bluuebunny/crossref_metadata_2025_split huggingface dataset:
Encoding Variability: When Pattern Reactivation Does Not Benefit Context Memory
Authors: Sievers Carolin , Smith Fraser W. , Saada Janak , Simons Jon S. , Renoult Louis 
Published: March 2019

AbstractA growing body of evidence suggests that neural pattern reactivation supports successful memory formation across multiple study episodes. Previous studies investigating the beneficial effects of repeated encoding typically presented the same stimuli repeatedly under the same encoding task instructions. In contrast, repeating stimuli in different contexts is associated with superior item memory, but poorer memory for contextual features varying across repetitions. In the present functional magnetic-resonance imaging (fMRI) study, we predicted dissociable mechanisms to underlie the successful formation of context memory when the context in which stimuli are repeated is either held constant or varies at each stimulus presentation. Twenty participants studied names of famous people four times, either in the same task repeatedly, or in four different encoding tasks. This was followed by a surprise recognition memory test, including a source judgement about the encoding task. Behaviourally, different task encoding compared to same task encoding was associated with fewer correct context memory judgements but also better item memory, as reflected in fewer misses. Searchlight representational similarity analysis revealed fMRI pattern reactivation in the posterior cingulate cortex to be higher for correct compared to incorrect source memory judgements in the same task condition, with the opposite pattern being observed in the different task condition. It was concluded that higher levels of pattern reactivation in the posterior cingulate cortex index generalisation across context information, which in turn may improve item memory performance during encoding variability but at the cost of contextual features.
Supervised dimension reduction for large-scale “omics” data with censored survival outcomes under possible non-proportional hazards
Authors: Spirko-Burns Lauren , Devarajan Karthik 
Published: March 2019

AbstractThe past two decades have witnessed significant advances in high-throughput “omics” technologies such as genomics, proteomics, metabolomics, transcriptomics and radiomics. These technologies have enabled simultaneous measurement of the expression levels of tens of thousands of features from individual patient samples and have generated enormous amounts of data that require analysis and interpretation. One specific area of interest has been in studying the relationship between these features and patient outcomes, such as overall and recurrence-free survival, with the goal of developing a predictive “omics” profile. Large-scale studies often suffer from the presence of a large fraction of censored observations and potential time-varying effects of features, and methods for handling them have been lacking. In this paper, we propose supervised methods for feature selection and survival prediction that simultaneously deal with both issues. Our approach utilizes continuum power regression (CPR) - a framework that includes a variety of regression methods - in conjunction with the parametric or semi-parametric accelerated failure time (AFT) model. Both CPR and AFT fall within the linear models framework and, unlike black-box models, the proposed prognostic index has a simple yet useful interpretation. We demonstrate the utility of our methods using simulated and publicly available cancer genomics data.
Neuroanatomical Correlates in Bilinguals: The Case of Children and Elderly
Authors: García-Pentón Lorna , Fernández Yuriem , Duñabeitia Jon Andoni , Pérez Alejandro , Carreiras Manuel 
Published: March 2019

ABSTRACTHow bilingualism modulates brain areas beyond the language regions is still controversial. Through a comprehensive set of analyses on brain structure, we investigated brain differences between Basque-Spanish bilinguals and monolinguals in children and the elderly, the most sensitive target groups to detect potential brain differences. In particular, we employed Diffusion MRI in combination with T1-MRI, network-based statistics and a graph-theoretical approach to investigate differences between bilinguals and monolinguals in structural connectivity and topological properties of brain networks. Additionally, regional grey and white matter structural differences between groups were examined. The findings suggest that the effects of bilingualism on brain structure are not solid but unstable. However, lifetime experience of active bilingualism may lead to increased neural reserve in ageing, since better global network graph-efficiency has been observed in the elderly lifelong bilinguals compared to monolinguals.
Prediction of inter-residue contacts with DeepMetaPSICOV in CASP13
Authors: Kandathil Shaun M. , Greener Joe G. , Jones David T. 
Published: March 2019

