| 349 record(s) printed from Clarivate Web of Science |
| Record 1 of 349 | ||||||
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| Author(s): Uhlik, F (Uhlik, Filip); Slanina, Z (Slanina, Zdenek); Bao, LP (Bao, Lipiao); Akasaka, T (Akasaka, Takeshi); Lu, X (Lu, Xing); Adamowicz, L (Adamowicz, Ludwik) | ||||||
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| Abstract: Relative populations of three energy-lowest IPR (isolated-pentagon-rule) isomers of Eu@C-88 are computed using the Gibbs energy based on characteristics from density functional theory and MP2 calculations (M06-2X/3-21G similar to SDD entropy term, and the MP2=FU/6-31G*similar to SDD or B2PLYPD=FU/6-31 + G*similar to SDD energetics). The calculations predict coexistence of three isomers, in agreement with extraction using a polar solvent, and offer a possible explanation why the Eu@C (2)(27)-C-88 species should prevail with a non-polar solvent. Role of extraction solvents and catalysis is thus pointed out. | ||||||
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| Record 2 of 349 | ||||||
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| Author(s): Slanina, Z (Slanina, Zdenek); Uhlik, F (Uhlik, Filip); Feng, L (Feng, Lai); Adamowicz, L (Adamowicz, Ludwik) | ||||||
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| Abstract: The paper presents ongoing density-functional theory (DFT) computational support to research of hybrid perovskite solar cells to facilitate their understanding at molecular level. Very recently, doping by a iodine salt, namely 2,2 '-bis(trifluoromethyl)-[1,1 '-biphenyl]-4,4 '-diamine iodine BFBAI(2), has been described that improves the power conversion efficiency and enhances device stability. As structural characteristics of BFBAI(2) are not well known, they are supplied here through DFT calculations for both BFBAI(2) monomer and dimer. The geometry optimizations are performed at the M06-2X/3-21G level, and energetics is refined with the M06-2X/Def2QZVP treatment. The dimerization potential-energy change is calculated as -6.2 kcal/mol. BFBAI(2) exhibits highly non-uniform charge distribution, i.e., it is a clearly polar system that can strongly modulate surface conditions when adsorbed. The adsorption-energy gain for BFBAI(2) on CsPbI3 perovskite is DFT evaluated as -13.2 kcal/mol. | ||||||
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| Record 3 of 349 | ||||||
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| Author(s): Slanina, Z (Slanina, Zdenek); Uhlik, F (Uhlik, Filip); Feng, L (Feng, Lai); Adamowicz, L (Adamowicz, Ludwik) | ||||||
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| Abstract: Relative populations of the three energy-lowest IPR (isolated-pentagon-rule) isomers of Ho@C-82 under the high-temperature synthetic conditions are computed using the Gibbs energy based on characteristics from the density functional theory calculations (B3LYP/3-21G similar to SDD entropy term, B3LYP/6-31G* similar to SDD energetics). Two major species are predicted, Ho@C (2v ); 9-C-82 and Ho@C ( s )(c); 6-C-82, with rather comparable populations under supposed synthetic temperatures. Roles of the inter-isomeric thermodynamic equilibrium and solubility are discussed. | ||||||
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| Record 4 of 349 | ||||||||||||
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| Author(s): Slanina, Z (Slanina, Zdenek); Uhlik, F (Uhlik, Filip); Rodriguez-Zavala, JG (Rodriguez-Zavala, Jaime G.); Chiang, LY (Chiang, Long Y.); Adamowicz, L (Adamowicz, Ludwik) | ||||||||||||
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| Abstract: Model quantum chemical calculations are carried out for the relative populations of two low-energy C-60(OH)(32) isomers at moderate temperatures, consistently using both enthalpy and entropy components of the Gibbs energy, in order to understand the isomeric interplay at relevant synthetic conditions. The Gibbs energy is based on the M06-2X/6-311++G** energetics and M06-2X/3-21G entropy. Owing to the entropy effects, the relative populations of the C-60(OH)(32) isomers change quite fast so that the equimolarity between both species is reached already at a temperature of 266 K. The calculations indicate a strong sensitivity of the C-60(OH)(32) isomeric relative populations to temperature changes (a feature useful for yield optimization with a selected isomer). Calculated data on structure, charge distribution, electronic and IR vibrational spectra are presented, too. Possible roles of the inter-isomeric thermodynamic equilibrium and solubility are discussed. The results, the first of its type for polyhydroxylated fullerenes, are encouraging for further such studies with other isomeric fullerenols. | ||||||||||||
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| Record 5 of 349 | |||||||||
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| Author(s): Cuyacot, BR (Cuyacot, Ben Joseph R.); Foroutan-Nejad, C (Foroutan-Nejad, Cina) | |||||||||
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| Record 6 of 349 | ||||||
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| Author(s): Holusa, J (Holusa, Jakub); Nyvlt, D (Nyvlt, Daniel); Woronko, B (Woronko, Barbara); Matejka, M (Matejka, Michael); Stuchlik, R (Stuchlik, Radim) | ||||||
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| Abstract: Aeolian sediments and landforms represent a unique source of proxy data allowing the detailed research of palaeoenvironmental changes. For example, dune morphology and dune field patterns could reflect an influence of a wide range of conditions from palaeowind directions to topography. The Moravian Sahara dune field located in southern Moravia represents a unique archive reflecting the effects of these environmental variables, lying far away from the European sand belt which is the main area of interest for aeolian research in Europe. Here, we present the complex geospatial analysis of the dunes and their topography performed on Digital Terrain Models (DTM) from which their basic morphometrics (crest orientation, spacings between the dunes, and others) were obtained. Two groups of differently oriented transverse dunes have been distinguished, suggesting a significant twist in atmospheric circulation connected with the retreat of ice sheets following the Last Glacial Maximum. In addition, other local conditions such as the topography and sediment supply were found to exert a strong influence on the formation of dune field patterns. Thus, the results of the high-resolution DTMs presented here show their applicability to the highly detailed study of the influence of environmental conditions on the development of the aeolian dune fields. | ||||||
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| Record 7 of 349 | |||||||||||||||
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| Author(s): Boronski, JT (Boronski, Josef T.); Seed, JA (Seed, John A.); Hunger, D (Hunger, David); Woodward, AW (Woodward, Adam W.); van Slageren, J (van Slageren, Joris); Wooles, AJ (Wooles, Ashley J.); Natrajan, LS (Natrajan, Louise S.); Kaltsoyannis, N (Kaltsoyannis, Nikolas); Liddle, ST (Liddle, Stephen T.) | |||||||||||||||
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| Record 8 of 349 | |||||||||
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| Author(s): Repka, R (Repka, Radomir); Koutecky, P (Koutecky, Petr); Mendel, P (Mendel, Peter); Frelich, R (Frelich, Rudolf) | |||||||||
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| Abstract: This study examines an assumed hybrid between Gymnocalycium capillense and G. intertextum discovered in a mixed population of the putative parents at Villa Viso in Cordoba Province, Argentina. Eleven quantitative morphological characters (including two ratios) were measured in the natural populations of the presumed parental species and the assumed hybrid. Five of these characters differed between the parental species whereas the assumed hybrid usually showed intermediate values. Eleven qualitative morphological characters were compared for all three taxa, whereby two characters of the assumed hybrid were closer to G. intertextum, one character was closer to G. capillense, six characters were intermediate (but two of them closer to one presumed parent), and three characters were unique. The seed morphology is the most important character separating the subgenera of Gymnocalycium: the assumed hybrid is most similar in this regard to the nominate subgenus, but the seeds are larger than in both assumed parents and have a very broad hilum-micropylar region and conspicuous strophiole at the margin, like in the subgenus Trichomosemineum. Genome sizes estimated by means of flow cytometry shows that G. capillense is tetraploid and G. intertextum diploid, while the assumed hybrid plants are hexaploid (i.e. allopolyploid hybrids). Sequencing and phylogenetic analysis of a low-copy nuclear PHYC gene also revealed that this genomic region of the hybrid combines sequences present in G. capillense and G. intertextum. In combination with the morphological data, these results support the hybrid nature and parentage of the studied plants. The hybrid is formally described here as G. xapplanatum and is the first documented hybrid between the subgenera Gymnocalycium and Trichomosemineum. The results show the potential of allopolyploidy in which different subgenera participate for the evolution of the genus. | |||||||||
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| Record 9 of 349 | |||||||||
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| Author(s): Slama, V (Slama, Vladislav); Rajabi, S (Rajabi, Sayeh); Mancal, T (Mancal, Tomas) | |||||||||
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| Abstract: We investigate the prospect of using a two-dimensional material, fluorographene, to mimic the light-harvesting function of natural photosynthetic antennas. We show by quantum chemical calculations that isles of graphene in a fluorographene sheet can act as quasi-molecules similar to natural pigments from which the structures similar in function to photosynthetic antennas can be built. The graphene isles retain enough identity so that they can be used as building blocks to which intuitive design principles of natural photosynthetic antennas can be applied. We examine the excited state properties, stability, and interactions of these building blocks. Constraints put on the antenna structure by the two-dimensionality of the material as well as the discrete nature of fluorographene sheet are studied. We construct a hypothetical energetic funnel out of two types of quasi-molecules to show how a limited number of building blocks can be arranged to bridge the energy gap and spatial separation in excitation energy transfer. Energy transfer rates for a wide range of the system-environment interaction strengths are predicted. We conclude that conditions for the near unity quantum efficiency of energy transfer are likely to be fulfilled in fluorographene with the controlled arrangement of quasi-molecules. Published under an exclusive license by AIP Publishing. | |||||||||
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| Record 10 of 349 |
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| Author(s): Vojtech, J (Vojtech, Josef); Havlis, O (Havlis, Ondrej); Slapak, M (Slapak, Martin); Smotlacha, V (Smotlacha, Vladimir); Velc, R (Velc, Radek); Pospisil, P (Pospisil, Petr); Kundrat, J (Kundrat, Jan); Altmannova, L (Altmannova, Lada); Vohnout, R (Vohnout, Rudolf); Cizek, M (Cizek, Martin); Hrabina, J (Hrabina, Jan); Rerucha, S (Rerucha, Simon); Pravdova, L (Pravdova, Lenka); Lazar, J (Lazar, Josef); Cip, O (Cip, Ondrej); Slodicka, L (Slodicka, Lukas) |
| Edited by: Strojnik M |
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| Abstract: National time and frequency dissemination networks are being developed in many countries; also international connections are being established. In the contribution we present Czech Infrastructure for Time and Frequency as a noncommercial, open activity focused on the transfer of accurate time and very stable frequency using optical networks. The national optical infrastructure for time and frequency transfer is operated on top of the CESNET network infrastructure, to have operational cost under control. We also address actually running and planned upgrades and future development plans regarding wavelength bands and considered geographic extensions. We will also focus on creation of bidirectional dark channels on different wavebands within shared fibers together with bidirectional compensation of fiber losses. Single path bidirectional amplification utilizing lumped optical amplifiers is sensitive to feedback from fiber line like back scattering and reflections and in case of increased feedback can produce unwanted oscillations, which potentially interfere with parallel data transmissions. We will also briefly mention the CLONETS-DS project working on design study for coherent Pan-European time and frequency dissemination network, which would connect national networks and provide different services based on time and frequency for a wide range of users. |
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| Conference Sponsors: SPIE |
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| ISBN: 978-1-5106-5451-8; 978-1-5106-5450-1 |
| Record 11 of 349 | ||||||
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| Author(s): Jirankova, E (Jirankova, Eva); Lazecky, M (Lazecky, Milan) | ||||||
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| Abstract: Ground surface uplift was detected at the start of longwall mining, a significant part of which is situated in the shaft protection pillar Sever of the CSM Mine in the Czech Republic. The largest uplift was found to be 23 mm, by the levelling method of surface points with height connections to non-mined areas. Due to the length of the connection to the non-influenced area, precise levelling was chosen to observe the vertical displacements and prove the displacement values using a confidence interval with 5% risk. This article aims to clarify the cause of ground surface uplift during longwall mining. Therefore, the height changes of the given area were extracted also from satellite radar interferometry (InSAR). The changes of the observed ground surface were compared with the empirical subsidence. The largest difference between the measured and empirical surface subsidence was 85 mm and occurred in the period before the ground surface uplift. Spatiotemporal evaluation of the data was used to determine the presumed cause of the occurrence of surface uplift in the overburdened strata, due to previous mining activity and the subsequent unburdening of the rock mass. | ||||||
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| Record 12 of 349 | |||||||||
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| Author(s): Fuzik, T (Fuzik, Tibor); Moravcova, J (Moravcova, Jana); Kalynych, S (Kalynych, Sergei); Plevka, P (Plevka, Pavel) | |||||||||
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Abstract:
Globally distributed enterovirus 70 (EV70) causes local outbreaks of acute hemorrhagic conjunctivitis. The discharge from infected eyes enables the high-efficiency transmission of EV70 in overcrowded areas with low hygienic standards.
Enterovirus 70 (EV70) is a human pathogen belonging to the family Picornaviridae. EV70 is transmitted by eye secretions and causes acute hemorrhagic conjunctivitis, a serious eye disease. Despite the severity of the disease caused by EV70, its structure is unknown. Here, we present the structures of the EV70 virion, altered particle, and empty capsid determined by cryo-electron microscopy. The capsid of EV70 is composed of the subunits VP1, VP2, VP3, and VP4. The partially collapsed hydrophobic pocket located in VP1 of the EV70 virion is not occupied by a pocket factor, which is commonly present in other enteroviruses. Nevertheless, we show that the pocket can be targeted by the antiviral compounds WIN51711 and pleconaril, which block virus infection. The inhibitors prevent genome release by stabilizing EV70 particles. Knowledge of the structures of complexes of EV70 with inhibitors will enable the development of capsid-binding therapeutics against this virus. IMPORTANCE Globally distributed enterovirus 70 (EV70) causes local outbreaks of acute hemorrhagic conjunctivitis. The discharge from infected eyes enables the high-efficiency transmission of EV70 in overcrowded areas with low hygienic standards. Currently, only symptomatic treatments are available. We determined the structures of EV70 in its native form, the genome release intermediate, and the empty capsid resulting from genome release. Furthermore, we elucidated the structures of EV70 in complex with two inhibitors that block virus infection, and we describe the mechanism of their binding to the virus capsid. These results enable the development of therapeutics against EV70. |
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| Record 13 of 349 | ||||||
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| Author(s): Jiraskova, Y (Jiraskova, Y.); Pizurova, N (Pizurova, N.); Bursik, J (Bursik, J.); Friak, M (Friak, M.); Cizek, J (Cizek, J.); Vlasak, T (Vlasak, T.); Cegan, T (Cegan, T.); Nikodym, M (Nikodym, M.); Lunacek, J (Lunacek, J.) | ||||||
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| Abstract: The scanning electron microscopy, X-ray diffraction, positron annihilation spectroscopy, Mossbauer spectrometry, and measurements of magnetic characteristics by vibrating sample magnetometer complemented by theoretical simulations are applied in the present investigations of the Fe-Al-Co alloys with 25 at% Al and Co substituting Fe in amount of 15 at% or 25 at%. The alloys prepared by slightly different technologies resulting in different structural morphologies are subjected to thermal treatment followed by slow cooling and water cooling. It is shown that the alloy with lower Co content and the initial A2 structure is more sensitive to the thermal treatments from the viewpoints of changes in morphology, defects concentration and magnetic properties in comparison to the other one with the initial B2 structure. This is reflected almost in all experimentally obtained results.(c) 2022 Elsevier B.V. All rights reserved. | ||||||
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| Record 14 of 349 | |||||||||
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| Author(s): Kontkanen, OV (Kontkanen, Outi Vilhelmiina); Biriukov, D (Biriukov, Denys); Futera, Z (Futera, Zdenek) | |||||||||
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| Abstract: Metalloproteins, known to efficiently transfer electronic charge in biological systems, recently found their utilization in nanobiotechnological devices where the protein is placed into direct contact with metal surfaces. The feasibility of oxidation/reduction of the protein redox sites is affected by the reorganization free energies, one of the key parameters determining the transfer rates. While their values have been measured and computed for proteins in their native environments, i.e., in aqueous solution, the reorganization free energies of dry proteins or proteins adsorbed to metal surfaces remain unknown. Here, we investigate the redox properties of blue copper protein azurin, a prototypical redox-active metalloprotein previously probed by various experimental techniques both in solution and on metal/vacuum interfaces. We used a hybrid quantum mechanical/molecular mechanical computational technique based on density functional theory to explore protein dynamics, flexibility, and corresponding reorganization free energies in aqueous solution, vacuum, and on vacuum gold interfaces. Surprisingly, the reorganization free energy only slightly decreases when azurin is dried because the loss of the hydration shell leads to larger flexibility of the protein near its redox site. At the vacuum gold surfaces, the energetics of the structure relaxation depends on the adsorption geometry; however, significant reduction of the reorganization free energy was not observed. These findings have important consequences for the charge transport mechanism in vacuum devices, showing that the free energy barriers for protein oxidation remain significant even under ultra-high vacuum conditions. Published under an exclusive license by AIP Publishing.& nbsp; | |||||||||
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| Record 15 of 349 |
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| Author(s): Falginella, FL (Falginella, Francesco L.); Kravec, M (Kravec, Marek); Drabinova, M (Drabinova, Martina); Paclikova, P (Paclikova, Petra); Bryja, V (Bryja, Vitezslav); Vacha, R (Vacha, Robert) |
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| Abstract: Over the past decades an extensive effort has been made to provide a more comprehensive understanding of Wnt signaling, yet many regulatory and structural aspects remain elusive. Among these, the ability of Dishevelled (DVL) protein to relocalize at the plasma membrane is a crucial step in the activation of all Wnt pathways. The membrane binding of DVL was suggested to be mediated by the preferential interaction of its C-terminal DEP domain with phosphatidic acid (PA). However, due to the scarcity and fast turnover of PA, we investigated the role on the membrane association of other more abundant phospholipids. The combined results from compu-tational simulations and experimental measurements with various model phospholipid membranes, demonstrate that the membrane binding of DEP/DVL constructs is governed by the concerted action of generic electrostatics and finely-tuned intermolecular interactions with individual lipid species. In particular, while we confirmed the strong preference for PA lipid, we also observed a weak but non-negligible affinity for phosphatidylserine, the most abundant anionic phospholipid in the plasma membrane, and phosphatidylinositol 4,5-bisphosphate. The obtained molecular insight into DEP-membrane interaction helps to elucidate the relation between changes in the local membrane composition and the spatiotemporal localization of DVL and, possibly, other DEP-containing proteins. |
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| Record 16 of 349 | |||||||||
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| Author(s): Burska, KD (Burska, Karolina Dockalova); Rusnak, V (Rusnak, Vit); Oslejsek, R (Oslejsek, Radek) | |||||||||
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Abstract:
Puzzle-based training is a common type of hands-on activity accompanying formal and informal cybersecurity education, much like programming or other IT skills. However, there is a lack of tools to help the educators with the post-training data analysis.
Through a visualization design study, we designed the Training Analysis Tool that supports learning analysis of a single hands-on session. It allows an in-depth trainee comparison and enables the identification of flaws in puzzle assignments. We also performed a qualitative evaluation with cybersecurity experts and students. The participants apprised the positive influence of the tool on their workflows. Our insights and recommendations could aid the design of future tools supporting educators, even beyond cyber security. (C) 2021 Elsevier Ltd. All rights reserved. |
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| Record 17 of 349 | ||||||
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| Author(s): Ambrozova, K (Ambrozova, Klara); Laska, K (Laska, Kamil); Matejka, M (Matejka, Michael); Reuder, J (Reuder, Joachim) | ||||||
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| Abstract: Air temperature inversions are common features in Antarctica, especially in the interior where they are observed nearly year-round. Large temporal variability of air temperature inversion incidence is typical for the coastal areas and little is known about its occurrence in the Antarctic deglaciated areas. Here we present a 12-year-long time series of near-surface air temperature inversion derived from two automatic weather stations situated at different altitudes (10 and 375 m a.s.l.) in ice-free part of northern James Ross Island (Antarctic Peninsula). The highest monthly relative frequency of temperature inversions during 2006-2017 was observed in July (38%) when the range between minimum and maximum monthly frequencies reached 34%. Both the lowest monthly relative frequency of temperature inversions and the range were found in December with values of 7% and 15%, respectively. The correlation between mean lapse rate and selected mesoscale flow characteristics were tested. The highest correlations were found between lapse rate and specific humidity for the yearly means (0.69 in the 925 hPa pressure level). Negative correlation coefficients were established between lapse rate and air temperature in summer (- 0.65 in the 500 hPa pressure level). Finally, we also used the Weather and Research Forecasting (WRF) model to ascertain its ability to simulate situations as complicated as near-surface air temperature inversion formation in complex terrain. For a strong winter air temperature inversion, simulated air temperature was compared with in situ observations to assess the model performance. | ||||||
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| Record 18 of 349 | |||||||||
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| Author(s): De Gregorio, G (De Gregorio, G.); Knapp, F (Knapp, F.); Lo Iudice, N (Lo Iudice, N.); Vesely, P (Vesely, P.) | |||||||||
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| Abstract: Bulk and spectroscopic properties of He-4 are studied within an equation of motion phonon method. Such a method generates a basis of n-phonon (n = 0, 1, 2, 3...) states composed of tensor products of particle-hole Tamm-Dancoff phonons and then solves the full eigenvalue problem in such a basis. The method does not rely on any approximation and is free of any contamination induced by the center of mass, in virtue of a procedure exploiting the singular value decomposition of rectangular matrices. Two potentials, both derived from the chiral effective field theory, are adopted in a self-consistent calculation performed within a space including up to three phonons. The latter basis states are treated under a simplifying assumption. A comparative analysis with the experimental data points out the different performances of the two potentials. It shows also that the calculation succeeds only partially in the description of the spectroscopic properties and suggests a recipe for further improvements. | |||||||||
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| Record 19 of 349 | |||||||||
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| Author(s): Husak, M (Husak, Michal); Sajbanova, S (Sajbanova, Simona); Klimes, J (Klimes, Jiri); Jegorovc, A (Jegorovc, Alexandr) | |||||||||
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| Abstract: Validation of a method for distinguishing between salts and cocrystals based on dispersion-corrected density functional theory is presented. Existing related works (van de Streek & Neumann, 2010; LeBlanc et al., 2018) indicate that this approach is problematic and leads to incorrect results in multiple situations. The method suggested here is based on the geometry optimization of an artificially constructed wrong structure (hydrogen atom placed in salt position near the potential acceptor for cocrystals and vice versa cocrystal position with hydrogen atom placed near the potential donor of the salts). The verification of the method is based on comparison of the results with an experimentally confirmed correct hydrogen position. Calculations were performed on 173 selected structures of salts and 96 cocrystals with Delta pK(a) in the critical <-1, 4 > range. The range was chosen to test the method on the most problematic structures. When the artificial wrong model did not converge to the correct one (salt to cocrystal and vice versa), it was tested whether the correct model converged to the correct one in addition. The results confirmed that the most widely used functional (PBE) tends to generate false salt results. All salts converged to the salt from cocrystal initial models. Sixteen cocrystals showed local energy minima for both the salt and cocrystal states. Eighteen cocrystals always converged to salt. Rules were identified under which the results can be considered reliable: when a cocrystal starting model converges to cocrystal, the structure is certainly cocrystal. When both the cocrystal and salt models converge to salt for a long hydrogen-bond (longer than 2.613 angstrom) the structure is most likely salt. For short hydrogen bonds it is not possible to distinguished reliably between salt and cocrystal using the dispersion-corrected PBE functional. Additional calculations were performed with more advanced functionals for 18 problematic structures detected in the screening as well as for four more mentioned in the literature. The results show that the rSCAN functional (Bartok & Yates, 2019) improves the agreement with the experiment. Further improvement was observed by using hybrid functionals (PBE0, PBE50), which were tested on structures that gave incorrect results with rSCAN. The described method for distinguishing salts from cocrystals can be useful for enhancing the information given by structure solutions from powder, the verification of structure solutions from single crystals and studies related to crystal structure prediction. | |||||||||
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| Record 20 of 349 | |||||||||
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| Author(s): Matas, M (Matas, Martin); Farhadizadeh, A (Farhadizadeh, Alireza); Houska, J (Houska, Jiri) | |||||||||
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| Abstract: We study the hard and electrically conductive multicomponent diboride Ti0.25Zr0.25Hf0.25Ta0.25B2 with high thermal stability by ab-initio calculations. We focus on the effect of defects (either vacancies or C atoms, both relevant for numerous experiments including our own) on material characteristics. Different types, concentrations and distributions of defects were investigated, and the configurations leading to the lowest formation energies were identified. We show that the replacement of B by C is more unfavorable than the formation of B vacancies. We show that vacancies prefer to coalesce into a larger planar void, minimizing the number of broken B-B bonds and the volume per atom, while carbon substitutions at boron sites do not prefer coalescence and tend to minimize the number of C-C bonds. We show the effect of vacancies on mechanical and electronic properties, and use the results to explain experimental data. | |||||||||
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| Record 21 of 349 | |||||||||
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| Author(s): Ketolainen, T (Ketolainen, Tomi); Karlicky, F (Karlicky, Frantisek) | |||||||||
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| Abstract: We use time-dependent density functional theory together with the HSE06 hybrid functional to investigate the optical and excitonic properties of two-dimensional transition metal carbides, MXenes. We determine reliable optical gaps, optical absorbance spectra, and exciton features for a set of eight semiconducting MXenes. The optical gaps of Sc2CF2, Cr2CF2, Cr2C(OH)(2), and anti-ferromagnetic Mn2CO2 (1.9-2.3 eV) lie in the energy region of visible (VIS) light. Sc2C(OH)(2), Ti2C, Ti2CO2, and ferromagnetic Mn2CO2 with smaller optical gaps (0.4-1.2 eV) well absorb solar radiation, including VIS light. Moreover, Ti2C and ferromagnetic Mn2CO2 show high monolayer absorbance of 10-20% in the 1-3 eV energy range. Finally, we analyse the excitons in MXenes and find that the first bright excitons of Sc- and Ti-based MXenes are strongly localized in k-space while the corresponding excitons of Cr- and Mn-based systems are delocalized. | |||||||||
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| Record 22 of 349 | ||||||
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| Author(s): Clo, J (Clo, Josselin) | ||||||
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| Abstract: Whole-genome duplication is a common mutation in eukaryotes with far-reaching phenotypic effects. The resulting morphological, physiological and fitness consequences and how they affect the survival probability of polyploid lineages are intensively studied, but little is known about the effect of genome doubling on the evolutionary potential of populations. Historically, it has been argued polyploids should be less able to adapt because gene duplication dilutes the effects of alleles, such that polyploids are less likely to evolve new adaptive gene complexes compared with diploids. In this paper, I investigate the short- and long-term consequences of genome doubling on the additive genetic variance of populations. To do so, I extended the classical models of quantitative traits under stabilizing selection to study the evolution of the additive variance of the trait under study after a shift from diploidy to tetraploidy. I found that, for realistic allele-dosage effects, polyploidization is associated with an initial decrease in adaptive potential. In the long term, the better masking of recessive deleterious mutations associated with polyploidy compensates for the initial decrease in additive variance. The time for the tetraploid populations to reach or exceed the additive variance of their diploid progenitors is generally lower than 200 generations. These results highlight that polyploidization per se has a negligible negative effect on the adaptive potential of populations in the short term, and a substantial positive effect in the long term. | ||||||
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| Record 23 of 349 | ||||||||||||
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| Author(s): Czernek, J (Czernek, Jiri); Brus, J (Brus, Jiri); Czernekova, V (Czernekova, Vladimira) | ||||||||||||
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| Abstract: The gas-phase value of the dissociation energy (D-0) is a key parameter employed in both experimental and theoretical descriptions of noncovalent complexes. The D-0 data were obtained for a set of mid-sized organic dimers in their global minima which was located using geometry optimizations that applied ample basis sets together with either the conventional second-order Moller-Plesset (MP2) method or several dispersion-corrected density-functional theory (DFT-D) schemes. The harmonic vibrational zero-point (VZP) and deformation energies from the MP2 calculations were combined with electronic energies from the coupled cluster theory with singles, doubles, and iterative triples [CCSD(T)] extrapolated to the complete basis set (CBS) limit to estimate D-0 with the aim of inspecting values that were most recently measured, and an analogous comparison was performed using the DFT-D data. In at least one case (namely, for the aniline...methane cluster), the D-0 estimate that employed the CCSD(T)/CBS energies differed from experiment in the way that could not be explained by a possible deficiency in the VZP contribution. Curiously, one of the DFT-D schemes (namely, the B3LYP-D3/def2-QZVPPD) was able to reproduce all measured D-0 values to within 1.0 kJ/mol from experimental error bars. These findings show the need for further measurements and computations of some of the complexes. In order to facilitate such studies, the physical nature of intermolecular interactions in the investigated dimers was analyzed by means of the DFT-based symmetry-adapted perturbation theory. Published under an exclusive license by AIP Publishing. | ||||||||||||
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| Record 24 of 349 | |||||||||||||||
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| Author(s): Montagud-Camps, V (Montagud-Camps, Victor); Hellinger, P (Hellinger, Petr); Verdini, A (Verdini, Andrea); Papini, E (Papini, Emanuele); Franci, L (Franci, Luca); Landi, S (Landi, Simone) | |||||||||||||||
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| Abstract: In plasma turbulence, energy and cross helicity are transferred across scales at a constant rate as a consequence of nonlinear interactions. In incompressible magnetohydrodynamics (MHD), the energy cascade rate of both quantities can be computed by means of the temporal evolution of second-order structure functions, known as Karman-Howarth-Monin (KHM) equations. In the present work, we derive the KHM equation to compute the energy cascade rate of cross helicity in compressible MHD. Using three-dimensional direct numerical simulations, we validate the equation and use it to measure the cross-helicity turbulence properties. Our results show a slower development of the cross-helicity cascade with respect to the energy one and the presence of inverse cascades of energy and cross helicity at large scales when in the presence of a strong mean field. We propose the relation of these phenomena with the longer duration of geomagnetic storms after the arrival of solar winds with large cross helicity and the observation of patchy inertial ranges displaying positive and negative cascade rates for certain solar wind intervals. | |||||||||||||||
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| Record 25 of 349 |
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| Author(s): Chatterjee, B (Chatterjee, Banhi); Skolimowski, J (Skolimowski, Jan); Byczuk, K (Byczuk, Krzysztof) |
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| Abstract: We study interference patterns and Friedel oscillations (FO) due to scattering from two or more localized impurities and scattering from extended inhomogeneities in the two-dimensional lattice systems of interacting fermions. Correlations between particles are accounted for by using an approximate method based on the real-space dynamical mean-field theory and a homogeneous self-energy approximation (HSEA), where the site-dependent part of the self-energy is neglected. We find that the interference maxima and minima change systematically as we vary the relative distance between the two impurities. At the same time, the increase of the interaction does not shift the position of interference fringes but only reduces their intensities. A comparison with the single impurity cases clearly shows complex patterns in FO fringes induced by additional multiple scattering processes. In the case of an extended steplike potential the system becomes more homogeneous when the interaction increases. FO and interference patterns are not present in the Mott insulating phase in both single and many impurity models. |
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| Record 26 of 349 | |||||||||
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| Author(s): Kabelka, I (Kabelka, Ivo); Georgiev, V (Georgiev, Vasil); Marx, L (Marx, Lisa); Pajtinka, P (Pajtinka, Peter); Lohner, K (Lohner, Karl); Pabst, G (Pabst, Georg); Dimova, R (Dimova, Rumiana); Vacha, R (Vacha, Robert) | |||||||||
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| Abstract: We previously speculated that the synergistically enhanced antimicrobial activity of Magainin 2 and PGLa is related to membrane adhesion, fusion, and further membrane remodeling. Here we combined computer simulations with time-resolved in vitro fluorescence microscopy, cryoelectron microscopy, and small-angle X-ray scattering to interrogate such morphological and topological changes of vesicles at nanoscopic and microscopic length scales in real time. Coarse grained simulations revealed formation of an elongated and bent fusion zone between vesicles in the presence of equimolar peptide mixtures. Vesicle adhesion and fusion were observed to occur within a few seconds by cryoelectron microscopy and corroborated by small-angle X-ray scattering measurements. The latter experiments indicated continued and time-extended structural remodeling for individual peptides or chemically linked peptide heterodimers but with different kinetics. Fluorescence microscopy further captured peptide-dependent adhesion, fusion, and occasional bursting of giant unilamellar vesicles a few seconds after peptide addition. The synergistic interactions between the peptides shorten the time response of vesicles and enhance membrane fusogenic and disruption properties of the equimolar mixture compared with the individual peptides. | |||||||||
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| Record 27 of 349 | ||||||
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| Author(s): Novotny, M (Novotny, Michal); Tykalova, T (Tykalova, Tereza); Ruzickova, H (Ruzickova, Hana); Ruzicka, E (Ruzicka, Evzen); Dusek, P (Dusek, Petr); Rusz, J (Rusz, Jan) | ||||||
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| Abstract: Even though hypomimia is a hallmark of Parkinson's disease (PD), objective and easily interpretable tools to capture the disruption of spontaneous and deliberate facial movements are lacking. This study aimed to develop a fully automatic video-based hypomimia assessment tool and estimate the prevalence and characteristics of hypomimia in de-novo PD patients with relation to clinical and dopamine transporter imaging markers. For this cross-sectional study, video samples of spontaneous speech were collected from 91 de-novo, drug-naive PD participants and 75 age and sex-matched healthy controls. Twelve facial markers covering areas of forehead, nose root, eyebrows, eyes, lateral canthal areas, cheeks, mouth, and jaw were used to quantitatively describe facial dynamics. All patients were evaluated using Movement Disorder Society-Unified PD Rating Scale and Dopamine Transporter Single-Photon Emission Computed Tomography. Newly developed automated facial analysis tool enabled high-accuracy discrimination between PD and controls with area under the curve of 0.87. The prevalence of hypomimia in de-novo PD cohort was 57%, mainly associated with dysfunction of mouth and jaw movements, and decreased variability in forehead and nose root wrinkles (p < 0.001). Strongest correlation was found between reduction of lower lip movements and nigro-putaminal dopaminergic loss (r = 0.32, p = 0.002) as well as limb bradykinesia/rigidity scores (r = -0.37 p < 0.001). Hypomimia represents a frequent, early marker of motor impairment in PD that can be robustly assessed via automatic video-based analysis. Our results support an association between striatal dopaminergic deficit and hypomimia in PD. | ||||||
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| Record 28 of 349 | ||||||||||||
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| Author(s): Irziqat, B (Irziqat, Bahaaeddin); Berger, J (Berger, Jan); Cebrat, A (Cebrat, Aleksandra); Mendieta-Moreno, JI (Mendieta-Moreno, Jesus I.); Sundar, MS (Sundar, Mothuku Shyam); Bedekar, AV (Bedekar, Ashutosh V. V.); Ernst, KH (Ernst, Karl-Heinz) | ||||||||||||
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| Abstract: Despite the vast development of stereochemistry it remains a great challenge to predict the fate of homochiral or heterochiral recognition in crystallization from racemic solution or melt. Using the well-defined model system of racemic trioxaundecahelicene on a Cu(100) surface in ultrahigh vacuum, the chiral recognition of this heterohelicene has been investigated by means of state-of-the-art scanning probe microscopy. The combination of scanning tunneling microscopy and tuning fork-based non-contact atomic force microscopy allowed assignment of the absolute configuration of single 7,12,17-trioxa[11]helicene molecules in their two-dimensional assemblies. At very low coverages, homochiral van der Waals-bonded tetramers are observed. These also constitute the building blocks of the completely filled monolayer, which is a 2D conglomerate of homochiral domains. The interpretation of the adsorption geometries was supported by density-functional theory calculations and molecular dynamics simulations, predicting a stronger interaction energy for homochiral structures over the heterochiral assembly. The striking similarity to heptahelicene on the same surface suggests that chiral recognition is dominated by the footprint interaction of the molecules with the metallic substrate. | ||||||||||||
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| Record 29 of 349 | ||||||
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| Author(s): Suthar, P (Suthar, Pawan); Trojanek, F (Trojanek, Frantisek); Maly, P (Maly, Petr); Derrien, TJY (Derrien, Thibault J-Y); Kozok, M (Kozak, Martin) | ||||||
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Abstract:
Nonlinear optical response of materials exposed to strong nonresonant light fields leads to production of high energy photons whose spectra contain fingerprints of the coherent electron dynamics in the material. In this paper we investigate how the high harmonic spectra generated in crystalline silicon are linked to specific properties of its band structure. By comparing the polarization anisotropy of high harmonic spectra for two distinct frequencies of the driving pulses we show that the anisotropy has two sources. When driven by mid-infrared light, the signal at specific photon energies is enhanced by the presence of Van Hove singularities in the joint density of states of silicon. With near-infrared driving pulses, in contrast, the high harmonic yield is mainly influenced by the anisotropy of the reduced mass of electron-hole pair, which is related to the nonresonant excitation probability. The experimental results are compared with numerical calculations using time-dependent density functional theory.
High harmonic generation in solids has been intensively studied for compact extreme ultraviolet light sources and for understanding of the inner workings of solids. In this study, the authors conducted polarization-resolved nonlinear spectroscopy of silicon with numerical calculations and uncovered the significant influence of van Hove singularities on the processes of high harmonic generation. |
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| Author(s): Trapl, D (Trapl, Dalibor); Krupicka, M (Krupicka, Martin); Visnovsky, V (Visnovsky, Vladimir); Hozzova, J (Hozzova, Jana); Ol'ha, J (Ol'ha, Jaroslav); Krenek, A (Krenek, Ales); Spiwok, V (Spiwok, Vojtech) | ||||||||||||
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| Abstract: The accuracy of biomolecular simulations depends on the accuracy of an empirical molecular mechanics potential known as a force field: a set of parameters and expressions to estimate the potential from atomic coordinates. Accurate parametrization of force fields for small organic molecules is a challenge due to their high diversity. One of the possible approaches is to apply a correction to the existing force fields. Here, we propose an approach to estimate the density functional theory (DFT)-derived force field correction which is calculated during the run of molecular dynamics without significantly affecting its speed. Using the formula known as a property map collective variable, we approximate the force field correction by a weighted average of this force field correction calculated only for a small series of reference structures. To validate this method, we used seven AMBER force fields, and we show how it is possible to convert one force field to behave like the other one. We also present the force field correction for the important anticancer drug Imatinib as a use case example. Our method appears to be suitable for adjusting the force field for general drug-like molecules. We provide a pipeline that generates the correction; this pipeline is available at https://pmcvff-correction.cerit-sc.cz/. | ||||||||||||
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| Record 31 of 349 | |||||||||
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| Author(s): Lopez-Carballeira, D (Lopez-Carballeira, Diego); Raymakers, J (Raymakers, Jorne); Artemenko, A (Artemenko, Anna); Lenaerts, R (Lenaerts, Ruben); Cermak, J (Cermak, Jan); Kulicek, J (Kulicek, Jaroslav); Nicley, SS (Nicley, Shannon S.); Kromka, A (Kromka, Alexander); Haenen, K (Haenen, Ken); Maes, W (Maes, Wouter); Rezek, B (Rezek, Bohuslav) | |||||||||
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| Abstract: Organic-based photovoltaic devices emerged as a complementary technology to silicon solar cells with specific advantages in terms of cost, ease of deployment, semi-transparency, and performance under low and diffuse light conditions. In this work, thin-film boron-doped diamond (B:NCD) electrodes are employed for their useful op-tical, electronic, and chemical properties, as well as stability and environmental safety. A set of oligothiophene perylene diimide (nT-PDI) donor-acceptor chromophores is designed and synthesized in order to investigate the influence of the oligothiophene spacer length when the nT-PDI molecule is attached to a B:NCD electrode. The chromophores are anchored to the diamond surface via diazonium grafting followed by Sonogashira cross -coupling. X-ray photoelectron spectroscopy shows that the surface coverage decreases with increasing oligo-thiophene length. Density functional theory (DFT/TDDFT) calculations reveal the upright nT-PDI orientation and the most efficient photogenerated charge separation and injection to diamond for elongated oligothiophene chains (8T-PDI). Yet, the maximum photovoltage is obtained for an intermediate oligothiophene length (3T-PDI), providing an optimum between decreasing transport efficiency and increasing efficiency of charge separation and reduced recombination with increasing oligothiophene length. Holes transferred from nT-PDI to diamond persist there even after the illumination is switched off. Such features may be beneficial for application in solar cells. | |||||||||
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| Record 32 of 349 | |||||||||
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| Author(s): Rubes, M (Rubes, Miroslav); Trachta, M (Trachta, Michal); Vaculik, J (Vaculik, Jan); Bulanek, R (Bulanek, Roman); Bludsky, O (Bludsky, Ota) | |||||||||
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| Abstract: The zeolite frameworks (FER, TON, CHA, and IFR) with a large diversity of the IR band shapes in the OH stretching region were investigated by combined use of FT-IR spectroscopy and DFT calculations. The analysis of various isolated Brunsted acid sites was performed with a model based on Boltzmann weighted relative energies and OH frequencies obtained by the omega/r correlation method. This approach has recently been used to reveal the non-statistical incorporation of aluminum into the H-MOR framework. The model correctly predicts the band shapes of H-FER and H-TON zeolites in the free OH region of the FT-IR spectra. For H-CHA and H-IFR, however, the mutual BAS interactions cannot be ignored even for high Si/Al ratios, which renders the concept of isolated BAS inadequate. Thus, the periodic calculations of adsorption and catalytic properties of zeotype frameworks should always be carried out with extended models mimicking real heteroatom distribution in these materials. | |||||||||
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| Record 33 of 349 |
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| Author(s): Liu, HM (Liu, Huimei); Chaloupka, J (Chaloupka, Jiri); Khaliullin, G (Khaliullin, Giniyat) |
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| Abstract: We present an analytical study of the exchange interactions between pseudospin one-half d(5) ions in honeycomb lattices with edge-shared octahedra. Various exchange channels involving Hubbard U, charge-transfer excitations, and cyclic exchange are considered. Hoppings within t(2g) orbitals as well as between t(2g) and e(g) orbitals are included. Special attention is paid to the trigonal crystal field Delta effects on the exchange parameters. The obtained exchange Hamiltonian is dominated by ferromagnetic Kitaev interaction K within a wide range of Delta. It is found that a parameter region close to the charge-transfer insulator regime and with a small Delta is most promising to realize the Kitaev spin liquid phase. Two representative honeycomb materials Na2IrO3 and alpha-RuCl3 are discussed based on our theory. We have found that both materials share dominant ferromagnetic K and positive nondiagonal Gamma values. However, their Heisenberg J terms have opposite signs: AFM J > 0 in Na2IrO3 and FM J < 0 in alpha-RuCl3. This brings different magnetic fluctuations and results in their different magnetization behaviors and spin excitation spectra. Proximity to FM state due to the large FM J is emphasized in alpha-RuCl3. The differences between the exchange couplings of these two materials originate from the opposite Delta values, indicating that the crystal field can serve as an efficient control parameter to tune the magnetic properties of d(5) spin-orbit Mott insulators. |
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| Author(s): Finstrlova, A (Finstrlova, Adela); Maslanova, I (Maslanova, Ivana); Blasdel Reuter, BG (Blasdel Reuter, Bob G.); Doskar, J (Doskar, Jiri); Gotz, F (Goetz, Friedrich); Pantucek, R (Pantucek, Roman) | ||||||||||||||||||
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Abstract:
Kayviruses are polyvalent broad host range staphylococcal phages with a potential to combat staphylococcal infections. However, the implementation of rational phage therapy in medicine requires a thorough understanding of the interactions between bacteriophages and pathogens at omics level. To evaluate the effect of a phage used in therapy on its host bacterium, we performed differential transcriptomic analysis by RNA-Seq from bacteriophage K of genus Kayvirus infecting two Staphylococcus aureus strains, prophage-less strain SH1000 and quadruple lysogenic strain Newman. The temporal transcriptional profile of phage K was comparable in both strains except for a few loci encoding hypothetical proteins. Stranded sequencing revealed transcription of phage noncoding RNAs that may play a role in the regulation of phage and host gene expression. The transcriptional response of S. aureus to phage K infection resembles a general stress response with differential expression of genes involved in a DNA damage response. The host transcriptional changes involved upregulation of nucleotide, amino acid and energy synthesis and transporter genes and downregulation of host transcription factors. The interaction of phage K with variable genetic elements of the host showed slight upregulation of gene expression of prophage integrases and antirepressors. The virulence genes involved in adhesion and immune evasion were only marginally affected, making phage K suitable for therapy. IMPORTANCE Bacterium Staphylococcus aureus is a common human and veterinary pathogen that causes mild to life-threatening infections. As strains of S. aureus are becoming increasingly resistant to multiple antibiotics, the need to search for new therapeutics is urgent. A promising alternative to antibiotic treatment of staphylococcal infections is a phage therapy using lytic phages from the genus Kayvirus. Here, we present a comprehensive view on the phage-bacterium interactions on transcriptomic level that improves the knowledge of molecular mechanisms underlying the Kayvirus lytic action. The results will ensure safer usage of the phage therapeutics and may also serve as a basis for the development of new antibacterial strategies.
Bacterium Staphylococcus aureus is a common human and veterinary pathogen that causes mild to life-threatening infections. As strains of S. aureus are becoming increasingly resistant to multiple antibiotics, the need to search for new therapeutics is urgent. |
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| Author(s): Palacek, S (Palacek, S.); Beseda, M (Beseda, M.); Kalus, R (Kalus, R.); Benhenni, M (Benhenni, M.); Gadea, FX (Gadea, F. X.); Leininger, T (Leininger, T.); Yousfi, M (Yousfi, M.) | ||||||
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| Abstract: A detailed dynamical study is presented for N-2(+)/He collisions running in the electronic ground state of the collision complex. Hybrid, quantum-classical dynamical calculations have been performed considering a broad range of collision energies (E-coll = 0.01-100 eV) and various initial rotational-vibrational excitations of the N-2(+) ion. Both non-reactive and reactive (N-2(+) collision-induced dissociation) cross-sections have been calculated with the momentum-transfer approximation applied to the former ones. A thorough comparison with pseudo-experimental data obtained from mobility measurements reported in the literature via an inverse-method approach has been performed and the effect of the rotational alignment of the N-2(+) ion on calculated cross-sections has been assessed and analyzed. | ||||||
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| Record 36 of 349 | ||||||
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| Author(s): Chrenko, O (Chrenko, O.); Chametla, RO (Chametla, R. O.); Nesvorny, D (Nesvorny, D.); Flock, M (Flock, M.) | ||||||
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Abstract:
Context. The occurrence rate of observed sub-Neptunes has a break at 0.1 au, which is often attributed to a migration trap at the inner rim of protoplanetary disks where a positive co-rotation torque prevents inward migration.
