bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allele imbalance in mRNA is selected in tumorigenesis, results from epigenetic alterations and has prognostic relevance
Authors: Palou-Márquez Guillermo , Pericot-Masdevall Pere , Supek Fran 
Published: September 2024

AbstractAllelic imbalance (AI) in levels of mRNAs that originated from the paternal and maternal copies of a gene can contribute to phenotypic variation and influence disease traits, including cancer. It is widely appreciated that AI at the DNA level, resulting from somatic copy number alterations (CNA) in tumors, generates second-hit events by which tumor suppressor genes are inactivated and oncogenes are activated; the somatic CNAs are also a known cause of AI at the mRNA level. Apart from CNA, other mechanisms could lead to AI in mRNA expression and also drive cancer evolution. By integrating genomic and transcriptomic pan-cancer data, we show that mRNA AI favoring the mutant allele in driver genes is subject to positive selection, generating second-hit events often independently of somatic CNA. The mRNA AI events associate with worse overall survival across all cancer types, outperforming other predictive markers. Various instances of mRNA AI are explained by the epigenetic changes in DNA accessibility and DNA methylation, affecting alleles differently. While we do not rule out that the driver somatic mutations themselves could induce allele-specific expression (we show an example of splicing-altering mutations, selected in various cancer genes), our study suggests that epigenetic alterations commonly act as second-hit events, generating mRNA allelic imbalances that drive cancer and identify new prognostic markers.
Conflicting roles of cell geometry, microtubule deflection and orientation-dependent dynamic instability in cortical array organization
Authors: Tian Tim Y.Y. , Wasteneys Geoffrey O. , Macdonald Colin B. , Cytrynbaum Eric N. 
Published: September 2024

AbstractThe self-organization of cortical microtubule arrays within plant cells is an emergent phenomenon with important consequences for the synthesis of the cell wall, cell shape, and subsequently the structure of plants. Mathematical modelling and experiments have elucidated the underlying processes involved. There has been recent interest in the influence of geometric cues on array orientation, be it direct (cell shape) or indirect (tension in the membrane). However, the mechanical influence of membrane curvature on these elastic filaments has largely been ignored. A previous model was proposed to describe how the anchoring process may control the deflection of individual microtubules seeking to minimize bending on a cylindrical cell. We implement this process into a model of interacting microtubules and find the cell curvature influence should be significant: the array favours orientations parallel to the direction of elongation rather than the expected transverse direction. Even without elasticity, the geometry of large cells hinders robust microtubule organization. These results suggest the necessity of additional processes to overcome these factors. We propose a simple model of orientation-dependent catastrophe in the context of cellulose microfibrils impeding microtubule polymerization and find a moderate impedance to be sufficient to generate transverse arrays despite the geometric influences.
Investigation of risk factors associated withAncylostomaspp. infection and the benzimidazole F167Y resistance marker polymorphism in dogs from the United States
Authors: Jimenez Castro Pablo D. , Willcox Jennifer L. , Rochani Haresh , Richmond Holly L. , Martinez Heather E. , Lozoya Cecilia E. , Savard Christian , Leutenegger Christian M. 
Published: September 2024

