bluuebunny/crossref_metadata_2025_split huggingface dataset:
Specifications of the ACMG/AMP variant curation guidelines for the analysis of germlineATMsequence variants
Authors: Richardson Marcy E. , Holdren Megan , Brannan Terra , de la Hoya Miguel , Spurdle Amanda B. , Tavtigian Sean V. , Young Colin C. , Zec Lauren , Hiraki Susan , Anderson Michael J. , Walker Logan C. , McNulty Shannon , Turnbull Clare , Tischkowitz Marc , Schon Katherine , Slavin Thomas , Foulkes William D. , Cline Melissa , Monteiro Alvaro N. , Pesaran Tina , Couch Fergus J. 
Published: May 2024

AbstractThe ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer (HBOP) Variant Curation Expert Panel (VCEP) is composed of internationally recognized experts in clinical genetics, molecular biology and variant interpretation. This VCEP made specifications for ACMG/AMP guidelines for the ataxia telangiectasia mutated (ATM) gene according to the Food and Drug Administration (FDA)-approved ClinGen protocol. These gene-specific rules forATMwere modified from the American College of Medical Genetics and Association for Molecular Pathology (ACMG/AMP) guidelines and were tested against 33ATMvariants of various types and classifications in a pilot curation phase. The pilot revealed a majority agreement between the HBOP VCEP classifications and the ClinVar-deposited classifications. Six pilot variants had conflicting interpretations in ClinVar and reevaluation with the VCEP’sATM-specific rules resulted in four that were classified as benign, one as likely pathogenic and one as a variant of uncertain significance (VUS) by the VCEP, improving the certainty of interpretations in the public domain. Overall, 28 the 33 pilot variants were not VUS leading to an 85% classification rate. The ClinGen-approved, modified rules demonstrated value for improved interpretation of variants inATM.
Epigenome-wide association study, meta-analysis and risk profiling of whole blood in Parkinson’s disease
Authors: Lie Ingeborg Haugesag , Tan Manuela , Andersen Maren Stolp , Toft Mathias , Pihlstrøm Lasse 
Published: May 2024

AbstractAn increasing body of evidence indicates altered DNA methylation in Parkinson’s disease (PD), yet the reproducibility and utility of such methylation changes are largely unexplored. We conducted an epigenome-wide association study (EWAS) in whole blood, including 280 PD and 279 control participants from Oslo, Norway. In meta-analysis with data from the Parkinson’s Progression Markers Initiative (PPMI) and a previously published whole blood PD EWAS (total N=3068) we confirmSLC7A11hypermethylation and nominate a novel suggestive differentially methylated CpG nearLPIN1. A joint multiscore risk profiling model incorporating polygenic risk and methylation-based estimates of epigenetic PD risk, smoking and leukocyte proportions differentiated patients from control participants with an area under the receiver-operator curve or 0.82 in the Oslo cohort and 0.65 in PPMI. Our results highlight the power of DNA methylation profiling to capture multiple aspects of disease risk, indicating a biomarker potential for precision medicine in neurodegenerative disorders.
Temporal rules of fear memory cooperation and competition
Authors: Madeira Natália , Campelo Inês , Fonseca Rosalina 
Published: May 2024

AbstractMemory consolidation is highly influenced by ongoing experiences. We explore the temporal rules that determine whether events are cooperatively associated or competitively separated. We show that neutral events are associated with fearful events if they occur within less than 30 minutes. In some individuals, memory association can lead to a competitive suppression of the fearful response by the neutral event. Activation of the thalamic MGm inputs to the lateral amygdala, led to an increase in memory association, whereas manipulation of the cortical inputs had no effect. Introducing a third event leads to competition depending on the temporal relationship between the initial association and the competitive event. Our results show a critical temporal rule of memory association, modulated by thalamic activity that shapes fear memory consolidation.
Polyphosphate mobilization influences the ability ofCryptococcus neoformansto cause disease in a murine model of cryptococcosis
Authors: Bhalla Kabir , León-Hing Eddy Sánchez , Huang Yu-Hsuan , French Victoria , Hu Guanggan , Wang Jennifer , Kretschmer Matthias , Qu Xianya , Moreira Raphaell , Foster E. Johan , Johnson Pauline , Kronstad James W. 
Published: May 2024

