bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toward a generalized Bienenstock-Cooper-Munro rule for spatiotemporal learning via triplet-STDP in memristive devices
Authors: Wang Zhongqiang , Zeng Tao , Ren Yanyun , Lin Ya , Xu Haiyang , Zhao Xiaoning , Liu Yichun , Ielmini Daniele 
Published: March 2020

AbstractThe close replication of synaptic functions is an important objective for achieving a highly realistic memristor-based cognitive computation. The emulation of neurobiological learning rules may allow the development of neuromorphic systems that continuously learn without supervision. In this work, the Bienenstock-Cooper-Munro learning rule, as a typical case of spike-rate-dependent plasticity, is mimicked using a generalized triplet-spike-timing-dependent plasticity scheme in a WO3−x memristive synapse. It demonstrates both presynaptic and postsynaptic activities and remedies the absence of the enhanced depression effect in the depression region, allowing a better description of the biological counterpart. The threshold sliding effect of Bienenstock-Cooper-Munro rule is realized using a history-dependent property of the second-order memristor. Rate-based orientation selectivity is demonstrated in a simulated feedforward memristive network with this generalized Bienenstock-Cooper-Munro framework. These findings provide a feasible approach for mimicking Bienenstock-Cooper-Munro learning rules in memristors, and support the applications of spatiotemporal coding and learning using memristive networks.
Single-molecule imaging reveals molecular coupling between transcription and DNA repair machinery in live cells
Authors: Ho Han Ngoc , van Oijen Antoine M. , Ghodke Harshad 
Published: March 2020

AbstractThe Escherichia coli transcription-repair coupling factor Mfd displaces stalled RNA polymerase and delivers the stall site to the nucleotide excision repair factors UvrAB for damage detection. Whether this handoff from RNA polymerase to UvrA occurs via the Mfd-UvrA2-UvrB complex or alternate reaction intermediates in cells remains unclear. Here, we visualise Mfd in actively growing cells and determine the catalytic requirements for faithful recruitment of nucleotide excision repair proteins. We find that ATP hydrolysis by UvrA governs formation and disassembly of the Mfd-UvrA2 complex. Further, Mfd-UvrA2-UvrB complexes formed by UvrB mutants deficient in DNA loading and damage recognition are impaired in successful handoff. Our single-molecule dissection of interactions of Mfd with its partner proteins inside live cells shows that the dissociation of Mfd is tightly coupled to successful loading of UvrB, providing a mechanism via which loading of UvrB occurs in a strand-specific manner.
500 microkelvin nanoelectronics
Authors: Sarsby Matthew , Yurttagül Nikolai , Geresdi Attila 
Published: March 2020

AbstractFragile quantum effects such as single electron charging in quantum dots or macroscopic coherent tunneling in superconducting junctions are the basis of modern quantum technologies. These phenomena can only be observed in devices where the characteristic spacing between energy levels exceeds the thermal energy, kBT, demanding effective refrigeration techniques for nanoscale electronic devices. Commercially available dilution refrigerators have enabled typical electron temperatures in the 10 to 100 mK regime, however indirect cooling of nanodevices becomes inefficient due to stray radiofrequency heating and weak thermal coupling of electrons to the device substrate. Here, we report on passing the millikelvin barrier for a nanoelectronic device. Using a combination of on-chip and off-chip nuclear refrigeration, we reach an ultimate electron temperature of Te = 421 ± 35 μK and a hold time exceeding 85 h below 700 μK measured by a self-calibrated Coulomb-blockade thermometer.
Polycyclic aromatic chains on metals and insulating layers by repetitive [3+2] cycloadditions
Authors: Riss Alexander , Richter Marcus , Paz Alejandro Pérez , Wang Xiao-Ye , Raju Rajesh , He Yuanqin , Ducke Jacob , Corral Eduardo , Wuttke Michael , Seufert Knud , Garnica Manuela , Rubio Angel , V. Barth Johannes , Narita Akimitsu , Müllen Klaus , Berger Reinhard , Feng Xinliang , Palma Carlos-Andres , Auwärter Willi 
Published: March 2020

