bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasma and ovarian metabolomic responses to chronic stress in female mice
Authors: Zeleznik Oana A. , Huang Tianyi , Patel Chirag J. , Poole Elizabeth M. , Clish Clary B. , Armaiz-Pena Guillermo N. , Nagaraja Archana S. , Eliassen A. Heather , Shutta Katherine H. , Balasubramanian Raji , Kubzansky Laura D. , Hankinson Susan E. , Sood Anil K. , Tworoger Shelley S. 
Published: January 2022

AbstractBackgroundChronic stress may affect metabolism of amino acids, lipids, and other small molecule metabolites, but these alterations may differ depending on tissue evaluated. We examined metabolomic changes in plasma and ovarian tissue samples from female mice due to chronic stress exposure.MethodsAt 12 weeks old, healthy, female, C57 black mice were randomly assigned to three weeks of chronic stress using daily restraint (2 hours/day; n=9) or normal care (n=10). Metabolomic profiling was conducted on plasma and ovarian tissues. Using the Wilcoxon Rank Test, Metabolite Set Enrichment Analysis, and Differential Network Analysis we identified metabolomic alterations occurring in response to restraint stress. All p-values were corrected for multiple testing using the false discovery rate approach.ResultsIn plasma, individual lysophosphatidylcholines (positively) and the metabolite classes carnitines (positively), diacylglycerols and triacylglycerols (inversely) were associated with restraint stress (adjusted-p’s<0.2). In contrast, diacylglycerols and triacylglycerols were increased while carnitines were decreased in ovarian tissue from stressed mice (adjusted-p’s<0.2). However, several metabolites (cholesteryl esters, phosphatidylcholines/ phosphatidylethanolamines plasmalogens and multiple amino acids) were consistently inversely associated with restraint stress in plasma and ovarian tissue (adjusted-p’s<0.2).ConclusionWe identified differences in multiple lipid and amino acid metabolites in plasma and ovarian tissue of female mice after exposure to chronic stress. Some affected metabolites (primarily triacylglycerols and diacylglycerols) exhibited opposite associations with chronic stress in plasma (a marker of systemic influences) versus in ovarian tissue (representing local changes), suggesting research to understand the biological impact of chronic stress needs to consider both systemic and tissue-specific alterations.
Modelling the distribution of rare invertebrates by correcting class imbalance and spatial bias
Authors: Gaul Willson , Sadykova Dinara , White Hannah J. , León-Sánchez Lupe , Caplat Paul , Emmerson Mark C. , Yearsley Jon M. 
Published: January 2022

AbstractAimSoil arthropods are important decomposers and nutrient cyclers, but are poorly represented on national and international conservation Red Lists. Opportunistic biological records for soil invertebrates are often sparse, and contain few observations of rare species but a relatively large number of non-detection observations (a problem known as class imbalance). Robinson et al. (2018) proposed a method for sub-sampling non-detection data using a spatial grid to improve class balance and spatial bias in bird data. For taxa that are less intensively sampled, datasets are smaller, which poses a challenge because under-sampling data removes information. We tested whether spatial under-sampling improved prediction performance of species distribution models for millipedes, for which large datasets are not available. We also tested whether using environmental predictor variables provided additional information beyond what is captured by spatial position for predicting species distributions.LocationIsland of Ireland.MethodsWe tested the spatial under-sampling method of Robinson et al. (2018) by using biological records to train species distribution models of rare millipedes.ResultsUsing spatially under-sampled training data improved species distribution model sensitivity (true positive rate) but decreased model specificity (true negative rate). The decrease in specificity was minimal for rarer species and was accompanied by substantial increases in sensitivity. For common species, specificity decreased more, and sensitivity increased less, making spatial under-sampling most useful for rare species. Geographic coordinates were as good as or better than environmental variables for predicting distributions of two out of six species.Main ConclusionsSpatial under-sampling improved prediction performance of species distribution models for rare soil arthropod species. Spatial under-sampling was most effective for rarer species. The good prediction performance of models using geographic coordinates is promising for modeling distributions of poorly studied species for which little is known about ecological or physiological determinants of occurrence.
Encoding of speech in convolutional layers and the brain stem based on language experience
Authors: Beguš Gašper , Zhou Alan , Zhao T. Christina 
Published: January 2022