AbstractAncylostoma caninumis the most significant intestinal nematode parasite of dogs. We acquired fecal surveillance data using molecular diagnostics in a large population of dogs in the United States (US). A diagnostic test using real-time PCR (qPCR) forAncylostomaspp. and allele-specific qPCR detecting the SNP F167Y was used in 885,424 canine fecal samples collected between March 2022 and December 2023. Overall,Ancylostomaspp. had a prevalence of 1.76% (15,537/885,424), with the highest observed in the South 3.73% (10,747/287,576), and the lowest in the West 0.45% (632/140,282). Within the subset ofAncylostomaspp.-detected dogs used for further analysis, the F167Y SNP had an overall prevalence of 14.2% with the highest in the West and the lowest in the Midwest (10.76%). The greyhound breed exhibited a higher prevalence ofAncylostomaspp. infections (17.03%) and a higher prevalence of the F167Y polymorphism (33.6%) compared to non-greyhound breeds (13.7% and 2.08%), respectively, but were not associated with the highest breed risk for the F167Y polymorphism. Sex did not influence hookworm infection nor F167Y polymorphism prevalence. Intact dogs had a prevalence of hookworm infection and F167Y polymorphism of 2.51% and 14.6%, respectively. Puppies showed increased prevalence of hookworms (3.70%) and the F167Y SNP (17.1%). Greyhounds, bluetick coonhounds, and boerboels had the highest relative risks (RR) for hookworm infection, while Cavalier King Charles spaniels, Havanese, and shiba inus had the lowest. The top and bottom three with the highest and lowest RR for the F167Y SNP were the old English sheepdog, American foxhound, and toy poodle Toy, and shih tzu, Maltese, and Australian cattle dogs, respectively. This study highlights the value of an accessible diagnostic qPCR test with fast turnaround times in unraveling the molecular epidemiology of hookworms and benzimidazole resistance, as well as explore potentially important risk factors associated with infection in medicalized dogs.Highlights- Greyhounds had the highest RR relative risk forAncylostomaspp., but only fourth for theA. caninumF167Y polymorphism.- The highest prevalence ofAncylostomaspp. in the United States was in the South.- The West had the lowest prevalence forAncylostomaspp., but the highest prevalence for theA. caninumF167Y SNP.- Puppies had the highest prevalence and AOR forAncylostomaspp. and F167Y polymorphism.
Navigating a double school-to-work transition: how do Chinese graduate students decide where to start their careers after studying abroad?
Authors: Dong Di , Akkermans Jos , Khapova Svetlana N. 
Published: September 2024

PurposeThis exploratory research aims to unravel how Chinese international students form their decisions regarding the school-to-work transition (sometimes also referred to as the university-to-work transition) when studying abroad.Design/methodology/approachThe authors use the concepts of school-to-work transition and cultural approaches to investigate how Chinese graduate students make career decisions to navigate the school-to-work transition in the context of international mobility. The authors' empirical study is based on 30 semi-structured interviews conducted with Chinese graduate students studying in the Netherlands.FindingsThe authors discovered four patterns with two major subgroups among Chinese students studying in the universities in the Netherlands based on their initial intentions: return-return, open-return, open-stay and stay-stay. These patterns made sense when navigating the school-to-work transition: participants experienced varied international experiences, cultural perceptions and acknowledgment influences when enhancing employability and shaping their career decisions. Participants in the return-return and stay-stay groups indicated strong resilience and consistency in achieving their goals and strongly focused on long-term objectives. However, participants' open-return decision demonstrated a thoughtful alignment of personal goals and knowledge of the possible beneficial influence they may have in their home country. Open-stay participants utilized the overseas study opportunity to finalize their decisions and increase their employability in the local labor market, thereby creating a transition from university to work in the host country.Originality/valueThe authors highlight the way Chinese graduate students manage their international experience and provide novel insights into the role played by the cultural characteristics of their home country and host country.
Investigating the role of path architecture complexity in users’ movement patterns in hospital circulation systems: case studies in Golestan, Iran
Authors: Saeidi Maryam , Siyahkali Mahsa Delshad , Moradinasab Hossein , Naseri Gholamhossein 
Published: September 2024

Purpose
This study aims to explore how users’ movement is influenced by different hospital ward layouts, by using space syntax theory. This study also compared four circulation patterns to find the best one for the study goal.

Design/methodology/approach
The authors used both qualitative and quantitative methods to study how users’ wayfinding in hospitals depends on various indicators and factors. The study used Depth Map software to do case studies and then analyzed the indicators from theoretical foundations and used the Pearson Test to check the correlation between indicators. This study also looked at Iran’s Ministry of Health standards for ward layouts. Finally, the results obtained from the research data were compared to achieve a suitable model based on the research objectives.

Findings
The linear-patterned plan was the best for easy wayfinding and accessibility among four patterns. The optimal hospital circulation patterns can improve wayfinding and reduce wayfinding problems and user movement.

