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| Author(s): Mrazkova, J (Mrazkova, Jana); Sistek, P (Sistek, Petr); Lochman, J (Lochman, Jan); Holla, LI (Izakovicova Holla, Lydie); Danek, Z (Danek, Zdenek); Linhartova, PB (Borilova Linhartova, Petra) | |||||||||||||||||||||
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| Abstract: Mannose-binding lectin (MBL) deficiency caused by the variability in the MBL2 gene is responsible for the susceptibility to and severity of various infectious and autoimmune diseases. A combination of six single nucleotide polymorphisms (SNPs) has a major impact on MBL levels in circulation. The aim of this study is to design and validate a sensitive and economical method for determining MBL2 haplogenotypes. The SNaPshot assay is designed and optimized to genotype six SNPs (rs1800451, rs1800450, rs5030737, rs7095891, rs7096206, rs11003125) and is validated by comparing results with Sanger sequencing. Additionally, an algorithm for online calculation of haplogenotype combinations from the determined genotypes is developed. Three hundred and twenty-eight DNA samples from healthy individuals from the Czech population are genotyped. Minor allele frequencies (MAFs) in the Czech population are in accordance with those present in the European population. The SNaPshot assay for MBL2 genotyping is a high-throughput, cost-effective technique that can be used in further genetic-association studies or in clinical practice. Moreover, a freely available online application for the calculation of haplogenotypes from SNPs is developed within the scope of this project. | |||||||||||||||||||||
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| Record 2 of 414 | ||||||
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| Author(s): Hubacek, O (Hubacek, Ondrej); Sourek, G (Sourek, Gustav); Zelezny, F (Zelezny, Filip) | ||||||
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| Abstract: We investigate the state-of-the-art in score-based soccer match outcome modelling to identify the top-performing methods across diverse classes of existing approaches to the problem. Namely, we bring together various statistical methods based on Poisson and Weibull distributions and several general ranking algorithms (Elo, Steph ratings, Gaussian-OD ratings) as well as domain-specific rating systems (Berrar ratings, pi-ratings). We review, reimplement and experimentally compare these diverse competitors altogether on the largest database of soccer results available to identify true leaders. Our results reveal that the individual predictions, as well as the overall performances, are very similar across the top models tested, likely suggesting the limits of this generic approach to score-based match outcome modelling. No study of a similar scale has previously been done. | ||||||
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| Record 3 of 414 | ||||||
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| Author(s): Lee, GKC (Lee, Gary Kwok Cheong); Bienzle, D (Bienzle, Dorothee); Keller, SM (Keller, Stefan Matthias); Hwang, MH (Hwang, Mei-Hua); Darzentas, N (Darzentas, Nikos); Chang, HY (Chang, Haiyang); Ratsep, E (Ratsep, Emily); Egan, R (Egan, Rebecca); Beeler-Marfisi, J (Beeler-Marfisi, Janet) | ||||||
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| Abstract: Background Lymphocytic neoplasms with frequent reactive lymphocytes are uncommonly reported in dogs, and can pose a diagnostic challenge. Different diagnostic modalities such as cytology, flow cytometry, histopathology, immunohistochemistry, and clonality testing, are sometimes required for a diagnosis. This report illustrates the value of using a multi-modal diagnostic approach to decipher a complex lymphocytic tumor, and introduces immune repertoire sequencing as a diagnostic adjunct. Case presentation A 10-month-old Great Dane was referred for marked ascites. Cytologic analysis of abdominal fluid and hepatic aspirates revealed a mixed lymphocyte population including numerous large lymphocytes, yielding a diagnosis of lymphoma. Flow cytometrically, abdominal fluid lymphocytes were highly positive for CD4, CD5, CD18, CD45, and MHC II, consistent with T cell lymphoma. Due to a rapidly deteriorating clinical condition, the dog was euthanized. Post mortem histologic evaluation showed effacement of the liver by aggregates of B cells surrounded by T cells, suggestive of hepatic T cell-rich large B cell lymphoma. Immune repertoire sequencing confirmed the presence of clonal B cells in the liver but not the abdominal fluid, whereas reactive T cells with shared, polyclonal immune repertoires were found in both locations. Conclusions T cell-rich large B cell lymphoma is a rare neoplasm in dogs that may be challenging to diagnose and classify due to mixed lymphocyte populations. In this case, the results of histopathology, immunohistochemistry and immune repertoire sequencing were most consistent with a hepatic B cell neoplasm and reactive T cells exfoliating into the abdominal fluid. Immune repertoire sequencing was helpful in delineating neoplastic from reactive lymphocytes and characterizing repertoire overlap in both compartments. The potential pitfalls of equating atypical cytomorphology and monotypic marker expression in neoplasia are highlighted. | ||||||
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| Record 4 of 414 | |||||||||
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| Author(s): Hozzova, J (Hozzova, Jana); Filipovic, J (Filipovic, Jiri); Nezarat, A (Nezarat, Amin); Ol'ha, J (Ol'ha, Jaroslav); Petrovic, F (Petrovic, Filip) | |||||||||
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Abstract:
We have developed several autotuning benchmarks in CUDA that take into account performance-relevant source-code parameters and reach near peak-performance on various GPU architectures. We have used them during the development and evaluation of a search method for tuning space proposed in [1]. With our framework Kernel Tuning Toolkit, freely available at Github, we measured computation times and hardware performance counters on several GPUs for the complete tuning spaces of five benchmarks. These data, which we provide here, might benefit research of search algorithms for the tuning spaces of GPU codes or research of relation between applied code optimization, hardware performance counters, and GPU kernels' performance.
Moreover, we describe the scripts we used for robust evaluation of our searcher and comparison to others in detail. In particular, the script that simulates the tuning, i.e., replaces time-demanding compiling and executing the tuned kernels with a quick reading of the computation time from our measured data, makes it possible to inspect the convergence of tuning search over a large number of experiments. These scripts, freely available with our other codes, make it easier to experiment with search algorithms and compare them in a robust and reproducible way. During our research, we generated models for predicting values of performance counters from values of tuning parameters of our benchmarks. Here, we provide the models themselves and describe the scripts we implemented for their training. These data might benefit researchers who want to reproduce or build on our research. (C) 2021 The Authors. Published by Elsevier Inc. |
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| Record 5 of 414 | |||||||||
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| Author(s): Sopko, B (Sopko, Bruno); Tejral, G (Tejral, Gracian); Bitti, G (Bitti, Guissepe); Abate, M (Abate, Marianna); Medvedikova, M (Medvedikova, Martina); Hajduch, M (Hajduch, Marian); Chloupek, J (Chloupek, Jan); Fajmonova, J (Fajmonova, Jolana); Skoric, M (Skoric, Misa); Amler, E (Amler, Evzen); Erban, T (Erban, Tomas) | |||||||||
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| Abstract: The broad-spectrum herbicide, glyphosate, is considered safe for animals because it selectively affects the shikimate pathway that is specific to plants and microorganisms. We sought a previously unknown mechanism to explain the concerns that glyphosate exposure can negatively affect animals, including humans. Computer modeling showed a probable interaction between glyphosate and eukaryotic translation elongation factor 1 subunit alpha 1 (eEF1 alpha 1), which was confirmed by microcalorimetry. Only restricted, nondisrupted spermatogenesis in rats was observed after chronic glyphosate treatments (0.7 and 7 mg/L). Cytostatic and antiproliferative effects of glyphosate in GC-1 and SUP-B15 cells were indicated. Meta-analysis of public health data suggested a possible effect of glyphosate use on sperm count. The in silico, in vitro, and in vivo experimental results as well as the metastatistics indicate side effects of chronic glyphosate exposure. Together, these findings indicate that glyphosate delays protein synthesis through an interaction with eEF1 alpha 1, thereby suppressing spermatogenesis and cell growth. | |||||||||
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| Record 6 of 414 | |||||||||||||||
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| Author(s): Avila, J (Avila, Jocasta); Cervinka, C (Cervinka, Ctirad); Dugas, PY (Dugas, Pierre-Yves); Padua, AAH (Padua, Agilio A. H.); Gomes, MC (Costa Gomes, Margarida) | |||||||||||||||
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| Abstract: Porous ionic liquids prepared from phosphonium-based ionic liquids and metal-organic frameworks (MOFs) are fluid in large ranges of temperature including ambient. It is shown that the ion pairs are too voluminous to enter the pores of the MOF, so the porous liquids remain several months as suspensions with permanent free volume, capable of absorbing large quantities of gases. The increase in gas absorption, when compared with the pure ionic liquids, is proportional to the amount of porous solid in suspension. Structural features of the MOFs and of the ionic liquids are maintained in the suspensions. Thermodynamic analysis and molecular simulations show that the driving force for gas absorption by the porous ionic liquids is energetic as well as structural being controlled by gas-solid affinity or by the porous liquid free volume. The enthalpy of gas absorption allows easy regeneration of the porous liquid in all cases. The dissolved gases fluidify the porous ionic liquids, different gases having distinct effects on mass transport. The molecular mechanisms that explain the stability of the suspensions and their capacity for gas absorption are identified and point toward easy design rules that will enable numerous applications of these innovative materials as reaction or separation media. | |||||||||||||||
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| Record 7 of 414 | ||||||
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| Author(s): Rubes, M (Rubes, Miroslav); Koudelkova, E (Koudelkova, Eva); Vaculik, J (Vaculik, Jan); Trachta, M (Trachta, Michal); Bulanek, R (Bulanek, Roman); Bludsky, O (Bludsky, Ota) | ||||||
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| Abstract: H-MOR zeolites with different Si/Al ratios were investigated by the combined use of FT-IR spectroscopy, calorimetry, and periodic DFT calculations. Our analysis of 14 different Br?nsted acid sites (BAS) was carried out with the ?/r correlation method parameterized to reproduce the OH band shape for the high silica H-MOR(32) sample. The estimated populations clearly show that the Al distribution exhibits non-statistical behavior. The preferential incorporation of Al into the T3 and T4 framework positions is in excellent agreement with the X-ray study of Alberti et al. on natural mordenites. This suggests that the Al distribution is very similar in both high silica and aluminum rich MOR materials. The analysis of H-MOR with lower Si/Al ratios is complicated by the interaction of the adjacent BAS. This effect leads to significant changes in relative energies that determine populations of the individual sites. Our interpretation of the experimental data is further supported by a very good agreement between calculated CO adsorption enthalpies and calorimetric measurements. An anomalously large dispersion stabilization is found for adsorption complexes located in the side pocket of the MOR framework. | ||||||
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| Record 8 of 414 | ||||||
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| Author(s): Nakahara, S (Nakahara, Shinichi); Matos-Maravi, P (Matos-Maravi, Pavel); Schwartz, J (Schwartz, Johanna); Willmott, KR (Willmott, Keith R.) | ||||||
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The field of systematics and our understanding of phylogenetic relationships have been invigorated by the use of molecular data, but analyses based on DNA sequence data are not always corroborated by diagnostic morphological characters. In particular, several taxonomic changes in butterflies (Papilionoidea) have been made solely on the basis of molecular data without identifying morphological synapomorphies that might have aided in diagnosing taxa from butterfly collections or specimens with no accessible DNA. We here focus on the butterfly genus Pseudodebis Forster, 1964 in the so- called 'Taygetis clade', which is one of the major clades in the diverse Neotropical nymphalid subtribe Euptychiina. We inferred the evolution of a male genitalic character using the most comprehensive molecular phylogeny for the 'Taygetis clade' to date. This approach allowed us to identify a synapomorphy for Pseudodebis Forster, 1964, which can be used to morphologically diagnose this genus and to distinguish it from other genera in the 'Taygetis clade'. In addition, we describe two new species of Pseudodebis, P. nakamurai Nakahara & Willmott, sp. nov. and P. pieti Nakahara & Willmott, sp. nov., recovered as sister species based on molecular data, with an estimated time of divergence of 0.3 Ma (Bayesian confidence interval 0.03-1.61 Ma). Despite the low genetic divergence between these two Pseudodebis species, they can be readily distinguished by wing morphology. Pseudodebis nakamurai, sp. nov. and P. pieti, sp. nov. occur in partial sympatry across an elevational gradient along the western Andes, and the inferred recent speciation event might be related to a shift in elevation and possibly a change in larval hostplant preference.
urn:lsid:zoobank.org:pub:38B4AF76-79E9-4D4D-BF16-FCD8F53A7277 |
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| Record 9 of 414 | ||||||||||||
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| Author(s): Wos, G (Wos, Guillaume); Choudhury, RR (Choudhury, Rimjhim Roy); Kolar, F (Kolar, Filip); Parisod, C (Parisod, Christian) | ||||||||||||
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| Abstract: Background Plant genomes can respond rapidly to environmental changes and transposable elements (TEs) arise as important drivers contributing to genome dynamics. Although some elements were reported to be induced by various abiotic or biotic factors, there is a lack of general understanding on how environment influences the activity and diversity of TEs. Here, we combined common garden experiment with short-read sequencing to investigate genomic abundance and expression of 2245 consensus TE sequences (containing retrotransposons and DNA transposons) in an alpine environment in Arabidopsis arenosa. To disentangle general trends from local differentiation, we leveraged four foothill-alpine population pairs from different mountain regions. Seeds of each of the eight populations were raised under four treatments that differed in temperature and irradiance, two factors varying with elevation. RNA-seq analysis was performed on leaves of young plants to test for the effect of elevation and subsequently of temperature and irradiance on expression of TE sequences. Results Genomic abundance of the 2245 consensus TE sequences varied greatly between the mountain regions in line with neutral divergence among the regions, representing distinct genetic lineages of A. arenosa. Accounting for intraspecific variation in abundance, we found consistent transcriptomic response for some TE sequences across the different pairs of foothill-alpine populations suggesting parallelism in TE expression. In particular expression of retrotransposon LTR Copia (e.g. Ivana and Ale clades) and LTR Gypsy (e.g. Athila and CRM clades) but also non-LTR LINE or DNA transposon TIR MuDR consistently varied with elevation of origin. TE sequences responding specifically to temperature and irradiance belonged to the same classes as well as additional TE clades containing potentially stress-responsive elements (e.g. LTR Copia Sire and Tar, LTR Gypsy Reina). Conclusions Our study demonstrated that the A. arenosa genome harbours a considerable diversity of TE sequences whose abundance and expression response varies across its native range. Some TE clades may contain transcriptionally active elements responding to a natural environmental gradient. This may further contribute to genetic variation between populations and may ultimately provide new regulatory mechanisms to face environmental challenges. | ||||||||||||
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| Record 10 of 414 | ||||||||||||
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| Author(s): Modrzejewski, M (Modrzejewski, Marcin); Yourdkhani, S (Yourdkhani, Sirous); Smiga, S (Smiga, Szymon); Klimes, J (Klimes, Jiri) | ||||||||||||
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| Abstract: The many-body expansion (MBE) of energies of molecular clusters or solids offers a way to detect and analyze errors of theoretical methods that could go unnoticed if only the total energy of the system was considered. In this regard, the interaction between the methane molecule and its enclosing dodecahedral water cage, CH4 center dot center dot center dot(H2O)(20), is a stringent test for approximate methods, including density functional theory (DFT) approximations. Hybrid and semilocal DFT approximations behave erratically for this system, with three- and four-body nonadditive terms having neither the correct sign nor magnitude. Here, we analyze to what extent these qualitative errors in different MBE contributions are conveyed to post-Kohn-Sham random-phase approximation (RPA), which uses approximate Kohn-Sham orbitals as its input. The results reveal a correlation between the quality of the DFT input states and the RPA results. Moreover, the renormalized singles energy (RSE) corrections play a crucial role in all orders of the many-body expansion. For dimers, RSE corrects the RPA underbinding for every tested Kohn-Sham model: generalized-gradient approximation (GGA), meta-GGA, (meta-)GGA hybrids, as well as the optimized effective potential at the correlated level. Remarkably, the inclusion of singles in RPA can also correct the wrong signs of three- and four-body nonadditive energies as well as mitigate the excessive higher-order contributions to the many-body expansion. The RPA errors are dominated by the contributions of compact clusters. As a workable method for large systems, we propose to replace those compact contributions with CCSD(T) energies and to sum up the remaining many-body contributions up to infinity with supermolecular or periodic RPA. As a demonstration of this approach, we show that for RPA(PBE0)+RSE it suffices to apply CCSD(T) to dimers and 30 compact, hydrogen-bonded trimers to get the methane-water cage interaction energy to within 1.6% of the reference value. | ||||||||||||
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| Record 11 of 414 | ||||||||||||||||||||||||||||||
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| Author(s): Cahlik, A (Cahlik, Ales); Hellerstedt, J (Hellerstedt, Jack); Mendieta-Moreno, JI (Mendieta-Moreno, Jesus, I); Svec, M (Svec, Martin); Santhini, VM (Santhini, Vijai M.); Pascal, S (Pascal, Simon); Soler-Polo, D (Soler-Polo, Diego); Erlingsson, SI (Erlingsson, Sigurdur, I); Vyborny, K (Vyborny, Karel); Mutombo, P (Mutombo, Pingo); Marsalek, O (Marsalek, Ondrej); Siri, O (Siri, Olivier); Jelinek, P (Jelinek, Pavel) | ||||||||||||||||||||||||||||||
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| Abstract: In hydrogen-bonded systems, nuclear quantum effects such as zero-point motion and tunneling can significantly affect their material properties through underlying physical and chemical processes. Presently, direct observation of the influence of nuclear quantum effects on the strength of hydrogen bonds with resulting structural and electronic implications remains elusive, leaving opportunities for deeper understanding to harness their fascinating properties. We studied hydrogen-bonded one-dimensional quinonediimine molecular networks which may adopt two isomeric electronic configurations via proton transfer. Herein, we demonstrate that concerted proton transfer promotes a delocalization of pi-electrons along the molecular chain, which enhances the cohesive energy between molecular units, increasing the mechanical stability of the chain and giving rise to distinctive electronic in-gap states localized at the ends. These findings demonstrate the identification of a class of isomeric hydrogen-bonded molecular systems where nuclear quantum effects play a dominant role in establishing their chemical and physical properties. This identification is a step toward the control of mechanical and electronic properties of low-dimensional molecular materials via concerted proton tunneling. | ||||||||||||||||||||||||||||||
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| Record 12 of 414 | ||||||
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| Author(s): Kana, T (Kana, T.); Cermak, J (Cermak, J.); Kral, L (Kral, L.) | ||||||
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| Abstract: We have performed ab initio calculations with equilibrium supercells of the Mg2Ni compound and its hydride Mg2NiH4 doped with elements X = Al, Ga, In, Si, Ge and Sn. Two concentrations of X in both structures have been set: (1) every 16th, and (2) every fourth Ni atom has been substituted by X. Total energy calculations yielded the Mg2NiH4 hydrogen absorption enthalpy DHabs according to the chemical reaction Mg2Ni + 2H(2) -> Mg2NiH4. Reduction of the hydrogen absorption enthalpy was reported for both concentrations of X. When doping the Mg2NiH4 hydride with X = In in a low concentration (1), the value of hydrogen desorption enthalpy decreases from 68.22 to 55.96 kJ(mol H-2)(-1). Doping with X = In in a high concentration (2) further decreases the hydrogen desorption enthalpy to 5.50 kJ(mol H-2)(-1). Further, the electronic structure of Mg-2(Ni-In)H-4 hydride with a low In concentration indicates weaker Ni-H bonds in comparison with the pristine Mg2NiH4. Attraction between H and In atoms induced enhanced bonding between Mg and H atoms compared to the pristine Mg2NiH4. (C) 2021 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved. | ||||||
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| Author(s): Opekar, S (Opekar, Stanislav); Kvicala, J (Kvicala, Jaroslav); Moos, M (Moos, Martin); Pejchal, V (Pejchal, Vladimir); Simek, P (Simek, Petr) | ||||||||||||
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| Abstract: The protection of carboxyl groups by esterification has been the most common method in macroscale and microscale chemistries. The esterification is usually conducted under anhydrous conditions; however, in biological chemistry and related fields, the reaction is of major concern in aqueous environments. Immediate esterification of the carboxyl in aqueous alcoholic media driven by an alkyl chloroformate and pyridine has been such a method which has found widespread use in many research and industrial laboratories. Nevertheless, the reaction mechanism has not yet been investigated, to our knowledge, and is not well understood. Herein, we describe the reaction intermediates and demonstrate that the reaction proceeds via a continual formation of the N-acylpyridinium intermediate decomposed by several reaction channels to the final ester. The understanding of the mechanism could encourage novel laboratory applications of this important esterification method. | ||||||||||||
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| Record 14 of 414 | |||||||||
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| Author(s): Hofierka, J (Hofierka, Jaroslav); Klimes, J (Klimes, Jiri) | |||||||||
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| Abstract: We calculate binding energies of four molecular solids using the Hartree-Fock (HF) and second-order Moller-Plesset perturbation theory (MP2). We obtain the energies within many-body expansion (MBE) as well as using periodic boundary conditions (PBC) to compare both approaches. The systems we study are methane, carbon dioxide, ammonia, and methanol. We use tight convergence settings to obtain the binding energies with a high precision, we estimate the uncertainties to be only few tenths of percent. We discuss several issues that affect the quality of the results and which need to be considered to reach high precision for both MBE and within PBC. For example, HF as well as MP2 energies within PBC benefited from the use of real-space Coulomb cut-off technique, the convergence of energies within MBE was improved by modifying the order of summation. Finally, numerical noise made the evaluation of some of the MBE contributions difficult and the effect was reduced by using smaller basis sets for the less critical terms. | |||||||||
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| Record 15 of 414 | ||||||
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| Author(s): Kabelka, I (Kabelka, Ivo); Brozek, R (Brozek, Radim); Vacha, R (Vacha, Robert) | ||||||
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| Abstract: The selective permeability of cellular membranes is a crucial property for controlled transport into and out of cells. Molecules that can bypass the cellular machinery and spontaneously translocate across membranes could be used as therapeutics or drug carriers. Peptides are a prominent class of such molecules, which include natural and man-developed antimicrobial and cell-penetrating peptides. However, the necessary peptide properties for translocation remain elusive. Computer simulations could uncover these properties once we have a good collective variable (CV) that accurately describes the translocation process. Here, we developed a new CV, which includes a description of peptide insertion, local membrane deformation, and peptide internal degrees of freedom related to its charged groups. By comparison of CVs, we demonstrated that all these components are necessary for an accurate description of peptide translocation. Moreover, the advantages and disadvantages of three common methods for free-energy calculations with our CV were evaluated using the MARTINI coarse-grained model: umbrella sampling, umbrella sampling with replica exchange, and metadynamics. The developed CV leads to the reliable and effective calculation of the free energy of peptide translocation, and thus, it could be useful in the design of spontaneously translocating peptides. | ||||||
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| Record 16 of 414 | |||||||||||||||
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| Author(s): Kohelova, E (Kohelova, Eliska); Marikova, J (Marikova, Jana); Korabecny, J (Korabecny, Jan); Hulcova, D (Hulcova, Daniela); Kucera, T (Kucera, Tomas); Jun, D (Jun, Daniel); Chlebek, J (Chlebek, Jakub); Jenco, J (Jenco, Jaroslav); Safratova, M (Safratova, Marcela); Hrabinova, M (Hrabinova, Martina); Ritomska, A (Ritomska, Aneta); Malanik, M (Malanik, Milan); Perinova, R (Perinova, Rozalie); Breiterova, K (Breiterova, Katerina); Kunes, J (Kunes, Jiri); Novakova, L (Novakova, Lucie); Opletal, L (Opletal, Lubomir); Cahlikova, L (Cahlikova, Lucie) | |||||||||||||||
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| Abstract: Twenty known Amaryllidaceae alkaloids of various structural types, and one undescribed alkaloid of narcikachnine-type, named narcieliine (3), have been isolated from fresh bulbs of Zephyranthes citrina. The chemical structures of the isolated alkaloids were elucidated by a combination of MS, HRMS, 1D and 2D NMR, and CD spectroscopic techniques, and by comparison with literature data. The absolute configuration of narcieliine (3) has also been determined. Compounds isolated in a sufficient quantity were evaluated for their in vitro acetylcholinesterase (AChE; E.C. 3.1.1.7), butyrylcholinesterase (BuChE; E.C. 3.1.1.8), and prolyl oligopeptidase (POP; E.C. 3.4.21.26) inhibition activities. Significant human AChE/BuChE (hAChE/hBuChE) inhibitory activity was demonstrated by the newly described alkaloid narcieliine (3), with IC50 values of 18.7 +/- 2.3 mu M and 1.34 +/- 0.31 mu M, respectively. This compound is also predicted to cross the blood-brain barrier (BBB) through passive diffusion. The in vitro data were further supported by in silico studies of 3 in the active site of hAChE/hBuChE. | |||||||||||||||
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| Record 17 of 414 | ||||||||||||||||||
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| Author(s): Oslejsek, R (Oslejsek, Radek); Rusnak, V (Rusnak, Vit); Burska, K (Burska, Karolina); Svabensky, V (Svabensky, Valdemar); Vykopal, J (Vykopal, Jan); Cegan, J (Cegan, Jakub) | ||||||||||||||||||
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| Abstract: Hands-on training is an effective way to practice theoretical cybersecurity concepts and increase participants' skills. In this article, we discuss the application of visual analytics principles to the design, execution, and evaluation of training sessions. We propose a conceptual model employing visual analytics that supports the sensemaking activities of users involved in various phases of the training life cycle. The model emerged from our long-term experience in designing and organizing diverse hands-on cybersecurity training sessions. It provides a classification of visualizations and can be used as a framework for developing novel visualization tools supporting phases of the training life-cycle. We demonstrate the model application on examples covering two types of cybersecurity training programs. | ||||||||||||||||||
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| Record 18 of 414 | |||||||||
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| Author(s): Friak, M (Friak, Martin); Pavlu, J (Pavlu, Jana); Sob, M (Sob, Mojmir) | |||||||||
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| Abstract: We have performed an ab initio study of vacancy-induced changes in thermodynamic, structural and magnetic properties of single-phase ferromagnetic Fe2CoAl with a chemically disordered (i) two-sublattice B2 phase or (ii) single-sublattice A2 phase. The two polymorphs of slightly non-stoichiometric Fe2CoAl (Fe27Co14Al13) were modeled by two different 54-atom supercells with atoms distributed according to the special quasi-random structure (SQS) concept. Both the lower-energy B2 phase and a higher-energy A2 phase possess elastic constants that correspond to an auxetic material that is mechanically stable. The properties of vacancies were computed by systematically removing different atoms (one at a time) from the supercells and quite wide ranges of values of vacancy-related characteristics were obtained. The increase in the level of disorder (when changing from the B2 to the A2 phase) results in an increase in the scatter of calculated values. The Fe and Co vacancies have lower vacancy formation energies than the Al ones. The total magnetic moment of the supercell decreases when introducing Fe and Co vacancies but it increases due to Al ones. The latter findings can be partly explained by an increase of the local magnetic moment of Fe atoms when the number of Al atoms in the first neighbor shell of Fe atoms is reduced, such as due to Al vacancies.</p> | |||||||||
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| Record 19 of 414 | |||||||||||||||
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| Author(s): Yordanov, D (Yordanov, Dancho); Deneva, V (Deneva, Vera); Georgiev, A (Georgiev, Anton); Vassilev, N (Vassilev, Nikolay); Vala, M (Vala, Martin); Zhivkov, I (Zhivkov, Ivaylo); Antonov, L (Antonov, Liudmil) | |||||||||||||||
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| Abstract: Two new 4-OH coumarin based rotary switches, containing fixed carbonyl groups in the rotor, have been synthesized and their properties have been studied by combined use of DFT calculations and molecular spectroscopy (UV-Vis absorbance and emission, NMR). It was found that the structure of the stator (naphthyl in 2 or quinolyl moiety in 3) and solvents polarity do not influence their azo-hydrazone tautomerism. Both compounds exist as keto (hydrazone) tautomers. The NMR data indicate a mixture of E (major) and Z (minor) keto form isomers in solution. The results are in very good agreement with ground state DFT calculations. The keto tautomers exhibit different emission behavior depending on the structure of the stators. Comparing to 2, more intensive emission and higher lifetime was observed in 3, where the formation of intramolecular hydrogen bonding of the hydrazone NH with the N atom of quinoline restricts the rotation of the stator. According to the spectral data and the TDDFT analysis the observed emission originates from the excitation of the keto tautomers and does not include excited state proton transfer. It was shown that the protonation is a suitable stimulus for E/Z switching in 2, where a possible mechanism is sketched. In the case of 3, the addition of acid leads to the pmtonation of the quinolyl nitrogen atom, which slightly affects the E/Z isomerization ratio. | |||||||||||||||
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| Record 20 of 414 | ||||||
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| Author(s): Merino, R (Merino, Raul); Pospisil, J (Pospisil, Jan); Sobotka, T (Sobotka, Tomas); Sottinen, T (Sottinen, Tommi); Vives, J (Vives, Josep) | ||||||
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| Abstract: The research presented in this paper provides an alternative option pricing approach for a class of rough fractional stochastic volatility models. These models are increasingly popular between academics and practitioners due to their surprising consistency with financial markets. However, they bring several challenges alongside. Most noticeably, even simple nonlinear financial derivatives as vanilla European options are typically priced by means of Monte-Carlo (MC) simulations which are more computationally demanding than similar MC schemes for standard stochastic volatility models. In this paper, we provide a proof of the prediction law for general Gaussian Volterra processes. The prediction law is then utilized to obtain an adapted projection of the future squared volatility - a cornerstone of the proposed pricing approximation. Firstly, a decomposition formula for European option prices under general Volterra volatility models is introduced. Then we focus on particular models with rough fractional volatility and we derive an explicit semi-closed approximation formula. Numerical properties of the approximation for a popular model - the rBergomi model - are studied and we propose a hybrid calibration scheme which combines the approximation formula alongside MC simulations. This scheme can significantly speed up the calibration to financial markets as illustrated on a set of AAPL options. | ||||||
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| Record 21 of 414 | ||||||||||||
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| Author(s): Scheirich, P (Scheirich, P.); Pravec, P (Pravec, P.); Kusnirak, P (Kusnirak, P.); Hornoch, K (Hornoch, K.); McMahon, J (McMahon, J.); Scheeres, DJ (Scheeres, D. J.); Capek, D (Capek, D.); Pray, DP (Pray, D. P.); Kucakova, H (Kucakova, H.); Galad, A (Galad, A.); Vrastil, J (Vrastil, J.); Krugly, YN (Krugly, Yu N.); Moskovitz, N (Moskovitz, N.); Avner, LD (Avner, L. D.); Skiff, B (Skiff, B.); McMillan, RS (McMillan, R. S.); Larsen, JA (Larsen, J. A.); Brucker, MJ (Brucker, M. J.); Tubbiolo, AF (Tubbiolo, A. F.); Cooney, WR (Cooney, W. R.); Gross, J (Gross, J.); Terrell, D (Terrell, D.); Burkhonov, O (Burkhonov, O.); Ergashev, KE (Ergashev, K. E.); Ehgamberdiev, SA (Ehgamberdiev, Sh A.); Fatka, P (Fatka, P.); Durkee, R (Durkee, R.); Schunova, EL (Schunova, E. Lilly); Inasaridze, RY (Inasaridze, R. Ya); Ayvazian, VR (Ayvazian, V. R.); Kapanadze, G (Kapanadze, G.); Gaftonyuk, NM (Gaftonyuk, N. M.); Sanchez, JA (Sanchez, J. A.); Reddy, V (Reddy, V); McGraw, L (McGraw, L.); Kelley, MS (Kelley, M. S.); Molotov, IE (Molotov, I. E.) | ||||||||||||
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Abstract:
We obtained thorough photometric observations of two binary near-Earth asteroids (66391) Moshup = 1999 KW4 and (88710) 2001 SL9 taken from 2000 to 2019. We modeled the data and derived physical and dynamical properties of the binary systems. For (66391) 1999 KW4, we derived its mutual orbit's pole, semimajor axis and eccentricity that are in agreement with radar-derived values (Ostro et al., 2006. Science, 314, 1276-1280). However, we found that the data are inconsistent with a constant orbital period and we obtained unique solution with a quadratic drift of the mean anomaly of the satellite of -0.65 +/- 0.16 deg./yr2 (all quoted uncertainties correspond to 3 sigma). This means that the semimajor axis of the mutual orbit of the components of this binary system, determined a = 2.548 +/- 0.015 km by Ostro et al. (2006), increases in time with a mean rate of 1.2 +/- 0.3 cm/yr.
For (88710) 2001 SL9, we determined that the mutual orbit has a pole within 10. of (L, B) = (302 degrees, 73 degrees) (ecliptic coordinates), and is close to circular (eccentricity < 0.07). The data for this system are also inconsistent with a constant orbital period and we obtained two solutions for the quadratic drift of the mean anomaly: 2.8 +/- 0.2 and 5.2 +/- 0.2 deg./yr(2), implying that the semimajor axis of the mutual orbit of the components (estimated a similar to 1.6 km) decreases in time with a mean rate of 2.8 +/- 0.2 or 5.1 +/- 0.2 cm/yr for the two solutions, respectively. The expanding orbit of (66391) 1999 KW4 may be explained by mutual tides interplaying with binary YORP (BYORP) effect (McMahon and Scheeres, 2010a. Icarus 209, 494-509). However, a modeling of the BYORP drift using radar-derived shapes of the binary components predicted a much higher value of the orbital drift than the observed one. It suggests that either the radar-derived shape model of the secondary is inadequate for computing the BYORP effect, or the present theory of BYORP overestimates it. It is possible that the BYORP coefficient has instead an opposite sign than predicted; in that case, the system may be moving into an equilibrium between the BYORP and the tides. In the case of (88710) 2001 SL9, the BYORP effect is the only known physical mechanism that can cause the inward drift of its mutual orbit. Together with the binary (175706) 1996 FG3 which has a mean anomaly drift consistent with zero, implying a stable equilibrium between the BYORP effect and mutual body tides (Scheirich et al., 2015. Icarus 245, 56-63), we now have three distinct cases of well observed binary asteroid systems with their long-term dynamical models inferred. They indicate a presence of all the three states of the mutual orbit evolution - equilibrium, expanding and contracting - in the population of near-Earth binary asteroids. |
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| Record 22 of 414 | |||||||||
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| Author(s): Sukenik, L (Sukenik, Lukas); Mukhamedova, L (Mukhamedova, Liya); Prochazkova, M (Prochazkova, Michaela); Skubnik, K (Skubnik, Karel); Plevka, P (Plevka, Pavel); Vacha, R (Vacha, Robert) | |||||||||
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| Abstract: Virus-like nanoparticles are protein shells similar to wild-type viruses, and both aim to deliver their content into a cell. Unfortunately, the release mechanism of their cargo/genome remains elusive. Pores on the symmetry axes were proposed to enable the slow release of the viral genome. In contrast, cryo-EM images showed that capsids of nonenveloped RNA viruses can crack open and rapidly release the genome. We combined in vitro cryo-EM observations of the genome release of three viruses with coarse-grained simulations of generic virus-like nanoparticles to investigate the cargo/genome release pathways. Simulations provided details on both slow and rapid release pathways, including the success rates of individual releases. Moreover, the simulated structures from the rapid release pathway were in agreement with the experiment. Slow release occurred when interactions between capsid subunits were long-ranged, and the cargo/genome was noncompact. In contrast, rapid release was preferred when the interaction range was short and/or the cargo/genome was compact. These findings indicate a design strategy of virus-like nanoparticles for drug delivery. | |||||||||
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| Record 23 of 414 | ||||||||||||
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| Author(s): Bohutinska, M (Bohutinska, Magdalena); Vlcek, J (Vlcek, Jakub); Yair, S (Yair, Sivan); Laenen, B (Laenen, Benjamin); Konecna, V (Konecna, Veronika); Fracassetti, M (Fracassetti, Marco); Slotte, T (Slotte, Tanja); Kolar, F (Kolar, Filip) | ||||||||||||
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| Abstract: Parallel adaptation provides valuable insight into the predictability of evolutionary change through replicated natural experiments. A steadily increasing number of studies have demonstrated genomic parallelism, yet the magnitude of this parallelism varies depending on whether populations, species, or genera are compared. This led us to hypothesize that the magnitude of genomic parallelism scales with genetic divergence between lineages, but whether this is the case and the underlying evolutionary processes remain unknown. Here, we resequenced seven parallel lineages of two Arabidopsis species, which repeatedly adapted to challenging alpine environments. By combining genome-wide divergence scans with modelbased approaches, we detected a suite of 151 genes that show parallel signatures of positive selection associated with alpine colonization, involved in response to cold, high radiation, short season, herbivores, and pathogens. We complemented these parallel candidates with published gene lists from five additional alpine Brassicaceae and tested our hypothesis on a broad scale spanning similar to 0.02 to 18 My of divergence. Indeed, we found quantitatively variable genomic parallelism whose extent significantly decreased with increasing divergence between the compared lineages. We further modeled parallel evolution over the Arabidopsis candidate genes and showed that a decreasing probability of repeated selection on the same standing or introgressed alleles drives the observed pattern of divergence-dependent parallelism. We therefore conclude that genetic divergence between populations, species, and genera, affecting the pool of shared variants, is an important factor in the predictability of genome evolution. | ||||||||||||
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| Record 24 of 414 | ||||||||||||
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| Author(s): Futas, J (Futas, Jan); Oppelt, J (Oppelt, Jan); Burger, PA (Burger, Pamela Anna); Horin, P (Horin, Petr) | ||||||||||||
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| Abstract: Cytotoxic T cells and natural killer cells can kill target cells based on their expression and release of perforin, granulysin, and granzymes. Genes encoding these molecules have been only poorly annotated in camelids. Based on bioinformatic analyses of genomic resources, sequences corresponding to perforin, granulysin, and granzymes were identified in genomes of camelids and related ungulate species, and annotation of the corresponding genes was performed. A phylogenetic tree was constructed to study evolutionary relationships between the species analyzed. Re-sequencing of all genes in a panel of 10 dromedaries and 10 domestic Bactrian camels allowed analyzing their individual genetic polymorphisms. The data showed that all extant Old World camelids possess functional genes for two pore-forming proteins (PRF1, GNLY) and six granzymes (GZMA, GZMB, GZMH, GZMK, GZMM, and GZMO). All these genes were represented as single copies in the genome except the GZMH gene exhibiting interspecific differences in the number of loci. High protein sequence similarities with other camelid and ungulate species were observed for GZMK and GZMM. The protein variability in dromedaries and Bactrian camels was rather low, except for GNLY and chymotrypsin-like granzymes (GZMB, GZMH). | ||||||||||||
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| Record 25 of 414 | ||||||
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| Author(s): Foroutan-Nejad, C (Foroutan-Nejad, Cina) | ||||||
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| Abstract: In this work bonding and aromaticity of triply bonded atoms of group 13 elements (M M, M = B and Al) in recently characterized B2Al3-, Na3Al2-, and Na4Al2 are studied. Here, I show that although molecular orbital-based analyses characterize triple bonds, the electropositive nature of group 13 elements gives these bonds unique characteristics. The bond orders derived from the delocalization index, topology of the electron density, and local characteristics of (3, -1) critical points, as defined within the context of quantum theory of atoms in molecules, do not conform with those of ordinary triple bonds. In Na3Al2- and Na4Al2 clusters non-nuclear attractors form between the electropositive Al atoms acting like pseudo atoms. The bond between boron atoms in B2Al3- is more similar to an ordinary triple covalent bond benefiting from the exchange-correlation component of the interatomic interaction energy as defined via interacting quantum atom theory. However, extreme electrostatic repulsion between negatively charged boron atoms attenuates this bond. Finally, current density analysis suggests that B2Al3- is a magnetic aromatic system, nearly 50% more aromatic compared to benzene. | ||||||
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| Record 26 of 414 | |||||||||
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| Author(s): Maafi, N (Maafi, Negar); Pidany, F (Pidany, Filip); Marikova, J (Marikova, Jana); Korabecny, J (Korabecny, Jan); Hulcova, D (Hulcova, Daniela); Kucera, T (Kucera, Tomas); Schmidt, M (Schmidt, Monika); Al Shammari, L (Al Shammari, Latifah); Spulak, M (Spulak, Marcel); Catapano, MC (Catapano, Maria Carmen); Mecava, M (Mecava, Marko); Prchald, L (Prchald, Lukas); Kunes, J (Kunes, Jiri); Janousek, J (Janousek, Jiri); Kohelova, E (Kohelova, Eliska); Jenco, J (Jenco, Jaroslav); Novakova, L (Novakova, Lucie); Cahlikova, L (Cahlikova, Lucie) | |||||||||
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| Abstract: Alzheimer's disease (AD) is the most common neurodegenerative disorder, characterized by neuronal loss and cognitive impairment. Currently, very few drugs are available for AD treatment, and a search for new therapeutics is urgently needed. Thus, in the current study, twenty-eight new derivatives of montanine-type Amaryllidaceae alkaloids were synthesized and evaluated for their ability to inhibit human recombinant acetylcholinesterase (hAChE) and butyrylcholinesterase (hBuChE). Three derivatives (1n, 1o, and 1p) with different substitution patterns demonstrated significant selective inhibitory potency for hAChE (IC50 < 5 mu M), and one analog, 1v, showed selective hBuChE inhibition activity (IC50 = 1.73 +/- 0.05 mu M). The prediction of CNS availability, as disclosed by the BBB score, suggests that the active compounds in this survey should be able pass through the blood-brain barrier (BBB). Cytotoxicity screening and docking studies were carried out for the two most pronounced cholinesterase inhibitors, 1n and 1v. | |||||||||
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| Record 27 of 414 | ||||||||||||||||||
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| Author(s): Kalcic, F (Kalcic, Filip); Zgarbova, M (Zgarbova, Michala); Hodek, J (Hodek, Jan); Chalupsky, K (Chalupsky, Karel); Dracinsky, M (Dracinsky, Martin); Dvorakova, A (Dvorakova, Alexandra); Strme, T (Strme, Timotej); Sebestik, J (Sebestik, Jaroslav); Baszczynski, O (Baszczynski, Ondrej); Weber, J (Weber, Jan); Mertlikova-Kaiserova, H (Mertlikova-Kaiserova, Helena); Janeba, Z (Janeba, Zlatko) | ||||||||||||||||||
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| Abstract: This study describes the discovery of novel prodrugs bearing tyrosine derivatives instead of the phenol moiety present in FDA-approved tenofovir alafenamide fumarate (TAF). The synthesis was optimized to afford diastereomeric mixtures of novel prodrugs in one pot (yields up to 86%), and the epimers were resolved using a chiral HPLC column into fast-eluting and slow-eluting epimers. In human lymphocytes, the most efficient tyrosine-based prodrug reached a single-digit picomolar EC50 value against HIV-1 and nearly 300-fold higher selectivity index (SI) compared to TAF. In human hepatocytes, the most efficient prodrugs exhibited subnanomolar EC50 values for HBV and up to 26-fold higher SI compared to TAF. Metabolic studies demonstrated markedly higher cellular uptake of the prodrugs and substantially higher levels of released tenofovir inside the cells compared to TAF. These promising results provide a strong foundation for further evaluation of the reported prodrugs and their potential utility in the development of highly potent antivirals. | ||||||||||||||||||
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| Record 28 of 414 | |||||||||
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| Author(s): Czernek, J (Czernek, Jiri); Brus, J (Brus, Jiri) | |||||||||
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| Abstract: The liquid state NMR chemical shift of protons is a parameter frequently used to characterize host-guest complexes. Its theoretical counterpart, that is, the H-1 NMR chemical shielding affected by the solvent (H-1 CS), may provide important insights into spatial arrangements of supramolecular systems, and it can also be reliably obtained for challenging cases of an aggregation of aromatic and antiaromatic molecules in solution. This computational analysis is performed for the complex of coronene and an antiaromatic model compound in acetonitrile by employing the GIAO-B3LYP-PCM approach combined with a saturated basis set. Predicted H-1 CS values are used to generate volumetric data, whose properties are thoroughly investigated. The H-1 CS isosurface, corresponding to a value of the proton chemical shift taken from a previous experimental study, is described. The presence of the H-1 CS isosurface should be taken into account in deriving structural information about supramolecular hosts and their encapsulation of small molecules. | |||||||||
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| Record 29 of 414 | ||||||||||||||||||||||||
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| Author(s): Martin-Fuentes, C (Martin-Fuentes, Cristina); Urgel, JI (Urgel, Jose, I); Edalatmanesh, S (Edalatmanesh, Shayan); Rodriguez-Sanchez, E (Rodriguez-Sanchez, Eider); Santos, J (Santos, Jose); Mutombo, P (Mutombo, Pingo); Biswas, K (Biswas, Kalyan); Lauwaet, K (Lauwaet, Koen); Gallego, JM (Gallego, Jose M.); Miranda, R (Miranda, Rodolfo); Jelinek, P (Jelinek, Pavel); Martin, N (Martin, Nazario); Ecija, D (Ecija, David) | ||||||||||||||||||||||||
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| Abstract: Among the plethora of polycyclic structures that have emerged in recent years, indenofluorenes comprise a unique class of compounds due to their potential in organic electronic systems such as OLEDs, OFETs, and OPVCs. However, the synthesis of fully conjugated indenofluorenes without bulky groups on the apical carbons under standard chemistry conditions is not easily accessible. In this regard, on-surface synthesis has appeared as a newly developing field of research, which exploits the use of well-defined solid surfaces as confinement templates to initiate and develop chemical reactions. Here, we demonstrate the successful fabrication of indeno[1,2-b]fluorene pi-conjugated polymers linked via cumulene-like connections on well-defined metallic surfaces under ultra-high vacuum conditions. The structure and electronic properties of the formed polymers have been precisely characterized by scanning tunneling microscopy, noncontact atomic force microscopy and scanning tunneling spectroscopy, complemented by computational investigations. | ||||||||||||||||||||||||
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| Record 30 of 414 | ||||||||||||||||||
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| Author(s): Kotaskova, I (Kotaskova, Iva); Syrovatka, V (Syrovatka, Vit); Obrucova, H (Obrucova, Hana); Videnska, P (Videnska, Petra); Zwinsova, B (Zwinsova, Barbora); Hola, V (Hola, Veronika); Blastikova, E (Blastikova, Eva); Ruzicka, F (Ruzicka, Filip); Freiberger, T (Freiberger, Tomas) | ||||||||||||||||||
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| Abstract: Actinotignum schaalii is an emerging, opportunistic pathogen and its connection to non-infectious diseases and conditions, such as prostate or bladder cancer, or chronic inflammation has been proposed. Here, we analyzed 297 urine, ureteral and urinary catheter samples from 128 patients by Polymerase Chain Reaction followed by Denaturing Gradient Gel Electrophoresis and Sequencing (PCR-DGGE-S), and culture, and 29 of these samples also by 16S rRNA Illumina sequencing, to establish A. schaalii's prevalence in urinary tract-related samples, its relation to other bacteria, and its potential association with patients' conditions and samples' characteristics. A. schaalii-positive samples were significantly more diverse than A. schaalii negative and between-group diversity was higher than intra-group. Propionimicrobium lymphophilum, Fusobacterium nucleatum, Veillonella sp., Morganella sp., and Aerococcus sp. were significantly more often present in A. schaalii-positive samples; thus, we suggest these species are A. schaalii's concomitants, while Enterobacter and Staphylococcaceae were more often identified in A. schaalii-negative samples; therefore, we propose A. schaalii and these species are mutually exclusive. Additionally, a significantly higher A. schaalii prevalence in patients with ureter stricture associated hydronephrosis (p = 0.020) was noted. We suggest that A. schaalii could be an early polybacterial biofilm colonizer, together with concomitant species, known for pro-inflammatory features. | ||||||||||||||||||
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| Record 31 of 414 | |||||||||||||||
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| Author(s): Liu, XS (Liu, Xunshan); Matej, A (Matej, Adam); Kratky, T (Kratky, Tim); Mendieta-Moreno, JI (Mendieta-Moreno, Jesus, I); Gunther, S (Guenther, Sebastian); Mutombo, P (Mutombo, Pingo); Decurtins, S (Decurtins, Silvio); Aschauer, U (Aschauer, Ulrich); Repp, J (Repp, Jascha); Jelinek, P (Jelinek, Pavel); Liu, SX (Liu, Shi-Xia); Patera, LL (Patera, Laerte L.) | |||||||||||||||
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| Abstract: Regiospecific C-H activation is a promising approach to achieve extended polymers with tailored structures. While a recent on-surface synthetic approach has enabled regioselective homocoupling of heteroaromatic molecules, only small oligomers have been achieved. Herein, selective C-H activation for dehydrogenative C-C couplings of hexaazatriphenylene by Scholl reaction is reported for the first time. By combining low-temperature scanning tunneling microscopy (STM) and atomic force microscopy (AFM), we revealed the formation of one-dimensional polymers with a double-chain structure. The details of the growth process are rationalized by density functional theory (DFT) calculations, pointing out a cooperative catalytic action of Na and Ag adatoms in steering the C-H selectivity for the polymerization. | |||||||||||||||
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| Record 32 of 414 | ||||||||||||||||||
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| Author(s): Sarmento, MJ (Sarmento, Maria J.); Owen, MC (Owen, Michael C.); Ricardo, JC (Ricardo, Joana C.); Chmelova, B (Chmelova, Barbora); Davidovic, D (Davidovic, David); Mikhalyov, I (Mikhalyov, Ilya); Gretskaya, N (Gretskaya, Natalia); Hof, M (Hof, Martin); Amaro, M (Amaro, Mariana); Vacha, R (Vacha, Robert); Sachl, R (Sachl, Radek) | ||||||||||||||||||
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| Abstract: Gangliosides form an important class of receptor lipids containing a large oligosaccharide headgroup whose ability to self-organize within lipid membranes results in the formation of nanoscopic platforms. Despite their biological importance, the molecular basis for the nanoscopic segregation of gangliosides is not clear. In this work, we investigated the role of the ganglioside headgroup on the nanoscale organization of gangliosides. We studied the effect of the reduction in the number of sugar units of the ganglioside oligosaccharide chain on the ability of gangliosides GM(1), GM(2), and GM(3) to spontaneously self-organize into lipid nanodomains. To reach nanoscopic resolution and to identify molecular forces that drive ganglioside segregation, we combined an experimental technique, Forster resonance energy transfer analyzed by Monte-Carlo simulations offering high lateral and trans-bilayer resolution with molecular dynamics simulations. We show that the ganglioside headgroup plays a key role in ganglioside self-assembly despite the negative charge of the sialic acid group. The nanodomains range from 7 to 120 nm in radius and are mostly composed of the surrounding bulk lipids, with gangliosides being a minor component of the nanodomains. The interactions between gangliosides are dominated by the hydrogen bonding network between the head-groups, which facilitates ganglioside clustering. The N-acetylgalactosamine sugar moiety of GM(2), however, seems to impair the stability of these clusters by disrupting hydrogen bonding of neighboring sugars, which is in agreement with a broad size distribution of GM(2) nanodomains. The simulations suggest that the formation of nanodomains is likely accompanied by several conformational changes in the gangliosides, which, however, have little impact on the solvent exposure of these receptor groups. Overall, this work identifies the key physicochemical factors that drive nanoscopic segregation of gangliosides. | ||||||||||||||||||
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| Record 33 of 414 | |||||||||
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| Author(s): Uhrova, M (Uhrova, M.); Mikula, O (Mikula, O.); Bennett, NC (Bennett, N. C.); Van Daele, P (Van Daele, P.); Pialek, L (Pialek, L.); Bryja, J (Bryja, J.); Visser, JH (Visser, J. H.); van Vuuren, BJ (van Vuuren, B. Jansen); Sumbera, R (Sumbera, R.) | |||||||||
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| Abstract: African mole-rats (Bathyergidae) are an intensively studied family of subterranean rodents including three highly social and three solitary genera. Although their phylogenetic interrelations are clear, genetic diversity and the number of species within each genus is much less certain. Among the solitary genera, Heliophobius and Georychus were for a long time considered as monotypic, but molecular studies demonstrated strong phylogeographic structure within each genus and proposed that they represent complexes of cryptic species. The present study reevaluates their internal genetic/phylogenetic structure using a combination of methodological approaches. We generated datasets of one mitochondrial and six specifically selected nuclear markers as well as of a large number of double digest restriction site associated (ddRAD) loci and then applied species delimitation analyses based on the multispecies coalescent model or clustering on co-ancestry matrices. The population structure was largely congruent across all analyses, but the methods differed in their resolution scale when determining distinct gene pools. While the multispecies coalescent model distinguished five Georychus and between eleven to thirteen Heliophobius gene pools in both Sanger sequenced and ddRAD loci, two clustering algorithms revealed significantly finer or coarser structure in ddRAD based co-ancestry matrices. Tens of clusters were distinguished by fineRADstructure and one (in Georychus) or two clusters (in Heliophobius) by Infomap. The divergence dating of the bathyergid phylogeny estimated that diversification within both genera coincided with the onset of the Pleistocene and was likely driven by repeated large-scale climatic changes. Based on this updated genetic evidence, we suggest recognizing one species of Georychus and two species of Heliophobius, corresponding to a northern and southern major lineage, separated by the Eastern Arc Mountains. Yet, the final taxonomic revision should await integrated evidence stemming from e.g. morphological, ecological, or behavioral datasets. | |||||||||
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| Record 34 of 414 | ||||||||||||||||||
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| Author(s): Cheng, Y (Cheng, Yu); Vechtova, P (Vechtova, Pavlina); Fussy, Z (Fussy, Zoltan); Sterba, J (Sterba, Jan); Linhartova, Z (Linhartova, Zuzana); Rodina, M (Rodina, Marek); Tuckova, V (Tuckova, Vladimira); Gela, D (Gela, David); Samarin, AM (Samarin, Azin Mohagheghi); Lebeda, I (Lebeda, Ievgen); Xin, MM (Xin, Miaomiao); Zhang, SP (Zhang, Songpei); Rahi, D (Rahi, Deepali); Linhart, O (Linhart, Otomar) | ||||||||||||||||||
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| Abstract: The purpose of the current study was to analyze phenotypic and functional characteristics of common carp (Cyprinus carpio) spermatozoa during in vitro aging and to investigate whether global DNA methylation is affected by sperm aging. Milt was collected from five individual males, stored in vitro on ice in a refrigerator for up to 96 h post stripping (HPS) and used to fertilize eggs with intervals of 1, 24 and 96 h. Computer-assisted sperm analysis and a S3e Cell Sorter was employed to determine the spermatozoa phenotypic characteristics (motility, velocity, concentration and viability). In addition, pH and osmolality of the seminal fluid and the capacity of the spermatozoa to fertilize, hatching rate and health of the resulting embryos were examined at different aging times. Whole-genome bisulfite sequencing was used to compare the global and gene-specific DNA methylation in fresh and aged spermatozoa. The results demonstrated that spermatozoa aging in common carp significantly affects their performance and thus the success of artificial fertilization. The methylation level at the cytosine-phosphate-guanine (CpG) sites increased significantly with 24 HPS spermatozoa compared to the fresh group at 1 HPS and then decreased significantly at 96 HPS. A more detailed investigation of gene specific differences in the DNA methylation was hindered by incomplete annotation of the C. carpio genome in the public databases. | ||||||||||||||||||
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| Record 35 of 414 | |||||||||||||||||||||||||||
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| Author(s): Sorzano, COS (Sorzano, Carlos Oscar S.); Jimenez-Moreno, A (Jimenez-Moreno, Amaya); Maluenda, D (Maluenda, David); Ramirez-Aportela, E (Ramirez-Aportela, Erney); Martinez, M (Martinez, Marta); Cuervo, A (Cuervo, Ana); Melero, R (Melero, Robert); Conesa, JJ (Javier Conesa, Jose); Sanchez-Garcia, R (Sanchez-Garcia, Ruben); Strelak, D (Strelak, David); Filipovic, J (Filipovic, Jiri); Fernandez-Gimenez, E (Fernandez-Gimenez, Estrella); de Isidro-Gomez, F (de Isidro-Gomez, Federico); Herreros, D (Herreros, David); Conesa, P (Conesa, Pablo); del Cano, L (del Cano, Laura); Fonseca, Y (Fonseca, Yunior); de la Morena, JJ (Jimenez de la Morena, Jorge); Macias, JR (Ramon Macias, Jose); Losana, P (Losana, Patricia); Marabini, R (Marabini, Roberto); Carazo, JM (Carazo, Jose-Maria) | |||||||||||||||||||||||||||
| Edited by: Owens RJ | |||||||||||||||||||||||||||
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| Abstract: Cryo-electron microscopy has established as a mature structural biology technique to elucidate the three-dimensional structure of biological macromolecules. The Coulomb potential of the sample is imaged by an electron beam, and fast semi-conductor detectors produce movies of the sample under study. These movies have to be further processed by a whole pipeline of image-processing algorithms that produce the final structure of the macromolecule. In this chapter, we illustrate this whole processing pipeline putting in value the strength of "meta algorithms," which are the combination of several algorithms, each one with different mathematical rationale, in order to distinguish correctly from incorrectly estimated parameters. We show how this strategy leads to superior performance of the whole pipeline as well as more confident assessments about the reconstructed structures. The "meta algorithms" strategy is common to many fields and, in particular, it has provided excellent results in bioinformatics. We illustrate this combination using the workflow engine, Scipion. | |||||||||||||||||||||||||||
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| ISBN: 978-1-0716-1406-8; 978-1-0716-1405-1 | |||||||||||||||||||||||||||
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| Record 36 of 414 | ||||||
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| Author(s): Ottley, T (Ottley, Tom); Blockeel, TL (Blockeel, Tom L.); Kucera, J (Kucera, Jan) | ||||||
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| Abstract: Introduction An unfamiliar member of the Pottiaceae discovered near Goginan in Cardiganshire, Wales, UK, was identified as Bryoerythrophyllum campylocarpum sensu lato. An earlier collection from a wood in East Cork, Ireland, was subsequently confirmed as belonging to the same species. This moss is primarily a tropical and subtropical species and is very rare in Europe. Methods Both the Irish and Welsh plants were initially identified by morphological comparison with herbarium specimens of Bryoerythrophyllum campylocarpum from other areas of its distribution. Identification was confirmed by assessment of molecular affinities using two chloroplast markers, rps4 and trnM-trnV. Key results and conclusions Molecular and morphological affinities are presented and discussed. Comparisons are made with similar species and notes on identification are presented. Bryoerythrophyllum campylocarpum, as currently circumscribed, is confirmed as a member of the Irish and British bryophyte floras; however, both the molecular and morphological variation of specimens attributed to this species suggest that it is a collective taxon comprising at least three lineages which will probably need to be described as species in the future. The possible origins of the Irish and Welsh plants are considered. | ||||||
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| Record 37 of 414 | |||||||||
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| Author(s): Shamayeva, K (Shamayeva, Katsiaryna); Spurna, K (Spurna, Karin); Kulik, N (Kulik, Natalia); Kale, D (Kale, Deepika); Munko, O (Munko, Oksana); Spurny, P (Spurny, Pavel); Zayats, V (Zayats, Vasilina); Ludwig, J (Ludwig, Jost) | |||||||||
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| Abstract: The yeast Trk1 polypeptide, like other members of the Superfamily of K Transporters (SKT proteins) consists of four Membrane-Pore-Membrane motifs (MPMs A-D) each of which is homologous to a single K-channel subunit. SKT proteins are thought to have evolved from ancestral K-channels via two gene duplications and thus single MPMs might be able to assemble when located on different polypeptides. To test this hypothesis experimentally we generated a set of partial gene deletions to create alleles encoding one, two, or three MPMs, and analysed the cellular localisation and interactions of these Trk1 fragments using GFP tags and Bimolecular Fluorescence Complementation (BiFC). The function of these partial Trk1 proteins either alone or in combinations was assessed by expressing the encoding genes in a K+-uptake deficient strain lacking also the K-channel Tok1 (trk1 , trk2,tok1 Delta) and (i) analysing their ability to promote growth in low media and (ii) by ion flux measurements using "microelectrode based ion flux estimation" (MIFF). We found that proteins containing only one or two MPM motifs can interact with each other and assemble with a polypeptide consisting of the rest of the Trk system to form a functional K+-translocation system. | |||||||||
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| Record 38 of 414 | |||||||||||||||
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| Author(s): Wetzel, MH (Wetzel, Marius Holger); Rabending, TT (Rabending, Tina Trixy); Friak, M (Friak, Martin); Vsianska, M (Vsianska, Monika); Sob, M (Sob, Mojmir); Leineweber, A (Leineweber, Andreas) | |||||||||||||||
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| Abstract: Although the general instability of the iron nitride gamma '-Fe4N with respect to other phases at high pressure is well established, the actual type of phase transitions and equilibrium conditions of their occurrence are, as of yet, poorly investigated. In the present study, samples of gamma '-Fe4N and mixtures of alpha Fe and gamma '-Fe4N powders have been heat-treated at temperatures between 250 and 1000 degrees C and pressures between 2 and 8 GPa in a multi-anvil press, in order to investigate phase equilibria involving the gamma ' phase. Samples heat-treated at high-pressure conditions, were quenched, subsequently decompressed, and then analysed ex situ. Microstructure analysis is used to derive implications on the phase transformations during the heat treatments. Further, it is confirmed that the Fe-N phases in the target composition range are quenchable. Thus, phase proportions and chemical composition of the phases, determined from ex situ X-ray diffraction data, allowed conclusions about the phase equilibria at high-pressure conditions. Further, evidence for the low-temperature eutectoid decomposition gamma '->alpha+epsilon ' is presented for the first time. From the observed equilibria, a P-T projection of the univariant equilibria in the Fe-rich portion of the Fe-N system is derived, which features a quadruple point at 5 GPa and 375 degrees C, above which gamma '-Fe4N is thermodynamically unstable. The experimental work is supplemented by ab initio calculations in order to discuss the relative phase stability and energy landscape in the Fe-N system, from the ground state to conditions accessible in the multi-anvil experiments. It is concluded that gamma '-Fe4N, which is unstable with respect to other phases at 0 K (at any pressure), has to be entropically stabilised in order to occur as stable phase in the system. In view of the frequently reported metastable retention of the gamma ' phase during room temperature compression experiments, energetic and kinetic aspects of the polymorphic transition gamma 'epsilon ' are discussed. | |||||||||||||||
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| Record 39 of 414 | |||||||||
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| Author(s): Sourek, G (Sourek, Gustav); Zelezny, F (Zelezny, Filip); Kuzelka, O (Kuzelka, Ondrej) | |||||||||
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| Abstract: We introduce a declarative differentiable programming framework, based on the language of Lifted Relational Neural Networks, where small parameterized logic programs are used to encode deep relational learning scenarios through the underlying symmetries. When presented with relational data, such as various forms of graphs, the logic program interpreter dynamically unfolds differentiable computation graphs to be used for the program parameter optimization by standard means. Following from the declarative, relational logic-based encoding, this results into a unified representation of a wide range of neural models in the form of compact and elegant learning programs, in contrast to the existing procedural approaches operating directly on the computational graph level. We illustrate how this idea can be used for a concise encoding of existing advanced neural architectures, with the main focus on Graph Neural Networks (GNNs). Importantly, using the framework, we also show how the contemporary GNN models can be easily extended towards higher expressiveness in various ways. In the experiments, we demonstrate correctness and computation efficiency through comparison against specialized GNN frameworks, while shedding some light on the learning performance of the existing GNN models. | |||||||||
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| Record 40 of 414 | ||||||||||||||||||
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| Author(s): Prochazkova, M (Prochazkova, Michaela); Fuzik, T (Fuzik, Tibor); Grybchuk, D (Grybchuk, Danyil); Falginella, FL (Falginella, Francesco Luca); Podesvova, L (Podesvova, Lucie); Yurchenko, V (Yurchenko, Vyacheslav); Vacha, R (Vacha, Robert); Plevka, P (Plevka, Pavel) | ||||||||||||||||||
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Abstract:
Leishmania parasites cause a variety of symptoms, including mucocutaneous leishmaniasis, which results in the destruction of the mucous membranes of the nose, mouth, and throat. The species of Leishmania carrying Leishmania RNA virus 1 (LRV1), from the family Totiviridae, are more likely to cause severe disease and are less sensitive to treatment than those that do not contain the virus. Although the importance of LRV1 for the severity of leishmaniasis was discovered a long time ago, the structure of the virus remained unknown. Here, we present a cryo-electron microscopy reconstruction of the virus-like particle of LRV1 determined to a resolution of 3.65 angstrom. The capsid has icosahedral symmetry and is formed by 120 copies of a capsid protein assembled in asymmetric dimers. RNA genomes of viruses from the family Totiviridae are synthetized, but not capped at the 5' end, by virus RNA polymerases. To protect viral RNAs from degradation, capsid proteins of the L-A totivirus cleave the 5' caps of host mRNAs, creating decoys to overload the cellular RNA quality control system. Capsid proteins of LRV1 form positively charged clefts, which may be the cleavage sites for the 5' cap of Leishmania mRNAs. The putative RNA binding site of LRV1 is distinct from that of the related L-A virus. The structure of the LRV1 capsid enables the rational design of compounds targeting the putative decapping site. Such inhibitors may be developed into a treatment for mucocutaneous leishmaniasis caused by LRV1-positive species of Leishmania.
