bluuebunny/crossref_metadata_2025 huggingface dataset:
Draft Genome Assemblies and Annotations ofAgrypnia vestitaWalker, andHesperophylax magnusBanks Reveal Substantial Repetitive Element Expansion in Tube Case-making Caddisflies (Insecta: Trichoptera)
Authors: Olsen Lindsey K. , Heckenhauer Jacqueline , Sproul John S. , Dikow Rebecca B. , Gonzalez Vanessa L. , Kweskin Matthew P. , Taylor Adam M. , Wilson Seth B. , Stewart Russell J. , Zhou Xin , Holzenthal Ralph , Pauls Steffen U. , Frandsen Paul B.
Published: November 2020

Trichoptera (caddisflies) play an essential role in freshwater ecosystems; for instance, larvae process organic material from the water and are food for a variety of predators. Knowledge on the genomic diversity of caddisflies can facilitate comparative and phylogenetic studies thereby allowing scientists to better understand the evolutionary history of caddisflies. While Trichoptera are the most diverse aquatic insect order, they remain poorly represented in terms of genomic resources. To date, all long-read based genomes have been sequenced from individuals in the retreat-making suborder, Annulipalpia, leaving ∼275 Ma of evolution without high-quality genomic resources. Here, we report the first long-read basedde novogenome assemblies of two tube case-making Trichoptera from the suborder Integripalpia,Agrypnia vestitaWalker andHesperophylax magnusBanks. We find that these tube case-making caddisflies have genome sizes that are at least three-fold larger than those of currently sequenced annulipalpian genomes and that this pattern is at least partly driven by major expansion of repetitive elements. InH. magnus, long interspersed nuclear elements (LINEs) alone exceed the entire genome size of some annulipalpian counterparts suggesting that caddisflies have high potential as a model for understanding genome size evolution in diverse insect lineages.

Significance

There is a lack of genomic resources for aquatic insects. So far, only three high-quality genomes have been assembled, all from individuals in the retreat-making suborder Annulipalpia. In this article, we report the first high-quality genomes of two case-making species from the suborder Integripalpia, which are essential for studying genomic diversity across this ecologically diverse insect order. Our research reveals larger genome sizes in the tube case-makers (suborder Integripalpia, infraorder Phryganides), accompanied by a disproportionate increase of repetitive DNA. This suggests that genome size is at least partly driven by a major expansion of repetitive elements. Our work shows that caddisflies have high potential as a model for understanding how genomic diversity might be linked to functional diversification and forms the basis for detailed studies on genome size evolution in caddisflies.

Data deposition

This project has been deposited at NCBI under the Bioproject ID: PRJNA668166
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

Understanding 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

Both 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

Both 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

The 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

Streptococcus 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

Antimicrobial 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

Intestinal 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

To 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

Mechanical 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.
Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages
Authors: Hughes Jennifer F. , Skaletsky Helen , Pyntikova Tatyana , Koutseva Natalia , Raudsepp Terje , Brown Laura G. , Bellott Daniel W. , Cho Ting-Jan , Dugan-Rocha Shannon , Khan Ziad , Kremitzki Colin , Fronick Catrina , Graves-Lindsay Tina A. , Fulton Lucinda , Warren Wesley C. , Wilson Richard K. , Owens Elaine , Womack James E. , Murphy William J. , Muzny Donna M. , Worley Kim C. , Chowdhary Bhanu P. , Gibbs Richard A. , Page David C.
Published: November 2020

Studies of Y Chromosome evolution have focused primarily on gene decay, a consequence of suppression of crossing-over with the X Chromosome. Here, we provide evidence that suppression of X–Y crossing-over unleashed a second dynamic: selfish X–Y arms races that reshaped the sex chromosomes in mammals as different as cattle, mice, and men. Using super-resolution sequencing, we explore the Y Chromosome of Bos taurus (bull) and find it to be dominated by massive, lineage-specific amplification of testis-expressed gene families, making it the most gene-dense Y Chromosome sequenced to date. As in mice, an X-linked homolog of a bull Y-amplified gene has become testis-specific and amplified. This evolutionary convergence implies that lineage-specific X–Y coevolution through gene amplification, and the selfish forces underlying this phenomenon, were dominatingly powerful among diverse mammalian lineages. Together with Y gene decay, X–Y arms races molded mammalian sex chromosomes and influenced the course of mammalian evolution.
Treatment response and tumor evolution: lessons from an extended series of multianalyte liquid biopsies in a metastatic breast cancer patient
Authors: Welter Lisa , Xu Liya , McKinley Dillon , Dago Angel E. , Prabakar Rishvanth K. , Restrepo-Vassalli Sara , Xu Kevin , Rodriguez-Lee Mariam , Kolatkar Anand , Nevarez Rafael , Ruiz Carmen , Nieva Jorge , Kuhn Peter , Hicks James
Published: November 2020

