bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recent Endemic Coronavirus Infection Associates With Higher SARS-CoV-2 Cross-Reactive Fc Receptor Binding Antibodies
Authors: Bean David J. , Liang Yan Mei , Sagar Manish 
Published: October 2024

ABSTRACTRecent documented infection with an endemic coronavirus (eCoV) associates with less severe coronavirus disease 2019 (COVID-19), yet the immune mechanism behind this protection has not been fully explored. We measured both antibody and T cell responses against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in SARS-CoV-2 naïve individuals classified into two groups, either with or without presumed recent eCoV infections. There was no difference in neutralizing antibodies and T cell responses against SARS-CoV-2 antigens between the two groups. SARS-CoV-2 naïve individuals with recent presumed eCoV infection, however, had higher levels of Fc receptor (FcR) binding antibodies against eCoV spikes (S) and SARS-CoV-2 S2. There was also a significant correlation between eCoV and SARS-CoV-2 FcR binding antibodies. Recent eCoV infection boosts cross-reactive antibodies that can mediate Fc effector functions, and this may play a role in the observed heterotypic immune protection against severe COVID-19.
Comparative study on the virulence of mycobacteriophages
Authors: Rubino Ilaria , Guerrero-Bustamante Carlos A. , Harrison Melissa , Co Sheila , Tetreau Isobel , Ordoubadi Mani , Larsen Sasha E. , Coler Rhea N. , Vehring Reinhard , Hatfull Graham F. , Sauvageau Dominic 
Published: October 2024

AbstractThe global tuberculosis (TB) epidemic affected 10 million people and caused 1.3 million deaths in 2022 alone. Multidrug-resistant TB is successfully treated in less than 60% of cases by long, expensive and aggressive treatments. Mycobacteriophages, viruses that can infect bacteria such asMycobacterium tuberculosis—the species responsible for TB, have the potential to redefine TB prevention and treatments. However, the development of phage-based products necessitates the assessment of numerous parameters, including virulence and adsorption, to ensure their performance and quality. In this work, we characterized the virulence of three different mycobacteriophages (Fionnbharth, Muddy and D29), alone and as cocktails, against a TB model host (Mycobacterium smegmatis) under planktonic and early-stage biofilm growth conditions. Phage D29 and cocktails containing D29 had the highest virulence under all conditions. Interestingly, phages Fionnbharth and Muddy and their combination showed higher virulence against early-stage biofilm than against the planktonic phenotype. Adsorption assays indicated that all three phages had lower adsorption efficiencies on the early-stage biofilm phenotype than on the planktonic one, suggesting a reduced availability of receptors in the former. Given that, despite these lower adsorption efficiencies, the virulence of the phages and phage cocktails was either unchanged or higher against the early-stage biofilm, this phenotype must display properties that are favorable to other steps of the infection process. These results inform us on the dynamics of mycobacteriophage infections, alone and in cocktail formulations, under different host growth conditions, and serve as a basis for the development of phage products targeting mycobacteria biofilms.
Mechanistic genotype-phenotype translation using hierarchical transformers
Authors: Lee Ingoo , Wallace Zach , Park Sungjoon , Nam Hojung , Majithia Amit R. , Ideker Trey 
Published: October 2024

AbstractGenome-wide association studies have linked millions of genetic variants to biomedical phenotypes, but their utility has been limited by a lack of mechanistic understanding and widespread epistatic interactions. Recently, Transformer models have emerged as a powerful general-purpose architecture in machine learning, with potential to address these and other challenges. Accordingly, here we introduce the Genotype-to-Phenotype Transformer (G2PT), a framework for modeling hierarchical information flow among variants, genes, multigenic functions, and phenotypes. As proof-of-concept, we use G2PT to model the genetics of TG/HDL (triglycerides to high-density lipoprotein cholesterol), an indicator of metabolic health. G2PT learns to predict this trait via high attention to genetic variants underlying 24 functions, including immune response and cholesterol transport, with accuracy exceeding state-of-the-art. It implicates unexpected epistatic interactions, including those among APOC1 and CETP. This work positions Hierarchical Transformers as a general approach to functionally interpret polygenic risk. The source code is available athttps://github.com/idekerlab/G2PT.
Identification of Cyclin L1 as a host factor regulating Hepatitis B Virus replication
Authors: Owino Collins Oduor , Narmada Balakrishnan Chakrapani , Lin Gian Yi , Kim Aw Pauline Poh , Ganesh Nivrithi , Siying Jovi Tan , Plissonnier Marie-Laure , Matan Thangavelu Thangavelu , Shirgaonkar Niranjan , Bifani Juan Pablo , Levrero Massimo , Periyasamy Giridharan , Lim Seng Gee , DasGupta Ramanuj 
Published: October 2024

