bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNaseH-based ribodepletion of total planarian RNA improves detection of longer and non-polyadenylated transcripts
Authors: Barai Pallob , Biswas Shishir , Verma Prince , Duncan Elizabeth M. 
Published: July 2024

AbstractThe overwhelming majority of RNA species isolated from cells or tissues using organic extraction are ribosomal RNAs (rRNA), whereas a relatively small percentage are messenger RNAs (mRNA). For studies that seek to detect mRNA transcripts and measure changes in their expression, this lopsided ratio of desired transcripts to undesired transcripts creates a significant challenge to obtaining sensitive and reproducible results. One method for improving mRNA detection is to selectively amplify polyadenylated (polyA) mRNA molecules when generating RNA-seq libraries, a strategy that is generally very successful in many species. However, this strategy is less effective when starting with total RNA from some species e.g., the planarian speciesSchmidtea mediterranea(S.med), as it generates libraries that still contain significant and variable amounts of rRNA reads. Further, commercially available ribodepletion kits do not efficiently deplete rRNAs from these samples because their sequences are divergent from mammalian rRNAs. Here we report a customized, optimized, and economical ribodepletion strategy than allows the generation of comprehensive RNA-seq libraries with less than one percent rRNA contamination. We show that this method improves transcript detection, particularly for those without polyA tails (e.g., core histones) and those that are relatively long (e.g., microtubule motor proteins). Using this custom ribodepletion approach, we also detected many transcripts that are not represented in the most recent set of S.med gene annotations, including a subset that are likely expressed transposable elements (TEs). To facilitate future differential expression analyses of these newly identified loci, we created both an annotation file of the new loci we identified and a bioinformatic pipeline for generating additional annotations from future libraries. As significant recent research shows that TE activation is regulated and functionally important, the resources provided here will provide a starting point for investigating such mechanisms in planarians and other species with less conserved rRNA sequences.
Using Multimodal Data Collection System as a Research Tool in the Major Depressive Disorder Analysis: a cross-sectional study protocol
Authors: Li Hongbo , Ji Yifu , Xu Linxiang , Yang Jiaoyun , Du Yang , Hu Min , An Ning 
Published: July 2024

ABSTRACTIntroductionPrevious studies have established that depressive syndromes can be detected using machine learning methods, with multimodal data being essential. Multimodal data facilitates the extraction of characteristics such as gaze tracking, a reliable depression indicator. Our study employs high-quality video and other multimodal data from patients diagnosed with depression. Our study uses a multimodal data collection system (MDC) to understand the complex indicators of depression.ObjectiveThis paper outlines our protocol for deploying a multimodal data collection system within an In-Person Clinical Assessment environment. The system gathers high-definition videos, real-time vital signs, and voice recordings for future extraction of critical information such as eye gaze patterns. We aim to scale our model to provide portable depression risk analyses, facilitating timely intervention and encouraging patients to seek professional assistance.Methods and AnalysisWe have conducted sessions with 70 participants diagnosed with depression. Each participant undergoes DSM-5 interviews and engages with our multimodal data collection system. Participants respond to five on-screen scales while being recorded. To our knowledge, no other protocol has combined multimodal data collection and various stimuli in depression data collection.Ethics and DisseminationEthical approval was provided by the National Health Commission of the PRC, Hefei Fourth People’s Hospital Ethics Committee (HSY-IRB-YJ-YYYX-JYF001). Results will be published in a peer-reviewed journal and presented at academic conferences.
Combining individual and wastewater whole genome sequencing improves SARS-CoV-2 surveillance
Authors: Troendle Evan P. , Lee Andrew J. , Reyne Marina I. , Allen Danielle M. , Bridgett Stephen J. , Radulescu Clara H. , Glenn Michael , Wilkins John-Paul , Rubino Francesco , Nejad Behnam Firoozi , McSparron Cormac , Niebel Marc , Fairley Derek J. , Creevey Christopher J. , McKinley Jennifer M. , Skvortsov Timofey , Gilpin Deirdre F. , McGrath John W. , Bamford Connor G. G. , Simpson David A. 
Published: July 2024

