bluuebunny/crossref_metadata_2025_split huggingface dataset:
Larger GPU-accelerated brain simulations with procedural connectivity
Authors: Knight James C , Nowotny Thomas 
Published: April 2020

AbstractLarge-scale simulations of spiking neural network models are an important tool for improving our understanding of the dynamics and ultimately the function of brains. However, even small mammals such as mice have on the order of 1 × 1012synaptic connections which, in simulations, are each typically charaterized by at least one floating-point value. This amounts to several terabytes of data – an unrealistic memory requirement for a single desktop machine. Large models are therefore typically simulated on distributed supercomputers which is costly and limits large-scale modelling to a few privileged research groups. In this work, we describe extensions to GeNN – our Graphical Processing Unit (GPU) accelerated spiking neural network simulator – that enable it to ‘procedurally’ generate connectivity and synaptic weights ‘on the go’ as spikes are triggered, instead of storing and retrieving them from memory. We find that GPUs are well-suited to this approach because of their raw computational power which, due to memory bandwidth limitations, is often under-utilised when simulating spiking neural networks. We demonstrate the value of our approach with a recent model of the Macaque visual cortex consisting of 4.13 × 106neurons and 24.2 × 109synapses. Using our new method, it can be simulated on a single GPU – a significant step forward in making large-scale brain modelling accessible to many more researchers. Our results match those obtained on a supercomputer and the simulation runs up to 35 % faster on a single high-end GPU than previously on over 1000 supercomputer nodes.
vmPFC drives hippocampal processing during autobiographical memory recall regardless of remoteness
Authors: McCormick Cornelia , Barry Daniel N. , Jafarian Amirhossein , Barnes Gareth R. , Maguire Eleanor A. 
Published: April 2020

AbstractOur ability to recall past experiences, autobiographical memories (AMs), is crucial to cognition, endowing us with a sense of self and underwriting our capacity for autonomy. Traditional views assume that the hippocampus orchestrates event recall, whereas recent accounts propose that the ventromedial prefrontal cortex (vmPFC) instigates and coordinates hippocampal-dependent processes. Here we sought to characterise the dynamic interplay between hippocampus and vmPFC during AM recall to adjudicate between these perspectives. Leveraging the high temporal resolution of magnetoencephalography, we found that the left hippocampus and the vmPFC showed the greatest power changes during AM retrieval. Moreover, responses in the vmPFC preceded activity in the hippocampus during initiation of AM recall, except during retrieval of the most recent AMs. The vmPFC drove hippocampal activity during recall initiation and also as AMs unfolded over subsequent seconds, and this effect was evident regardless of AM age. These results re-cast the positions of the hippocampus and the vmPFC in the AM retrieval hierarchy, with implications for theoretical accounts of memory processing and systems-level consolidation.
Cis-regulatory similarities in the zebrafish and human pancreas uncover potential disease-related enhancers
Authors: Bordeira-Carriço R. , Teixeira J. , Duque M. , Galhardo M. , Ribeiro D. , Dominguez-Acemel R. , Firbas P. N. , Tena J. J. , Eufrasio A. , Marques J. , Ferreira F. , Freitas T. , Carneiro F. , Goméz-Skarmeta J. L. , Bessa J. 
Published: April 2020

Introductory paragraphThe pancreas is a central organ for human diseases that have a dramatic societal burden, such as pancreatic cancer and diabetes1,2. Non-coding cis-regulatory elements (CREs) of DNA control gene expression3,4, being required for proper pancreas function. Most disease-associated alleles5,6are non-coding, often overlapping with CREs5, suggesting that alterations in these regulatory sequences contribute to human pancreatic diseases by impairing gene expression. However, functional testing of CREsin vivois not fully explored. Here we analysed histone modifications, transcription, chromatin accessibility and interactions, to identify zebrafish pancreas CREs and their human functional equivalents, uncovering disease-associated sequences across species. We found a human pancreatic enhancer whose deletion impairs the tumour suppressor geneARID1Aexpression, conferring a potential tumour suppressor role to this non-coding sequence. Additionally, we identified a zebrafishptf1adistal enhancer which deletion generates pancreatic agenesis, demonstrating the causality of this condition in humans7and the interspecies functional equivalency of enhancers.
Neutrophil to Lymphocyte Ratio (NLR) in captive chimpanzees (Pan troglodytes): The effects of sex, age, and rearing
Authors: Neal Webb Sarah J. , Schapiro Steven J. , Sherwood Chet C. , Raghanti Mary Ann , Hopkins William D. 
Published: April 2020