Aims. We argue that conditions in inner disk regions are such that sub-Neptunes are likely to open gaps, lose the support of the co-rotation torque as their co-rotation regions become depleted, and the trapping efficiency then becomes uncertain. We study what it takes to trap such gap-opening planets at the inner disk rim. Methods. We performed 2D locally isothermal and non-isothermal hydrodynamic simulations of planet migration. A viscosity transition was introduced in the disk to (i) create a density drop and (ii) mimic the viscosity increase as the planet migrated from a dead zone towards a region with active magneto-rotational instability (MRI). We chose TOI-216b as a Neptune-like upper-limit test case, but we also explored different planetary masses, both on fixed and evolving orbits. Results. For planet-to-star mass ratios q similar or equal to (4-8) x 10(-5), the density drop at the disk rim becomes reshaped due to a gap opening and is often replaced with a small density bump centred on the planet's co-rotation. Trapping is possible only if the bump retains enough gas mass and if the co-rotation region becomes azimuthally asymmetric, with an island of librating streamlines that accumulate a gas overdensity ahead of the planet. The overdensity exerts a positive torque that can counteract the negative torque of spiral arms. Under suitable conditions, the overdensity turns into a Rossby vortex. In our model, efficient trapping depends on the alpha viscosity and its contrast across the viscosity transition. In order to trap TOI-216b, alpha(DZ) = 10(-3) in the dead zone requires alpha(MRI) greater than or similar to 5 x 10(-2) in the MRI-active zone. If alpha(DZ) = 5 x 10(-4), alpha(MRI) greater than or similar to 7.5 x 10(-2) is needed. Conclusions. We describe a new regime of a migration trap relevant for massive (sub-)Neptunes that puts valuable constraints on the levels of turbulent stress in the inner part of their natal disks. |
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| Record 37 of 349 |
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| Author(s): Meltzer, T (Meltzer, T.); Masin, Z (Masin, Z.) |
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| Abstract: We introduce a new variational R-matrix model called polarization-consistent coupled Hartree-Fock (PC-CHF). The PC-CHF model describes polarization and multi-channel effects in polyatomic molecules, whilst using a simple Hartree-Fock-like description of the ionic states. Furthermore, the model is constructed in a self-consistent manner meaning that all of the target states implied by the polarization configurations are included. The PC-CHF model is applied to three molecular targets ranging from small to intermediate i.e., H2O, N2O and formic acid (HCOOH) and the results are compared against other established R-matrix models as well as data from the literature. |
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| Author(s): Sorzano, COS (Sorzano, C. O. S.); Jimenez-Moreno, A (Jimenez-Moreno, A.); Maluenda, D (Maluenda, D.); Martinez, M (Martinez, M.); Ramirez-Aportela, E (Ramirez-Aportela, E.); Krieger, J (Krieger, J.); Melero, R (Melero, R.); Cuervo, A (Cuervo, A.); Conesa, J (Conesa, J.); Filipovic, J (Filipovic, J.); Conesa, P (Conesa, P.); del Cano, L (del Cano, L.); Fonseca, YC (Fonseca, Y. C.); Jimenez-de la Morena, J (Jimenez-de la Morena, J.); Losana, P (Losana, P.); Sanchez-Garcia, R (Sanchez-Garcia, R.); Strelak, D (Strelak, D.); Fernandez-Gimenez, E (Fernandez-Gimenez, E.); de Isidro-Gomez, FP (de Isidro-Gomez, F. P.); Herreros, D (Herreros, D.); Vilas, JL (Vilas, J. L.); Marabini, R (Marabini, R.); Carazo, JM (Carazo, J. M.) | ||||||||||||||||||
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| Abstract: Cryo-electron microscopy (cryoEM) has become a well established technique to elucidate the 3D structures of biological macromolecules. Projection images from thousands of macromolecules that are assumed to be structurally identical are combined into a single 3D map representing the Coulomb potential of the macromolecule under study. This article discusses possible caveats along the image-processing path and how to avoid them to obtain a reliable 3D structure. Some of these problems are very well known in the community. These may be referred to as sample-related (such as specimen denaturation at interfaces or non-uniform projection geometry leading to underrepresented projection directions). The rest are related to the algorithms used. While some have been discussed in depth in the literature, such as the use of an incorrect initial volume, others have received much less attention. However, they are fundamental in any data-analysis approach. Chiefly among them, instabilities in estimating many of the key parameters that are required for a correct 3D reconstruction that occur all along the processing workflow are referred to, which may significantly affect the reliability of the whole process. In the field, the term overfitting has been coined to refer to some particular kinds of artifacts. It is argued that overfitting is a statistical bias in key parameter-estimation steps in the 3D reconstruction process, including intrinsic algorithmic bias. It is also shown that common tools (Fourier shell correlation) and strategies (gold standard) that are normally used to detect or prevent overfitting do not fully protect against it. Alternatively, it is proposed that detecting the bias that leads to overfitting is much easier when addressed at the level of parameter estimation, rather than detecting it once the particle images have been combined into a 3D map. Comparing the results from multiple algorithms (or at least, independent executions of the same algorithm) can detect parameter bias. These multiple executions could then be averaged to give a lower variance estimate of the underlying parameters. | ||||||||||||||||||
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| Record 39 of 349 | ||||||
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| Author(s): Merkerova, MD (Merkerova, Michaela Dostalova); Klema, J (Klema, Jiri); Kundrat, D (Kundrat, David); Szikszai, K (Szikszai, Katarina); Krejcik, Z (Krejcik, Zdenek); Hrustincova, A (Hrustincova, Andrea); Trsova, I (Trsova, Iva); Le, AV (Anh Vu Le); Cermak, J (Cermak, Jaroslav); Jonasova, A (Jonasova, Anna); Belickova, M (Belickova, Monika) | ||||||
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| Abstract: Background/Aim: Prediction of response to azacitidine (AZA) treatment is an important challenge in hematooncology. In addition to protein coding genes (PCGs), AZA efficiency is influenced by various noncoding RNAs (ncRNAs), including long ncRNAs (lncRNAs), circular RNAs (circRNAs), and transposable elements (TEs). Materials and Methods: RNA sequencing was performed in patients with myelodysplastic syndromes or acute myeloid leukemia before AZA treatment to assess contribution of ncRNAs to AZA mechanisms and propose novel disease prediction biomarkers. Results: Our analyses showed that lncRNAs had the strongest predictive potential. The combined set of the best predictors included 14 lncRNAs, and only four PCGs, one circRNA, and no TEs. Epigenetic regulation and recombinational repair were suggested as crucial for AZA response, and network modeling defined three deregulated lncRNAs (CTC-482H14.5, RP11-419K12.2, and RP11-736I24.4) associated with these processes. Conclusion: The expression of various ncRNAs can influence the effect of AZA and new ncRNA-based predictive biomarkers can be defined. | ||||||
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| Record 40 of 349 | ||||||
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| Author(s): Hurta, M (Hurta, Martin); Drahosova, M (Drahosova, Michaela); Mrazek, V (Mrazek, Vojtech) | ||||||
| Edited by: Rudolph G; Kononova AV; Aguirre H; Kerschke P; Ochoa G; Tusar T | ||||||
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| Abstract: The aim of this work is to design a hardware-efficient implementation of data preprocessing in the task of levodopa-induced dyskinesia classification. In this task, there are three approaches implemented and compared: 1) evolution of magnitude approximation using Cartesian genetic programming, 2) design of preprocessing unit using two-population coevolution (2P-CoEA) of cartesian programs and fitness predictors, which are small subsets of training set, and 3) a design using three-population coevolution (3P-CoEA) combining compositional coevolution of preprocessor and classifier with coevolution of fitness predictors. Experimental results show that all of the three investigated approaches are capable of producing energy-saving solutions, suitable for implementation in hardware unit, with a quality comparable to baseline software implementation. Design of approximate magnitude leads to correctly working solutions, however, more energy-demanding than other investigated approaches. 3P-CoEA is capable of designing both preprocessor and classifier compositionally while achieving smaller solutions than the design of approximate magnitude. Presented 2P-CoEA results in the smallest and the most energy-efficient solutions along with producing a solution with significantly better classification quality for one part of test data in comparison with the software implementation. | ||||||
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| ISBN: 978-3-031-14714-2; 978-3-031-14713-5 |
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| Author(s): Wos, G (Wos, Guillaume); Mackova, L (Mackova, Lenka); Kubikova, K (Kubikova, Katerina); Kolar, F (Kolar, Filip) | |||||||||
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| Abstract: Premise Endoreduplication, nonheritable duplication of a nuclear genome, is widespread in plants and plays a role in developmental processes related to cell differentiation. However, neither ecological nor cytological factors influencing intraspecific variation in endoreduplication are fully understood. Methods We cultivated plants covering the range-wide natural diversity of diploid and tetraploid populations of Arabidopsis arenosa in common conditions to investigate the effect of original ploidy level on endoreduplication. We also raised plants from several foothill and alpine populations from different lineages and of both ploidies to test for the effect of elevation. We determined the endoreduplication level in leaves of young plants by flow cytometry. Using RNA-seq data available for our populations, we analyzed gene expression analysis in individuals that differed in endoreduplication level. Results We found intraspecific variation in endoreduplication that was mainly driven by the original ploidy level of populations, with significantly higher endoreduplication in diploids. An effect of elevation was also found within each ploidy, yet its direction exhibited rather regional-specific patterns. Transcriptomic analysis comparing individuals with high vs. low endopolyploidy revealed a majority of differentially expressed genes related to the stress and hormone response and to modifications especially in the cell wall and in chloroplasts. Conclusions Our results support the general assumption of higher potential of low-ploidy organisms to undergo endoreduplication and suggest that endoreduplication is further integrated within the stress response pathways for a fine-tune adjustment of the endoreduplication process to their local environment. | |||||||||
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| Record 42 of 349 | ||||||||||||||||||
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| Author(s): Matys, M (Matys, M.); Bulanov, SV (Bulanov, S., V); Kucharik, M (Kucharik, M.); Jirka, M (Jirka, M.); Nikl, J (Nikl, J.); Kecova, M (Kecova, M.); Proska, J (Proska, J.); Psikal, J (Psikal, J.); Korn, G (Korn, G.); Klimo, O (Klimo, O.) | ||||||||||||||||||
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| Abstract: In this work, we investigate the application of the plasma shutters for heavy ion acceleration driven by a high-intensity laser pulse. We use particle-in-cell and hydrodynamic simulations. The laser pulse, transmitted through the opaque shutter, gains a steep-rising front and its peak intensity is locally increased at the cost of losing part of its energy. These effects have a direct influence on subsequent ion acceleration from the ultrathin target behind the shutter. In our 3D simulations of silicon nitride plasma shutter and a silver target, the maximal energy of high-Z ions increases significantly when the shutter is included for both linearly and circularly polarized laser pulses. Moreover, application of the plasma shutter for linearly polarized pulse results in focusing of ions toward the laser axis in the plane perpendicular to the laser polarization. The generated high energy ion beam has significantly lower divergence compared to the broad ion cloud, generated without the shutter. The effects of prepulses are also investigated assuming a double plasma shutter. The first shutter can withstand the assumed sub-ns prepulse (treatment of ns and ps prepulses by other techniques is assumed) and the pulse shaping occurs via interaction with the second shutter. On the basis of our theoretical findings, we formulated an approach toward designing a double plasma shutter for high-intensity and high-power laser pulses and built a prototype. | ||||||||||||||||||
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| Record 43 of 349 | ||||||||||||
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| Author(s): Zadnik, M (Zadnik, Martin); Wrona, J (Wrona, Jan); Hynek, K (Hynek, Karel); Cejka, T (Cejka, Tomas); Husak, M (Husak, Martin) | ||||||||||||
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| Abstract: Network-based monitoring and intrusion detection systems generate a high number of alerts reporting the suspicious activity of IP addresses. The majority of alerts are dropped due to their low relevance, low priority, or due to high number of alerts themselves. We assume that these alerts still contain valuable information, namely, about the coordination of IP addresses. Knowledge of the coordinated IP addresses improves situational awareness and reflects the requirement of security analysts as well as automated reasoning tools to have as much contextual information as possible to make an informed decision. To validate our assumption, we introduce a novel method to discover the groups of coordinated IP addresses that exhibit a temporal correlation of their alerts. We evaluate our method on data from a real sharing platform reporting approximately 1.5 million alerts per day. The results show that our method can indeed discover groups of truly coordinated IP addresses. | ||||||||||||
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| Record 44 of 349 | |||||||||
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| Author(s): Yildiz, B (Yildiz, Bugra); Erkisi, A (Erkisi, Aytac); Surucu, G (Surucu, Gokhan) | |||||||||
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| Abstract: In this study, magnetic and electronic nature, optical behavior, and elasticity properties of YMnS2 compound have been investigated by using density functional theory (DFT). The compound belongs to the chalcopyrite family having tetragonal crystal structure with 122 (I-42d) space group. Firstly, the optimization process has been done for ferromagnetic, antiferromagnetic, and paramagnetic orders to find most stable magnetic order and the formation energies have been determined. Negative formation energies prove that our compound is energetically synthesizable and structurally stable. For this compound, plotted energy change with respect to volume curves show that ferromagnetic order is most stable. It is understood from the electronic band structure obtained with Perdew-Burke-Ernzerhof functional within Generalized Graident Approximation, which has 1.27 eV band gap for spin-up orientation and metallic for spin-down orientation, so overall YMnS2 compound has a half metallic nature. Moreover, the electronic band structure has been obtained with HSE06 functionals that indicates the half-metallic nature with 3.20 eV band gap in spin-up orientation and metallic nature in spin-down orientation. To understand optical properties, frequency dependent complex dielectric functions have been determined. Then, some optical properties have been investigated using the imaginary and real parts of the dielectric function. In addition to that, YMnS2 compound is mechanically stable according to Born-Huang stability criteria. Also, this new chalcopyrite compound is considered to be ductile, which is important for its use in technological applications. | |||||||||
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| Record 45 of 349 |
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| Author(s): Radil, J (Radil, Jan); Vojtech, J (Vojtech, Josef) |
| Book Group Author(s): IEEE |
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| Abstract: In this contribution, the mutual interference of bidirectional Erbium doped fiber amplification of coherent optical frequency transfer and Raman amplification used for high speed data transmission, will be investigated experimentally. |
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| Conference Sponsors: IEEE, European Frequency & Time Forum, SFMC, IEEE Ultroson, Ferroelectr & Frequency Control Soc |
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| ISBN: 978-1-6654-9718-3 |
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| Author(s): Padilla-Garcia, N (Padilla-Garcia, Nelida); Sramkova, G (Sramkova, Gabriela); Zaveska, E (Zaveska, Eliska); Slenker, M (Slenker, Marek); Clo, J (Clo, Josselin); Zeisek, V (Zeisek, Vojtech); Lucanova, M (Lucanova, Magdalena); Rurane, I (Rurane, Ieva); Kolar, F (Kolar, Filip); Marhold, K (Marhold, Karol) | |||||||||||||||||||||
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| Abstract: Aim Although whole-genome duplication (WGD) is an important speciation force, we still lack a consensus on the role of niche differentiation in polyploid evolution. In addition, the role of genome doubling per se vs. later divergence on polyploid niche evolution remains obscure. One reason for this might be that the intraspecific genetic structure of polyploid complexes and interploidy gene flow is often neglected in ecological studies. Here, we aim to investigate to which extent these evolutionary processes impact our inference on niche differentiation of autopolyploids. Location Europe. Taxon Arabidopsis arenosa (Brassicaceae). Methods Leveraging a total of 352 cytotyped populations of diploid-autotetraploid A. arenosa, we examined differences among climatic niches of diploid and tetraploid lineages both globally, and independently for each tetraploid lineage with respect to the niche of its evolutionary closest relative. Then, we tested whether there was an effect of additional interploidy introgression from other sympatric but ancestrally divergent diploid lineages of A. arenosa on climatic niches of tetraploids. Results Ecological niche shift of tetraploids is only detected when the assignment of populations to intraspecific genetic lineages is considered. We found different patterns of climatic niche evolution (i.e. niche conservatism, contraction or expansion) in each tetraploid lineage when compared to its evolutionary closest relatives. We observed an effect of interploidy gene flow in patterns of climatic niche evolution of the tetraploid ruderal lineage of A. arenosa. Main conclusions The niche shift of tetraploids in A. arenosa is not driven by WGD per se but rather reflects dynamic post-WGD evolution in the species, involving tetraploid migration out of their ancestral area and interploidy introgression with other diploid lineages. Our study supports that evolutionary processes following WGD-which usually remain undetected by studies neglecting evolutionary history of polyploids-may play a key role in the adaptation of polyploids to challenging environments. | |||||||||||||||||||||
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| Author(s): Mendieta-Moreno, JI (Mendieta-Moreno, Jesus, I); Mallada, B (Mallada, Benjamin); de la Torre, B (de la Torre, Bruno); Cadart, T (Cadart, Timothee); Kotora, M (Kotora, Martin); Jelinek, P (Jelinek, Pavel) | |||||||||||||||||||||
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| Abstract: Chemical transformation of polyaromatic hydrocarbon (PAH) molecules following different reaction strategies has always been the focus of organic synthesis. In this work, we report the synthesis of a PAH molecule, formation of which consists of an unusual C-C bond cleavage accompanied by a complex pi-conjugated molecular scaffold rearrangement. We demonstrate that the complex chemical transformation is steered by concerted motion of individual Au-0 gold atoms on a supporting Au(111) surface. This observation underpins the importance of single-atom catalysis mediated by adatoms in on-surface synthesis as well as catalytic activity of single Au-0 atoms facilitating cleavage of covalent carbon bonds. | |||||||||||||||||||||
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| Record 48 of 349 | |||||||||
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| Author(s): Hantova, K (Hantova, Kamila); Houska, J (Houska, Jiri) | |||||||||
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| Abstract: Crystalline zinc oxide thin films are important due to a combination of optical transparency, electrical conductivity, and piezoelectric and pyroelectric properties. These functional properties are improved with increasing perfection of the crystalline structure. In this paper, classical molecular dynamics with a reactive force field was used to simulate the atom-by-atom growth of ZnOx films on a crystalline template. Contrary to previous modeling studies, the effect of a wide range of process parameters (elemental ratio x, kinetic energy of arriving atoms, and fraction of fast atoms in the particle flux) on the film crystallinity was investigated. All the parameters were found to have a significant impact. Counterintuitively, the highest crystal quality was obtained for slightly overstoichiometric films with x > 1. The results provide a quantitative insight into the role of individual deposition parameters, and the identification of their optimum values facilitates a further improvement of the film properties. | |||||||||
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| Author(s): Krizek, F (Krizek, Filip); Reimers, S (Reimers, Sonka); Kaspar, Z (Kaspar, Zdenek); Marmodoro, A (Marmodoro, Alberto); Michalicka, J (Michalicka, Jan); Man, O (Man, Ondrej); Edstrom, A (Edstrom, Alexander); Amin, OJ (Amin, Oliver J.); Edmonds, KW (Edmonds, Kevin W.); Campion, RP (Campion, Richard P.); Maccherozzi, F (Maccherozzi, Francesco); Dhesi, SS (Dhesi, Samjeet S.); Zubac, J (Zubac, Jan); Kriegner, D (Kriegner, Dominik); Carbone, D (Carbone, Dina); Zelezny, J (Zelezny, Jakub); Vyborny, K (Vyborny, Karel); Olejnik, K (Olejnik, Kamil); Novak, V (Novak, Vit); Rusz, J (Rusz, Jan); Idrobo, JC (Idrobo, Juan-Carlos); Wadley, P (Wadley, Peter); Jungwirth, T (Jungwirth, Tomas) | ||||||||||||||||||||||||||||||||||||||||||
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| Abstract: The interest in understanding scaling limits of magnetic textures such as domain walls spans the entire field of magnetism from its physical fundamentals to applications in information technologies. Here, we explore antifer-romagnetic CuMnAs in which imaging by x-ray photoemission reveals the presence of magnetic textures down to nanoscale, reaching the detection limit of this established microscopy in antiferromagnets. We achieve atomic resolution by using differential phase-contrast imaging within aberration-corrected scanning transmission electron microscopy. We identify abrupt domain walls in the antiferromagnetic film corresponding to the Neel order reversal between two neighboring atomic planes. Our work stimulates research of magnetic textures at the ultimate atomic scale and sheds light on electrical and ultrafast optical antiferromagnetic devices with magnetic field-insensitive neuromorphic functionalities. | ||||||||||||||||||||||||||||||||||||||||||
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| Author(s): Matasovic, L (Matasovic, Lujo); Panic, B (Panic, Barbara); Bubas, M (Bubas, Matej); Vancik, H (Vancik, Hrvoj); Biljan, I (Biljan, Ivana); Roncevic, I (Roncevic, Igor) | |||||||||
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| Abstract: Using the dinitrosobenzene polymer (1) as a model, we explore how the electronic, transport, and optical properties of a conjugated organic semiconductor can be modulated. Combining computational and experimental tools, we explore the effects of solid-state packing, backbone torsion, surface adsorption, the conjugation in the aromatic core, and substituents. The band gap (E-g) and optical spectrum of 1 are calculated using both GW-BSE with zero-gap renormalization (ZGR) and hybrid TD-DFT, with the former method predicting a value (2.41 eV) in excellent agreement with our diffuse reflectance spectroscopy measurements (2.39 eV). Using GW-BSE-ZGR, changes occurring upon solid-state packing are separated into a contribution arising from (i) the change in the torsional angle and (ii) the change in the screened Coulombic interaction, which strongly affects the exciton binding energies. Comprehensive hybrid TD-DFT calculations find that the effects of substituents on E-g and on transport properties can mostly be explained through changes in the torsional angle theta, and predict a linear dependence between theta and E-g. Extending the conjugation in the aromatic core is found to enhance transport properties and narrow E-g, identifying future synthetic targets. Atomic force microscopy and spectroscopic ellipsometry are used to study 1 adsorbed to a (111) gold surface (1@Au), with the latter method showing a significant narrowing of the band gap to 0.68 eV, in good agreement with TD-DFT predictions. | |||||||||
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| Author(s): He, JJ (He, Junjie); Li, S (Li, Shuo); Zhou, LJ (Zhou, Liujiang); Frauenheim, T (Frauenheim, Thomas) | |||||||||||||||
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| Abstract: Ultrafast optical control of magnetism had great potential to revolutionizemagnetic storage technology and spintronics, but for now, its potential remains mostlyuntapped in two-dimensional (2D) magnets. Here, using the state-of-the-art real-time time-dependent density functional theory (rt-TDDFT), we demonstrate that an ultrafast laser pulsecan induce a ferromagnetic state in nonmagnetic MoSe2monolayers interfaced with van derWaals (vdW) ferromagnetic MnSe2. Our results show that the transient ferromagnetism inMoSe2derives from photoinduced direct ultrafast interlayer spin transfer from Mn to Mo via avdW-coupled interface, albeit with a delay of approximately a few femtoseconds. This delaywas strongly dependent on laser duration and interlayer coupling, which could be used to tunethe amplitude and rate spin transfer. Furthermore, we have also shown that ferromagneticstates can be photoinduced in other transition metal dichalcogenides (TMDs), such as PtS2and TaSe2monolayers. Overall, ourfindings provide crucial physical insights for exploringlight-induced interlayer spin and charge dynamics in 2D magnetic systems | |||||||||||||||
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| Record 52 of 349 | ||||||||||||
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| Author(s): Kolarikova, A (Kolarikova, Alena); Kutalkova, E (Kutalkova, Eva); Bus, V (Bus, Vaclav); Witasek, R (Witasek, Roman); Hrncirik, J (Hrncirik, Josef); Ingr, M (Ingr, Marek) | ||||||||||||
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| Abstract: Hyaluronic acid (HA) is a natural polysaccharide present in the connective tissues of vertebrates, often used in the cosmetics and pharmaceutical industries. HA is a strongly hydrophilic macromolecule forming highly swollen random coils in aqueous solutions. Although some authors reported the secondary and tertiary structures of HA chain, others brought convincing evidence contradicting this hypothesis. This study aims at investigation of the stability and dynamics of the temporary duplex HA structures at different NaCl concentrations by molecular dynamics (MD) simulations. The tendency to duplex formation grows with NaCl concentration reaching its maximum at 0.6 M. This profile is a result of two counteracting NaCl-concentration dependent phenomena, the growing electrostatic-repulsion screening on one side and the disturbance of hydrogen-bonds formation on the other side. Although the weak intermolecular attraction cannot lead to long-lived secondary and tertiary structures, it may influence the properties of large HA macromolecules and concentrated HA solutions. | ||||||||||||
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| Record 53 of 349 | ||||||||||||
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| Author(s): Dockal, J (Dockal, Jan); Lisal, M (Lisal, Martin); Moucka, F (Moucka, Filip) | ||||||||||||
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| Abstract: Understanding the microscopic behavior of aqueous electrolyte solutions in contact with graphene and related carbon surfaces is important in electrochemical technologies, such as capacitive deionization or supercapacitors. In this work, we focus on preferential adsorption of ions in mixed alkali-halide electrolytes containing different fractions of Li+/Na+ or Li+/K+ and/or Na+/K+ cations with Cl- anions dissolved in water. We performed molecular dynamics simulations of the solutions in contact with both neutral and positively and negatively charged graphene surfaces under ambient conditions, using the effectively polarizable force field. The simulations show that large ions are often intuitively attracted to oppositely charged electrodes. In contrast, the adsorption behavior of small ions tends to be counterintuitive. In mixed-cation solutions, one of the cations always supports the adsorption of the other cation, while the other cation weakens the adsorption of the first cation. In mixed-cation solutions containing large and small cations simultaneously, adsorption of the larger cations varies dramatically with the electrode charge in an intuitive way, while adsorption of the smaller cations changes oppositely, i.e., in a counterintuitive way. For (Li/K)Cl mixed-cation solutions, these effects allow the control of Li+ adsorption by varying the electrode charge, whereas, for LiCl single-salt solutions, Li+ adsorption is nearly independent of the electrode charge. We rationalize this cation-cation lever effect as a result of a competition between three driving forces: (i) direct graphene-ion interactions, (ii) the strong tendency of the solutions to saturate the network of non-covalent intermolecular bonds, and (iii) the tendency to suppress local charge accumulation in any region larger than typical interparticle distances. We analyze the driving forces in detail using a general method for intermolecular bonding based on spatial distribution functions and different contributions to the total charge density profiles. The analysis helps to predict whether an ion is more affected by each of the three driving forces, depending on the strength of the ion solvation shells and the compatibility between the contributions of the charge density profiles due to the ion and water molecules. This approach is general and can also be applied to other solutions under different thermodynamic conditions. | ||||||||||||
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| Record 54 of 349 | ||||||||||||||||||
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| Author(s): Kobera, L (Kobera, Libor); Dedecek, J (Dedecek, Jiri); Klein, P (Klein, Petr); Tabor, E (Tabor, Edyta); Brus, J (Brus, Jiri); Fishchuk, AV (Fishchuk, Anna, V); Sklenak, S (Sklenak, Stepan) | ||||||||||||||||||
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| Abstract: Framework Al-FR Lewis sites represent a substantial portion of active sites in H-BEA zeolite catalysts activated at low temperatures. We studied their nature by Al-27 WURST-QCPMG nuclear magnetic resonance (NMR) and proposed a plausible mechanism of their formation based on periodic density functional theory calculations constrained by H-1 MAS, Al-27 WURST-QCPMG, and Si-29 MAS NMR experiments and FTIR measurements. Our results show that the electron-pair acceptor of Al-FR Lewis sites corresponds to an Al-TRI atom tricoordinated to the zeolite framework, which adsorbs a water molecule. This Al-TRI-OH2 complex is reflected in Al-27 NMR resonance with delta(iso) = 70 +/- 5 ppm and C-Q = 13 +/- 2 MHz. In addition, the Al-TRI atom with adsorbed acetonitrile-d(3) (the probe of Al-FR Lewis sites in FTIR spectroscopy) exhibits a similar Al-27 NMR resonance. We suggest that these Al-FR Lewis sites are formed from Al-OH-Si-O-Si-O-Si-OH-Al sequences located in 12-rings (i.e., close unpaired Al atoms). Published under an exclusive license by AIP Publishing. | ||||||||||||||||||
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| Record 55 of 349 | ||||||||||||
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| Author(s): Synoradzki, K (Synoradzki, K.); Skokowski, P (Skokowski, P.); Frackowiak, L (Frackowiak, L.); Koterlyn, M (Koterlyn, M.); Sebesta, J (Sebesta, J.); Legut, D (Legut, D.); Tolinski, T (Tolinski, T.) | ||||||||||||
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| Abstract: We present the magnetic, specific heat, electrical resistivity, and thermoelectric power measurements for the intermetallic compound CeSi1.2Ga0.8. This composition belongs to the series CeSi2-xGax, which exhibits diverse magnetic orderings and different crystallographic structures depending on the substitution level x. It has been previously suggested that for 0.0 < x < 1.3 the compounds crystallize in the alpha-ThSi2 type structure and for 0.7 < x < 1.3 they order ferromagnetically below 14 K. Our complementary studies for x = 0.8 reveal that it is a complex system due to the Kondo scattering competing with the RKKY interactions. The transition from the paramagnetic to the ferromagnetic state takes place at T-C = 12.5(1) K. Moreover, the Seebeck coefficient and electrical resistivity show not only an anomaly related to the magnetic transition, but also a broad maximum at-90 K related to the crystal field effect. The case of x = 0.8 is of special interest as it is at the crossing of the characteristic temperatures, i.e. T-ord (magnetic ordering temperature)similar to & nbsp; T-K (Kondo temperature) similar to 10 K. Additionally, ab initio electronic structure calculations were performed allowing us to determine phase stability, (revealing two stable phases -alpha-GdSi2-type and alpha-ThSi2-type structures) as well as spin and orbital moment decomposition on Ce-states for both considered structures. | ||||||||||||
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| Record 56 of 349 | ||||||
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| Author(s): Fanta, R (Fanta, Roman); Dubecky, M (Dubecky, Matus) | ||||||
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| Record 57 of 349 | ||||||
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| Author(s): Beseda, M (Beseda, M.); Palacek, S (Palacek, S.); Gadea, FX (Gadea, F. X.); Leininger, T (Leininger, T.); Kalus, R (Kalus, R.); Benhenni, M (Benhenni, M.); Yousfi, M (Yousfi, M.) | ||||||
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| Abstract: As a first step towards realistic modeling of transport properties of the N-2(+) ion in helium gas, detailed investigations of the electronic structure of the ion as well as the N-2(+) /He collision complex have been performed with the main focus on computational efficiency and accuracy. A broad range of correlation consistent basis sets and representative orbital spaces have been considered for both computationally cheap multi-configuration self -consistent field (MCSCF) methods and benchmark multi-reference configuration interaction (MRCI) approaches. It has been found that the computationally advantageous MCSCF approach, even if combined with basis sets of moderate sizes, leads to an acceptable accuracy and is thus suitable for direct dynamics simulations of N+2 /He collisions to be addressed in subsequent works. | ||||||
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| Record 58 of 349 | ||||||||||||
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| Author(s): Nguyen, NT (Nhat-Tien Nguyen); Nguyen, HN (Hong-Nhu Nguyen); Le, AT (Anh-Tu Le); Nguyen, ND (Nhan Duc Nguyen); Do, DT (Dinh-Thuan Do); Voznak, M (Voznak, Miroslav) | ||||||||||||
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| Abstract: The evolution of non-orthogonal multiple access (NOMA) has raised many opportunities for massive connectivity with less latency in signal transmissions at great distances. We aim to integrate NOMA with a satellite communications network to evaluate system performance under the impacts of imperfect channel state information and co-channel interference from nearby systems. In our considered system, two users perform downlink communications under power-domain NOMA. We analyzed the performance of this system with two modes of shadowing effect: heavy shadowing and average shadowing. The detailed performance was analyzed in terms of the outage probability and ergodic capacity of the system. We derive closed-form expressions and performed a numerical analysis. We discover that the performance of two destinations depends on the strength of the transmit power at the satellite. However, floor outage occurs because the system depends on other parameters, such as satellite link modes, noise levels, and the number of interference sources. To verify the authenticity of the derived closed-form expressions, we also perform Monte-Carlo simulations. | ||||||||||||
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| Record 59 of 349 | |||||||||||||||||||||
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| Author(s): Nguyen, TN (Nguyen, Tan N.); Duy, TT (Duy, Tran Trung); Tran, PT (Tran, Phuong T.); Voznak, M (Voznak, Miroslav); Li, XW (Li, Xingwang); Poor, HV (Poor, H. Vincent) | |||||||||||||||||||||
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| Abstract: Full-duplex communication offers enhanced spectral efficiency for relay deployment, but suffers from the inherent self-interference from the strong transmit signal coupling to the sensitive receive chain. In this article, we propose a self-energy recycling (S-ER) protocol for full-duplex multi-relay networks, in which the energy from self-interference is harvested back at the relay for future use. Furthermore, two amplify-and-forward (AF) relay selection algorithms, namely, partial relay selection (PRS) and full relay selection (FRS) are introduced to enhance the reliability of the proposed systems. For PRS, the best relay is selected based on just the knowledge of the channels from the source to all relays, while in FRS, the best relay is selected based on the end-to-end signal-to-noise ratio, which requires knowledge of all source-relay and relay-destination links. We provide a thorough analysis on the outage performance and the spectrum efficiency of the proposed algorithms in both cases: all channel gains are independently but non-identically distributed (i.n.d.) (case 1) or independently, identically distributed (i.i.d.) (case 2) Rayleigh random variables. It is shown that SER and FRS can significantly enhance the performance of FD networks and avoid the outage floor when the number of relays increases, while the outage probability (OP) in PRS case reaches an outage floor. In addition, the end-to-end signal-to-noise ratio in both cases can be minimized if an optimal power-splitting factor is selected. All analytical results are verified by Monte Carlo simulation. | |||||||||||||||||||||
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| Record 60 of 349 | ||||||||||||
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| Author(s): Midlik, A (Midlik, Adam); Varekova, IH (Varekova, Ivana Hutarova); Hutar, J (Hutar, Jan); Chareshneu, A (Chareshneu, Aliaksei); Berka, K (Berka, Karel); Svobodova, R (Svobodova, Radka) | ||||||||||||
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| Abstract: Every protein family has a set of characteristic secondary structures. However, due to individual variations, a single structure is not enough to represent the whole family. OverProt can create a secondary structure consensus, showing the general fold of the family as well as its variation. Our server provides precomputed results for all CATH superfamilies and user-defined computations, visualized by an interactive viewer, which shows the secondary structure element type, length, frequency of occurrence, spatial variability and beta-connectivity. | ||||||||||||
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| Record 61 of 349 | |||||||||
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| Author(s): Kumar, TPR (Kumar, T. P. Ragesh); Nag, P (Nag, P.); Rankovic, M (Rankovic, M.); Luxford, TFM (Luxford, T. F. M.); Kocisek, J (Kocisek, J.); Masin, Z (Masin, Z.); Fedor, J (Fedor, J.) | |||||||||
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| Abstract: We experimentally show that N-H bond cleavage in the pyrrole molecule following resonant electron attachment is allowed and controlled by the motion of the atoms which are not dissociating, namely, of the carbon-attached hydrogen atoms. We use this fact to steer the efficiency of this bond cleavage. In order to interpret the experimental findings, we have developed a method for locating all resonant and virtual states of an electron-molecule system in the complex plane, based on all-electron R-matrix scattering calculations. Mapping these as a function of molecular geometry allows us to separate two contributing dissociation mechanisms: a pi*resonance formation inducing strong bending deformations and a nonresonant sigma* mechanism originating in a virtual state. The coupling between the two mechanisms is enabled by the out-of-plane motion of the C-H bonds, and we show that it must happen on an ultrafast (few fs) time scale. | |||||||||
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| Record 62 of 349 | |||||||||
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| Author(s): Sklenak, S (Sklenak, Stepan); Groizard, T (Groizard, Thomas); Jirglova, H (Jirglova, Hana); Sazama, P (Sazama, Petr); Dedecek, J (Dedecek, Jiri) | |||||||||
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| Abstract: Distant binuclear cationic M(II) centers in transitionmetal-exchanged zeolites were shown to activate dioxygen by its splitting at room temperature to form a pair of very active oxygen species (i.e., alpha-oxygens) able to subsequently oxidize methane to methanol at room temperature. Selective oxidations of methane and other hydrocarbons are of extreme importance because of their potential for the transformation of hydrocarbons to valuable products. The reactivity of the alpha-oxygens with dihydrogen was investigated to obtain insight into the reactivity of these unique species. The reduction of Fe(IV)=O centers of pairs of distant alpha-oxygen atoms is a model reaction that allows for the study of the effect of the proximity of the other Fe(IV)=O site on the reactivity of the alpha-oxygen. The reduction by dihydrogen is also the key reaction for the quantification of these unique sites by temperature-programmed reduction (TPR) techniques. Our study reveals that (i) there is no direct concurrent reaction of both the Fe(IV)=O centers of pairs of the distant alpha-oxygen atoms with a molecule of dihydrogen; (ii) first, one Fe(IV)=O site of a pair of the distant alpha-oxygen atoms reacts with H-2(g) to form a water molecule, which is adsorbed on the Fe(II) cation while the other Fe(IV)=O site is intact. Afterward, one of the two H atoms of the adsorbed water molecule migrates to yield two Fe(III)OH groups, which subsequently react with another molecule of dihydrogen to give two water molecules, each adsorbed on one Fe(II) cation; (iii) an isolated Fe(IV)=O site is reduced by the same mechanism as the first Fe(IV)=O site of a pair of the distant alpha-oxygen atoms to yield H2O adsorbed on the Fe(II) cation; and (iv) lower reducibility of the Fe(IV)=O centers of pairs of the distant alpha-oxygen atoms with respect to the isolated Fe(IV)=O sites. | |||||||||
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| Record 63 of 349 |
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| Author(s): Vojtech, J (Vojtech, Josef); Vohnout, R (Vohnout, Rudolf); Havlis, O (Havlis, Ondrej); Pospisil, P (Pospisil, Petr); Slapak, M (Slapak, Martin); Velc, R (Velc, Radek); Altmannova, L (Altmannova, Lada); Horvath, T (Horvath, Tomas); Kundrat, J (Kundrat, Jan); Hazlinsky, M (Hazlinsky, Michal); Andriantsarazo, E (Andriantsarazo, Elizabeth); Ridlichowski, P (Ridlichowski, Piotr) |
| Edited by: Deacon KS; Meyers RE |
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| Abstract: This contribution focuses on experimental verification of the QKD system deployment in a multi-domain network environment managed by Czech and Polish National Research and Educational Network (NREN) operators. We demonstrate full functionality of such a solution for transmission of secret keys in boundary conditions, and with this we open up new possibilities for further use of extremely secure communication between two neighboring network entities, and the services built upon it. Moreover, we have shared the cross-border link among strong QKD service channels, accurate time, and classical data channels together with weak quantum channel to reduce the total number of optical fibers needed for transmission. To our knowledge, this is the first shared cross-border QKD transmission in the region of Central and Eastern Europe (CEE). |
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| Conference Sponsors: SPIE |
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| ISBN: 978-1-5106-5461-7; 978-1-5106-5460-0 |
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| Author(s): Kolejak, P (Kolejak, Pierre); Lezier, G (Lezier, Geoffrey); Postava, K (Postava, Kamil); Lampin, JF (Lampin, Jean-Francois); Tiercelin, N (Tiercelin, Nicolas); Vanwolleghem, M (Vanwolleghem, Mathias) | ||||||||||||
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| Abstract: Polarization control of THz light is of paramount interest for the numerous applications offered in this frequency range. Recent developments in THz spintronic emitters allow for a very efficient broadband emission, and especially unique is their ability of THz polarization switching through magnetization control of the ferromagnetic layer. Here we present an improved scheme to achieve full 360 degrees nearly coherent polarization rotation that does not require multipolar or rotating external magnetic bias nor complex cascaded emitters. By replacing the FM layer of the spintronic emitter with a carefully designed FeCo/TbCo2/FeCo anisotropic heterostructure, we experimentally demonstrate Stoner-Wohlfarth-like coherent rotation of the THz polarization over a full 2 pi azimuth only by a bipolar variation of the strength of the hard axis field, and with only a negligible decrease in the emission efficiency as compared to standard Pt/CoFeB/W inverse spin Hall emitters. THz measurements are in agreement with our model of the nonperfect Stoner-Wohlfarth behavior. These emitters are well adapted for the implementation of polarimetric characterization not requiring any mechanically rotating polarizing elements. An example is given with the characterization of the birefringence in a quartz plate. | ||||||||||||
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| Record 65 of 349 | |||||||||
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| Author(s): Bakovic, V (Bakovic, Vid); Hoglund, A (Hoglund, Andrey); Cerezo, MLM (Cerezo, Maria Luisa Martin); Henriksen, R (Henriksen, Rie); Wright, D (Wright, Dominic) | |||||||||
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| Abstract: How sexual selection affects the genome ultimately relies on the strength and type of selection, and the genetic architecture of the involved traits. While associating genotype with phenotype often utilizes standard trait morphology, trait representations in morphospace using geometric morphometric approaches receive less focus in this regard. Here, we identify genetic associations to a sexual ornament, the comb, in the chicken system (Gallus gallus). Our approach combined genome-wide genotype and gene expression data (>30k genes) with different aspects of comb morphology in an advanced intercross line (F8) generated by crossing a wild-type Red Junglefowl with a domestic breed of chicken (White Leghorn). In total, 10 quantitative trait loci were found associated to various aspects of comb shape and size, while 1,184 expression QTL were found associated to gene expression patterns, among which 98 had overlapping confidence intervals with those of quantitative trait loci. Our results highlight both known genomic regions confirming previous records of a large effect quantitative trait loci associated to comb size, and novel quantitative trait loci associated to comb shape. Genes were considered candidates affecting comb morphology if they were found within both confidence intervals of the underlying quantitative trait loci and eQTL. Overlaps between quantitative trait loci and genome-wide selective sweeps identified in a previous study revealed that only loci associated to comb size may be experiencing on-going selection under domestication. | |||||||||
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| Author(s): Benda, J (Benda, J.); Masin, Z (Masin, Z.); Gorfinkiel, JD (Gorfinkiel, J. D.) | |||||||||
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| Abstract: We employ the recently developed multiphoton R-matrix method for molecular above-threshold photoionization to obtain second-order ionization amplitudes that govern the interference in RABITT experiments. This allows us to extract RABITT time delays that are in better agreement with nonperturbative time-dependent simulations of this process than the typically used combination of first-order (Wigner) delays and asymptotic corrections. We calculate molecular-frame as well as orientation-averaged RABITT delays for H-2, N-2, CO2, H2O, and N2O and analyze the origin of various structures in the time delays including the effects of partial-wave interference, shape resonances, and orientation averaging. Time delays for B and C states of CO2+ are strongly affected by absorption of the second (IR) photon in the ion. This effect corresponds to an additional contribution tau(coupl) to the asymptotic approximation for the RABITT delays tau approximate to tau(mol) + tau(c) + tau(coupl). Applicability of the asymptotic theory depends on the target and IR photon energy but typically starts at approximately 30-35 eV of XUV photon energy. | |||||||||
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| Record 67 of 349 | |||||||||||||||
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| Author(s): Makoveev, A (Makoveev, Anton); Prochazka, P (Prochazka, Pavel); Shahsavar, A (Shahsavar, Azin); Kormos, L (Kormos, Lukas); Krajnak, T (Krajnak, Tomas); Stara, V (Stara, Veronika); Cechal, J (Cechal, Jan) | |||||||||||||||
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| Abstract: Self-assembly and on-surface synthesis are vital strategies used for fabricating surface-confined 1D or 2D su-pramolecular nanoarchitectures with atomic precision. In many systems, the resulting structure is determined by the kinetics of the processes involved, i.e., reaction rate, on-surface diffusion, nucleation, and growth, all of which are typically governed by temperature. However, other external factors have been only scarcely harnessed to control the on-surface chemical reaction kinetics and self-assembly. Here, we show that a low-energy electron beam can be used to steer chemical reaction kinetics and induce the growth of molecular phases unattainable by thermal annealing. The electron beam provides a well-controlled means of promoting the elementary reaction step, i.e., deprotonation of carboxyl groups. The reaction rate increases with the increasing electron beam energy beyond the threshold energy of 6 eV. Our results offer the novel prospect of controlling self-assembly, enhancing the rate of reaction steps selectively, and thus altering the kinetic rate hierarchy. | |||||||||||||||
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| Record 68 of 349 |
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| Author(s): Gebauer, M (Gebauer, Marek); Blejchar, T (Blejchar, Tomas); Brzobohaty, T (Brzobohaty, Tomas); Karasek, T (Karasek, Tomas); Nevrela, M (Nevrela, Miroslav) |
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| Abstract: The energy efficiency of machines is nowadays an intensively studied problem. The efficiency of the induction motor is dominantly influenced by the rotor's and stator winding's temperature. The main goal of the research presented in this paper is to develop a methodology based on Computational Fluid Dynamics (CFD) analysis of internal and external aerodynamics, which is necessary for the optimisation of cooling of the induction motors. In this paper, the theoretical, as well as the numerical study of the internal and external aerodynamics of the induction motor, is described and verified by the experimental measurements. In the CFD-based numerical study, the Reynolds-averaged Navier-Stokes (RANS) turbulence modelling approach was applied to the flow field simulations inside and outside the induction motor. The complexity of the solved problem is increased not only by the geometric asymmetry but also by the flow's asymmetric character caused by the fan's rotation to cool the motor casing. This increases demand, especially on computational resources, as it is impossible to create a simplified numerical model incorporating symmetry. The volume flow of the cooling air and velocity between ribs was measured for the experimental study. Comparing the results of the Computational Fluid Dynamics (CFD) simulations and data obtained from the experimental measurement, we concluded that the results of CFD simulations are in good relationship with the results of experimental measurement and analytical approximations. An experimentally validated CFD model of the induction motor, the so-called digital twin, will be in the future used for virtual optimisation of the new designs concerning minimising losses and maximising efficiency, respectively. |
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| Record 69 of 349 | |||||||||
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| Author(s): Jilek, Z (Jilek, Z.); Caloud, J (Caloud, J.); Zikan, P (Zikan, P.); Obrusnik, A (Obrusnik, A.); Trunec, D (Trunec, D.) | |||||||||
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| Abstract: Two numerical models were used to study the function of an emissive (electron-emitting) probe-the PIC/MC model and the thermal model. The PIC/MC model was used to calculate the I-V characteristics of the emissive probe. The calculations were focussed on the determination of the floating potential of the probe, which increases with increasing probe temperature. It was found that the floating potential can reach the value of the plasma potential, and it can even be higher than the plasma potential. The dependence of the floating potential on probe temperature is linear in the vicinity of the plasma potential, and the slope of this dependence changes when the floating potential equals the plasma potential. The potential profiles near the probe were also calculated and it was found that the space charge effects can be neglected for the plasma parameters studied (electron density 10(14)-10(16) m(-3), electron temperature 2500-40 000 K, probe temperature up to 2500 K). The thermal model was used for the calculation of the dependence of probe temperature and potential profiles on DC current passing through the probe (and heating the probe). The thermal model was based on the heat equation, which was solved using the finite element method. Finally, the results from both the above-mentioned models were combined to obtain the dependencies of floating potential on probe heating DC current. | |||||||||
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| Record 70 of 349 |
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| Author(s): Meca, O (Meca, Ondrej); Riha, L (Riha, Lubomir); Jansik, B (Jansik, Branislav); Brzobohaty, T (Brzobohaty, Tomas) |
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| Abstract: This paper presents an algorithm for highly-parallel loading and processing of unstructured mesh databases in a distributed memory environment of large HPC clusters without collecting data into a single process. The algo-rithm is proved effective, having linear speedup in the large dataset limit. Demonstrated on Ansys CDB, EnSight, VTK Legacy, and XDMF databases, we show that it is possible to efficiently reconstruct meshes with 800 million nodes and 500 million elements in several seconds on thousands of processors, even from databases that were not designed to be read in parallel. The algorithm is implemented in our MESIO library that can be used as (i) an efficient parallel loader (e.g. for numerical physical solvers) or as (ii) a high performing parallel converter be-tween mesh databases. |
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| Record 71 of 349 | ||||||||||||
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| Author(s): Postulka, J (Postulka, Jan); Slavicek, P (Slavicek, Petr); Pysanenko, A (Pysanenko, Andriy); Poterya, V (Poterya, Viktoriya); Farnik, M (Farnik, Michal) | ||||||||||||
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| Abstract: Nanoparticles can serve as an efficient reaction environment for bimolecular reactions as the reactants concentrate either inside the nanoparticle or on the surface of the nanoparticle. The reaction rate is then controlled by the rate of formation of the reaction pairs. We demonstrate this concept on the example of electron-induced reactions in hydrogen peroxide. We consider two types of nanoparticle environments: solid argon particles, only weakly interacting with the hydrogen peroxide reactant, and ice particles with a much stronger interaction. The formation of hydrogen peroxide dimers is investigated via classical molecular dynamics (MD) simulations on a microsecond timescale. With a modified force field for hydrogen peroxide, we found out a fast formation and stabilization of the hydrogen peroxide dimer for argon nanoparticles, while the reaction pair was formed reversibly at a much slower rate on the water nanoparticles. We have further investigated the electron-induced reactions using non-adiabatic ab initio MD simulations, identifying the possible reaction products upon the ionization or electron attachment. The major reaction path in all cases corresponded to a proton transfer. The computational findings are supported by mass spectrometry experiments, where large Ar-M and (H2O)(M) nanoparticles are generated, and several hydrogen peroxide molecules are embedded on these nanoparticles in a pickup process. Subsequently, the nanoparticles are ionized either positively by 70 eV electrons or negatively by electron attachment at electron energies below 5 eV. The recorded mass spectra demonstrate the efficient coagulation of H2O2 on Ar-M, while it is quite limited on (H2O)(M). | ||||||||||||
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| Record 72 of 349 | |||||||||||||||||||||
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| Author(s): Lukova, K (Lukova, K.); Kolesnikova, L (Kolesnikova, L.); Koucky, J (Koucky, J.); Vavra, K (Vavra, K.); Kania, P (Kania, P.); Guillemin, JC (Guillemin, J-C); Urban, S (Urban, S.) | |||||||||||||||||||||
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Abstract:
Aims. The recent detection of cyanomethanimine in the interstellar medium makes its methyl derivative, 2-iminopropanenitrile (CH3C(CN)NH), a promising candidate for an interstellar detection. The aim of this work is to extend the current knowledge of the laboratory rotational spectrum to higher frequencies, which is an essential prerequisite for an identification of the molecular species in the interstellar medium by millimetre-wave astronomy.
Methods. The room-temperature rotational spectrum of 2-iminopropanenitrile has been measured in several frequency regions between 128 and 329 GHz. The A-E splittings of the rotational transitions arising from the methyl top internal rotation were analysed employing the ERHAM and XIAM programs. Results. A dataset of approximately 900 newly assigned rotational transitions in the ground state of the Z isomer and a set of refined molecular constants, including the internal rotation parameters, are reported. Moreover, this work provides the first spectral characterisation of the less stable E isomer ground state, as well as the three lowest-lying vibrationally excited states of the Z isomer, v(21) = 1, v(14) = 1, and v(20) = 1. This comprehensive spectroscopic study will allow a search for 2-iminopropanenitrile in the millimetre-wave surveys of interstellar sources, such as those recorded by the Atacama Large Millimeter/submillimeter Array. |
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| Author(s): Ritacco, I (Ritacco, Ida); Camellone, MF (Camellone, Matteo Farnesi); Caporaso, L (Caporaso, Lucia); Detz, H (Detz, Hermann); Butera, V (Butera, Valeria) | ||||||
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| Abstract: Catalytic CO2 conversion to fuels and chemicals is important for mitigating the climate change and reducing the dependence on fossil resources. In order to achieve this goal on a large industrial level, effective catalysts need to be developed. Among them, gallium nitride (GaN) and related Mg-doped and In-alloyed systems have been proven as efficient materials for the reduction of highly stable CO2 molecules. This work presents a density functional theory (DFT) investigation, performing periodic boundary condition (PBC) calculations which allow to employ a more extended surface for a detailed analysis of the CO2 coverage, and the effect of Mg doping and In alloying on the CO2 adsorption and its conversion to CO. The results show the great potential of GaN(100) surfaces to simultaneously bind and strongly activate multiple CO2 molecules, which is a crucial aspect for an efficient CO2 conversion process. Moreover, the presence of Mg-dopant on the top layer is found to be more beneficial for the CO2 adsorption and activation with respect to both the pristine and In-alloyed system, and this effect is further improved by the inclusion of a second impurity on the top layer. In line with the previous experimental findings, these calculations support the potential of pristine GaN(100) to catalyze the CO2-to-CO reduction. The results presented here offer crucial information for the development of more efficient and selective catalysts for the CO2 reduction. | ||||||
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| Record 74 of 349 | ||||||
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| Author(s): Simonik, M (Simonik, Marek); Krumnikl, M (Krumnikl, Michal) | ||||||
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| Abstract: We present CrossInfoMobileNet, a hand pose estimation convolutional neural network based on CrossInfoNet, specifically tuned to mobile phone processors through the optimization, modification, and replacement of computationally critical CrossInfoNet components. By introducing a state-of-the-art MobileNetV3 network as a feature extractor and refiner, replacing ReLU activation with a better performing H-Swish activation function, we have achieved a network that requires 2.37 times less multiply-add operations and 2.22 times less parameters than the CrossInfoNet network, while maintaining the same error on the state-of-the-art datasets. This reduction of multiply-add operations resulted in an average 1.56 times faster real-world performance on both desktop and mobile devices, making it more suitable for embedded applications. The full source code of CrossInfoMobileNet including the sample dataset and its evaluation is available online through Code Ocean. | ||||||
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| Record 75 of 349 |
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| Author(s): Ponimatkin, G (Ponimatkin, Georgy); Labbe, Y (Labbe, Yann); Russell, B (Russell, Bryan); Aubry, M (Aubry, Mathieu); Sivic, J (Sivic, Josef) |
| Book Group Author(s): IEEE COMP SOC |
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| Abstract: We introduce FocalPose, a neural render-and-compare method for jointly estimating the camera-object 6D pose and camera focal length given a single RGB input image depicting a known object. The contributions of this work are twofold. First, we derive a focal length update rule that extends an existing state-of-the-art render-and-compare 6D pose estimator to address the joint estimation task. Second, we investigate several different loss functions for jointly estimating the object pose and focal length. We find that a combination of direct focal length regression with a re-projection loss disentangling the contribution of translation, rotation, and focal length leads to improved results. We show results on three challenging benchmark datasets that depict known 3D models in uncontrolled settings. We demonstrate that our focal length and 6D pose estimates have lower error than the existing state-of-the-art methods. |
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| Conference Sponsors: IEEE, CVF, IEEE Comp Soc |
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| ISBN: 978-1-6654-6946-3 |
| Record 76 of 349 | |||||||||
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| Author(s): Dostal, Z (Dostal, Zdenek); Horak, D (Horak, David); Kruzik, J (Kruzik, Jakub); Brzobohaty, T (Brzobohaty, Tomas); Vlach, O (Vlach, Oldrich) | |||||||||
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| Abstract: The unpreconditioned hybrid domain decomposition method was recently shown to be a competitive solver for linear elliptic PDE problems discretized by structured grids. Here, we plug H-TFETI-DP (hybrid total finite element tearing and interconnecting dual primal) method into the solution of huge boundary elliptic variational inequalities. We decompose the domain into subdomains that are discretized and then interconnected partly by Lagrange multipliers and partly by edge averages. After eliminating the primal variables, we get a quadratic programming problem with a well-conditioned Hessian and bound and equality constraints that is effectively solvable by specialized algorithms. We prove that the procedure enjoys optimal, i.e., asymptotically linear complexity. The analysis uses recently established bounds on the spectrum of the Schur complements of the clusters interconnected by edge/face averages. The results extend the scope of scalability of massively parallel algorithms for the solution of variational inequalities and show the outstanding efficiency of the H-TFETI-DP coarse grid split between the primal and dual variables. | |||||||||
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| Record 77 of 349 | ||||||
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| Author(s): Klajmon, M (Klajmon, Martin); Cervinka, C (Cervinka, Ctirad) | ||||||
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| Abstract: Molecular dynamics simulations are used for predictions of the glass transition temperatures for a test set of five aprotic ionic liquids. Glass transitions are localized with the trend-shift method, analyzing volumetric and transport properties of bulk amorphous phases. A classical nonpolarizable all-atom OPLS force-field model developed by Canongia Lopes and Padua (CL&P) is employed as a starting level of theory for all calculations. Alternative approaches of charge scaling and the Drude oscillator model, accounting for atomic polarizability either implicitly or explicitly, respectively, are used to investigate the sensitivity of the glass transition temperatures to induction effects. The former nonpolarizable model overestimates the glass transition temperature by tens of Kelvins (37 K on average). The charge-scaling technique yields a significant improvement, and the best estimations were achieved using polarizable simulations with the Drude model, which yielded an average deviation of 11 K. Although the volumetric data usually exhibit a lesser trend shift upon vitrification, their lower statistical uncertainty enables to predict the glass transition temperature with lower uncertainty than the ionic self-diffusivities, the temperature dependence of which is usually more scattered. Additional analyses of the simulated data were also performed, revealing that the Drude model predicts lower densities for most subcooled liquids but higher densities for the glasses than the original CL&P, and that the Drude model also invokes some longer-range organization of the subcooled liquid, greatly impacting the temperature trend of ionic self-diffusivities in the low-temperature region. | ||||||
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| Record 78 of 349 | ||||||||||||
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| Author(s): Fazio, P (Fazio, Peppino); Mehic, M (Mehic, Miralem); Voznak, M (Voznak, Miroslav) | ||||||||||||
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| Abstract: Mobility is a key aspect of modern networking systems. To determine how to better manage the available resources, many architectures aim to a priori know the future positions of mobile nodes. This can be determined, for example, from mobile sensors in a smart city environment or wearable devices carried by pedestrians. If we consider infrastructure networks, frequently changing the coverage cell may lead to service disruptions if a predictive approach is not deployed in the system. All predictive systems are based on the storage of old mobility samples to adequately train the model. Our focus is based on the possibility to determine an approach for adaptively sampling mobility patterns based on the intrinsic features of the human/node behavior. Several works in the literature examine mobility prediction mobile networks, but all of them are dedicated to the study of time features in mobility traces: none took into account the spectral content of historical mobility patterns for predictive purposes. In contrast, we take into account this spectral content in mobility samples. Through a set of wavelet transforms, we adapted the sampling frequency dynamically and obtained a considerable set of advantages (space, energy, accuracy, etc.). In fact, this issue covers an important role in the IoT paradigm, where energy consumption is one of the main variables requiring optimization (frequent and unnecessary mobility samplings can disrupt battery life). We performed several simulations using real-world traces to confirm the merit of our proposal. | ||||||||||||
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| Record 79 of 349 |
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| Author(s): Vetesnik, A (Vetesnik, Ales); Vencovsky, V (Vencovsky, Vaclav); Gummer, AW (Gummer, Anthony W.) |
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| Abstract: The basilar membrane in the cochlea can be modeled as an array of fluid coupled segments driven by stapes vibration and by the undamping nonlinear force simulating cochlear amplification. If stimulated with two tones, the model generates additional tones due to nonlinear distortion. These distortion products (DPs) can be transmitted into the ear canal and produce distortion-product otoacoustic emissions (DPOAEs) known to be generated in the healthy ear of various vertebrates. This study presents a solution for DPs in a two-dimensional nonlinear cochlear model with cochlear roughness-small irregularities in the impedance along the basilar membrane, which may produce additional DPs due to coherent reflection. The solution allows for decomposition of various sources of DPs in the model. In addition to the already described nonlinear-distortion and coherent-reflection mechanisms of DP generation, this study identifies a long-latency DPOAE component due to perturbation of nonlinear force. DP wavelets that are coherently reflected due to impedance irregularities travel toward the stapes across the primary generation region of DPs and there evoke perturbation of the nonlinear undamping force. The ensuing DP wavelets have opposite phase to the wavelets arising from coherent reflection, which results in partial cancellation of the coherent-reflection DP wavelets. (C) 2022 Author(s). |
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| Record 80 of 349 | ||||||||||||
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| Author(s): Alebachew, N (Alebachew, Nigussie); Murthy, HCA (Murthy, H. C. Ananda); Abdissa, B (Abdissa, Bedassa); Demissie, TB (Demissie, Taye B.); von Eschwege, KG (von Eschwege, Karel G.); Langner, EHG (Langner, Ernst H. G.); Coetsee-Hugo, L (Coetsee-Hugo, Liza) | ||||||||||||
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| Abstract: This study presents the simultaneous exfoliation and modification of heterostructured copper oxide incorporated sulfur doped graphitic carbon nitride (CuO@S-doped g-C3N4) nanocomposites (NCs) synthesized via chemical precipitation and pyrolysis techniques. The results revealed that the approach is feasible and highly efficient in producing 2-dimensional CuO@S-doped g-C3N4 NCs. The findings also showed a promising technique for enhancing the optical and electrical properties of bulk g-C3N4 by combining CuO nanoparticles (NPs) with S-doped g-C3N4. The crystallite and the average size of the NCs were validated using X-ray diffraction (XRD) studies. Incorporation of the cubical structured CuO on flower shaped S-doped-g-C3N4 was visualized and characterized through XRD, HR-SEM/EDS/SED, FT-IR, BET, UV-Vis/DRS, PL, XPS and impedance spectroscopy. The agglomerated NCs had various pore sizes, shapes and nanosized crystals, while being photo-active in the UV-vis range. The synergistic effect of CuO and S-doped g-C3N4 as co-modifiers greatly facilitates the electron transfer process between the electrolyte and the bare glassy carbon electrode. Specific surface areas of the NCs clearly revealed modification of bulk S-doped g-C3N4 when CuO NPs are incorporated with S-doped g-C3N4, providing a suitable environment for the binder-free decorated electrode with sensing behavior for hazardous pollutants. This was tested for the preparation of a 4-nitrophenol sensor. | ||||||||||||
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| Record 81 of 349 | |||||||||
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| Author(s): Tran, TN (Thanh-Nam Tran); Nguyen, TL (Thanh-Long Nguyen); Voznak, M (Voznak, Miroslav) | |||||||||
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| Abstract: In long-range wireless communication networks, the fading channels described in channel state information are strongly related to distance and the path loss exponent and represent a major challenge in delivering the performance required to support emerging applications. Conveniently, multiple antennas and cooperative relays are efficient solutions that can combat fading channels, thereby improving networking capacity and transmission reliability. This study investigated the use of multi-antenna unmanned aerial vehicle (UAV)s as aerial Internet of Things (IoT) relays and employed their direct line-of-sight benefits to assist IoT wireless networks. To improve the outage probability, system throughput, and energy efficiency (EE), we first considered a combination of transmit antenna selection at the transmitter and the selection combining technique at the receiver to determine the best channel from the pre-coding channel matrix. Using a practical model in a three-dimensional earth environment in combination with the K-means algorithm, we then investigated optimal UAV placement to obtain optimal channel state information for the non-orthogonal multiple access (NOMA) -IoT device cluster globally, thereby ensuring the quality of service for the IoT devices. We introduced a max-successive interference cancellation-min-rate framework for non-ordered NOMA devices, thus deriving theoretical expressions in novel closed forms for two independent scenarios: (i) Rayleigh and (ii) Nakagami- m fading channels. By optimizing the UAV placement, the investigated results applied to the UAV scheme delivered better performance in a NOMA-IoT network than in a terrestrial relay (TR) scheme. Finally, the study examines a variety of models and presents algorithms for Monte Carlo simulations to verify the theoretical results. | |||||||||
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| Record 82 of 349 | |||||||||
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| Author(s): Feng, ZX (Feng, Zexin); Zhou, XR (Zhou, Xiaorong); Smejkal, L (Smejkal, Libor); Wu, L (Wu, Lei); Zhu, ZW (Zhu, Zengwei); Guo, HX (Guo, Huixin); Gonzalez-Hernandez, R (Gonzalez-Hernandez, Rafael); Wang, XN (Wang, Xiaoning); Yan, H (Yan, Han); Qin, PX (Qin, Peixin); Zhang, X (Zhang, Xin); Wu, HJ (Wu, Haojiang); Chen, HY (Chen, Hongyu); Meng, Z (Meng, Ziang); Liu, L (Liu, Li); Xia, ZC (Xia, Zhengcai); Sinova, J (Sinova, Jairo); Jungwirth, T (Jungwirth, Tomas); Liu, ZQ (Liu, Zhiqi) | |||||||||
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Abstract:
The anomalous Hall effect is a time-reversal symmetry-breaking magneto-electronic phenomenon originally discovered in ferromagnets. Recently, ruthenium dioxide (RuO2) with a compensated antiparallel magnetic order has been predicted to generate an anomalous Hall effect of comparable strength to ferromagnets. The phenomenon arises from an altermagnetic phase of RuO2 with a characteristic alternating spin polarization in both real-space crystal structure and momentum-space band structure. Here we report an anomalous Hall effect in RuO2 with an anomalous Hall conductivity exceeding 1,000 omega(-1) cm(-1). We combine the vector magnetometry and magneto-transport measurements of epitaxial RuO2 films of different crystallographic orientations. We show that the anomalous Hall effect dominates over an ordinary Hall contribution, and a contribution due to a weak field-induced magnetization. Our results could lead to the exploration of topological Berry phases and dissipationless quantum transport in crystals of abundant elements and with a compensated antiparallel magnetic order.
By combining vector magnetometry and magneto-transport measurements of epitaxial films with different crystallographic orientations, an anomalous Hall effect can be measured in collinear altermagnetic ruthenium dioxide with an anomalous Hall conductivity exceeding 1,000 omega(-1) cm(-1). |
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| Author(s): Wang, YJ (Wang, Yijun); Legut, D (Legut, Dominik); Liu, XP (Liu, Xiaopeng); Li, YY (Li, Yiyao); Li, CX (Li, Chenxi); Sun, YL (Sun, Yiliu); Zhang, RF (Zhang, Ruifeng); Zhang, QF (Zhang, Qianfan) | ||||||||||||
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| Abstract: Magnetic two-dimensional materials have great potential in the preparation of nanoelectronic and spintronic devices. Recently, a new two-dimensional material with no corresponding bulk-structure, MoSi2N4, has been prepared, attracting public attention to the XA2Z4 series of materials. Naturally, doping with 3d magnetic element will result in various magnetic orderings. In our work, we replaced the Mo element with different transition-metal elements whose property varies from magnetic to nonmagnetic and screened out a variety of two-dimensional exchange scenarios. Then, we provided an analysis that shows the existence of a huge on-site Coulomb interaction at 3d orbitals which is strongly related to the Mott transition and therefore causes the superexchange interaction. | ||||||||||||
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| Record 84 of 349 | ||||||
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| Author(s): Zrigui, S (Zrigui, Salah); de Camargo, RY (de Camargo, Raphael Y.); Legrand, A (Legrand, Arnaud); Trystram, D (Trystram, Denis) | ||||||
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| Abstract: Job scheduling in high-performance computing platforms is a hard problem that involves uncertainties on both the job arrival process and their execution times. Users typically provide only loose upper bounds for job execution times, which are not so useful for scheduling heuristics based on processing times. Previous studies focused on applying regression techniques to obtain better execution time estimates, which worked reasonably well and improved scheduling metrics. However, these approaches require a long period of training data.& nbsp;In this work, we propose a simpler approach by classifying jobs as small or large and prioritizing the execution of small jobs over large ones. Indeed, small jobs are the most impacted by queuing delays, but they typically represent a light load and incur a small burden on the other jobs. The classifier operates online and learns by using data collected over the previous weeks, facilitating its deployment and enabling a fast adaptation to changes in the workload characteristics.& nbsp;We evaluate our approach using four scheduling policies on seven HPC platform workload traces. We show that: first, incorporating such classification reduces the average bounded slowdown of jobs in all scenarios, second, in most considered scenarios, the improvements are comparable to the ideal hypothetical situation where the scheduler would know in advance the exact running time of jobs. (C)& nbsp;2022 Elsevier Inc. All rights reserved. | ||||||
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| Author(s): Holy, V (Holy, Vladimir); Tomanova, P (Tomanova, Petra) | |||||||||
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| Abstract: The price clustering phenomenon manifesting itself as an increased occurrence of specific prices is widely observed and well documented for various financial instruments and markets. In the literature, however, it is rarely incorporated into price models. We consider that there are several types of agents trading only in specific multiples of the tick size resulting in an increased occurrence of these multiples in prices. For example, stocks on the NYSE and NASDAQ exchanges are traded with precision to one cent but multiples of five cents and ten cents occur much more often in prices. To capture this behavior, we propose a discrete price model based on a mixture of double Poisson distributions with dynamic volatility and dynamic proportions of agent types. The model is estimated by the maximum likelihood method. In an empirical study of DJIA stocks, we find that higher instantaneous volatility leads to weaker price clustering at the ultra-high frequency. This is in sharp contrast with results at low frequencies which show that daily realized volatility has a positive impact on price clustering. | |||||||||
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| Record 86 of 349 | |||||||||
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| Author(s): Butera, V (Butera, Valeria); Mazzone, G (Mazzone, Gloria); Detz, H (Detz, Hermann) | |||||||||
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| Abstract: A new family of bis[pyrrolyl Ru(II)] triad scaffolds, consisting of two [Ru(bpy)(2)](2+) centers separated by a variety of organic linkers, has been recently reported as efficient compounds for in vitro photodynamic therapy (PDT). Among all the complexes, the one carrying the pyrenyl group in the organic linker, namely 4 h, has emerged as an extremely potent photosensitizer for in vitro PDT. Here, we present a computational study based on both DFT and TDA-TDDFT methods, to investigate the photochemical properties of this promising complex. In order to evaluate the influence of the organic chromophore on the photochemical properties, our investigation was further extended to the complex 4 e, whose linker includes the benzothiadiazole group, which has yielded the longest-wavelength absorption maxima overall (but with a reduced intensity compared to 4 h). Eventually, the role of the second [Ru(bpy)(2)](2+) moiety was evaluated by comparison with the mononuclear complex. | |||||||||
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| Record 87 of 349 | ||||||||||||
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| Author(s): Lampart, M (Lampart, Marek); Lampartova, A (Lampartova, Alzbeta); Orlando, G (Orlando, Giuseppe) | ||||||||||||
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| Abstract: The objective of this paper is the study of the dynamical properties analysis of an original specification of the classical Cournot heterogeneous model with optimal response; specifically, a new approach that considers ordinal utility instead of cardinal monetary amounts is proposed where the classical decision of quantity is disentangled from the decision on imitation. The analysis is performed by means of bifurcation diagrams, the 0-1 test for chaos, power spectral density, histograms, and trajectory analysis. For this purpose, a new perturbation parameter epsilon of the initial condition is introduced, and together with the intensity of choice parameter beta determining the share of responders vs imitators, the system is researched. Depending on epsilon and beta, extreme reach dynamics, and coexisting attractors, periodic and chaotic trajectories are investigated through massive simulations. Those dynamics represent alternation between stability, cycles and chaos in the market. As the dynamics are completely endogenous, it means that swings in economy are intrinsic to the system and that they may persist unless controlled. | ||||||||||||
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| Record 88 of 349 | ||||||
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| Author(s): Cammarata, A (Cammarata, Antonio); Kaintz, M (Kaintz, Matus); Polcar, T (Polcar, Tomas) | ||||||
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| Abstract: Diamond-based compounds are ideal materials to build nanoengineered devices with wide applicability in nanophotonics, optomechanics, photovoltaics and electronics, where tuning the width and the character of the electronic band gap is paramount. While the available information is focused on specific aspects of the material preparation and response, a general understanding of how the entangled geometric and electronic properties determine the characteristics of the band gap is missing. The present work aims to tackle this challenge by means of first principle simulations. We show that specific charge distributions in the ion environment determine the width of the band gap; in order to control it, we suggest how to select suitable dopant atomic types and how to impose specific structural deformations. We also propose different routes to switch the character of the band gap from indirect to direct. The results pave new avenues aimed to design diamond-based nanostructured materials with targeted optical and electronic properties. The outcomes of the present work are general and can therefore be promptly applied to the study of optical and electronic materials irrespective of their chemical composition and atomic topology. | ||||||
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| Record 89 of 349 | |||||||||||||||||||||||||||||||||||||||||||||
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| Author(s): Zatopkova, M (Zatopkova, Martina); Sevcikova, T (Sevcikova, Tereza); Fanfani, V (Fanfani, Viola); Chyra, Z (Chyra, Zuzana); Rihova, L (Rihova, Lucie); Bezdekova, R (Bezdekova, Renata); Zihala, D (Zihala, David); Growkova, K (Growkova, Katerina); Filipova, J (Filipova, Jana); Cerna, L (Cerna, Lucie); Broskevicova, L (Broskevicova, Lucie); Kryukov, F (Kryukov, Fedor); Minarik, J (Minarik, Jiri); Smejkalova, J (Smejkalova, Jana); Maisnar, V (Maisnar, Vladimir); Harvanova, L (Harvanova, Lubica); Pour, L (Pour, Ludek); Jungova, A (Jungova, Alexandra); Popkova, T (Popkova, Tereza); Bago, JR (Bago, Juli Rodriguez); Sithara, AA (Sithara, Anjana Anilkumar); Hrdinka, M (Hrdinka, Matous); Jelinek, T (Jelinek, Tomas); Simicek, M (Simicek, Michal); Stracquadanio, G (Stracquadanio, Giovanni); Hajek, R (Hajek, Roman) | |||||||||||||||||||||||||||||||||||||||||||||
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| Record 90 of 349 | |||||||||
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| Author(s): Tran, TN (Thanh-Nam Tran); Ho, VC (Van-Cuu Ho); Vo, TP (Thoai Phu Vo); Tran, KNN (Khanh Ngo Nhu Tran); Voznak, M (Voznak, Miroslav) | |||||||||
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| Abstract: The requirements of low latency, low cost, less energy consumption, high flexibility, high network capacity, and high data safety are crucial challenges for future Internet of Things (IoT) wireless networks. Motivated by these challenges, this study deals with a novel design of green-cooperative IoT network, which employed coupled relays consisting of one IoT relay selected for forwarding signals to multiple IoT devices while another IoT relay transmitted jamming signals to an eavesdropper. For flexibility, all IoT nodes were powered by solar energy enough to sustain themselves, in order to consume less energy. To reach low latency, the study adopted the emerging non-orthogonal multiple access technique to serve multiple IoT devices simultaneously. Furthermore, the study adopted the simultaneous wireless information and power transfer technique which transmits wireless data for information processing and energy for energy harvesting. The study sketched a novel transmission block time period framework which plotted how a signal could travel via an individual IoT model. Maximizing the achievable bit-rate of IoT devices was considered to improve network capacity and data safety as well. Aiming at enhancing secrecy performance, a rest IoT relay played a role as a friendly jammer to transmit a jamming signal to an eavesdropper using energy harvested from the power splitting protocol. The results achieved in this study showed that the proposed model satisfied the requirements of future green IoT wireless networks. Derivatives leading to closed-form expressions are presented and verified by simulation results. The investigated results demonstrated that a friendly jammer based on radio frequency and energy harvesting strongly forces the intercept probability performance of the eavesdropper towards one, while outage probability performance of IoT devices towards zero showed that the signal to noise ratio tends to infinity. | |||||||||
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| Record 91 of 349 | ||||||
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| Author(s): Watschinger, R (Watschinger, Raphael); Merta, M (Merta, Michal); Of, G (Of, Guenther); Zapletal, J (Zapletal, Jan) | ||||||
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| Abstract: We present a novel approach to the parallelization of the parabolic fast multipole method for a space-time boundary element method for the heat equation. We exploit the special temporal structure of the involved operators to provide an efficient distributed parallelization with respect to time and with a one-directional communication pattern. On top, we apply a task-based shared memory parallelization and Single Instruction Multiple Data vectorization. In the numerical tests we observe high efficiencies of our parallelization approach. | ||||||
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| Record 92 of 349 | |||||||||
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| Author(s): Malik, J (Malik, Jiri); Soucek, O (Soucek, Ondrej) | |||||||||
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| Abstract: Purpose This paper aims to propose a semi-analytical benchmarking framework for enthalpy-based methods used in problems involving phase change with latent heat. The benchmark is based on a class of semi-analytical solutions of spatially symmetric Stefan problems in an arbitrary spatial dimension. Via a public repository this study provides a finite element numerical code based on the FEniCS computational platform, which can be used to test and compare any method of choice with the (semi-)analytical solutions. As a particular demonstration, this paper uses the benchmark to test several standard temperature-based implementations of the enthalpy method and assesses their accuracy and stability with respect to the discretization parameters. Design/methodology/approach The class of spatially symmetric semi-analytical self-similar solutions to the Stefan problem is found for an arbitrary spatial dimension, connecting some of the known results in a unified manner, while providing the solutions' existence and uniqueness. For two chosen standard semi-implicit temperature-based enthalpy methods, the numerical error assessment of the implementations is carried out in the finite element formulation of the problem. This paper compares the numerical approximations to the semi-analytical solutions and analyzes the influence of discretization parameters, as well as their interdependence. This study also compares accuracy of these methods with other traditional approach based on time-explicit treatment of the effective heat capacity with and without iterative correction. Findings This study shows that the quantitative comparison between the semi-analytical and numerical solutions of the symmetric Stefan problems can serve as a robust tool for identifying the optimal values of discretization parameters, both in terms of accuracy and stability. Moreover, this study concludes that, from the performance point of view, both of the semi-implicit implementations studied are equivalent, for optimal choice of discretization parameters, they outperform the effective heat capacity method with iterative correction in terms of accuracy, but, by contrast, they lose stability for subcritical thickness of the mushy region. Practical implications The proposed benchmark provides a versatile, accessible test bed for computational methods approximating multidimensional phase change problems. The supplemented numerical code can be directly used to test any method of choice against the semi-analytical solutions. Originality/value While the solutions of the symmetric Stefan problems for individual spatial dimensions can be found scattered across the literature, the unifying perspective on their derivation presented here has, to the best of the authors' knowledge, been missing. The unified formulation in a general dimension can be used for the systematic construction of well-posed, reliable and genuinely multidimensional benchmark experiments. | |||||||||
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| Record 93 of 349 | |||||||||
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| Author(s): Yang, CJ (Yang, C. J.); Jiang, WG (Jiang, W. G.); Burrello, S (Burrello, S.); Grasso, M (Grasso, M.) | |||||||||
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| Abstract: We propose a novel idea to construct an effective interaction under energy-density-functional (EDF) theories which is adaptive to the enlargement of the model space. Guided by effective field theory principles, iterations of interactions as well as enlargements of the model space through particle-hole excitations are carried out for infinite nuclear matter and selected closed-shell nuclei (4He, 16O, 40Ca, 56Ni, and 100Sn) up to next-to-leading order. Our approach provides a new way for handling the nuclear matter and finite nuclei within the same scheme, with advantages from both EDF and ab initio approaches. | |||||||||
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| Record 94 of 349 | |||||||||||||||
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| Author(s): Matej, Z (Matej, Zdenek); Kostal, M (Kostal, Michal); Majerle, M (Majerle, Mitja); Ansorge, M (Ansorge, Martin); Losa, E (Losa, Evzen); Zmeskal, M (Zmeskal, Marek); Schulc, M (Schulc, Martin); Simon, J (Simon, Jan); Stefanik, M (Stefanik, Milan); Novak, J (Novak, Jan); Koliadko, D (Koliadko, Daniil); Cvachovec, F (Cvachovec, Frantisek); Mravec, F (Mravec, Filip); Prenosil, V (Prenosil, Vaclav); Zach, V (Zach, Vaclav); Czakoj, T (Czakoj, Tomas); Rypar, V (Rypar, Vojtech); Capote, R (Capote, Roberto) | |||||||||||||||
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| Abstract: Dosimetry cross sections are fundamental quantities for proper determination of the neutron fluences in points of interest under heavy radiation load. One of the critical applications is the Reactor Pressure Vessel aging management, related to the correct estimation of its residual lifetime or for many non-reactor applications including neutron dosimetry of accelerator-based fields or space applications. The neutron flux of neutrons above 12 MeV in reference to fission spectra is below 1%. Therefore, new reference neutron fields with average energy above 5 MeV should be developed for the validation of neutron dosimetry cross sections up to 60 MeV. This paper presents the testing of a new methodology for the use of quasi monoenergetic neutron fields, where different sensitivity allows validations of the dosimetry cross section at energies much higher than the average energy of around 2 MeV typical of fission spectra. The exact shape of the neutron spectrum in the tested fields is measured by stilbene spectrometry. The total flux is determined from Ni and Al flux monitors. The developed methodology was applied to the validation of selected reactions from the IRDFF-II library showing satisfactory agreement. | |||||||||||||||
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| Record 95 of 349 | ||||||
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| Author(s): Sabol, R (Sabol, Radoslav); Horak, A (Horak, Ales) | ||||||
| Edited by: Sojka P; Horak A; Kopecek I; Pala K | ||||||
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Abstract:
The style and vocabulary of social media communication, such as chats, discussions or comments, differ vastly from standard languages. Specifically in internal business communication, the texts contain large amounts of language mixins, professional jargon and occupational slang, or colloquial expressions. Standard natural language processing tools thus mostly fail to detect basic text processing attributes such as the prevalent language of a message or communication or their sentiment.
