bluuebunny/crossref_metadata_2025_split huggingface dataset:
An integrated strain-level analytic pipeline utilizing longitudinal metagenomic data
Authors: Zhou Boyan , Wang Chan , Putzel Gregory , Hu Jiyuan , Liu Menghan , Wu Fen , Chen Yu , Pironti Alejandro , Li Huilin 
Published: September 2024

ABSTRACT

With the development of sequencing technology and analytic tools, studying within-species variations enhances the understanding of microbial biological processes. Nevertheless, most existing methods designed for strain-level analysis lack the capability to concurrently assess both strain proportions and genome-wide single nucleotide variants (SNVs) across longitudinal metagenomic samples. In this study, we introduce LongStrain, an integrated pipeline for the analysis of large-scale metagenomic data from individuals with longitudinal or repeated samples. In LongStrain, we first utilize two efficient tools, Kraken2 and Bowtie2, for the taxonomic classification and alignment of sequencing reads, respectively. Subsequently, we propose to jointly model strain proportions and shared haplotypes across samples within individuals. This approach specifically targets tracking a primary strain and a secondary strain for each subject, providing their respective proportions and SNVs as output. With extensive simulation studies of a microbial community and single species, our results demonstrate that LongStrain is superior to two genotyping methods and two deconvolution methods across a majority of scenarios. Furthermore, we illustrate the potential applications of LongStrain in the real data analysis of The Environmental Determinants of Diabetes in the Young study and a gastric intestinal metaplasia microbiome study. In summary, the proposed analytic pipeline demonstrates marked statistical efficiency over the same type of methods and has great potential in understanding the genomic variants and dynamic changes at strain level. LongStrain and its tutorial are freely available online at
https://github.com/BoyanZhou/LongStrain
.

IMPORTANCE
The advancement in DNA-sequencing technology has enabled the high-resolution identification of microorganisms in microbial communities. Since different microbial strains within species may contain extreme phenotypic variability (e.g., nutrition metabolism, antibiotic resistance, and pathogen virulence), investigating within-species variations holds great scientific promise in understanding the underlying mechanism of microbial biological processes. To fully utilize the shared genomic variants across longitudinal metagenomics samples collected in microbiome studies, we develop an integrated analytic pipeline (LongStrain) for longitudinal metagenomics data. It concurrently leverages the information on proportions of mapped reads for individual strains and genome-wide SNVs to enhance the efficiency and accuracy of strain identification. Our method helps to understand strains’ dynamic changes and their association with genome-wide variants. Given the fast-growing longitudinal studies of microbial communities, LongStrain which streamlines analyses of large-scale raw sequencing data should be of great value in microbiome research communities.
Heterogeneous effects of Medicaid coverage on cardiovascular risk factors: secondary analysis of randomized controlled trial
Authors: Inoue Kosuke , Athey Susan , Baicker Katherine , Tsugawa Yusuke 
Published: September 2024

Abstract

Objectives

To investigate whether health insurance generated improvements in cardiovascular risk factors (blood pressure and hemoglobin A
1c
(HbA
1c
) levels) for identifiable subpopulations, and using machine learning to identify characteristics of people predicted to benefit highly.

Design
Secondary analysis of randomized controlled trial.

Setting
Medicaid insurance coverage in 2008 for adults on low incomes (defined as lower than the federal-defined poverty line) in Oregon who were uninsured.

Participants
12 134 participants from the Oregon Health Insurance Experiment with in-person data for health outcomes for both treatment and control groups.

Interventions
Health insurance (Medicaid) coverage.

Main outcomes measures

The conditional local average treatment effects of Medicaid coverage on systolic blood pressure and HbA
1c
using a machine learning causal forest algorithm (with instrumental variables). Characteristics of individuals with positive predicted benefits of Medicaid coverage based on the algorithm were compared with the characteristics of others. The effect of Medicaid coverage was calculated on blood pressure and HbA
1c
among individuals with high predicted benefits.

Results

In the in-person interview survey, mean systolic blood pressure was 119 (standard deviation 17) mm Hg and mean HbA
1c
concentrations was 5.3% (standard deviation 0.6%). Our causal forest model showed heterogeneity in the effect of Medicaid coverage on systolic blood pressure and HbA
1c
. Individuals with lower baseline healthcare charges, for example, had higher predicted benefits from gaining Medicaid coverage. Medicaid coverage significantly lowered systolic blood pressure (−4.96 mm Hg (95% confidence interval −7.80 to −2.48)) for people predicted to benefit highly. HbA
1c
was also significantly reduced by Medicaid coverage for people with high predicted benefits, but the size was not clinically meaningful (−0.12% (−0.25% to −0.01%)).