AbstractIn this article, we describe our efforts in contact prediction in the CASP13 experiment. We employed a new deep learning-based contact prediction tool, DeepMetaPSICOV (or DMP for short), together with new methods and data sources for alignment generation. DMP evolved from MetaPSICOV and DeepCov and combines the input feature sets used by these methods as input to a deep, fully convolutional residual neural network. We also improved our method for multiple sequence alignment generation and included metagenomic sequences in the search. We discuss successes and failures of our approach and identify areas where further improvements may be possible. DMP is freely available at:https://github.com/psipred/DeepMetaPSICOV.
Progressive recruitment of distal MEC-4 channels determines touch response strength inC. elegans
Authors: Katta S. , Sanzeni A. , Das A. , Vergassola M. , Goodman M.B. 
Published: March 2019

AbstractTouch deforms, or strains, the skin beyond the immediate point of contact. The spatiotemporal nature of the touch-induced strain fields depend on the mechanical properties of the skin and the tissues below. Somatosensory neurons that sense touch branch out within the skin and rely on a set of mechano-electrical transduction channels distributed within their dendrites to detect mechanical stimuli. Here, we sought to understand how tissue mechanics shape touch-induced mechanical strain across the skin over time and how individual channels located in different regions of the strain field contribute to the overall touch response. We leveragedC. elegans’touch receptor neurons (TRNs) as a simple model amenable toin vivowhole-cell patch clamp recording and an integrated experimental-computational approach to dissect the mechanisms underlying the spatial and temporal dynamics that we observed. Consistent with the idea that strain is produced at a distance, we show that delivering strong stimuli outside the anatomical extent of the neuron is sufficient to evoke MRCs. The amplitude and kinetics of the MRCs depended on both stimulus displacement and speed. Finally, we found that the main factor responsible for touch sensitivity is the recruitment of progressively more distant channels by stronger stimuli, rather than modulation of channel open probability. This principle may generalize to somatosensory neurons with more complex morphologies.SummaryThrough experiment and simulation, Kattaet al. reveal that pushing faster and deeper recruits more and more distant mechano-electrical transduction channels during touch. The net result is a dynamic receptive field whose size and shape depends on tissue mechanics, stimulus parameters, and channel distribution within sensory neurons.
Genomic landscape of the global oak phylogeny
Authors: Hipp Andrew L. , Manos Paul S. , Hahn Marlene , Avishai Michael , Bodénès Cathérine , Cavender-Bares Jeannine , Crowl Andrew , Deng Min , Denk Thomas , Fitz-Gibbon Sorel , Gailing Oliver , González-Elizondo M. Socorro , González-Rodríguez Antonio , Grimm Guido W. , Jiang Xiao-Long , Kremer Antoine , Lesur Isabelle , McVay John D. , Plomion Christophe , Rodríguez-Correa Hernando , Schulze Ernst-Detlef , Simeone Marco C. , Sork Victoria L. , Valencia-Avalos Susana 
Published: March 2019

SummaryThe tree of life is highly reticulate, with the history of population divergence buried amongst phylogenies deriving from introgression and lineage sorting. In this study, we test the hypothesis that there are regions of the oak (Quercus, Fagaceae) genome that are broadly informative about phylogeny and investigate global patterns of oak diversity.We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing ca. 250 oak species to infer a time-calibrated phylogeny of the world’s oaks. We use reversible-jump MCMC to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20,000 RAD-seq loci back to a recently published oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny.Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification due to climatic transitions or ecological opportunity.The support we find for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.
On Transformative Adaptive Activation Functions in Neural Networks for Gene Expression Inference
Authors: Kunc Vladimír , Kléma Jiří 
Published: March 2019

