bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene-based microbiome representation enhances host phenotype classification
Authors: Deschênes Thomas , Tohoundjona Fred Wilfried Elom , Plante Pier-Luc , Di Marzo Vincenzo , Raymond Frédéric 
Published: July 2023

ABSTRACT

With the concomitant advances in both the microbiome and machine learning fields, the gut microbiome has become of great interest for the potential discovery of biomarkers to be used in the classification of the host health status. Shotgun metagenomics data derived from the human microbiome is composed of a high-dimensional set of microbial features. The use of such complex data for the modeling of host-microbiome interactions remains a challenge as retaining
de novo
content yields a highly granular set of microbial features. In this study, we compared the prediction performances of machine learning approaches according to different types of data representations derived from shotgun metagenomics. These representations include commonly used taxonomic and functional profiles and the more granular gene cluster approach. For the five case-control datasets used in this study (Type 2 diabetes, obesity, liver cirrhosis, colorectal cancer, and inflammatory bowel disease), gene-based approaches, whether used alone or in combination with reference-based data types, allowed improved or similar classification performances as the taxonomic and functional profiles. In addition, we show that using subsets of gene families from specific functional categories of genes highlight the importance of these functions on the host phenotype. This study demonstrates that both reference-free microbiome representations and curated metagenomic annotations can provide relevant representations for machine learning based on metagenomic data.

IMPORTANCE
Data representation is an essential part of machine learning performance when using metagenomic data. In this work, we show that different microbiome representations provide varied host phenotype classification performance depending on the dataset. In classification tasks, untargeted microbiome gene content can provide similar or improved classification compared to taxonomical profiling. Feature selection based on biological function also improves classification performance for some pathologies. Function-based feature selection combined with interpretable machine learning algorithms can generate new hypotheses that can potentially be assayed mechanistically. This work thus proposes new approaches to represent microbiome data for machine learning that can potentiate the findings associated with metagenomic data.
Hospital admissions linked to SARS-CoV-2 infection in children and adolescents: cohort study of 3.2 million first ascertained infections in England
Authors: Wilde Harrison , Tomlinson Christopher , Mateen Bilal A , Selby David , Kanthimathinathan Hari Krishnan , Ramnarayan Padmanabhan , Du Pre Pascale , Johnson Mae , Pathan Nazima , Gonzalez-Izquierdo Arturo , Lai Alvina G , Gurdasani Deepti , Pagel Christina , Denaxas Spiros , Vollmer Sebastian , Brown Katherine 
Published: July 2023

Abstract

Objective
To describe hospital admissions associated with SARS-CoV-2 infection in children and adolescents.

Design
Cohort study of 3.2 million first ascertained SARS-CoV-2 infections using electronic health care record data.

Setting
England, July 2020 to February 2022.

Participants
About 12 million children and adolescents (age <18 years) who were resident in England.

Main outcome measures
Ascertainment of a first SARS-CoV-2 associated hospital admissions: due to SARS-CoV-2, with SARS-CoV-2 as a contributory factor, incidental to SARS-CoV-2 infection, and hospital acquired SARS-CoV-2.

Results
3 226 535 children and adolescents had a recorded first SARS-CoV-2 infection during the observation period, and 29 230 (0.9%) infections involved a SARS-CoV-2 associated hospital admission. The median length of stay was 2 (interquartile range 1-4) days) and 1710 of 29 230 (5.9%) SARS-CoV-2 associated admissions involved paediatric critical care. 70 deaths occurred in which covid-19 or paediatric inflammatory multisystem syndrome was listed as a cause, of which 55 (78.6%) were in participants with a SARS-CoV-2 associated hospital admission. SARS-CoV-2 was the cause or a contributory factor in 21 000 of 29 230 (71.8%) participants who were admitted to hospital and only 380 (1.3%) participants acquired infection as an inpatient and 7855 (26.9%) participants were admitted with incidental SARS-CoV-2 infection. Boys, younger children (<5 years), and those from ethnic minority groups or areas of high deprivation were more likely to be admitted to hospital (all P<0.001). The covid-19 vaccination programme in England has identified certain conditions as representing a higher risk of admission to hospital with SARS-CoV-2: 11 085 (37.9%) of participants admitted to hospital had evidence of such a condition, and a further 4765 (16.3%) of participants admitted to hospital had a medical or developmental health condition not included in the vaccination programme’s list.