IMPORTANCE Twelve million people worldwide suffer from leishmaniasis, resulting in more than 30 thousand deaths annually. The disease has several variants that differ in their symptoms. The mucocutaneous form, which leads to disintegration of the nasal septum, lips, and palate, is caused predominantly by Leishmania parasites carrying Leishmania RNA virus 1 (LRV1). Here, we present the structure of the LRV1 capsid determined using cryo-electron microscopy. Capsid proteins of a related totivirus, L-A virus, protect viral RNAs from degradation by cleaving the 5' caps of host mRNAs. Capsid proteins of LRV1 may have the same function. We show that the LRV1 capsid contains positively charged clefts that may be sites for the cleavage of mRNAs of Leishmania cells. The structure of the LRV1 capsid enables the rational design of compounds targeting the putative mRNA cleavage site. Such inhibitors may be used as treatments for mucocutaneous leishmaniasis. |
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| Record 41 of 414 | |||||||||
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| Author(s): Navratil, M (Navratil, Michal); Cisarova, I (Cisarova, Ivana); Stepnicka, P (Stepnicka, Petr) | |||||||||
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| Abstract: Introducing a ferrocene moiety into a molecule results in the incorporation of a metal center and a redox active moiety. This contribution describes the synthesis of FcN(CH2PPh2)(2) (1; Fc=ferrocenyl), a ferrocene analog of the widely studied bis-phosphane pincer ligands, RN(CH2PPh2)(2). Compound 1 was studied as a ligand in complexes of Group 10 and 11 metal ions. The following compounds were synthesized and characterized using a combination of spectroscopic methods and single-crystal X-ray diffraction analysis: the square planar complexes [MX2(1-kappa P-2,P')] (M/X=Ni/Cl, Pd/Cl, Pd/Br, Pd/I and Pt/Cl) and the tetrahedral complexes [M(1-kappa P-2,P')(2)]X (M/X=Cu/PF6, Ag/SbF6 and Au/SbF6). Furthermore, a pair of open and cyclic digold(I) complexes containing bis-phosphane 1 as a P,P-bridging ligand, viz. [(mu(P,P')-1)(AuCl)(2)] and [(mu(P,P')-1)(2)Au-2][SbF6](2), were isolated. Ligand 1, the corresponding phosphane selenide 1-Se and all complexes (except for the poorly soluble [(mu(P,P')-1)(2)Au-2][SbF6] and unstable [Ag(1-kappa P-2,P')(2)][SbF6]) were further analyzed by cyclic voltammetry. | |||||||||
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| Record 42 of 414 | ||||||
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| Author(s): Semrad, H (Semrad, Hugo); Mazal, C (Mazal, Ctibor); Munzarova, M (Munzarova, Marketa) | ||||||
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| Abstract: The experimentally motivated question of the acetylene bromoboration mechanism was addressed in order to suggest possible radical isomerization pathways for the syn-adduct. Addition-elimination mechanisms starting with a bromine radical attack at the "bromine end" or the "boron end" of the C=C bond were considered. Dispersion-corrected DFT and MP2 methods with the SMD solvation model were employed using three all-electron bases as well as the ECP28MWB ansatz. The rate-determining, elimination step had a higher activation energy (12 kcal mol(-1)) in case of the "bromine end" attack due to intermediate stabilization at both the MP2 and DFT levels. In case of the "boron end" attack, two modes of C-C bond rotation were followed and striking differences in MP2 vs. DFT potential energy surfaces were observed. Employing MP2, addition was followed by either a 180 degrees rotation through an eclipsed conformation of vicinal bromine atoms or by an opposite rotation avoiding that conformation, with 5 kcal mol(-1) of elimination activation energy. Within B3LYP, the addition and rotation proceeded simultaneously, with a 9 (7) kcal mol(-1) barrier for rotation involving (avoiding) eclipsed conformation of vicinal bromines. For weakly bound complexes, ZPE corrections with MP2 revealed significant artifacts when diffuse bases were included, which must be considered in the Gibbs free energy profile interpretation. | ||||||
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| Record 43 of 414 |
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| Author(s): Vavra, J (Vavra, Jan); Hromada, M (Hromada, Martin); Lukas, L (Lukas, Ludek); Dworzecki, J (Dworzecki, Jacek) |
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| Abstract: Technology has become an integral part of contemporary society. The current transition from an industrial so-ciety to an information society is accompanied by the implementation of new technologies in every part of human activity. Increasing pressure to apply ICT in critical infrastructure resulted in the creation of new vul-nerabilities. Traditional safety approaches are ineffective in a considerable number of cases. Therefore, machine learning another evolutionary step that provides robust solutions for extensive and sophisticated systems. The article focuses on cybersecurity research for industrial control systems that are widely used in the field of critical information infrastructure. Moreover, cybernetic protection for industrial control systems is one of the most important security types for a modern state. We present an adaptive solution for defense against cyber-attacks, which also consider the specifics of the industrial control systems environment. Moreover, the experiments are based on four machine learning algorithms (artificial neural network, recurrent neural network LSTM, isolation forest, and algorithm OCSVM). The proposed anomaly detection system utilizes multiple techniques and pro-cesses as preprocessing techniques, optimization techniques, and processes required for result interpretation. These procedures allow the creation of an adaptable and robust system that meets the need for industrial control systems. |
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| Record 44 of 414 | ||||||||||||
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| Author(s): Basak, D (Basak, Dipmalya); Smythe, L (Smythe, Lucy); Herchel, R (Herchel, Radovan); Murrie, M (Murrie, Mark); Nemec, I (Nemec, Ivan); Ray, D (Ray, Debashis) | ||||||||||||
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| Abstract: Two new families of cobalt(II/III)-lanthanide(III) coordination aggregates have been reported: tetranuclear [Ln(2)(III)Co(2)(III)L(2)(N-BuDEA)(2)(O2CCMe3)(4)(H2O)(2)]center dot(MeOH)(n)center dot(H2O)(m) (Ln = Gd, 1; Tb, 2; Dy, 3; n=2, m=10 for 1 and 2; n=6, m=2 for 3) and pentanuclear Ln(2)(III)Co(II)Co(2)(III)L(2)(N-BuDEA)(2)(O2CCMe3)(6)(MeOH)(2) (Ln = Dy, 4; Ho, 5) formed from the reaction of two aggregation assisting ligands H2L (o-vanillin oxime) and N-BuDEAH(2) (N-butyldiethanolamine). A change in preference from a lower to higher nuclearity structure was observed on going across the lanthanide series brought about by the variation in the size of the Ln(III) ions. An interesting observation was made for the varying sequence of addition of the ligands into the reaction medium paving the way to access both structural types for Ln = Dy. HRMS (+ve) of solutions gave further insight into the formation of the aggregates via different pathways. The tetranuclear complexes adopt a modified butterfly structure with a more complex bridging network while trapping of an extra Co-II ion in the pentanuclear complexes destroys this arrangement putting the Co-Co-Co axis above the Ln-Ln axis. Direct current (dc) magnetic susceptibility measurements reveal weak antiferromagnetic coupling in 1. Complexes 2 and 5 display no slow magnetic relaxation, whereas complexes 3 and 4 display out-of-phase signals at low temperature in ac susceptibility measurements. All compounds were analyzed with DFT and CASSCF calculations and informations about the single-ion anisotropies and mutual 4f-4f/4f-3d magnetic interactions were derived. | ||||||||||||
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| Record 45 of 414 | ||||||
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| Author(s): Dolezal, R (Dolezal, Rafael) | ||||||
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| Abstract: Nowadays, advanced computational chemistry methods offer various strategies for revealing prospective hit structures in drug development essentially through accurate binding free energy predictions. After the era of molecular docking and quantitative structure-activity relationships, much interest has been lately oriented to perturbed molecular dynamic approaches like replica exchange with solute tempering and free energy perturbation (REST/FEP) and the potential of the mean force with adaptive biasing and accelerated weight histograms (PMF/AWH). Both of these receptor-based techniques can exploit exascale CPU&GPU supercomputers to achieve high throughput performance. In this fundamental study, we have compared the predictive power of a panel of supercomputerized molecular modelling methods to distinguish the major binding modes and the corresponding binding free energies of a promising tacrine related potential antialzheimerics in human acetylcholinesterase. The binding free energies were estimated using flexible molecular docking, molecular mechanics/generalized Born surface area/Poisson-Boltzmann surface area (MM/GBSA/PBSA), transmutation REST/FEP with 12 x 5 ns/lambda windows, annihilation FEP with 20 x 5 ns/lambda steps, PMF with weight histogram analysis method (WHAM) and 40 x 5 ns samples, and PMF/AWH with 10 x 100 ns replicas. Confrontation of the classical approaches such as canonical molecular dynamics and molecular docking with alchemical calculations and steered molecular dynamics enabled us to show how large errors in Delta G predictions can be expected if these in silico methods are employed in the elucidation of a common case of enzyme inhibition. Communicated by Ramaswamy H. Sarma | ||||||
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| Record 46 of 414 |
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| Author(s): Schwarz, M (Schwarz, Marek); Vohradsky, J (Vohradsky, Jiri); Panek, J (Panek, Josef) |
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| Abstract: A Summary: We present a web service for improving characterization of non-coding RNAs (ncRNAs) from NCBI BLAST outputs, based on a command-line application rboAnalyzer. Briefly, the application extends subject sequences of selected high scoring pairs (HSPs) in BLAST output to their plausible full length, and predicts their homology and secondary structures. The aim of the application is to aid to characterize subject RNAs in HSPs that come uncharacterized in BLAST output. The main advantages of the web-server are easy use and interactive analysis with search, filtering and data export options. |
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| Record 47 of 414 | ||||||||||||
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| Author(s): Dey, S (Dey, Shuvankar); Modi, K (Modi, Krunal); Panchal, U (Panchal, Urvi); Panchal, M (Panchal, Manthan); Jain, VK (Jain, Vinod K.) | ||||||||||||
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| Abstract: We demonstrate an azacalix[4]arene based bifunctional probe, viz. bisnaphthylated-azacalix[4]arene (BNAC) for the selective recognition of molecular toxins such as monocrotophos (MCP) and N-methyl-4-nitroaniline (MNA). The photophysical properties, especially the emission studies were introduced for monitoring the host-guest complexation. Noteworthy, the emission responses of the host exclusively alter according to the functionalities attached to the guest molecules. For instance, MCP being electronrich enhances the emission intensity of BNAC upon complexation by donating electrons to the electrophilic sites of the receptor. Inversely, MNA having electron-withdrawing nitro groups readily interacts with the highly conjugated naphthalene rings and suppresses the emission maxima of the receptor through photoinduced electron transfer (PET). Job's plot reveals both MNA and MCP exhibit 1:1 stoichiometry upon complexation with BNAC. Computational studies including molecular docking and DFT calculations were carried out to predict the binding affinity, plausible host-guest interactions and to investigate the binding mechanism. (C) 2021 Elsevier B.V. All rights reserved. | ||||||||||||
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| Record 48 of 414 | ||||||||||||||||||||||||||||||||||||||||||
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| Author(s): Muller, K (Muller, Karel); Dobrev, PI (Dobrev, Petre Ivanov); Pencik, A (Pencik, Ales); Hosek, P (Hosek, Petr); Vondrakova, Z (Vondrakova, Zuzana); Filepova, R (Filepova, Roberta); Malinska, K (Malinska, Katerina); Brunoni, F (Brunoni, Federica); Helusova, L (Helusova, Lenka); Moravec, T (Moravec, Tomas); Retzer, K (Retzer, Katarzyna); Harant, K (Harant, Karel); Novak, O (Novak, Ondrej); Hoyerova, K (Hoyerova, Klara); Petrasek, J (Petrasek, Jan) | ||||||||||||||||||||||||||||||||||||||||||
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| Abstract: Together with auxin transport, auxin metabolism is a key determinant of auxin signaling output by plant cells. Enzymatic machinery involved in auxin metabolism is subject to regulation based on numerous inputs, including the concentration of auxin itself. Therefore, experiments characterizing altered auxin availability and subsequent changes in auxin metabolism could elucidate the function and regulatory role of individual elements in the auxin metabolic machinery. Here, we studied auxin metabolism in auxin-dependent tobacco BY- 2 cells. We revealed that the concentration of N-( 2-oxindole-3-acetyl)-L- aspartic acid (oxIAA-Asp), the most abundant auxin metabolite produced in the control culture, dramatically decreased in auxin- starved BY-2 cells. Analysis of the transcriptome and proteome in auxin- starved cells uncovered significant downregulation of all tobacco ( Nicotiana tabacum) homologs of Arabidopsis (Arabidopsis thaliana) DIOXYGENASE FOR AUXIN OXIDATION 1 (DAO1), at both transcript and protein levels. Auxin metabolism profiling in BY-2 mutants carrying either siRNA- silenced or CRISPR- Cas9-mutated NtDAO1, as well as in dao1-1 Arabidopsis plants, showed not only the expected lower levels of oxIAA, but also significantly lower abundance of oxIAA- Asp. Finally, ability of DAO1 to oxidize IAA-Asp was confirmed by an enzyme assay in AtDAO1-producing bacterial culture. Our results thus represent direct evidence of DAO1 activity on IAA amino acid conjugates. | ||||||||||||||||||||||||||||||||||||||||||
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| Record 49 of 414 | |||||||||||||||
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| Author(s): Mikula, O (Mikula, Ondrej); Nicolas, V (Nicolas, Violaine); Sumbera, R (Sumbera, Radim); Konecny, A (Konecny, Adam); Denys, C (Denys, Christiane); Verheyen, E (Verheyen, Erik); Bryjova, A (Bryjova, Anna); Lemmon, AR (Lemmon, Alan R.); Lemmon, EM (Lemmon, Emily Moriarty); Bryja, J (Bryja, Josef) | |||||||||||||||
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| Abstract: The tribe Arvicanthini (Muridae: Murinae) is a highly diversified group of rodents (ca. 100 species) and with 18 African genera (plus one Asiatic) represents probably the most successful adaptive radiation of extant mammals in Africa. They colonized a broad spectrum of habitats (from rainforests to semi-deserts) in whole sub-Saharan Africa and their members often belong to most abundant parts of mammal communities. Despite intensive efforts, the phylogenetic relationships among major lineages (i.e. genera) remained obscured, which was likely caused by the intensive radiation of the group, dated to the Late Miocene. Here we used genomic scale data (377 nuclear loci; 581,030 bp) and produced the first fully resolved species tree containing all currently delimited genera of the tribe. Mitogenomes were also extracted, and while the results were largely congruent, there was less resolution at basal nodes of the mitochondrial phylogeny. Results of a fossil-based divergence dating analysis suggest that the African radiation started early after the colonization of Africa by a single arvicanthine ancestor from Asia during the Messinian stage (ca. 7 Ma), and was likely linked with a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forest, while many others successfully colonized broad spectrum of new open habitats (e.g. savannas, wetlands or montane moorlands) that appeared at the beginning of Pliocene. One lineage even evolved partially arboricolous life style in savanna woodlands, which allowed them to re-colonize equatorial forests. We also discuss delimitation of genera in Arvicanthini and propose corresponding taxonomic changes. | |||||||||||||||
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| Author(s): Herreros, D (Herreros, David); Lederman, RR (Lederman, Roy R.); Krieger, J (Krieger, James); Jimenez-Moreno, A (Jimenez-Moreno, Amaya); Martinez, M (Martinez, Marta); Myska, D (Myska, David); Strelak, D (Strelak, David); Filipovic, J (Filipovic, Jiri); Bahar, I (Bahar, Ivet); Carazo, JM (Carazo, Jose Maria); Sanchez, COS (Sanchez, Carlos Oscar S.) | |||||||||||||||
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| Abstract: Structural biology has evolved greatly due to the advances introduced in fields like electron microscopy. This image-capturing technique, combined with improved algorithms and current data processing software, allows the recovery of different conformational states of a macromolecule, opening new possibilities for the study of its flexibility and dynamic events. However, the ensemble analysis of these different conformations, and in particular their placement into a common variable space in which the differences and similarities can be easily recognized, is not an easy matter. To simplify the analysis of continuous heterogeneity data, this work proposes a new automatic algorithm that relies on a mathematical basis defined over the sphere to estimate the deformation fields describing conformational transitions among different structures. Thanks to the approximation of these deformation fields, it is possible to describe the forces acting on the molecules due to the presence of different motions. It is also possible to represent and compare several structures in a low-dimensional mapping, which summarizes the structural characteristics of different states. All these analyses are integrated into a common framework, providing the user with the ability to combine them seamlessly. In addition, this new approach is a significant step forward compared with principal component analysis and normal mode analysis of cryo-electron microscopy maps, avoiding the need to select components or modes and producing localized analysis. | |||||||||||||||
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| Record 51 of 414 | |||||||||||||||||||||||||||
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| Author(s): Su, J (Su, Jie); Fan, W (Fan, Wei); Mutombo, P (Mutombo, Pingo); Peng, XN (Peng, Xinnan); Song, ST (Song, Shaotang); Ondracek, M (Ondracek, Martin); Golub, P (Golub, Pavlo); Brabec, J (Brabec, Jiri); Veis, L (Veis, Libor); Telychko, M (Telychko, Mykola); Jelinek, P (Jelinek, Pavel); Wu, JS (Wu, Jishan); Lu, J (Lu, Jiong) | |||||||||||||||||||||||||||
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| Abstract: The ability to engineer geometrically well-defined antidots in large triangulene homologues allows for creating an entire family of triangulene quantum rings (TQRs) with tunable high-spin ground state, crucial for next-generation molecular spintronic devices. Herein, we report the synthesis of an open-shell [7]triangulene quantum ring ([7]TQR) molecule on Au(111) through the surface-assisted cyclodehydrogenation of a rationally designed kekulene derivative. Bond-resolved scanning tunneling microscopy (BR-STM) unambiguously imaged the molecular backbone of a single [7]TQR with a triangular zigzag edge topology, which can be viewed as [7]triangulene decorated with a coronene-like antidot in the center. Additionally, dI/dV mapping reveals that both inner and outer zigzag edges contribute to the edge-localized and spin-polarized electronic states of [7]TQR. Both experimental results and spin-polarized density functional theory calculations indicate that [7]TQR retains its open-shell septuple ground state (S = 3) on Au(111). This work demonstrates a new route for the design of high-spin graphene quantum rings for future quantum devices. | |||||||||||||||||||||||||||
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| Record 52 of 414 | ||||||
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| Author(s): Vojtech, J (Vojtech, Josef); Smotlacha, V (Smotlacha, Vladimir); Havlis, O (Havlis, Ondrej); Slapak, M (Slapak, Martin); Kundrat, J (Kundrat, Jan); Bhowmick, S (Bhowmick, Sarbojeet); Vohnout, R (Vohnout, Rudolf); Velc, R (Velc, Radek); Altmannova, L (Altmannova, Lada); Horvath, T (Horvath, Tomas); Cizek, M (Cizek, Martin); Hrabina, J (Hrabina, Jan); Rerucha, S (Rerucha, Simon); Pravdova, L (Pravdova, Lenka); Lazar, J (Lazar, Josef); Cip, O (Cip, Ondrej); Kuna, A (Kuna, Alexander); Roztocil, J (Roztocil, Jaroslav) | ||||||
| Edited by: Baldini F; Homola J; Lieberman RA | ||||||
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| Abstract: Article summarizes past and continuous development, and especially current state of Czech national research infrastructure for Clock Network Services and future development plans. The focus is on used transmission means and stabilization techniques, available and planned wavelength bands and also plans for geographic extensions. | ||||||
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| Conference Sponsors: ELI Beamlines, Laserlab Europe, European Opt Soc, HiLASE Ctr | ||||||
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| ISBN: 978-1-5106-4379-6 |
| Record 53 of 414 | ||||||
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| Author(s): Vohradsky, J (Vohradsky, Jiri); Schwarz, M (Schwarz, Marek); Ramaniuk, O (Ramaniuk, Olga); Ruiz-Larrabeiti, O (Ruiz-Larrabeiti, Olatz); Hausnerova, VV (Vankova Hausnerova, Viola); Sanderova, H (Sanderova, Hana); Krasny, L (Krasny, Libor) | ||||||
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| Abstract: The exponential increase in the number of conducted studies combined with the development of sequencing methods have led to an enormous accumulation of partially processed experimental data in the past two decades. Here, we present an approach using literature-mined data complemented with gene expression kinetic modeling and promoter sequence analysis. This approach allowed us to identify the regulon of Bacillus subtilis sigma factor SigB of RNA polymerase (RNAP) specifically expressed during germination and outgrowth. SigB is critical for the cell's response to general stress but is also expressed during spore germination and outgrowth, and this specific regulon is not known. This approach allowed us to (i) define a subset of the known SigB regulon controlled by SigB specifically during spore germination and outgrowth, (ii) identify the influence of the promoter sequence binding motif organization on the expression of the SigB-regulated genes, and (iii) suggest additional sigma factors co-controlling other SigB-dependent genes. Experiments then validated promoter sequence characteristics necessary for direct RNAP-SigB binding. In summary, this work documents the potential of computational approaches to unravel new information even for a well-studied system; moreover, the study specifically identifies the subset of the SigB regulon, which is activated during germination and outgrowth. | ||||||
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| Record 54 of 414 | ||||||
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| Author(s): Jarosik, J (Jarosik, Jiri); Wagner, V (Wagner, Vladimir); Majerle, M (Majerle, Mitja); Chudoba, P (Chudoba, Petr); Burianova, N (Burianova, Nicola); Stefanik, M (Stefanik, Milan) | ||||||
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| Abstract: This paper describes cross-section measurements by means of the neutron activation method using an accelerator-driven fast neutron source at the Nuclear Physics Institute of the Czech Academy of Sciences in Rel. It extends previous studies published in papers (Vrzalova et al. (2013); Chudoba et al. (2018)). A quasimonoenergetic neutron source based on the p+Li(C) reaction was used to irradiate Al, Au, Bi, Co, NaF, and Y samples with neutrons at the energies of 17.5(10) MeV, 19.8(9) MeV and 27.5(7) MeV. Irradiated foils were analyzed by means of gamma-ray spectrometry and reaction yields were obtained. Cross sections of several fast neutron-induced reactions were determined on the basis of the measurement of neutron spectra and their corresponding reaction yields. The production cross sections of isomeric states were determined as well. This paper also describes the measurements of the positron emitters using annihilation gamma-ray spectrometry. The sources of uncertainties in the various parts of the experiment are discussed. The resulting cross sections might be useful for the further development of advanced nuclear reactors and fast neutron dosimetry. | ||||||
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| Record 55 of 414 | ||||||||||||
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| Author(s): Svozilik, V (Svozilik, Vladislav); Krakovska, AS (Svozilikova Krakovska, Aneta); Bitta, J (Bitta, Jan); Jancik, P (Jancik, Petr) | ||||||||||||
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| Abstract: Knowing the relationship between pollution sources and air pollution concentrations is crucial. Mathematical modeling is a suitable method for the assessment of this relationship. The aim of this research was to compare the results of the Analytical Dispersion Modelling Supercomputer System (ADMOSS), which is used for air pollution modeling in large areas, with the results of moss biomonitoring. For comparison purposes, air pollution mathematical modeling and the collection of moss samples for biomonitoring in the Czech-Polish-Slovak border area in the European Grouping of Territorial Cooperation (EGTC) Tritia were carried out. Moss samples were analyzed by multi-element instrumental neutron activation analysis (INAA). The INAA results were statistically processed using the correlation-matrix-based hierarchical clustering and correlation analysis of the biomonitoring results and ADMOSS results. Biomonitoring using bryophytes proved to be suitable for the verification of mathematical models of air pollution due to the ability of bryophytes to capture the long-term deposition of pollutants and the resulting possibility of finding the real distribution of pollutants in the area, as well as identify the specific chemical elements, the distribution of which coincides with the mathematical model. | ||||||||||||
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| Record 56 of 414 |
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| Author(s): Bhowmick, S (Bhowmick, Sarbojeet); Vojtech, J (Vojtech, Josef); Altmannova, L (Altmannova, Lada); Velc, R (Velc, Radek) |
| Edited by: Kalli K; Mendez A; Peterka P |
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| Abstract: Fibre based transmission of ultra-precise time and ultra-stable optical frequency is quickly becoming common reality, not only in the fibres used for research but also in other operational fibre networks. At the moment, a fibre represents the best precision of such transmissions. In order to achieve highest possible transmission stability up to 10-18 for 1000 s averaging, the bidirectional transmission within single fibre is required including exclusive optical amplification. We present here the use and results of Optical Time Domain Reflectometry (OTDR) technique for detection of disturbances as connector losses, reflections, bending etc. on live fibres with present Amplified Spontaneous Emission (ASE) from bidirectional Erbium Doped Fibre Amplifiers (EDFAs). |
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| Conference Sponsors: SPIE |
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| ISBN: 978-1-5106-4381-9 |
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| Author(s): Lopes, M (Lopes, Magno); Brejchova, K (Brejchova, Kristyna); Riecan, M (Riecan, Martin); Novakova, M (Novakova, Michaela); Rossmeisl, M (Rossmeisl, Martin); Cajka, T (Cajka, Tomas); Kuda, O (Kuda, Ondrej) | ||||||||||||
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| Abstract: Glucose tolerance represents a complex phenotype in which many tissues play important roles and interact to regulate metabolic homeostasis. Here, we perform an analysis of C-13(6)-glucose tissue distribution, which maps the metabolome and lipidome across 12 metabolically relevant mouse organs and plasma, with integrated C-13(6)-glucose-derived carbon tracing during oral glucose tolerance test (OGTT). We measure time profiles of water-soluble metabolites and lipids and integrate the global metabolite response into metabolic pathways. During the OGTT, glucose use is turned on with specific kinetics at the organ level, but fasting substrates like beta-hydroxybutyrate are switched off in all organs simultaneously. Timeline profiling of C-13-labeled fatty acids and triacylglycerols across tissues suggests that brown adipose tissue may contribute to the circulating fatty acid pool at maximal plasma glucose levels. The GTTAtlas interactive web application serves as a unique resource for the exploration of whole-body glucose metabolism and time profiles of tissue and plasma metabolites during the OGTT. | ||||||||||||
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| Record 58 of 414 |
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| Author(s): Vanura, P (Vanura, Petr); Sykora, D (Sykora, David); Uhlikova, T (Uhlikova, Tereza) |
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| Abstract: By using electrospray ionization mass spectrometry (ESI-MS), it was proven experimentally that the silver cation Ag+ forms with corannulene (C20H10) the cationic complex [Ag(C20H10)(2)](+). Further, applying quantum chemical DFT calculations, the most probable structures of the [Ag(C20H10)(2)](+) complex were derived. In the resulting complex the "central" cation Ag+, is located between two molecules of the corannulene ligand. Finally, the interaction energy, E(int), of the considered cation-pi complex [Ag(C20H10)(2)](+) was found to be -335.0 to -306.9 kJ/mol. |
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| Author(s): Schindler, O (Schindler, Ondrej); Racek, T (Racek, Tomas); Marsavelski, A (Marsavelski, Aleksandra); Koca, J (Koca, Jaroslav); Berka, K (Berka, Karel); Svobodova, R (Svobodova, Radka) | |||||||||||||||
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Abstract:
Background: Partial atomic charges find many applications in computational chemistry, chemoinformatics, bioinformatics, and nanoscience. Currently, frequently used methods for charge calculation are the Electronegativity Equalization Method (EEM), Charge Equilibration method (QEq), and Extended QEq (EQeq). They all are fast, even for large molecules, but require empirical parameters. However, even these advanced methods have limitations-e.g., their application for peptides, proteins, and other macromolecules is problematic. An empirical charge calculation method that is promising for peptides and other macromolecular systems is the Split-charge Equilibration method (SQE) and its extension SQE+q0. Unfortunately, only one parameter set is available for these methods, and their implementation is not easily accessible.
Results: In this article, we present for the first time an optimized guided minimization method (optGM) for the fast parameterization of empirical charge calculation methods and compare it with the currently available guided minimization (GDMIN) method. Then, we introduce a further extension to SQE, SQE+qp, adapted for peptide datasets, and compare it with the common approaches EEM, QEq EQeq, SQE, and SQE+q0. Finally, we integrate SQE and SQE+qp into the web application Atomic Charge Calculator II (ACC II), including several parameter sets. Conclusion: The main contribution of the article is that it makes SQE methods with their parameters accessible to the users via the ACC II web application (https://acc2.ncbr.muni.cz) and also via a command-line application. Furthermore, our improvement, SQE+qp, provides an excellent solution for peptide datasets. Additionally, optGM provides comparable parameters to GDMIN in a markedly shorter time. Therefore, optGM allows us to perform parameterizations for charge calculation methods with more parameters (e.g., SQE and its extensions) using large datasets. |
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| Record 60 of 414 | ||||||
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| Author(s): Tomasov, A (Tomasov, Adrian); Horvath, T (Horvath, Tomas); Munster, P (Munster, Petr); Holik, M (Holik, Martin); Oujersky, V (Oujersky, Vaclav) | ||||||
| Edited by: Herencsar H | ||||||
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| Abstract: Passive optical networks are a suitable and promising solution for the service delivery network, particularly for data, video, and voice communications. An optical distribution consists of passive elements (e.g., splitters, fibers), providing a cost-effective high bandwidth tree-like topology. This paper describes a new analysis system designed for an inspection of passive optical networks. The system uses an FPGA-accelerated network interface card to capture the communication from the optical network and machine learning models in order to evaluate the possible anomalies, errors, or attacks. | ||||||
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| ISBN: 978-1-6654-2933-7 |
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| Author(s): Chatterjee, B (Chatterjee, Banhi); Kolorenc, J (Kolorenc, Jindrich) | |||||||||
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| Abstract: The debate whether uranium 5f electrons are closer to being localized or itinerant in the ferromagnetic compound UGa2 is not yet fully settled. The experimentally determined magnetic moments are large, approximately 3 mu(B), suggesting the localized character of the 5f electrons. In the same time, one can identify signs of itinerant as well as localized behavior in various spectroscopic observations. The band theory, employing local exchange-correlation functionals, is biased toward itinerant 5f states and severely underestimates the moments. Using material-specific dynamical mean-field theory (DMFT), we probe how a less approximate description of electron-electron correlations improves the picture. We present two variants of the theory: starting either from spin-restricted (LDA) or spin-polarized (LSDA) band structure. We show that the L(S)DA+DMFT method can accurately describe the magnetic moments in UGa2 as long as the exchange interaction between the uranium 6d and 5 f electrons is preserved by a judicious choice of the spin-polarized double-counting correction. We discuss the computed electronic structure in relation to photoemission experiments and show how the correlations reduce the Sommerfeld coefficient of the electronic specific heat by shifting the 5 f states slightly away from the Fermi level. | |||||||||
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| Record 62 of 414 | ||||||||||||||||||||||||||||||||||||||||||||||||
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| Author(s): Al Mamun, A (Al Mamun, Abdullah); Pidany, F (Pidany, Filip); Hulcova, D (Hulcova, Daniela); Marikova, J (Marikova, Jana); Kucera, T (Kucera, Tomas); Schmidt, M (Schmidt, Monika); Catapano, MC (Catapano, Maria Carmen); Hrabinova, M (Hrabinova, Martina); Jun, D (Jun, Daniel); Muckova, L (Muckova, Lubica); Kunes, J (Kunes, Jiri); Janousek, J (Janousek, Jiri); Andrys, R (Andrys, Rudolf); Novakova, L (Novakova, Lucie); Perinova, R (Perinova, Rozalie); Maafi, N (Maafi, Negar); Soukup, O (Soukup, Ondrej); Korabecny, J (Korabecny, Jan); Cahlikova, L (Cahlikova, Lucie) | ||||||||||||||||||||||||||||||||||||||||||||||||
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| Abstract: Alzheimer's disease (AD) is a multifactorial neurodegenerative condition of the central nervous system (CNS) that is currently treated by cholinesterase inhibitors and the N-methyl-d-aspartate receptor antagonist, memantine. Emerging evidence strongly supports the relevance of targeting butyrylcholinesterase (BuChE) in the more advanced stages of AD. Within this study, we have generated a pilot series of compounds (1-20) structurally inspired from belladine-type Amaryllidaceae alkaloids, namely carltonine A and B, and evaluated their acetylcholinesterase (AChE) and BuChE inhibition properties. Some of the compounds exhibited intriguing inhibition activity for human BuChE (hBuChE), with a preference for BuChE over AChE. Seven compounds were found to possess a hBuChE inhibition profile, with IC50 values below 1 mu M. The most potent one, compound 6, showed nanomolar range activity with an IC50 value of 72 nM and an excellent selectivity pattern over AChE, reaching a selectivity index of almost 1400. Compound 6 was further studied by enzyme kinetics, along with in-silico techniques, to reveal the mode of inhibition. The prediction of CNS availability estimates that all the compounds in this survey can pass through the blood-brain barrier (BBB), as disclosed by the BBB score. | ||||||||||||||||||||||||||||||||||||||||||||||||
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| Record 63 of 414 | |||||||||
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| Author(s): Varekova, IH (Varekova, Ivana Hutarova); Hutar, J (Hutar, Jan); Midlik, A (Midlik, Adam); Horsky, V (Horsky, Vladimir); Hladka, E (Hladka, Eva); Svobodova, R (Svobodova, Radka); Berka, K (Berka, Karel) | |||||||||
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| Abstract: A Summary: Secondary structures provide a deep insight into the protein architecture. They can serve for comparison between individual protein family members. The most straightforward way how to deal with protein secondary structure is its visualization using 2D diagrams. Several software tools for the generation of 2D diagrams were developed. Unfortunately, they create 2D diagrams based on only a single protein. Therefore, 2D diagrams of two proteins from one family markedly differ. For this reason, we developed the 2DProts database, which contains secondary structure 2D diagrams for all domains from the CATH and all proteins from PDB databases. These 2D diagrams are generated based on a whole protein family, and they also consider information about the 3D arrangement of secondary structure elements. Moreover, 2DProts database contains multiple 2D diagrams, which provide an overview of a whole protein family's secondary structures. 2DProts is updated weekly and is integrated into CATH. | |||||||||
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| Record 64 of 414 | ||||||
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| Author(s): Zechovsky, J (Zechovsky, Jan); Mrozek, O (Mrozek, Ondrej); Samsonov, M (Samsonov, Maksim); Jambor, R (Jambor, Roman); Ruzicka, A (Ruzicka, Ales); Dostal, L (Dostal, Libor) | ||||||
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| Abstract: The reactivity of two lithium amides derived from bis-(2-pyridyl)amine (dpa)H or its methyl-substituted congener bis-(6-methyl-2-pyridyl)amine (Me-dpa)H, i.e. (dpa)Li (1) and (Me-dpa)Li (2), toward ECl2 (where E = Ge (dioxane complex) and Sn) is reported. This study produced both heteroleptic complexes (dpa)GeCl (3), [(dpa)SnCl](2) (4), and (Me-dpa)GeCl (5) and homoleptic complexes (dpa)(2)E (E = Ge (6) or Sn (7)) and (Me-dpa)(2)E (E = Ge (8) or Sn (9)). The structures of all complexes were established by single-crystal X-ray diffraction analysis showing significant differences depending on the E atom and ligand used. By contrast, in solution, the majority of compounds showed a fluxional behaviour as demonstrated by the NMR study. Finally, it turned out that the Me-dpa ligand, unlike dpa, is able to form ate complexes [(Me-dpa)(3)E]Li (E = Ge (10), Sn (11) or Pb (12)), whose structures were determined by single-crystal X-ray diffraction analysis. This study revealed the formation of two isomers for Ge and Sn complexes depending on the coordination preference of the lithium atom being coordinated either by nitrogen donors (10-12) or solely by the Ge or Sn electron lone pair (10a and 11a). Furthermore, the NMR experiments proved that the germanium complex 10 exhibits only limited stability in solution and decomposes to germylene 8 and lithium amide 2. | ||||||
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| Record 65 of 414 | ||||||
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| Author(s): Houska, J (Houska, Jiri); Rezek, J (Rezek, Jiri); Cerstvy, R (Cerstvy, Radomir) | ||||||
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| Abstract: The growth of crystalline ZrO2 is studied by a combined approach of atom-by-atom growth simulations, high-power impulse magnetron sputtering and conventional pulsed magnetron sputtering. We focus on the energy of arriving atoms of various elements, and investigate how does it affect the growth of ZrO2 crystals of various orientations. The results are correlated with quantities such as surface energy and horizontal periodicity of individual orientations. Simulations show that the growth of orientations characterized by high surface energy and short horizontal period, (001) in the first place, requires higher energy delivered by arriving atoms, and that the energy is more effectively delivered by heavy Zr than by light O. Experiments confirm that the relative preference of such orientations increases with increasing substrate bias voltage, increasing concentration of ions which are subsequently accelerated by the bias voltage, and synchronization of the pulsed bias voltage with the arrival of heavy Zr+ ions. The results are important for the preparation of crystalline ZrO2 of various orientations for various technological applications, and the fundamental reasons behind them make them relevant also for the growth of other crystalline materials. | ||||||
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| Record 66 of 414 | ||||||||||||
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| Author(s): Le, TP (Thi Phuong Le); Roncevic, I (Roncevic, Igor); Dracinsky, M (Dracinsky, Martin); Cisarova, I (Cisarova, Ivana); Solinova, V (Solinova, Veronika); Kasicka, V (Kasicka, Vaclav); Kaleta, J (Kaleta, Jiri) | ||||||||||||
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| Abstract: Herein we report the highly selective radical chlorination of 2,2-difluorobicyclo[1.1.1]pentane-1,3-dicarboxylic acid. Together with radical hydrodechlorination by TMS3SiH, four new bicyclo[1.1.1]pentane cages carrying two fluorine and one to three chlorine atoms in bridge positions have been obtained. The exact positions of all halogen atoms have been confirmed by X-ray diffraction. The acidity constants (pK(a)) for all new derivatives have been determined by capillary electrophoresis, and these experimental values show excellent agreement with pK(a)s predicted by DFT methods. Extensive DFT calculations have been used to rationalize the selective formation of four out of nine possible F2Cl1-4 isomers of bridge-halogenated bicyclo[1.1.1]pentanes and to obtain relative strain energies for all possible isomers. | ||||||||||||
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| Record 67 of 414 | |||||||||
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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: The singular value decomposition of rectangular matrices is shown to provide the recipe for removing the center of mass spurious admixtures from the multiphonon basis generated by an equation of motion method for solving the nuclear eigenvalue problem. It works for any single particle basis without any energy restriction on the selection of the configurations. Its effects on 4He are illustrated. (c) 2021 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Funded by SCOAP3. | |||||||||
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| Record 68 of 414 | |||||||||||||||||||||
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| Author(s): Tlaskal, V (Tlaskal, Vojtech); Brabcova, V (Brabcova, Vendula); Vetrovsky, T (Vetrovsky, Tomas); Lopez-Mondejar, R (Lopez-Mondejar, Ruben); Monteiro, LMO (Monteiro, Lummy Maria Oliveira); Saraiva, JP (Saraiva, Joao Pedro); da Rocha, UN (da Rocha, Ulisses Nunes); Baldrian, P (Baldrian, Petr) | |||||||||||||||||||||
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| Abstract: Deadwood represents significant carbon (C) stock in a temperate forests. Its decomposition and C mobilization is accomplished by decomposer microorganisms - fungi and bacteria - who also supply the foodweb of commensalist microbes. Due to the ecosystem-level importance of deadwood habitat as a C and nutrient stock with significant nitrogen fixation, the deadwood microbiome composition and function are critical to understanding the microbial processes related to its decomposition. We present a comprehensive suite of data packages obtained through environmental DNA and RNA sequencing from natural deadwood. Data provide a complex picture of the composition and function of microbiome on decomposing trunks of European beech (Fagus sylvatica L.) in a natural forest. Packages include deadwood metagenomes, metatranscriptomes, sequences of total RNA, bacterial genomes resolved from metagenomic data and the 16S rRNA gene and ITS2 metabarcoding markers to characterize the bacterial and fungal communities. This project will be of use to microbiologists, environmental biologists and biogeochemists interested in the microbial processes associated with the transformation of recalcitrant plant biomass. | |||||||||||||||||||||
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| Record 69 of 414 | ||||||
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| Author(s): Zaveska Drabkova, L (Zaveska Drabkova, Lenka); Honys, D (Honys, David); Motyka, V (Motyka, Vaclav) | ||||||
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| Abstract: In the complex process of homeostasis of phytohormones cytokinins (CKs), O-glucosylation catalyzed by specific O-glucosyltransferases represents one of important mechanisms of their reversible inactivation. The CK O-glucosyltransferases belong to a highly divergent and polyphyletic multigene superfamily of glycosyltransferases, of which subfamily 1 containing UDP-glycosyltransferases (UGTs) is the largest in the plant kingdom. It contains recently discovered O and P subfamilies present in higher plant species but not in Arabidopsis thaliana. The cis-zeatin O-glucosyltransferase (cisZOG) genes belong to the O subfamily encoding a stereo-specific O-glucosylation of cis-zeatin-type CKs. We studied different homologous genes, their domains and motifs, and performed a phylogenetic reconstruction to elucidate the plant evolution of the cisZOG gene. We found that the cisZOG homologs do not form a clear separate clade, indicating that diversification of the cisZOG gene took place after the diversification of the main angiosperm families, probably within genera or closely related groups. We confirmed that the gene(s) from group O is(are) not present in A. thaliana and is(are) also missing in the family Brassicaceae. However, cisZOG or its metabolites are found among Brassicaceae clade, indicating that remaining genes from other groups (UGT73-group D and UGT85-group G) are able, at least in part, to substitute the function of group O lost during evolution. This study is the first detailed evolutionary evaluation of relationships among different plant ZOGs within angiosperms. | ||||||
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| Record 70 of 414 | ||||||||||||||||||
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| Author(s): Nicolas, V (Nicolas, Violaine); Mikula, O (Mikula, Ondrej); Lavrenchenko, LA (Lavrenchenko, Leonid A.); Sumbera, R (Sumbera, Radim); Bartakova, V (Bartakova, Veronika); Bryjova, A (Bryjova, Anna); Meheretu, Y (Meheretu, Yonas); Verheyen, E (Verheyen, Erik); Missoup, AD (Missoup, Alain Didier); Lemmon, AR (Lemmon, Alan R.); Lemmon, EM (Lemmon, Emily Moriarty); Bryja, J (Bryja, Josef) | ||||||||||||||||||
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| Abstract: The tribe Praomyini is a diversified group including 64 species and eight extant rodent genera. They live in a broad spectrum of habitats across whole sub-Saharan Africa. Members of this tribe are often very abundant, they have a key ecological role in ecosystems, they are hosts of many potentially pathogenic microorganisms and comprise numerous agricultural pests. Although this tribe is well supported by both molecular and morphological data, its intergeneric relationships and the species contents of several genera are not yet fully resolved. Recent molecular data suggest that at least three genera in current sense are paraphyletic. However, in these studies the species sampling was sparse and the resolution of relationships among genera was poor, probably due to a fast radiation of the tribe dated to the Miocene and insufficient amount of genetic data. Here we used genomic scale data (395 nuclear loci = 610,965 bp long alignment and mitogenomes = 14,745 bp) and produced the first fully resolved species tree containing most major lineages of the Praomyini tribe (i.e. all but one currently delimited genera and major intrageneric clades). Results of a fossil-based divergence dating analysis suggest that the radiation started during the Messinian stage (ca. 7 Ma) and was likely linked to a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forests, while many others adapted to a broad spectrum of new open lowland and montane habitats that appeared at the beginning of Pliocene. Our analyses clearly confirmed the presence of three polyphyletic genera (Praomys, Myomyscus and Mastomys). We review current knowledge of these three genera and suggest corresponding taxonomic changes. To keep genera monophyletic, we propose taxonomic re-arrangements and delimit four new genera. Furthermore, we discovered a new highly divergent genetic lineage of Praomyini in southwestern Ethiopia, which is described as a new species and genus. | ||||||||||||||||||
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| Record 71 of 414 | ||||||
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| Author(s): Vondrous, O (Vondrous, Ondrej); Kocur, Z (Kocur, Zbynek); Hrad, J (Hrad, Jaromir) | ||||||
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| Abstract: This article presents a verification process of a new metric designed for transmission continuity optimization. Unlike the commonly used metrics, it focuses solely on flow continuity and sustainability, disregarding the maximization of throughput or minimization of latency. We base our metric on inter-packet gaps analysis and ordering of packets from multiple communication flows into a final flow. We also compare our metric with the commonly used one based on Jain's fairness index in cases when optimization of communication flow sustainability is the priority. We present the evaluation of results and analyze the data processing complexity. Moreover, we discuss the weaknesses and strengths of different approaches to communication flow optimization. | ||||||
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| Record 72 of 414 | ||||||
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| Author(s): Galgonek, J (Galgonek, Jakub); Vondrasek, J (Vondrasek, Jiri) | ||||||
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| Abstract: The Resource Description Framework (RDF), together with well-defined ontologies, significantly increases data interoperability and usability. The SPARQL query language was introduced to retrieve requested RDF data and to explore links between them. Among other useful features, SPARQL supports federated queries that combine multiple independent data source endpoints. This allows users to obtain insights that are not possible using only a single data source. Owing to all of these useful features, many biological and chemical databases present their data in RDF, and support SPARQL querying. In our project, we primary focused on PubChem, ChEMBL and ChEBI small-molecule datasets. These datasets are already being exported to RDF by their creators. However, none of them has an official and currently supported SPARQL endpoint. This omission makes it difficult to construct complex or federated queries that could access all of the datasets, thus underutilising the main advantage of the availability of RDF data. Our goal is to address this gap by integrating the datasets into one database called the Integrated Database of Small Molecules (IDSM) that will be accessible through a SPARQL endpoint. Beyond that, we will also focus on increasing mutual interoperability of the datasets. To realise the endpoint, we decided to implement an in-house developed SPARQL engine based on the PostgreSQL relational database for data storage. In our approach, data are stored in the traditional relational form, and the SPARQL engine translates incoming SPARQL queries into equivalent SQL queries. An important feature of the engine is that it optimises the resulting SQL queries. Together with optimisations performed by PostgreSQL, this allows efficient evaluations of SPARQL queries. The endpoint provides not only querying in the dataset, but also the compound substructure and similarity search supported by our Sachem project. Although the endpoint is accessible from an internet browser, it is mainly intended to be used for programmatic access by other services, for example as a part of federated queries. For regular users, we offer a rich web application called ChemWebRDF using the endpoint. The application is publicly available at https://idsm.elixir-czech.cz/chemweb/. | ||||||
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| Record 73 of 414 | ||||||
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| Author(s): Krticka, J (Krticka, J.); Kubat, J (Kubat, J.); Krtickova, I (Krtickova, I.) | ||||||
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| Abstract: Massive stars lose a significant fraction of mass during their evolution. However, the corresponding mass-loss rates are rather uncertain, especially for evolved stars. To improve this, we calculated global line-driven wind models for Galactic B supergiants. Our models predict radial wind structure and particularly the mass-loss rates and terminal velocities directly from basic stellar parameters. The hydrodynamic structure of the flow is consistently determined from the photosphere in nearly hydrostatic equilibrium to supersonically expanding wind. The radiative force is derived from the solution of the radiative transfer equation in the comoving frame. We provide a simple formula that predicts theoretical mass-loss rates as a function of stellar luminosity and effective temperature. The mass-loss rate of B supergiants slightly decreases with temperature down to about 22.5 kK, where the region of recombination of FeIV to FeIII starts to appear. In this region, which is about 5 kK wide, the mass-loss rate gradually increases by a factor of about 6. The increase of the mass-loss rate is associated with a gradual decrease of terminal velocities by a factor of about 2. We compared the predicted wind parameters with observations. While the observed wind terminal velocities are reasonably reproduced by the models, the situation with mass-loss rates is less clear. The mass-loss rates derived from observations that are uncorrected for clumping are by a factor of 3 to 9 higher than our predictions on cool and hot sides of the studied sample, respectively. These observations can be reconciled with theory assuming a temperature-dependent clumping factor that is decreasing toward lower effective temperatures. On the other hand, the mass-loss rate estimates that are not sensitive to clumping agree with our predictions much better. Our predictions are by a factor of about 10 lower than the values currently used in evolutionary models appealing for reconsideration of the role of winds in the stellar evolution. | ||||||
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| Record 74 of 414 | |||||||||
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| Author(s): Krepl, M (Krepl, Miroslav); Damberger, FF (Damberger, Fred Franz); von Schroetter, C (von Schroetter, Christine); Theler, D (Theler, Dominik); Pokorna, P (Pokorna, Pavlina); Allain, FHT (Allain, Frederic H-T); Sponer, J (Sponer, Jiri) | |||||||||
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| Abstract: The YTH domain of YTHDC1 belongs to a class of protein "readers", recognizing the N6-methyladenosine (m(6)A) chemical modification in mRNA. Static ensemble-averaged structures revealed details of N6-methyl recognition via a conserved aromatic cage. Here, we performed molecular dynamics (MD) simulations along with nuclear magnetic resonance (NMR) and isothermal titration calorimetry (ITC) to examine how dynamics and solvent interactions contribute to the m(6)A recognition and negative selectivity toward an unmethylated substrate. The structured water molecules surrounding the bound RNA and the methylated substrate's ability to exclude bulk water molecules contribute to the YTH domain's preference for m(6)A. Intrusions of bulk water deep into the binding pocket disrupt binding of unmethylated adenosine. The YTHDC1's preference for the 5'-Gm(6)A-3' motif is partially facilitated by a network of water-mediated interactions between the 2amino group of the guanosine and residues in the m(6)A binding pocket. The 5'-Im(6)A-3' (where I is inosine) motif can be recognized too, but disruption of the water network lowers affinity. The D479A mutant also disrupts the water network and destabilizes m(6)A binding. Our interdisciplinary study of the YTHDC1 protein-RNA complex reveals an unusual physical mechanism by which solvent interactions contribute toward m(6)A recognition. | |||||||||
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| Record 75 of 414 | ||||||
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| Author(s): Svehlova, K (Svehlova, Katerina); Luksan, O (Luksan, Ondrej); Jakubec, M (Jakubec, Martin); Curtis, EA (Curtis, Edward A.) | ||||||
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| Abstract: Functional DNA molecules are useful components in nanotechnology and synthetic biology. To expand the toolkit of functional DNA parts, in this study we used artificial evolution to identify a glowing deoxyribozyme called Supernova. This deoxyribozyme transfers a phosphate from a 1,2-dioxetane substrate to its 5' hydroxyl group, which triggers a chemiluminescent reaction and a flash of blue light. An engineered version of Supernova is only catalytically active in the presence of an oligonucleotide complementary to its 3' end, demonstrating that light production can be coupled to ligand binding. We anticipate that Supernova will be useful in a wide variety of applications, including as a signaling component in allosterically regulated sensors and in logic gates of molecular computers. | ||||||
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| Record 76 of 414 | |||||||||||||||||||||
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| Author(s): Zedek, F (Zedek, Frantisek); Vesely, P (Vesely, Pavel); Tichy, L (Tichy, Lubomir); Elliott, TL (Elliott, Tammy L.); Garbolino, E (Garbolino, Emmanuel); de Ruffray, P (de Ruffray, Patrice); Bures, P (Bures, Petr) | |||||||||||||||||||||
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| Record 77 of 414 | ||||||
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| Author(s): Butera, V (Butera, Valeria); Detz, H (Detz, Hermann) | ||||||
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| Abstract: The photochemical reduction of carbon dioxide (CO2) into methanol is very appealing since it requires sunlight as the only energy input. However, the development of highly selective and efficient photocatalysts is still very challenging. It has been reported that CO2 can be spontaneously activated on gallium nitride (GaN). Moreover, the photocatalytic activity for CO2 conversion into methanol can be drastically enhanced by incorporating a small amount of Mg dopant. In this work, density functional theory (DFT) based on a cluster model approach has been applied to further explore the photocatalytic activity of bare GaN towards CO2 adsorption and conversion. We extended the investigation of Mg-doping replacing one Ga atom with Mg on three different sites and evaluated the consequent effects on the band gaps and CO2 adsorption energies. Finally, we explore different routes leading to the production of methanol and evaluate the catalytic activity of bare GaN by applying the energetic span model (ESM) in order to identify the rate-determining states which are fundamental for suggesting modifications that can improve the photocatalytic activity of this promising material. | ||||||
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| Record 78 of 414 | |||||||||
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| Author(s): Midlik, A (Midlik, Adam); Navratilova, V (Navratilova, Veronika); Moturu, TR (Moturu, Taraka Ramji); Koca, J (Koca, Jaroslav); Svobodova, R (Svobodova, Radka); Berka, K (Berka, Karel) | |||||||||
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| Abstract: Protein structural families are groups of homologous proteins defined by the organization of secondary structure elements (SSEs). Nowadays, many families contain vast numbers of structures, and the SSEs can help to orient within them. Communities around specific protein families have even developed specialized SSE annotations, always assigning the same name to the equivalent SSEs in homologous proteins. A detailed analysis of the groups of equivalent SSEs provides an overview of the studied family and enriches the analysis of any particular protein at hand. We developed a workflow for the analysis of the secondary structure anatomy of a protein family. We applied this analysis to the model family of cytochromes P450 (CYPs)-a family of important biotransformation enzymes with a community-wide used SSE annotation. We report the occurrence, typical length and amino acid sequence for the equivalent SSE groups, the conservation/variability of these properties and relationship to the substrate recognition sites. We also suggest a generic residue numbering scheme for the CYP family. Comparing the bacterial and eukaryotic part of the family highlights the significant differences and reveals a well-known anomalous group of bacterial CYPs with some typically eukaryotic features. Our workflow for SSE annotation for CYP and other families can be freely used at address https://sestra.ncbr.muni.cz. | |||||||||
