bluuebunny/crossref_metadata_2025_split huggingface dataset:
Graspot: A graph attention network for spatial transcriptomics data integration with optimal transport
Authors: Gao Zizhan , Cao Kai , Wan Lin 
Published: February 2024

AbstractSpatial transcriptomics (ST) technologies enable the measurement of mRNA expression while simultaneously capturing spot locations. By integrating ST data, the 3D structure of a tissue can be reconstructed, yielding a comprehensive understanding of the tissue’s intricacies. Nevertheless, a computational challenge persists: how to remove batch effects while preserving genuine biological structure variations across ST data. To address this, we introduce Graspot, agraphattention network designed forspatial transcriptomics data integration with unbalancedoptimaltransport. Graspot adeptly harnesses both gene expression and spatial information to align common structures across multiple ST datasets. It embeds multiple ST datasets into a unified latent space, facilitating the partial alignment of spots from different slices. Demonstrating superior performance compared to existing methods on four real spatial transcriptomics datasets, Graspot excels in ST data integration, including tasks that require partial alignment. In particular, Graspot unveils subtle tumor microenvironment structures of breast cancer, and accurately aligns the spatio-temporal transcriptomics data to reconstruct human heart developmental processes. The code for Graspot is available athttps://github.com/zhan009/Graspot.
Rhinovirus infection of airway epithelial cells uncovers the non-ciliated subset as a likely driver of genetic susceptibility to childhood-onset asthma
Authors: Djeddi Sarah , Fernandez-Salinas Daniela , Huang George X. , Aguiar Vitor R. C. , Mohanty Chitrasen , Kendziorski Christina , Gazal Steven , Boyce Joshua , Ober Carole , Gern James , Barrett Nora , Gutierrez-Arcelus Maria 
Published: February 2024

AbstractAsthma is a complex disease caused by genetic and environmental factors. Epidemiological studies have shown that in children, wheezing during rhinovirus infection (a cause of the common cold) is associated with asthma development during childhood. This has led scientists to hypothesize there could be a causal relationship between rhinovirus infection and asthma or that RV-induced wheezing identifies individuals at increased risk for asthma development. However, not all children who wheeze when they have a cold develop asthma. Genome-wide association studies (GWAS) have identified hundreds of genetic variants contributing to asthma susceptibility, with the vast majority of likely causal variants being non-coding. Integrative analyses with transcriptomic and epigenomic datasets have indicated that T cells drive asthma risk, which has been supported by mouse studies. However, the datasets ascertained in these integrative analyses lack airway epithelial cells. Furthermore, large-scale transcriptomic T cell studies have not identified the regulatory effects of most non-coding risk variants in asthma GWAS, indicating there could be additional cell types harboring these “missing regulatory effects”. Given that airway epithelial cells are the first line of defense against rhinovirus, we hypothesized they could be mediators of genetic susceptibility to asthma. Here we integrate GWAS data with transcriptomic datasets of airway epithelial cells subject to stimuli that could induce activation states relevant to asthma. We demonstrate that epithelial cultures infected with rhinovirus significantly upregulate childhood-onset asthma-associated genes. We show that this upregulation occurs specifically in non-ciliated epithelial cells. This enrichment for genes in asthma risk loci, or ‘asthma heritability enrichment’ is also significant for epithelial genes upregulated with influenza infection, but not with SARS-CoV-2 infection or cytokine activation. Additionally, cells from patients with asthma showed a stronger heritability enrichment compared to cells from healthy individuals. Overall, our results suggest that rhinovirus infection is an environmental factor that interacts with genetic risk factors through non-ciliated airway epithelial cells to drive childhood-onset asthma.
Increased evolutionary rate in the Z-chromosome ofMorphobutterflies and implications for speciation
Authors: Villavicencio Manuela López , Ledamoisel Joséphine , Lopez-Roques Céline , Debat Vincent , Llaurens Violaine 
Published: February 2024

