bluuebunny/crossref_metadata_2025_split huggingface dataset:
Community Views of Determinants of Men’s Wellbeing in Guatemala: A Study Using Fuzzy Cognitive Mapping
Authors: Pizarro Katherine W. , Chomat Anne M. , Quieju Diego P. , López Bernardo Y. , Sarmiento Iván , LeBel Nicholas , Mancini Chloe , Andersson Neil , Groleau Danielle , Cockcroft Anne 
Published: January 2025

Background In post-conflict Guatemala, Indigenous men’s psychological distress has been linked to violence exposure, disrupted social support systems, and structural inequities. Purpose We aimed to document how communities themselves understand men’s wellbeing and the factors that influence men’s wellbeing. Research design and study sample Fuzzy Cognitive Mapping with 20 stakeholder groups in Santiago Atitlán and Cuilco, Guatemala defined men’s wellbeing in local terms and identified the influences community groups understood to promote and detract from men’s wellbeing. Participants mapped pathways through which influences affected wellbeing and weighted their relative perceived strength. Analysis The researchers used thematic analysis to summarise influences into 43 factors and used fuzzy transitive closure to calculate their net causal influence for each set of stakeholders. We compared perspectives of groups of adult men, adult women, and practitioners of Mayan medicine in Santiago Atitlán, with a primarily Indigenous population, to groups in Cuilco, with a primarily non-Indigenous population. We also compared perspectives across age groups in Santiago Atitlán. Results Across regions, maps highlighted the importance of family and social relations, emotional distress, substance use and physical health for men’s wellbeing. Basic resource insecurity and unemployment were top risk factors for men’s wellbeing in maps from Cuilco but had both risk and protective influences on men’s wellbeing in maps from Santiago Atitlán. Conclusions Findings challenge the focus on scale-up of individual biomedical interventions as the best strategy to reduce the burden of emotional distress in Guatemala and raise questions about standard development approaches that emphasize income generation and educational attainment above cultural continuity and social harmony.
Microbially produced imidazole propionate impairs prostate cancer progression through PDZK1
Authors: Jin Shengkai , Zhou Yuhua , Lv Jing , Lu Yichen , Zhang Yuwei , Li Menglu , Feng Ninghan 
Published: January 2025

Abstract

Background
A close relationship exists between castration-resistant prostate cancer (CRPC) and histidine metabolism by gut microbes. However, the effects of the histidine metabolite imidazole propionate (IMP) on prostate cancer (PCa) and its underlying mechanisms are not well understood.

Methods
We first assessed the effects of IMP on cell proliferation and migration at the cellular level. Subsequently, we investigated the mechanism of action of IMP using transcriptome sequencing, qPCR, and Western blot analysis. Finally, we validated our findings in vivo using a mouse model.

Results
Histidine had no effect on PCa cell proliferation; however, IMP significantly inhibited the proliferation and migration of PC3 and DU145 cells. Mechanistic studies indicate that IMP exerts its effects by upregulating PDZK1 expression, which subsequently inhibits the phosphorylation of the PI3K-AKT pathway.

Conclusions
In conclusion, IMP significantly inhibits the progression of PCa, offering new insights into potential treatments for CRPC.
TopoQual polishes circular consensus sequencing data and accurately predicts quality scores
Authors: Weerakoon Minindu , Lee Sangjin , Mitchell Emily , Heaton Haynes 
Published: January 2025

Abstract

Background
Pacific Biosciences (PacBio) circular consensus sequencing (CCS), also known as high fidelity (HiFi) technology, has revolutionized modern genomics by producing long (10 + kb) and highly accurate reads. This is achieved by sequencing circularized DNA molecules multiple times and combining them into a consensus sequence. Currently, the accuracy and quality value estimation provided by HiFi technology are more than sufficient for applications such as genome assembly and germline variant calling. However, there are limitations in the accuracy of the estimated quality scores when it comes to somatic variant calling on single reads.