Conclusions
Most SARS-CoV-2 associated hospital admissions in children and adolescents in England were due to SARS-CoV-2 or SARS-CoV-2 was a contributory factor. These results should inform future public health initiatives and research.
A framework for community health worker optimisation in conflict settings: prerequisites and possibilities from Northwest Syria
Authors: Habboush Ahmad , Ekzayez Abdulkarim , Gilmore Brynne 
Published: July 2023

BackgroundThe world will face a human resource gap of 10 million health workers in 2030. Community health workers (CHWs) can contribute to mitigating this workforce gap while improving equitable access to care and health outcomes. However, questions on how to best implement and optimise CHW programmes, especially across varied contexts, remain. As each context has its determinants for a successful CHW programme, this research identifies and assesses pertinent factors needed for optimal CHW programmes in conflict settings, specifically Northwest Syria.MethodsA mixed-methods study in Northwest Syria consisting of a literature and document review, semistructured interviews with CHWs’ team leaders and programme managers, key informant interviews with policymakers and a survey with CHWs was conducted across three research phases from 2018 to 2022. The three phases aimed to identify, refine and finalise a framework for CHW optimisation in humanitarian conflict contexts, respectively. Qualitative data were analysed thematically, and quantitative data were statistically analysed to identify critical trends.Results16 interviews and 288 surveys were conducted, supplemented by key reports and literature. The framework underwent two iterative rounds of refinement, reflecting varying stakeholders’ perceptions of CHW optimisation. The resulting framework presents important implementation factors with subthemes across identified topics of institutionalisation, integration and representation for CHW optimisation in Northwest Syria and other humanitarian conflict contexts. The presented factors are similar in various ways to other fragile low/middle-income country settings. However, in protracted conflict settings like Syria, careful consideration should be given to strategic dimensions such as integration and representation.ConclusionFor CHW programmes to impact health outcomes in humanitarian conflict settings, they require a set of implementation and design factors relevant to the context. The dynamics of humanitarian funding restrictions, health system capacity and governance structures confront achieving these requirements. Nevertheless, pioneering projects which use available resources are possible. Evidence is needed to understand the impact of CHWs’ interventions and further support implementation across humanitarian contexts.
Associations of serum aminotransferase and the risk of all-cause and cause-specific mortality in Chinese type 2 diabetes: a community-based cohort study
Authors: Su Jian , Guan Haoyu , Fan Xikang , Yu Hao , Qin Yu , Yang Jie , Zhu Zheng , Shen Chong , Pan Enchun , Lu Yan , Zhou Jin-Yi , Wu Ming 
Published: July 2023

ObjectiveInvestigating the associations of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) with all-cause, cardiovascular disease (CVD) and cancer mortality in a large cohort of community-dwelling patients with type 2 diabetes mellitus (T2DM).DesignCommunity-based prospective cohort study conducted between 2013 and 2014.Setting44 selected townships in Changshu and Huai’an City, Jiangsu province, China.Participants20340 participants with T2DM were recruited in Jiangsu province, China.MethodsWe use Cox proportional hazard models to estimate the HR and 95% CIs of associations of serum ALT and AST levels with all-cause and cause-specific mortality. Restricted cubic splines were used to explore the dose-response relationships between ALT and AST levels with mortality.ResultsALT and AST levels were inversely associated with CVD mortality, compared with the lowest quintile (Q1), the multivariable HRs of the highest quintile (Q5) was 0.82 (95% CI: 0.66 to 1.01, p for trend=0.022) and 0.78 (95% CI: 0.63 to 0.96, p for trend=0.022), respectively. Furthermore, the HRs for ALT levels in all-cause mortality were 0.90 (95% CI: 0.79 to 1.01, p for trend=0.018), and the HRs for AST levels in cancer mortality were 1.29 (95% CI: 1.02 to 1.63, p for trend=0.023). Stronger inverse effects of ALT and AST levels on all-cause mortality were observed in the older subgroup and in those with dyslipidaemia (all p for interaction <0.05). Further analysis based on gender showed that the associations between serum aminotransferases and the mortality risk were more significant in women and substantially attenuated in men.ConclusionOur findings suggested patients with T2DM with lower levels of ALT and AST had an increased risk of CVD mortality, which needs confirmation in future clinical trials.
Sharing voice during deliberative engagement to improve guideline adherence in dental clinics: findings from a qualitative evaluation of an online deliberative forum discussion
Authors: Gruß Inga , Dawson Tim , Kaplan Charles D , Pihlstrom Daniel J , Reich Sacha , Fellows Jeffrey L , Polk Deborah E 
Published: July 2023