AbstractCryptococcus neoformans, an invasive basidiomycete fungal pathogen, causes one of the most prevalent, life-threatening diseases in immunocompromised individuals and accounts for ∼15% of AIDS-associated deaths. A dire need for the development of novel antifungal drugs, vaccines, and improved diagnostics has emerged with the increased frequency of fungal infections. Therefore, understanding the pathogenesis ofC. neoformansand its interactions with the host immune system is critical for the development of therapeutics against cryptococcosis. Previous research demonstrated thatC. neoformanscells lacking polyphosphate (polyP), an immunomodulatory polyanionic storage molecule, display altered cell surface architecture. However, the relevance of surface changes and the role of polyP in the virulence ofC. neoformansremain unclear. Here we show that mutants lacking the polyphosphatases (Xpp1 and Epp1) are attenuated for virulence in a murine inhalational model of cryptococcosis, demonstrate reduced proliferation in host tissue, and provoke an altered immune response. An analysis of mutants lacking the polyphosphatases and the Vtc4 protein for polyP synthesis indicated that the Xpp1 and Epp1 contribute to the organization of the cell surface, virulence factor production, the response to stress, and mitochondrial function. Overall, we conclude that polyP mobilization plays a multifaceted role in the pathogenesis ofC. neoformans.Author SummaryCryptococcus neoformanscauses one of the most prevalent fungal diseases in people with compromised immune systems and accounts for 15-20% of AIDS-associated deaths worldwide. The continual increase in the incidence of fungal infections and limited treatment options necessitate the development of new antifungal drugs and improved diagnostics. Polyphosphate (polyP), an under-explored biopolymer, functions as a storage molecule, modulates the host immune response, and contributes to the ability of many fungal and bacterial pathogens to cause disease. However, the role of polyP in cryptococcal disease remains unclear. In this study, we report that the enzymes that regulate polyP synthesis and turnover contribute to the virulence ofC. neoformansin a mouse model of cryptococcosis. The polyphosphatases, Xpp1 and Epp1, influenced the survival ofC. neoformansin macrophages and altered the host immune response. The loss of Xpp1 and Epp1 led to changes in cell surface architecture, cell size, impaired growth, and defects in both mitochondrial function and the stress response ofC. neoformans.Thus, our work establishes polyP as a key factor in the disease caused byC. neoformans, and identifies polyP mobilization as a novel target to support new therapeutic approaches.
POLQ mediates replication-stress induced structural variant formation throughout common fragile sites during mitosis
Authors: Wilson Thomas E. , Ahmed Samreen , Winningham Amanda , Glover Thomas W. 
Published: May 2024

AbstractGenomic structural variants (SVs) greatly impact human health and disease, but much is unknown about their generative mechanisms, especially for the large class of nonrecurrent alterations. Common fragile sites (CFSs) are unstable loci that provide a model for SV formation, especially large deletions, under replication stress. We studied SV junction formation as it occurred in cells by applying error-minimized capture sequencing to CFS DNA harvested during replication stress. SV junctions formed throughout CFS genes at a 5-fold higher rate after cells passed from G2 into M-phase. Neither SV formation nor CFS expression depended on mitotic DNA synthesis (MiDAS), an error-prone form of conservative replication active at CFSs. Instead, analysis of tens of thousands ofde novoSV junctions combined with DNA repair pathway inhibition revealed a primary role for DNA polymerase theta (POLQ)-mediated end-joining (TMEJ) in M-phase SV formation. We propose an important role for TMEJ in nonrecurrent SV formation genome wide.
In vivoandin vitroanalysis of the role of the Prc protease in inducing mucoidy inPseudomonas aeruginosa
Authors: Sommerfield Alexis G. , Wang Michelle , Mamana Julia , Darwin Andrew J. 
Published: May 2024