Currently, clinical characterization of metastatic breast cancer is based on tissue samples taken at time of diagnosis. However, tissue biopsies are invasive and tumors are continuously evolving, which indicates the need for minimally invasive longitudinal assessment of the tumor. Blood-based liquid biopsies provide minimal invasive means for serial sampling over the course of treatment and the opportunity to adjust therapies based on molecular markers. Here, we aim to identify cellular changes that occur in breast cancer over the lifespan of an affected patient through single-cell proteomic and genomic analysis of longitudinally sampled solid and liquid biopsies. Three solid and 17 liquid biopsies from peripheral blood of an ER+/HER2− metastatic breast cancer patient collected over 4 years and eight treatment regimens were analyzed for morphology, protein expression, copy-number alterations, and single-nucleotide variations. Analysis of 563 single morphometrically similar circulating tumor cells (CTCs) and 13 cell-free DNA (cfDNA) samples along with biopsies of the primary and metastatic tumor revealed progressive genomic evolution away from the primary tumor profiles, along with changes in ER expression and the appearance of resistance mutations. Both the abundance and the genomic alterations of CTCs and cfDNA were highly correlated and consistent with genomic alterations in the tissue samples. We demonstrate that genomic evolution and acquisition of drug resistance can be detected in real time and at single-cell resolution through liquid biopsy analytes and highlight the utility of liquid biopsies to guide treatment decisions.
Spare Parts Procurement Planning at KM Trans Logistics
Authors: Roy Debjit , Bandyopadhyay Arindam
Published: November 2020

Inventory management plays a critical role in managing business profitability. Through this case, the participants will understand the role of managing inventory for timely workshop operations. Further, too much inventory can erode business margins and occupy storage space. This case also highlights the selection of an appropriate inventory review policy for managing the spare parts inventory.
Marco Crumbs BV
Authors: Soman Chetan A.
Published: November 2020

Marco Crumbs BV is in the process of introducing a new product and this is putting additional stress on already tense interface of marketing and operations functions. The company which was traditionally offering a limited but high volume product range is finding itself in a low volume, high variety situation. It appears that the traditional make-to-stock production system is not working and the company is thinking of combined make-to-order (MTO) and make-to-stock (MTS) production system. How to go about it?
Kunvarji Group
Authors: Roy Debjit , Maheshwari Atul
Published: November 2020

Kunvarji Group is on its way to transform from a commodity trading business to a service-driven business. To become an integrated service provider in the agri-supply chain, Kunvarji is by participating actively in procurement, trading, and now eyeing options for providing agri-storage services. Their dilemma reeled around the choice of storage that should be preferred for better returns: warehouse, cold storage, or silos? What should be Kunvarji's growth strategy?
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

Purpose

The 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/approach

HSDT 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.

Findings

The 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/implications

The present work considers the linear behavior of the laminated composite skew plate.

Originality/value

To 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

Purpose

The 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/approach

A 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.

Findings

The 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/implications

The scope of the study is limited to specific Indian manufacturing firms. The survey could not represent whole population of manufacturing sector.

Practical implications

The 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/value

This 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.
Reframing research access
Authors: Mamtora Jayshree , Pandey Prashant
Published: November 2020

Purpose

The paper describes how Charles Darwin University (CDU) used a three-pronged approach to better serve its researchers: it developed a single interface for improved accessibility and discoverability of its research outputs, consolidated its corresponding policies and procedures and implemented training programs to support the new portal. This in turn made its suite of research outputs more openly accessible and better discoverable. The intention was to make CDU research compliant with the FAIR (Findable, Accessible, Interoperable and Reusable) policy statement, affirming the need to make Australia's research more visible, thereby enabling better access, better collaboration locally and internationally and researchers more accountable to their community.

Design/methodology/approach

This paper uses case study methodology and a qualitative approach.

