bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insomnia, excessive daytime sleepiness, anxiety, depression and socioeconomic status among customer service employees in Canada
Authors: Sosso FA Etindele 
Published: August 2019

ABSTRACTObjectivesThe present study alerts on the potential effect of working full time in a call center as a risk factor for neuropsychiatric illnesses. It is the first study investigating deeply presence of anxiety, depression, insomnia and excessive daytime sleepiness among a large population of customer service employees. It has 3 specifics goals which were (1) document presence of sleep disorders among customer service advisors (2) document presence of anxiety and depression in this population (3) determine the influence of the socioeconomic status, duration in position and full time or part-time shift on the diseases above.FindingsIt was found that the majority of people working in customer service are undergraduate students or at a secondary/high school degree. They worked full time, are single and have reported at least two of the neuropsychiatric disorders assessed in the present study. Among customer service advisors enrolled in this study, all neuropsychiatric disorders investigated were present and significantly higher for those working full time. Perceived socioeconomic status (pSES) was almost similar for full time and part time workers with a mean score of 4.8 on the MacArthur scale of subjective social status. Results revealed that duration in position was an excellent predictor of insomnia, sleepiness and anxiety (respectively with R2=91,83%, R2=81,23% and R2=87,46%) but a moderate predictor of depression (R2=69,14%). The pSES was a moderate predictor of sleep disorders (respectively R2=62,04% for insomnia and R2=53,62% for sleepiness) but had a strong association with anxiety and depression (R2=82,95% for anxiety and R2=89,77% for depression). It was found that insomnia and anxiety are more prevalent for immigrants and international students compared to Canadians, while depression was similarly higher for Canadian and immigrants compared to international students. It was found that sleepiness has the same trend in the three subgroups.ConclusionCustomer service employees are exposed to a continuous stimulation of their cognitive functions in addition to different stressors which can progressively and silently damage the nervous system. Investigations on mental and physical health of customer service advisors are worthy of interest, and understanding how their work, their rotating shifts and their socioeconomic status influence their resilience and their performance at work; may help comprehension of similar health issues emerging in similar populations with similar occupations.
Relationships between landscape structure and the prevalence of two tick-borne infectious agents, Anaplasma phagocytophilum and Borrelia burgdorferi sensu lato, in small mammal communities
Authors: Perez Grégoire , Bastian Suzanne , Chastagner Amélie , Agoulon Albert , Rantier Yann , Vourc’h Gwenaël , Plantard Olivier , Butet Alain 
Published: August 2019

AbstractContextBy modifying ecosystems, land cover changes influence the emergence, the spread and the incidence of vector-borne diseases.ObjectiveThis study aimed at identifying associations between landscape structure and the prevalence of two tick-borne infectious agents, Anaplasma phagocytophilum and Borrelia burgdorferi s.l., in small mammal communities.MethodsSmall mammals were sampled in 24 sites along a gradient of woodland fragmentation and hedgerow network density, and screened for infectious agents with real-time PCR techniques. For each site, structural variables (composition and configuration) of the surrounding landscape at various scales (0-500 m) and variables of wooded habitats connectivity based on graph theory and least cost path distances for the two dominant species, bank voles (Myodes glareolus) and wood mice (Apodemus sylvaticus), were computed.ResultsThe A. phagocytophilum prevalence increased with wooded habitats cover (0-500 m), likely through host population size, and increased slightly with bank vole abundance, which has a higher reservoir competence than wood mouse. The B. burgdorferi s.l. prevalence increased with wooded ecotones only at local scales (50-100 m). Wooded habitats connectivity measures did not improve models built with simple land cover variables. A more marked spatial pattern was observed for the prevalence of A. phagocytophilum than B. burgdorferi s.l..ConclusionsThis study highlights the interest of considering together the ecology of infectious agents (e.g. host specificity) and the host species community ecology to better understand the influence of the landscape structure on the spatial distribution of vector-borne infectious agents.
Comparison of RNA Isolation Methods on RNA-Seq: Implications for Differential Expression and Meta-Analyses
Authors: Scholes Amanda N. , Lewis Jeffrey A. 
Published: August 2019

