bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patterns of crossover distribution inDrosophila mauritiananecessitate a re-thinking of the centromere effect on crossing over
Authors: Hawley R. Scott , Price Andrew , Li Hua , Jagannathan Madhav , Staber Cynthia , Hughes Stacie E. , Williams Stefanie , Perera Anoja , Egidy Rhonda R. , Lawlor Amanda , Miller Danny E. , Blumenstiel Justin P. 
Published: November 2024

AbstractWe present a SNP-based crossover map forDrosophila mauritiana. Using females derived by crossing two different strains ofD.mauritiana, we analyzed crossing over on all five major chromosome arms. Analysis of 105 male progeny allowed us to identify 327 crossover chromatids bearing single, double, or triple crossover events, representing 398 separate crossover events. We mapped these crossover sites along these five chromosome arms using a genome sequence map that includes the euchromatin-heterochromatin boundary. Confirming previous studies, we show that the overall crossover frequency inD.mauritianais higher than is seen inD.melanogaster. Much of the increase in exchange frequency inD.mauritianais due to a greatly diminished centromere effect. Using larval neuroblast metaphases fromD.mauritiana–D.melanogasterhybrids we show that the lengths of the pericentromeric heterochromatin do not differ substantially between the two species, and thus cannot explain the observed differences in crossover distribution. Using a new and robust maximum likelihood estimation tool for obtaining Weinstein tetrad distributions, we observed an increase in bivalents with two or more crossovers when compared toD.melanogaster. This increase in crossing over along the arms ofD.mauritianalikely reflects an expansion of the crossover-available euchromatin caused by the reduction in the centromere effect. The pattern of crossing over inD.mauritianaconflicts with the commonly accepted view of centromeres as polar suppressors of exchange (whose intensity is buffered by sequence non-specific heterochromatin) and demonstrates the importance of expanding such studies into other species of Drosophila.Article SummaryIn meiosis, homolog segregation is usually ensured by crossovers. The number and distribution of crossovers is in part regulated by cis-acting factors such as the cis- acting centromere effect, a polar suppression of exchange emanating from the vicinity of the centromere. We use SNP-based crossover mapping to show that inDrosophila mauritiana, the centromere effect is greatly reduced on four of the five major chromosome arms. We conclude that the centromere effect differs betweenDrosophila mauritianaandDrosophila melanogasterand that the ability to attenuate the centromere effect is not a general property of heterochromatin.
Inter-individual gene expression variability implies stable regulation of brain-biased genes across organs
Authors: Bucao Christabel F. , Aletti Consolée , Moretti Sébastien , Thompson Andrew W. , Racicot Brett L. , Wilson Catherine A. , Bobe Julien , Braasch Ingo , Guiguen Yann , Postlethwait John H. , Robinson-Rechavi Marc 
Published: November 2024