ObjectivesSelecting effective implementation strategies to support guideline-concordant dental care is a complex process. For this research project, an online deliberative forum brought together staff from dental clinics to discuss the strengths and weaknesses of implementation strategies and barriers to implementation of a component of a dental (pit-and-fissure) guideline. The goal was to determine whether deliberative engagement enabled participants’ sharing of promotive and prohibitive voice about implementation strategies to promote guideline-concordant care.DesignQualitative analysis of online chat transcripts of facilitated deliberations from 31 small group sessions.SettingKaiser Permanente Dental (KP Dental) in the USA.ParticipantsAll staff from 16 dental offices.ResultsThe directed content analysis revealed that participants shared prohibitive and promotive voice when offering critique of the barriers and the implementation strategies suggested by the researchers. The analysis also revealed that the focus of the deliberations often was not on the aspect of the pit-and-fissure guideline intended by the research team for deliberation.ConclusionsThe deliberative forum discussions were a productive venue to ask staff in dental clinics to share their perspectives on strategies to promote guideline-concordant care as well as barriers. Participants demonstrated prohibitive voice and engaged critically with the materials the research team had put together. An important limitation of the deliberation was that the discussion often centred around an aspect of the pit-and-fissure guideline that already was implemented well. To ensure a deliberation oriented towards resolving challenging aspects of the pit-and-fissure guideline, greater familiarity with the guideline would have been important, as well as more intimate knowledge of the current discrepancies in guideline-concordant care.Trial registration numberThis project is registered at ClinicalTrials.gov with IDNCT04682730. The trial was first registered on 18 December 2020.https://clinicaltrials.gov/ct2/show/NCT04682730.
Mental health awareness programmes to promote mental well-being at the workplace among workforce in the low-income and middle-income countries: a scoping review protocol
Authors: Luberenga Ibrahim , Kasujja Rosco , Vasanthan Lenny Thinagaran , Nyende Adam , Tumwebaze Eunice , Henry Joseph Leonard Joseph 
Published: July 2023

IntroductionAn understanding of the mental health awareness programmes among workforces in low/middle-income countries (LMICs) is lacking significantly in literature. Such understanding is crucial for the employers, government agencies and other stakeholders to initiate strategies to promote mental health and well-being at the workplace.ObjectiveThe main aim of this study is to conduct a scoping review to systematically map the research on the mental health awareness programmes among workforces in LMICs.MethodsA comprehensive search strategy for the articles published between 2000 and 2022 will be conducted in MEDLINE, PubMed, EBSCOhost, Wiley Online Library, Cochrane and JSTOR. Various study designs such as randomised control trials, non-randomised control trials, systematic reviews, scoping reviews and observational studies that report evidence on mental health awareness programmes among workforce in LMICs will be identified through specific strategy. Search outcomes will be exported to Endnote and duplication of studies will be removed. From the list of included studies, data such as characteristics of mental health programmes, common outcome measures and domains, and motivations underlying the establishment of existing mental health awareness programmes will be extracted and analysed.AnalysisThe search outcomes will be presented in a Preferred Reporting Items for Systematic Reviews and Meta-Analyses flow chart. The characteristics of the research studies on mental health programmes will be outlined using tables. The various outcome domains and outcome measures reported in the studies will be presented in a bubble chart showing different outcome measures categorised and collated under a specific outcome domain. The findings on the motivations and justifications underlying the establishment of mental health awareness programmes will be summarised using a thematic analysis.Trial registration numberhttps://doi.org/10.17605/OSF.IO/WPURK.
Community-based family peer navigator programme to facilitate linkage to coordinated specialty care for early psychosis among Black families in the USA: A protocol for a hybrid type I feasibility study
Authors: Oluwoye Oladunni , Stokes Bryony I , Burduli Ekaterina , Kriegel Liat S , Hoagwood Kimberly E 
Published: July 2023

