bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lethal clinical outcome and chemotherapy and immunotherapy resistance in patients with urothelial carcinoma with MDM2 amplification or overexpression
Authors: Jin Kaifeng , Ding Yawei , Xu Jingtong , Liu Zhaopei , Zeng Han , Su Xiaohe , Zhang Lingkai , Sun Jiaxing , Wu Yuzhen , Liu Hailong , Chang Yuan , Zhu Yu , Wang Zewei , Xu Le , Zhang Weijuan , Xu Jiejie 
Published: January 2025

BackgroundThe E3 ubiquitin ligase murine double minute 2 (MDM2) binds the p53 transcriptional activation domain and acts as a potent inhibitor ofTP53pathway, one of the three most crucial oncogenic pathways in urothelial carcinoma (UC). However, the clinical significance and impact on tumor immune contexture ofMDM2amplification in UC remain unclear.MethodsThis study analyzed 240 patients with UC with matched clinical annotations from two local cohorts (ZSHS cohort and FUSCC cohort). We assessed the correlation betweenMDM2status and clinical outcomes, therapeutic efficacy, and immunological characteristics by immunohistochemical analysis and targeted sequencing. Additionally, 2264 UC samples from five independent external cohorts, with genomic, transcriptomic, and clinical data, were used for validation.ResultsMDM2amplification (MDM2Amp) or protein overexpression (MDM2OE) was associated with inferior overall survival (ZSHS cohort, Log-rank p<0.001; FUSCC cohort, Log-rank p=0.030) and reduced response to platinum-based chemotherapy (ZSHS cohort, Log-rank p<0.001) as well as anti-PD-1/PD-L1 immunotherapy (FUSCC cohort, Log-rank p=0.016) in patients with UC, irrespective ofTP53/p53 status.MDM2amplification or overexpression was further linked to high-grade UC tumors with dedifferentiated morphology. In addition, UC withMDM2amplification or overexpression was associated with an immuno-evasive contexture characterized by lower proportion of tertiary lymphoid structure infiltration, lower abundance of CD8+T cells, IFN-γ+cells, GZMB+cells, and decreased expression of immune checkpoint molecules including programmed death-ligand 1 (PD-L1), programmed death-1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4).ConclusionsMDM2amplification or overexpression defines a lethal subset of patients with UC with inferior prognosis and resistance to both platinum-based chemotherapy and immunotherapy irrespective ofTP53/p53 status. These tumors are characterized by dedifferentiated morphology and an immunosuppressive microenvironment. Accurate assessment ofMDM2status can improve risk stratification and enable personalized genomics-guided treatment for patients with UC.
Low versus high initial oral glucocorticoid dose for lupus nephritis: a pooled analysis of randomised controlled clinical trials
Authors: Saxena Amit , Sorrento Cristina , Izmirly Peter , Sullivan Janine , Gamez-Perez Monica , Law Jammie , Belmont Howard Michael , Buyon Jill P 
Published: January 2025

ObjectiveTraditional initial treatment regimens for lupus nephritis (LN) used oral glucocorticoids (GC) in starting doses up to 1.0 mg/kg/day prednisone equivalent with or without a preceding intravenous methylprednisolone pulse. More recent management guidelines recommend lower starting oral GC doses following intravenous pulse therapy. As there have been no large studies directly comparing patients receiving low versus high initial oral GC doses, this pooled analysis of high-quality randomised controlled trials (RCTs) aims to evaluate differences in efficacy and safety.MethodsPublished data were analysed from RCTs that assessed variable GC doses in the standard of care (SOC) treatment arms. Patients receiving starting prednisone doses up to 0.5 mg/kg/day (low dose) were compared with 1.0 mg/kg/day (high dose). Complete renal response requiring urine protein-creatinine ratio <0.5 mg/mg (CRR 0.5), CRR or partial renal response (PRR), serious adverse events (SAE) and SAE due to infections at 12 months of treatment were compared between groups.Results417 patients from SOC arms of five studies were exposed to low-dose initial GC after intravenous pulse, while 521 patients from four studies were treated with high-dose oral GC. In patients with low-dose oral GC, 25.2% achieved CRR 0.5 at 12 months compared with 27.2% in high-dose groups, p=0.54. CRR or PRR was attained in 48.7% low-dose vs 43.6% high-dose patients, p=0.14. SAEs and infection SAEs were less common in the low-dose GC group (19.4% vs 31.6%, p<0.001 and 9.8% vs 16.5%, p=0.012, respectively).ConclusionsBased on pooled RCT data, there was no significant difference in 12-month renal responses between patients receiving low-dose prednisone following intravenous GC compared with those receiving initial high doses. SAEs were less frequent in patients receiving low-dose initial GC. These findings support the use of lower oral GC doses in LN treatment.
Evaluating factors impacting National Institutes of Health funding in pain medicine
Authors: Kurian Christopher , Kurian Emil , Orhurhu Vwaire , Korn Elizabeth , Salisu-Orhurhu Mariam , Mueller Ariel , Houle Timothy , Shen Shiqian 
Published: January 2025