AbstractPhenotypic variation among individuals plays a key role in evolution, since variation provides the material on which natural selection can act. One important link between genetic and phenotypic variation is gene expression. As for other phenotypes, the range of accessible expression variation is limited and biased by different evolutionary and developmental constraints. Gene expression variability broadly refers to the tendency of a gene to vary in expression (i.e., between individuals or cells) due to stochastic fluctuations or differences in genetic, epigenetic, or environmental factors, separately from the differences between e.g. organs. Variability due to biomolecular stochasticity (transcriptional ‘noise’) and cell-to-cell heterogeneity has been well-studied in isogenic populations of unicellular organisms such as bacteria and yeasts. However, for more complex organisms with multiple cells, tissues, and organs sharing the same genetic background, the interplay between inter-individual expression variability, gene and organ function, and gene regulation remains an open question. In this study, we used highly multiplexed 3’-end Bulk RNA Barcoding and sequencing (BRB-seq) to generate transcriptome profiles spanning at least nine organs in outbred individuals of three ray-finned fish species: zebrafish, Northern pike, and spotted gar. For each condition, we measured expression variation per gene independent of mean expression level. We observed that lowly variable genes are enriched in cellular housekeeping functions whereas highly variable genes are enriched in stimulus-response functions. Furthermore, genes with highly variable expression between individuals evolve under weaker purifying selection at the coding sequence level, indicating that intra-species gene expression variability predicts inter-species protein sequence divergence. Genes that are broadly expressed across organs tend to be both highly expressed and lowly variable between individuals, whereas organ-biased genes are typically highly variable within their top organ of expression. For genes with organ-biased expression profiles, we inferred differences in selective pressure on gene regulation depending on their top organ. We found that genes with peak expression in the brain have low inter-individual expression variability across non-nervous organs, suggesting stabilizing selection on regulatory evolution of brain-biased genes. Conversely, liver-biased genes have highly variable expression across organs, implying weaker regulatory constraints. These patterns show that gene regulatory mechanisms evolved differently based on constraints on the primary organ.
Genotype-immunophenotype relationships inNPM1-mutant AML clonal evolution uncovered by single cell multiomic analysis
Authors: Drucker Morgan , Lee Darren , Zhang Xuan , Kain Bailee , Bowman Michael , Nicolet Deedra , Wang Zhe , Stone Richard M. , Mrózek Krzysztof , Carroll Andrew J. , Starczynowski Daniel T. , Levine Ross L. , Byrd John C. , Eisfeld Ann-Kathrin , Salomonis Nathan , Grimes H. Leighton , Bowman Robert L. , Miles Linde A. 
Published: November 2024

AbstractAcute myeloid leukemia (AML) is a multi-clonal disease, existing as a milieu of clones with unique but related genotypes as initiating clones acquire subsequent mutations. However, bulk sequencing cannot fully capture AML clonal architecture or the clonal evolution that occurs as patients undergo therapy. To interrogate clonal evolution, we performed simultaneous single cell molecular profiling and immunophenotyping on 43 samples from 32NPM1-mutant AML patients at different stages of disease. Here we show that diagnosis and relapsed AML samples display similar clonal architecture patterns, but signaling mutations can drive increased clonal diversity specifically at relapse. We uncovered unique genotype-immunophenotype relationships regardless of disease state, suggesting leukemic lineage trajectories can be hard-wired by the mutations present. Analysis of longitudinal samples from patients on therapy identified dynamic clonal, transcriptomic, and immunophenotypic changes. Our studies provide resolved understanding of leukemic clonal evolution and the relationships between genotype and cell state in leukemia biology.
gen3DNet: An R Package for Generating 3D Network Models
Authors: Morrison Paul , Tang Tina , Lu Charles , Mollah Shamim 
Published: November 2024

AbstractMotivationNetworks are ubiquitous to organize and represent data in the real world such as the biomedical networks, social networks, etc. Due to the attractive property of networks which can explicitly capture the rich relationships among data samples, there is an increasing demand to transform linkage-free data to graph-structure data for efficient downstream analyses. Existing works typically focus on representing a single data object like gene expression profile in a homogeneous 2D network, which fail to deal with situations where two different data objects are involved to create a 3D heterogeneous network.ResultsIn this paper, we introduce an R package, gen3DNet (a generic version of the iPhDNet), for generating 3D network models from two correlated objects with shared common factors. Specifically, gen3DNet builds the relationships between samples and shared factors using the non-negative matrix factorization, where three clustering techniques are evaluated to determine the number of functional modules. In addition, it builds the relationships between samples from the two distinct data objects based on a partial least squares regression model. Usage of the package is illustrated through a real-world application.GitHub URLSource code is available athttps://github.com/mollahlab/gen3DNet
Vaccine-induced and hybrid immunity against SARS-CoV-2 variants of concern in two cohorts in Queensland, Australia (2021-2022)
Authors: Parry Rhys H. , Shang Yingjun , Sng Julian D.J. , McMillan Christopher L. D. , Modhiran Naphak , Amarilla Alberto A. , Isaacs Ariel , Liang Benjamin , Muller David A. , Rawle Daniel , Suhrbier Andreas , Anderson Stevie , Kelly Samuel , Watterson Daniel , Burr Lucy D. , Khromykh Alexander A. 
Published: November 2024