In the presented paper, we describe the development and evaluation of new modules specifically designed for language identification and sentiment analysis of informal business communication inside a large international company. Besides the details of the module architectures, we offer a detailed comparison with other state-of-the-art tools for the same purpose and achieve an improvement of 10-13% in accuracy with selected problematic datasets. |
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| Conference Sponsors: Masaryk Univ, Fac Informat, Univ W Bohemia, Fac Appl Sci, Int Speech Commun Assoc, Lex Comp Ltd, IBMC Eska Republika Spol s r o, Amazon Alexa | ||||||
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| ISBN: 978-3-031-16270-1; 978-3-031-16269-5 |
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| Author(s): Bulanek, R (Bulanek, Roman); Vaculik, J (Vaculik, Jan); Vesely, O (Vesely, Ondrej); Prech, J (Prech, Jan); Kubu, M (Kubu, Martin); Rubes, M (Rubes, Miroslav); Bludsky, O (Bludsky, Ota) | ||||||||||||
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| Abstract: The strength of Bronsted acid sites (BAS) affects the properties of 2D and hierarchical zeolites, but the relative contribution of internal and external BAS remains unknown. Accordingly, this study aims to assess the acidity of external and internal BAS in nanosponge-like MFI zeolites by comparatively analyzing hydrogen-deuterium exchange kinetics between zeolitic deuteroxyl groups and C2H6 molecules monitored by in-situ FTIR spectroscopy. For this purpose, (i) a sample pre-treatment procedure was specifically developed to deuterate only internal or only external acid sites using 2,6-di-tert-butylpyridine (DTBP) as a masking agent and (ii) DFT modeling of surface BAS was performed. Theoretical models of the thin MFI layer revealed that the external surface of MFI crystals contains three types of BAS: (i) BAS positioned in 5-membered rings, either shielded by silanol nests, rendering the site inaccessible for DTBP or yielding a very low adsorption energy for ethane, (ii) BAS pointing into the pores, due to the presence of aluminol, which hinders DTBP accessibility, or the BAS undergoes transformation to a three-coordinate aluminium site, and (iii) BAS accessible to both DTBP and ethane. The results from our kinetics measurements showed that H/D exchange at external BAS of nanosponge MFI zeolites is faster than at internal BAS (rate constants at 425 degrees C: 3.8 10(-3) vs. 2.4 10(-3) s(-1) for external and internal BAS, respectively), but this cannot be attributed to the effect of diffusion. Therefore, the differences in exchange kinetics between external and internal BAS are given by mutual interplay of subtle differences in the corresponding activation barriers (113 vs. 117 kJ/mol for external and internal BAS, respectively) and pre-exponential terms (1.09 10(6) vs. 1.45 10(6) s(-1) for external and internal BAS, respectively). | ||||||||||||
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| Record 97 of 349 | ||||||
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| Author(s): Butera, V (Butera, Valeria); Detz, H (Detz, Hermann) | ||||||
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| Abstract: Obtaining chemicals and fuels from the reduction of carbon dioxide (CO2) represents a promising strategy to mitigate the growing greenhouse gas emissions. Because of the high thermodynamic stability of CO2, the real challenge is the development of efficient and selective catalysts. In this regard, photocatalysis is receiving much attention because it exclusively relies on energy input from sunlight. Gallium nitride (GaN) semiconductors can effectively promote the CO2 reduction. Moreover, the addition on the semiconductor surfaces of transition metal nanoparticles, such as Rh and Pt, can further improve the efficiency and selectivity toward CH4 rather than CO, along with improving the optical absorptions in the visible spectral region by decreasing the wide band gap of the pristine GaN. Water is commonly used as an atomic hydrogen donor for CO2 reduction. In this regard, GaN was previously reported as an excellent photocatalyst for water oxidation. Here, we present a density functional theory investigation based on a cluster model approach to shed light on the effective role of the metal nanoparticles on the CO2 reduction in the presence of water. Our calculations have underlined a more favored dissociative adsorption of H2O with respect to CO2. Moreover, while the dissociative H2O adsorption on the GaN surface occurs without the involvement of the Rh metal, the role of the metal center in activating the CO2 molecule is found to be crucial. Highest occupied molecular orbital-lowest unoccupied molecular orbital gaps and calculated absorption spectra have shown that the presence of the adsorbed nanoparticles not only intensifies the absorption next to the UV region but also extends it to all visible regions. Particularly, while the presence of Rh exhibits a stronger light absorption property in the visible region, enhanced in the blue-green region, Pt nanoparticles have a clear red-shift effect. | ||||||
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| Record 98 of 349 | |||||||||||||||
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| Author(s): Siborova, M (Siborova, Marta); Fuzik, T (Fuzik, Tibor); Prochazkova, M (Prochazkova, Michaela); Novacek, J (Novacek, Jiri); Benesik, M (Benesik, Martin); Nilsson, AS (Nilsson, Anders S.); Plevka, P (Plevka, Pavel) | |||||||||||||||
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Abstract:
E. coli phage SU10 has a short non-contractile tail. Here, the authors show that after cell binding, nozzle proteins and tail fibers of SU10 change conformation to form a nozzle that enables the delivery of the phage DNA into the bacterial cytoplasm.
Escherichia coli phage SU10 belongs to the genus Kuravirus from the class Caudoviricetes of phages with short non-contractile tails. In contrast to other short-tailed phages, the tails of Kuraviruses elongate upon cell attachment. Here we show that the virion of SU10 has a prolate head, containing genome and ejection proteins, and a tail, which is formed of portal, adaptor, nozzle, and tail needle proteins and decorated with long and short fibers. The binding of the long tail fibers to the receptors in the outer bacterial membrane induces the straightening of nozzle proteins and rotation of short tail fibers. After the re-arrangement, the nozzle proteins and short tail fibers alternate to form a nozzle that extends the tail by 28 nm. Subsequently, the tail needle detaches from the nozzle proteins and five types of ejection proteins are released from the SU10 head. The nozzle with the putative extension formed by the ejection proteins enables the delivery of the SU10 genome into the bacterial cytoplasm. It is likely that this mechanism of genome delivery, involving the formation of the tail nozzle, is employed by all Kuraviruses. |
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| Record 99 of 349 | |||||||||
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| Author(s): Drahos, B (Drahos, Bohuslav); Herchel, R (Herchel, Radovan) | |||||||||
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| Abstract: A series of Ni(ii) complexes with pyridine-based macrocyclic ligand L (3,12,18-triaza-6,9-dioxabicyclo[12.3.1]octadeca-1(18),14,16-triene) with general formula [Ni(L)(X)(2)](0/2+) (X = Br- (1), I- (2), CH3CN (3), NCS- (4), imidazole (5)) was prepared and thoroughly investigated. X-ray molecular structures confirmed pentagonal bipyramidal geometry for all studied complexes with a strong Jahn-Teller distortion in the pentagonal equatorial plane and significantly elongated Ni-O distance(s) with a decrease of this distortion by varying axial coligands (CH3CN > Br- > I- > NCS- > imidazole). Direct current magnetic measurements revealed the easy-axis type of magnetic anisotropy with negative as well as positive axial zero-field-splitting parameter D ranging from +6.8 to -14.5 cm(-1), which remains not affected in the halogenido series Cl- & RARR; Br- & RARR; I-, but which increases in the series with N-axial ligands in order CH3CN & RARR; NCS- & RARR; imidazole. Theoretical calculations helped to elucidate (i) the final coordination numbers 6 + 1 for 1 and 2, and 5 + 2 for 2-5, (ii) the pattern of splitting of d-orbitals, contributions of excited states to the final D-values and their final signs, and (iii) the complexity in the variation of the D and E parameters with elongation of axial bond distances in such strongly distorted systems. The studied complexes did not show any alternating magnetic susceptibility signal, but it was clearly documented that the magnetic anisotropy of the pentagonal bipyramidal Ni(ii) complexes can be modulated/tuned by variation of axial coligands. Nevertheless, great care has to be taken for symmetry of the equatorial ligand field. | |||||||||
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| Record 100 of 349 | |||||||||
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| Author(s): Kessete, JM (Kessete, Jenbrie M.); Demissie, TB (Demissie, Taye B.); Chilume, M (Chilume, Misha); Mohammed, AM (Mohammed, Ahmed M.); Andrushchenko, V (Andrushchenko, Valery) | |||||||||
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| Abstract: CO2 conversion to value-added chemicals requires efficient catalytic CO2 reduction. Activation of CO2 using 14 phosphine-borane frustrated Lewis pair catalysts was done computationally using B3LYP-D3/6-31++G(d,p)/PCM/THF and M06-2X/6-311++G(d,p)/PCM/THF methods. We designed 14 catalysts, 12 of which exhibit better catalytic activity towards CO2 activation. Moreover, the catalytic mechanisms of compounds 12 and 4 were predicted, and they showed an efficient catalytic system for CO2 reduction to CO, HCHO and HCOOH. Catalysts 2, 3 and 4, with the same methylene linker, have activation energies of 20.5, 18.3 and 10.4 kcal/mol, respectively. This indicates that the catalytic activity of the compound is highly influenced by the ligand bound to borane and phosphine. Compound 4 with the CO2 activation energy of 10.4 kcal/mol is the most efficient catalyst for CO2 activation ever reported among phosphine-borane catalysts. The energy barriers for H-2 activation with catalyst 12 (Delta G(double dagger) = 26.6 kcal/mol) and 4 (Delta G(double dagger) = 34.0 kcal/mol) are higher than the HCOOH releasing activation energy. The designed compounds will help to synthesise efficient metal-free phosphine-borane catalysts. Our results also indicate that phosphine-borane catalysts are promising candidates for CO2 reduction and direct hydrogenation. | |||||||||
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| Record 101 of 349 | |||||||||
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| Author(s): Cvrcek, J (Cvrcek, Jan); Kubena, AA (Kubena, Ales Antonin); Jor, T (Jor, Tomas); Nanka, O (Nanka, Ondrej); Kaupova, SD (Kaupova, Sylva Drtikolova); Veleminsky, P (Veleminsky, Petr) | |||||||||
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| Abstract: In forensic contexts, sternal anatomical varieties represent useful tools for the identification of an individual, either by comparison of ante-mortem and post-mortem data, or by potential comparison of data from biologically related individuals. Sternal body variation is also used to detect the biological affinity of individuals in bioarchaeology. However, no study has been made available to date on the degree to which the overall shape of the sternal body reflects the degree of biological relatedness. We, therefore, analyzed the sternal body shape of 10 individuals with known genealogical data, members of one family over three generations including inbred individuals (19th-20th centuries, Bohemia, Czech Republic), and a control sample of 12 biologically unrelated individuals. First, closely biologically related individuals were compared with unrelated individuals based on 10 variables expressing the morphological characteristics of the sternum, and then all individuals were compared based on Fourier analysis depending on their degree of relationship. The results showed that there is a greater degree of shape similarity in biologically related individuals than in unrelated individuals, and variability decreases with an increasing degree of relatedness. Inbred individuals showed the lowest sternum-shape distances and degree of variability, while unrelated individuals, showed the highest distances and variability. Moreover, in some cases, the documented relationships were also supported by a similar morphology of the ossified and fused xiphoid process. Thus, sternal shape analysis expands the possibilities for individual identification and the detection of the biological affinity of individuals for both the forensic sciences and bioarchaeology. | |||||||||
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| Record 102 of 349 | ||||||
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| Author(s): Vazquez, H (Vazquez, Hector) | ||||||
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| Abstract: A method is presented that allows for the calculation using density functional theory (DFT) of the tunneling conductance of single molecule junctions for thousands of junction structures. With a single scaling parameter, conductance is evaluated from clusters consisting of the molecule bonded to one Au atom at each end. Junction geometries are obtained without any constraints from ab initio molecular dynamics simulations at room temperature. This method accurately reproduces standard DFT-based conductance values for several molecular and electrode structures while reducing the computational cost by a factor of similar to 400x, allowing for the conductance of tens of thousands of geometries to be computed. When applied to a pair of conjugated molecules, these large data sets quantify the effect on conductance of molecular structure or quantum chemical properties. This methodology enables reliable DFT-based conductance calculations at a negligible computational cost and opens the way to quantitative structure-conductance relationships. | ||||||
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| Record 103 of 349 | |||||||||
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| Author(s): Pinos, M (Pinos, Michal); Mrazek, V (Mrazek, Vojtech); Sekanina, L (Sekanina, Lukas) | |||||||||
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| Abstract: Automated neural architecture search (NAS) methods are now employed to routinely deliver high-quality neural network architectures for various challenging data sets and reduce the designer's effort. The NAS methods utilizing multi-objective evolutionary algorithms are especially useful when the objective is not only to minimize the network error but also to reduce the number of parameters (weights) or power consumption of the inference phase. We propose a multi-objective NAS method based on Cartesian genetic programming for evolving convolutional neural networks (CNN). The method allows approximate operations to be used in CNNs to reduce the power consumption of a target hardware implementation. During the NAS process, a suitable CNN architecture is evolved together with selecting approximate multipliers to deliver the best trade-offs between accuracy, network size, and power consumption. The most suitable 8 x N-bit approximate multipliers are automatically selected from a library of approximate multipliers. Evolved CNNs are compared with CNNs developed by other NAS methods on the CIFAR-10 and SVHN benchmark problems. | |||||||||
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| Record 104 of 349 |
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| Author(s): Dostal, Z (Dostal, Zdenek); Brzobohaty, T (Brzobohaty, Tomas); Vlach, O (Vlach, Oldrich); Meca, O (Meca, Ondrej); Sadowska, M (Sadowska, Marie) |
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| Abstract: We describe the three-level hybrid domain decomposition TFETI method and show that the condition number of an elastic cluster defined on a fixed cube domain, decomposed into m x m x m subdomains interconnected by the face's rigid body modes and discretized by a regular grid, increases proportionally to m. The estimates are plugged into the analysis of the unpreconditioned H-TFETI (hybrid) method and used to prove its numerical scalability for linear problems. The estimates show that the cost of the coarse problem decreases with m(6) v while the number of iterations increases only proportionally to root m. Numerical experiments show a large scope of scalability of H-TFETI. The results are also essential for solving huge contact problems. |
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| Record 105 of 349 | ||||||||||||
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| Author(s): Wittner, R (Wittner, Rudolf); Mascia, C (Mascia, Cecilia); Gallo, M (Gallo, Matej); Frexia, F (Frexia, Francesca); Muller, H (Mueller, Heimo); Plass, M (Plass, Markus); Geiger, J (Geiger, Jorg); Holub, P (Holub, Petr) | ||||||||||||
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| Abstract: Provenance is information describing the lineage of an object, such as a dataset or biological material. Since these objects can be passed between organizations, each organization can document only parts of the objects life cycle. As a result, interconnection of distributed provenance parts forms distributed provenance chains. Dependant on the actual provenance content, complete provenance chains can provide traceability and contribute to reproducibility and FAIRness of research objects. In this paper, we define a lightweight provenance model based on W3C PROV that enables generation of distributed provenance chains in complex, multi-organizational environments. The application of the model is demonstrated with a use case spanning several steps of a real-world research pipeline - starting with the acquisition of a specimen, its processing and storage, histological examination, and the generation/collection of associated data (images, annotations, clinical data), ending with training an AI model for the detection of tumor in the images. The proposed model has become an open conceptual foundation of the currently developed ISO 23494 standard on provenance for biotechnology domain. | ||||||||||||
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| Record 106 of 349 |
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| Author(s): Chametla, RO (Chametla, R. O.); Chrenko, O (Chrenko, O.) |
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| Abstract: We investigate the gravitational interaction between low- to intermediate-mass planets (M-p is an element of [0.06 - 210] M-circle plus) and two previously formed pressure bumps in a gas-dust protoplanetary disc. We explore how the disc structure changes due to planetinduced perturbations and also how the appearance of vortices affects planet migration. We use multifluid 2D hydrodynamical simulations and the dust is treated in the pressureless-fluid approximation, assuming a single grain size of 5 mu m. The initial surface density profiles containing two bumps are motivated by recent observations of the protoplanetary disc HD163296. When planets are allowed to migrate, either a single planet from the outer pressure maximum or two planets from each pressure maximum, the initial pressure bumps quickly spread and merge into a single bump which is radially wide and has a very low amplitude. The redistribution of the disc material is accompanied by the Rossby Wave Instability and an appearance of mini-vortices that merge in a short period of time to form a large vortex. The large vortex induces perturbations with a spiral wave pattern that propagate away from the vortex as density waves. We found that these vortex-induced spiral waves strongly interact with the spiral waves generated by the planet and we called this mechanism the 'Faraway Interaction'. It facilitates much slower and/or stagnant migration of the planets and it excites their orbital eccentricities in some cases. Our study provides a new explanation for how rocky planets can come to have a slow migration in protoplanetary discs where vortex formation occurs. |
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| Record 107 of 349 | ||||||||||||||||||
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| Author(s): Bryja, J (Bryja, Josef); Meheretu, Y (Meheretu, Yonas); Boratynski, Z (Boratynski, Zbyszek); Zeynu, A (Zeynu, Ali); Denys, C (Denys, Christiane); Mulualem, G (Mulualem, Getachew); Welegerima, K (Welegerima, Kiros); Bryjova, A (Bryjova, Anna); Kasso, M (Kasso, Mohammed); Kostin, DS (Kostin, Danila S.); Martynov, AA (Martynov, Aleksey A.); Lavrenchenko, LA (Lavrenchenko, Leonid A.) | ||||||||||||||||||
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| Abstract: The Afar Triangle in easternmost Africa is one of biogeographically important regions, whose recent biota is virtually unknown. Here we evaluated the level of evolutionary uniqueness of biodiversity of this region in a wide regional and continental biogeographical context, using rodents as a model group. By combining our recent collections with historical records, and based on genetic data and phylogenetic approaches, we specifically tested whether and to what extent the geographical isolation of the Afar Depression is reflected in allopatric diversification of arid-adapted mammals. We documented the presence of 16 rodent species (four are reported for the first time in Ethiopia and one rediscovered there after more than 100 years) and eight additional species are likely present based on literature data. Comparative phylogeographic analysis suggests that the Afar Triangle can be considered as a part of a larger Somalian biogeographical region, but its fauna is genetically distinct, including the presence of narrow Afar endemics. To a lesser extent, there are taxa with evolutionary affinities to the eastern Sahara-Sahelian region and to the southern Arabian Peninsula. Compared to the Ethiopian Highlands, the rodent fauna of Afar is relatively poor. However, similarly to highlands, the evolutionary distinctiveness of mammals in the Afar Triangle is very high and it can be considered a unique centre of endemism. Our first comprehensive summary of Afar rodents significantly fills the gap in the knowledge of the mammalian fauna of arid regions in Ethiopia and the Horn of Africa in general and highlights the significance of the region for nature conservation. | ||||||||||||||||||
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| Record 108 of 349 |
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| Author(s): Muraskova, V (Muraskova, Viera); Eigner, V (Eigner, Vaclav); Dusek, M (Dusek, Michal); Poplstein, J (Poplstein, Jakub); Sturala, J (Sturala, Jiri); Sedmidubsky, D (Sedmidubsky, David) |
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| Abstract: Mononuclear Fe(III) complex [FeL(N-3)]center dot CH3OH, where L2- is the dianion of an unsymmetrical propyl-ethyl pentadentate Schiff base ligand condensed from pyridoxal and N-(2-aminoethyl)propane-1,3-diamine, and dinuclear Fe(III) complex [{FeL'}(2)(mu-OCH3)(2)]center dot 2.5CH(3)OH center dot H2O, where L'(2-) is the dianion of tetradentate Schiff base ligand based on pyridoxal and ethylenediamine, have been synthesized and characterized by elemental analysis, X-ray structural analysis, FT-IR and mass spectrometry. Tetradentate pyridoxal Schiff base ligand L'(2-) of the dinuclear complex was generated in situ via iron-catalyzed oxidative C-N bond cleavage of the pentadentate Schiff base. The coordination geometry around the iron(III) centers of the complexes can be described as a distorted octahedron. Magnetic investigations of [FeL(N-3)]center dot CH3OH complex revealed that the octahedral Fe(III) center retains high-spin in the entire temperature range (2-300 K) and enabled the evaluation of the axial zerofield splitting (ZFS) parameter D = -1.78 cm(-1), intermolecular exchange parameter zj = -1.35 cm(-1) and temperature-independent paramagnetism chi(TIM) = 0.00029 cm(3) mol(-1). Magnetic investigations of [{FeL'}(2)(mu-OCH3)(2)]center dot 2.5CH(3)OH center dot H2O showed that Fe(III) centers are coupled by a strong antiferromagnetic interaction (J = -94.5 cm(-1)). The experimental magnetic properties of the complexes were compared with the data obtained from the density functional theory (DFT) calculations. |
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| Record 109 of 349 | ||||||||||||||||||
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| Author(s): Nguyen, TN (Tan Nhat Nguyen); Tran, DH (Tran, Dinh-Hieu); Van Chien, T (Trinh Van Chien); Phan, VD (Van-Duc Phan); Voznak, M (Voznak, Miroslav); Chatzinotas, S (Chatzinotas, Symeon) | ||||||||||||||||||
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| Abstract: This article investigates the security and reliability analysis for a novel satellite-terrestrial network. Specifically, a satellite attempts to transmit confidential information to a ground user via the support of multiple relay nodes in the presence of an eavesdropper that tries to overhear the information. A friendly jammer is deployed to improve the secure transmission between the satellite and the relays. Furthermore, satellite-to-relay generalized Rician fading channels and imperfect channel state information are deployed to examine a general system model. In this context, the closed-formed expressions for the outage probability and intercept probability are derived corresponding to an amplify-and-forward based relaying scheme, which is challenging and has not been studied before. Finally, the exactness of the mathematical analyses is validated through Monte Carlo simulations. Furthermore, the effects of various key parameters (e.g., channel estimation errors, satellite's transmit power, relay's transmit power, number of relays, and fading severity parameter) are examined. | ||||||||||||||||||
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| Record 110 of 349 | |||||||||
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| Author(s): Benacek, J (Benacek, Jan); Karlicky, M (Karlicky, Marian) | |||||||||
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| Abstract: Solar radio zebras are used in the determination of the plasma density and magnetic field in solar flare plasmas. Analyzing observed zebra stripes and assuming their generation by the double-plasma resonance (DPR) instability, high values of the gyro-harmonic number are found. In some cases they exceed one hundred, in disagreement with the DPR growth rates computed up to now, which decrease with increasing gyro-harmonic number. We address the question of how zebras with high values of the gyro-harmonic numbers s are generated. For this purpose, we compute the growth rates of the DPR instability in a very broad range of s, considering a loss-cone kappa-distribution of superthermal electrons and varying the losscone angle, electron energies, and background plasma temperature. We have numerically calculated the dispersion relations and the growth rates of the upper-hybrid waves and found that the growth rates increase with increasing gyro-harmonic numbers if the loss-cone angles are similar to 80 degrees. The highest growth rates for these loss-cone angles are obtained for velocity v(k) = 0.15 c. The growth rates as a function of the gyro-harmonic number still show well distinct peaks, which correspond to zebra-stripe frequencies. The contrast between peak growth rates and surrounding growth rate levels increases as the kappa index increases and the background temperature decreases. Zebras with high values of s can be generated in regions where loss-cone distributions of superthermal electrons with large loss-cone angles (similar to 80 degrees) are present. Furthermore, owing to the high values of s, the magnetic field is relatively weak and has a small spatial gradient in such regions. | |||||||||
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| Record 111 of 349 | ||||||
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| Author(s): Maldonado-Dominguez, M (Maldonado-Dominguez, Mauricio); Srnec, M (Srnec, Martin) | ||||||
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| Abstract: Hydrogen atom abstraction (HAA) is central to life, and its importance in synthetic chemistry continues to grow. Enzymes rely on HAA to trigger life-sustaining reaction cascades, and greener synthetic routes are attainable by in situ capture of the carbon-centered radicals generated by HAA. Despite the potential of HAA for the diversification of molecular complexity and the late-stage functionalization of bioactive compounds, readily applicable and reliable models translating experimentally or computationally accessible thermodynamic quantities into relative free energy barriers are missing. In this work, we discovered a complete thermodynamic basis for the description of HAA reactivity, which consists of three components. Besides, the traditional linear free energy relationship and the recently introduced factor of asynchronicity (Srnec et al., PNAS 2018, 115, E10287-E10294), we present the third thermodynamic component of H atom abstraction reactions: the factor of frustration that arises from the dissimilarity of the species competing over a hydrogen atom in their overall ability to acquire an electron and proton. Incorporating these nonclassical descriptors into a Marcus-type model, the approach herein presented allows nearly quantitative prediction of relative barriers in six sets of metal-oxo-mediated HAA reactions, outperforming existing methods even in a stringent test with >200 computational HAA reactions. | ||||||
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| Record 112 of 349 | |||||||||
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| Author(s): Vitek, A (Vitek, Ales); Kalus, R (Kalus, Rene) | |||||||||
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| Abstract: Classical Monte Carlo simulations in the isothermal-isobaric ensemble have been performed for the Hg-13 cluster with the main emphasis paid to structural changes in this cluster induced by elevated temperature and pressure. Broad ranges of temperatures and pressures have been considered so that a comprehensive picture of the structural changes in Hg-13 could be obtained and represented in the form of a phase diagram constructed in the temperature-pressure plane. The effect of the complex electronic structure of the cluster on its electronic ground state potential energy surface and equilibrium thermodynamics has been studied within a semi-empirical electronic structure model based on the diatomics-in-molecules approach. The involvement of (three) lowest excited electronic states has been revealed while the higher excited states available within this model do not contribute. | |||||||||
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| Record 113 of 349 | |||||||||
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| Author(s): Jakubec, M (Jakubec, Martin); Cisarova, I (Cisarova, Ivana); Karban, J (Karban, Jindrich); Sykora, J (Sykora, Jan) | |||||||||
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| Abstract: The effect of substitution on intermolecular interactions was investigated in a series of 1,6-anhydro-2,3-epimino-hexopyranoses. The study focused on the qualitative evaluation of intermolecular interactions using DFT calculations and the comparison of molecular arrangements in the crystal lattice. Altogether, ten crystal structures were compared, including two structures of C4-deoxygenated, four C4-deoxyfluorinated and four parent epimino pyranoses. It was found that the substitution of the original hydroxy group by hydrogen or fluorine leads to a weakening of the intermolecular interaction by approximately 4 kcal/mol. The strength of the intermolecular interactions was found to be in the following descending order: hydrogen bonding of hydroxy groups, hydrogen bonding of the amino group, interactions with fluorine and weak electrostatic interactions. The intermolecular interactions that involved fluorine atom were rather weak; however, they were often supported by other weak interactions. The fluorine atom was not able to substitute the role of the hydroxy group in molecular packing and the fluorine atoms interacted only weakly with the hydrogen atoms located at electropositive regions of the carbohydrate molecules. However, the fluorine interaction was not restricted to a single molecule but was spread over at least three other molecules. This feature is a base for similar molecule arrangements in the structures of related compounds, as we found for the C4-Fax and C4-Feq epimines presented here. | |||||||||
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| Record 114 of 349 | ||||||
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| Author(s): Kalina, J (Kalina, Jiri); White, KB (White, Kevin B.); Scheringer, M (Scheringer, Martin); Pribylova, P (Pribylova, Petra); Kukucka, P (Kukucka, Petr); Audy, O (Audy, Ondrej); Martinik, J (Martinik, Jakub); Klanova, J (Klanova, Jana) | ||||||
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| Abstract: Passive air sampling (PAS) has been used to monitor semivolatile organic compounds (SVOCs) for the past 20 years, but limitations and uncertainties persist in the derivation of effective sampling volumes, sampling rates, and concentrations. As a result, the comparability of atmospheric levels measured by PAS and concentrations measured by active air sampling (AAS) remains unclear. Long-term PAS data, without conversion into concentrations, provide temporal trends that are similar to, and consistent with, trends from AAS data. However, for more comprehensive environmental and human health assessments of SVOCs, it is also essential to harmonize and pool air concentration data from the major AAS and PAS monitoring networks in Europe. To address this need, we calculated and compared concentration data for 28 SVOCs (including organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), and polycyclic aromatic hydrocarbons (PAHs)) at the six monitoring sites in Europe with 10 years of co-located AAS (EMEP) and PAS (MONET) data: Birkenes, Kosetice, Pallas, Rao, Storhofoi, and Zeppelin. Atmospheric SVOC concentrations were derived from PAS data using the two most common computation models. Long-term agreement between the AAS and PAS data was strong for most SVOCs and sites, with 79% of the median PAS-derived concentrations falling within a factor of 3 of their corresponding AAS concentrations. However, in both models it is necessary to set a sampler-dependent correction factor to prevent underestimation of concentrations for primarily particle-associated SVOCs. In contrast, the models overestimate concentrations at sites with wind speeds that consistently exceed 4 m s(-1). We present two recommendations that, if followed, allow MONET PAS to provide sufficiently accurate estimates of SVOC concentrations in air so that they can be deployed together with AAS in regional and global monitoring networks. | ||||||
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| Record 115 of 349 | ||||||
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| Author(s): Svec, J (Svec, Jan); Fremund, A (Fremund, Adam); Bulin, M (Bulin, Martin); Lehecka, J (Lehecka, Jan) | ||||||
| Edited by: Sojka P; Horak A; Kopecek I; Pala K | ||||||
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| Abstract: Pre-trained models used in the transfer-learning scenario are recently becoming very popular. Such models benefit from the availability of large sets of unlabeled data. Two kinds of such models include the Wav2Vec 2.0 speech recognizer and T5 text-to-text transformer. In this paper, we describe a novel application of such models for dialog systems, where both the speech recognizer and the spoken language understanding modules are represented as Transformer models. Such composition outperforms the baseline based on the DNN-HMM speech recognizer and CNN understanding. | ||||||
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| Conference Sponsors: Masaryk Univ, Fac Informat, Univ W Bohemia, Fac Appl Sci, Int Speech Commun Assoc, Lex Comp Ltd, IBMC Eska Republika Spol s r o, Amazon Alexa | ||||||
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| ISBN: 978-3-031-16270-1; 978-3-031-16269-5 |
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| Author(s): Hou, DW (Hou, Dianwei); Heard, CJ (Heard, Christopher J.) | |||||||||
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| Abstract: The encapsulation of noble metal atoms into zeolites is a promising route to generate controlled size distributions of stable metal catalysts. Pinning of single metal atoms to particular binding sites represents the optimal atom-efficiency and is a desirous outcome, despite the propensity of metal clusters to sinter. Currently, sintering resistance of noble metals in siliceous and high-silica frameworks is incompletely understood, while the role of influencing factors such as adsorbates and metal element identity, have not been ascertained. Here, we investigate the nature of metal-zeolite interactions, via density functional global structure optimisation and kinetic Monte Carlo simulations of the binding and migration of Pt and Au in a siliceous zeolite with framework topology LTA. We show that strong binding of Pt atoms to the framework severely hinders migration, even in the absence of framework heteroatoms, while Au diffuses freely through the pore. Reducing agents CO and H-2 change the preferred binding site of Pt and flatten the potential energy surface, which reduces migration barriers and thereby promotes particle growth. PtCO is found to represent a compromise between strongly framework-bound Pt-1, and bulky, volatile Pt(CO)(x) clusters, exhibiting fast diffusion. This work provides an atomistic picture of single metal atom kinetics inside high-silica zeolites, which represent a fundamental basis for understanding nano-catalyst deactivation. | |||||||||
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| Record 117 of 349 | ||||||
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| Author(s): Shi, Y (Shi, Yu); Wei, B (Wei, Bo); Legut, D (Legut, Dominik); Du, SY (Du, Shiyu); Francisco, JS (Francisco, Joseph S.); Zhang, RF (Zhang, Ruifeng) | ||||||
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| Abstract: The exploration of cathode catalysts with low overpotentials for the carbon dioxide reduction reaction (CRR) and carbon dioxide evolution reaction (CER) is essential for Li-CO2 batteries. MXenes have been suggested as potential candidates owing to their high electrical conductivity and effective CO2 activation performance. Herein, the stability and bifunctional CRR/CER catalytic activities of bare MXene (M2C), oxygen-functionalized MXene (M2CO2), and single-atom (SA) modified M2CO2 are systemically investigated. Among bare MXenes, Mo2C exhibits the best catalytic activity, comparable to that of carbon nanotubes, whereas oxygen-functionalized MXene has poor activity. Notably, introducing an SA on the surface of oxygen-functionalized MXene decreases the overpotential by 12.2%-68.1%, which can even outperform graphene catalysts, suggesting their potential as bifunctional cathode catalysts in Li-CO2 batteries. This high activity is appropriate reactivity in origin, as highlighted by the volcano-type relationship between the Gibbs free energy and the overpotential for key steps. The descriptor xi, which is related to adsorption behavior, is effective in determining bifunctional catalytic activity, which depends on the ability of SA electrons to fill antibonding orbitals and SA-oxygen/carbon bonding. This work not only identifies promising MXene-based bifunctional CRR/CER catalysts but also provides a rational design rule for SA modified catalysts. | ||||||
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| Record 118 of 349 | |||||||||
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| Author(s): Abdellaoui, S (Abdellaoui, S.); Krticka, J (Krticka, J.); Kurfurst, P (Kurfurst, P.) | |||||||||
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Abstract:
Context. Fast rotating Wolf-Rayet stars are expected to be progenitors of long duration gamma-ray bursts. However, the observational test of this model is problematic. Spectral lines of Wolf-Rayet stars originate in expanding stellar wind, therefore a reliable spectroscopical determination of their rotational velocities is difficult. Intrinsic polarization of Wolf-Rayet stars due to the rotational modulation of the stellar wind may provide an indirect way to determine the rotational velocities of these stars. However, detailed wind models are required for this purpose.
Aims. We determine the intrinsic polarization of Wolf-Rayet stars from hydrodynamical wind models as a function of rotational velocity. Methods. We used 2.5D hydrodynamical simulations to calculate the structure of rotating winds of Wolf-Rayet stars. The simulations account for the deformation of the stellar surface due to rotation, gravity darkening, and nonradial forces. From the derived models, we calculated the intrinsic stellar polarization. The mass loss rate was scaled to take realistic wind densities of Wolf-Rayet stars into account. Results. The hydrodynamical wind models predict a prolate wind structure, which leads to a relatively low level of polarization. Even relatively large rotational velocities are allowed by observational constrains. The obtained wind structure is similar to that obtained previously for rotating optically thin winds. Conclusions. Derived upper limits of rotational velocities of studied Wolf-Rayet stars are not in conflict with the model of long duration gamma-ray bursts. |
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| Author(s): Miranda-Olvera, M (Miranda-Olvera, Montserrat); Arcos-Ramos, R (Arcos-Ramos, Rafael); Maldonado-Dominguez, M (Maldonado-Dominguez, Mauricio); Salmon, L (Salmon, Lionel); Molnar, G (Molnar, Gabor); Bousseksou, A (Bousseksou, Azzedine); Carreon-Castro, MD (del Pilar Carreon-Castro, Maria) | |||||||||||||||
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| Abstract: A set of small benzothiadiazole (BTD)-based derivatives with a D-A-D architecture were synthesized and characterized as building blocks of organic semiconducting materials by applying an experimental-theoretical approach. The four derivatives tend to self-assemble into highly ordered crystalline solids, with varying degrees of responsiveness to mechanical and thermal stimuli. The featured derivatives exhibit absorption maxima in solution and molar extinction coefficient values related to pi-pi* electronic transitions with minor solvatochromic responses, displaying broad fluorescence profiles with large Stokes shifts and high fluorescence quantum yields. In the solid-state, the BTD derivatives display absorption maxima in the visible range and intense fluorescence emission of the n-butoxy and fluorene derivatives. The stability of the one-electron reduced and oxidized forms of all compounds was assessed by means of cyclic voltammetry, which complemented by DFT calculations allowed the identification of one BTD derivative (BuO-BTD) as a strong candidate for use as an electron transport layer in organoelectronic devices. | |||||||||||||||
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| Record 120 of 349 | |||||||||||||||
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| Author(s): Santiago-Sampedro, GI (Santiago-Sampedro, Gerardo, I); Aguilar-Granda, A (Aguilar-Granda, Andres); Torres-Huerta, A (Torres-Huerta, Aaron); Flores-Alamo, M (Flores-Alamo, Marcos); Maldonado-Dominguez, M (Maldonado-Dominguez, Mauricio); Rodriguez-Molina, B (Rodriguez-Molina, Braulio); Iglesias-Arteaga, MA (Iglesias-Arteaga, Martin A.) | |||||||||||||||
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| Abstract: This work describes the synthesis and aggregation behavior of a dimeric bile acid derivative in which two steroid cores are bridged by a p-di(phenylethynyl)phenylene tluorophore. The studied compound contains three key characteristics: (a) restricted conformational equilibrium in solution, (b) efficient fluorescence conferred by the bridge, and (c) medium responsiveness encoded in the steroid fragments. The incorporation of the three components afforded a compound that generates nano- and micrometric spherical particles with aggregation-responsive fluorescence emission. The observed self-assembly process of the featured molecule was induced by the gradual addition of water to the tetrahydrofuran (THF) solution. This aggregation led to significant changes in fluorescence that went from two bands at lambda(em) values of 370 and 390 nm in pure THF to a new spectrum with two maxima at lambda(em) values of 395 and 418 nm at high water contents, without a decrease in emission. The observed changes can be ascribed to weakly coupled aggregation, a hypothesis supported by multiscale molecular modeling, which sheds light on the mechanism of the self-assembly of this unconventional amphiphile. | |||||||||||||||
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| Record 121 of 349 |
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| Author(s): Brodsky, L (Brodsky, Lukas); Vilimek, V (Vilimek, Vit); Sobr, M (Sobr, Miroslav); Kroczek, T (Kroczek, Tomas) |
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| Abstract: Supraglacial lakes (SGL) are a specific phenomenon of glaciers. They are important for ice dynamics, surface mass balance, and surface hydrology, especially during ongoing climate changes. The important characteristics of lakes are their water storage and drainage. Satellite-based remote sensing is commonly used not only to monitor the area but also to estimate the depth and volume of lakes, which is the basis for long-term spatiotemporal analysis of these phenomena. Lake depth retrieval from optical data using a physical model requires several basic assumptions such as, for instance, the water has little or no dissolved or suspended matter. Several authors using these assumptions state that they are also potential weaknesses, which remain unquantified in the literature. The objective of this study is to quantify the effect of maximum detectable lake depth for water with non-zero suspended particulate matter (SPM). We collected in-situ concurrent measurements of hyperspectral and lake depth observations to a depth of 8 m. Additionally, we collected water samples to measure the concentration of SPM. The results of empirical and physically based models proved that a good relationship still exists between the water spectra of SGL and the lake depth in the presence of 48 mg/L of SPM. The root mean squared error for the models ranged from 0.163 m (Partial Least Squares Regression-PLSR model) to 0.243 m (physically based model), which is consistent with the published literature. However, the SPM limited the maximum detectable depth to approximately 3 m. This maximum detectable depth was also confirmed by the theoretical concept of Philpot (1989). The maximum detectable depth decreases exponentially with an increase in the water attenuation coefficient g, which directly depends on the water properties. |
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| Record 122 of 349 | ||||||
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| Author(s): Oujezsky, V (Oujezsky, Vaclav); Horvath, T (Horvath, Tomas); Holik, M (Holik, Martin) | ||||||
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| Abstract: This paper presents a developed tool for automated security incident reporting in passive optical networks. This tool interacts with our programmable development card, developed detection modules, and TheHive project. The custom implementation of the solution has resulted in anomaly reporting templates for xPON networks that can be universally applied and new definitions of indicators of compromise. The custom implementation consists of a collector and middleware layer between the programmable card and Apache Kafka. | ||||||
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| Record 123 of 349 |
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| Author(s): Deeloed, W (Deeloed, Wanchai); Priamushko, T (Priamushko, Tatiana); Cizek, J (Cizek, Jakub); Suramitr, S (Suramitr, Songwut); Kleitz, F (Kleitz, Freddy) |
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| Abstract: In this work, defect-rich ordered mesoporous spinel oxides, including CoCo2O4, NiCo2O4, and ZnCo2O4, were developed as bifunctional electrocatalysts toward oxygen reduction and evolution reactions (ORR and OER, respectively). The materials are synthesized via nanocasting and modified by chemical treatment with 0.1 M NaBH4 solution to enhance the defect concentration. The synthesized samples have metal and oxygen divacancies (V-Co + V-O) as the primary defect sites, as indicated by positron annihilation lifetime spectroscopy (PALS). Cation substitution in the spinel structure induces a higher number of oxygen vacancies. The increased number of surface defects and the synergistic effect between two incorporated metals provide a high activity in both the OER and ORR in the case of NiCo2O4 and ZnCo2O4. Especially, ZnCo2O4 exhibits the highest OER/ORR activity. The defect engineering with 0.1 M NaBH4 solution results in a metal-hydroxylated surface (M-OH) and enhanced the catalytic activity for the post-treated metal oxides in the ORR and OER. This fundamental investigation of the defective structure of the mixed metal oxides offers some useful insights into further development of highly active electrocatalysts through defect engineering methods. |
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| Record 124 of 349 | |||||||||||||||||||||||||||||||||
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| Author(s): Juhas, M (Juhas, Martin); Bachtikova, A (Bachtikova, Andrea); Nawrot, DE (Nawrot, Daria Elzbieta); Hatokova, P (Hatokova, Paulina); Pallabothula, VSK (Pallabothula, Vinod Sukanth Kumar); Diepoltova, A (Diepoltova, Adela); Jandourek, O (Jandourek, Ondrej); Barta, P (Barta, Pavel); Konecna, K (Konecna, Klara); Paterova, P (Paterova, Pavla); Sestak, V (Sestak, Vit); Zitko, J (Zitko, Jan) | |||||||||||||||||||||||||||||||||
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| Abstract: Antimicrobial drug resistance is currently one of the most critical health issues. Pathogens resistant to last-resort antibiotics are increasing, and very few effective antibacterial agents have been introduced in recent years. The promising drug candidates are often discontinued in the primary stages of the drug discovery pipeline due to their unspecific reactivity (PAINS), toxicity, insufficient stability, or low water solubility. In this work, we investigated a series of substituted N-oxazolyl-and N-thiazolylcarboxamides of various pyridinecarboxylic acids. Final compounds were tested against several microbial species. In general, oxazole-containing compounds showed high activity against mycobacteria, especially Mycobacterium tuberculosis (best MICH37Ra = 3.13 mu g/mL), including the multidrug-resistant strains. Promising activities against various bacterial and fungal strains were also observed. None of the compounds was significantly cytotoxic against the HepG2 cell line. Experimental measurement of lipophilicity parameter log k'(w) and water solubility (log S) confirmed significantly (typically two orders in logarithmic scale) increased hydrophilicity/water solubility of oxazole derivatives in comparison with their thiazole isosteres. Mycobacterial beta-ketoacyl-acyl carrier protein synthase III (FabH) was suggested as a probable target by molecular docking and molecular dynamics simulations. | |||||||||||||||||||||||||||||||||
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| Record 125 of 349 | ||||||||||||
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| Author(s): Isci, R (Isci, Recep); Baysak, E (Baysak, Elif); Kesan, G (Kesan, Gurkan); Minofar, B (Minofar, Babak); Eroglu, MS (Eroglu, Mehmet S.); Duygulu, O (Duygulu, Ozgur); Gorkem, SF (Gorkem, Sultan F.); Ozturk, T (Ozturk, Turan) | ||||||||||||
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| Abstract: Non-covalent functionalization of single wall carbon nanotubes (SWCNTs) has been conducted using several binding agents with surface pi-interaction forces in recent studies. Herein, we present the first example of non-covalent functionalization of sidewalls of SWCNTs using thienothiophene (TT) derivatives without requiring any binding agents. Synthesized TT derivatives, TT-CN-TPA, TT-CN-TPA2 and TT-COOH-TPA, were attached directly to SWCNTs through non-covalent interactions to obtain new TT-based SWCNT hybrids, HYBRID 1-3. Taking advantage of the presence of sulfur atoms in the structure of TT, HYBRID 1, as a representative, was treated with Au nanoparticles for the adsorption of Au by sulfur atoms, which generated dear TEM images of the particles. The images indicated the attachment of TTs to the surface of SWCNTs. Thus, the presence of sulfur atoms in TT units made the binding of TTs to SWCNTs observable via TEM analysis through adsorption of Au nanoparticles by the sulfur atoms. Surface interactions between TTs and SWCNTs of the new hybrids were also clarified by classical molecular dynamic simulations, a quantum mechanical study, and SEM, TEM, AFM and contact angle (CA) analyses. The minimum distance between a TT and a SWCNT reached up to 3.5 angstrom, identified with strong peaks on a radial distribution function (RDF), while maximum interaction energies were raised to -316.89 kcal mol(-1), which were determined using density functional theory (DFT). | ||||||||||||
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| Record 126 of 349 | ||||||
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| Author(s): Bohacek, M (Bohacek, Matyas); Hruz, M (Hruz, Marek) | ||||||
| Book Group Author(s): IEEE COMP SOC | ||||||
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| Abstract: In this paper we present a system for word-level sign language recognition based on the Transformer model. We aim at a solution with low computational cost, since we see great potential in the usage of such recognition system on hand-held devices. We base the recognition on the estimation of the pose of the human body in the form of 2D landmark locations. We introduce a robust pose normalization scheme which takes the signing space in consideration and processes the hand poses in a separate local coordinate system, independent on the body pose. We show experimentally the significant impact of this normalization on the accuracy of our proposed system. We introduce several augmentations of the body pose that further improve the accuracy, including a novel sequential joint rotation augmentation. With all the systems in place, we achieve state of the art top-1 results on the WLASL and LSA64 datasets. For WLASL, we are able to successfully recognize 63.18 % of sign recordings in the 100-gloss subset, which is a relative improvement of 5 % from the prior state of the art. For the 300-gloss subset, we achieve recognition rate of 43.78 % which is a relative improvement of 3.8 %. With the LSA64 dataset, we report test recognition accuracy of 100 %. | ||||||
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| Conference Sponsors: IEEE, IEEE Comp Soc, CVF, Amazon, Google, Kitware, Mitre, Verisk | ||||||
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| ISBN: 978-1-6654-5824-5 |
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| Author(s): Kleparnik, P (Kleparnik, Petr); Zemcik, P (Zemcik, Pavel); Treeby, BE (Treeby, Bradley E.); Jaros, J (Jaros, Jiri) | ||||||
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| Abstract: This article presents a method to calculate the average acoustic intensity during ultrasound simulation using a new approach that exploits compression of intermediate results. One of the applications of high-intensity focused ultrasound (HIFU) simulations is the calculation of the thermal dose, which indicates the amount of tissue destroyed using a state-of-the-art k-space pseudospectral method. The thermal simulation is preceded by the calculation of the average intensity within the acoustic simulation. Due to the time staggering between the particle velocity and the acoustic pressure used in such simulations, the average intensity calculation is typically executed offline after the acoustic simulation consuming both disk space and time (the data can spread over terabytes). Our new approach calculates the average intensity during the acoustic simulation using the output coefficients of a new compression method which enables resolving the time staggering on-the-fly with huge disk space savings. To reduce RAM requirements, the article also presents a new 40-bit method for encoding compression complex coefficients. Experimental numerical simulations with the proposed method have shown that disk space requirements are up to 99% lower. The simulation speed was not significantly affected by the approach and the compression error did not affect the prediction accuracy of the thermal dose. From the standpoint of supercomputers, the new approach is significantly more economical. Saving computing resources increases the chances of real use of acoustic simulations in practice. The method can be applied to signals of a similar character, e.g., for electromagnetic radio waves. | ||||||
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| Record 128 of 349 | |||||||||||||||
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| Author(s): Lin, C (Lin, Chao); Feng, X (Feng, Xiang); Legut, D (Legut, Dominik); Liu, XP (Liu, Xiaopeng); Seh, ZW (Seh, Zhi Wei); Zhang, RF (Zhang, Ruifeng); Zhang, QF (Zhang, Qianfan) | |||||||||||||||
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| Abstract: Photocatalytic oxygen evolution reaction (OER) by 2D semiconductors is a promising strategy for efficient energy conversion. The newly discovered 2D semiconductors MA(2)Z(4) (M = transition metal, e.g., Mo, W; A = C, Si, and Ge; Z = N, P, and As) have shown characteristics of promising photocatalytic OER catalysts. Herein, an automated high-throughput workflow is proposed to efficiently screen MA(2)Z(4) photocatalytic OER catalysts, and further reveal the theoretical mechanism. The four criteria of semi-conductivity, bandgap width/band edge position, structural stability, and free energy change, are proposed to screen MA(2)Z(4) catalysts thermodynamically. The exciton properties and carrier mobility of these MA(2)Z(4) are further studied to explore the high-efficiency photocatalytic OER MA(2)Z(4) with low exciton binding energy and high effective mass ratio. It is found that the bandgap width of MA(2)Z(4) mainly depends on the strength of M-Z bonding and the redistribution of electrons, while the catalytic effect is closely related to the adsorption capacity of O atom. In particular, beta-ZrSi2N4 and beta-HfSi2N4 are screened as efficient photocatalytic OER catalysts. This work develops a fully automated method and contributes to a complete framework for screening high-efficiency photocatalytic OER catalysts. | |||||||||||||||
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| Record 129 of 349 | ||||||||||||||||||||||||
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| Author(s): Nazarizadeh, M (Nazarizadeh, Masoud); Peterka, J (Peterka, Jiri); Kubecka, J (Kubecka, Jan); Vasek, M (Vasek, Mojmir); Juza, T (Juza, Tomas); de Moraes, KR (de Moraes, Karlos Ribeiro); Cech, M (Cech, Martin); Holubova, M (Holubova, Michaela); Souza, AT (Souza, Allan T.); Blabolil, P (Blabolil, Petr); Muska, M (Muska, Milan); Tsering, L (Tsering, Lobsang); Barton, D (Barton, Daniel); Riha, M (Riha, Milan); Smejkal, M (Smejkal, Marek); Tuser, M (Tuser, Michal); Vejrik, L (Vejrik, Lukas); Frouzova, J (Frouzova, Jaroslava); Jaric, I (Jaric, Ivan); Prchalova, M (Prchalova, Marie); Vejrikova, I (Vejrikova, Ivana); Stefka, J (Stefka, Jan) | ||||||||||||||||||||||||
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| Abstract: Ligula intestinalis (Linnaeus, 1758) is a tapeworm parasite with a worldwide distribution that uses a wide variety of fish species as its second intermediate host. In the present study, we investigated the prevalence and population genetic structure of plerocercoids of L. intestinalis in five common cyprinoid species, roach Rutilus rutilus (Linnaeus), freshwater bream Abramis brama (Linnaeus), white bream Blicca bjoerkna (Linnaeus), bleak Alburnus alburnus (Linnaeus), and rudd Scardinius erythrophthalmus (Linnaeus), collected in six water bodies of the Czech Republic (Milada, Most, Medard, Jordan, kimov and Lipno). Of the six study sites, the highest frequency of parasitism was recorded in Lake Medard (15%). The overall prevalence rate among the species was as follows: roach > rudd > freshwater bream > bleak > white bream. Two mitochondrial genes (cytb and COI) were used to compare the population genetic structure of parasite populations using selected samples from the five fish species. The results of the phylogenetic analysis indicated that all populations of L. intestinalis were placed in Clade A, previously identified as the most common in Europe. At a finer scale, haplotype network and PCoA analyses indicated the possible emergence of host specificity of several mtDNA haplotypes to the freshwater bream. Moreover, pairwise Fixation indices (FST) revealed a significant genetic structure between the parasite population in freshwater bream and other host species. Parasite populations in roach not only showed the highest rate of prevalence but also depicted a maximum number of shared haplotypes with populations from bleak and rudd. Our results suggest that recent ecological differentiation might have influenced tapeworm populations at a fine evolutionary scale. Thus, the differences in prevalence between fish host species in different lakes might be influenced not only by the parasite's ecology, but also by its genetic diversity. | ||||||||||||||||||||||||
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| Record 130 of 349 | |||||||||||||||
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| Author(s): Mazier, A (Mazier, Arnaud); Bilger, A (Bilger, Alexandre); Forte, AE (Forte, Antonio E.); Peterlik, I (Peterlik, Igor); Hale, JS (Hale, Jack S.); Bordas, SPA (Bordas, Stephane P. A.) | |||||||||||||||
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| Abstract: In this paper we develop a framework for solving inverse deformation problems using the FEniCS Project finite-element software. We validate our approach with experimental imaging data acquired from a soft silicone beam under gravity. In contrast with inverse iterative algorithms that require multiple solutions of a standard elasticity problem, the proposed method can compute the undeformed configuration by solving only one modified elasticity problem. This modified problem has a complexity comparable to the standard one. The framework is implemented within an open-source pipeline enabling the direct and inverse deformation simulation directly from imaging data. We use the high-level unified form language (UFL) of the FEniCS Project to express the finite-element model in variational form and to automatically derive the consistent Jacobian. Consequently, the design of the pipeline is flexible: for example, it allows the modification of the constitutive models by changing a single line of code. We include a complete working example showing the inverse deformation of a beam deformed by gravity as supplementary material. | |||||||||||||||
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| Record 131 of 349 | |||||||||
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| Author(s): Navratil, M (Navratil, Michal); Cisarova, I (Cisarova, Ivana); Stepnicka, P (Stepnicka, Petr) | |||||||||
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| Abstract: Combining a phosphinoferrocene fragment with extended muItidonor moieties affords novel, flexible muftidonor pro-ligands. This contribution describes the synthesis of two structurally similar functional phosphines, Ph(2)PfcNHC(2)CH(2)PPh(2) (1) and Ph(2)PfcNHCH(2)CH(2)PPh(2) (2, fc = ferrocene-1,1'-diyl), and their coordination behaviour towards Pd(II). The former amidophosphine reacts with [PdCl2(MeCN)(2)] to produce the cheIate complex [PdCl2(1-kappa 2 P,P')] as a mixture of cis and trans isomers, which convert into bis-cheIate [PdCl2(Ph(2)PfcNC(O)CH2PPh2-kappa P-3,P',N)] upon reacting with a strong base (KOt-Bu). In contrast, the more flexible and more basic phosphinoamine 2 directly forms the cationic bis-cheIate complex [PdCl(2-kappa P-3,P',N)]CI via spontaneous self-ionisation. Subsequent halogen abstraction with Ag[SbF6] results either in counter ion exchange to give [PdCl(2-kappa Fe-3,P',P')][SbF6] or in the formation of a structurally unique complex [PdCl(2-kappa Fe-4,P,P', N)][SbF6](2) with an Fe -> Pd dative interaction, depending on the amount of silver(i) salt used (1 or 2 equiv.). | |||||||||
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| Record 132 of 349 | |||||||||||||||
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| Author(s): Vana, L (Vana, Lubomir); Jakubec, M (Jakubec, Martin); Sykora, J (Sykora, Jan); Cisarova, I (Cisarova, Ivana); Zadny, J (Zadny, Jaroslav); Storch, J (Storch, Jan); Cirkva, V (Cirkva, Vladimir) | |||||||||||||||
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| Abstract: A series of aza[n]helicenes (n = 4-7) was synthesized using a photocyclodehydrochlorination of 1-chloro-N-aryl-2- naphthamides as a general synthetic procedure introducing the nitrogen atom to the third ring of the helicene framework. The effect of the nitrogen presence in the helicene skeleton on the physicochemical properties of the prepared aza[n]helicenes was studied and compared to those of the parent carbo-analogues. The insertion of a nitrogen atom into the outer edge of the helicene molecule has a severe impact on certain physicochemical properties such as optical rotation, electrostatic potentials, and intermolecular interactions. On the other hand, some other properties such as UV/vis, fluorescence, and phosphorescence spectra remained almost unaffected when compared to the parent carbohelicenes. A nitrogen atom can be also used for further derivatization, which can lead to further modification of helicene properties, as manifested here in the fluorescence changes induced by protonation. | |||||||||||||||
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| Record 133 of 349 | |||||||||
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| Author(s): Rezac, J (Rezac, Jan) | |||||||||
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| Abstract: The Non-Covalent Interactions Atlas (https://www.nciatlas.org) has been extended with two data sets of benchmark interaction energies in complexes dominated by London dispersion. The D1200 data set of equilibrium geometries provides a thorough sampling of an extended chemical space, while the D442x10 set features dissociation curves for selected complexes. In total, they provide 5178 new CCSD(T)/CBS data points of the highest quality. The new data have been combined with previous NCIA data sets in a comprehensive test of dispersion-corrected DFT methods, identifying the ones that achieve high accuracy in all types of non-covalent interactions in a broad chemical space. Additional tests of dispersion-corrected MP2 and semiempirical QM methods are also reported. | |||||||||
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| Record 134 of 349 | ||||||
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| Author(s): Arasu, NP (Arasu, Narendra P.); Vazquez, H (Vazquez, Hector) | ||||||
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| Abstract: Interfaces between metals and organic materials play an essential role in molecular surface science, photovoltaics, or molecular electronics. Modeling the evolution of interface geometry over sufficiently long timescales requires an accurate parameterization of the relevant metal- molecule interactions. Here, we describe a method for calculating interface parameters from reference density functional theory calculations of small metal-molecule complexes. We apply this method to develop a parameter set for a series of metal-molecule-metal junctions. We study the dynamics of short oligophenyls with amine, methyl-sulfide, or direct Au-C links, which are bonded to Au(111) via small adatom structures. Nanosecond classical molecular dynamics simulations using the generated parameter set reveal insight into molecular degrees of freedom not accessible from ab initio molecular dynamics simulations. | ||||||
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| Record 135 of 349 | |||||||||
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| Author(s): Gazda, D (Gazda, D.); Htun, TY (Htun, T. Yadanar); Forssen, C (Forssen, C.) | |||||||||
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| Abstract: The energy levels of light hypernuclei are experimentally accessible observables that contain valuable information about the interaction between hyperons and nucleons. In this work we study strangeness S = -1 systems H-3,4(Lambda) and He-4,5(Lambda) using the ab initio no-core shell model (NCSM) with realistic interactions obtained from chiral effective field theory (chi EFT). In particular, we quantify the finite precision of theoretical predictions that can be attributed to nuclear physics uncertainties. We study both the convergence of the solution of the many-body problem (method uncertainty) and the regulator and calibration-data dependence of the nuclear chi EFT Hamiltonian (model uncertainty). For the former, we implement infrared correction formulas and extrapolate finite-space NCSM results to infinite model space. We then use Bayesian parameter estimation to quantify the resulting method uncertainties. For the latter, we employ a family of 42 realistic Hamiltonians and measure the standard deviation of predictions while keeping the leading-order hyperon-nucleon interaction fixed. Following this procedure we find that model uncertainties of ground-state Lambda separation energies amount to approximate to 20 (100) keV in H-3(Lambda) (H-4(Lambda), He) and approximate to 400 keV in He-5(Lambda). Method uncertainties are comparable in magnitude for the H-4(Lambda), He 1(+) excited states and He-5(Lambda), which are computed in limited model spaces, but otherwise are much smaller. This knowledge of expected theoretical precision is crucial for the use of binding energies of light hypernuclei to infer the elusive hyperon-nucleon interaction. | |||||||||
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| Record 136 of 349 | ||||||
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| Author(s): Najman, P (Najman, Pavel); Zemcik, P (Zemcik, Pavel) | ||||||
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| Abstract: We have proposed a novel method for vehicle speed estimation using a calibrated and synchronized pair of stereo cameras. In a newly proposed method, we first localize the vehicle by detecting and tracking its license plate in a series of stereo images; then, we triangulate the vehicle position along its trajectory; and finally, we compute its speed based on the trajectory and time. The experiments show that the proposed method overcomes state-of-the-art results with a mean error of approximately 0.05 km/h, a standard deviation of less than 0.20 km/h, and a maximum absolute error of less than 0.75 km/h. For the purpose of evaluation, we have recorded a dataset that contains over 600 vehicles whose trajectories were recorded and for which their ground truth speed was obtained from a pair of single beam LIDARs in optical gate configuration. Using the presented method, the speed was measured for over 99 % of the recorded vehicles. Others were rejected by the method mainly due to their short trajectories, obstructed license plates or frame errors that would adversely affect the precision of the measurement. | ||||||
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| Record 137 of 349 | ||||||
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| Author(s): Premus, J (Premus, Jan); Gallovic, F (Gallovic, Frantisek); Ampuero, JP (Ampuero, Jean-Paul) | ||||||