Results
To address the challenge of inaccurate quality scores for somatic variant calling, we introduce TopoQual, a novel tool designed to enhance the accuracy of base quality predictions. TopoQual leverages techniques including partial order alignments (POA), topologically parallel bases, and deep learning algorithms to polish consensus sequences. Our results demonstrate that TopoQual corrects approximately 31.9% of errors in PacBio consensus sequences. Additionally, it validates base qualities up to q59, which corresponds to one error in 0.9 million bases. These improvements will significantly enhance the reliability of somatic variant calling using HiFi data.

Conclusion
TopoQual represents a significant advancement in genomics by improving the accuracy of base quality predictions for PacBio HiFi sequencing data. By correcting a substantial proportion of errors and achieving high base quality validation, TopoQual enables confident and accurate somatic variant calling. This tool not only addresses a critical limitation of current HiFi technology but also opens new possibilities for precise genomic analysis in various research and clinical applications.
Sherlock-Genome: an R Shiny application for genomic analysis and visualization
Authors: Klein Alyssa , Zhong Jun , Landi Maria Teresa , Zhang Tongwu 
Published: January 2025

Abstract

Motivation
Next-generation sequencing technologies, such as whole genome sequencing (WGS), have become prominent in cancer genomics. However, managing, visualizing, and integratively analyzing WGS results across various bioinformatic pipelines remains challenging, particularly for non-bioinformaticians, hindering the usability of WGS data for biological discovery.

Results
We developed Sherlock-Genome, an R Shiny app for data harmonization, visualization, and integrative analysis of WGS-based cancer genomics studies. Following FAIR principles, Sherlock-Genome provides a platform and guidelines for managing and sharing finalized sample-level WGS analysis results, enabling users to upload results, inspect analyses locally, and perform integrative analyses. It includes modules for major cancer genomic analyses, allowing interactive data visualizations and integrative analyses with other data types. Sherlock-Genome supports both local and cloud deployment, facilitating the sharing of results for related publications. This tool has the potential to be widely adopted in cancer genomics, significantly enhancing the accessibility and usability of sample-level WGS analysis results for comprehensive biological discovery and research advancements.

Availability and implementation
The source code and installation instructions for Sherlock-Genome can be accessed via Github https://github.com/xtmgah/Sherlock-Genome. Documentation and data requirements for user project data can also be found on the same GitHub page.
‘It's about collaboration’: a whole-systems approach to understanding and promoting movement in Suffolk
Authors: Brinkley A. J. , Cusimano K. M. , Freeman P. , Southall-Edwards R. , Gladwell V. F. 
Published: January 2025

Abstract

Background
Population-levels of physical activity have remained stagnant for years. Previous approaches to modify behaviour have broadly neglected the importance of whole-systems approaches. Our research aimed to (i) understand, (ii) map, (iii) identify the leverage points, and (iv) develop solutions surrounding participation in physical activity across an English rural county.

Methods
A systems-consortium of partners from regional and local government, charities, providers, deliverers, advocacy groups, and health and social care, and public health engaged in our research, which consisted of two-phases. Within Phase 1, we used secondary data, insight-work, a narrative review, participatory workshops, and interviews in a pluralistic style to map the system-representing physical activity. Phase 2 began with an initial analysis using markers from social network analysis and the Action Scales Model. This analysis informed a participatory workshop, to identify leverage points, and develop solutions for change within the county.

Results
The systems-map is constructed from biological, financial, and psychological individual factors, interpersonal factors, systems partners, built, natural and social environmental factors, and policy and structural factors. Our initial analysis found 13 leverage points to review within our participatory workshop. When appraised by the group, (i) local governing policies, (ii) shared policies, strategies, vision, and working relationships, (iii) shared facilities (school, sport, community, recreation), and (iv) funding were deemed most important to change. Within group discussions, participants stressed the importance and challenges associated with shared working relationships, a collective vision, and strategy, the role of funding, and management of resources. Actions to leverage change included raising awareness with partners beyond the system, sharing policies, resources, insight, evidence, and capacity, and collaborating to co-produce a collective vision and strategy.

