bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simultaneous Modeling of Reaction Times and Brain Dynamics in a Spatial Cuing Task
Authors: Steinkamp Simon R. , Fink Gereon R. , Vossel Simone , Weidner Ralph 
Published: November 2020

AbstractUnderstanding how brain activity translates into behavior is a grand challenge in neuroscientific research. Simultaneous computational modeling of both measures offers to address this question. The extension of the dynamic causal modeling (DCM) framework for BOLD responses to behavior (bDCM) constitutes such a modeling approach. However, only very few studies have employed and evaluated bDCM, and its application has been restricted to binary behavioral responses, limiting more general statements about its validity.This study used bDCM to model reaction times in a spatial attention task, which involved two separate runs with either horizontal or vertical stimulus configurations. We recorded fMRI data and reaction times (n=29) and compared bDCM to classical DCM and a behavioral Rescorla-Wagner model using goodness of fit-statistics and machine learning methods.Data showed that bDCM performed equally well as classical DCM when modeling BOLD responses and better than the Rescorla Wagner model when modeling reaction times. Notably, only using bDCM’s parameters enabled classification of the horizontal and vertical runs suggesting that bDCM seems to be more sensitive than the other models. Although our data also revealed practical limitations of the current bDCM approach that warrant further investigation, we conclude that bDCM constitutes a promising method for investigating the link between brain activity and behavior.
Amplification, not spreading limits rate of tau aggregate accumulation in Alzheimer’s disease
Authors: Meisl Georg , Zuo Yukun , Allinson Kieren , Rittman Timothy , DeVos Sarah , Sanchez Justin S. , Xu Catherine K , Duff Karen E , Johnson Keith A. , Rowe James B , Hyman Bradley T , Knowles Tuomas P J , Klenerman David 
Published: November 2020

AbstractBoth the replication of protein aggregates and their spreading throughout the brain are implicated in the progression of Alzheimer’s disease (AD). However, the rates of these processes are unknown and the identity of the rate-determining process in humans has therefore remained elusive. By bringing together chemical kinetics with measurements of tau seeds and aggregates across brain regions, we are able to quantify their replication rate in human brains. Remarkably, we obtain comparable rates in several different datasets, with 5 different methods of tau quantification, from seed amplification assaysin vitroto tau PET studies in living patients. Our results suggest that the overall rate of accumulation of tau in neocortical regions is limited not by spreading between brain regions but by local replication, which doubles the number of seeds every ~5 years. Thus, we propose that limiting local replication constitutes the most promising strategy to control tau accumulation during AD.
Conformational dynamics of α-synuclein during the interaction with phospholipid nanodiscs by Millisecond Hydrogen Deuterium Exchange Mass Spectrometry
Authors: Oganesyan Irina , Lento Cristina , Tandon Anurag , Wilson Derek J. 
Published: November 2020

AbstractBoth normal and pathological functions of α-synuclein (αSN), an abundant protein in the central and peripheral nervous system, have been linked to its interaction with membrane lipid bilayers. The ability to characterize structural transitions of αSN upon membrane complexation will clarify molecular mechanisms associated with αSN-linked pathologies, including Parkinson’s disease (PD), Multiple Systems Atrophy and other synucleinopathies. In this work, Time-Resolved ElectroSpray Ionization Hydrogen/ Deuterium Exchange Mass Spectrometry (TRESI-HDX-MS) was employed to acquire a detailed picture of αSN’s conformational transitions as it undergoes complexation with nanodisc membrane mimics. Using this approach, αSN interactions with DMPC nanodiscs were shown to be rapid exchanging and to have a little impact on the αSN conformational ensemble. Interactions with nanodiscs containing lipids known to promote amyloidogenesis (e.g., POPG), on the other hand, were observed to induce substantial and specific changes in the αSN conformational ensemble. Ultimately, we identify a region corresponding residues 19-28 and 45-57 of the αSN sequence that is uniquely impacted by interactions with ‘amyloidogenic’ lipid membranes and may therefore play a critical role in pathogenic aggregation.
Seasonal variations in soil fungal communities and co-occurrence networks along an altitudinal gradient in the cold temperate zone of China: A case study on Oakley Mountain
Authors: Ji Li , Zhang Yan , Yang Yuchun , Yang Lixue 
Published: November 2020