AbstractTechnical variation across different batches of RNA-seq experiments can clearly produce spurious signals of differential expression and reduce our power to detect true differences. Thus, it is important to identify major sources of these so-called “batch effects” to eliminate them from study design. Based on the different chemistries of “classic” phenol extraction of RNA compared to common commercial RNA isolation kits, we hypothesized that specific mRNAs may be preferentially extracted depending upon method, which could masquerade as differential expression in downstream RNA-seq analyses. We tested this hypothesis and found that phenol extraction preferentially isolated membrane-associated mRNAs, thus resulting in spurious signals of differential expression. Within a self-contained experimental batch (e.g. control versus treatment), the method of RNA isolation had little effect on the ability to identify differentially expressed transcripts. However, we suggest that researchers performing meta-analyses across different experimental batches strongly consider the RNA isolation methods for each experiment.
Development of structure-function coupling in human brain networks during youth
Authors: Baum Graham L. , Cui Zaixu , Roalf David R. , Ciric Rastko , Betzel Richard F. , Larsen Bart , Cieslak Matthew , Cook Philip A. , Xia Cedric H. , Moore Tyler M. , Ruparel Kosha , Oathes Desmond , Alexander-Bloch Aaron , Shinohara Russell T. , Raznahan Armin , Gur Raquel E. , Gur Ruben C. , Bassett Danielle S. , Satterthwaite Theodore D. 
Published: August 2019

ABSTRACTThe protracted development of structural and functional brain connectivity within distributed association networks coincides with improvements in higher-order cognitive processes such as working memory. However, it remains unclear how white matter architecture develops during youth to directly support coordinated neural activity. Here, we characterize the development of structure-function coupling using diffusion-weighted imaging and n-back fMRI data in a sample of 727 individuals (ages 8-23 years). We found that spatial variability in structure-function coupling aligned with cortical hierarchies of functional specialization and evolutionary expansion. Furthermore, hierarchy-dependent age effects on structure-function coupling localized to transmodal cortex in both cross-sectional data and a subset of participants with longitudinal data (n=294). Moreover, structure-function coupling in rostrolateral prefrontal cortex was associated with executive performance, and partially mediated age-related improvements in executive function. Together, these findings delineate a critical dimension of adolescent brain development, whereby the coupling between structural and functional connectivity remodels to support functional specialization and cognition.
Structured Reviews for Data and Knowledge Driven Research
Authors: Queralt-Rosinach Núria , Stupp Gregory S. , Li Tong Shu , Mayers Michael , Hoatlin Maureen E. , Might Matthew , Good Benjamin M. , Su Andrew I. 
Published: August 2019

AbstractMotivationHypothesis generation is a critical step in research and a cornerstone in the rare disease field. Research is most efficient when those hypotheses are based on the entirety of knowledge known to date. Systematic review articles are commonly used in biomedicine to summarize existing knowledge and contextualize experimental data. But the information contained within review articles is typically only expressed as free-text, which is difficult to use computationally. Researchers struggle to navigate, collect and remix prior knowledge as it is scattered in several silos without seamless integration and access. This lack of a structured information framework hinders research by both experimental and computational scientists.ResultsTo better organize knowledge and data, we built a structured review article that is specifically focused on NGLY1 Deficiency, an ultra-rare genetic disease first reported in 2012. We represented this structured review as a knowledge graph, and then stored this knowledge graph in a Neo4j database to simplify dissemination, querying, and visualization of the network. Relative to free-text, this structured review better promotes the principles of findability, accessibility, interoperability, and reusability (FAIR). In collaboration with domain experts in NGLY1 Deficiency, we demonstrate how this resource can improve the efficiency and comprehensiveness of hypothesis generation. We also developed a read-write interface that allows domain experts to contribute FAIR structured knowledge to this community resource. In contrast to traditional free-text review articles, this structured review exists as a living knowledge graph that is curated by humans and accessible to computational analyses. Finally, we have generalized this workflow into modular and repurposable components that can be applied to other domain areas. This NGLY1 Deficiency-focused network is publicly available athttp://ngly1graph.org/.Availability and implementationSource code and network data files are at:https://github.com/SuLab/ngly1-graphandhttps://github.com/SuLab/bioknowledge-reviewer.Contactasu@scripps.edu
Empirically Constrained Network Models for Contrast-dependent Modulation of Gamma Rhythm in V1
Authors: Zachariou Margarita , Roberts Mark , Lowet Eric , De Weerd Peter , Hadjipapas Avgis 
Published: August 2019