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| Record 79 of 414 | ||||||
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| Author(s): Kulhanek, J (Kulhanek, Jonas); Derner, E (Derner, Erik); Babuska, R (Babuska, Robert) | ||||||
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| Abstract: Visual navigation is essential for many applications in robotics, from manipulation, through mobile robotics to automated driving. Deep reinforcement learning (DRL) provides an elegant map-free approach integrating image processing, localization, and planning in one module, which can be trained and therefore optimized for a given environment. However, to date, DRL-based visual navigation was validated exclusively in simulation, where the simulator provides information that is not available in the real world, e.g., the robot's position or segmentation masks. This precludes the use of the learned policy on a real robot. Therefore, we present a novel approach that enables a direct deployment of the trained policy on real robots. We have designed a new powerful simulator capable of domain randomization. To facilitate the training, we propose visual auxiliary tasks and a tailored reward scheme. The policy is fine-tuned on images collected from real-world environments. We have evaluated the method on a mobile robot in a real office environment. The training took approximately 30 hours on a single GPU. In 30 navigation experiments, the robot reached a 0.3-meter neighbourhood of the goal in more than 86.7% of cases. This result makes the proposed method directly applicable to tasks like mobile manipulation. | ||||||
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| Record 80 of 414 | |||||||||||||||
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| Author(s): Wos, G (Wos, Guillaume); Bohutinska, M (Bohutinska, Magdalena); Noskova, J (Noskova, Jana); Mandakova, T (Mandakova, Terezie); Kolar, F (Kolar, Filip) | |||||||||||||||
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| Abstract: Parallel adaptation results from the independent evolution of similar traits between closely related lineages and allows us to test to what extent evolution is repeatable. Similar gene expression changes are often detected but the identity of genes shaped by parallel selection and the causes of expression parallelism remain largely unknown. By comparing genomes and transcriptomes of four distinct foothill-alpine population pairs across four treatments, we addressed the genetic underpinnings, plasticity and functional consequences of gene expression parallelism in alpine adaptation. Seeds of eight populations of Arabidopsis arenosa were raised under four treatments that differed in temperature and irradiance, factors varying strongly with elevation. Parallelism in differential gene expression between the foothill and alpine ecotypes was quantified by RNA-seq in leaves of young plants. By manipulating temperature and irradiance, we also tested for parallelism in plasticity (i.e., gene-environment interaction, GEI). In spite of global non-parallel patterns transcriptome wide, we found significant parallelism in gene expression at the level of individual loci with an over-representation of genes involved in biotic stress response. In addition, we demonstrated significant parallelism in GEI, indicating a shared differential response of the originally foothill versus alpine populations to environmental variation across mountain regions. A fraction of genes showing expression parallelism also encompassed parallel outliers for genomic differentiation, with greater enrichment of such variants in cis-regulatory elements in some mountain regions. In summary, our results suggest frequent evolutionary repeatability in gene expression changes associated with the colonization of a challenging environment that combines constitutive expression differences and plastic interaction with the surrounding environment. | |||||||||||||||
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| Record 81 of 414 | |||||||||||||||
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| Author(s): Modrak, M (Modrak, Martin); Burkner, PC (Buerkner, Paul-Christian); Sieger, T (Sieger, Tomas); Slisz, T (Slisz, Tomas); Vasakova, M (Vasakova, Martina); Meseznikov, G (Meseznikov, Grigorij); Casas-Mendez, LF (Casas-Mendez, Luis Fernando); Vajter, J (Vajter, Jaromir); Taborsky, J (Taborsky, Jan); Kubricht, V (Kubricht, Viktor); Suk, D (Suk, Daniel); Horejsek, J (Horejsek, Jan); Jedlicka, M (Jedlicka, Martin); Mifkova, A (Mifkova, Adriana); Jaros, A (Jaros, Adam); Kubiska, M (Kubiska, Miroslav); Vachalova, J (Vachalova, Jana); Sin, R (Sin, Robin); Veverkova, M (Veverkova, Marketa); Pospisil, Z (Pospisil, Zbysek); Vohryzkova, J (Vohryzkova, Julie); Pokrievkova, R (Pokrievkova, Rebeka); Hrusak, K (Hrusak, Kristian); Christozova, K (Christozova, Kristina); Leos-Barajas, V (Leos-Barajas, Vianey); Fiser, K (Fiser, Karel); Hyanek, T (Hyanek, Tomas) | |||||||||||||||
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| Abstract: We collected a multi-centric retrospective dataset of patients (N = 213) who were admitted to ten hospitals in Czech Republic and tested positive for SARS-CoV-2 during the early phases of the pandemic in March-October 2020. The dataset contains baseline patient characteristics, breathing support required, pharmacological treatment received and multiple markers on daily resolution. Patients in the dataset were treated with hydroxychloroquine (N = 108), azithromycin (N = 72), favipiravir (N = 9), convalescent plasma (N = 7), dexamethasone (N = 4) and remdesivir (N = 3), often in combination. To explore association between treatments and patient outcomes we performed multiverse analysis, observing how the conclusions change between defensible choices of statistical model, predictors included in the model and other analytical degrees of freedom. Weak evidence to constrain the potential efficacy of azithromycin and favipiravir can be extracted from the data. Additionally, we performed external validation of several proposed prognostic models for Covid19 severity showing that they mostly perform unsatisfactorily on our dataset. | |||||||||||||||
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| Record 82 of 414 | |||||||||||||||
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| Author(s): Havlenova, T (Havlenova, Tereza); Skaroupkova, P (Skaroupkova, Petra); Miklovic, M (Miklovic, Matus); Behounek, M (Behounek, Matej); Chmel, M (Chmel, Martin); Jarkovska, D (Jarkovska, Dagmar); Sviglerova, J (Sviglerova, Jitka); Stengl, M (Stengl, Milan); Kolar, M (Kolar, Michal); Novotny, J (Novotny, Jiri); Benes, J (Benes, Jan); Cervenka, L (Cervenka, Ludek); Petrak, J (Petrak, Jiri); Melenovsky, V (Melenovsky, Vojtech) | |||||||||||||||
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| Abstract: Mechanisms of right ventricular (RV) dysfunction in heart failure (HF) are poorly understood. RV response to volume overload (VO), a common contributing factor to HF, is rarely studied. The goal was to identify interventricular differences in response to chronic VO. Rats underwent aorto-caval fistula (ACF)/sham operation to induce VO. After 24 weeks, RV and left ventricular (LV) functions, gene expression and proteomics were studied. ACF led to biventricular dilatation, systolic dysfunction and hypertrophy affecting relatively more RV. Increased RV afterload contributed to larger RV stroke work increment compared to LV. Both ACF ventricles displayed upregulation of genes of myocardial stress and metabolism. Most proteins reacted to VO in a similar direction in both ventricles, yet the expression changes were more pronounced in RV (p(slope): < 0.001). The most upregulated were extracellular matrix (POSTN, NRAP, TGM2, CKAP4), cell adhesion (NCAM, NRAP, XIRP2) and cytoskeletal proteins (FHL1, CSRP3) and enzymes of carbohydrate (PKM) or norepinephrine (MAOA) metabolism. Downregulated were MYH6 and FAO enzymes. Therefore, when exposed to identical VO, both ventricles display similar upregulation of stress and metabolic markers. Relatively larger response of ACF RV compared to the LV may be caused by concomitant pulmonary hypertension. No evidence supports RV chamber-specific regulation of protein expression in response to VO. | |||||||||||||||
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| Record 83 of 414 | |||||||||
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| Author(s): Zimmermann, T (Zimmermann, Tomas); Sebesta, F (Sebesta, Filip); Burda, JV (Burda, Jaroslav, V) | |||||||||
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| Abstract: This review emphasizes the necessity to perform additional Legendre transformation of the free energy for a correct thermodynamic description of reactions in the environment with constant pH. The power of this new thermodynamic potential (Gibbs-Alberty free energy Delta GA(0)) is demonstrated on three examples. First example, a DFT-based study of interaction of cisplatin with glycine, demonstrates the grand canonical character of the potential, which is manifested by the fact that Delta GA(0) energy is not dependent on a concrete form of molecules (protonated or deprotonated) used for energy evaluation. This independence on concrete molecular form strongly contradicts to the standard quantum-mechanical approach where only a single protonation state is used to represent each molecule. Second example, the reaction of hydroxo form of cisplatin with methionine which exhibits quite interesting pH dependency, demonstrates that it is possible to predict metal coordination sites of the amino acid based on proton (hydronium) concentration in solution: in neutral environment the metal binds to thio-group, in basic solutions to amino-group of the amino acid, and in acidic solutions to carboxyl group. This prediction is in the remarkable agreement with the pH-dependent migration of the coordination site observed experimentally in Reedijk laboratory. The final example is the combination of the approach with QM/MM MD simulations of the interaction of (hydrated) mercury cation with thymine. In this reaction, Delta GA(0) changes from endergonic to exergonic when the pH passes from acidic to basic values. (C) 2021 Elsevier B.V. All rights reserved. | |||||||||
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| Record 84 of 414 | |||||||||
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| Author(s): Borthakur, P (Borthakur, Priyakshree); Aryafard, M (Aryafard, Meysam); Zara, Z (Zara, Zeenat); David, R (David, Reha); Minofar, B (Minofar, Babak); Das, MR (Das, Manash R.); Vithanage, M (Vithanage, Meththika) | |||||||||
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| Abstract: Experimental and computational investigations have been conducted in this study to assess the influence of municipal waste pyrolyzed biochar impregnated clay composites on antibiotic removal as a material for wastewater treatment and simultaneous value-addition for waste. The surface potential (zeta potential) of the pristine biochar and composite samples are found to be within the range similar to 10 to similar to -40 mV in the pH range 2-10. The presence of different inorganic salt solutions influences the electrophoretic mobility of the dispersed phase in a suspension, as well as its zeta potential. In addition of Na+ salt solutions, the Na+ ions undergo electrostatic interaction with the negatively charged biochar samples and form a double layer at the interface of biochar and ionic salt solution. Molecular dynamics simulations have been employed to understand experimental findings, ions adsorption and solute-solvent interactions at the molecular level of two biochar B7 (seven benzene rings, one methoxy, one aldehyde and two hydroxyls groups) and B17 (seventeen benzene rings, one methoxy, two hydroxyls and two carboxylic acid groups) in salts aqueous solutions. The results confirm that hydroxyls and carboxylate groups of biochar are responsible for solute-solvent interactions. Successful removal of tetracycline antibiotics is observed with 26 mg/g maximum adsorption capacity with montmorillonite biochar composite. This study confirms that interactions between amide and hydroxyl groups of tetracycline with hydroxyl and carboxylate groups of biochar play the key role in the adsorption process. The solution pH and presence of different background electrolytes effectively influence the process of solute-solvent interactions as well as adsorption efficacy towards tetracycline adsorption. | |||||||||
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| Record 85 of 414 | |||||||||||||||
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| Author(s): Pokorny, V (Pokorny, Vaclav); Stejfa, V (Stejfa, Vojtech); Pavlicek, J (Pavlicek, Jan); Klajmon, M (Klajmon, Martin); Fulem, M (Fulem, Michal); Ruzicka, K (Ruzicka, Kvetoslav) | |||||||||||||||
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| Abstract: As a continuation of our effort to establish reliable thermodynamic data for important industrial solvents, dimethoxymethane (CAS RN: 109-87-5), 1,2-dimethoxyethane (CAS RN: 110-71-4), 2-methoxyethanol (CAS RN: 109-86-4), and 2-ethoxyethanol (CAS RN: 110-80-5) were studied. Vapor pressure was measured by ebulliometry for dimethoxymethane and by static method for 1,2-dimethoxyethane, 2-methoxyethanol, and 2-ethoxyethanol. Heat capacities in the liquid phase of all four compounds were measured by Tian-Calvet calorimetry in the temperature interval (262-358) K. In the case of dimethoxymethane and 1,2-dimethoxyethane, this interval was shortened because of their volatility. The thermodynamic properties in the ideal gaseous state were calculated using the methods of statistical thermodynamics based on calculated fundamental vibrational frequencies and molecular structure data. Calculated ideal-gas heat capacities and experimental data on vapor pressures, liquid phase heat capacities, and vaporization enthalpies were treated simultaneously to obtain a consistent thermodynamic description. Comparisons with literature values are shown for all measured and derived properties. Furthermore, the developed recommended data were used to identify new molecular parameters for the studied solvents within the PC-SAFT (perturbed-chain statistical associating fluid theory) equation of state and to compare their performance with those published in earlier papers; improved performance of the new parameters was achieved. | |||||||||||||||
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| Record 86 of 414 | ||||||
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| Author(s): Prerovska, T (Prerovska, Tereza); Pavlu, A (Pavlu, Anna); Hancharyk, D (Hancharyk, Dzianis); Rodionova, A (Rodionova, Anna); Vavrikova, A (Vavrikova, Anna); Spiwok, V (Spiwok, Vojtech) | ||||||
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| Abstract: Arabinogalactan proteins are very abundant, heavily glycosylated plant cell wall proteins. They are intensively studied because of their crucial role in plant development as well as their function in plant defence. Research of these biomacromolecules is complicated by the lack of tools for their analysis and characterisation due to their extreme heterogeneity. One of the few available tools for detection, isolation, characterisation, and functional studies of arabinogalactan proteins is Yariv reagents. Yariv reagent is a synthetic aromatic glycoconjugate originally prepared as an antigen for immunization. Later, it was found that this compound can precipitate arabinogalactan proteins, namely, their ss-D-(1 -> 3)-galactan structures. Even though this compound has been intensively used for decades, the structural basis of arabinogalactan protein precipitation by Yariv is not known. Multiple biophysical studies have been published, but none of them attempted to elucidate the three-dimensional structure of the Yariv-galactan complex. Here we use a series of molecular dynamics simulations of systems containing one or multiple molecules of ss-D-galactosyl Yariv reagent with or without oligo ss-D-(1 -> 3)-galactan to predict the structure of the complex. According to our model of Yariv-galactan complexes, Yariv reagent forms stacked oligomers stabilized by pi-pi and CH/pi interactions. These oligomers may contain irregularities. Galactan structures crosslink these Yariv oligomers. The results were compared with studies in literature. | ||||||
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| Record 87 of 414 | ||||||||||||
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| Author(s): Svoboda, M (Svoboda, Martin); Jimenez, SMG (Jimenez, M. Guadalupe S.); Kowalski, A (Kowalski, Adam); Cooke, M (Cooke, Michael); Mendoza, C (Mendoza, Cesar); Lisal, M (Lisal, Martin) | ||||||||||||
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| Abstract: Bilayers, self-assembled by cationic surfactants and fatty alcohols in water, are the basic units of lamellar gel networks - creamy formulations extensively used in cosmetics and pharmaceutics. Mesoscopic modelling and study of the bilayers formed by single- or double-tail cationic surfactants (CTAC or DHDAC), and fatty alcohols (FAs) in the lamellar fluid and gel phases were employed. Fatty alcohols with alkyl tail equal to or greater than the surfactant alkyl tail, i.e., C(16)FA or C(18)FA and C(22)FA, were considered. A model formulation was explored with the FA concentration greater than that of the surfactant and the structure of the fluid and gel bilayers in tensionless state characterised via the density profiles across the bilayers, orientational order parameters of the surfactant and FA chains, intrinsic analysis of the bilayer interfaces, and bending rigidity. The intrinsic analysis allows identification and quantification of the coexistence of the interdigitated and non-interdigitated phases present within the gel bilayers. The FA chains were found to conform the primary scaffolding of the bilayers while the surfactant chains tessellate bilayer monolayers from their water-hydrophobic interface. Further, the overlap of the FA chains from the apposed monolayers of the fluid bilayers rises with increasing FA length. Finally, the prevalence of the non-interdigitated phase over the interdigitated phase within the gel bilayers becomes enhanced upon the FA length increase with a preference of the surfactant chains to reside in the non-interdigitated phase rather than the interdigitated phase. | ||||||||||||
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| Record 88 of 414 | ||||||
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| Author(s): Jochim, B (Jochim, Bethany); Zohrabi, M (Zohrabi, M.); Gaire, B (Gaire, B.); 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: Employing a coincidence three-dimensional momentum imaging technique, we investigate the ultrafast, intense laser-induced dissociation of a metastable NO2+ ion beam into N+ + O+. Based on the kinetic energy release and angular distributions, measured using both 774-nm and second-order-harmonic 387-nm pulses, we show that the main processes driving dissociation in pulses of about 1014 W/cm(2) peak intensity are one- and two-photon transitions from the X-2 Pi+ ground state to the A(2)Pi first-excited state. First-order perturbation theory calculations also corroborate these findings. | ||||||
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| Record 89 of 414 | |||||||||
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| Author(s): Matveieva, M (Matveieva, Mariia); Polishchuk, P (Polishchuk, Pavel) | |||||||||
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| Abstract: Interpretation of QSAR models is useful to understand the complex nature of biological or physicochemical processes, guide structural optimization or perform knowledge-based validation of QSAR models. Highly predictive models are usually complex and their interpretation is non-trivial. This is particularly true for modern neural networks. Various approaches to interpretation of these models exist. However, it is difficult to evaluate and compare performance and applicability of these ever-emerging methods. Herein, we developed several benchmark data sets with end-points determined by pre-defined patterns. These data sets are purposed for evaluation of the ability of interpretation approaches to retrieve these patterns. They represent tasks with different complexity levels: from simple atom-based additive properties to pharmacophore hypothesis. We proposed several quantitative metrics of interpretation performance. Applicability of benchmarks and metrics was demonstrated on a set of conventional models and end-to-end graph convolutional neural networks, interpreted by the previously suggested universal ML-agnostic approach for structural interpretation. We anticipate these benchmarks to be useful in evaluation of new interpretation approaches and investigation of decision making of complex "black box" models. | |||||||||
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| Record 90 of 414 | |||||||||||||||
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| Author(s): Matas, M (Matas, Martin); Prochazka, M (Prochazka, Michal); Vlcek, J (Vlcek, Jaroslav); Houska, J (Houska, Jiri) | |||||||||||||||
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| Abstract: Amorphous HfMSiBCN materials (M = Y, Ho, Ta, Mo or an enhanced Hf content instead of any other M) are investigated by ab initio calculations and magnetron sputtering. We focus on combining the high-temperature stability and oxidation resistance of these materials with optimised mechanical, optical and electrical properties. First, we predict the corresponding trends by calculating the effect of the M choice and fraction on formation energy (E-form) and mechanical properties of MN and HfxM1-xN crystals. We discuss the dependence of E-form(HfxM1-xN) on the crystal structure and the distribution of Hf and M in the metal sublattice. The mechanical properties calculated for MN correlate with those measured for HfMSiBCN. The driving force towards N incorporation, decreasing with the periodic-table group number of M according to the calculated E-form (MN), correlates with the measured increasing electrical conductivity and extinction coefficient of HfMSiBCN. Second, we model the amorphous HfMSiBCN materials themselves by ab initio molecular dynamics. The calculated band gap, localisation of electronic states and bonding preferences of M also correspond to the increasing metallicity with respect to the periodic-table group number of M and confirm the possibility of predicting the trends in characteristics of HfMSiBCN using those of MN. Third, we study the measured HfMSiBCN properties as functions of each other and identify sputter target compositions leading to hard films with high electrical conductivity at a relatively low extinction coefficient. The results are important for the design of hard, conductive and/or transparent high-temperature coatings. (C) 2021 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved. | |||||||||||||||
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| Record 91 of 414 | |||||||||||||||
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| Author(s): Bohacek, J (Bohacek, Jan); Raudensky, M (Raudensky, Miroslav); Astrouski, I (Astrouski, Ilya); Karimi-Sibaki, E (Karimi-Sibaki, Ebrahim) | |||||||||||||||
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Abstract:
Polymeric hollow-fiber heat exchangers are a sound alternative to metallic plate fin counterparts. Plastic heat exchangers weigh much less, have significantly larger surface area per unit volume, are corrosion/ erosion resistant and electrically non-conductive, have a reduced ecological footprint, and are likely to be substantially cheaper.
A good passive chilled beam type heat exchanger requires its heat transfer surfaces to be distributed in optimal positions so that the thermal performance is maximized. For that purpose, a Lattice-Boltzmann model was setup in the open-source code Palabos to calculate natural convection triggered around a chilled beam made of many parallel hollow fibers with cold water running inside. In the simulations, the horizontal and vertical pitches between fibers were varied to eventually find their dimensionless optima of 6.9 and 1.3, respectively, for the Rayleigh number of 2.3. The numerical results were validated in the experiment as well as in the well-established ANSYS FLUENT. (c) 2021 Elsevier Ltd. All rights reserved. |
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| Record 92 of 414 | ||||||
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| Author(s): Zapletal, J (Zapletal, Jan); Watschinger, R (Watschinger, Raphael); Of, G (Of, Guenther); Merta, M (Merta, Michal) | ||||||
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| Abstract: The presented paper concentrates on the boundary element method (BEM) for the heat equation in three spatial dimensions. In particular, we deal with tensor product space-time meshes allowing for quadrature schemes analytic in time and numerical in space. The spatial integrals can be treated by standard BEM techniques known from three dimensional stationary problems. The contribution of the paper is twofold. First, we provide temporal antiderivatives of the heat kernel necessary for the assembly of BEM matrices and the evaluation of the representation formula. Secondly, the presented approach has been implemented in a publicly available library besthea allowing researchers to reuse the formulae and BEM routines straightaway. The results are validated by numerical experiments in an HPC environment. | ||||||
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| Record 93 of 414 | |||||||||||||||||||||
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| Author(s): Koubova, J (Koubova, Justina); Pangracova, M (Pangracova, Marie); Jankasek, M (Jankasek, Marek); Luksan, O (Luksan, Ondrej); Jehlik, T (Jehlik, Tomas); Brabcova, J (Brabcova, Jana); Jedlicka, P (Jedlicka, Pavel); Krivanek, J (Krivanek, Jan); Capkova Frydrychova, R (Capkova Frydrychova, Radmila); Hanus, R (Hanus, Robert) | |||||||||||||||||||||
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| Abstract: Kings and queens of termites, like queens of other advanced eusocial insects, are endowed with admirable longevity, which dramatically exceeds the life expectancies of their non-reproducing nest-mates and related solitary insects. In the quest to find the mechanisms underlying the longevity of termite reproductives, we focused on somatic maintenance mediated by telomerase. This ribonucleoprotein is well established for pro-longevity functions in vertebrates, thanks primarily to its ability of telomere extension. However, its participation in lifespan regulation of insects, including the eusocial taxa, remains understudied. Here, we report a conspicuous increase of telomerase abundance and catalytic activity in the somatic organs of primary and secondary reproductives of the termite Prorhinotermes simplex and confirm a similar pattern in two other termite species. These observations stand in contrast with the telomerase downregulation characteristic for most adult somatic tissues in vertebrates and also in solitary insects and non-reproducing castes of termites. At the same time, we did not observe caste-specific differences in telomere lengths that might explain the differential longevity of termite castes. We conclude that although the telomerase activation in termite reproductives is in line with the broadly assumed association between telomerase and longevity, its direct phenotypic impact remains to be elucidated. | |||||||||||||||||||||
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| Record 94 of 414 | ||||||
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| Author(s): Sindelka, K (Sindelka, Karel); Limpouchova, Z (Limpouchova, Zuzana); Prochazka, K (Prochazka, Karel) | ||||||
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| Abstract: Using coarse-grained dissipative particle dynamics (DPD) with explicit electrostatics, we performed (i) an extensive series of simulations of the electrostatic co-assembly of asymmetric oppositely charged copolymers composed of one (either positively or negatively charged) polyelectrolyte (PE) block A and one water-soluble block B and (ii) studied the solubilization of positively charged porphyrin derivatives (P+) in the interpolyelectrolyte complex (IPEC) cores of co-assembled nanoparticles. We studied the stoichiometric mixtures of 137 A(10)(+)B(25) and 137 A(10)(-)B(25) chains with moderately hydrophobic A blocks (DPD interaction parameter a(AS)=35) and hydrophilic B blocks (a(BS)=25) with 10 to 120 P+ added (a(PS)=39). The P+ interactions with other components were set to match literature information on their limited solubility and aggregation behavior. The study shows that the moderately soluble P+ molecules easily solubilize in IPEC cores, where they partly replace PE+ and electrostatically crosslink PE- blocks. As the large P+ rings are apt to aggregate, P+ molecules aggregate in IPEC cores. The aggregation, which starts at very low loadings, is promoted by increasing the number of P+ in the mixture. The positively charged copolymers repelled from the central part of IPEC core partially concentrate at the core-shell interface and partially escape into bulk solvent depending on the amount of P+ in the mixture and on their association number, A(S). If A(S) is lower than the ensemble average < A(S)>(n), the copolymer chains released from IPEC preferentially concentrate at the core-shell interface, thus increasing A(S), which approaches < A(S)>(n). If A(S) > < A(S)>(n), they escape into the bulk solvent. | ||||||
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| Record 95 of 414 | |||||||||||||||||||||
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| Author(s): Vondrak, T (Vondrak, Tihana); Oliveira, L (Oliveira, Ludmila); Novak, P (Novak, Petr); Koblizkova, A (Koblizkova, Andrea); Neumann, P (Neumann, Pavel); Macas, J (Macas, Jiri) | |||||||||||||||||||||
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| Abstract: Repeat-rich regions of higher plant genomes are usually associated with constitutive heterochromatin, a specific type of chromatin that forms tightly packed nuclear chromocenters and chromosome bands. There is a large body of cytogenetic evidence that these chromosome regions are often composed of tandemly organized satellite DNA. However, comparatively little is known about the sequence arrangement within heterochromatic regions, which are difficult to assemble due to their repeated nature. Here, we explore long-range sequence organization of heterochromatin regions containing the major satellite repeat CUS-TR24 in the holocentric plant Cuscuta europaea. Using a combination of ultra-long read sequencing with assembly-free sequence analysis, we reveal the complex structure of these loci, which are composed of short arrays of CUS-TR24 interrupted frequently by emerging simple sequence repeats and targeted insertions of a specific lineage of LINE retrotransposons. These data suggest that the organization of satellite repeats constituting heterochromatic chromosome bands can be more complex than previously envisioned, and demonstrate that heterochromatin organization can be efficiently investigated without the need for genome assembly. (C) 2021 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. | |||||||||||||||||||||
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| Record 96 of 414 | ||||||||||||||||||||||||
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| Author(s): Strelak, D (Strelak, David); Jimenez-Moreno, A (Jimenez-Moreno, Amaya); Vilas, JL (Vilas, Jose L.); Ramirez-Aportela, E (Ramirez-Aportela, Erney); Sanchez-Garcia, R (Sanchez-Garcia, Ruben); Maluenda, D (Maluenda, David); Vargas, J (Vargas, Javier); Herreros, D (Herreros, David); Fernandez-Gimenez, E (Fernandez-Gimenez, Estrella); de Isidro-Gomez, FP (de Isidro-Gomez, Federico P.); Horacek, J (Horacek, Jan); Myska, D (Myska, David); Horacek, M (Horacek, Martin); Conesa, P (Conesa, Pablo); Fonseca-Reyna, YC (Fonseca-Reyna, Yunior C.); Jimenez, J (Jimenez, Jorge); Martinez, M (Martinez, Marta); Harastani, M (Harastani, Mohamad); Jonic, S (Jonic, Slavica); Filipovic, J (Filipovic, Jiri); Marabini, R (Marabini, Roberto); Carazo, JM (Carazo, Jose M.); Sorzano, COS (Sorzano, Carlos O. S.) | ||||||||||||||||||||||||
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| Abstract: Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the world. During its 25 years of existence, Xmipp underwent multiple changes and updates. While there were many publications related to new programs and functionality added to Xmipp, there is no single publication on the Xmipp as a package since 2013. In this article, we give an overview of the changes and new work since 2013, describe technologies and techniques used during the development, and take a peek at the future of the package.</p> | ||||||||||||||||||||||||
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| Record 97 of 414 | ||||||||||||||||||
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| Author(s): Pokorny, V (Pokorny, Vaclav); Stejfa, V (Stejfa, Vojtech); Klajmon, M (Klajmon, Martin); Fulem, M (Fulem, Michal); Ruzicka, K (Ruzicka, Kvetoslav) | ||||||||||||||||||
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| Abstract: Vapor pressures for liquid 1-heptanol (CAS RN: 111-70-6), 1-octanol (CAS RN: 111-87-5), 1-nonanol (CAS RN: 143-08-8), and 1-decanol (CAS RN: 112-30-1) were measured by a static method near ambient temperatures over an operating pressure range from 0.5 to 1270 Pa, thus complementing literature vapor pressure data obtained by ebulliometry at higher temperatures. Liquid heat capacities of 1-octanol, 1-nonanol, and 1-decanol were determined by Tian-Calvet calorimetry. Ideal-gas thermodynamic properties of 1-alkanols up to 1-heptanol were obtained by a combination of quantum chemistry and statistical mechanics and validated against available experimental data. Ideal-gas heat capacities and entropies for longer homologues were obtained by deriving a methylene increment due to having a too complex conformational shape for analogical treatment. The thermodynamic consistency of available data was validated by simultaneous correlation of selected vapor pressures, literature enthalpies of vaporization, and heat capacity differences between the ideal gaseous and the liquid phase. The results are represented by the Cox equation and compared with available literature data. Moreover, the results were used to examine the perturbed-chain statistical associating fluid theory (PC-SAFT) equation of state for its performance in describing vapor pressures, enthalpies of vaporization, residual liquid heat capacities, and liquid densities of neat 1-alkanols from 1-hexanol to 1-decanol. A new PC-SAFT parameter set for each of them was also regressed that improves the PC-SAFT performance for the studied properties in comparison to existing parameters published in the literature. | ||||||||||||||||||
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| Record 98 of 414 | |||||||||||||||||||||
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| Author(s): Kratochvil, M (Kratochvil, Matous); Ciganek, M (Ciganek, Martin); Yumusak, C (Yumusak, Cigdem); Seelajaroen, H (Seelajaroen, Hathaichanok); Cisarova, I (Cisarova, Ivana); Fabry, J (Fabry, Jan); Vala, M (Vala, Martin); Lunak, S (Lunak, Stanislav); Weiter, M (Weiter, Martin); Sariciftci, NS (Sariciftci, Niyazi Serdar); Krajcovic, J (Krajcovic, Jozef) | |||||||||||||||||||||
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| Abstract: Optical and semiconducting properties of vacuum-deposited thin films of four hydrogen-bonded pigments were studied. Well-known 1,4-diketo-3,6-diphenyl-pyrrolo-[3,4-c]-pyrrole (Ph-DPP) and 1,4-diketo-3,6-(thiophen-2yl)-pyrrolo-[3,4-c]-pyrrole (Th-DPP) were transformed to their 1,4-dithioketo heteroanalogues (Ph-DTPP and ThDTPP) using Lawesson's reagent. X-ray single crystal structure determination confirmed the presence of CS-HN hydrogen bonds and a similar stack formation in both DTPPs, leading to relatively high decomposition temperatures, about 350 degrees C. According to density functional theory (DFT) calculations, thionation left HOMO (pi-type) level almost unchanged, considerably destabilized non-bonding orbital (n-orbital) localized on thioketo group, and significantly decreased LUMO (pi*-type) energy. Evolution of HOMO and LUMO energies was confirmed by cyclic voltammetry, establishing LUMO energy at -4.5 eV for both DTPPs, while a signature of high-lying n-orbital was detected through n pi* transition in the far-red/near-infrared area of absorption spectra, interpreted with help of time dependent DFT calculations on monomer and stacked dimer geometry. The lowest optical band-gap among the pigments under study was found to be 1.4 eV for Ph-DTPP thin film. Field effect mobilities, determined on a bottom-gate top-contact transistor, show DPPs as p-type and DTPPs as n-type semiconductors. The highest electron mobility mu e = 0.018 cm2 V-1 s- 1 was obtained for Ph-DTPP film in the device with aluminium source and drain electrodes. | |||||||||||||||||||||
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| Record 99 of 414 | ||||||
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| Author(s): Bera, K (Bera, Krishnendu) | ||||||
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Abstract:
Drug repurposing requires a limited resource, cost-effective and faster method to combat severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Therefore, this in silico studies attempts to identify the drug-likeness properties of ravidasvir, an II/III phase clinical trial chronic hepatitis C drug against 3-Chymotrypsin-like protease (3CL(pro)) of SARS-CoV-2 to combat the ongoing coronavirus disease 2019 (COVID-19) pandemic. This protease is predominantly involved in virus replication cycle; hence it is considered as a potent drug target. The molecular docking results showed that ravidasvir was found to be potent inhibitors of 3CL(pro) with scoring function based binding energy is -26.7 kJ/mol. Further dynamic behaviour of apo form and complex form of ravidasvir with 3CL(pro) were studied using molecular dynamics (MD) simulations over 500 ns each, total 2 mu s time scale. The motion of the protein was studied using principal component analysis of the MD simulation trajectories. The binding free energy calculated using MM/PBSA method from the MD simulation trajectory was -190.3 +/- 70.2 kJ/mol and -106.0 +/- 26.7 kJ/mol for GROMOS96 54A7 and AMBER99SB-ILDN force field, respectively. This in silico studies suggesting ravidasvir might be a potential lead molecule against SARS-CoV-2 for further optimization and drug development to combat the life-threatening COVID-19 pandemic.
Communicated by Ramaswamy H. Sarma |
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| Record 100 of 414 | ||||||||||||
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| Author(s): Fedosov, VE (Fedosov, Vladimir E.); Fedorova, AV (Fedorova, Alina, V); Larrain, J (Larrain, Juan); Santos, MB (Santos, Marina B.); Stech, M (Stech, Michael); Kucera, J (Kucera, Jan); Brinda, JC (Brinda, John C.); Tubanova, DY (Tubanova, Dolgor Ya); Von Konrat, M (Von Konrat, Matt); Ignatova, EA (Ignatova, Elena A.); Ignatov, MS (Ignatov, Michael S.) | ||||||||||||
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| Abstract: Molecular phylogenetic reconstructions of Rhabdoweisiaceae based on plastid (trnS-rps4 and trnL-F) and mitochondrial (narL5) DNA sequences and a comprehensive taxon sampling were performed, including 15 out of 16 genera currently attributed to the family, taxa recently found belonging to Rhabdoweisiaceae and expanded outgroups from related families of Dicranidae. The suggested revised delimitation of the family comprises Camptodontium (previously referred to Dicranaceae), three subaquatic species currently classified in Blindia (Seligeriaceae), and Glyphomitrium (previously referred to Ptychomitriaceae, Erpodiaceae or its own family) and Eucamptodon perichctetialis (the type species of the genus, previously referred to Dicnemonaceae). The emended delimitation of Rhabdoweisiaceae thus adds to the already high morphological heterogeneity resulting from the divergent evolution of specialized traits in different lineages of epiphytes and saxicolous hygrophytes. Taxonomic inferences from the phylogenetic analyses include segregation of three new genera, Pseudoblindia (for species currently recognized as Kiaeria falcata, Blindia robusta, B. lewinskyae and B. inundata), Ripariella (for Kiaeria riparia) and Brideliella (for Oncophorus wahlenbergii, O. demetrii and Symblepharis lindigii). Hollia is reinstated for the dicnemonoid Australasian species previously classified in Eucamptodon. Additionally, we propose to merge (1) Oreoweisia, Pocsiella and Pseudohyophila with Cynodontium, and (2) Kiaeria as. withArctoa. Furthermore, we propose to limit Oncophorus to a virens and a integerrimus and expand the circumscription of Symblepharis to accommodate O. crispifolius, O. dendrophilus, O. elongatus and a raui. The generic status and inclusion in Rhabdoweisiaceae are confirmed for Cnestrum and the recently described Notocynodontium, and the exclusion of Amphidium, Dichodontium, Holodontium and Hymenolomct from the family is supported. | ||||||||||||
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| Record 101 of 414 | ||||||
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| Author(s): Ortiz, D (Ortiz, David); Pekar, S (Pekar, Stano); Dianat, M (Dianat, Malahat) | ||||||
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| Abstract: RAD sequencing yields large amounts of genome-wide data at a relatively low cost and without requiring previous taxon-specific information, making it ideal for evolutionary studies of highly diversified and neglected organisms. However, concerns about information decay with phylogenetic distance have discouraged its use for assessing supraspecific relationships. Here, using Double Digest Restriction Associated DNA (ddRAD) data, we perform the first deep-level approach to the phylogeny of Zodarion, a highly diversified spider genus. We explore the impact of loci and taxon filtering across concatenated and multispecies coalescent reconstruction methods and investigate the patterns of information dropout in reference to both the time of divergence and the mitochondrial divergence between taxa. We found that relaxed loci-filtering and nested taxon-filtering strategies maximized the amount of molecular information and improved phylogenetic inference. As expected, there was a clear pattern of allele dropout towards deeper time and mitochondrial divergences, but the phylogenetic signal remained strong throughout the phylogeny. Therefore, we inferred topologies that were almost fully resolved, highly supported, and noticeably congruent between setups and inference methods, which highlights overall inconsistency in the taxonomy of Zodarion. Because Zodarion appears to be among the oldest and most mitochondrially diversified spider genera, our results suggest that ddRAD data show high potential for inferring intra-generic relationships across spiders and probably also in other taxonomic groups. | ||||||
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| Record 102 of 414 | |||||||||
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| Author(s): Slanina, Z (Slanina, Zdenek); Uhlik, F (Uhlik, Filip); Adamowicz, L (Adamowicz, Ludwik); Pan, CW (Pan, Changwang); Lu, X (Lu, Xing) | |||||||||
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| Abstract: The hydrogen-peroxide encapsulation into C-60 is evaluated using the DFT (M06-2X) and B2PLYPD as well MP2 calculations in the standard 6-31++G** and 6-311++G** basis sets. The H2O2 encapsulation is attractive, yielding an energy gain of about 12 kcal/mol. Such substantial encapsulation energy could allow for the high-temperature and high pressure synthesis (originally used for encapsulation of rare gases in fullerenes) of H2O2@C-60 which has otherwise been observed only in a form of encapsulation into an open-cage C-60 derivative. The calculated structural characteristics and IR vibrational spectrum are presented, too. | |||||||||
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| Record 103 of 414 | |||||||||
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| Author(s): Jirka, M (Jirka, M.); Klimo, O (Klimo, O.); Matys, M (Matys, M.) | |||||||||
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| Abstract: A substantial increase in local laser intensity is observed in the near field behind a plasma shutter. This increase is caused by the interference of the diffracted light at the relativistic plasma aperture and it is studied both analytically and using numerical simulations. This effect is only accessible in the regime of relativistically induced transparency and thus it requires a careful choice of laser and target parameters. The theoretical estimates for the maximum field strength and its spatial location as a function of target and laser parameters are provided and compared with simulation results. Our full 3D particle-in-cell simulations indicate that the laser intensity may be increased roughly by an order of magnitude, improving the feasibility of strong field QED research with the present generation of lasers. | |||||||||
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| Record 104 of 414 | ||||||||||||||||||||||||
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| Author(s): Said, M (Said, Mahmoud); Holusova, K (Holusova, Katerina); Farkas, A (Farkas, Andras); Ivanizs, L (Ivanizs, Laszlo); Gaal, E (Gaal, Eszter); Capal, P (Capal, Petr); Abrouk, M (Abrouk, Michael); Martis-Thiele, MM (Martis-Thiele, Mihaela M.); Kalapos, B (Kalapos, Balazs); Bartos, J (Bartos, Jan); Friebe, B (Friebe, Bernd); Dolezel, J (Dolezel, Jaroslav); Molnar, I (Molnar, Istvan) | ||||||||||||||||||||||||
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| Abstract: Breeding of agricultural crops adapted to climate change and resistant to diseases and pests is hindered by a limited gene pool because of domestication and thousands of years of human selection. One way to increase genetic variation is chromosome-mediated gene transfer from wild relatives by cross hybridization. In the case of wheat (Triticum aestivum), the species of genus Aegilops are a particularly attractive source of new genes and alleles. However, during the evolution of the Aegilops and Triticum genera, diversification of the D-genome lineage resulted in the formation of diploid C, M, and U genomes of Aegilops. The extent of structural genome alterations, which accompanied their evolution and speciation, and the shortage of molecular tools to detect Aegilops chromatin hamper gene transfer into wheat. To investigate the chromosome structure and help develop molecular markers with a known physical position that could improve the efficiency of the selection of desired introgressions, we developed single-gene fluorescence in situ hybridization (FISH) maps for M- and U-genome progenitors, Aegilops comosa and Aegilops umbellulata, respectively. Forty-three ortholog genes were located on 47 loci in Ae. comosa and on 52 loci in Ae. umbellulata using wheat cDNA probes. The results obtained showed that M-genome chromosomes preserved collinearity with those of wheat, excluding 2 and 6M containing an intrachromosomal rearrangement and paracentric inversion of 6ML, respectively. While Ae. umbellulata chromosomes 1, 3, and 5U maintained collinearity with wheat, structural reorganizations in 2, 4, 6, and 7U suggested a similarity with the C genome of Aegilops markgrafii. To develop molecular markers with exact physical positions on chromosomes of Aegilops, the single-gene FISH data were validated in silico using DNA sequence assemblies from flow-sorted M- and U-genome chromosomes. The sequence similarity search of cDNA sequences confirmed 44 out of the 47 single-gene loci in Ae. comosa and 40 of the 52 map positions in Ae. umbellulata. Polymorphic regions, thus, identified enabled the development of molecular markers, which were PCR validated using wheat-Aegilops disomic chromosome addition lines. The single-gene FISH-based approach allowed the development of PCR markers specific for cytogenetically mapped positions on Aegilops chromosomes, substituting as yet unavailable segregating map. The new knowledge and resources will support the efforts for the introgression of Aegilops genes into wheat and their cloning. | ||||||||||||||||||||||||
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| Author(s): Nepovimova, E (Nepovimova, Eugenie); Svobodova, L (Svobodova, Lucie); Dolezal, R (Dolezal, Rafael); Hepnarova, V (Hepnarova, Vendula); Junova, L (Junova, Lucie); Jun, DI (Jun, Daniel); Korabecny, J (Korabecny, Jan); Kucera, T (Kucera, Tomas); Gazova, Z (Gazova, Zuzana); Motykova, K (Motykova, Katarina); Kubackova, J (Kubackova, Jana); Bednarikova, Z (Bednarikova, Zuzana); Janockova, J (Janockova, Jana); Jesus, C (Jesus, Catarina); Cortes, L (Cortes, Luisa); Pina, J (Pina, Joao); Rostohar, D (Rostohar, Danijela); Serpa, C (Serpa, Carlos); Soukup, O (Soukup, Ondrej); Aitken, L (Aitken, Laura); Hughes, RE (Hughes, Rebecca E.); Musilek, K (Musilek, Kamil); Muckova, L (Muckova, Lubica); Jost, P (Jost, Petr); Chvojkova, M (Chvojkova, Marketa); Vales, K (Vales, Karel); Valis, M (Valis, Martin); Chrienova, Z (Chrienova, Zofia); Chalupova, K (Chalupova, Katarina); Kuca, K (Kuca, Kamil) | |||||||||||||||||||||||||||||||||||||||
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| Abstract: A series of tacrine - benzothiazole hybrids incorporate inhibitors of acetylcholinesterase (AChE), amyloid beta (A beta) aggregation and mitochondrial enzyme ABAD, whose interaction with AO leads to mitochondrial dysfunction, into a single molecule. In vitro, several of 25 final compounds exerted excellent anti-AChE properties and interesting capabilities to block A beta aggregation. The best derivative of the series could be considered 10w that was found to be highly potent and selective towards AChE with the IC50 value in nanomolar range. Moreover, the same drug candidate exerted absolutely the best results of the series against ABAD, decreasing its activity by 23% at 100 mu M concentration. Regarding the cytotoxicity profile of highlighted compound, it roughly matched that of its parent compound - 6-chlorotacrine. Finally, 10w was forwarded for in vivo scopolamine-induced amnesia experiment consisting of Morris Water Maze test, where it demonstrated mild procognitive effect. Taking into account all in vitro and in vivo data, highlighted derivative 10w could be considered as the lead structure worthy of further investigation. | |||||||||||||||||||||||||||||||||||||||
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| Record 106 of 414 | ||||||
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| Author(s): Psikal, J (Psikal, J.) | ||||||
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| Abstract: In this paper, we report on multiple phases of efficient laser-driven ion acceleration from near-critical density plasma of Gaussian density profile. Tracking of high-energy accelerated ions in multidimensional particle-in-cell simulations reveals the development of accelerating fields affecting the particles and the contribution of each acceleration phase to final ion energies. While the acceleration of ions occurs in a short time interval when a steep (infinite) density gradient is present, the accelerating field affecting the most energetic ions has unexpected local maxima about 50 fs after the moment when ultrashort (30 fs) laser pulse completely left the target with smooth density gradients. This field can be attributed to the apex of electron filament created behind the transmitted laser pulse. Full 3D simulation confirms the observations in 2D simulations in terms of ion acceleration mechanisms. However, it shows a substantial reduction of maximum achievable ion energies and a larger angular spread of accelerated ions compared with 2D approach, which demonstrates the necessity of using computationally demanding full 3D geometry for similar numerical studies. | ||||||
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| Record 107 of 414 | ||||||||||||||||||
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| Author(s): Kutalkova, E (Kutalkova, Eva); Hrncirik, J (Hrncirik, Josef); Witasek, R (Witasek, Roman); Ingr, M (Ingr, Marek); Huerta-Angeles, G (Huerta-Angeles, Gloria); Hermannova, M (Hermannova, Martina); Velebny, V (Velebny, Vladimir) | ||||||||||||||||||
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| Abstract: In this work, low molecular weight (17 kDa) hyaluronan was modified by dodecanoyl substituents. The activation of dodecanoic acid was mediated by benzoyl chloride towards the preparation of a mixed anhydride, which reacts in a second step with HA in water mixed with an organic solvent. The effect of the cosolvent was studied and showed an even distribution of substituents and higher reaction rate in water: 1,4-dioxane compared to water:tert-butanol where substituents occupy adjacent positions. The chemical characterization of the prepared derivatives was elucidated by NMR, FTIR spectroscopy, thermal analyses, and gas chromatography, while the distribution of substituents was evaluated by enzymatic degradation. Molecular-dynamics simulations reveal opposite solvent separations around HA and dodecanoyl chains, that is stronger in water:tert-butanol solution. The resulting incompatibility of solvation-shells of the two entities repels the reaction intermediates from the HA chain and drives them towards the already bound substituents, explaining the observed differences in the distribution evenness. Thus, the influence of the solvent on the reaction selectivity is observed by shielding reactive sites around HA. Therefore, a control of the distribution of the substituents was obtained by defining the concentration of HA and used cosolvent. | ||||||||||||||||||
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| Record 108 of 414 | |||||||||||||||||||||
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| Author(s): Kiss, MA (Kiss, Marton A.); Perina, M (Perina, Miroslav); Bazgier, V (Bazgier, Vaclav); May, NV (May, Nora V.); Baji, A (Baji, Adam); Jorda, R (Jorda, Radek); Frank, E (Frank, Eva) | |||||||||||||||||||||
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| Abstract: One of the main directions of steroid research is the preparation of modified derivatives in which, in addition to changes in physicochemical properties, receptor binding is significantly altered, thus a bioactivity different from that of the parent compound predominates. In the frame of this work, 2-arylidene derivatives were first synthesized by regioselective modification of the A-ring of natural sex hormone, 5 alpha-dihydrotestosterone (DHT). After Claisen-Schmidt condensations of DHT with (hetero)aromatic aldehydes in alkaline EtOH, heterocyclizations of the alpha,beta-enones were performed with 3-amino-1,2,4-triazole, 3-aminopyrazole and 3-amino-5-methylpyrazole in the presence of t-BuOK in DMF to afford 7 '-epimeric mixtures of A-ring-fused azolo-dihydropyrimidines, respectively. Depending on the electronic demand of the substituents of the arylidene moiety, spontaneous or 2,3-dichloro-5,6-dicyanobenzoquinone (DDQ)-induced oxidation of the heteroring led to triazolo[1,5-a]pyrimidines and pyrazolo[1,5-a]pyrimidines in good yields, while, using the Jones reagent as a strong oxidant, 17oxidation also occurred. The crystal structures of an arylidene and a triazolopyrimidine product have been determined by single crystal X-ray diffraction and both were found to crystallize in the monoclinic crystal system at P21 space group. Most derivatives were found to diminish the transcriptional activity of androgen receptor (AR) in reporter cell line. The candidate compound (17 beta-hydroxy-2-(4-chloro)benzylidene-5 alpha-androstan-3-one, 2f) showed to suppress androgen-mediated AR transactivation in a dose-dependent manner. We confirmed the cellular interaction of 2f with AR, described the binding in AR-binding cavity by the flexible docking and showed the ability of the compound to suppress the expression of AR-regulated genes in two prostate cancer cell lines. | |||||||||||||||||||||
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| Record 109 of 414 | |||||||||
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| Author(s): Labajova, N (Labajova, Nad'a); Baranova, N (Baranova, Natalia); Jurasek, M (Jurasek, Miroslav); Vacha, R (Vacha, Robert); Loose, M (Loose, Martin); Barak, I (Barak, Imrich) | |||||||||
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| Abstract: DivIVA is a protein initially identified as a spatial regulator of cell division in the model organism Bacillus subtilis, but its homologues are present in many other Gram-positive bacteria, including Clostridia species. Besides its role as topological regulator of the Min system during bacterial cell division, DivIVA is involved in chromosome segregation during sporulation, genetic competence, and cell wall synthesis. DivIVA localizes to regions of high membrane curvature, such as the cell poles and cell division site, where it recruits distinct binding partners. Previously, it was suggested that negative curvature sensing is the main mechanism by which DivIVA binds to these specific regions. Here, we show that Clostridioides difficile DivIVA binds preferably to membranes containing negatively charged phospholipids, especially cardiolipin. Strikingly, we observed that upon binding, DivIVA modifies the lipid distribution and induces changes to lipid bilayers containing cardiolipin. Our observations indicate that DivIVA might play a more complex and so far unknown active role during the formation of the cell division septal membrane. | |||||||||
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| Record 110 of 414 | ||||||
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| Author(s): Rud, OV (Rud, Oleg V.); Landsgesell, J (Landsgesell, Jonas); Holm, C (Holm, Christian); Kosovan, P (Kosovan, Peter) | ||||||
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| Abstract: Hydrogels immersed in salty solutions induce partitioning of small ions that can be exploited for water desalination. This partitioning also affects the H+ ions, leading to a decrease of the pH in the gel as compared to supernatant solution. When using weak polyelectrolyte gels, this lower pH may decrease their ionization degree, and hence diminish their desalination capacity. Using the recently developed grand-reaction ensemble, we performed particle-based computer simulations of a gel in contact with a reservoir of salt solution at pH similar or equal to 7. We showed that the effect of ion partitioning on the ionization degree is negligible, as long as the salinity of the reservoir is high. However, when the reservoir salinity approaches that of fresh water, the ionization degree of weak polyelectrolyte gel is significantly decreased, thus making it a less efficient desalination agent. Furthermore, we demonstrated that the ionization degree of the gel is decreased upon compression. However, up to pressures of approximately 30 bar this does not significantly affect the ion partitioning. Our result predict that weak polyelectrolyte hydrogels, such as the often employed poly(acrylic acid), can be efficiently used to lower the salinity of sea- or brackish water, while they will be inefficient in desalinating water of low salinity. | ||||||
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| Record 111 of 414 | ||||||||||||
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| Author(s): Vosahlo, P (Vosahlo, Petr); Radal, L (Radal, Lea); Labonde, M (Labonde, Marine); Cisarova, I (Cisarova, Ivana); Roger, J (Roger, Julien); Pirio, N (Pirio, Nadine); Hierso, JC (Hierso, Jean-Cyrille); Stepnicka, P (Stepnicka, Petr) | ||||||||||||
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| Abstract: Anionic phosphinoferrocene amidosulfonates bearing sterically demanding tert-butyl substituents in positions 3 and 3' of the ferrocene scaffold, viz. rac-(Et3NH)[Fe(eta(5)-tBuC(5)H(3)PR(2))-(eta(5)-tBuC(5)H(3)C(O)NHCH2SO3)] (R = phenyl, cyclohexyl), were synthesized by amidation of the corresponding phosphinocarboxylic acids, [Fe(eta(5)-tBuC(5)H(3)PR(2))(eta(5)-tetBuC(5)H(3)CO(2)H)]. These ditopic polar phosphinoferrocenes and their non-tert-butylated analogues have been used as ligands to prepare zwitterionic (eta(3)-ally) palladium(II) complexes [Pd(eta(3)-C3H5){Fe(eta(5)-R'C5H3PR2)(eta(5)-R'C5H3C(O)NHCH2SO3)}] (R' = H, tBu; R = Ph, Cy). Depending on the isolation procedure and crystallization conditions, some complexes were isolated in two isomeric forms which differed in the coordination of the amidosulfonate pendant group, where either amide or sulfonated oxygen ligated the Pd(II) center. The preference for coordination of the amide or sulfonate oxygen atoms has been explained by the interplay of electrostatic and solvation effects and further supported by DFT calculations. The (eta(3)-ally)Pd-II complexes have been applied as defined precatalysts for Pd-catalyzed C-H arylation of an unprotected indole with aryl iodides in polar solvents. Under the optimized reaction conditions at 100 degrees C in water, C2-arylation proceeded selectively with various aryl iodides to produce the respective 2-arylindoles in acceptable yields at a low catalyst loading (1 mol % Pd) and in the absence of any phase transfer agent. The catalyst possessing tert-butyl groups at the ferrocene core and an electron-rich dicyclohexylphosphino group exhibited the best catalytic performance. | ||||||||||||
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| Record 112 of 414 | |||||||||
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| Author(s): Hon, J (Hon, Jiri); Marusiak, M (Marusiak, Martin); Martinek, T (Martinek, Tomas); Kunka, A (Kunka, Antonin); Zendulka, J (Zendulka, Jaroslav); Bednar, D (Bednar, David); Damborsky, J (Damborsky, Jiri) | |||||||||
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Abstract:
Motivation: Poor protein solubility hinders the production of many therapeutic and industrially useful proteins. Experimental efforts to increase solubility are plagued by low success rates and often reduce biological activity. Computational prediction of protein expressibility and solubility in Escherichia coli using only sequence information could reduce the cost of experimental studies by enabling prioritization of highly soluble proteins.