AbstractThe biogeography of soil fungi has attracted much attention in recent years; however, studies on this topic have mainly focused on mid- and low-altitude regions. The seasonal patterns of soil fungal community structure and diversity along altitudinal gradients under the unique climatic conditions at high latitudes remain unclear, which limits our insight into soil microbial interactions and the mechanisms of community assembly. In this study, Illumina MiSeq sequencing was used to investigate the spatiotemporal changes in soil fungal communities along an altitudinal gradient (from 750 m to 1420 m) on Oakley Mountain in the northern Greater Khingan Mountains. Altitude had significant impacts on the relative abundances of the dominant phyla and classes of soil fungi, and the interaction of altitude and season significantly affected the relative abundances of Ascomycota and Basidiomycota. The number of soil fungal taxa and Faith’s phylogenetic diversity (PD) index tended to monotonically decline with increasing elevation. Soil moisture (SM), soil temperature (ST) and pH were the main factors affecting fungal community structure in May, July and September, respectively. The soil dissolved organic carbon (DOC) content significantly shaped the soil fungal community composition along the altitudinal gradient throughout the growing season. Compared to that in May and July, the soil fungal network in September had more nodes and links, a higher average degree and a higher average clustering coefficient. The nine module nodes in the co-occurrence network were all Ascomycota taxa, and the identities of the keystone taxa of soil fungi in the network showed obvious seasonality. Our results demonstrated that altitude has stronger effects than season on soil fungal community structure and diversity at high latitudes. In addition, the co-occurrence network of soil fungi exhibited obvious seasonal succession, which indicated that the keystone taxa of soil fungi exhibit niche differentiation among seasons.
MrvR, a Group BStreptococcusTranscription Factor that Controls Multiple Virulence Traits
Authors: Dammann Allison N. , Chamby Anna B. , Catomeris Andrew J. , Davidson Kyle M. , Tettelin Hervé , van Pijkeren Jan-Peter , Gopalakrishna Kathyayini P. , Keith Mary F. , Elder Jordan L. , Ratner Adam J. , Hooven Thomas A. 
Published: November 2020

AbstractStreptococcus agalactiae(group BStreptococcus; GBS) remains a dominant cause of serious neonatal infections. One aspect of GBS that renders it particularly virulent during the perinatal period is its ability to invade the chorioamniotic membranes and persist in amniotic fluid, which is nutritionally deplete and rich in fetal immunologic factors such as antimicrobial peptides. We used next-generation sequencing of transposon-genome junctions (Tn-seq) to identify five GBS genes that promote survival in the presence of human amniotic fluid. We confirmed our Tn-seq findings using a novel CRISPR inhibition (CRISPRi) gene expression knockdown system. This analysis showed that one gene, which encodes a GntR-class transcription factor that we named MrvR, conferred a significant fitness benefit to GBS in amniotic fluid. We generated an isogenic targeted knockout of themrvRgene, which we found to have a growth defect in amniotic fluid relative to the wild type parent strain. In addition to growing poorly in amniotic fluid, the knockout also showed a significant biofilm defectin vitro. Subsequentin vivostudies showed that, while the knockout was able to cause persistent murine vaginal colonization, pregnant mice colonized with the knockout strain did not develop preterm labor despite consistent GBS invasion of the uterus and the fetoplacental units. In contrast, pregnant mice colonized with wild type GBS consistently deliver prematurely. Similarly, in a sepsis model in which 87% of mice infected with wild type GBS died within three days, none of the mice infected with the knockout strain died. In order to better understand the mechanism by which this newly identified transcription factor controls GBS virulence, we performed electrophoresis mobility shift assays with recombinant MrvR and whole-genome transcriptomic analysis on the knockout and wild type strains. We show that MrvR binds to its own promoter region, suggesting likely self-regulation. RNA-seq revealed that the transcription factor affects expression of a wide range of genes across the GBS chromosome. Nucleotide biosynthesis and salvage pathways were highly represented among the set of differentially expressed genes, suggesting a linkage between purine or pyrimidine availability and activity of MrvR in multiple GBS virulence traits.
Unbiased antimicrobial resistance detection from clinical bacterial isolates using proteomics
Authors: Blumenscheit Christian , Pfeifer Yvonne , Werner Guido , John Charlyn , Schneider Andy , Lasch Peter , Doellinger Joerg 
Published: November 2020