Originality/value
By pioneering space syntax in hospital research, this study unveils the novel interaction between path architecture and user movement. It gives new insights into current trends, helping architects, administrators and policymakers improve health-care design, efficiency and patient experience.
Large-scale agile security practices in software engineering
Authors: Ascenção Cláudia , Teixeira Henrique , Gonçalves João , Almeida Fernando 
Published: September 2024

Purpose
Security in large-scale agile is a crucial aspect that should be carefully addressed to ensure the protection of sensitive data, systems and user privacy. This study aims to identify and characterize the security practices that can be applied in managing large-scale agile projects.

Design/methodology/approach
A qualitative study is carried out through 18 interviews with 6 software development companies based in Portugal. Professionals who play the roles of Product Owner, Scrum Master and Scrum Member were interviewed. A thematic analysis was applied to identify deductive and inductive security practices.

Findings
The findings identified a total of 15 security practices, of which 8 are deductive themes and 7 are inductive. Most common security practices in large-scale agile include penetration testing, sensitive data management, automated testing, threat modeling and the implementation of a DevSecOps approach.

Originality/value
The results of this study extend the knowledge about large-scale security practices and offer relevant practical contributions for organizations that are migrating to large-scale agile environments. By incorporating security practices at every stage of the agile development lifecycle and fostering a security-conscious culture, organizations can effectively address security challenges in large-scale agile environments.
Embracing the future of interactive marketing with contactless technology: evidence from tourism businesses
Authors: Ku Edward C.S. 
Published: September 2024

PurposeThis study explores how predictor variables (value congruence and customer–AI-assisted exchanges) lead tourism businesses to meet customer needs through contactless technology and enhance their willingness to pay more.Design/methodology/approachThe research model was designed from the perspective of consumer-brand relationships and acceptance of AI device use. This study collected and analyzed 647 valid questionnaires using the structural equation modeling (SEM) approach.FindingsThe findings indicate that value congruence and customer-AI-assisted exchanges (CAIX) affect intimacy. Intimacy affects satisfaction and the willingness to pay more for contactless technological services. Moreover, brand trust and sensory brand experience play a role in moderating contactless technological services.Originality/valueEffective interactions between customers and AI-assisted services significantly contribute to overall satisfaction. When AI systems can understand and respond appropriately to customer queries, needs, and preferences, they enhance customer experience and satisfaction levels, increasing overall customer satisfaction with AI services.
Drivers of the use of digital platforms by Portuguese parishes – how small government entities struggle with the demand for transparency
Authors: Gomes Patrícia , Budding Tjerk , Fernandes Maria J. 
Published: September 2024

PurposeThe provision of online information through the use of digital platforms (websites and social networks) can be helpful for public sector organisations to promote transparency and accountability, thereby bringing it closer to citizens, more accessible and with higher added value for society. Whereas the call for government transparency is manifest and seems to be equal for all parts of government, this paper investigates whether small government entities are able to cope with this demand. In addition, the drivers of digital platforms are investigated in the context of Portuguese parishes.Design/methodology/approachThe paper follows a quantitative research approach based on an original data set with more than 3,000 observations collected in two different time periods (2015 and 2020), which looks at the parishes’ use of website and Facebook.FindingsFindings show that about half of Portuguese parishes, which are mostly small entities with on average fewer than 3,500 inhabitants, have an institutional website, whereas almost three out of four have Facebook. The empirical analyses reveal that a lack of organisational capacity of small entities can be an obstacle for the use of an institutional website and of Facebook. Furthermore, factors from the provider side (e.g. being part of a merger, participation in previous elections) and the user side (e.g. having access to broadband internet) are also found to have an influence on the adoption, use, and dropping of a digital platform.Originality/valueThe use of an original data set with more than 3,000 observations, and the research of the influence of size as a proxy of organisational capacity on the presence of parishes on the internet and Facebook, are innovative elements of this paper. In addition, this study adds to the knowledge about the influence of organisational, political, and socio-demographic characteristics on the use of digital platforms by small government entities.Peer reviewThe peer review history for this article is available at: https://publons.com/publon/10.1108/OIR-04-2023-0171
Parameters of sustainability: a systematic literature review and bibliometric analysis with respect to micro enterprises
Authors: Biswas Bappaditya , Gupta Rohan Prasad , Sharma Mantosh 
Published: September 2024