ABSTRACTBackgroundRobust methods to track pathogens support public health surveillance. Both wastewater (WW) and individual whole genome sequencing (WGS) are used to assess viral variant diversity and spread. However, their relative performance and the information provided by each approach have not been sufficiently quantified. Therefore, we conducted a comparative evaluation using extensive individual and wastewater longitudinal SARS-CoV-2 WGS datasets in Northern Ireland (NI).MethodsWGS of SARS-CoV-2 was performed on >4k WW samples and >23k individuals across NI from 14thNovember 2021 to 11thMarch 2023. SARS-CoV-2 RNA was amplified using the ARTIC nCov-2019 protocol and sequenced on an Illumina MiSeq. Wastewater data were analysed using Freyja to determine variant compositions, which were compared to individual data through time series and correlation analyses. Inter-programme agreements were evaluated by mean absolute error (MAE) calculations. WW treatment plant (WWTP) performances were ranked by mean MAE. Volatile periods were identified using numerical derivative analyses. Geospatial spreading patterns were determined by horizontal curve shifting.FindingsStrong concordance was observed between wastewater and individual variant compositions and distributions, influenced by sequencing rate and variant diversity. Overall variant compositions derived from individual sequences and each WWTP were regionally clustered rather than dominated by local population size. Both individual and WW sequencing detected common nucleotide substitutions across many variants and complementary additional substitutions. Conserved spreading patterns were identified using both approaches.InterpretationBoth individual and wastewater WGS effectively monitor SARS-CoV-2 variant dynamics. Combining these approaches enhances confidence in predicting the composition and spread of major variants, particularly with higher sequencing rates. Each method detects unique mutations, and their integration improves overall genome surveillance.FundingIndividual sequencing was funded via the Belfast Health and Social Care Trust (Department of Health for Northern Ireland) and the COVID-19 Genomics UK (COG-UK) consortium, which was supported by the Medical Research Council (MRC), UK Research and Innovation (UKRI), the National Institute for Health Research (NIHR), the Department of Health and Social Care (DHSC), and the Wellcome Sanger Institute. The NI Wastewater Surveillance Programme was funded by the Department of Health for Northern Ireland. EPT was supported through the COG-UK Early Career Funding Scheme.
Validation of rectal swabbing for total and aerobic gut microbiota study
Authors: Marin Julie , Bertoye Paul Albin , Birgy Andre , Dziri Samira , Lescat Mathilde 
Published: July 2024

AbstractIn microbiota research, whole stool sampling is the conventional approach but can be problematic or infeasible for certain patients. This study aims to validate the use of rectal swabbing as an alternative method for microbiota analysis and determine optimal storage conditions suitable for various clinical settings, including intensive care units. We evaluated different sampling techniques, conservation media and storage temperatures. Our findings indicated that rectal swabs yield microbiota diversity comparable to whole stool samples. Notably, storage conditions significantly impacted microbiota profiles, with increasedE. coliandEnterococcus sp. quantifications observed at room temperature. Consequently, we recommend immediate refrigeration of rectal swabs to reliably assess aerobic and total microbiota, particularly for patients requiring urgent care such as antibiotic treatment.ImportanceWe developed a pragmatic approach to study total and aerobic gut microbiota, applicable in numerous clinical units such as intensive care or emergency units, where whole stool sampling is often impractical. This approach employs ESwab™ devices which are already commonly used in hospital.
Classification of human actin pathological variants usingC. elegansCRISPR-generated models
Authors: Hecquet Théo , Arbogast Nadine , Suhner Delphine , Goetz Anaïs , Amann Grégory , Yürekli Selin , Marangoni Fiona , Greve Johannes N. , Di Donato Nataliya , Reymann Anne-Cécile 
Published: July 2024

AbstractActin plays a crucial role in diverse physiological processes via the formation of dynamic networks that determine cellular shape and mechanical properties.De novovariants in cytoskeletal β- and γ-actin, encoded by humanACTBandACTG1genes, lead to a wide range of rare diseases, termed Non-Muscle Actinopathies (NMA). Variants include missense, frameshift, truncating variants up to whole gene deletions and induce diverse symptoms. So far, the high clinical variability and genotype-phenotype correlations in NMA remain largely unresolved. To address this question, we used CRISPR to insert in theC. eleganshomologueact-2gene ninede novomutations identified in patients. Using these animal models, we performed a quantitative multiscale characterisation. We uncovered a variety of perturbations: actin network defects at the micro scale, cell scale abnormalities, morphogenesis failure, as well as weaker behavioural phenotypes. Importantly, the range of developmental defects observed correlates with the severity of patients’ symptoms. Thus, we provide evidence that aC. elegans- based approach represents a new way to investigate the mechanisms underlying NMA physiopathology or ultimately screen for therapeutic strategies.
Intertwined charge and spin density waves in a topological kagome material
Authors: Chen Y. , Gaudet J. , Marcus G. G. , Nomoto T. , Chen T. , Tomita T. , Ikhlas M. , Suzuki H. S. , Zhao Y. , Chen W. C. , Strempfer J. , Arita R. , Nakatsuji S. , Broholm C. 
Published: July 2024

Using neutrons and x rays we show the topological kagome antiferromagnet Mn3Sn for T<285K forms a homogeneous spin and charge ordered state comprising a longitudinally polarized spin density wave with wave vector kβ=kβĉ, a helical modulated version of the room temperature antichiral magnetic order with kχ=kχĉ, and charge density waves with wave vectors 2kβ,2kχ, and kβ+kχ. Though kχ and kβ coincide for 200K<T<230K, they exhibit distinct continuous Tdependencies before locking to commensurate values of kβ=112c* and kχ=548c* at lowT. Density functional theory indicates this complex modulated state may be associated with the nesting of Fermi surfaces from correlated flat kagome bands, which host Weyl nodes that are annihilated as it forms.