BackgroundWhile many medical specialties have established links between bibliometric indices, academic rank, leadership roles, and National Institutes of Health (NIH) funding, there exists a gap within the field of pain medicine. The purpose of our study is to examine the impact of research productivity (h-index, m-index, publications, citations), professional degrees (PhD, MPH, MBA), leadership positions (program director, division chief, chairman), and faculty demographics (gender, nationality of training) on attaining NIH grant funding among pain medicine faculty.MethodsA complete list of 98 civilian pain medicine programs was included in the study. Between September 1, 2022, and December 30, 2022, departmental websites were accessed to accrue a list of pain medicine faculty listings. Publicly available information was used to extract research productivities, professional degrees, leadership positions, faculty demographics, and NIH grant funding. Descriptive statistics were used for analysis, with NIH funding status as the primary outcome.ResultsA total of 696 pain physicians within the academic community were identified. Markers of research productivity such as a higher h- or m-index, larger number of publications and citations, PhD status, and being senior faculty (full professor, division chief, or chairman) were independently associated with NIH funding. There was no statistical difference (p>0.05) among males and females in the number of R grants received.ConclusionsWe have identified many factors associated with NIH funding status and failed to find significant gender disparities in NIH funding. These findings allow for chronic pain programs to have another set of tools to attract, promote, and retain faculty.
Sleep quality and coping styles among nurses working in tertiary cancer institutions: a mixed-method study
Authors: Pai Shubha , Suvvari Praneeth , Kodisharapu Praveen Kumar , Rayani Basanth Kumar , Palat Gayatri 
Published: January 2025

IntroductionProviding nursing care is a challenging job which may lead to serious effects on sleep quality, thereby leading to lower work productivity and reduced job satisfaction. Therefore, it becomes increasingly important to adopt effective and adaptive coping strategies to deal with day-to-day stress and to improve sleep.AimThis study aimed to assess the sleep quality of nurses and the coping styles employed by them to deal with the stressors at the workplace.MethodsThis cross-sectional study included (n=125) nurses working across different wards and intensive care units in two cancer hospitals. The sleep quality was assessed using the Pittsburgh Sleep Quality Index, while brief COPE was used to assess the coping styles. Stress was assessed using a Likert scale.ResultsThe results indicated that the majority of the nurses (59.2%) had poor sleep quality. However, most nurses employed problem-focused coping (70.4%) compared with emotion-focused (21.6%) and avoidant coping (8%). Poor sleep quality was found to have significant association with problem-focused coping (r=0.27), emotion-focused coping (r=0.25) and stress (r=0.42). A thematic analysis of the responses resulted in the emergence of eight major themes causing stress including management issues, novelty of job, family stress, health, work-life balance, workload, interpersonal relations and career growth.ConclusionPoor sleep quality was observed in more than half of the nurses who participated in this study. This can be attributed to several reasons mostly relating to work stress. Thus, it becomes increasingly important to address these issues and provide adequate support on an organisational level to improve their psychological well-being.
Dual antiplatelet therapy with ticagrelor vs clopidogrel in patients with TIA or minor stroke with or without symptomatic carotid artery stenosis: a post hoc analysis of the CHANCE-2 trial
Authors: Xie Xuewei , Jing Jing , Wang Anxin , Xu Qin , Zhao Xingquan , Lin Jinxi , Chen Pan , Jiang Yong , Wang Yilong , Li Hao , Meng Xia , Wang Yongjun 
Published: January 2025