Purpose
The purpose of this paper is to perform a thorough analysis of the literature on the parameters of sustainability of the micro-enterprises. It seeks to provide an organizing framework to identify research gaps and future directions. Using data from Web of Science and Scopus, the study offers insights into key trends, authorship and thematic shifts, informing future research design and positioning.

Design/methodology/approach
Researchers used a systematic review methodology, gathering data from Web of Science and Scopus databases. R Studio software facilitated bibliometric analysis. This study scrutinized research papers to construct an organizing framework and identify thematic trends in sustainability parameters for micro-enterprises.

Findings
The review presents a comprehensive overview of sustainability parameters in micro-enterprises, revealing significant research trends, key authors, countries and journals. It identifies gaps and suggests future research directions, aiding in the design and positioning of forthcoming studies in this domain.

Research limitations/implications
Limitations may include the scope of databases accessed and potential biases in the selected literature. Future studies could explore additional databases or incorporate qualitative analyses for deeper insights into sustainability parameters in micro-enterprises.

Practical implications
This study offers practical insights for policymakers, practitioners and researchers by highlighting key sustainability parameters in micro-enterprises. It informs decision-making processes concerning resource allocation, policy formulation and support mechanisms for sustainable development.

Social implications
Understanding sustainability parameters in micro-enterprises has significant social implications, particularly for vulnerable groups like craftsmen, women and young entrepreneurs. By addressing these parameters, interventions can enhance livelihoods and contribute to broader socio-economic development.

Originality/value
By providing a thorough analysis of sustainability factors in micro-enterprises and applying bibliometric analysis to shed light on research trends, this paper adds to the body of literature. Its organized framework identifies gaps and guides future research, offering value to scholars, policymakers and practitioners invested in sustainable development at the grassroots level.
Engaging healthcare teams to increase access to medications for opioid use disorder
Authors: Oberman Rebecca S. , Huynh Alexis K. , Cummings Kelsey , Resnick Adam , Taylor Stephanie L. , Bergman Alicia A. , Chang Evelyn T. 
Published: September 2024

AbstractObjectiveTo assess the effectiveness of evidence‐based quality improvement (EBQI) as an implementation strategy to expand the use of medications for opioid use disorder (MOUD) within nonspecialty settings.Data Sources and Study SettingWe studied eight facilities in one Veteran Health Administration (VHA) region from October 2015 to September 2022 using administrative data.Study DesignInitially a pilot, we sequentially engaged seven of eight facilities from April 2018 to September 2022 using EBQI, consisting of multilevel stakeholder engagement, technical support, practice facilitation, and data feedback. We established facility‐level interdisciplinary quality improvement (QI) teams and a regional‐level cross‐facility collaborative. We used a nonrandomized stepped wedge design with repeated cross sections to accommodate the phased implementation. Using aggregate facility‐level data from October 2015 to September 2022, we analyzed changes in patients receiving MOUD using hierarchical multiple logistic regression.Data Collection/Extraction MethodsEligible patients had an opioid use disorder (OUD) diagnosis from an outpatient or inpatient visit in the previous year. Receiving MOUD was defined as having been prescribed an opioid agonist or antagonist treatment or a visit to an opioid substitution clinic.Principal FindingsThe probability of patients with OUD receiving MOUD improved significantly over time for all eight facilities (average marginal effect [AME]: 0.0057, 95% CI: 0.0044, 0.0070) due to ongoing VHA initiatives, with the probability of receiving MOUD increasing by 0.577 percentage points, on average, each quarter, totaling 16 percentage points during the evaluation period. The seven facilities engaging in EBQI experienced, on average, an additional 5.25 percentage point increase in the probability of receiving MOUD (AME: 0.0525, 95%CI: 0.0280, 0.0769). EBQI duration was not associated with changes.ConclusionsEBQI was effective for expanding access to MOUD in nonspecialty settings, resulting in increases in patients receiving MOUD exceeding those associated with temporal trends. Additional research is needed due to recent MOUD expansion legislation.
Reliable technique for acromion density assessment on CT
Authors: Su Shu , Chen Xiao , Warby Sarah , Tate Julie , Brooke Penelope , Barwood Shane , Hoy Gregory , Soo Brendan , Dallalana Richard , Wright Warwick , Rotstein Andrew H 
Published: September 2024