BackgroundApproximately 70% of Black/African American family members report no contact with mental health providers prior to initial diagnosis and the receipt of services for early psychosis. Black families often encounter barriers and experience delays on the pathway to coordinated specialty care programmes for early psychosis.Methods and analysisThis mixed-methods study will (1) develop and refine a family peer navigator (FPN) for Black families designed to increase access and engagement in coordinated specialty care and (2) pilot-test FPN for Black families with 40 family members with loved ones at risk for psychosis in a randomised trial to assess the acceptability and feasibility. Families will be randomised to FPN (n=20) or a low-intensive care coordination (n=20). Other outcomes include proposed treatment targets (eg, knowledge, social connectedness), preliminary impact outcomes (time to coordinated specialty care programmes, initial family engagement), and implementation outcomes (acceptability, feasibility, appropriateness).Ethics and disseminationEthics approval has been obtained from Washington State University Institutional Review Board and informed consent will be obtained from all participants. This study will establish an innovative culturally responsive FPN programme and implementation strategy, and generate preliminary data to support a larger hybrid effectiveness-implementation trial. Study findings will be presented at conferences and in peer-reviewed journals.Trial registration numberNCT05284721.
Behavioural deficits of autism spectrum disorder and associations with different gene clusters: a study with the whole-genome transmission disequilibrium test
Authors: Guo Qi , Xia Lu , Guo Ruolan , Xu Wenjian , Zhang Yue , Zhao Chunlin , Zhang Peng , Bai Ting , Ni Xin , Hao Chanjuan , Xia Kun , Li Wei 
Published: July 2023

BackgroundAutism spectrum disorder (ASD) is a diverse neurodevelopmental disease primarily distinguished by limited and stereotyped activities as well as impaired social interaction. Due to the high heritability of ASD, research on the disorder has emphasised on identifying the underlying genetic and epigenetic aetiology. Many ASD loci have been identified by genome-wide association studies (GWASs). However, GWASs are more susceptible to bias due to population stratification. Moreover, GWASs barely reflect the genetic aetiology of subtypes of behavioural deficits.MethodsWe applied whole-genome transmission disequilibrium test (TDT) to reveal the gene sets that are significantly associated with the four behavioural subtypes of restricted repetitive behaviours in 334 ASD trios. We further mapped the clustered genes to pathways and enriched the SFARI genes in these pathways.ResultsFour unique gene clusters (181 genes in total) that are related to four different behavioural subtypes in ASD were identified. 23 SFARI genes were enriched in these four clusters. Through pathway analysis, nine non-SFARI genes (CNDP1, ETNK1,ITPKB,KCNQ5,PDE4D,PDGFRA,PPARGC1A,ULK2,SYNJ2) were found to be linked to the SFARI genes, which may contribute to the development of ASD. Furthermore, we found that the mTOR pathway enriched with theCNDP1, PDE4D,ULK2genes is associated with neurodevelopment.ConclusionsWhole-genome TDT test is a unique tool in clustering genes related to ASD subtypes of behavioural deficits. Several new candidate genes for ASD are revealed by pathway analysis of the clustered genes. These findings are useful for understanding the underlying mechanism of ASD.
Alcohol use and internal migration in Nepal: a cross-sectional study
Authors: Ghimire Dirgha J , Cole Faith , Hermosilla Sabrina , Axinn William G , Benjet Corina 
Published: July 2023