Background and purposeSymptomatic internal carotid artery stenosis (sCAS) is an essential cause of transient ischaemic attack (TIA) or minor stroke. We aimed to evaluate whether the superiority of aspirin-ticagrelor over aspirin-clopidogrel varies between patients with sCAS or not.MethodsThis was a post-hoc analysis of the High-Risk Patients with Acute Nondisabling Cerebrovascular Events-II (CHANCE-2) trial, all of which wereCYP2C19loss-of-function alleles carriers. The primary exposures of interest were the treatment group and sCAS status. The primary efficacy endpoint was the new stroke assessed within 90 days.ResultsA total of 5920 (92.3%) from 6412 were analysed, including 197 (3.3%) with sCAS and 5723 (96.7%) without sCAS. Stroke recurrence occurred in 13 (12.15%) and 11 (12.22%) patients with sCAS who received aspirin-ticagrelor and aspirin-clopidogrel, respectively (adjusted HR, 1.04; 95% CI, 0.46 to 2.36; p=0.930). Among patients without sCAS, there were 158 cases (5.52%) of new strokes in the aspirin-ticagrelor group and 222 cases (7.76%) in the aspirin-clopidogrel group (HR, 0.70; 95% CI, 0.57 to 0.86; p=0.0006). The treatment-by-sCAS subtype was not significant (p=0.405).ConclusionsGenotype-guided dual antiplatelet treatment with aspirin-ticagrelor may be beneficial for preventing recurrent strokes in patients without sCAS; however, it appears less effective in those with sCAS. No significant interaction was found between the treatment and sCAS subtypes.Trial registration numberNCT04078737.
Repository for extended dark matter object constraints
Authors: Croon Djuna , Sevillano Muñoz Sergio 
Published: January 2025

AbstractExtended dark matter objects (EDOs) are popular dark matter candidates that interact gravitationally with the Standard Model. These gravitational interactions can be used to constrain their allowed parameter space. However, EDOs can have different formation mechanisms, sizes, and shapes, requiring a case-by-case analysis when studying their impact on different areas of cosmology. We thus present a repository of all available bounds for these objects, with a code that allows plotting user-defined combinations of all up-to-date bounds for a given shape and different radii. We propose a standard for the EDOs’ mass profiles so that different sets of bounds are consistent with each other, and provide instructions on using the code and contributing to the repository.
Quantum technology master’s: a shortcut to the quantum industry?
Authors: Goorney Simon , Muñoz Borja , Sherson Jacob 
Published: January 2025

AbstractIn this article, we investigate a growing trend in the worldwide Quantum Technology (QT) education landscape, that of the development of master’s programs, intended to provide graduates with the knowledge and skills to take a job in the quantum industry, while serving a much shorter timeline than a doctoral degree. Through a global survey, we identified 86 master’s programs, with substantial growth since 2021. Over time master’s have become increasingly interdisciplinary, organised by multiple faculties or through joint degree programs, and offer more hands-on experiences such as internships in companies. Information from program organisers and websites suggests that the intended career destinations of their graduates are a diverse range of industries, and therefore master’s programs may be a boon to the industrialisation of quantum technologies. Finally, we identify a range of national efforts to grow the quantum workforce of many countries, “quantum program enhancements”, which augment the content of existing study programs with quantum content. This may further contribute to the growth and viability of master’s programs as a route to the quantum industry.
Earnings attainment in the three main cities of Southeastern Brazil: social networks and communities of worship
Authors: Higgins Silvio Segundo Salej , Neves Jorge Alexandre Barbosa , Mattar Luciano 
Published: January 2025