Conclusions
Our findings highlight the importance and provide insight into the early phase of a whole-systems approach to promoting physical activity. Our whole-systems approach within Suffolk needs to consider methods to (i) grow and maintain the systems-consortium, (ii) create a sustainable means to map the system and identify leverage points within it, and (iii) monitor and evaluate change.
Spectral framework using modified shifted Chebyshev polynomials of the third-kind for numerical solutions of one- and two-dimensional hyperbolic telegraph equations
Authors: Sayed S. M. , Mohamed A. S. , Abo-Eldahab E. M. , Youssri Y. H. 
Published: January 2025

Abstract
This investigation discusses a numerical approach to solving the hyperbolic telegraph equation in both one and two dimensions. Applying the Galerkin method is the basis of this approach. We use appropriate combinations of third-kind modified shifted Chebyshev polynomials (3KMSCPs) as basis functions to transform the governing partial differential equations into a collection of algebraic equations. Through spectral Galerkin techniques, we establish the convergence error to demonstrate that our algorithm is more effective and efficient. Five examples are examined to verify the effectiveness and resilience of the applied method by comparing errors and illustrating the results. Our results show that the current numerical solutions align closely with exact solutions. The current algorithm is simple to set up and is better suited to solving certain difficult partial differential equations.
Management of acute bacterial meningitis in a limited resource setting: an Egyptian consensus model
Authors: Zaky Samy , Elbadry Mohamed , Saeed Maysaa A. , Fathelbab Hanaa , Abdelsalam Fatma , Abdel-Hamid Mohammed Gamal , Eid Alshaimaa , Bakr Asmaa , Maher Amira , Abdelrahman Mona Mohammed , Metwally Mohamed A. , Berengy Mahmoud Saad , AlMowafy Enaam Ali , Goabar Hassan , Baki Amin Abdel , Corie Ahmed , Hammad Osama , Elsharkawy Entesar , Saad Ahmed , Ali-Eldin Fatma , Mahdy Ahmed , Zaky Ramadan , Hammad Reham , Essmat Gamal 
Published: January 2025

Abstract
Acute bacterial meningitis (ABM) is an emerging disease with high morbidity and mortality. It is a globally serious disease and is considered endemic in Egypt, affecting all age groups and being common in low-standard and overcrowded areas. Early and appropriate antimicrobial therapy is crucial for suspected bacterial meningitis, even before the causative pathogen is identified. This is because definitive laboratory confirmation can take several days and may not always be successful. Those who do recover, especially if there was delayed appropriate intervention, can have permanent disabilities, such as brain damage, hearing loss, and learning disabilities. Rapid intervention in such cases is mandatory, which is not easy in countries with limited income due to weak capabilities and resources. Therefore, we are in dire need of making an Egyptian consensus that suits our country as a low-resource one, in order to facilitate and speed up the process of managing such cases. This consensus-based paper is under the supervision of the Egyptian Society of Fever comprising clinicians, microbiologists, epidemiologists, and public health representatives. They convened to assess the current situation and develop a new consensus on the management of ABM, taking into consideration the human and health potential of Egypt. All the experts who participated in writing and directing this conference belong to different Egyptian universities, and their main clinical interest was infectious diseases. Others work in fever hospitals that are affiliated with the Ministry of Health. They collaborated on the statements` writing, reviewing, and voting to reach the final version. Each statement was voted as strongly, moderately, or weekly recommended. Each statement should have a predefined score of 80% agreement to be accepted and reported in this consensus.

Conclusion

This Egyptian consensus model offers a feasible and context-specific approach to managing ABM, aiming to improve outcomes and reduce disparities in resource-limited settings.
A Novel Facile and Efficient Prophylaxis Avenue of Chitosan Oligosaccharide/PLGA Based Polydatin Loaded Nanoparticles Against Bleomycin-Induced Lung Inflammation in Experimental Rat Model
Authors: Alnagar Ahmed Nashaat , Motawea Amira , Zaghloul Randa A. , Eldesoqui Mamdouh , Abu Hashim Irhan Ibrahim 
Published: January 2025