ABSTRACTBackground & AimsUnderstanding the regulatory interactions between Hepatitis B virus (HBV) and human host factors is key to the development of next-generation host-directed antiviral therapies and achieving a functional HBV cure. In this study, we aimed to investigate HBV-induced alterations in host gene expression in primary human hepatocytes (PHH) to identify host-specific factors that are regulated and exploited by the virus for replication and survival.MethodsWe performed whole transcriptome sequencing (WTS) of HBV-infected PHH to identify host pathways that could potentially influence the HBV life cycle. RNA-interference-based validation of putative targets to evaluate the function of dysregulated candidate genes resulted in the identification of Cyclin L1 (CCNL1) as a key host factor.ResultsRNAi-knockdown ofCCNL1revealed that it is essential for HBV gene expression, including HBV-surface antigen (HBsAg). Mechanistically, we found that CCNL1 can phosphorylate the C-terminal domain (CTD) of RNA Polymerase II (RNAPII) at serine 2 (S2), likely to regulate HBV transcription. Furthermore, the knockdown of CCNL1 inhibited the binding of total and phospho- (Ser2-Ser5) RNAPII, pan-acetylated H3ac, and H3K27ac to HBV cccDNA, implicating its function in the regulation of cccDNA-dependent viral transcription. Finally, enhanced CCNL1 expression in chronic hepatitis B patients, as compared to those with resolved infection, underscores a functional link between this host factor and CHB.ConclusionOur data demonstrates that CCNL1 regulates HBV RNA transcription and replication by modulating RNAPII phosphorylation and activity, making it a potential host susceptibility factor for HBV.LAY SUMMARYHepatitis B requires human host cell factors and biological processes to establish an efficient infection. Identifying host factors that support and/or restrict HBV infection is essential for understanding the molecular basis of chronic HBV infection and for developing host-targeting anti-HBV drugs. Here, we report thatCCNL1can serve as a potential host susceptibility factor for HBV, as reduced CCNL1 function results in reduced viral replication and gene expression.Graphical SummaryGraphical summary, highlighting the approach and validation experiments. From whole transcriptomics analysis, we identified known HBV-host factors such as SRPK1, CDK1, NXF1 among others as well as new factors such as CCNL1. Employing various RNAi approaches and different cell models including primary human hepatocytes, we validated the role of CCNL1 during HBV infection cycle. Pull-down experiments followed by ChIP-PCR further showed a reduction in cccDNA-based transcription upon knockdown of CCNL1.Graphical abstract
Evolutionary rescue during extreme drought
Authors: Anstett Daniel N. , Anstett Julia , Sheth Seema N. , Moxley Dylan R. , Jahani Mojtaba , Huang Kaichi , Todesco Marco , Jordan Rebecca , Lazaro-Guevara Jose Miguel , Rieseberg Loren H. , Angert Amy L. 
Published: October 2024