ABSTRACTComparing artificial neural networks with outputs of neuroimaging techniques has recently seen substantial advances in (computer) vision and text-based language models. Here, we propose a framework to compare biological and artificial neural computations of spoken language representations and propose several new challenges to this paradigm. The proposed technique is based on a similar principle that underlies electroencephalography (EEG): averaging of neural (artificial or biological) activity across neurons in the time domain, and allows to compare encoding of any acoustic property in the brain and in intermediate convolutional layers of an artificial neural network. Our approach allows a direct comparison of responses to a phonetic property in the brain and in deep neural networks that requires no linear transformations between the signals. We argue that the brain stem response (cABR) and the response in intermediate convolutional layers to the exact same stimulus are highly similar and quantify this observation. The proposed technique not only reveals similarties, but also allows for analysis of the encoding of actual acoustic properties in the two signals: we compare peak latency (i) in cABR relative to the stimulus in the brain stem and in (ii) intermediate convolutional layers relative to the input/output in deep convolutional networks. We also examine and compare the effect of prior language exposure on the peak latency in cABR and in intermediate convolutional layers. Substantial similarities in peak latency encoding between the human brain and intermediate convolutional networks emerge based on results from eight trained networks (including a replication experiment). The proposed technique can be used to compare encoding between the human brain and intermediate convolutional layers for any acoustic property and for other neuroimaging techniques.
A Single Intranasal Dose of Bacterial Therapeutics to Calves Confers Longitudinal Modulation of the Nasopharyngeal Microbiota
Authors: Amat Samat , Timsit Edouard , Workentine Matthew , Schwinghamer Timothy , van der Meer Frank , Guo Yongmei , Alexander Trevor 
Published: January 2022

AbstractTo address the emergence of antimicrobial-resistant pathogens in livestock, microbiome-based strategies are increasingly being sought to reduce antimicrobial use. Here, we describe the intranasal application of bacterial therapeutics (BTs) for mitigating bovine respiratory disease (BRD) and used structural equation modeling to investigate the causal networks after BT application. Beef cattle received i) an intranasal cocktail of previously characterized BT strains, ii) an injection of metaphylactic antimicrobial (tulathromycin), or iii) intranasal saline. Despite being transient colonizers, inoculated BT strains induced longitudinal modulation of the nasopharyngeal bacterial microbiota while showing no adverse effect on animal health. The BT-mediated changes in bacteria included reduced diversity and richness and strengthened cooperative and competitive interactions. In contrast, tulathromycin increased bacterial diversity and antibiotic resistance, and disrupted bacterial interactions. Overall, a single intranasal dose of BTs can modulate the bovine respiratory microbiota, highlighting that microbiome-based strategies have the potential in being utilized to mitigate BRD in feedlot cattle.
Regulation of PDF receptor signaling controlling daily locomotor rhythms in Drosophila
Authors: Li Weihua , Trigg Jennifer S. , Taghert Paul H. 
Published: January 2022