Results: A new tool for sequence-based prediction of soluble protein expression in E.coli, SoluProt, was created using the gradient boosting machine technique with the TargetTrack database as a training set. When evaluated against a balanced independent test set derived from the NESG database, SoluProt's accuracy of 58.5% and AUC of 0.62 exceeded those of a suite of alternative solubility prediction tools. There is also evidence that it could significantly increase the success rate of experimental protein studies. |
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| Record 113 of 414 |
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| Author(s): Chareshneu, A (Chareshneu, Aliaksei); Pant, P (Pant, Purbaj); Ramos, RJT (Ramos, Ravi Jose Tristao); Sehmal, D (Sehmal, David); Gokbel, T (Gokbel, Tugrul); Ionescu, CM (Ionescu, Crina-Maria); Koca, J (Koca, Jaroslav) |
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| Abstract: Nicotinic acetylcholine receptors (nAChRs) comprise a large and ancient family of allosteric ion channels mediating synaptic transmission. The vast knowledge about nAChRs has become difficult to navigate. NAChRDB is a web-accessible resource of curated residue-level functional annotations of neuromuscular nAChRs. Interactive three-dimensional (3D) visualization and sequence alignment give further context to this rich and growing collection of experimental observations and computational predictions. NAChRDB is freely available at https://crocodile.ncbr.muni.cz/Apps/NAChRDB/, with interactive tutorials and regular updates to the content and web interface. No installation or user registration is required. NAChRDB is accessible through any modern internet browser on desktops and mobile devices. By providing immediate and systematic access to practical knowledge gained through decades of research, NAChRDB represents a powerful educational tool and helps guide discovery by revealing gaps in current knowledge and aiding the interpretation of results of molecular and structural biology experiments or computational studies. |
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| Record 114 of 414 | ||||||||||||
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| Author(s): Palenikova, V (Palenikova, Veronika); Frolikova, M (Frolikova, Michaela); Valaskova, E (Valaskova, Eliska); Postlerova, P (Postlerova, Pavla); Komrskova, K (Komrskova, Katerina) | ||||||||||||
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| Abstract: Integrins are transmembrane receptors that facilitate cell adhesion and cell-extracellular matrix communication. They are involved in the sperm maturation including capacitation and gamete interaction, resulting in successful fertilization. alpha V integrin belongs to the integrin glycoprotein superfamily, and it is indispensable for physiological spermiogenesis and testosterone production. We targeted the gene and protein expression of the alpha V integrin subunit and described its membrane localization in sperm. Firstly, in mouse, we traced alpha V integrin gene expression during spermatogenesis in testicular fraction separated by elutriation, and we detected gene activity in spermatogonia, spermatocytes, and round spermatids. Secondly, we specified alpha V integrin membrane localization in acrosome-intact and acrosome-reacted sperm and compared its pattern between mouse, pig, and human. Using immunodetection and structured illumination microscopy (SIM), the alpha V integrin localization was confined to the plasma membrane covering the acrosomal cap area and also to the inner acrosomal membrane of acrosome-intact sperm of all selected species. During the acrosome reaction, which was induced on capacitated sperm, the alpha V integrin relocated and was detected over the whole sperm head. Knowledge of the integrin pattern in mature sperm prepares the ground for further investigation into the pathologies and related fertility issues in human medicine and veterinary science. | ||||||||||||
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| Record 115 of 414 | ||||||||||||
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| Author(s): Dias, CAR (Rocha Dias, Cayo Augusto); Kuhn, GCS (Kuhn, Gustavo C. S.); Svartman, M (Svartman, Marta); Dos Santos, JE (Dos Santos Junior, Jose Eustaquio); Santos, FR (Santos, Fabricio Rodrigues); Pinto, CM (Pinto, Christian Miguel); Perini, FA (Perini, Fernando Araujo) | ||||||||||||
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| Abstract: Didelphis species have been shown to exhibit very conservative karyotypes, which mainly differ in their constitutive heterochromatin, known to be mostly composed by repetitive DNAs. In this study, we used genome skimming data combined with computational pipelines to identify the most abundant repetitive DNA families of Lutreolina crassicaudata and all six Didelphis species. We found that transposable elements (TEs), particularly LINE-1, endogenous retroviruses, and SINEs, are the most abundant mobile elements in the studied species. Despite overall similar TE proportions, we report that species of the D. albiventris group consistently present a less diverse TE composition and smaller proportions of LINEs and LTRs in their genomes than other studied species. We also identified four new putative satDNAs (sat206, sat907, sat1430 and sat2324) in the genomes of Didelphis species, which show differences in abundance and nucleotide composition. Phylogenies based on satDNA sequences showed well supported relationships at the species (sat1430) and groups of species (sat206) level, recovering topologies congruent with previous studies. Our study is one of the first attempts to present a characterization of the most abundant families of repetitive DNAs of Lutreolina and Didelphis species providing insights into the repetitive DNA composition in the genome landscape of American marsupials. | ||||||||||||
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| Record 116 of 414 | |||||||||||||||||||||||||||||||||
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| Author(s): Wu, SZ (Wu, Shangze); Zurauskas, J (Zurauskas, Jonas); Domanski, M (Domanski, Michal); Hitzfeld, PS (Hitzfeld, Patrick S.); Butera, V (Butera, Valeria); Scott, DJ (Scott, Daniel J.); Rehbein, J (Rehbein, Julia); Kumar, A (Kumar, Ajeet); Thyrhaug, E (Thyrhaug, Erling); Hauer, J (Hauer, Juergen); Barham, JP (Barham, Joshua P.) | |||||||||||||||||||||||||||||||||
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| Abstract: As a combination of visible light photoredox catalysis and synthetic organic electrochemistry, electrochemically-mediated photoredox catalysis emerged as a powerful synthetic technique in recent years, overcoming fundamental limitations of electrochemistry and photoredox catalysis in the single electron transfer activation of small organic molecules. Herein we report a tunable class of electroactivated photoredox catalyst, tri(para-substituted)biarylamines, that become superoxidants in their photoexcited states even able to oxidize molecules beyond the solvent window limits of cyclic voltammetry (such as polyfluorobenzene and trifluorotoluene). Furthermore, we demonstrate that precomplexation not only permits the excited state photochemistry of tris(para-substituted)biarylaminium cations to overcome picosecond lifetime, but enables and rationalizes the surprising photochemistry of their higher-order doublet (D-n) excited states, unlocking extremely high oxidative potentials (up to a record-breaking similar to+4.4 V vs. SCE). | |||||||||||||||||||||||||||||||||
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| Record 117 of 414 | ||||||
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| Author(s): Kundrat, J (Kundrat, Jan); Vasko, M (Vasko, Michal); Krejci, R (Krejci, Radek); Kubernat, V (Kubernat, Vaclav); Pecka, T (Pecka, Tomas); Havlis, O (Havlis, Ondrej); Slapak, M (Slapak, Martin); Jedlinsky, J (Jedlinsky, Jaroslav); Vojtech, J (Vojtech, Josef) | ||||||
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| Abstract: We present an implementation of streaming telemetry of optical metrics within open hardware reconfigurable add/drop multiplexers (ROADMs). Our key achievements are sub-second updates of high-resolution spectrum scans, and we demonstrate a sustained telemetry stream of the full C-band with a sub-GHz resolution. The telemetry streaming is implemented over a standard, Internet Engineering Task Force (IETF)-defined protocol (YANG Push) in collaboration with an open-source YANG software stack and device-specific code. As the telemetry collector, we used a common time series database (TSDB) along with a visualization dashboard. We also extended the Open Network Operating System (ONOS) software-defined network (SDN) controller to act as a telemetry receiver. (C) 2021 Optical Society of America under the terms of the OSA Open Access Publishing Agreement | ||||||
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| Record 118 of 414 | |||||||||
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| Author(s): Tehrani, ZA (Aliakbar Tehrani, Zahra); Rulisek, L (Rulisek, Lubomir); Cerny, J (Cerny, Jiri) | |||||||||
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| Abstract: Human stimulator of interferon genes (hSTING) is a signaling adaptor protein that triggers innate immune system by response to cytosolic DNA and second messenger cyclic dinucleotides (CDNs). Natural CDNs contain purine nucleobase with different phosphodiester linkage types (3 '-3 ', 2 '-2 ' or mixed 2 '-3 '-linkages) and exhibit different binding affinity towards hSTING, ranging from micromolar to nanomolar. High-affinity CDNs are considered as suitable candidates for treatment of chronic hepatitis B and cancer. We have used molecular dynamics simulations to investigate dynamical aspects of binding of natural CDNs (specifically, 2'-2'-cGAMP, 2'-3'-cGAMP, 3'-3'-cGAMP, 3'-3'-c-di-AMP, and 3'-3'-c-di-GMP) with hSTING(wt) protein. Our results revealed that CDN/hSTING(wt) interactions are controlled by the balance between fluctuations (conformational changes) in the CDN ligand and the protein dynamics. Binding of different CDNs induces different degrees of conformational/dynamics changes in hSTING(wt) ligand binding cavity, especially in alpha(1)-helices, the so-called lid region and alpha(2)-tails. The ligand residence time in hSTING(wt) protein pocket depends on different contribution of R232 and R238 residues interacting with oxygen atoms of phosphodiester groups in ligand, water distribution around interacting charged centers (in protein residues and ligand) and structural stability of closed conformation state of hSTING(wt) protein. These findings may perhaps guide design of new compounds modulating hSTING activity. Communicated by Ramaswamy H. Sarma | |||||||||
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| Record 119 of 414 | |||||||||
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| Author(s): Valentova, L (Valentova, L'ubica); Gallovic, F (Gallovic, Frantisek); Hok, S (Hok, Sebastien) | |||||||||
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| Abstract: Empirical ground-motion prediction equations (GMPEs) lack a sufficient number of measurements at near-source distances. Seismologists strive to supplement the missing data by physics-based strong ground-motion modeling. Here, we build a database of similar to 3000 dynamic rupture scenarios, assuming a vertical strike-slip fault of 36 x 20 km embedded in a 1D layered elastic medium and linear slip-weakening friction with heterogeneous parameters along the fault. The database is built by a Monte Carlo procedure to follow median and variability of Next Generation Attenuation-West2 Project GMPEs by Boore et al. (2014) at Joyner-Boore distances 10-80 km. The synthetic events span a magnitude range of 5.8-6.8 and have static stress drops between 5 and 40 MPa. These events are used to simulate ground motions at near-source stations within 5 km from the fault. The synthetic ground motions saturate at the near-source distances, and their variability increases at the near stations compared to the distant ones. In the synthetic database, the within event and between-event variability are extracted for the near and distant stations employing a mixed-effect model. The within-event variability is lower than its empirical value, only weakly dependent on period, and generally larger for the near stations than for the distant ones. The between-event variability is by 1/4 lower than its empirical value at periods > 1 s. We show that this can be reconciled by considering epistemic error in M-w when determining GMPEs, which is not present in the synthetic data. | |||||||||
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| Record 120 of 414 | ||||||||||||||||||
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| Author(s): Marques, SM (Marques, Sergio M.); Supolikova, L (Supolikova, Lucie); Molcanova, L (Molcanova, Lenka); Smejkal, K (Smejkal, Karel); Bednar, D (Bednar, David); Slaninova, I (Slaninova, Iva) | ||||||||||||||||||
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| Abstract: Multidrug resistance (MDR) is a common problem when fighting cancer with chemotherapy. P-glycoprotein (P-gp, or MDR1) is an active pump responsible for the efflux of xenobiotics out of the cell, including anti-cancer drugs. It is a validated target against MDR. No crystal structure of the human P-gp is available to date, and only recently several cryo-EM structures have been solved. In this paper, we present a comprehensive computational approach that includes constructing the full-length three-dimensional structure of the human P-gp and its refinement using molecular dynamics. We assessed its flexibility and conformational diversity, compiling a dynamical ensemble that was used to dock a set of lignan compounds, previously reported as active P-gp inhibitors, and disclose their binding modes. Based on the statistical analysis of the docking results, we selected a system for performing the structure-based virtual screening of new potential P-gp inhibitors. We tested the method on a library of 87 natural flavonoids described in the literature, and 10 of those were experimentally assayed. The results reproduced the theoretical predictions only partially due to various possible factors. However, at least two of the predicted natural flavonoids were demonstrated to be effective P-gp inhibitors. They were able to increase the accumulation of doxorubicin inside the human promyelocytic leukemia HL60/MDR cells overexpressing P-gp and potentiate the antiproliferative activity of this anti-cancer drug. | ||||||||||||||||||
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| Record 121 of 414 |
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| Author(s): Grabner, M (Grabner, Martin); Nithyanandan, K (Nithyanandan, Kanagaraj); Peterka, P (Peterka, Pavel); Koska, P (Koska, Pavel); Jasim, AA (Jasim, Ali. A.); Honzatko, P (Honzatko, Pavel) |
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| Abstract: The cladding pumping within a double-clad fiber structure is an effective technique to convert high-power multimode beam into high-power, almost diffraction limited beam. Since the pump efficiency is limited by the presence of higher skew-ray modes, geometrical perturbations are used to scramble the modes and to achieve a higher overlap of the electromagnetic field with the doped core. In this paper, the combined effect of fiber coiling and twisting is investigated in the double-clad fiber structure with the octagonal shape of an inner cladding. Electromagnetic field propagation through fibers with different cross-section areas, bending radii and twisting rates is numerically simulated using finite element beam propagation method. Holmium-doped double-clad fiber pumped in tandem configuration at wavelength 1950 nm is selected as an example. Nontrivial dependence of pump absorption on bending radius with the presence of local maxima is revealed. The observed impact of fiber coiling and twisting increases with the size of the cross-section area of the inner cladding. |
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| Record 122 of 414 | ||||||||||||||||||
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| Author(s): Chumova, Z (Chumova, Zuzana); Zaveska, E (Zaveska, Eliska); Hlouskova, P (Hlouskova, Petra); Ponert, J (Ponert, Jan); Schmidt, PA (Schmidt, Philipp-Andre); Certner, M (Certner, Martin); Mandakova, T (Mandakova, Terezie); Travnicek, P (Travnicek, Pavel) | ||||||||||||||||||
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| Abstract: Although the evolutionary drivers of genome size change are known, the general patterns and mechanisms of plant genome size evolution are yet to be established. Here we aim to assess the relative importance of proliferation of repetitive DNA, chromosomal variation (including polyploidy), and the type of endoreplication for genome size evolution of the Pleurothallidinae, the most species-rich orchid lineage. Phylogenetic relationships between 341 Pleurothallidinae representatives were refined using a target enrichment hybrid capture combined with high-throughput sequencing approach. Genome size and the type of endoreplication were assessed using flow cytometry supplemented with karyological analysis and low-coverage Illumina sequencing for repeatome analysis on a subset of samples. Data were analyzed using phylogeny-based models. Genome size diversity (0.2-5.1 Gbp) was mostly independent of profound chromosome count variation (2n = 12-90) but tightly linked with the overall content of repetitive DNA elements. Species with partial endoreplication (PE) had significantly greater genome sizes, and genomic repeat content was tightly correlated with the size of the non-endoreplicated part of the genome. In PE species, repetitive DNA is preferentially accumulated in the non-endoreplicated parts of their genomes. Our results demonstrate that proliferation of repetitive DNA elements and PE together shape the patterns of genome size diversity in orchids. | ||||||||||||||||||
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| Record 123 of 414 | |||||||||||||||||||||
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| Author(s): Krijt, J (Krijt, Jakub); Sokolova, J (Sokolova, Jitka); Silhavy, J (Silhavy, Jan); Mlejnek, P (Mlejnek, Petr); Kubovciak, J (Kubovciak, Jan); Liska, F (Liska, Frantisek); Malinska, H (Malinska, Hana); Huttl, M (Huettl, Martina); Markova, I (Markova, Irena); Krizkova, M (Krizkova, Michaela); Stipanuk, MH (Stipanuk, Martha H.); Krizek, T (Krizek, Tomas); Ditroi, T (Ditroi, Tamas); Nagy, P (Nagy, Peter); Kozich, V (Kozich, Viktor); Pravenec, M (Pravenec, Michal) | |||||||||||||||||||||
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| Abstract: Increased plasma total cysteine (tCys) has been associated with obesity and metabolic syndrome in human and some animal studies but the underlying mechanisms remain unclear. In this study, we aimed at evaluating the effects of high cysteine diet administered to SHR-CRP transgenic rats, a model of metabolic syndrome and inflammation. SHR-CRP rats were fed either standard (3.2 g cystine/kg diet) or high cysteine diet (HCD, enriched with additional 4 g L-cysteine/kg diet). After 4 weeks, urine, plasma and tissue samples were collected and parameters of metabolic syndrome, sulfur metabolites and hepatic gene expression were evaluated. Rats on HCD exhibited similar body weights and weights of fat depots, reduced levels of serum insulin, and reduced oxidative stress in the liver. The HCD did not change concentrations of tCys in tissues and body fluids while taurine in tissues and body fluids, and urinary sulfate were significantly increased. In contrast, betaine levels were significantly reduced possibly compensating for taurine elevation. In summary, increased Cys intake did not induce obesity while it ameliorated insulin resistance in the SHR-CRP rats, possibly due to beneficial effects of accumulating taurine. | |||||||||||||||||||||
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| Record 124 of 414 | |||||||||
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| Author(s): Slanina, Z (Slanina, Zdenek); Uhlik, F (Uhlik, Filip); Akasaka, T (Akasaka, Takeshi); Lu, X (Lu, Xing); Adamowicz, L (Adamowicz, Ludwik) | |||||||||
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| Abstract: Relative equilibrium populations of the IPR (isolated-pentagon-rule) isomers of Gd@C-82 under the high-temperature synthetic conditions are calculated. The calculations are based on the Gibbs energy derived using characteristics from the density functional theory calculations (B3LYP/3-21G similar to SDD entropy term, B2PLYPD/6-31+G* similar to SDD energetics). In agreement with observations, Gd@C (2v )(9)-C(82 )is the prevailing isomer while Gd@C ( s )(c; 6)-C-82 is predicted as a minor species. | |||||||||
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| Record 125 of 414 | |||||||||
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| Author(s): Zalis, S (Zalis, Stanislav); Heyda, J (Heyda, Jan); Sebesta, F (Sebesta, Filip); Winkler, JR (Winkler, Jay R.); Gray, HB (Gray, Harry B.); Vlcek, A (Vlcek, Antonin) | |||||||||
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| Abstract: Hole hopping through tryptophan/tyrosine chains enables rapid unidirectional charge transport over long distances. We have elucidated structural and dynamical factors controlling hopping speed and efficiency in two modified azurin constructs that include a rhenium(I) sensitizer, Re(His)(CO)(3)(dmp)(+), and one or two tryptophans (W-1, W-2). Experimental kinetics investigations showed that the two closely spaced (3 to 4 angstrom) intervening tryptophans dramatically accelerated long-range electron transfer (ET) from Cu-I to the photoexcited sensitizer. In our theoretical work, we found that time-dependent density-functional theory (TDDFT) quantum mechanics/molecular mechanics/molecular dynamics (QM/MM/MD) trajectories of low-lying triplet excited states of ReI(His)(CO)(3)(dmp)+-W-1(-W-2) exhibited crossings between sensitizer-localized (*Re) and charge-separated [ReI(His)(CO)(3)(dmp(center dot-))/(W1(center dot+) or W2(center dot+))] (CS1 or CS2) states. Our analysis revealed that the distances, angles, and mutual orientations of ET-active cofactors fluctuate in a relatively narrow range in which the cofactors are strongly coupled, enabling adiabatic ET. Water-dominated electrostatic field fluctuations bring *Re and CS1 states to a crossing where *Re(CO)(3)(dmp)(+)<- W-1 ET occurs, and CS1 becomes the lowest triplet state. ET is promoted by solvation dynamics around *Re(CO)(3)(dmp)+(W-1); and CS1 is stabilized by Re(dmp(center dot-))/W-1(center dot+) electron/hole interaction and enhanced W-1(center dot+) solvation. The second hop, W-1(center dot+)<- W-2, is facilitated by water fluctuations near the W-1/W-2 unit, taking place when the electrostatic potential at W-2 drops well below that at W1(center dot+). Insufficient solvation and reorganization around W2 make W-1(center dot+)<- W-2 ET endergonic, shifting the equilibrium toward W-1(center dot+) and decreasing the charge-separation yield. We suggest that multiscale TDDFT/MM/MD is a suitable technique to model the simultaneous evolution of photogenerated excited-state manifolds. | |||||||||
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| Record 126 of 414 | |||||||||
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| Author(s): Rozhon, J (Rozhon, Jan); Rezac, F (Rezac, Filip); Jalowiczor, J (Jalowiczor, Jakub); Behan, L (Behan, Ladislav) | |||||||||
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| Abstract: With the increased number of Software-Defined Networking (SDN) installations, the data centers of large service providers are becoming more and more agile in terms of network performance efficiency and flexibility. While SDN is an active and obvious trend in a modern data center design, the implications and possibilities it carries for effective and efficient network management are not yet fully explored and utilized. With most of the modern Internet traffic consisting of multimedia services and media-rich content sharing, the quality of multimedia communications is at the center of attention of many companies and research groups. Since SDN-enabled switches have an inherent feature of monitoring the flow statistics in terms of packets and bytes transmitted/lost, these devices can be utilized to monitor the essential statistics of the multimedia communications, allowing the provider to act in case of network failing to deliver the required service quality. The internal packet processing in the SDN switch enables the SDN controller to fetch the statistical information of the particular packet flow using the PacketIn and Multipart messages. This information, if preprocessed properly, can be used to estimate higher layer interpretation of the link quality and thus allowing to relate the provided quality of service (QoS) to the quality of user experience (QoE). This article discusses the experimental setup that can be used to estimate the quality of speech communication based on the information provided by the SDN controller. To achieve higher accuracy of the result, latency characteristics are added based on the exploiting of the dummy packet injection into the packet stream and/or RTCP packet analysis. The results of the experiment show that this innovative approach calculates the statistics of each individual RTP stream, and thus, we obtain a method for dynamic measurement of speech quality, where when quality decreases, it is possible to respond quickly by changing routing at the network level for each individual call. To improve the quality of call measurements, a Convolutional Neural Network (CNN) was also implemented. This model is based on two standard approaches to measuring the speech quality: PESQ and E-model. However, unlike PESQ/POLQA, the CNN-based model can take delay into account, and unlike the E-model, the resulting accuracy is much higher. | |||||||||
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| Record 127 of 414 | |||||||||||||||||||||
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| Author(s): Sillitoe, I (Sillitoe, Ian); Bordin, N (Bordin, Nicola); Dawson, N (Dawson, Natalie); Waman, VP (Waman, Vaishali P.); Ashford, P (Ashford, Paul); Scholes, HM (Scholes, Harry M.); Pang, CSM (Pang, Camilla S. M.); Woodridge, L (Woodridge, Laurel); Rauer, C (Rauer, Clemens); Sen, N (Sen, Neeladri); Abbasian, M (Abbasian, Mahnaz); Le Cornu, S (Le Cornu, Sean); Lam, SD (Lam, Su Datt); Berka, K (Berka, Karel); Varekova, IH (Varekova, Ivana Hutarova); Svobodova, R (Svobodova, Radka); Lees, J (Lees, Jon); Orengo, CA (Orengo, Christine A.) | |||||||||||||||||||||
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| Abstract: CATH (https:// www.cathdb.info) identifies domains in protein structures from wwPDB and classifies these into evolutionary superfamilies, thereby providing structural and functional annotations. There are two levels: CATH-B, a daily snapshot of the latest domain structures and superfamily assignments, and CATH+, with additional derived data, such as predicted sequence domains, and functionally coherent sequence subsets (Functional Families or FunFams). The latest CATH+ release, version 4.3, significantly increases coverage of structural and sequence data, with an addition of 65,351 fully-classified domains structures (+15%), providing 500 238 structural domains, and 151 million predicted sequence domains (+59%) assigned to 5481 superfamilies. The FunFam generation pipeline has been re-engineered to cope with the increased influx of data. Three times more sequences are captured in FunFams, with a concomitant increase in functional purity, information content and structural coverage. FunFam expansion increases the structural annotations provided for experimental GO terms (+59%). We also present CATH-FunVar web-pages displaying variations in protein sequences and their proximity to known or predicted functional sites. We present two case studies (1) putative cancer drivers and (2) SARS-CoV-2 proteins. Finally, we have improved links to and from CATH including SCOP, InterPro, Aquaria and 2DProt. | |||||||||||||||||||||
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| Record 128 of 414 |
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| Author(s): Houser, J (Houser, Josef); Kozmon, S (Kozmon, Stanislav); Mishra, D (Mishra, Deepti); Hammerova, Z (Hammerova, Zuzana); Wimmerova, M (Wimmerova, Michaela); Koca, J (Koca, Jaroslav) |
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| Record 129 of 414 | ||||||||||||||||||
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| Author(s): Fussy, Z (Fussy, Zoltan); Vinopalova, M (Vinopalova, Martina); Treitli, SC (Treitli, Sebastian Cristian); Panek, T (Panek, Tomas); Smejkalova, P (Smejkalova, Pavla); Cepicka, I (Cepicka, Ivan); Dolezal, P (Dolezal, Pavel); Hampl, V (Hampl, Vladimir) | ||||||||||||||||||
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| Abstract: Although the mitochondria of extant eukaryotes share a single origin, functionally these organelles diversified to a great extent, reflecting lifestyles of the organisms that host them. In anaerobic protists of the group Meta-monada, mitochondria are present in reduced forms (also termed hydrogenosomes or mitosomes) and a complete loss of mitochondrion in Monocercomonoides exilis (Metamonada:Preaxostyla) has also been reported. Within metamonads, retortamonads from the gastrointestinal tract of vertebrates form a sister group to parasitic dip -lomonads (e.g. Giardia and Spironucleus) and have also been hypothesized to completely lack mitochondria. We obtained transcriptomic data from Retortamonas dobelli and R. caviae and searched for enzymes of the core metabolism as well as mitochondrion-and parasitism-related proteins. Our results indicate that retortamonads have a streamlined metabolism lacking pathways for metabolites they are probably capable of obtaining from prey bacteria or their environment, reminiscent of the biochemical arrangement in other metamonads. Retor-tamonads were surprisingly found do encode homologs of components of Giardia?s remarkable ventral disk, as well as homologs of regulatory NEK kinases and secreted lytic enzymes known for involvement in host coloni-zation by Giardia. These can be considered pre-adaptations of these intestinal microorganisms to parasitism. Furthermore, we found traces of the mitochondrial metabolism represented by iron-sulfur cluster assembly subunits, subunits of mitochondrial translocation and chaperone machinery and, importantly, [FeFe]-hy-drogenases and hydrogenase maturases (HydE, HydF and HydG). Altogether, our results strongly suggest that a remnant mitochondrion is still present. | ||||||||||||||||||
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| Author(s): Jaros, M (Jaros, Milan); Riha, L (Riha, Lubomir); Strakos, P (Strakos, Petr); Spetko, M (Spetko, Matej) | ||||||
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Abstract:
This article presents a solution to path tracing of massive scenes on multiple GPUs. Our approach analyzes the memory access pattern of a path tracer and defines how the scene data should be distributed across up to 16 CPUs with minimal effect on performance. The key concept is that the parts of the scene that have the highest amount of memory accesses are replicated on all GPUs.
We propose two methods for maximizing the performance of path tracing when working with partially distributed scene data. Both methods work on the memory management level and therefore path tracer data structures do not have to be redesigned, making our approach applicable to other path tracers with only minor changes in their code. As a proof of concept, we have enhanced the open-source Blender Cycles path tracer. The approach was validated on scenes of sizes up to 169 GB. We show that only 1 5% of the scene data needs to be replicated to all machines for such large scenes. On smaller scenes we have verified that the performance is very close to rendering a fully replicated scene. In terms of scalability we have achieved a parallel efficiency of over 94% using up to 16 GPUs. |
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| Record 131 of 414 | |||||||||
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| Author(s): Vacek, J (Vacek, Jan); Vostalova, J (Vostalova, Jitka); Papouskova, B (Papouskova, Barbora); Skarupova, D (Skarupova, Denisa); Kos, M (Kos, Martin); Kabelac, M (Kabelac, Martin); Storch, J (Storch, Jan) | |||||||||
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| Abstract: In this contribution, a comprehensive study of the redox transformation, electronic structure, stability and photoprotective properties of phytocannabinoids is presented. The non-psychotropic cannabidiol (CBD), cannabigerol (CBG), cannabinol (CBN), cannabichromene (CBC), and psychotropic tetrahydrocannabinol (THC) isomers and iso-THC were included in the study. The results show that under aqueous ambient conditions at pH 7.4, non-psychotropic cannabinoids are slight or moderate electron-donors and they are relatively stable, in the following order: CBD > CBG >= CBN > CBC. In contrast, psychotropic Delta(9)-THC degrades approximately one order of magnitude faster than CBD. The degradation (oxidation) is associated with the transformation of OH groups and changes in the double-bond system of the investigated molecules. The satisfactory stability of cannabinoids is associated with the fact that their OH groups are fully protonated at pH 7.4 (pKa is >= 9). The instability of CBN and CBC was accelerated after exposure to UVA radiation, with CBD (or CBG) being stable for up to 24 h. To support their topical applications, an in vitro dermatological comparative study of cytotoxic, phototoxic and UVA or UVB photoprotective effects using normal human dermal fibroblasts (NHDF) and keratinocytes (HaCaT) was done. NHDF are approx. twice as sensitive to the cannabinoids' toxicity as HaCaT. Specifically, toxicity IC50 values for CBD after 24 h of incubation are 7.1 and 12.8 mu M for NHDF and HaCaT, respectively. None of the studied cannabinoids were phototoxic. Extensive testing has shown that CBD is the most effective protectant against UVA radiation of the studied cannabinoids. For UVB radiation, CBN was the most effective. The results acquired could be used for further redox biology studies on phytocannabinoids and evaluations of their mechanism of action at the molecular level. Furthermore, the UVA and UVB photoprotectivity of phytocannabinoids could also be utilized in the development of new cannabinoid-based topical preparations. | |||||||||
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| Record 132 of 414 |
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| Author(s): Vydana, HK (Vydana, Hari Krishna); Karafiat, M (Karafiat, Martin); Burget, L (Burget, Lukas); Cernocky, H (Cernocky, Honza) |
| Book Group Author(s): Assoc Computat Linguist |
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| Abstract: The paper describes BUT's English to German offline speech translation (ST) systems developed for IWSLT2021. They are based on jointly trained Automatic Speech Recognition-Machine Translation models. Their performances is evaluated on MustC-Common test set. In this work, we study their efficiency from the perspective of having a large amount of separate ASR training data and MT training data, and a smaller amount of speech-translation training data. Large amounts of ASR and MT training data are utilized for pretraining the ASR and MT models. Speechtranslation data is used to jointly optimize ASR-MT models by defining an end-to-end differentiable path from speech to translations. For this purpose, we use the internal continuous representations from the ASR-decoder as the input to MT module. We show that speech translation can be further improved by training the ASR-decoder jointly with the MT-module using large amount of text-only MT training data. We also show significant improvements by training an ASR module capable of generating punctuated text, rather than leaving the punctuation task to the MT module. |
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| Conference Sponsors: Assoc Computat Linguist |
| ISBN: 978-1-954085-74-9 |
| Record 133 of 414 |
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| Author(s): Haslinger, J (Haslinger, Jaroslav); Kucera, R (Kucera, Radek); Motyckova, K (Motyckova, Kristina); Satek, V (Satek, Vaclav) |
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| Abstract: The paper deals with the Stokes flow subject to the threshold leak boundary conditions in two and three space dimensions. The velocity-pressure formulation leads to the inequality type problem that is approximated by the P1-bubble/P1 mixed finite elements. The resulting algebraic system is nonsmooth. It is solved by the path-following variant of the interior point method, and by the active-set implementation of the semi-smooth Newton method. Inner linear systems are solved by the preconditioned conjugate gradient method. Numerical experiments illustrate scalability of the algorithms. The novelty of this work consists in applying dual strategies for solving the problem. |
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| Record 134 of 414 | ||||||
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| Author(s): Vojtech, J (Vojtech, Josef); Havlis, O (Havlis, Ondrej); Slapak, M (Slapak, Martin); Smotlacha, V (Smotlacha, Vladimir); Horvath, T (Horvath, Tomas); ALtmannova, L (ALtmannova, Lada); Velc, R (Velc, Radek); Kundrat, J (Kundrat, Jan); Vohnout, R (Vohnout, Rudolf); Bhowmick, S (Bhowmick, Sarbojeet); Hazlinsky, M (Hazlinsky, Michal); Cizek, M (Cizek, Martin); Hrabina, J (Hrabina, Jan); Pravdova, L (Pravdova, Lenka); Cip, O (Cip, Ondrej); Roztocil, J (Roztocil, Jaroslav) | ||||||
| Edited by: Strojnik M | ||||||
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| Abstract: Precise time and ultra-stable optical frequency transfers over fiber networks are deployed relatively often these days. When size of such infrastructure for precise time and frequency bidirectional transmission is becoming significant, aspects associated with infrastructure operational cost and time needed for deployment of time and frequency transmission must be considered. First can be decreased via fiber sharing with telecommunication traffic, however spectral allocation must be considered carefully to avoid mutual disturbance of time and frequency transmission versus data and allow future accommodation of growing demands. In text, we show and discuss alternative spectral bands to be used for time and frequency transmission. Time to deployment can be quite excessive especially when transmission must be established via multiple networks or network domains, also there is a chance of blocking. In case of precise time and optical radio frequency transmission it is possible to use conversion from optical to electrical and back to optical domain with wavelength change. This possibility removes danger of blocking and improves time to deployment for such services. We also address possibility to change wavelength or just extend reach by using simple re-amplify and reshape approach. | ||||||
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| ISBN: 978-1-5106-4499-1; 978-1-5106-4498-4 |
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| Author(s): Lopez-Echartea, E (Lopez-Echartea, Eglantina); Suman, J (Suman, Jachym); Smrhova, T (Smrhova, Tereza); Ridl, J (Ridl, Jakub); Pajer, P (Pajer, Petr); Strejcek, M (Strejcek, Michal); Uhlik, O (Uhlik, Ondrej) | |||||||||||||||||||||
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| Abstract: Certain industrial chemicals accumulate in the environment due to their recalcitrant properties. Bioremediation uses the capability of some environmental bacteria to break down these chemicals and attenuate the pollution. One such bacterial strain, designated Pvy, was isolated from sediment samples from a lagoon in Romania located near an oil refinery due to its capacity to degrade dibenzofuran (DF). The genome sequence of the Pvy strain was obtained using an Oxford Nanopore MiniION platform. According to the consensus 16S rRNA gene sequence that was compiled from six 16S rRNA gene copies contained in the genome and orthologous average nucleotide identity (OrthoANI) calculation, the Pvy strain was identified as Pseudomonas veronii, which confirmed the identification obtained with the aid of MALDI-TOF mass spectrometry and MALDI BioTyper. The genome was analyzed with respect to enzymes responsible for the overall biodegradative versatility of the strain. The Pvy strain was able to derive carbon from naphthalene (NP) and several aromatic compounds of natural origin, including salicylic, protocatechuic, p-hydroxybenzoic, trans-cinnamic, vanillic, and indoleacetic acids or vanillin, and was shown to degrade but not utilize DF. In total seven loci were found in the Pvy genome, which enables the strain to participate in the degradation of these aromatic compounds. Our experimental data also indicate that the transcription of the NP-dioxygenase alpha-subunit gene (ndoB), carried by the plasmid of the Pvy strain, is inducible by DF. These features make the Pvy strain a potential candidate for various bioremediation applications. | |||||||||||||||||||||
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| Author(s): Sen, HS (Sen, H. S.); Polcar, T (Polcar, T.) | |||||||||
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| Abstract: The alpha particles, which appear during the nuclear reactions and are transformed into He atoms, are often implanted into (or produced in) the structural materials causing deterioration of the mechanical properties. Moreover, they precipitate into high-pressure He bubbles, further decreasing the strength. Metallic alloys with a high density of interfaces and/or grain boundaries can reduce or even heal the defects caused by irradiation; nevertheless, the detrimental effect of He atoms is still a concern and diffusion of He atoms in the vicinity of interfaces is the subject of active research. Here, we present an ab initio study to explore how the electric field influences the diffusion of He atoms in (HCP-BCC) Zr-Nb metallic multilayer composite before they start to agglomerate. Motivated by our previous work, where we showed that He atoms tend to agglomerate into the regions with low electron density, we utilized the shift of electrons inside Zr-Nb multilayer system due to the external field to manipulate the migration of He atoms in a preferred direction. The results indicate that He atoms can be guided along the direction of the field out of the system, especially along [00 02] direction in HCP-Zr. (C) 2021 Elsevier B.V. All rights reserved. | |||||||||
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| Author(s): Skodova-Sverakova, I (Skodova-Sverakova, Ingrid); Zahonova, K (Zahonova, Kristina); Juricova, V (Juricova, Valeria); Danchenko, M (Danchenko, Maksym); Moos, M (Moos, Martin); Barath, P (Barath, Peter); Prokopchuk, G (Prokopchuk, Galina); Butenko, A (Butenko, Anzhelika); Lukacova, V (Lukacova, Veronika); Kohutova, L (Kohutova, Lenka); Buckova, B (Buckova, Barbora); Horak, A (Horak, Ales); Faktorova, D (Faktorova, Drahomira); Horvath, A (Horvath, Anton); Simek, P (Simek, Petr); Lukes, J (Lukes, Julius) | ||||||||||||||||||||||||||||||||||||||||||
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| Abstract: Background The phylum Euglenozoa is a group of flagellated protists comprising the diplonemids, euglenids, symbiontids, and kinetoplastids. The diplonemids are highly abundant and speciose, and recent tools have rendered the best studied representative, Diplonema papillatum, genetically tractable. However, despite the high diversity of diplonemids, their lifestyles, ecological functions, and even primary energy source are mostly unknown. Results We designed a metabolic map of D. papillatum cellular bioenergetic pathways based on the alterations of transcriptomic, proteomic, and metabolomic profiles obtained from cells grown under different conditions. Comparative analysis in the nutrient-rich and nutrient-poor media, as well as the absence and presence of oxygen, revealed its capacity for extensive metabolic reprogramming that occurs predominantly on the proteomic rather than the transcriptomic level. D. papillatum is equipped with fundamental metabolic routes such as glycolysis, gluconeogenesis, TCA cycle, pentose phosphate pathway, respiratory complexes, beta-oxidation, and synthesis of fatty acids. Gluconeogenesis is uniquely dominant over glycolysis under all surveyed conditions, while the TCA cycle represents an eclectic combination of standard and unusual enzymes. Conclusions The identification of conventional anaerobic enzymes reflects the ability of this protist to survive in low-oxygen environments. Furthermore, its metabolism quickly reacts to restricted carbon availability, suggesting a high metabolic flexibility of diplonemids, which is further reflected in cell morphology and motility, correlating well with their extreme ecological valence. | ||||||||||||||||||||||||||||||||||||||||||
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| Record 138 of 414 | ||||||
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| Author(s): Srsen, S (Srsen, Stepan); Slavicek, P (Slavicek, Petr) | ||||||
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| Abstract: Nuclear densities are frequently represented by an ensemble of nuclear configurations or points in the phase space in various contexts of molecular simulations. The size of the ensemble directly affects the accuracy and computational cost of subsequent calculations of observable quantities. In the present work, we address the question of how many configurations do we need and how to select them most efficiently. We focus on the nuclear ensemble method in the context of electronic spectroscopy, where thousands of sampled configurations are usually needed for sufficiently converged spectra. The proposed representative sampling technique allows for a dramatic reduction of the sample size. By using an exploratory method, we model the density from a large sample in the space of transition properties. The representative subset of nuclear configurations is optimized by minimizing its Kullback-Leibler divergence to the full density with simulated annealing. High-level calculations are then performed only for the selected subset of configurations. We tested the algorithm on electronic absorption spectra of three molecules: (E)-azobenzene, the simplest Criegee intermediate, and hydrated nitrate anion. Typically, dozens of nuclear configurations provided sufficiently accurate spectra. A strongly forbidden transition of the nitrate anion presented the most challenging case due to rare geometries with disproportionately high transition intensities. This problematic case was easily diagnosed within the present approach. We also discuss various exploratory methods and a possible extension to dynamical simulations. | ||||||
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| Record 139 of 414 | ||||||||||||||||||||||||
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| Author(s): Vicar, T (Vicar, Tomas); Chemelik, J (Chemelik, Jiri); Jakubicek, R (Jakubicek, Roman); Chmelikova, L (Chmelikova, Larisa); Gumulec, J (Gumulec, Jaromir); Balvan, J (Balvan, J. A. N.); Provaznik, I (Provaznik, I. V. O.); Kolar, R (Kolar, Radim) | ||||||||||||||||||||||||
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| Abstract: In this paper, a novel U-Net-based method for robust adherent cell segmentation for quantitative phase microscopy image is designed and optimised. We designed and evaluated four specific post-processing pipelines. To increase the transferability to different cell types, non-deep learning transfer with adjustable parameters is used in the post-processing step. Additionally, we proposed a self-supervised pretraining technique using nonlabelled data, which is trained to reconstruct multiple image distortions and improved the segmentation performance from 0.67 to 0.70 of object-wise intersection over union. Moreover, we publish a new dataset of manually labelled images suitable for this task together with the unlabelled data for self-supervised pretraining. (c) 2021 Optical Society of America under the terms of the OSA Open Access Publishing Agreement | ||||||||||||||||||||||||
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| Record 140 of 414 | |||||||||
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| Author(s): Jirik, M (Jirik, Miroslav); Hacha, F (Hacha, Filip); Gruber, I (Gruber, Ivan); Palek, R (Palek, Richard); Mirka, H (Mirka, Hynek); Zelezny, M (Zelezny, Milos); Liska, V (Liska, Vaclav) | |||||||||
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| Abstract: Liver volumetry is an important tool in clinical practice. The calculation of liver volume is primarily based on Computed Tomography. Unfortunately, automatic segmentation algorithms based on handcrafted features tend to leak segmented objects into surrounding tissues like the heart or the spleen. Currently, convolutional neural networks are widely used in various applications of computer vision including image segmentation, while providing very promising results. In our work, we utilize robustly segmentable structures like the spine, body surface, and sagittal plane. They are used as key points for position estimation inside the body. The signed distance fields derived from these structures are calculated and used as an additional channel on the input of our convolutional neural network, to be more specific U-Net, which is widely used in medical image segmentation tasks. Our work shows that this additional position information improves the results of the segmentation. We test our approach in two experiments on two public datasets of Computed Tomography images. To evaluate the results, we use the Accuracy, the Hausdorff distance, and the Dice coefficient. Code is publicly available at: https://gitlab.com/hachaf/liver-segmentation.git. | |||||||||
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| Record 141 of 414 | |||||||||
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| Author(s): Jalowiczor, J (Jalowiczor, Jakub); Rozhon, J (Rozhon, Jan); Voznak, M (Voznak, Miroslav) | |||||||||
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| Abstract: The technologies of the Internet of Things (IoT) have an increasing influence on our daily lives. The expansion of the IoT is associated with the growing number of IoT devices that are connected to the Internet. As the number of connected devices grows, the demand for speed and data volume is also greater. While most IoT network technologies use cloud computing, this solution becomes inefficient for some use-cases. For example, suppose that a company that uses an IoT network with several sensors to collect data within a production hall. The company may require sharing only selected data to the public cloud and responding faster to specific events. In the case of a large amount of data, the off-loading techniques can be utilized to reach higher efficiency. Meeting these requirements is difficult or impossible for solutions adopting cloud computing. The fog computing paradigm addresses these cases by providing data processing closer to end devices. This paper proposes three possible network architectures that adopt fog computing for LoRaWAN because LoRaWAN is already deployed in many locations and offers long-distance communication with low-power consumption. The architecture proposals are further compared in simulations to select the optimal form in terms of total service time. The resulting optimal communication architecture could be deployed to the existing LoRaWAN with minimal cost and effort of the network operator. | |||||||||
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| Record 142 of 414 | ||||||
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| Author(s): Butera, V (Butera, Valeria); Detz, H (Detz, Hermann) | ||||||
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| Abstract: In order to provide alternative paths for the CO2 conversion processes, we present a quantum-chemical investigation of the CO2 hydrogenation to methanol catalyzed by the recently proposed diphosphine-ruthenium(ii) cationic complex, named Ru2, in presence of carboxylic acids. Our results have shown that, in absence of carboxylate anion, CO2 molecule is not activated towards the hydride nucleophilic attack and, consequently, its hydrogenation does not occur. On the other hand, the addition of carboxylic acid 1) allows the replacement of the p-cymene ligand and, therefore, the formation of the active metal-carboxylate specie proposed experimentally, and 2) activates the CO2 molecule, thus confirming the experimental suggestion that carboxylic acid acts as promoter. Moreover, the influence of the size of the carbon chain in the carboxylate acid has been also investigated and rationalized. Eventually, DFT calculations have been carried out to explore the experimentally proposed catalytic cycle for the CO2 hydrogenation to methanol. | ||||||
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| Record 143 of 414 | |||||||||
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| Author(s): Desai, AL (Desai, Ajay L.); Bhatt, K (Bhatt, Keyur); Modi, KM (Modi, Krunal M.); Patel, NP (Patel, Nihal P.); Panchal, M (Panchal, Manthan); Kongor, A (Kongor, Anita); Patel, CN (Patel, Chirag N.); Liska, A (Liska, Alan) | |||||||||
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| Abstract: Interaction of a novel calix[4]pyrrole bearing carboxylic acid functionality (ABCP) has been investigated towards amino acids in methanol. The ABCP-Tryptophan complex produces a blue shift in absorption spectra based on charge transfer mediated recognition. Additionally, the density functional theory calculations could substantiate possible mechanism for the 1:1 binding of Tryptophan with ABCP theoretically. Moreover, other parameters such as stability, softness, hardness and chemical potential have been calculated to know about the binding behaviour of ABCP as host and Tryptophan as guest. The Natural Bond Orbital and TDDFT calculation facilitates to understand the proper binding mechanism in reference to experimental results. | |||||||||
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| Record 144 of 414 | ||||||||||||
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| Author(s): Loiseau, O (Loiseau, Oriane); Machado, TM (Machado, Talita Mota); Paris, M (Paris, Margot); Koubinova, D (Koubinova, Darina); Dexter, KG (Dexter, Kyle G.); Versieux, LM (Versieux, Leonardo M.); Lexer, C (Lexer, Christian); Salamin, N (Salamin, Nicolas) | ||||||||||||
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| Abstract: The tropics hold at least an order of magnitude greater plant diversity than the temperate zone, yet the reasons for this difference are still subject to debate. Much of tropical plant diversity is in highly speciose genera and understanding the drivers of such high species richness will help solve the tropical diversity enigma. Hybridization has recently been shown to underlie many adaptive radiations, but its role in the evolution of speciose tropical plant genera has received little attention. Here, we address this topic in the hyperdiverse Bromeliaceae genus Vriesea using genome skimming data covering the three genomic compartments. We find evidence for hybridization in ca. 11% of the species in our dataset, both within the genus and between Vriesea and other genera, which is commensurate with hybridization underlying the hyperdiversity of Vriesea, and potentially other genera in Tillandsioideae. While additional genomic research will be needed to further clarify the contribution of hybridization to the rapid diversification of Vriesea, our study provides an important first data point suggesting its importance to the evolution of tropical plant diversity. | ||||||||||||
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| Record 145 of 414 | |||||||||
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| Author(s): Tran, TN (Thanh-Nam Tran); Voznak, M (Voznak, Miroslav); Fazio, P (Fazio, Peppino); Ho, VC (Van-Cuu Ho) | |||||||||
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| Abstract: In this study, we examine an emerging Multiple-Input-Multiple-Output (MIMO) Non-Orthogonal Multiple Access (NOMA) network which combines Transmit Antenna Selection (TAS) and Simultaneous Wireless Information and Power Transfer (SWIPT) protocols. A pre-coding channels matrix was designed to aid the TAS protocol. We deployed a strong user as a relay to assist a weak user. Three cooperative MIMO-NOMA network scenarios were investigated. In the first scenario, we assumed the relay was deployed with (i) Decode-and-Forward (DF), (ii) Amplify-and-Forward (AF) with Fixed Gain (FG) and (iii) AF with a Variable Gain (VG) protocols to improve system performance over the first scenario. In scenario (iii), we investigated an amplify coefficient based on the maximum of instantaneous CSI and obtained the Outage Probability (OP) in novel closed form. The analytical results showed that although the Base Station (BS) sent information and energy at the same instant, the OP performance at the relay was sufficient due to assistance from multi-antennas and the TAS protocol. However, the OP performance at the user under cooperation with a relay using the AF-VG protocol achieved better system performance | |||||||||
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| Record 146 of 414 | |||||||||||||||||||||
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| Author(s): Andrikopoulos, PC (Andrikopoulos, Prokopis C.); Chaudhari, AS (Chaudhari, Aditya S.); Liu, YL (Liu, Yingliang); Konold, PE (Konold, Patrick E.); Kennis, JTM (Kennis, John T. M.); Schneider, B (Schneider, Bohdan); Fuertes, G (Fuertes, Gustavo) | |||||||||||||||||||||
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| Abstract: Photosensory receptors containing the flavin-binding light-oxygen-voltage (LOV) domain are modular proteins that fulfil a variety of biological functions ranging from gene expression to phototropism. The LOV photocycle is initiated by blue-light and involves a cascade of intermediate species, including an electronically excited triplet state, that leads to covalent bond formation between the flavin mononucleotide (FMN) chromophore and a nearby cysteine residue. Subsequent conformational changes in the polypeptide chain arise due to the remodelling of the hydrogen bond network in the cofactor binding pocket, whereby a conserved glutamine residue plays a key role in coupling FMN photochemistry with LOV photobiology. Although the dark-to-light transition of LOV photosensors has been previously addressed by spectroscopy and computational approaches, the mechanistic basis of the underlying reactions is still not well understood. Here we present a detailed computational study of three distinct LOV domains: EL222 from Erythrobacter litoralis, AsLOV2 from the second LOV domain of Avena sativa phototropin 1, and RsLOV from Rhodobacter sphaeroides LOV protein. Extended protein-chromophore models containing all known crucial residues involved in the initial steps (femtosecond-to-microsecond) of the photocycle were employed. Energies and rotational barriers were calculated for possible rotamers and tautomers of the critical glutamine side chain, which allowed us to postulate the most energetically favoured glutamine orientation for each LOV domain along the assumed reaction path. In turn, for each evolving species, infrared difference spectra were constructed and compared to experimental EL222 and AsLOV2 transient infrared spectra, the former from original work presented here and the latter from the literature. The good agreement between theory and experiment permitted the assignment of the majority of observed bands, notably the similar to 1635 cm(-1) transient of the adduct state to the carbonyl of the glutamine side chain after rotation. Moreover, both the energetic and spectroscopic approaches converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and more so for AsLOV2, while for RsLOV the glutamine keeps its initial configuration. Additionally, the computed infrared shifts of the glutamine and interacting residues could guide experimental research addressing early events of signal transduction in LOV proteins. | |||||||||||||||||||||
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| Author(s): Munster, L (Munster, Lukas); Fojtu, M (Fojtu, Michaela); Capakova, Z (Capakova, Zdenka); Muchova, M (Muchova, Monika); Musilova, L (Musilova, Lenka); Vaculovic, T (Vaculovic, Tomas); Balvan, J (Balvan, Jan); Kuritka, I (Kuritka, Ivo); Masarik, M (Masarik, Michal); Vicha, J (Vicha, Jan) | |||||||||||||||||||||||||||
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| Abstract: Study provides an in-depth analysis of the structure-function relationship of polysaccharide anticancer drug carriers and points out benefits and potential drawbacks of differences in polysaccharide glycosidic bonding, branching and drug binding mode of the carriers. Cellulose, dextrin, dextran and hyaluronic acid have been regioselectively oxidized to respective dicarboxylated derivatives, allowing them to directly conjugate cisplatin, while preserving their major structural features intact. The structure of source polysaccharide has crucial impact on conjugation effectiveness, carrier capacity, drug release rates, in vitro cytotoxicity and cellular uptake. For example, while branched structure of dextrin-based carrier partially counter the undesirable initial burst release, it also attenuates the cellular uptake and the cytotoxicity of carried drug. Linear polysaccharides containing beta-(1 -> 4) glycosidic bonds and oxidized at C2 and C3 (cellulose and hyaluronate) have the best overall combination of structural features for improved drug delivery applications including potentiation of the cisplatin efficacy towards malignances. | |||||||||||||||||||||||||||
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| Record 148 of 414 | ||||||||||||||||||||||||
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| Author(s): Skalicky, T (Skalicky, Tomas); Alves, JMP (Alves, Joao M. P.); Morais, AC (Morais, Anderson C.); Reznarova, J (Reznarova, Jana); Butenko, A (Butenko, Anzhelika); Lukes, J (Lukes, Julius); Serrano, MG (Serrano, Myrna G.); Buck, GA (Buck, Gregory A.); Teixeira, MMG (Teixeira, Marta M. G.); Camargo, EP (Camargo, Erney P.); Sanders, M (Sanders, Mandy); Cotton, JA (Cotton, James A.); Yurchenko, V (Yurchenko, Vyacheslav); Kostygov, AY (Kostygov, Alexei Y.) | ||||||||||||||||||||||||
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| Abstract: Trypanosomatids of the subfamily Strigomonadinae bear permanent intracellular bacterial symbionts acquired by the common ancestor of these flagellates. However, the cospeciation pattern inherent to such relationships was revealed to be broken upon the description of Angomonas ambiguus, which is sister to A. desouzai, but bears an endosymbiont genetically close to that of A. deanei. Based on phylogenetic inferences, it was proposed that the bacterium from A. deanei had been horizontally transferred to A. ambiguus. Here, we sequenced the bacterial genomes from two A. ambiguus isolates, including a new one from Papua New Guinea, and compared them with the published genome of the A. deanei endosymbiont, revealing differences below the interspecific level. Our phylogenetic analyses confirmed that the endosymbionts of A. ambiguus were obtained from A. deanei and, in addition, demonstrated that this occurred more than once. We propose that coinfection of the same blowfly host and the phylogenetic relatedness of the trypanosomatids facilitate such transitions, whereas the drastic difference in the occurrence of the two trypanosomatid species determines the observed direction of this process. This phenomenon is analogous to organelle (mitochondrion/plastid) capture described in multicellular organisms and, thereafter, we name it endosymbiont capture. | ||||||||||||||||||||||||
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| Author(s): Jirsova, D (Jirsova, Dagmar); Koubkova, B (Koubkova, Bozena); Jirounkova, E (Jirounkova, Eliska); Vorel, J (Vorel, Jiri); Zhou, X (Zhou, Xing); Ding, XJ (Ding, Xuejuan); Gelnar, M (Gelnar, Milan); Kasny, M (Kasny, Martin) | ||||||
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| Abstract: Paradiplozoon opsariichthydis (Jiang, Wu et Wang, 1984) Jiang, Wu et Wang, 1989 (Platyhelminthes, Monogenea, Diplozoidae) is blood-feeding parasite from the gills of Asian cyprinid fish Opsariichthys bidens Gunther, 1873. In this study, we present a morphological redescription of P. opsariichthydis neotype main morphological features e. g. size of body and clamps due to the fact that the type material is missing. We decided to supplement morphological descriptions by the relevant molecular data (internal transcribed spacer - ITS2) related to P. opsariichthydis adult worm isolates and other representatives of genus Paradiplozoon to cross verify our findings. In addition to that, this study also brings an attention to the host identification. Thus, parasite data were complemented by the determinant cytochrome oxidase b (cytb) sequences of its hosts. All novel sequences are deposited in GenBank. This combination of the morphological and molecular data related to both the parasite and its host seems to be the optimal approach to the general process of (re)description of highly host-specific parasitic organisms, which can then lead to a meaningful phylogenetic analysis. | ||||||
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| Record 150 of 414 | ||||||||||||
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| Author(s): Ha, DH (Duy-Hung Ha); Duy, TT (Tran Trung Duy); Son, PN (Pham Ngoc Son); Thuong, LT (Thuong Le-Tien); Voznak, M (Voznak, Miroslav) | ||||||||||||
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| Abstract: In this paper, we propose secure relaying transmission protocols using rateless codes, where a source sends encoded packets to two intended destinations via help of intermediate relays. Employing non-orthogonal multiple access, two encoded packets can be sent to the destinations at the same time. In addition, two partial relay selection methods are studied to enhance reliability of the data transmission at the first and second hops. For protecting the source-relay and relay-destination transmission against an eavesdropper, cooperative jamming technique is employed. Particularly, in the first phase of each data transmission cycle, the remaining relays (except the selected relay) are used to transmit artificial noise on the eavesdropper, and cooperate with the selected relay to cancel interference components. In the second phase, trusted nodes that are near the destinations are employed to play a role as the cooperative jammers. For a fair performance comparison, we design a simple transmit power allocation for the transmitter and jammer nodes at the first and second phases. We also propose an adaptive power allocation method, where fractions of the transmit power are appropriately allocated to the signals, relying on instantaneous channel gains between the selected relay and the destinations. This paper also derives exact closed-form formulas of outage probability and intercept probability over Rayleigh fading channel. All the performance analysis is then validated by Monte-Carlo simulations. The obtained results clearly show a trade-off between security and reliability that can be enhanced by optimally designing the system parameters. | ||||||||||||
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| Record 151 of 414 | |||||||||
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| Author(s): Tran, TN (Tran, Thanh-Nam); Voznak, M (Voznak, Miroslav) | |||||||||
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| Abstract: The article proposes a new switchable coupled relay model for massive MIMO-NOMA networks. The model equips a much greater number of antennas on the coupled relays to dramatically improve capacity and Energy Efficiency (EE). Each relay in a coupled relay is selected and delivered into a single transmission block to serve multiple devices. This paper also plots a new diagram of two transmission blocks which illustrates energy harvesting and signal processing. To optimize the system performance of a massive MIMO-NOMA network, i.e., Outage Probability (OP) and system throughput, this paper deploys a Transmit Antenna Selection (TAS) protocol to select the best received signals from the pre-coding channel matrices. In addition, to achieve better EE, Simultaneously Wireless Information Power Transmit (SWIPT) is implemented. Specifically, this paper derives the novel theoretical analysis in closed-form expressions, i.e., OP, system throughput and EE from a massive MIMO-NOMA network aided by switchable coupled relays. The theoretical results obtained from the closed-form expressions show that a massive MIMO-NOMA network achieves better OP and greater capacity and expends less energy than the MIMO technique. Finally, independent Monte Carlo simulations verified the theoretical results. | |||||||||
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| Record 152 of 414 |
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| Author(s): Samas, P (Samas, Peter); Hauber, ME (Hauber, Mark E.); Honza, M (Honza, Marcel) |
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| Abstract: The capability of hosts to reject the odd egg from their nest is one of the key defenses against avian brood parasitism. Considerable research effort has been devoted to exploring which phenotypic traits of eggshells facilitate to cue the recognition of the parasitic egg. Here we have reviewed studies addressing salient egg traits involved in the rejection of foreign eggs and used a formal meta-analysis to quantify their relative importance. Hosts appear to rely to a large extent on eggshell color traits, followed by maculation patterns. Hosts respond with similar rates of egg rejection to natural vs. model eggs and when breeding in both closed and open nests. Analyses of experiments on hosts of Cuculus and Molothrus parasites, the two best studied brood parasitic lineages with different co-evolutionary histories, yield similar conclusions. We also identify several poorly studied potential egg recognition cues, such as odor or weight, and recommend exploring even the visual traits in more detail, including chromatic and achromatic contrasts or experimentally manipulated egg maculation characteristics. Recent technological and sensory ecological advances open many new research avenues to experimentally examine the role of diverse egg characteristics in antiparasite defenses. |
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| Record 153 of 414 | ||||||||||||
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| Author(s): Slivova, M (Slivova, Martina); Voznak, M (Voznak, Miroslav); Tovarek, J (Tovarek, Jaromir); Partila, P (Partila, Pavol) | ||||||||||||
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| Abstract: The article proposes a new speaker liveness test for speech verification systems. Biometric authentication systems based on speaker verification are often subject to presentation attacks which use the target speaker's recorded speech. We propose a liveness test which uses CNN isolated word ASR as a countermeasure to repel attacks during the verification process. The liveness test incorporates the extraction of MFCC coefficients and the CNN classifier. Reliability of the recognition of isolated words is verified against a validation dataset of various sizes. The achieved results verified the system's reliability, which decreased slightly as the size of the keyword dataset increased. The proposed method represents a simple and effective security component against presentation attacks for existing SV systems. | ||||||||||||
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| Record 154 of 414 | ||||||||||||
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| Author(s): Vrabec, R (Vrabec, Rudolf); Marikova, J (Marikova, Jana); Locarek, M (Locarek, Miroslav); Korabecny, J (Korabecny, Jan); Hulcova, D (Hulcova, Daniela); Hostalkova, A (Hostalkova, Anna); Kunes, J (Kunes, Jiri); Chlebek, J (Chlebek, Jakub); Kucera, T (Kucera, Tomas); Hrabinova, M (Hrabinova, Martina); Jun, D (Jun, Daniel); Soukup, O (Soukup, Ondrej); Andrisano, V (Andrisano, Vincenza); Jenco, J (Jenco, Jaroslav); Safratova, M (Safratova, Marcela); Novakova, L (Novakova, Lucie); Opletal, L (Opletal, Lubomir); Cahlikova, L (Cahlikova, Lucie) | ||||||||||||
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| Abstract: One undescribed indole alkaloid together with twenty-two known compounds have been isolated from aerial parts of Vinca minor L. (Apocynaceae). The chemical structures of the isolated alkaloids were determined by a combination of MS, HRMS, 1D, and 2D NMR techniques, and by comparison with literature data. The NMR data of several alkaloids have been revised, corrected, and missing data have been supplemented. Alkaloids isolated in sufficient quantity were screened for their in vitro acetylcholinesterase (AChE; E.C. 3.1.1.7) and butyrylcholinesterase (BuChE; E.C. 3.1.1.8) inhibitory activity. Selected compounds were also evaluated for prolyl oligopeptidase (POP; E.C. 3.4.21.26), and glycogen synthase 3 beta-kinase (GSK-3 beta; E.C. 2.7.11.26) inhibition potential. Significant hBuChE inhibition activity has been shown by (- )-2-ethyl-3[2-(3-ethylpiperidinyl)-ethyl]-1Hindole with an IC50 value of 0.65 +/- 0.16 mu M. This compound was further studied by enzyme kinetics, along with in silico techniques, to reveal the mode of inhibition. This compound is also predicted to cross the blood-brain barrier (BBB) through passive diffusion. | ||||||||||||
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| Record 155 of 414 | |||||||||
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| Author(s): Van, HT (Van, Hoang Thien); Van, QN (Van, Quyet-Nguyen); Le, DH (Le, Danh Hong); Van, HP (Van, Hoang-Phuong); Jalowiczor, J (Jalowiczor, Jakub); Nguyen, HS (Nguyen, Hoang-Sy); Voznak, M (Voznak, Miroslav) | |||||||||
