bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tau accumulates in Crohn’s disease gut
Authors: Prigent Alice , Chapelet Guillaume , de Lataillade Adrien de Guilhem , Oullier Thibauld , Durieu Emilie , Bourreille Arnaud , Duchalais Emilie , Hardonnière Kévin , Neunlist Michel , Noble Wendy , Kerdine-Römer Saadia , Derkinderen Pascal , Rolli-Derkinderen Malvyne 
Published: March 2020

AbstractA sizeable body of evidence has recently emerged to suggest that gastrointestinal inflammation might be involved in the development of Parkinson’s disease. There is now strong epidemiological and genetical evidence linking Parkinson’s disease to inflammatory bowel diseases and we recently demonstrated that the neuronal protein alpha-synuclein, which is critically involved in Parkinson’s disease pathophysiology, is upregulated in inflamed segments of Crohn’s colon. The microtubule associated protein tau is another neuronal protein critically involved in neurodegenerative disorders but, in contrast to alpha-synuclein, no data are available about its expression and phosphorylation patterns in inflammatory bowel diseases. Here, we examined the expression levels of tau isoforms, their phosphorylation profile and truncation in colon biopsy specimens from 16 Crohn’s disease and 6 ulcerative colitis patients and compared them to samples from 16 controls. Additional experiments were performed in full thickness segments of colon of 5 Crohn’s disease and 5 control subjects, in primary cultures of rat enteric neurons and in Nrf2 knockout mice. Our results show the upregulation of two main human tau isoforms in the enteric nervous system in Crohn’s disease but not in ulcerative colitis. This upregulation was not transcriptionally regulated but instead likely resulted from a decrease in protein clearance via an Nrf2 pathway. Our findings, which provide the first detailed characterization of tau in Crohn’s disease, suggest that the key proteins involved in neurodegenerative disorders such as alpha-synuclein and tau, might also play a role in Crohn’s disease.
Cortical Depth-Dependent Modeling of Visual Hemodynamic Responses
Authors: Lacy T.C. , Robinson P.A. , Aquino K.M. , Pang J.C. 
Published: March 2020

AbstractA physiologically based three-dimensional (3D) hemodynamic model is used to predict the experimentally observed blood oxygen level dependent (BOLD) responses versus the cortical depth induced by visual stimuli. Prior 2D approximations are relaxed in order to analyze 3D blood flow dynamics as a function of cortical depth. Comparison of the predictions with experimental data for typical stimuli demonstrates that the full 3D model matches at least as well as previous approaches while requiring significantly fewer assumptions and model parameters (e.g., there is no more need to define depth-specific parameter values for spatial spreading, peak amplitude, and hemodynamic velocity).
Co-contraction uses dual control of agonist-antagonist muscles to improve motor performance
Authors: Saliba Christopher M. , Rainbow Michael J. , Selbie W. Scott , Deluzio Kevin J. , Scott Stephen H. 
Published: March 2020

AbstractCo-contraction of agonist-antagonist muscles is commonly observed when performing difficult motor tasks. The benefit of co-contraction is thought to be zero-delay corrections to unexpected disturbances from increased intrinsic muscle impedance. We used upper-limb postural and tracking tasks to characterize the effects of co-contraction on motor corrections to loads applied to the limb. We systematically controlled pre-perturbation muscle activity and showed that co-contraction improves subsequent corrective responses in both tasks. However, substantial improvements in the corrective response are only observed at the time when neural feedback pathways can also contribute. We demonstrate that muscle impedance appears to play a minor role in improving performance. Instead, co-contraction engages a dual agonist-antagonist control strategy to counter disturbances, that is distinct from the control strategy used when not co-contracting or selectively pre-activating a single muscle group. Critically, we showed that this dual agonist-antagonist control strategy improved performance even at low levels of co-contraction.
MeRIP-seq and RNA-seq data of mycelium and spore ofAscosphaera apis, a widespread bee fungal pathogen
Authors: Du Yu , Jiang Haibin , Zhu Zhiwei , Wang Jie , Chen Huazhi , Xiong Cuiling , Zheng Yanzhen , Chen Dafu , Guo Rui 
Published: March 2020