Abstract
Lung inflammation is a hallmark of several respiratory diseases. Despite the great effectiveness of the synthetic antiinflammatory agents, they cause potential side effects. Polydatin (PD), a natural phytomedicine, has antioxidant and antiinflammatory effects. Its clinical applications are hindered due to poor aqueous solubility, low bioavailability, and rapid metabolism by first-pass effect. Herein, we report the development of a novel chitosan oligosaccharide-coated PD-loaded Poly dl-lactide-co-glycolide nanoparticles (COS-coated PD/PLGA NPs) against a bleomycin-induced pulmonary inflammation in a rat model. The NPs exhibited a small particle size of 188.57 ± 5.68 nm and a high zeta potential of + 18.13 ± 2.75 mV with spherical architecture and sustained release pattern of PD. In vivo studies in bleomycin-induced lung inflammation in a rat model revealed the superior prophylactic activity of COS-coated PD/PLGA NPs over the free drug (PD) as demonstrated by histopathological and immunohistochemical analyses, alongside biochemical assays evaluating oxidative stress biomarkers and inflammatory cytokine levels. Overall, the optimized COS-coated PD/PLGA NPs formulation offers a promising prophylactic platform against many respiratory diseases.

Graphical Abstract
Genetic Variants Associated With the Biochemical Response to Vitamin D3 in the Multi-Ethnic Study of Atherosclerosis
Authors: Best Cora M , Li Xiaohui , Rotter Jerome I , Prince David K , Hsu Simon , Hoofnagle Andrew N , Siscovick David , Taylor Kent D , Williams Kayleen , Michos Erin D , Psaty Bruce M , Shea Steven , Rice Kenneth M , Watson Karol E , Allen Norrina B , Tracy Russell P , Robinson-Cohen Cassianne , de Boer Ian H , Kestenbaum Bryan R 
Published: January 2025

Abstract

Context
The response to treatment with vitamin D varies between patients.

Objective
To identify genetic variants associated with the biochemical response to vitamin D3 supplementation.

Design
Randomized placebo-controlled trial conducted between 2017 and 2019.

Setting
The trial was nested in an ongoing community-based cohort study, the Multi-Ethnic Study of Atherosclerosis.

Intervention
2000 International Units of vitamin D3 or placebo daily for 16 weeks.

Participants
The analytic sample included 427 participants assigned to vitamin D3 (mean age, 73 years; 54% females) and was 36% White, 33% Black, 18% Hispanic, and 14% Chinese.

Main Outcome Measures
The biochemical response to vitamin D3 included changes in serum concentrations of 1,25-dihydroxyvitamin D3 [1,25(OH)2D3], PTH, and 25-hydroxyvitamin D3 [25(OH)D3].

Results
In genome-wide analyses, single nucleotide polymorphisms in 8 regions of the genome had significant association (P &lt; 5E-08) with 1 of the traits (2 with change in 1,25(OH)2D3, 1 with change in PTH, and 5 with change in 25(OH)D3). rs16867276 within an intergenic region on 2q31 was associated with change in serum 1,25(OH)2D3 (+8.37 pg/mL difference per effect allele; P = 4.93E-08) and was the only locus that achieved genome-wide significance in transethnic meta-analysis. rs114044709 adjacent to FAM20A, which encodes a protein required for biomineralization, was associated with change in PTH among Black participants (+20.32 pg/mL difference per effect allele; P = 1.34E-08). In candidate analyses, single nucleotide polymorphisms within SULT2A1 and CYP24A1 had significant association (P &lt; .05÷36 = .0014) with the changes in 1,25(OH)2D3 and PTH, respectively.

Conclusion
Our results reveal potential new pathways of vitamin D regulation that require replication in other vitamin D trials.
BMP and STRA8 act collaboratively to ensure correct mitotic-to-meiotic transition in the fetal mouse ovary
Authors: Cheung Fiona K. M. , Feng Chun-Wei Allen , Crisp Clare , Mishina Yuji , Spiller Cassy M. , Bowles Josephine 
Published: January 2025