AbstractIn humans, neutrophil to lymphocyte ratio (NLR) has been used as a clinical tool in diagnosis and/or prognosis of a variety of cancers and medical conditions, as well as in measuring physiological stress over time. Given the close phylogenetic relationship and physical similarities between humans and apes, NLR may similarly be a useful diagnostic tool in assessing chimpanzee health. Only one study has examined NLR in apes, reporting that NLR increased with age and was affected by body-mass index and sex. In the current study, we examined changes in NLR data from longitudinal health records for 443 chimpanzees in two captive chimpanzee populations. Using these data, we analyzed intra-individual changes and inter-individual differences in NLR as a function of age, rearing history, and sex. Contrary to previous studies in humans and the one previous study in chimpanzees, NLR values did not change over a 10-year timespan within individual chimpanzees. However, cross-sectional comparisons revealed a significant quadratic relationship between age and NLR with the highest values during mid-life (20-30 years of age) and the lowest values in younger and older individuals. Additionally, males and mother-reared individuals had higher NLR than females and nursery-reared chimpanzees, respectively. Lastly, males and those with higher NLR values died at younger ages. These findings may suggest that NLR can be used a predictor of longevity in chimpanzees. However, given the complexities of these relationships, more research is needed to determine the utility of NLR as a diagnostic health tool for use in chimpanzees.
In silicodesign and validation of commercial kit GPS™ CoVID-19 dtec-RT-qPCR Test under criteria of UNE/EN ISO 17025:2005 and ISO/IEC 15189:2012
Authors: Martínez-Murcia Antonio , Bru Gema , Navarro Aaron , Ros-Tárraga Patricia , García-Sirera Adrián , Pérez Laura 
Published: April 2020

ABSTRACTBackgroundThe Corona Virus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has become a serious infectious disease affecting human health worldwide and rapidly declared a pandemic by WHO. Early, several RT-qPCR were designed by using only the first SARS-CoV-2 genome sequence.ObjectivesA few days later, when additional SARS-CoV-2 genome were retrieved, the kit GPS™ CoVID-19 dtec-RT-qPCR Test was designed to provide a highly specific detection method and commercially available worldwide. The kit was validated following criteria recommended by the UNE/EN ISO 17025:2005 and ISO/IEC 15189:2012.MethodsThe present study approached thein silicospecificity of the GPS™ CoVID-19 dtec-RT-qPCR Test and RT-qPCR designs currently published. The empirical validation parameters specificity (inclusivity/exclusivity), quantitative phase analysis (10-106copies), reliability (repeatability/reproducibility) and sensitivity (detection/quantification limits) were evaluated for a minimum of 10-15 assays. Diagnostic validation was achieved by two independent reference laboratories, the Instituto de Salud Carlos III (ISCIII), (Madrid, Spain) and the Public Health England (PHE; Colindale, London, UK).ResultsThe GPS™ RT-qPCR primers and probe showed the highest number of mismatches with the closet related non-SARS-CoV-2 coronavirus, including some indels. The kits passed all parameters of validation with strict acceptance criteria. Results from reference laboratories 100% correlated with these obtained by suing reference methods and received an evaluation with 100% of diagnostic sensitivity and specificity.ConclusionsThe GPS™ CoVID-19 dtec-RT-qPCR Test, available with full analytical and diagnostic validation, represents a case of efficient transfer of technology being successfully used since the pandemic was declared. The analysis suggested the GPS™ CoVID-19 dtec-RT-qPCR Test is the more exclusive by far.
PtrR (YneJ) is a novelE. colitranscription factor regulating the putrescine stress response and glutamate utilization
Authors: Rodionova Irina A. , Gao Ye , Sastry Anand , Monk Jonathan , Wong Nicholas , Szubin Richard , Lim Hyungyu , Zhang Zhongge , Saier Milton H. , Palsson Bernhard 
Published: April 2020