ABSTRACTAscosphaera apisis widespread fungal pathogen of honeybee larvae, causing chalkbrood, a chronic disease that weakens bee health and colony productivity. In this article, mecylia and spores ofA. apiswere respectively purified followed by RNA isolation, cDNA library construction, MeRIP-seq and RNA-seq. A total of 62,551,172, 41,773,158, 49,535,092 and 61,569,610 raw reads were produced from Aam_IP, Aas_IP, Aam_input and Aas_input groups, respectively. After quality control, 58,484,368, 37,381,432, 44,655,434 and 58,739,742 clean reads were obtained. Furthermore, 47,706,205, 31,356,690, 35,259,810 and 44,319,061 clean reads were mapped to the reference genome ofA. apis, including 39,337,036, 26,731,957, 31,987,396 and 40,017,855 unique mapped reads, and 8,369,169, 4,624,733, 3,272,414 and 4,301,206 multiple mapped reads. Among them, 96.31%, 96.51%, 96.82% and 97.11% of clean reads were mapped to exons; 2.09%, 2.31%,1.83% and 1.81% to introns; 1.60%, 1.18%, 1.35% and 1.08% to intergenic regions.Value of the dataThe data can be used to investigate the relationship between the m6A modification extent and the transcript level in theA. apistranscriptome.This dataset contributes to transcriptome-wide characterization of the m6A distributing patterns in mRNAs and non-coding RNAs inA. apismycelium and spore.Current data benefits new functions of m6A modification in the transcripts extensively modified by m6A inA. apismycelium and spore.Our data could be used to characterize differential patterns of the m6A methylation between mycelium and spore ofA. apis.
Ebola virus requires phosphatidylserine scrambling activity for efficient budding and optimal infectivity
Authors: Acciani Marissa D. , Lay-Mendoza Maria F. , Havranek Katherine E. , Duncan Avery M. , Iyer Hersha , Linn Olivia L. , Brindley Melinda A. 
Published: March 2020

AbstractEbola virus (EBOV) interacts with cells using two categories of cell surface receptors, C-type lectins and phosphatidylserine (PS) receptors. PS receptors typically bind to apoptotic cell membrane PS and orchestrate the uptake and clearance of apoptotic bodies. Many viruses coated with PS-containing lipid envelopes, acquired during budding from host cells, can also exploit these receptors for internalization. PS is restricted to the inner leaflet of the plasma membrane in homeostatic cells, an orientation that would be unfavorable for PS receptor-mediated uptake if conserved on the viral envelope. Therefore, it is theorized that viral infection induces host cell PS externalization to the outer leaflet during replication. Cells have several membrane scramblase enzymes that enrich outer leaflet PS when activated. Here, we investigate two scramblases, TMEM16F and XKR8, as possible mediators of cellular and viral envelope surface PS levels during recombinant VSV/EBOV-GP replication and EBOV virus-like particle (VLP) production. We found that rVSV/EBOV-GP and EBOV VLPs produced in XKR8 knockout cells contain decreased levels of PS in their outer leaflets. ΔXKR8-made rVSV/EBOV-GP is 70% less efficient at infecting cells through apoptotic mimicry compared to viruses made in parental cells. Our data suggest that virion surface PS acquisition requires XKR8 activity, whereas TMEM16F activity is not essential. Unexpectedly, we observed defective rVSV/G, rVSV/EBOV-GP, and EBOV VLP budding in ΔXKR8 cells, suggesting that phospholipid scrambling via XKR8 enhances both Ebola infectivity and budding efficiency. Overexpression of XKR8 dramatically increased budding activity, suggesting outer leaflet PS is required for both particle production and increased infectivity.ImportanceThe Democratic Republic of the Congo experienced its deadliest Ebola outbreak from 2018 to 2020, with 3,444 confirmed cases and 2,264 deaths (as of March 12, 2020). Owing to the extensive damage that these outbreaks have caused in Africa, as well as its future epidemic potential, Ebola virus (EBOV) ranks among the top eight priority pathogens outlined by the WHO in 2018. A comprehensive understanding of Ebola entry pathways into target cells is critical for antiviral development and outbreak control. Thus far, host-cell scramblases TMEM16F and XKR8 have each been named as the sole mediator of Ebola envelope surface phosphatidylserine (PS). We assessed the contributions of these proteins using CRISPR knockout cells and two EBOV models: rVSV/EBOV-GP and EBOV VLPs. We observed that XKR8 is required for optimal EBOV envelope PS levels, PS receptor engagement, and particle budding across all viral models, whereas TMEM16F did not play a major role.
A convex optimization framework for gene-level tissue network estimation with missing data and its application in understanding disease architecture
Authors: Dey Kushal K. , Mazumder Rahul 
Published: March 2020

