bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Oxford Nanopore Technology-Based Hepatitis B Virus Sequencing Protocol Suitable For Genomic Surveillance Within Clinical Diagnostic Settings
Authors: Tshiabuila Derek , Choga Wonderful , James San E. , Maponga Tongai , Preiser Wolfgang , van Zyl Gert , Moir Monika , van Wyk Stephanie , Giandhari Jennifer , Pillay Sureshnee , Anyaneji Ugochukwu J. , Lessells Richard J. , Naidoo Yeshnee , Sanko Tomasz Janusz , Wilkinson Eduan , Tegally Houriiyah , Baxter Cheryl , Martin Darren P. , de Oliveira Tulio 
Published: January 2024

AbstractChronic hepatitis B virus (HBV) infection remains a significant public health concern, particularly in Africa, where there is a substantial burden. HBV is an enveloped virus, with isolates being classified into ten phylogenetically distinct genotypes (A – J) determined based on full-genome sequence data or reverse hybridization-based diagnostic tests. In practice, limitations are noted in that diagnostic sequencing, generally using Sanger sequencing, tends to focus only on the S-gene, yielding little or no information on intra-patient HBV genetic diversity with very low-frequency variants and reverse hybridization detects only known genotype-specific mutations. To resolve these limitations, we developed an Oxford Nanopore Technology (ONT)-based HBV genotyping protocol suitable for clinical virology, yielding complete HBV genome sequences and extensive data on intra-patient HBV diversity. Specifically, the protocol involves tiling-based PCR amplification of HBV sequences, library preparation using the ONT Rapid Barcoding Kit, ONT GridION sequencing, genotyping using Genome Detective software, recombination analysis using jpHMM and RDP5 software, and drug resistance profiling using Geno2pheno software. We prove the utility of our protocol by efficiently generating and characterizing high-quality near full-length HBV genomes from 148 left-over diagnostic Hepatitis B patient samples obtained in the Western Cape province of South Africa, providing valuable insights into the genetic diversity and epidemiology of HBV in this region of the world.
Differential gene expression analysis of spatial transcriptomic experiments using spatial mixed models
Authors: Ospina Oscar E. , Soupir Alex C. , Manjarres-Betancur Roberto , Gonzalez-Calderon Guillermo , Yu Xiaoqing , Fridley Brooke L. 
Published: January 2024

AbstractSpatial transcriptomics (ST) assays represent a revolution in the way the architecture of tissues is studied, by allowing for the exploration of cells in their spatial context. A common element in the analysis is the delineation of tissue domains or “niches” followed by the detection of differentially expressed genes to infer the biological identity of the tissue domains or cell types. However, many studies approach differential expression analysis by using statistical approaches often applied in the analysis of non-spatial scRNA data (e.g., two-sample t-tests, Wilcoxon rank sum test), hence neglecting the spatial dependency observed in ST data. In this study, we show that applying linear mixed models with spatial correlation structures using spatial random effects effectively accounts for the spatial autocorrelation and reduces inflation of type-I error rate that is observed in non-spatial based differential expression testing. We also show that spatial linear models with an exponential correlation structure provide a better fit to the ST data as compared to non-spatial models, particularly for spatially resolved technologies that quantify expression at finer scales (i.e., single-cell resolution).
An unconventional regulatory circuitry involving Aurora B controls anaphase onset and error-free chromosome segregation in trypanosomes
Authors: Ballmer Daniel , Lou Hua Jane , Ishii Midori , Turk Benjamin E. , Akiyoshi Bungo 
Published: January 2024

AbstractAccurate chromosome segregation during mitosis requires that all chromosomes establish stable bi-oriented attachments with the spindle apparatus. Kinetochores form the interface between chromosomes and spindle microtubules and as such are under tight control by complex regulatory circuitry. As part of the chromosomal passenger complex (CPC), the Aurora B kinase plays a central role within this circuitry by destabilizing improper kinetochore-microtubule attachments and relaying the attachment status to the spindle assembly checkpoint, a feedback control system that delays the onset of anaphase by inhibiting the anaphase-promoting complex/cyclosome. Intriguingly, Aurora B is conserved even in kinetoplastids, an evolutionarily divergent group of eukaryotes, whose kinetochores are composed of a unique set of structural and regulatory proteins. Kinetoplastids do not have a canonical spindle checkpoint and it remains unclear how their kinetochores are regulated to ensure the fidelity and timing of chromosome segregation. Here, we show inTrypanosoma brucei, the kinetoplastid parasite that causes African sleeping sickness, that inhibition of Aurora B using an analogue-sensitive approach arrests cells in metaphase, with a reduction in properly bi-oriented kinetochores. Aurora B phosphorylates several kinetochore proteinsin vitro, including the N-terminal region of the divergent Bub1-like protein KKT14. Depletion of KKT14 partially overrides the cell cycle arrest caused by Aurora B inhibition, while overexpression of a non-phosphorylatable KKT14 protein results in a prominent delay in the metaphase-to-anaphase transition. Finally, we demonstrate using a nanobody-based system that re-targeting the catalytic module of the CPC to the outer kinetochore is sufficient to promote mitotic exit but causes massive chromosome mis-segregation in anaphase. Our results indicate that the CPC and KKT14 are involved in an unconventional pathway controlling mitotic exit and error-free chromosome segregation in trypanosomes.
Boosting entrepreneurial competences beyond business and management–related disciplines. The case of engineering programs
Authors: Berbegal-Mirabent Jasmina , Gil-Doménech Dolors , Manresa Alba 
Published: January 2024