ABSTRACTAlthough polyamines, such as putrescine (Ptr), induce envelope stress for bacteria, they are important as nitrogen and carbon sources. Ptr utilization inEscherichia coliinvolves protein glutamylation, and glutamate stands at a crossroads between catabolism and anabolism. This communication reports that the transcription factor YneJ, here renamed PtrR, is involved in the regulation of a small regulatory RNA gene,fnrS, and an operon,yneIHGF, encoding succinate-semialdehyde dehydrogenase, Sad (YneI), glutaminase, GlsB (YneH), and several other genes. TheyneIpromoter is activated during putrescine utilization under nitrogen/carbon starvation conditions, and we show that PtrR is important for the putrescine stress response. It is also a repressor offnrSgene expression, involved in the cascade regulation of mRNA synthesis for themarAandsodBgenes, involved in antibiotic responses. PtrR transcriptional regulation offnrSleads to a regulatory cascade induced by this small RNA that affects mRNA levels ofompFand the multidrug resistance regulator, MarA. We propose that PtrR functions as a dual activator/repressor, and that its regulation is important for the responses to different stress conditions involving L-glutamine/L-glutamate and putrescine utilization.IMPORTANCEPutrescine is an important source of nitrogen for many organisms, but it also induces stress. Although its metabolism has been studied extensively, the regulatory mechanisms that control the stress response are still poorly understood. This study reveals that the HTH-type transcriptional regulator, YneJ inEscherichia coli, here re-named PtrR, is important for the putrescine stress response, in part because it plays a role in outer membrane porin regulation as a sensor in a regulatory cascade. Direct PtrR transcriptional regulation of thefnrS, yneI (sad), gltSandptrRgenes is documented and rationalized, and nine PtrR binding sites were identified using ChIP-Exo. AptrRmutant exhibited altered resistance to a tetracycline group of antibiotics under microaerophilic conditions, suggesting that PtrR indirectly controls expression of porin genes such asompF.
Advanced Rock Climbers Exhibit Greater Finger Force and Resistance to Fatigue Compared to Novices During Treadwall Climbing
Authors: Ferrara Philip F. , Becker James , Seifert John G. 
Published: April 2020

AbstractBackgroundThe purpose of the study was to investigate the effects of rock climbing experience on time to fatigue (TTF), finger flexor force production relative to body weight (REL FP), and changes in finger flexor muscle activity during tread wall climbing.MethodsEight advanced and seven novice sport rock climbers performed a climbing protocol on a treadwall system. The protocol consisted of climbing for six 5-minute intervals or until voluntary failure. A mounted force plate was used to measure finger force production before and after the climbing protocol. Subjects performed a 20-second maximum voluntary isometric contraction (MVIC) against the force plate with the dominant and non-dominant fingertips in a common climbing hand configuration known as a half crimp. Muscle activity was monitored with electromyographic electrodes placed bilaterally over the subject’s flexor digitorum superficialis. Median frequency (MF) and root mean square (RMS) were analyzed. The treadwall was set at a difficulty of 9 IRCRA/5.9 YDS. It rotated at 7 m/min and was fixed at 7° overhanging.ResultsSignificant group differences were observed in subject characteristics, TTF (30±0 vs. 25.7±3.6 min), REL FP (5.6±1.2 vs. 3.2±0.9 N/kg BW), ΔFP (+1.5±12.3% vs. -31±16%), and ΔMF (+6.3±22.4% vs. -17.6±10.9%).ConclusionThe results of this study demonstrate that advanced climbers possess greater finger flexor force production and resistance to fatigue compared to novices during bouts of climbing on a treadwall system. This may be attributed to physiological changes due to years of training, such as metabolic adaptations and oxygenation capacity in the forearm musculature.
Subtelomeric regions and a repeat-rich chromosome harbor multicopy effector gene clusters with variable conservation in multiple plant pathogenicColletotrichumspecies
Authors: Gan Pamela , Hiroyama Ryoko , Tsushima Ayako , Masuda Sachiko , Shibata Arisa , Ueno Akiko , Kumakura Naoyoshi , Narusaka Mari , Hoat Trinh Xuan , Narusaka Yoshihiro , Takano Yoshitaka , Shirasu Ken 
Published: April 2020