Findings

CDU Library collaborated with the University’s Research Office in undertaking a series of strategies towards reframing access to its research. The partners migrated their research collections into a single, new, integrated interface; developed new policies and consolidated existing ones; and to this end, rolled out a training and educational program for the research community. The intention of the program was to introduce the Pure repository to new researchers and to train all staff to self archive and curate their own research outputs. This new streamlined approach ensured a more comprehensive and timely availability and accessibility of the University's research outputs.

Originality/value

A single source of truth was established through the migration of iCDU’s research collections, ensuring data quality was maintained. At the start of this project, there were few institutions in Australia using the Pure system, and even fewer using it as their sole repository for displaying research outputs.
Organization member action proximity and attributions for managerial crisis response failure
Authors: Carson Jack , Waddingham Jacob , Mackey Jeremy
Published: November 2020

Purpose

The purpose of this research is to describe organization members' attributions for managerial responses to obviously externally caused crises. The authors draw from attribution theory research and the actor-observer bias to argue that organization members' proximity to managerial crisis response is a key determinant of organization members' affective and behavioral outcomes following a crisis.

Design/methodology/approach

The authors develop a conceptual dual-process model of attributions that explains why organization members' judgments of managerial responsibility and associated outcomes differ depending on organization members' proximity to crisis response action.

Findings

The authors focus on organization members' attributions for the failure of managerial crisis responses to obviously externally caused crisis events. The authors present propositions regarding the impact of organization members' potential biases on their attributions for managerial crisis response. Then, the authors delineate how action proximity can assuage negative outcomes of managerial crisis response failure by encouraging an attitude of understanding and awareness of situational challenges.

Originality/value

The authors diverge from prior applications of attribution theory to crisis management by focusing on organization members' attributions of managerial crisis response failure, rather than attributions for the initial cause of the crisis itself. The authors also extend prior work that primarily focuses on crisis response strategies by instead elaborating on how organization members' attributions operate in the wake of their management's failure to effectively respond to an obviously externally caused crisis.
Dying in lockdown
Authors: Wallace Tina
Published: November 2020

Purpose

This study aims to share a personal viewpoint on the hardship imposed by lockdown measure.

Design/methodology/approach

A personal experience of losing a loved one during the Covid-19 lockdown in England.

Findings

The costs of lockdown go far beyond the economic ones.

Originality/value

A unique, personal perspective.
Friends or Foes? Bilateral Relationships and Ownership Choice in Cross‐border Acquisitions by Emerging Market Firms
Authors: Yoon Hyungseok (David) , Peillex Jonathan , Buckley Peter J.
Published: November 2020

Emerging market firms (EMFs) are increasingly recognized as a heterogeneous group of business enterprises, providing a unique context for examining the predictive power of existing theories. Drawing on real options and internalization theories, this paper predicts the contrasting effect of bilateral relationships on EMFs' ownership choice in cross‐border acquisitions. The conflicting conjectures are tested using data consisting of almost 1,000 cross‐border acquisition deals. Our results show that weak economic, political and military relationships between acquiring and target countries induce EMFs to opt for full acquisitions. The findings support the view of internalization theory, highlighting that EMFs prefer full ownership over partial ownership by coping with the political risk derived from weak bilateral relationships.
Progressing policy toward a risk/need informed sanctioning model
Authors: D'Amato Christopher , Silver Ian A. , Newsome Jamie , Latessa Edward J.
Published: November 2020

Research Summary

This study examined whether risk/need assessment results coincided with the placement of defendants into six types of sanctions among convicted adults from 11 counties in one state. Crosstabulations highlighted that individuals’ risk/need levels corresponded to the placement of low‐risk/need individuals to probation and high‐risk/need individuals to prison; however, intermediate sanctions were rarely used for any risk/need level and some low‐ and moderate‐risk/need individuals were sentenced to prison when convicted of offenses that do not typically result in incarceration.

Policy Implications

The results suggest that courts should adopt an evidence‐informed sanctioning model by using risk/need assessments to inform sentencing decisions. Further, states should utilize intermediate sanctions more often to divert individuals convicted of less serious offenses from prison. Finally, judges should avoid sentencing low‐risk/need individuals to prison whenever possible. These changes could help courts to better match individuals’ risk/need level to sanctions.
MiR‐423‐5p aggravates lung adenocarcinoma via targeting CADM1
Authors: Huang Yuzhen , Feng Ganzhu
Published: November 2020

Background

At present, microRNAs and its downstream genes have been regarded as influential indicators in various malignancies. Therefore, the aim of this study was to explore the relationship and molecular mechanism of the miR‐423‐5p and its downstream gene CADM1 in the LUAD.