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| Abstract: This manuscript investigates the system performance of hybrid wireless and power line communication networks for indoor Internet of Things applications. Differentiating itself from the existing literature, the performance of the direct link and dual-hop energy harvesting relay-aided links is analyzed under the condition of indoor fading modeled by log-normal distribution. Moreover, the manuscript presents the analytical expressions of the successful transmission probability of the deployed opportunistic decode-and-forward and amplify-and-forward relay selection scheme, and validates them with Monte Carlo simulations. Moreover, the impact of different system parameters on the successful transmission probability is revealed. For the considered hybrid system, in general, the opportunistic decode-and-forward relaying scheme outperforms the opportunistic amplify-and-forward relaying scheme. As importantly, increasing the source to relay distance and power splitting ratio over certain limits significantly deteriorates the system performance, indicated by the decrease in the successful transmission probability. | |||||||||
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| Record 156 of 414 | ||||||
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| Author(s): Sevcik, L (Sevcik, Lukas); Voznak, M (Voznak, Miroslav) | ||||||
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| Abstract: Video quality evaluation needs a combined approach that includes subjective and objective metrics, testing, and monitoring of the network. This paper deals with the novel approach of mapping quality of service (QoS) to quality of experience (QoE) using QoE metrics to determine user satisfaction limits, and applying QoS tools to provide the minimum QoE expected by users. Our aim was to connect objective estimations of video quality with the subjective estimations. A comprehensive tool for the estimation of the subjective evaluation is proposed. This new idea is based on the evaluation and marking of video sequences using the sentinel flag derived from spatial information (SI) and temporal information (TI) in individual video frames. The authors of this paper created a video database for quality evaluation, and derived SI and TI from each video sequence for classifying the scenes. Video scenes from the database were evaluated by objective and subjective assessment. Based on the results, a new model for prediction of subjective quality is defined and presented in this paper. This quality is predicted using an artificial neural network based on the objective evaluation and the type of video sequences defined by qualitative parameters such as resolution, compression standard, and bitstream. Furthermore, the authors created an optimum mapping function to define the threshold for the variable bitrate setting based on the flag in the video, determining the type of scene in the proposed model. This function allows one to allocate a bitrate dynamically for a particular segment of the scene and maintains the desired quality. Our proposed model can help video service providers with the increasing the comfort of the end users. The variable bitstream ensures consistent video quality and customer satisfaction, while network resources are used effectively. The proposed model can also predict the appropriate bitrate based on the required quality of video sequences, defined using either objective or subjective assessment. | ||||||
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| Record 157 of 414 | ||||||||||||
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| Author(s): Dong, B (Dong, Bo); Yu, YL (Yu, Yanling); Slanina, Z (Slanina, Zdenek); Wang, F (Wang, Feng); Lian, YF (Lian, Yongfu); Uhlik, F (Uhlik, Filip); Feng, L (Feng, Lai) | ||||||||||||
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| Abstract: Carbide clusterfullerenes (CCFs) have been of great concern due to their potential applications in materials science, in which the internal carbide cluster plays vital roles in the stability and properties of CCF. However, there still remains a debate about what configuration is ideal for the internal carbide cluster. In this work, we isolated two isomers (I and II) of Ho2C94 and studied them by means of mass spectrometry, UV-vis-NIR spectroscopy, and cyclic/differential pulse voltammetry. A combined study of single-crystal X-ray diffraction (SC-XRD) and density functional theory (DFT) computation ascertains isomer-I as Ho2C2@C-2(61)-C-92 , in which the Ho2C2 cluster displays variable configurations from planar zigzag to folded butterfly with very small distortion energy (similar to 10 kJ/mol) This study hence confirms that the internal carbide cluster is intrinsically flexible over a broad geometrical range in a relatively large fullerene cage, where the nanoscale compression effect is almost negligible. | ||||||||||||
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| Record 158 of 414 | ||||||
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| Author(s): Pavlik, V (Pavlik, Vaclav); Shore, SN (Shore, Steven N.) | ||||||
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| Abstract: Aims. We aim to investigate the consequences of a fast massive stellar remnant - a black hole (BH) or a neutron star (NS) - encountering a planetary system.Methods. We modelled a close encounter between the actual Solar System (SS) and a 2 M-circle dot NS and a 10 M-circle dot BH, using a few-body symplectic integrator. We used a range of impact parameters, orbital phases at the start of the simulation derived from the current SS orbital parameters, encounter velocities, and incidence angles relative to the plane of the SS.Results. We give the distribution of possible outcomes, such as when the SS remains bound, when it suffers a partial or complete disruption, and in which cases the intruder is able to capture one or more planets, yielding planetary systems around a BH or a NS. We also show examples of the long-term stability of the captured planetary systems. | ||||||
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| Record 159 of 414 | |||||||||
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| Author(s): Tran, TN (Tran, Thanh-Nam); Vo, TP (Vo, Thoai Phu); Fazio, P (Fazio, Peppino); Voznak, M (Voznak, Miroslav) | |||||||||
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| Abstract: We present the design for an ultra-low latency and low energy Internet of Things (IoT) network inspired by the emerging cooperative Non-Orthogonal Multiple Access (NOMA) wireless communication technique. The IoT network model consists of a source at the center of the network, a near device inside the network, and a far device outside the network. The far device is in the near proximity of the near device, however. We deploy the near device as a relay to assist the far device. The near device is assumed to be a low energy node. As a result, the near device cannot forward signals to the far device through its own power. We therefore design the IoT network to apply the Simultaneous Wireless Information and Power Transfer (SWIPT) technique so that the near device would be able to harvest energy and use it to forward signals. Two cooperative IoT network scenarios are examined: Half-Duplex (HD) and Full-Duplex (FD) relaying, each with and without eavesdroppers. The design also exploits Power Splitting (PS) factors for fairness in Quality of Service (QoS) for the devices. Novel analysis expressions are obtained accuracy and approximation of closed-forms for Outage Probability (OP), secrecy OP, system throughput and Jain's fairness index. The analysis results are proved and verified by Monte Carlo simulation results. | |||||||||
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| Record 160 of 414 | ||||||||||||||||||
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| Author(s): Vinklarek, IS (Vinklarek, Ivo S.); Suchan, J (Suchan, Jiri); Rakovsky, J (Rakovsky, Jozef); Moriova, K (Moriova, Kamila); Poterya, V (Poterya, Viktoriya); Slavicek, P (Slavicek, Petr); Farnik, M (Farnik, Michal) | ||||||||||||||||||
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| Abstract: We investigate the photodissociation dynamics of the C-Cl bond in chloroalkanes CH3Cl, n-C3H7Cl, i-C3H7Cl, n-C5H11Cl, combining velocity map imaging (VMI) experiment and direct ab initio dynamical simulations. The Cl fragment kinetic energy distributions (KEDs) from the VMI experiment exhibit a single peak with maximum close to 0.8 eV, irrespective of the alkyl chain length and C-Cl bond position. In contrary to CH3Cl, where less than 10% of the available energy is deposited into the internal excitation of the CH3 fragment, for all higher chloroalkanes around 40% to 60% of the available energy goes into the alkyl fragment excitation. We apply the classical hard spheres and spectator model to explain the energy partitioning, and compare the classical approach with direct ab initio dynamics simulations. The alkyl chain appears to be a soft, energy absorbing unit. We further investigate the role of the spin-orbit effects on the excitation and dynamics. Combining our experimental data with theory allows us to derive the probability of the direct absorption into the triplet electronic state as well as the probabilities for intersystem crossing. The results indicate an increasing direct absorption into the triplet state with increasing alkyl chain length. | ||||||||||||||||||
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| Record 161 of 414 | ||||||||||||||||||||||||
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| Author(s): Zarsky, V (Zarsky, Vojtech); Klimes, V (Klimes, Vladimir); Paces, J (Paces, Jan); Vlcek, C (Vlcek, Cestmir); Hradilova, M (Hradilova, Miluse); Benes, V (Benes, Vladimir); Nyvltova, E (Nyvltova, Eva); Hrdy, I (Hrdy, Ivan); Pyrih, J (Pyrih, Jan); Mach, J (Mach, Jan); Barlow, L (Barlow, Lael); Stairs, CW (Stairs, Courtney W.); Eme, L (Eme, Laura); Hall, N (Hall, Neil); Elias, M (Elias, Marek); Dacks, JB (Dacks, Joel B.); Roger, A (Roger, Andrew); Tachezy, J (Tachezy, Jan) | ||||||||||||||||||||||||
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| Abstract: The transition of free-living organisms to parasitic organisms is a mysterious process that occurs in all major eukaryotic lineages. Parasites display seemingly unique features associated with their pathogenicity; however, it is important to distinguish ancestral preconditions to parasitism from truly new parasite-specific functions. Here, we sequenced the genome and transcriptome of anaerobic free-living Mastigamoeba balamuthi and performed phylogenomic analysis of four related members of the Archamoebae, including Entamoeba histolytica, an important intestinal pathogen of humans. We aimed to trace gene histories throughout the adaptation of the aerobic ancestor of Archamoebae to anaerobiosis and throughout the transition from a free-living to a parasitic lifestyle. These events were associated with massive gene losses that, in parasitic lineages, resulted in a reduction in structural features, complete losses of some metabolic pathways, and a reduction in metabolic complexity. By reconstructing the features of the common ancestor of Archamoebae, we estimated preconditions for the evolution of parasitism in this lineage. The ancestor could apparently form chitinous cysts, possessed proteolytic enzyme machinery, compartmentalized the sulfate activation pathway in mitochondrion-related organelles, and possessed the components for anaerobic energy metabolism. After the split of Entamoebidae, this lineage gained genes encoding surface membrane proteins that are involved in host-parasite interactions. In contrast, gene gains identified in the M. balamuthi lineage were predominantly associated with polysaccharide catabolic processes. A phylogenetic analysis of acquired genes suggested an essential role of lateral gene transfer in parasite evolution (Entamoeba) and in adaptation to anaerobic aquatic sediments (Mastigamoeba). | ||||||||||||||||||||||||
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| Record 162 of 414 | |||||||||
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| Author(s): Lopez Marin, MA (Lopez Marin, Marco Antonio); Strejcek, M (Strejcek, Michal); Junkova, P (Junkova, Petra); Suman, J (Suman, Jachym); Santrucek, J (Santrucek, Jiri); Uhlik, O (Uhlik, Ondrej) | |||||||||
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| Abstract: A bacterial species is best characterized after its isolation in a pure culture. This is an arduous endeavor for many soil microorganisms, but it can be simplified by several techniques for improving culturability: for example, by using growth-promoting factors. We investigated the potential of a Micrococcus luteus culture supernatant containing resuscitation-promoting factor (SRpf) to increase the number and diversity of cultured bacterial taxa from a nutrient-rich compost soil. Phosphate-buffered saline and inactivated SRpf were included as controls. After agitation with SRpf at 28 degrees C for 1 day, the soil suspension was diluted and plated on two different solid, oligotrophic media: tenfold diluted Reasoner's 2A agar (R2A) and soil extract-based agar (SA). Colonies were collected from the plates to assess the differences in diversity between different treatments and cultivation media. The diversity on both R2A and SA was higher in the SRpf-amended extracts than the controls, but the differences on R2A were higher. Importantly, 51 potentially novel bacterial species were isolated on R2A and SA after SRpf treatment. Diversity in the soil extracts was also determined by high-throughput 16S rRNA amplicon sequencing, which showed an increase in the abundance of specific taxa before their successful cultivation. Conclusively, SRpf can effectively enhance the growth of soil bacterial species, including those hitherto uncultured. | |||||||||
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| Record 163 of 414 |
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| Author(s): Tichy, O (Tichy, Ondrej); Burda, JV (Burda, Jaroslav, V) |
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| Abstract: Vertical absorption spectra of selected molecules (pyrimidine nucleobases and 5-azacytosin, 2-amino-1,3,5-triazine, 2,4-diamino-1,3,5-triazine, 2,4,6-triamino-1,3,5-triazine, and s-triazine) were performed using TD-DFT, post-HF, and semiempirical OM2/MNDO methods. From comparing a relatively large set of functionals from the different rungs of Jacob's DFT ladder, the important role of the exact exchange interaction is demonstrated. TD-DFT results with the omega B2GP-PLYP functional (and a few others) are comparable with the post-HF methods. An important finding is also a good accuracy of the semiempirical OM2 approximation, which is used for estimations of lifetimes of the excited states for the same set of molecules. The lifetimes' determination is based on a stochastical treatment of a swarm of MD trajectories. The time-dependent Schrodinger equation is solved for the electronic degrees of freedom while the dynamics of nuclei is treated classically in each trajectory step applying Tully's fewest switch algorithm. The probability of individual states in time is determined and compared with both experimental and computational studies. Our results are in fair accord with available experiments. The nucleobases relatively quickly deactivate - all the relaxation times are below 0.5 ps (in very good accord with measured values). Much longer lifetimes (a few hundred ps) were obtained for other molecules: 5-azacytosin, 2,4-diamino-1,3,5-triazine, and 2,4,6-triamino-1,3,5-triazine. Also, in agreement with experimental data, 2-amino-1,3,5-triazine returns to the ground state on a nanosecond scale. (C) 2021 Elsevier B.V. All rights reserved. |
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| Record 164 of 414 | |||||||||
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| Author(s): Benacek, J (Benacek, Jan); Munoz, PA (Munoz, Patricio A.); Buchner, J (Buechner, Jorg) | |||||||||
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| Abstract: Electromagnetic waves due to electron-positron clouds (bunches), created by cascading processes in pulsar magnetospheres, have been proposed to explain the pulsar radio emission. In order to verify this hypothesis, we utilized for the first time Particle-in-Cell (PIC) code simulations to study the nonlinear evolution of electron-positron bunches dependant on the initial relative drift speeds of electrons and positrons, plasma temperature, and distance between the bunches. For this sake, we utilized the PIC code ACRONYM with a high-order field solver and particle weighting factor, appropriate to describe relativistic pair plasmas. We found that the bunch expansion is mainly determined by the relative electron-positron drift speed. Finite drift speeds were found to cause the generation of strong electrostatic superluminal waves at the bunch density gradients that reach up to E similar to 7.5 x 10(5) V cm(-1) (E/(m ( e ) c omega ( p ) e (-1)) similar to 4.4) and strong plasma heating. As a result, up to 15% of the initial kinetic energy is transformed into the electric field energy. Assuming the same electron and positron distributions, we found that the fastest (in the bunch reference frame) particles of consecutively emitted bunches eventually overlap in momentum (velocity) space. This overlap causes two-stream instabilities that generate electrostatic subluminal waves with electric field amplitudes reaching up to E similar to 1.9 x 10(4) V cm(-1) (E/(m ( e ) c omega ( p ) e (-1)) similar to 0.11). We found that in all simulations the evolution of electron-positron bunches may lead to the generation of electrostatic superluminal or subluminal waves, which, in principle, can be behind the observed electromagnetic emissions of pulsars in the radio wave range. | |||||||||
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| Record 165 of 414 | ||||||||||||
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| Author(s): Mangiola, S (Mangiola, Stefano); Thomas, EA (Thomas, Evan A.); Modrak, M (Modrak, Martin); Vehtari, A (Vehtari, Aki); Papenfuss, AT (Papenfuss, Anthony T.) | ||||||||||||
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| Abstract: Relative transcript abundance has proven to be a valuable tool for understanding the function of genes in biological systems. For the differential analysis of transcript abundance using RNA sequencing data, the negative binomial model is by far the most frequently adopted. However, common methods that are based on a negative binomial model are not robust to extreme outliers, which we found to be abundant in public datasets. So far, no rigorous and probabilistic methods for detection of outliers have been developed for RNA sequencing data, leaving the identification mostly to visual inspection. Recent advances in Bayesian computation allow large-scale comparison of observed data against its theoretical distribution given in a statistical model. Here we propose ppcseq, a key quality-control tool for identifying transcripts that include outlier data points in differential expression analysis, which do not follow a negative binomial distribution. Applying ppcseq to analyse several publicly available datasets using popular tools, we show that from 3 to 10 percent of differentially abundant transcripts across algorithms and datasets had statistics inflated by the presence of outliers. | ||||||||||||
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| Record 166 of 414 |
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| Author(s): Trnka, A (Trnka, Alfred); Samas, P (Samas, Peter) |
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| Abstract: There is increasing evidence of social information transfer about predation risk in foraging animal groups. However, little is known about whether individuals also acquire such information from non-members of their own group. We experimentally manipulated the perceived threat and heterospecific cues about low predation risk in the house sparrow, Passer domesticus, by presenting stuffed dummies of the Eurasian sparrowhawk, Accipiter nisus, and the Eurasian tree sparrow, Passer montanus, at the feeder. Data were collected during winter 2016/2017 in two private yards in south-west and north Slovakia, where 1677 individuals in 83 flocks were observed at two feeders. We found no evidence for heterospecific information use in foraging single-species flocks of house sparrows. We suggest that strong bonds created among flock members may explain the observed pattern. |
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| Record 167 of 414 | |||||||||||||||
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| Author(s): Tin, PT (Tin, Phu Tran); Phan, V (Phan, Van-Duc); Nguyen, TN (Nguyen, Tan N.); Tu, LT (Tu, Lam-Thanh); Minh, BV (Minh, Bui Vu); Voznak, M (Voznak, Miroslav); Fazio, P (Fazio, Peppino) | |||||||||||||||
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| Abstract: In the present paper, we investigate the performance of the simultaneous wireless information and power transfer (SWIPT) based cooperative cognitive radio networks (CCRNs). In particular, the outage probability is derived in the closed-form expressions under the opportunistic partial relay selection. Different from the conventional CRNs in which the transmit power of the secondary transmitters count merely on the aggregate interference measured on the primary networks, the transmit power of the SWIPT-enabled transmitters is also constrained by the harvested energy. As a result, the mathematical framework involves more correlated random variables and, thus, is of higher complexity. Monte Carlo simulations are given to corroborate the accuracy of the mathematical analysis and to shed light on the behavior of the OP with respect to several important parameters, e.g., the transmit power and the number of relays. Our findings illustrate that increasing the transmit power and/or the number of relays is beneficial for the outage probability. | |||||||||||||||
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| Record 168 of 414 |
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| Author(s): Futera, Z (Futera, Zdenek) |
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| Abstract: The charge transport properties of biological molecules like peptides and proteins are intensively studied for the great flexibility, redox-state variability, long-range efficiency, and biocompatibility of potential bioelectronic applications. Yet, the electronic interactions of biomolecules with solid metal surfaces, determining the conductivities of the biomolecular junctions, are hard to predict and usually unavailable. Here, we present accurate adsorption structures and energies, electronic band alignment, and interfacial electronic coupling data for all 20 natural amino acids computed using the DFT+sigma scheme based on the vdW-DF and OT-RSH functionals. For comparison, data obtained using the popular PBE functional are provided as well. Tryptophan, compared to other amino acids, is shown to be distinctly exceptional in terms of the electronic properties related to charge transport. Its high adsorption energy, frontier-orbital levels aligned relatively close to the Fermi energy of gold and strong interfacial electronic coupling make it an ideal candidate for facilitating charge transfer on such heterogeneous interfaces. Although the amino acids in peptides and proteins are affected by the structural interactions hindering their contact with the surface, knowledge of the single-molecule surface interactions is necessary for a detailed understanding of such structural effects and tuning of potential applications. |
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| Record 169 of 414 | ||||||||||||
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| Author(s): Spetko, M (Spetko, Matej); Vysocky, O (Vysocky, Ondrej); Jansik, B (Jansik, Branislav); Riha, L (Riha, Lubomir) | ||||||||||||
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| Abstract: Nvidia is a leading producer of GPUs for high-performance computing and artificial intelligence, bringing top performance and energy-efficiency. We present performance, power consumption, and thermal behavior analysis of the new Nvidia DGX-A100 server equipped with eight A100 Ampere microarchitecture GPUs. The results are compared against the previous generation of the server, Nvidia DGX-2, based on Tesla V100 GPUs. We developed a synthetic benchmark to measure the raw performance of floating-point computing units including Tensor Cores. Furthermore, thermal stability was investigated. In addition, Dynamic Frequency and Voltage Scaling (DVFS) analysis was performed to determine the best energy-efficient configuration of the GPUs executing workloads of various arithmetical intensities. Under the energy-optimal configuration the A100 GPU reaches efficiency of 51 GFLOPS/W for double-precision workload and 91 GFLOPS/W for tensor core double precision workload, which makes the A100 the most energy-efficient server accelerator for scientific simulations in the market. | ||||||||||||
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| Record 170 of 414 | |||||||||
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| Author(s): Dvorackova, O (Dvorackova, Olga); Chval, Z (Chval, Zdenek) | |||||||||
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| Abstract: Kinetics of the hydration reaction and the bonding properties of the trans-[Pt(NH3)(2)(NH2X)Cl](+) complexes (X=H, CH3, F, Cl, Br, NH2, NO2, OH, dimethylamine (DMA), cyclopropyl (CyP), cyclohexyl (CyH)) were studied theoretically by DFT methodology in the gas phase and the water solution. The electron-donating and electron-withdrawing X substituents lower and increase, respectively, the activation free energy (Delta G(not equal)) and Pt-trans ligand binding energies (BEs) to a similar extent as meta and para substituents of the pyridine ligand studied previously (ACS Omega, 2020, 5, 11768). For the saturated hydrocarbon X substituents (X=H, CH3, CyP, CyH), the Delta G(not equal) values and Pt-trans ligand BEs decrease with the logarithm of the X substituent size being best quantified by the number of electrons. The additivity of the substituent effects was studied on the NF3 ligand and worked well for ligand charges and Pt-trans ligand BEs. The influence of chelation was evaluated by the comparison of the CyH system and the complexes with the cyclohexanediamine (DACH) ligand. Finally, the effect of isomerization was studied on the complexes with the 1,2-bis(aminomethyl)cyclobutane (BAMCB) ligand. Thus, this study also evaluates the influence of the non-leaving ligands present in cisplatin, oxaliplatin, lobaplatin, JM118, and JM11 drugs on the reactivity of the Pt(II) complexes in the same ligand environment. | |||||||||
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| Record 171 of 414 | ||||||||||||||||||
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| Author(s): Payne, DT (Payne, Daniel T.); Labuta, J (Labuta, Jan); Futera, Z (Futera, Zdenek); Brezina, V (Brezina, Vaclav); Hanykova, L (Hanykova, Lenka); Chahal, MK (Chahal, Mandeep K.); Hill, JP (Hill, Jonathan P.) | ||||||||||||||||||
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| Abstract: Molecular rotors are an important class of dynamic molecules which have been studied not only for their possible uses as components of molecular machines but also because of potential applications as probes of local viscosity in biological media, especially self-assembled membranes. For the former, factors affecting rotational motility are critical while for the latter the rotor activity must be complexed with an output signal (often fluorescence) for reporting of local conditions. Molecular single stator-double rotor activity of an oxidized resorcinarene (fuchsonarene) macrocycle containing unsaturated hemiquinonoid groups at its meso positions was investigated. Fuchsonarenes contain two hemiquinonoid substituents at diagonally-opposed meso-positions with two electron rich phenol groups at the remaining meso-positions between the hemiquinonoid groups. All meso-substituents are in proximity at one side of the resorcinarene macrocycle (so-called rccc-type isomer) with rotational activity of the phenol meso-substituents. Rotation rates of the phenol moieties can be controlled by varying temperature, solvent polarity and acidity of the medium of study with rotation being thermally activated in neutral and acidic media and tunable in the range from 2 s(-1) to 20 000 s(-1). Experimental and computational data indicate that rotation of the mobile phenol meso-substituents is remotely affected by interactions with acidic solvents at the carbonyl CvO groups of macrocyclic acetyloxy groups, which occurs with the emergence of a lower energy electronic absorption band whose intensity is correlated with both the acidity of the medium and the rotation rate of the phenol substituents. Time-dependent DFT calculations suggest that the low energy band is due to a molecular conformational adjustment affecting electronic conjugation caused by strong interaction of macrocyclic acetyloxy carbonyl groups with the acid medium. The work presents a molecular mechanical model for estimating solution acidity and also gives insight into a possible method for modulating rotor activity in molecular machines. | ||||||||||||||||||
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| Record 172 of 414 | ||||||||||||||||||
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| Author(s): Stadlbauer, P (Stadlbauer, Petr); Islam, B (Islam, Barira); Otyepka, M (Otyepka, Michal); Chen, JL (Chen, Jielin); Monchaud, D (Monchaud, David); Zhou, J (Zhou, Jun); Mergny, JL (Mergny, Jean-Louis); Sponer, J (Sponer, Jiri) | ||||||||||||||||||
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| Abstract: Guanine quadruplex nucleic acids (G4s) are involved in key biological processes such as replication or transcription. Beyond their biological relevance, G4s find applications as biotechnological tools since they readily bind hemin and enhance its peroxidase activity, creating a G4-DNAzyme. The biocatalytic properties of G4-DNAzymes have been thoroughly studied and used for biosensing purposes. Despite hundreds of applications and massive experimental efforts, the atomistic details of the reaction mechanism remain unclear. To help select between the different hypotheses currently under investigation, we use extended explicit-solvent molecular dynamics (MD) simulations to scrutinize the G4/hemin interaction. We find that besides the dominant conformation in which hemin is stacked atop the external G-quartets, hemin can also transiently bind to the loops and be brought to the external G-quartets through diverse delivery mechanisms. The simulations do not support the catalytic mechanism relying on a wobbling guanine. Similarly, the catalytic role of the iron-bound water molecule is not in line with our results; however, given the simulation limitations, this observation should be considered with some caution. The simulations rather suggest tentative mechanisms in which the external G-quartet itself could be responsible for the unique H2O2-promoted biocatalytic properties of the G4/hemin complexes. Once stacked atop a terminal G-quartet, hemin rotates about its vertical axis while readily sampling shifted geometries where the iron transiently contacts oxygen atoms of the adjacent G-quartet. This dynamics is not apparent from the ensemble-averaged structure. We also visualize transient interactions between the stacked hemin and the G4 loops. Finally, we investigated interactions between hemin and on-pathway folding intermediates of the parallel-stranded G4 fold. The simulations suggest that hemin drives the folding of parallel-stranded G4s from slip-stranded intermediates, acting as a G4 chaperone. Limitations of the MD technique are briefly discussed. | ||||||||||||||||||
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| Record 173 of 414 | ||||||
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| Author(s): Slaninakova, T (Slaninakova, Terezia); Antol, M (Antol, Matej); Olha, J (Olha, Jaroslav); Kana, V (Kana, Vojtech); Dohnal, V (Dohnal, Vlastislav) | ||||||
| Edited by: Reyes N; Connor R; Kriege N; Kazempour D; Bartolini I; Schubert E; Chen JJ | ||||||
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Abstract:
Metric indexes are traditionally used for organizing unstructured or complex data to speed up similarity queries. The most widely-used indexes cluster data or divide space using hyper-planes. While searching, the mutual distances between objects and the metric properties allow for the pruning of branches with irrelevant data - this is usually implemented by utilizing selected anchor objects called pivots. Recently, we have introduced an alternative to this approach called Learned Metric Index. In this method, a series of machine learning models substitute decisions performed on pivots - the query evaluation is then determined by the predictions of these models. This technique relies upon a traditional metric index as a template for its own structure - this dependence on a pre-existing index and the related overhead is the main drawback of the approach.
In this paper, we propose a data-driven variant of the Learned Metric Index, which organizes the data using their descriptors directly, thus eliminating the need for a template. The proposed learned index shows significant gains in performance over its earlier version, as well as the established indexing structure M-index. |
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| ISBN: 978-3-030-89657-7; 978-3-030-89656-0 |
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| Author(s): Vasicek, J (Vasicek, J.); Vitolo, R (Vitolo, R.) | ||||||
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| Abstract: The purpose of the paper is to show that, in low dimensions, the WDVV equations are bi-Hamiltonian. The invariance of the bi-Hamiltonian formalism is proved for N = 3. More examples in higher dimensions show that the result might hold in general. The invariance group of the bi-Hamiltonian pairs that we find for WDVV equations is the group of projective transformations. The significance of projective invariance of WDVV equations is discussed in detail. The computer algebra programs that were used for calculations throughout the paper are provided in a GitHub repository. | ||||||
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| Record 175 of 414 | |||||||||
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| Author(s): Gallo, G (Gallo, Gianpiero); Mihanovic, A (Mihanovic, Ana); Roncevic, I (Roncevic, Igor); Dinnebier, R (Dinnebier, Robert); Vancik, H (Vancik, Hrvoj) | |||||||||
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| Abstract: Crystal and molecular structure of poly(1,4-phenyleneazine-N,N-dioxide) (PDNB, 1), obtained from polymerization of 1,4-dinitrosobenzene, is investigated by X-ray powder diffraction (XRPD) and DFT calculations. Starting with the determined crystal structure, we have calculated the electronic structure of the polymer, which reveals that 1 is potentially a wide-bandgap (WBG) semiconductor with a band gap of 2.3 eV. Its calculated electronic spectrum with the absorbance at 400 nm is in good agreement with the experimental data. A highly organized crystal structure with linear chains of polymer indicates possible anisotropic electronic properties that could be useful in molecular photoelectronics (e.g OLEDs). Photolysis of 1 at cryogenic temperatures yields dinitrosobenzene monomers, which re-polymerize at higher temperatures. After this reversible photo-thermal cycle, the starting polymorph of 1 is recovered. Thermal analysis (TG/DSC/DTA) and in situ XRPD measurements show the high thermal stability of 1 until around 150 degrees C. | |||||||||
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| Record 176 of 414 | |||||||||||||||
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| Author(s): Paloncyova, M (Paloncyova, Marketa); Cechova, P (Cechova, Petra); Srejber, M (Srejber, Martin); Kuhrova, P (Kuhrova, Petra); Otyepka, M (Otyepka, Michal) | |||||||||||||||
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| Abstract: Recent advances in RNA-based medicine have provided new opportunities for the global current challenge, i.e., the COVID-19 pandemic. Novel vaccines are based on a messenger RNA (mRNA) motif with a lipid nanoparticle (LNP) vector, consisting of high content of unique pH-sensitive ionizable lipids (ILs). Here we provide molecular insights into the role of the ILs and lipid mixtures used in current mRNA vaccines. We observed that the lipid mixtures adopted a nonlamellar organization, with ILs separating into a very disordered, pH-sensitive phase. We describe structural differences of the two ILs leading to their different congregation, with implications for the vaccine stability. Finally, as RNA interacts preferentially with IL-rich phases located at the regions with high curvature of lipid phase, local changes in RNA flexibi l i t y and base pairing are induced by lipids. A proper atomistic understanding of RNA-lipid interactions may enable rational tailoring of LNP composition for efficient RNA delivery. | |||||||||||||||
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| Record 177 of 414 | ||||||||||||
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| Author(s): Veverka, J (Veverka, Jakub); Lukac, F (Lukac, Frantisek); Kadzielawa, AP (Kadzielawa, Andrzej P.); Koller, M (Koller, Martin); Chlup, Z (Chlup, Zdenek); Hadraba, H (Hadraba, Hynek); Karlik, M (Karlik, Miroslav); Legut, D (Legut, Dominik); Vontorova, J (Vontorova, Jirina); Chraska, T (Chraska, Tomas); Vilemova, M (Vilemova, Monika) | ||||||||||||
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| Abstract: The application of non-equilibrium methods such as Mechanical Alloying and Field Assisted Sintering enables the formation of a single solid solution in immiscible systems, or the ones characterized by a miscibility gap. This work shows that W-Cr solid solution can be used as an intermediate step to produce ultrafine-grained composite alloys with rod-like microstructural features. It is shown that a significant increase in strength can be achieved without an increase in hardness using this top-down material design. | ||||||||||||
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| Record 178 of 414 | ||||||||||||
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| Author(s): Rogers, BA (Rogers, Bradley A.); Okur, HI (Okur, Halil, I); Yan, CY (Yan, Chuanyu); Yang, TL (Yang, Tinglu); Heyda, J (Heyda, Jan); Cremer, PS (Cremer, Paul S.) | ||||||||||||
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Abstract:
Weakly hydrated anions solubilize macromolecules but cause small molecules that are made from identical chemical constituents to precipitate out of aqueous solutions. Now, this phenomenon has been understood by demonstrating that the binding of anions to polymers is regulated by molecular curvature and interfacial water structure.
Weakly hydrated anions help to solubilize hydrophobic macromolecules in aqueous solutions, but small molecules comprising the same chemical constituents precipitate out when exposed to these ions. Here, this apparent contradiction is resolved by systematically investigating the interactions of NaSCN with polyethylene oxide oligomers and polymers of varying molecular weight. A combination of spectroscopic and computational results reveals that SCN- accumulates near the surface of polymers, but is excluded from monomers. This occurs because SCN- preferentially binds to the centre of macromolecular chains, where the local water hydrogen-bonding network is disrupted. These findings suggest a link between ion-specific effects and theories addressing how hydrophobic hydration is modulated by the size and shape of a hydrophobic entity. |
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| Record 179 of 414 | ||||||||||||
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| Author(s): Balaz, P (Balaz, Pavel); Pasciak, M (Pasciak, Marek); Hlinka, J (Hlinka, Jiri) | ||||||||||||
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| Abstract: Melting of a particle lattice in two dimensional systems substantially differs from the one in three dimensions. The most prominent theory of the lattice melting in 2D, formulated by Kosterlitz, Thouless, Halperin, Nelson, and Young (KTHNY), describes the solid-liquid phase transition as a two-step process, where the solid phase turns into the liquid via the hexatic phase. The microscopic nature of this process lies in the excitation and unbinding of topological defects in the 2D lattice. The KTHNY melting scenario has been observed in number of 2D physical systems. Here, we theoretically analyze the melting process of a Neel skyrmion lattice by means of numerical simulations using a model of lacunar spinel GaV4S8 hosting hexagonal skyrmion lattice at low temperatures. We show that topological defects are excited in such skyrmion lattice causing its melting via the hexatic phase in agreement with the KTHNY theory. | ||||||||||||
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| Record 180 of 414 | |||||||||||||||||||||
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| Author(s): Nguyen, NT (Nhat-Tien Nguyen); Nguyen, HN (Hong-Nhu Nguyen); Nguyen, NL (Ngoc-Long Nguyen); Le, AT (Anh-Tu Le); Do, DT (Dinh-Thuan Do); Voznak, M (Voznak, Miroslav) | |||||||||||||||||||||
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| Abstract: In the paper, we present a study on the performance analysis of a non-orthogonal multiple access (NOMA) underlay cognitive hybrid satellite-terrestrial relaying network (CSTRN) and highlight the performance gaps between multiple users. The satellite source communicates with users by enabling cognitive radio scheme to forward signals to secondary destinations on the ground which belong to dedicated groups following the principle of NOMA. In this scenario, the secondary source acts a relay and employs Amplify and Forward (AF) mode to serve distant NOMA users under a given interference constraint. To characterize the transmission environment, the shadowed-Rician fading and Nakagami-m fading models are widely adopted to the relevant hybrid channels. To provide detailed examination of the system performance metrics, we aim to derive closed-form formulas for the outage probability of the secondary destinations in the presence of the primary interference power constraint imposed by the adjacent primary satellite network. Finally, our simulation results showed that a greater number of antennas, better quality of wireless channels and power allocation factors exhibit the main effects on system performance. | |||||||||||||||||||||
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| Record 181 of 414 | ||||||||||||||||||
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| Author(s): Montagud-Camps, V (Montagud-Camps, Victor); Nemec, F (Nemec, Frantisek); Safrankova, J (Safrankova, Jana); Nemecek, Z (Nemecek, Zdenek); Verdini, A (Verdini, Andrea); Grappin, R (Grappin, Roland); Papini, E (Papini, Emanuele); Franci, L (Franci, Luca) | ||||||||||||||||||
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| Abstract: Observations of proton density fluctuations of the solar wind at 1 au have shown the presence of a decade-long transition region of the density spectrum above sub-ion scales, characterized by a flattening of the spectral slope. We use the proton density fluctuations data collected by the BMSW instrument on-board the Spektr-R satellite in order to delimit the plasma parameters under which the transition region can be observed. Under similar plasma conditions to those in observations, we carry out 3D compressible magnetohydrodynamics (MHD) and Hall-MHD numerical simulations and find that Hall physics is necessary to generate the transition region. The analysis of the k omega power spectrum in the Hall-MHD simulation indicates that the flattening of the density spectrum is associated with fluctuations having frequencies smaller than the ion cyclotron frequency. | ||||||||||||||||||
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| Record 182 of 414 | ||||||||||||||||||||||||||||||
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| Author(s): Navrkalova, V (Navrkalova, Veronika); Plevova, K (Plevova, Karla); Hynst, J (Hynst, Jakub); Pal, K (Pal, Karol); Mareckova, A (Mareckova, Andrea); Reigl, T (Reigl, Tomas); Jelinkova, H (Jelinkova, Hana); Vrzalova, Z (Vrzalova, Zuzana); Stranska, K (Stranska, Kamila); Pavlova, S (Pavlova, Sark); Panovska, A (Panovska, Anna); Janikova, A (Janikova, Andrea); Doubek, M (Doubek, Michael); Kotaskova, J (Kotaskova, Jana); Pospisilova, S (Pospisilova, Sarka) | ||||||||||||||||||||||||||||||
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| Abstract: B-cell neoplasms represent a clinically heterogeneous group of hematologic malignancies with considerably diverse genomic architecture recently endorsed by next-generation sequencing (NGS) studies. Because multiple genetic defects have a potential or confirmed clinical impact, a tendency toward more comprehensive testing of diagnostic, prognostic, and predictive markers is desired. This study introduces the design, validation, and implementation of an integrative, custom-designed, capture-based NGS panel titled LYmphoid NeXt-generation sequencing (LYNX) for the analysis of standard and novel molecular markers in the most common lymphoid neoplasms (chronic lymphocytic leukemia, acute lymphoblastic leukemia, diffuse large B-cell lymphoma, follicular lymphoma, and mantle cell lymphoma). A single LYNX test provides the following: i) accurate detection of mutations in all coding exons and splice sites of 70 lymphoma-related genes with a sensitivity of 5% variant allele frequency, ii) reliable identification of large genome-wide (>6 Mb) and recurrent chromosomal aber-rations (>300 kb) in at least 20% of the clonal cell fraction, iii) the assessment of immunoglobulin and T-cell receptor gene rearrangements, and iv) lymphoma-specific translocation detection. Dedicated bioinformatic pipelines were designed to detect all markers mentioned above. The LYNX panel repre-sents a comprehensive, up-to-date tool suitable for routine testing of lymphoid neoplasms with research and clinical applicability. It allows a wide adoption of capture-based targeted NGS in clinical practice and personalized management of patients with lymphoproliferative diseases. | ||||||||||||||||||||||||||||||
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| Record 183 of 414 | ||||||
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| Author(s): Klajmon, M (Klajmon, Martin); Cervinka, C (Cervinka, Ctirad) | ||||||
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| Abstract: Y Molecular dynamics simulations are performed for a test set of 20 aprotic ionic liquids to investigate whether including an explicit polarizability model in the force field leads to higher accuracy and reliability of the calculated phase behavior properties, especially the enthalpy of fusion. A classical nonpolarizable all-atom optimized potentials for liquid simulations (OPLS) force-field model developed by Canongia Lopes and Padua (CL&P) serves as a reference level of theory. Polarizability is included either in the form of Drude oscillators, resulting in the CL&P-D models, or in the framework of the atomic multipole optimized energetics for biomolecular application (AMOEBA) force field with polarizable atomic sites. Benchmarking of the calculated fusion enthalpy values against the experimental data reveals that overall the nonpolarizable CL&P model and polarizable CL&P-D models perform similarly with average deviations of about 30%. However, fusion enthalpies from the CL&P-D models exhibit a stronger correlation with their experimental counterparts. The least successful predictions are interestingly obtained from AMOEBA (deviation ca. 60%), which may indicate that a reparametrization of this force-field model is needed to achieve improved predictions of the fusion enthalpy. In general, all FF models tend to underestimate the fusion enthalpies. In addition, quantum chemical calculations are used to compute the electronic cohesive energies of the crystalline phases of the ionic liquids and of the interaction energies within the ion pair. Significant positive correlations are found between the fusion enthalpy and the cohesive energies. The character of the present anions predetermines the magnitude of individual mechanistic components of the interaction energy and related enthalpic and cohesive properties. | ||||||
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| Record 184 of 414 | ||||||
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| Author(s): Bharadwaz, P (Bharadwaz, Priyam); Maldonado-Dominguez, M (Maldonado-Dominguez, Mauricio); Srnec, M (Srnec, Martin) | ||||||
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| Abstract: Bifurcating reactions yield two different products emerging from one single transition state and are therefore archetypal examples of reactions that cannot be described within the framework of the traditional Eyring's transition state theory (TST). With the growing number and importance of these reactions in organic and biosynthetic chemistry, there is also an increasing demand for a theoretical tool that would allow for the accurate quantification of reaction outcome at low cost. Here, we introduce such an approach that fulfils these criteria, by evaluating bifurcation selectivity through the energy distribution within the reactive mode of the key transition state. The presented method yields an excellent agreement with experimentally reported product ratios and predicts the correct selectivity for 89% of nearly 50 various cases, covering pericyclic reactions, rearrangements, fragmentations and metal-catalyzed processes as well as a series of trifurcating reactions. With 71% of product ratios determined within the error of less than 20%, we also found that the methodology outperforms three other tested protocols introduced recently in the literature. Given its predictive power, the procedure makes reaction design feasible even in the presence of complex non-TST chemical steps. | ||||||
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| Record 185 of 414 | ||||||
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| Author(s): Halfar, R (Halfar, Radek); Lawson, BAJ (Lawson, Brodie A. J.); dos Santos, RW (dos Santos, Rodrigo Weber); Burrage, K (Burrage, Kevin) | ||||||
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| Abstract: Cardiac fibrosis and other scarring of the heart, arising from conditions ranging from myocardial infarction to ageing, promotes dangerous arrhythmias by blocking the healthy propagation of cardiac excitation. Owing to the complexity of the dynamics of electrical signalling in the heart, however, the connection between different arrangements of blockage and various arrhythmic consequences remains poorly understood. Where a mechanism defies traditional understanding, machine learning can be invaluable for enabling accurate prediction of quantities of interest (measures of arrhythmic risk) in terms of predictor variables (such as the arrangement or pattern of obstructive scarring). In this study, we simulate the propagation of the action potential (AP) in tissue affected by fibrotic changes and hence detect sites that initiate re-entrant activation patterns. By separately considering multiple different stimulus regimes, we directly observe and quantify the sensitivity of re-entry formation to activation sequence in the fibrotic region. Then, by extracting the fibrotic structures around locations that both do and do not initiate re-entries, we use neural networks to determine to what extent re-entry initiation is predictable, and over what spatial scale conduction heterogeneities appear to act to produce this effect. We find that structural information within about 0.5 mm of a given point is sufficient to predict structures that initiate re-entry with more than 90% accuracy. | ||||||
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| Author(s): Dunlop, D (Dunlop, David); Vecera, M (Vecera, Milos); Gyepes, R (Gyepes, Robert); Kubat, P (Kubat, Pavel); Lang, K (Lang, Kamil); Horacek, M (Horacek, Michal); Pinkas, J (Pinkas, Jiri); Simkova, L (Simkova, Ludmila); Liska, A (Liska, Alan); Lamac, M (Lamac, Martin) | ||||||||||||||||||||||||
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| Abstract: Cationic group 4 metallocene complexes with pendant imine and pyridine donor groups were prepared as stable crystalline [B(C6F5)(4)](-) salts either by protonation of the intramolecularly bound ketimide moiety in neutral complexes [(eta(5)-C5Me5){eta(5)-C5H4CMe2CMe2C(R)=N-kappa N}MCl] (M = Ti, Zr, Hf; R = t-Bu, Ph) by PhNMe2H+[B(C6F5)(4)](-) to give [(eta(C5Me5)-C-5){eta(5)-C5H4CMe2CMe2C(R)=NH-kappa N}MCl](+)[B(C6F5)(4)]or by chloride ligand abstraction from the complexes [(eta(C5Me5)-C-5) (eta(5)-C5H4CMe2CH2C5H4N-kappa N)MCl2] (M = Ti, Zr) by Li [ B(C6F5)(4)]center dot 2. 5 Et2O to give [(eta(5)-C5Me5)(eta(5)center dot C5H4Me2CH2C5H4N-kappa N)MCl](+)[B(C6F5)(4)](-). Solid state structures of the new compounds were established by X-ray diffraction analysis, and their electrochemical behavior was studied by cyclic voltammetry. The cationic complexes of Zr and Hf, compared to the corresponding neutral species, exhibited significantly enhanced luminescence predominantly from triplet ligand-to-metal ((LMCT)-L-3) excited states with lifetimes up to 62 mu s and quantum yields up to 58% in the solid state. DFT calculations were performed to explain the structural features and optical and electrochemical properties of the complexes. | ||||||||||||||||||||||||
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| Record 187 of 414 | ||||||
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| Author(s): Biriukov, D (Biriukov, Denys); Futera, Z (Futera, Zdenek) | ||||||
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| Abstract: Gaining accurate molecular descriptions of metal/bio interfaces is a necessary step toward numerous important applications, particularly in electrochemistry and bionanotechnology. Here, using atomistic molecular dynamics simulations and free energy calculations with the GolP-CHARMM force field, we investigate how applied static electric field disturbs the structure of an aqueous Au (111)/amino acid (AA) interface. We show that adsorption of positively charged AAs (arginine, histidine, and lysine) is more affected by the external electric field than that of negatively charged (aspartic and glutamic acids) and charge-neutral AAs (alanine, glycine, tryptophan, and asparagine). The adsorption free energies of positively charged AAs can vary within 55% when static fields of up to 0.5 V/angstrom are applied, in contrast to considerably weaker responses of negatively charged and charge-neutral AAs (up to 25%). The difference arises from the role of a charged side chain in the adsorption on the gold surface. Positively charged amines adsorb stronger than negatively charged carboxylates, and this fact together with the trend within positively charged AAs (arginine > histidine > lysine) is related to the affinity of their side chains for Au (111) surfaces and ability to replace water molecules in the first adsorption layer. The adsorption via a deprotonated carboxyl group is less favorable, indirect, and facilitated by hydrogen bonding with the adsorbed water, while the positive amines directly interact with surface gold atoms. This eventually leads to relatively weaker adsorption of negatively charged AAs and their smaller response to the external electric fields due to solvent-induced electrostatic screening. These fundamental results provide a useful insight into the molecular arrangement at the electrified biointerfaces with gold, which can help to interpret electrochemical phenomena and advance bioelectronic applications. | ||||||
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| Record 188 of 414 | ||||||||||||
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| Author(s): Chamorro, VC (Chamorro, Victor Cruces); Tempra, C (Tempra, Carmelo); Jungwirth, P (Jungwirth, Pavel) | ||||||||||||
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| Abstract: Small differences in physical and chemical properties of H2O and D2O, such as melting and boiling points or pK(a), can be traced back to a slightly stronger hydrogen bonding in heavy versus normal water. In particular, deuteration reduces zero-point vibrational energies as a demonstration of nuclear quantum effects. In principle, computationally demanding quantum molecular dynamics is required to model such effects. However, as already demonstrated by Feynmann and Hibbs, zero-point vibrations can be effectively accounted for by modifying the interaction potential within classical dynamics. In the spirit of the Feymann-Hibbs approach, we develop here two water models for classical molecular dynamics by fitting experimental differences between H2O and D2O. We show that a three-site SPCE-based model accurately reproduces differences between properties of the two water isotopes, with a four-site TIP4P-2005/based model in addition capturing also the absolute values of key properties of heavy water. The present models are computationally simple enough to allow for extensive simulations of biomolecules in heavy water relevant, for example, for experimental techniques such as NMR or neutron scattering. | ||||||||||||
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| Record 189 of 414 | ||||||
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| Author(s): Gu, YJ (Gu, Yan-Jun); Bulanov, SV (Bulanov, Sergei V.) | ||||||
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| Abstract: Magnetic reconnection driven by laser plasma interactions attracts great interests in the recent decades. Motivated by the rapid development of the laser technology, the ultra strong magnetic field generated by the laser-plasma accelerated electrons provides unique environment to investigate the relativistic magnetic field annihilation and reconnection. It opens a new way for understanding relativistic regimes of fast magnetic field dissipation particularly in space plasmas, where the large scale magnetic field energy is converted to the energy of the nonthermal charged particles. Here we review the recent results in relativistic magnetic reconnection based on the laser and collisionless plasma interactions. The basic mechanism and the theoretical model are discussed. Several proposed experimental setups for relativistic reconnection research are presented. | ||||||
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| Record 190 of 414 | ||||||||||||
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| Author(s): Cizkova, D (Cizkova, Dagmar); Dureje, L (Dureje, Ludovit); Pialek, J (Pialek, Jaroslav); Kreisinger, J (Kreisinger, Jakub) | ||||||||||||
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| Abstract: Data on the gut microbiota (GM) of wild animals are key to studies on evolutionary biology (host-GM interactions under natural selection), ecology and conservation biology (GM as a fitness component closely connected to the environment). Wildlife GM sampling often requires non-invasive techniques or sampling from dead animals. In a controlled experiment profiling microbial 16S rRNA in 52 house mice (Mus musculus) from eight families and four genetic backgrounds, we studied the effects of live- and snap-trapping on small mammal GM and evaluated the suitability of microbiota from non-fresh faeces as a proxy for caecal GM. We compared CM from individuals sampled 16-18 h after death with those in live traps and caged controls, and caecal and faecal GM collected from mice in live-traps. Sampling delay did not affect GM composition, validating data from fresh cadavers or snap-trapped animals. Animals trapped overnight displayed a slight but significant difference in GM composition to the caged controls, though the change only had negligible effect on GM diversity, composition and inter-individual divergence. Hence, the trapping process appears not to bias GM profiling. Despite their significant difference, caecal and faecal microbiota were correlated in composition and, to a lesser extent, diversity. Both showed congruent patterns of inter-individual divergence following the natural structure of the dataset. Thus, the faecal microbiome represents a good non-invasive proxy of the caecal microbiome, making it suitable for detecting biologically relevant patterns. However, care should be taken when analysing mixed datasets containing both faecal and caecal samples. | ||||||||||||
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| Record 191 of 414 | |||||||||||||||||||||
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| Author(s): Radaszkiewicz, T (Radaszkiewicz, Tomasz); Noskova, M (Noskova, Michaela); Gomoryova, K (Gomoryova, Kristina); Blanarova, OV (Blanarova, Olga Vondalova); Radaszkiewicz, KA (Radaszkiewicz, Katarzyna Anna); Pickova, M (Pickova, Marketa); Vichova, R (Vichova, Rachel); Gybel, T (Gybel, Tomas); Kaiser, K (Kaiser, Karol); Demkova, L (Demkova, Lucia); Kucerova, L (Kucerova, Lucia); Barta, T (Barta, Tomas); Potessil, D (Potessil, David); Zdrahal, Z (Zdrahal, Zbynek); Soucek, K (Soucek, Karel); Bryja, V (Bryja, Vitezslav) | |||||||||||||||||||||
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| Abstract: RNF43 is an E3 ubiquitin ligase and known negative regulator of WNT/beta-catenin signaling. We demonstrate that RNF43 is also a regulator of noncanonical WNT5A-induced signaling in human cells. Analysis of the RNF43 interactome using BioID and immunoprecipitation showed that RNF43 can interact with the core receptor complex components dedicated to the noncanonical Wnt pathway such as ROR1, ROR2, VANGL1, and VANGL2. RNF43 triggers VANGL2 ubiquitination and proteasomal degradation and clathrin-dependent internalization of ROR1 receptor and inhibits ROR2 activation. These activities of RNF43 are physiologically relevant and block pro-metastatic WNT5A signaling in melanoma. RNF43 inhibits responses to WNT5A, which results in the suppression of invasive properties of melanoma cells. Furthermore, RNF43 prevented WNT5A-assisted development of resistance to BRAF V600E and MEK inhibitors. Next, RNF43 acted as melanoma suppressor and improved response to targeted therapies in vivo. In line with these findings, RNF43 expression decreases during melanoma progression and RNF43-low patients have a worse prognosis. We conclude that RNF43 is a newly discovered negative regulator of WNT5A-mediated biological responses that desensitizes cells to WNT5A. | |||||||||||||||||||||
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| Record 192 of 414 | ||||||
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| Author(s): Muraskova, V (Muraskova, Viera); Eigner, V (Eigner, Vaclav); Dusek, M (Dusek, Michal); Sedmidubsky, D (Sedmidubsky, David) | ||||||
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| Abstract: Three complexes, [FeLCl]Cl center dot H2O, [Co2L2H3O2]Cl center dot 8H(2)O, and [CoLN3], where L2- is the dianion of an asymmetric propyl-ethyl pentadentate Schiff base ligand condensed from pyridoxal and N-(2-aminoethyl)propane-1,3-diamine, have been synthesized and characterized by elemental analysis, FT-IR and mass spectroscopy. Crystal structures of the complexes along with the Schiff base were determined by X-ray diffraction. (HNMR)-H-1 spectrum of the Schiff base has been obtained. The coordination polyhedra of all three complexes can be expressed as distorted octahedra. Magnetic investigations of [FeLCl]Cl center dot H2O complex confirmed high-spin state over the whole temperature range (5-300 K) and allowed the evaluation of the axial zero-field splitting (ZFS) parameter D = -0.97 cm(-1), intermolecular exchange parameter zj = -0.88 cm(-1) and temperature-independent paramagnetism chi(TIM) = 0.00025 cm(3)mol(-1). The low-spin state of Co(III) was stabilized in diamagnetic [Co2L2H3O2]Cl center dot 4.8H(2)O and [CoLN3] complexes. Redox potentials of the Schiff base and the complexes were investigated by cycling voltammetry on the GC electrode in dry acetonitrile. The experimental magnetic properties of the complexes [FeLCl]Cl center dot H2O and [CoLN3] were compared with the theoretical ones calculated using density functional theory (DFT). (C) 2021 Elsevier Ltd. All rights reserved. | ||||||
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| Record 193 of 414 | ||||||||||||
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| Author(s): Strejckova, B (Strejckova, Beata); Milec, Z (Milec, Zbynek); Holusova, K (Holusova, Katefina); Capal, P (Capal, Petr); Vojtkova, T (Vojtkova, Tereza); Cegan, R (Cegan, Radim); Safar, J (Safar, Jan) | ||||||||||||
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| Abstract: The VERNALIZATION1 (VRN1) gene encodes a MADS-box transcription factor and plays an important role in the cold-induced transition from the vegetative to reproductive stage. Allelic variability of VRN1 homoeologs has been associated with large differences in flowering time. The aim of this study was to investigate the genetic variability of VRN1 homoeologs (VRN-A1, VRN-B1 and VRN-D1). We performed an in-depth sequence analysis of VRN1 homoeologs in a panel of 105 winter and spring varieties of hexaploid wheat. We describe the novel allele Vrn-B1f with an 836 bp insertion within intron 1 and show its specific expression pattern associated with reduced heading time. We further provide the complete sequence of the Vrn-A1b allele, revealing a 177 bp insertion in intron 1, which is transcribed into an alternative splice variant. Copy number variation (CNV) analysis of VRN1 homoeologs showed that VRN-B1 and VRN-D1 are present in only one copy. The copy number of recessive vrn-A1 ranged from one to four, while that of dominant Vrn-A1 was one or two. Different numbers of Vrn-A1a copies in the spring cultivars Branisovicka IX/49 and Bastion did not significantly affect heading time. We also report on the deletion of secondary structures (G-quadruplex) in promoter sequences of cultivars with more vrn-A1 copies. | ||||||||||||
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| Record 194 of 414 | ||||||||||||
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| Author(s): Gutten, O (Gutten, Ondrej); Jurecka, P (Jurecka, Petr); Tehrani, ZA (Tehrani, Zahra Aliakbar); Budesinsky, M (Budesinsky, Milos); Rezac, J (Rezac, Jan); Rulisek, L (Rulisek, Lubomir) | ||||||||||||
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| Abstract: Performance of computational methods in modelling cyclic dinucleotides - an important and challenging class of compounds - has been evaluated by two different benchmarks: (1) gas-phase conformational energies and (2) qualitative agreement with NMR observations of the orientation of the chi-dihedral angle in solvent. In gas-phase benchmarks, where CCSD(T) and DLPNO-CCSD(T) methods have been used as the reference, most of the (dispersion corrected) density functional approximations are accurate enough to justify prioritizing computational cost and compatibility with other modelling options as the criterion of choice. NMR experiments of 3 ' 3 '-c-di-AMP, 3 ' 3 '-c-GAMP, and 3 ' 3 '-c-di-GMP show the overall prevalence of the anti-conformation of purine bases, but some population of syn-conformations is observed for guanines. Implicit solvation models combined with quantum-chemical methods struggle to reproduce this behaviour, probably due to a lack of dynamics and explicitly modelled solvent, leading to structures that are too compact. Molecular dynamics simulations overrepresent the syn-conformation of guanine due to the overestimation of an intramolecular hydrogen bond. Our combination of experimental and computational benchmarks provides "error bars" for modelling cyclic dinucleotides in solvent, where such information is generally difficult to obtain, and should help gauge the interpretability of studies dealing with binding of cyclic dinucleotides to important pharmaceutical targets. At the same time, the presented analysis calls for improvement in both implicit solvation models and force-field parameters. | ||||||||||||
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| Record 195 of 414 | |||||||||||||||
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| Author(s): Kohout, P (Kohout, Petr); Sudova, R (Sudova, Radka); Brabcova, V (Brabcova, Vendula); Vosolsobe, S (Vosolsobe, Stanislav); Baldrian, P (Baldrian, Petr); Albrechtova, J (Albrechtova, Jana) | |||||||||||||||
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| Abstract: Belowground litter derived from tree roots has been shown as a principal source of soil organic matter in coniferous forests. Fate of tree root necromass depends on fungal communities developing on the decaying roots. Local environmental conditions which affect composition of tree root mycobiome may also influence fungal communities developing on decaying tree roots. Here, we assessed fungal communities associated with decaying roots of Picea abies decomposing in three microhabitats: soil with no vegetation, soil with ericoid shrubs cover, and P. abies deadwood, for a 2-year period. Forest microhabitat showed stronger effect on structuring fungal communities associated with decaying roots compared to living roots. Some ericoid mycorrhizal fungi showed higher relative abundance on decaying roots in soils under ericoid shrub cover, while saprotrophic fungi had higher relative abundance in roots decomposing inside deadwood. Regardless of the studied microhabitat, we observed decline of ectomycorrhizal fungi and increase of endophytic fungi during root decomposition. Interestingly, we found substantially more fungal taxa with unknown ecology in late stages of root decomposition, indicating that highly decomposed roots may represent so far overlooked niche for soil fungi. Our study shows the importance of microhabitats on the fate of the decomposing spruce roots. | |||||||||||||||
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| Record 196 of 414 | ||||||
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| Author(s): Arasu, NP (Arasu, Narendra P.); Vazquez, H (Vazquez, Hector) | ||||||
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| Abstract: Antiaromatic molecules have been predicted to exhibit increased electron transport properties when placed between two nanoelectrodes compared to their aromatic analogues. While some studies have demonstrated this relationship, others have found no substantial increase. We use atomistic simulations to establish a general relationship between the electronic spectra of aromatic, antiaromatic, and quinoidal molecules and illustrate its implications for electron transport. We compare the electronic properties of a series of aromatic-antiaromatic counterparts and show that antiaromaticity effectively p-dopes the aromatic electronic spectra. As a consequence, the conducting properties of aromatic-antiaromatic analogues are closely related. For similar attachment points to the electrodes, an interference feature is expected in the HOMO-LUMO gap of one whenever it is absent in the other one. We demonstrate how the relative conductance of aromatic-antiaromatic pairs can be tuned and even reversed through the choice of chemical linker groups. Our work provides a general picture relating connectivity, (anti)aromaticity, and quantum interference and establishes new design rules for single molecule circuits. | ||||||
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| Record 197 of 414 |
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| Author(s): Dostal, Z (Dostal, Zdenek); Brzobohaty, T (Brzobohaty, Tomas); Vlach, O (Vlach, Oldrich) |
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| Abstract: Bounds on the spectrum of Schur complements of subdomain stiffness matrices with respect to the interior variables are key ingredients of the convergence analysis of FETI (finite element tearing and interconnecting) based domain decomposition methods. Here we give bounds on the regular condition number of Schur complements of 'floating' clusters arising from the discretization of 3D Laplacian on a cube decomposed into cube subdomains. The results show that the condition number of the cluster defined on a fixed domain decomposed into m x m x m cube subdomains connected by face and optionally edge averages increases proportionally to m. The estimates support scalability of unpreconditioned H-FETI-DP (hybrid FETI dual-primal) method. Though the research is most important for the solution of variational inequalities, the results of numerical experiments indicate that unpreconditioned H-FETI-DP with large clusters can be useful also for the solution of huge linear problems. |
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| Record 198 of 414 |
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| Author(s): Capek, J (Capek, Jan); Cuaresma, JC (Cuaresma, Jesus Crespo); Holler, J (Holler, Johannes); Schuster, P (Schuster, Philip) |
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| Abstract: We estimate fiscal multipliers for Austria in a framework of model uncertainty emanating from the choice of a particular econometric model. We present a comprehensive framework that allows to assess the effects of different multiplier definitions and choices related to the data, the model employed, and further technical choices associated with the specification of the model exert on fiscal multiplier estimates. The mean present-value government spending multiplier over all models entertained, based on around 3,000 estimates, is 0.68. Estimates of the peak spending multiplier for Austria tend to be larger than present-value spending multipliers, with a mean value of 0.85. The magnitude of the present-value tax multiplier is relatively high, with an average value across specifications of -1.12 and the mean peak tax multiplier is -0.54 for all specifications used. |
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| Record 199 of 414 |
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| Author(s): Pilat, M (Pilat, Martin) |
| Book Group Author(s): IEEE Comp Soc |
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Abstract:
The problem of coordinating the charging of electric vehicles gains more importance as the number of such vehicles grows. In this paper, we develop a method for the training of controllers for the coordination of EV charging. In contrast to most existing works on this topic, we require the controllers to preserve the privacy of the users, therefore we do not allow any communication from the controller to any third party.