AbstractMembers of theColletotrichum gloeosporioidesspecies complex are causal agents of anthracnose in a wide range of commercially important plants. To provide an in-depth overview of its diversity, we sequenced the genomes of fungi belonging to this group, including multiple strains ofC. fructicola(Cf) andC. siamense(Cs), as well as representatives of three previously unsequenced species,C. aenigma(Ca),C. tropicaleandC. viniferum. Comparisons between multipleCfandCsstrains led to the identification of accessory regions that show variable conservation in both lineages. These accessory regions encode effector candidate genes, including homologs of previously characterized effectors, organized in clusters of conserved synteny with copy number variations in different strains ofCf, CsandCa. Analysis of highly contiguous assemblies ofCf, CsandCastrains revealed the association of such accessory effector gene clusters with subtelomeric regions and repeat-rich minichromosomes and provided evidence of gene transfer between these two genomic compartments. In addition, expression analysis indicated that paralogs associated with clusters of conserved synteny showed a tendency for correlated gene expression. These data highlight the importance of subtelomeric regions and repeat-rich chromosomes to the genome plasticity ofColletotrichumfungi.
Self-Reported Sleep Relates to Microstructural Hippocampal Decline in β-Amyloid Positive Adults Beyond Genetic Risk
Authors: Grydeland Håkon , Sederevičius Donatas , Wang Yunpeng , Bartrés-Faz David , Bertram Lars , Dobricic Valerija , Düzel Sandra , Ebmeier Klaus P. , Lindenberger Ulman , Nyberg Lars , Pudas Sara , Sexton Claire E. , Solé-Padullés Cristina , Walhovd Kristine B. , Fjell Anders M. 
Published: April 2020

AbstractBackgroundTo test the hypothesis that worse self-reported sleep relates to memory decay and reduced hippocampal integrity as indexed by increased intra-hippocampal water diffusion, and that the relations are stronger in the presence of β-amyloid (Aβ) accumulation, a marker of Alzheimer’s disease (AD) pathology.MethodsTwo-hundred and forty-three cognitively healthy participants, aged 19-81 years, completed the Pittsburgh Sleep Quality Index, and 2 diffusion tensor imaging sessions, on average 3 years apart, allowing measures of decline in hippocampal microstructural integrity as indexed by increased mean diffusivity. We measured memory decay using delayed recall from the California Verbal Learning Test.18F-Flutemetamol positron emission tomography, in 108 participants above 44 years of age, yielded 23 Aβ positive. Genotyping enabled controlling forAPOEε4 status, and polygenic scores for sleep efficiency and AD.ResultsWorse global sleep quality and sleep efficiency related to more rapid reduction in hippocampal microstructural integrity over time. Focusing on sleep efficiency, the relation was stronger in presence of Aβ accumulation. Sleep efficiency related to memory decay indirectly via hippocampal integrity decline. The results were not explained by genetic risk for sleep efficiency and AD.ConclusionsPoor self-reported sleep efficiency related to decline in hippocampal integrity, especially in the presence of Aβ accumulation. Poor sleep and hippocampal microstructural decline may partly explain memory decline in older adults with Aβ pathology. The relationships were not explained by genetic risk. Poor self-reported sleep efficiency might constitute a risk factor for AD, although the causal mechanisms driving the of observed associations remain unknown.
Microsaccades during high speed continuous visual search
Authors: Martin Jacob G. , Davis Charles E. , Riesenhuber Maximilian , Thorpe Simon J. 
Published: April 2020