AbstractIntroductionAcromial stress fracture (ASF) is an uncommon but acknowledged complication of reverse total shoulder arthroplasty (RTSA). There is no standardised method to directly measure the bone mineral density of the acromion to allow a detailed analysis of the potential mechanism of ASF. The aim is to establish a reliable and reproducible technique for measurement of acromial density on computer tomography (CT).MethodsA retrospective review on CT scans obtained for three groups of patients: those planned for RTSA (n = 26); age and gender‐matched non‐operative (n = 26); and young non‐operative patients (n = 28) were performed. Standardised axial images of 1 mm thickness at 1 mm increments were created following horizontal straightening on the coronal and sagittal views. To assess inter‐rater reliability, two senior CT radiographers performed density measurements using standard region of interest (ROI) tool on the CTs with the ROI placed on the mid (ROI 1) and posterior (ROI 2) acromion. ROIs were selected as the most common locations for acromion fracture post RTSA. Measurements were repeated at least 6 weeks apart. Intra‐class coefficients (ICC) were used to determine intra‐ and inter‐rater reliability.ResultsICCs demonstrated good to high intra‐rater and inter‐rater reliability for both ROI 1 and ROI 2 across all three groups. The lower margin of 95% confidence intervals was more than 0 for all intra‐class coefficients.ConclusionThis study demonstrates a reliable method of measuring acromion density on CT. This method can be used to assess bone mineral density in the clinical setting and in future studies investigating ASF following RTSA.
Characterizing Spanish‐speaking patients’ patient‐centered care experiences in the emergency department
Authors: Schwei Rebecca J. , Geiger Gabriella , Mirrielees Jenn , Center Alexandra , Enemuoh Alyana , Portillo Recinos Ashley , Arias Franchesca , Lor Maichou , Shah Manish N. , Wiegmann Douglas , Pulia Michael S. 
Published: September 2024

AbstractBackgroundPatient‐centered care (PCC) is an essential component of high‐quality health, yet patients with non–English language preferences (NELP) experience worse PCC outcomes. Additionally, there are likely unique aspects to PCC for patients with NELP in the emergency department (ED). To inform the development of strategies to improve PCC for NELP in the ED, we sought to understand how Spanish‐speaking ED patients experience care and the factors that influenced their perceptions of the patient‐centeredness of that care.MethodsWe conducted a single‐center qualitative study using semistructured interviews with adult, Spanish‐speaking patients who had been discharged home from the ED. Interviews were conducted using an interview guide, recorded, transcribed, and analyzed iteratively in Spanish using inductive and deductive thematic analysis.ResultsWe conducted 19 interviews with participants from 24 to 72 years old. Participants were born in seven different Spanish‐speaking countries. Participants identified three domains of PCC: patient, medical team's skills, and system. Several of the identified themes such as shared decision making, open communication, compassionate care, and coordination of follow‐up care are often incorporated into PCC definitions. However, other themes, including uncertainty leading to fear, use of professional interpreters to promote understanding, receiving equitable care, technical proficiency, and efficiency of care expand upon existing domains in PCC definitions.ConclusionsWe now have a more nuanced understanding of how Spanish‐speaking patients with NELP experience PCC in the ED and what matters to them. Several of the themes identified in this analysis add details about what matters to patients within the domains of previous PCC definitions. This suggests that the conceptualization of PCC may vary based on the setting where care is provided and the population who is receiving this care. Future work should consider patient population and setting when conceptualizing PCC.