ABSTRACTEach day and in conjunction with ambient daylight conditions, neuropeptide PDF regulates the phase and amplitude of locomotor activity rhythms in Drosophila through its receptor, PDFR, a Family B G protein-coupled receptor (GPCR). We studied the in vivo process by which PDFR signaling turns off, by converting as many as half of the 28 potential sites of phosphorylation in its C terminal tail to a non-phosphorylatable residue (alanine). We report that many such sites are conserved evolutionarily, and their conversion creates a specific behavioral syndrome opposite to loss-of-function phenotypes previously described for pdfr. That syndrome includes increases in the amplitudes of both Morning and Evening behavioral peaks, as well as multi-hour delays of the Evening phase. The precise behavioral effects were dependent on day-length, and most effects mapped to conversion of only a few, specific serine residues near the very end of the protein and specific to its A isoform. Behavioral phase delays under entraining conditions were often, but not always correlated with increases in circadian period. The behavioral phenotypes produced by the most severe PDFR variant were ligand-dependent in vivo, and not a consequence of changes to their pharmacological properties, nor of changes in their surface expression, as measured in vitro. The mechanisms underlying termination of PDFR signaling are complex, subject to regulation that is modified by season, and central to a better understanding of the peptidergic modulation of behavior.AUTHOR SUMMARYIn multi-cellular organisms, circadian pacemakers create output as a series of phase markers across the 24 hour day to allow other cells to pattern diverse aspects of daily rhythmic physiology and behavior. Within circadian pacemaker circuits, neuropeptide signaling is essential to help promote coherent circadian outputs. In the fruit fly Drosophila 150 neurons are dedicated circadian clocks and they all tell the same time. In spite of such strong synchronization, they provide diverse phasic outputs in the form of their discrete, asynchronous neuronal activity patterns. Neuropeptide signaling breaks the clock-generated symmetry and drives many pacemakers away from their preferred activity period in the morning. Each day, neuropeptide PDF is released by Morning pacemakers and delays the phase of activity of specific other pacemakers to later parts of the day or night. When and how the PDF that is released in the morning stops acting is unknown. Furthermore, timing of signal termination is not fixed because day length changes each day, hence the modulatory delay exerted by PDF must itself be regulated. Here we test a canonical model of G protein-coupled receptor physiology to ask how PDF receptor signaling is normally de-activated. We use behavioral measures to define sequence elements of the receptor whose post-translational modifications (e.g., phosphorylation) may define the duration of receptor signaling.
Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line
Authors: Han Shunhua , Dias Guilherme B. , Basting Preston J. , Viswanatha Raghuvir , Perrimon Norbert , Bergman Casey M. 
Published: January 2022

ABSTRACTAnimal cell lines cultured for extended periods often undergo extreme genome restructuring events, including polyploidy and segmental aneuploidy that can impede de novo whole-genome assembly (WGA). In Drosophila, many established cell lines also exhibit massive proliferation of transposable elements (TEs) relative to wild-type flies. To better understand the role of transposition during long-term animal somatic cell culture, we sequenced the genome of the tetraploid Drosophila S2R+ cell line using long-read and linked-read technologies. Relative to comparable data from inbred whole flies, WGAs for S2R+ were highly fragmented and generated variable estimates of TE content across sequencing and assembly technologies. We therefore developed a novel WGA-independent bioinformatics method called “TELR” that identifies, locally assembles, and estimates allele frequency of TEs from long-read sequence data (https://github.com/bergmanlab/telr). Application of TELR to a ∼130x PacBio dataset for S2R+ revealed many haplotype-specific TE insertions that arose by somatic transposition in cell culture after initial cell line establishment and subsequent tetraploidization. Local assemblies from TELR also allowed phylogenetic analysis of paralogous TE copies within the S2R+ genome, which revealed that proliferation of different TE families during cell line evolution in vitro can be driven by single or multiple source lineages. Our work provides a model for the analysis of TEs in complex heterozygous or polyploid genomes that are not amenable to WGA and yields new insights into the mechanisms of genome evolution in animal cell culture.
mTORC2 loss in oligodendrocyte progenitor cells results in regional hypomyelination in the central nervous system
Authors: Dahl Kristin D. , Hathaway Hannah A. , Almeida Adam R. , Bourne Jennifer , Brown Tanya L. , Finseth Lisbet T. , Wood Teresa L. , Macklin Wendy B. 
Published: January 2022