ABSTRACTInPseudomonas aeruginosa,alginate biosynthesis gene expression is inhibited by the transmembrane anti-sigma factor MucA, which sequesters the AlgU sigma factor. Cell envelope stress initiates cleavage of the MucA periplasmic domain by site-1 protease AlgW, followed by further MucA degradation to release AlgU. However, after colonizing the lungs of people with cystic fibrosis,P. aeruginosaconverts to a mucoid form that produces alginate constitutively. Mucoid isolates often havemucAmutations, with the most common beingmucA22, which truncates the periplasmic domain. MucA22 is degraded constitutively, and genetic studies suggested that the Prc protease is responsible. Some studies also suggested that Prc contributes to induction in strains with wild type MucA, whereas others suggested the opposite. However, missing from all previous studies is a demonstration that Prc cleaves any protein directly, which leaves open the possibility that the effect of aprcnull mutation is indirect. To address the ambiguities and shortfalls, we reevaluated the roles of AlgW and Prc as MucA and MucA22 site-1 proteases.In vivoanalyses using three different assays, and two different inducing conditions, all suggested that AlgW is the only site-1 protease for wild type MucA in any condition. In contrast, genetics suggested that AlgW or Prc act as MucA22 site-1 proteases in inducing conditions, whereas Prc is the only MucA22 site-1 protease in non-inducing conditions. For the first time, we also show that Prc is unable to degrade the periplasmic domain of wild type MucA, but does degrade the mutated periplasmic domain of MucA22 directly.IMPORTANCEAfter colonizing the lungs of individuals with cystic fibrosis,P. aeruginosaundergoes mutagenic conversion to a mucoid form, worsening the prognosis. Most mucoid isolates have a truncated negative regulatory protein MucA, which leads to constitutive production of the extracellular polysaccharide alginate. The protease Prc has been implicated, but not shown, to degrade the most common MucA variant, MucA22, to trigger alginate production. This work provides the first demonstration that the molecular mechanism of Prc involvement is direct degradation of the MucA22 periplasmic domain, and perhaps other truncated MucA variants as well. MucA truncation and degradation by Prc might be the predominant mechanism of mucoid conversion in cystic fibrosis infections, suggesting that Prc activity could be a useful therapeutic target.
Quantification and optimization of travel time for ethnic minority populations in cancer clinical trials
Authors: Lee H , Trevino JG , Terry MB , Winkfield K , Janowitz T 
Published: May 2024

ABSTRACTOf all minority racial and ethnic groups, Hispanic populations are most under-represented in trials compared to the general US population. Transportation and socioeconomic burdens are two important inter-related quantifiable and modifiable variables associated with decreased clinical trial participation for underrepresented populations. In this study, Hispanic population sizes and socioeconomic deprivation indices of catchment areas within simulated 30-minute driving distances from all major U.S. cancer trial sites (N=78) and all U.S. hospitals (N=7,623) were calculated using OpenStreetMap and U.S. census data. In the proximity of major trial sites Hispanic ethnicity representation varied across a wide range (64% to 2%) and Hispanic populations were underrepresented compared to the national average in almost 2/3 of the sites (n=50). The cities with the highest number of hospitals identified with catchment populations of >60%, >40% or >20% Hispanic representation were San Antonio TX, Houston TX, and New York NY respectively. Data-driven analyses can quantify and optimize measurable factors associated with decreased clinical trial participation for under-represented populations and may aid selection of trial sites to enable participation.
Combating green innovation in Italian luxury hotels: combination of social cognitive theory and natural resource-based view
Authors: Aslam Nadia , Shi Da , Sahibzada Umar Farooq 
Published: May 2024