AbstractThe vast potential of organic materials for electronic, optoelectronic and spintronic devices entails substantial interest in the fabrication of π-conjugated systems with tailored functionality directly at insulating interfaces. On-surface fabrication of such materials on non-metal surfaces remains to be demonstrated with high yield and selectivity. Here we present the synthesis of polyaromatic chains on metallic substrates, insulating layers, and in the solid state. Scanning probe microscopy shows the formation of azaullazine repeating units on Au(111), Ag(111), and h-BN/Cu(111), stemming from intermolecular homo-coupling via cycloaddition reactions of CN-substituted polycyclic aromatic azomethine ylide (PAMY) intermediates followed by subsequent dehydrogenation. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry demonstrates that the reaction also takes place in the solid state in the absence of any catalyst. Such intermolecular cycloaddition reactions are promising methods for direct synthesis of regioregular polyaromatic polymers on arbitrary insulating surfaces.
Molecular vibrations reduce the maximum achievable photovoltage in organic solar cells
Authors: Panhans Michel , Hutsch Sebastian , Benduhn Johannes , Schellhammer Karl Sebastian , Nikolis Vasileios C. , Vangerven Tim , Vandewal Koen , Ortmann Frank 
Published: March 2020

AbstractThe low-energy edge of optical absorption spectra is critical for the performance of solar cells, but is not well understood in the case of organic solar cells (OSCs). We study the microscopic origin of exciton bands in molecular blends and investigate their role in OSCs. We simulate the temperature dependence of the excitonic density of states and low-energy absorption features, including low-frequency molecular vibrations and multi-exciton hybridisation. For model donor-acceptor blends featuring charge-transfer excitons, our simulations agree very well with temperature-dependent experimental absorption spectra. We unveil that the quantum effect of zero-point vibrations, mediated by electron-phonon interaction, causes a substantial exciton bandwidth and reduces the open-circuit voltage, which is predicted from electronic and vibronic molecular parameters. This effect is surprisingly strong at room temperature and can substantially limit the OSC’s efficiency. Strategies to reduce these vibration-induced voltage losses are discussed for a larger set of systems and different heterojunction geometries.
Chromosome organization by a conserved condensin-ParB system in the actinobacterium Corynebacterium glutamicum
Authors: Böhm Kati , Giacomelli Giacomo , Schmidt Andreas , Imhof Axel , Koszul Romain , Marbouty Martial , Bramkamp Marc 
Published: March 2020

AbstractHigher-order chromosome folding and segregation are tightly regulated in all domains of life. In bacteria, details on nucleoid organization regulatory mechanisms and function remain poorly characterized, especially in non-model species. Here, we investigate the role of DNA-partitioning protein ParB and SMC condensin complexes in the actinobacterium Corynebacterium glutamicum. Chromosome conformation capture reveals SMC-mediated long-range interactions around ten centromere-like parS sites clustered at the replication origin (oriC). At least one oriC-proximal parS site is necessary for reliable chromosome segregation. We use chromatin immunoprecipitation and photoactivated single-molecule localization microscopy to show the formation of distinct, parS-dependent ParB-nucleoprotein subclusters. We further show that SMC/ScpAB complexes, loaded via ParB at parS sites, mediate chromosomal inter-arm contacts (as previously shown in Bacillus subtilis). However, the MukBEF-like SMC complex MksBEFG does not contribute to chromosomal DNA-folding; instead, this complex is involved in plasmid maintenance and interacts with the polar oriC-tethering factor DivIVA. Our results complement current models of ParB-SMC/ScpAB crosstalk and show that some condensin complexes evolved functions that are apparently uncoupled from chromosome folding.
Playing games with multiple access channels
Authors: Leditzky Felix , Alhejji Mohammad A. , Levin Joshua , Smith Graeme 
Published: March 2020