AbstractIn the central nervous system (CNS), oligodendrocyte progenitor cells (OPCs) differentiate into mature oligodendrocytes to generate myelin, which is essential for normal nervous system function. OPC differentiation is driven by signaling pathways such as mTOR (Mechanistic Target of Rapamycin), which functions in two distinct complexes: mTOR complex 1 (mTORC1) and mTOR complex 2 (mTORC2), containing Raptor or Rictor respectively. In the current studies, mTORC2 signaling was selectively deleted from OPCs in PDGFRα-Cre X Rictorfl/fl mice. This study examined developmental myelination in male and female mice, comparing the impact of mTORC2 deletion in the corpus callosum and spinal cord. In both corpus callosum and spinal cord, Rictor loss in OPCs resulted in early reduction in myelin RNAs and some myelin proteins. However, these deficits rapidly recovered in spinal cord, where normal myelin abundance and thickness was noted at post-natal day 21 and 1.5 months. By contrast, the losses in corpus callosum resulted in severe hypomyelination, and increased unmyelinated axons. The current studies focus on uniquely altered signaling pathways following mTORC2 loss in developing oligodendrocytes. A major mTORC2 substrate is phospho-Akt-S473, which was significantly reduced throughout development in both corpus callosum and spinal cord at all ages measured, yet this had little impact in spinal cord. Loss of mTORC2 signaling resulted in decreased expression of actin regulators such as gelsolin in corpus callosum, but only minimal loss in spinal cord. The current study establishes a regionally-specific role for mTORC2 signaling in OPCs, particularly in the corpus callosum.Significance StatementmTORC1 and mTORC2 signaling have differential impact on myelination in the central nervous system. Numerous studies identify a role for mTORC1, but deletion of Rictor (mTORC2 signaling) in late-stage oligodendrocytes had little impact on myelination in the CNS. However, the current studies establish that deletion of mTORC2 signaling from oligodendrocyte progenitor cells results in reduced myelination of brain axons. These studies also establish a regional impact of mTORC2, with little change in spinal cord in these conditional Rictor deletion mice. Importantly, in both, brain and spinal cord, mTORC2 downstream signaling targets were impacted by Rictor deletion. Yet, these signaling changes had little impact on myelination in spinal cord, while they resulted in long term alterations in myelination in brain.
Hemato-vascular specification requiresarnt1andarnt2genes in zebrafish embryos
Authors: Edwards Hailey E. , Edgington Mary Jane , Souder Jaclyn P. , Gorelick Daniel A. 
Published: January 2022

ABSTRACTDuring embryonic development, a subset of cells in the mesoderm germ layer are specified as hemato- vascular progenitor cells, which then differentiate into endothelial cells and hematopoietic stem and progenitor cells. In zebrafish, the transcription factornpas4l, also known ascloche, is required for the specification of hemato-vascular progenitor cells. However, it is unclear ifnpas4lis the sole factor at the top of the hemato-vascular specification cascade. Here we show thatarnt1andarnt2genes are required for hemato-vascular specification. We found thatarnt1;arnt2double homozygous mutant zebrafish embryos (herein calledarnt1/2mutants), but notarnt1orarnt2single mutants, lack blood cells and most vascular endothelial cells.arnt1/2mutants have reduced or absent expression ofetsrpandtal1, the earliest known endothelial and hematopoietic transcription factor genes.npas4land thearntgenes are PAS domain-containing bHLH transcription factors that function as dimers. We found that Npas4l binds both Arnt1 and Arnt2 proteinsin vitro, consistent with the idea that PAS domain- containing bHLH transcription factors act in a multimeric complex to regulate gene expression. Our results demonstrate thatnpas4l,arnt1andarnt2act together to regulate endothelial and hematopoietic cell fate, where each gene is necessary, but by itself not sufficient, to drive hemato-vascular specification. Our results also demonstrate thatarnt1andarnt2act redundantly in a transcriptional complex containingnpas4l, but do not act redundantly when interacting with another PAS domain- containing bHLH transcription factor, the aryl hydrocarbon receptor. Altogether, our data enhance our understanding of hemato-vascular specification and the function of PAS domain-containing bHLH transcription factors.
Multi-sensor optimal deployment based efficient and synchronous data acquisition in large three-dimensional physical similarity simulation
Authors: Hao Yuyu , Li Shugang , Zhang Tianjun 
Published: January 2022

Purpose
This paper aims to propose a deployment optimization and efficient synchronous acquisition method for compressive stress sensors used by stress distribution law research based on the genetic algorithm and numerical simulations. The authors established a new method of collecting the mining compressive stress-strain distribution data to address the problem of the number of sensors and to optimize the sensor locations in physical similarity simulations to improve the efficiency and accuracy of data collection.