AbstractGenes with correlated expression across individuals in multiple tissues are potentially informative for systemic genetic activity spanning these tissues. In this context, the tissue-level gene expression data across multiple subjects from the Genotype Tissue Expression (GTEx) Project is a valuable analytical resource. Unfortunately, the GTEx data is fraught with missing entries owing to subjects often contributing only a subset of tissues. In such a scenario, standard techniques of correlation matrix estimation with or without data imputation do not perform well. Here we proposeRobocov, a novel convex optimization-based framework for robustly learning sparse covariance or inverse covariance matrices for missing data problems.Robocovproduces more interpretable and less cluttered visual representation of correlation and causal structure in both simulation settings and GTEx data analysis. Simulation experiments also show thatRobocovestimators have a lower false positive rate than competing approaches for missing data problems. Genes prioritized based on the average value ofRobocovcorrelations or partial correlations across tissues are enriched for pathways related to systemic activities such as signaling pathways, heat stress factor, immune function and circadian clock. Furthermore, SNPs linked to these prioritized genes provide unique signal for blood-related traits; in comparison, no disease signal is observed for SNPs linked to genes prioritized by the standard correlation estimator.Robocovis an important stand-alone statistical tool for sparse correlation and causal network estimation for data with missing entries; and when applied to GTEx data, it provides insights into both genetic and autoimmune disease architectures.
Neuron-specific cilia loss alters locomotor responses to amphetamine
Authors: Ramos Carlos , Roberts Jonté B. , Jasso Kalene R. , Ten Eyck Tyler W. , Setlow Barry , McIntyre Jeremy C. 
Published: March 2020

AbstractThe neural mechanisms that underlie responses to drugs of abuse are complex, and impacted by a number of neuromodulatory peptides. Within the past ten years it has been discovered that several of the receptors for neuromodulators are enriched in the primary cilia of neurons. Primary cilia are microtubule-based organelles that project from the surface of nearly all mammalian cells, including neurons. Despite what we know about cilia, our understanding of how cilia regulate neuronal function and behavior is still limited. The primary objective of this study was to investigate the contributions of primary cilia on specific neuronal populations to behavioral responses to amphetamine. To test the consequences of cilia loss on amphetamine-induced locomotor activity we selectively ablated cilia from dopaminergic or GAD2-GABAergic neurons in mice. Cilia loss had no effect on baseline locomotion in either mouse strain. Both female and male mice lacking cilia on dopaminergic neurons showed significantly reduced responses to acute administration of 3.0 mg/kg amphetamine compared to wildtype mice. In contrast, changes in the locomotor response to amphetamine in mice lacking cilia on GAD2-GABAergic neurons were primarily driven by reductions in locomotor activity in males. Following repeated amphetamine administration (1.0 mg/kg/day over 5 days), mice lacking cilia on GAD2-GABAergic neurons exhibited enhanced sensitization of the locomotor stimulant response to the drug, whereas mice lacking cilia on dopaminergic neurons did not differ from their wildtype controls. These results indicate that cilia play neuron-specific roles in both acute and neuroplastic responses to psychostimulant drugs of abuse.
Structural manipulations of a shelter resource reveal underlying preference functions in a shell-dwelling cichlid fish
Authors: Bose Aneesh P. H. , Windorfer Johannes , Böhm Alex , Ronco Fabrizia , Indermaur Adrian , Salzburger Walter , Jordan Alex 
Published: March 2020