AbstractFollowing the field of insertion into the labor market, we tested the classic hypothesis of the strength of weak ties in the three largest cities in the Southeast Region of Brazil, with a focus on communities of religious worship. A survey was carried out in 2021 with 900 questionnaires divided equally among the three cities, weighted considering the size of the population and the distribution of religious affiliation. We investigated: (1) whether the strength of ties leverages the labor insertion of adults; (2) whether religious cult communities operate as mechanisms for the circulation of opportunities in the labor market. The data were analyzed with Heckman’s two-stage correction models to mitigate possible censoring biases. Controlling by seniority in the position and participation of three sampled cities in gross national product, inter alia, the results show that strong ties, as predicted by the strength of ties theory, are associated with lower earnings. At the same time, obtaining a paid job through another cult member is negatively associated with earnings. However, when testing our main hypothesis, we found that in the three largest cities in the Southeast Region of Brazil the religious embeddedness, composed of strong ties, high worship attendance and religious motivations coming from maternal ties, operate plausibly in labor market as favorable screen mechanism associated with higher earnings.
DFAST_QC: quality assessment and taxonomic identification tool for prokaryotic Genomes
Authors: Elmanzalawi Mohamed , Fujisawa Takatomo , Mori Hiroshi , Nakamura Yasukazu , Tanizawa Yasuhiro 
Published: January 2025

Abstract
Background
Accurate taxonomic classification in genome databases is essential for reliable biological research and effective data sharing. Mislabeling or inaccuracies in genome annotations can lead to incorrect scientific conclusions and hinder the reproducibility of research findings. Despite advances in genome analysis techniques, challenges persist in ensuring precise and reliable taxonomic assignments. Existing tools for genome verification often involve extensive computational resources or lengthy processing times, which can limit their accessibility and scalability for large-scale projects. There is a need for more efficient, user-friendly solutions that can handle diverse datasets and provide accurate results with minimal computational demands. This work aimed to address these challenges by introducing a novel tool that enhances taxonomic accuracy, offers a user-friendly interface, and supports large-scale analyses.

Results
We introduce a novel tool for the quality control and taxonomic classification tool of prokaryotic genomes, called DFAST_QC, which is available as both a command-line tool and a web service. DFAST_QC can quickly identify species based on NCBI and GTDB taxonomies by combining genome-distance calculations using MASH with ANI calculations using Skani. We evaluated DFAST_QC's performance in species identification and found it to be highly consistent with existing taxonomic standards, successfully identifying species across diverse datasets. In several cases, DFAST_QC identified potential mislabeling of species names in public databases and highlighted discrepancies in current classifications, demonstrating its capability to uncover errors and enhance taxonomic accuracy. Additionally, the tool’s efficient design allows it to operate smoothly on local machines with minimal computational requirements, making it a practical choice for large-scale genome projects.

Conclusions
DFAST_QC is a reliable and efficient tool for accurate taxonomic identification and genome quality control, well-suited for large-scale genomic studies. Its compatibility with limited-resource environments, combined with its user-friendly design, ensures seamless integration into existing workflows. DFAST_QC's ability to refine species assignments in public databases highlights its value as a complementary tool for maintaining and enhancing the accuracy of taxonomic data in genomic research. The web version is available at https://dfast.ddbj.nig.ac.jp/dqc/submit/, and the source code for local use can be found at https://github.com/nigyta/dfast_qc.
Antifungal, toxicological, and colorimetric properties of Origanum vulgare, Moringa oleifera, and Cinnamomum verum essential oils mixture against Egyptian Prince Yusuf Palace deteriorative fungi
Authors: Mohamed Asmaa Alhussein , Ahmed Mahgoub A. , Korayem Abdallah S. , Abu-Hussien Samah H. , Rashidy Wael Bakry 
Published: January 2025