AbstractHere we present experimentally constrained computational models of gamma rhythm and use these to investigate gamma oscillation instability. To this end, we extracted empirical constraints for PING (Pyramidal Interneuron Network Gamma) models from monkey single-unit and LFP responses recorded during contrast variation. These constraints implied weak rather than strong PING, connectivity between excitatory (E) and inhibitory (I) cells within specific bounds, and input strength variations that modulated E but not I cells. Constrained models showed valid behaviours, including gamma frequency increases with contrast and power saturation or decay at high contrasts. The route to gamma instability involved increased heterogeneity of E cells with increasing input triggering a breakdown of I cell pacemaker function. We illustrate the model’s capacity to resolve disputes in the literature. Our work is relevant for the range of cognitive operations to which gamma oscillations contribute and could serve as a basis for future, more complex models.
Neurons expressing pathological Tau protein trigger dramatic changes in microglial morphology and dynamics
Authors: Hassan-Abdi Rahma , Brenet Alexandre , Bennis Mohamed , Yanicostas Constantin , Soussi-Yanicostas Nadia 
Published: August 2019

AbstractMicroglial cells, the resident macrophages of the brain, are important players in the pathological process of numerous neurodegenerative disorders, including tauopathies, a heterogeneous class of diseases characterized by intraneuronal Tau aggregates. However, microglia response in Tau pathologies remains poorly understood. Here we exploit a genetic zebrafish model of tauopathy, combined with live microglia imaging, to investigate the behaviour of microglia in vivo in the disease context. Results show that while microglia were almost immobile and displayed long and highly dynamic branches in a wild-type context, in presence of diseased neurons cells became highly mobile and displayed morphological changes, with highly mobile cell bodies together with fewer and shorter processes. We also imaged, for the first time to our knowledge, the phagocytosis of apoptotic tauopathic neurons by microglia in vivo and observed that microglia engulfed about as twice materials as in controls. Finally, genetic ablation of microglia in zebrafish tauopathy model significantly increased Tau hyperphosphorylation, suggesting that microglia provide neuroprotection to diseased neurons. Our findings demonstrate for the first time the dynamics of microglia in contact with tauopathic neurons in vivo and open perspectives for the real-time study of microglia in many neuronal diseases.
Musculoskeletal fat imaging and quantification by high-resolution metabolite cycling magnetic resonance spectroscopic imaging at 3 T: A fast method to generate separate distribution maps of lipid components
Authors: Alhulail Ahmad A. , Patterson Debra A. , Xia Pingyu , Zhou Xiaopeng , Lin Chen , Thomas M. Albert , Dydak Ulrike , Emir Uzay E. 
Published: August 2019

AbstractPurposeTo provide a rapid, non-invasive fat quantification technique capable of producing separate lipid component maps.MethodsThe calf muscles in 5 healthy adolescents (age 12-16 years; BMI = 20 ± 3 Kg/m2) were scanned by two different fat fraction (FF) quantification methods. A high-resolution, density-weighted concentric ring trajectory (DW-CRT) metabolite cycling (MC) magnetic resonance spectroscopic imaging (MRSI) technique was implemented to collect data with 0.25 mL resolution within 3 minutes and 16 seconds. For comparative purposes, the standard Dixon technique was performed. The two techniques were compared using structural similarity (SSIM) analysis. Additionally, the difference in the distribution of each lipid over the adolescent calf muscles was assessed based on the MRSI data.ResultsThe proposed MRSI technique provided individual FF maps for eight musculoskeletal lipids identified by LCModel analysis (L09, L11, L13, L15, L21, L23, L53, and L55) with mean SSIM indices of 0.19, 0.04, 0.03, 0.50, 0.45, 0.04, 0.07, and 0.12, respectively compared to that of Dixon’s FF map. Further analysis of voxels with zero SSIM demonstrated an increased sensitivity of FF lipid maps from data acquired using this MRSI technique over the standard Dixon technique. The trend of lipid spatial distribution over calf muscles was consistent with previously published findings in adults.ConclusionThe advantages of this MRSI technique make it a useful tool when individual lipid FF maps are desired within a short scanning time.
Blockade of stromal Gas6 alters cancer cell plasticity, activates NK cells and inhibits pancreatic cancer metastasis
Authors: Ireland Lucy , Luckett Teifion , Schmid Michael C. , Mielgo Ainhoa 
Published: August 2019