AbstractMotivationGene expression profiling was made cheaper by the NIH LINCS program that profiles only ~1, 000 selected landmark genes and uses them to reconstruct the whole profile. The D–GEX method employs neural networks to infer the whole profile. However, the original D–GEX can be further significantly improved.ResultsWe have analyzed the D–GEX method and determined that the inference can be improved using a logistic sigmoid activation function instead of the hyperbolic tangent. Moreover, we propose a novel transformative adaptive activation function that improves the gene expression inference even further and which generalizes several existing adaptive activation functions. Our improved neural network achieves average mean absolute error of 0.1340 which is a significant improvement over our reimplementation of the original D–GEX which achieves average mean absolute error 0.1637
Cell BLAST: Searching large-scale scRNA-seq databases via unbiased cell embedding
Authors: Cao Zhi-Jie , Wei Lin , Lu Shen , Yang De-Chang , Gao Ge 
Published: March 2019

AbstractAn effective and efficient cell-querying method is critical for integrating existing scRNA-seq data and annotating new data. Herein, we present Cell BLAST, an accurate and robust cell-querying method. Powered by a well-curated reference database and a user-friendly Web server, Cell BLAST (http://cblast.gao-lab.org) provides a one-stop solution for real-world scRNA-seq cell querying and annotation.
Estimating and accounting for genotyping errors in RAD-seq experiments
Authors: Bresadola Luisa , Link Vivian , Buerkle C. Alex , Lexer Christian , Wegmann Daniel 
Published: March 2019

AbstractIn non-model organisms, evolutionary questions are frequently addressed using reduced representation sequencing techniques due to their low cost, ease of use, and because they do not require genomic resources such as a reference genome. However, evidence is accumulating that such techniques may be affected by specific biases, questioning the accuracy of obtained genotypes, and as a consequence, their usefulness in evolutionary studies. Here we introduce three strategies to estimate genotyping error rates from such data: through the comparison to high quality genotypes obtained with a different technique, from individual replicates, or from a population sample when assuming Hardy-Weinberg equilibrium. Applying these strategies to data obtained with Restriction site Associated DNA sequencing (RAD-seq), arguably the most popular reduced representation sequencing technique, revealed per-allele genotyping error rates that were much higher than sequencing error rates, particularly at heterozygous sites that were wrongly inferred as homozygous. As we exemplify through the inference of genome-wide and local ancestry of well characterized hybrids of two Eurasian poplar (Populus) species, such high error rates may lead to wrong biological conclusions. By properly accounting for these error rates in downstream analyses, either by incorporating genotyping errors directly or by recalibrating genotype likelihoods, we were nevertheless able to use the RAD-seq data to support biologically meaningful and robust inferences of ancestry among Populus hybrids. Based on these findings, we strongly recommend carefully assessing genotyping error rates in reduced representation sequencing experiments, and to properly account for these in downstream analyses, for instance using the tools presented here.
Whisker map organization in somatosensory cortex of awake, behaving mice
Authors: Wang Han Chin , LeMessurier Amy M. , Feldman Daniel E. 
Published: March 2019

SUMMARYThe whisker map in rodent somatosensory cortex is well characterized under anesthesia, but its organization during awake sensation, when cortical coding can differ strongly, is unknown. Using a novel behavioral task, we measured whisker receptive fields and maps in awake mice with 2-photon calcium imaging in vivo. During a whisker-attentive task, layer 2/3 pyramidal neurons were sharply tuned, with cells tuned to different whiskers intermixed in each column. This salt-and-pepper organization consisted of small clusters of similarly-tuned neurons superimposed on a mean subcolumnar map. Parvalbumin interneurons had broader tuning, and were more homogeneously tuned to the columnar whisker. During a sound-attentive task, whisker tuning of pyramidal cells was less heterogeneous in each column, and firing correlations increased. Thus, behavioral demands modulate fine-scale map structure, and decorrelate the whisker map during whisker-attentive behavior.
Inter-subject pattern analysis: a straightforward and powerful scheme for group-level MVPA
Authors: Wang Qi , Cagna Bastien , Chaminade Thierry , Takerkart Sylvain 
Published: March 2019