AbstractThe evolution of reproductive isolation between populations shapes divergence in genome structure and content: comparing the genomes of closely-related species can thus enlighten the speciation process. Comparisons of genomes of allopatricvs. sympatric species sharing similarvs. dissimilar ecological niches allows to specifically investigate the effect of reinforcement and ecological specialization on genome evolution. In the butterfly genusMorpho, several species can be found in sympatry presenting specialisation in different microhabitats and temporal niches. Here, we sequenced, assembled and annotated the genomes of 8Morphospecies and used previously published genomes of three otherMorphospecies to study genomic rearrangements and signatures of positive selection. We found extensive chromosomal rearrangements in the Z chromosome compared to the autosomes, particularly among closely related sympatric species occupying similar niches, pointing at the putative role of inversions in preventing gene flow at a postzygotic level. We also detected a higher proportion of genes under positive selection on the Z-chromosome compared to the autosomes, suggesting a potential role of the Z-chromosome in driving adaptive evolution inMorpho. Finally, because of the divergence in daily activities between species, we studied the evolution of eight genes involved in the circadian clock and detected a signature of positive selection on the genePeriod, located in the Z chromosome. By studying the evolution of genome structure and coding sequences, our study indicates fast evolution of the Z-chromosome, partly driven by selection, throughout this genus, highlighting the putative implication of this sexual chromosome on pre and post-zygotic isolation.
Longitudinal changes in anthropometric, physiological, and physical qualities of international women’s rugby league players
Authors: Scantlebury Sean , Costello Nessan , Owen Cameron , Chantler Sarah , Ramirez Carlos , Zabaloy Santiago , Collins Neil , Allen Hayden , Phillips Gemma , Alexander Marina , Barlow Matthew , Williams Emily , Mackreth Peter , Barrow Stuart , Clarke Anthony , Samuels Benjamin , Roe Stephanie , Blake Cameron , Jones Ben 
Published: February 2024

AbstractThis is the first study to assess longitudinal changes in anthropometric, physiological, and physical qualities of international women’s rugby league players. Thirteen forwards and 11 backs were tested three times over a 10-month period. Assessments included: standing height and body mass, body composition measured by dual x-ray absorptiometry (DXA), a blood panel, resting metabolic rate (RMR) assessed by indirect calorimetry, aerobic capacity (i.e., VLO2max) evaluated by an incremental treadmill test, and isometric force production measured by a force plate. During the pre-season phase, lean mass increased significantly by ∼2% for backs (testing point 1: 47 kg; testing point 2: 48 kg) and forwards (testing point 1: 50 kg; testing point 2: 51 kg) (p = ≤ 0.05). Backs significantly increased their VLO2max by 22% from testing point 1 (40 ml·kg−1·min−1) to testing point 3 (49 ml·kg−1·min−1) (p = ≤ 0.04). The VLO2max of forwards increased by 10% from testing point 1 (41 ml·kg−1·min−1) to testing point 3 (45 ml·kg−1·min−1), however this change was not significant (p = ≥ 0.05). Body mass (values represent the range of means across the three testing points) (backs: 68 kg; forwards: 77-78 kg), fat mass percentage (backs: 25-26%; forwards: 30-31%), resting metabolic rate (backs: 7 MJ·day−1; forwards: 7 MJ·day−1), isometric mid-thigh pull (backs: 2106-2180 N; forwards: 2155-2241 N), isometric bench press (backs: 799-822 N; forwards: 999-1024 N), isometric prone row (backs: 625-628 N; forwards: 667-678 N) and bloods (backs: ferritin 21-29 ug/L, haemoglobin 137-140 g/L, iron 17-21 umol/L, transferrin 3 g/L, transferring saturation 23-28%; forwards: ferritin 31-33 ug/L, haemoglobin 141-145 g/L, iron 20-23 umol/L, transferrin 3 g/L, transferrin saturation 26-31%) did not change (p = ≥ 0.05). This study provides novel longitudinal data which can be used to better prepare women rugby league players for the unique demands of their sport, underpinning female athlete health.
TNFpromoter hypomethylation is associated with mucosal inflammation in IBD and anti-TNF response
Authors: Levic Daniel S. , Niedzwiecki Donna , Kandakatla Apoorva , Karlovich Norah S. , Juneja Arjun , Park Jieun , Stolarchuk Christina , Adams Shanté , Willer Jason R. , Schaner Matthew R. , Lian Grace , Beasley Caroline , Marjoram Lindsay , Flynn Ann D. , Valentine John F. , Onken Jane E. , Sheikh Shehzad Z. , Davis Erica E. , Evason Kimberley J. , Garman Katherine S. , Bagnat Michel 
Published: February 2024