PurposeThe objective of this investigation is to examine the correlation between green transformational leadership (GTL) and organizational green innovation (GI) by employing a mediation model. Drawing upon the social cognitive theory and natural resource-based view, the present study explores the role of green creativity (GC) as a mediating variable in the relationship between GTL and GI in the hotel industry.Design/methodology/approachThe research was conducted in Italian luxury hotels to assess the efficacy of our conceptual framework among workers in the hospitality industry. The study utilized a three-wave 2-week time-lagged design (N = 303). In addition, the study also intends to apply the Partial Least Squares – Structural Equation Modelling (PLS-SEM) and the fuzzy qualitative comparative analysis (fsQCA) to have distinctive discernment into model rapport.FindingsThe results of the study indicate the linkage between GTL and GI. Furthermore, the study also found the partial mediation of GC of employees. The results show numerous combinations using fsQCA that can be utilized to increase green performance (GP).Originality/valueThe study helps the hotel industry maximize its performance by unravelling irregular relationships. Therefore, it contributes by explaining previously unexplored factors and elucidating causal recipes to build a higher GP base through GTL, GC and GI. The research findings hold significant implications for comprehending the effects of GTL on organizational GI as well as its influence on GP. The limitations of the study are discussed for avenues of future research.
A comprehensive review of techniques for documenting artificial intelligence
Authors: Königstorfer Florian 
Published: May 2024

Purpose
Companies are increasingly benefiting from artificial intelligence (AI) applications in various domains, but also facing its negative impacts. The challenge lies in the lack of clear governance mechanisms for AI. While documentation is a key governance tool, standard software engineering practices are inadequate for AI. Practitioners are unsure about how to document AI, raising questions about the effectiveness of current documentation guidelines. This review examines whether AI documentation guidelines meet regulatory and industry needs for AI applications and suggests directions for future research.

Design/methodology/approach
A structured literature review was conducted. In total, 38 papers from top journals and conferences in the fields of medicine and information systems as well as journals focused on fair, accountable and transparent AI were reviewed.

Findings
This literature review contributes to the literature by investigating the extent to which current documentation guidelines can meet the documentation requirements for AI applications from regulatory bodies and industry practitioners and by presenting avenues for future research. This paper finds contemporary documentation guidelines inadequate in meeting regulators’ and professionals’' expectations. This paper concludes with three recommended avenues for future research.

Originality/value
This paper benefits from the insights from comprehensive and up-to-date sources on the documentation of AI applications.
A gender-specific view on entrepreneurial recovery – effects on and responses of micro-entrepreneurs during the COVID-19 pandemic in Germany
Authors: Terstriep Judith , Schäfer Susann , David Alexandra , Rieger-Fels Markus , García Schmidt Armando , Kay Rosemarie , Rosenberger Theresa 
Published: May 2024

Purpose
Given the adversity of the COVID-19 pandemic, there remains an incomplete understanding of the gender disparities in the affectedness and recovery of micro-entrepreneurs from the crisis. Consequently, this paper aims to scrutinise gender disparities in the initial repercussions of the crisis and throughout the recovery phase.

Design/methodology/approach
Acknowledging the interconnectedness of micro-entrepreneurs’ professional and private spheres, the study adopts a mixed-methods approach combining a representative quantitative study with qualitative data from 36 semi-structured interviews with self-employed individuals in Germany amidst the COVID-19 crisis.

Findings
The findings indicate a gender gap in the impact and recovery trajectory, particularly affecting female entrepreneurs in caregiving roles beyond immediate financial repercussions. These disparities did not result in more pronounced business measures for recovery but rather involved more experimentation and prosocial behaviours, with a preference for alternatives to state aid, such as personal reserves and social networks.