AbstractAntimicrobial resistance (AMR) poses an increasing challenge for therapy and clinical management of bacterial infections. Currently, antimicrobial resistance detection often relies on phenotypic assays, which are performed independently from species identification. Although genomics-based approaches are increasingly being proposed as possible alternatives for resistance detection, the analysis of proteins should be superior to gene or transcript sequencing when it comes to phenotype prediction from molecular data as the actual resistance against antibiotics is almost exclusively mediated by proteins. In this study, we present a unbiased proteomics workflow for detecting both, bacterial species and AMR related proteins in the absence of secondary antibiotic cultivation in less than 4 h from a primary culture. The method was validated using a sample cohort of 7 bacterial species and 11 AMR determinants represented by 13 protein isoforms which resulted in a sensitivity of 98 % (100 % with vancomycin inference) and a specificity of 100 % with respect to AMR determinants. This proof-of concept study suggests a high application potential of untargeted proteomics in clinical microbiology.
An Integrated Workflow for Enhanced Taxonomic and Functional Coverage of the Mouse Faecal Metaproteome
Authors: Nalpas Nicolas , Hoyles Lesley , Anselm Viktoria , Ganief Tariq , Martinez-Gili Laura , Grau Cristina , Droste-Borel Irina , Davidovic Laetitia , Altafaj Xavier , Dumas Marc-Emmanuel , Macek Boris 
Published: November 2020

AbstractIntestinal microbiota plays a key role in shaping host homeostasis by regulating metabolism, immune responses and behaviour. Its dysregulation has been associated with metabolic, immune and neuropsychiatric disorders and is accompanied by changes in bacterial metabolic regulation. Although proteomics is well suited for analysis of individual microbes, metaproteomics of faecal samples is challenging due to the physical structure of the sample, presence of contaminating host proteins and coexistence of hundreds of microorganisms. Furthermore, there is a lack of consensus regarding preparation of faecal samples, as well as downstream bioinformatic analyses following metaproteomics data acquisition. Here we assess sample preparation and data analysis strategies applied to mouse faeces in a typical mass spectrometry-based metaproteomic experiment. We show that subtle changes in sample preparation protocols may influence interpretation of biological findings. Two-step database search strategies led to significant underestimation of false positive protein identifications. Unipept software provided the highest sensitivity and specificity in taxonomic annotation of the identified peptides of unknown origin. Comparison of matching metaproteome and metagenome data revealed a positive correlation between protein and gene abundances. Notably, nearly all functional categories of detected protein groups were differentially abundant in the metaproteome compared to what would be expected from the metagenome, highlighting the need to perform metaproteomics when studying complex microbiome samples.
PseudotimeDE: inference of differential gene expression along cell pseudotime with well-calibrated p-values from single-cell RNA sequencing data
Authors: Song Dongyuan , Li Jingyi Jessica 
Published: November 2020