BackgroundAlcohol use is a leading cause of disease. Although low- and middle-income countries (LMICs) have lower per capita alcohol consumption, the alcohol-attributable disease burden is high in these settings with consumption increasing. LMICs are also experiencing unprecedented levels of internal migration, potentially increasing mental stress, changing social restrictions on drinking, and increasing alcohol availability. We assessed the relationship between internal migration, opportunity to drink, and the transition from first use to regular alcohol use and alcohol use disorders (AUD) in Nepal, a low-income, South Asian country.MethodsA representative sample of 7435 individuals, aged 15–59 from Nepal were interviewed in 2016–2018 (93% response rate) with clinically validated measures of alcohol use and disorders and life history calendar measures of lifetime migration experiences. Discrete-time hazard models assessed associations between migration and alcohol use outcomes.ResultsNet of individual sociodemographic characteristics, internal migration was associated with increased odds of opportunity to drink (OR 1.32, 95% CI 1.14 to 1.53), onset of regular alcohol use given lifetime use (OR 1.29, 95% CI 1.13 to 1.48) and AUD given lifetime use (OR 1.24, 95% CI 0.99 to 1.57). The statistically significant association between internal migration and opportunity to drink was specific to females, whereas the associations between migration and regular use and disorder were statistically significant for males.ConclusionsDespite high rates of internal migration worldwide, most research studying migration and alcohol use focuses on international migrants. Findings suggest that internal migrants are at increased risk to transition into alcohol use and disorders. Support services for internal migrants could prevent problematic alcohol use among this underserved population.
Method to share learning in real time at scientific meetings: lessons from the IHI-BMJ International Conference on Quality and Safety
Authors: Figueroa Johanna , McPherson Marianne E , Henriks Göran , Mountford James , Barker Pierre 
Published: July 2023

BackgroundCapturing and disseminating key learnings on emerging themes for conference participants is challenging, yet also presents a significant opportunity to distill, share and discuss learning in real time with conference organisers and attendees. The Institute for Healthcare Improvement (IHI) andBritish Medical Journal(BMJ) collaborate annually to convene a Health Quality and Safety conference attracting 1000 to 3000 attendees each year.AimTo test a learning system that harvested and synthesised the key lessons shared by conference participants at the 2022 IHI-BMJ Gothenburg Forum, and to disseminate this content.MethodsTwelve invited Forum attendees collected and shared their ‘breakthrough learnings’ via electronic survey. Three IHI team members synthesised the participants’ responses into themes that were shared and refined in real time at an in-person Forum session including 35 additional participants.ResultsParticipants shared four learning themes: collaboration and co-production, trust, meaningful communication about data, and broadening the scope of the Science of Improvement field to multi-disciplinary and multi-system approaches.ConclusionsCollection of key learning on emerging topics of interest to the health system improvement community is feasible and yielded information both for dissemination and real-time learning. While not representing the full scope of the conference learnings, the content resonated with an additional group of reviewers at the conclusion of the conference and has guided planning for the next annual meeting. This approach may be helpful in capturing key themes for discussion and planning by similar improvement communities.
Gravitational ringing and superradiant instabilities of the Kerr-like black holes in a dark matter halo
Authors: Liu Dong , Yang Yi , Övgün Ali , Long Zheng-Wen , Xu Zhaoyi 
Published: July 2023

AbstractSupermassive black holes from the center of galaxy may be immersed in a dark matter halo. This dark matter halo may form a “cusp” structure around the black hole and disappear at a certain distance from the black hole. Based on this interesting physical background, we use the continued fraction method to study gravitational ringring of the Kerr-like black holes immersed in a dark matter halo, i.e., quasinormal modes (QNM) and quasibound states (QBS). We consider these gravitational ringring of black holes both in cold dark matter (CDM) model and scalar field dark matter (SFDM) model at the LSB galaxy, and compare them with Kerr black hole. By testing the states of QNM/QBS frequencies with different parameters l, m, a, we confirm the existence of the superradiant instabilities when the black holes both in CDM model and SFDM model. Besides, we also study the impacts of dark matter parameters on the QNM/QBS of black holes at the specific circumstances. In the future, these results may be used for gravitational wave detection of supermassive black holes, and may provide an effective method for detecting the existence of dark matter.