AbstractCommunication networks have multiple users, each sending and receiving messages. A multiple access channel (MAC) models multiple senders transmitting to a single receiver, such as the uplink from many mobile phones to a single base station. The optimal performance of a MAC is quantified by a capacity region of simultaneously achievable communication rates. We study the two-sender classical MAC, the simplest and best-understood network, and find a surprising richness in both a classical and quantum context. First, we find that quantum entanglement shared between senders can substantially boost the capacity of a classical MAC. Second, we find that optimal performance of a MAC with bounded-size inputs may require unbounded amounts of entanglement. Third, determining whether a perfect communication rate is achievable using finite-dimensional entanglement is undecidable. Finally, we show that evaluating the capacity region of a two-sender classical MAC is in fact NP-hard.
Distinct roles for H4 and H2A.Z acetylation in RNA transcription in African trypanosomes
Authors: Kraus Amelie J. , Vanselow Jens T. , Lamer Stephanie , Brink Benedikt G. , Schlosser Andreas , Siegel T. Nicolai 
Published: March 2020

AbstractDespite histone H2A variants and acetylation of histones occurring in almost every eukaryotic organism, it has been difficult to establish direct functional links between canonical histones or H2A variant acetylation, deposition of H2A variants and transcription. To disentangle these complex interdependent processes, we devised a highly sensitive strategy for quantifying histone acetylation levels at specific genomic loci. Taking advantage of the unusual genome organization inTrypanosoma brucei, we identified 58 histone modifications enriched at transcription start sites (TSSs). Furthermore, we found TSS-associated H4 and H2A.Z acetylation to be mediated by two different histone acetyltransferases, HAT2 and HAT1, respectively. Whereas depletion of HAT2 decreases H2A.Z deposition and shifts the site of transcription initiation, depletion of HAT1 does not affect H2A.Z deposition but reduces total mRNA levels by 50%. Thus, specifically reducing H4 or H2A.Z acetylation levels enabled us to reveal distinct roles for these modifications in H2A.Z deposition and RNA transcription.
Machine learning for cluster analysis of localization microscopy data
Authors: Williamson David J. , Burn Garth L. , Simoncelli Sabrina , Griffié Juliette , Peters Ruby , Davis Daniel M. , Owen Dylan M. 
Published: March 2020

AbstractQuantifying the extent to which points are clustered in single-molecule localization microscopy data is vital to understanding the spatial relationships between molecules in the underlying sample. Many existing computational approaches are limited in their ability to process large-scale data sets, to deal effectively with sample heterogeneity, or require subjective user-defined analysis parameters. Here, we develop a supervised machine-learning approach to cluster analysis which is fast and accurate. Trained on a variety of simulated clustered data, the neural network can classify millions of points from a typical single-molecule localization microscopy data set, with the potential to include additional classifiers to describe different subtypes of clusters. The output can be further refined for the measurement of cluster area, shape, and point-density. We demonstrate this approach on simulated data and experimental data of the kinase Csk and the adaptor PAG in primary human T cell immunological synapses.
Reproductive tract extracellular vesicles are sufficient to transmit intergenerational stress and program neurodevelopment
Authors: Chan Jennifer C. , Morgan Christopher P. , Adrian Leu N. , Shetty Amol , Cisse Yasmine M. , Nugent Bridget M. , Morrison Kathleen E. , Jašarević Eldin , Huang Weiliang , Kanyuch Nickole , Rodgers Ali B. , Bhanu Natarajan V. , Berger Dara S. , Garcia Benjamin A. , Ament Seth , Kane Maureen , Neill Epperson C. , Bale Tracy L. 
Published: March 2020

AbstractExtracellular vesicles (EVs) are a unique mode of intercellular communication capable of incredible specificity in transmitting signals involved in cellular function, including germ cell maturation. Spermatogenesis occurs in the testes, behind a protective barrier to ensure safeguarding of germline DNA from environmental insults. Following DNA compaction, further sperm maturation occurs in the epididymis. Here, we report reproductive tract EVs transmit information regarding stress in the paternal environment to sperm, potentially altering fetal development. Using intracytoplasmic sperm injection, we found that sperm incubated with EVs collected from stress-treated epididymal epithelial cells produced offspring with altered neurodevelopment and adult stress reactivity. Proteomic and transcriptomic assessment of these EVs showed dramatic changes in protein and miRNA content long after stress treatment had ended, supporting a lasting programmatic change in response to chronic stress. Thus, EVs as a normal process in sperm maturation, can also perform roles in intergenerational transmission of paternal environmental experience.
The ribosome-associated complex RAC serves in a relay that directs nascent chains to Ssb
Authors: Zhang Ying , Valentín Gesé Genís , Conz Charlotte , Lapouge Karine , Kopp Jürgen , Wölfle Tina , Rospert Sabine , Sinning Irmgard 
Published: March 2020