AbstractTo investigate molecular mechanisms underlying cell state changes, a crucial analysis is to identify differentially expressed (DE) genes along the pseudotime inferred from single-cell RNA-sequencing data. However, existing methods do not account for pseudotime inference uncertainty, and they have either ill-posedp-values or restrictive models. Here we propose PseudotimeDE, a DE gene identification method that adapts to various pseudotime inference methods, accounts for pseudotime inference uncertainty, and outputs well-calibratedp-values. Comprehensive simulations and real-data applications verify that PseudotimeDE outperforms existing methods in false discovery rate control and power.
Fascin1 empowers YAP mechanotransduction and promotes cholangiocarcinoma development
Authors: Pocaterra Arianna , Ament Cindy , Ribback Silvia , Chen Xin , Evert Matthias , Calvisi Diego F. , Dupont Sirio 
Published: November 2020

AbstractMechanical forces control cell behavior, including cancer progression. Cells sense forces through actomyosin and YAP, but what regulators of actin mechanotransduction play relevant roles in vivo remains unclear. Here we identify the Fascin1 F-actin bundling protein as a key factor sustaining YAP activation in response to ECM mechanical cues. This is relevant in the mouse liver, where Fascin1 regulates YAP-dependent hepatocyte dedifferentiation. Moreover, Fascin1 is required in the AKT/NICD system and sufficient together with AKT to induce cholangiocarcinomas in mice, recapitulating genetic YAP requirements, and its expression in intrahepatic cholangiocarcinomas correlates with aggressiveness and poor patient prognosis. We propose that Fascin1 represents a pro-oncogenic mechanism that can be exploited during intrahepatic cholangiocarcinoma development to overcome a mechanical tumor-suppressive environment.
Buckling of laminated composite skew plate using FEM and machine learning methods
Authors: Mishra Bharat Bhushan , Kumar Ajay , Samui Pijush , Roshni Thendiyath 
Published: November 2020

PurposeThe purpose of this paper is to attempt the buckling analysis of a laminated composite skew plate using the C0finite element (FE) model based on higher-order shear deformation theory (HSDT) in conjunction with minimax probability machine regression (MPMR) and multivariate adaptive regression spline (MARS).Design/methodology/approachHSDT considers the third-order variation of in-plane displacements which eliminates the use of shear correction factor owing to realistic parabolic transverse shear stresses across the thickness coordinate. At the top and bottom of the plate, zero transverse shear stress condition is imposed. C0FE model based on HSDT is developed and coded in formula translation (FORTRAN). FE model is validated and found efficient to create new results. MPMR and MARS models are coded in MATLAB. Using skew angle (α), stacking sequence (Ai) and buckling strength (Y) as input parameters, a regression problem is formulated using MPMR and MARS to predict the buckling strength of laminated composite skew plates.FindingsThe results of the MPMR and MARS models are in good agreement with the FE model result. MPMR is a better tool than MARS to analyze the buckling problem.Research limitations/implicationsThe present work considers the linear behavior of the laminated composite skew plate.Originality/valueTo the authors’ best of knowledge, there is no work in the literature on the buckling analysis of a laminated composite skew plate using C0FE formulation based on third-order shear deformation theory in conjunction with MPMR and MARS. These machine-learning techniques increase efficiency, reduce the computational time and reduce the cost of analysis. Further, an equation is generated with the MARS model via which the buckling strength of the laminated composite skew plate can be predicted with ease and simplicity.
Discrepancies in transgender persons (protection of rights) act, 2018: a comparative study of transgender’s rights in Pakistan and India
Authors: Fazi Muhammad Abdullah , Bibi Maryam 
Published: November 2020

Purpose
Comparison.

Design/methodology/approach
Qualitative, Analytical.

Findings
The paper will suggest where the Pakistani legislation will have to be amended without affecting the core subject of the transgender rights in Pakistan.