AbstractMultivariate pattern analysis (MVPA) has become vastly popular for analyzing functional neuroimaging data. At the group level, two main strategies are used in the literature. The standard one is hierarchical, combining the outcomes of within-subject decoding results in a second-level analysis. The alternative one, inter-subject pattern analysis, directly works at the group-level by using, e.g, a leave-one-subject-out cross-validation. This study provides a thorough comparison of these two group-level decoding schemes, using both a large number of artificial datasets where the size of the multivariate effect and the amount of inter-individual variability are parametrically controlled, as well as two real fMRI datasets comprising respectively 15 and 39 subjects. We show that these two strategies uncover distinct significant regions with partial overlap, and that inter-subject pattern analysis is able to detect smaller effects and to facilitate the interpretation. The core source code and data are openly available, allowing to fully reproduce most of these results.
Information decomposition of multichannel EMG to map functional interactions in the distributed motor system
Authors: Boonstra Tjeerd W , Faes Luca , Kerkman Jennifer N , Marinazzo Daniele 
Published: March 2019

AbstractThe central nervous system needs to coordinate multiple muscles during postural control. Functional coordination is established through the neural circuitry that interconnects different muscles. Here we used multivariate information decomposition of multichannel EMG acquired from 14 healthy participants during postural tasks to investigate the neural interactions between muscles. A set of information measures were estimated from an instantaneous linear regression model and a time-lagged VAR model fitted to the EMG envelopes of 36 muscles. We used network analysis to quantify the structure of functional interactions between muscles and compared them across experimental conditions. Conditional mutual information and transfer entropy revealed sparse networks dominated by local connections between muscles. We observed significant changes in muscle networks across postural tasks localized to the muscles involved in performing those tasks. Information decomposition revealed distinct patterns in task-related changes: unimanual and bimanual pointing were associated with reduced transfer to the pectoralis major muscles, but an increase in total information compared to no pointing, while postural instability resulted in increased information, information transfer and information storage in the abductor longus muscles compared to normal stability. These findings show robust patterns of directed interactions between muscles that are task-dependent and can be assessed from surface EMG recorded during static postural tasks. We discuss directed muscle networks in terms of the neural circuitry involved in generating muscle activity and suggest that task-related effects may reflect gain modulations of spinal reflex pathways.
A new cryo-EM system for electron 3D crystallography by eEFD
Authors: Yonekura Koji , Ishikawa Tetsuya , Maki-Yonekura Saori 
Published: March 2019

AbstractA new cryo-EM system has been developed and investigated for use in protein electron 3D crystallography. The system provides parallel illumination of a coherent 300 kV electron beam to a sample, filters out energy-loss electrons through the sample with an in-column energy filter, and allows rotational data collection on a fast camera. It also possesses motorized cryo-sample loading and automated liquid-nitrogen filling for cooling of multiple samples. To facilitate its use, we developed GUI programs for efficient operation and accurate structure analysis. Here we report on the performance of the system and first results for thin 3D crystals of the protein complexes, catalase and membrane protein complex ExbBD. Data quality is remarkably improved with this approach, which we name eEFD (electron energy-filtered diffraction of 3D crystals), compared with those collected at 200 kV without energy filtration. Key advances include precise control of the microscope and recordings of lens fluctuations, which the programs process and respond to. We also discuss the merits of higher-energy electrons and filtration of energy-loss electrons in electron 3D crystallography.
Inter-joint and temporal coordination change in very slow walking
Authors: Little Virginia L. , McGuirk Theresa E. , Patten Carolynn 
Published: March 2019