PurposeThis study addresses the challenge of integrating entrepreneurial competences development into the traditionally structured engineering curriculum, recognizing its potential contribution to job creation. Specifically, this study proposes a course design that intersects project management and entrepreneurial disciplines, adopting a challenge-based learning approach.Design/methodology/approachConsidering a list of common features that entrepreneurs and engineers—in the role of project managers—should excel at, and building upon the principles of experiential learning, this study proposes and describes a course design that is expected to help engineering students develop entrepreneurial competences. Through a series of assessment instruments and descriptive statistics, the study evaluates its implementation in a pilot test applied in a Project Management course at a Spanish university.FindingsThe results demonstrate a significant improvement in students' entrepreneurial competences after completing the course. Noteworthy variations in receptiveness to skill development among different personality profiles are observed. Gender differences are minimal, with the exception of women exhibiting heightened self-perception in the autonomy dimension.Originality/valueThis study explores the common features shared by two often-disconnected disciplines, namely engineering and entrepreneurship. It suggests that integrating both perspectives through a challenge-based course design can enhance entrepreneurial competences among engineering students without compromising the specific knowledge gained from engineering programs. Engaging students in such pedagogical experiences not only fosters entrepreneurial competences but also contributes to their professional and personal growth.
Configuring mobile app update strategy for growth: An empirical analysis of a landscape search model
Authors: Wang Fei , Nan Ning , Zhao Jing 
Published: January 2024

PurposeThis study attempts to discover effective strategies for mobile commerce applications (apps) to grow their consumer base by releasing app strategic updates. Drawing on the landscape search model from strategy research, this study conceptualizes mobile app update strategy as three interdependent decisions, i.e. what business elements are changed in an app strategic update, how substantial the changes are and when strategic updates are released relative to the competitive environment.Design/methodology/approachUsing a field data set of 1,500 strategic updates of seven rival apps in the mobile travel market, this study integrated fuzzy set qualitative comparative analysis (fsQCA) with econometric analysis to analyze how app strategic update decisions interdependently influence app performance.FindingsThis study identified three effective and one ineffective mobile app update strategies from the mixed-method analysis, which verified the complex interdependency of app strategic update decisions. A general takeaway from these strategies is that a complex strategy problem on the mobile platform must be solved with respect to the constraints and capabilities of mobile technology.Originality/valueThis study moves beyond a linear view of the relationship between app update frequency and app performance and provides a holistic view of how and why app strategic update decisions mutually influence one another in their impact on app performance. This work makes contributions by identifying interdependency as a conceptual bridge between strategy and mobile app literature and developing an empirically testable version of the landscape search model.
How can I serve you better? Unlocking the digital D2C barriers for regional food products
Authors: Joshi Shivam , Sengar Anita , Nautiyal Atri 
Published: January 2024

PurposeThe digital direct-to-consumer (D2C) approach has seen widespread adoption across many industries, but its application to regional food products has been slower. This study aims to identify and rank the most significant challenges to the widespread use of digital D2C for regional food products.Design/methodology/approachA multi-criteria decision-making method called a fuzzy analytic hierarchy process (FAHP) was used to determine the order in which these obstacles were evaluated. Thirty-five barriers were identified and categorized into six categories named technological, operational, sociocultural, financial, market and institutional and regulatory barriers.FindingsMarket barriers ranked as the top barrier, and the technological barrier ranked the least significant amongst the main barrier categories for the adoption of digital D2C model for the regional food products. Lack of consumer awareness ranked number one globally, and lack of government subsidies ranked the least amongst the thirty-five identified barriers. Operational barriers came out to be second most significant barrier followed by institutional and regulatory barrier, sociocultural barrier, financial barrier and technological barrier.Research limitations/implicationsThe findings of this research were derived through a numerical examination of data gathered from the Indian setting. It follows that the technological, sociocultural, financial, market, operational and institutional constraints, among others, outlined here are all unique to India. Because of the unique nature of the Indian setting, the results of this study can only be used there and not elsewhere. It is possible that future research will broaden the aims of this one and refine its methodology. Digital D2C adoption for regional food products may be prioritized and ranked using quantitative and qualitative data sources like ANP and TOPSIS. It is possible that similar studies may be conducted in nations which have a different set of operational, technological, sociocultural market and financial and regulatory barriers. Conceptual framework can be formed by integrating TAM and TPB to understand the buying behavior of regional food products via digital D2C.Originality/valueThis research is the first to identify challenges to the widespread use of the digital D2C model for regional food products. Policymakers and other interested parties can use this information to better understand the difficulties of expanding the distribution of regional food products beyond their immediate regions.
Unlocking the relationships between developmental human resource practices, psychological collectivism and knowledge hiding: the moderating role of affective organizational commitment
Authors: Yang Chengchuan , Tang Chunyong , Xu Nan , Lai Yanzhao 
Published: January 2024