ABSTRACTHere, we provide an analysis of the microsaccades that occurred during continuous visual search and targeting of small faces that we pasted either into cluttered background photos or into a simple gray background. Subjects continuously used their eyes to target singular 3-degree upright or inverted faces in changing scenes. As soon as the participant’s gaze reached the target face, a new face was displayed in a different and random location. Regardless of the experimental context (e.g. background scene, no background scene), or target eccentricity (from 4 to 20 degrees of visual angle), we found that the microsaccade rate dropped to near zero levels within only 12 milliseconds after trial onset. There were almost never any microsaccades before the saccade to the face. One subject completed 118 consecutive trials without a single microsaccade. However, in about 20% of the trials, there was a single corrective microsaccade that occurred almost immediately after the preceding saccade’s offset. These corrective microsaccades were task oriented because their facial landmark targeting distributions matched those of saccades within both the upright and inverted face conditions. Our findings show that a single feedforward pass through the visual hierarchy for each stimulus is likely all that is needed to effectuate prolonged continuous visual search. In addition, we provide evidence that microsaccades can serve perceptual functions like correcting saccades or effectuating task-oriented goals during continuous visual search.
Develope Micro clonal -propagation protocol forOxytenanthera abyssinica A.Rich. Munroto large scale micro-propagation
Authors: Admas Adugnaw , Kidane Berhane , Admasu Melaku , Misga Tesaka 
Published: April 2020

ABSTRACTIn Ethiopia,Oxytenanthera abyssinica A.Rich. Munrohas varies economic importance. However, conventional propagation methods ofO. abyssinicaare generally inefficient due to their low multiplication rate, time consuming, labor intensive, and too costly. The objective of this study was to develop a protocol for mass micropropagation of O. abyssinica through seed culture. Murashige and Skoog (MS) medium augmented with 6-Benzylaminopurine (BAP) was used for shoot initiation and multiplication. For in vitro rooting, MS medium supplemented with 3-Indole –butric acid (IBA) was used.In shoot initiation experiment all viable seeds were proliferated in 5-7 days of culturing. In shoot multiplication at 0.004 g/L BAP was Sucssefuly shoot multiplied, also best root responding were found at 0.005 g/l IBA.The present optimized protocol enables for any acters who needs large numbers of low land bamboo seedling for industery, small and micro enterprize or for reafforestation programms.
Rational design of protein-specific folding modifiers
Authors: Das Anirban , Yadav Anju , Gupta Mona , Purushotham R , Terse Vishram L. , Vishvakarma Vicky , Singh Sameer , Nandi Tathagata , Mandal Kalyaneswar , Gosavi Shachi , Das Ranabir , Koti Ainavarapu Sri Rama , Maiti Sudipta 
Published: April 2020

AbstractProtein folding can go wrongin vivoandin vitro, with significant consequences for the living cell and the pharmaceutical industry, respectively. Here we propose a general design principle for constructing small peptide-based protein-specific folding modifiers. We construct a ‘xenonucleus’, which is a pre-folded peptide that resembles the folding nucleus of a protein, and demonstrate its activity on the folding of ubiquitin. Using stopped-flow kinetics, NMR spectroscopy, Förster Resonance Energy transfer, single-molecule force measurements, and molecular dynamics simulations, we show that the ubiquitin xenonucleus can act as an effective decoy for the native folding nucleus. It can make the refolding faster by 33 ± 5% at 3 M GdnHCl. In principle, our approach provides a general method for constructing specific, genetically encodable, folding modifiers for any protein which has a well-defined contiguous folding nucleus.
Subcortical Circuits Mediate Communication Between Primary Sensory Cortical Areas
Authors: Lohse Michael , Dahmen Johannes C. , Bajo Victoria M. , King Andrew J. 
Published: April 2020

AbstractIntegration of information across the senses is critical for perception and is a common property of neurons in the cerebral cortex, where it is thought to arise primarily from corticocortical connections. Much less is known about the role of subcortical circuits in shaping the multisensory properties of cortical neurons. We show that stimulation of the whiskers causes widespread suppression of sound-evoked activity in mouse primary auditory cortex (A1). This suppression depends on the primary somatosensory cortex (S1), and is implemented through a descending circuit that links S1, via the auditory midbrain, with thalamic neurons that project to A1. Furthermore, a direct pathway from S1 has a facilitatory effect on auditory responses in higher-order thalamic nuclei that project to other brain areas. Crossmodal corticofugal projections to the auditory midbrain and thalamus therefore play a pivotal role in integrating multisensory signals and in enabling communication between different sensory cortical areas.