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| Abstract: Transient fault slip spans time scales from tens of seconds of earthquake rupture to years of aseismic afterslip. So far, seismic and geodetic recordings of these two phenomena have primarily been studied separately and mostly with a focus on kinematic aspects, which limits our physical understanding of the interplay between seismic and aseismic slip. Here, we use a Bayesian dynamic source inversion method, based on laboratory-derived friction laws, to constrain fault stress and friction properties by joint quantitative modeling of coseismic and postseismic observations. Analysis of the well-recorded 2014 South Napa, California earthquake shows how the stressing and frictional conditions on the fault govern the spatial separation between shallow coseismic and postseismic slip, the progression of afterslip driving deep off-fault aftershocks, and the oblique ribbon-like rupture shape. Such inferences of stress and frictional rheology can advance our understanding of earthquake physics and pave the way for self-consistent cross-scale seismic hazard assessment. | ||||||
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| Record 138 of 349 | ||||||
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| Author(s): Cizek, J (Cizek, Jakub); Vlasak, T (Vlasak, Tomas); Melikhova, O (Melikhova, Oksana) | ||||||
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| Abstract: Lattice defects in refractory metal high-entropy alloy HfNbTaTiZr are investigated using positron lifetime spectroscopy combined with coincidence Doppler broadening (CDB) spectroscopy. Annealing of HfNbTaTiZr alloy at 1000 degrees C results in full recovery of defects and formation of single-phase random solid solution characterized by the bulk positron lifetime of 141 ps. This value is in accordance with the theoretical estimation. Quenching of the alloy from high temperature prevents recovery of thermally equilibrium vacancies and enables to retain a high concentration of vacancies in the sample at ambient temperature. For single vacancies in the HfNbTaTiZr alloy, a characteristic positron lifetime of 212 ps is measured, which is significantly shorter than the value estimated by theoretical calculations. It indicates that there is considerable ion relaxation around vacancies. The CDB spectroscopy investigations reveal that vacancies in HfNbTaTiZr alloy are not distributed randomly but are preferentially coupled with Hf solutes. | ||||||
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| Record 139 of 349 | ||||||||||||
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| Author(s): Sangvirotjanapat, S (Sangvirotjanapat, Sunisa); Fer, T (Fer, Tomas); Denduangboripant, J (Denduangboripant, Jessada); Newman, MF (Newman, Mark F.) | ||||||||||||
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| Abstract: A molecular systematic study of Globba section Nudae (Zingiberaceae) using ITS and matK sequences identifies three major clades, Globba subsection Nudae, G. subsection Mediocalcaratae and a new subsection, Globba subsection Pelecantherae, which is described here. The two species belonging in this subsection, Globba pelecanthera and Globba securifer, which are both new, are described. Rectangular anther appendages are reported in Globba for the first time. Evidence of hybridisation is given. The morphological characters of the flowers, which are likely to be important in pollination, are discussed. | ||||||||||||
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| Record 140 of 349 | |||||||||||||||||||||
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| Author(s): Jaulmes, F (Jaulmes, Fabien); Ficker, O (Ficker, Ondrej); Weinzettl, V (Weinzettl, Vladimir); Komm, M (Komm, Michael); Grover, O (Grover, Ondrej); Seidl, J (Seidl, Jakub); Zadvitskiy, G (Zadvitskiy, Georgiy); Macusova, E (Macusova, Eva); Panek, R (Panek, Radomir) | |||||||||||||||||||||
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| Abstract: In the future COMPASS Upgrade (Vondracek et al. in Fusion Eng Des 169:112490, https://doi.org/10.1016/j.fusengdes.2021.112490, 2021) tokamak (R-0 = 0.894 m, B-t similar to 5 T), three distinct types of edge transport bather are anticipated: ELMy H-mode, EDA H-mode and I-mode. The main auxiliary heating system used to access H-mode will be Neutral Beam Injection (NBI) power. The NBI will have a nominal injection energy of 80 keV at a maximum injection radius R-tan = 0.6 m. A significant neutron yield will occur from the interaction of the beam with the plasma background. Using our orbit-following code EBdyna (Jaulmes et al. in Nucl Fusion 61, 046012, https://doi.org/10.1088/1741-4326/abd41b, 2021), we calculate the trajectories of the NBI ions during the complete thermalization process, calculate the amount of NBI ions losses and evaluate the neutron rate in steady state from the beam-plasma and beam-beam interaction. Combining it with the thermal yield, we can derive detailed synthetic spectrogram of the energy distribution of the neutrons. The markers can be further used to provide synthetic neutron spectrometer diagnostics data. Due to the reduction of the simulated neutron count seen by the detectors when the peaking of the neutron source is lower, we anticipate the need for absolute-calibration in order to recover quantitative results. | |||||||||||||||||||||
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| Record 141 of 349 |
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| Author(s): Vacek, J (Vacek, Jan); Zatloukalova, M (Zatloukalova, Martina); Kabelac, M (Kabelac, Martin) |
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| Abstract: In this Opinion, redox transformations of bioactive electron donors and electron acceptors, especially reactive electro-philes, are discussed. The mutual balance and their coopera-tive effects, together with an extensive battery of antioxidant/ prooxidant enzymes, is responsible for maintaining the redox homeostasis of the cell. Electrochemical approaches play a key role in the investigation of these molecules, especially in research of their physico-chemical properties, their stability/ reactivity and ability to interact with other cellular components such as nucleic acids, proteins (enzymes and cell receptors) and lipid membranes. The interaction of electron acceptors/ donors is the basis for an understanding of highly complex and dynamic systems for homeostasis control and the cell response to stress conditions. |
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| Record 142 of 349 | ||||||||||||
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| Author(s): Brus, J (Brus, Jiri); Czernek, J (Czernek, Jiri); Urbanova, M (Urbanova, Martina); Cervinka, C (Cervinka, Ctirad) | ||||||||||||
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| Abstract: In crystalline molecular solids, in the absence of strong intermolecular interactions, entropy-driven processes play a key role in the formation of dynamically modulated transient phases. Specifically, in crystalline simvastatin, the observed fully reversible enantiotropic behavior is associated with multiple order-disorder transitions: upon cooling, the dynamically disordered high-temperature polymorphic Form I is transformed to the completely ordered low-temperature polymorphic Form III via the intermediate (transient) modulated phase II. This behavior is associated with a significant reduction in the kinetic energy of the rotating and flipping ester substituents, as well as a decrease in structural ordering into two distinct positions. In transient phase II, the conventional three-dimensional structure is modulated by periodic distortions caused by cooperative conformation exchange of the ester substituent between the two states, which is enabled by weakened hydrogen bonding. Based on solid-state NMR data analysis, the mechanism of the enantiotropic phase transition and the presence of the transient modulated phase are documented. | ||||||||||||
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| Record 143 of 349 | ||||||||||||||||||||||||||||||
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| Author(s): Alcaraz, AJG (Alcaraz, Alper James G.); Baraniuk, S (Baraniuk, Shaina); Mikulasek, K (Mikulasek, Kamil); Park, B (Park, Bradley); Lane, T (Lane, Taylor); Burbridge, C (Burbridge, Connor); Ewald, J (Ewald, Jessica); Potesil, D (Potesil, David); Xia, JG (Xia, Jianguo); Zdrahal, Z (Zdrahal, Zbynek); Schneider, D (Schneider, David); Crump, D (Crump, Doug); Basu, N (Basu, Niladri); Hogan, N (Hogan, Natacha); Brinkmann, M (Brinkmann, Markus); Hecker, M (Hecker, Markus) | ||||||||||||||||||||||||||||||
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| Abstract: Current approaches in chemical hazard assessment face significant challenges because they rely on live animal testing, which is time-consuming, expensive, and ethically questionable. These concerns serve as an impetus to develop new approach methodologies (NAMs) that do not rely on live animal tests. This study explored a molecular benchmark dose (BMD) approach using a 7-day embryo-larval fathead minnow (FHM) assay to derive transcriptomic points-of-departure (tPODs) to predict apical BMDs of fluoxetine (FLX), a highly prescribed and potent selective serotonin reuptake inhibitor frequently detected in surface waters. Fertilized FHM embryos were exposed to graded concentrations of FLX (confirmed at < LOD, 0.19, 0.74, 3.38, 10.2, 47.5 mu g/L) for 32 days. Subsets of fish were subjected to omics and locomotor analyses at 7 days post-fertilization (dpf) and to histological and biometric measurements at 32 dpf. Enrichment analyses of transcriptomics and proteomics data revealed significant perturbations in gene sets associated with serotonergic and axonal functions. BMD analysis resulted in tPOD values of 0.56 mu g/L (median of the 20 most sensitive gene-level BMDs), 5.0 mu g/L (tenth percentile of all gene-level BMDs), 7.51 mu g/L (mode of the first peak of all gene-level BMDs), and 5.66 mu g/L (pathway-level BMD). These tPODs were protective of locomotor and reduced body weight effects (LOEC of 10.2 mu g/L) observed in this study and were reflective of chronic apical BMDs of FLX reported in the literature. Furthermore, the distribution of gene-level BMDs followed a bimodal pattern, revealing disruption of sensitive neurotoxic pathways at low concentrations and metabolic pathway perturbations at higher concentrations. This is one of the first studies to derive protective tPODs for FLX using a short-term embryo assay at a life stage not considered to be a live animal under current legislations. | ||||||||||||||||||||||||||||||
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| Record 144 of 349 | |||||||||
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| Author(s): Kriz, K (Kriz, Kristian); Rezac, J (Rezac, Jan) | |||||||||
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| Abstract: The SH250x10 dataset presented here extends the Non-Covalent Interactions Atlas database (https://www.nciatlas.org) to complexes bound by sigma-hole interactions - halogen, chalcogen and pnictogen bonds. It comprises 250 complexes where Cl, Br, I, S, Se, P and As interact with diverse electron donors. An accurate CCSD(T)/CBS benchmark is provided for ten points along a dissociation curve of each complex. The SH250x10 set is used in testing a wide variety of DFT functionals and semiempirical quantum-mechanical methods. In DFT calculations, the new data set exposes large errors of some functionals related to exaggerated charge transfer. The size and diversity of the data set have also been exploited in the reparametrization of a halogen-bond correction for the PM6 semiempirical method. | |||||||||
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| Record 145 of 349 | ||||||||||||||||||
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| Author(s): Praks, P (Praks, Pavel); Lampart, M (Lampart, Marek); Praksova, R (Praksova, Renata); Brkic, D (Brkic, Dejan); Kozubek, T (Kozubek, Tomas); Najser, J (Najser, Jan) | ||||||||||||||||||
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| Abstract: In this paper, we analyze the interpretable models from real gasification datasets of the project "Centre for Energy and Environmental Technologies" (CEET) discovered by symbolic regression. To evaluate CEET models based on input data, two different statistical metrics to quantify their accuracy are usually used: Mean Square Error (MSE) and the Pearson Correlation Coefficient (PCC). However, if the testing points and the points used to construct the models are not chosen randomly from the continuum of the input variable, but instead from the limited number of discrete input points, the behavior of the model between such points very possibly will not fit well the physical essence of the modelled phenomenon. For example, the developed model can have unexpected oscillatory tendencies between the used points, while the usually used statistical metrics cannot detect these anomalies. However, using dynamic system criteria in addition to statistical metrics, such suspicious models that do fit well-expected behavior can be automatically detected and abandoned. This communication will show the universal method based on dynamic system criteria which can detect suitable models among all those which have good properties following statistical metrics. The dynamic system criteria measure the complexity of the candidate models using approximate and sample entropy. The examples are given for waste gasification where the output data (percentage of each particular gas in the produced mixture) is given only for six values of the input data (temperature in the chamber in which the process takes place). In such cases instead, to produce expected simple spline-like curves, artificial intelligence tools can produce inappropriate oscillatory curves with sharp picks due to the known tendency of symbolic regression to produce overfitted and relatively more complex models if the nature of the physical model is simple. | ||||||||||||||||||
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| Record 146 of 349 | |||||||||
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| Author(s): Cizek, J (Cizek, J.); Melikhova, O (Melikhova, O.); Vlasak, T (Vlasak, T.); Hruska, P (Hruska, P.); Stary, D (Stary, D.); Lukac, F (Lukac, F.) | |||||||||
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| Abstract: A B S T R A C T Severe distortions of crystalline lattice represent an inherent feature of complex concentrated alloys (CCAs). Lattice distortions are caused by atomic size differences of alloy constituent ions which are distributed randomly over the lattice sites. It is believed that lattice distortions play the key role in extraordinary properties of CCAs. However, characterization of lattice distortions is difficult since they occur on the atomic scale and have a stochastic nature. In the present work we employ positron annihilation spectroscopy for characterization of lattice distortions in series of 18 refractory metal CCAs with the bcc structure. Our study revealed that the bulk positron lifetime increases with increasing magnitude of lattice distortions. It indicates that positron delocalized in the lattice can be used as a probe of lattice distortions in CCAs since it is located with higher probability in interstitial regions with extended open volume. This experimental observation is supported by theoretical calculations of positron lifetimes in CCAs. Moreover, it was confirmed that lattice distortions cause strengthening of CCAs. | |||||||||
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| Record 147 of 349 | ||||||
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| Author(s): Arasu, NP (Arasu, Narendra P.); Vazquez, H (Vazquez, Hector) | ||||||
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| Abstract: Interfaces between metals and organic materials play an essential role in molecular surface science, photovoltaics, or molecular electronics. Modeling the evolution of interface geometry over sufficiently long timescales requires an accurate parameterization of the relevant metal- molecule interactions. Here, we describe a method for calculating interface parameters from reference density functional theory calculations of small metal-molecule complexes. We apply this method to develop a parameter set for a series of metal-molecule-metal junctions. We study the dynamics of short oligophenyls with amine, methyl-sulfide, or direct Au-C links, which are bonded to Au(111) via small adatom structures. Nanosecond classical molecular dynamics simulations using the generated parameter set reveal insight into molecular degrees of freedom not accessible from ab initio molecular dynamics simulations. | ||||||
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| Record 148 of 349 | ||||||||||||
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| Author(s): Lunkad, R (Lunkad, Raju); Biehl, P (Biehl, Philip); Murmiliuk, A (Murmiliuk, Anastasiia); Blanco, PM (Blanco, Pablo M.); Mons, P (Mons, Peter); Stepanek, M (Stepanek, Miroslav); Schacher, FH (Schacher, Felix H.); Kosovan, P (Kosovan, Peter) | ||||||||||||
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| Abstract: We synthesized three different polyzwitterions-poly(N,N-diallyl glutamate) (PDAGA), poly(dehydroalanine) (PDha), and poly(2-(imidazol-1-yl)acrylic acid) (PImAA)-and investigated how their ionization states respond to changes in solution pH. We used molecular simulations to determine how the net charge per monomer and the ionization states of individual acidic and basic groups differ from the ideal (Henderson-Hasselbalch) behavior. To complement the theoretical predictions, we performed potentiometric titrations and zeta-potential measurements of all studied polyzwitterions. By comparing these experiments with theoretical predictions, we could show that molecular simulations can predict and explain the origin of the differences between the effective and bare pK(a) values of individual titratable groups. Furthermore, we have shown that it is not possible to obtain these effective pK(a) values directly from the equivalence point recognition criterion (ERC), commonly used in potentiometric titrations. However, the effective pK(a) values can be reliably obtained by calculating the net charge per monomer from the potentiometric titration curves and validating these results against theoretical predictions. The approach we propose works reliably for polyzwitterions in which the ionization response is dominated by electrostatic interactions, such as PDAGA or PDha; however, it fails if other specific interactions contribute significantly, such as in the case of PImAA. | ||||||||||||
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| Record 149 of 349 |
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| Author(s): Krticka, J (Krticka, J.); Kubat, J (Kubat, J.); Krtickova, I (Krtickova, I) |
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| Abstract: Wind-fed high-mass X-ray binaries are powered by accretion of the radiatively driven wind of the luminous component on the compact star. Accretion-generated X-rays alter the ionization state of the wind. Because higher ionization states drive the wind less effectively, X-ray ionization may brake acceleration of the wind. This causes a decrease in the wind terminal velocity and mass flux in the direction toward the X-ray source. Here we study the effect of X-ray ionization on the stellar wind of B supergiants. We determine the binary parameters for which the X-ray irradiation significantly influences the stellar wind. This can be conveniently studied in diagrams that plot the optical depth parameter versus the X-ray luminosity. For low optical depths or for high X-ray luminosities, X-ray ionization leads to a disruption in the wind aimed toward the X-ray source. Observational parameters of high-mass X-ray binaries with B-supergiant components appear outside the wind disruption zone. The X-ray feedback determines the resulting X-ray luminosity. We recognize two states with a different level of feedback. For low X-ray luminosities, ionization is weak, and the wind is not disrupted by X-rays and flows at large velocities, consequently the accretion rate is relatively low. On the other hand, for high X-ray luminosities, the X-ray ionization disrupts the flow braking the acceleration, the wind velocity is low, and the accretion rate becomes high. These effects determine the X-ray luminosity of individual binaries. Accounting for the X-ray feedback, estimated X-ray luminosities reasonably agree with observational values. We study the effect of small-scale wind inhomogeneities (clumping), showing that clumping weakens the effect of X-ray ionization by increasing recombination and the mass-loss rate. This effect is particularly important in the region of the so-called bistability jump. We show that ultraluminous X-ray binaries with LX less than or similar to 10(40) erg s(-1) may be powered by accretion of a B-supergiant wind on a massive black hole. |
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| Record 150 of 349 | ||||||
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| Author(s): Matzner, F (Matzner, Filip) | ||||||
| Edited by: Fieldsend JE | ||||||
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| Abstract: Echo State Networks represent a type of recurrent neural network with a large randomly generated reservoir and a small number of readout connections trained via linear regression. The most common topology of the reservoir is a fully connected network of up to thousands of neurons. Over the years, researchers have introduced a variety of alternative reservoir topologies, such as a circular network or a linear path of connections. When comparing the performance of different topologies or other architectural changes, it is necessary to tune the hyperparameters for each of the topologies separately since their properties may significantly differ. The hyperparameter tuning is usually carried out manually by selecting the best performing set of parameters from a sparse grid of predefined combinations. Unfortunately, this approach may lead to underperforming configurations, especially for sensitive topologies. We propose an alternative approach of hyperparameter tuning based on the Covariance Matrix Adaptation Evolution Strategy (CMA-ES). Using this approach, we have improved multiple topology comparison results by orders of magnitude suggesting that topology alone does not play as important role as properly tuned hyperparameters. | ||||||
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| Conference Sponsors: Assoc Comp Machinery, ACM SIGEVO | ||||||
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| ISBN: 978-1-4503-9237-2 |
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| Author(s): Egorova, E (Egorova, Ekaterina); Vydana, HK (Vydana, Hari Krishna); Burget, L (Burget, Lukas); Cernocky, JH (Cernocky, Jan Honza) | |||||||||
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| Abstract: We propose a new end-to-end architecture for automatic speech recognition that expands the "listen, attend and spell" (LAS) paradigm. While the main word-predicting network is trained to predict words, the secondary, speller network, is optimized to predict word spellings from inner representations of the main network (e.g. word embeddings or context vectors from the attention module). We show that this joint training improves the word error rate of a word-based system and enables solving additional tasks, such as out-of-vocabulary word detection and recovery. The tests are conducted on LibriSpeech dataset consisting of 1000 h of read speech. | |||||||||
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| Record 152 of 349 | |||||||||||||||
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| Author(s): Erlebach, A (Erlebach, Andreas); Nachtigall, P (Nachtigall, Petr); Grajciar, L (Grajciar, Lukas) | |||||||||||||||
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| Abstract: The computational discovery and design of zeolites is a crucial part of the chemical industry. Finding highly accurate while computational feasible protocol for identification of hypothetical siliceous frameworks that could be targeted experimentally is a great challenge. To tackle this challenge, we trained neural network potentials (NNP) with the SchNet architecture on a structurally diverse database of density functional theory (DFT) data. This database was iteratively extended by active learning to cover not only low-energy equilibrium configurations but also high-energy transition states. We demonstrate that the resulting reactive NNPs retain DFT accuracy for thermodynamic stabilities, vibrational properties, as well as reactive and non-reactive phase transformations. As a showcase, we screened an existing zeolite database and revealed >20k additional hypothetical frameworks in the thermodynamically accessible range of zeolite synthesis. Hence, our NNPs are expected to be essential for future high-throughput studies on the structure and reactivity of siliceous zeolites. | |||||||||||||||
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| Author(s): Colville, C (Colville, Carly); Alcaraz, AJ (Alcaraz, Alper James); Green, D (Green, Derek); Park, B (Park, Bradley); Xia, JG (Xia, Jianguo); Soufan, O (Soufan, Othman); Hruska, P (Hruska, Pavel); Potesil, D (Potesil, David); Zdrahal, Z (Zdrahal, Zbynek); Crump, D (Crump, Doug); Basu, N (Basu, Niladri); Hogan, N (Hogan, Natacha); Hecker, M (Hecker, Markus) | ||||||||||||||||||
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| Abstract: Current ecotoxicity testing programs are impeded as they predominantly rely on slow and expensive animal tests measuring adverse outcomes. Therefore, new approach methodologies (NAMs) increasingly involve short-term mechanistic assays that employ molecular endpoints to predict adverse outcomes of regulatory relevance. This study aimed to elucidate the application of NAMs in adult fathead minnows using fluoxetine (FLX) as a model compound. Fish were exposed to three FLX concentrations (measured: 2.42, 10.7, and 56.7 mu gL(-1)) and a control. After 96 h, molecular toxicity signatures were characterized using proteomics and transcriptomics analyses in livers and brains of a sub-set of fish. The remaining fish were sampled at 21 days and assessed for liver histopathology and morphometric measurements. Fecundity was monitored throughout the study. In the livers, 56.7 mu gL(-1) FLX caused enrichment of PPAR signaling in the proteome and fatty acid-related pathways in the transcriptome, potential upstream responses that led to lipid-type vacuolation of hepatocytes, observed via histopathology. Upregulated genes in the brain suggested alterations in serotonin-related signaling processes and reproductive behaviour, which may explain the observed signifi-cant decrease in fecundity. While the relationships between molecular responses and adverse outcomes remain complex, this research provided important insights into the mechanistic toxicity of FLX. | ||||||||||||||||||
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| Record 154 of 349 | ||||||
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| Author(s): Tonka, T (Tonka, Tomas); Walterova, L (Walterova, Lucie); Hejna, O (Hejna, Ondrej); Curn, V (Curn, Vladislav) | ||||||
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| Record 155 of 349 | ||||||||||||
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| Author(s): Wenskat, M (Wenskat, Marc); Cizek, J (Cizek, Jakub); Liedke, MO (Liedke, Maciej Oskar); Butterling, M (Butterling, Maik); Stiehl, M (Stiehl, Martin); Semione, GDL (Semione, Guilherme Dalla Lana); Backes, C (Backes, Constanze); Bate, C (Bate, Christopher); Melikhova, O (Melikhova, Oksana); Hirschmann, E (Hirschmann, Eric); Wagner, A (Wagner, Andreas); Weise, H (Weise, Hans); Stierle, A (Stierle, Andreas); Aeschlimann, M (Aeschlimann, Martin); Hillert, W (Hillert, Wolfgang) | ||||||||||||
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| Abstract: In recent years, superconducting radio-frequency (SRF) cavities have been considered as candidates for qubits in quantum computing, showing longer photon lifetimes and, therefore, longer decoherence times of a cavity stored qubit compared to many other realizations. In modern particle accelerators, SRF cavities are the workhorse. Continuous research and development efforts are being undertaken to improve their properties, i.e., to increase the accelerating field and lower the surface resistance, which in turn increase the energy reach and duty cycle of accelerators. While some experimental milestones have been achieved, the mechanisms behind the still observed losses remain not fully understood. In this contribution we are going to show that a recently reported temperature treatment of Nb SRF cavities in the temperature range of 573-673 K, which reduces the residual surface resistance to unprecedented values, is linked to a reorganization of the niobium oxide and near-surface vacancy structure and that this reorganization can explain the observed improved performance in both applications, quantum computing and SRF cavities. | ||||||||||||
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| Record 156 of 349 | ||||||
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| Author(s): Bering, K (Bering, Klaus); Pazderka, M (Pazderka, Michal) | ||||||
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| Abstract: We investigate a new algebra-based approach of finding Grassmannian formulas for scattering amplitudes. Our prime motivation is massive amplitudes of 4D N . = 4 SYM, and therefore we consider a 6D Grassmannian formula, where we can take advantage of massless kinematics. We next use symmetry arguments, and in particular, 6D dual conformal symmetry generalized to arbitrary dual conformal weights. Assuming a rational ansatz in terms of Plucker coordinates (i.e. minors) for the integrand, this approach leads to a set of algebraic equations. As an example, we explicitly find the solution for 4-point scattering amplitudes up to proportionality constants. | ||||||
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| Record 157 of 349 | ||||||||||||
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| Author(s): Roncevic, I (Roncevic, Igor); Kaletova, E (Kaletova, Eva); Varga, K (Varga, Katarina); Cisarova, I (Cisarova, Ivana); Bastl, Z (Bastl, Zdenek); Jiang, JC (Jiang, Jyh-Chiang); Kaleta, J (Kaleta, Jiri) | ||||||||||||
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| Abstract: The present study has identified molecular bending as an important factor thathas a profound effect on the self-assembly of originally rod-shaped organic molecules on a(111) gold surface. This was demonstrated on three specifically designed rigid molecular rodscarrying archetypal anchoring groups (pyridyl units and thiols) on one terminus. These rodswere used to prepare corresponding self-assembled monolayers (SAMs), and a combinationof various analytical techniques revealed that originally straight molecular rods that were bentonce adsorbed on a metallic surface, acquiring a characteristic"J-shape". Extensive densityfunctional theory calculations, includingin silicoreconstruction of such SAMs on (111) gold,clearly confirmed experimental observations. | ||||||||||||
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| Record 158 of 349 | ||||||
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| Author(s): Nesvorny, D (Nesvorny, David); Chrenko, O (Chrenko, Ondrej); Flock, M (Flock, Mario) | ||||||
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| Abstract: TOI-216 is a pair of close-in planets with orbits deep in the 2:1 mean motion resonance. The inner Neptune-class planet (TOI-216b) is near 0.12 au (orbital period P (b) similar or equal to 17 days) and has a substantial orbital eccentricity (e (b) similar or equal to 0.16) and large libration amplitude (A ( psi ) similar or equal to 60 degrees) in the resonance. The outer planet (TOI-216c) is a gas giant on a nearly circular orbit. We carry out N-body simulations of planet migration in a protoplanetary gas disk to explain the orbital configuration of TOI-216 planets. We find that TOI-216b's migration must have been halted near its current orbital radius to allow for a convergent migration of the two planets into the resonance. For the inferred damping-to-migration timescale ratio tau ( e )/tau ( a ) similar or equal to 0.02, overstable librations in the resonance lead to a limit cycle with A ( psi ) similar or equal to 80 degrees and e (b) < 0.1. The system could have remained in this configuration for the greater part of the protoplanetary disk lifetime. If the gas disk was removed from inside out, this would have reduced the libration amplitude to A ( psi ) similar or equal to 60 degrees and boosted e (b) via the resonant interaction with TOI-216c. Our results suggest a relatively fast inner-disk removal (similar to 10(5) yr). Another means of explaining the large libration amplitude is stochastic stirring from a (turbulent) gas disk. For that to work, overstable librations would need to be suppressed, tau ( e )/tau ( a ) similar or equal to 0.05, and very strong turbulent stirring (or some other source of large stochastic forcing) would need to overcome the damping effects of gas. Hydrodynamical simulations can be performed to test these models. | ||||||
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| Record 159 of 349 |
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| Author(s): Beranek, J (Beranek, Jakub); Bohm, S (Bohm, Stanislav); Cima, V (Cima, Vojtech) |
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| Abstract: Task graphs provide a simple way to describe scientific workflows (sets of tasks with dependencies) that can be executed on both HPC clusters and in the cloud. An important aspect of executing such graphs is the used scheduling algorithm. Many scheduling heuristics have been proposed in existing works; nevertheless, they are often tested in oversimplified environments. We provide an extensible simulation environment designed for prototyping and benchmarking task schedulers, which contains implementations of various scheduling algorithms and is open-sourced, in order to be fully reproducible. We use this environment to perform a comprehensive analysis of workflow scheduling algorithms with a focus on quantifying the effect of scheduling challenges that have so far been mostly neglected, such as delays between scheduler invocations or partially unknown task durations. Our results indicate that network models used by many previous works might produce results that are off by an order of magnitude in comparison to a more realistic model. Additionally, we show that certain implementation details of scheduling algorithms which are often neglected can have a large effect on the scheduler's performance, and they should thus be described in great detail to enable proper evaluation. |
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| Record 160 of 349 |
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| Author(s): Markopoulos, A (Markopoulos, Alexandros); Beremlijski, P (Beremlijski, Petr); Vlach, O (Vlach, Oldrich); Sadowska, M (Sadowska, Marie) |
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| Abstract: The present paper deals with the numerical solution of 3D shape optimization problems in frictional contact mechanics. Mathematical modelling of the Coulomb friction problem leads to an implicit variational inequality which can be written as a fixed point problem. Furthermore, it is known that the discretized problem is uniquely solvable for small coefficients of friction. Since the considered problem is nonsmooth, we exploit the generalized Mordukhovich's differential calculus to compute the needed subgradient information.The state problem is solved using successive approximations combined with the Total FETI (TFETI) method. The latter is based on tearing the bodies into "floating " subdomains, discretization by finite elements, and solving the resulting quadratic programming problem by augmented Lagrangians.The presented numerical experiments demonstrate our method's power and the importance of the proper modelling of 3D frictional contact problems. The state problem solution and the sensitivity analysis process were implemented in parallel. |
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| Record 161 of 349 |
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| Author(s): Nemec, T (Nemec, Tomas) |
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| Abstract: Nucleation rates for droplet formation in water vapor are measured in molecular dynamics (MD) simulations of SPC/E and TIP4P/2005 water by monitoring individual nucleation events. The nucleation process is simulated in the NPT ensemble to evaluate the steady-state nucleation rate in accordance with the assumptions of classical nucleation theory (CNT). Nucleation rates measured between 300 and 425 K for the SPC/E model, and between 325 and 475 K for the TIP4P/2005 model, agree with the CNT predictions roughly within the standard deviation of the MD measurements of the nucleation rates. |
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| Record 162 of 349 | |||||||||||||||
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| Author(s): Beranek, T (Beranek, Tomas); Jakubec, M (Jakubec, Martin); Sykora, J (Sykora, Jan); Cisarova, I (Cisarova, Ivana); Zadny, J (Zadny, Jaroslav); Storch, J (Storch, Jan) | |||||||||||||||
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| Abstract: A synthetic strategy toward phosphahelicenes containing a terminal phosphinine ring has been explored. The 4-phenyl-6-methyl-2-phospha[7]helicene was prepared from start-ing 2-bromobenzo[c]phenanthrene in 12% overall yield in 12 steps. The synthetic approach involves introduction of the phosphorus function prior to photocyclization forming the final helicene skeleton, followed by the formation of a phosphorus hexacycle. The structure of the first phosphahelicene with a terminal phosphinine ring was confirmed by X-ray crystallography. | |||||||||||||||
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| Record 163 of 349 | |||||||||||||||
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| Author(s): Das, NR (Das, Nilima R.); Bera, K (Bera, Krishnendu); Sharma, T (Sharma, Tripti); Toropova, AP (Toropova, Alla P.); Toropov, AA (Toropov, Andrey A.); Achary, PGR (Achary, P. Ganga Raju) | |||||||||||||||
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| Abstract: QSAR modelling based on several computational approaches has been effectively executed in the fields of pharmaceutical, eco-toxicity of industrial chemicals and materials science, etc. In this article a single optimal descriptor based QSAR models have been built. The therapeutic activity of a set of 105 molecules as inhibitors to HIF-1A (Hypoxia-inducible factor 1-alpha) were analyzed, as HIF is an important enzyme in promoting tumor growth and metastasis. Molecular docking was also implemented to estimate the binding capability of the studied molecules. QSAR model validation parameters and the docking results helped to identify the ligands that have high inhibition capability against HIF-1A. The molecular docking results exhibited that the ligand-105 showed better inhibition for C alpha atoms of HIF-1A with a binding energy of-40.1664 kJ/mol. Molecular dynamics (MD) simulations over 50 ns were used to investigate the dynamic behaviour of the apo form and complex form of ligand-105 with HIF-1A. The binding free energy determined from the MD simulation trajectory using the MM/ PBSA technique was-94.010+/-19.462 kJ/mol. | |||||||||||||||
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| Record 164 of 349 | ||||||
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| Author(s): Pazourkova, L (Pazourkova, Lenka); Martynkova, GS (Martynkova, Grazyna Simha); Supova, M (Supova, Monika) | ||||||
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| Abstract: Bioapatites (A) from natural bones are used as implants for bone grafts or powder bone fillings. The main advantage of A obtained from natural bones is the best ratio of Ca and P in comparison with synthetic bioapatites. Second component, Ca-deficient hydroxyapatite (CDH), is biocompatible and cheap material that is very often used not only in biological applications, but also for ceramic utilization. In this study we used the surface of bioapatite as a substrate for the CDH deposition. Calcinated A's at several temperatures were subsequently crushed in mortar or milled in jet mill. The Ca-deficient hydroxyapatite was prepared by easy precipitation route on bioapatite surface. The final modified A's structure was characterised using X-ray powder diffraction, infrared spectroscopy with Fourier transformation and scanning electron microscopy. The results show that interactions between CDH and A are probably by physical and non-bonding base. Copyright (C) 2022 Elsevier Ltd. All rights reserved. | ||||||
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| Record 165 of 349 | ||||||
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| Author(s): Eremenko, ZE (Eremenko, Z. E.); Pashynska, VA (Pashynska, V. A.); Kuznetsova, KS (Kuznetsova, K. S.); Shaposhnikova, A (Shaposhnikova, A.); Minofar, B (Minofar, B.) | ||||||
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| Abstract: We combined the microwave dielectrometry method for the complex permittivity experimental study of aqueous Human Serum Albumin (HSA) solutions and a molecular dynamics simulation of similar mod-elling aqueous solutions. Using microwave dielectrometry we obtained that the real and imaginary parts of complex permittivity of all studied solutions (HSA water solutions, HSA water solutions with NaCl or glucose) decrease at the HSA concentration growing. The molecular dynamics simulation of HSA aqueous solutions showed that the increase of the HSA concentration causes the number of H-bound increase between water and protein molecules and leads to complex permittivity value decrease for the tested solutions. Thus, the molecular dynamics simulation results are in good agreement with microwave dielectrometry experimental data for HSA aqueous solutions with the addition of NaCl and glucose. Our study can be applied in the ecological investigations of wastewater samples owing to demonstrated sensitivity of complex permittivity parameters measured to the small changes of the concentration in the solutions.(c) 2022 Elsevier B.V. All rights reserved. | ||||||
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| Record 166 of 349 | ||||||||||||||||||
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| Author(s): Vasilopoulos, Y (Vasilopoulos, Yannis); Heyda, J (Heyda, Jan); Rohlicek, J (Rohlicek, Jan); Skorepova, E (Skorepova, Eliska); Zvonicek, V (Zvonicek, Vitek); Soos, M (Soos, Miroslav) | ||||||||||||||||||
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| Abstract: In drug manufacturing, solvent-based methods are used for the crystallization of active pharmaceutical ingredients (APIs). Often, the solvent interacts with the API resulting in the formation of a new solid compound, the solvate. When desolvation occurs upon heating, it might result in the formation of new solid forms with significantly different physicochemical properties. Therefore, in this work, we study the desolvation kinetics by combining in situ powder X-ray diffraction (PXRD), all-atom molecular dynamics (MD) simulations, and macroscopic solid-state reaction kinetics modeling. The fluorobenzene (FB) solvate of Bruton's tyrosine kinase inhibitor Ibrutinib (IBR) was used as a model system. While the macroscopic solid-state modeling provides information about the desolvation kinetics, the MD simulations were used to trace individual FB molecules inside the crystal lattice. The activation energy of confined solvent diffusion, obtained by MD simulations, agrees well with results of the macroscopic solid-state reaction kinetics modeling. In addition, MD simulations provided detailed information about the IBR-FB interactions at the nanoscale. The mechanism revealed is that the solvent molecules diffusion, controlled by distinct open-close gating conformational changes of the drug, triggers the desolvation throughout the crystal lattice. | ||||||||||||||||||
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| Record 167 of 349 | |||||||||
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| Author(s): Lunak, S (Lunak, Stanislav, Jr.); Weiter, M (Weiter, Martin); Vala, M (Vala, Martin) | |||||||||
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| Abstract: Stacked centrosymmetrical dimers and simultaneously H-bonded and stacked hexamers of thiophene-substituted diketopyrrolopyrrole (ThDPP) were studied using DFT as models for crystals with slipped-stacked molecules in 1D columns. Eight stacked dimer arrangements were found, six of which are driven by the minimisation of electron repulsion and realised by placing the partially negatively charged atoms of the diketopyrrolopyrrole rings below the centre of an adjacent thiophene ring. Four of these stacks are related to N,N'-dialkylated derivatives of ThDPP found in the literature, while a further one is related to an N,N'-diacylated derivative. An analogous set of eight stacks was discovered computationally for phenyl-substituted DPP (PhDPP), four of which are known among H-bonded DPP pigments, and one more among N,N'-dialkylated PhDPP derivatives. The results shed more light on the mechanisms that drive the formation of stacks between nonaromatic (DPP) and aromatic (Th, Ph) rings. The excitation energies of the lowest four singlet states computed by TD DFT enabled excitonic coupling and energy separation between Frenkel-resonance-type and charge-transfer states to be established, depending on the equilibrium stack geometry. | |||||||||
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| Record 168 of 349 | ||||||||||||
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| Author(s): Prochazka, K (Prochazka, Karel); Limpouchova, Z (Limpouchova, Zuzana); Stepanek, M (Stepanek, Miroslav); Sindelka, K (Sindelka, Karel); Lisal, M (Lisal, Martin) | ||||||||||||
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| Abstract: This review article is addressed to a broad community of polymer scientists. We outline and analyse the fundamentals of the dissipative particle dynamics (DPD) simulation method from the point of view of polymer physics and review the articles on polymer systems published in approximately the last two decades, focusing on their impact on macromolecular science. Special attention is devoted to polymer and polyelectrolyte self- and co-assembly and self-organisation and to the problems connected with the implementation of explicit electrostatics in DPD numerical machinery. Critical analysis of the results of a number of successful DPD studies of complex polymer systems published recently documents the importance and suitability of this coarse-grained method for studying polymer systems. | ||||||||||||
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| Record 169 of 349 | |||||||||
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| Author(s): Kocman, R (Kocman, Radim); Krivka, Z (Krivka, Zbynek); Meduna, A (Meduna, Alexander); Nagy, B (Nagy, Benedek) | |||||||||
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| Abstract: Jumping finite automata and sensing 5' -> 3' Watson-Crick finite automata are finite-state models of computation which allow to process the input word not only in the strictly left-to-right manner. In this paper a new combined model of them is presented. The accepting power of the newmodel is studied and compared with the originalmodels and also other well-known language families. Furthermore, the paper investigates changes in the accepting power when commonly studied restrictions from Watson-Crick finite automata, e.g., all states are final, are applied to this combined model. In the end, the paper presents a comprehensive hierarchy of all related language families. | |||||||||
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| Record 170 of 349 | ||||||
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| Author(s): Klajmon, M (Klajmon, Martin) | ||||||
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| Abstract: A pair of popular thermodynamic models for pharmaceutical applications, namely, the perturbed-chain statistical associating fluid theory (PC-SAFT) equation of state and the conductor-like screening model for real solvents (COSMO-RS) are thoroughly benchmarked for their performance in predicting the solubility of active pharmaceutical ingredients (APIs) in pure solvents. The ultimate goal is to provide an illustration of what to expect from these progressive frameworks when applied to the thermodynamic solubility of APIs based on activity coefficients in a purely predictive regime without specific experimental solubility data (the fusion properties of pure APIs were taken from experiments). While this kind of prediction represents the typical modus operandi of the first-principles-aided COSMO-RS, PC-SAFT is a relatively highly parametrized model that relies on experimental data, against which its pure-substance and binary interaction parameters (k(ij)) are fitted. Therefore, to make this benchmark as fair as possible, we omitted any binary parameters of PC-SAFT (i.e., k(ij) = 0 in all cases) and preferred pure-substance parameter sets for APIs not trained to experimental solubility data. This computational approach, together with a detailed assessment of the obtained solubility predictions against a large experimental data set, revealed that COSMO-RS convincingly outperformed PC-SAFT both qualitatively (i.e., COSMO-RS was better in solvent ranking) and quantitatively, even though the former is independent of both substance- and mixture-specific experimental data. Regarding quantitative comparison, COSMO-RS outperformed PC-SAFT for 9 of the 10 APIs and for 63% of the API-solvent systems, with root-mean-square deviations of the predicted data from the entire experimental data set being 0.82 and 1.44 log units, respectively. The results were further analyzed to expand the picture of the performance of both models with respect to the individual APIs and solvents. Interestingly, in many cases, both models were found to qualitatively incorrectly predict the direction of deviations from ideality. Furthermore, we examined how the solubility predictions from both models are sensitive to different API parametrizations. | ||||||
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| Record 171 of 349 | ||||||
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| Author(s): Pauk, K (Pauk, Karel); Lunak, S (Lunak, Stanislav, Jr.); Ruzicka, A (Ruzicka, Ales); Markova, A (Markova, Aneta); Teichmanova, K (Teichmanova, Katerina); Mausova, A (Mausova, Anna); Kratochvil, M (Kratochvil, Matous); Smolka, R (Smolka, Rastislav); Mikysek, T (Mikysek, Tomas); Weiter, M (Weiter, Martin); Imramovsky, A (Imramovsky, Ales); Vala, M (Vala, Martin) | ||||||
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| Abstract: The solid-state fluorescence (SSF) of eight DPA-DPS-EWG derivatives (DPA = diphenylamino, DPS = 2,5-diphenyl-stilbene building block, EWG = electron withdrawing group) was studied. Varying the strength of the EWG enabled the tuning of the LUMO energy within a range broader than 1 eV, while the simultaneous changes of HOMO energy were less than 0.1 eV, according to cyclic voltammetry. The fluorescence maxima in dichloromethane laid between 483 and 752 nm and exhibited monoexponential decay and a photoluminescence quantum yield (PLQY) always higher than 35%. Six derivatives with a SSF PLQY higher than 10% in polycrystalline powder form continuously covered the range from 475 to 733 nm. Three components of SSF multiexponential decay, obtained by time-resolved fluorescence spectroscopy, were ascribed to exciton migration to nonfluorescent traps, and monomer-like and aggregate fluorescence. The character of the emitting aggregates was evaluated by quantum chemical modelling based on time-dependent density functional theory computations, carried out on the dimer arrangements obtained by X-ray diffractometry of the single crystals. | ||||||
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| Record 172 of 349 | |||||||||||||||
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| Author(s): Ondel, L (Ondel, Lucas); Yusuf, B (Yusuf, Bolaji); Burget, L (Burget, Lukas); Saraclar, M (Saraclar, Murat) | |||||||||||||||
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| Abstract: This work investigates subspace non-parametric models for the task of learning a set of acoustic units from unlabeled speech recordings. We constrain the base-measure of a Dirichlet-Process mixture with a phonetic subspace-estimated from other source languages-to build an educated prior, thereby forcing the learned acoustic units to resemble phones of known source languages. Two types of models are proposed: (i) the Subspace HMM (SHMM) which assumes that the phonetic subspace is the same for every language, (ii) the Hierarchical-Subspace HMM (H-SHMM) which relaxes this assumption and allows to have a language-specific subspace estimated on the unlabeled target data. These models are applied on 3 languages: English, Yoruba and Mboshi and they are compared with various competitive acoustic units discovery baselines. Experimental results show that both subspace models outperform other systems in terms of clustering quality and segmentation accuracy. Moreover, we observe that the H-SHMM provides results superior to the SHMM supporting the idea that language-specific priors are preferable to language-agnostic priors for acoustic unit discovery. | |||||||||||||||
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| Record 173 of 349 | |||||||||||||||
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| Author(s): Khirsariya, P (Khirsariya, Prashant); Pospisil, P (Pospisil, Patrik); Maier, L (Maier, Lukas); Boudny, M (Boudny, Miroslav); Babas, M (Babas, Martin); Kroutil, O (Kroutil, Ondrej); Mraz, M (Mraz, Marek); Vacha, R (Vacha, Robert); Paruch, K (Paruch, Kamil) | |||||||||||||||
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| Abstract: Histone methyltransferase DOT1L is an attractivetherapeutic target for the treatment of hematological malignancies.Here, we report the design, synthesis, and profiling of new DOT1Linhibitors based on nonroutine carbocyclic C-nucleoside scaffolds.The experimentally observed SAR was found to be nontrivial asseemingly minor changes of individual substituents resulted insignificant changes in the affinity to DOT1L. Molecular modelingsuggested that these trends could be related to significantconformational changes of the protein upon interaction with theinhibitors. The compounds22and (-)-53(MU1656), carbocyclicC-nucleoside analogues of the natural nucleoside derivativeEPZ004777, and the clinical candidateEPZ5676(pinometostat)potently and selectively inhibit DOT1L in vitro as well as in the cell. The most potent compoundMU1656was found to be moremetabolically stable and significantly less toxic in vivo than pinometostat itself. | |||||||||||||||
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| Record 174 of 349 | |||||||||
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| Author(s): Glick-Magid, A (Glick-Magid, Ayala); Forssen, C (Forssen, Christian); Gazda, D (Gazda, Daniel); Gazit, D (Gazit, Doron); Gysbers, P (Gysbers, Peter); Navratil, P (Navratil, Petr) | |||||||||
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| Abstract: Precision measurements of beta-decay observables offer the possibility to search for deviations from the Standard Model. A possible discovery of such deviations requires accompanying first-principles calculations. Here we compute the nuclear structure corrections for the beta-decay of He-6 which is of central interest in several experimental efforts. We employ the impulse approximation together with wave functions calculated using the ab initio no-core shell model with potentials based on chiral effective field theory. We use these state-of-the-art calculations to give a novel and comprehensive analysis of theoretical uncertainties. We find that nuclear corrections, which we compute within the sensitivity of future experiments, create significant deviation from the naive Gamow-Teller predictions, making their accurate assessment essential in searches for physics beyond the Standard Model. (C) 2022 The Author(s). Published by Elsevier B.V. | |||||||||
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| Record 175 of 349 | ||||||||||||
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| Author(s): Matouskova, E (Matouskova, Eva); Drsata, T (Drsata, Tomas); Pfeifferova, L (Pfeifferova, Lucie); Sponer, J (Sponer, Jiri); Reblova, K (Reblova, Kamila); Lankas, F (Lankas, Filip) | ||||||||||||
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| Abstract: Kink-turns are highly bent internal loop motifs commonly found in the ribosome and other RNA complexes. They frequently act as binding sites for proteins and mediate tertiary interactions in larger RNA structures. Kink-turns have been a topic of intense research, but their elastic properties in the folded state are still poorly understood. Here we use extensive all-atom molecular dynamics simulations to parameterize a model of kink-turn in which the two flanking helical stems are represented by effective rigid bodies. Time series of the full set of six interhelical coordinates enable us to extract minimum energy shapes and harmonic stiffness constants for kink-turns from different RNA functional classes. The analysis suggests that kink-turns exhibit isotropic bending stiffness but are highly anisotropic with respect to lateral displacement of the stems. The most flexible lateral displacement mode is perpendicular to the plane of the static bend. These results may help understand the structural adaptation and mechanical signal transmission by kink-turns in complex natural and artificial RNA structures. | ||||||||||||
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| Record 176 of 349 | |||||||||
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| Author(s): Ahn, KH (Ahn, Kyo-Hoon); Marmodoro, A (Marmodoro, Alberto); Hejtmanek, J (Hejtmanek, Jirl); Jirak, Z (Jirak, Zdenek); Knizek, K (Knizek, Karel) | |||||||||
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| Abstract: A canted ferromagnetic arrangement with a long-range-ordered antiferromagnetic component is predicted for the metallic SrRuO3 orthoperovskite based on local-density-approximation-type electronic-structure calculation including on-site Coulomb repulsion U and spin-orbit coupling. The electronic state of Ru4+ ions and the nature of nonzero orbital momentum are analyzed in detail. With regard to the density of states at the Fermi level, the value of the magnetic moment, and the easy axis along the a-axis in a Pbnm setting, a good agreement with the experimental data is achieved for U = 1 eV. The calculated parameters of magnetic exchange, including the anisotropic and antisymmetric terms, are used to determine the magnon spectra. It is shown that notable anisotropic exchange in SrRuO3 is responsible for a gap of 1.7 meV at the Gamma point of the magnon spectra, found previously by inelastic neutron diffraction. The origin of the spin canting that is confined within the ab-plane follows from the presence of the Dzyaloshinskii-Moriya interaction associated with the antisymmetric exchange. | |||||||||
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| Record 177 of 349 |
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| Author(s): Kuptsov, KA (Kuptsov, K. A.); Antonyuk, MN (Antonyuk, M. N.); Sheveyko, AN (Sheveyko, A. N.); Bondarev, AV (Bondarev, A. V.); Ignatov, SG (Ignatov, S. G.); Slukin, PV (Slukin, P. V.); Dwivedi, P (Dwivedi, P.); Fraile, A (Fraile, A.); Polcar, T (Polcar, T.); Shtansky, DV (Shtansky, D. V.) |
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| Abstract: High-entropy coatings (HECs) are of a great interest for the protection of structural steels and alloys used in the costal and offshore areas. Here, thick, dense, and uniform Fe-Cr-Ni-Co-(Cu) coatings with a crack-free surface have been successfully deposited on AISI 420S steel by vacuum electro-spark deposition using CrNiCo and CrNiCoCu electrodes. The coatings consist of columnar grains (approximately 300 nm in diameter) and subgrains (10-50 nm thick) of an fcc phase and spherical inclusions of mixed SiO2 + (Cr,Ti)2O3 oxide, 30-50 nm in size. Although Cu is an element prone to segregation, the experimental results show that Cu does not form its own phase and is in the metal solid solution. Molecular dynamics simulation shows that Cu has a slight tendency to self-clustering and form Cu-rich clusters in FeCrNiCo-Cu HECs. However, several regions enriched in Cu are observed in the FeCrNiCo-Cu samples. FeCrNiCo coatings tested in artificial seawater and the Black Sea exhibited enhanced corrosion resistance. In tribocorrosion tests, FeCrNiCo-(Cu) coatings performed better than steel substrate due to faster recovery of a passive film. The addition of Cu has a positive effect on the antibacterial activity of FeCrNiCo coatings against Gram-positive B. cereus Arc30 and B. cereus F strains. |
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| Author(s): Skvara, J (Skvara, Jirf); Nezbeda, I (Nezbeda, Ivo) | ||||||
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| Abstract: Thermodynamic and structural properties of TIP4P/ice water have been studied in detail in the region of the expected occurrence of the second critical point. Various structure order parameters along with the Delaunay tessellation and density histogram have been used with a focus on their ability and mutual con-sistency to provide the necessary information. Whereas density histograms clearly show the bimodal dis-tribution corresponding to the coexistence of two metastable density states, most of the standard structural parameters provided only information about the increase in the level of molecular order with lowered temperature. Only the parameter called the local structure index and parameters based on the Delaunay tessellation provided information consistent with the density histogram. The bimodality in these parameters has been connected to the anomalous behavior of the isothermal compressibility which increases in the supercooled region gaining the k-shape form which a sign of the presence of the critical point. In addition, an attempt to link the structures of supercooled water to that of an underlying disor-dered ice is made.(c) 2022 Elsevier B.V. All rights reserved. | ||||||
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| Record 179 of 349 |
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| Author(s): Martisko, J (Martisko, Jakub); Meduna, A (Meduna, Alexander); Krivka, Z (Krivka, Zbynek) |
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| Abstract: The L(PSCG) = L(CS) problem asks whether propagating scattered context grammars and context sensitive grammars are equivalent. The presented paper reformulates and answers this problem in terms of CD grammar systems. More specifically, it characterizes the family of context sensitive languages by two-component CD grammar systems with propagating scattered context rules. |
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| Record 180 of 349 |
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| Author(s): Mosner, L (Mosner, Ladislav); Plchot, O (Plchot, Oldrich); Burget, L (Burget, Lukas); Cernocky, J' (Cernocky, Jan ''Honza'') |
| Book Group Author(s): IEEE |
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| Abstract: Motivated by unconsolidated data situation and the lack of a standard benchmark in the field, we complement our previous efforts and present a comprehensive corpus designed for training and evaluating text-independent multi-channel speaker verification systems. It can be readily used also for experiments with dereverberation, denoising, and speech enhancement. We tackled the ever-present problem of the lack of multi-channel training data by utilizing data simulation on top of clean parts of the Voxceleb corpus. The development and evaluation trials are based on a retransmitted Voices Obscured in Complex Environmental Settings (VOiCES) corpus, which we modified to provide multi-channel trials. We publish full recipes that create the dataset from public sources as the MultiSV dataset, and we provide results with two of our multi-channel speaker verification systems with neural network-based beamforming based either on predicting ideal binary masks or the more recent Conv-TasNet. |
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| Conference Sponsors: Inst Elect & Elect Engineers, Inst Elect & Elect Engineers Signal Proc Soc |
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| ISBN: 978-1-6654-0540-9 |
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| Author(s): Antonov, AP (Antonov, Alexander P.); Vorac, D (Vorac, David); Ryabov, A (Ryabov, Artem); Maass, P (Maass, Philipp) | |||||||||||||||
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| Abstract: In crowded systems, particle currents can be mediated by propagating collective excitations which are generated as rare events, are localized, and have a finite lifetime. The theoretical description of such excitations is hampered by the problem of identifying complex many-particle transition states, calculation of their free energies, and the evaluation of propagation mechanisms and velocities. Here we show that these problems can be tackled for a highly jammed system of hard spheres in a periodic potential. We derive generation rates of collective excitations, their anomalously high velocities, and explain the occurrence of an apparent jamming transition and its strong dependence on the system size. The particle currents follow a scaling behavior, where for small systems the current is proportional to the generation rate and for large systems given by the geometric mean of the generation rate and velocity. Our theoretical approach is widely applicable to dense nonequilibrium systems in confined geometries. It provides new perspectives for studying dynamics of collective excitations in experiments. | |||||||||||||||
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| Record 182 of 349 | |||||||||||||||||||||||||||
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| Author(s): Honza, M (Honza, Marcel); Kolecek, J (Kolecek, Jaroslav); Pialek, L (Pialek, Lubomir); Pialkova, R (Pialkova, Radka); Pozgayova, M (Pozgayova, Milica); Prochazka, P (Prochazka, Petr); Stetkova, G (Stetkova, Gabriela); Jelinek, V (Jelinek, Vaclav); Hughes, AE (Hughes, Anna E.); Sulc, M (Sulc, Michal) | |||||||||||||||||||||||||||
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| Abstract: In some populations of the host of brood parasites, more than two parasite eggs may be laid in a single nest. This phenomenon is known as multiple parasitism, representing a cost to both the host and parasite. In this study, we analysed a long-term dataset (2007-2021) focusing on multiple parasitism of the common cuckoo (Cuculus canorus) parasitizing the great reed warbler (Acrocephalus arundinaceus). The annual parasitism rate was on average 54.3% and varied between 5.8% and 92.2%, depending on the year. Out of 720 parasitized nests, double parasitism was recorded in 172 (23.9%) nests, triple in 51 (7.1%) nests, quadruple in 10 (1.3%) nests, and, exceptionally, in the years of heavy parasitism (about 90%), quintuple parasitism was recorded in three (0.4%) nests. The rate of multiple parasitism ranged from 0 to 63% inter-annually and strongly correlated with the parasitism rate and the total number of parasite eggs found. Furthermore, the number of cuckoo eggs laid per one nest increased with the decreasing daily availability of host nests that were at a suitable breeding stage for parasitism. Both genetic and egg phenotype analyses revealed that no cuckoo female laid more than one egg in the same host nest. Using data on long-term parasite-host interactions and from continuous video recording, as well as progressive methods to assign parasite offspring thus helped us better understand various aspects of multiple parasitism in hosts heavily parasitized by an evictor brood parasite. Significance statement Laying more parasite eggs in one host nest (i.e. multiple parasitism) is common in brood parasites whose nestlings share the nest with nestmates. In the species where the parasite's nestling kills its nest mates, multiple parasitism should be rare because it is costly for the parasite. However, in host populations with high parasitism rates, multiple parasitism occurs more often than predicted. Using long-term and video-recording data, we quantified multiple parasitism in the common cuckoo across years and host egg-laying sequences. We found that the rate of multiple parasitism is positively related to the parasitism rate and that the lower the number of nests suitable for parasitism, the higher the number of parasite eggs in one nest. Based on genetic and egg phenotype analyses, we also showed that individual parasitic females avoid laying in the nests they had already parasitized. | |||||||||||||||||||||||||||
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| Record 183 of 349 | |||||||||||||||||||||
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| Author(s): Vazquez-Chavez, J (Vazquez-Chavez, Josue); Martinez-Torres, FC (Martinez-Torres, Fatima C.); Navarro-Huerta, A (Navarro-Huerta, Armando); Flores-Alamo, M (Flores-Alamo, Marcos); Maldonado-Dominguez, M (Maldonado-Dominguez, Mauricio); Blahut, J (Blahut, Jan); Stocek, JR (Stocek, Jakub Radek); Dracinsky, M (Dracinsky, Martin); Rodriguez-Molina, B (Rodriguez-Molina, Braulio); Iglesias-Arteaga, MA (Iglesias-Arteaga, Martin A.) | |||||||||||||||||||||
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| Abstract: The dimeric steroid SMR-3, featuring a 1,4-phenyldiboronic ester flanked by two pregnan-triol frameworks, was synthesized to explore the intramolecular dynamics of its central component. The structural data from single-crystal X-ray diffraction studies and the Hirshfeld analyses indicate small steric effects around the aromatic ring that should favor the intended motion. However, solid-state NMR data obtained through VT 13C{1H} CPMAS and 2H spin-echo experiments, using the deuterated analogue SMR-3D4, revealed that this component is rigid even at temperatures where other reported steroidal molecular rotors experience fast rotation (85 degrees C). A combination of classical molecular dynamics, molecular mechanics, and correlated ab initio calculations allowed us to distinguish the steric and electronic factors that restrict the potential motion in this compound. The experimental and computational data reveal that electronic components dominate the behavior and are responsible for the high rotational barrier in the SMR-3 crystal. | |||||||||||||||||||||
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| Record 184 of 349 |
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| Author(s): Vanura, P (Vanura, Petr); Sykora, D (Sykora, David); Bohm, S (Bohm, Stanislav); Uhlikova, T (Uhlikova, Tereza) |
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Abstract:
Electrospray ionisation mass spectrometry was used to investigate the cation-pi interaction of Tl+ with [7]helicene. Further, applying quantum mechanical calculations in the frame of the density functional theory, applying B3LYP functional with Def2TZVP basis set, the most probable structure of the [7]helicene-Tl+ complex was derived. In the resulting complex, the 'central' cation Tl+ is bounded between two terminal benzene rings of the parent [7]helicene ligand via cation-pi interaction. In such conformation, the [7]helicene creates a tweezer for Tl+ ion. The interaction energy, E(int), of this cation-7 complex was calculated to be -160 kJ/mol, which is consistent with the formation of the considered cationic complex species. Other structures were also found and generally lie energetically about 19-24 kJ/mol above the tweezer complex.