AbstractThe conserved ribosome-associated complex (RAC) consisting of Zuo1 (Hsp40) and Ssz1 (non-canonical Hsp70) acts together with the ribosome-bound Hsp70 chaperone Ssb in de novo protein folding at the ribosomal tunnel exit. Current models suggest that the function of Ssz1 is confined to the support of Zuo1, however, it is not known whether RAC by itself serves as a chaperone for nascent chains. Here we show that, via its rudimentary substrate binding domain (SBD), Ssz1 directly binds to emerging nascent chains prior to Ssb. Structural and biochemical analyses identify a conserved LP-motif at the Zuo1 N-terminus forming a polyproline-II helix, which binds to the Ssz1-SBD as a pseudo-substrate. The LP-motif competes with nascent chain binding to the Ssz1-SBD and modulates nascent chain transfer. The combined data indicate that Ssz1 is an active chaperone optimized for transient, low-affinity substrate binding, which ensures the flux of nascent chains through RAC/Ssb.
Highly selective phonon diffusive scattering in superionic layered AgCrSe2
Authors: Wang Chen , Chen Yue 
Published: March 2020

AbstractSuperionic materials that exhibit coexistence of rigid crystalline lattices and liquid-like fluctuating substructures have emerged as promising thermoelectric materials. The inadequate understanding of the phonon behavior in the superionic state, however, still prevents further revealing of the underlying correlation between the thermally induced liquid-like atomic dynamics and anomalous thermal transport properties. Herein, by adopting a hybrid scheme to directly characterize anharmonic phonon quasiparticles from ab-initio molecular dynamics, we manifest that low-energy transverse phonons dominated by Ag atoms totally collapse, whereas longitudinal optical phonons remain largely intact during the superionic transition. The ultralow thermal conductivity originates from the atomic level structural heterogeneity can be ultimately attributed to diffusive phonon dynamics. Our study also reveals that the extremely large selective phonon diffusive scattering can be counteracted by hydrostatic pressure induced deactivation of the liquid-like flow of Ag atoms. These results demonstrate the decisive role of ion superionicity in phonon scattering across superionic transition and may pave the way for new phonon engineering strategies in related superionic materials.
CD4+ Th immunogenicity of the Ascaris spp. secreted products
Authors: Ebner Friederike , Morrison Eliot , Bertazzon Miriam , Midha Ankur , Hartmann Susanne , Freund Christian , Álvaro-Benito Miguel 
Published: March 2020

AbstractAscaris spp. is a major health problem of humans and animals alike, and understanding the immunogenicity of its antigens is required for developing urgently needed vaccines. The parasite-secreted products represent the most relevant, yet complex (>250 proteins) antigens ofAscaris spp. as defining the pathogen-host interplay. We applied an in vitro antigen processing system coupled to quantitative proteomics to identify potential CD4+Thcell epitopes inAscaris-secreted products. This approach considerably restricts the theoretical list of epitopes using conventional CD4+Thcell epitope prediction tools. We demonstrate the specificity and utility of our approach on two sets of candidate lists, allowing us identifying hits excluded by either one or both computational methods. More importantly, one of the candidates identified experimentally, clearly demonstrates the presence of pathogen-reactive T cells in healthy human individuals against these antigens. Thus, our work pipeline identifies the first human T cell epitope againstAscaris spp. and represents an easily adaptable platform for characterization of complex antigens, in particular for those pathogens that are not easily amenable for in vivo experimental validation.
The distinctive structure and composition of arterial and venous thrombi and pulmonary emboli
Authors: Chernysh Irina N. , Nagaswami Chandrasekaran , Kosolapova Sofia , Peshkova Alina D. , Cuker Adam , Cines Douglas B. , Cambor Carolyn L. , Litvinov Rustem I. , Weisel John W. 
Published: March 2020