AbstractThe spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the main target for vaccine development, as antibodies generated against the spike protein are the most immunodominant and neutralizing against the virus. However, variants of concern (VOC), often containing multiple mutations within neutralizing epitopes, confer immune evasion of the response generated by current SARS-CoV-2 vaccines. To assess the immunogenicity and virus-neutralisation ability of antibodies induced by individual or combination of Vaxzevria (AstraZeneca: AZ) and Comirnaty (Pfizer: PZ) vaccines and of a hybrid immunity induced in people who were also infected with SARS-CoV-2, longitudinal sera samples of participants recruited through the David Serisier Research biobank (Mater Research Hospital) or at the University of Queensland were collected. ELISA with a panel of purified Spike proteins from ancestral, alpha, delta and omicron BA.1 and BA.2 VOCs showed significantly (by ∼2 to 6-fold) reduced IgG antibody titres against Spike proteins from Omicron BA.1 and BA.2 compared to ancestral strain regardless of the number of vaccinations or presence of infection. Neutralisation assays showed reduced activity against delta and omicron BA.1, BA.5 and BA.5 VOCs. However, the differences were in general less pronounced than in the ELISA assay and some were not statistically significant, particularly after four (two AZ and two PZ) vaccinations. We also generated by circular polymerase extension reaction an attenuated SARS-CoV-2 strain with deletion of all accessory genes, ORF 3, 6, 7 and 8, based on the ancestral (QLD02) virus backbone (QLD02Δ3678) and validated it in virus-neutralization assays with our panel of sera samples. We showed the attenuation of the QLD02Δ3678virus in Vero E6 and human Caco2 cells. We demonstrated that neutralization assays with the wild-type QLD02 virus and QLD02Δ3678virus were concordant, providing a safe platform for neutralisation assays in BSL2/PC2 settings.
Documenting trends in blockchain technology adoption: a systematic review
Authors: Isiaku Labaran , Muhammad Abubakar Sadiq , Kefas Hyelda Ibrahim , Isiaku Hamza Haruna 
Published: November 2024

Purpose
This study aims to critically analyze existing research on blockchain technology adoption, examining the dominant models and methodologies used, the primary domains where blockchain is applied and the emerging opportunities across various sectors.

Design/methodology/approach
Using a methodical systematic review approach, the authors meticulously examined a pool of 1,322 collected articles, subjecting 38 studies to rigorous assessment. Through this comprehensive analysis, the authors unveiled the key models and influential factors that intricately shape the trajectory of blockchain adoption.

Findings
The primary models identified for investigating blockchain adoption were the technology acceptance model and technology–organization–environment. Apart from the core variables within these models, the pivotal determinants influencing various blockchain applications include perceived trust, perceived cost and social influence. In addition, this study highlights supply chain management as a prominent domain for blockchain application adoption.

Practical implications
Understanding these influential factors and models can guide practical decisions and aid stakeholders in formulating effective strategies for blockchain adoption in diverse sectors.

Originality/value
This study contributes to advancing the understanding of blockchain adoption dynamics by unveiling the prevalent models and determinants shaping adoption. This study offers valuable insights into the factors influencing the use and adoption of blockchain technologies across diverse sectors.
Lean readiness factors for higher education
Authors: Kakouris Andreas , Sfakianaki Eleni , Kapaj Matilda 
Published: November 2024

Purpose
This paper aims to identify the readiness factors (RFs) required for the deployment of lean initiatives within the context of higher education (HE), a field not yet significantly explored.

Design/methodology/approach
This research employed a Systematic Literature Review (SLR) to thoroughly identify and consolidate all relevant scholarly literature concerning lean practices and readiness in the context of HE. Subsequently, a three-phase Delphi study was conducted to evaluate and enhance the findings of the SLR.

Findings
The results indicate the following seven RFs for use in HE: leadership/top management, changing environment and organisational culture, lean initiatives linked with the strategic agenda of the educational institute, employee empowerment and engagement, student value, supplier relations and continuous improvement.