[GRAPHICS] . |
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| Record 185 of 349 | ||||||||||||
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| Author(s): Kandziora, M (Kandziora, Martha); Sklenar, P (Sklenar, Petr); Kolar, F (Kolar, Filip); Schmickl, R (Schmickl, Roswitha) | ||||||||||||
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| Abstract: A major challenge in phylogenetics and -genomics is to resolve young rapidly radiating groups. The fast succession of species increases the probability of incomplete lineage sorting (ILS), and different topologies of the gene trees are expected, leading to gene tree discordance, i.e., not all gene trees represent the species tree. Phylogenetic discordance is common in phylogenomic datasets, and apart from ILS, additional sources include hybridization, whole-genome duplication, and methodological artifacts. Despite a high degree of gene tree discordance, species trees are often well supported and the sources of discordance are not further addressed in phylogenomic studies, which can eventually lead to incorrect phylogenetic hypotheses, especially in rapidly radiating groups. We chose the high-Andean Asteraceae genus Loricaria to shed light on the potential sources of phylogenetic discordance and generated a phylogenetic hypothesis. By accounting for paralogy during gene tree inference, we generated a species tree based on hundreds of nuclear loci, using Hyb-Seq, and a plastome phylogeny obtained from off-target reads during target enrichment. We observed a high degree of gene tree discordance, which we found implausible at first sight, because the genus did not show evidence of hybridization in previous studies. We used various phylogenomic analyses (trees and networks) as well as the D-statistics to test for ILS and hybridization, which we developed into a workflow on how to tackle phylogenetic discordance in recent radiations. We found strong evidence for ILS and hybridization within the genus Loricaria. Low genetic differentiation was evident between species located in different Andean cordilleras, which could be indicative of substantial introgression between populations, promoted during Pleistocene glaciations, when alpine habitats shifted creating opportunities for secondary contact and hybridization. | ||||||||||||
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| Record 186 of 349 |
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| Author(s): Soucek, T (Soucek, Tomas); Alayrac, JB (Alayrac, Jean-Baptiste); Miech, A (Miech, Antoine); Laptev, I (Laptev, Ivan); Sivic, J (Sivic, Josef) |
| Book Group Author(s): IEEE COMP SOC |
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| Abstract: Human actions often induce changes of object states such as "cutting an apple", "cleaning shoes" or "pouring coffee". In this paper, we seek to temporally localize object states (e.g. "empty" and "full" cup) together with the corresponding state-modifying actions ("pouring coffee") in long uncurated videos with minimal supervision. The contributions of this work are threefold. First, we develop a self-supervised model for jointly learning state-modifying actions together with the corresponding object states from an uncurated set of videos from the Internet. The model is self-supervised by the causal ordering signal, i.e. initial object state -> manipulating action -> end state. Second, to cope with noisy uncurated training data, our model incorporates a noise adaptive weighting module supervised by a small number of annotated still images, that allows to efficiently filter out irrelevant videos during training. Third, we collect a new dataset with more than 2600 hours of video and 34 thousand changes of object states, and manually annotate a part of this data to validate our approach. Our results demonstrate substantial improvements over prior work in both action and object state-recognition in video. |
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| Conference Sponsors: IEEE, CVF, IEEE Comp Soc |
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| ISBN: 978-1-6654-6946-3 |
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| Author(s): Giacobelli, VG (Giacobelli, Valerio G.); Fujishima, K (Fujishima, Kosuke); Lepsik, M (Lepsik, Martin); Tretyachenko, V (Tretyachenko, Vyacheslav); Kadava, T (Kadava, Tereza); Makarov, M (Makarov, Mikhail); Bednarova, L (Bednarova, Lucie); Novak, P (Novak, Petr); Hlouchova, K (Hlouchova, Klara) | |||||||||||||||
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| Abstract: RNA-peptide/protein interactions have been of utmost importance to life since its earliest forms, reaching even before the last universal common ancestor (LUCA). However, the ancient molecular mechanisms behind this key biological interaction remain enigmatic because extant RNA-protein interactions rely heavily on positively charged and aromatic amino acids that were absent (or heavily under-represented) in the early pre-LUCA evolutionary period. Here, an RNA-binding variant of the ribosomal uL11 C-terminal domain was selected from an approximately 10(10) library of partially randomized sequences, all composed of ten prebiotically plausible canonical amino acids. The selected variant binds to the cognate RNA with a similar overall affinity although it is less structured in the unbound form than the wild-type protein domain. The variant complex association and dissociation are both slower than for the wild-type, implying different mechanistic processes involved. The profile of the wild-type and mutant complex stabilities along with molecular dynamics simulations uncovers qualitative differences in the interaction modes. In the absence of positively charged and aromatic residues, the mutant uL11 domain uses ion bridging (K+/Mg2+) interactions between the RNA sugar-phosphate backbone and glutamic acid residues as an alternative source of stabilization. This study presents experimental support to provide a new perspective on how early protein-RNA interactions evolved, where the lack of aromatic/basic residues may have been compensated by acidic residues plus metal ions. | |||||||||||||||
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| Record 188 of 349 | ||||||
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| Author(s): Rzepiela, K (Rzepiela, Kacper); Kaminsky, J (Kaminsky, Jakub); Buczek, A (Buczek, Aneta); Broda, MA (Broda, Malgorzata A.); Kupka, T (Kupka, Teobald) | ||||||
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| Abstract: The quality of theoretical NMR shieldings calculated at the quantum-chemical level depends on various theoretical aspects, of which the basis set type and size are among the most important factors. Nevertheless, not much information is available on the basis set effect on theoretical shieldings of the NMR-active nuclei of the third row. Here, we report on the importance of proper basis set selection to obtain accurate and reliable NMR shielding parameters for nuclei from the third row of the periodic table. All calculations were performed on a set of eleven compounds containing the elements Na, Mg, Al, Si, P, S, or Cl. NMR shielding tensors were calculated using the SCF-HF, DFT-B3LYP, and CCSD(T) methods, combined with the Dunning valence aug-cc-pVXZ, core-valence aug-cc-pCVXZ, Jensen polarized-convergent aug-pcSseg-n and Karlsruhe x2c-Def2 basis set families. We also estimated the complete basis set limit (CBS) values of the NMR parameters. Widely scattered nuclear shieldings were observed for the Dunning polarized-valence basis set, which provides irregular convergence. We show that the use of Dunning core-valence or Jensen basis sets effectively reduces the scatter of theoretical NMR results and leads to their exponential-like convergence to CBS. We also assessed the effect of vibrational, temperature, and relativistic corrections on the predicted shieldings. For systems with single bonds, all corrections are relatively small, amounting to less than 4% of the CCSD(T)/CBS value. Vibrational and temperature corrections were less reliable for H3PO and HSiCH due to the high anharmonicity of the molecules. An abnormally high relativistic correction was observed for phosphorus in PN, reaching similar to 20% of the CCSD(T)/CBS value, while the correction was less than 7% for other tested molecules. | ||||||
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| Record 189 of 349 | |||||||||
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| Author(s): Kaletova, E (Kaletova, Eva); Hurtado, CS (Santos Hurtado, Carina); Cisarova, I (Cisarova, Ivana); Teat, SJ (Teat, Simon J.); Kaleta, J (Kaleta, Jiri) | |||||||||
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| Abstract: Herein we introduce fully modular synthesis leading to three representative examples of rigid molecular rods that are intended to form sturdy monolayers on various surfaces. These molecules contain two triptycene units that are designed to interlock into a compact "double-decker" structure. Two of the three final products provided suitable crystals for X-ray diffraction (analyzed on synchrotron), allowing deeper insight into packing in the 3-D crystal lattice. The acidity of all three compounds were determined by capillary electrophoresis, and the pK(a) values ranged between 2.06-2.53. All three rigid rods easily formed Langmuir-Blodgett monolayers (LBMs) on the water-air interfaces, with the area per molecule equal to 55-59 angstrom(2)/molecule, suggesting tight intermolecular packing. The thickness of all three films reached similar to 19 angstrom after transfer to a gold (111) surface, meaning that individual molecules are tilted maximally 38 degrees from the axis perpendicular to the surface. The structure of one of these films on a gold (111) surface was visualized by AFM. These geometrically unique molecules represent promising platforms with a wide scope of applicability in the supramolecular architecture. | |||||||||
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| Author(s): Vanura, P (Vanura, Petr); Sykora, D (Sykora, David); Uhlikova, T (Uhlikova, Tereza) | ||||||
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| Abstract: Electrospray ionization mass spectrometry was used to investigate the cation-pi interaction of Ag+ cation with [2.2]paracyclophane. It was found that cationic Ag.([2.2]paracyclophane)(+) and Ag.([2.2]paracyclophane)(2)(+) complex species are formed in the gas phase. Further, applying quantum mechanical calculations in the frame of the density functional theory, using B3LYP functional with Def2TZVP basis set, the most probable structures of the proved Ag+ - [2.2]paracyclophane complexes were derived. In the Ag.([2.2]paracyclophane)(+) complex, the cation Ag+ is bounded to three carbon atoms of one benzene ring of [2.2]paracyclophane ligand via cation-pi interaction. Quite analogously is bonded also second [2.2]paracyclophane molecule in Ag.([2.2]paracyclophane)(2)(+) complex. The interaction energy, E(int), of Ag.([2.2]paracyclophane)(+) complex was calculated to be -220.79 kJ/mol, E(int) of Ag.([2.2]paracyclophane)(2)(+) complex is -362.67 kJ/mol. It is consistent with the formation of the considered Ag+ - [2.2]paracyclophane complex species. | ||||||
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| Record 191 of 349 |
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| Author(s): Klinec, D (Klinec, Dusan); Sys, M (Sys, Marek); Kubicek, K (Kubicek, Karel); Svenda, P (Svenda, Petr); Matyas, V (Matyas, Vashek) |
| Edited by: DiVimercati SDC; Samarati P |
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| Abstract: The output of cryptographic functions, be it encryption routines or hash functions, should be statistically indistinguishable from a truly random data for an external observer. The property can be partially tested automatically using batteries of statistical tests. However, it is not easy in practice: multiple incompatible test suites exist, with possibly overlapping and correlated tests, making the statistically robust interpretation of results difficult. Additionally, a significant amount of data processing is required to test every separate cryptographic function. Due to these obstacles, no large-scale systematic analysis of the the round-reduced cryptographic functions w.r.t their input mixing capability, which would provide an insight into the behaviour of the whole classes of functions rather than few selected ones, was yet published. We created a framework to consistently run 414 statistical tests and their variants from the commonly used statistical testing batteries (NIST STS, Dieharder, TestU01, and BoolTest). Using the distributed computational cluster providing required significant processing power, we analyzed the output of 109 round-reduced cryptographic functions (hash, lightweight, and block-based encryption functions) in the multiple configurations. scrutinizing the mixing property of each one. As a result, we established the fraction of a function's rounds with still detectable bias (a.k.a. security margin) when analyzed by randomness statistical tests. |
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| ISBN: 978-989-758-590-6 |
| Record 192 of 349 | |||||||||||||||||||||||||||
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| Author(s): Balarynova, J (Balarynova, Jana); Klcova, B (Klcova, Barbora); Sekaninoa, J (Sekaninova, Jana); Kobrlova, L (Kobrlova, Lucie); Cechova, MZ (Cechova, Monika Zajacova); Krejci, P (Krejci, Petra); Leonova, T (Leonova, Tatiana); Gorbach, D (Gorbach, Daria); Ihling, C (Ihling, Christian); Smrzova, L (Smrzova, Lucie); Trneny, O (Trneny, Oldrich); Frolov, A (Frolov, Andrej); Bednar, P (Bednar, Petr); Smykal, P (Smykal, Petr) | |||||||||||||||||||||||||||
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| Abstract: Seed coats serve as protective tissue to the enclosed embryo. As well as mechanical there are also chemical defence functions. During domestication, the property of the seed coat was altered including the removal of the seed dormancy. We used a range of genetic, transcriptomic, proteomic and metabolomic approaches to determine the function of the pea seed polyphenol oxidase (PPO) gene. Sequencing analysis revealed one nucleotide insertion or deletion in the PPO gene, with the functional PPO allele found in all wild pea samples, while most cultivated peas have one of the three nonfunctional ppo alleles. PPO functionality cosegregates with hilum pigmentation. PPO gene and protein expression, as well as enzymatic activity, was downregulated in the seed coats of cultivated peas. The functionality of the PPO gene relates to the oxidation and polymerisation of gallocatechin in the seed coat. Additionally, imaging mass spectrometry supports the hypothesis that hilum pigmentation is conditioned by the presence of both phenolic precursors and sufficient PPO activity. Taken together these results indicate that the nonfunctional polyphenol oxidase gene has been selected during pea domestication, possibly due to better seed palatability or seed coat visual appearance. | |||||||||||||||||||||||||||
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| Record 193 of 349 | |||||||||||||||||||||
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| Author(s): Kari, N (Kari, Nuerguli); Zannotti, M (Zannotti, Marco); Giovannetti, R (Giovannetti, Rita); Reha, D (Reha, David); Minofar, B (Minofar, Babak); Abliz, S (Abliz, Shawket); Yimit, A (Yimit, Abliz) | |||||||||||||||||||||
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| Abstract: Metal effects on the gas sensing behavior of metal complexes of 5,10,15,20-tetrakis(4-hydroxyphenyl)porphyrin (THPP) thin film was investigated in terms of detecting NO2 gas by the planar optical waveguide. For this purpose, several THPP and metal complexes were synthesized with different central metal ions: Co(II), Ni(II), Cu(II), and Zn(II). Planar optical gas sensors were fabricated with the metalloporphyrins deposited on K+ ion-exchanged soda-lime glass substrate with the spin coating method serving as host matrices for gas interaction. All of the THPP complex's films were fully characterized by UV-Vis, IR and XPS spectroscopy, and the laser light source wavelength was selected at 520 and 670 nm. The results of the planar optical waveguide sensor show that the Zn-THPP complex exhibits the strongest response with the lowest detectable gas concentration of NO2 gas for both 520 nm and 670 nm. The Ni-THPP and Co-THPP complexes display good efficiency in the detection of NO2, while, on the other hand, Cu-THPP shows a very low interaction with NO2 gas, with only 50 ppm and 200 ppm detectable gas concentration for 520 nm and 670 nm, respectively. In addition, molecular dynamic simulations and quantum mechanical calculations were performed, proving to be coherent with the experimental results. | |||||||||||||||||||||
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| Record 194 of 349 | ||||||
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| Author(s): Fukal, J (Fukal, Jiri); Zgarbova, M (Zgarbova, Marie); Jurecka, P (Jurecka, Petr); Sebera, J (Sebera, Jakub); Sychrovsky, V (Sychrovsky, Vladimir) | ||||||
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| Abstract: Interpretation of 3JP,H3 ' NMR scalar spin-spin coupling constants in DNA becomes more reliable by including distinct structural states such as BI and BII, using the weighted-static or, better still, the recently implemented adiabatic-MD (Ad-MD) method. The calculation method employs an adiabatic ("Ad") dependence of 3JP,H3 ' coupling on NMR-assigned torsion angle, euro, weighted by P(euro) probability distribution calculated by molecular dynamics (MD). Ad-MD calculations enable cross-validation of the bsc1, OL15, and OL21 force fields and various parametrizations of the Karplus equation describing the depend-ence of 3JP,H3 ' coupling on euro torsion (KE). The mean absolute deviation of Ad-MD 3JP,H3 ' couplings from the experimental values in Dickerson-Drew DNA is comparable to the scatter of 3JP,H3 ' couplings among four separate NMR experiments. A commonly accepted assumption of homogeneity of one kind of structure-dynamic state within DNA (BI or BII) is questionable because the principal characteristics of relevant P(euro) probabilities (shapes and positioning) vary with DNA sequence. The theory outlined in the present work sets limits to future reparameterization of MD force fields, as relevant to NMR data. | ||||||
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| Record 195 of 349 | ||||||||||||
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| Author(s): Ma, S (Ma, Shuo); Liu, JZ (Liu, Jin-Zhong); Zhang, Y (Zhang, Yu); Hu, QS (Hu, Qingshun); Lu, GL (Lu, Guo-Liang) | ||||||||||||
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| Abstract: We performed new photometric observations for two contact binaries (i.e., CRTS J025408.1+265957 and CRTS J012111.1+272933), which were observed by the 1.0 m telescope at Xingjiang Astronomical Observatory. From our light curves and several survey data, we derived several sets of photometric solutions. We found that CRTS J025408.1+265957 and CRTS J012111.1+272933 were A- and W-type W UMa, respectively. The results imply that the spot migrates or disappears in the two contact binaries, which were identified by chromospheric activity emissions (e.g., H-alpha emission) from LAMOST spectra. From the O-C curves, the orbital periods of the two contact binaries may be increasing, which is interpreted by the mass transfer from the less massive component to the more massive one. With mass transferring, the two contact binaries may evolve from the contact configurations to semi-detached ones as predicted by the theory of thermal relaxation oscillation. | ||||||||||||
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| Record 196 of 349 |
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| Author(s): Mosner, L (Mosner, Ladislav); Plchot, O (Plchot, Oldrich); Burget, L (Burget, Lukas); Cernocky, J' (Cernocky, Jan ''Honza'') |
| Book Group Author(s): IEEE |
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| Abstract: We focus on the problem of speaker recognition in far-field multi-channel data. The main contribution is introducing an alternative way of predicting spatial covariance matrices (SCMs) for a beamformer from the time domain signal. We propose to use ConvTasNet, a well-known source separation model, and we adapt it to perform speech enhancement by forcing it to separate speech and additive noise. We experiment with using the STFT of Conv-TasNet outputs to obtain SCMs of speech and noise, and finally, we fine-tune this multi-channel frontend w.r.t. speaker verification objective. We successfully tackle the problem of the lack of a realistic multi-channel training set by using simulated data of MultiSV corpus. The analysis is performed on its retransmitted and simulated test parts. We achieve consistent improvements with a 2.7 times smaller model than the baseline based on a scheme with mask estimating NN. |
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| Conference Sponsors: Inst Elect & Elect Engineers, Inst Elect & Elect Engineers Signal Proc Soc |
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| ISBN: 978-1-6654-0540-9 |
| Record 197 of 349 | ||||||||||||||||||
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| Author(s): Panacek, D (Panacek, David); Zdrazil, L (Zdrazil, Luka); Langer, M (Langer, Michal); Sedajova, V (Sedajova, Veronika); Bad'ura, Z (Bad'ura, Zdeak); Zoppellaro, G (Zoppellaro, Georgio); Yang, QY (Yang, Qiuyue); Nguyen, EP (Nguyen, Emily P.); Alvarez-Diduk, R (Alvarez-Diduk, Ruslan); Hruby, V (Hruby, Viterslav); Kolarik, J (Kolarik, Jan); Chalmpes, N (Chalmpes, Nikolaos); Bourlinos, AB (Bourlinos, Athanasios B.); Zboril, R (Zboril, Radek); Merkoci, A (Merkoci, Arben); Bakandritsos, A (Bakandritsos, Aristides); Otyepka, M (Otyepka, Michal) | ||||||||||||||||||
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| Abstract: Access to clean water for drinking, sanitation, and irrigation is a major sustainable development goal of the United Nations. Thus, technologies for cleaning water and quality-monitoring must become widely accessible and of low-cost, while being effective, selective, sustainable, and eco-friendly. To meet this challenge, hetero-bifunctional nanographene fluorescent beacons with high-affinity pockets for heavy metals are developed, offering top-rated and selective adsorption for cadmium and lead, reaching 870 and 450 mg g(-1), respectively. The heterobifunctional and multidentate pockets also operate as selective gates for fluorescence signal regulation with sub-nanomolar sensitivity (0.1 and 0.2 nm for Pb2+ and Cd2+, respectively), due to binding affinities as low as those of antigen-antibody interactions. Importantly, the acid-proof nanographenes can be fully regenerated and reused. Their broad visible-light absorption offers an additional mode for water-quality monitoring based on ultra-low cost and user-friendly reagentless paper detection with the naked-eye at a limit of detection of 1 and 10 ppb for Pb2+ and Cd2+ ions, respectively. This work shows that photoactive nanomaterials, densely-functionalized with strong, yet selective ligands for targeted contaminants, can successfully combine features such as excellent adsorption, reusability, and sensing capabilities, in a way to extend the material's applicability, its life-cycle, and value-for-money. | ||||||||||||||||||
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| Record 198 of 349 | ||||||||||||||||||
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| Author(s): Klein, P (Klein, Petr); Dedecek, J (Dedecek, Jiri); Thomas, HM (Thomas, Haunani M.); Whittleton, SR (Whittleton, Sarah R.); Klimes, J (Klimes, Jiri); Brus, J (Brus, Jiri); Kobera, L (Kobera, Libor); Bryce, DL (Bryce, David L.); Sklenak, S (Sklenak, Stepan) | ||||||||||||||||||
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| Abstract: Zeolites are crystalline microporous aluminosilicates of paramount importance. The siting of cations balancing the negative charge of framework Al affects the catalytic and sorption properties of cation-exchanged zeolites. The siting of Na+ cations in dehydrated Si-rich ferrierite zeolites is investigated by Na-23 (ultra)-high-field (MQ)MAS NMR spectroscopy together with DFT to obtain the Na+ siting and the local structure of nine Na+ cationic sites formed by two 6-rings and two 8-rings having one Al atom located in different framework T sites. The occupation of the Na+ cationic sites is not controlled by their relative energies but by the kinetics of the Na+ ion-exchange. Na-23 solid-state NMR spectroscopy alone can determine the ring forming the Na+ site but not which T site is occupied by Al in that ring. The developed methodology represents a highly promising tool for the analysis of the Na+ arrangements in zeolites and other crystalline matrices. | ||||||||||||||||||
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| Record 199 of 349 |
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| Author(s): Asim, A (Asim, Arslan); Cada, M (Cada, Michael) |
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| Abstract: In this paper, a new plasmonic absorbing metasurface sensor has been proposed to determine glucose concentrations. Surface Plasmon Resonance (SPR) shift has been used as the indicator of glucose concentration. The sensor employs metal-dielectric-metal configuration along with metal nano-cylinders to provide near unity absorption in the near infrared wavelength range (1800- 2200 nm). The absorption frequency shifts when the sensor is surrounded by materials of different refractive indices. The structure has been investigated through Finite Difference Time Domain (FDTD) simulations. The results show reflectance and absorbance peaks with different analyte concentrations. The sensor displays a linear response along with sensitivity and Figure of Merit (FOM) equal to almost 500 nm/RIU and 11.82 RIU-1, respectively. The proposed sensor has potential applications in food and biomedical industries. |
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| Record 200 of 349 | ||||||
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| Author(s): Chen, Q (Chen, Q.); Maslarova, D (Maslarova, Dominika); Wang, J (Wang, J.); Li, S (Li, S.); Umstadter, D (Umstadter, D.) | ||||||
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| Abstract: Mutual injection of electron beams into two laser plasma wakefields was observed experimentally when driv-ing laser pulses interfered in plasma at a small crossing angle and were slightly relatively delayed, approximately by one pulse duration. Particle-in-cell simulations revealed that the mutual injection was sensitive to the spatial overlap of the laser pulses, which therefore could be used to control the mutual injection. The dual synchronized, femtosecond electron beams are potentially useful for pump-probe experiments in ultrafast science. In addition, out-of-axis ring-shaped electron beams were detected in both experiments and simulations. | ||||||
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| Record 201 of 349 |
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| Author(s): Barticka, V (Barticka, Vojtech); Prazak, O (Prazak, Ondrej); Konopik, M (Konopik, Miloslav); Sido, J (Sido, Jakub) |
| Edited by: Sojka P; Horak A; Kopecek I; Pala K |
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| Abstract: This paper describes the experimental evaluation of several attribution methods on two NLP tasks: Sentiment analysis and multi-label document classification. Our motivation is to find the best method to use with Transformers to interpret model decisions. For this purpose, we introduce two new evaluation datasets. The first one is derived from Stanford Sentiment Treebank, where the sentiment of individual words is annotated along with the sentiment of the whole sentence. The second dataset comes from Czech Text Document Corpus, where we added keyword information assigned to each category. The keywords were manually assigned to each document and automatically propagated to categories via PMI. We evaluate each attribution method on several models of different sizes. The evaluation results are reasonably consistent across all models and both datasets. It indicates that both datasets with proposed evaluation metrics are suitable for interpretability evaluation. We show how the attribution methods behave concerning model size and task. We also consider practical applications - we show that while some methods perform well, they can be replaced with slightly worse-performing methods requiring significantly less time to compute. |
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| Conference Sponsors: Masaryk Univ, Fac Informat, Univ W Bohemia, Fac Appl Sci, Int Speech Commun Assoc, Lex Comp Ltd, IBMC Eska Republika Spol s r o, Amazon Alexa |
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| ISBN: 978-3-031-16270-1; 978-3-031-16269-5 |
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| Author(s): Martinovic, T (Martinovic, Tomas); Fulnecek, J (Fulnecek, Jan) | ||||||
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| Abstract: Detection of the high impedance fault caused by vegetation is one of the biggest challenges brought by the usage of covered conductors in medium voltage overhead power lines. One of the accompanying events of long-term contact of vegetation with the XLPE insulation is partial discharge which damages the insulation. Current systems for the detection of partial discharge have two major problems: the price and difficult installation. In this paper, an approach for the detection of the partial discharge from the data collected by the antenna is described. This approach is focused on the small computational demand and low false positive rate. Thanks to the small computational requirements, it can be run on the remote gateway devices which are collecting the data from the antenna. It is composed of four steps: outlier detection, outlier clustering, feature extraction, and classification. It is shown that this approach greatly improves the detection rate and lowers false positives compared to the previous algorithm used for partial discharge detection based on the data from an antenna, making it fit to use in the production environment. | ||||||
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| Record 203 of 349 | ||||||||||||||||||
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| Author(s): Koucky, J (Koucky, J.); Kolesnikova, L (Kolesnikova, L.); Lukova, K (Lukova, K.); Vavra, K (Vavra, K.); Kania, P (Kania, P.); Coutens, A (Coutens, A.); Loison, JC (Loison, J-C); Jorgensen, JK (Jorgensen, J. K.); Belloche, A (Belloche, A.); Urban, S (Urban, S.) | ||||||||||||||||||
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Abstract:
Context. Several sugar-like molecules have been found in the interstellar medium (ISM). The molecule studied in this work, 2-hydroxyprop-2-enal, is among the candidates to be searched for, as it is a dehydration product of C-3 sugars and contains structural motifs that are typical for some interstellar molecules. Furthermore, it has recently been predicted that it is more abundant in the ISM than its tentatively detected isomer 3-hydroxypropenal.
Aims. So far, only low-frequency microwave data of 2-hydroxyprop-2-enal have been published. The aim of this work is to deepen our knowledge about the millimetre-wave spectrum of 2-hydroxyprop-2-enal, enabling its detailed search towards astronomical objects. In particular, we target the solar-type protostar IRAS 16293-2422 and the star-forming region Sagittarius (Sgr) B2(N). Methods. The rotational spectrum of 2-hydroxyprop-2-enal was measured and analysed in the frequency regions of 128-166 GHz and 285-329 GHz. The interstellar exploration towards IRAS 16293-2422 was based on the Atacama Large Millimeter/submillimeter Array (ALMA) data of the Protostellar Interferometric Line Survey (PILS). We also used the imaging spectral line survey ReMoCA performed with ALMA towards Sgr B2(N) to search for 2-hydroxyprop-2-enal in the ISM. We modelled the astronomical spectra under the assumption of local thermodynamic equilibrium (LTE). Results. We provide laboratory analysis of hundreds of rotational transitions of 2-hydroxyprop-2-enal in the ground state and the lowest lying excited vibrational state. We report its non-detection towards IRAS 16293 B. The 2-hydroxyprop-2-ena1/3-hydroxypropenal abundance ratio is estimated to be <0.9-1.3, in agreement with the predicted value of -1.4. We report the non-detection of 2-hydroxyprop-2-enal towards the hot molecular core Sgr B2(N1), and we did not detect the related aldehydes 2-hydroxypropanal and 3-hydroxypropenal either. We find that these three molecules are at least nine, four, and ten times less abundant than acetaldehyde in this source, respectively. Conclusions. Despite the non-detections of 2-hydroxyprop-2-enal, the results of this work represent a significant improvement on previous investigations in the microwave region and meet the requirements for further searches for this molecule in the ISM. |
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| Author(s): Man, M (Man, Matej); Wild, J (Wild, Jan); Macek, M (Macek, Martin); Kopecky, M (Kopecky, Martin) | |||||||||||||||
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Abstract:
Increasingly available high-resolution digital elevation models (DEMs) facilitate the use of line-scale topographic variables as proxies for microclimatic effects not captured by the coarse-grained macroclimate datasets. Species distributions and community assembly rules are, however directly shaped by microclimate and not by topography. DEM-derived topography, sometimes combined with vegetation structure, is thus widely used as a proxy for microclimatic effects in ecological research and conservation applications. however, the suitability of such a strategy has not been evaluated against in situ measured microclimate and species composition. Because bryophytes are highly sensitive to microclimate, they are ideal model organisms for such evaluation.
To provide this much needed evaluation, we simultaneously recorded bryophyte species composition, microclimate, and forest vegetation structure at 218 sampling sites distributed across topographically complex sandstone landscape. Using a LiDAR-based DEM with a 1 m resolution, we calculated eleven topographic variables serving as a topographic proxy for microclimate. To characterize vegetation structure, we used hemispherical photographs and LiDAR canopy height models. Finally, we calculated eleven microclimatic variables from a continuous two-year time- series of air and soil temperature and soil moisture. To evaluate topography and vegetation structure as substitutes for the ecological effect of measured microclimate, we partitioned the variation in bryophyte species composition and richness explained by microclimate, topography, and vegetation structure. In situ measured microclimate was clearly the most important driver of bryophyte assemblages in temperate coniferous forests. The most bryophyte-relevant variables were growing degree days, maximum air temperature, and mean soil moisture. Our results thus showed that topographic variables, even when derived from high-resolution LiDAR data and combined with in situ sampled vegetation structure, cannot fully substitute effects of in situ measured microclimate on forest bryophytes. |
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| Author(s): Ponomarev, I (Ponomarev, I); Polcar, T (Polcar, T.); Nicolini, P (Nicolini, P.) | |||||||||
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| Abstract: We present a new reactive force field (ReaxFF) parameter set for simulations of Mo-S structures. We compare our parameterization to the state-of-the-art ones in their performance against density functional theory (DFT) benchmarks and MoS2 crystallization simulations. Our new force field matches DFT data significantly better than any previously published force fields and provides a realistic layered MoS2 structure in crystallization simulations. It significantly improves the state-of-the-art force fields, which tend to crystalline in the experimentally unknown rock-salt MoS structure. Therefore, our new force field is a good candidate for further development and inclusion of other practically relevant elements, such as O, C, N, and H, which can be used to study the formation and tribological or catalytical properties of molybdenum disulfide. | |||||||||
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| Record 206 of 349 | |||||||||
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| Author(s): Janousek, B (Janousek, Bohuslav); Gogela, R (Gogela, Roman); Bacovsky, V (Bacovsky, Vaclav); Renner, SS (Renner, Susanne S.) | |||||||||
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| Abstract: Microscopically dimorphic sex chromosomes in plants are rare, reducing our ability to study them. One difficulty has been the paucity of cultivatable species pairs for cytogenetic, genomic and experimental work. Here, we study the newly recognized sisters Coccinia grandis and Coccinia schimperi, both with large Y chromosomes as we here show for Co. schimperi. We built genetic maps for male and female Co. grandis using a full-sibling family, inferred gene sex-linkage, and, with Co. schimperi transcriptome data, tested whether X- and Y-alleles group by species or by sex. Most sex-linked genes for which we could include outgroups grouped the X- and Y-alleles by species, but some 10% instead grouped the two species' X-alleles. There was no relationship between XY synonymous-site divergences in these genes and gene position on the non-recombining part of the X, suggesting recombination arrest shortly before or after species divergence, here dated to about 3.6 Ma. Coccinia grandis and Co. schimperi are the species pair with the most heteromorphic sex chromosomes in vascular plants (the condition in their sister remains unknown), and future work could use them to study mechanisms of Y chromosome enlargement and parallel degeneration, or to test Haldane's rule about lower hybrid fitness in the heterogametic sex.This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'. | |||||||||
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| Record 207 of 349 | ||||||
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| Author(s): Zizien, A (Zizien, Adam); Fliegel, K (Fliegel, Karel) | ||||||
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| Abstract: Recent developments in the field of plenoptic imaging have directly coincided with standardisation efforts. Such efforts are in no small part reliant on quality evaluations. For traditional imaging modalities, such as static images and videos, subjective evaluations have played a very important part. The goal of most objective quality evaluations has been the correlation performance with subjective results. However, plenoptic modalities enable applications that rely more on the objective rather than subjective quality. As such, it is necessary to examine the performance of currently used objective quality metrics. The paper provides a study on the predictive abilities of objective quality metrics on the quality of light field disparity map estimation. The study measures the influence of distortions on light field disparity estimations; furthermore, the study examines how well can objective quality metrics predict the quality of the resulting disparity maps. None of the tested metrics showed satisfactory prediction performance. Thus, two metric fusion algorithms were also examined to see if either can further improve prediction accuracy. The metric fusion algorithms showed that the prediction can be significantly improved. A novel objective quality metric that would correlate well with both subjective and objective results could thus be introduced. | ||||||
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| Record 208 of 349 | ||||||||||||
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| Author(s): Simonova, Z (Simonova, Zuzana); Porubova, L (Porubova, Ludmila); Verner, A (Verner, Adam); Gabor, R (Gabor, Roman); Vilamova, Z (Vilamova, Zuzana); Dobrocka, E (Dobrocka, Edmund); Cieslar, M (Cieslar, Miroslav); Krbeckova, V (Krbeckova, Veronika); Dedkova, KP (Dedkova, Katerina Peterek); Svoboda, L (Svoboda, Ladislav); Bednar, J (Bednar, Jiri); Dvorsky, R (Dvorsky, Richard); Seidlerova, J (Seidlerova, Jana) | ||||||||||||
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| Abstract: Our simple technique of polymer/metal-based material preparation produces very promising material, and we outline that this material can be suitable for the potential wound healing multilayered dressing. In our research we focused on these main issues: (1) the preparation of silver nanowire-like structures using gallic acid (GA); (2) direct silver nanowire-like structure crystallization of co-polymer L-lactide and epsilon-caprolactone (PLCL) electrospun fiber and (3) evaluation of the material cytotoxicity on the Vero cell line. Synthesized silver nanowire-like width varied from 30 to 100 nm and the hexagonal particles had sizes from 80 to 300 nm. The detected structures were crystalline cubic silver and were similarly synthesized during both batch synthesis and direct synthesis on the PLCL fibers. The amount of the silver spread within the fibrous membrane was approximately 1.1 wt. % in the sample, moreover, the silver incorporation had no influence on the polymer structure, which was confirmed by FTIR measurement. The cytotoxicity testing estimated that cell survival increased with decreased concentration of GA and silver in the PLCL matrix and the silver-based sample in 50 % MTT extraction concentration maintained required non-cytotoxic properties. | ||||||||||||
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| Record 209 of 349 | |||||||||||||||
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| Author(s): Bim, D (Bim, Daniel); Navratil, M (Navratil, Michal); Gutten, O (Gutten, Ondrej); Konvalinka, J (Konvalinka, Jan); Kutil, Z (Kutil, Zsofia); Culka, M (Culka, Martin); Navratil, V (Navratil, Vaclav); Alexandrova, AN (Alexandrova, Anastassia N.); Barinka, C (Barinka, Cyril); Rulisek, L (Rulisek, Lubomir) | |||||||||||||||
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| Abstract: Quantum and molecular mechanics (QM/MM) and QM-only (cluster model) modeling techniques represent the two workhorses in mechanistic understanding of enzyme catalysis. One of the stringent tests for QM/MM and/or QM approaches is to provide quantitative answers to real-world biochemical questions, such as the effect of single-point mutations on enzyme kinetics. This translates into predicting the relative activation energies to 1-2 kcal.mol(-1) accuracy; such predictions can be used for the rational design of novel enzyme variants with desired/improved characteristics. Herein, we employ glutamate carboxypeptidase II (GCPII), a dizinc metallopeptidase, also known as the prostate specific membrane antigen, as a model system. The structure and activity of this major cancer antigen have been thoroughly studied, both experimentally and computationally, which makes it an ideal model system for method development. Its reaction mechanism is quite well understood: the reaction coordinate comprises a "tetrahedral intermediate" and two transition states and experimental activation Gibbs free energy of similar to 17.5 kcal.mol(-1) can be inferred for the known k(cat) approximate to 1 s(-1). We correlate experimental kinetic data (including the E424H variant, newly characterized in this work) for various GCPII mutants (k(cat) = 8.6 x 10(-5) s(-1) to 2.7 s(-1)) with the energy profiles calculated by QM/MM and QM-only (cluster model) approaches. We show that the near-quantitative agreement between the experimental values and the calculated activation energies (Delta H double dagger) can be obtained and recommend the combination of the two protocols: QM/MM optimized structures and cluster model (QM) energetics. The trend in relative activation energies is mostly independent of the QM method (DFT functional) used. Last but not least, a satisfactory correlation between experimental and theoretical data allows us to provide qualitative and fairly simple explanations of the observed kinetic effects which are thus based on a rigorous footing. | |||||||||||||||
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| Record 210 of 349 |
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| Author(s): Lebeda, M (Lebeda, Miroslav); Vlcak, P (Vlcak, Petr); Drahokoupil, J (Drahokoupil, Jan) |
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| Abstract: Density functional theory (DFT), molecular dynamics (MD) with referential modified embedded-atom method (MEAM) potential, and in-house built DFT-genetic algorithm (DFT-GA) have been used to derive the influence of N interstitials in alpha-Ti and N vacancies in 8-TiN on structural and mechanical properties. A DFT-GA was applied to find the low energy distributions of N interstitials/vacancies within their experimentally observed concentration ranges, and for each distribution the lattice parameters and bulk modulus were determined by DFT and MD. For 8-TiN phase, we observed increasing lattice parameters and bulk modulus with decreasing number of N vacancies by DFT and MD in agreement with experimental references. For alpha-Ti phase, DFT lattice parameters a and c were increasing with increasing number of N interstitials in correspondence with experimental data, but the lattice parameter c by MD was decreasing. This indicated that the used referential parametrization of MEAM may not be suitable for this type of calculation. Bulk modulus of alpha-Ti was observed to be increasing with increasing concentration of N interstitials by both methods, which agreed with experimental references. In addition, to illustrate how the obtained dependencies may provide expected values across the depth of the alpha-Ti target modified by N ion implantation, we extrapolated them on the N depth concentration distribution computed by MD. |
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| Record 211 of 349 | ||||||||||||
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| Author(s): Praus, P (Praus, Petr); Rehackova, L (Rehackova, Lenka); Cizek, J (Cizek, Jakub); Smykalova, A (Smykalova, Aneta); Kostejn, M (Kostejn, Martin); Pavlovsky, J (Pavlovsky, Jiri); Edelmannova, MF (Edelmannova, Miroslava Filip); Koci, K (Koci, Kamila) | ||||||||||||
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| Abstract: Graphitic carbon nitride (C3N4) was synthesised from melamine at 550 degrees C for 4 h in the argon atmosphere and then was reheated for 1-3 h at 500 degrees C in argon. Two band gaps of 2.04 eV and 2.47 eV were observed in all the synthetized materials. Based on the results of elemental and photoluminescence analyses, the lower band gap was found to be caused by the formation of vacancies. Specific surface areas of the synthetized materials were 15-18 m(2)g(-1) indicating that no thermal exfoliation occurred. The photocatalytic activity of these materials was tested for hydrogen generation. The best photocatalyst showed 3 times higher performance (1547 mu mol/g) than bulk C3N4 synthetized in the air (547 mu mol/g). This higher activity was explained by the presence of carbon (V-C) and nitrogen (V-N) vacancies grouped in their big complexes 2V(C) + 2V(N) (observed by positron annihilation spectroscopy). The effect of an inert gas on the synthesis of C3N4 was demonstrated using Graham ' s law of ammonia diffusion. This study showed that the synthesis of C3N4 from nitrogen-rich precursors in the argon atmosphere led to the formation of vacancy complexes beneficial for hydrogen generation, which was not referred so far. | ||||||||||||
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| Record 212 of 349 | ||||||
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| Author(s): Socha, P (Socha, Petr); Miskovsky, V (Miskovsky, Vojtech); Novotny, M (Novotny, Martin) | ||||||
| Book Group Author(s): IEEE | ||||||
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| Abstract: Side-channel attacks pose a severe threat to cryptographic implementations, allowing the attacker to recover secret information based on physical observations of the cryptographic device. Correlation Power Analysis is considered to be one of the most powerful attacks in the non-profiled scenario. In this paper, we consider the distance/Brownian correlation instead of the traditionally used Pearson coefficient. We give a fair comparison of our novel approach attacking AES on three different FPGA platforms and we discuss the distance correlation potential in the context of side-channel analysis. | ||||||
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| Conference Sponsors: EUROMICRO, MANT, MECOnet, Univ Montenegro, Eindhoven Tech Univ, Univ Zagreb, Univ Belgrade, Ind Syst Inst, Minist Montenegro, Cikom, Elkon, SMART4ALL | ||||||
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| ISBN: 978-1-6654-6828-2 |
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| Author(s): Vavra, K (Vavra, K.); Kolesnikova, L (Kolesnikova, L.); Belloche, A (Belloche, A.); Garrod, RT (Garrod, R. T.); Koucky, J (Koucky, J.); Uhlikova, T (Uhlikova, T.); Lukova, K (Lukova, K.); Guillemin, JC (Guillemin, J-C); Kania, P (Kania, P.); Muller, HSP (Mueller, H. S. P.); Menten, KM (Menten, K. M.); Urban, S (Urban, S.) | ||||||||||||||||||||||||
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Abstract:
Context. The interstellar detections of isocyanic acid (HNCO), methyl isocyanate (CH3NCO), and very recently also ethyl isocyanate (C2H5NCO) invite the question of whether or not vinyl isocyanate (C2H3NCO) can be detected in the interstellar medium. There are only low-frequency spectroscopic data (<40 GHz) available for this species in the literature, which makes predictions at higher frequencies rather uncertain, which in turn hampers searches for this molecule in space using millimeter (mm) wave astronomy.
Aims. The aim of the present study is on one hand to extend the laboratory rotational spectrum of vinyl isocyanate to the mm wave region and on the other to search, for the first time, for its presence in the high-mass star-forming region Sgr B2, where other isocyanates and a plethora of complex organic molecules are observed. Methods. We recorded the pure rotational spectrum of vinyl isocyanate in the frequency regions 127.5-218 and 285-330 GHz using the Prague mm wave spectrometer. The spectral analysis was supported by high-level quantum-chemical calculations. On the astronomy side, we assumed local thermodynamic equilibrium to compute synthetic spectra of vinyl isocyanate and to search for it in the ReMoCA survey performed with the Atacama Large Millimeter/submillimeter Array (ALMA) toward the high-mass star-forming protocluster Sgr B2(N). Additionally, we searched for the related molecule ethyl isocyanate in the same source. Results. Accurate values for the rotational and centrifugal distortion constants are reported for the ground vibrational states of trans and cis vinyl isocyanate from the analysis of more than 1000 transitions. We report nondetections of vinyl and ethyl isocyanate toward the main hot core of Sgr B2(N). We find that vinyl and ethyl isocyanate are at least 11 and 3 times less abundant than methyl isocyanate in this source, respectively. Conclusions. Although the precise formation mechanism of interstellar methyl isocyanate itself remains uncertain, we infer from existing astrochemical models that our observational upper limit for the CH3NCO:C2H5NCO ratio in Sgr B2(N) is consistent with ethyl isocyanate being formed on dust grains via the abstraction or photodissociation of an H atom from methyl isocyanate, followed by the addition of a methyl radical. The dominance of such a process for ethyl isocyanate production, combined with the absence of an analogous mechanism for vinyl isocyanate, would indicate that the ratio C2H3NCO:C2H5NCO should be less than unity. Even though vinyl isocyanate was not detected toward Sgr B2(N), the results of this work represent a significant improvement on previous low-frequency studies and will help the astronomical community to continue searching for this species in the Universe. |
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| Record 214 of 349 | |||||||||||||||
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| Author(s): Marchisio, A (Marchisio, Alberto); Mrazek, V (Mrazek, Vojtech); Massa, A (Massa, Andrea); Bussolino, B (Bussolino, Beatrice); Martina, M (Martina, Maurizio); Shafique, M (Shafique, Muhammad) | |||||||||||||||
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| Abstract: Neural Architecture Search (NAS) algorithms aim at finding efficient Deep Neural Network (DNN) architectures for a given application under given system constraints. DNNs are computationally-complex as well as vulnerable to adversarial attacks. In order to address multiple design objectives, we propose RoHNAS, a novel NAS framework that jointly optimizes for adversarial-robustness and hardware-efficiency of DNNs executed on specialized hardware accelerators. Besides the traditional convolutional DNNs, RoHNAS additionally accounts for complex types of DNNs such as Capsule Networks. For reducing the exploration time, RoHNAS analyzes and selects appropriate values of adversarial perturbation for each dataset to employ in the NAS flow. Extensive evaluations on multi - Graphics Processing Unit (GPU) - High Performance Computing (HPC) nodes provide a set of Pareto-optimal solutions, leveraging the tradeoff between the above-discussed design objectives. For example, a Pareto-optimal DNN for the CIFAR-10 dataset exhibits 86.07% accuracy, while having an energy of 38.63 mJ, a memory footprint of 11.85 MiB, and a latency of 4.47 ms. | |||||||||||||||
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| Record 215 of 349 | |||||||||
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| Author(s): Kunesova, M (Kunesova, Marie); Rezackova, M (Rezackova, Marketa) | |||||||||
| Edited by: Sojka P; Horak A; Kopecek I; Pala K | |||||||||
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| Abstract: Prosodic boundaries in speech are of great relevance to both speech synthesis and audio annotation. In this paper, we apply the wav2vec 2.0 framework to the task of detecting these boundaries in speech signal, using only acoustic information. We test the approach on a set of recordings of Czech broadcast news, labeled by phonetic experts, and compare it to an existing text-based predictor, which uses the transcripts of the same data. Despite using a relatively small amount of labeled data, the wav2vec2 model achieves an accuracy of 94% and F1 measure of 83% on within-sentence prosodic boundaries (or 95% and 89% on all prosodic boundaries), outperforming the text-based approach. However, by combining the outputs of the two different models we can improve the results even further. | |||||||||
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| Conference Sponsors: Masaryk Univ, Fac Informat, Univ W Bohemia, Fac Appl Sci, Int Speech Commun Assoc, Lex Comp Ltd, IBMC Eska Republika Spol s r o, Amazon Alexa | |||||||||
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| ISBN: 978-3-031-16270-1; 978-3-031-16269-5 |
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| Author(s): Kadam, RG (Kadam, Ravishankar G.); Ye, TN (Ye, Tian-Nan); Zaoralova, D (Zaoralova, Dagmar); Medved, M (Medved, Miroslav); Sharma, P (Sharma, Priti); Lu, YF (Lu, Yangfan); Zoppellaro, G (Zoppellaro, Giorgio); Tomanec, O (Tomanec, Ondrrej); Otyepka, M (Otyepka, Michal); Zboril, R (Zboril, Radek); Hosono, H (Hosono, Hideo); Gawande, MB (Gawande, Manoj B.) | |||||||||
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| Abstract: Inorganic electrides have been proved to be efficient hosts for incorporating transition metals, which can effectively act as active sites giving an outstanding catalytic performance. Here, it is demonstrated that a reusable and recyclable (for more than 7 times) copper-based intermetallic electride catalyst (LaCu0.67Si1.33), in which the Cu sites activated by anionic electrons with low-work function are uniformly dispersed in the lattice framework, shows vast potential for the selective C-H oxidation of industrially important hydrocarbons and cycloaddition of CO2 with epoxide. This leads to the production of value-added cyclic carbonates under mild reaction conditions. Importantly, the LaCu0.67Si1.33 catalyst enables much higher turnover frequencies for the C-H oxidation (up to 25 276 h(-1)) and cycloaddition of CO2 into epoxide (up to 800 000 h(-1)), thus exceeding most nonnoble as well as noble metal catalysts. Density functional theory investigations have revealed that the LaCu0.67Si1.33 catalyst is involved in the conversion of N-hydroxyphthalimide (NHPI) into the phthalimido-N-oxyl (PINO), which then triggers selective abstraction of an H atom from ethylbenzene for the generation of a radical susceptible to further oxygenation in the presence of O-2. | |||||||||
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| Record 217 of 349 | ||||||||||||
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| Author(s): Bonnassieux, E (Bonnassieux, Etienne); Sweijen, F (Sweijen, Frits); Brienza, M (Brienza, Marisa); Rajpurohit, K (Rajpurohit, Kamlesh); Riseley, CJ (Riseley, Christopher John); Bonafede, A (Bonafede, Annalisa); Jackson, N (Jackson, Neal); Morabito, LK (Morabito, Leah K.); Brunetti, G (Brunetti, Gianfranco); Harwood, J (Harwood, Jeremy); Kappes, A (Kappes, Alex); Rottgering, HJ (Rottgering, Huub J.); Tasse, C (Tasse, Cyril); van Weeren, R (van Weeren, Reinout) | ||||||||||||
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| Abstract: 3C295 is a bright, compact steep spectrum source with a well-studied integrated radio spectral energy distribution (SED) from 132 MHz to 15 GHz. However, spatially resolved spectral studies have been limited due to a lack of high resolution images at low radio frequencies. These frequencies are crucial for measuring absorption processes, and anchoring the overall spectral modelling of the radio SED. In this paper, we use International LOw-Frequency ARray (LOFAR) Telescope (ILT) observations of 3C295 to study its spatially resolved spectral properties with sub-arcsecond resolution at 132 MHz. Combining our new 132 MHz observation with archival data at 1.6, 4.8, and 15 GHz, we are able to carry out a resolved radio spectral analysis. The spectral properties of the hotspots provides evidence for low frequency flattening. In contrast, the spectral shape across the lobes is consistent with a Jaffe-Perola spectral ageing model. Using the integrated spectral information for each component, we then fitted low-frequency absorption models to the hotspots, finding that both free-free absorption and synchrotron self-absorption models provide a better fit to the data than a standard power law. Although we can say there is low-frequency absorption present in the hotspots of 3C295, future observations with the Low Band Antenna of the ILT at 55 MHz may allow us to distinguish the type of absorption. | ||||||||||||
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| Record 218 of 349 | |||||||||||||||||||||
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| Author(s): Kovarovic, V (Kovarovic, Vojtech); Sedlacek, I (Sedlacek, Ivo); Petras, P (Petras, Petr); Kralova, S (Kralova, Stanislava); Maslanova, I (Maslanova, Ivana); Svec, P (Svec, Pavel); Neumann-Schaal, M (Neumann-Schaal, Meina); Botka, T (Botka, Tibor); Gelbicova, T (Gelbicova, Tereza); Stankova, E (Stankova, Eva); Doskar, J (Doskar, Jiri); Pantucek, R (Pantucek, Roman) | |||||||||||||||||||||
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| Abstract: Staphylococci from the Staphylococcus intermedius-Staphylococcus hyicus species group include numerous animal pathogens and are an important reservoir of virulence and antimicrobial resistance determinants. Due to their pathogenic potential, they are possible causative agents of zoonoses in humans; therefore, it is important to address the properties of these strains. Here we used a polyphasic taxonomic approach to characterize the coagulase-negative staphylococcal strain NRL/St 03/464(T), isolated from the nostrils of a healthy laboratory rat during a microbiological screening of laboratory animals. The 16S rRNA sequence, MALDI-TOF mass spectrometry and positive urea hydrolysis and beta-glucuronidase tests clearly distinguished it from closely related Staphylococcus spp. All analyses have consistently shown that the closest relative is Staphylococcus chromogenes; however, values of digital DNA-DNA hybridization Staphylococcus species. Whole-genome sequencing and expert annotation of the genome revealed the presence of novel variable genetic elements, including two plasmids named pSR9025A and pSR9025B, prophages, genomic islands and a composite transposon that may confer selective advantages to other bacteria and enhance their survival. Based on phenotypic, phylogenetic and genomic data obtained in this study, the strain NRL/St 03/464(T) (= CCM 9025(T) = LMG 31873(T) = DSM 111348(T)) represents a novel species with the suggested name Staphylococcus ratti sp. nov. | |||||||||||||||||||||
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| Author(s): Zara, Z (Zara, Zeenat); Mishra, D (Mishra, Deepti); Pandey, SK (Pandey, Saurabh Kumar); Csefalvay, E (Csefalvay, Eva); Fadaei, F (Fadaei, Fatemeh); Minofar, B (Minofar, Babak); Reha, D (Reha, David) | ||||||||||||
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| Abstract: The effect of aqueous solutions of selected ionic liquids solutions on Ideonella sakaiensis PETase with bis(2-hydroxyethyl) terephthalate (BHET) substrate were studied by means of molecular dynamics simulations in order to identify the possible effect of ionic liquids on the structure and dynamics of enzymatic Polyethylene terephthalate (PET) hydrolysis. The use of specific ionic liquids can potentially enhance the enzymatic hydrolyses of PET where these ionic liquids are known to partially dissolve PET. The aqueous solution of cholinium phosphate were found to have the smallest effect of the structure of PETase, and its interaction with (BHET) as substrate was comparable to that with the pure water. Thus, the cholinium phosphate was identified as possible candidate as ionic liquid co-solvent to study the enzymatic hydrolyses of PET. | ||||||||||||
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| Author(s): Barna, B (Barna, B.); Palous, J (Palous, J.); Ehlerova, S (Ehlerova, S.); Wunsch, R (Wunsch, R.); Morris, MR (Morris, M. R.); Vermot, P (Vermot, P.) | ||||||
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| Abstract: The way supermassive black holes (SMBHs) in Galactic Centres (GCs) accumulate their mass is not completely determined. At large scales, it is governed by galactic encounters, mass inflows connected to spirals arms and bars, or due to expanding shells from supernova (SN) explosions in the central parts of galaxies. The investigation of the latter process requires an extensive set of gas dynamical simulations to explore the multidimensional parameter space needed to frame the phenomenon. The aims of this paper are to extend our investigation of the importance of SNe for inducing accretion on to an SMBH and carry out a comparison between the fully hydrodynamic code flash and the much less computationally intensive code ring, which uses the thin shell approximation. We simulate 3D expanding shells in a gravitational potential similar to that of the GC with a variety of homogeneous and turbulent environments. In homogeneous media, we find convincing agreement between flash and ring in the shapes of shells and their equivalent radii throughout their whole evolution until they become subsonic. In highly inhomogeneous, turbulent media, there is also a good agreement of shapes and sizes of shells, and of the times of their first contact with the central 1-pc sphere, where we assume that they join the accretion flow. The comparison supports the proposition that an SN occurring at a galactocentric distance of 5 pc typically drives 1-3 M-circle dot into the central 1 pc around the GC. | ||||||
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| Record 221 of 349 | ||||||||||||||||||
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| Author(s): Cuyacot, BR (Cuyacot, Ben Joseph R.); Novotny, J (Novotny, Jan); Berger, RJF (Berger, Raphael J. F.); Komorovsky, S (Komorovsky, Stanislav); Marek, R (Marek, Radek) | ||||||||||||||||||
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| Abstract: Relativistic effects are known to alter the chemical bonds and spectroscopic properties of heavy-element compounds. In this work, we introduce the concept of spin-orbit (SO) electronegativity of a heavy atom, as reflected by an SO-induced change in the interatomic distance between the heavy atom (HA) and a neighboring light atom (LA). We provide a transparent interpretation of these SO effects by using the concept of spin-orbit electron deformation density (SO-EDD). Spin-orbit coupling at the HA induces rearrangement of the electron density for the scalar-relativistically optimized geometry that, in turn, exerts a new force on the LA. The resulting expansion or contraction of the HA-LA bond depends on the nature and electron configuration of the HA. In addition, we quantify the change in atomic electronegativity induced by SO coupling for a series of hydrides, thereby complementing the SO-EDD picture. The trends in the SO-induced electronegativity and the HA-LA bond length across the periodic table of elements are demonstrated and interpreted, and also linked, intuitively, with the SO-induced NMR shielding at the LA. | ||||||||||||||||||
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| Record 222 of 349 | |||||||||
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| Author(s): Cuypers, LN (Cuypers, Laura N.); Cizkova, D (Cizkova, Dagmar); de Bellocq, JG (de Bellocq, Joelle Gouy) | |||||||||
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| Abstract: Mammarenaviruses are bi-segmented RNA viruses. They encompass viruses responsible for several severe diseases in humans. While performing a de novo assembly of a new virus found in a wild single-striped grass mouse in Tanzania, we found a single S but two divergent L segments. Natural co-infections, common within reptarenaviruses in captivity, were never reported for mammarenaviruses and never in a wild sample. This finding can have implications for virus evolution as co-infection could trigger viral recombination/reassortment in natural reservoirs. | |||||||||
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| Record 223 of 349 | ||||||
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| Author(s): Sachl, L (Sachl, L.); Velimsky, J (Velimsky, J.); Fullea, J (Fullea, J.); Martinec, Z (Martinec, Z.) | ||||||
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| Abstract: The interaction of the oceanic tidal flow with the Earth's main magnetic field provides a powerful natural source of electromagnetic (EM) energy suitable for suboceanic upper-mantle electrical conductivity sounding. In this paper, we have developed and tested a new frequency-domain, spherical harmonic-finite element approach to the inverse problem of global EM induction. It is set up for an effective inversion of satellite-observed tidally induced magnetic field in terms of 3-D structure of the electrical conductivity in the suboceanic upper mantle. Before proceeding to the inversion of Swarm-derived models of tidal magnetic signatures, we have performed a series of parametric studies, using the 3-D conductivity model WINTERC-e as a testbed. The WINTERC-e model has been derived using state-of-the-art laboratory conductivity measurements of mantle minerals, and thermal and compositional model of the lithosphere and upper mantle WINTERC-G. The latter model is based on the inversion of global surface waveforms, satellite gravity and gradiometry measurements, surface elevation and heat flow data in a thermodynamically self-consistent framework. Therefore, the WINTERC-e model, independent of any EM data, represents an ideal target for synthetic tests of the 3-D EM inversion. We tested the impact of the truncation degree of the spherical-harmonic expansion of the M-2 tidal signal, the effect of random noise in synthetic data and inclusion of the N-2 and O-1 tidal constituents on the ability to recover the suboceanic upper-mantle conductivity structure. We demonstrate that with suitable regularization we can successfully reconstruct the 3-D upper-mantle conductivity beneath world oceans. In the ideal noise-free case, the correlation coefficient between the target and recovered conductivity is greater than 0.8 in the 150-270 km depth range. | ||||||
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| Record 224 of 349 | ||||||
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| Author(s): Rud, OV (Rud, Oleg, V); Kazakov, AD (Kazakov, Alexander D.); Nova, L (Nova, Lucie); Uhlik, F (Uhlik, Filip) | ||||||
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| Abstract: We model a process of seawater desalination that employs compression of a weak polyelectrolyte hydrogel as the drawing force for ion transfer. We model seawater as an aqueous solution containing mono- and divalent ions, Na+, Cl-, and Ca2+. We demonstrate that the compression of hydrogel in equilibrium with a bath containing such a solution creates two types of ion flow. The first type is the exchange of divalent Ca2+ by monovalent Na+. The charge density during this process is preserved, so that per one absorbed Ca2+ two Na+ are released. The second type is the desalination itself which leads to the uptake of Na+ and Cl- pairs from the surrounding solution. The first flow predominates when Ca2+ are in excess; however, as their fraction in the solution decreases, desalination flow becomes more significant. We have shown that although the gel is a weak polyelectrolyte, its compression in the presence of divalent ions does not influence its ionization degree. This is caused by a significant screening of electrostatic interactions by divalent ions. When the density of Ca2+ is small, the gel compression may lead to its discharge and to the release of counterions, which shows up in an increase of the solution ionic strength. | ||||||
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| Record 225 of 349 | |||||||||
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| Author(s): Friak, M (Friak, Martin); Mazalova, M (Mazalova, Martina); Turek, I (Turek, Ilja); Schneeweiss, O (Schneeweiss, Oldrich); Kastil, J (Kastil, Jiri); Kamarad, J (Kamarad, Jiri); Sob, M (Sob, Mojmir) | |||||||||
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| Abstract: We have performed an ab initio study of disordered ferrimagnetic Ni1.9375Mn1.5625Sn0.5 martensite. Employing the supercell approach combined with the special quasi-random structure concept for modeling of disordered states we have determined thermodynamic, magnetic, structural, elastic and vibrational properties of the studied material. Its atomic and magnetic configuration is found to exhibit a pressure-induced increase of the total magnetic moment, i.e. the total magnetic moment increases with decreasing volume. This peculiar trend is revealed despite of the fact that the magnitudes of local magnetic moments of atoms decrease (or stay constant) with decreasing volume. The origin of the identified phenomena may be related to (i) the ferrimagnetic nature of the magnetic state when the parallel and antiparallel magnetic moments nearly compensate each other and (ii) chemical disorder that leads to different local atomic environments and, consequently, also to different local magnetic moments and their different response to hydrostatic pressures (the antiparallel moments are more sensitive). The studied state is mechanically and dynamically stable (no imaginary-frequency phonons) but, regarding its thermodynamic stability, it is an excited state. | |||||||||
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| Record 226 of 349 | |||||||||||||||
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| Author(s): Smejkal, L (Smejkal, Libor); MacDonald, AH (MacDonald, Allan H.); Sinova, J (Sinova, Jairo); Nakatsuji, S (Nakatsuji, Satoru); Jungwirth, T (Jungwirth, Tomas) | |||||||||||||||
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Abstract:
Only in recent years has the Hall effect been predicted and observed in materials with antiferromagnetic order. This Review systematically organizes the current understanding of anomalous antiferromagnetic materials that generate a Hall effect, discussing these systems in the broad context of spintronics, topological condensed matter and multipole magnetism.