Published by the American Physical Society
2024
The employee-related antecedents of work performance: exploring a three-sided model for Human Resources Management
Authors: Ferrari Filippo 
Published: July 2024

PurposeThis research paper aims to integrate the employee-related factors that empirical literature considers antecedents of performance (skills, work motivation, personal characteristics) into a multiple linear regression model, and to test such a model in order to measure the level of each individual factor on the performance.Design/methodology/approachQuantitative, multisource research approach. After testing the validity of the model with a Confirmatory Factor Analysis, this research applies the multiple linear regression model Work performance = a(Skills) + b(Work Motivation) + c(Personal Characteristics) + e(constant) to two different samples of workers: chemical technicians (N = 63) and salespeople (N = 61).FindingsThis study confirms the factorial structure of the antecedents of work performance, showing that skills, motivation, and personal characteristics are three general employee-related factors underlying work performance. The statistical analysis highlights a variance in performance between 40 and 65% explained by employee-related factors, hence leaving 35–60% as due to factors outside the model (firm/environment-related and/or job-related factors, or other skills and personal characteristics not considered in the model). The study also highlights that employee-related factors sometimes affect performance differently than job designers' expectations, and sometimes even negatively.Research limitations/implicationsThe equation was tested on two case studies, so further explorations are needed. Furthermore, the approach adopted is inductive thus describing performance as it is, not as it should be. Therefore, it explains the best actual performance of workers, not the ideal performance.Practical implicationsThe equation tested here represents a simple and valid tool to guide many Human Resource Management practices, such as; selection, training, development, and career orientation.Social implicationsFindings provide a valid indication for designing and managing human resource management systems more even-handedly, from an organizational and employee point of view. In doing so, it drives organizations towards a better Person/Job fit.Originality/valueThe study represents one of the first attempts to take into consideration multiple factors simultaneously in explaining work performance.
Not for us? Vocational training in the social and policy space in Sierra Leone
Authors: Harris Jamelia 
Published: July 2024

PurposeThis paper explores the attractiveness of TVET in Sierra Leone, a post-conflict West African country. It aims to unpack structural factors which contribute to the low repute of TVET.Design/methodology/approachThe paper uses qualitative interviews with employers, government and third sector organisations, focus group discussions with young Sierra Leoneans and analysis of key government policy documents. Thematic analysis was used to analyse the data, and the empirical analysis is grounded in Social Learning Theory of Career Decision Making and Social Cognitive Career Theory. The paper is interdisciplinary, drawing on literature from economics, psychology, political science and development studies.FindingsThe paper argues that TVET is in low repute in Sierra Leone owing to low prioritisation by the national government in terms of policy focus, budgetary allocations and provision of training facilities; the proliferation and continuation of a post-war style of TVET programmes by development partners which initially targeted ex-combatants and thus carry reputational baggage; and colonial legacies of preferences for university education and white-collar jobs.Originality/valueThe research contributes to the academic and policy discourse by providing new empirical insights from an under-studied country (and region), and arguably one where evidence-based policy is much needed.
Expressing opinions about information security in an organization: the spiral of silence theory perspective
Authors: Petrič Gregor , Orehek Špela 
Published: July 2024

Purpose
Expressing views on organizational information security (IS) by employees is vital for improving security processes, policies and trainings, while non-communication may conceal the true state of the human factor of IS and lead to security breaches. The purpose of this paper is to introduce the concept of opinion expressing about organizational IS, provide an explanatory model based on the theory of spiral of silence and offer its empirical validation.

Design/methodology/approach
Data from a web-based survey among the employees of one the universities in the European Union (n = 504) was analyzed with regression analysis to investigate the proposed hypotheses.

Findings
The study reveals that employees with positive opinions about IS will be more willing to share their opinions with coworkers and management. However, when employees perceive that their pro-IS opinions are not shared by other coworkers, they will remain silent, which increases the risk of problematic opinions spreading throughout the organization.

Research limitations/implications
The study highlights the need to focus on the communication perspectives of organizational information security, an area often overlooked in the human factor of information security research.