AbstractBackground and aimsInflammatory Bowel Diseases (IBD) are chronic inflammatory conditions influenced heavily by environmental factors. DNA methylation is a form of epigenetic regulation linking environmental stimuli to gene expression changes and inflammation. Here, we investigated how DNA methylation of theTNFpromoter differs between inflamed and uninflamed mucosa of IBD patients, including anti-TNF responders and non-responders.MethodsWe obtained mucosal biopsies from 200 participants (133 IBD and 67 controls) and analyzedTNFpromoter methylation using bisulfite sequencing, comparing inflamed with uninflamed segments, in addition to paired inflamed/uninflamed samples from individual patients. We conducted similar analyses on purified intestinal epithelial cells from bowel resections. We also comparedTNFmethylation levels of inflamed and uninflamed mucosa from a separate cohort of 15 anti-TNF responders and 17 non-responders. Finally, we sequenced DNA methyltransferase genes to identify rare variants in IBD patients and functionally tested them using rescue experiments in a zebrafish genetic model of DNA methylation deficiency.ResultsTNFpromoter methylation levels were decreased in inflamed mucosa of IBD patients and correlated with disease severity. Isolated IECs from inflamed tissue showed proportional decreases inTNFmethylation. Anti-TNF non-responders showed lower levels ofTNFmethylation than responders in uninflamed mucosa. Our sequencing analysis revealed two missense variants inDNMT1, one of which had reduced functionin vivo.ConclusionsOur study reveals an association ofTNFpromoter hypomethylation with mucosal inflammation, suggesting that IBD patients may be particularly sensitive to inflammatory environmental insults affecting DNA methylation. Together, our analyses indicate thatTNFpromoter methylation analysis may aid in the characterization of IBD status and evaluation of anti-TNF therapy response.
Pangenome-wide association study reveals selective absence of CRISPR genes (Rv2816c-19c) in drug-resistantMycobacterium tuberculosis
Authors: Bhalla Nikhil , Nanda Ranjan Kumar 
Published: February 2024

AbstractBackgroundThe drug resistance development inMycobacterium tuberculosis(Mtb) is attributed to the acquisition of mutations in the drug target genes. However, the role of the differential presence of non-essential accessory genes is relatively unexplored and Pan Genome-Wide Association Study (Pan-GWAS) can identify these gene sets that could contribute to drug resistance development in Mtb.MethodologyPublicly available Whole Genome Sequencing (WGS) data of clinical Mtb isolates (n=2601) from TB endemic countries (India, China, Zambia, Pakistan) were used in this study. The Mtb WGS data was de novo assembled, filtered for contamination, scaffolded into longer contigs, and functionally annotated. All analyses, including Gene repertoire and Pan-GWAS, were conducted using open-source tools, and the Benjamin Hochberg test was applied to identify genes having significant association with drug-resistant Mtb isolates.ResultsOut of 2601 Mtb WGS data sets, 2184 qualified as high-quality and were used for Pan-GWAS analysis (drug-resistant n=1386; drug-sensitive n=798). A set of 3784 core genes, 123 softcore genes, 224 shell genes, and 762 cloud genes were identified. Sets of 33 and 39 genes showed a positive and a negative association with drug-resistant isolates, respectively, with high significance (p-value < 0.01). Gene ontology cluster analysis indicated a compromised bacterial immune system and impaired DNA repair in drug-resistant compared to the sensitive isolates. Multidrug efflux pump repressor genes (Rv3830c and Rv3855c) were also absent in the drug-resistant Mtb isolates. The absence of CRISPR-associated genes (Rv2816c-19c) is reported in other drug-resistant microbes, and a similar pattern is observed in Mtb.ConclusionsThis study sheds light on Mtb genes involved in drug resistance emergence and could be helpful in better understanding of host-pathogen interactions, identification of novel drug targets and diagnostics.
Organizational justice, job satisfaction and academic rank: a moderating mediation study on employee commitment in Ethiopian public universities
Authors: Gollagari Ramakrishna , Birega Temesgen , Mishra Santap Sanhari 
Published: February 2024