Design/methodology/approach
First, numerical simulations were used to obtain the compressive stress distribution curve under specific mining conditions. Second, by comparing the mean square error between a fitted curve and simulation data for different numbers of sensors, a genetic algorithm was used to optimize the three-dimensional (3D) spatial deployment of sensors. Third, the authors designed an efficient synchronous acquisition module to allow distributed sensors to achieve synchronous and efficient acquisition of hundreds of data points through a built-in on-board database and a synchronous sampling communication structure.

Findings
The sensor deployment scheme was established through the genetic algorithm, A synchronous and selective data acquisition method was established for reduced the amount of sensor data required under synchronous acquisition and improved the system acquisition efficiency. The authors obtained a 3D compressive stress distribution when the advancement was 200 m on a large-scale 3D physical similarity simulation platform.

Originality/value
The proposed method provides a new optimization method for sensor deployment in physical similarity simulations, which improves the efficiency and accuracy of system data acquisition, providing accurate acquisition data for experimental data analysis.
The impact of COVID-19 on destination visit intention and local food consumption
Authors: Dedeoğlu Bekir Bora , Mariani Marcello , Shi Fangfang , Okumus Bendegul 
Published: January 2022

PurposeThis paper aims to investigate the relationships between motivation and intention to consume local food and between intention to consume local food and intention to visit the destination of that food's origin while examining the moderating effect of risk perception associated with coronavirus disease 2019 (COVID-19).Design/methodology/approachData were collected from two samples of potential Chinese tourists in the contexts of Italian and Thai food. Data obtained from 264 Chinese respondents for Italian food and 277 Chinese respondents for Thai food were analyzed. Partial least squares structural equation modeling was utilized to test the research model.FindingsThe results indicate that, while motivational factors such as cultural experience, novelty and sensory appeal influence potential Chinese tourists' intention to consume Italian food, motivational factors such as cultural experience, health concern, novelty and sensory appeal influence tourists' intention to consume Thai food. The authors found that intention to consume local food positively influences tourists' intention to visit both destinations (Italy and Thailand). Moreover, tourists' risk perceptions of COVID-19 negatively moderate the effect of cultural experience and novelty on the intention to consume Italian food. Regarding the intention to consume Thai food, the authors found that tourists' risk perceptions have a diminishing effect on all motivational factors.Originality/valueThis pioneering study examines the role of COVID-19-related risk perception on the relationships among motivation of local food consumption, intention of local food consumption and destination visit intention in the context of two destination countries. It reveals cross-country differences of the negative effect pertaining to the risk perceptions of COVID-19, which has important implications for international destination marketing.
Workplace incivility and its socio-demographic determinants in India
Authors: Chaudhary Richa , Lata Madhu , Firoz Mantasha 
Published: January 2022

Purpose
The purpose of this study is to present an empirical account of the prevalence and socio-demographic determinants of workplace incivility (experienced and instigated) in the Indian workplace.

Design/methodology/approach
The study sample consisted of 1,133 employees working in service organizations mainly banks, hotels, academic institutions and information technology firms. The authors tested the proposed model on the same set of respondents in two different studies. The phenomenon of instigated incivility and its determinants were examined in Study 1, while Study 2 looked at experienced incivility and its antecedents. The data were analyzed using univariate, bivariate, and multivariate statistical operations in SPSS 24.

Findings
The results of both studies revealed that employees’ age, gender, educational qualification, position, nature of the organization, type of the organization and duration of working hours significantly predict the onset of workplace incivility. Nevertheless, marital status and tenure failed to predict the manifestation of uncivil behaviors in the organization.

Research limitations/implications
The scope of this study was restricted to the Indian service sector with a focus on only two types of workplace incivility (instigated and experienced).

Practical implications
The managers are advised to be mindful of employees’ socio-demographic differences while devising interventions to tackle the issues of uncivil acts at work.

Originality/value
This study is one of the pioneer attempts to explore the impact of socio-demographic factors on employees’ tendency to instigate and experience incivility at work in India. In doing so, the study enriches the scant literature on workplace incivility by establishing the role of individual differences in determining the occurrence of incivility in the workplace.