AbstractPurposeVery slow walking has been suggested to be a distinctively different motor behavior than walking at comfortable gait speeds. While kinematic and spatiotemporal gait parameters are known to scale with gait speed, inter-joint coordination during swing remains consistent, at least across comfortable speeds. The purpose of this study was to determine whether coordination patterns serving limb clearance and shortening differ with very slow walking, providing additional support for the premise that very slow walking represents a unique motor behavior.MethodsWe assessed nine healthy adults walking overground at their self-selected speed and two-to-three progressively slower speeds. We collected lower extremity kinematics with 3D motion analysis and quantified joint motion contributions to limb clearance and shortening. We investigated changes in coordination using linear mixed models to determine magnitude and timing differences of joint influence across walking speeds.ResultsHip and knee influences serving limb clearance reduced considerably with slower walking speeds. Similarly, knee influence on limb shortening reduced with very slow walking. Importantly, ankle influence remained unchanged across gait speeds for limb shortening and reduced subtly for limb clearance. Temporally, joint influences on limb clearance varied across walking speeds. Specifically, the temporal order of peak hip and knee influences reversed between comfortable and very slow walking. For limb shortening the timing of ankle influence remained unchanged while the timing of knee influence occurred later in the gait cycle for slower walking speeds.ConclusionsOur results demonstrate temporal coordination and the relative joint contributions serving limb clearance and shortening differ with very slow walking providing additional evidence that slow walking may be a behavior distinct from walking at comfortable speeds.
Segregation of floricolous ants along latitudinal and urbanization gradients
Authors: Vergnes Alan , Rome Quentin , Gayral Inès , Fontaine Colin 
Published: March 2019

AbstractRecent call has been made to study the biogeography of species interactions in order to better understand ecosystems’ states and processes, as well as their response to global anthropogenic disturbances. Ants (Formicidae) are a dominant group of arthropods with a central role in ecosystem functioning. Many ant species, those feeding on liquids, are floricolous and consume nectar. The biogeography of ant-flower interactions is still poorly studied and especially in temperate area. Here we quantify variations in ant-flower interaction frequency in response to latitudinal and urbanization gradients at a country scale.We used data from a flower-visitor monitoring program that includes pictures on 2511 flower plants across Continental France (Mainland) and over 4 years. We analysed the occurrence of the ant-flower interactions along two gradients: latitude and urbanization, this for 10 ant taxa corresponding to different taxonomical level (from family to species).Ants visited 26 % of the sampled plants. Most of the observed ant-flower interaction involved the subfamily Formicinae (82.1 %), followed by Myrmicinae and Dolichoderinae (6.9 % and 4.6 % respectively). Globally, (i) the probability of occurrence was negatively related to latitudes (ii) and to urbanization at lower latitude. (iii) Responses to latitude among sub families, genus and species level responses were segregated and taxonomically aggregated.At lower taxonomic levels we found clear latitudinal niche partitioning among ant taxa suggesting that competition, on both evolutionary and ecological time scales, is a major process structuring ant communities. Finally, our results highlight that the effects of large scale perturbation like urbanization can vary and affect latitudinal gradient.
Neutral genomic signatures of host-parasite coevolution
Authors: Živković Daniel , John Sona , Verin Mélissa , Stephan Wolfgang , Tellier Aurélien 
Published: March 2019

AbstractCoevolution is a selective process of reciprocal adaptation between antagonistic or mutualistic symbionts and their host. Classic population genetics theory predicts the signatures of selection at the interacting loci but not the neutral genome-wide polymorphism patterns. We here build a coevolutionary model with cyclic changes in the host and parasite population sizes. Using an analytical framework, we investigate if and when these population size changes can be observed in the neutral site frequency spectrum of the host and parasite full genome data. We show that polymorphism data sampled over time can capture the changes in the population size of the parasite but not of the host because genetic drift and mutations occur on different time scales in the coevolving species. This is due to the small parasite population size at the onset of the coevolutionary history subsequently undergoing a series of strong bottlenecks. We also show that tracking coevolutionary cycles is more likely for a small amount of parasite per host and for multiple parasite generations per host generation. Our results demonstrate that time sampling of host and parasite full genome data are crucial to infer the co-demographic history of interacting species.