ABSTRACT
A successful mitosis-to-meiosis transition in germ cells is essential for fertility in sexually reproducing organisms. In mice and humans, it has been established that expression of STRA8 is crucial for meiotic onset in both sexes. Here, we show that BMP signalling is also essential, not for STRA8 induction but for correct meiotic progression in female mouse fetal germ cells. Largely in agreement with evidence from primordial germ cell-like cells (PGCLCs) in vitro, germ cell-specific deletion of BMP receptor 1A (BMPR1A; ALK3) caused aberrant retention of pluripotency marker OCT4 and meiotic progression was compromised; however, the timely onset of Stra8 and STRA8 expression was unaffected. Comparing the transcriptomes of Bmpr1a-cKO and Stra8-null models, we reveal interplay between the effects of BMP signalling and STRA8 function. Our results verify a role for BMP signalling in instructing germ cell meiosis in female mice in vivo, and shed light on the regulatory mechanisms underlying fetal germ cell development.
The Effects of Gymnastics Programs with Different Cognitive Loads on Working Memory and Prefrontal Cortex Oxygenation: A Randomized Controlled Trial
Authors: Lin Chih-Chien , Kao Shih-Chun , Hung Chiao-Ling , Tsai Chia-Liang , Huang Chung-Ju , Chang Yu-Kai , Hung Tsung-Min 
Published: January 2025

ABSTRACT

Purpose
This study used functional near-infrared spectroscopy (fNIRS) to investigate the effects of gymnastics programs with high versus low cognitive load on children's visuospatial working memory (VSWM) and prefrontal cortex (PFC) oxygenation.

Methods
Eighty-one healthy children aged 7 to 10 from Taipei City were randomly assigned to high cognitive load (HG), low cognitive load (LG), and control (SC) groups. The HG and LG groups underwent an 8-week gymnastics program with different levels of cognitive load, while the SC group participated in a static course. Pre- and post-intervention assessments included VSWM tests and simultaneous monitoring of PFC oxyhemoglobin (HbO) concentration.

Results
The results showed time-related improvements in response accuracy and d-prime (d') from the pretest to posttest for both the HG and LG groups but not for the SC group. Additionally, the HG group demonstrated higher response accuracy and d' compared to the SC group at the posttest. Although VSWM-related HbO concentration was higher during task conditions requiring higher WM load compared to low WM load, no intervention effect was found. Further correlation analysis controlling for intervention-related fitness changes revealed positive associations between time-related changes in VSWM performance (response accuracy and d') and HbO concentration across all participants, with a similar correlation between response accuracy and HbO remaining specifically in the HG group but not other groups.

Conclusions
These findings suggest that a 8-week gymnastics program can enhance VSWM performance and such cognitive benefits may be maximized by incorporating higher cognitive loads into the intervention. Despite the positive correlations between time-related changes in PFC oxygenation and VSWM performance, the gymnastics programs did not alter task-related PFC oxygenation, suggesting that intervention-induced VSWM improvement may not be solely dependent on changes in task-related PFC oxygenation.
Performance-Management-Systeme: Immer noch die „Rituals of Verification“ oder schon Multidimensionale Integrierte Informationssysteme?
Authors: Pidun Tim 
Published: January 2025

Zusammenfassung
Die Digitale Transformation (DT) mit ihrem Haupttreiber Informationstechnologie (IT) ist eine zentrale Herausforderung für Unternehmen und Behörden. Eine ihrer Haupteffekte ist die Verbesserung der Entscheidungsunterstützung in Organisationen. Die u. a. wichtigsten Informationssysteme zur Unterstützung des Managements sind dabei Performance-Management-Systeme (PMS), insbesondere wird der Einsatz von Softwareanwendungen zur Automatisierung von PMS gefordert. Dieser Beitrag sammelt in einem strukturierten Review erste Forschungsergebnisse zu Anforderungen an PMS und bereits nutzbarer Softwarelösungen. Im Ergebnis lassen sich spezialisierte Lösungen finden, die allerdings bestehende Nachteile nicht überwinden sowie generelle Ansätze, deren Einsatz im Bereich der PMS noch nicht verbreitet ist. Eine vollintegrierte multidimensionale Lösung, die allen Anforderungen genügt, ist dagegen derzeit nicht sichtbar und bedürfte der Konstruktion.