PurposeThis study aims to draw on social exchange theory and reciprocity norm to examine the direct effects and mechanisms through which developmental human resources (HR) practices influence employee knowledge hiding behaviors. Additionally, the authors investigate the mediating role of psychological collectivism and the moderating role of affective organizational commitment.Design/methodology/approachTo test the research model, the authors employed a three-stage time-lagged study design and surveyed a sample of 302 employees in China. The authors utilized confirmatory factor analysis, hierarchical regression analysis and the bootstrapping method using statistical product and service solutions (SPSS) and analysis of moment structures (AMOS) to test the hypotheses.FindingsThe findings indicate the following: (1) Developmental HR practices are negatively associated with playing dumb and evasive hiding, but positively linked with rationalized hiding; (2) Psychological collectivism serves as a mediating factor in the relationship between developmental HR practices and knowledge hiding; (3) Affective organizational commitment not only moderates the relationship between developmental HR practices and psychological collectivism, but also reinforces the indirect impact of developmental HR practices on knowledge hiding.Originality/valueThis study offers a fresh perspective on previous research regarding the impact of developmental HR practices on employee behavior. Furthermore, it provides practical recommendations for organizations to enhance knowledge management by fostering stronger emotional connections between employees and the organization.
Cultural change in servitization – a conceptual review and framework
Authors: Biesinger Benjamin , Hadwich Karsten , Bruhn Manfred 
Published: January 2024

Purpose (Digital) servitization, referring to service-driven strategies and their increasing implementation in manufacturing, is one of the most rapidly growing areas in industrial service research. However, the cultural change involved in successful servitization is a phenomenon that is widely observed but poorly understood. This research aims to clarify the processes of social construction as manufacturers change their organizational culture to transform into industrial service providers.Design/methodology/approachThis research takes a systematic approach to integrate disparate literature on servitization into a cohesive framework for cultural change, which is purposefully augmented by rationale culled from organizational learning and sensemaking literature.Findings The organizational learning framework for cultural change in servitization introduces a dynamic perspective on servitizing organizations by explaining social processes between organizational and member-level cultural properties. It identifies three major cultural orientations toward service, digital and learning that govern successful servitization.Originality/value This research contributes to the servitization literature by presenting a new approach to reframe and explore cultural change processes across multiple levels, thus providing a concrete starting point for further research in this area.
A scoping review: Inquiring into the potency of response source credibility (RSC) towards enhancing crisis response strategies
Authors: Dominic Egede Dominion , Mahamed Mastura , Abdullah Zulhamri , Hashim Norliana Binti 
Published: January 2024

AbstractIt is paramount to consider that organizations are not immune to crises. Communicating solutions to the cataclysm is indispensable when the response source is credible. Our article answers recent calls for more research into the efficacy of organizational response source credibility (RSC) during crises and maintaining reputation. RSC (trustworthiness) is one of the indispensable prerequisites for achieving effective result‐oriented crisis response strategies and sustaining reputation in times of crisis. This article is a scoping review regarding the potential of RSC on crisis response strategies. The findings from this review raises the awareness of the crisis managers about the relevance of source credibility towards making crisis response effective and maintaining reputation during a crisis situation. This article provides insights to help crisis managers, institutions and policy‐makers develop specific effective crisis response strategies using a credible source to boost stakeholders' confidence and maintain a good reputation during an organizational crisis. This article fills the gap in the crisis communication domain concerning the limited amount of information regarding factors that influence the efficacy of crisis response strategies. The originality of this article is validated by the systematic scoping review used.
Community‐scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing
Authors: Cerk Klara , Ugalde‐Salas Pablo , Nedjad Chabname Ghassemi , Lecomte Maxime , Muller Coralie , Sherman David J. , Hildebrand Falk , Labarthe Simon , Frioux Clémence 
Published: January 2024