AbstractPopulations declining due to climate change may need to evolve to persist. While evolutionary rescue has been demonstrated in theory and the lab, its relevance to natural populations facing climate change remains unknown. Here we link rapid evolution and population dynamics in scarlet monkeyflower,Mimulus cardinalis, during an exceptional drought. We leverage whole-genome sequencing across 55 populations to identify climate-associated loci. Simultaneously we track demography and allele frequency change throughout the drought. We establish range-wide population decline during the drought, geographically variable rapid evolution, and variable population recovery that is predictable by both standing genetic variation and rapid evolution at climate-associated loci. These findings demonstrate evolutionary rescue in the wild, showing that genomic variability at adaptive, but not neutral loci, predicts population recovery.
Enriched environment requires remodeling of hippocampal perineuronal nets to trigger memory improvement in Alzheimer’s mouse model
Authors: Bouisset Guillaume , Tixier Fanny J. , Dupak Tatiana , Lejards Camille , Verret Laure 
Published: October 2024

AbstractAlzheimer’s disease (AD) is a major neurodegenerative disorder influenced by both genetic and environmental factors. Engaging in mentally stimulating activities is believed to reduce cognitive decline by establishing a cognitive reserve, though the underlying neurobiological mechanisms remain elusive. In this study, we explore the role of parvalbumin-expressing inhibitory neurons (PV) and their associated perineuronal nets (PNN) in cognitive deficits observed in AD. Using the Tg2576 mouse model, we demonstrate that 10 days of exposure to an enriched environment (EE) significantly restores spatial and social memory, accompanied by an increase in PV and PV/PNN cell populations in the hippocampus. Notably, preventing PV/PNN remodeling in the CA1 region during EE abolishes the spatial memory improvements, whereas localized neuregulin-1 (NRG1) injections induce PV/PNN remodeling and restore memory function. These findings suggest that hippocampal PV/PNN remodeling is essential for the cognitive benefits of EE in AD, highlighting this neuronal population as a critical substrate for cognitive reserve. This study provides new insights into the mechanisms by which environmental factors may mitigate cognitive decline in AD, offering potential avenues for therapeutic interventions.Highlights:10-day environmental enrichment increases PV+ and PV+/PNN+ in the hippocampus of Tg2576 mouse model of ADBlocking PV/PNN remodeling during EE prevents memory recovery in Tg2576 miceEnhancing PV/PNN remodeling with NRG1 leads to restored memory in Tg2576 micePV/PNN remodeling in area CA1 affects spatial memory, while in CA2, it impacts social memory
Analyzing barriers for organic food consumption in India: a DEMATEL-based approach
Authors: Thanki Shashank , Guru Sunita , Shah Bhavin 
Published: October 2024

PurposePopularity of organic food and food products is growing across the globe due to rising awareness towards health and environment, leading to quality life. However, the multitude of challenges associated with the purchase and consumption of organic food remain insufficiently addressed within the context of developing nations, such as India. This study attempts to fill this gap by identifying the crucial barriers and analyzing them further to establish contextual relationships among them.Design/methodology/approachIn total, 18 barriers identified with a literature review are classified into 6 major barriers (constructs) using exploratory factor analysis (EFA). Further, fuzzy decision-making trial and evaluation laboratory (DEMATEL) approach is employed to relegate these barriers and sub-barriers into the cause-and-effect group. Moreover, causal relationships among these barriers are also established to assist organic food producers and food processing industries in developing the strategies to overcome these barriers.FindingsThe study results indicate that “acceptability,” “preferability” and “reachability” are the most prominent barriers. Moreover, “reachability’ is the leading cause group barrier, while “acceptability” is the major effect group barrier. “Usualness,” “visibility” and “readiness” of the organic food exhibit significant challenges in the organic food consumption.Practical implicationsThe findings of this study act as a roadmap and guiding principle for various stakeholders, such as organic food manufacturers, organic food processing industries, government policymaking bodies and food certification agencies, in organizations and government regulatory agencies for devising and implementing targeted strategies to enhance the accessibility, appeal and, in turn, adoption and consumption of organic foods. This successively contributes to broader efforts in improving public health and ensuring sustainable agricultural practices.Originality/valueThe contribution of this study is two-fold. First, it investigates the interdependences among the organic food consumption barriers. Second, it provides policy-related recommendations to enhance the consumption of organic food, especially in India.
Framework for implementing an Agile-BIM in Brazilian public organizations based on the value-focused thinking method
Authors: Menezes-Firmino Maria Júlia , Alencar Luciana Hazin , Olbina Svetlana 
Published: October 2024