Methods

The pcDNA‐CADM1 was used to construct the CADM1 overexpressed cell model. The cell proliferation was determined by CCK‐8 and EdU assays and the cell metastasis was performed by wound scratch and transwell chamber assays. The relationship between miR‐423‐5p and CADM1 were determined by bioinformatics, luciferase reporter and western blot assays.

Results

The results revealed that the CADM1 was downregulated in LUAD tissues and cell lines. CADM1 overexpression markedly repressed the cell proliferation, migration and invasion. Moreover, the results of bioinformatics, luciferase reporter and WB assays showed that CADM1 was a target gene of miR‐423‐5p and the miR‐423‐5p expression was negatively associated with CADM1 in LUAD cell lines. Finally, rescue experiments revealed that downregulation of CADM1 could antagonize the functions of miR‐423‐5p inhibitor on cell proliferation and metastasis. These results indicated that miR‐423‐5p aggravated lung adenocarcinoma via downregulation of CADM1 expression.

Conclusions

Downregulation of CADM1 could antagonize the functions of miR‐423‐5p inhibitor on cell proliferation and metastasis. miR‐423‐5p aggravated lung adenocarcinoma via downregulation of CADM1 expression.
Utility of coagulation analyses to assess thromboprophylaxis with dalteparin in intensive care unit patients
Authors: Andersen Nina Gjerde , Mowinckel Marie‐Christine , Sunde Kjetil , Sandset Per Morten , Beitland Sigrid
Published: November 2020

Background

The aim of this study was to evaluate the utility of coagulation analyses to assess thromboprophylaxis with dalteparin in intensive care unit (ICU) patients.

Methods

Prospective observational study of ICU patients receiving dalteparin prophylaxis at Oslo University Hospital in Norway. Trough and peak antithrombin, protein C, anti‐factor Xa activity (aFXa), d‐dimer, thromboelastography, calibrated automated thrombogram and microparticles were analysed. Levels were compared in patients with and without venous thromboembolism (VTE), major bleeding, acute kidney injury (AKI) with use of renal replacement therapy (RRT) and variable dalteparin dose.

Results

Among 50 included patients (76% male, mean age 62 years) five (10%) developed VTE and eight (16%) major bleeding. Median through aFXa level was 0.03 (0.02‐0.05) IU/mL, and 48 (96%) of patients were within and two (4%) above target range. Peak aFXa level was 0.21 (0.13‐0.29) IU/mL, the number of patients below, within and above prophylactic range were 21 (42%), 25 (50%) and four (8%). Peak aFXa levels were similar in patients with and without VTE (0.18 vs 0.21 IU/L, P = .72), major bleeding (0.22 vs 0.21 IU/mL, P = .38) and AKI with RRT (0.18 vs 0.24, P = .13), but lower in patients receiving dalteparin 5000 IU od compared to 7500 IU od (0.19 vs 0.30 IU/mL, P < .01).

Conclusions

Intensive care unit patients receiving dalteparin prophylaxis had half of patients within prophylactic peak aFXa target range. Peak aFXa levels was affected by administered dalteparin dose, but not presence of VTE, major bleeding or AKI with RRT.
Government's Say‐on‐pay Policy and Corporate Risk‐taking: Evidence from China
Authors: Su Kun , Jiang Haiyan , Tian Gary
Published: November 2020

This paper investigates whether the restriction on executive compensation in Chinese state‐owned enterprises (SOEs) imposed by the Government's say‐on‐pay schemes is conducive to corporate risk taking. Using a sample of listed SOEs over the period 2005–2018, we find that the restriction on executive compensation is negatively associated with corporate risk taking, suggesting that regulatory intervention in executive pay may produce unintended consequences. Our analyses also demonstrate that this negative regulatory effect on corporate risk taking is driven by listed SOEs in the growth stage of the business life cycle and by those in the provinces with a significant degree of government intervention. An additional test shows that the negative effect of the pay restriction on risk taking disappears in the SOEs in which managers hold shares, suggesting that an alignment of interests between managers and other shareholders mitigates the negative effect of the pay restriction. Our finding is robust to a batch of tests to alleviate the concerns about self‐selection and reverse causality.
Basophils and their effector molecules in allergic disorders
Authors: Miyake Kensuke , Shibata Sho , Yoshikawa Soichiro , Karasuyama Hajime
Published: November 2020