Practical implications
By identifying such factors, the present study acknowledges the strategic nature of lean and recognises that its full strategic benefits can only be realised when properly implemented at a macro-level.

Originality/value
The authors believe that this is the first attempt to provide a consolidated list of RFs in the context of HE validated by a group of experts. This study expands the knowledge of lean in HE contexts, benefiting both researchers and professionals. For researchers, it provides a valuable foundation for further study of the implementation of lean programs. For professionals and practitioners, it offers insights for better preparation that are crucial for the sustainability of lean initiatives leading to overall improved performance.
Environmental knowledge influencing pro-environmental behavior among university students: a serial mediation and MGA approach
Authors: Mago Monita , Yadav Mandeep , Sharma Sukriti , Kaur Harshdeep 
Published: November 2024

Purpose
The study aims to investigate the mediating role played by environmental attitude and environmental sensitivity in the influence of environmental knowledge on pro-environmental behavior. Specifically, the study examined whether both environmental attitude and environmental sensitivity act as serial mediators between environmental knowledge and pro-environmental behavior. This study also explored whether there are gender differences in how environmental knowledge affects pro-environmental behavior through environmental attitude and environmental sensitivity.

Design/methodology/approach
A survey tool was distributed to university students in the northern region of India who had studied environmental studies as a compulsory subject during one of their semesters in their higher education program. A total of 558 responses were analyzed through nonparametric partial least squares multigroup analysis using PLS-SEM.

Findings
The results indicated that environmental knowledge significantly affected pro-environmental behavior. Moreover, environmental attitude and environmental sensitivity played significant mediating roles between environmental knowledge and pro-environmental behavior. Additionally, the results showed that the serial mediation effect of environmental attitude and environmental sensitivity in the relationship between environmental knowledge and pro-environmental behavior was significant. However, the findings did not show any significant gender difference in how environmental knowledge influences pro-environmental behavior, mediated serially by environmental attitude and environmental sensitivity.

Originality/value
Although vast literature is available on the relationship between environmental knowledge and pro-environmental behavior, a few studies have shown environmental attitude and environmental sensitivity as mediators. In addition, this study fills the gap in the existing research by exploring how environmental attitude and sensitivity serially mediate the nexus between environmental knowledge and pro-environmental behavior, particularly across genders.
Digital transformation capability and employee turnover intentions: the role of knowledge management capability and digital leadership
Authors: Mohammad Al Montaser , Awain Ali Mohsin Salim Ba , Jaboob Ali Said , Mkheimer Ibrahim , Menhat Masha 
Published: November 2024

PurposeThe primary objective of this research is to examine the effects of digital transformation capability (DTC) on employee turnover intention (ETI) in Jordanian universities. Based on the social cognitive theory (SCT). The study also investigates the mediated moderation role of knowledge management capability (KMC) and digital leadership (DL) in the relationship between DTC and ETI.Design/methodology/approachA survey questionnaire was used to obtain data from 384 faculty members at Jordanian universities in Jordan, and the SmartPLS4 and SPSS software were used to test the hypotheses.FindingsThe results reveal that DTC significantly mitigates ETI through providing a favourable environment for knowledge sharing and innovation. Using DL as a moderator, the results show that the relationship between DTC and ETI becomes stronger in the presence of high DL.Originality/valueThis research uniquely integrates SCT to explore the combined impact of DTC, KMC and DL on faculty turnover intentions at Jordanian universities. It offers novel viewpoints on retaining academic staff by implementing smart digital attempts.
Driving a motor vehicle and living with a mental health condition: The personal and professional experiences of consumer lived experience staff
Authors: Dun Carolyn , Palmer Catherine , Turville Megan 
Published: November 2024