PurposeThis research purpose was to develop a Value-Focused Thinking (VFT)-based framework for implementing an Agile-BIM in public institutions in Brazil. The framework is used for structuring an action plan for implementing the Agile-BIM.Design/methodology/approachThe methodology used to structure the Agile-BIM implementation framework is based on the VFT method, which enables a decision-maker’s strategic, fundamental and means-end objectives for the context analyzed to be more easily identified and better understood. The network developed shapes the decision context, shows possible paths toward achieving the fundamental objectives and guides the institution under study on the implementation process. Based on the networks of two decision-makers and the implementation factors identified, the Agile-BIM implementation framework is proposed.FindingsThe study developed an Agile-BIM implementation framework that provides guidance for creating an Agile-BIM implementation plan in a public sector construction project and supports decision-making, in addition to clarifying the decision context for decision-makers and other actors involved. The framework consists of three main dimensions: “Project Stakeholder,” “Technology Infrastructure” and “Standardization and Procedures.” Each dimension comprises several factors that contribute to the Agile-BIM implementation process. The findings show that a structured approach to Agile-BIM implementation can support institutions in achieving a smooth and structured transition to BIM usage, thereby ensuring enhanced performance and compliance with legal requirements.Practical implicationsThe proposed framework can support the assessment of organizational needs and serves as a basis for guiding the implementation of Agile-BIM in public institutions. This framework for Agile-BIM implementation can guide other public institutions in formulating their action plans for implementing Agile-BIM. The framework demonstrates potential for being applicable in different contexts and being able to adapt to these. It can be transferred to other emerging and/or developing countries that are seeking to embrace Agile-BIM while considering the requisite adjustments inherent to each organization.Originality/valueThe originality of this study lies in addressing the implementation of BIM in the public sector as a decision problem and using the values of the manager who is in charge in the institution to structure the Agile-BIM implementation, based on the VFT method. Furthermore, it proposes an implementation framework that integrates agile methodologies and BIM, known as Agile-BIM.
How family businesses transfer their values across generation: a conceptual framework
Authors: Agnihotri Arpita , Bhattacharya Saurabh 
Published: October 2024

Purpose
Recognising the value of sustaining virtuous values in family business across generations, this paper aims to provide a conceptual framework and propose a mediated-moderated mechanism through which family members’ traits, such as family size and parenting style, influence the extent to which family business’s virtuous values transfer across generations.

Design/methodology/approach
The paper is based on systematic literature that was conducted using specific keyword searches in the business source databases of Emerald, ProQuest, ScienceDirect, EBSCOhost and SpringerLink.

Findings
This paper leads to a conceptual framework proposing a mediating relationship between family members’ traits and the transfer of virtuous values to the next generation. Further, two parallel mediators are proposed, moderated by traits of family members’ offspring, such as the age gap and gender of offspring.

Research limitations/implications
This paper proposes a conceptual framework focusing on transferring virtuous values across generations in the family business. It investigates family members’ traits, such as the size of the family and parenting style, to comprehend the family members’ traits and the transfer of virtuous values relationship.

Practical implications
The proposed conceptual framework should form the basis of interventions adopted by family business members to enhance the transfer to virtuous values across generations by positively impacting their moral self-efficacy and affective commitment to virtuous values.

Originality/value
Prior research on family businesses has primarily explored transgenerational succession. However, sustaining virtuous values across generations is equally important to retain a business’s legacy. Very limited scholarly attention has focused on these virtuous values in family business.
Caught in the deglobalisation crosswind? De-risking by “China+1” or “In-China-For-China”
Authors: Day Steven James , Godsell Janet , Shou Yongyi 
Published: October 2024