Originality/value
Novel idea of comparing Pakistani law with an identical Indian law on transgender has been proposed.
An empirical investigation of supply chain operations reference model practices and supply chain performance
Authors: Kottala Sri Yogi , Herbert Kotzab 
Published: November 2020

PurposeThe purpose of this paper is to develop and validate a scale measurement of supply chain operations reference (SCOR)-related performance indicators and proposed constructs, SCOR-related performance indicators as practices within the Indian manufacturing sector.Design/methodology/approachA literature-based model on SCOR processes with five constructs and respective performance indicators was empirically validated by using a structured questionnaire. A total of 155 respondents among Indian manufacturing sector participated in this research, and the returned questionnaires were analyzed by using structural equation modeling.FindingsThe study established a relationship among the SCOR-related performance indicators and overall supply chain performance indicators (OSCPI). The moderation effect of demographic characteristics, namely, employee size, company age and type of company showed significant differences between SCOR-related performance indicators and overall supply chain indicators.Research limitations/implicationsThe scope of the study is limited to specific Indian manufacturing firms. The survey could not represent whole population of manufacturing sector.Practical implicationsThe findings assist managers/supply chain practitioners in improving the performance measures identified using the standard framework, i.e., SCOR processes, overall supply chain performance measures as standard practices for Indian manufacturing sector for a profitable and sustainable business growth in global environment.Originality/valueThis research holds a value for suggested practices under SCOR processes and the proposed model for OSCPI, a path finder/performance measurement tool for supply chain professionals in the Indian context.
Emotional configurations of politicization in social justice movements
Authors: Curnow Joe , Vea Tanner 
Published: November 2020

Purpose
This paper aims to trace how emotion shapes the sense that is made of politics and how politicization can remake and re-mark emotion, giving it new meaning in context. This paper brings together theories of politicization and emotional configurations in learning to interrogate the role emotion plays in the learning of social justice activists.

Design/methodology/approach
Drawing on sociocultural learning perspectives, the paper traces politicization processes across the youth climate movement (using video-based interaction analysis) and the animal rights movement (using ethnographic interviews and participant observation).

Findings
Emotional configurations significantly impacted activists’ politicization in terms of what was learned conceptually, the kinds of practices – including emotional practices – that were taken up collectively, the epistemologies that framed social justice work, and the identities that were made salient in collective action. In turn, politicization reshaped how social justice activists made sense of emotion in the course of activist practice.

Social implications
This study is valuable for theorizing social justice learning, so social movement facilitators and educators might design spaces where learning about gender, racialization, colonialism and/or human/more-than-human relations can thrive. By attending to emotional configurations, this study can help facilitate a design that supports and sustains learning for justice.

Originality/value
Emotion remains under-theorized and under-analyzed in the learning sciences, despite indications that emotion enables and constrains particular learning opportunities. This paper proposes new ways of understanding emotion and politicization as co-constitutive processes for learning scientists interested in politics and social justice.
Safety climate of UAE petroleum industry: a cross-validation using confirmatory factor analytic approach
Authors: Almazrouei Mohmaed , Khalid Khalizani , Davidson Ross 
Published: November 2020

Purpose
The purpose of this paper is to develop and validate a safety climate scale for measuring the safety climate in the oil and gas industry.

Design/methodology/approach
The scale developed through conducting a literature review about the safety climate and constructing a question pool. The number of items was reduced to 51 after performing a screening process. Explanatory factor analysis (EFA) and confirmatory factor analysis (CFA) were performed to examine the scale’s construct validity.

Findings
CFA loadings were statistically significant. All Cronbach’s alpha (a) and composite reliability values support the construct reliability. The outcomes showed acceptable convergent and discriminant validity: AVEs showed acceptable values, and the square roots of AVE values showed higher values than the construct correlation values. Furthermore, all factor loadings exceeded 0.50, and the t-values were statistically significant. CFA loadings were statistically significant.

Originality/value
The safety climate measuring scale of 43-instrument items produced in this study is reliable and valid for the oil and gas industry.