AbstractIntroductionDriving a motor vehicle is an important activity for people living with a mental health condition, as it can support engagement in the community as part of recovery. There is little research exploring mental health consumers' experiences with driving and no found research on the role of mental health lived experience staff in assisting consumers with safe driving. It is essential to learn about consumers' experiences of driving to know the supports they find useful in understanding their driver responsibilities and self‐regulating their driving through periods of changing health and wellness. This study explored the personal and professional experiences of lived experience consumer staff related to driving a motor vehicle while also living with a mental health condition.MethodThe research was guided by the interpretive paradigm and codesign principles. Qualitative data were derived from semi‐structured interviews with (n = 9) lived experience consumers working in a public mental health service. Data were thematically analysed.Consumer and community involvementOur research team involved consumer and occupational therapy coresearchers.FindingsFive main themes were identified: (1) Driving means freedom and independence, (2) A nuanced understanding about the impact of mental health on driving, (3) I/we can manage: A range of strategies, (4) Driving is not something mental health staff tend to discuss, and (5) Do not beat around the bush, just talk about it.ConclusionConsumers want support and direct conversations about driving and their mental health, medication side effects, and strategies to gain their licence, maintain, or return to driving. Alongside mental health clinicians, consumer lived experience staff could play a vital role in supporting safe driving.
Knowledge co‐production praxis in sustainability science: Insights from three contexts
Authors: Ligtermoet Emma 
Published: November 2024

AbstractKnowledge co‐production is needed as never before to support social change in the face of climate, water, biodiversity, and other sustainability crises. Co‐production brings together diverse groups and their ways of knowing to generate new knowledges and practices that reconfigure or generate transformative social changes and that invite reflexivity. Within sustainability sciences, tensions exist between descriptive, analytical framings of co‐production used to interrogate knowledge‐power relations and instrumental or normative framings used to build such relations. The former has been criticised for being overly descriptive and difficult to translate into policy outcomes and the latter for failing to sufficiently interrogate power dynamics and for perpetuating existing inequities. As researchers, how are we to navigate this tension? Co‐production praxis involves reconfiguring knowledge‐power relations for just and transformative social changes. I suggest what is needed is a critical lens on those relations to underpin and guide feasible and action‐oriented processes and outcomes for such changes. In three ways, I present and reflect on co‐production contexts with different temporal, spatial and epistemological characteristics. These contexts are analysing historical co‐production of knowledge of coastal freshwater floodplain Country of the Northern Territory, facilitating the Kunwinjku Seasons calendar and enabling reflexive co‐production praxis with sustainability science researchers at a national science institution. I demonstrate the need within each context to weave analytical, practical, and reflexive work to reconfigure fairer societal outcomes and to pay greater attention to socio‐institutional changes arising from our engaged work.
Molecular identification of Fusarium species in commercial vanilla and crop wild relatives in Colombia
Authors: Rodríguez‐Bastidas Jayerlin , Manrique‐Barros Santiago , Riascos‐Ortiz Donald , Mosquera‐Espinosa Ana T. , Flanagan Nicola S. 
Published: November 2024

AbstractVanilla is an economically important crop for low‐lying humid tropical regions, but cultivated plants face serious phytosanitary problems. Fusarium wilt is a devastating disease affecting vanilla crops, caused by the fungal pathogens Fusarium oxysporum f. sp. vanillae (Fov) and F. oxysporum f. sp. radicis‐vanillae (Forv), part of the F. oxysporum species complex (FOSC). We characterized 29 fungal isolates from a vanilla crop and crop wild relatives (CWR) using molecular (EF1‐α and ITS‐rRNA loci) and morphological traits. Fusarium was the predominant genus, followed by Colletotrichum and Clonostachys. Four Fusarium species were identified: F. oxysporum (37.9%), Fusarium solani (20.7%), Fusarium pseudocircinatum (13.8%) and Fusarium concentricum (10.3%). The latter three species were isolated only from CWR and may represent latent pathogens. Fov was isolated from both the crop and CWR, while a Forv‐affiliated isolate was also found in a vanilla crop, marking the first report in the neotropical region. The EF1‐α locus provided greater genotype resolution, as well as having reference sequences for Forv. However, the fungal barcode ITS locus is widely applied. We recommend the continued use of both loci for Fusarium diagnosis in vanilla to facilitate early detection and the development of effective integrated crop management strategies.