PurposeOrganizational justice and its impact on employee commitment have received a lot of attention these days. The objective of this study is to see the effect of job satisfaction as a mediator in the relationship between organizational justice and employee commitment. Also, the role of academic rank as a moderator in the model is probed.Design/methodology/approachA moderating mediation structural equation model was used for randomly collected cross-section data on 285 employees from public universities in Ethiopia. Necessary condition analysis (NCA) was employed to check the importance of the variables. The Gaussian copula approach was used to check endogeneity in the structural model.FindingsNCA confirms the importance of organizational justice and employee satisfaction as the independent variables. The Gaussian copula approach reveals no endogeneity problems in the structural model. The results supported the partial mediating role of job satisfaction in organizational justice and academic staff’s commitment. Moreover, though staff rank is not a necessary condition, it plays the role of moderator in the relationship between academic staff’s job satisfaction and commitment.Practical implicationsThis paper affirms that public institutions must implement fair initiatives and procedures to promote academic staff satisfaction and commitment.Originality/valueThis is the first study to check the job rank as a moderator in the model comprising organization justice, employee commitment and satisfaction. Moreover, application of NCA and Gaussian copula adds to methodological innovation.
Empowering the next generation of women in interior design in the United Arab Emirates through competitive education: a curriculum review
Authors: Pasina Irene , Corti Emanuela , Eldanaf Taher , Abdullah Dalal 
Published: February 2024

PurposeThis paper explores the impact of interior design education and its effectiveness in the work environment for women in the United Arab Emirates (UAE), as they are the primary recipients of interior design programs. The analysis focuses on the role of women in interior design in the Gulf countries and the update of an interior design program curriculum as part of the continuous development program requested by the UAE Commission of Academic Accreditation (CAA) of the national Ministry of Education (MoE).Design/methodology/approachThe research adopts different methodologies: an academic annual effectiveness report (AER), requirements of relevant international and regional accreditation bodies and a double round of surveys and interviews with female students, alumni, instructors and professionals.FindingsThe article collects and compares data from different perspectives, from the academic to the professional point of view, discussing challenges and opportunities for female students in contemporary interior design in the UAE. After collecting the necessary feedback on the strengths and weaknesses of the bachelor’s program, a set of informed recommendations has been developed, approved and introduced during the academic year 2022/2023. At the end of the year, a second feedback from faculty and external reviewers was gathered and analyzed, providing preliminary insights into the effectiveness of the curricular revisions and highlighting the significant benefits for the female students.Originality/valueThe paper discusses the comprehensive and up-to-date combination of traditional elements, innovative approaches and sustainable practices, alongside the strategic planning of the United Arab Emirates, proposed to enhance female learning experiences while reinforcing their skills and competencies for their future careers.
The moderating role of women directors in politically connected companies on the performance of Liberian companies
Authors: Neves Maria Elisabete , Guedes Rui , Proença Catarina , Lozano Belen 
Published: February 2024

Purpose
The purpose of this paper is to analyse the impact of political connections and gender diversity on the performance of Iberian companies as a singular market and considering Portugal and Spain separately.

Design/methodology/approach
The authors used panel data methodology, specifically GMM system estimation model by Arellano and Bond (1991) for the period from 2015 to 2020.

Findings
Results show that the performance of listed Iberian companies is influenced by political connections, by gender diversity and that gender diversity has a mitigating effect on the effects of political connections in each country. The mitigating effect of women is evident in both Portugal and Spain, as they are more cautious and principled, which is valued by short-term investors interested in an immediate investment. However, considering the Iberian Peninsula as a whole, the results indicate that – in the long term – women's political relationships can benefit performance through a better reputation and image, which can lead to better social and economic results in the long term.