The Hall effect, in which a current flows perpendicular to an electrical bias, has been prominent in the history of condensed matter physics. Appearing variously in classical, relativistic and quantum guises, the Hall effect has - among other roles - contributed to the establishment of the band theory of solids, to research on new phases of interacting electrons and to the phenomenology of topological condensed matter. The dissipationless Hall current requires time-reversal symmetry breaking. When this symmetry breaking is due to an externally applied magnetic field, the effect is referred to as the ordinary Hall effect; when it is due to a non-zero internal magnetization (ferromagnetism), it is referred to as the anomalous Hall effect. The Hall effect has not usually been associated with antiferromagnetic order. More recently, however, theoretical predictions and experimental observations have identified large Hall effects in some compensated magnetic crystals, governed by neither of the global magnetic-dipole symmetry-breaking mechanisms mentioned above. The goal of this Review is to systematically organize the present understanding of anomalous antiferromagnetic materials that generate a Hall effect - which we call anomalous Hall antiferromagnets - and to discuss this class of materials in a broader fundamental and applied research context. Our motivation is twofold: first, because Hall effects that are not governed by magnetic-dipole symmetry breaking are at odds with the traditional understanding of the phenomenon, the topic deserves attention on its own. Second, this new incarnation of the Hall effect has placed it again in the middle of an emerging field in physics, at the intersection of multipole magnetism, topological condensed matter and spintronics. |
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| Record 227 of 349 | ||||||
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| Author(s): Bubenikova, J (Bubenikova, Jana); Futas, J (Futas, Jan); Oppelt, J (Oppelt, Jan); Plasil, M (Plasil, Martin); Vodicka, R (Vodicka, Roman); Burger, PA (Burger, Pamela A.); Horin, P (Horin, Petr) | ||||||
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| Abstract: Natural killer (NK) cells belong to the innate immune system. The germline-encoded natural killer cell receptors represent activating and inhibitory receptors regulating multiple NK cell activities. The natural cytotoxicity receptors (NCRs) are activating natural cytotoxicity triggering receptors 1, 2, and 3 (NKp46, NKp44, and NKp30), encoded by the genes NCR1, NCR2, and NCR3, respectively. NCRs may be expressed in different cell types engaged in mechanisms of innate and adaptive immunity. The family Felidae, comprising the domestic cat and a wide variety of free-ranging species represents a well-suited model for biomedical and evolutionary studies. We characterized the NCR1, NCR2, and NCR3 genes in a panel of felid species. We confirmed the presence of potentially functional genes NCR1, NCR2, and NCR3 in all species. All three genes are conserved within the family and are similar to other phylogenetically related mammalian families. The NCR1 and NCR2 phylogenetic trees based on both nucleotide and protein sequences corresponded to the current zoological taxonomy, with some exceptions suggesting effects of different selection pressures in some species. Highly conserved NCR3 sequences did not allow a robust phylogenetic analysis. Most interspecific differences both at the nucleotide and protein level were found in NCR2. Within species, the most polymorphic CDS was detected in NCR1. Selection analyses indicated the effects of purifying selection on individual amino acid sites in all three genes. In stray cats, a rather high intraspecific diversity was observed. | ||||||
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| Record 228 of 349 | |||||||||||||||
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| Author(s): Sowlati-Hashjin, S (Sowlati-Hashjin, Shahin); Sadek, V (Sadek, Vojtech); Sadjadi, S (Sadjadi, SeyedAbdolreza); Karttunen, M (Karttunen, Mikko); Martin-Pendas, A (Martin-Pendas, Angel); Foroutan-Nejad, C (Foroutan-Nejad, Cina) | |||||||||||||||
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| Abstract: Recent discovery of an unusual bond between Na and B in NaBH3- motivated us to look for potentially similar bonds, which remained unnoticed among systems isoelectronic with NaBH3-. Here, we report a novel family of collective interactions and a measure called exchange-correlation interaction collectivity index (ICIXC; ICI is an element of [0, 1]) to characterize the extent of collective versus pairwise bonding. Unlike conventional bonds in which ICIXC remains close to one, in collective interactions ICIXC may approach zero. We show that collective interactions are commonplace among widely used organometallics, as well as among boron and aluminum complexes with the general formula [M(a+)AR(3)](b-) (A: C, B or Al). In these species, the metal atom interacts more efficiently with the substituents (R) on the central atoms than the central atoms (A) upon forming efficient collective interactions. Furthermore, collective interactions were also found among fluorine atoms of XFn systems (X: B or C). Some of organolithium and organomagnesium species have the lowest ICIXC among the more than 100 studied systems revealing the fact that collective interactions are rather a rule than an exception among organometallic species. | |||||||||||||||
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| Record 229 of 349 | ||||||
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| Author(s): Jochim, B (Jochim, Bethany); Zohrabi, M (Zohrabi, M.); Gaire, B (Gaire, B.); Anis, F (Anis, F.); Uhlikova, T (Uhlikova, Tereza); Carnes, KD (Carnes, K. D.); Wells, E (Wells, E.); Esry, BD (Esry, B. D.); Ben-Itzhak, I (Ben-Itzhak, I.) | ||||||
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| Abstract: We study laser-induced dissociation of a metastable NO2+ ion-beam target into N+ + O+, focusing on the prominent contribution by molecules breaking parallel to the polarization at high peak laser intensity (similar to 10(15) W/cm(2)). Our experimental results and time-dependent Schrodinger equation calculations show that, contrary to commonly held intuition that electronic transitions always prevail, the dominant process underlying this highly aligned dissociation is a multiphoton permanent-dipole transition involving only the electronic ground state and leading to its vibrational continuum. Strong-field permanent-dipole transitions should thus be considered generally, as they may play a significant role in other heteronuclear molecules. Moreover, their role should only grow in importance for longer wavelengths, a trending direction in ultrafast laser studies. | ||||||
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| Record 230 of 349 | |||||||||||||||||||||
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| Author(s): Cavallin, I (Cavallin, Ivana); Bartosovic, M (Bartosovic, Marek); Skalicky, T (Skalicky, Tomas); Rengaraj, P (Rengaraj, Praveenkumar); Demko, M (Demko, Martin); Schmidt-Dengler, MC (Schmidt-Dengler, Martina Christina); Drino, A (Drino, Aleksej); Helm, M (Helm, Mark); Vanacova, S (Vanacova, Stepanka) | |||||||||||||||||||||
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| Abstract: Transfer RNAs acquire a large plethora of chemical modifications. Among those, modifications of the anticodon loop play important roles in translational fidelity and tRNA stability. Four human wobble U-containing tRNAs obtain 5-methoxycarbonylmethyluridine (mcm(5)U(34)) or 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)U(34)), which play a role in decoding. This mark involves a cascade of enzymatic activities. The last step is mediated by alkylation repair homolog 8 (ALKBH8). In this study, we performed a transcriptome-wide analysis of the repertoire of ALKBH8 RNA targets. Using a combination of HITS-CLIP and RIP-seq analyses, we uncover ALKBH8-bound RNAs. We show that ALKBH8 targets fully processed and CCA modified tRNAs. Our analyses uncovered the previously known set of wobble U-containing tRNAs. In addition, both our approaches revealed ALKBH8 binding to several other types of noncoding RNAs, in particular C/D box snoRNAs. | |||||||||||||||||||||
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| Record 231 of 349 | ||||||||||||
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| Author(s): Koloniuk, I (Koloniuk, Igor); Matyasova, A (Matyasova, Alena); Brazdova, S (Brazdova, Sara); Vesela, J (Vesela, Jana); Pribylova, J (Pribylova, Jaroslava); Franova, J (Franova, Jana); Elena, SF (Elena, Santiago F.) | ||||||||||||
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| Abstract: Advances in high-throughput sequencing methods have boosted the discovery of multistrain viral infections in diverse plant systems. This phenomenon appears to be pervasive for certain viral species. However, our knowledge of the transmission aspects leading to the establishment of such mixed infections is limited. Recently, we reported a mixed infection of a single strawberry plant with strawberry mottle virus (SMoV), strawberry crinkle virus (SCV) and strawberry virus 1 (StrV-1). While SCV and StrV-1 are represented by two and three molecular variants, respectively, SmoV has three different RNA1 and RNA2 segments. In this study, we focus on virus acquisition by individual adult aphids of the Aphis gossypii, Aphis forbesi and Chaetosiphon fragaefolii species. Single-aphid transmission trials are performed under experimental conditions. Both different viruses and individual virus strains show varying performances in single aphid acquisition. The obtained data suggests that numerous individual transmission events lead to the establishment of multistrain infections. These data will be important for the development of epidemiological models in plant virology. | ||||||||||||
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| Record 232 of 349 | ||||||||||||
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| Author(s): Pysanenko, A (Pysanenko, Andriy); Farnikova, K (Farnikova, Karolina); Lengyel, J (Lengyel, Jozef); Pluharova, E (Pluharova, Eva); Farnik, M (Farnik, Michal) | ||||||||||||
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| Abstract: Mixed nitric acid/water clusters with dimethylamine (DMA) represent a suitable model system for understanding acid-base chemistry in atmospherically relevant clusters. We investigate these clusters in a detailed molecular-beam experiment accompanied by ab initio calculations. The (HNO3)(M)(H2O)(N) clusters are produced by supersonic expansion into vacuum and doped by DMA molecules in a pickup process. Two complementary mass spectrometry approaches are employed to analyze the resulting (DMA)(K)(HNO3)(M)(H2O)(N) clusters: (i) electron impact ionization at 70 eV to form positive cluster ions and (ii) low-energy electron attachment at 0-10 eV to form negative clusters. The positive ion spectra contain mainly protonated (DMA)(k)(HNO3)(m)H+ clusters with k = m + 1, whereas the negative ones are dominated by (DMA)(k)(HNO3)(m)NO3- with m >= k, followed by (DMA)(k)(HNO3)(m)NO2- (m > k) ions with low abundances. These observations are rationalized by our calculations, which exhibit the tendency of the mixed clusters to maximize the number DMA center dot H+ and NO3- ions in the clusters. In the neutral clusters, this is fulfilled for 1 : 1 ratio of DMA and HNO3, while the positively charged (DMA)(k)(HNO3)(m)H+ clusters satisfy this condition for k = m + 1. The protonated clusters always contain the DMA center dot H+ moiety. For the negatively charged cluster ions, thermochemistry supports the prevailing formation of NO3- and m >= k ion composition. Furthermore, the NO3--containing cluster ions can form when an electron attaches to the protonated moiety of the DMA center dot H+center dot center dot center dot NO3- ion pair in the cluster, which leads to H atom evaporation. From the gas phase HNO3 molecule, where NO2- is formed exclusively upon an electron attachment, the tendency to form NO3- increases to hydrated HNO3 clusters, where both NO2- and NO3- ions are generated in approximately equal abundances, to the DMA doped clusters, where NO3- strongly prevails NO2-. | ||||||||||||
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| Record 233 of 349 | |||||||||||||||||||||||||||||||||
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| Author(s): Zhukouskaya, H (Zhukouskaya, Hanna); Blanco, PM (Blanco, Pablo M.); Cernochova, Z (Cernochova, Zulfiya); Ctverackova, L (Ctverackova, Lucie); Stano, R (Stano, Roman); Pavlova, E (Pavlova, Ewa); Vetrik, M (Vetrik, Miroslav); Cernoch, P (Cernoch, Peter); Filipova, M (Filipova, Marcela); Slouf, M (Slouf, Miroslav); Stepanek, M (Stepanek, Miroslav); Hruby, M (Hruby, Martin); Kosovan, P (Kosovan, Peter); Panek, J (Panek, Jiri) | |||||||||||||||||||||||||||||||||
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| Abstract: ABSTRACT: We developed acid-functionalized glycogen conjugates as supramolecular carriers for efficient encapsulation and inhibition of a model cationic peptide melittin-the main component of honeybee venom. For this purpose, we synthesized and characterized a set of glycogens, functionalized to various degrees by several different acid groups. These conjugates encapsulate melittin up to a certain threshold amount, beyond which they precipitate. Computer simulations showed that sufficiently functionalized conjugates electrostatically attract melittin, resulting in its efficient encapsulation in a broad pH range around the physiological pH. Hemolytic assays confirmed in vitro that the effective inhibition of melittin's hemolytic activity occurs for highly functionalized samples, whereas no inhibition is observed when using low-functionalized conjugates. It can be concluded that functional glycogens are promising carriers for cationic molecular cargos or antidotes against animal venoms under conditions, in which suitable properties such as biodegradability and biocompatibility are crucial. | |||||||||||||||||||||||||||||||||
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| Record 234 of 349 | |||||||||||||||
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| Author(s): Obertik, R (Obertik, Robert); Chudoba, J (Chudoba, Josef); Sturala, J (Sturala, Jiri); Tarabek, J (Tarabek, Jan); Ludvikova, L (Ludvikova, Lucie); Slanina, T (Slanina, Tomas); Konig, B (Koenig, Burkhard); Cibulka, R (Cibulka, Radek) | |||||||||||||||
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| Abstract: Catalyst recovery is an integral part of photoredox catalysis. It is often solved by adding another component-a sacrificial agent-whose role is to convert the catalyst back into its original oxidation state. However, an additive may cause a side reaction thus decreasing the selectivity and overall efficiency. Herein, we present a novel approach towards chemoselective photooxidation reactions based on suitable solvent-acetonitrile acting simultaneously as an electron acceptor for catalyst recovery, and on anaerobic conditions. This is allowed by the unique properties of the catalyst, 7,8-dimethoxy-3-methyl-5-phenyl-5-deazaflavinium chloride existing in both strongly oxidizing and reducing forms, whose strength is increased by excitation with visible light. Usefulness of this system is demonstrated in chemoselective dehydrogenations of 4-methoxy- and 4-chlorobenzyl alcohols to aldehydes without over-oxidation to benzoic acids achieving yields up to 70 %. 4-Substituted 1-phenylethanols were oxidized to ketones with yields 80-100 % and, moreover, with yields 31-98 % in the presence of benzylic methyl group, diphenylmethane or thioanisole which are readily oxidized in the presence of oxygen but these were untouched with our system. Mechanistic studies based on UV-Vis spectro-electrochemistry, EPR and time-resolved spectroscopy measurements showed that the process involving an electron release from an excited deazaflavin radical to acetonitrile under formation of solvated electron is crucial for the catalyst recovery. | |||||||||||||||
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| Record 235 of 349 | |||||||||||||||||||||
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| Author(s): Carretti, E (Carretti, Ettore); Vacca, V (Vacca, V.); O'Sullivan, SP (O'Sullivan, S. P.); Heald, GH (Heald, G. H.); Horellou, C (Horellou, C.); Rottgering, HJA (Rottgering, H. J. A.); Scaife, AMM (Scaife, A. M. M.); Shimwell, TW (Shimwell, T. W.); Shulevski, A (Shulevski, A.); Stuardi, C (Stuardi, C.); Vernstrom, T (Vernstrom, T.) | |||||||||||||||||||||
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| Abstract: We used the rotation measure (RM) catalogue derived from the LOFAR Two-metre Sky Survey Data Release 2 (LoTSS DR2) at 144MHz to measure the evolution with redshift of the extragalactic RM (RRM: Residual RM) and the polarization fraction (p) of sources in low-density environments. We also measured the same at 1.4 GHz by cross-matching with the NRAO VLA Sky Survey RM catalogue. We find that RRM versus redshift is flat at 144 MHz, but, once redshift-corrected, it shows evolution at high significance. Also, p evolves with redshift with a decrement by a factor of similar to 8 at z similar to 2. Comparing the 144-MHz and 1.4-GHz data, we find that the observed RRM and p are most likely to have an origin local to the source at 1.4 GHz, while a cosmic web filament origin is favoured at 144 MHz. If we attribute the entire signal to filaments, we infer a mean rest-frame RRM per filament of RRM0,f = 0.71 +/- 0.07 rad m(-2) and a magnetic field per filament of B-f = 32 +/- 3 nG. This is in agreement with estimates obtained with a complementary method based on synchrotron emission stacking, and with cosmological simulations if primordial magnetic fields are amplified by astrophysical source field seeding. The measurement of an RRM0, f supports the presence of diffuse baryonic gas in filaments. We also estimated a conservative upper limit of the filament magnetic turbulence of sigma(RRM0,f) = 0.039 +/- 0.001 rad m(-2), concluding that the ordered magnetic field component dominates in filaments. | |||||||||||||||||||||
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| Record 236 of 349 | ||||||
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| Author(s): Fraile, A (Fraile, Alberto); Dwivedi, P (Dwivedi, Prashant); Bonny, G (Bonny, Giovanni); Polcar, T (Polcar, Tomas) | ||||||
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| Abstract: The atomistic mechanisms of damage initiation during high velocity (v up to 9 km s(-1), kinetic energies up to 200 keV) impacts of W projectiles on a W surface have been investigated using parallel molecular-dynamics simulations involving large samples (up to 40 million atoms). Various aspects of the high velocity impacts, where the projectile and part of the target material undergo massive plastic deformation, breakup, melting, and vaporization, are analyzed. Different stages of the penetration process have been identified through a detailed examination of implantation, crater size and volume, sputtered atoms, and dislocations created by the impacts. The crater volume increases linearly with the kinetic energy for a given impactor; and the total dislocation length (TDL) increases with the kinetic energy but depends on the size of the impactor. We found that the TDL does not depend on the used interatomic potential. The results are rationalized based on the physical properties of bcc W. | ||||||
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| Record 237 of 349 | ||||||||||||
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| Author(s): Simsova-Zamecnikova, M (Simsova-Zamecnikova, M.); Soldan, P (Soldan, P.); Gustafsson, M (Gustafsson, M.) | ||||||||||||
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| Abstract: Context. Radiative association is a possible way of sodium chloride (NaCl) formation in interstellar and related environments. Theoretical studies are essential since laboratory experiments are unavailable and difficult to perform. Aims. The total rate coefficient was calculated for the formation of NaCl by radiative association at 30-750 K. Methods. We included two contributing processes for the total rate-coefficient computation. One of them takes the nonadiabatic coupling between the two lowest (1)sigma(+) states, X-1 sigma(+) and Beta(1)sigma(+), into account. The other one was calculated conventionally as a single channel and started in the continuum of the A(1)pi state. The individual rate coefficients were calculated from cross sections obtained up to 0.8 eV, which enabled us to calculate the rate coefficients up to 750 K. The cross section was also calculated for a one-state process within the X-1 sigma(+) state. Results. The nonadiabatic coupling enhances the formation of NaCl by radiative association by two orders of magnitude at about 30 K and by around one order of magnitude at about 750 K. The single-channel process starting in the continuum of the A(1) pi state starts to contribute above around 200 K. The one-state transition model, within the X-1 sigma(+) state, is not an adequate approximation for collisions in (1)sigma(+) symmetry. Instead, these collisions are treated in the diabatic representation in the total rate-coefficient calculation. Conclusions. The calculated total rate-coefficient function at 30-750 K can improve the astrochemical reaction networks for the CRL 2688, IRC+10216, and Orion SrcI environments, where NaCl was detected before. | ||||||||||||
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| Record 238 of 349 | |||||||||||||||
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| Author(s): Kyvala, L (Kyvala, L.); Havela, L (Havela, L.); Kadzielawa, AP (Kadzielawa, A. P.); Legut, D (Legut, D.) | |||||||||||||||
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| Abstract: GGA+U has been used as a framework for computational study of UH2, and alpha- and ,B-UH3, exploring specific features of the polar U-H bonding and its influence on magnetic and cohesion properties, including elastic parameters and vibrational properties. The description of the U-5 f states with direct Coulomb U = 0.5 eV and equal exchange J = 0.5 eV not only reproduce equilibrium volumes but provides a realistic description of total magnetic moments, consisting of smaller spin and larger antiparallel orbital components. For UH(2 )and alpha-UH3, the spin-axis is aligned along the [111] direction. For ,B-UH3, there is a significant difference between both size and orientation U moments of atoms at the 2 a and 6 c Wyckoff positions. The former has U moments aligned along [111], while in the latter, not fixed to any specific direction by symmetry, they deviate by 10 . The method corroborates previous bonding analyses, indicating a prominent hybridization and charge transfer, affecting the 6 d and 7 s states of U, being partly transferred to the H-1 s states, revealed by the Bader analysis. Analyzing individual effective inter-site magnetic coupling parameters it was possible to identify sources of relatively high Curie temperatures of 170 K for both UH(3 )variants and 120 K for UH2. Our results give predictions of elastic coefficients (consistent with the known bulk modulus in the case of ,B-UH3) and phonon densities of states, yielding expected infrared, Raman, and Hyper Raman active modes. (C) 2022 Elsevier B.V. All rights reserved. | |||||||||||||||
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| Record 239 of 349 | |||||||||||||||
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| Author(s): Schmiedova, L (Schmiedova, Lucie); Tomasek, O (Tomasek, Oldrich); Pinkasova, H (Pinkasova, Hana); Albrecht, T (Albrecht, Tomas); Kreisinger, J (Kreisinger, Jakub) | |||||||||||||||
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| Abstract: Quality and quantity of food items consumed has a crucial effect on phenotypes. In addition to direct effects mediated by nutrient resources, an individual's diet can also affect the phenotype indirectly by altering its gut microbiota, a potent modulator of physiological, immunity and cognitive functions. However, most of our knowledge of diet-microbiota interactions is based on mammalian species, whereas little is still known about these effects in other vertebrates. We developed a metabarcoding procedure based on cytochrome c oxidase I high-throughput amplicon sequencing and applied it to describe diet composition in breeding colonies of an insectivorous bird, the barn swallow (Hirundo rustica). To identify putative diet-microbiota associations, we integrated the resulting diet profiles with an existing dataset for faecal microbiota in the same individual. Consistent with previous studies based on macroscopic analysis of diet composition, we found that Diptera, Hemiptera, Coleoptera and Hymenoptera were the dominant dietary components in our population. We revealed pronounced variation in diet consumed during the breeding season, along with significant differences between nearby breeding colonies. In addition, we found no difference in diet composition between adults and juveniles. Finally, our data revealed a correlation between diet and faecal microbiota composition, even after statistical control for environmental factors affecting both diet and microbiota variation. Our study suggests that variation in diet induce slight but significant microbiota changes in a non-mammalian host relying on a narrow spectrum of items consumed. | |||||||||||||||
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| Record 240 of 349 | |||||||||
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| Author(s): Smejkal, L (Smejkal, Libor); Sinova, J (Sinova, Jairo); Jungwirth, T (Jungwirth, Tomas) | |||||||||
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| Abstract: Recent series of theoretical and experimental reports have driven attention to time-reversal symmetry -breaking spintronic and spin-splitting phenomena in materials with collinear-compensated magnetic order incompatible with conventional ferromagnetism or antiferromagnetism. Here we employ an approach based on nonrelativistic spin-symmetry groups that resolves the conflicting notions of unconventional ferromagnetism or antiferromagnetism by delimiting a third basic collinear magnetic phase. We derive that all materials hosting this collinear-compensated magnetic phase are characterized by crystal-rotation symmetries connecting opposite-spin sublattices separated in the real space and opposite-spin electronic states separated in the momentum space. We describe prominent extraordinary characteristics of the phase, including the alternating spin-splitting sign and broken time-reversal symmetry in the nonrelativistic band structure, the planar or bulk d-, g-, or i-wave symmetry of the spin-dependent Fermi surfaces, spin -degenerate nodal lines and surfaces, band anisotropy of individual spin channels, and spin-split general, as well as time-reversal invariant momenta. Guided by the spin-symmetry principles, we discover in ab initio calculations outlier materials with an extraordinary nonrelativistic spin splitting, whose eV-scale and momentum dependence are determined by the crystal potential of the nonmagnetic phase. This spin -splitting mechanism is distinct from conventional relativistic spin-orbit coupling and ferromagnetic exchange, as well as from the previously considered anisotropic exchange mechanism in compensated magnets. Our results, combined with our identification of material candidates for the phase ranging from insulators and metals to a parent crystal of cuprate superconductors, underpin research of novel quantum phenomena and spintronic functionalities in high-temperature magnets with light elements, vanishing net magnetization, and strong spin coherence. In the discussion, we argue that the conflicting notions of unconventional ferromagnetism or antiferromagnetism, on the one hand, and our symmetry-based delimitation of the third phase, on the other hand, favor a distinct term referring to the phase. The alternating spin polarizations in both the real-space crystal structure and the momentum-space band structure characteristic of this unconventional magnetic phase suggest a term altermagnetism. We point out that d-wave altermagnetism represents a realization of the long-sought-after counterpart in magnetism of the unconventional d-wave superconductivity. | |||||||||
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| Record 241 of 349 | |||||||||
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| Author(s): Medvedev, N (Medvedev, Nikita); Volkov, AE (Volkov, Alexander E.) | |||||||||
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| Abstract: Atomic heating in a solid takes place after an impact of a swift heavy ion within a time of electronic cooling there, i.e., similar to 100 fs. This implies an extremely fast electron-ion energy exchange ( "electron-phonon coupling ") necessary for the production of detected ion tracks. In contrast, laser irradiation experiments and calculations show too slow electron-phonon energy exchange to cause structural changes detected in swift heavy ion tracks in solids. We demonstrate that this contradiction can be resolved by taking into account that electron-phonon coupling is not the sole mechanism of energy exchange between electrons and ions in condensed matter. Excitation of the electronic system alters the potential energy surface of atoms, causing them to accelerate and increase their kinetic energy at ultrashort times. Published under an exclusive license by AIP Publishing. | |||||||||
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| Record 242 of 349 | ||||||||||||
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| Author(s): Muenster, L (Muenster, Lukas); Capakova, Z (Capakova, Zdenka); Humpolicek, P (Humpolicek, Petr); Kuritka, I (Kuritka, Ivo); Christensen, BE (Christensen, Bjorn E.); Vicha, J (Vicha, Jan) | ||||||||||||
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| Abstract: Sequential periodate-chlorite oxidation of sodium hyaluronate to 2,3-dicarboxylated hyaluronate (DCH), a novel biocompatible and highly functionalized derivative bearing additional pair of -COOH groups at C2 and C3 carbons of oxidized ?-glucuronic acid units, is investigated. The impact of various reaction parameters (time, oxidizer concentration, and molar amount) on DCH's composition, molecular weight, degree of oxidation, and cytotoxicity are investigated to guide the synthesis of DCH derivatives of desired properties. Subsequently, fully (99%) and partially (70%) oxidized DCH derivatives were compared to untreated sodium hyaluronate in terms of anticancer drug cisplatin loading efficacy, carrier capacity, drug release rates, and cytotoxicity towards healthy and cancerous cell lines. DCH derivatives were found to be superior in every aspect, having nearly twice the carrier capacity, significantly slower release rates, and higher efficacy. DCH is thus a highly interesting hyaluronate derivative with an adjustable degree of oxidation, molecular weight, and great potential for further modifications. | ||||||||||||
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| Record 243 of 349 | |||||||||||||||||||||||||||
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| Author(s): Rybakiewicz-Sekita, R (Rybakiewicz-Sekita, Renata); Toman, P (Toman, Petr); Ganczarczyk, R (Ganczarczyk, Roman); Drapala, J (Drapala, Jakub); Ledwon, P (Ledwon, Przemyslaw); Banasiewicz, M (Banasiewicz, Marzena); Skorka, L (Skorka, Lukasz); Matyjasiak, A (Matyjasiak, Anna); Zagorska, M (Zagorska, Malgorzata); Pron, A (Pron, Adam) | |||||||||||||||||||||||||||
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| Abstract: Five D-pi-A-pi-D compounds consisting of the same donor unit (dithieno[3,2-b:2',3'-d]pyrrole, DTP), the same pi-linker (2,5-thienylene), and different acceptors of increasing electron-withdrawing ability (1,3,4-thiadiazole (TD), benzo[c]-[1,2,5]thiadiazole (BTD), 2,5-dihydropyrrolo[3,4-c]pyrrole-1,4-dione (DPP), 1,2,4,5-tetrazine (TZ), and benzo[lmn][3,8]-phenanthroline-1,3,6,8(2H,7H)-tetraone (NDI)) were synthesized. DTP-TD, DTP-BTD, and DTP-DPP turned out to be interesting luminophores emitting either yellow (DTP-TD) or near-infrared (DTP-BTD and DTP-DPP) radiation in dichloromethane solutions. The emission bands were increasingly bathochromically shifted with increasing solvent polarity. Electrochemically determined electron affinities (vertical bar EA vertical bar s) were found to be strongly dependent on the nature of the acceptor changing from 2.86 to 3.84 eV for DTP-TD and DTP-NDI, respectively, while the ionization potential (IP) values varied only weakly. Experimental findings were strongly supported by theoretical calculations, which correctly predicted the observed solvent dependence of the emission spectra. Similarly, the calculated IP and EA values were in excellent agreement with the experiment. DTP-TD, DTP-BTD, DTP-TZ, and DTP-NDI could be electropolymerized to yield polymers of very narrow electrochemical band gap and characterized by redox states differing in color coordinates and lightness. Poly(DTP-NDI) and poly(DTP-TD) showed promising electrochromic behavior, not only providing a rich color palette in the visible but also exhibiting near-infrared (NIR) electrochromism. | |||||||||||||||||||||||||||
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| Record 244 of 349 | ||||||||||||
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| Author(s): Hervo-Hansen, S (Hervo-Hansen, Stefan); Heyda, J (Heyda, Jan); Lund, M (Lund, Mikael); Matubayasi, N (Matubayasi, Nobuyuki) | ||||||||||||
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| Abstract: The contributions from anions and cations from salt are inseparable in their perturbation of molecular systems by experimental and computational methods, rendering it difficult to dissect the effects exerted by the anions and cations individually. Here we investigate the solvation of a small molecule, caffeine, and its perturbation by monovalent salts from various parts of the Hofmeister series. Using molecular dynamics and the energy-representation theory of solvation, we estimate the solvation free energy of caffeine and decompose it into the contributions from anions, cations, and water. We also decompose the contributions arising from the solute-solvent and solute-ions interactions and that from excluded volume, enabling us to pin-point the mechanism of salt. Anions and cations revealed high contrast in their perturbation of caffeine solvation, with the cations salting-in caffeine via binding to the polar ketone groups, while the anions were found to be salting-out via perturbations of water. In agreement with previous findings, the perturbation by salt is mostly anion dependent, with the magnitude of the excluded-volume effect found to be the governing mechanism. The free-energy decomposition as conducted in the present work can be useful to understand ion-specific effects and the associated Hofmeister series. | ||||||||||||
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| Record 245 of 349 | ||||||
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| Author(s): Ghosh, S (Ghosh, Srikrishna); Manchon, A (Manchon, Aurelien); Zelezny, J (Zelezny, Jakub) | ||||||
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| Abstract: Ferromagnetic spin valves and tunneling junctions are crucial for spintronics applications and are one of the most fundamental spintronics devices. Motivated by the potential unique advantages of antiferromagnets for spintronics, we theoretically study here junctions built out of noncollinear antiferromagnets. We demonstrate a large and robust magnetoresistance and spin-transfer torque capable of ultrafast switching between parallel and antiparallel states of the junction. In addition, we show that a new type of self-generated torque appears in the noncollinear junctions. | ||||||
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| Record 246 of 349 | |||||||||
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| Author(s): Jenista, J (Jenista, Jiri); Chau, SW (Chau, Shiu-Wu); Chien, SW (Chien, Sheng-Wei); Zivny, O (Zivny, Oldrich); Takana, H (Takana, Hidemasa); Nishiyama, H (Nishiyama, Hideya); Bartlova, M (Bartlova, Milada); Aubrecht, V (Aubrecht, Vladimir); Murphy, AB (Murphy, Anthony B.) | |||||||||
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| Abstract: This study presents a numerical model of the hybrid-stabilized argon-steam thermal DC plasma torch of a new design for generating an argon-steam plasma suitable for efficient abatement of persistent perfluorinated compounds. The model includes the discharge region and the plasma jet flowing to the surrounding steam atmosphere contained in a plasma-chemical chamber. Compared to previous studies, the torch had a smaller nozzle diameter (5.3 mm) and a reduced input power (20-40 kW) and arc current (120-220 A). The outlet region for the plasma jet extends to 20 cm downstream of the exit nozzle. Fluid dynamic and thermal characteristics together with diffusion of argon, hydrogen and oxygen species, and distribution of plasma species in the discharge and the plasma jet are obtained for currents from 120 to 220 A. The results of the calculations show that the plasma jet exhibits high spatiotemporal fluctuations in the shear layer between the plasma jet and colder steam atmosphere. The most abundant species in the plasma jet are hydrogen and oxygen atoms near the jet center, and molecules of H-2, O-2 and OH in colder surrounding regions. Satisfactory agreement is obtained with measurements of the radial temperature and electron number density profiles near the jet center close to the nozzle exit. | |||||||||
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| Record 247 of 349 | |||||||||||||||
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| Author(s): Chen, Q (Chen, Qiang); Maslarova, D (Maslarova, Dominika); Wang, JZ (Wang, Junzhi); Lee, SX (Lee, Shao Xian); Horny, V (Horny, Vojtech); Umstadter, D (Umstadter, Donald) | |||||||||||||||
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| Abstract: We show the first experiment of a transverse laser interference for electron injection into the laser plasma accelerators. Simulations show such an injection is different from previous methods, as electrons are trapped into later acceleration buckets other than the leading ones. With optimal plasma tapering, the dephasing limit of such unprecedented electron beams could be potentially increased by an order of magnitude. In simulations, the interference drives a relativistic plasma grating, which triggers the splitting of relativistic-intensity laser pulses and wakefield. Consequently, spatially dual electron beams are accelerated, as also confirmed by the experiment. | |||||||||||||||
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| Record 248 of 349 | |||||||||
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| Author(s): Dockal, J (Dockal, Jan); Lisal, M (Lisal, Martin); Moucka, F (Moucka, Filip) | |||||||||
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| Abstract: We develop and study polarizable microscopic models, force fields, for molecular simulations of alkali halide electrolyte aqueous solutions, their crystals, and phase equilibria. We start from the AH/BK3 force fields of Kiss and Baranyai (P. T. Kiss and A. A. Baranyai, J. Chem. Phys. 2014, 141, 114501), which we refine using an approach for determining ion-ion interaction parameters, directly targeting experimental values of the lattice energy, pressure at a given density, and bulk and shear moduli of anhydrous electrolyte crystals. We apply the approach to 16 alkali-halide salts crystallizing in the face-centered cubic rock salt structure. As a result, we obtain force fields which predict rather accurately properties of crystals including their chemical potentials, properties of aqueous solutions including their static permittivity, and aqueous solubility. The force fields can thus find applications in molecular simulations of alkali halide aqueous electrolytes, their interfaces, phase equilibria, metastable states, and other cases where less accurate models may exhibit various undesirable features such as excessive ion pairing, spurious precipitation, or incorrect low mobility. (c) 2022 Elsevier B.V. All rights reserved. | |||||||||
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| Record 249 of 349 | |||||||||||||||||||||
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| Author(s): Lowe, B (Lowe, Benjamin); Hellerstedt, J (Hellerstedt, Jack); Matej, A (Matej, Adam); Mutombo, P (Mutombo, Pingo); Kumar, D (Kumar, Dhaneesh); Ondracek, M (Ondracek, Martin); Jelinek, P (Jelinek, Pavel); Schiffrin, A (Schiffrin, Agustin) | |||||||||||||||||||||
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| Abstract: Selective activation and controlled functionalization of C-H bonds in organic molecules is one of the most desirable processes in synthetic chemistry. Despite progress in heterogeneous catalysis using metal surfaces, this goal remains challenging due to the stability of C-H bonds and their ubiquity in precursor molecules, hampering regioselectivity. Here, we examine the interaction between 9,10-dicyanoanthracene (DCA) molecules and Au adatoms on a Ag(111) surface at room temperature (RT). Characterization via low-temperature scanning tunneling microscopy, spectroscopy, and noncontact atomic force microscopy, supported by theoretical calculations, revealed the formation of organometallic DCA-Au-DCA dimers, where C atoms at the ends of the anthracene moieties are bonded covalently to single Au atoms. The formation of this organometallic compound is initiated by a regioselective cleaving of C-H bonds at RT. Hybrid quantum mechanics/molecular mechanics calculations show that this regioselective C-H bond cleaving is enabled by an intermediate metal-organic complex which significantly reduces the dissociation barrier of a specific C-H bond. Harnessing the catalytic activity of single metal atoms, this regioselective on-surface C-H activation reaction at RT offers promising routes for future synthesis of functional organic and organometallic materials. | |||||||||||||||||||||
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| Record 250 of 349 | ||||||
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| Author(s): Meszaros, Z (Meszaros, Zuzana); Petraskova, L (Petraskova, Lucie); Kulik, N (Kulik, Natalia); Pelantova, H (Pelantova, Helena); Bojarova, P (Bojarova, Pavla); Kren, V (Kren, Vladimir); Slamova, K (Slamova, Kristyna) | ||||||
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| Abstract: Fungal beta-N-acetylhexosaminidases of the CAZy family 20 of glycoside hydrolases are well-established tools for the enzymatic synthesis of a wide variety of natural and modified oligosaccharides and glycoconjugates. In order to increase their synthetic efficiency, the beta-N-acetylhexosaminidase from Aspergillus oryzae (AoHex) was employed as a model enzyme for enzyme engineering aiming at shifting the reaction course from hydrolysis toward transglycosylation. Specifically, nine mutant variants of AoHex were designed by molecular modeling based on its crystal structure and molecular dynamics simulations. The selected mutation hotspots included the tyrosine residue at the active site, which stabilizes the transition state of the reaction, and two residues at the aglycone-binding site, which were replaced by tryptophan residues to increase the hydrophobicity of this subsite. Besides the individual mutants, combined double-mutant variants were also prepared and characterized. As a result, eight out of the studied new AoHex variants had transglycosidase activity, with V306W/Y445N AoHex being a superior transglycosidase with a transglycosylation-to-hydrolysis ratio greater than 110, which is entirely unique among the hypertransglycosylating glycosidase mutants including the GH20 beta-N-acetylhexosaminidases. | ||||||
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| Record 251 of 349 | ||||||
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| Author(s): Korinek, T (Korinek, Tomas); Frana, K (Frana, Karel); Hujer, J (Hujer, Jan); Skarohlid, J (Skarohlid, Jan) | ||||||
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| Abstract: A fine near-wall resolution plays a crucial role in simulations of unsteady heat transfer from a wall. A generation of fine structured grids for a complex domain is cumbersome and requires an enormous number of grid points and a local grid refinement is a possible technique for a grid point reduction. The present study addresses numerical simulations of impinging jet heat transfer on locally refined computational grids using the Scale-Resolving-Simulation methods (DES, LES and PANS). The study is performed at a Reynolds number Re = 23000 and two nozzle-plate distances H/D = 2 and H/D = 6. DES and the PANS model with f(k) = 0.25 predicted results closest to experimental data. However, DES significantly over-predicted heat transfer at the location r/D = 1 - 2 in the small nozzle-plate distance case (H/D = 2). The decrease of physical resolution in the PANS model resulted in the over-prediction of heat transfer close to the nozzle axis. In conclusion, the influence of the local refinement in the perpendicular direction was rather low compared to the longitudinal direction. Moreover, the local grid refinement improved results predicted by LES and DES in the small nozzle-plate distance case. | ||||||
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| Author(s): Brezina, K (Brezina, Krystof); Kostal, V (Kostal, Vojtech); Jungwirth, P (Jungwirth, Pavel); Marsalek, O (Marsalek, Ondrej) | |||||||||||||||
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| Abstract: The benzene radical anion is a molecular ion pertinent to several organic reactions, including the Birch reduction of benzene in liquid ammonia. The species exhibits a dynamic Jahn-Teller effect due to its open-shell nature and undergoes pseudorotation of its geometry. Here, we characterize the complex electronic structure of this condensed-phase system based on ab initio molecular dynamics simulations and GW calculations of the benzene radical anion solvated in liquid ammonia. Using detailed analysis of the molecular and electronic structure, we find that the spatial character of the excess electron of the solvated radical anion follows the underlying Jahn-Teller distortions of the molecular geometry. We decompose the electronic density of states to isolate the contribution of the solute and to examine the response of the solvent to its presence. Our findings show the correspondence between instantaneous molecular structure and spin density; provide important insights into the electronic stability of the species, revealing that it is, indeed, a bound state in the condensed phase; and offer electronic densities of states that aid in the interpretation of experimental photoelectron spectra. | |||||||||||||||
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| Record 253 of 349 | |||||||||
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| Author(s): Yang, MY (Yang, Mengyao); Ozdemir, Z (Ozdemir, Zulal); Kim, H (Kim, Heejeong); Nah, S (Nah, Sanghee); Andris, E (Andris, Erik); Li, XS (Li, Xingshu); Wimmer, Z (Wimmer, Zdenek); Yoon, J (Yoon, Juyoung) | |||||||||
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| Abstract: Combating biofilm infections remains a challenge due to the shield and acidic conditions. Herein, an acid-responsive nanoporphyrin (PN3-NP) based on the self-assembly of a water-soluble porphyrin derivative (PN3) is constructed. Additional kinetic control sites formed by the conjugation of the spermine molecules to a porphyrin macrocycle make PN3 self-assemble into stable nanoparticles (PN3-NP) in the physiological environment. Noteworthily, near-infrared (NIR) fluorescence monitoring and synergistic photodynamic therapy (PDT) and photothermal therapy (PTT) effects of PN3-NP can be triggered by the acidity in biofilms, accompanied by intelligent transformation into dot-like nanospheres. Thus, damage to normal tissue is effectively avoided and accurate diagnosis and treatment of biofilms is achieved successfully. The good results of fluorescence imaging-guided photo-ablation of antibiotic-resistant strains methicillin-resistant Staphylococcus aureus (MRSA) biofilms verify that PN3-NP is a promising alternative to antibiotics. Meanwhile, this strategy also opens new horizons to engineer smart nano-photosensitizer for accurate diagnosis and treatment of biofilms. | |||||||||
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| Record 254 of 349 | |||||||||||||||
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| Author(s): Nakonieczny, DS (Nakonieczny, Damian S.); Antonowicz, M (Antonowicz, Magdalena); SimhaMartynkova, G (SimhaMartynkova, Grazyna); Kern, F (Kern, Frank); Pazourkova, L (Pazourkova, Lenka); Erfurt, K (Erfurt, Karol); Hupsch, M (Hupsch, Michal) | |||||||||||||||
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| Abstract: The aim of this study was to conduct artificial ageing tests on polymer-ceramic composites prepared from polyamide PA-12 polymer matrix for medical applications and three different variants of ceramic fillers: zirconia, alumina and cenospheres. Before ageing, the samples were subjected to ethyl oxide sterilization. The composite variants were prepared for 3D printing using the fused deposition modeling method. The control group consisted of unsterilized samples. Samples were subjected to artificial ageing in a high-pressure autoclave. Ageing conditions were calculated from the modified Hammerlich Arrhenius kinetic equation. Ageing was carried out in artificial saliva. After ageing the composites were subjected to mechanical (tensile strength, hardness, surface roughness) testing, chemical and structural (MS, FTIR) analysis, electron microscopy observations (SEM/EDS) and absorbability measurements. | |||||||||||||||
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| Record 255 of 349 | ||||||||||||||||||||||||
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| Author(s): Nakonieczny, DS (Nakonieczny, Damian S.); Martynkova, GS (Martynkova, Grazyna Simha); Hundakova, M (Hundakova, Marianna); Kratosova, G (Kratosova, Gabriela); Holesova, S (Holesova, Sylva); Kupkova, J (Kupkova, Jana); Pazourkova, L (Pazourkova, Lenka); Majewska, J (Majewska, Justyna) | ||||||||||||||||||||||||
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| Abstract: The alumina and zirconia surfaces were pretreated with chemical etching using alkaline mixtures of ammonia, hydrogen peroxide and sodium hydroxide, and followed with application of the powder layer of Ca-deficient hydroxyapatite (CDH). The influence of etching bath conditions time and concentration on surface development, chemical composition and morphology of medicinal ceramic powders were studied. The following analyses were performed: morphology (scanning electron microscopy), phase composition (X-ray diffraction analysis), changes in binding interactions and chemical composition (FT-Infrared and Energy dispersive spectroscopies). Both types of etchants did not expose the original phase composition changes or newly created phases for both types of ceramics. Subsequent decoration of the surface with hydroxyapatite revealed differences in the morphological appearance of the layer on both ceramic surfaces. The treated zirconia surface accepted CDH as a flowing layer on the surface, while the alumina was decorated with individual CDH aggregates. The goal of this study was to focus further on the ceramic fillers for polymer-ceramic composites used as a biomaterial in dental prosthetics. | ||||||||||||||||||||||||
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| Record 256 of 349 | |||||||||
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| Author(s): Uhlirova, T (Uhlirova, T.); Zamastil, J (Zamastil, J.); Benda, J (Benda, J.) | |||||||||
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| Abstract: We propose the use of Sturmian basis set for relativistic atomic structure calculations. We describe a numerically stable algebraic calculation of one-and two-particle radial integrals. The method is illustrated on the basis set independent calculation of energies, electric dipole moments, hyperfine integrals and parity non-conserving (PNC) amplitude for Cs in Dirac-Hartree-Fock approximation with frozen core orbitals. The previously reported results for electric dipole moments and PNC amplitude are found to be strongly basis dependent. Program summary Program title: PASC CPC Library link to program files: https://doi .org /10 .17632 /xycmhhcr5h .1 Licensing provisions: MIT Programming language: Fortran 2008 Nature of problem: Precise atomic measurements require reliable and highly accurate atomic structure calculations. Here we deal with the problem of numerical stability of the atomic integrals and basis set independence of the calculations. Solution method: The radial parts of the electronic orbitals are expanded in a discrete Sturmian functions that are eigenfunctions of one of the generators of the so(2, 1) Lie algebra. This algebraic structure is used to deduce algebraic relations between the radial parts of the atomic integrals. This leads to numerically stable calculation, which in turn allows to achieve basis set independence. Additional comments including restrictions and unusual features: The method is currently restricted to the Dirac-Hartree-Fock method. However, this limitation will be lifted in future versions, which will be extended with the coupled clusters method. (C) 2022 Elsevier B.V. All rights reserved. | |||||||||
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| Record 257 of 349 | ||||||
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| Author(s): Skoupy, V (Skoupy, Viktor); Lukes-Gerakopoulos, G (Lukes-Gerakopoulos, Georgios) | ||||||
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| Abstract: The detection of gravitational waves from extreme mass ratio inspirals (EMRIs) by the future space based gravitational-wave detectors demands the generation of accurate enough waveform templates. Since the spin of the smaller secondary body cannot be neglected for the detection and parameter estimation of EMRIs, we study its influence on the phase of the gravitational waves from EMRIs with a spinning secondary. We focus on generic eccentric equatorial orbits around a Kerr black hole. To model the spinning secondary object, we use the Mathisson-Papapetrou-Dixon equations in the pole-dipole approximation. Furthermore, we linearize in spin the orbital variables and the gravitational-wave fluxes from the respective orbits. We obtain these fluxes by using the Teukolsky formalism in the frequency domain. We derive the evolution equations for the spin-induced corrections to the adiabatic evolution of an inspiral. Finally, through their numerical integration, we find the gravitational-wave phase shift between an inspiral of a spinning and a nonspinning body. | ||||||
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| Record 258 of 349 |
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| Author(s): Vaczi, P (Vaczi, Peter); Bartak, M (Bartak, Milos) |
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| Abstract: The study brings data on monitoring of spectral refectance signatures of different com-ponents of Antarctic terrestrial vegetation by using a high-resolution multispectral im-ages. The aim of the study was to compare several spots of a vegetation oasis by mapping vegetation cover using an UAV approach. This study provides data on vege-tation distribution within a long-term research plot (LTRP) located at the northern coast of James Ross Island (Antarctica). Apart from normalized difference vegetation index (NDVI), 10 spectral reflectance indices (NDVI, NDVIRed-edge, RGBVI, NGRDI, ExG, TGI MSR, MSRRed-edge, Clgreen, ClRed-edge, GLI) were evaluated for different spots representing vegetation classes dominated by different Antarctic autotrophs. The UAV application and spectral reflectance indices proved their capability to detect and map small-area vegetated patches (with the smallest area of 10 cm2) dominated by different Antarctic autotrophs, and identify their classes (moss / lichens / biological soil crusts / microbio-logical mats / stream bottom microbiological mats). The methods used in our study re-vealed sufficiently high resolution of particular vegetation-covered surfaces and the spectral indices provided important indicators for environmental characteristics of the long-term research plot at the James Ross Island, Antarctica. |
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| Record 259 of 349 | |||||||||
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| Author(s): Chrienova, Z (Chrienova, Zofia); Nepovimova, E (Nepovimova, Eugenie); Andrys, R (Andrys, Rudolf); Dolezal, R (Dolezal, Rafael); Janockova, J (Janockova, Jana); Muckova, L (Muckova, Lubica); Fabova, L (Fabova, Lenka); Soukup, O (Soukup, Ondrej); Oleksak, P (Oleksak, Patrik); Valis, M (Valis, Martin); Korabecny, J (Korabecny, Jan); Marco-Contelles, J (Marco-Contelles, Jose); Kuca, K (Kuca, Kamil) | |||||||||
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| Abstract: Twenty-four novel compounds bearing tetrahydroacridine and N-propargyl moieties have been designed, synthesised, and evaluated in vitro for their anti-cholinesterase and anti-monoamine oxidase activities. Propargyltacrine 23 (IC50 = 21 nM) was the most potent acetylcholinesterase (AChE) inhibitor, compound 20 (IC50 = 78 nM) showed the best inhibitory human butyrylcholinesterase (hBChE) profile, and ligand 21 afforded equipotent and significant values on both ChEs (human AChE [hAChE]: IC50 = 0.095 +/- 0.001 mu M; hBChE: IC50 = 0.093 +/- 0.003 mu M). Regarding MAO inhibition, compounds 7, 15, and 25 demonstrated the highest inhibitory potential towards hMAO-B (IC50 = 163, 40, and 170 nM, respectively). In all, compounds 7, 15, 20, 21, 23, and 25 exhibiting the most balanced pharmacological profile, were submitted to permeability and cell viability tests. As a result, 7-phenoxy-N-(prop-2-yn-1-yl)-1,2,3,4-tetrahydroacridin-9-amine hydrochloride (15) has been identified as a permeable agent that shows a balanced pharmacological profile [IC50 (hAChE) = 1.472 +/- 0.024 mu M; IC50 (hBChE) = 0.659 +/- 0.077 mu M; IC50 (hMAO-B) = 40.39 +/- 5.98 nM], and consequently, as a new hit-ligand that deserves further investigation, in particular in vivo analyses, as the preliminary cell viability test results reported here suggest that this is a relatively safe therapeutic agent. | |||||||||
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| Record 260 of 349 | ||||||||||||||||||
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| Author(s): Bouda, M (Bouda, Martin); Huggett, BA (Huggett, Brett A.); Prats, KA (Prats, Kyra A.); Wason, JW (Wason, Jay W.); Wilson, JP (Wilson, Jonathan P.); Brodersen, CR (Brodersen, Craig R.) | ||||||||||||||||||
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| Abstract: The earliest vascular plants had stems with a central cylindrical strand of water-conducting xylem, which rapidly diversified into more complex shapes. This diversification is understood to coincide with increases in plant body size and branching; however, no selection pressure favoring xylem strand-shape complexity is known. We show that incremental changes in xylem network organization that diverge from the cylindrical ancestral form lead to progressively greater drought resistance by reducing the risk of hydraulic failure. As xylem strand complexity increases, independent pathways for embolism spread become fewer and increasingly concentrated in more centrally located conduits, thus limiting the systemic spread of embolism during drought. Selection by drought may thus explain observed trajectories of xylem strand evolution in the fossil record and the diversity of extant forms. | ||||||||||||||||||
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| Record 261 of 349 | |||||||||||||||
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| Author(s): Daghbouj, N (Daghbouj, N.); Sen, HS (Sen, H. S.); Callisti, M (Callisti, M.); Vronka, M (Vronka, M.); Karlik, M (Karlik, M.); Duchon, J (Duchon, J.); Cech, J (Cech, J.); Havranek, V (Havranek, V); Polcar, T (Polcar, T.) | |||||||||||||||
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| Abstract: Tailoring interfaces is a powerful way of reducing the accumulation of radiation defects. Understanding strain evolution induced by ion bombardment in nuclear materials with high interface density is crucial for next-generation reactors since induced defects are responsible for volumetric swelling and catastrophic failure. X-ray and selected-area diffraction patterns (SADPs) measurements reveal, after Cu implantation, that a relatively high out-of-plane strain is created in thin Zr/Nb-6 multilayers, while thick Zr/Nb96 is barely distorted. The absence of layer deformation in Zr/Nb-96 is explained by local TEM strain mapping showing the presence of two oppositely distorted regions (inner and interface-affected regions) within one layer producing only a small overall strain, whereas the whole individual layers of Zr/Nb-6 are affected by the interface manifesting high strain. Using MD simulations, the types of defects responsible for layer distortion are identified. The opposite distortion within the layer is attributed to the inequality of the defect flux from the inner to interface-affected region due to the difference in migration energy barriers of the point defects. Moreover, the interface sink efficiency (defect annihilation) is determined for Zr/Nb as an illustration which provides a strategy for designing new derivate structures of multilayers with high radiation damage resistance. (c) 2022 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved. | |||||||||||||||
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| Record 262 of 349 | ||||||
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| Author(s): Arzt, M (Arzt, Matthias); Deschamps, J (Deschamps, Joran); Schmied, C (Schmied, Christopher); Pietzsch, T (Pietzsch, Tobias); Schmidt, D (Schmidt, Deborah); Tomancak, P (Tomancak, Pavel); Haase, R (Haase, Robert); Jug, F (Jug, Florian) | ||||||
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| Abstract: We present LABKIT, a user-friendly Fiji plugin for the segmentation of microscopy image data. It offers easy to use manual and automated image segmentation routines that can be rapidly applied to single- and multi-channel images as well as to timelapse movies in 2D or 3D. LABKIT is specifically designed to work efficiently on big image data and enables users of consumer laptops to conveniently work with multiple-terabyte images. This efficiency is achieved by using ImgLib2 and BigDataViewer as well as a memory efficient and fast implementation of the random forest based pixel classification algorithm as the foundation of our software. Optionally we harness the power of graphics processing units (GPU) to gain additional runtime performance. LABKIT is easy to install on virtually all laptops and workstations. Additionally, LABKIT is compatible with high performance computing (HPC) clusters for distributed processing of big image data. The ability to use pixel classifiers trained in LABKIT via the ImageJ macro language enables our users to integrate this functionality as a processing step in automated image processing workflows. Finally, LABKIT comes with rich online resources such as tutorials and examples that will help users to familiarize themselves with available features and how to best use LABKIT in a number of practical real-world use-cases. | ||||||
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| Record 263 of 349 | |||||||||||||||||||||
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| Author(s): Dobesova, L (Dobesova, Lucie); Gier, T (Gier, Theresa); Kopecna, O (Kopecna, Olga); Pagacova, E (Pagacova, Eva); Vicar, T (Vicar, Tomas); Bestvater, F (Bestvater, Felix); Toufar, J (Toufar, Jiri); Bacikova, A (Bacikova, Alena); Kopel, P (Kopel, Pavel); Fedr, R (Fedr, Radek); Hildenbrand, G (Hildenbrand, Georg); Falkova, I (Falkova, Iva); Falk, M (Falk, Martin); Hausmann, M (Hausmann, Michael) | |||||||||||||||||||||
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| Abstract: (1) Background: In oncology research, a long-standing discussion exists about pros and cons of metal nanoparticle-enhanced radiotherapy and real mechanisms behind the tumor cell response to irradiation (IR) in presence of gold nanoparticles (GNPs). A better understanding of this response is, however, necessary to develop more efficient and safety nanoparticle (NP) types designed to disturb specific processes in tumor cells. (2) Aims and Methods: We combined 3D confocal microscopy and super-resolution single molecule localization microscopy (SMLM) to analyze, at the multiscale, the early and late effects of 10 nm-GNPs on DNA double strand break (DSB) induction and repair in tumor cells exposed to different doses of photonic low-LET (linear energy transfer) radiation. The results were correlated to different aspects of short and long-term cell viability. SkBr3 breast cancer cells (selected for the highest incidence of this cancer type among all cancers in women, and because most breast tumors are treated with IR) were incubated with low concentrations of GNPs and irradiated with Co-60 gamma-rays or 6 MV X-rays. In numerous post-irradiation (PI) times, ranging from 0.5 to 24 h PI, the cells were spatially (3D) fixed and labeled with specific antibodies against gamma H2AX, 53BP1 and H3K9me3. The extent of DSB induction, multi-parametric micro- and nano-morphology of gamma H2AX and 53BP1 repair foci, DSB repair kinetics, persistence of unrepaired DSBs, nanoscale clustering of gamma H2AX and nanoscale (hetero)chromatin re-organization were measured by means of the mentioned microscopy techniques in dependence of radiation dose and GNP concentration. (3) Results: The number of gamma H2AX/53BP1 signals increased after IR and an additional increase was observed in GNP-treated (GNP(+)) cells compared to untreated controls. However, this phenomenon reflected slight expansion of the G2-phase cell subpopulation in irradiated GNP(+) specimens instead of enhanced DNA damage induction by GNPs. This statement is further supported by some micro- and nano-morphological parameters of gamma H2AX/53BP1 foci, which slightly differed for cells irradiated in absence or presence of GNPs. At the nanoscale, Ripley's distance frequency analysis of SMLM signal coordinate matrices also revealed relaxation of heterochromatin (H3K9me3) clusters upon IR. These changes were more prominent in presence of GNPs. The slight expansion of radiosensitive G2 cells correlated with mostly insignificant but systematic decrease in post-irradiation survival of GNP(+) cells. Interestingly, low GNP concentrations accelerated DSB repair kinetics; however, the numbers of persistent gamma H2AX/53BP1 repair foci were slightly increased in GNP(+) cells. (4) Conclusions: Low concentrations of 10-nm GNPs enhanced the G2/M cell cycle arrest and the proportion of radiosensitive G2 cells, but not the extent of DNA damage induction. GNPs also accelerated DSB repair kinetics and slightly increased presence of unrepaired gamma H2AX/53BP1 foci at 24 h PI. GNP-mediated cell effects correlated with slight radiosensitization of GNP(+) specimens, significant only for the highest radiation dose tested (4 Gy). | |||||||||||||||||||||
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| Record 264 of 349 | ||||||||||||
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| Author(s): Simonova, Z (Simonova, Zuzana); Krbeckova, V (Krbeckova, Veronika); Vilamova, Z (Vilamova, Zuzana); Dobrocka, E (Dobrocka, Edmund); Klejdus, B (Klejdus, Borivoj); Cieslar, M (Cieslar, Miroslav); Svoboda, L (Svoboda, Ladislav); Bednar, J (Bednar, Jiri); Dvorsky, R (Dvorsky, Richard); Seidlerova, J (Seidlerova, Jana) | ||||||||||||
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| Abstract: A wide range of methods can be used for nature-inspired metallic nanoparticle (NP) synthesis. These syntheses, however, are ongoing in the presence of diverse mixtures of different chemical compounds, and all or only a few of these contribute to resultant particle properties. Herein, the linden (Tilia sp.) inflorescence leachate and pure citric and protocatechuic acids were chosen for Ag-AgCl nanoparticle (NP) synthesis, and the resultant particles were then compared. We focused on the following four issues: (1) preparation of Ag-AgCl NPs using the Tilia sp.-based phytosynthetic protocol, (2) analytical determination of the common phenolic, nonphenolic, and inorganic profiles of three Tilia sp. types from different harvesting locations, (3) preparation of Ag-AgCl NPs using a mixture of citric and protocatechuic acids based on chromatographic evaluation, and (4) comparison of Tilia-based and organic acid-based syntheses. Our research confirms that the Tilia organic and inorganic profiles in biomasses are influenced by the harvesting location, and the three sites influenced both the morphology and final NP size. Our processing method was uniform, and this enabled great Ag-AgCl NP reproducibility for each specific biomass. We were then able to prove that the simplified organic acid-based synthesis produced even smaller NPs than Tilia-based synthesis. These findings provide better understanding of the significant influence on NP final properties resulting from other organic acids contained in the linden. | ||||||||||||
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| Record 265 of 349 | |||||||||
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| Author(s): Zhang, WD (Zhang, Wenda); Dovciak, M (Dovciak, Michal); Bursa, M (Bursa, Michal); Karas, V (Karas, Vladimir); Matt, G (Matt, Giorgio); Ursini, F (Ursini, Francesco) | |||||||||
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| Abstract: High-sensitivity X-ray polarimetric observations of black hole X-ray binaries, which will soon become available with the launches of space-borne X-ray observatories with sensitive X-ray polarimeters, will be able to put independent constraints on the black hole as well as the accretion flow, and possibly break degeneracies that cannot be resolved by spectral/timing observations alone. In this work, we perform a series of general relativistic Monte Carlo radiative transfer simulations to study the expected polarization properties of X-ray radiation emerging from lamp-post coronae in black hole X-ray binaries. We find that the polarization degree of the coronal emission of black hole X-ray binaries is sensitive to the spin of the black hole, the height of the corona, and the dynamics of the corona. | |||||||||
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| Record 266 of 349 | ||||||
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| Author(s): Fiedler, D (Fiedler, David); Certicky, M (Certicky, Michal); Alonso-Mora, J (Alonso-Mora, Javier); Pechoucek, M (Pechoucek, Michal); Cap, M (Cap, Michal) | ||||||
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| Abstract: Mobility-on-demand (MoD) systems consist of a fleet of shared vehicles that can be hailed for one-way point-to-point trips. The total distance driven by the vehicles and the fleet size can be reduced by employing ridesharing, i.e., by assigning multiple passengers to one vehicle. However, finding the optimal passenger-vehicle assignment in an MoD system is a hard combinatorial problem. In this work, we demonstrate how the VGA method, a recently proposed systematic method for ridesharing, can be used to compute the optimal passenger-vehicle assignments and corresponding vehicle routes in a massive-scale MoD system. In contrast to existing works, we solve all passenger-vehicle assignment problems to optimality, regularly dealing with instances containing thousands of vehicles and passengers. Moreover, to examine the impact of using optimal ridesharing assignments, we compare the performance of an MoD system that uses optimal assignments against an MoD system that uses assignments computed using insertion heuristic and against an MoD system that uses no ridesharing. We found that the system that uses optimal ridesharing assignments subject to the maximum travel delay of 4 minutes reduces the vehicle distance driven by 57% compared to an MoD system without ridesharing. Furthermore, we found that the optimal assignments result in a 20% reduction in vehicle distance driven and 5% lower average passenger travel delay compared to a system that uses insertion heuristic. | ||||||
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| Record 267 of 349 | |||||||||||||||
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| Author(s): Medvedev, N (Medvedev, Nikita); Akhmetov, F (Akhmetov, Fedor); Rymzhanov, RA (Rymzhanov, Ruslan A.); Voronkov, R (Voronkov, Roman); Volkov, AE (Volkov, Alexander E.) | |||||||||||||||
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| Abstract: The authors present a concurrent Monte Carlo (MC)-molecular dynamics (MD) approach to modeling matter response to excitation of its electronic system at nanometric scales. The two methods are combined on-the-fly at each time step in one code, TREKIS-4. The MC model describes the arrival of irradiation (a photon, an electron, or a fast ion). It traces induced cascades of secondary electrons and holes, and their energy exchange with atoms due to scattering. The excited atomic system is simulated with an MD model. An efficient way is proposed to account for nonthermal effects in the electron-atom energy transfer in covalent materials via the conversion of the potential energy of the electronic ensemble into the kinetic energy of atoms. Such a combined MC-MD approach enables a time-resolved tracing of the excitation kinetics of both, the electronic and atomic systems, and their simultaneous response to a deposited dose. As a proof-of-principle, it is shown that the proposed method describes atomic dynamics after X-ray irradiation in good agreement with tight-binding MD. The model also allows gaining insights into the atomic system behavior during the energy deposition from a nonequilibrium electronic system excited by an ion impact. | |||||||||||||||
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| Record 268 of 349 | ||||||||||||
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| Author(s): Simsova, M (Simsova nee Zamecnikova, Martina); Gustafsson, M (Gustafsson, Magnus); Soldan, P (Soldan, Pavel) | ||||||||||||
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| Abstract: Collisions of sodium and chlorine atoms and of their ions are studied within the diabatic two-state picture at energies below and above the ionic threshold with focus on the processes of radiative association, chemiionisation, and mutual neutralisation. The radiative-association cross sections as functions of collision energy are calculated up to 4.6 eV in the case of neutral atoms and up to 3.12 eV in the case of ions. The non-radiative charge-exchange cross sections as functions of collision energy are calculated up to 12 eV for chemiionisation and up to 10.52 eV for mutual neutralisation. The corresponding radiative-association rate coefficients are then determined up to 5300 K for the radiative association of neutral atoms and non-radiative charge-exchange and up to 3615 K for the radiative association of ions. Contribution of many Fano-Feshbach-type resonances is included to the rate coefficient of neutral-atom radiative association. The chemiionisation rate coefficients were calculated from 1000 K to 5300 K. The process of mutual neutralisation exhibits the largest cross sections and also the largest rate coefficients with values around 10(-9) cm(3) s(-1) at all calculated temperatures, 120-5300 K. | ||||||||||||
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| Record 269 of 349 | |||||||||||||||
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| Author(s): Correa, CA (Correa, Cinthia Antunes); Poupon, M (Poupon, Morgane); Petricek, V (Petricek, Vaclav); Tarasenko, R (Tarasenko, Robert); Mihalik, M (Mihalik, Matus); Legut, D (Legut, Dominik); Wdowik, UD (Wdowik, Urszula D.); Orendacova, A (Orendacova, Alzbeta) | |||||||||||||||
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| Abstract: Cu(tn)Cl-2 belongs to fa m i l y of molecular magnets with low-dimensional magnetism mediated by hydrogen bonds. Here, the X-ray diffraction, electron paramagnetic resonance, specific heat measurements, and ab initio calculations performed within the framework of density functional theory have been employed to investigate the structural phase transition in Cu(tn)Cl-2. Satellite reflections in the X-ray diffraction patter n from single crystals, visible anomaly in the specific heat measured in a zero magnetic field, rapid growth of the EPR resonance line width, along with the increase of the g-factors in the vici n i t y of 160 K are indicative of the structural phase transition in Cu(tn)Cl-2. Our results reveal that this system undergoes transition from a disordered structure of the Pnma symmetry to a modulated structure with the Pnma(0 beta 0)s00 superspace group. The transition is reversible and driven by the reorientation of the diaminopropane ligands. The density functional theory studies support results of our specific heat measurements. | |||||||||||||||
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| Author(s): Hruz, M (Hruz, Marek); Gruber, I (Gruber, Ivan); Kanis, J (Kanis, Jakub); Bohacek, M (Bohacek, Matyas); Hlavac, M (Hlavac, Miroslav); Krnoul, Z (Krnoul, Zdenek) | |||||||||||||||||||||
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| Abstract: In this paper, we dive into sign language recognition, focusing on the recognition of isolated signs. The task is defined as a classification problem, where a sequence of frames (i.e., images) is recognized as one of the given sign language glosses. We analyze two appearance-based approaches, I3D and TimeSformer, and one pose-based approach, SPOTER. The appearance-based approaches are trained on a few different data modalities, whereas the performance of SPOTER is evaluated on different types of preprocessing. All the methods are tested on two publicly available datasets: AUTSL and WLASL300. We experiment with ensemble techniques to achieve new state-of-the-art results of 73.84% accuracy on the WLASL300 dataset by using the CMA-ES optimization method to find the best ensemble weight parameters. Furthermore, we present an ensembling technique based on the Transformer model, which we call Neural Ensembler. | |||||||||||||||||||||
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| Record 271 of 349 | ||||||||||||
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| Author(s): Nemirovich, T (Nemirovich, Tatiana); Kostal, V (Kostal, Vojtech); Copko, J (Copko, Jakub); Martinek, T (Martinek, Tomas); Slanina, T (Slanina, Tomas); Jungwirth, P (Jungwirth, Pavel) | ||||||||||||
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| Abstract: Birch reduction is a time-proven way to hydrogenate aromatic hydrocarbons (such as benzene), which relies on the reducing power of electrons released from alkali metals into liquid ammonia. We have succeeded to characterize the key intermediates of the Birch reduction process -the solvated electron and dielectron and the benzene radical anion -using cyclic voltammetry and photoelectron spectroscopy, aided by electronic structure calculations. In this way, we not only quantify the electron binding energies of these species, which are decisive for the mechanism of the reaction, but also use Birch reduction as a case study to directly connect the two seemingly unrelated experimental techniques. | ||||||||||||
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| Record 272 of 349 |
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| Author(s): Lehecka, J (Lehecka, Jan); Psutka, JV (Psutka, Josef, V); Psutka, J (Psutka, Josef) |
| Edited by: Sojka P; Horak A; Kopecek I; Pala K |
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| Abstract: Czech is a very specific language due to its large differences between the formal and the colloquial form of speech. While the formal (written) form is used mainly in official documents, literature, and public speeches, the colloquial (spoken) form is used widely among people in casual speeches. This gap introduces serious problems for ASR systems, especially when training or evaluating ASR models on datasets containing a lot of colloquial speech, such as the MALACH project. In this paper, we are addressing this problem in the light of a new paradigm in end-to-end ASR systems - recently introduced self-supervised audio Transformers. Specifically, we are investigating the influence of colloquial speech on the performance of Wav2Vec 2.0 models and their ability to transcribe colloquial speech directly into formal transcripts. We are presenting results with both formal and colloquial forms in the training transcripts, language models, and evaluation transcripts. |
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| Conference Sponsors: Masaryk Univ, Fac Informat, Univ W Bohemia, Fac Appl Sci, Int Speech Commun Assoc, Lex Comp Ltd, IBMC Eska Republika Spol s r o, Amazon Alexa |
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| ISBN: 978-3-031-16270-1; 978-3-031-16269-5 |
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| Author(s): Kaschner, M (Kaschner, Martin); Kafka, V (Kafka, Vladimir); Marcisovsky, M (Marcisovsky, Michal); Stanek, P (Stanek, Pavel); Svihra, P (Svihra, Peter) | ||||||
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| Abstract: Radon detectors based on an electrostatic collection of polonium and detection of its alpha decay are a popular choice for the measurement of radon activity. Due to the nature of Rn-222 decays, 88% of radon progeny have a positive charge, thus enabling their collection on an electrode. A simulation software focused on the drift and diffusion of ions in an electric field has been developed, providing a tool to study and characterise such detectors. It has been found that one such device achieves only 44% collection efficiency, caused by the loss of a large fraction of the ions before reaching the collection diode. An improvement of the design is therefore proposed, changing the placement of the sensor resulted in an simulated increase of the collection efficiency up to 93%. Preliminary measurements performed using prototypes of these detectors confirm the results of the simulations. | ||||||
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| Author(s): Zenisek, J (Zenisek, Jaroslav); Ondracka, P (Ondracka, Pavel); Cencnal, J (Cencnal, Jan); Soucek, P (Soucek, Pavel); Holec, D (Holec, David); Vasina, P (Vasina, Petr) | |||||||||||||||||||||
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| Abstract: In this paper, we critically evaluate the applicability of the procedure proposed in [Mirzaei et al., Surf. Coat. Technol. 358 (2019) 843-849] which is based on the fitting of the XPS spectrum of amorphous W-B-C material into three components with fixed peak positions to get the relative amount of W-W, W-B, and W-C bonds. We show that W-W bonds substantially influence positions of the peak components. We have verified this assumption by generating a set of models of amorphous W-B-C with different compositions (W:B:C ratio) and calculating the W 4f core electron binding energies employing ab initio methods. This enabled us to formulate the relationship between the W 4f electron binding energies (BE) and the local atomic environments of W atoms. Our analysis confirms the expected W 4f chemical shifts in W-B-C caused by W-B and W-C bonds and reveals that W-W bonds shift the W 4f electronic states in the same direction as W-B bonds, which has substantial implications for the correct interpretation of the measured XPS spectra. | |||||||||||||||||||||
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| Record 275 of 349 | ||||||
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| Author(s): Olha, J (Olha, Jaroslav); Slaninakova, T (Slaninakova, Terezia); Gendiar, M (Gendiar, Martin); Antol, M (Antol, Matej); Dohnal, V (Dohnal, Vlastislav) | ||||||
| Edited by: Skopal T; Falchi F; Lokoc J; Sapino ML; Bartolini I; Patella M | ||||||
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Abstract:
Despite the constant evolution of similarity searching research, it continues to face challenges stemming from the complexity of the data, such as the curse of dimensionality and computationally expensive distance functions. Various machine learning techniques have proven capable of replacing elaborate mathematical models with simple linear functions, often gaining speed and simplicity at the cost of formal guarantees of accuracy and correctness of querying.