Basophils are the rarest granulocytes which represent <1% of peripheral blood leukocytes. Basophils bear several phenotypic similarities to tissue‐resident mast cells and therefore had been erroneously considered as blood‐circulating mast cells. However, recent researches have revealed that basophils play nonredundant roles in allergic inflammation, protective immunity against parasitic infections and regulation of innate and acquired immunity. Basophils are recruited to inflamed tissues and activated in an IgE‐dependent or IgE‐independent manner to release a variety of effector molecules. Such molecules, including IL‐4, act on various types of cells and play versatile roles, including the induction and termination of allergic inflammation and the regulation of immune responses. Recent development of novel therapeutic agents has enabled us to gain further insights into basophil biology in human disorders. In this review, we highlight the recent advances in the field of basophil biology with a particular focus on the role of basophils in allergic inflammation. Further studies on basophils and their effector molecules will help us identify novel therapeutic targets for treating allergic disorders.
First‐trimester maternal serum biomarkers and the risk of cerebral palsy
Authors: Peris Monique , Reid Susan M , Dobie Stephen , Bonacquisto Leo , Shepherd Daisy A , Amor David J
Published: November 2020

Aim

To investigate whether combined first‐trimester screening (cFTS) biomarkers are associated with cerebral palsy (CP) and to identify CP characteristics associated with abnormal biomarker levels.

Method

In this retrospective case–control data linkage study, we matched mothers of 435 singletons with CP from a population register to their cFTS records and selected 10 singleton pregnancy controls per case. We compared mean and abnormal levels (expressed as multiples of the median [MoMs]) of pregnancy‐associated plasma protein‐A (PAPP‐A), beta subunit of human chorionic gonadotrophin (β‐hCG), and nuchal translucency between cases and controls and between CP subgroups.

Results

Compared with control pregnancies, CP pregnancies had lower mean levels of PAPP‐A (0.95 vs 1.01 MoM, p=0.02) and β‐hCG (0.93 vs 0.99 MoM, p=0.02). Biomarker levels in CP pregnancies were 1.8 times more likely to be associated with abnormally low levels of PAPP‐A (p<0.01), 1.4 times for β‐hCG (p=0.12), and 2.6 times for low PAPP‐A and β‐hCG together (p=0.04). In cases with CP, an abnormally low PAPP‐A level was associated with moderate preterm birth, low Apgar scores, and Gross Motor Function Classification System level V. Low β‐hCG was associated with very low birthweight.

Interpretation

Low first‐trimester biomarker levels suggest a role for early pregnancy factors in some causal pathways to CP.

What this paper adds

Low first‐trimester levels of biomarkers in maternal serum are associated with later cerebral palsy (CP).

Early pregnancy factors have potential importance in causal pathways to CP.

Causal pathways involving preterm birth, term neonatal encephalopathy, and genetic syndromes may be implicated.
Explainable artificial intelligence enhances the ecological interpretability of black‐box species distribution models
Authors: Ryo Masahiro , Angelov Boyan , Mammola Stefano , Kass Jamie M. , Benito Blas M. , Hartig Florian
Published: November 2020

Species distribution models (SDMs) are widely used in ecology, biogeography and conservation biology to estimate relationships between environmental variables and species occurrence data and make predictions of how their distributions vary in space and time. During the past two decades, the field has increasingly made use of machine learning approaches for constructing and validating SDMs. Model accuracy has steadily increased as a result, but the interpretability of the fitted models, for example the relative importance of predictor variables or their causal effects on focal species, has not always kept pace. Here we draw attention to an emerging subdiscipline of artificial intelligence, explainable AI (xAI), as a toolbox for better interpreting SDMs. xAI aims at deciphering the behavior of complex statistical or machine learning models (e.g. neural networks, random forests, boosted regression trees), and can produce more transparent and understandable SDM predictions. We describe the rationale behind xAI and provide a list of tools that can be used to help ecological modelers better understand complex model behavior at different scales. As an example, we perform a reproducible SDM analysis in R on the African elephant and showcase some xAI tools such as local interpretable model‐agnostic explanation (LIME) to help interpret local‐scale behavior of the model. We conclude with what we see as the benefits and caveats of these techniques and advocate for their use to improve the interpretability of machine learning SDMs.