In order to train the controllers, we use the idea of imitation learning - we first find an optimum solution for a relaxed version of the problem using quadratic optimization and then train the controllers to imitate this solution. We also investigate the effects of regularization of the optimum solution on the performance of the controllers. The method is evaluated on realistic data and shows improved performance and training speed compared to similar controllers trained using evolutionary algorithms. |
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| Conference Sponsors: IEEE, IEEE Comp Soc, Biol Artificial Intelligence Fdn |
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| ISBN: 978-1-6654-0898-1 |
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| Author(s): Li, Q (Li, Qian); Stoica, VA (Stoica, Vladimir A.); Pasciak, M (Pasciak, Marek); Zhu, Y (Zhu, Yi); Yuan, YK (Yuan, Yakun); Yang, TN (Yang, Tiannan); McCarter, MR (McCarter, Margaret R.); Das, S (Das, Sujit); Yadav, AK (Yadav, Ajay K.); Park, S (Park, Suji); Dai, C (Dai, Cheng); Lee, HJ (Lee, Hyeon Jun); Ahn, Y (Ahn, Youngjun); Marks, SD (Marks, Samuel D.); Yu, SK (Yu, Shukai); Kadlec, C (Kadlec, Christelle); Sato, T (Sato, Takahiro); Hoffmann, MC (Hoffmann, Matthias C.); Chollet, M (Chollet, Matthieu); Kozina, ME (Kozina, Michael E.); Nelson, S (Nelson, Silke); Zhu, DL (Zhu, Diling); Walko, DA (Walko, Donald A.); Lindenberg, AM (Lindenberg, Aaron M.); Evans, PG (Evans, Paul G.); Chen, LQ (Chen, Long-Qing); Ramesh, R (Ramesh, Ramamoorthy); Martin, LW (Martin, Lane W.); Gopalan, V (Gopalan, Venkatraman); Freeland, JW (Freeland, John W.); Hlinka, J (Hlinka, Jirka); Wen, HD (Wen, Haidan) | ||||||||||||||||||||||||
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| Abstract: The collective dynamics of topological structures(1-6) are of interest from both fundamental and applied perspectives. For example, studies of dynamical properties of magnetic vortices and skyrmions(3,4) have not only deepened our understanding of many-body physics but also offered potential applications in data processing and storage(7). Topological structures constructed from electrical polarization, rather than electron spin, have recently been realized in ferroelectric superlattices(5,6), and these are promising for ultrafast electric-field control of topological orders. However, little is known about the dynamics underlying the functionality of such complex extended nanostructures. Here, using terahertz-field excitation and femtosecond X-ray diffraction measurements, we observe ultrafast collective polarization dynamics that are unique to polar vortices, with orders-of-magnitude higher frequencies and smaller lateral size than those of experimentally realized magnetic vortices(3). A previously unseen tunable mode, hereafter referred to as a vortexon, emerges in the form of transient arrays of nanoscale circular patterns of atomic displacements, which reverse their vorticity on picosecond timescales. Its frequency is considerably reduced (softened) at a critical strain, indicating a condensation (freezing) of structural dynamics. We use first-principles-based atomistic calculations and phase-field modelling to reveal the microscopic atomic arrangements and corroborate the frequencies of the vortex modes. The discovery of subterahertz collective dynamics in polar vortices opens opportunities for electric-field-driven data processing in topological structures with ultrahigh speed and density. | ||||||||||||||||||||||||
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| Record 201 of 414 | |||||||||
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| Author(s): Vana, L (Vana, Lubomir); Jakubec, M (Jakubec, Martin); Sykora, J (Sykora, Jan); Cisarova, I (Cisarova, Ivana); Storch, J (Storch, Jan); Cirkva, V (Cirkva, Vladimir) | |||||||||
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| Abstract: A novel methodology for the synthesis of aza[n]-phenacenes was successfully developed utilizing photocyclodehydro-chlorination reaction of 2-chloro-N-aryl-1-naphthamides. In these key intermediates, the factors influencing the photoreaction were studied. The target aza[n]phenacenes were obtained by triflation or chlorination from prepared phenanthridinones, followed by hydrogenation. The introduction of a nitrogen atom into a phenacene skeleton induced changes in the physicochemical properties. The important properties of prepared aza[n]phenacenes (n = 4-6) were studied experimentally and by density functional theory calculations and were compared to those of their carbo analogues. Furthermore, some important features of the crystalline aza[n]phenacenes were investigated, including intermolecular interaction in the crystal lattice and the increased solubility or decreased melting points. | |||||||||
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| Record 202 of 414 | |||||||||
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| Author(s): Skoupy, V (Skoupy, Viktor); Lukes-Gerakopoulos, G (Lukes-Gerakopoulos, Georgios) | |||||||||
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| Abstract: We use the frequency and time domain Teukolsky formalism to calculate gravitational-wave fluxes from a spinning body on a bound eccentric equatorial orbit around a Kerr black hole. The spinning body is represented as a point particle following the pole-dipole approximation of the Mathisson-Papapetrou-Dixon equations. Reformulating these equations we are not only able to find the trajectory of a spinning particle in terms of its constants of motion, but also to provide a method to calculate the azimuthal and the radial frequency of this trajectory. Using these orbital quantities, we introduce the machinery to calculate through the frequency domain Teukolsky formalism the energy and the angular momentum fluxes at infinity, and at the horizon, along with the gravitational strain at infinity. We crosscheck the results obtained from the frequency domain approach with the results obtained from a time domain Teukolsky equation solver called Teukode. | |||||||||
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| Record 203 of 414 | ||||||||||||
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| Author(s): Ebeling, R (Ebeling, Rene); Arasu, NP (Arasu, Narendra P.); Bensch, L (Bensch, Lisa); Lammers, BS (Schulze Lammers, Bertram); Mayer, B (Mayer, Bernhard); Muller, TJJ (Mueller, Thomas J. J.); Vazquez, H (Vazquez, Hector); Karthauser, S (Karthaeuser, Silvia) | ||||||||||||
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| Abstract: Donor-acceptor molecules are a subject of great attention due to their immense potential in molecular electronics and photovoltaics. Despite numerous extensive studies demonstrating their functionality in solution, the donor-acceptor character is usually lost upon adsorption on a conducting substrate. Here the concept of breaking the conjugation between the donor and acceptor unit by insertion of a bridge is used. Furthermore, the bridge introduces a kink into the dyad and thus, reduces the possibility of hybridization with the substrate. A donor-bridge-acceptor dyad composed of carbazole and phenalenone units joined through a flexible bridge is synthesized and deposited on a Pt(111) surface. Its electronic properties are investigated with a combination of low temperature scanning tunneling microscope measurements and density functional theory simulations. Two preferential adsorption configurations are identified, in which individual molecules form strong bonds to the substrate and to a Pt adatom. Differential conductance measurements and atomistic simulations evidence the preservation of a reduced donor-acceptor character upon adsorption of the molecule, where this reduction is ascribed to the strong molecule-metal hybridization. Our results highlight the changes in donor-acceptor character of the dyad induced by the substrate and provide guidelines for the use of donor-bridge-acceptor molecules as functional units in solid-state devices. | ||||||||||||
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| Record 204 of 414 | |||||||||
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| Author(s): Fukal, J (Fukal, Jiri); Budesinsky, M (Budesinsky, Milos); Pav, O (Pav, Ondrej); Jurecka, P (Jurecka, Petr); Zgarbova, M (Zgarbova, Marie); Sebera, J (Sebera, Jakub); Sychrovsky, V (Sychrovsky, Vladimir) | |||||||||
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| Abstract: A method for averaging of NMR parameters by molecular dynamics (MD) has been derived from the method of statistical averaging in MD snapshots, benchmarked and applied to structurally dynamic interpretation of the P-31 NMR shift (delta(31P)) in DNA phosphates. The method employs adiabatic dependence of an NMR parameter on selected geometric parameter(s) that is weighted by MD-calculated probability distribution(s) for the geometric parameter(s) (Ad-MD method). The usage of Ad-MD for polymers is computationally convenient when one pre-calculated structural dependence of an NMR parameter is employed for all chemically equivalent units differing only in dynamic behavior. The Ad-MD method is benchmarked against the statistical averaging method for delta(31P) in the model phosphates featuring distinctively different structures and dynamic behavior. The applicability of Ad-MD is illustrated by calculating P-31 NMR spectra in the Dickerson-Drew DNA dodecamer. delta(31P) was calculated with the B3LYP/IGLO-III/PCM(water) and the probability distributions for the torsion angles adjacent to the phosphorus atoms in the DNA phosphates were calculated using the OL15 force field. | |||||||||
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| Record 205 of 414 | |||||||||||||||||||||
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| Author(s): Loubalova, Z (Loubalova, Zuzana); Fulka, H (Fulka, Helena); Horvat, F (Horvat, Filip); Pasulka, J (Pasulka, Josef); Malik, R (Malik, Radek); Hirose, M (Hirose, Michiko); Ogura, A (Ogura, Atsuo); Svoboda, P (Svoboda, Petr) | |||||||||||||||||||||
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Abstract:
A set of three papers reports that the piRNA pathway is essential for mammalian female fertility based on genetic perturbation experiments performed in golden hamsters.
PIWI-interacting RNAs (piRNAs) support the germline by suppressing retrotransposons. Studies of the pathway in mice have strongly shaped the view that mammalian piRNAs are essential for male but not for female fertility. Here, we report that the role of the piRNA pathway substantially differs in golden hamsters (Mesocricetus auratus), the piRNA pathway setup of which more closely resembles that of other mammals, including humans. The loss of the Mov10l1 RNA helicase-an essential piRNA biogenesis factor-leads to striking phenotypes in both sexes. In contrast to mice, female Mov10l1(-/-) hamsters are sterile because their oocytes do not sustain zygotic development. Furthermore, Mov10l1(-/-) male hamsters have impaired establishment of spermatogonia accompanied by transcriptome dysregulation and an expression surge of a young retrotransposon subfamily. Our results show that the mammalian piRNA pathway has essential roles in both sexes and its adaptive nature allows it to manage emerging genomic threats and acquire new critical roles in the germline. |
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| Record 206 of 414 | ||||||||||||
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| Author(s): Subadini, S (Subadini, Suchismita); Bera, K (Bera, Krishnendu); Hritz, J (Hritz, Jozef); Sahoo, H (Sahoo, Harekrushna) | ||||||||||||
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| Abstract: The importance of macromolecules paves the way towards a detailed molecular level investigation as all most all cellular processes occurring at the interior of cells in the form of proteins, enzymes, and other biological molecules are significantly affected because of their crowding. Thus, exploring the role of crowding environment on the denaturation and renaturation kinetics of protein molecules is of great importance. Here, CRABP I (cellular retinoic acid binding protein I) is employed as a model protein along with different molecular weights of Polyethylene glycol (PEG) as molecular crowders. The experimental evaluations are done by accessing the protein secondary structure analysis using circular dichroism (CD) spectroscopy and unfolding kinetics using intrinsic fluorescence of CRABP I at 37 degrees C to mimic the in vivo crowding environment. The unfolding kinetics results indicated that both PEG 2000 and PEG 4000 act as stabilizers by retarding the unfolding kinetic rates. Both kinetic and stability outcomes presented the importance of crowding environment on stability and kinetics of CRABP I. The molecular dynamics (MD) studies revealed that thirteen PEG 2000 molecules assembled during the 500 ns simulation, which increases the stability and percentage of beta-sheet. The experimental findings are well supported by the molecular dynamics simulation results. | ||||||||||||
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| Record 207 of 414 | ||||||||||||
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| Author(s): Bischoff, M (Bischoff, Marie); Biriukov, D (Biriukov, Denys); Predota, M (Predota, Milan); Marchioro, A (Marchioro, Arianna) | ||||||||||||
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| Abstract: Ion-specific effects play a crucial role in controlling the stability of colloidal systems and regulating interfacial processes. Although mechanistic pictures have been developed to explain the electrostatic structure of solid/water colloidal interfaces, ion-specific effects remain poorly understood. Here we quantify the average interfacial water orientation and the electrostatic surface potential around 100 nm SiO2 and TiO2 colloidal particles in the presence of NaCl, RbCl, and CaCl2 using polarimetric angle-resolved second harmonic scattering. We show that these two parameters can be used to establish the ion adsorption mechanism in a low ionic strength regime (<1 mM added salt). The relative differences between salts as a function of the ionic strength demonstrate cation- and surface-specific preferences for inner- vs outer-sphere adsorption. Compared to monovalent Rb+ and Na+, Ca2+ is found to be preferentially adsorbed as outer-sphere on SiO2 surfaces, while a dominant inner-sphere adsorption is observed for Ca2+ on TiO2. Molecular dynamics simulations performed on crystalline SiO2 and TiO2 surfaces support the experimental conclusions. This work contributes to the understanding of the electrostatic environment around colloidal nanoparticles on a molecular level by providing insight into ion-specific effects with micromolar sensitivity. | ||||||||||||
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| Record 208 of 414 |
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| Author(s): Rican, O (Rican, Oldrich); Dragova, K (Dragova, Klara); Almiron, A (Almiron, Adriana); Casciotta, J (Casciotta, Jorge); Gottwald, J (Gottwald, Jens); Pialek, L (Pialek, Lubomir) |
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| Abstract: Crenicichla is the largest and most widely distributed genus of Neotropical cichlids. Here, we analyze a mtDNA dataset comprising 681 specimens (including Teleocichla, a putative ingroup of Crenicichla) and 77 out of 105 presently recognized valid species (plus 10 out of 36 nominal synonyms plus over 50 putatively new species) from 129 locations in 31 major river drainages throughout the whole distribution of the genus in South America. Based on these data we make an inventory of diversity and highlight taxa and biogeographic areas worthy of further sampling effort and conservation protection. Using three methods of molecular species delimitation, we find between 126 and 168 species-like clusters, i.e., an average increase of species diversity of 65-121% with a range of increase between species groups. The increase ranges from 0% in the Missioneira and Macrophthama groups, through 25-40% (Lacustris group), 50-87% (Reticulata group, Teleocichla), 68-168% (Saxatilis group), 125-200% (Wallacii group), and 158-241% in the Lugubris group. We found a high degree of congruence between clusters derived from the three used methods of species delimitation. Overall, our results recognize substantially underestimated diversity in Crenicichla including Teleocichla. Most of the newly delimited putative species are from the Amazon-Orinoco-Guiana (AOG) core area (Greater Amazonia) of the Neotropical region, especially from the Brazilian and Guiana shield areas of which the former is under the largest threat and largest degree of environmental degradation of all the Amazon. |
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| Record 209 of 414 | ||||||
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| Author(s): Guzi, M (Guzi, Martin); Huber, P (Huber, Peter); Mikula, S (Mikula, Stepan) | ||||||
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| Abstract: We analyze the long-term impact of the resettlement of the Sudetenland after World War II on residential migration. This event involved expulsion of ethnic Germans and an almost complete depopulation of an area of a country and its rapid resettlement by 2 million Czech inhabitants. Results based on a regression discontinuity design show a highly persistent higher population churn and thus a lower attachment of residents to their region in resettled areas. Descriptive evidence also indicates that resettled settlements still have fewer local club memberships, less frequently organize local social events and had lower turnout in municipal elections until the 1990s. This thus suggests persistently lower levels of local social capital. This finding is consistent with recent theoretical models that suggest a highly persistent impact of the destruction of local social capital on residential migration. | ||||||
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| Record 210 of 414 | |||||||||
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| Author(s): Nemec, A (Nemec, Alexandr); Radolfova-Krizova, L (Radolfova-Krizova, Lenka); Maixnerova, M (Maixnerova, Martina); Nemec, M (Nemec, Matej); Spanelova, P (Spanelova, Petra); Safrankova, R (Safrankova, Renata); Sedo, O (Sedo, Ondrej); Lopes, BS (Lopes, Bruno S.); Higgins, PG (Higgins, Paul G.) | |||||||||
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| Abstract: This study aimed to define the taxonomic position and structure of a novel, taxonomically unique group of 26 Acinetobacter strains, provisionally designated Taxon 24 (T24). The strains were recovered from soil and freshwater ecosystems (n = 21) or animals (n = 5) in Czechia, Scotland, Germany, the Netherlands and Turkey between 1993 and 2015. They were non-glucose-acidifying, nonhemolytic, nonproteolytic, growing at 32 degrees C and on acetate and ethanol as single carbon sources, but not on 4-hydroxybenzoate and mostly not at 37 degrees C. Their whole-genome sequences were 3.0-3.7 Mb in size, with GC contents of 39.8-41.3%. Based on core genome phylogenetic analysis, the 26 strains formed a distinct Glade within the genus Acinetobacter, with strongly supported subclades termed T24A (n = 11), T24B (n = 8), T24C (n = 2), T24D (n = 3) and T24E (n = 2). The internal genomic ANIb values for these subclades were >94.8%, while the ANIb values between them were <92.5%. The results of MALDI-TOF MS-based analyses agreed with this classification. The five subclades differed from each other in the results of one to six carbon source assimilation tests. Given the genomic and phenotypic distinctness, internal coherence, numbers of available strains and geographically diverse origin of T24A and T24B, we propose the names Acinetobacter terrae sp. nov. and Acinetobacter terrestris sp. nov. for these two taxa, respectively. The type strains are ANC 4282(v) (= CCM 8986(T) = CCUG 73811(T) = CNCTC 8082(T)) and ANC 4471(T) (= CCM 8985(T) = CCUG 73812(T) = CNCTC 8093(T)), respectively. We conclude that these two species together with the other T24 strains represent a widely dispersed Acinetobacter Glade primarily associated with terrestrial ecosystems. (C) 2021 Elsevier GmbH. All rights reserved. | |||||||||
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| Record 211 of 414 |
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| Author(s): Dostal, Z (Dostal, Zdenek); Vlach, O (Vlach, Oldrich) |
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| Abstract: Augmented Lagrangian method is a well established tool for the solution of optimization problems with equality constraints. If combined with effective algorithms for the solution of bound constrained quadratic programming problems, it can solve efficiently very large problems with bound and linear equality constraints. The point of this paper is to show that the performance of the algorithm can be essentially improved by enhancing the information on the free set of current iterates into the reorthogonalization of equality constraints. The improvement is demonstrated on the numerical solution of a large problem arising from the application of domain decomposition methods to the solution of discretized elliptic variational inequality describing a variant of Hertz's two-body contact problem. (C) 2021 Elsevier B.V. All rights reserved. |
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| Record 212 of 414 |
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| Author(s): Ahmad, T (Ahmad, Touqeer); Emami, E (Emami, Ebrahim); Cadik, M (Cadik, Martin); Bebis, G (Bebis, George) |
| Book Group Author(s): IEEE |
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| Abstract: Skyline plays a pivotal role in mountainous visual geo-localization and localization/navigation of planetary rovers/UAVs and virtual/augmented reality applications. We present a novel mountainous skyline detection approach where we adapt a shallow learning approach to learn a set of filters to discriminate between edges belonging to sky-mountain boundary and others coming from different regions. Unlike earlier approaches, which either rely on extraction of explicit feature descriptors and their classification, or fine-tuning general scene parsing deep networks for sky segmentation, our approach learns linear filters based on local structure analysis. At test time, for every candidate edge pixel, a single filter is chosen from the set of learned filters based on pixel's structure tensor, and then applied to the patch around it. We then employ dynamic programming to solve the shortest path problem for the resultant multistage graph to get the sky-mountain boundary. The proposed approach is computationally faster than earlier methods while providing comparable performance and is more suitable for resource constrained platforms e.g., mobile devices, planetary rovers and UAVs. We compare our proposed approach against earlier skyline detection methods using four different data sets. Our code is available at https://github.com/TouqeerAhmad/skyline detection. |
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| Conference Sponsors: Int Neural Network Soc, IEEE Computat Intelligence Soc |
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| ISBN: 978-0-7381-3366-9 |
| Record 213 of 414 |
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| Author(s): Matousek, J (Matousek, Jindrich); Tihelka, D (Tihelka, Daniel) |
| Book Group Author(s): IEEE |
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| Abstract: In this paper, we continue to investigate the use of machine learning for the automatic detection of glottal closure instants (GCIs) from raw speech. We compare several deep one-dimensional convolutional neural network architectures on the same data and show that the InceptionV3 model yields the best results on the test set. On publicly available databases, the proposed 1D InceptionV3 outperforms XGBoost, a non-deep machine learning model, as well as other traditional GCI detection algorithms. |
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| Conference Sponsors: IEEE, Inst Elect & Elect Engineers, Signal Proc Soc |
| ISBN: 978-1-7281-7605-5 |
| Record 214 of 414 | ||||||
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| Author(s): Zubac, J (Zubac, Jan); Kaspar, Z (Kaspar, Zdenek); Krizek, F (Krizek, Filip); Forster, T (Foerster, Tobias); Campion, RP (Campion, Richard P.); Novak, V (Novak, Vit); Jungwirth, T (Jungwirth, Tomas); Olejnik, K (Olejnik, Kamil) | ||||||
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| Abstract: Antiferromagnetic spintronics allows us to explore storing and processing information in magnetic crystals with vanishing magnetization. In this paper, we investigate magnetoresistance effects in antiferromagnetic CuMnAs upon switching into high-resistive states using electrical pulses. By employing magnetic field sweeps up to 14 T and magnetic field pulses up to similar to 60 T, we reveal hysteretic phenomena and changes in the magnetoresistance, as well as the resilience of the switching signal in CuMnAs to the high magnetic field. These properties of the switched state are discussed in the context of recent studies of antiferromagnetic textures in CuMnAs. | ||||||
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| Record 215 of 414 | |||||||||
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| Author(s): Antol, M (Antol, Matej); Ol'ha, J (Ol'ha, Jaroslav); Slaninakova, T (Slaninakova, Terezia); Dohnal, V (Dohnal, Vlastislav) | |||||||||
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| Abstract: The main paradigm of similarity searching in metric spaces has remained mostly unchanged for decades - data objects are organized into a hierarchical structure according to their mutual distances, using representative pivots to reduce the number of distance computations needed to efficiently search the data. We propose an alternative to this paradigm, using machine learning models to replace pivots, thus posing similarity search as a classification problem, which stands in for numerous expensive distance computations. Even a relatively naive implementation of this idea is more than competitive with state-of-the-art methods in terms of speed and recall, proving the concept as viable and showing great potential for its future development. (C) 2021 Elsevier Ltd. All rights reserved. | |||||||||
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| Record 216 of 414 | ||||||||||||||||||
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| Author(s): Landovsky, T (Landovsky, Tomas); Babor, M (Babor, Martin); Cejka, J (Cejka, Jan); Eigner, V (Eigner, Vaclav); Dvorakova, H (Dvorakova, Hana); Krupicka, M (Krupicka, Martin); Lhotak, P (Lhotak, Pavel) | ||||||||||||||||||
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| Abstract: Oxidized phenoxathiin-based macrocycles, easily accessible thiacalix[4]arene derivatives, consist of a unique set of structural elements representing a key prerequisite for the unexpected reactivity described in this paper. As proposed, the internal strain, imposed by the presence of a heterocyclic moiety, together with a number of electron-withdrawing groups (SO2) opens the way to the cleavage of the macrocyclic skeleton through a cascade of three SNAr reactions triggered by the nucleophilic attack of an SH- anion. The whole transformation, which is unparalleled in classical calixarene chemistry, leads to unique linear sulfinic acid derivatives with a rearranged phenoxathiin moiety that can serve as building blocks for macrocyclic systems of a new type. | ||||||||||||||||||
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| Record 217 of 414 | ||||||||||||||||||
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| Author(s): Vojacek, L (Vojacek, Libor); Ibrahim, F (Ibrahim, Fatima); Hallal, A (Hallal, Ali); Dieny, B (Dieny, Bernard); Chshiev, M (Chshiev, Mairbek) | ||||||||||||||||||
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| Abstract: Magnetic tunnel junctions with perpendicular anisotropy form the basis of the spin-transfer torque magnetic random-access memory (STT MRAM), which is nonvolatile, fast, dense, and has quasi-infinite write endurance and low power consumption. Based on density-functional-theory (DFT) calculations, we propose an alternative design of magnetic tunnel junctions comprising Fe(n)Co(m)Fe(n)|MgO storage layers [n and m denote the number of monolayers (ML)] with greatly enhanced perpendicular magnetic anisotropy (PMA) up to several mJ/m(2), leveraging the interfacial perpendicular anisotropy of Fe vertical bar MgO along with a strain-induced bulk PMA discovered within bcc Co. This giant enhancement dominates the demagnetizing energy when increasing the film thickness. The tunneling magnetoresistance (TMR) estimated from the Julliere model is comparable with that of the pure Fe vertical bar MgO case. We discuss the advantages and pitfalls of a real-life fabrication of the structure and propose the Fe(3ML)Co(4ML)Fe(3ML) as a storage layer for MgO-based STT MRAM cells. The large PMA in strained bcc Co is explained in the framework of second-order perturbation theory by the MgO-imposed strain and consequent changes in the energies of d(yz) and d(z2) minority-spin bands. | ||||||||||||||||||
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| Record 218 of 414 | |||||||||
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| Author(s): Novotna, B (Novotna, Barbora); Hola, L (Hola, Lucie); Stas, M (Stas, Monika); Gutten, O (Gutten, Ondrej); Smola, M (Smola, Miroslav); Zavrel, M (Zavrel, Martin); Vavrina, Z (Vavrina, Zdenek); Budesinsky, M (Budesinsky, Milos); Liboska, R (Liboska, Radek); Chevrier, F (Chevrier, Florian); Dobias, J (Dobias, Juraj); Boura, E (Boura, Evzen); Rulisek, L (Rulisek, Lubomir); Birkus, G (Birkus, Gabriel) | |||||||||
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| Abstract: The 3'-5', 3'-5' cyclic dinucleotides (3'3'CDNs) are bacterial second messengers that can also bind to the stimulator of interferon genes (STING) adaptor protein in vertebrates and activate the host innate immunity. Here, we profiled the substrate specificity of four bacterial dinucleotide synthases from Vibrio cholerae (DncV), Bacillus thuringiensis (btDisA), Escherichia coli (dgcZ), and Thermotoga maritima (tDGC) using a library of 33 nucleoside-5'-triphosphate analogues and then employed these enzymes to synthesize 24 3'3'CDNs. The STING affinity of CDNs was evaluated in cell-based and biochemical assays, and their ability to induce cytokines was determined by employing human peripheral blood mononuclear cells. Interestingly, the prepared heterodimeric 3'3'CDNs bound to the STING much better than their homodimeric counterparts and showed similar or better potency than bacterial 3'3'CDNs. We also rationalized the experimental findings by in-depth STING-CDN structure-activity correlations by dissecting computed interaction free energies into a set of well-defined and intuitive terms. To this aim, we employed state-of-the-art methods of computational chemistry, such as quantum mechanics/molecular mechanics (QM/MM) calculations, and complemented the computed results with the {STING:3'3'c-di-ara-AMP} X-ray crystallographic structure. QM/MM identified three outliers (mostly homodimers) for which we have no clear explanation of their impaired binding with respect to their heterodimeric counterparts, whereas the R-2 = 0.7 correlation between the computed Delta G(int_ref)' and experimental Delta T-m's for the remaining ligands has been very encouraging. | |||||||||
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| Record 219 of 414 | |||||||||||||||
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| Author(s): Chin, HT (Chin, Hao-Ting); Klimes, J (Klimes, Jiri); Hu, IF (Hu, I-Fan); Chen, DR (Chen, Ding-Rui); Nguyen, HT (Nguyen, Hai-Thai); Chen, TW (Chen, Ting-Wei); Ma, SW (Ma, Shao-Wei); Hofmann, M (Hofmann, Mario); Liang, CT (Liang, Chi-Te); Hsieh, YP (Hsieh, Ya-Ping) | |||||||||||||||
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Abstract:
We here report on the direct observation of ferroelectric properties of water ice in its 2D phase. Upon nanoelectromechanical confinement between two graphene layers, water forms a 2D ice phase at room temperature that exhibits a strong and permanent dipole which depends on the previously applied field, representing clear evidence for ferroelectric ordering. Characterization of this permanent polarization with respect to varying water partial pressure and temperature reveals the importance of forming a monolayer of 2D ice for ferroelectric ordering which agrees with ab-initio and molecular dynamics simulations conducted. The observed robust ferroelectric properties of 2D ice enable novel nanoelectromechanical devices that exhibit memristive properties. A unique bipolar mechanical switching behavior is observed where previous charging history controls the transition voltage between low-resistance and high-resistance state. This advance enables the realization of rugged, non-volatile, mechanical memory exhibiting switching ratios of 10(6), 4 bit storage capabilities and no degradation after 10,000 switching cycles.
Ferroelectric ordering of water has been at the heart of intense debates due to its importance in enhancing our understanding of the condensed matter. Here, the authors observe ferroelectric properties of water ice in a two dimensional phase under confinement between two graphene layers. |
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| Author(s): Alcaraz, AJG (Alcaraz, Alper James G.); Mikulasek, K (Mikulasek, Kamil); Potesil, D (Potesil, David); Park, B (Park, Bradley); Shekh, K (Shekh, Kamran); Ewald, J (Ewald, Jessica); Burbridge, C (Burbridge, Connor); Zdrahal, Z (Zdrahal, Zbynek); Schneider, D (Schneider, David); Xia, JG (Xia, Jianguo); Crump, D (Crump, Doug); Basu, N (Basu, Niladri); Hecker, M (Hecker, Markus) | |||||||||||||||
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| Abstract: There is an urgent demand for more efficient and ethical approaches in ecological risk assessment. Using 17 alpha-ethinylestradiol (EE2) as a model compound, this study established an embryo benchmark dose (BMD) assay for rainbow trout (RBT; Oncorhynchus mykiss) to derive transcriptomic points-of-departure (tPODs) as an alternative to live-animal tests. Embryos were exposed to graded concentrations of EE2 (measured: 0, 1.13, 1.57, 6.22, 16.3, 55.1, and 169 ng/L) from hatch to 4 and up to 60 days post-hatch (dph) to assess molecular and apical responses, respectively. Whole proteome analyses of alevins did not show clear estrogenic effects. In contrast, transcriptomics revealed responses that were in agreement with apical effects, including excessive accumulation of intravascular and hepatic proteinaceous fluid and significant increases in mortality at 55.1 and 169 ng/L EE2 at later time points. Transcriptomic BMD analysis estimated the median of the 20th lowest geneBMD to be 0.18 ng/L, the most sensitive tPOD. Other estimates (0.78, 3.64, and 1.63 ng/L for the 10th percentile geneBMD, first peak geneBMD distribution, and median geneBMD of the most sensitive over-represented pathway, respectively) were within the same order of magnitude as empirically derived apical PODs for EE2 in the literature. This 4-day alternative RBT embryonic assay was effective in deriving tPODs that are protective of chronic effects of EE2. | |||||||||||||||
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| Record 221 of 414 | ||||||||||||||||||
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| Author(s): Tabor, E (Tabor, Edyta); Lemishka, M (Lemishka, Mariia); Olszowka, JE (Olszowka, Joanna E.); Mlekodaj, K (Mlekodaj, Kinga); Dedecek, J (Dedecek, Jiri); Andrikopoulos, PC (Andrikopoulos, Prokopis C.); Sklenak, S (Sklenak, Stepan) | ||||||||||||||||||
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| Abstract: Activation of dioxygen is of extreme importance due to its potential for transformation of methane to valuable products and applications in other selective oxidation reactions. Distant binuclear cationic Fe(II) centers in Fe-ferrierite were shown to split dioxygen at room temperature to form a pair of very active oxygen species (i.e., alpha-oxygens) and subsequently oxidize methane to methanol at room temperature as well. Our study reveals that the activity in splitting dioxygen represents a general property of the distant binuclear cationic Fe(II) centers stabilized in the aluminosilicate matrix. Computational models of the ferrierite, beta, A, and mordenite zeolites with various Al sitings in the rings forming the cationic sites were investigated by periodic DFT calculations including molecular dynamics simulations. The results reveal that the Fe(II) sites stabilized in various zeolite matrices can split dioxygen if the two cationic sites forming the distant binuclear Fe(II) centers (i) face each other, (ii) are parallel, and (iii) are axial, and (iv) the Fe center dot center dot center dot Fe distance lies in a narrow range from ca. 7 to ca. 8 A (ca. 7-ca. 10 A for the distance between the two rings (forming the corresponding cationic sites) in empty zeolites since this distance is equal to or larger than the Fe center dot center dot center dot Fe distances). Our study opens the possibility of developing Fe-zeolite-based systems for the dioxygen activation employed for direct oxidations using various zeolite matrices. | ||||||||||||||||||
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| Record 222 of 414 | |||||||||
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| Author(s): Brazdil, T (Brazdil, Tomas); Gallo, M (Gallo, Matej); Nenutil, R (Nenutil, Rudolf); Kubanda, A (Kubanda, Andrej); Toufar, M (Toufar, Martin); Holub, P (Holub, Petr) | |||||||||
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| Abstract: The diagnosis of solid tumors of epithelial origin (carcinomas) represents a major part of the workload in clinical histopathology. Carcinomas consist of malignant epithelial cells arranged in more or less cohesive clusters of variable size and shape, together with stromal cells, extracellular matrix, and blood vessels. Distinguishing stroma from epithelium is a critical component of artificial intelligence (AI) methods developed to detect and analyze carcinomas. In this paper, we propose a novel automated workflow that enables large-scale guidance of AI methods to identify the epithelial component. The workflow is based on re-staining existing hematoxylin and eosin (H&E) formalin-fixed paraffin-embedded sections by immunohistochemistry for cytokeratins, cytoskeletal components specific to epithelial cells. Compared to existing methods, clinically available H&E sections are reused and no additional material, such as consecutive slides, is needed. We developed a simple and reliable method for automatic alignment to generate masks denoting cytokeratin-rich regions, using cell nuclei positions that are visible in both the original and the re-stained slide. The registration method has been compared to state-of-the-art methods for alignment of consecutive slides and shows that, despite being simpler, it provides similar accuracy and is more robust. We also demonstrate how the automatically generated masks can be used to train modern AI image segmentation based on U-Net, resulting in reliable detection of epithelial regions in previously unseen H&E slides. Through training on real-world material available in clinical laboratories, this approach therefore has widespread applications toward achieving AI-assisted tumor assessment directly from scanned H&E sections. In addition, the re-staining method will facilitate additional automated quantitative studies of tumor cell and stromal cell phenotypes. | |||||||||
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| Record 223 of 414 | |||||||||||||||
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| Author(s): de Ruiter, I (de Ruiter, Iris); Leseigneur, G (Leseigneur, Guillaume); Rowlinson, A (Rowlinson, Antonia); Wijers, RAMJ (Wijers, Ralph A. M. J.); Drabent, A (Drabent, Alexander); Intema, HT (Intema, Huib T.); Shimwell, TW (Shimwell, Timothy W.) | |||||||||||||||
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| Abstract: We present a search for transient radio sources on time-scales of 2-9 yr at 150 MHz. This search is conducted by comparing the first Alternative Data Release of the TIFR GMRT Sky Survey (TGSS ADR1) and the second data release of the LOFAR Two-metre Sky Survey (LoTSS DR2). The overlapping survey area covers 5570 deg(2) on the sky, or 14 per cent of the total sky. We introduce a method to compare the source catalogues that involves a pair match of sources, a flux density cutoff to meet the survey completeness limit and a newly developed compactness criterion. This method is used to identify both transient candidates in the TGSS source catalogue that have no counterpart in the LoTSS catalogue and transient candidates in LoTSS without a counterpart in TGSS. We find that imaging artefacts and uncertainties and variations in the flux density scales complicate the transient search. Our method to search for transients by comparing two different surveys, while taking into account imaging artefacts around bright sources and misaligned flux scales between surveys, is universally applicable to future radio transient searches. No transient sources were identified, but we are able to place an upper limit on the transient surface density of <5.4 x 10(-4) deg(-2) at 150 MHz for compact sources with an integrated flux density over 100 mJy. Here we define a transient as a compact source with flux density greater than 100 mJy that appears in the catalogue of one survey without a counterpart in the other survey. | |||||||||||||||
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| Record 224 of 414 | |||||||||||||||
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| Author(s): Ament, K (Ament, Kevin); Kowitsch, N (Koewitsch, Nicolas); Hou, DW (Hou, Dianwei); Gotsch, T (Goetsch, Thomas); Krohnert, J (Kroehnert, Jutta); Heard, CJ (Heard, Christopher J.); Trunschke, A (Trunschke, Annette); Lunkenbein, T (Lunkenbein, Thomas); Armbruster, M (Armbruester, Marc); Breu, J (Breu, Josef) | |||||||||||||||
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| Abstract: Ultrathin layers of oxides deposited on atomically flat metal surfaces have been shown to significantly influence the electronic structure of the underlying metal, which in turn alters the catalytic performance. Upscaling of the specifically designed architectures as required for technical utilization of the effect has yet not been achieved. Here, we apply liquid crystalline phases of fluorohectorite nanosheets to fabricate such architectures in bulk. Synthetic sodium fluorohectorite, a layered silicate, when immersed into water spontaneously and repulsively swells to produce nematic suspensions of individual negatively charged nanosheets separated to more than 60 nm, while retaining parallel orientation. Into these galleries oppositely charged palladium nanoparticles were intercalated whereupon the galleries collapse. Individual and separated Pd nanoparticles were thus captured and sandwiched between nanosheets. As suggested by the model systems, the resulting catalyst performed better in the oxidation of carbon monoxide than the same Pd nanoparticles supported on external surfaces of hectorite or on a conventional Al2O3 support. XPS confirmed a shift of Pd 3d electrons to higher energies upon coverage of Pd nanoparticles with nanosheets to which we attribute the improved catalytic performance. DFT calculations showed increasing positive charge on Pd weakened CO adsorption and this way damped CO poisoning. | |||||||||||||||
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| Record 225 of 414 | ||||||||||||
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| Author(s): Kroutil, O (Kroutil, Ondrej); Nguyen, DV (Nguyen, D. Vinh); Volanek, J (Volanek, Jirf); Kucera, A (Kucera, Ales); Predota, M (Predota, Milan); Vranova, V (Vranova, Valerie) | ||||||||||||
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| Abstract: Classical molecular dynamics (CMD) simulations were used to describe clinoptilolite/electrolyte interface with an atomistic resolution. The most abundant (010) surface cut was chosen together with two forms of clinoptilolite (CL) skeleton: neutral siliceous form (CL-SIL) and charged natural form with aluminum substitutions (CLSUB). Structural properties of adsorbed water molecules, sodium, and ammonium cations are described in very detail and compared to the experimental findings. It is shown that the structure of water molecules and ions near the surface is significantly influenced by the framework charge. To improve our understanding of CL(010)/ electrolyte interactions, umbrella sampling (US) simulations were performed to get free energies of adsorption of Na+ and NH4+ cations. These are compared with complementary experimental numbers obtained by batch adsorption experiments. The qualitative agreement was found but the origins of quantitative disagreement are discussed. | ||||||||||||
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| Record 226 of 414 |
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| Author(s): Kucharikova, H (Kucharikova, Hana); Dobrovolna, P (Dobrovolna, Pavlina); Lochmanova, G (Lochmanova, Gabriela); Zdrahal, Z (Zdrahal, Zbynek) |
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| Abstract: Histone post-translational modifications (hPTMs) are epigenetic marks that strongly affect numerous processes, including cell cycling and protein interactions. They have been studied by both antibody- and MS-based methods for years, but the analyses are still challenging, mainly because of the diversity of histones and their modifications arising from high contents of reactive amine groups in their amino acid sequences. Here, we introduce use of trimethylacetic anhydride (TMA) as a new reagent for efficient histone derivatization, which is a requirement for bottom-up proteomic hPTM analysis. TMA can denyatize unmodified amine groups of lysine residues and amine groups generated at peptide N-termini by trypsin digestion. The derivatization is facilitated by microwave irradiation, which also reduces incubation times to minutes. We demonstrate that histone derivatization with TMA reliably provides high yields of fully derivatized peptides and thus is an effective alternative to conventional methods. TMA afforded more than 98% and 99% labeling efficiencies for histones H4 and H3, respectively, thereby enabling accurate quantification of peptide forms. Trimethylacetylation substantially improves chromatographic separation of peptide forms, which is essential for direct quantification based on signals extracted from MS1 data. For this purpose, software widely applied by the proteomics community can be used without additional computational development. Thorough comparison with widely applied propionylation highlights the advantages of TMA-based histone derivatization for monitoring hPTMs in biological samples. |
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| Record 227 of 414 | |||||||||
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| Author(s): Smak, P (Smak, Pavel); Tvaroska, I (Tvaroska, Igor); Koca, J (Koca, Jaroslav) | |||||||||
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| Abstract: Tyrosine sulfation alters the biological activity of many proteins involved in different physiological and pathophysiological conditions, such as non-specific immune reaction, response to inflammation and ischemia, targeting of leukocytes and stem cells, or the formation of cancer metastases. Tyrosine sulfation is catalyzed by the enzymes tyrosylprotein sulfotransferases (TPST). In this study, we used QM/MM Car-Parrinello metadynamics simulations together with QM/MM potential energy calculations to investigate the catalytic mechanism of isoform TPST-1. The structural changes along the reaction coordinate are analyzed and discussed. Furthermore, both the methods supported the S(N)2 type of catalytic mechanism. The reaction barrier obtained from CPMD metadynamics was 12.8 kcal mol(-1), and the potential energy scan led to reaction barriers of 11.6 kcal mol(-1) and 13.7 kcal mol(-1) with the B3LYP and OPBE functional, respectively. The comparison of the two methods (metadynamics and potential energy scan) may be helpful for future mechanistic studies. The insight into the reaction mechanism of TPST-1 might help with the rational design of transition-state TPST inhibitors. | |||||||||
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| Record 228 of 414 |
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| Author(s): Hokr, M (Hokr, Milan); Balvin, A (Balvin, Ales) |
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| Abstract: Understanding evolution of groundwater hydraulic and chemical conditions is important for safety assessment of radioactive waste disposal. Perturbations to groundwater can occur due to the construction and operation of the underground facility. The initial perturbations and their recovery after the tunnel closure were observed in the Groundwater REcovery Experiment in Tunnel (GREET) in Mizunami, Japan, at 500-m depth in granite. In a 100m-long tunnel, 50 m was isolated by building a plug. Aside from other measurement and exploration data, groundwater pressures and chemical composition were monitored in boreholes with 24 packer sections. This work used numerical modelling to better understand and be able to predict the observed water flow and solute transport phenomena. The model covered 100-m scale around the tunnel and was divided into a continuum farfield domain and a near-field domain with deterministic discrete fractures and matrix blocks. A mixed-hybrid finite element solution was used with independent degrees of freedom for 3D and 2D elements. Modelling started with a blind prediction followed by a calibration (inverse model) for drainage and flooding experiment phases. The inverse hydraulic model fitted the more/less communicating sections and estimated transmissivity and conductivity parameters that are consistent for the two phases. The model sensitivity on transport parameters was insufficient for the inverse model, which can use only simplified measured evolution to avoid noisy data. |
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| Record 229 of 414 | ||||||
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| Author(s): Tesikova, J (Tesikova, Jana); Krasova, J (Krasova, Jarmila); de Bellocq, JG (de Bellocq, Joelle Gouy) | ||||||
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| Abstract: Rodents are a speciose group of mammals with strong zoonotic potential. Some parts of Africa are still underexplored for the occurrence of rodent-borne pathogens, despite this high potential. Angola is at the convergence of three major biogeographical regions of sub-Saharan Africa, each harbouring a specific rodent community. This rodent-rich area is, therefore, strategic for studying the diversity and evolution of rodent-borne viruses. In this study we examined 290 small mammals, almost all rodents, for the presence of mammarenavirus and hantavirus RNA. While no hantavirus was detected, we found three rodent species positive for distinct mammarenaviruses with a particularly high prevalence in Namaqua rock rats (Micaelamys namaquensis). We characterised four complete virus genomes, which showed typical mammarenavirus organisation. Phylogenetic and genetic distance analyses revealed: (i) the presence of a significantly divergent strain of Luna virus in Angolan representatives of the ubiquitous Natal multimammate mouse (Mastomys natalensis), (ii) a novel Okahandja-related virus associated with the Angolan lineage of Micaelamys namaquensis for which we propose the name Bitu virus (BITV) and (iii) the occurrence of a novel Mobala-like mammarenavirus in the grey-bellied pygmy mouse (Mus triton) for which we propose the name Kwanza virus (KWAV). This high virus diversity in a limited host sample size and in a relatively small geographical area supports the idea that Angola is a hotspot for mammarenavirus diversity. | ||||||
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| Record 230 of 414 | ||||||||||||
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| Author(s): Guo, XY (Guo, Xinyi); Mandakova, T (Mandakova, Terezie); Trachtova, K (Trachtova, Karolina); Ozudogru, B (Ozudogru, Baris); Liu, JQ (Liu, Jianquan); Lysak, MA (Lysak, Martin A.) | ||||||||||||
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| Abstract: Pervasive hybridization and whole-genome duplications (WGDs) influenced genome evolution in several eukaryotic lineages. Although frequent and recurrent hybridizations may result in reticulate phylogenies, the evolutionary events underlying these reticulations, including detailed structure of the ancestral diploid and polyploid genomes, were only rarely reconstructed. Here, we elucidate the complex genomic history of a monophyletic clade from the mustard family (Brassicaceae), showing contentious relationships to the early-diverging clades of this model plant family. Genome evolution in the crucifer tribe Biscutelleae (similar to 60 species, 5 genera) was dominated by pervasive hybridizations and subsequent genome duplications. Diversification of an ancestral diploid genome into several divergent but crossable genomes was followed by hybridizations between these genomes. Whereas a single genus (Megadenia) remained diploid, the four remaining genera originated by allopolyploidy (Biscutella, Lunaria, Ricotia) or autopolyploidy (Heldreichia). The contentious relationships among the Biscutelleae genera, and between the tribe and other early diverged crucifer lineages, are best explained by close genomic relatedness among the recurrently hybridizing ancestral genomes. By using complementary cytogenomics and phylogenomics approaches, we demonstrate that the origin of a monophyletic plant clade can be more complex than a parsimonious assumption of a single WGD spurring postpolyploid cladogenesis. Instead, recurrent hybridization among the same and/or closely related parental genomes may phylogenetically interlink diploid and polyploid genomes despite the incidence of multiple independent WGDs. Our results provide new insights into evolution of early-diverging Brassicaceae lineages and elucidate challenges in resolving the contentious relationships within and between land plant lineages with pervasive hybridization and WGDs. | ||||||||||||
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| Record 231 of 414 | |||||||||||||||
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| Author(s): Nieves, P (Nieves, P.); Arapan, S (Arapan, S.); Zhang, SH (Zhang, S. H.); Kadzielawa, AP (Kadzielawa, A. P.); Zhang, RF (Zhang, R. F.); Legut, D (Legut, D.) | |||||||||||||||
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Abstract:
MAELAS is a computer program for the calculation of magnetocrystalline anisotropy energy, anisotropic magnetostrictive coefficients and magnetoelastic constants in an automated way. The method originally implemented in version 1.0 of MAELAS was based on the length optimization of the unit cell, proposed by Wu and Freeman, to calculate the anisotropic magnetostrictive coefficients. We present here a revised and updated version (v2.0) of MAELAS, where we added a new methodology to compute anisotropic magnetoelastic constants from a linear fitting of the energy versus applied strain. We analyze and compare the accuracy of both methods showing that the new approach is more reliable and robust than the one implemented in version 1.0, especially for non-cubic crystal symmetries. This analysis also helps us find that the accuracy of the method implemented in version 1.0 could be improved by using deformation gradients derived from the equilibrium magnetoelastic strain tensor, as well as potential future alternative methods like the strain optimization method. Additionally, we clarify the role of the demagnetized state in the fractional change in length, and derive the expression for saturation magnetostriction for polycrystals with trigonal, tetragonal and orthorhombic crystal symmetry. In this new version, we also fix some issues related to trigonal crystal symmetry found in version 1.0.