AbstractThe increasing demand for sustainable alternatives to conventional antifungal agents has prompted extensive research into the antifungal properties of plant essential oils (EOs). This study investigates the use of EOs mixture (Origanum vulgare, Moringa oleifera, and Cinnamomum verum) for controlling fungal deterioration in wall paintings at the archaeological Youssef Kamal Palace in Nag Hammadi, Egypt. Fungal isolates were collected from deteriorated wall paintings and identified using phenotypic and genotypic analyses. Aspergillus sp. was found to be the predominant species (50%), followed by Penicillium sp. (16.7%), Fusarium sp. (16.7%), and others. They were genetically identified to be Aspergillus oryzae, Aspergillus niger, Penicillium chrysogenum, Fusarium solani, Alternaria alternata, Botrytis cinerea, and Trichoderma viride. The antifungal activity of three individual oils (oregano, moringa and cinnamon) was evaluated against the most predominant A. niger strain. Out of the three oils, oregano oil showed the strongest antifungal effect with an inhibition zone diameter (IZD) of 4.5 cm followed by moringa (3.5 cm) and cinnamon (3.2 cm). A mixture design approach optimized the EOs combination, with the most effective composition being (44% oregano, 46% moringa, 10% cinnamon), yielding an IZD of 6.5 cm. The optimized EOs mixture demonstrated complete inhibition against all tested fungal strains. The minimal inhibitory concentration tests showed varying efficacies against different fungal strains, with MIC values ranging from 125 to 500 µg/mL. GC-MS analysis identified the major bioactive compounds: carvacrol (83.25%) in oregano, trans-13-octadecenoic acid (22.62%) in moringa, and cinnamaldehyde (24.42%) in cinnamon. Cytotoxicity testing on human skin fibroblasts (HSF) showed minimal toxicity of EOs mixture with 87.64% cell viability at 100 µg/ml. Colorimetric measurements revealed some colour changes in experimental painting samples, particularly with cinnamon oil on white pigment (ΔE = 9.64) and moringa oil on a yellow pigment (ΔE = 16.31). However, oregano oil consistently showed the least impact across all pigments. These findings demonstrate the potential of the EOs combination as an effective, eco-friendly approach to mitigating fungal deterioration in wall paintings, contributing to sustainable conservation strategies for cultural heritage preservation.
Organizational readiness for implementation: a qualitative assessment to explain survey responses
Authors: McClam Maria , Workman Lauren , Walker Timothy J. , Dias Emanuelle M. , Craig Derek W. , Padilla Joe R. , Lamont Andrea E. , Wandersman Abraham , Fernandez Maria E. 
Published: January 2025

Abstract
Background
One factor considered essential to successful implementation is organizational readiness. The purpose of this study was to explore ways to improve the measurement of organizational readiness, and in particular to refine a preliminary measure based on the Readiness = Motivation x innovation Specific Capacity x General Capacity (R = MC2) heuristic. We assessed the experiences of staff in Federally Qualified Health Centers (FQHC) implementing evidence-based interventions (EBIs) designed to increase colorectal cancer screening (CRCS) who previously completed the survey and aimed to understand their perspectives on why our data were positively skewed.

Methods
We conducted a series of qualitative interviews with FQHC employees who had previously completed the readiness survey and/or been involved with the distribution of the readiness survey. Interviews were conducted via Zoom, recorded, transcribed. Data was analyzed using an inductive approach to identify key emergent themes.

Results
Analyses revealed numerous contributors to high organizational readiness assessment scores including concerns about confidentiality, social desirability bias, knowledge of respondents about the survey content, and the survey format. Specific to the survey format, we found that survey length and response scaling likely impacted scores and the overall survey experience. Lastly, some participants shared that the tendency for high scores may reflect actual perceptions because FQHC staff are passionate, work well in teams, and typically have already worked hard to improve CRCS rates through evidence-based interventions.

Conclusion
Study findings reinforce the importance of collaborative and community-engaged survey design and the need to address the common challenges dissemination and implementation surveys may be vulnerable to. Lessons learned can be applied to other measurement work and surveys conducted across public health research. The findings will inform continued organizational readiness measure development and have implications for measurement of other factors influencing implementation.