Originality/value
To the best of the authors’ knowledge, this paper is original and covers an important gap in the literature when considering political connections and women's impact on these connections as determinants of the performance of Iberian companies.
Theory-practice gap of capitation payment in the Indonesian national health insurance: toward universal health coverage
Authors: Putri Nuzulul Kusuma , Purwaningrum Farah , Thabrany Hasbullah , Khotimah Eva Husnul 
Published: February 2024

PurposeThis study aims to present a comprehensive integrative review of capitation payment for primary healthcare (PHC) in the Indonesian national health insurance (Jaminan Kesehatan Nasional,JKN).Design/methodology/approachWhittemore and Knafl’s integrative review method is used within this review and analysis framework. Multiple types of academic literature were included in this review, including all studies related to capitation payment in the JKN from 2014 until 2022.FindingsThis review found that several practices of capitation payments in the JKN in Indonesia deviate from basic economic concept of capitation. It does not yet incentivize PHC to create a competitive environment in attracting members and it does not incentivize health promotion and prevention. Moreover, the capitation model uses the same scope of primary care services for all PHC throughout the country – which in fact has disparities in providing 155 medical conditions as required competencies for PHC. The authors recommend that the JKN apply bottom-up costing and pricing methods to set market prices of capitation rates.Originality/valueThis is the first study that reviews theory-practice gap of the capitation payment model using an integrative review that covers academic literature, journal articles and regulations in Indonesia.
Having your career path decided too early: the effects of high school track on education-occupation mismatch
Authors: Botezat Alina , Incaltarau Cristian , Diac Sabina Ana , Grosu Alexandra Claudia 
Published: February 2024

PurposeThis paper aims to extend the scope of previous studies on education-occupation mismatch to explicitly focus on the role high school track choices have on the risk of being mismatched in the labor market.Design/methodology/approachThe paper uses the most exhaustive available database regarding the early-career paths of university graduates in Romania. Using a novel matching technique, entropy balancing (EB), our study relies on multinomial logit models and logit regressions to estimate the effect of the completed high school track on the likelihood of being mismatched in the labor market. The empirical analysis focuses on two types of education-occupation mismatches: horizontal and vertical mismatches.FindingsWe show that studying a different field in college compared to the completed high school track increases the risk of being skill mismatched in the first job after graduation. Five years after college graduation, the influence of the high school track fades, while being skill mismatched in the first employment plays a more important role. In contrast, we find no evidence that pursuing a college major unrelated to the completed high school track increases the probability of being overeducated. However, being overeducated in the first job increases the risk of being overeducated five years later.Originality/valueThe study brings new reliable evidence on the extent to which high school track choices may contribute to the risk of being mismatched in the labor market.
Data literacy in the new EU DigComp 2.2 framework how DigComp defines competences on artificial intelligence, internet of things and data
Authors: Van Audenhove Leo , Vermeire Lotte , Van den Broeck Wendy , Demeulenaere Andy 
Published: February 2024

Purpose
The purpose of this paper is to analyse data literacy in the new Digital Competence Framework for Citizens (DigComp 2.2). Mid-2022 the Joint Research Centre of the European Commission published a new version of the DigComp (EC, 2022). This new version focusses more on the datafication of society and emerging technologies, such as artificial intelligence. This paper analyses how DigComp 2.2 defines data literacy and how the framework looks at this from a societal lens.

Design/methodology/approach
This study critically examines DigComp 2.2, using the data literacy competence model developed by the Knowledge Centre for Digital and Media Literacy Flanders-Belgium. The examples of knowledge, skills and attitudes focussing on data literacy (n = 84) are coded and mapped onto the data literacy competence model, which differentiates between using data and understanding data.

Findings
Data literacy is well-covered in the framework, but there is a stronger emphasis on understanding data rather than using data, for example, collecting data is only coded once. Thematically, DigComp 2.2 primarily focusses on security and privacy (31 codes), with less attention given to the societal impact of data, such as environmental impact or data fairness.

Originality/value
Given the datafication of society, data literacy has become increasingly important. DigComp is widely used across different disciplines and now integrates data literacy as a required competence for citizens. It is, thus, relevant to analyse its views on data literacy and emerging technologies, as it will have a strong impact on education in Europe.