PurposeForeign firms in China, particularly those from the Global West, are in a difficult position as deglobalisation and strained international relations create risk. This paper offers research avenues on how operations and supply chain management scholars can analyse the risk factors, de-risking practices, and de-risking outcomes of foreign firms in China.Design/methodology/approachThis paper is primarily based on interviews with managers of foreign firms’ subsidiaries and joint ventures in China between late 2019 and early 2024 and employs institutional theory to develop a conceptual framework.FindingsSix risk factors motivating foreign firms to consider “China+1” (diversification and multi-sourcing) or “In-China-For-China” (localisation with potential bifurcation) are identified. Four pathways focusing on politics, locations, technologies, and people enable further investigation of these de-risking strategies.Originality/valueThis is the first paper to take a deeper look at perceptions, worries, and considerations of foreign firms in China and offers specific recommendations for impactful research.
How green HRM practices foster green competitive advantage through big data analytics capability and are amplified by managerial environmental concern
Authors: Shaikh Sonia Najam , Zhen Li , Sohu Jan Muhammad , Soomro Sanam , Akhtar Sadaf , Kherazi Fatima Zahra , Najam Suman 
Published: October 2024

PurposeIn today’s business landscape, drawing upon the critical role of environmental sustainability, this study investigates the intricate relationship between green human resource management practices (GHRMP), big data analytics capability (BDAC), green competitive advantage (GCA) and environmental performance (EP), further moderated by managerial environmental concern (MEC).Design/methodology/approachThis study employs a quantitative approach using the latest version of SmartPLS 4 version 4.0.9.6 on a data sample of 467 participants representing a diverse range of manufacturing SMEs. Data were collected from managers and directors using a structured questionnaire and analyzed using structural equation modeling (SEM). This study contributes to the existing knowledge by integrating GHRMP and BDAC within the GCA framework, providing a comprehensive understanding of how these practices enhance SME`s sustainability.FindingsThe findings provide valuable insights into the manufacturing sector, aiming to enhance SMEs' green competitive advantage. Implementing GHRMP fosters environmental awareness within the workforce, and building BDAC allows for effectively translating that GHRMP into actionable insights, maximizing the potential for achieving GCA. Furthermore, recognizing MEC’s moderating role strengthens positive environmental outcomes associated with GCA. The findings confirm that GHRMP and BDAC are valuable resources and key drivers contributing to competitive advantage in sustainability of enterprises.Practical implicationsFor SMEs, our findings suggest that strategically integrating GHRMP with BDAC not only boosts environmental stewardship but also improves operational efficiency and market positioning. This research outlines actionable steps for SMEs aiming to achieve sustainability targets while enhancing profitability. This research provides actionable insights for SMEs in strategic decision-making and policy formulation, aiding SMEs in navigating the complexities of sustainable development effectively.Originality/valueThis study contributes to the existing knowledge by integrating GHRMP and BDAC within the GCA framework, providing a robust theoretical explanation of how HRM practices and BDAC help SMEs gain green competitiveness. The implication of this study reveals that SMEs implementing and integrating green HRM practices with advanced data analytics are more likely to gain competitive advantage. This study draws theoretical support from the resource-based view (RBV) theory, positing that a firm’s sustainable competitive advantage stems from its unique and valuable resources and capabilities that are difficult for competitors to imitate or substitute.
Portfolio location-related decisions: do proximities matter?
Authors: Iturrioz-Landart Cristina , Aragón-Amonarriz Cristina , Garmendia-Lazcano Aitor 
Published: October 2024

PurposeThis paper aims to examine the relationships between how family owners perceive different aspects of proximity to their territory of origin and the location-related decisions of family business portfolios.Design/methodology/approachBy using the data collected from 112 family business portfolios (FBP), the authors carry out an empirical analysis to test the proposed hypotheses. The results are robust across a battery of robustness analyses performed by the authors.FindingsThe analysis reveals a heterogeneous relationship between the different dimensions of proximity and the maintenance and location of portfolio business units. Specifically, we reveal that entrepreneurial families’ social and institutional proximities to their founding territory have a positive influence on their decisions related to investing and maintaining their business portfolio.Originality/valueThese findings open the black box of how business decisions are affected by how business owners perceive their contexts, providing new insights into how corporate decisions in understudied business organisations, business groups, are shaped by the ownership’s proximity to territories.