AbstractAlthough arterial and venous thromboembolic disorders are among the most frequent causes of mortality and morbidity, there has been little description of how the composition of thrombi and emboli depends on their vascular origin and age. We quantified the structure and composition of arterial and venous thrombi and pulmonary emboli using high-resolution scanning electron microscopy. Arterial thrombi contained a surprisingly large amount of fibrin, in addition to platelets. The composition of pulmonary emboli mirrored the most distal part of venous thrombi from which they originated, which differed from the structure of the body and head of the same thrombi. All thrombi and emboli contained few biconcave red blood cells but many polyhedrocytes or related forms of compressed red blood cells, demonstrating that these structures are a signature of clot contraction in vivo. Polyhedrocytes and intermediate forms comprised the major constituents of venous thrombi and pulmonary emboli. The structures within all of the thrombi and emboli were very tightly packed, in contrast to clots formed in vitro. There are distinctive, reproducible differences among arterial and venous thrombi and emboli related to their origin, destination and duration, which may have clinical implications for the understanding and treatment of thrombotic disorders.
The X-Ray Emission Effectiveness of Plasma Mirrors: Reexamining Power-Law Scaling for Relativistic High-Order Harmonic Generation
Authors: Edwards Matthew R. , Mikhailova Julia M. 
Published: March 2020

AbstractUltrashort pulsed lasers provide uniquely detailed access to the ultrafast dynamics of physical, chemical, and biological systems, but only a handful of wavelengths are directly produced by solid-state lasers, necessitating efficient high-power frequency conversion. Relativistic plasma mirrors generate broadband power-law spectra, that may span the gap between petawatt-class infrared laser facilities and x-ray free-electron lasers; despite substantial theoretical work the ultimate efficiency of this relativistic high-order-harmonic generation remains unclear. We show that the coherent radiation emitted by plasma mirrors follows a power-law distribution of energy over frequency with an exponent that, even in the ultrarelativistic limit, strongly depends on the ratio of laser intensity to plasma density and exceeds the frequently quoted value of −8/3 over a wide range of parameters. The coherent synchrotron emission model, when adequately corrected for the finite width of emitting electron bunches, is not just valid for p-polarized light and thin foil targets, but generally describes relativistic harmonic generation, including at normal incidence and with finite-gradient plasmas. Our numerical results support the ω−4/3 scaling of the synchrotron emission model as a limiting efficiency of the process under most conditions. The highest frequencies that can be generated with this scaling are usually restricted by the width of the emitting electron bunch rather than the Lorentz factor of the fastest electrons. The theoretical scaling relations developed here suggest, for example, that with a 20-PW 800-nm driving laser, 1 TW/harmonic can be produced for 1-keV photons.
Association of induced abortion with hypertensive disorders of pregnancy risk among nulliparous women in China: a prospective cohort study
Authors: Su Yinhua , Xie Xiaoping , Zhou Yanfang , Lin Hong , Li Yamei , Feng Na , Luo Jiayou 
Published: March 2020

AbstractThe relationship between induced abortion(IA) and hypertensive disorders of pregnancy(HDP) is inconclusive. Few studies have been conducted in China. In order to clarify the association between previous IA and risk of HDP, including gestational hypertension(GH) and pre-eclampsia(PE), we performed a community-based prospective cohort study enrolling 5191 eligible nulliparous women in selected 2 districts and 11 towns of Liuyang from 2013 to 2015. Multivariable logistic regression was conducted to examine whether IA was associated with HDP, GH and PE. Of the gravidea, 1378(26.5%) had a previous IA and 258(5.0%) diagnosed with HDP, including 141(2.7%) GH and 117(2.3%) PE. The difference in the incidence of GH and PE between gravidae having one versus those with two or more IAs was minimal. After adjustment for maternal age, body mass index at first antenatal visit, education, virus infection and history of medical disorders, previous IA was significantly associated with HDP (OR = 0.67, 95%CI = 0.49 to 0.91) and PE (OR = 0.61, 95%CI = 0.38 to 0.97), but not with GH (OR = 0.73, 95%CI = 0.49 to 1.10). Additional adjustment for occupation, living area, anemia, gestational diabetes mellitus, psychological stress, conception climate and infant sex, multivariable analysis provided similar results. In conclusion, previous IA was associated with a lower risk of PE among nulliparous women.