AbstractMany animals can modify the environments in which they live, thereby changing the selection pressures they experience. A common example of such niche-construction is the use, creation, or modification of environmental resources for use as nests or shelters. Because these resources often have correlated structural elements, it can be difficult to disentangle the relative contribution of these elements to resource choice, and the preference functions underlying niche-construction behaviour remain hidden. Here, we present an experimental paradigm that uses 3D-scanning, -modelling, and -printing to create replicas of structures that differ with respect to key structural attributes. We show that a niche-constructing, shelldwelling cichlid fish,Neolamprologus multifasciatus, has strong open-ended preference functions for exaggerated shell replicas. Fish preferred shells that were fully intact and either enlarged, lengthened, or had widened apertures. Shell intactness was the most important structural attribute, followed by shell length, then aperture width. We disentangle the relative roles of different shell attributes, which are tightly correlated in the wild, but nevertheless differentially influence shelter choice and therefore niche construction in this species. We highlight the broad utility of our approach when compared to more traditional methods (e.g. two-choice tasks) for studying animal decision-making in a range of contexts.
Spatial integration during active tactile sensation drives elementary shape perception
Authors: Brown Jennifer , Antón Oldenburg Ian , Telian Gregory I. , Griffin Sandon , Voges Mieke , Jain Vedant , Adesnik Hillel 
Published: March 2020

SummaryActive haptic sensation is critical for object identification and manipulation, such as for tool use in humans, or prey capture in rodents. The neural circuit basis for recognizing objects through active touch alone is poorly understood. To address this gap, we combined optogenetics, two photon imaging, and high-speed behavioral tracking in mice solving a novel surface orientation discrimination task with their whiskers. We found that orientation discrimination required animals to summate input from multiple whiskers specifically along the whisker arc. Many animals discriminated the orientation of the stimulusper se, as their performance was invariant to the specific location of the presented stimulus. Two photon imaging showed that populations of neurons in the barrel cortex encoded each of the discriminated orientations, and this coding depended on integration over the whisker array. Finally, acute optogenetic inactivation of the barrel cortex strongly impaired surface orientation discrimination, and even cell-type specific optogenetic suppression of layer 4 excitatory neurons degraded performance, implying a role for superficial layers in this computation. These data suggest a model in which spatial summation over an active haptic array generates representations of an object’s surface orientations. These computations may facilitate the encoding of complex three-dimensional objects during active exploration.
Efficacy ofMethylobacterium oryzaeSupplementedSargassum wightiiSeaweed Liquid Fertilizer on Chilly and Tomato Plant Growth
Authors: Murugan Athiappan , Rubavathi Anandan , Visali Kannan , Neginah Vijayasingh 
Published: March 2020

AbstractLiquid seaweed fertilizer gaining interest due to their use in crop productivity. The present study was designed to evaluate the impact ofMethylobacterium oryzaeamended liquid seaweed fertilizer on domestic plants like chilly and tomato. TheSargassum wightiimethanolic extract was maximum (137 mg/g) among other solvent tested. Extract showed 0.456mg/mL, 1.587 mg/mL, 0.78 mg/g, 5.27 mg/g, 0.63 mg/mL, 0.98 mg/mL, 0.285 g/mL and 0.546 μg/mL of total phenolic, total flavonoids, total chlorophyll, total carotenoids, total protein, total carbohydrates, total lipids and total aminoacids respectively. The maximum survival ofMethylobacterium oryzaewas observed at 40 % ofSargassum wightiiSLF extract with 3%Methylobacterium oryzaeculture concentration and has viability of 750 × 106CFU/l after 6 months. Impact of foliar sprayed liquid fertilizer on the chlorophyll, internode and shoot length had been promising over seed soaked.
Molecular Typing of Human Respiratory Adenoviruses with Universal PCR and Sequencing Primers for Three Major Capsid Genes: Penton base, Hexon, and Fiber
Authors: Zhang Jing , Sridhar Siddhartha , Lau Susanna K. P. , Liu June , Ou Junxian , Yan Yuqian , Zhao Shan , Lan Wendong , Guan Wenyi , Wu Jianguo , Woo Patrick C. Y. , Seto Donald , Zhang Qiwei 
Published: March 2020