Program summary Program title: MAELAS CPC Library link to program files: https://doi.org/10.17632/gxcdg3z7t6.2 Developer's repository link: https://github.com/pnieyes2019/MAELAS Code Ocean capsule: https://codeocean.com/capsule/2689126 Licensing provisions: BSD 3-clause Programming language: Python3 Journal reference of previous version: P. Nieves, S. Arapan, S.H. Zhang, A.P. K4dzielawa, R.F. Zhang and D. Legut, Comput. Phys. Commun. 264, 107964 (2021) Does the new version supersede the previous version?: Yes Reasons for the new version: To implement a more accurate methodology to compute magnetoelastic constants and magnetostrictive coefficients, and fix some issues related to trigonal crystal symmetry. Summary of revisions: New method to calculate magnetoelastic constants and magnetostrictive coefficients derived from the magnetoelastic energy. Correction of the trigonal crystal symmetry. Implementation of the saturation magnetostriction for polycrystals with trigonal, tetragonal and orthorhombic crystal symmetry. In the visualization tool MAELASviewer, we included the possibility to choose the type of reference demagnetized state in the calculation of the fractional change in length. Nature of problem: To calculate anisotropic magnetostrictive coefficients and magnetoelastic constants in an automated way based on Density Functional Theory methods. Solution method: In the first stage, the unit cell is relaxed through a spin-polarized calculation without spin-orbit coupling (SOC). Next, after a crystal symmetry analysis, a set of deformed lattice and spin configurations are generated using the pymatgen library [1]. The energy of these states is calculated by the Vienna Ab-initio Simulation Package (VASP) [2], including SOC. The anisotropic magnetoelastic constants are derived from the fitting of these energies to a linear polynomial. Finally, if the elastic tensor is provided [3], then the magnetostrictive coefficients are also calculated from the theoretical relations between elastic and magnetoelastic constants. Additional comments including restrictions and unusual features: This version supports the following crystal systems: Cubic (point groups 432, (4) over bar 3m, m (3) over barm), Hexagonal (6mm, 622, (6) over bar 2m, 6/mmm), Trigonal (32, 3m, (3) over barm), Tetragonal (4mm, (4) over bar 22, 42m, 4/mmm) and Orthorhombic (222, 2mm, mmm). (C) 2021 Elsevier B.V. All rights reserved. |
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| Record 232 of 414 |
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| Author(s): Vitek, A (Vitek, Ales); Sarmanova, M (Sarmanova, Martina); Kalus, R (Kalus, Rene) |
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| Abstract: Parallel-tempering Monte Carlo calculations have been performed for the Hg8 cluster in an isothermal-isobaric ensemble. Temperature and pressure dependent cluster residual heat capacity and Pearson correlation coefficient for cluster energy and volume have been calculated over a broad range of cluster temperatures and external pressures using a 2D multiple histogram method. Calculated data have subsequently been used in investigations of structural changes in Hg8 induced by increased pressure and temperature. A global picture of these changes is provided in the form of a cluster temperature-pressure phase diagram. |
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| Author(s): Svec, P (Svec, Petr); Samsonov, MA (Samsonov, Maksim A.); Ruzickova, Z (Ruzickova, Zdenka); Brus, J (Brus, Jiri); Ruzicka, A (Ruzicka, Ales) | ||||||||||||
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| Abstract: Stannylenes of L2Sn type bearing either C,N-chelating (1, L = L-CN = 2-(N,N-dimethylaminomethyl)phenyl) or bulky amido (2, L = L-N = N(SiMe3)(2)) ligands react with cyanogen bromide (Br-C N) via an oxidative-addition reaction to give monomeric six-coordinate (L-CN)(2)Sn(Br)CN (1a) and four-coordinate (L-N)(2)Sn(Br) CN (2a) stannanes in moderate yields. In solution, both 1a and 2a undergo instantaneous bromido-cyanido ligand redistribution reactions, leading to mixtures containing 1a, (L-CN)(2)SnBr2 (1b) and (L-CN)(2)Sn(CN)(2) (1c) or 2a, (L-N)(2)SnBr2 (2b) and (L-N)(2)Sn(CN)(2) (2c), respectively. The prepared species were characterised by multinuclear NMR spectroscopy in solution (1a-c and 2a-c) and in the solid state (1a-c). The crystal structures of 1a/b/c, 2a/b/c and sole 2b were determined by XRD analyses. DFT calculations and QTAIM analysis were also carried out to corroborate the experimental results. | ||||||||||||
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| Author(s): Nguyen, NT (Nguyen, Nhat-Tien); Le, TTT (Le, Thien T. T.); Nguyen, HH (Nguyen, Huy-Hung); Voznak, M (Voznak, Miroslav) | ||||||||||||||||||
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| Abstract: Underwater wireless sensor networks are currently seeing broad research in various applications for human benefits. Large numbers of sensor nodes are being deployed in rivers and oceans to monitor the underwater environment. In the paper, we propose an energy-efficient clustering multi-hop routing protocol (EECMR) which can balance the energy consumption of these nodes and increase their network lifetime. The network area is divided into layers with regard to the depth level. The data sensed by the nodes are transmitted to a sink via a multi-hop routing path. The cluster head is selected according to the depth of the node and its residual energy. To transmit data from the node to the sink, the cluster head aggregates the data packet of all cluster members and then forwards them to the upper layer of the sink node. The simulation results show that EECMR is effective in terms of network lifetime and the nodes' energy consumption. | ||||||||||||||||||
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| Author(s): Christe, C (Christe, Camille); Boluda, CG (Boluda, Carlos G.); Koubinova, D (Koubinova, Darina); Gautier, L (Gautier, Laurent); Naciri, Y (Naciri, Yamama) | ||||||
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| Abstract: Some tropical plant families, such as the Sapotaceae, have a complex taxonomy, which can be resolved using Next Generation Sequencing (NGS). For most groups however, methodological protocols are still missing. Here we identified 531 monocopy genes and 227 Short Tandem Repeats (STR) markers and tested them on Sapotaceae using target capture and NGS. The probes were designed using two genome skimming samples from Capurodendron delphinense and Bemangidia lowryi, both from the Tseboneae tribe, as well as the published Manilkara zapota transcriptome from the Sapotoideae tribe. We combined our probes with 261 additional ones previously published and designed for the entire angiosperm group. On a total of 792 low-copy genes, 638 showed no signs of paralogy and were used to build a phylogeny of the family with 231 individuals from all main lineages. A highly supported topology was obtained at high taxonomic ranks but also at the species level. This phylogeny revealed the existence of more than 20 putative new species. Single nucleotide polymorphisms (SNPs) extracted from the 638 genes were able to distinguish lineages within a species complex and to highlight geographical structuration. STR were recovered efficiently for the species used as reference (C. delphinense) but the recovery rate decreased dramatically with the phylogenetic distance to the focal species. Altogether, the new loci will help reaching a sound taxonomic understanding of the family Sapotaceae for which many circumscriptions and relationships are still debated, at the species, genus and tribe levels. | ||||||
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| Record 236 of 414 | ||||||||||||
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| Author(s): Mayorquin-Torres, MC (Mayorquin-Torres, Martha C.); Maldonado-Dominguez, M (Maldonado-Dominguez, Mauricio); Flores-Alamo, M (Flores-Alamo, Marcos); Iglesias-Arteaga, MA (Iglesias-Arteaga, Martin A.) | ||||||||||||
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| Abstract: The synthesis of six dimeric spiroketals bearing an estradiol half fused to the 5 alpha- or 5 beta-epimers of androstane, cholestane, and spirostane nuclei is described. The synthetic procedure comprises the Sonogashira- coupling of different steroid alkynes with 2-iodoestradiol 17-monoacetate, followed by Pd-catalyzed spiroketalization. The structural characterization of the obtained hybrid dimers was performed using a combination of 1D and 2D NMR techniques, and was assisted by DFT calculations. Single crystal X-ray diffraction of one of the obtained compounds confirmed the proposed structures. | ||||||||||||
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| Record 237 of 414 | ||||||||||||||||||||||||
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| Author(s): Sehnal, D (Sehnal, David); Bittrich, S (Bittrich, Sebastian); Deshpande, M (Deshpande, Mandar); Svobodova, R (Svobodova, Radka); Berka, K (Berka, Karel); Bazgier, V (Bazgier, Vaclav); Velankar, S (Velankar, Sameer); Burley, SK (Burley, Stephen K.); Koca, J (Koca, Jaroslav); Rose, AS (Rose, Alexander S.) | ||||||||||||||||||||||||
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| Abstract: Large biomolecular structures are being determined experimentally on a daily basis using established techniques such as crystallography and electron microscopy. In addition, emerging integrative or hybrid methods (I/HM) are producing structural models of huge macromolecular machines and assemblies, sometimes containing 100s of millions of non-hydrogen atoms. The performance requirements for visualization and analysis tools delivering these data are increasing rapidly. Significant progress in developing online, web-native three-dimensional (3D) visualization tools was previously accomplished with the introduction of the LiteMol suite and NGL Viewers. Thereafter, Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of LiteMol (developed by PDBe) and NGL (developed by RCSB PDB). The web-native Mol* Viewer enables 3D visualization and streaming of macromolecular coordinate and experimental data, together with capabilities for displaying structure quality, functional, or biological context annotations. High-performance graphics and data management allows users to simultaneously visualise up to hundreds of (superimposed) protein structures, stream molecular dynamics simulation trajectories, render cell-level models, or display huge I/HM structures. It is the primary 3D structure viewer used by PDBe and RCSB PDB. It can be easily integrated into third-party services. Mol* Viewer is open source and freely available at https://molstar.org/. | ||||||||||||||||||||||||
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| Record 238 of 414 | ||||||
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| Author(s): Ledvinka, T (Ledvinka, Tomas); Khirnov, A (Khirnov, Anton) | ||||||
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| Abstract: We report on a numerical study of gravitational waves undergoing gravitational collapse due to their self-interaction. We consider several families of asymptotically flat initial data which, similar to the well-known Choptuik's discovery, can be fine-tuned between dispersal into empty space and collapse into a black hole. We find that near-critical spacetimes exhibit behavior similar to scalar-field collapse: For different families of initial data, we observe universal "echoes" in the form of irregularly repeating, approximate, scaled copies of the same piece of spacetime. | ||||||
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| Record 239 of 414 | |||||||||||||||
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| Author(s): Foltyn, L (Foltyn, Ladislav); Vysocky, J (Vysocky, Jan); Prettico, G (Prettico, Giuseppe); Beloch, M (Beloch, Michal); Praks, P (Praks, Pavel); Fulli, G (Fulli, Gianluca) | |||||||||||||||
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| Abstract: Electrical distribution networks are facing an energy transition which entails an increase of decentralised renewable energy sources and electric vehicles. The resulting temporal and spatial uncertainty in the generation/load patterns challenges the operations of an infrastructure not designed for such a transition. In this situation, Optimal Power Flow methods can play a key role in identifying system weak points and supporting efficient management of the electrical networks, including the distribution level. In this work, to support distribution system operators' decision-making process, we aim at attaining a quasi-optimal solution in the shortest time possible in an electrical network experiencing a large growth of distributed energy sources. We propose an optimisation method based on a modified version of a genetic algorithm and the Python pandapower package. The method is tested on a model of a real urban meshed network of a large Czech city. The optimisation method minimises the total operating costs of the distribution network by controlling selected network components and parameters, namely the transformer tap changers and the active power demand at consumption nodes. The results of our method are compared with the exact solution showing that a close-to-optimal solution of the observed problem can be reached in a relatively short time. (c) 2021 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). | |||||||||||||||
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| Record 240 of 414 | |||||||||||||||
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| Author(s): Caballer, M (Caballer, Miguel); Antonacci, M (Antonacci, Marica); Sustr, Z (Sustr, Zdenek); Perniola, M (Perniola, Michele); Molto, G (Molto, German) | |||||||||||||||
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| Abstract: Virtual clusters are widely used computing platforms than can be deployed in multiple cloud platforms. The ability to dynamically grow and shrink the number of nodes has paved the way for customised elastic computing both for High Performance Computing and High Throughput Computing workloads. However, elasticity is typically restricted to a single cloud site, thus hindering the ability to provision computational resources from multiple geographically distributed cloud sites. To this aim, this paper introduces an architecture of open-source components that coherently deploy a virtual elastic cluster across multiple cloud sites to perform large-scale computing. These hybrid virtual elastic clusters are automatically deployed and configured using an Infrastructure as Code (IaC) approach on a distributed hybrid testbed that spans different organizations, including on-premises and public clouds, supporting automated tunneling of communications across the cluster nodes with advanced VPN topologies. The results indicate that cluster-based computing of embarrassingly parallel jobs can benefit from hybrid virtual clusters that aggregate computing resources from multiple cloud back-ends and bring them together into a dedicated, albeit virtual network. | |||||||||||||||
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| Record 241 of 414 | ||||||
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| Author(s): Lampart, M (Lampart, Marek); Zapomel, J (Zapomel, Jaroslav) | ||||||
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| Abstract: In this work, the combination of the 0-1 test for chaos and approximate entropy is applied to a newly established mechanical model instead of the Lyapunov exponent exploration on huge simulations reached on the supercomputer Salomon (Czech Republic). This procedure is applied to the mechanical systems modeled by a system of non-autonomous ordinary differential equations that detects the type of trajectories generated when the system parameters are changed. This new mechanical system is formed by an impact element hanging on a flexible rope, and a moving belt, etc. This contact system with impacts and dry friction is based on numerous industrial applications such as stones falling on a moving conveyor belt. The mathematical model's systems of equations have three degrees of freedom: two of them correspond to the position of the impact body center of gravity and the third one to the angular rotation. As the main aim, it is shown that the investigated systems exhibit a full range of trajectory types, meaning it can act in both a regular and irregular way. These results are supported by bifurcation diagrams and phase portraits for a suitable choice of drive parameters: the excitation frequency and amplitude. | ||||||
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| Record 242 of 414 | ||||||||||||
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| Author(s): Polak, J (Polak, Jakub); Moravek, P (Moravek, Pavel); Brkljaca, Z (Brkljaca, Zlatko); Vazdar, M (Vazdar, Mario); Cibulka, I (Cibulka, Ivan); Heyda, J (Heyda, Jan) | ||||||||||||
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| Abstract: The effect of increasing temperature and pressure is studied for aqueous guanidinium chloride (GdmCl) at infinite dilutions. Experimentally determined partial molar volumes are combined with classical molecular dynamics simulations of GdmCl and the detailed analysis of the hydration structure is presented. We find that Gdm(+) ion behaves differently than Cl- ion in terms of overall hydration structure, where Gdm(+) has an anisotropic hydration shell compared to an isotropically hydrated Cl- ion. The difference in the hydration structure between the ions is also visible in the corresponding Kirkwood-Buff integrals and in temperature and pressure effects on single ion standard molar volumes. The detailed analysis shows a unique behavior of Gdm(+) hydration structure which at the same time displays both hydrophilic and hydrophobic response to increase in temperature and pressure. (C) 2021 Elsevier Ltd. | ||||||||||||
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| Record 243 of 414 | ||||||
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| Author(s): Hovorkova, M (Hovorkova, Michaela); Kulik, N (Kulik, Natalia); Konvalinkova, D (Konvalinkova, Dorota); Petraskova, L (Petraskova, Lucie); Kren, V (Kren, Vladimir); Bojarova, P (Bojarova, Pavla) | ||||||
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| Abstract: Glycosidases that cleave oligosaccharides can also synthesize the glycosidic bond. Site-directed mutagenesis of the catalytic nucleophile commonly abolishes their hydrolytic activity, affording glycosynthases that use glycosyl fluorides as substrates. Here, the synthetic ability of beta-galactosidase from Bacillus circulans isoform A (BgaD-A; EC 3.2.1.23, GH2) was investigated by site-directed mutagenesis. The cold-shock expression ensured selective induction and correct folding. Three mutants were constructed at the active-site catalytic nucleophile E532 as putative glycosynthases. However, none of the mutants could process alpha-galactosyl fluoride as a galactosyl donor. With only negligible hydrolytic activity, two mutants selectively synthesized azido-functionalized N-acetyllactosamine using the p-nitrophenyl beta-d-galactoside as a galactosyl donor. Thus, they behaved as transglycosidases. This study demonstrates that substitution at the catalytic nucleophile for the assembly of glycosynthases is not unrestrictedly versatile and that the effect of mutagenesis on synthetic abilities depends on the relative orientations of amino acids in the enzyme active site. | ||||||
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| Record 244 of 414 | ||||||
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| Author(s): Lampart, M (Lampart, Marek); Zapomel, J (Zapomel, Jaroslav) | ||||||
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| Abstract: In the field of mechanical engineering, conveyors and moving belts are frequently used machine parts. In many working regimes, they are subjected to sudden loading, which can be a source of irregular motion in the impacting bodies and undesirable behavior in the working machine. This paper deals with a mechanical model where colisions between an impact body and a moving belt take place. The impact body is constrained by a flexible rope, the upper end of which is excited by a slider in the vertical direction. The behavior of the system was investigated in terms of its dependence on the amplitude and frequency of excitation given by the movement of the slider, and the eccentricity of the center of gravity of the impact body. Outputs of the computations indicate that different combinations of the analyzed parameters lead to high complexity of the system's movement. The bifurcation analysis shows multiple periodic areas changed by chaotic regions. The research carried out provides more details about the behavior and properties of strongly nonlinear mechanical systems resulting from impacts and dry friction. The obtained information will enable designers to propose parameters for industrial machines that make it possible to avoid their working at undesirable operating levels. | ||||||
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| Record 245 of 414 | |||||||||
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| Author(s): Knizek, K (Knizek, K.); Novak, P (Novak, P.); Jirak, Z (Jirak, Z.) | |||||||||
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| Abstract: We have studied the origin of magnetic interaction in e-Fe2O3 by ab-initio electronic structure calculations. The exchange integrals of the Heisenberg Hamiltonian have been calculated using the methods based on the density functional theory (DFT) employing generalized gradient approximation (GGA) with orbital dependent potential extension for 3d electrons of Fe (GGA + U method). The calculations confirm the ground antiferromagnetic (AFM) state with two Fe3+ sublattices oriented up (Fe2 and Fe3) and two Fe3+ sublattices oriented down (Fe1 and Fe4). The calculated exchange integrals, including also the intra-sublattice ones, are all of AFM type. Their strength weighted by the number of neighbors is larger between the Fe sublattices with opposite spins than between the sublattices with equal spin directions. The notable exception is a strong exchange integral between the neighboring tetrahedrally-coordinated sites within the Fe4 sublattice, which effectively decreases the molecular field imposed on Fe4 sites by neighboring sites of other sublattices, namely the antiparallelly oriented Fe2 and Fe3. For this reason, the ordered magnetic moment of Fe4 exhibits the fastest decrease with increasing temperature among the sublattices, leading to an uncompensated AFM arrangement in e-Fe2O3. Considering the competition of the inter- and intra-sublattice exchange integrals and applying symmetry arguments, we infer that the collinear AFM ground state of e-Fe2O3 is prone to an intrinsic canting within the sublattices, retaining at the same time the magnetic group symmetry Pna ' 2(1)'. | |||||||||
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| Record 246 of 414 | |||||||||||||||
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| Author(s): Alcaraz, AJG (Alcaraz, Alper James G.); Potesil, D (Potesil, David); Mikulasek, K (Mikulasek, Kamil); Green, D (Green, Derek); Park, B (Park, Bradley); Burbridge, C (Burbridge, Connor); Bluhm, K (Bluhm, Kerstin); Soufan, O (Soufan, Othman); Lane, T (Lane, Taylor); Pipal, M (Pipal, Marek); Brinkmann, M (Brinkmann, Markus); Xia, JG (Xia, Jianguo); Zdrahal, Z (Zdrahal, Zbynek); Schneider, D (Schneider, David); Crump, D (Crump, Doug); Basu, N (Basu, Niladri); Hogan, N (Hogan, Natacha); Hecker, M (Hecker, Markus) | |||||||||||||||
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| Abstract: There is increasing pressure to develop alternative ecotoxicological risk assessment approaches that do not rely on expensive, time-consuming, and ethically questionable live animal testing. This study aimed to develop a comprehensive early life stage toxicity pathway model for the exposure of fish to estrogenic chemicals that is rooted in mechanistic toxicology. Embryo-larval fathead minnows (FHM; Pimephales promelas) were exposed to graded concentrations of 17 alpha-ethinylestradiol (water control, 0.01% DMSO, 4, 20, and 100 ng/L) for 32 days. Fish were assessed for transcriptomic and proteomic responses at 4 days post-hatch (dph), and for histological and apical end points at 28 dph. Molecular analyses revealed core responses that were indicative of observed apical outcomes, including biological processes resulting in overproduction of vitellogenin and impairment of visual development. Histological observations indicated accumulation of proteinaceous fluid in liver and kidney tissues, energy depletion, and delayed or suppressed gonad development. Additionally, fish in the 100 ng/L treatment group were smaller than controls. Integration of omics data improved the interpretation of perturbations in early life stage FHM, providing evidence of conservation of toxicity pathways across levels of biological organization. Overall, the mechanism-based embryo-larval FHM model showed promise as a replacement for standard adult live animal tests. | |||||||||||||||
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| Record 247 of 414 | ||||||||||||||||||
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| Author(s): Morina, F (Morina, Filis); Mijovilovich, A (Mijovilovich, Ana); Koloniuk, I (Koloniuk, Igor); Pencik, A (Pencik, Ales); Gruz, J (Gruz, Jiri); Novak, O (Novak, Ondrej); Kupper, H (Kupper, Hendrik) | ||||||||||||||||||
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| Abstract: Phomopsis. longicolla is a hemibiotrophic fungus causing significant soybean yield loss worldwide. To reveal the role of zinc in plant-pathogen interactions, soybean seedlings were grown hydroponically with a range of Zn concentrations, 0.06 mu M (deficient, Zn0), 0.4 mu M (optimal growth), 1.5 mu M, 4 mu M, 12 mu M, and toxic 38 mu M, and were subsequently inoculated with P. longicolla via the roots. In vivo analysis of metal distribution in tissues by micro-X-ray fluorescence showed local Zn mobilization in the root maturation zone in all treatments. Decreased root and pod biomass, and photosynthetic performance in infected plants treated with 0.4 mu M Zn were accompanied with accumulation of Zn, jasmonoyl-L-isoleucine (JA-Ile), jasmonic acid, and cell wall-bound syringic acid ((cw)SyA) in roots. Zn concentration in roots of infected plants treated with 1.5 mu M Zn was seven-fold higher than in the 0.4 mu M Zn treatment, which together with accumulation of JA-Ile, (cw)SyA, cell wall-bound vanilic acid and leaf jasmonates contributed to maintaining photosynthesis and pod biomass. Host-pathogen nutrient competition and phenolics accumulation limited the infection in Zn-deficient plants. The low infection rate in Zn 4 mu M-treated roots correlated with salicylic and 4-hydroxybenzoic acid, and cell wall-bound p-coumaric acid accumulation. Zn toxicity promoted pathogen invasion and depleted cell wall-bound phenolics. The results show that manipulation of Zn availability improves soybean resistance to P. longicolla by stimulating phenolics biosynthesis and stress-inducible phytohormones. | ||||||||||||||||||
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| Record 248 of 414 | |||||||||||||||
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| Author(s): Kartha, KK (Kartha, Kalathil K.); Takai, A (Takai, Atsuro); Futera, Z (Futera, Zdenek); Labuta, J (Labuta, Jan); Takeuchi, M (Takeuchi, Masayuki) | |||||||||||||||
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| Abstract: Elucidation of dynamics of molecular rotational motion is an essential part and challenging area of research. We demonstrate reversible diastereomeric interconversion of a molecular rotor composed of overcrowded butterfly-shape alkene (FDF). Its inherent dual rotatory motion (two rotors, one stator) with interconversion between two diastereomers, chiral trans-FDF and meso cis-FDF forms, has been examined in detail upon varying temperatures and solvents. The free energy profile of 180 degrees revolution of one rotor part has a bimodal shape with unevenly positioned maxima (transition states). FDF in aromatic solvents adopts preferentially meso cis-conformation, while in non-aromatic solvents a chiral trans-conformation is more abundant owing to the solvent interactions with peripheral hexyl chains (solvophobic effect). Moderate correlations between the trans-FDF/cis-FDF ratio and solvent parameters, such as refractive index, polarizability, and viscosity were found. | |||||||||||||||
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| Record 249 of 414 | ||||||
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| Author(s): Jirka, M (Jirka, M.); Sasorov, P (Sasorov, P.); Bulanov, SS (Bulanov, S. S.); Korn, G (Korn, G.); Rus, B (Rus, B.); Bulanov, SV (Bulanov, S., V) | ||||||
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| Abstract: The question of whether an electron radiating its energy away during the interaction with a laser can reach the region of highest intensity with energy high enough to make a number of different phenomena observable is one of the most studied and most important in strong field quantum electrodynamics. Here a simple analytical estimate for an average electron energy evolution is proposed and benchmarked against particle-in-cell simulations. Furthermore, these results are used to estimate the electron and laser pulse properties required to make vacuum Cherenkov emission observable. | ||||||
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| Record 250 of 414 | ||||||
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| Author(s): Zeman, V (Zeman, Vaclav); Kliegr, T (Kliegr, Tomas); Svatek, V (Svatek, Vojtech) | ||||||
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| Abstract: AMIE+ is a state-of-the-art algorithm for learning rules from RDF knowledge graphs (KGs). Based on association rule learning, AMIE+ constituted a breakthrough in terms of speed on large data compared to the previous generation of ILP-based systems. In this paper we present several algorithmic extensions to AMIE+, which make it faster, and the support for data pre-processing and model post-processing, which provides a more comprehensive coverage of the linked data mining process than does the original AMIE+ implementation. The main contributions are related to performance improvement: (1) the top-k approach, which addresses the problem of combinatorial explosion often resulting from a hand-set minimum support threshold, (2) a grammar that allows to define fine-grained patterns reducing the size of the search space, and (3) a faster projection binding reducing the number of repetitive calculations. Other enhancements include the possibility to mine across multiple graphs, the support for discretization of continuous values, and the selection of the most representative rules using proven rule pruning and clustering algorithms. Benchmarks show reductions in mining time of up to several orders of magnitude compared to AMIE+. | ||||||
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| Record 251 of 414 | |||||||||
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| Author(s): Parez, S (Parez, Stanislav); Travnickova, T (Travnickova, Tereza); Svoboda, M (Svoboda, Martin); Aharonov, E (Aharonov, Einat) | |||||||||
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| Abstract: Shear strain localization into shear bands is associated with velocity weakening instabilities and earthquakes. Here, we simulate steady-state plane-shear flow of numerical granular material (gouge), confined between parallel surfaces. Both constant shear stress and constant strain-rate boundary conditions are tested, and the two types of boundary conditions are found to yield distinct velocity profiles and friction laws. The inertial number, I, exerts the largest control on the layers' behavior, but additional dependencies of friction on normal stress and thickness of the layer are observed under constant stress boundary condition. We find that shear-band localization, which is present in the quasistatic regime (I < 10(-3)) in rate-controlled shear, is absent under stress-controlled loading. In the latter case, flow ceases when macroscopic friction coefficient approaches the quasistatic friction value. The inertial regime that occurs at higher inertial numbers (I > 10(-3)) is associated with distributed shear, and friction and porosity that increase with shear rate (rate-strengthening regime). The finding that shear under constant stress boundary condition produces the inertial, distributed shear but never quasistatic, localized deformation is rationalized based on low fluctuations of shear forces in granular contacts for stress-controlled loading. By examining porosity within and outside a shear band, we also provide a mechanical reason why the transition between quasistatic and inertial shear coincides with the transition between localized and distributed strain. | |||||||||
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| Record 252 of 414 | ||||||||||||
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| Author(s): Zatloukalova, M (Zatloukalova, Martina); Jedinak, L (Jedinak, Lukas); Riman, D (Riman, Daniel); Frankova, J (Frankova, Jana); Novak, D (Novak, David); Cytryniak, A (Cytryniak, Adrianna); Nazaruk, E (Nazaruk, Ewa); Bilewicz, R (Bilewicz, Renata); Vrba, J (Vrba, Jiri); Papouskova, B (Papouskova, Barbora); Kabelac, M (Kabelac, Martin); Vacek, J (Vacek, Jan) | ||||||||||||
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| Abstract: Lipid nitroalkenes - nitro-fatty acids (NO2-FAs) are formed in vivo via the interaction of reactive nitrogen species with unsaturated fatty acids. The resulting electrophilic NO2-FAs play an important role in redox homeostasis and cellular stress response. This study investigated the physicochemical properties and reactivity of two NO2-FAs: 9/10-nitrooleic acid (1) and its newly prepared 1-monoacyl ester, (E)-2,3-hydroxypropyl 9/10-nitrooctadec-9-enoate (2), both synthesized by a direct radical nitration approach. Compounds 1 and 2 were investigated in an aqueous medium and after incorporation into lipid nanoparticles prepared from 1-monoolein, cubosomes 1@CUB and 2@CUB. Using an electrochemical analysis and LC-MS, free 1 and 2 were found to be unstable under acidic conditions, and their degradation occurred in an aqueous environment within a few minutes or hours. This degradation was associated with the production of the NO radical, as confirmed by fluorescence assay. In contrast, preparations 1@CUB and 2@CUB exhibited a significant increase in the stability of the loaded 1 and 2 up to several days to weeks. In addition to experimental data, density functional theory-based calculation results on the electronic structure and structural variability (open and closed configuration) of 1 and 2 were obtained. Finally, experiments with a human HaCaT keratinocyte cell line demonstrated the ability of 1@CUB and 2@CUB to penetrate through the cytoplasmic membrane and modulate cellular pathways, which was exemplified by the Keap1 protein level monitoring. Free 1 and 2 and the cubosomes prepared from them showed cytotoxic effect on HaCaT cells with IC50 values ranging from 1 to 8 mu M after 24 h. The further development of cubosomal preparations with embedded electrophilic NO2-FAs may not only contribute to the field of fundamental research, but also to their application using an optimized lipid delivery vehicle. | ||||||||||||
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| Record 253 of 414 | |||||||||
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| Author(s): Smydke, J (Smydke, Jan); Csaszar, AG (Csaszar, Attila G.) | |||||||||
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| Abstract: Generalization of an earlier reduced-density-matrix-based vibrational assignment algorithm is given, applicable for systems exhibiting both large-amplitude motions, including tunneling, and degenerate vibrational modes. The algorithm developed is used to study the structure of the excited vibrational wave functions of the ammonia molecule, (NH3)-N-14. Characterization of the complex dynamics of systems with several degenerate vibrations requires reconsidering the traditional degenerate-mode description given by vibrational angular momentum quantum numbers and switching to a symmetry-based approach that directly predicts state degeneracy and uncovers relations between degenerate modes. Out of the 600 distinct vibrational eigenstates of ammonia obtained by a full-dimensional variational computation, the developed methodology allows for the assignment of about 500 with meaningful labels. This study confirms that vibrationally excited states truly have modal character recognizable up to very high energies even for the non-trivial case of ammonia, a molecule which exhibits a tunneling motion and has two two-dimensional normal modes. The modal characteristics of the excited states and the interplay of the vibrational modes can be easily visualized by the reduced-density matrices, giving an insight into the complex modal behavior directed by symmetry. | |||||||||
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| Record 254 of 414 | ||||||||||||||||||||||||
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| Author(s): Harazim, M (Harazim, Marketa); Pialek, L (Pialek, Lubomir); Pikula, J (Pikula, Jiri); Seidlova, V (Seidlova, Veronika); Zukal, J (Zukal, Jan); Bachorec, E (Bachorec, Erik); Bartonicka, T (Bartonicka, Tomas); Kokurewicz, T (Kokurewicz, Tomasz); Martinkova, N (Martinkova, Natalia) | ||||||||||||||||||||||||
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| Abstract: The challenges of surviving periods of increased physiological stress elicit selective pressures that drive adaptations to overcome hardships. Bats in the Palearctic region survive winter in hibernation. We sampled single nucleotide polymorphisms (SNPs) in hibernating Myotis myotis bats using double-digest restriction site-associated DNA sequencing and we associated the genomic variability with the observed phenotypes reflecting hibernation site preference, body condition and bat health during hibernation. We did not observe genotype associations between the detrended body condition index, representing fat reserves, and functional genes involved in fat metabolism. Bat body surface temperature, reflecting roost selection, or roost warmth relative to the climate at the site did not show any associations with the sampled genotypes. We found SNPs with associations to macroclimatic variables, characterising the hibernaculum, and blood biochemistry, related to health of the bat. The genes in proximity of the associated SNPs were involved in metabolism, immune response and signal transduction, including chaperones, apoptosis and autophagy regulators and immune signalling molecules. The genetic adaptations included adaptation to tissue repair and protection against tissue damage. | ||||||||||||||||||||||||
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| Record 255 of 414 | ||||||||||||
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| Author(s): Sladkova, KP (Pleiner Sladkova, K.); Soucek, O (Soucek, O.); Behounkova, M (Behounkova, M.) | ||||||||||||
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| Abstract: We propose a new model of Enceladus' tiger stripes in which the ice shell is modeled as an elastic system with Coulomb-type frictional interfaces subjected to periodic tidal loading. We find that the diurnal tides produce a complex pattern of stress anomalies, characterized by a length scale of tens of km and the peak values exceeding 100 kPa. Friction delays the response of the system to tidal loading and leads to an asymmetry between the compression and extension phases. This asymmetry results in additional stress, constant in time and comparable in magnitude to the cyclic stress. This static stress field is characterized by compression in the direction perpendicular to the faults and may influence the evolution of the south polar region on geological time scales. The total heat flow generated by friction is 0.1-1 GW, accounting for only a small fraction of the heat power emitted from the tiger stripes. | ||||||||||||
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| Record 256 of 414 | ||||||||||||||||||||||||||||||
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| Author(s): Ivanko, I (Ivanko, Iryna); Mahun, A (Mahun, Andrii); Kobera, L (Kobera, Libor); Cernochova, Z (Cernochova, Zulfiya); Pavlova, E (Pavlova, Ewa); Toman, P (Toman, Petr); Pientka, Z (Pientka, Zbynek); Stepanek, P (Stepanek, Petr); Tomsik, E (Tomsik, Elena) | ||||||||||||||||||||||||||||||
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| Abstract: A new method for poly (3, 4-ethylenedioxythiophene) (PEDOT) synthesis based on acid-assisted polymerization is proposed, and the optical and structural properties of the obtained material are explored. Special attention is given to the effect of the polar Bronsted acid on the formation of oligomer/polymer chains and their ability to assemble into nanoobjects. By using H-1 and C-13 NMR spectroscopy (in the liquid and solid state), the formation of PEDOT in a neutral state was proven. Matrix-assisted laser desorption/ionization-time-of-flight, static light scattering, and dynamic light scattering spectroscopies were used to determine the M-w and size of PEDOT nanoobjects. Moreover, we used density functional theory calculations to seek a correlation between the length of the PEDOT oligomer chain and the position of its lowest-energy absorption peak S-1. All calculations were performed in concentrated formic acid and compared with calculations in the gas phase. In addition, we demonstrate a correlation between the photoluminescence (PL) from individual PEDOT chains and that from PEDOT chains assembled into nanoobjects. While individual PEDOT chains show four PL peaks, the assembled PEDOT nanoobjects show only one PL peak. Tuning the process of self-assembly for individual PEDOT chains is a promising way to control the properties of a polymer material. | ||||||||||||||||||||||||||||||
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| Record 257 of 414 | ||||||
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| Author(s): Medvedev, N (Medvedev, Nikita); Chalupsky, J (Chalupsky, Jaromir); Juha, L (Juha, Libor) | ||||||
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| Abstract: We study the behavior of poly(methyl methacrylate) (PMMA) exposed to femtosecond pulses of extreme ultraviolet and X-ray laser radiation in the single-shot damage regime. The employed microscopic simulation traces induced electron cascades, the thermal energy exchange of electrons with atoms, nonthermal modification of the interatomic potential, and a triggered atomic response. We identify that the nonthermal hydrogen decoupling triggers ultrafast fragmentation of PMMA strains at the absorbed threshold dose of ~0.07 eV/atom. At higher doses, more hydrogen atoms detach from their parental molecules, which, at the dose of ~0.5 eV/atom, leads to a complete separation of hydrogens from carbon and oxygen atoms and fragmentation of MMA molecules. At the dose of ~0.7 eV/atom, the band gap completely collapses indicating that a metallic liquid is formed with complete atomic disorder. An estimated single-shot ablation threshold and a crater depth as functions of fluence agree well with the experimental data collected. | ||||||
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| Record 258 of 414 | |||||||||
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| Author(s): Lasota, M (Lasota, Martin); Sidlof, P (Sidlof, Petr); Kaltenbacher, M (Kaltenbacher, Manfred); Schoder, S (Schoder, Stefan) | |||||||||
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| Abstract: In an aeroacoustic simulation of human voice production, the effect of the sub-grid scale (SGS) model on the acoustic spectrum was investigated. In the first step, incompressible airflow in a 3D model of larynx with vocal folds undergoing prescribed two-degree-of-freedom oscillation was simulated by laminar and Large-Eddy Simulations (LES), using the One-Equation and Wall-Adaptive Local-Eddy (WALE) SGS models. Second, the aeroacoustic sources and the sound propagation in a domain composed of the larynx and vocal tract were computed by the Perturbed Convective Wave Equation (PCWE) for vowels [u:] and [i:]. The results show that the SGS model has a significant impact not only on the flow field, but also on the spectrum of the sound sampled 1 cm downstream of the lips. With the WALE model, which is known to handle the near-wall and high-shear regions more precisely, the simulations predict significantly higher peak volumetric flow rates of air than those of the One-Equation model, only slightly lower than the laminar simulation. The usage of the WALE SGS model also results in higher sound pressure levels of the higher harmonic frequencies. | |||||||||
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| Record 259 of 414 | ||||||||||||
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| Author(s): Manthei, AC (Manthei, Alina C.); Benacek, J (Benacek, Jan); Munoz, PA (Munoz, Patricio A.); Buchner, J (Buechner, Joerg) | ||||||||||||
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| Abstract: Context. Several important mechanisms that explain coherent pulsar radio emission rely on streaming (or beam) instabilities of the relativistic pair plasma in a pulsar magnetosphere. However, it is still not clear whether the streaming instability by itself is sufficient to explain the observed coherent radio emission. Due to the relativistic conditions that are present in the pulsar magnetosphere, kinetic instabilities could be quenched. Moreover, uncertainties regarding specific model-dependent parameters impede conclusions concerning this question.Aims. We aim to constrain the possible parameter range for which a streaming instability could lead to pulsar radio emission, focusing on the transition between strong and weak beam models, beam drift speed, and temperature dependence of the beam and background plasma components.Methods. We solve a linear relativistic kinetic dispersion relation appropriate for pulsar conditions in a more general way than in previous studies, considering a wider parameter range. In doing so, we provide a theoretical prediction of maximum and integrated growth rates as well as of the fractional bandwidth of the most unstable waves for the investigated parameter ranges. The analytical results are validated by comparison with relativistic kinetic particle-in-cell (PIC) numerical simulations.Results. We obtain growth rates as a function of background and beam densities, temperatures, and streaming velocities while finding a remarkable agreement of the linear dispersion predictions and numerical simulation results in a wide parameter range. Monotonous growth is found when increasing the beam-to-background density ratio. With growing beam velocity, the growth rates firstly increase, reach a maximum and decrease again for higher beam velocities. A monotonous dependence on the plasma temperatures is found, manifesting in an asymptotic behaviour when reaching colder temperatures. A simultaneous change of both temperatures proves not to be a mere linear superposition of both individual temperature dependences. We show that the generated waves are phase-coherent by calculating the fractional bandwidth.Conclusions. Plasma streaming instabilities of the pulsar pair plasma can efficiently generate coherent radio signals if the streaming velocity is ultra-relativistic with Lorentz factors in the range 13< gamma< 300, if the background and beam temperatures are small enough (inverse temperatures rho(0); rho (1)>= 1, i.e., T-0; T-1 <= 6x10(9)), and if the beam-to-background plasma density ratio n(1)/(gamma (b)n(0)) exceeds 10(-3), which means that n(1)/n(0) has to be between 1.3 and 20% (depending on the streaming velocity). | ||||||||||||
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| Record 260 of 414 | |||||||||||||||||||||
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| Author(s): Tlaskal, V (Tlaskal, Vojtech); Brabcova, V (Brabcova, Vendula); Vetrovsky, T (Vetrovsky, Tomas); Jomura, M (Jomura, Mayuko); Lopez-Mondejar, R (Lopez-Mondejar, Ruben); Monteiro, LMO (Monteiro, Lummy Maria Oliveira); Saraiva, JP (Saraiva, Joao Pedro); Human, ZR (Rainier Human, Zander); Cajthaml, T (Cajthaml, Tomas); da Rocha, UN (da Rocha, Ulisses Nunes); Baldrian, P (Baldrian, Petr) | |||||||||||||||||||||
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Abstract:
Forests accumulate and store large amounts of carbon (C), and a substantial fraction of this stock is contained in deadwood. This transient pool is subject to decomposition by deadwood-associated organisms, and in this process it contributes to CO2 emissions. Although fungi and bacteria are known to colonize deadwood, little is known about the microbial processes that mediate carbon and nitrogen (N) cycling in deadwood. In this study, using a combination of metagenomics, metatranscriptomics, and nutrient flux measurements, we demonstrate that the decomposition of deadwood reflects the complementary roles played by fungi and bacteria. Fungi were found to dominate the decomposition of deadwood and particularly its recalcitrant fractions, while several bacterial taxa participate in N accumulation in deadwood through N fixation, being dependent on fungal activity with respect to deadwood colonization and C supply. Conversely, bacterial N fixation helps to decrease the constraints of deadwood decomposition for fungi. Both the CO2 efflux and N accumulation that are a result of a joint action of deadwood bacteria and fungi may be significant for nutrient cycling at ecosystem levels. Especially in boreal forests with low N stocks, deadwood retention may help to improve the nutritional status and fertility of soils.
IMPORTANCE Wood represents a globally important stock of C, and its mineralization importantly contributes to the global C cycle. Microorganisms play a key role in deadwood decomposition, since they possess enzymatic tools for the degradation of recalcitrant plant polymers. The present paradigm is that fungi accomplish degradation while commensalist bacteria exploit the products of fungal extracellular enzymatic cleavage, but this assumption was never backed by the analysis of microbial roles in deadwood. This study clearly identifies the roles of fungi and bacteria in the microbiome and demonstrates the importance of bacteria and their N fixation for the nutrient balance in deadwood as well as fluxes at the ecosystem level. Deadwood decomposition is shown as a process where fungi and bacteria play defined, complementary roles. |
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| Record 261 of 414 | ||||||
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| Author(s): Dedicova, S (Dedicova, Sarka); Dockal, J (Dockal, Jan); Moucka, F (Moucka, Filip); Jirsak, J (Jirsak, Jan) | ||||||
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| Abstract: Molecular dynamics simulations are carried out to investigate the structure of a single poly(oxyethylene) (POE) chain in aqueous and methanolic solutions in a strong external electric field. The conformational changes of the polymer chain induced by the strong external electric field are monitored by measuring the radius of gyration, the components of the gyration tensor, the end-to-end distance, dihedral angle distribution, and the helical content. The isotropic coil size measures, i. e., the radius of gyration and the end-to-end distance mostly decrease with growing intensity of the electric field except a small increase occurring between 0 and 1 V/nm in water. Therefore, in most cases the field compresses the polymer coil. Nevertheless, the deformation is anisotropic, leading to an average spheroid which is prolate in water (again with the exception of fields less or equal to 1 V/nm) and oblate in methanol. Analysis of dihedrals suggests that POE chain's partially helical structure is promoted at electric fields above 1 V/nm. Changes caused by the strong external electric field in the solvent-solvent and solvent-polymer hydrogen-bonding structure are monitored by measuring the number of hydrogen bonds, their strength, and the volume of the bonding region. Results show non-trivial, solvent-specific effects, which are yet to be fully understood. (C) 2021 Elsevier B.V. All rights reserved. | ||||||
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| Record 262 of 414 | ||||||
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| Author(s): Broz, M (Broz, M.); Chrenko, O (Chrenko, O.); Nesvorny, D (Nesvorny, D.); Dauphas, N (Dauphas, N.) | ||||||
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| Abstract: The massive cores of the giant planets are thought to have formed in a gas disk by the accretion of pebble-sized particles whose accretional cross-section was enhanced by aerodynamic gas drag(1,2). A commonly held view is that the terrestrial planet system formed later (30-200 Myr after the dispersal of the gas disk) by giant collisions of tens of lunar-to Mars-sized protoplanets(3,4). Here we propose, instead, that the terrestrial planets of the Solar System formed earlier by the gas-driven convergent migration of protoplanets towards similar to 1 au. To investigate situations in which convergent migration occurs and determine the thermal structure of the gas and pebble disks in the terrestrial planet zone, we developed a radiation-hydrodynamic model with realistic opacities(5,6). We find that protoplanets grow in the first 10 Myr by mutual collisions and pebble accretion, and gain orbital eccentricities by gravitational scattering and the hot-trail effect(7,8). The orbital structure of the inner Solar System is well reproduced in our simulations, including its tight mass concentration at 0.7-1 au and the small sizes of Mercury and Mars. The early-stage protosolar disk temperature exceeds 1,500 K inside 0.4 au, implying that Mercury grew in a highly reducing environment next to the evaporation lines of iron and silicates, influencing Mercury's bulk composition(9). A dissipating gas disk, however, is cold, and pebbles drifting from larger heliocentric distances would deliver volatile elements. | ||||||
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| Record 263 of 414 | |||||||||
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| Author(s): Futera, Z (Futera, Zdenek); English, NJ (English, Niall J.) | |||||||||
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| Abstract: The high-pressure solid phase of water known as ice VII has recently attracted a lot of attention when its presence was detected in large exoplanets, their icy satellites, and even in Earth's mantle. Moreover, a transition of ice VII to the superionic phase can be triggered by external electric fields. Here, we investigate the dielectric responses of ice VII to applied oscillating electric fields of various frequencies employing non-equilibrium ab initio molecular dynamics. We focus on the dynamical properties of a dipole-ordered ice VII structure, for which we explored external-field-induced electronic polarisation and the vibrational spectral density of states (VDOS). These analyses are important for the understanding of collective motions in the ice-VII lattice and the electronic properties of this exotic water phase. | |||||||||
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| Record 264 of 414 | |||||||||||||||
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| Author(s): Dannegger, T (Dannegger, Tobias); Berritta, M (Berritta, Marco); Carva, K (Carva, Karel); Selzer, S (Selzer, Severin); Ritzmann, U (Ritzmann, Ulrike); Oppeneer, PM (Oppeneer, Peter M.); Nowak, U (Nowak, Ulrich) | |||||||||||||||
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| Abstract: We explore the possibility of ultrafast, coherent all-optical magnetization switching in antiferromagnets by studying the action of the inverse Faraday effect in CrPt, an easy-plane antiferromagnet. Using a combination of density-functional theory and atomistic spin dynamics simulations, we show how a circularly polarized laser pulse can switch the order parameter of the antiferromagnet within a few hundred femtoseconds. This nonthermal switching takes place on an elliptical path, driven by the staggered magnetic moments induced by the inverse Faraday effect and leading to reliable switching between two perpendicular magnetic states. | |||||||||||||||
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| Record 265 of 414 | ||||||||||||
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| Author(s): Pokorny, V (Pokorny, Vaclav); Stejfa, V (Stejfa, Vojtech); Ruzicka, K (Ruzicka, Kvetoslav); Cervinka, C (Cervinka, Ctirad) | ||||||||||||
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| Abstract: Hydrogen bonding in liquids of the constitution isomers of heptan-1-ol mixed with 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquids (ILs), [C(n)mim][NTf2], is investigated using both computational and experimental techniques. All-atom non-polarizable molecular-dynamics (MD) simulations predict that the hydrogen bonds gradually decay with increasing temperature. This decay is more pronounced for the branched alcohols and in the presence of the ionic liquids. The primary and linear isomer, heptan-1-ol, and its tertiary and bulky analogue 3-ethylpentan-3-ol are identified as the opposite extremes of the spectrum of hydrogen bonding stability in the bulk liquid. While neat heptan-1-ol exhibits strong hydrogen bonding at 350 K, 3-ethylpentan-3-ol is prone to hydrogen bonding decay already at 300 K. The presence of ionic liquids is found to affect the hydrogen bonding comparably as a 50 K temperature increase. Since the heat capacities of the associating liquids are very sensitive to any variation in hydrogen bonding strength and to the character of the hydrogen-bonded clusters in the bulk liquid, the calorimetric effort provides useful experimental data to confirm the results predicted by MD simulations. In this work, excess heat capacity is measured for equimolar single-phase mixtures of alcohols and ILs, and it differs largely in its sign and magnitude for individual heptanol isomers. Temperature trends of the excess heat capacities suggest that the stability of hydrogen bonding for individual heptanol isomers is temperature-shifted, based on their capability of hydrogen bonding. The predicted hierarchy of hydrogen bonding in individual alcohols and its impact on the excess heat capacity trends are qualitatively confirmed via thermodynamic modelling of the associative contribution to the excess heat capacities. These terms are found to predetermine the observed non-monotonous excess heat capacity trends. | ||||||||||||
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| Record 266 of 414 | ||||||
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| Author(s): Oncak, M (Oncak, Milan); Cosic, R (Cosic, Rajko); Kalus, R (Kalus, Rene) | ||||||
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| Abstract: A comparative study has been performed to assess the reliability of a diatomics-in-molecules (DIM) representation of the potential energy surfaces in calculations of the photoabsorption spectra of selected charged helium clusters, He+N (N = 3, 4,10). Results of the computationally cheap DIM approach have been compared to data resulting from accurate ab initio methods (MRCI, EOM-CCSD) and extended basis sets (up to d-aug-cc-pVQZ). Both single-point calculations and averaged photoabsorption spectra calculations have been performed to observe the effect of approximations employed within the DIM approach. DIM predictions of photoabsorption spectra are in a fairly good agreement with the ab initio ones, which seems to indicate that the semi-empirical DIM approach is suitable for simulating larger ionic helium clusters for which more elaborate ab initio models are not practicable. | ||||||
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| Record 267 of 414 | |||||||||
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| Author(s): Peterkova, K (Peterkova, Katerina); Durnik, I (Durnik, Ivo); Marek, R (Marek, Radek); Plavec, J (Plavec, Janez); Podbevsek, P (Podbevsek, Peter) | |||||||||
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| Abstract: Several sequences forming G-quadruplex are highly conserved in regulatory regions of genomes of different organisms and affect various biological processes like gene expression. Diverse G-quadruplex properties can be modulated via their interactionwith small polyaromatic molecules such as pyrene. To investigate how pyrene interacts with G-rich DNAs, we incorporated deoxyuridine nucleotide(s) with a covalently attached pyrene moiety (U-py) into a model system that forms parallel G-quadruplex structures. We individually substituted terminal positions and positions in the pentaloop of the c-kit2 sequence originating from the KIT proto-oncogene with U-py and performed a detailed NMR structural study accompanied with molecular dynamic simulations. Our results showed that incorporation into the pentaloop leads to structural polymorphism and in some cases also thermal destabilization. In contrast, terminal positions were found to cause a substantial thermodynamic stabilization while preserving topology of the parent c-kit2 G-quadruplex. Thermodynamic stabilization results from pi-pi stacking between the polyaromatic core of the pyrene moiety and guanine nucleotides of outer G-quartets. Thanks to the prevalent overall conformation, our structures mimic the G-quadruplex found in human KIT proto-oncogene and could potentially have antiproliferative effects on cancer cells. | |||||||||
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| Author(s): Medvedev, N (Medvedev, N.); Babaev, P (Babaev, P.); Chalupsky, J (Chalupsky, J.); Juha, L (Juha, L.); Volkov, AE (Volkov, A. E.) | ||||||||||||
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| Abstract: Polyethylene (PE) irradiated with femtosecond extreme ultraviolet or X-ray laser pulses in a single-shot damage regime is studied theoretically. The employed microscopic simulation tool XTANT-3 traces nonequilibrium electron kinetics, energy exchange between electrons and atoms, nonthermal modification of interatomic potential, and the induced atomic response. It is found that the nonthermal detachment of hydrogen atoms in bulk PE starts at the threshold deposited dose of similar to 0.05 eV per atom. With an increase in the dose, more hydrogen atoms detach from the carbon backbone. At a dose of similar to 0.3 eV per atom, hydrogen behaves like a liquid flowing around carbon chains. It is accompanied by the appearance of defect energy levels within the band gap. At a dose of similar to 0.5 eV per atom, carbon chains actively bend and cross-link. In the range of doses from similar to 0.5 eV per atom to similar to 0.9 eV per atom, the electronic excitation induces formation of new carbon structures embedded in the hydrogen liquid, such as benzene-like rings. The band gap collapses at such doses, merging the valence and the conduction bands. Finally, at doses above similar to 0.9 eV per atom, the carbon subsystem also melts into liquid. All of these damage mechanisms are mainly nonthermal, triggered by promotion of electrons from the valence into the conduction band of PE. At high doses, however, thermal electron-ion coupling is extremely fast causing equilibration of the electronic and the ionic temperatures within a hundred femtoseconds. | ||||||||||||
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| Record 269 of 414 | |||||||||
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| Author(s): Futera, Z (Futera, Zdenek); English, NJ (English, Niall J.) | |||||||||
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| Abstract: The dynamical properties of physically and chemically adsorbed water molecules at pristine hematite-(001) surfaces have been studied by means of nonequilibrium ab initio molecular dynamics (NE-AIMD) in the NVT ensemble at room temperature, in the presence of externally applied, uniform static electric fields of increasing intensity. The dissociation of water molecules to form chemically adsorbed species was scrutinized, in addition to charge redistribution and Grotthus proton hopping between water molecules. Dynamical properties of the adsorbed water molecules and OH- and H3O+ ions were gauged, such as the hydrogen bonds between protons in water molecules and the bridging oxygen atoms at the hematite surface, as well as the interactions between oxygen atoms in adsorbed water molecules and iron atoms at the hematite surface. The development of Helmholtz charge layers via water breakup at Fe2O3-hematite/water interfaces is also an interesting feature, with the development of protonic conduction on the surface and more bulk-like water. | |||||||||
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| Author(s): Mraz, K (Mraz, Krystof); Bohacek, J (Bohacek, Jan); Resl, O (Resl, Ondrej); Chabicovsky, M (Chabicovsky, Martin); Karimi-Sibaki, E (Karimi-Sibaki, Ebrahim) | |||||||||||||||
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| Abstract: This paper presents a novel method to determine the effective thermal conductivity of porous oxides formed on steel. This advanced approach enables more accurate numerical modeling of the oxide layer impact on the spray cooling of steel. Although the thermal conductivity of the oxide layer is highly influenced by the porous structure of iron oxides, the microstructure of the oxide layer was generally not considered in the studies of the thermal conductivity. In this paper a detailed 3D finite element model of the oxide layer based on a data acquired by computed tomography was created. The image acquisition and image processing are described. An unconventional method of converting image voxels directly into finite elements was used. Two distinct segmentation approaches were implemented and results of simulations were averaged. Obtained temperature-dependent results of the effective conductivity of the oxide layer was used as an input material parameter for the subsequent numerical simulation of the spray cooling of steel. The impact of the oxide layer with different thicknesses was quantified by plotting the temperature-dependent effective heat transfer coefficient. The limitations of the commonly used alternative analytical approach were identified. | |||||||||||||||
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| Record 271 of 414 | ||||||||||||||||||
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| Author(s): Unikandanunni, V (Unikandanunni, Vivek); Medapalli, R (Medapalli, Rajasekhar); Fullerton, EE (Fullerton, Eric E.); Carva, K (Carva, Karel); Oppeneer, PM (Oppeneer, Peter M.); Bonetti, S (Bonetti, Stefano) | ||||||||||||||||||
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Abstract:
We investigate the ultrafast spin dynamics in an epitaxial hcp(1
1 <mml:mo><overbar></mml:mover>00) cobalt thin film. By performing pump-probe magneto-optical measurements with the magnetization along either the easy or hard magnetic axis, we determine the demagnetization and recovery time for the two axes. We observe an average of 33% slower dynamics along the easy magnetization axis, which we attribute to magneto-crystalline anisotropy of the electron-phonon coupling, supported by our ab initio calculations. This points toward an unambiguous and previously undisclosed role of anisotropic electron-lattice coupling in ultrafast magnetism. |
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| Record 272 of 414 | ||||||||||||
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| Author(s): Tolba, AH (Tolba, Amal Hassan); Krupicka, M (Krupicka, Martin); Chudoba, J (Chudoba, Josef); Cibulka, R (Cibulka, Radek) | ||||||||||||
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| Abstract: We report an effective, operationally simple, and environmentally friendly system for the synthesis of tertiary amides by the oxidative coupling of aromatic or aliphatic aldehydes with amines mediated by riboflavin tetraacetate (RFTA), an inexpensive organic photocatalyst, and visible light using oxygen as the sole oxidant. The method is based on the oxidative power of an excited flavin catalyst and the relatively low oxidation potential of the hemiaminal formed by amine to aldehyde addition. | ||||||||||||
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| Record 273 of 414 | |||||||||||||||||||||||||||
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| Author(s): Kolecek, J (Kolecek, Jaroslav); Pialkova, R (Pialkova, Radka); Pialek, L (Pialek, Lubomir); Sulc, M (Sulc, Michal); Hughes, AE (Hughes, Anna E.); Brlik, V (Brlik, Vojtech); Prochazka, P (Prochazka, Petr); Pozgayova, M (Pozgayova, Milica); Capek, M (Capek, Miroslav); Sosnovcova, K (Sosnovcova, Katerina); Stetkova, G (Stetkova, Gabriela); Valterova, R (Valterova, Radka); Honza, M (Honza, Marcel) | |||||||||||||||||||||||||||
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| Abstract: Understanding egg-laying behaviour of brood parasites in space and time can improve our knowledge of interactions between hosts and parasites. However, no studies have combined information on the laying activity of an obligate brood parasite with detailed information on the distribution of host nests within an area and time period. Here, we used molecular methods and analysis of egg phenotypes to determine maternal identity of common cuckoo, Cuculus canorus, eggs and chicks found in the nests of four species of Acrocephalus warblers in consecutive years. The median size of a cuckoo female laying area (calculated as a minimum convex polygon) was correlated negatively with the density of host nests and positively with the number of eggs assigned to a particular female. Cuckoo female laying areas overlapped to a large extent and their size and location did not change between years. Cuckoo females preferentially parasitized host nests located close to their previously parasitized nests and were mostly host specific except for two that parasitized two host species. Future studies should focus on sympatric host and parasite communities with variable densities across different brood-parasitic systems to investigate how population density of hosts affects fitness and evolution of brood parasites. For instance, it remains unknown whether female parasites moving to new sites need to meet a threshold density of a potential host. In addition, young females may be more limited in their egg laying, particularly with respect to the activity of other parasites and hosts, than older females. (c) 2021 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved. | |||||||||||||||||||||||||||
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| Record 274 of 414 | |||||||||
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| Author(s): Oprsal, I (Oprsal, Ivo); Thun, J (Thun, Johannes); Burjanek, J (Burjanek, Jan); Fah, D (Faeh, Donat) | |||||||||
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Abstract:
The Alpe di Roscioro, is a site of an unstable rock slope located above the village of Preonzo in southern Switzerland. There have been numerous rock-slope failures with a major event that happened in May 2012. After that event, several seismic stations were set up at the site of the remaining highly fractured and unstable rock mass. The analysis of continuous seismic recordings has shown a high number of permanent micro-deformations and tilts, recorded by a seismometer located on top of the unstable part of the slope. In terms of the ground motion, the directions of these disturbances are parallel to the mean strike of the mapped fracture network, implying a connection to the ongoing deformations of the rock mass. The static deformation field of the fractured rock mass is modeled by finite-difference method (FD). The FD method enables us to apply a reciprocal approach by tilting the affected body of block 1, closest to the stable massif, by measured values and observing the deformations below the seismometer and in the neighboring blocks. The numerical model explains the following features observed in situ: feature 1. The combination of the horizontal displacement and tilt observed approximately at the same measurement point; feature 2. The block 1 center of rotation is shifted towards SSE by similar to 10 m off its center; feature 3. The sensors placed on the stable massif did not record any micro-deformation and tilt signals above the background noise.