AbstractPancreatic ductal adenocarcinoma (PDA) is one of the deadliest cancers due to its aggressive and metastatic nature. PDA is characterized by a rich tumor stroma with abundant macrophages, fibroblasts and collagen deposition that can represent up to 90% of the tumor mass. Activation of the tyrosine kinase receptor AXL and expression of its ligand growth arrest-specific protein 6 (Gas6) correlate with a poor prognosis and increased metastasis in pancreatic cancer patients. Gas6 is a multifunctional protein that can be secreted by several cell types and regulates multiple processes, including cancer cell plasticity, angiogenesis and immune cell functions. However, the role of Gas6 in pancreatic cancer metastasis has not been fully investigated. In these studies we find that, in pancreatic tumors, Gas6 is mainly produced by tumor associated macrophages (TAMs) and cancer associated fibroblasts (CAFs) and that pharmacological blockade of Gas6 partially reverses epithelial-to-mesenchymal transition (EMT) of tumor cells and supports NK cell activation, thereby inhibiting pancreatic cancer metastasis. Our data suggest that Gas6 simultaneously acts on both the tumor cells and the NK cells to support pancreatic cancer metastasis. This study supports the rationale for targeting Gas6 in pancreatic cancer and use NK cells as a potential biomarker for response to anti-Gas6 therapy.
Chemistry of cation hydration and conduction in a skeletal muscle ryanodine receptor
Authors: Wu Zhaolong , Liu Congcong , Yu Hua , Kang Duan , Ma Yinping , Li Xuemei , Zhang Lei , Fan Chun , Li Xin-Zheng , Song Chen , Yin Chang-Cheng , Mao Youdong 
Published: August 2019

AbstractRyanodine receptors (RyRs) are Ca2+-regulated Ca2+channels of 2.2-megadalton in muscles and neurons for calcium signaling. How Ca2+regulates ion conduction in the RyR channels remains elusive. We determined a 2.6-Å cryo-EM structure of rabbit skeletal muscle RyR1, and used multiscale dynamics simulations to elucidate cation interactions with RyR1. We investigated 21 potential cation-binding sites that may together rationalize biphasic Ca2+response of RyR1. The selectivity filter captures a cation hydration complex by hydrogen-bonding with both the inner and outer hydration shells of water molecules. Molecular dynamics simulations suggest that adjacent Ca2+ions moving in concert along ion-permeation pathway are separated by at least two cation-binding sites. Our analysis reveals that RyR1 has been evolved to favor its interactions with two hydration shells of cations.
E3 Ligase UBR5 HECT domain mutations in lymphoma control maturation of B cells via alternative splicing
Authors: Swenson Samantha A. , Gilbreath Tyler J. , Vahle Heather , Hynes-Smith R. Willow , Graham Jared H. , Law Henry Chun Hin , Woods Nicholas T. , Green Michael R. , Buckley Shannon M. 
Published: August 2019

ABSTRACTCoordination of a number of molecular mechanisms including transcription, alternative splicing, and class switch recombination are required to facilitate development, activation, and survival of B cells. Disruption of these pathways can result in malignant transformation. Recently, next generation sequencing has identified a number of novel mutations in mantle cell lymphoma (MCL) patients including the ubiquitin E3 ligase UBR5. Approximately 18% of MCL patients were found to have mutations in UBR5 with the majority of mutations within the HECT domain of the protein which can accept and transfer ubiquitin molecules to the substrate. Determining if UBR5 controls the maturation of B cells is important to fully understand malignant transformation to MCL. To elucidate the role of UBR5 in B cell maturation and activation we generated a conditional mutant disrupting UBR5’s C-terminal HECT domain. Loss of the UBR5 HECT domain leads to a block in maturation of B cells in the spleen and up-regulation of proteins associated with mRNA splicing via the spliceosome. Our studies reveal a novel role of UBR5 in B cell maturation by regulating alternative splicing of key transcripts during B cell development and suggests UBR5 mutations may promote mantle cell lymphoma initiation.KEY POINTSUtilizing a novel mouse model mimicking MCL patient mutations, the loss of UBR5’s HECT domain causes alterations in B cell development.UBR5 mutations lead to stabilization of UBR5 and aberrant splicing.
vH+-ATPase-induced intracellular acidification is critical to glucose-stimulated insulin secretion
Authors: Naik Akshata R. , Formosa Brent J. , Pulvender Rishika G. , Liyanaarachchi Asiri G. , Jena Bhanu P. 
Published: August 2019