Practical implications
The results highlight the need to examine the gap between the dominant climate of opinion about IS in the organization and the display of compliant IS behaviors in order to strengthen IS endeavors. Organizations are encouraged to facilitate open dialogue about IS processes, policies and training and implement mechanisms for considering employees’ feedback in order to improve the organization’s IS.

Originality/value
The study contributes to a growing body of research that moves beyond viewing employees merely as subjects of compliance, recognizing instead their agency in IS issues that can enhance organizational resilience. To the best of the authors’ knowledge, this is the first study to apply the spiral of silence theory in the IS field, thereby helping to overcome the lack of communication science perspectives in organizational IS research.
Exploring the nexus of industry dynamism, climate risk exposure and mental health and well-being of owners of small and micro-sized suppliers: implications for sustainable supply chain management
Authors: Bag Surajit , Sarkar Abhigyan , Sarkar Juhi Gahlot , Rogers Helen , Srivastava Gautam 
Published: July 2024

PurposeAlthough climate change-related risks affect all stakeholders along the supply chain, the potential impact on small and micro-sized suppliers is incredibly excessive. The corresponding toll of these climate risk threats on the mental health and well-being of owners of small and micro-sized suppliers can adversely affect their participation in sustainability efforts, ultimately impacting the firm's performance. This often-overlooked dynamic forms the core of our research. We probe into two pivotal aspects: how industry dynamism and climate risk affect the mental health and well-being of owners of small and micro-sized suppliers and how, in turn, dictate involvement and, consequently, supply chain sustainability performance. This is further nuanced by the moderating role of the abusive behavior of buyers.Design/methodology/approachOur study is built on resource dependency theory and the supporting empirical evidence is fortified by a mixed-methods sequential explanatory design. This study comprises three phases. In the first phase, our experiment examines the effect of industry dynamism and climate risk exposure on sustainable supply chain management performance. Hypotheses H1a and H1b are tested in the first phase. The second phase involves using a survey and structural equation modeling to test the comprehensiveness of the model. Here, the relationship between industry dynamism, climate risk exposure, mental health and well-being of owners of small and micro-sized supplier firms, supplier involvement and sustainable supply chain management (H2–H7) is tested in the second phase. In the third phase, we adopt a qualitative approach to verify and provide descriptive explanations of phase two findings.FindingsOur findings underscore the significance of small and micro-sized suppliers in sustainability, offering invaluable insights for both theoretical understanding and practical implementation. Our study highlights that buyers must allocate sufficient resources to support small and micro-sized supplier firms and collaborate closely to address climate change and its impacts.Practical implicationsThe key takeaway from this study is that buyer firms should consider SDG 3, which focuses on the good health and well-being of their employees and the mental health and well-being of owners of small and micro-sized suppliers in their upstream supply chain. This approach enhances sustainability performance in supply chains.Originality/valueThis is one of the first studies that shows that industry dynamism and climate risk exposure can negatively impact small and micro-sized suppliers in the presence of a contextual element, i.e. abusive behavior of buyers, and ultimately, it negatively impacts sustainable supply chain performance dimensions.
Project success factors for leadership practices and communication: challenges in the construction sector
Authors: Rehan Ashok , Thorpe David , Heravi Amirhossein 
Published: July 2024

PurposeThe study examines the project success factors for leadership behavioural practices and communication impacting project success, providing empirical evidence to address the challenges in the digitalized environment in the Australian construction sector.Design/methodology/approachA quantitative approach was employed to collect survey data from 109 project managers and followers (project engineers, supervisors, team members, and senior managers) with diverse project management experience in the construction sector. An exploratory factors analysis/multivariate regression/relative importance index/t-test was used to identify the key project success factors and validate the study's results.FindingsData analysis identified four key project success factors: (1) Relationship Management, (2) Leading by Example, (3) Self-Management, and (4) Effective Communication, along with seventeen “behavioural practices attributes” impacting project success positively and significantly and emphasizing inclusiveness, relationship building, self-feedback objectivity, sharing information, collaboratively resolving disputes, and controlling emotions that significantly impact project success.Practical implicationsThe study's results will address the industry's challenges in the complex digitalized environment and specific issues experienced in the construction industry: delays and inefficiencies, supply chain management, communication barriers with multicultural workforce and safety protocols implementation, regulatory and safety compliance, infrastructure demands, skills shortages, sustainability, and new technology adoption to achieve project success.Originality/valueThe quantification of research findings, employing an innovative approach, underscores the distinctive nature of this study. The key success factors will help formulate innovative practices using stakeholder analysis, communication plans, conflict resolution strategies, promoting collaboration, safety leadership, providing cultural awareness, and enhancing the decision-making process to face challenges in the construction sector.