In the light of the numerical modeling, the weak coupling between the micro-tilt active block 1 and neighboring media explains the absence of detected events in the reference stations placed on the stable massif. The simplified "shear and bending" force system FD model, indicates that the aftermath of the May 2012 main failure consisted of numerous episodic elementary relaxations of the SSE part of block 1 after the collapse of its NNW compartment, which was previously connected to it. |
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| Record 275 of 414 | ||||||||||||||||||
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| Author(s): Konecny, L (Konecny, Lukas); Vicha, J (Vicha, Jan); Komorovsky, S (Komorovsky, Stanislav); Ruud, K (Ruud, Kenneth); Repisky, M (Repisky, Michal) | ||||||||||||||||||
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| Abstract: The simulation of X-ray absorption spectra requires both scalar and spin-orbit (SO) relativistic effects to be taken into account, particularly near L- and M-edges where the SO splitting of core p and d orbitals dominates. Four-component Dirac-Coulomb Hamiltonian-based linear damped response time-dependent density functional theory (4c-DR-TDDFT) calculates spectra directly for a selected frequency region while including the relativistic effects variationally, making the method well suited for X-ray applications. In this work, we show that accurate X-ray absorption spectra near L-2,L-3- and M-4,M-5-edges of closed-shell transition metal and actinide compounds with different central atoms, ligands, and oxidation states can be obtained by means of 4c-DR-TDDFT. While the main absorption lines do not change noticeably with the basis set and geometry, the exchange-correlation functional has a strong influence with hybrid functionals performing the best. The energy shift compared to the experiment is shown to depend linearly on the amount of Hartee-Fock exchange with the optimal value being 60% for spectral regions above 1000 eV, providing relative errors below 0.2% and 2% for edge energies and SO splittings, respectively. Finally, the methodology calibrated in this work is used to reproduce the experimental L-2,L-3-edge X-ray absorption spectra of [RuCl2(DMSO)(2)(Im)(2)] and [WCl4(PMePh2)(2)], and resolve the broad bands into separated lines, allowing an interpretation based on ligand field theory and double point groups. These results support 4c-DR-TDDFT as a reliable method for calculating and analyzing X-ray absorption spectra of chemically interesting systems, advance the accuracy of state-of-the art relativistic DFT approaches, and provide a reference for benchmarking more approximate techniques. | ||||||||||||||||||
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| Record 276 of 414 | |||||||||||||||
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| Author(s): Fernandes, SPS (Fernandes, Soraia P. S.); Kovar, P (Kovar, Petr); Psenicka, M (Psenicka, Milan); Silva, AMS (Silva, Artur M. S.); Salonen, LM (Salonen, Laura M.); Espina, B (Espina, Begona) | |||||||||||||||
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| Abstract: Microcystins (MCs), produced by Microcystis sp, are the most commonly detected cyanotoxins in freshwater, and due to their toxicity, worldwide distribution, and persistence in water, an improvement in the monitoring programs for their early detection and removal from water is necessary. To this end, we investigate the performance of three covalent organic frameworks (COFs), TpBD(CF3)(2), TpBD-(NO2)(2), and TpBD-(NH2)(2), for the adsorption of the most common and/or toxic MC derivatives, MC-LR, MC-RR, MC-LA, and MC-YR, from water. While MC-LR and MC-YR can be efficiently adsorbed using all three COF derivatives, high adsorption efficiencies were found for the most lipophilic toxin, MCLA, with TpBD-(NH2)(2), and the most hydrophilic one, MC-RR, with TpBD-(NO2). Theoretical calculations revealed that MC-LA and MC-RR have a tendency to be located mainly on the COF surface, interacting through hydrogen bonds with the amino and nitro functional groups of TpBD-(NH2)(2) and TpBD-(NO2)(2), respectively. TpBD-(NO2)(2) outperforms the adsorbent materials reported for the capture of MC-RR, resulting in an increase in the maximum adsorption capacity by one order of magnitude. TpBD-(NH2)(2) is reported as the first efficient adsorbent material for the capture of MC-LA. Large differences in desorption efficiencies were observed for the MCs with different COFs, highlighting the importance of COF-adsorbate interactions in the material recovery. Herein we show that efficient capture of these toxins from water can be achieved through the proper selection of the COF material. More importantly, this study demonstrates that by careful choice of COF functionalities, specific compounds can be targeted or excluded from a group of analogues, providing insight into the design of more efficient and selective adsorbent materials. | |||||||||||||||
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| Record 277 of 414 | ||||||||||||
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| Author(s): Watfa, D (Watfa, D.); Delagrange, R (Delagrange, R.); Kadlecova, A (Kadlecova, A.); Ferrier, M (Ferrier, M.); Kasumov, A (Kasumov, A.); Bouchiat, H (Bouchiat, H.); Deblock, R (Deblock, R.) | ||||||||||||
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| Abstract: We probe the high frequency emission of a carbon nanotube based Josephson junction and compare it to its dc Josephson current. The ac emission is probed by coupling the carbon nanotube to an on-chip detector (a superconductor-insulator-superconductor junction), via a coplanar waveguide resonator. The measurement of the photoassisted current of the detector gives direct access to the signal emitted by the carbon nanotube. We focus on the gate regions that exhibit Kondo features in the normal state and demonstrate that when the dc supercurrent is enhanced by the Kondo effect, the ac Josephson effect is strongly reduced. This result is compared to numerical renormalization group theory and is attributed to a transition between the singlet ground state and the doublet excited state which is enabled only when the junction is driven out-ofequilibrium by a voltage bias. | ||||||||||||
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| Record 278 of 414 | ||||||||||||||||||
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| Author(s): Zahonova, K (Zahonova, Kristina); Lax, G (Lax, Gordon); Sinha, SD (Sinha, Savar D.); Leonard, G (Leonard, Guy); Richards, TA (Richards, Thomas A.); Lukes, J (Lukes, Julius); Wideman, JG (Wideman, Jeremy G.) | ||||||||||||||||||
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| Abstract: Background The supergroup Euglenozoa unites heterotrophic flagellates from three major clades, kinetoplastids, diplonemids, and euglenids, each of which exhibits extremely divergent mitochondrial characteristics. Mitochondrial genomes (mtDNAs) of euglenids comprise multiple linear chromosomes carrying single genes, whereas mitochondrial chromosomes are circular non-catenated in diplonemids, but circular and catenated in kinetoplastids. In diplonemids and kinetoplastids, mitochondrial mRNAs require extensive and diverse editing and/or trans-splicing to produce mature transcripts. All known euglenozoan mtDNAs exhibit extremely short mitochondrial small (rns) and large (rnl) subunit rRNA genes, and absence of tRNA genes. How these features evolved from an ancestral bacteria-like circular mitochondrial genome remains unanswered. Results We sequenced and assembled 20 euglenozoan single-cell amplified genomes (SAGs). In our phylogenetic and phylogenomic analyses, three SAGs were placed within kinetoplastids, 14 within diplonemids, one (EU2) within euglenids, and two SAGs with nearly identical small subunit rRNA gene (18S) sequences (EU17/18) branched as either a basal lineage of euglenids, or as a sister to all euglenozoans. Near-complete mitochondrial genomes were identified in EU2 and EU17/18. Surprisingly, both EU2 and EU17/18 mitochondrial contigs contained multiple genes and one tRNA gene. Furthermore, EU17/18 mtDNA possessed several features unique among euglenozoans including full-length rns and rnl genes, six mitoribosomal genes, and nad11, all likely on a single chromosome. Conclusions Our data strongly suggest that EU17/18 is an early-branching euglenozoan with numerous ancestral mitochondrial features. Collectively these data contribute to untangling the early evolution of euglenozoan mitochondria. | ||||||||||||||||||
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| Record 279 of 414 | |||||||||||||||
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| Author(s): Grillova, L (Grillova, Linda); Robinson, MT (Robinson, Matthew T.); Chanthongthip, A (Chanthongthip, Anisone); Vincent, AT (Vincent, Antony T.); Nieves, C (Nieves, Cecilia); Oppelt, J (Oppelt, Jan); Mariet, JF (Mariet, Jean-Francois); Lorioux, C (Lorioux, Celine); Vongsouvath, M (Vongsouvath, Manivanh); Mayxay, M (Mayxay, Mayfong); Phonemeexay, O (Phonemeexay, Ooyanong); Rattanavong, S (Rattanavong, Sayaphet); Phommasone, K (Phommasone, Koukeo); Douangnouvong, A (Douangnouvong, Anousone); Smajs, D (Smajs, David); Veyrier, FJ (Veyrier, Frederic J.); Newton, PN (Newton, Paul N.); Picardeau, M (Picardeau, Mathieu) | |||||||||||||||
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Abstract:
BackgroundAlthough Southeast Asia is one of the most leptospirosis afflicted regions, little is known about the diversity and molecular epidemiology of the causative agents of this widespread and emerging zoonotic disease. Methodology/Principal findingsWe used whole genome sequencing to examine genetic variation in 75 Leptospira strains isolated from patients in the Lao PDR (Laos) between 2006 and 2017.Eleven serogroups from 4 Leptospira species and 43 cgMLST-defined clonal groups (CGs) were identified. The most prevalent CG was CG272 (n = 18, 26.8%), composed of L. interrogans serogroup Autumnalis isolates. This genotype was recovered throughout the 12-year period and was associated with deaths, and with a large outbreak in neighbouring Thailand. Genome analysis reveals that the CG272 strains form a highly clonal group of strains that have, for yet unknown reasons, recently spread in Laos and Thailand. Additionally, accessory genes clearly discriminate CG272 strains from the other Leptospira strains. Conclusions/SignificanceThe present study reveals a high diversity of Leptospira genotypes in Laos, thus extending our current knowledge of the pan- and core-genomes of these life-threatening pathogens. Our results demonstrate that the CG272 strains belong to a unique clonal group, which probably evolved through clonal expansion following niche adaptation. Additional epidemiological studies are required to better evaluate the spread of this genotype in Southeast Asia. To further investigate the key factors driving the virulence and spread of these pathogens, more intense genomic surveillance is needed, combining detailed clinical and epidemiological data.
Author summaryPathogenic Leptospira are the causative agents for leptospirosis, a neglected and emerging zoonosis occurring worldwide. In this study, we investigated the genetic diversity of Leptospira strains isolated from patients over a 12-year period in Lao PDR. Our genome analysis revealed a high diversity of Leptospira genotypes in this endemic country for leptospirosis, including a group of clonal strains which was responsible for a large outbreak in neighboring Thailand. Further progress in our understanding of the epidemiology of Leptospira circulating genotypes should contribute to the implementation of prevention and intervention measures to reduce the risk of leptospirosis transmission. |
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| Author(s): Novotny, J (Novotny, Jan); Jeremias, L (Jeremias, Lukas); Nimax, P (Nimax, Patrick); Komorovsky, S (Komorovsky, Stanislav); Heinmaa, I (Heinmaa, Ivo); Marek, R (Marek, Radek) | |||||||||||||||||||||
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| Abstract: Nuclear magnetic resonance (NMR) spectroscopy of paramagnetic molecules provides detailed information about their molecular and electron-spin structure. The paramagnetic NMR spectrum is a very rich source of information about the hyperfine interaction between the atomic nuclei and the unpaired electron density. The Fermi-contact contribution to ligand hyperfine NMR shifts is particularly informative about the nature of the metal-ligand bonding and the structural arrangements of the ligands coordinated to the metal center. In this account, we provide a detailed experimental and theoretical NMR study of compounds of Cr(III) and Cu(II) coordinated with substituted acetylacetonate (acac) ligands in the solid state. For the first time, we report the experimental observation of extremely paramagnetically deshielded C-13 NMR resonances for these compounds in the range of 900-1200 ppm. We demonstrate an excellent agreement between the experimental NMR shifts and those calculated using relativistic density-functional theory. Crystal packing is shown to significantly influence the NMR shifts in the solid state, as demonstrated by theoretical calculations of various supramolecular clusters. The resonances are assigned to individual atoms in octahedral Cr(acac)(3) and square-planar Cu(acac)(2) compounds and interpreted by different electron configurations and magnetizations at the central metal atoms resulting in different spin delocalizations and polarizations of the ligand atoms. Further, effects of substituents on the C-13 NMR resonance of the ipso carbon atom reaching almost 700 ppm for Cr(acac)(3) compounds are interpreted based on the analysis of Fermi-contact hyperfine contributions. | |||||||||||||||||||||
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| Author(s): Benda, J (Benda, Jakub); Masin, Z (Masin, Zdenek) | ||||||
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| Abstract: We formulate a computationally efficient time-independent method based on the multi-electron molecular R-matrix formalism. This method is used to calculate transition matrix elements for the multi-photon ionization of atoms and molecules under the influence of a perturbative field. The method relies on the partitioning of space which allows us to calculate the infinite-range free-free dipole integrals analytically in the outer region, beyond the range of the initial bound wave function. This approach is valid for an arbitrary order, that is, any number of photons absorbed both in the bound and the continuum part of the spectrum (below- and above-threshold ionization). We calculate generalized multi-photon cross sections and angular distributions of different systems (H, He, H2, CO2) and validate our approach by comparison with data from the literature. | ||||||
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| Author(s): Mangiola, S (Mangiola, Stefano); McCoy, P (McCoy, Patrick); Modrak, M (Modrak, Martin); Souza-Fonseca-Guimaraes, F (Souza-Fonseca-Guimaraes, Fernando); Blashki, D (Blashki, Daniel); Stuchbery, R (Stuchbery, Ryan); Keam, SP (Keam, Simon P.); Kerger, M (Kerger, Michael); Chow, K (Chow, Ken); Nasa, C (Nasa, Chayanica); Le Page, M (Le Page, Melanie); Lister, N (Lister, Natalie); Monard, S (Monard, Simon); Peters, J (Peters, Justin); Dundee, P (Dundee, Phil); Williams, SG (Williams, Scott G.); Costello, AJ (Costello, Anthony J.); Neeson, PJ (Neeson, Paul J.); Pal, B (Pal, Bhupinder); Huntington, ND (Huntington, Nicholas D.); Corcoran, NM (Corcoran, Niall M.); Papenfuss, AT (Papenfuss, Anthony T.); Hovens, CM (Hovens, Christopher M.) | |||||||||||||||
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| Abstract: Background Prostate cancer is caused by genomic aberrations in normal epithelial cells, however clinical translation of findings from analyses of cancer cells alone has been very limited. A deeper understanding of the tumour microenvironment is needed to identify the key drivers of disease progression and reveal novel therapeutic opportunities. Results In this study, the experimental enrichment of selected cell-types, the development of a Bayesian inference model for continuous differential transcript abundance, and multiplex immunohistochemistry permitted us to define the transcriptional landscape of the prostate cancer microenvironment along the disease progression axis. An important role of monocytes and macrophages in prostate cancer progression and disease recurrence was uncovered, supported by both transcriptional landscape findings and by differential tissue composition analyses. These findings were corroborated and validated by spatial analyses at the single-cell level using multiplex immunohistochemistry. Conclusions This study advances our knowledge concerning the role of monocyte-derived recruitment in primary prostate cancer, and supports their key role in disease progression, patient survival and prostate microenvironment immune modulation. | |||||||||||||||
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| Author(s): Hariki, A (Hariki, Atsushi); Ahn, KH (Ahn, Kyo-Hoon); Kunes, J (Kunes, Jan) | |||||||||
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| Abstract: We present a computational study of PbCoO3 at ambient and elevated pressure. We employ the static and dynamic treatment of local correlation in the form of density functional theory + U (DFT+U) and + dynamical mean-field theory (DFT+DMFT). Our results capture the experimentally observed crystal structures and identify the unsaturated Pb 6s - O 2p bonds as the driving force beyond the complex physics of PbCoO3. We provide a geometrical analysis of the structural distortions and we discuss their implications, in particular the internal doping, which triggers a transition between phases with and without local moments and a site-selective Mott transition in the low-pressure phase. | |||||||||
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| Author(s): Prokacheva, VM (Prokacheva, Varvara M.); Rud, OV (Rud, Oleg V.); Uhlik, F (Uhlik, Filip); Borisov, OV (Borisov, Oleg V.) | |||||||||
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| Abstract: By this article, we continue studying weak polyelectrolyte hydrogels and their application as a desalination agent. We modeled the desalination process as a four-step reversible thermodynamic cycle transferring ions from a low salinity solution to a high salinity one. The cycle implies reversibility at any stage, therefore the method can achieve the maximum thermodynamic efficiency, comparable to the reverse osmosis. As a driving force for ions movement, we use the fact that compression of the gel leads to a decrease in the gel ionization degree, and therefore to a release of ions entrapped in the gel. We considered the gel composed of ionogenic units modified by hydrophobic pendants and showed that this modification significantly increases the number of transferred ions. This increase is caused by a first-order phase transition originated from an interplay between repulsive electrostatic and attractive steric interactions. The transition happens during hydrogel compression. At a certain pressure, the gel collapses abruptly, changing its volume almost to that of a dry state, and releases almost all ions collected inside. Employing the phase transition allows us to model the desalination cycle, which transfers a much larger number of ions and works at rather low pressures <10bar. | |||||||||
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| Record 285 of 414 |
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| Author(s): Cmejla, J (Cmejla, Jaroslav); Kounovsky, T (Kounovsky, Tomas); Gannot, S (Gannot, Sharon); Koldovsky, Z (Koldovsky, Zbynek); Tandeitnik, P (Tandeitnik, Pinchas) |
| Book Group Author(s): IEEE |
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| Abstract: We introduce a database of multi-channel recordings performed in an acoustic lab with adjustable reverberation time. The recordings provide detailed information about room acoustics for positions of a source within a confined area. In particular, the main positions correspond to 4104 vertices of a cube-shaped dense grid within a 46 x 36 x 32 cm volume. The database can serve for simulations of a real-world situations and as a tool for detailed analyses of beampatterns of spatial processing methods. It could be used also for training and testing of mathematical models of the acoustic field. |
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| Conference Sponsors: European Assoc Signal Proc |
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| ISBN: 978-9-0827-9705-3 |
| Record 286 of 414 |
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| Author(s): Ghodrati, H (Ghodrati, Hanieh); Allolio, C (Allolio, Christoph) |
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| Abstract: Noncovalent functionalization of semiconductors is an effective way to modify their electronic properties. In this paper, we determine factors that sensitize the band gap of phosphorene, a representative two-dimensional (2D) material, to the permittivity of the solvent. This enables an ab initio design approach for polarity sensing devices. Charge transfer (CT) to certain cationic conjugated acceptor substrates is highly sensitive to the solvation at the surface. This provides regulation of their acceptor properties by the solvent, which turns out to have a large effect on the material's band gap. As a result, we predict that highly electropositive cationic adsorbates, such as aromatic viologens, have the potential for polarity sensing across a wide range of permittivities. Time-dependent density-functional theory (TD-DFT) calculations of their absorption spectra on phosphorene using hybrid functionals show solvent-sensitive excitations inside the near-infrared (NIR) region, as is desirable for high penetration bioimaging. We compare our results to a representative set of acceptor molecules, including well-established electron acceptors like tetracyanoquinodimethane(TCNQ), that do not exhibit significant polarity response. |
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| Record 287 of 414 | |||||||||
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| Author(s): Hauerova, R (Hauerova, Radka); Hauer, T (Hauer, Tomas); Kastovsky, J (Kastovsky, Jan); Komarek, J (Komarek, Jiri); Lepsova-Skacelova, O (Lepsova-Skacelova, Olga); Mares, J (Mares, Jan) | |||||||||
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| Abstract: Oscillatoria has long been known to be polyphyletic. After recent resequencing of the reference strain for this genus, many Oscillatoria-like groups phylogenetically distant from the type species O. princeps remained unresolved. Here we describe one of these groups as a new genus Tenebriella. Most of the studied strains originate from Central Europe, where they are able to form prominent microbial mats. Despite the overall Oscillatoria-like morphology, Tenebriella can be distinguished by darker trichomes and forms a separate monophyletic clade in phylogenies inferred from the 16S rRNA gene and two additional loci (rpoC1, rbcLX). Within Tenebriella we recognize two new species differing from each other by morphological and ecological characteristics. First species does not fit any known taxon description, and thus is described as a new species T. amphibia. The latter one corresponds with the information available for Oscillatoria curviceps Agardh ex Gomont, and thus new combination T. curviceps is proposed. The phylogenetic analyses of the 16S-23S ITS region together with the comparison of the hypothetical secondary structures confirmed recognition of these two species and additionally revealed presence of a morphologically cryptic species Tenebriella sp. The results corroborate frequent recurrence of convergent morphotypes in the evolution of cyanobacteria and justify further exploration even of the intensively studied European freshwaters using molecular phylogenetics to discover new and ecologically relevant taxa. | |||||||||
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| Author(s): Marakatti, VS (Marakatti, Vijaykumar S.); Klimes, J (Klimes, Jiri); Kasinathan, P (Kasinathan, Palraj); Sorathia, K (Sorathia, Kesha); Tew, DP (Tew, David P.); Gaigneaux, EM (Gaigneaux, Eric M.) | |||||||||||||||
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| Abstract: The choice of an appropriate solvent in heterogeneous catalysis is not always straightforward but it affects significantly the activity and selectivity in organic reactions. Here we show that the acceptor number (AN) and donor number (DN) make the selection of solvent robust and competitive compared to traditional solvent properties such as dielectric constant, polarity and nature. The conversion rates measured in selected acid or base-catalysed reactions in the liquid phase (alkylation, acylation, esterification, condensation) consistently vary with the AN or DN of the solvents in which they are achieved. The impact of the AN and DN in these reactions was understood by addressing the interactions between the catalyst, solvents, and reactants through spectroscopic (FTIR and UV-vis) techniques and DFT simulations. The association between the AN and DN, and the catalytic performance is shown to proceed via the strength of the non-covalent hydrogen bond established between the partners of the reaction. The strength of hydrogen bonds of the solvent with the catalyst influences the acid sites of the catalyst directly and by this means plays a crucial role during the reaction. These findings build strong fundamental scientific information on the solvent effects in heterogeneous catalysis. | |||||||||||||||
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| Record 289 of 414 | ||||||||||||
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| Author(s): Yahagi, Y (Yahagi, Yuta); Miura, D (Miura, Daisuke); Sakuma, A (Sakuma, Akimasa); Zelezny, J (Zelezny, Jakub) | ||||||||||||
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| Abstract: The spin Hall effect (SHE) is responsible for electrical spin current generation, which is a key concept of modern spintronics. We present a theoretical study of an extrinsic mechanism of SHE arising from a spindependent s-d scattering in ferromagnets. In order to investigate the spin conductivity in a ferromagnetic 3d alloy model, we employ a microscopic transport theory based on the Kubo formula and the averaged T-matrix approximation. From the model, we derived an extrinsic mechanism that contributes to both the SHE and the time-reversal odd SHE known as the magnetic SHE. This mechanism can be understood as the contribution from anisotropic (spatial-dependent) spin-flip scattering due to the combination of the orbital-dependent anisotropic shape of s-d hybridization and spin flipping, with the orbital shift caused by spin-orbit interaction with the d orbitals. We also show that this mechanism is valid under crystal-field splitting among the d orbitals in either the cubic or tetragonal symmetry. | ||||||||||||
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| Record 290 of 414 | ||||||||||||||||||
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| Author(s): Bora, P (Bora, Pablo); Gahurova, L (Gahurova, Lenka); Masek, T (Masek, Tomas); Hauserova, A (Hauserova, Andrea); Potesil, D (Potesil, David); Jansova, D (Jansova, Denisa); Susor, A (Susor, Andrej); Zdrahal, Z (Zdrahal, Zbynek); Ajduk, A (Ajduk, Anna); Pospisek, M (Pospisek, Martin); Bruce, AW (Bruce, Alexander W.) | ||||||||||||||||||
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| Abstract: Successful specification of the two mouse blastocyst inner cell mass (ICM) lineages (the primitive endoderm (PrE) and epiblast) is a prerequisite for continued development and requires active fibroblast growth factor 4 (FGF4) signaling. Previously, we identified a role for p38 mitogen-activated protein kinases (p38-MAPKs) during PrE differentiation, but the underlying mechanisms have remained unresolved. Here, we report an early blastocyst window of p38-MAPK activity that is required to regulate ribosome-related gene expression, rRNA precursor processing, polysome formation and protein translation. We show that p38-MAPK inhibition-induced PrE phenotypes can be partially rescued by activating the translational regulator mTOR. However, similar PrE phenotypes associated with extracellular signal-regulated kinase (ERK) pathway inhibition targeting active FGF4 signaling are not affected by mTOR activation. These data indicate a specific role for p38-MAPKs in providing a permissive translational environment during mouse blastocyst PrE differentiation that is distinct from classically reported FGF4-based mechanisms. Bora et al. show that an early blastocyst window of p38-MAPK activity regulates ribosome-related gene expression, rRNA precursor processing, polysome formation, and protein translation. This study suggests a distinct role of p38-MAPKs for providing a permissive translational environment during mouse blastocyst primitive endoderm differentiation. | ||||||||||||||||||
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| Record 291 of 414 | ||||||
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| Author(s): Pusztai, M (Pusztai, Martin); Skaloud, P (Skaloud, Pavel) | ||||||
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| Abstract: Until recently, there was no agreement on species delimitation within the morphologically similar chrysophycean genera Uroglena, Uroglenopsis and Urostipulosphaera. In this study, we aimed at a modern taxonomic revision based on the combination of morphological characters (ultrastructure of cysts, cell and colony features) and a multigene phylogeny (SSU, ITS rDNA and rbcL sequences), with ecology taken into account. Of more than 650 explored localities, only approximately one in 10 hosted a viable and detectable population of these colonial chrysophytes at the time of sampling. We established and examined 189 short-term cultures along with single colony isolates, derived mostly from blooming or encysting populations. We obtained the cyst morphology for four species and two lineages of Uroglena, two species of Uroglenopsis, and four species of Urostipulosphaera. A total of 12 resolved lineages could be attributed to previously described species or new species (Uroglena imitata sp. nov., Urostipulosphaera granulata sp. nov.). Based on our molecular analyses and morphological observations, we assign all the previously described Uroglena-like taxa to newly recognized genera and propose a key to identification. Consequently, Uroglena now includes 16 species and two varieties, Uroglenopsis contains four species and Urostipulosphaera encompasses nine species. Within Uroglena and Urostipulosphaera, species are defined by the ultrastructure of their cysts. On the contrary, as Uroglenopsis has simple cysts, species are defined by cell and colony characteristics. | ||||||
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| Record 292 of 414 | |||||||||||||||
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| Author(s): Bera, K (Bera, Krishnendu); Reeda, VSJ (Reeda, V. S. Jeba); Babila, PR (Babila, P. R.); Dinesh, DC (Dinesh, Dhurvas Chandrasekaran); Hritz, J (Hritz, Jozef); Karthick, T (Karthick, T.) | |||||||||||||||
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| Abstract: The work attempts to recognise the possible inhibitors against Papain-like protease (PLpro) and 3-Chymotrypsin-like protease (3CL(pro)) of SARS-CoV-2 to combat infectious COVID-19 virus using in silico studies. These two proteases are predominantly involved in the virus replication cycle; hence they are considered as potential drug targets. The virtual dock screening was performed for 53 selected drugs. The drugs with higher binding energy and oriented in the vicinity of active binding sites were selected for finding thermal stability using molecular dynamics (MD) simulation. The docking result reflects that the drugs A17 (Dasabuvir) and A34 (Methisazone) bind with PLpro and the drugs A17 and A53 (Vaniprevir) bind with 3CL(pro) with higher binding affinities. The MD simulation and principal component analysis show that the drug A17 has stable dynamic behaviour with both proteins over the 300 ns time-scale. The binding free energy of complexes was predicted from the last 100 ns trajectories using MM/PBSA. The predicted binding free energy of PLPro-A17 (Dasabuvir) and PLpro-A34 complexes (Methisazone) were -16.1 kcal/mol and -12.3 kcal/mol, respectively and -41.3 kcal/mol and -11.9 kcal/mol for 3CL(pro)-A17 (Dasabuvir) and 3CL(pro)-A53 (Vaniprevir) complexes, respectively. However, further experimental validation is required to confirm their inhibitory activities against SARS-CoV-2 causing COVID-19. | |||||||||||||||
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| Record 293 of 414 | |||||||||||||||||||||
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| Author(s): Gonzalez-Hernandez, R (Gonzalez-Hernandez, Rafael); Smejkal, L (Smejkal, Libor); Vyborny, K (Vyborny, Karel); Yahagi, Y (Yahagi, Yuta); Sinova, J (Sinova, Jairo); Jungwirth, T (Jungwirth, Tomas); Zelezny, J (Zelezny, Jakub) | |||||||||||||||||||||
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| Abstract: Spin-current generation by electrical means is among the core phenomena driving the field of spintronics. Using ab initio calculations we show that a room-temperature metallic collinear antiferro-magnet RuO2 allows for highly efficient spin-current generation, arising from anisotropically spin-split bands with conserved up and down spins along the Neel vector axis. The zero net moment antiferromagnet acts as an electrical spin splitter with a 34 degrees propagation angle between spin-up and spin-down currents. The corresponding spin conductivity is a factor of 3 larger than the record value from a survey of 20 000 nonmagnetic spin-Hall materials. We propose a versatile spin-splitter-torque concept circumventing limitations of spin-transfer and spin-orbit torques in present magnetic memory devices. | |||||||||||||||||||||
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| Record 294 of 414 | |||||||||
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| Author(s): Gonzalez-Rodriguez, E (Gonzalez-Rodriguez, Edgar); Guzman-Juarez, B (Guzman-Juarez, Brenda); Miranda-Olvera, M (Miranda-Olvera, Montserrat); Carreon-Castro, MD (Carreon-Castro, Maria del Pilar); Maldonado-Dominguez, M (Maldonado-Dominguez, Mauricio); Arcos-Ramos, R (Arcos-Ramos, Rafael); Farfan, N (Farfan, Norberto); Santillan, R (Santillan, Rosa) | |||||||||
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| Abstract: A family of eight rc-extended push-pull coumarins with cross-conjugated (amide) and directly conjugated (p-phenylene, alkyne, alkene) bridges were synthesized through a convergent strategy. Using an experimentally calibrated computational protocol, their UV-Visible light absorption and emission spectra in solution were investigated. Remarkably, amide-, alkyne- and alkene-bridges undergo comparable vertical excitations. The different nature of these bridges manifests during excited-state relaxation and fluorescence. We predict that these molecules can serve as building blocks for p-type semiconductors with low reorganization energies, below 0.2 eV. Since solid-state self-assembly is crucial for this application, we examined the effect of the rc-bridge over the supramolecular organization in this family of compounds to determine if stacking prevails in these rc-extended coumarin derivatives. Amide and alkyne spacers allow coplanar conformations which crystallize readily; p-phenylene hinders planarity yet allows facile crystallization; alkene-bridged molecules eluded all crystallization attempts. All the crystals obtained feature dense face-to-face 1t-stacking with 3.5-3.7 A interlayer distances, expected to facilitate charge transfer processes in the solid state. (c) 2021 Elsevier B.V. All rights reserved. | |||||||||
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| Record 295 of 414 | |||||||||
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| Author(s): Tosner, Z (Tosner, Zdenek); Brandl, MJ (Brandl, Matthias J.); Blahut, J (Blahut, Jan); Glaser, SJ (Glaser, Steffen J.); Reif, B (Reif, Bernd) | |||||||||
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| Abstract: Dipolar recoupling is a central concept in the nuclear magnetic resonance spectroscopy of powdered solids and is used to establish correlations between different nuclei by magnetization transfer. The efficiency of conventional cross-polarization methods is low because of the inherent radio frequency (rf) field inhomogeneity present in the magic angle spinning (MAS) experiments and the large chemical shift anisotropies at high magnetic fields. Very high transfer efficiencies can be obtained using optimal control-derived experiments. These sequences had to be optimized individually for a particular MAS frequency. We show that by adjusting the length and the rf field amplitude of the shaped pulse synchronously with sample rotation, optimal control sequences can be successfully applied over a range of MAS frequencies without the need of reoptimization. This feature greatly enhances their applicability on spectrometers operating at differing external fields where the MAS frequency needs to be adjusted to avoid detrimental resonance effects. | |||||||||
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| Record 296 of 414 |
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| Author(s): Fornuskova, A (Fornuskova, Alena); Hiadlovska, Z (Hiadlovska, Zuzana); Macholan, M (Macholan, Milos); Pialek, J (Pialek, Jaroslav); de Bellocq, JG (de Bellocq, Joelle Gouy) |
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| Abstract: Lymphocytic choriomeningitis virus (LCMV) is an Old World mammarenavirus found worldwide because of its association with the house mouse. When LCMV spills over to immunocompetent humans, the virus can cause aseptic meningitis; in immunocompromised persons, systemic infection and death can occur. Central Europe is a strategic location for the study of LCMV evolutionary history and host specificity because of the presence of a hybrid zone (genetic barrier) between 2 house mouse subspecies, Mus musculus musculus and M. musculus domesticus. We report LCMV prevalence in natural mouse populations from a Czech Republic-Germany transect and genomic characterization of 2 new LCMV variants from the Czech Republic. We demonstrate that the main division in the LCMV phylogenetic tree corresponds to mouse host subspecies and, when the virus is found in human hosts, the mouse subspecies found at the spillover location. Therefore, LCMV strains infecting humans can be predicted by the genetic structure of house mice. |
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| Record 297 of 414 | |||||||||
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| Author(s): Elsayed, M (Elsayed, Mohamed); Staab, TEM (Staab, Torsten E. M.); Cizek, J (Cizek, Jakub); Krause-Rehberg, R (Krause-Rehberg, Reinhard) | |||||||||
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| Abstract: To study the vacancy-solute-atom interaction, diluted Al-In and Al-Sn alloys with 0.005 and 0.025 at.% indium/tin cast from very high purity elements were investigated by positron annihilation spectroscopy (PAS). Therefore, the alloys have been solution heat treated at temperatures ranging from 320 to 620 degrees C and then rapidly quenched into ice water freezing-in most thermal vacancies. Positron annihilation life-time (PALS) and coincidence Doppler broadening spectroscopies (CDBS) were combined to unambiguously identify vacancy-solute-atom complexes. For enabling a direct comparison to experiment, we did employ ab-initio DFT calculations of vacancy-solute-atom complexes providing relaxed atomic coordinates, which are used to calculate PAS annihilation parameters. In the as-quenched state vacancy-solute-atom pairs as well as vacancy clusters were observed in both alloys for all concentrations. During isochronal annealing vacancy clusters, formed during quenching, dissolved at about 130 degrees C, leaving vacancy-solute-atoms complexes as the only remaining defects. Thus, we could unambiguously identify those by a combination of PALS and CDBS with ab-initio calculations. Employing isothermal annealing the binding energy E-B of vacancies to In and Sn solute atoms was determined experimentally by PALS as well as by ab-initio calculations. We find from our experiments E-B = (0.20 +/- 0.03) and (0.32 +/- 0.10) eV for In and Sn, respectively, which is in very good agreement with our ab-initio calculations giving 0.23 and 0.26 eV, respectively. Our results clearly identified vacancy-In/Sn complexes as responsible for the retardation of vacancy migration after quenching. The vacancies bound to In and Sn solute-atoms are released around 150 degrees C shifting, when added to AlCu alloys as trace elements, the transport of copper atoms to higher temperatures necessary for the formation of finely distributed "precipitates", which efficiently strengthen this kind of alloys. (C) 2021 The Authors. Published by Elsevier Ltd on behalf of Acta Materialia Inc. | |||||||||
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| Author(s): Kmentova, N (Kmentova, Nikol); Hahn, C (Hahn, Christoph); Koblmuller, S (Koblmuller, Stephan); Zimmermann, H (Zimmermann, Holger); Vorel, J (Vorel, Jiri); Artois, T (Artois, Tom); Gelnar, M (Gelnar, Milan); Vanhove, MPM (Vanhove, Maarten P. M.) | |||||||||||||||
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| Abstract: Simple Summary Species richness in open water areas is generally lower than in coastal zones. Fish parasites have been targeted as biological tags potentially magnifying biological patterns of their hosts including long-distance migrations notoriously difficult to trace. Lake Tanganyika (Africa) is an ideal place to study general mechanisms of host-parasite interactions in an open water environment and Cichlidogyrus, a monogenean flatworm lineage also present in Lake Tanganyika, has been proposed as a model system to study parasite-host relationships. The present study revealed the lake-wide occurrence (600 km) of Cichlidogyrus casuarinus, a parasite with a broad host range infecting pelagic fishes endemic to Lake Tanganyika. Our comparative approach highlighted incongruence between morphological and genetic differentiation of the populations of Cichlidogyrus casuarinus. Our results show a limitation of the parasite's magnifying potential for the focal host species due to the parasites' broad host range including highly mobile host species. Using different sequencing technologies, the study further provides the first assessment of the genetic variation of mitochondrial data in Cichlidogyrus showing contrasting patterns within and between parasite species. Given the now considerable baseline knowledge on its morphological and genetic variation, we propose C. casuarinus as a model to study (1) mechanisms driving host range and (2) the role of phenotypic plasticity in diversification and speciation. Little phylogeographic structure is presumed for highly mobile species in pelagic zones. Lake Tanganyika is a unique ecosystem with a speciose and largely endemic fauna famous for its remarkable evolutionary history. In bathybatine cichlid fishes, the pattern of lake-wide population differentiation differs among species. We assessed the congruence between the phylogeographic structure of bathybatine cichlids and their parasitic flatworm Cichlidogyrus casuarinus to test the magnifying glass hypothesis. Additionally, we evaluated the use of a PoolSeq approach to study intraspecific variation in dactylogyrid monogeneans. The lake-wide population structure of C. casuarinus ex Hemibates stenosoma was assessed based on a portion of the cox1 gene combined with morphological characterisation. Additionally, intraspecific mitogenomic variation among 80 parasite samples from one spatially constrained metapopulation was assessed using shotgun NGS. While no clear geographic genetic structure was detected in parasites, both geographic and host-related phenotypic variation was apparent. The incongruence with the genetic north-south gradient observed in H. stenosoma may be explained by the broad host range of this flatworm including eupelagic bathybatine host species that form panmictic populations across the lake. In addition, we present the first parasite mitogenome from Lake Tanganyika and propose a methodological framework for studying the intraspecific mitogenomic variation of dactylogyrid monogeneans. | |||||||||||||||
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| Author(s): Starha, P (Starha, Pavel); Drahos, B (Drahos, Bohuslav); Herchel, R (Herchel, Radovan) | ||||||||||||
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| Abstract: Complex cis-[PtI2(NH3)(pic)] (1; pic = 2-methylpyridine), a diiodido analogue of clinically studied picoplatin (2), is unstable in solution, which is intriguingly connected with the release of its pic ligand. This observation complicates the biological testing of e.g. cytotoxicity in human cancer cells for 1. | ||||||||||||
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| Author(s): Gregor, J (Gregor, Jiri); Radilova, K (Radilova, Katerina); Brynda, J (Brynda, Jiri); Fanfrlik, J (Fanfrlik, Jindrich); Konvalinka, J (Konvalinka, Jan); Kozisek, M (Kozisek, Milan) | |||||||||||||||
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| Abstract: Influenza A virus (IAV) encodes a polymerase composed of three subunits: PA, with endonuclease activity, PB1 with polymerase activity and PB2 with host RNA five-prime cap binding site. Their cooperation and stepwise activation include a process called cap-snatching, which is a crucial step in the IAV life cycle. Reproduction of IAV can be blocked by disrupting the interaction between the PB2 domain and the five-prime cap. An inhibitor of this interaction called pimodivir (VX-787) recently entered the third phase of clinical trial; however, several mutations in PB2 that cause resistance to pimodivir were observed. First major mutation, F404Y, causing resistance was identified during preclinical testing, next the mutation M431I was identified in patients during the second phase of clinical trials. The mutation H357N was identified during testing of IAV strains at Centers for Disease Control and Prevention. We set out to provide a structural and thermodynamic analysis of the interactions between cap-binding domain of PB2 wild-type and PB2 variants bearing these mutations and pimodivir. Here we present four crystal structures of PB2-WT, PB2-F404Y, PB2-M431I and PB2-H357N in complex with pimodivir. We have thermodynamically analysed all PB2 variants and proposed the effect of these mutations on thermodynamic parameters of these interactions and pimodivir resistance development. These data will contribute to understanding the effect of these missense mutations to the resistance development and help to design next generation inhibitors. | |||||||||||||||
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| Record 301 of 414 | |||||||||||||||||||||||||||||||||
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| Author(s): Mullett, MS (Mullett, Martin S.); Drenkhan, R (Drenkhan, Rein); Adamson, K (Adamson, Kalev); Boron, P (Boron, Piotr); Lenart-Boron, A (Lenart-Boron, Anna); Barnes, I (Barnes, Irene); Tomsovsky, M (Tomsovsky, Michal); Janosikova, Z (Janosikova, Zuzana); Adamcikova, K (Adamcikova, Katarina); Ondruskova, E (Ondruskova, Emilia); Queloz, V (Queloz, Valentin); Piskur, B (Piskur, Barbara); Musolin, DL (Musolin, Dmitry L.); Davydenko, K (Davydenko, Kateryna); Georgieva, M (Georgieva, Margarita); Schmitz, S (Schmitz, Sophie); Kacergius, A (Kacergius, Audrius); Ghelardini, L (Ghelardini, Luisa); Kranjec Orlovic, J (Kranjec Orlovic, Jelena); Muller, M (Muller, Michael); Oskay, F (Oskay, Funda); Hauptman, T (Hauptman, Tine); Halasz, A (Halasz, Agnes); Markovskaja, S (Markovskaja, Svetlana); Solheim, H (Solheim, Halvor); Vuorinen, M (Vuorinen, Martti); Heinzelmann, R (Heinzelmann, Renate); Hamelin, RC (Hamelin, Richard C.); Konecny, A (Konecny, Adam) | |||||||||||||||||||||||||||||||||
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| Abstract: Dothistroma septosporum, the primary causal agent of Dothistroma needle blight, is one of the most significant foliar pathogens of pine worldwide. Its wide host and environmental ranges have led to its global success as a pathogen and severe economic damage to pine forests in many regions. This comprehensive global population study elucidated the historical migration pathways of the pathogen to reveal the Eurasian origin of the fungus. When over 3800 isolates were examined, three major population clusters were revealed: North America, Western Europe, and Eastern Europe, with distinct subclusters in the highly diverse Eastern European cluster. Modeling of historical scenarios using approximate Bayesian computation revealed the North American cluster was derived from an ancestral population in Eurasia. The Northeastern European subcluster was shown to be ancestral to all other European clusters and subclusters. The Turkish subcluster diverged first, followed by the Central European subcluster, then the Western European cluster, which has subsequently spread to much of the Southern Hemisphere. All clusters and subclusters contained both mating-types of the fungus, indicating the potential for sexual reproduction, although asexual reproduction remained the primary mode of reproduction. The study strongly suggests the native range of D. septosporum to be in Eastern Europe (i.e., the Baltic and Western Russia) and Western Asia. | |||||||||||||||||||||||||||||||||
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| Record 302 of 414 | |||||||||
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| Author(s): Pokorny, V (Pokorny, Vladislav); Novotny, T (Novotny, Tomas) | |||||||||
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| Abstract: Interacting single-level quantum dots connected to BCS superconducting leads represent a well-controllable system to study the interplay between the correlation effects and the electron pairing that can result in a 0 - pi (singlet-doublet) quantum phase transition (QPT). The physics of this system can be well described by the impurity Anderson model. We present an analysis of the statistics of the perturbation expansion order of the continuous-time hybridization expansion quantum Monte Carlo algorithm in the vicinity of such a first-order impurity QPT. By calculating the moments of the histograms of the expansion order which deviate from the ideal Gaussian shape, we provide an insight into the thermodynamic mixing of the two phases at low but finite temperatures, which is reflected in the bimodal nature of the histograms. | |||||||||
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| Record 303 of 414 | |||||||||
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| Author(s): Nekovar, F (Nekovar, Frantisek); Faigl, J (Faigl, Jan); Saska, M (Saska, Martin) | |||||||||
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| Abstract: This letter concerns optimal power transmission line inspection formulated as a proposed generalization of the traveling salesman problem for a multi-route one-depot scenario. The problem is formulated for an inspection vehicle with a limited travel budget. Therefore, the solution can be composed of multiple runs to provide full coverage of the given power lines. Besides, the solution indicates how many vehicles can perform the inspection in a single run. The optimal solution of the problem is solved by the proposed IntegerLinear Programming (ILP) formulation, which is, however, very computationally demanding. Therefore, the computational requirements are addressed by the combinatorial metaheuristic. The employed greedy randomized adaptive search procedure is significantly less demanding while providing competitive solutions and scales better with the problem size than the ILP-based approach. The proposed formulation and algorithms are demonstrated in a real-world scenario to inspect power line segments at the electrical substation. | |||||||||
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| Record 304 of 414 | ||||||
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| Author(s): Belohoubek, J (Belohoubek, Jan); Fiser, P (Fiser, Petr); Schmidt, J (Schmidt, Jan) | ||||||
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| Abstract: Physical attacks, namely invasive, observation, and combined, represent a great challenge for today's digital design. Successful class of strategies adopted by industry, allowing hiding data dependency of the side channel emissions in CMOS is based on balancing. Although attacks on CMOS dynamic power represent a class of state-ofthe-art attacks, vulnerabilities exploiting data dependency in CMOS static power and light-modulated static power were recently presented. In this paper, we describe structures and techniques developed to enhance and balance the power imprint of the traditional static CMOS bulk structures under invasive light attack. The novel standard cells designed according to the presented techniques in the TSMC180nm technology node were used to synthesize the dual-rail AES SBOX block. The behavior of the AES SBOX block composed of the novel cells is compared to classical approaches. Usage of novel cells enhances circuit security under invasive light attack while preserving comparable circuit resistance against state-of-the-art power attacks. | ||||||
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| Record 305 of 414 | ||||||
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| Author(s): Ortiz, D (Ortiz, David); Pekar, S (Pekar, Stano); Bilat, J (Bilat, Julia); Alvarez, N (Alvarez, Nadir) | ||||||
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| Abstract: Genomic data provide unprecedented power for species delimitation. However, current implementations are still time and resource consuming. In addition, bioinformatic processing is contentious and its impact on downstream analyses is insufficiently understood. Here we employ ddRAD sequencing and a thorough sampling for species delimitation in Zodarion styliferum, a widespread Iberian ant-eating spider. We explore the influence of the loci filtering strategy on the downstream phylogenetic analyses, genomic clustering and coalescent species delimitation. We also assess the accuracy of one mitochondrial (COI) and one nuclear (ITS) barcode for fast and inexpensive species delineation in the group. Our genomic data strongly support two morphologically cryptic but ecologically divergent lineages, mainly restricted to the central-eastern and western parts of the Iberian Peninsula, respectively. Larger matrices with more missing data showed increased genomic diversity, supporting that bioinformatic strategies to maximize matrix completion disproportionately exclude loci with the highest mutation rates. Moderate loci filtering gave the best results across analyses: although larger matrices returned concatenated phylogenies with higher support, middle-sized matrices performed better in genetic structure analyses. COI displayed high diversity and a conspicuous barcode gap, revealing 13 mitochondrial lineages. Mitonuclear discordance is consistent with ancestral isolation in multiple groups, probably in glacial refugia, followed by range expansion and secondary contact that produced genomic homogenization. Several apparently (unidirectionally) introgressed specimens further challenge the accuracy of species identification through mitochondrial barcodes in the group. Conversely, ITS failed to separate both lineages of Z. styliferum. This study shows an extreme case of mitonuclear discordance that highlights the limitations of single molecular barcodes for species delimitation, even in presence of distinct barcode gaps, and brings new light on the effects of parameterization on shallow-divergence studies using RAD data. | ||||||
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| Record 306 of 414 | ||||||
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| Author(s): Montes, E (Montes, Enrique); Vazquez, H (Vazquez, Hector) | ||||||
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| Abstract: We investigate, using density functional theory (DFT), the electronic and conducting properties of benzenediamine connected to gold electrodes via different tip structures. We examine a series of binding motifs to the electrodes and calculate the junction spectral properties. We consider corrections to the position of molecular resonances at the junction and discuss different approaches to the calculation of these shifts. We relate the magnitude of these corrections to resonance energies to the atomistic structure of the tip. Benzenediamine DFT-based transmission spectra can be well approximated by a Lorentzian model involving only the highest occupied molecular orbital (HOMO). We show how benzenediamine calculated conductance values in quantitative agreement with previous experiments can be achieved from the combination of DFT-based spectra and corrections to the DFT-based HOMO energy and an accessible Lorentzian model. | ||||||
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| Record 307 of 414 | |||||||||||||||||||||
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| Author(s): Diachkov, MV (Diachkov, Mikhail V.); Ferrer, K (Ferrer, Karoll); Oklestkova, J (Oklestkova, Jana); Rarova, L (Rarova, Lucie); Bazgier, V (Bazgier, Vaclav); Kvasnica, M (Kvasnica, Miroslav) | |||||||||||||||||||||
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| Abstract: Brassinosteroids are a class of plant hormones that regulate a broad range of physiological processes such as plant growth, development and immunity, including the suppression of biotic and abiotic stresses. In this paper, we report the synthesis of new brassinosteroid analogues with a nitrogen-containing side chain and their biological activity on Arabidopis thaliana. Based on molecular docking experiments, two groups of brassinosteroid analogues were prepared with short and long side chains in order to study the impact of side chain length on plants. The derivatives with a short side chain were prepared with amide, amine and ammonium functional groups. The derivatives with a long side chain were synthesized using amide and ammonium functional groups. A total of 25 new brassinosteroid analogues were prepared. All 25 compounds were tested in an Arabidopsis root sensitivity bioassay and cytotoxicity screening. The synthesized substances showed no significant inhibitory activity compared to natural 24-epibrassinolide. In contrast, in low concentration, several compounds (8a, 8b, 8e, 16e, 22a and 22e) showed interesting growth-promoting activity. The cytotoxicity assay showed no toxicity of the prepared compounds on cancer and normal cell lines. | |||||||||||||||||||||
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| Record 308 of 414 | |||||||||||||||||||||||||||
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| Author(s): Liao, MZ (Liao, Mengzhou); Nicolini, P (Nicolini, Paolo); Du, LJ (Du, Luojun); Yuan, JH (Yuan, Jiahao); Wang, SP (Wang, Shuopei); Yu, H (Yu, Hua); Tang, J (Tang, Jian); Cheng, P (Cheng, Peng); Watanabe, K (Watanabe, Kenji); Taniguchi, T (Taniguchi, Takashi); Gu, L (Gu, Lin); Claerbout, VEP (Claerbout, Victor E. P.); Silva, A (Silva, Andrea); Kramer, D (Kramer, Denis); Polcar, T (Polcar, Tomas); Yang, R (Yang, Rong); Shi, DX (Shi, Dongxia); Zhang, GY (Zhang, Guangyu) | |||||||||||||||||||||||||||
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Abstract:
MoS2/graphite and MoS2/h-BN interfaces are shown to have ultra-low friction coefficients, whereas edges and interface steps mainly contribute to the friction force.
Two-dimensional heterostructures are excellent platforms to realize twist-angle-independent ultra-low friction due to their weak interlayer van der Waals interactions and natural lattice mismatch. However, for finite-size interfaces, the effect of domain edges on the friction process remains unclear. Here we report the superlubricity phenomenon and the edge-pinning effect at MoS2/graphite and MoS2/hexagonal boron nitride van der Waals heterostructure interfaces. We found that the friction coefficients of these heterostructures are below 10(-6). Molecular dynamics simulations corroborate the experiments, which highlights the contribution of edges and interface steps to friction forces. Our experiments and simulations provide more information on the sliding mechanism of finite low-dimensional structures, which is vital to understand the friction process of laminar solid lubricants. |
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| Record 309 of 414 | ||||||||||||||||||||||||
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| Author(s): Johnson, F (Johnson, F.); Boldrin, D (Boldrin, D.); Zemen, J (Zemen, J.); Pesquera, D (Pesquera, D.); Kim, J (Kim, J.); Moya, X (Moya, X.); Zhang, H (Zhang, H.); Singh, HK (Singh, H. K.); Samathrakis, I (Samathrakis, I.); Cohen, LF (Cohen, L. F.) | ||||||||||||||||||||||||
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| Abstract: The anomalous Hall effect (AHE) has been shown to be present in certain non-collinear antiferromagnets due to their symmetry-breaking magnetic structure, and its magnitude is dependent primarily on the non-zero components of the Berry curvature. In the non-collinear antiferromagnet Mn3NiN, the Berry phase contribution has been predicted to have strong strain dependence, although in practice, direct observation may be obscured by other strain-related influences-for instance, magnetic phase transitions mediated by strain. To unravel the various contributions, we examine the thickness and temperature dependence of the AHE for films grown on the piezoelectric substrate BaTiO3. We observe a systematic reduction in T-N due to increased compressive strain as film thickness is reduced and a linear decrease in the AHE magnitude as the films are cooled from their ferrimagnetic phase above T-N to their antiferromagnetic phase below. At 190 K, we applied an electric field across a 0.5 mm thick BaTiO3 substrate with a 50 nm thick Mn3NiN film grown on top and we demonstrate that at the coercive field of the piezoelectric substrate, the tensile in-plane strain is estimated to be of the order of 0.15%, producing a 20% change in AHE. Furthermore, we show that this change is, indeed, dominated by the intrinsic strain dependence of the Berry curvature. | ||||||||||||||||||||||||
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| Record 310 of 414 | |||||||||||||||
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| Author(s): Dolezal, P (Dolezal, Petr); Cejpek, P (Cejpek, Petr); Tsutsui, S (Tsutsui, Satoshi); Kaneko, K (Kaneko, Koji); Legut, D (Legut, Dominik); Carva, K (Carva, Karel); Javorsky, P (Javorsky, Pavel) | |||||||||||||||
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| Abstract: The interaction between phonons and 4f electrons, which is forming a new quantum state (quasi-bound state) beyond Born-Oppenheimer approximation, is very prominent and lattice dynamics plays here a key role. There is only a small number of compounds in which the experimental observation suggest such a scenario. One of these compounds is CePd2Al2. Here the study of phonon dispersion curves of (Ce,La)Pd2Al2 at 1.5, 7.5, 80 and 300 K is presented. The inelastic X-ray scattering technique was used for mapping the phonon modes at X and Z points as well as in ? and Delta directions, where the symmetry analysis of phonon modes was performed. The measured spectra are compared with the theoretical calculation, showing very good agreement. The measurements were performed in several Brillouin zones allowing the reconstruction of phonon dispersion curves. The results are discussed with respect to the magneto-elastic interaction and are compared with other cerium compounds. The phonon mode symmetry A(1g) was found to be unaffected by the interaction, which is in contrast to previous assumptions. | |||||||||||||||
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| Record 311 of 414 | |||||||||
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| Author(s): Zalom, P (Zalom, Peter); Novotny, T (Novotny, Tomas) | |||||||||
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| Abstract: We elaborate on the recently introduced concept of the reentrant Kondo effect in quantum impurities/dots coupled to hybrid metal-semiconductor contacts [G. Diniz et al., Phys. Rev. B 101, 125115 (2020)]. By noticing the equivalence of the originally suggested semiconducting arrangement to an analogous three-terminal quantum dot setup with a normal and two phase-biased superconducting leads introduced in our recent work [P. Zalom et al., Phys. R. i3 103, 035419 (2021)], we put this effect into a new physical context, which gives us a fresh look on the problem. First, we identify the superconducting counterpart of the reentrant Kondo effect and, consequently, reveal its fragility with respect to an underlying doublet-singlet quantum phase transition induced by the particle-hole asymmetry of the reservoir densities of states. This is pertinent (even if previously unnoticed) also in the original as well as extended semiconducting setups, where it puts stringent conditions on the symmetry of the contact density of states. Furthermore, we analyze the experimental feasibility of observing the reentrant Kondo effect in its superconducting realization concluding that even present-day experiments might see the onset of the reentrant behavior, but fully developed Kondo features cannot be reached due to the required vast separation of energy/temperature scales. | |||||||||
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| Record 312 of 414 | |||||||||
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| Author(s): Mic, V (Mic, Vladimir); Racek, T (Racek, Tomas); Krenek, A (Krenek, Ales); Zezula, P (Zezula, Pavel) | |||||||||
| Edited by: Reyes N; Connor R; Kriege N; Kazempour D; Bartolini I; Schubert E; Chen JJ | |||||||||
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| Abstract: Contemporary challenges for efficient similarity search include complex similarity functions, the curse of dimensionality, and large sizes of descriptive features of data objects. This article reports our experience with a database of protein chains which form (almost) metric space and demonstrate the following extreme properties. Evaluation of the pairwise similarity of protein chains can take even tens of minutes, and has a variance of six orders of magnitude. The minimisation of a number of similarity comparisons is thus crucial, so we propose a generic three stage search engine to solve it. We improve the median searching time 73 times in comparison with the search engine currently employed for the protein database in practice. | |||||||||
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| Conference Host: TU Dortmund | |||||||||
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| ISBN: 978-3-030-89657-7; 978-3-030-89656-0 |
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| Author(s): Mihola, O (Mihola, Ondrej); Landa, V (Landa, Vladimir); Pratto, F (Pratto, Florencia); Brick, K (Brick, Kevin); Kobets, T (Kobets, Tatyana); Kusari, F (Kusari, Fitore); Gasic, S (Gasic, Srdjan); Smagulova, F (Smagulova, Fatima); Grey, C (Grey, Corinne); Flachs, P (Flachs, Petr); Gergelits, V (Gergelits, Vaclav); Tresnak, K (Tresnak, Karel); Silhavy, J (Silhavy, Jan); Mlejnek, P (Mlejnek, Petr); Camerini-Otero, RD (Camerini-Otero, R. Daniel); Pravenec, M (Pravenec, Michal); Petukhova, GV (Petukhova, Galina V.); Trachtulec, Z (Trachtulec, Zdenek) | |||||||||||||||
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| Abstract: Background Vertebrate meiotic recombination events are concentrated in regions (hotspots) that display open chromatin marks, such as trimethylation of lysines 4 and 36 of histone 3 (H3K4me3 and H3K36me3). Mouse and human PRDM9 proteins catalyze H3K4me3 and H3K36me3 and determine hotspot positions, whereas other vertebrates lacking PRDM9 recombine in regions with chromatin already opened for another function, such as gene promoters. While these other vertebrate species lacking PRDM9 remain fertile, inactivation of the mouse Prdm9 gene, which shifts the hotspots to the functional regions (including promoters), typically causes gross fertility reduction; and the reasons for these species differences are not clear. Results We introduced Prdm9 deletions into the Rattus norvegicus genome and generated the first rat genome-wide maps of recombination-initiating double-strand break hotspots. Rat strains carrying the same wild-type Prdm9 allele shared 88% hotspots but strains with different Prdm9 alleles only 3%. After Prdm9 deletion, rat hotspots relocated to functional regions, about 40% to positions corresponding to Prdm9-independent mouse hotspots, including promoters. Despite the hotspot relocation and decreased fertility, Prdm9-deficient rats of the SHR/OlaIpcv strain produced healthy offspring. The percentage of normal pachytene spermatocytes in SHR-Prdm9 mutants was almost double than in the PWD male mouse oligospermic sterile mutants. We previously found a correlation between the crossover rate and sperm presence in mouse Prdm9 mutants. The crossover rate of SHR is more similar to sperm-carrying mutant mice, but it did not fully explain the fertility of the SHR mutants. Besides mild meiotic arrests at rat tubular stages IV (mid-pachytene) and XIV (metaphase), we also detected postmeiotic apoptosis of round spermatids. We found delayed meiosis and age-dependent fertility in both sexes of the SHR mutants. Conclusions We hypothesize that the relative increased fertility of rat versus mouse Prdm9 mutants could be ascribed to extended duration of meiotic prophase I. While rat PRDM9 shapes meiotic recombination landscapes, it is unnecessary for recombination. We suggest that PRDM9 has additional roles in spermatogenesis and speciation-spermatid development and reproductive age-that may help to explain male-specific hybrid sterility. | |||||||||||||||
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| Record 314 of 414 |
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| Author(s): Karafiatova, M (Karafiatova, Miroslava); Bednarova, M (Bednarova, Martina); Said, M (Said, Mahmoud); Cizkova, J (Cizkova, Jana); Holusova, K (Holusova, Katerina); Blavet, N (Blavet, Nicolas); Bartos, J (Bartos, Jan) |
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| Abstract: More than a centu |