ABSTRACTSwelling of secretory vesicles is critical for the regulated expulsion of intra-vesicular contents from cells during secretion. At the secretory vesicle membrane of the exocrine pancreas and neurons, GTP-binding G proteins, vH+-ATPase, potassium channels and AQP water channels, are among the players implicated in vesicle volume regulation. Here we report in insulin secreting MIN6 cells, the requirement of vH+-ATPase-mediated intracellular acidification, on glucose-stimulated insulin release. MIN6 cells exposed to the vH+-ATPase inhibitor Bafilomycin A show decreased acidification of the cytosolic compartment that include insulin-carrying granules. Additionally, a loss of insulin granule association with the cell plasma membrane is demonstrated and results in a decrease in glucose-stimulated insulin secretion and accumulation of intracellular insulin. These results suggest that vH+-ATPase-mediated intracellular acidification is required both at the level of secretory vesicles and the cell plasma membrane for cell secretion.
Predicting the global mammalian viral sharing network using phylogeography
Authors: Albery Gregory F , Eskew Evan A , Ross Noam , Olival Kevin J 
Published: August 2019

AbstractUnderstanding interspecific viral transmission is key to understanding viral ecology and evolution, disease spillover into humans, and the consequences of global change. Prior work has demonstrated that macroecological factors drive viral sharing in some mammalian groups, but analyses have never attempted to predict viral sharing in a pan-mammalian context. Here we show that host phylogenetic similarity and geographic range overlap are strong, nonlinear predictors of viral sharing among species across the entire mammal class. Using these traits, we predict global viral sharing patterns across 4196 mammal species and show that our simulated network successfully predicts viral sharing and reservoir host status using internal validation and an external dataset. We predict high rates of mammalian viral sharing in the tropics, particularly among rodents and bats, and that within- and between-order sharing differs geographically and taxonomically. Our results emphasize the importance of macroecological factors in shaping mammalian viral communities, and provide a robust, general model to predict viral host range and guide pathogen surveillance and conservation efforts.
Intraspecific genomic variation and local adaptation in a young hybrid species
Authors: Cuevas Angélica , Ravinet Mark , Sætre Glenn-Peter , Eroukhmanoff Fabrice 
Published: August 2019

ABSTRACTHybridization increases genetic variation, hence hybrid species may have a strong evolutionary potential once their admixed genomes have stabilized and incompatibilities have been purged. Yet, little is known about how such hybrid lineages evolve at the genomic level following their formation, in particular the characteristics of their adaptive potential, i.e. constraints and facilitations of diversification. Here we investigate how the Italian sparrow (Passer italiae), a homoploid hybrid species, has evolved and locally adapted to its variable environment. Using restriction site-associated DNA sequencing (RAD-seq) on several populations across the Italian peninsula, we evaluate how genomic constraints and novel genetic variation have influenced population divergence and adaptation. We show that population divergence within this hybrid species has evolved in response to climatic variation. As in non-hybrid species, climatic differences may even reduce gene flow between populations, suggesting ongoing local adaptation. We report outlier genes associated with adaptation to climatic variation, known to be involved in beak morphology in other species. Most of the strongly divergent loci among Italian sparrow populations seem not to be differentiated between its parent species, the house and Spanish sparrow. Within the parental species, population divergence has occurred mostly in loci where different alleles segregate in the parent species, unlike in the hybrid, suggesting that novel combinations of parental alleles in the hybrid have not necessarily enhanced its evolutionary potential. Rather, our study suggests that constraints linked to incompatibilities may have restricted the evolution of this admixed genome, both during and after hybrid species formation.