AbstractHuman adenoviruses (HAdVs) within species B, C, and E include the predominant types responsible for highly contagious and potentially severe respiratory infections. The traditional method to type these pathogens was based on virus neutralization and hemagglutination assays using antisera, which is both time-consuming and difficult, particularly due to the non-availability of reagents. Molecular typing based on partial characterization of HAdV hexon, as well as the restriction enzyme analysis (REA) of the genomics DNA, is difficult to identify recombinants. Here, a rapid, simple, and cost-effective molecular typing of respiratory HAdVs is presented. This incorporates three pairs of universal PCR primers that target the variable regions of the three major capsid genes,i.e. hexon, penton base and fiber genes. The protocol developed enables detection and typing of respiratory HAdVs within species B, C, and E, as well as of some strains within species D and F. Using this method, we surveyed a total of 100 children with acute respiratory infection caused by HAdVs in Hong Kong, Summer 2014 (July to October). 100 Throat swab specimens were collected. The samples were analyzed by PCR and the sequences were characterized by BLAST. HAdVs were detected in 98 out of 100 (98%) samples. The predominant HAdV type was species B type 3. Among the patients, 74 were of HAdV-B3 (74%), 10 were of HAdV-E4 (10%), 6 were of HAdV-C2 (21.7%), 2 were of HAdV-C6 (2%), 1 were of HAdV-B7 (2%), 1 were of HAdV-C1 (74%), and 2 were of recombinant types. The developed method allows the rapid identification of HAdVs with recombinant genomes, and bypasses the need for whole genome data, for the real-time surveillance of circulating adenovirus strains in immediate outbreaks and populations by clinical microbiologists, public health officers, and epidemiologists.
Unsupervised learning and clustered connectivity enhance reinforcement learning in spiking neural networks
Authors: Weidel Philipp , Duarte Renato , Morrison Abigail 
Published: March 2020

ABSTRACTReinforcement learning is a learning paradigm that can account for how organisms learn to adapt their behavior in complex environments with sparse rewards. However, implementations in spiking neuronal networks typically rely on input architectures involving place cells or receptive fields. This is problematic, as such approaches either scale badly as the environment grows in size or complexity, or presuppose knowledge on how the environment should be partitioned. Here, we propose a learning architecture that combines unsupervised learning on the input projections with clustered connectivity within the representation layer. This combination allows input features to be mapped to clusters; thus the network self-organizes to produce task-relevant activity patterns that can serve as the basis for reinforcement learning on the output projections. On the basis of the MNIST and Mountain Car tasks, we show that our proposed model performs better than either a comparable unclustered network or a clustered network with static input projections. We conclude that the combination of unsupervised learning and clustered connectivity provides a generic representational substrate suitable for further computation.
OmicsDB::Pathogens - A database for exploring functional networks of plant pathogens
Authors: Hansen Bjoern Oest , Olsson Stefan 
Published: March 2020

AbstractPlant pathogens are a great threat to food security. To combat them we need an understanding of how they work. Integrating large-scale omics datasets such as genomes and transcriptomes has been shown to provide deeper insights into many aspects of molecular biology. For a better understanding of plant pathogens, we aim to construct a platform for accessing genomic and gene co-expression networks for a range of pathogens and reference species. Currently we have integrated genomic and transcriptomics data from 10 species (Fusarium graminearum, Ustilago maydis, Blumeria graminis, Neurospora crassa, Schizosaccharomyces pombe, Saccharomyces cerevisiae, Escherichia coli, Arabidopsis thaliana, Mus musculus and Homo sapiens).Here we introduce OmicsDB::Pathogens (http://pathogens.omicsdb.org), a publicly available web portal with an underlying database containing genomic, and transcriptomic data and analysis tools. It allows non-bioinformaticians to browse genomic data and inspect and compare biological networks across species.The information is modelled in a graph-based database, enabling flexibility for querying and future extensions. Tools such as BLAST and Cytoscape.js are available together with the option of performing GO enrichment analysis. The database also enables the user to browse information such as Orthologs, Protein domains and publications citing a given gene.Herein we describe how to use this platform for generating hypotheses for the function of a gene.Availability and ImplementationCurrently, Omicsdb supports networks for 10 organisms and is freely available for public use athttp://pathogens.omicsdb.org