The authors explore the potential of this research trend by presenting a lightweight solution for the complex problem of 3D protein structure search. The solution consists of three steps - (i) transformation of 3D protein structural information into very compact vectors, (ii) use of a probabilistic model to group these vectors and respond to queries by returning a given number of similar objects, and (iii) a final filtering step which applies basic vector distance functions to refine the result. |
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| ISBN: 978-3-031-17849-8; 978-3-031-17848-1 |
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| Author(s): Konecna, KP (Konecna, Klara Prikrylova); Kilar, A (Kilar, Agata); Kovacikova, P (Kovacikova, Petra); Fajkus, J (Fajkus, Jiri); Sykorova, E (Sykorova, Eva); Fojtova, M (Fojtova, Miloslava) | ||||||
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| Abstract: ARM was identified previously as an interaction partner of the telomerase protein subunit (TERT) in Arabidopsis thaliana. To investigate the interconnection between ARM and telomerase and to identify ARM cellular functions, we analyzed a set of arm mutant lines and arm/tert double mutants. Telomere length was not affected in arm single mutant plants, in contrast to double mutants. In the second generation of homozygous arm-1/tert double mutants following the heterozygous state during the double mutant construction, telomeres shortened dramat-ically, even below levels in tert plants displaying severe morphological defects. Intriguingly, homozygous arm-1/ tert double mutants with short telomeres grew without obvious phenotypic changes for next two generations. Then, in agreement with the onset of phenotypic changes in tert, morphological defects were timed to the 5th arm-1/tert homozygous generation. RNAseq analyses of arm-1/tert and respective single mutants displayed markedly overlapping sets of differentially expressed genes in arm-1/tert double mutant and arm-1 single mutant lines, indicating a dominant effect of the ARM mutation. RNAseq data further implied ARM involvement in circadian rhythms, responses to drugs and to biotic and abiotic stimuli. In agreement with it, we observed sensitivity of arm-1 single mutant to the heat stress during germination. Altogether, our results suggest ARM involvement in crucial cellular processes without evidencing its role in the telomerase canonical function. | ||||||
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| Record 277 of 349 | ||||||||||||
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| Author(s): Gustafsson, DIR (Gustafsson, Daniel R.); Najer, T (Najer, Tomas); Zou, FS (Zou, Fasheng); Bush, SE (Bush, Sarah E.) | ||||||||||||
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| Abstract: The ischnoceran chewing lice known from bulbuls are discussed and revised, and 18 new species are described. These are: Brueelia celer sp. nov. from Pycnonotus cafer bengalensis Blyth, 1845 and Pycnonotus cafer primrosei Deignan, 1949; Brueelia colindalei sp. nov. from Hemixos castanonotus canipennis Seebohm, 1890; Brueelia doisuthepensis sp. nov. from Alophoixus ochraceus ochraceus (Moore, 1858); Brueelia galeata sp. nov. from Alophoixus pallidus henrici (Oustalet, 1896); Brueelia hermetica sp. nov. from Pycnonotus barbatus layardi Gurney, 1879; Brueelia leiae sp. nov. from Alophoixus flaveolus burmanicus (Oates, 1899); Brueelia robertrankini sp. nov. from Pycnonotus jocosus jocosus (Linnaeus, 1758) and Pycnonotus jocosus pattani Deignan, 1948; Brueelia yunnanensis sp. nov. from Ixos mcclellandii similis (Rothschild, 1921); Guimaraesiella brunneomarginata sp. nov. from Pycnonotus goiaver samarensis Rand & Rabor, 1960 and Pycnonotus goiaver personatus Hume, 1873; Guimaraesiella caligogularis sp. nov. from Pycnonotus plumosus plumosus Blyth, 1845 and Alophoixus bres tephrogenys (Jardine & Selby, 1833); Guimaraesiella cinnamomea sp. nov. from Iole propinqua propinqua (Oustalet, 1903) and Iole viridescens cinnamomeoventris Baker, 1917; Guimaraesiella ixi sp. nov. from Ixos mcclellandii peracensis (Hartert & Butler, 1898); Guimaraesiella lorica sp. nov. from Hypsipetes leucocephalus nigerrimus Gould, 1863; Guimaraesiella mayoensis sp. nov. from Hypsipetes everetti everetti (Tweeddale, 1877); Guimaraesiella phlaoalopha sp. nov. from Alophoixus pallidus henrici (Oustalet, 1896); Philopteroides holosternus sp. nov. from Pycnonotus goiavier goiavier (Scopoli, 1786); Philopteroides longiclypeatus sp. nov. from Hypsipetes everretti samarensis Rand & Rabor, 1959; Philopteroides haerixos sp. nov. from Ixos mcclellandii holtii (Swinhoe, 1861) and Alophoixus pallidus henrici (Oustalet, 1896). The following new host records are provided: Hemixos castanonotus canipennis Seebohm, 1890, for Guimaraesiella flavala (Najer & Sychra in Najer et al., 2012); Pycnonotus blanfordi conradi (Finsch in Finsch & Conrad, 1873) for Philopteroides cucphuongensis Mey, 2004. Philopterus cucphuongensis is tentatively redescribed and illustrated based on specimens from a non-type host species. The species descriptions of the following species are amended slightly, based on re-examinations of type specimens: Brueelia alophoixi Sychra in Sychra et al., 2009; Guimaraesiella cucphuongensis (Najer & Sychra in Najer et al., 2012); Guimaraesiella flavala (Najer & Sychra in Najer et al., 2012). We propose to move Philopterus hiyodori Uchida, 1949, to the genus Craspedorrhynchus Keler, 1938. The species Sturnidoecus acutifrons (Uchida, 1949) and Penenirmus guldum (Ansari, 1955) are considered species inquirenda. An updated checklist of ischnoceran lice known from bulbuls is provided, as well as a key to all ischnoceran species known from bulbuls. | ||||||||||||
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| Record 278 of 349 | ||||||
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| Author(s): Lunkad, R (Lunkad, Raju); da Silva, FLB (Barroso da Silva, Fernando L.); Kosovan, P (Kosovan, Peter) | ||||||
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| Abstract: The mechanism of protein-polyelectrolyte complexation on the wrong side of the isoelectric point has long puzzled researchers. Two alternative explanations have been proposed in the literature: (a) the charge-patch (CP) mechanism, based on the inhomogeneous distribution of charges on the protein, and (b) the charge-regulation (CR) mechanism, based on the variable charge of weak acid and base groups, which may invert the protein charge in the presence of another highly charged object. To discern these two mechanisms, we simulated artificially constructed short peptides, containing acidic and basic residues, arranged in a blocklike or alternating sequence. Our simulations of these peptides, interacting with polyelectrolytes, showed that charge patch and charge regulation alone can both lead to adsorption on the wrong side of the pI value. Their simultaneous presence enhances adsorption, whereas their absence prevents adsorption. Our simulation results were rationalized by following the variation of the charge regulation capacity and dipole moments of these peptides with the pH. Specifically for lysozyme, we found that charge patch prevails at physiological pH, whereas charge regulation prevails near the pI, thereby explaining seemingly contradicting conclusions in the literature. By applying the same approach to other proteins, we developed a general framework for assessing the role of the CP and CR mechanisms in existing case studies and for predicting how various proteins interact with polyelectrolytes at different pH values. | ||||||
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| Record 279 of 349 | |||||||||
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| Author(s): Michal, P (Michal, Pavel); Kapitan, J (Kapitan, Josef); Kessler, J (Kessler, Jiri); Bour, P (Bour, Petr) | |||||||||
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| Abstract: Vibrational frequencies of modes involving intermolecular motions in liquids are relatively small, in the Raman scattering close to the excitation frequency, and the bands may merge into a diverging uninterpretable signal. Raman optical activity (ROA) spectral shapes in this region, however, are structured more and may better reflect the nature of the studied systems. To understand the origin of the signal and its relation to the molecules, ROA spectra of six chiral neat liquids are recorded and analyzed on the basis of molecular dynamics and density functional theory computations. The theory of Raman scattering of liquids is discussed and adapted for modeling based on clusters and periodic boundary conditions. A plain cluster approach is compared to a crystal-like model. The results show that the low-frequency optical activity can be reliably modeled and related to the structure. However, momentary arrangement of molecules leads to large variations of optical activity, and a relatively large number of geometries need to be averaged for accurate simulations. The intermolecular modes are intertwined with intramolecular ones and start to dominate as the frequency goes down. The low-frequency ROA signal thus reflects the chemical composition and coupled with the modeling it provides a welcome means to study the structure and interactions of chiral liquids. | |||||||||
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| Record 280 of 349 |
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| Author(s): Moravec, P (Moravec, Prokop); Zavadil, L (Zavadil, Lukas); Starecek, J (Starecek, Jakub); Kratky, T (Kratky, Tomas); Danek, T (Danek, Tomas); Abrahamek, P (Abrahamek, Petr) |
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| Abstract: Partload regimes of all types of centrifugal pumps are strongly and unfavorably affected by an influence of an inlet recirculation. This negative phenomenon usually occurs at pump suctions, when a circumferential velocity component of the fluid flow (derived from a rotational speed of a rotor) is dominant over an axial velocity component. Such physical effect goes hand in hand with a creation of a pump-head instability, a decrease of an overall efficiency, an excessive noise and pressure pulsations and even a possible cavitation formation. The introduced technical problem was tested/examined for a radial centrifugal pump Ns375 with a volute (spiral casing) and an axial intake domain with two potential countermeasures. Both, a physical experiment and transient numerical simulations were employed and compared on crucial levels. |
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| Record 281 of 349 |
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| Author(s): Breuer, JP (Breuer, Jean-Paul); Galgoczi, G (Galgoczi, Gabor); Fioretti, V (Fioretti, Valentina); Zlamal, J (Zlamal, Jakub); Liska, P (Liska, Petr); Werner, N (Werner, Norbert); Santin, G (Santin, Giovanni); Boudin, N (Boudin, Nathalie); Ferreira, I (Ferreira, Ivo); Guainazzi, M (Guainazzi, Matteo); von Kienlin, A (von Kienlin, Andreas); Lotti, S (Lotti, Simone); Mineo, T (Mineo, Teresa); Molendi, S (Molendi, Silvano); Perinati, E (Perinati, Emanuele) |
| Edited by: DenHerder JWA; Nikzad S; Nakazawa K |
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| Abstract: The last generation of X-ray focusing telescopes operating outside the Earth's radiation belt discovered that optics were able to focus not only astrophysical X-ray photons, but also low-energy heliophysical protons entering the Field of View (FOV). This "soft proton" contamination affects around 40% of the observation time of XMMNewton. The ATHENA Charged Particle Diverter (CPD) was designed to use magnetic fields to move these soft protons away from the FOV of the detectors, separating the background-contributing ions in the focused beam from the photons of interest. These magnetically deflected protons can hit other parts of the payload and scatter back to the focal plane instruments. Evaluating the impact of this secondary scattering with accurate simulations is essential for the CPD scientific assessment. However, while Geant4 simulations of grazing soft proton scattering on X-ray mirrors have been recently validated, the scattering on the unpolished surfaces of the payload (e.g. the baffle or the diverter itself) is still to be verified with experimental results. Moreover, the roughness structure can affect the energy and angle of the scattered protons, with a scattering efficiency depending on the specific target volume. Using Atomic Force Microscopy to take nanometer-scale surface roughness measurements from different materials and coating samples, we use Geant4 together with the CADMesh library to shoot protons at these very detailed surface roughness models to understand the effects of different material surface roughnesses, coatings, and compositions on proton energy deposition and scattering angles. We compare and validate the simulation results with laboratory experiments, and propose a framework for future proton scattering experiments. |
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| Conference Sponsors: SPIE |
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| ISBN: 978-1-5106-5344-3; 978-1-5106-5343-6 |
| Record 282 of 349 |
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| Author(s): Smith, DJB (Smith, D. J. B.); Krause, MG (Krause, M. G.); Hardcastle, MJ (Hardcastle, M. J.); Drake, AB (Drake, A. B.) |
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| Abstract: We report new observations of 'Hanny's Voorwerp' (hereafter HV) taken from the second data release of the LOFAR Two-metre Sky Survey (LoTSS). HV is a highly-ionized region in the environs of the galaxy IC2497, first discovered by the Galaxy Zoo project. The new 150 MHz observations are considered in the context of existing multi frequency radio data and archival narrow-band imaging from the Hubble Space Telescope, centred on the [O iii] emission line. The combined sensitivity and spatial resolution of the LoTSS data - which far exceed what was previously available at radio frequencies - reveal clear evidence for large-scale extended emission emanating from the nucleus of IC2497. The radio jet appears to have punched a hole in the neutral gas halo, in a region co-located with HV. The new 150 MHz data, alongside newly-processed archival 1.64 GHz eVLA data, reveal that the extended emission has a steep spectrum, implying an age >10(8) yr. The jet supplying the extended 150 MHz structure must have 'turned off' long before the change in X-ray luminosity reported in recent works. In this picture, a combination of jet activity and the influence of the radiatively efficient active galactic nucleus are responsible for the unusual appearance of HV. |
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| Author(s): Grybchuk, D (Grybchuk, Danyil); Prochazkova, M (Prochazkova, Michaela); Fuzik, T (Fuzik, Tibor); Konovalovas, A (Konovalovas, Aleksandras); Serva, S (Serva, Saulius); Yurchenko, V (Yurchenko, Vyacheslav); Plevka, P (Plevka, Pavel) | |||||||||||||||
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Abstract:
L-BC virus persists in the budding yeast Saccharomyces cerevisiae, whereas other viruses from the family Totiviridae infect a diverse group of organisms including protists, fungi, arthropods, and vertebrates. The presence of totiviruses alters the fitness of the host organisms, for example, by maintaining the killer system in yeast or increasing the virulence of Leishmania guyanensis. Despite the importance of totiviruses for their host survival, there is limited information about Totivirus structure and assembly. Here we used cryo-electron microscopy to determine the structure of L-BC virus to a resolution of 2.9 angstrom. The L-BC capsid is organized with icosahedral symmetry, with each asymmetric unit composed of two copies of the capsid protein. Decamers of capsid proteins are stabilized by domain swapping of the C-termini of subunits located around icosahedral fivefold axes. We show that capsids of 9% of particles in a purified L-BC sample were open and lacked one decamer of capsid proteins. The existence of the open particles together with domain swapping within a decamer provides evidence that Totiviridae capsids assemble from the decamers of capsid proteins. Furthermore, the open particles may be assembly intermediates that are prepared for the incorporation of the virus (+) strand RNA.
A 2.9 angstrom resolution structure of the L-BC virus provides insight into the contacts between capsid proteins and the mechanism of capsid assembly. |
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| Record 284 of 349 |
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| Author(s): Krejci, J (Krejci, Jan); Straka, O (Straka, Ondrej); Vyskocil, J (Vyskocil, Jiri); Jirik, M (Jirik, Miroslav); Dahmen, U (Dahmen, Uta) |
| Book Group Author(s): IEEE |
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| Abstract: This paper deals with the problem of tracking multiple objects, in which each object is known to belong to a unique class. We follow the tracking by detection paradigm and assume that the object detector provides scores in addition to each detection. The problem is tackled as simultaneous classification and tracking using random finite sets. Inspired by the multi-Bernoulli mixture (MBM) filter, we propose a solution to the problem by modifying the target birth process. To simplify the implementation and to mitigate the computational costs, we develop tractable solutions with linear complexity. The algorithms are subsequently used for visual tracking of surgical instruments. As a by-product, we derive the prediction step of the Bernoulli filter using the probability generating functionals (PGFLs). |
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| Conference Sponsors: William Demant Fdn, SAAB, Mitsubishi Elect Res Lab, Ericsson, Metron, Verizon, Nordic Inertial, UMS Skeldar, ACTIA Nordic, Arriver, NIRA Dynam, Int Soc Informat Fus, IEEE AESS, Linkoping, ACTIA, Real Labs Res |
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| Author(s): Krupova, M (Krupova, Monika); Leszczenko, P (Leszczenko, Patrycja); Sierka, E (Sierka, Ewa); Hamplova, SE (Emma Hamplova, Sara); Pelc, R (Pelc, Radek); Andrushchenko, V (Andrushchenko, Valery) | ||||||||||||||||||
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| Abstract: Vibrational circular dichroism (VCD) spectroscopy has been widely used to study (bio)molecules in solution. However, its solid-state applications have been restricted due to experimental limitations and artifacts. Having overcome some of them, the first VCD study of nucleoside crystals is now presented. A two-orders-of-magnitude enhancement of VCD signal was observed due to high molecular order in the crystals and resulting supramolecular chirality. This allowed to obtain high-quality VCD spectra within minutes using minute amounts of samples. The VCD technique is extremely sensitive in detecting changes in a crystal order and is able to distinguish different hydration states of crystals. This elevates it to a new level, as a fast and efficient tool to study chiral crystalline samples. This study demonstrates that VCD is capable of near-instantaneous detection of hydration polymorphs and crystal degradation, which is of substantial interest in pharmaceutical industry (quality and stability control). | ||||||||||||||||||
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| Record 286 of 349 | |||||||||||||||
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| Author(s): Nikitin, D (Nikitin, Dmitri); Mican, J (Mican, Jan); Toul, M (Toul, Martin); Bednar, D (Bednar, David); Peskova, M (Peskova, Michaela); Kittova, P (Kittova, Patricia); Thalerova, S (Thalerova, Sandra); Vitecek, J (Vitecek, Jan); Damborsky, J (Damborsky, Jiri); Mikulik, R (Mikulik, Robert); Fleishman, SJ (Fleishman, Sarel J.); Prokop, Z (Prokop, Zbynek); Marek, M (Marek, Martin) | |||||||||||||||
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| Abstract: Cardio-and cerebrovascular diseases are leading causes of death and disability, resulting in one of the highest socio-economic burdens of any disease type. The discovery of bacterial and human plasminogen activators and their use as thrombolytic drugs have revolutionized treatment of these pathologies. Fibrin specific agents have an advantage over non-specific factors because of lower rates of deleterious side effects. Specifically, staphylokinase (SAK) is a pharmacologically attractive indirect plasminogen activator protein of bacterial origin that forms stoichiometric noncovalent complexes with plasmin, promoting the conversion of plasminogen into plasmin. Here we report a computer-assisted re-design of the molecular surface of SAK to increase its affinity for plasmin. A set of computationally designed SAK mutants was produced recombinantly and biochemically characterized. Screening revealed a pharmacologically interesting SAK mutant with-7-fold enhanced affinity toward plasmin,-10-fold improved plasmin selectivity and moderately higher plasmin-generating efficiency in vitro. Collectively, the results obtained provide a framework for SAK engineering using computational affinity-design that could pave the way to next-generation of effective, highly selective, and less toxic thrombolytics.(c) 2022 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). | |||||||||||||||
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| Record 287 of 349 |
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| Author(s): Fedosov, VE (Fedosov, Vladimir E.); Shkurko, AV (Shkurko, Anna, V); Fedorova, AV (Fedorova, Alina, V); Ignatova, EA (Ignatova, Elena A.); Solovyeva, EN (Solovyeva, Evgeniya N.); Brinda, JC (Brinda, John C.); Ignatov, MS (Ignatov, Michael S.); Kucera, J (Kucera, Jan) |
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| Abstract: We present an integrative molecular and morphological study of subaquatic representatives of the genus Pseudohygrohypnum (Pylaisiaceae, Bryophyta), supplemented by distribution modelling of the revealed phylogenetic lineages. Phylogenetic analyses of nuclear and plastid datasets combined with the assemble species by automatic partitioning (ASAP) algorithm revealed eight distinct species within the traditionally circumscribed P. eugyrium and P. subeugyrium. These species are therefore yet another example of seemingly widely distributed taxa that harbour molecularly well-differentiated lineages with narrower distribution ranges. Studied accessions that were previously assigned to P. eugyrium form three dearly allopatric lineages, associated with temperate regions of Europe, eastern North America and eastern Asia. Remarkably, accessions falling under the current morphological concept of P. subeugyrium were shown to be even more diverse, containing five phylogenetic lineages. Three of these lineages occur under harsh Asian continental climates from cool-temperate to Arctic regions, while the remaining two, referred to P. subeugyrium s.str. and P. purpurascens, have more oceanic North Atlantic and East Asian distributions. Niche identity and similarity tests suggested no similarity in the distributions of the phylogenetically related lineages but revealed the identity of two East Asian species and the similarity of two pairs of unrelated species. A morphological survey confirmed the distinctness of all eight phylogenetic lineages, requiring the description of five new species. Pseudohygrohypnum appalachianum and P. orientale are described for North American and East Asian plants of P. eugyrium s.l., while P. sibiricum, P. subarcticum and P. neglectum are described for the three continental, predominantly Asian lineages of P. subeugyrium s.l. Our results highlight the importance of nontropical Asia as a center of bryophyte diversity. Phylogenic dating suggests that the diversification of subaquatic Pseudohygrohypnum lineages appeared in late Miocene, while mesophilous species of the genus split before Miocene cooling, in climatic conditions dose to those where the ancestor of Pseudohygrohypnum appeared. We speculate that radiation of the P. subeugyrium complex in temperate Asia might have been driven by progressive cooling, aridification, and increases in seasonality, temperature and humidity gradients. Our results parallel those of several integrative taxonomic studies of North Asian mosses, which have resulted in a number of newly revealed species. These include various endemics from continental areas of Asia suggesting that the so-called Rapoport's rule of low diversity and wide distribution range in subpolar regions might not be applicable to bryophytes. Rather, the strong climatic oscillations in these regions may have served as a driving force of speciation and niche divergence. |
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| Record 288 of 349 | ||||||
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| Author(s): Sokolova, M (Sokolova, Marina); Sestakova, H (Sestakova, Hana); Truksa, M (Truksa, Martin); Safarik, M (Safarik, Martin); Hadravova, R (Hadravova, Romana); Bour, P (Bour, Petr); Sebestik, J (Sebestik, Jaroslav) | ||||||
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| Abstract: Oxidative stress may cause extended tyrosine posttranslational modifications of peptides and proteins. The 3-nitro-L-tyrosine (Nit), which is typically formed, affects protein behavior during neurodegenerative processes, such as Alzheimer's and Parkinson's diseases. Such metabolic products may be conveniently detected at very low concentrations by surface enhanced Raman spectroscopy (SERS). Previously, we have explored the SERS detection of the Nit NO2 bending vibrational bands in a presence of hydrogen chloride (Niederhafner et al., Amino Acids 53:517-532, 2021, ibid). In this article, we describe performance of a new SERS substrate, "pink silver", synthesized photochemically. It provides SERS even without the HCl induction, and the acid further decreases the detection limit about 9 times. Strong SERS bands were observed in the asymmetric (1550-1475 cm(-1)) and symmetric (1360-1290 cm(-1)) NO stretching in the NO2 group. The bending vibration was relatively weak, but appeared stronger when HCl was added. The band assignments were supported by density functional theory modeling. | ||||||
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| Record 289 of 349 | ||||||
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| Author(s): Heger, T (Heger, Tomas); Zatloukal, M (Zatloukal, Marek); Kubala, M (Kubala, Martin); Strnad, M (Strnad, Miroslav); Gruz, J (Gruz, Jiri) | ||||||
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| Abstract: Members of the Viola genus play important roles in traditional Asian herbal medicine. This study investigates the ability of Viola odorata L. extracts to inhibit Na+,K+-ATPase, an essential animal enzyme responsible for membrane potential maintenance. The root extract of V. odorata strongly inhibited Na+,K+-ATPase, while leaf and seeds extracts were basically inactive. A UHPLC-QTOF-MS/MS metabolomic approach was used to identify the chemical principle of the root extract's activity, resulting in the detection of 35,292 features. Candidate active compounds were selected by correlating feature area with inhibitory activity in 14 isolated fractions. This yielded a set of 15 candidate compounds, of which 14 were preliminarily identified as procyanidins. Commercially available procyanidins (B1, B2, B3 and C1) were therefore purchased and their ability to inhibit Na+,K+-ATPase was investigated. Dimeric procyanidins B1, B2 and B3 were found to be inactive, but the trimeric procyanidin C1 strongly inhibited Na+,K+-ATPase with an IC50 of 4.5 mu M. This newly discovered inhibitor was docked into crystal structures mimicking the Na3E1 similar to P center dot ADP and K2E2 center dot P-i states to identify potential interaction sites within Na+,K+-ATPase. Possible binding mechanisms and the principle responsible for the observed root extract activity are discussed. | ||||||
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| Record 290 of 349 | ||||||||||||||||||||||||
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| Author(s): Tulpova, Z (Tulpova, Zuzana); Kovarik, A (Kovarik, Ales); Toegelova, H (Toegelova, Helena); Navratilova, P (Navratilova, Pavla); Kapustova, V (Kapustova, Veronika); Hribova, E (Hribova, Eva); Vrana, J (Vrana, Jan); Macas, J (Macas, Jiri); Dolezel, J (Dolezel, Jaroslav); Simkova, H (Simkova, Hana) | ||||||||||||||||||||||||
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| Abstract: Three out of four RNA components of ribosomes are encoded by 45S ribosomal DNA (rDNA) loci, which are organized as long head-to-tail tandem arrays of nearly identical units, spanning several megabases of sequence. Due to this structure, the rDNA loci are the major sources of gaps in genome assemblies, and gene copy number, sequence composition, and expression status of particular arrays remain elusive, especially in complex genomes harboring multiple loci. Here we conducted a multi-omics study to decipher the 45S rDNA loci in hexaploid bread wheat. Coupling chromosomal genomics with optical mapping, we reconstructed individual rDNA arrays, enabling locus-specific analyses of transcription activity and methylation status from RNA- and bisulfite-sequencing data. We estimated a total of 6,650 rDNA units in the bread wheat genome, with approximately 2,321, 3,910, 253, and 50 gene copies located in short arms of chromosomes 1B, 6B, 5D, and 1A, respectively. Only 1B and 6B loci contributed substantially to rRNA transcription at a roughly 2:1 ratio. The ratio varied among five tissues analyzed (embryo, coleoptile, root tip, primary leaf, mature leaf), being the highest (2.64:1) in mature leaf and lowest (1.72:1) in coleoptile. Cytosine methylation was considerably higher in CHG context in the silenced 5D locus as compared with the active 1B and 6B loci. In conclusion, a fine genomic organization and tissue-specific expression of rDNA loci were deciphered, for the first time, in a complex polyploid species. The results are discussed in the context of wheat evolution and transcription regulation. | ||||||||||||||||||||||||
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| Record 291 of 349 | ||||||
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| Author(s): Priban, P (Priban, Pavel); Smid, J (Smid, Jakub); Mistera, A (Mistera, Adam); Kral, P (Kral, Pavel) | ||||||
| Edited by: Sojka P; Horak A; Kopecek I; Pala K | ||||||
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| Abstract: This paper deals with cross-lingual sentiment analysis in Czech, English and French languages. We perform zero-shot cross-lingual classification using five linear transformations combined with LSTM and CNN based classifiers. We compare the performance of the individual transformations, and in addition, we confront the transformation-based approach with existing state-of-the-art BERT-like models. We show that the pre-trained embeddings from the target domain are crucial to improving the cross-lingual classification results, unlike in the monolingual classification, where the effect is not so distinctive. | ||||||
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| Conference Sponsors: Masaryk Univ, Fac Informat, Univ W Bohemia, Fac Appl Sci, Int Speech Commun Assoc, Lex Comp Ltd, IBMC Eska Republika Spol s r o, Amazon Alexa | ||||||
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| ISBN: 978-3-031-16270-1; 978-3-031-16269-5 |
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| Author(s): Hudecova, J (Hudecova, Jana); Kapitan, J (Kapitan, Josef); Dracinsky, M (Dracinsky, Martin); Michal, P (Michal, Pavel); Profant, V (Profant, Vaclav); Bour, P (Bour, Petr) | |||||||||||||||
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| Abstract: The histidine residue has an exceptional affinity for metals, but solution structure of its complexes are difficult to study. For zinc and nickel complexes, Raman and Raman optical activity (ROA) spectroscopy methods to investigate the link between spectral shapes and the geometry were used. The spectra were recorded and interpreted on the basis of ionic equilibria, molecular dynamics, ab initio molecular dynamics, and density functional theory. For zwitterionic histidine the dominant tautomer was determined by the decomposition of experimental spectra into calculated subspectra. An octahedral structure was found to prevail for the ZnHis(2) complex in solution, in contrast to a tetrahedral arrangement in the crystal phase. The solution geometry of NiHis(2) is more similar to the octahedral structure found by X-ray. The Raman and ROA structural determinations of metal complexes are dependent on extensive computations, but reveal unique information about the studied systems. | |||||||||||||||
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| Record 293 of 349 | ||||||
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| Author(s): Vymetal, J (Vymetal, Jiri); Vondrasek, J (Vondrasek, Jiri) | ||||||
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| Abstract: Computer simulations of biomolecules such as molecular dynamics often suffer from insufficient sampling. Due to limited computational resources, insufficient sampling prevents obtaining proper equilibrium distributions of observed properties. To deal with this problem, we proposed a simulation protocol for efficient resampling of collected off-equilibrium trajectories. These trajectories are utilized for the initial mapping of the conformational space, which is later properly resampled by the introduced Iterative Landmark-Based Umbrella Sampling (ILBUS) method. Reconstruction of static equilibrium properties is achieved by the multistate Bennett acceptance ratio (MBAR) method, which enables efficient use of simulated data. The ILBUS protocol is geometry-based and does not demand any additional collective variable or a dimensional-reduction technique. The only requirement is a set of suitably spaced reference conformations, which serve as landmarks in the mapped conformational space. Additionally, the ILBUS protocol encompasses an iterative process that optimizes the force constant used in the umbrella sampling simulation. Such tuning is an inherent feature of the protocol and does not need to be performed by the user in advance. Furthermore, even the simulations with suboptimal force constants can be used in estimates by MBAR. We demonstrate the feasibility and the performance of this approach in the study of the conformational landscape of the alanine dipeptide, met-enkephalin, and adenylate kinase. | ||||||
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| Record 294 of 349 | |||||||||
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| Author(s): Kolar, MH (Kolar, Michal H.); Nagy, G (Nagy, Gabor); Kunkel, J (Kunkel, John); Vaiana, SM (Vaiana, Sara M.); Bock, LV (Bock, Lars, V); Grubmuller, H (Grubmueller, Helmut) | |||||||||
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| Abstract: The ribosome is a fundamental biomolecular complex that synthesizes proteins in cells. Nascent proteins emerge from the ribosome through a tunnel, where they may interact with the tunnel walls or small molecules such as antibiotics. These interactions can cause translational arrest with notable physiological consequences. Here, we studied the arrest caused by the regulatory peptide VemP, which is known to form alpha-helices inside the ribosome tunnel near the peptidyl transferase center under specific conditions. We used all-atom molecular dynamics simulations of the entire ribosome and circular dichroism spectroscopy to study the driving forces of helix formation and how VemP causes the translational arrest. To that aim, we compared VemP dynamics in the ribosome tunnel with its dynamics in solution. We show that the VemP peptide has a low helical propensity in water and that the propensity is higher in mixtures of water and trifluorethanol. We propose that helix formation within the ribosome is driven by the interactions of VemP with the tunnel and that a part of VemP acts as an anchor. This anchor might slow down VemP progression through the tunnel enabling alpha-helix formation, which causes the elongation arrest. | |||||||||
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| Record 295 of 349 | |||||||||
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| Author(s): Chumova, Z (Chumova, Zuzana); Belyayev, A (Belyayev, Alexander); Mandakova, T (Mandakova, Terezie); Zeisek, V (Zeisek, Vojtech); Hodkova, E (Hodkova, Eva); Semberova, K (Semberova, Kristyna); Euston-Brown, D (Euston-Brown, Douglas); Travnicek, P (Travnicek, Pavel) | |||||||||
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| Abstract: Non-coding repetitive DNA (repeatome) is an active part of the nuclear genome, involved in its structure, evolution and function. It is dominated by transposable elements (TEs) and satellite DNA and is prone to the most rapid changes over time. The TEs activity presumably causes the global genome reorganization and may play an adaptive or regulatory role in response to environmental challenges. This assumption is applied here for the first time to plants from the Cape Floristic hotspot to determine whether changes in repetitive DNA are related to responses to a harsh, but extremely species-rich environment. The genus Pteronia (Asteraceae) serves as a suitable model group because it shows considerable variation in genome size at the diploid level and has high and nearly equal levels of endemism in the two main Cape biomes, Fynbos and Succulent Karoo. First, we constructed a phylogeny based on multiple low-copy genes that served as a phylogenetic framework for detecting quantitative and qualitative changes in the repeatome. Second, we performed a comparative analysis of the environments of two groups of Pteronia differing in their TEs bursts. Our results suggest that the environmental transition from the Succulent Karoo to the Fynbos is accompanied by TEs burst, which is likely also driving phylogenetic divergence. We thus hypothesize that analysis of rapidly evolving repeatome could serve as an important proxy for determining the molecular basis of lineage divergence in rapidly radiating groups. | |||||||||
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| Author(s): Changmai, P (Changmai, Piya); Jaisamut, K (Jaisamut, Kitipong); Kampuansai, J (Kampuansai, Jatupol); Kutanan, W (Kutanan, Wibhu); Altinisik, NES (Altinisik, N. Ezgi S.); Flegontova, O (Flegontova, Olga); Inta, AS (Inta, Angkhana S.); Yuencue, E (Yuencue, Eren); Boonthai, WS (Boonthai, Worrawit S.); Pamjav, H (Pamjav, Horolma); Reich, DS (Reich, David S.); Flegontov, P (Flegontov, Pavel) | |||||||||||||||||||||
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Abstract:
The great ethnolinguistic diversity found today in mainland Southeast Asia (MSEA) reflects multiple migration waves of people in the past. Maritime trading between MSEA and India was established at the latest 300 BCE, and the formation of early states in Southeast Asia during the first millennium CE was strongly influenced by Indian culture, a cultural influence that is still prominent today. Several ancient Indian-influenced states were located in present-day Thailand, and various populations in the country are likely to be descendants of people from those states. To systematically explore Indian genetic heritage in MSEA populations, we generated genome-wide SNP data (using the Affymetrix Human Origins array) for 119 present-day individuals belonging to 10 ethnic groups from Thailand and co-analyzed them with published data using PCA, ADMIXTURE, and methods relying on f-statistics and on autosomal haplotypes. We found low levels of South Asian admixture in various MSEA populations for whom there is evidence of historical connections with the ancient Indian-influenced states but failed to find this genetic component in present-day hunter-gatherer groups and relatively isolated groups from the highlands of Northern Thailand. The results suggest that migration of Indian populations to MSEA may have been responsible for the spread of Indian culture in the region. Our results also support close genetic affinity between Kra-Dai-speaking (also known as Tai-Kadai) and Austronesian-speaking populations, which fits a linguistic hypothesis suggesting cladality of the two language families.
Author summaryMainland Southeast Asia is a region with great ethnolinguistic diversity. We studied genetic population history of present-day mainland Southeast Asian populations using genome-wide SNP data. We generated new data for ten present-day ethnic groups from Thailand, which we further combined with published data from mainland and island Southeast Asians and worldwide populations. We revealed South Asian genetic admixture in various mainland Southeast Asian ethnic groups which are influenced by Indian culture but failed to find it in groups that remained culturally isolated until recently. Our finding suggests that migrations of Indian people in the past may have been responsible for the spread of Indian culture in mainland Southeast Asia. We also found support for a close genetic affinity between Kra-Dai- and Austronesian-speaking populations, which fits a linguistic hypothesis suggesting cladality of the two language families. |
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| Author(s): Lubos, M (Lubos, Marta); Mrazkova, L (Mrazkova, Lucie); Gwozdiakova, P (Gwozdiakova, Petra); Picha, J (Picha, Jan); Budesinsky, M (Budesinsky, Milos); Jiracek, J (Jiracek, Jiri); Kaminsky, J (Kaminsky, Jakub); Zakova, L (Zakova, Lenka) | |||||||||||||||
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| Abstract: Preptin is a 34-amino-acid-long peptide derived from the E-domain of a precursor of insulin-like growth factor 2 (pro-IGF2) with bone-anabolic and insulin secretion amplifying properties. Here, we describe the synthesis, structures, and biological activities of six shortened analogues of human preptin. Eight- and nine-amino-acid-long peptide amides corresponding to the C-terminal part of human preptin were stabilised by two types of staples to induce a higher proportion of helicity in their secondary structure. We monitored the secondary structure of the stapled peptides using circular dichroism. The biological effect of the structural changes was determined afterwards by the ability of peptides to stimulate the release of intracellular calcium ions. We confirmed the previous observation that the stabilisation of the disordered conformation of human preptin has a deleterious effect on biological potency. However, surprisingly, one of our preptin analogues, a nonapeptide stabilised by olefin metathesis between positions 3 and 7 of the amino acid chain, had a similar ability to stimulate calcium ions' release to the full-length human preptin. Our findings could open up new ways to design new preptin analogues, which may have potential as drugs for the treatment of diabetes and osteoporosis. | |||||||||||||||
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| Record 298 of 349 |
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| Author(s): Zheng, ZY (Zheng, Zhiyang); Xu, TF (Xu, Tengfei); Legut, D (Legut, Dominik); Zhang, RF (Zhang, Ruifeng) |
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| Abstract: High-throughput (HT) computations and machine learning (ML) algorithms are two fundamental approaches in data-driven paradigms to predict various properties of solids due to their efficiency in data creation and model construction, which however are usually used individually and lack generalization and flexibility. In this paper, we propose a scheme combining HT computations for the efficient creation of consistent data and ML algorithms for the fast construction of surrogate models to screen B-N solids' stability and mechanical properties at ambient and high pressures. Employing HT computations, a standardized database of formation enthalpy, elasticity and ideal strength of thousands of B-N structures with high precision is first established. Then several ML models are comparatively built employing the XGBoost approach with the consideration of four descriptors, i.e., sine matrix, Ewald sum matrix, SOAP, and MBTR. Our results suggest the MBTR provides more accurate estimates of various physical properties except for bulk modulus, which is evaluated with greater precision by the Ewald sum matrix. To further improve the model interpretability, based on the brittleness/ductility criterion of materials, a symbolic model with strong physical significance is successfully built for the ideal strength of the B-N solids through the key descriptors screened by the ML methods, showing great accuracy. Our research demonstrates the possibility of building high-efficient ML models and compact symbolic physical models by incorporating consistent data through HT computations for high accuracy in predicting the thermodynamic and mechanical properties of strong solids with high precision, providing a pathway for inverse design of novel materials. |
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| Author(s): Ryabov, A (Ryabov, Artem); Tasinkevych, M (Tasinkevych, Mykola) | ||||||
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| Abstract: Catalytically active macromolecules are envisioned as key building blocks in the development of artificial nanomotors. However, theory and experiments report conflicting findings regarding their dynamics. The lack of consensus is mostly caused by the limited understanding of the specifics of self-propulsion mechanisms at the nanoscale. Here, we study a generic model of a self-propelled nanoparticle that does not rely on a particular mechanism. Instead, its main assumption is the fundamental symmetry of microscopic dynamics of chemical reactions: the principle of microscopic reversibility. Significant consequences of this assumption arise if we subject the particle to the action of an external time-periodic force. The particle diffusion coefficient then becomes enhanced compared to the unbiased dynamics. The enhancement can be controlled by the force amplitude and frequency. We also derive the power spectrum of particle trajectories. Among the new effects stemming from the microscopic reversibility are the enhancement of the spectrum at all frequencies and sigmoid-shaped transitions and a peak at characteristic frequencies of rotational diffusion and external forcing. Microscopic reversibility is a generic property of a broad class of chemical reactions. Therefore, we expect that the presented results will motivate new experimental studies aimed at testing our predictions. This could provide new insights into the dynamics of catalytic macromolecules. Published under an exclusive license by AIP Publishing. | ||||||
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| Record 300 of 349 | ||||||||||||
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| Author(s): Zrimsek, M (Zrimsek, Masa); Kucharikova, H (Kucharikova, Hana); Draganic, K (Draganic, Kristina); Dobrovolna, P (Dobrovolna, Pavlina); Spornberger, VH (Spornberger, Verena Heiss); Winkelmayer, L (Winkelmayer, Lisa); Hassler, MR (Hassler, Melanie R.); Lochmanova, G (Lochmanova, Gabriela); Zdrahal, Z (Zdrahal, Zbynek); Egger, G (Egger, Gerda) | ||||||||||||
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| Abstract: Histone deacetylases (HDACs) target acetylated lysine residues in histone and non-histone proteins. HDACs are implicated in the regulation of genomic stability, cell cycle, cell death and differentiation and thus critically involved in tumorigenesis. Further, HDACs regulate T-cell development and HDAC inhibitors (HDACis) have been approved for clinical use in some T-cell malignancies. Still, the exact targets and mechanisms of HDAC inhibition in cancer are understudied. We isolated tumor cell lines from a transgenic mouse model of anaplastic large cell lymphoma (ALCL), a rare T-cell lymphoma, and abrogated HDAC activity by treatment with the HDACis Vorinostat and Entinostat or Cre-mediated deletion of Hdac1. Changes in overall protein expression as well as histone and protein acetylation were measured following Hdac1 deletion or pharmacological inhibition using label-free liquid chromatography mass spectrometry (LC-MS/MS). We found changes in overall protein abundance and increased acetylation of histones and non-histone proteins, many of which were newly discovered and associated with major metabolic and DNA damage pathways. For non-histone acetylation, we mapped a total of 1204 acetylated peptides corresponding to 603 proteins, including chromatin modifying proteins and transcription factors. Hyperacetylated proteins were involved in processes such as transcription, RNA metabolism and DNA damage repair (DDR). The DDR pathway was majorly affected by hyperacetylation following HDAC inhibition. This included acetylation of H2AX, PARP1 and previously unrecognized acetylation sites in TP53BP1. Our data provide a comprehensive view of the targets of HDAC inhibition in malignant T cells with general applicability and could have translational impact for the treatment of ALCL with HDACis alone or in combination therapies. | ||||||||||||
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| Record 301 of 349 | ||||||||||||
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| Author(s): Vedantham, HK (Vedantham, H. K.); Callingham, JR (Callingham, J. R.); Shimwell, TW (Shimwell, T. W.); Benz, AO (Benz, A. O.); Hajduk, M (Hajduk, M.); Ray, TP (Ray, T. P.); Tasse, C (Tasse, C.); Drabent, A (Drabent, A.) | ||||||||||||
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| Abstract: The empirical relationship between the nonthermal 5 GHz radio luminosity and the soft X-ray luminosity of active stellar coronae, canonically called the Gudel-Benz relationship, has been a cornerstone of stellar radio astronomy, as it explicitly ties the radio emission to the coronal heating mechanisms. The relationship extends from microflares on the Sun to the coronae of the most active stars suggesting that active coronae are heated by a flare-like process. The relationship is thought to originate from a consistent partition of the available flare energy into relativistic charges, which emit in the radio-band via the incoherent gyrosynchrotron mechanism, and heating of the bulk coronal plasma, which emits in the X-ray band via the Bremsstrahlung mechanism. Consequently, coherent emission from stellar and substellar objects is not expected to adhere to this empirical relationship, as it is observed in ultracool dwarf stars and brown dwarfs. Here we report a population of radio-detected chromospherically active stars that surprisingly follow the Gudel-Benz relationship despite their radio emission being classified as coherent emission by virtue of its high circularly polarized fraction and high brightness temperature. Our results prompt a reexamination of the physics behind the Gudel-Benz relationship, its implication for the mechanism of coronal heating and particle acceleration in active stars, and the phenomenological connection between solar and stellar flares. | ||||||||||||
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| Record 302 of 349 | ||||||
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| Author(s): Liu, XP (Liu, Xiaopeng); Legut, D (Legut, Dominik); Zhang, QF (Zhang, Qianfan) | ||||||
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| Abstract: The development of spintronic and quantum computing has inspired researchers to search for single-molecule magnets with stable structures that could be modulated repetitively. Modulation and utilization of the magnetic state of a single-molecule magnet is essential for quantum information manipulation. Moreover, in order to better design quantum information devices, it is important to explore the influence of the molecular structure on the spin center theoretically. In the present work, through density functional theory calculations, we systematically studied the spin-orbit coupling effect in the Cu-nickelocene-Cu magnetic molecular junction, and clarified the strain effect on the magnetic anisotropy energy (MAE) by developing the theoretical model based on spin-orbital coupling interaction. We quantitatively demonstrated that the tensile strain can lead to an abnormal increase of the MAE. Furthermore, it is found that the shift of the deep energy level and the change of the composition of d-orbitals in the hybrid molecular orbitals are the key factors to determine the strength of the spin-orbit coupling. This method will be widely applicable for the construction of similar magnetic molecular junction components. | ||||||
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| Record 303 of 349 | |||||||||||||||||||||
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| Author(s): Kitner, M (Kitner, Miloslav); Thines, M (Thines, Marco); Sedlarova, M (Sedlarova, Michaela); Vaculna, L (Vaculna, Lucie); Ban, R (Ban, Rita); Korosi, K (Korosi, Katalin); Iwebor, M (Iwebor, Maria); Antonova, T (Antonova, Tatiana); Ali, T (Ali, Tahir); Nadvornik, P (Nadvornik, Petr); Lebeda, A (Lebeda, Ales); Spring, O (Spring, Otmar) | |||||||||||||||||||||
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| Abstract: Plasmopara halstedii is a biotrophic parasite of sunflower (Helianthus annuus). We genetically analysed 162 P. halstedii samples collected between 1982 and 2018, representing a 3500 km west-east transect across Europe, from France to the Krasnodar region in southern Russia. To assess the population genetic structure among P. halstedii isolates, we sequenced two mitochondrial regions (cox1 and cox2), in addition to analysing eight polymorphic simple sequence repeat (SSR, microsatellite) markers. Sequencing of cox2 enabled comparison of our data with recent SSR-based studies to provide further evidence for differences among P. halstedii strains infecting different hosts (H. annuus, H. x laetiflorus, Rudbeckia spp.). There are two different lineages infecting H. annuus that we resolved on a neighbour-joining tree, which also corresponded to a discriminant analysis of principal components. This suggests at least two independent introductions of P. halstedii on sunflower. We observed no relationship between the phylogenetic placement of the individual samples and virulence characteristics, indicating independent evolution of virulence phenotypes. Both genetic markers clearly separated P. halstedii samples originating from H. annuus and H. x laetiflorus, suggesting these might represent distinct species. | |||||||||||||||||||||
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| Record 304 of 349 | ||||||||||||
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| Author(s): Miroshkina, ON (Miroshkina, Olga N.); Eggert, B (Eggert, Benedikt); Lill, J (Lill, Johanna); Beckmann, B (Beckmann, Benedikt); Koch, D (Koch, David); Hu, MY (Hu, Michael Y.); Lojewski, T (Lojewski, Tobias); Rauls, S (Rauls, Simon); Scheibel, F (Scheibel, Franziska); Taubel, A (Taubel, Andreas); Sob, M (Sob, Mojmir); Ollefs, K (Ollefs, Katharina); Gutfleisch, O (Gutfleisch, Oliver); Wende, H (Wende, Heiko); Gruner, ME (Gruner, Markus E.); Friak, M (Friak, Martin) | ||||||||||||
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| Abstract: We have performed a combined experimental and theoretical investigation of the vibrational properties of Ni2MnSn Heusler alloys. Sn-partial vibrational density of states (VDOS) of 119Sn was measured by nuclear resonant inelastic x-ray scattering at temperatures of 15 and 300 K, while magnetism and local environment of Sn was resolved by 119Sn Mossbauer spectroscopy. Using density functional theory, we associate the peaks in the VDOS with particular features in the element-resolved phonon dispersion of L21 ordered Ni2MnSn. The good agreement between theory and experiment in the low-energy region provides the evidence that the inversion of optical modes at I' involving the displacement of Ni and the heavier main group element atoms, which was predicted previously for other Ni-Mn-based Heusler compounds, is also a characteristic property of Ni2MnSn. Introducing different types of magnetic and antisite disorder in our calculations results in a distinctive redistribution and broadening of the Sn-VDOS, suggesting that considering partial disorder further improves the agreement with the experiment in particular at the highest phonon energies. | ||||||||||||
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| Record 305 of 349 | ||||||
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| Author(s): Vymetal, J (Vymetal, Jiri); Mertova, K (Mertova, Katerina); Bousova, K (Bousova, Kristyna); Sulc, J (Sulc, Josef); Tripsianes, K (Tripsianes, Konstantinos); Vondrasek, J (Vondrasek, Jiri) | ||||||
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| Abstract: Proteins are naturally formed by domains edging their functional and structural properties. A domain out of the context of an entire protein can retain its structure and to some extent also function on its own. These properties rationalize construction of artificial fusion multidomain proteins with unique combination of various functions. Information on the specific functional and structural characteristics of individual domains in the context of new artificial fusion proteins is inevitably encoded in sequential order of composing domains defining their mutual spatial positions. So the challenges in designing new proteins with new domain combinations lie dominantly in structure/function prediction and its context dependency. Despite the enormous body of publications on artificial fusion proteins, the task of their structure/function prediction is complex and nontrivial. The degree of spatial freedom facilitated by a linker between domains and their mutual orientation driven by noncovalent interactions is beyond a simple and straightforward methodology to predict their structure with reasonable accuracy. In the presented manuscript, we tested methodology using available modeling tools and computational methods. We show that the process and methodology of such prediction are not straightforward and must be done with care even when recently introduced AlphaFold II is used. We also addressed a question of benchmarking standards for prediction of multidomain protein structures-x-ray or Nuclear Magnetic Resonance experiments. On the study of six two-domain protein chimeras as well as their composing domains and their x-ray structures selected from PDB, we conclude that the major obstacle for justified prediction is inappropriate sampling of the conformational space by the explored methods. On the other hands, we can still address particular steps of the methodology and improve the process of chimera proteins prediction. | ||||||
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| Record 306 of 349 | ||||||||||||
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| Author(s): Blahut, J (Blahut, Jan); Brandl, MJ (Brandl, Matthias J.); Pradhan, T (Pradhan, Tejaswini); Reif, B (Reif, Bernd); Tosner, Z (Tosner, Zdenek) | ||||||||||||
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| Abstract: Recently, proton-detected magic-angle spinning (MAS) solid-state nuclear magnetic resonance (NMR) spectroscopy has become an attractive tool to study the structure and dynamics of insoluble proteins at atomic resolution. The sensitivity of the employed multidimensional experiments can be systematically improved when both transversal components of the magnetization are transferred simultaneously after an evolution period. The method of preservation of equivalent pathways has been explored in solution-state NMR; however, it does not find widespread application due to relaxation issues connected with increased molecular size. We present here for the first time heteronuclear transverse mixing sequences for correlation experiments at moderate and fast MAS frequencies. Optimal control allows to boost the signal-to-noise ratio (SNR) beyond the expected factor of root 2 for each indirect dimension. In addition to the carbon-detected sensitivity-enhanced 2D NCA experiment, we present a novel proton detected, doubly sensitivity-enhanced 3D hCANH pulse sequence for which we observe a 3-fold improvement in SNR compared to the conventional experimental implementation. The sensitivity gain turned out to be essential to unambiguously characterize a minor fibril polymorph of a human lambda-III immunoglobulin light chain protein that escaped detection so far. | ||||||||||||
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| Record 307 of 349 |
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| Author(s): Bellinvia, E (Bellinvia, Erica); Garcia-Gonzalez, J (Garcia-Gonzalez, Judith); Cifrova, P (Cifrova, Petra); Martinek, J (Martinek, Jan); Sikorova, L (Sikorova, Lenka); Havelkova, L (Havelkova, Lenka); Schwarzerova, K (Schwarzerova, Katerina) |
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| Abstract: Protein complex Arp2/3 has a conserved role in the nucleation of branched actin filaments. It is constituted of seven subunits, including actin-like subunits ARP2 and ARP3 plus five other subunits called Arp2/3 Complex Component 1 to 5, which are not related to actin. Knock-out plant mutants lacking individual plant ARP2/3 subunits have a typical phenotype of distorted trichomes, altered pavement cells shape and defects in cell adhesion. While knock-out mutant Arabidopsis plants for most ARP2/3 subunits have been characterized before, Arabidopsis plant mutants missing ARPC1 and ARPC3 subunits have not yet been described. Using CRISPR/Cas9, we generated knock-out mutants lacking ARPC1 and ARPC3 subunits. We confirmed that the loss of ARPC1 subunits results in the typical ARP2/3 mutant phenotype. However, the mutants lacking ARPC3 subunits resulted in plants with surprisingly different phenotypes. Our results suggest that plant ARP2/3 complex function in trichome shaping does not require ARPC3 subunit, while the fully assembled complex is necessary for the establishment of correct cell adhesion in the epidermis. |
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| Record 308 of 349 | ||||||||||||||||||
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| Author(s): Planas-Iglesias, J (Planas-Iglesias, Joan); Opaleny, F (Opaleny, Filip); Ulbrich, P (Ulbrich, Pavol); Stourac, J (Stourac, Jan); Sanusi, Z (Sanusi, Zainab); Pinto, GP (Pinto, Gaspar P.); Schenkmayerova, A (Schenkmayerova, Andrea); Byska, J (Byska, Jan); Damborsky, J (Damborsky, Jiri); Kozlikova, B (Kozlikova, Barbora); Bednar, D (Bednar, David) | ||||||||||||||||||
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Abstract:
The transplantation of loops between structurally related proteins is a compelling method to improve the activity, specificity and stability of enzymes. However, despite the interest of loop regions in protein engineering, the available methods of loop-based rational protein design are scarce. One particular difficulty related to loop engineering is the unique dynamism that enables them to exert allosteric control over the catalytic function of enzymes. Thus, when engaging in a transplantation effort, such dynamics in the context of protein structure need consideration. A second practical challenge is identifying successful excision points for the transplantation or grafting. Here, we present LoopGrafter (https://loschmidt.chemi.muni.cz/loopgrafter/), a web server that specifically guides in the loop grafting process between structurally related proteins. The server provides a step-by-step interactive procedure in which the user can successively identify loops in the two input proteins, calculate their geometries, assess their similarities and dynamics, and select a number of loops to be transplanted. All possible different chimeric proteins derived from any existing recombination point are calculated, and 3D models for each of them are constructed and energetically evaluated. The obtained results can be interactively visualized in a user-friendly graphical interface and downloaded for detailed structural analyses.
[GRAPHICS] . |
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| Record 309 of 349 | |||||||||
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| Author(s): Roberts, ID (Roberts, I. D.); van Weeren, RJ (van Weeren, R. J.); Timmerman, R (Timmerman, R.); Botteon, A (Botteon, A.); Gendron-Marsolais, M (Gendron-Marsolais, M.); Ignesti, A (Ignesti, A.); Rottgering, HJA (Rottgering, H. J. A.) | |||||||||
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| Abstract: In this paper we report the first identification of jellyfish galaxies in the Perseus cluster (Abell 426). We identified four jellyfish galaxies (LEDA 2191078, MCG +07-07-070, UGC 2654, UGC 2665) within the central 2 degrees x2 degrees (2.6  Mpc x 2.6  Mpc) of Perseus based on the presence of one-sided radio continuum tails that were detected at 144  MHz by the LOw Frequency ARray (LOFAR). The observed radio tails, as well as the orientation of morphological features in the rest-frame optical, are consistent with these four galaxies being impacted by ram pressure stripping as they orbit through the Perseus intracluster medium. By combining the LOFAR imaging at 144 MHz with 344 MHz imaging from the Karl G. Jansky Very Large Array, we derived spectral indices for the disks and the stripped tails of these jellyfish galaxies. We show that the spectral indices over the galaxy disks are quite flat, while the indices of the stripped tails are substantially steeper. We also identified a number of compact H alpha + [NII] sources with narrowband imaging from the Isaac Newton Telescope. These sources are brighter along the leading side of the galaxy (i.e., opposite to the direction of the stripped tail), which is consistent with ram pressure induced star formation. Lastly, consistent with previous works in other clusters, we find that these jellyfish galaxies show enhanced radio luminosities for their observed star formation rates. Given the small distance to the Perseus cluster (D  similar to  70  Mpc, 1 '' similar or equal to  340  pc), these galaxies are excellent candidates for multiwavelength follow-up observations to probe the impact of ram pressure stripping on galaxy star formation at subkiloparsec scales. | |||||||||
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| Record 310 of 349 | |||||||||
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| Author(s): Sipr, O (Sipr, O.); Mankovsky, S (Mankovsky, S.); Vackar, J (Vackar, J.); Ebert, H (Ebert, H.); Marmodoro, A (Marmodoro, A.) | |||||||||
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| Abstract: Laves RFe2 compounds, where R is a rare earth, exhibit technologically relevant properties associated with the interplay between their lattice geometry and magnetism. We apply ab initio calculations to explore how magnetic properties of Fe in RFe2 systems vary with temperature. We found that the ratio between the orbital magnetic moment mu orb and the spin magnetic moment mu spin increases with increasing temperature for YFe2, GdFe2, TbFe2, DyFe2, and HoFe2. This increase is significant and it should be experimentally observable by means of x-ray magnetic circular dichroism. We conjecture that the predicted increase of the mu orb/mu spin ratio with temperature is linked to the reduction of hybridization between same-spin-channel states of atoms with fluctuating magnetic moments and to the associated increase of their atomic-like character. | |||||||||
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| Record 311 of 349 | ||||||||||||
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| Author(s): Dockal, J (Dockal, Jan); Lisal, M (Lisal, Martin); Moucka, F (Moucka, Filip) | ||||||||||||
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| Abstract: The interactions of graphene electrodes with aqueous solutions of electrolytes play important roles in many technologies such as capacitive deionisation. Particularly important is the surface adsorption of ions due to the electric potential of the electrode. In this paper, we have studied structural changes in several prototypical aqueous solutions of electrolytes (NaCl, KCl, and LiCl) in contact with graphene induced by its either positive or negative electric charge, under ambient conditions. We have carried out molecular-dynamics simulations using the most accurate interaction models available. We have analysed the solution structure using an advanced analysis of the intermolecular bonding, and also standard properties such as density and charge density profiles, electrostatic potential, and screening functions. Our results show that the graphene charge has nearly no translational effect on water molecules, whereas it significantly changes their orientations, and the effect on ions' distributions differ from solution to solution. Larger ions, whose hydration shells are weaker, are affected directly in an intuitive fashion, i.e., cations are attracted by negatively charged graphene and vice versa, whereas effects on smaller ions may vary and may be even counterintuitive, e.g., the number of chlorine anions in aqueous KCl in contact with negatively charged graphene is greater when compared to neutral graphene. The surplus of chlorine anions adsorbed on a positively charged electrode strengthens the structure of water and counterintuitively rotates the water molecules in the second layer pointing their electric dipoles preferentially to the electrode. The surplus of cations due to a negatively charged electrode is accompanied by a weakening of the water structure in the case of larger ions, whereas in the case of the lithium cation the structure is stronger due to the direct effects of the graphene charge on water molecules. Regardless of the graphene charge, the total number of intermolecular bonds connected with a single water molecule is nearly independent of the distance from the graphene surface and the same applies to the number of intermolecular bonds connected with a single ion, which means that whenever a particle loses an intermolecular bond it nearly always forms a new bond as a compensation. (C) 2022 Elsevier B.V. All rights reserved. | ||||||||||||
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| Author(s): Ignesti, A (Ignesti, A.); Brunetti, G (Brunetti, G.); Shimwell, T (Shimwell, T.); Gitti, M (Gitti, M.); Birzan, L (Birzan, L.); Botteon, A (Botteon, A.); Bruggen, M (Brueggen, M.); de Gasperin, F (de Gasperin, F.); Di Gennaro, G (Di Gennaro, G.); Edge, AC (Edge, A. C.); Riseley, CJ (Riseley, C. J.); Rottgering, HJA (Roettgering, H. J. A.); van Weeren, RJ (van Weeren, R. J.) | |||||||||||||||
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Abstract:
Context. Radio observations represent a powerful probe of the physics occurring in the intracluster medium (ICM) because they trace the relativistic cosmic rays in the cluster magnetic fields, or within galaxies themselves. By probing the low-energy cosmic rays, low-frequency radio observations are especially interesting because they unveil emission powered by low-efficiency particle acceleration processes, which are believed to play a crucial role in the origin of diffuse radio emission.
Aims. We investigate the origin of the radio mini-halo at the centre of the galaxy cluster 2A0335+096 and its connection to the central galaxy and the sloshing cool core. We also study the properties of the head-tail galaxy GB6 B0335+096 hosted in the cluster to explore the life cycle of the relativistic electrons in its radio tails. Methods. We used new LOw Frequency ARray (LOFAR) observations from the LOFAR Two-meter Sky Survey at 144 MHz to map the low-frequency emission with a high level of detail. The new data were combined with archival Giant Metrewave Radio Telescope and Chandra observations to carry out a multi-wavelength study. Results. We have made the first measurement of the spectral index of the mini-halo (alpha=-1.2 +/- 0.1 between 144 MHz and 1.4 GHz) and the lobes of the central source (alpha similar or equal to-1.5 +/- 0.1 between 144 and 610 MHz). Based on the low-frequency radio emission morphology with respect to the thermal ICM, we propose that the origin of the diffuse radio emission is linked to the sloshing of the cool core. The new data reveal the presence of a megaparsec-long radio tail associated with GB6 B0335+096. The observed projected length is a factor 3 longer than the expected cooling length, with evidence of flattening in the spectral index trend along the tail. Therefore, we suggest that the electrons towards the end of the tail are kept alive by the ICM gentle re-acceleration. |
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| Record 313 of 349 |
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| Author(s): Kumar, PR (Kumar, P. Ragesh); Nag, P (Nag, P.); Rankovic, M (Rankovic, M.); Luxford, FM (Luxford, F. M.); Kocisek, J (Kocisek, J.); Masin, Z (Masin, Z.); Fedor, J (Fedor, J.) |
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| Abstract: We experimentally show that N-H bond cleavage in the pyrrole molecule following resonant electron attachment is allowed and controlled by the motion of the atoms which are not dissociating, namely, of the carbon-attached hydrogen atoms. We use this fact to steer the efficiency of this bond cleavage. In order to interpret the experimental findings, we have developed a method for locating all resonant and virtual states of an electron-molecule system in the complex plane, based on all-electron R-matrix scattering calculations. Mapping these as a function of molecular geometry allows us to separate two contributing dissociation mechanisms: a pi* resonance formation inducing strong bending deformations and a nonresonant sigma* mechanism originating in a virtual state. The coupling between the two mechanisms is enabled by the out-of-plane motion of the C-H bonds, and we show that it must happen on an ultrafast (few fs) time scale. |
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| Author(s): Vicar, T (Vicar, Tomas); Chmelik, J (Chmelik, Jiri); Navratil, J (Navratil, Jiri); Kolar, R (Kolar, Radim); Chmelikova, L (Chmelikova, Larisa); Cmiel, V (Cmiel, Vratislav); Jagos, J (Jagos, Jiri); Provaznik, I (Provaznik, Ivo); Masarik, M (Masarik, Michal); Gumulec, J (Gumulec, Jaromir) | |||||||||||||||||||||||||||
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| Abstract: Cell viscoelastic properties are affected by the cell cycle, differentiation, and pathological processes such as malignant transformation. Therefore, evaluation of the mechanical properties of the cells proved to be an approach to obtaining information on the functional state of the cells. Most of the currently used methods for cell mechanophenotyping are limited by low robustness or the need for highly expert operation. In this paper, the system and method for viscoelasticity measurement using shear stress induction by fluid flow is described and tested. Quantitative phase imaging (QPI) is used for image acquisition because this technique enables one to quantify optical path length delays introduced by the sample, thus providing a label free objective measure of morphology and dynamics. Viscosity and elasticity determination were refined using a new approach based on the linear system model and parametric deconvolution. The proposed method allows high-throughput measurements during live-cell experiments and even through a time lapse, whereby we demonstrated the possibility of simultaneous extraction of shear modulus, viscosity, cell morphology, and QPI-derived cell parameters such as circularity or cell mass. Additionally, the proposed method provides a simple approach to measure cell refractive index with the same setup, which is required for reliable cell height measurement with QPI, an essential parameter for viscoelasticity calculation. Reliability of the proposed viscoelasticity measurement system was tested in several experiments including cell types of different Young/shear modulus and treatment with cytochalasin D or docetaxel, and an agreement with atomic force microscopy was observed. The applicability of the proposed approach was also confirmed by a time-lapse experiment with cytochalasin D washout, whereby an increase of stiffness corresponded to actin repolymerization in time. | |||||||||||||||||||||||||||
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| Author(s): Cuciti, V (Cuciti, V); de Gasperin, F (de Gasperin, F.); Bruggen, M (Brueggen, M.); Vazza, F (Vazza, F.); Brunetti, G (Brunetti, G.); Shimwell, TW (Shimwell, T. W.); Edler, HW (Edler, H. W.); van Weeren, RJ (van Weeren, R. J.); Botteon, A (Botteon, A.); Cassano, R (Cassano, R.); Di Gennaro, G (Di Gennaro, G.); Gastaldello, F (Gastaldello, F.); Drabent, A (Drabent, A.); Rottgering, HJA (Roettgering, H. J. A.); Tasse, C (Tasse, C.) | |||||||||||||||
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| Abstract: The central regions of galaxy clusters are permeated by magnetic fields and filled with relativistic electrons(1). When clusters merge, the magnetic fields are amplified and relativistic electrons are re-accelerated by turbulence in the intracluster medium(2,)(3). These electrons reach energies of 1-10 GeV and, in the presence of magnetic fields, produce diffuse radio halos(4) that typically cover an area of around 1 Mpc(2). Here we report observations of four clusters whose radio halos are embedded in much more extended, diffuse radio emission, filling a volume 30 times larger than that of radio halos. The emissivity in these larger features is about 20 times lower than the emissivity in radio halos. We conclude that relativistic electrons and magnetic fields extend far beyond radio halos, and that the physical conditions in the outer regions of the clusters are quite different from those in the radio halos. | |||||||||||||||
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| Record 316 of 349 | ||||||||||||||||||
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| Author(s): Heesen, V (Heesen, V); Staffehl, M (Staffehl, M.); Basu, A (Basu, A.); Beck, R (Beck, R.); Stein, M (Stein, M.); Tabatabaei, FS (Tabatabaei, F. S.); Hardcastle, MJ (Hardcastle, M. J.); Chyzy, KT (Chyzy, K. T.); Shimwell, TW (Shimwell, T. W.); Adebahr, B (Adebahr, B.); Beswick, R (Beswick, R.); Bomans, DJ (Bomans, D. J.); Botteon, A (Botteon, A.); Brinks, E (Brinks, E.); Bruggen, M (Brueggen, M.); Dettmar, RJ (Dettmar, R-J); Drabent, A (Drabent, A.); de Gasperin, F (de Gasperin, F.); Gurkan, G (Guerkan, G.); Heald, GH (Heald, G. H.); Horellou, C (Horellou, C.); Nikiel-Wroczynski, B (Nikiel-Wroczynski, B.); Paladino, R (Paladino, R.); Piotrowska, J (Piotrowska, J.); Rottgering, HJA (Roettgering, H. J. A.); Smith, DJB (Smith, D. J. B.); Tasse, C (Tasse, C.) | ||||||||||||||||||
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Abstract:
Context. Cosmic rays and magnetic fields are key ingredients in galaxy evolution, regulating both stellar feedback and star formation. Their properties can be studied with low-frequency radio continuum observations that are free from thermal contamination.