Originality/value
Unveiling the dual influence of economic and social factors as essential for female entrepreneurs’ recovery from the crisis adds to the literature by providing a comprehensive understanding of gender-specifics.
Implementing artificial intelligence across task types: constraints of automation and affordances of augmentation
Authors: Mazurova Elena , Standaert Willem 
Published: May 2024

PurposeThis study aims to uncover the constraints of automation and the affordances of augmentation related to implementing artificial intelligence (AI)-powered systems across different task types: mechanical, thinking and feeling.Design/methodology/approachQualitative study involving 45 interviews with various stakeholders in artistic gymnastics, for which AI-powered systems for the judging process are currently developed and tested. Stakeholders include judges, gymnasts, coaches and a technology vendor.FindingsWe identify perceived constraints of automation, such as too much mechanization, preciseness and inability of the system to evaluate artistry or to provide human interaction. Moreover, we find that the complexity and impreciseness of the rules prevent automation. In addition, we identify affordances of augmentation such as speedier, fault-less, more accurate and objective evaluation. Moreover, augmentation affords to provide an explanation, which in turn may decrease the number of decision disputes.Research limitations/implicationsWhile the unique context of our study is revealing, the generalizability of our specific findings still needs to be established. However, the approach of considering task types is readily applicable in other contexts.Practical implicationsOur research provides useful insights for organizations that consider implementing AI for evaluation in terms of possible constraints, risks and implications of automation for the organizational practices and human agents while suggesting augmented AI-human work as a more beneficial approach in the long term.Originality/valueOur granular approach provides a novel point of view on AI implementation, as our findings challenge the notion of full automation of mechanical and partial automation of thinking tasks. Therefore, we put forward augmentation as the most viable AI implementation approach. In addition, we developed a rich understanding of the perception of various stakeholders with a similar institutional background, which responds to recent calls in socio-technical research.
Navigating diversity: identity perceptions and workplace dynamics
Authors: Qureshi Fareed ud din 
Published: May 2024

Purpose
This study aims to investigate the impact of dissimilarity perceptions, specifically related to religious identity and socioeconomic class, on identity disclosure behavior within the workplace. It also explores the relationship between disclosure behavior and perceptions of workplace ostracism. The study further examines the moderating roles of psychological safety climate and diversity-focused human resource (HR) practices in these dynamics.

Design/methodology/approach
Using quantitative methods, this confirmatory study analyzes the relationships between dissimilarity perceptions, identity disclosure behavior, workplace ostracism perceptions, psychological safety climate and diversity-focused HR policies. Hypotheses are tested to understand the effects of these variables in the workplace context.

Findings
The findings reveal that subjective dissimilarity perceptions are negatively associated with identity disclosure behavior. In addition, disclosure behavior is positively linked to perceptions of workplace ostracism. Surprisingly, the study finds that the psychological safety climate moderates the relationship between dissimilarity perceptions and identity disclosure behavior, showing a positive relationship when psychological safety climate perceptions are high. Furthermore, perceptions of diversity-focused HR policies moderate the relationship between disclosure behavior and perceptions of workplace ostracism, indicating a weakened relationship when diversity-focused HR practices are perceived as stronger.

Originality/value
This study contributes to the understanding of workplace diversity, inclusion and management by emphasizing the role of subjective dissimilarity perceptions, identity disclosure behavior and workplace ostracism. It explores the moderating influence of psychological safety climate and diversity-focused HR practices, offering valuable insights for both theory and practical strategies in the context of diversity management.
African Continental Free Trade Area Agreement investor protection and capital market in Africa
Authors: Ajibo Collins Chikodili 
Published: May 2024

Purpose
The purpose of this paper is to explore the modalities for the curtailment of expropriation of investment in the course of implementation of the African Continental Free Trade Area (AfCFTA) Agreement and to ensure that the African capital markets contribute robustly to economic growth.

Design/methodology/approach
The paper relies on the doctrinal approach to assess the state of play and the prospects for the future.

Findings
The paper found that African capital markets are fragmented and continue to suffer from poor investor protection which lowers market confidence.

Originality/value
The paper offers new insights on the regulatory approaches to foster investor protection in light of the emergence of the AfCFTA, regulation of executive compensation and need for harmonization of best practices across African markets.