AbstractBuilding models is essential for understanding the functions and dynamics of microbial communities. Metabolic models built on genome‐scale metabolic network reconstructions (GENREs) are especially relevant as a means to decipher the complex interactions occurring among species. Model reconstruction increasingly relies on metagenomics, which permits direct characterisation of naturally occurring communities that may contain organisms that cannot be isolated or cultured. In this review, we provide an overview of the field of metabolic modelling and its increasing reliance on and synergy with metagenomics and bioinformatics. We survey the means of assigning functions and reconstructing metabolic networks from (meta‐)genomes, and present the variety and mathematical fundamentals of metabolic models that foster the understanding of microbial dynamics. We emphasise the characterisation of interactions and the scaling of model construction to large communities, two important bottlenecks in the applicability of these models. We give an overview of the current state of the art in metagenome sequencing and bioinformatics analysis, focusing on the reconstruction of genomes in microbial communities. Metagenomics benefits tremendously from third‐generation sequencing, and we discuss the opportunities of long‐read sequencing, strain‐level characterisation and eukaryotic metagenomics. We aim at providing algorithmic and mathematical support, together with tool and application resources, that permit bridging the gap between metagenomics and metabolic modelling.
Relationship between patterns of immunohistochemical conventional neuroendocrine markers and efficacy of immune check point inhibitors in patients with extensive disease small cell lung cancer
Authors: Iida Yuko , Wakuda Kazushige , Kawata Takuya , Morita Meiko , Sekikawa Motoki , Doshita Kosei , Yabe Michitoshi , Kodama Hiroaki , Miura Keita , Morikawa Noboru , Mamesaya Nobuaki , Kobayashi Haruki , Ko Ryo , Ono Akira , Kenmotsu Hirotsugu , Naito Tateaki , Murakami Haruyasu , Gon Yasuhiro , Takahashi Toshiaki 
Published: January 2024

AbstractBackgroundWhich patients benefit from the addition of immune checkpoint inhibitors (ICIs) to chemotherapy for small cell lung cancer (SCLC) remains unclear. There have been few reports on the efficacy of ICIs based on conventional immunohistochemical neuroendocrine (NE) markers (synaptophysin, chromogranin A, and neural cell adhesion molecule [NCAM]). In the present study, we aimed to analyze the relationship between the expression of immunohistochemical NE markers and the efficacy of ICIs in patients with extensive disease (ED)‐SCLC, to assess whether conventional NE markers are predictive of ICIs.MethodsPatients with untreated ED‐SCLC who received first‐line therapy at the Shizuoka Cancer Center between November 2002 and July 2021 were retrospectively reviewed. We evaluated the efficacy of first‐line chemotherapy according to the expression status of each immunohistochemical NE marker in patients treated with ICI plus chemotherapy (ICI‐chemo group) and with chemotherapy alone (chemo group).ResultsA total of 227 patients were included in the ICI‐chemo and chemo groups, respectively. The progression‐free survival (PFS) tended to be better in patients in the ICI‐chemo group than those treated with chemotherapy alone in patients with NE marker‐positive SCLC. In particular, it was statistically significant in patients with chromogranin A‐positive SCLC (p = 0.036). In patients with NE marker‐negative SCLC, no significant differences were observed in PFS between the two groups. There were no significant differences in overall survival (OS), regardless of the expression of any conventional NE marker.ConclusionOur study suggests that the efficacy of ICIs in addition to chemotherapy may be poor in patients with NE marker‐negative SCLC.
Behavioural interactions between co‐habiting females and their impact on productivity and offspring sex ratios in the coffee berry borer, Hypothenemus hampei
Authors: Myrie Ameka , Biedermann Peter , Oettler Jan , Robinson Dwight , Schultner Eva 
Published: January 2024

Abstract
The coffee berry borer (CBB) Hypothenemus hampei (Ferrari) (Coleoptera: Curculionidae: Scolytinae) has invaded all coffee‐producing regions of the world and causes substantial economic losses every year. A single female beetle typically infests one coffee berry, which her offspring consume over the course of development. Offspring then engage in sib‐mating before daughters fly off to infest new berries.
We assessed infestation rates across different locations in Jamaica and found a strong positive correlation between double infestation and overall infestation rate, suggesting that females prefer to breed alone but will tolerate sharing a berry under resource constraints.
Using an artificial habitat to study productivity and behaviour in the laboratory, we found that single females produced significantly more offspring per capita than two females, suggesting that co‐habitation is costly. Accordingly, co‐habiting females spent a significant proportion of their time engaged in antagonistic interactive behaviours such as pushing. When daughter beetles were given the opportunity to stay with their mothers or to infest a new berry, they tended to leave.
In contrast to some related beetle species, which exhibit gregariousness and even cooperative behaviour, beneficial social interactions in the CBB appear to be limited to parental care.