Aims. We define a sample of 76 nearby (<30 Mpc) galaxies with rich ancillary data in the radio continuum and infrared from the CHANG-ES and KINGFISH surveys, which will be observed with the LOFAR Two-metre Sky Survey (LoTSS) at 144 MHz. Methods. We present maps for 45 of them as part of the LoTSS data release 2 (LoTSS-DR2), where we measure integrated flux densities and study integrated and spatially resolved radio spectral indices. We investigate the radio-star formation rate (SFR) relation using SFRs derived from total infrared and H alpha + 24-mu m emission. Results. The radio-SFR relation at 144 MHz is clearly super-linear with L-144mHz proportional to SFR1,4-1,5. The mean integrated radio spectral index between 144 and approximate to 1400 MHz is <alpha > = -0.56 +/- 0.14, in agreement with the injection spectral index for cosmic ray electrons (CRE5). However, the radio spectral index maps show variation of spectral indices with flatter spectra associated with star-forming regions and steeper spectra in galaxy outskirts and, in particular, in extra-planar regions. We found that galaxies with high SFRs have steeper radio spectra; we find similar correlations with galaxy size, mass, and rotation speed. Conclusions. Galaxies that are larger and more massive are better electron calorimeters, meaning that the CRE lose a higher fraction of their energy within the galaxies. This explains the super-linear radio-SFR relation, with more massive, star-forming galaxies being radio bright. We propose a semi-calorimetric radio-SFR relation that employs the galaxy mass as a proxy for the calorimetric efficiency. |
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| Record 317 of 349 | ||||||
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| Author(s): Arias, M (Arias, M.); Botteon, A (Botteon, A.); Bassa, CG (Bassa, C. G.); van der Jagt, S (van der Jagt, S.); van Weeren, RJ (van Weeren, R. J.); O'Sullivan, SP (O'Sullivan, S. P.); Bosschaart, Q (Bosschaart, Q.); Dullaart, RS (Dullaart, R. S.); Hardcastle, MJ (Hardcastle, M. J.); Hessels, JWT (Hessels, J. W. T.); Shimwell, T (Shimwell, T.); Slob, MM (Slob, M. M.); Sturm, JA (Sturm, J. A.); Tasse, C (Tasse, C.); Theijssen, NCMA (Theijssen, N. C. M. A.); Vink, J (Vink, J.) | ||||||
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| Abstract: We report the discovery of a ring of low surface brightness radio emission around the Calvera pulsar, a high Galactic latitude, isolated neutron star, in the LOFAR Two-metre Sky Survey (LoTSS). It is centered at alpha = 14h11m12(s).6, delta = +79 degrees 23 ' 15 '', has inner and outer radii of 14 '.2 and 28 '.4, and has an integrated flux density at 144 MHz of 1.08 +/- 0.15 Jy. The ring center is offset by 4 '.9 from the location of the Calvera pulsar. Observations with the Isaac Newton Telescope in the H alpha band show no coincident optical emission, but they do show a small (similar to 20 '') optical structure internal to the ring. We consider three possible interpretations for the ring: that it is an H II region, a supernova remnant (SNR), or an odd radio circle (ORC). The positional coincidence of the ring, the pulsar, and an X-ray-emitting non-equilibrium ionization plasma previously detected lead us to prefer the SNR interpretation. If the source is indeed a SNR and if its association with the Calvera pulsar is confirmed, then Calvera's SNR, or G118.4+37.0, will be one of few SNRs in the Galactic halo. | ||||||
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| Author(s): Simonte, M (Simonte, M.); Andernach, H (Andernach, H.); Bruggen, M (Brueggen, M.); Schwarz, DJ (Schwarz, D. J.); Prandoni, I (Prandoni, I); Willis, AG (Willis, A. G.) | |||||||||
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| Abstract: Giant radio galaxies (GRGs) are radio galaxies that have projected linear extents of more than 700 kpc or 1 Mpc, depending on definition. We have carried out a careful visual inspection in search of GRGs of the Bootes LOw-Frequency ARray Deep Field image at 150 MHz. We identified 74 GRGs with a projected size larger than 0.7 Mpc of which 38 are larger than 1 Mpc. The resulting GRG sky density is about 2.8 (1.43) GRGs per square degree for GRGs with linear size larger than 0.7 (1) Mpc. We studied their radio properties and the accretion state of the host galaxies using deep optical and infrared survey data and determined flux densities for these GRGs from available survey images at both 54 MHz and 1.4 GHz to obtain integrated radio spectral indices. We show the location of the GRGs in the P-D diagram. The accretion mode on to the central black holes of the GRG hosts is radiatively inefficient suggesting that the central engines are not undergoing massive accretion at the time of the emission. Interestingly, 14 out of 35 GRGs for which optical spectra are available show a moderate star-formation rate (10-100 M-circle dot yr(-1)). Based on the number density of optical galaxies taken from the Dark Energy Spectroscopic Instrument survey DR9 photometric redshift catalogue, we found no significant differences between the environments of GRGs and other radio galaxies, at least for redshift up to z = 0.7. | |||||||||
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| Record 319 of 349 | ||||||||||||||||||||||||||||||
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| Author(s): Stundlova, J (Stundlova, Jana); Hospodarska, M (Hospodarska, Monika); Luksikova, K (Luksikova, Karolina); Volenikova, A (Volenikova, Anna); Pavlica, T (Pavlica, Tomas); Altmanova, M (Altmanova, Marie); Richter, A (Richter, Annekatrin); Reichard, M (Reichard, Martin); Dalikova, M (Dalikova, Martina); Pelikanova, S (Pelikanova, Sarka); Marta, A (Marta, Anatolie); Simanovsky, SA (Simanovsky, Sergey A.); Hirman, M (Hirman, Matyas); Jankasek, M (Jankasek, Marek); Dvorak, T (Dvorak, Tomas); Bohlen, J (Bohlen, Joerg); Rab, P (Rab, Petr); Englert, C (Englert, Christoph); Nguyen, P (Nguyen, Petr); Sember, A (Sember, Alexandr) | ||||||||||||||||||||||||||||||
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| Abstract: Homomorphic sex chromosomes and their turnover are common in teleosts. We investigated the evolution of nascent sex chromosomes in several populations of two sister species of African annual killifishes, Nothobranchius furzeri and N. kadleci, focusing on their under-studied repetitive landscape. We combined bioinformatic analyses of the repeatome with molecular cytogenetic techniques, including comparative genomic hybridization, fluorescence in situ hybridization with satellite sequences, ribosomal RNA genes (rDNA) and bacterial artificial chromosomes (BACs), and immunostaining of SYCP3 and MLH1 proteins to mark lateral elements of synaptonemal complexes and recombination sites, respectively. Both species share the same heteromorphic XY sex chromosome system, which thus evolved prior to their divergence. This was corroborated by sequence analysis of a putative master sex determining (MSD) gene gdf6Y in both species. Based on their divergence, differentiation of the XY sex chromosome pair started approximately 2 million years ago. In all populations, the gdf6Y gene mapped within a region rich in satellite DNA on the Y chromosome long arms. Despite their heteromorphism, X and Y chromosomes mostly pair regularly in meiosis, implying synaptic adjustment. In N. kadleci, Y-linked paracentric inversions like those previously reported in N. furzeri were detected. An inversion involving the MSD gene may suppress occasional recombination in the region, which we otherwise evidenced in the N. furzeri population MZCS-121 of the Limpopo clade lacking this inversion. Y chromosome centromeric repeats were reduced compared with the X chromosome and autosomes, which points to a role of relaxed meiotic drive in shaping the Y chromosome repeat landscape. We speculate that the recombination rate between sex chromosomes was reduced due to heterochiasmy. The observed differences between the repeat accumulations on the X and Y chromosomes probably result from high repeat turnover and may not relate closely to the divergence inferred from earlier SNP analyses. | ||||||||||||||||||||||||||||||
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| Author(s): Ignesti, A (Ignesti, Alessandro); Vulcani, B (Vulcani, Benedetta); Poggianti, BM (Poggianti, Bianca M.); Moretti, A (Moretti, Alessia); Shimwell, T (Shimwell, Timothy); Botteon, A (Botteon, Andrea); van Weeren, RJ (van Weeren, Reinout J.); Roberts, ID (Roberts, Ian D.); Fritz, J (Fritz, Jacopo); Tomicic, N (Tomicic, Neven); Peluso, G (Peluso, Giorgia); Paladino, R (Paladino, Rosita); Gitti, M (Gitti, Myriam); Muller, A (Mueller, Ancla); McGee, S (McGee, Sean); Gullieuszik, M (Gullieuszik, Marco) | ||||||||||||||||||||||||||||||
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| Abstract: Jellyfish galaxies, characterized by long filaments of stripped interstellar medium extending from their disks, are the prime laboratories to study the outcomes of ram pressure stripping. At radio wavelengths, they often show unilateral emission extending beyond the stellar disk, and an excess of radio luminosity with respect to that expected from their current star formation rate. We present new 144 MHz images provided by the LOFAR Two-metre Sky Survey for a sample of six galaxies from the GASP survey. These galaxies are characterized by a high global luminosity at 144 MHz (6-27 x 10(22) W Hz(-1)), in excess compared to their ongoing star formation rate. The comparison of radio and H alpha images smoothed with a Gaussian beam corresponding to similar to 10 kpc reveals a sublinear spatial correlation between the two emissions with an average slope of k = 0.50. In their stellar disk we measure k = 0.77, which is close to the radio-to-star formation linear relation. We speculate that, as a consequence of the ram pressure, in these jellyfish galaxies cosmic ray transport is more efficient than in normal galaxies. Radio tails typically have higher radio-to-H alpha ratios than the disks, thus we suggest that the radio emission is boosted by electrons stripped from the disks. In all galaxies, the star formation rate has decreased by a factor <= 10 within the last similar to 10(8) yr. The observed radio emission is consistent with the past star formation, so we propose that this recent decline may be the cause of their radio luminosity-to-star formation rate excess. | ||||||||||||||||||||||||||||||
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| Record 321 of 349 | |||||||||||||||
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| Author(s): Dave, Z (Dave, Zankruti); Blanarova, OV (Blanarova, Olga Vondalova); Cada, S (Cada, Stepan); Janovska, P (Janovska, Pavlina); Zezula, N (Zezula, Nikodem); Behal, M (Behal, Martin); Hanakova, K (Hanakova, Katerina); Ganji, SR (Ganji, Sri Ranjani); Krejci, P (Krejci, Pavel); Gomoryova, K (Gomoryova, Kristina); Peschelova, H (Peschelova, Helena); Smida, M (Smida, Michal); Zdrahal, Z (Zdrahal, Zbynek); Pavlova, S (Pavlova, Sarka); Kotaskova, J (Kotaskova, Jana); Pospisilova, S (Pospisilova, Sarka); Bryja, V (Bryja, Vitezslav) | |||||||||||||||
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| Abstract: Chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL) are malignancies characterized by the dependence on B-cell receptor (BCR) signaling and by the high expression of ROR1, the cell surface receptor for Wnt-5a. Both, BCR and ROR1 are therapeutic targets in these diseases and the understanding of their mutual cross talk is thus of direct therapeutic relevance. In this study we analyzed the role of Lyn, a kinase from the Src family participating in BCR signaling, as a mediator of the BCR-ROR1 crosstalk. We confirm the functional interaction between Lyn and ROR1 and demonstrate that Lyn kinase efficiently phosphorylates ROR1 in its kinase domain and aids the recruitment of the E3 ligase c-CBL. We show that ROR1 surface dynamics in migrating primary CLL cells as well as chemotactic properties of CLL cells were inhibited by Lyn inhibitor dasatinib. Our data establish Lyn-mediated phosphorylation of ROR1 as a point of crosstalk between BCR and ROR1 signaling pathways. | |||||||||||||||
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| Record 322 of 349 | |||||||||||||||||||||
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| Author(s): Daloz, AS (Daloz, Anne Sophie); Schwingshackl, C (Schwingshackl, Clemens); Mooney, P (Mooney, Priscilla); Strada, S (Strada, Susanna); Rechid, D (Rechid, Diana); Davin, EL (Davin, Edouard L.); Katragkou, E (Katragkou, Eleni); de Noblet-Ducoudre, N (de Noblet-Ducoudre, Nathalie); Belda, M (Belda, Michal); Halenka, T (Halenka, Tomas); Breil, M (Breil, Marcus); Cardoso, RM (Cardoso, Rita M.); Hoffmann, P (Hoffmann, Peter); Lima, DCA (Lima, Daniela C. A.); Meier, R (Meier, Ronny); Soares, PMM (Soares, Pedro M. M.); Sofiadis, G (Sofiadis, Giannis); Strandberg, G (Strandberg, Gustav); Toelle, MH (Toelle, Merja H.); Lund, MT (Lund, Marianne T.) | |||||||||||||||||||||
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| Abstract: Seasonal snow cover plays a major role in the climate system of the Northern Hemisphere via its effect on land surface albedo and fluxes. In climate models the parameterization of interactions between snow and atmosphere remains a source of uncertainty and biases in the representation of local and global climate. Here, we evaluate the ability of an ensemble of regional climate models (RCMs) coupled with different land surface models to simulate snow- atmosphere interactions over Europe in winter and spring. We use a previously defined index, the snow-albedo sensitivity index (SASI), to quantify the radiative forcing associated with snow cover anomalies. By comparing RCM-derived SASI values with SASI calculated from reanalyses and satellite retrievals, we show that an accurate simulation of snow cover is essential for correctly reproducing the observed forcing over middle and high latitudes in Europe. The choice of parameterizations, and primarily the choice of the land surface model, strongly influences the representation of SASI as it affects the ability of climate models to simulate snow cover accurately. The degree of agreement between the datasets differs between the accumulation and ablation periods, with the latter one presenting the greatest challenge for the RCMs. Given the dominant role of land surface processes in the simulation of snow cover during the ablation period, the results suggest that, during this time period, the choice of the land surface model is more critical for the representation of SASI than the atmospheric model. | |||||||||||||||||||||
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| Author(s): Vondracek, O (Vondracek, Oldrich); Mikes, L (Mikes, Libor); Talacko, P (Talacko, Pavel); Leontovyc, R (Leontovyc, Roman); Bulantova, J (Bulantova, Jana); Horak, P (Horak, Petr) | ||||||||||||
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| Abstract: Schistosome invasive stages, cercariae, leave intermediate snail hosts, penetrate the skin of definitive hosts, and transform to schistosomula which migrate to the final location. During invasion, cercariae employ histolytic and other bioactive products of specialized holocrine secretory cells - postacetabular (PA) and circumacetabular (CA) penetration glands. Although several studies attempted to characterize protein composition of the in vitro-induced gland secretions in Schistosoma mansoni and Schistosoma japonicum, the results were somewhat inconsistent and dependent on the method of sample collection and processing. Products of both gland types mixed during their secretion did not allow localization of identified proteins to a particular gland. Here we compared proteomes of separately isolated cercarial gland cells of the avian schistosome Trichobilharzia szidati, employing laser-assisted microdissection and shotgun LC-MS/MS, thus obtaining the largest dataset so far of the representation and localization of cercarial penetration gland proteins. We optimized the methods of sample processing with cercarial bodies (heads) first. Alizarin-pre-stained, chemically non-fixed samples provided optimal results of MS analyses, and enabled us to distinguish PA and CA glands for microdissection. Using 7.5 x 106 lm3 sample volume per gland replicate, we identified 3347 peptides assigned to 792 proteins, from which 461 occurred in at least two of three replicates in either gland type (PA = 455, 40 exclusive; CA = 421, six exclusive; 60 proteins differed significantly in their abundance between the glands). Peptidases of five catalytic types accounted for ca. 8% and 6% of reliably identified proteins in PA and CA glands, respectively. Invadolysin, nardilysin, cathepsins B2 and L3, and elastase 2b orthologs were the major gland endopeptidases. Two cystatins and a serpin were highly abundant peptidase inhibitors in the glands. While PA glands generally had rich enzymatic equipment, CA glands were conspicuously abundant in venom allergen-like proteins. (c) 2022 The Author(s). Published by Elsevier Ltd on behalf of Australian Society for Parasitology. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). | ||||||||||||
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| Author(s): Vodak, R (Vodak, Rostislav); Furst, T (Furst, Tomas); Sir, M (Sir, Miloslav); Kmec, J (Kmec, Jakub) | ||||||
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| Abstract: Semi-continuum modelling of unsaturated porous media flow is based on representing the porous medium as a grid of non-infinitesimal blocks that retain the character of a porous medium. This approach is similar to the hybrid/multiscale modelling. Semi-continuum model is able to physically correctly describe diffusion-like flow, finger-like flow, and the transition between them. This article presents the limit of the semi-continuum model as the block size goes to zero. In the limiting process, the retention curve of each block scales with the block size and in the limit becomes a hysteresis operator of the Prandtl-type used in elasto-plasticity models. Mathematical analysis showed that the limit of the semi-continuum model is a hyperbolic-parabolic partial differential equation with a hysteresis operator of Prandl's type. This limit differs from the standard Richards' equation, which is a parabolic equation and is not able to describe finger-like flow. | ||||||
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| Author(s): Ivanizs, L (Ivanizs, Laszlo); Marcotuli, I (Marcotuli, Ilaria); Rakszegi, M (Rakszegi, Marianna); Kalapos, B (Kalapos, Balazs); Szoke-Pazsi, K (Szoke-Pazsi, Kitti); Farkas, A (Farkas, Andras); Turkosi, E (Turkosi, Edina); Gaal, E (Gaal, Eszter); Kruppa, K (Kruppa, Klaudia); Kovacs, P (Kovacs, Peter); Darko, E (Darko, Eva); Szakacs, E (Szakacs, Eva); Said, M (Said, Mahmoud); Capal, P (Capal, Petr); Dolezel, J (Dolezel, Jaroslav); Gadaleta, A (Gadaleta, Agata); Molnar, I (Molnar, Istvan) | ||||||||||||||||||
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| Abstract: Grain dietary fiber content is an important health-promoting trait of bread wheat. A dominant dietary fiber component of wheat is the cell wall polysaccharide arabinoxylan and the goatgrass Aegilops biuncialis has high beta-glucan content, which makes it an attractive gene source to develop wheat lines with modified fiber composition. In order to support introgression breeding, this work examined genetic variability in grain beta-glucan, pentosan, and protein content in a collection of Ae. biuncialis. A large variation in grain protein and edible fiber content was revealed, reflecting the origin of Ae. biuncialis accessions from different eco-geographical habitats. Association analysis using DArTseq-derived SNPs identified 34 QTLs associated with beta-glucan, pentosan, water-extractable pentosan, and protein content. Mapping the markers to draft chromosome assemblies of diploid progenitors of Ae. biuncialis underlined the role of genes on chromosomes 1M(b), 4M(b), and 5M(b)in the formation of grain beta-glucan content, while other QTLs on chromosome groups 3, 6, and 1 identified genes responsible for total- and water-extractable pentosan content. Functional annotation of the associated marker sequences identified fourteen genes, nine of which were identified in other monocots. The QTLs and genes identified in the present work are attractive targets for chromosome-mediated gene transfer to improve the health-promoting properties of wheat-derived foods. | ||||||||||||||||||
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| Author(s): Vavra, O (Vavra, Ondrej); Damborsky, J (Damborsky, Jiri); Bednar, D (Bednar, David) | ||||||
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| Abstract: Acceleration of chemical reactions by the enzymes optimized using protein engineering represents one of the key pillars of the contribution of biotechnology towards sustainability. Tunnels and channels of enzymes with buried active sites enable the exchange of ligands, ions, and water molecules between the outer environment and active site pockets. The efficient exchange of ligands is a fundamental process of biocatalysis. Therefore, enzymes have evolved a wide range of mechanisms for repetitive conformational changes that enable periodic opening and closing. Protein-ligand interactions are traditionally studied by molecular docking, whereas molecular dynamics is the method of choice for studying conformational changes and ligand transport. However, computational demands make molecular dynamics impractical for screening purposes. Thus, several approximative methods have been recently developed to study interactions between a protein and ligand during the ligand transport process. Apart from identifying the best binding modes, these methods also provide information on the energetics of the transport and identify problematic regions limiting the ligand passage. These methods use approximations to simulate binding or unbinding events rapidly (calculation times from minutes to hours) and provide energy profiles that can be used to rank ligands or pathways. Here we provide a critical comparison of available methods, showcase their results on sample systems, discuss their practical applications in molecular biotechnologies and outline possible future developments. | ||||||
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| Author(s): Edler, HW (Edler, H. W.); de Gasperin, F (de Gasperin, F.); Brunetti, G (Brunetti, G.); Botteon, A (Botteon, A.); Cuciti, V (Cuciti, V); van Weeren, RJ (van Weeren, R. J.); Cassano, R (Cassano, R.); Shimwell, TW (Shimwell, T. W.); Bruggen, M (Brueggen, M.); Drabent, A (Drabent, A.) | |||||||||||||||
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Abstract:
Context. Abell 1033 is a merging galaxy cluster of moderate mass (M-500 = 3.24 x 10(14) M-circle dot). It hosts a broad variety of diffuse radio sources that are linked to different astrophysical phenomena. The most peculiar phenomenon is an elongated feature with an ultra-steep spectrum that is the prototype of the category of gently reenergized tails (GReET). Furthermore, the cluster hosts sources that were previously classified as a radio phoenix and a radio halo.
Aims. We aim to improve the understanding of the cosmic-ray acceleration mechanisms in galaxy clusters in a frequency and mass range that has been poorly explored so far. Methods. To investigate the ultra-steep synchrotron emission in the cluster, we performed a full direction-dependent calibration of a LOFAR observation centered at 54 MHz. We analyzed this observation together with recalibrated data of the LOFAR Two-meter Sky Survey at 144 MHz and an archival GMRT observation at 323 MHz. We performed a spectral study of the radio galaxy tail that is connected to the GReET to test whether the current interpretation of the source agrees with observational evidence below 100 MHz. Additionally, we employed a Markov chain Monte Carlo code to fit the halo surface brightness profile at different frequencies. Results. We report an extreme spectral curvature for the GReET. The spectral index flattens from alpha(323MHz)(144MHz) approximate to -4 to alpha(144MHz)(54MHz) approximate to -2. This indicates the presence of a cutoff in the electron energy spectrum. At the cluster center, we detect the radio halo at 54, 144, and at lower significance at 323 MHz. We categorize it as an ultra-steep spectrum radio halo with a low-frequency spectral index alpha = -1.65 +/- 0.17. Additionally, with a radio power of P-150MHz = 1.22 +/- 0.13 x 10(25) W Hz(-1), it is found to be significantly above the correlations of radio power to cluster mass reported in the literature. Furthermore, the synchrotron spectrum of the halo is found to further steepen between 144 and 323 MHz, in agreement with the presence of a break in the electron spectrum, which is a prediction of homogeneous reacceleration models. |
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| Author(s): Pasini, T (Pasini, T.); Edler, HW (Edler, H. W.); Bruggen, M (Brueggen, M.); de Gasperin, F (de Gasperin, F.); Botteon, A (Botteon, A.); Rajpurohit, K (Rajpurohit, K.); van Weeren, RJ (van Weeren, R. J.); Gastaldello, F (Gastaldello, F.); Gaspari, M (Gaspari, M.); Brunetti, G (Brunetti, G.); Cuciti, V (Cuciti, V.); Nanci, C (Nanci, C.); di Gennaro, G (di Gennaro, G.); Rossetti, M (Rossetti, M.); Dallacasa, D (Dallacasa, D.); Hoang, DN (Hoang, D. N.); Riseley, CJ (Riseley, C. J.) | ||||||||||||||||||||||||||||||
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Context. Radio observations of galaxy clusters reveal a plethora of diffuse, steep-spectrum sources related to the re-acceleration of cosmic-ray electrons, such as halos, relics, and phoenices. In this context, the LOw Frequency ARray Low-Band Antenna (LOFAR-LBA) Sky Survey (LoLSS) provides the most sensitive images of the sky at 54 MHz to date, allowing us to investigate re-acceleration processes in a poorly explored frequency regime.
Aims. We study diffuse radio emission in the galaxy cluster Abell 1550, with the aim of constraining particle re-acceleration in the intra-cluster medium. Methods. We exploited observations at four different radio frequencies: 54, 144, 400, and 1400 MHz. To complement our analysis, we made use of archival Chandra X-ray data. Results. At all frequencies we detect an ultra-steep spectrum radio halo (S-nu proportional to nu(-1.6)) with an extent of similar to 1.2 Mpc at 54 MHz. Its morphology follows the distribution of the thermal intra-cluster medium inferred from the Chandra observation. West of the centrally located head-tail radio galaxy, we detect a radio relic with a projected extent of similar to 500 kpc. From the relic, a similar to 600 kpc long bridge departs and connects with the halo. Between the relic and the radio galaxy, we observe what is most likely a radio phoenix, given its curved spectrum. The phoenix is connected to the tail of the radio galaxy through two arms, which show a nearly constant spectral index for similar to 300 kpc. Conclusions. The halo could be produced by turbulence induced by a major merger, with the merger axis lying in the NE-SW direction. This is supported by the position of the relic, whose origin could be attributed to a shock propagating along the merger axis. It is possible that the same shock has also produced the phoenix through adiabatic compression, while we propose that the bridge could be generated by electrons which were pre-accelerated by the shock, and then re-accelerated by turbulence. Finally, we detect hints of gentle re-energisation in the two arms that depart from the tail of the radio galaxy. |
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| Author(s): Pomakov, VP (Pomakov, V. P.); O'Sullivan, SP (O'Sullivan, S. P.); Bruggen, M (Brueggen, M.); Vazza, F (Vazza, F.); Carretti, E (Carretti, E.); Heald, GH (Heald, G. H.); Horellou, C (Horellou, C.); Shimwell, T (Shimwell, T.); Shulevski, A (Shulevski, A.); Vernstrom, T (Vernstrom, T.) | ||||||||||||||||||
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| Abstract: Faraday rotation studies of distant radio sources can constrain the evolution and the origin of cosmic magnetism. We use data from the LOFAR Two-Metre Sky Survey: Data Release 2 (LoTSS DR2) to study the dependence of the Faraday rotation measure (RM) on redshift. By focusing on radio sources that are close in terms of their projection on the sky, but physically unrelated ('random pairs'), we measure the RM difference, Delta RM, between the two sources. Thus, we isolate the extragalactic contribution to Delta RM from other contributions. We present a statistical analysis of the resulting sample of random pairs and find a median absolute RM difference vertical bar Delta RM vertical bar =(1.79 +/- 0.09) rad m(-2), with vertical bar Delta RM vertical bar uncorrelated both with respect to the redshift difference of the pair and the redshift of the nearer source, and a median excess of random pairs over physical pairs of (1.65 +/- 0.10) rad m(-2). We seek to reproduce this result with Monte Carlo simulations assuming a non-vanishing seed cosmological magnetic field and a redshift evolution of the comoving magnetic field strength that varies as (1 + z)(-gamma). We find the best-fitting results B-0 = B-comoving (z = 0) less than or similar to (2.0 +/- 0.2) nG and gamma less than or similar to 4.5 +/- 0.2 that we conservatively quote as upper limits due to an unmodelled but non-vanishing contribution of local environments to the RM difference. A comparison with cosmological simulations shows our results to be incompatible with primordial magnetogenesis scenarios with uniform seed fields of order nG. | ||||||||||||||||||
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| Author(s): Brozova, V (Brozova, Viktorie); Prockow, J (Prockow, Jaroslaw); Zaveska Drabkova, L (Zaveska Drabkova, Lenka) | |||||||||
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| Abstract: Juncaceae is a cosmopolitan family belonging to the cyperid clade of Poales together with Cyperaceae and Thurniaceae. These families have global economic and ethnobotanical significance and are often keystone species in wetlands around the world, with a widespread cosmopolitan distribution in temperate and arctic regions in both hemispheres. Currently, Juncaceae comprises more than 474 species in eight genera: Distichia, Juncus, Luzula, Marsippospermum, Oreojuncus, Oxychloe center dot, Patosia and Rostkovia. The phylogeny of cyperids has not been studied before in a complex view based on most sequenced species from all three families. In this study, most sequenced regions from chloroplast (rbcL, trnL, trnL-trnF) and nuclear (ITS1-5.8S-ITS2) genomes were employed from more than a thousand species of cyperids covering all infrageneric groups from their entire distributional range. We analyzed them by maximum parsimony, maximum likelihood, and Bayesian inference to revise the phylogenetic relationships in Juncaceae and Cyperaceae. Our major results include the delimitation of the most problematic paraphyletic genus Juncus, in which six new genera are recognized and proposed to recover monophyly in this group: Juncus, Verojuncus, gen. nov., Juncinella, gen. et stat. nov., Alpinojuncus, gen. nov., Australojuncus, gen. nov., Boreojuncus, gen. nov. and Agathryon, gen. et stat. nov. For these genera, a new category, Juncus supragen. et stat. nov., was established. This new classification places most groups recognized within the formal Juncus clade into natural genera that are supported by morphological characters. | |||||||||
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| Record 331 of 349 |
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| Author(s): An, ZY (An, Zheyi); Xie, SS (Xie, Shanshan); Ondrejkovic, P (Ondrejkovic, Petr); Marton, P (Marton, Pavel); de Prado, E (de Prado, Esther); Yokota, H (Yokota, Hiroko); Ren, W (Ren, Wei); Ye, ZG (Ye, Zuo-Guang); Glazer, AM (Glazer, A. M.); Pasciak, M (Pasciak, Marek); Zhang, N (Zhang, Nan) |
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| Abstract: PbZr1-xTixO3 exhibits an antiferroelectric-ferroelectric phase boundary at the composition x - 0.06. Around this boundary, several questions need to be answered, such as the stabilizations of different phases with a small amount of compositional difference, the sequence of phase transitions, the coexistence of crystal structures, and potential applications. In this work, we have carried out systematic structural investigations of single crystals and ceramics with several compositions across the phase boundary. The phase diagram for x 0.07 has been established. A complex phase coexistence is found near the phase boundary, which leads to an unusual transition sequence. It is confirmed that Pbam and R3c structures maintain a subtle balance at the phase boundary, which may be perturbed by a slight change in the concentration or external stimuli. These findings provide unique insights into understanding the antiferroelectric-ferroelectric competition and, hence, into designing alternative materials for energy storage and conversion. |
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| Author(s): Navratilova, P (Navratilova, Pavla); Toegelova, H (Toegelova, Helena); Tulpova, Z (Tulpova, Zuzana); Kuo, YT (Kuo, Yi-Tzu); Stein, N (Stein, Nils); Dolezel, J (Dolezel, Jaroslav); Houben, A (Houben, Andreas); Simkova, H (Simkova, Hana); Mascher, M (Mascher, Martin) | |||||||||||||||
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| Abstract: The first gapless, telomere-to-telomere (T2T) sequence assemblies of plant chromosomes were reported recently. However, sequence assemblies of most plant genomes remain fragmented. Only recent breakthroughs in accurate long-read sequencing have made it possible to achieve highly contiguous sequence assemblies with a few tens of contigs per chromosome, that is a number small enough to allow for a systematic inquiry into the causes of the remaining sequence gaps and the approaches and resources needed to close them. Here, we analyse sequence gaps in the current reference genome sequence of barley cv. Morex (MorexV3). Optical map and sequence raw data, complemented by ChIP-seq data for centromeric histone variant CENH3, were used to estimate the abundance of centromeric, ribosomal DNA, and subtelomeric repeats in the barley genome. These estimates were compared with copy numbers in the MorexV3 pseudomolecule sequence. We found that almost all centromeric sequences and 45S ribosomal DNA repeat arrays were absent from the MorexV3 pseudomolecules and that the majority of sequence gaps can be attributed to assembly breakdown in long stretches of satellite repeats. However, missing sequences cannot fully account for the difference between assembly size and flow cytometric genome size estimates. We discuss the prospects of gap closure with ultra-long sequence reads. | |||||||||||||||
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| Record 333 of 349 | ||||||||||||||||||
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| Author(s): Hert, D (Hert, Daniel); Baca, T (Baca, Tomas); Petracek, P (Petracek, Pavel); Kratky, V (Kratky, Vit); Spurny, V (Spurny, Vojtech); Petrlik, M (Petrlik, Matej); Vrba, M (Vrba, Matous); Zaitlik, D (Zaitlik, David); Stoudek, P (Stoudek, Pavel); Walter, V (Walter, Viktor); Stepan, P (Stepan, Petr); Horyna, J (Horyna, Jiri); Pritzl, V (Pritzl, Vaclav); Silano, G (Silano, Giuseppe); Licea, DB (Licea, Daniel Bonilla); Stibinger, P (Stibinger, Petr); Penicka, R (Penicka, Robert); Nascimento, T (Nascimento, Tiago); Saska, M (Saska, Martin) | ||||||||||||||||||
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| Abstract: This paper presents a family of autonomous Unmanned Aerial Vehicles (UAVs) platforms designed for a diverse range of indoor and outdoor applications. The proposed UAV design is highly modular in terms of used actuators, sensor configurations, and even UAV frames. This allows to achieve, with minimal effort, a proper experimental setup for single, as well as, multi-robot scenarios. Presented platforms are intended to facilitate the transition from simulations, and simplified laboratory experiments, into the deployment of aerial robots into uncertain and hard-to-model real-world conditions. We present mechanical designs, electric configurations, and dynamic models of the UAVs, followed by numerous recommendations and technical details required for building such a fully autonomous UAV system for experimental verification of scientific achievements. To show strength and high variability of the proposed system, we present results of tens of completely different real-robot experiments in various environments using distinct actuator and sensory configurations. | ||||||||||||||||||
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| Author(s): Blaha, J (Blaha, Jan); Skalova, T (Skalova, Tereza); Kalouskova, B (Kalouskova, Barbora); Skorepa, O (Skorepa, Ondrej); Cmunt, D (Cmunt, Denis); Grobarova, V (Grobarova, Valeria); Pazicky, S (Pazicky, Samuel); Polachova, E (Polachova, Edita); Abreu, C (Abreu, Celeste); Stransky, J (Stransky, Jan); Koval, T (Koval, Tomas); Duskova, J (Duskova, Jarmila); Zhao, YG (Zhao, Yuguang); Harlos, K (Harlos, Karl); Hasek, J (Hasek, Jindrich); Dohnalek, J (Dohnalek, Jan); Vanek, O (Vanek, Ondrej) | |||||||||||||||||||||||||||
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Abstract:
NKR-P1 is an inhibitory receptor on the surface of natural killer cells, and its engagement with the ligand LLT1 on activated monocytes and B cells triggers NK cell self-tolerance and other immunological processes. Here authors set up a comprehensive, structure-based model of NKR-P1-LLT1 interaction that involves NKR-P1 homodimer formation and subsequent bridging of two LLT1 molecules.
Signaling by the human C-type lectin-like receptor, natural killer (NK) cell inhibitory receptor NKR-P1, has a critical role in many immune-related diseases and cancer. C-type lectin-like receptors have weak affinities to their ligands; therefore, setting up a comprehensive model of NKR-P1-LLT1 interactions that considers the natural state of the receptor on the cell surface is necessary to understand its functions. Here we report the crystal structures of the NKR-P1 and NKR-P1:LLT1 complexes, which provides evidence that NKR-P1 forms homodimers in an unexpected arrangement to enable LLT1 binding in two modes, bridging two LLT1 molecules. These interaction clusters are suggestive of an inhibitory immune synapse. By observing the formation of these clusters in solution using SEC-SAXS analysis, by dSTORM super-resolution microscopy on the cell surface, and by following their role in receptor signaling with freshly isolated NK cells, we show that only the ligation of both LLT1 binding interfaces leads to effective NKR-P1 inhibitory signaling. In summary, our findings collectively support a model of NKR-P1:LLT1 clustering, which allows the interacting proteins to overcome weak ligand-receptor affinity and to trigger signal transduction upon cellular contact in the immune synapse. |
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| Author(s): Choutka, J (Choutka, Jan); Kratochvil, M (Kratochvil, Michal); Cisarova, I (Cisarova, Ivana); Pohl, R (Pohl, Radek); Kaminsky, J (Kaminsky, Jakub); Parkan, K (Parkan, Kamil) | |||||||||||||||
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| Abstract: Modification of the carbohydrate scaffold is an important theme in drug and vaccine discovery. Therefore, the preparation of novel types of glycomimetics is of interest in synthetic carbohydrate chemistry. In this manuscript, we present an early investigation of the synthesis, structure, and conformational behaviour of (1 -> 1)-Si-disaccharides as a novel type of glycomimetics arising from the replacement of interglycosidic oxygen with a dimethyl-, methylpropyl-, or diisopropylsilyl linkage. We accomplished the preparation of this unusual group of umpoled compounds by the reaction of lithiated glycal or 2-oxyglycal units with dialkyldichlorosilanes. We demonstrated the good stability of the "Si-glycosidic" linkage under acidic conditions even at elevated temperatures. Next, we described the conformational landscape of these compounds by the combination of in silico modelling with spectroscopic and crystallographic methods. Finally, we explained the observed conformational flexibility of these compounds by the absence of gauche stabilizing effects that are typically at play in natural carbohydrates. | |||||||||||||||
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| Author(s): Said, M (Said, Mahmoud); Capal, P (Capal, Petr); Farkas, A (Farkas, Andras); Gaal, E (Gaal, Eszter); Ivanizs, L (Ivanizs, Laszlo); Friebe, B (Friebe, Bernd); Dolezel, J (Dolezel, Jaroslav); Molnar, I (Molnar, Istvan) | ||||||
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| Abstract: Breeding of wheat adapted to new climatic conditions and resistant to diseases and pests is hindered by a limited gene pool due to domestication and thousands of years of human selection. Annual goatgrasses (Aegilops spp.) with M and U genomes are potential sources of the missing genes and alleles. Development of alien introgression lines of wheat may be facilitated by the knowledge of DNA sequences of Aegilops chromosomes. As the Aegilops genomes are complex, sequencing relevant Aegilops chromosomes purified by flow cytometric sorting offers an attractive route forward. The present study extends the potential of chromosome genomics to allotetraploid Ae. biuncialis and Ae. geniculata by dissecting their M and U genomes into individual chromosomes. Hybridization of FITC-conjugated GAA oligonucleotide probe to chromosomes suspensions of the two species allowed the application of bivariate flow karyotyping and sorting some individual chromosomes. Bivariate flow karyotype FITC vs. DAPI of Ae. biuncialis consisted of nine chromosome-populations, but their chromosome content determined by microscopic analysis of flow sorted chromosomes indicated that only 7M(b) and 1U(b) could be sorted at high purity. In the case of Ae. geniculata, fourteen chromosome-populations were discriminated, allowing the separation of nine individual chromosomes (1M(g), 3M(g), 5M(g), 6M(g), 7M(g), 1U(g), 3U(g), 6U(g), and 7U(g)) out of the 14. To sort the remaining chromosomes, a partial set of wheat-Ae. biuncialis and a whole set of wheat-Ae. geniculata chromosome addition lines were also flow karyotyped, revealing clear separation of the GAA-rich Aegilops chromosomes from the GAA-poor A- and D-genome chromosomes of wheat. All of the alien chromosomes represented by individual addition lines could be isolated at purities ranging from 74.5% to 96.6% and from 87.8% to 97.7%, respectively. Differences in flow karyotypes between Ae. biuncialis and Ae. geniculata were analyzed and discussed. Chromosome-specific genomic resources will facilitate gene cloning and the development of molecular tools to support alien introgression breeding of wheat. | ||||||
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| Author(s): Jancik, J (Jancik, Jan); Pospisil, J (Pospisil, Jan); Kratochvil, M (Kratochvil, Matous); Truksa, J (Truksa, Jan); Altamura, D (Altamura, Davide); Giannini, C (Giannini, Cinzia); Weiter, M (Weiter, Martin); Blasi, D (Blasi, Davide); Lukes, V (Lukes, Vladimir); Glowacki, ED (Glowacki, Eric D.); Krajcovic, J (Krajcovic, Jozef) | ||||||||||||
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| Abstract: The investigation of poly(3-alkylthiophenes) (P3ATs) has gained great attention in the last decades. Here, we present the synthesis, experimental and theoretical study of the novel regioregular poly(3-adamantylmethylthiophene) (PMAT) and poly(3-adamantylethylthiophene) (PEAT), characterised by a bulky adamantane side group. The prepared compounds are solution-processable in common organic solvents, possess excellent thermal stability up to 491 degrees C and have unique chemical endurance. The molecular ordering of the polymers was investigated by the GIWAXS technique, and PMAT was found to have the higher content of crystalline phase. The experimental absorption and fluorescence spectra of investigated polymers indicate a higher rigidity of the adamantane side group with respect to torsional rotation in solutions and in thin layers. Electrical measurements exhibit charge carrier mobilities comparable to poly(3-hexylthiophene) (P3HT). In contrast to P3HT, adamantyl-substituted polymers show quasi-reversible reduction alongside the expected quasi -reversible oxidation, which in theory supports the ability to transport both types of electric charges. The newly synthetized regioregular adamantane substituted polythiophenes are serious competitors for a wide range of applications in electronics and optoelectronics. | ||||||||||||
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| Author(s): Pinto, GP (Pinto, Gaspar P.); Hendrikse, NM (Hendrikse, Natalie M.); Stourac, J (Stourac, Jan); Damborsky, J (Damborsky, Jiri); Bednar, D (Bednar, David) | |||||||||
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| Abstract: The development of microbial products for cancer treatment has been in the spotlight in recent years. In order to accelerate the lengthy and expensive drug development process, in silico screening tools are systematically employed, especially during the initial discovery phase. Moreover, considering the steadily increasing number of molecules approved by authorities for commercial use, there is a demand for faster methods to repurpose such drugs. Here we present a review on virtual screening web tools, such as publicly available databases of molecular targets and libraries of ligands, with the aim to facilitate the discovery of potential anticancer drugs based on microbial products. We provide an entry-level step-by-step description of the workflow for virtual screening of microbial metabolites with known protein targets, as well as two practical examples using freely available web tools. The first case presents a virtual screening study of drugs developed from microbial products using Caver Web, a web tool that performs docking along a tunnel. The second case comprises a comparative analysis between a wild type isocitrate dehydrogenase 1 and a mutant that results in cancer, using the recently developed web tool PredictSNPOnco. In summary, this review provides the basic and essential background information necessary for virtual screening experiments, which may accelerate the discovery of novel anticancer drugs. | |||||||||
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| Author(s): Botteon, A (Botteon, A.); Shimwell, TW (Shimwell, T. W.); Cassano, R (Cassano, R.); Cuciti, V (Cuciti, V.); Zhang, X (Zhang, X.); Bruno, L (Bruno, L.); Camillini, L (Camillini, L.); Natale, R (Natale, R.); Jones, A (Jones, A.); Gastaldello, F (Gastaldello, F.); Simionescu, A (Simionescu, A.); Rossetti, M (Rossetti, M.); Akamatsu, H (Akamatsu, H.); van Weeren, RJ (van Weeren, R. J.); Brunetti, G (Brunetti, G.); Bruggen, M (Bruggen, M.); Groeneveld, C (Groeneveld, C.); Hoang, DN (Hoang, D. N.); Hardcastle, MJ (Hardcastle, M. J.); Ignesti, A (Ignesti, A.); Di Gennaro, G (Di Gennaro, G.); Bonafede, A (Bonafede, A.); Drabent, A (Drabent, A.); Rottgering, HJA (Rottgering, H. J. A.); Hoeft, M (Hoeft, M.); de Gasperin, F (de Gasperin, F.) | ||||||||||||||||||||||||||||||
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Abstract:
Context. Relativistic electrons and magnetic fields permeate the intra-cluster medium (ICM) and manifest themselves as diffuse sources of synchrotron emission observable at radio wavelengths, namely radio halos and radio relics. Although there is broad consensus that the formation of these sources is connected to turbulence and shocks in the ICM, the details of the required particle acceleration, the strength and morphology of the magnetic field in the cluster volume, and the influence of other sources of high-energy particles are poorly known.
Aims. Sufficiently large samples of radio halos and relics, which would allow us to examine the variation among the source population and pinpoint their commonalities and differences, are still missing. At present, due to the physical properties of the sources and the capabilities of existing facilities, large numbers of these sources are easiest to detect at low radio frequencies, where they shine brightly. Methods. We examined the low-frequency radio emission from all 309 clusters in the second catalog of Planck Sunyaev Zel'dovich detected sources that lie within the 5634 deg 2 covered by the Second Data Release of the LOFAR Two-meter Sky Survey (LoTSS-DR2). We produced LOFAR images at different resolutions, with and without discrete sources subtracted, and created overlays with optical and X-ray images before classifying the diffuse sources in the ICM, guided by a decision tree. Results. Overall, we found 83 clusters that host a radio halo and 26 that host one or more radio relics (including candidates). About half of them are new discoveries. The detection rate of clusters that host a radio halo and one or more relics in our sample is 30 +/- 11% and 10 +/- 6%, respectively. Extrapolating these numbers, we anticipate that once LoTSS covers the entire northern sky it will provide the detection of 251 +/- 92 clusters that host a halo and 83 +/- 50 clusters that host at least one relic from Planck clusters alone. All images and results produced in this work are publicly available via the project website. |
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| Author(s): Mingo, B (Mingo, B.); Croston, JH (Croston, J. H.); Best, PN (Best, P. N.); Duncan, KJ (Duncan, K. J.); Hardcastle, MJ (Hardcastle, M. J.); Kondapally, R (Kondapally, R.); Prandoni, I (Prandoni, I); Sabater, J (Sabater, J.); Shimwell, TW (Shimwell, T. W.); Williams, WL (Williams, W. L.); Baldi, RD (Baldi, R. D.); Bonato, M (Bonato, M.); Bondi, M (Bondi, M.); Dabhade, P (Dabhade, P.); Gurkan, G (Gurkan, G.); Ineson, J (Ineson, J.); Magliocchetti, M (Magliocchetti, M.); Miley, G (Miley, G.); Pierce, JCS (Pierce, J. C. S.); Rottgering, HJA (Rottgering, H. J. A.) | |||||||||||||||||||||||||||
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| Abstract: Radio-loud active galaxies have two accretion modes [radiatively inefficient (RI) and radiatively efficient (RE)], with distinct optical and infrared signatures, and two jet dynamical behaviours, which in arcsec- to arcmin-resolution radio surveys manifest primarily as centre- or edge-brightened structures [Fanaroff-Riley (FR) class I and II]. The nature of the relationship between accretion mode and radio morphology (FR class) has been the subject of long debate. We present a comprehensive investigation of this relationship for a sample of 286 well-resolved radio galaxies in the LOFAR Two-metre Sky Survey Deep Fields (LoTSS-Deep) first data release, for which robust morphological and accretion mode classifications have been made. We find that two-thirds of luminous FRII radio galaxies are RI, and identify no significant differences in the visual appearance or source dynamic range (peak/mean surface brightness) of the RI and RE FRIIs, demonstrating that both RI and RE systems can produce FRII structures. We also find a significant population of low-luminosity FRIIs (predominantly RI), supporting our earlier conclusion that FRII radio structures can be produced at all radio luminosities. We demonstrate that in the luminosity range where both morphologies are present, the probability of producing FRI or FRII radio morphology is directly linked to stellar mass, while across all morphologies and luminosities, RE accretion occurs in systems with high specific star formation rate, presumably because this traces fuel availability. In summary, the relationship between accretion mode and radio morphology is very indirect, with host-galaxy environment controlling these two key parameters in different ways. | |||||||||||||||||||||||||||
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| Author(s): Rudnick, L (Rudnick, L.); Bruggen, M (Brueggen, M.); Brunetti, G (Brunetti, G.); Cotton, WD (Cotton, W. D.); Forman, W (Forman, W.); Jones, TW (Jones, T. W.); Nolting, C (Nolting, C.); Schellenberger, G (Schellenberger, G.); van Weeren, R (van Weeren, R.) | ||||||||||||||||||||||||
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| Abstract: Thin synchrotron-emitting filaments are increasingly seen in the intracluster medium (ICM). We present the first example of a direct interaction between a magnetic filament, a radio jet, and a dense ICM clump in the poor cluster A194. This enables the first exploration of the dynamics and possible histories of magnetic fields and cosmic rays in such filaments. Our observations are from the MeerKAT Galaxy Cluster Legacy Survey and the LOFAR Two-Meter Sky Survey. Prominent 220 kpc long filaments extend east of radio galaxy 3C40B, with very faint extensions to 300 kpc, and show signs of interaction with its northern jet. They curve around a bend in the jet and intersect the jet in Faraday depth space. The X-ray surface brightness drops across the filaments; this suggests that the relativistic particles and fields contribute significantly to the pressure balance and evacuate the thermal plasma in a similar to 35 kpc cylinder. We explore whether the relativistic electrons could have streamed along the filaments from 3C40B, and present a plausible alternative whereby magnetized filaments are (a) generated by shear motions in the large-scale, post-merger ICM flow, (b) stretched by interactions with the jet and flows in the ICM, amplifying the embedded magnetic fields, and (c) perfused by re-energized relativistic electrons through betatron-type acceleration or diffusion of turbulently accelerated ICM cosmic-ray electrons. We use the Faraday depth measurements to reconstruct some of the 3D structures of the filameGnts and of 3C40A and B. | ||||||||||||||||||||||||
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| Author(s): Marques, SM (Marques, Sergio M.); Slanska, M (Slanska, Michaela); Chmelova, K (Chmelova, Klaudia); Chaloupkova, R (Chaloupkova, Radka); Marek, M (Marek, Martin); Clark, S (Clark, Spencer); Damborsky, J (Damborsky, Jiri); Kool, ET (Kool, Eric T.); Bodnar, D (Bodnar, David); Prokop, Z (Prokop, Zbynek) | ||||||||||||||||||
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| Abstract: HaloTag labeling technology has introduced unrivaled potential in protein chemistry and molecular and cellular biology. A wide variety of ligands have been developed to meet the specific needs of diverse applications, but only a single protein tag, DhaAHT, is routinely used for their incorporation. Following a systematic kinetic and computational analysis of different reporters, a tetramethyirhodamine- and three 4-stilbazolium-based fluorescent ligands, we showed that the mechanism of incorporating different ligands depends both on the binding step and the efficiency of the chemical reaction. By studying the different haloalkane dehalogenases DhaA, LinB, and DmmA, we found that the architecture of the access tunnels is critical for the kinetics of both steps and the ligand specificity. We showed that highly efficient labeling with specific ligands is achievable with natural dehalogenases. We propose a simple protocol for selecting the optimal protein tag for a specific Iigand from the wide pool of available enzymes with diverse access tunnel architectures. The application of this protocol eliminates the need for expensive and laborious protein engineering. | ||||||||||||||||||
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| Author(s): Volny, J (Volny, Jiri); Charvatova, K (Charvatova, Katerina); Veis, M (Veis, Martin); Holy, V (Holy, Vaclav); Vondracek, M (Vondracek, Martin); Honolka, J (Honolka, Jan); Duverger-Nedellec, E (Duverger-Nedellec, Elen); Schusser, J (Schusser, Jakub); D'Souza, SW (D'Souza, Sunil W.); Minar, J (Minar, Jan); Pientka, JM (Pientka, James M.); Marmodoro, A (Marmodoro, Alberto); Vyborny, K (Vyborny, Karel); Uhlirova, K (Uhlirova, Klara) | |||||||||||||||||||||||||||||||||
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| Abstract: Synthesis of single-crystalline NaMnAs is reported, and we confirm its high quality by x-ray photoemission spectra. Magnetometry results are consistent with previous findings of antiferromagnetic order. The electronic structure was further studied using optical transmittance and by theoretical modeling using local-density approximation (LDA) extended to LDA + U for the purpose of determining the Heisenberg model parameters. Optical transmittance measurements confirm theoretical predictions that NaMnAs is a semiconductor. The Neel temperature was determined from temperature dependence of susceptibility, in agreement with our Monte Carlo simulations. | |||||||||||||||||||||||||||||||||
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| Author(s): Hutschenreuter, S (Hutschenreuter, S.); Anderson, CS (Anderson, C. S.); Betti, S (Betti, S.); Bower, GC (Bower, G. C.); Brown, JA (Brown, J-A); Bruggen, M (Brueggen, M.); Carretti, E (Carretti, E.); Clarke, T (Clarke, T.); Clegg, A (Clegg, A.); Costa, A (Costa, A.); Croft, S (Croft, S.); Eck, CV (Eck, C., V); Gaensler, BM (Gaensler, B. M.); De Gasperin, F (de Gasperin, F.); Haverkorn, M (Haverkorn, M.); Heald, G (Heald, G.); Hull, CLH (Hull, C. L. H.); Inoue, M (Inoue, M.); Johnston-Hollitt, M (Johnston-Hollitt, M.); Kaczmarek, J (Kaczmarek, J.); Law, C (Law, C.); Ma, YK (Ma, Y. K.); MacMahon, D (MacMahon, D.); Mao, A (Mao, S. A.); Riseley, C (Riseley, C.); Roy, S (Roy, S.); Shanahan, R (Shanahan, R.); Shimwell, T (Shimwell, T.); Stil, J (Stil, J.); Sobey, C (Sobey, C.); O'Sullivan, SP (O'Sullivan, S. P.); Tasse, C (Tasse, C.); Vacca, V (Vacca, V.); Vernstrom, T (Vernstrom, T.); Williams, PKG (Williams, P. K. G.); Wright, M (Wright, M.); Ensslin, TA (Ensslin, T. A.) | |||||||||||||||||||||||||||
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| Abstract: Aims. This work provides an update to existing reconstructions of the Galactic Faraday rotation sky by processing almost all Faraday rotation data sets available at the end of the year 2020. Observations of extra-Galactic sources in recent years have further illuminated the previously underconstrained southern celestial sky, as well as parts of the inner disc of the Milky Way, along with other regions. This has culminated in an all-sky data set of 55 190 data points, thereby comprising a significant expansion on the 41 330 used in previous works. At the same time, this novelty makes an updated separation of the Galactic component a promising enterprise. The increased source density allows us to present our results in a resolution of about 1.3 x 10(-2) deg(2) (46.8 arcmin(2)), which is a twofold increase compared to previous works. Methods. As for previous Faraday rotation sky reconstructions, this work is based on information field theory, namely, a Bayesian inference scheme for field-like quantities that handles noisy and incomplete data. Results. In contrast to previous reconstructions, we find a significantly thinner and pronounced Galactic disc with small-scale structures exceeding values of several thousand rad m(-2). The improvements can mainly be attributed to the new catalog of Faraday data, but are also supported by advances in correlation structure modeling within numerical information field theory. We also provide a detailed discussion on the statistical properties of the Faraday rotation sky and we investigate correlations with other data sets. | |||||||||||||||||||||||||||
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| Author(s): Zuo, S (Zuo, Sheng); Yadala, R (Yadala, Ramakrishna); Yang, F (Yang, Fen); Talbert, P (Talbert, Paul); Fuchs, J (Fuchs, Joerg); Schubert, V (Schubert, Veit); Ahmadli, U (Ahmadli, Ulkar); Rutten, T (Rutten, Twan); Pecinka, A (Pecinka, Ales); Lysak, MA (Lysak, Martin A.); Lermontova, I (Lermontova, Inna) | |||||||||||||||||||||
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| Abstract: KINETOCHORE NULL2 (KNL2) plays key role in the recognition of centromeres and new CENH3 deposition. To gain insight into the origin and diversification of the KNL2 gene, we reconstructed its evolutionary history in the plant kingdom. Our results indicate that the KNL2 gene in plants underwent three independent ancient duplications in ferns, grasses, and eudicots. Additionally, we demonstrated that previously unclassified KNL2 genes could be divided into two clades alpha KNL2 and beta KNL2 in eudicots and gamma KNL2 and delta KNL2 in grasses, respectively. KNL2s of all clades encode the conserved SANTA domain, but only the alpha KNL2 and gamma KNL2 groups additionally encode the CENPC-k motif. In the more numerous eudicot sequences, signatures of positive selection were found in both alpha KNL2 and beta KNL2 clades, suggesting recent or ongoing adaptation. The confirmed centromeric localization of beta KNL2 and mutant analysis suggests that it participates in loading of new CENH3, similarly to alpha KNL2. A high rate of seed abortion was found in heterozygous beta knl2 plants and the germinated homozygous mutants did not develop beyond the seedling stage. Taken together, our study provides a new understanding of the evolutionary diversification of the plant kinetochore assembly gene KNL2, and suggests that the plant-specific duplicated KNL2 genes are involved in centromere and/or kinetochore assembly for preserving genome stability. | |||||||||||||||||||||
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| Author(s): Kunka, A (Kunka, Antonin); Lacko, D (Lacko, David); Stourac, J (Stourac, Jan); Damborsky, J (Damborsky, Jiri); Prokop, Z (Prokop, Zbynek); Mazurenko, S (Mazurenko, Stanislav) | |||||||||
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Abstract:
The importance of the quantitative description of protein unfolding and aggregation for the rational design of stability or understanding the molecular basis of protein misfolding diseases is well established. Protein thermostability is typically assessed by calorimetric or spectroscopic techniques that monitor different complementary signals during unfolding. The CalFitter webserver has already proved integral to deriving invaluable energy parameters by global data analysis. Here, we introduce CalFitter 2.0, which newly incorporates singular value decomposition (SVD) of multi-wavelength spectral datasets into the global fitting pipeline. Processed time- or temperature-evolved SVD components can now be fitted together with other experimental data types. Moreover, deconvoluted basis spectra provide spectral fingerprints of relevant macrostates populated during unfolding, which greatly enriches the information gains of the CalFitter output. The SVD analysis is fully automated in a highly interactive module, providing access to the results to users without any prior knowledge of the underlying mathematics. Additionally, a novel data uploading wizard has been implemented to facilitate rapid and easy uploading of multiple datasets. Together, the newly introduced changes significantly improve the user experience, making this software a unique, robust, and interactive platform for the analysis of protein thermal denaturation data. The webserver is freely accessible at https://loschmidt.chemi.muni.cz/calfitter.
[GRAPHICS] . |
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| Author(s): Zahonova, K (Zahonova, Kristina); Treitli, SC (Treitli, Sebastian Cristian); Le, T (Le, Tien); Skodova-Sverakova, I (Skodova-Sverakova, Ingrid); Hanouskova, P (Hanouskova, Pavla); Cepicka, I (Cepicka, Ivan); Tachezy, J (Tachezy, Jan); Hampl, V (Hampl, Vladimir) | |||||||||||||||||||||||||||
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| Abstract: Background Mitochondria and peroxisomes are the two organelles that are most affected during adaptation to microoxic or anoxic environments. Mitochondria are known to transform into anaerobic mitochondria, hydrogenosomes, mitosomes, and various transition stages in between, collectively called mitochondrion-related organelles (MROs), which vary in enzymatic capacity. Anaerobic peroxisomes were identified only recently, and their putatively most conserved function seems to be the metabolism of inositol. The group Archamoebae includes anaerobes bearing both anaerobic peroxisomes and MROs, specifically hydrogenosomes in free-living Mastigamoeba balamuthi and mitosomes in the human pathogen Entamoeba histolytica, while the organelles within the third lineage represented by Pelomyxa remain uncharacterized. Results We generated high-quality genome and transcriptome drafts from Pelomyxa schiedti using single-cell omics. These data provided clear evidence for anaerobic derivates of mitochondria and peroxisomes in this species, and corresponding vesicles were tentatively identified in electron micrographs. In silico reconstructed MRO metabolism harbors respiratory complex II, electron-transferring flavoprotein, a partial TCA cycle running presumably in the reductive direction, pyruvate:ferredoxin oxidoreductase, [FeFe]-hydrogenases, a glycine cleavage system, a sulfate activation pathway, and an expanded set of NIF enzymes for iron-sulfur cluster assembly. When expressed in the heterologous system of yeast, some of these candidates localized into mitochondria, supporting their involvement in the MRO metabolism. The putative functions of P. schiedti peroxisomes could be pyridoxal 5 '-phosphate biosynthesis, amino acid and carbohydrate metabolism, and hydrolase activities. Unexpectedly, out of 67 predicted peroxisomal enzymes, only four were also reported in M. balamuthi, namely peroxisomal processing peptidase, nudix hydrolase, inositol 2-dehydrogenase, and d-lactate dehydrogenase. Localizations in yeast corroborated peroxisomal functions of the latter two. Conclusions This study revealed the presence and partially annotated the function of anaerobic derivates of mitochondria and peroxisomes in P. schiedti using single-cell genomics, localizations in yeast heterologous systems, and transmission electron microscopy. The MRO metabolism resembles that of M. balamuthi and most likely reflects the state in the common ancestor of Archamoebae. The peroxisomal metabolism is strikingly richer in P. schiedti. The presence of myo-inositol 2-dehydrogenase in the predicted peroxisomal proteome corroborates the situation in other Archamoebae, but future experimental evidence is needed to verify additional functions of this organelle. | |||||||||||||||||||||||||||
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| Author(s): Gasic, S (Gasic, Srdjan); Mihola, O (Mihola, Ondrej); Trachtulec, Z (Trachtulec, Zdenek) | ||||||
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| Abstract: Aneuploidy (abnormal chromosome number) accompanies reduced ovarian function in humans and mice, but the reasons behind this concomitance remain underexplored. Some variants in the human gene encoding histone-3-lysine-4,36-trimethyltransferase PRDM9 are associated with aneuploidy, and other variants with ovarian function reduced by premature ovarian failure (POF), but no link between POF and aneuploidy has been revealed. SHR/OlaIpcv rat females lacking PRDM9 manifest POF-a reduced follicle number, litter size, and reproductive age. Here, we explored this model to test how POF relates to oocyte euploidy. The mutant rat females displayed increased oocyte aneuploidy and embryonic death of their offspring compared to controls. Because rat PRDM9 positions meiotic DNA breaks, we investigated the repair of these breaks. Fertile control rodents carry pachytene oocytes with synapsed homologous chromosomes and repaired breaks, while sterile Prdm9-deficient mice carry pachytene-like oocytes with many persisting breaks and asynapsed chromosomes. However, most PRDM9-lacking rat oocytes displayed a few persisting breaks and non-homologous synapsis (NHS). HORMAD2 protein serves as a barrier to sister-chromatid repair and a signal for the synapsis and DNA repair checkpoints. NHS but not asynapsis was associated with HORMAD2 levels similar to the levels on rat pachytene chromosomes with homologous synapsis. NHS was accompanied by crossing-over decreased below the minimum that is essential for euploidy. We argue that the increased mutant rat aneuploidy is due to NHS, which allows some oocytes to pass meiotic checkpoints without one crossing-over per chromosomal pair, leading to segregation errors, and thereby NHS links POF to aneuploidy. | ||||||
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| Author(s): Maschmann, D (Maschmann, Daniel); Melchior, AL (Melchior, Anne-Laure); Combes, F (Combes, Francoise); Ciraulo, BM (Ciraulo, Barbara Mazzilli); Freundlich, J (Freundlich, Jonathan); Halle, A (Halle, Anaelle); Drabent, A (Drabent, Alexander) | |||||||||||||||
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| Abstract: The respective contributions of gas accretion, galaxy interactions, and mergers to the mass assembly of galaxies, as well as the evolution of their molecular gas and star-formation activity are still not fully understood. In a recent work, a large sample of double-peak (DP) emission-line galaxies have been identified from the SDSS. While the two peaks could represent two kinematic components, they may be linked to the large bulges that their host galaxies tend to have. Star-forming DP galaxies display a central star-formation enhancement and have been discussed as compatible with a sequence of recent minor mergers. In order to probe merger-induced star-formation mechanisms, we conducted observations of the molecular-gas content of 35 star-forming DP galaxies in the upper part of the main sequence (MS) of star formation (SF) with the IRAM 30 m telescope. Including similar galaxies 0.3 dex above the MS and with existing molecular-gas observations from the literature, we finally obtained a sample of 52 such galaxies. We succeeded in fitting the same kinematic parameters to the optical ionised- and molecular-gas emission lines for ten (19%) galaxies. We find a central star-formation enhancement resulting most likely from a galaxy merger or galaxy interaction, which is indicated by an excess of gas extinction found in the centre. This SF is traced by radio continuum emissions at 150 MHz, 1.4 GHz, and 3 GHz, all three of which are linearly correlated in log with the CO luminosity with the same slope. The 52 DP galaxies are found to have a significantly larger amount of molecular gas and longer depletion times, and hence a lower star-formation efficiency, than the expected values at their distance of the MS. The large bulges in these galaxies might be stabilising the gas, hence reducing the SF efficiency. This is consistent with a scenario of minor mergers increasing the mass of bulges and driving gas to the centre. We also excluded the inwards-directed gas migration and central star-formation enhancement as the origin of a bar morphology. Hence, these 52 DP galaxies could be the result of recent minor mergers that funnelled molecular gas towards their centre, triggering SF, but with moderate efficiency. | |||||||||||||||
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