Conclusions
Although Medicaid coverage did not improve cardiovascular risk factors on average, substantial heterogeneity was noted in the effects within that population. Individuals with high predicted benefits were more likely to have no or low prior healthcare charges, for example. Our findings suggest that Medicaid coverage leads to improved cardiovascular risk factors for some, particularly for blood pressure, although those benefits may be diluted by individuals who did not experience benefits.
Public attitudes to emergency care treatment plans: a population survey of Great Britain
Authors: Underwood Martin , Noufaily Angela , Bain Chris , Harlock Jenny , Griffiths Frances , Huxley Caroline , Perkins Gavin , Rees Sophie , Slowther Anne-Marie 
Published: September 2024

ObjectivesTo measure community attitudes to emergency care and treatment plans (ECTPs).DesignPopulation survey.SettingGreat Britain.ParticipantsAs part of the British Social Attitudes Survey, sent to randomly selected addresses in Great Britain, 1135 adults completed a module on ECTPs. The sample was nationally representative in terms of age and location, 619 (55%) were female and 1005 (89%) were of white origin.Outcome measuresPeople’s attitudes having an ECTP for themselves now, and in the future; how comfortable they might be having a discussion about an ECTP and how they thought such a plan might impact on their future care.ResultsPredominantly, respondents were in favour of people being able to have an ECTP, with 908/1135 (80%) being at least somewhat in favour. People in good health were less likely than those with activity-limiting chronic disease to want a plan at present (52% vs 64%, OR 1.78 (95% CI 1.30 to 2.45) p<0.001). Developing a long-term condition or becoming disabled would lead 42% (467/1112) and 43% (481/1112) of individuals, respectively, to want an ECTP. More, 634/1112 (57%) would want an ECTP if they developed a life-threatening condition. Predominantly, 938/1135 (83%) respondents agreed that an ECTP would help avoid their family needing to make difficult decisions on their behalf, and 939/1135 (83%) that it would ensure doctors and nurses knew their wishes. Nevertheless, a small majority—628/1135 (55%)—agreed that there was a serious risk of the plan being out of date when needed. A substantial minority—330/1135 (29%)—agreed that an ECTP might result in them not receiving life-saving treatment.ConclusionsThere is general support for the use of ECTPs by people of all ages. Nevertheless, many respondents felt these might be out of date when needed and prevent people receiving life-saving treatment.
Mapping resilience: a scoping review on mediators and moderators of childhood adversity with a focus on gender patterns
Authors: Bornscheuer Lisa , Gauffin Karl , Almquist Ylva B 
Published: September 2024

BackgroundChildhood adversity is associated with a host of negative health and socioeconomic outcomes far into adulthood. The process of avoiding such outcomes is often referred to as resilience. Mapping resilience comprehensively and across contexts is highly relevant to public health, as it is a step towards understanding environments and interventions that contribute to preventing or reversing negative outcomes after early adverse experiences.ObjectivesThis review scoped out the literature on resilience factors in relation to adulthood outcomes as diverse as mental health and educational attainment. Our aim was to understand where there is untapped research potential, by examining the current evidence base on resilience factors in terms of (a) resources that can buffer the impact of childhood adversity and (b) the pathways linking adversity to long-term outcomes. Furthermore, we aimed to identify gender patterns in these resources and pathways, which has not been a primary interest of reviews on resilience to date, and which can add to our understanding of the different ways in which resilience may unfold.Eligibility criteriaStudies had to include an adversity experienced in childhood, an outcome considered indicative of resilience in adulthood, and at least one putative resilience factor, which had to be approached via mediation or moderation analysis. We considered cohort, case–control and cross-sectional studies.Sources of evidenceWe searched PubMed, Scopus and PsycINFO and included original, peer-reviewed articles published before 20 July 2023 in English, German, French, Spanish, Dutch and Swedish.Charting methodsAll three authors collaborated on the extraction of information relevant to answering the research questions. The results were visually and narratively summarised.ResultsWe included 102 studies. Traditionally anchored in the field of psychology, the resilience literature focuses heavily on individual-level resilience factors. Gender was considered in approximately 22% of included studies and was always limited to comparisons between men and women. There is no evidence that childhood adversity impacts men and women differently in the long term, but there is some evidence for gender differences in resilience factors.ConclusionsThere is untapped potential in resilience research. By considering structural-level factors simultaneously with individual-level factors, and including gender as one of the elements that shape resilience, we can map resilience as a heterogeneous, multilevel process from a public health perspective. This would complement the extensive existing literature on individual-level factors and help reframe resilience as a concept that can be intervened on at a structural level, and that is subject to societal norms and forces, such as gender. There is a lack of quantitative studies including transgender and gender-non-conforming persons.
Accessibility of TB diagnostic services at primary healthcare clinics in the eThekwini district, South Africa: a geospatial analysis
Authors: Dlangalala Thobeka , Musekiwa Alfred , Mckelly David , Baloyi Ethel , Mashamba-Thompson Tivani Phosa 
Published: September 2024

BackgroundImproving geographic access can aid in managing tuberculosis (TB) by enabling early diagnosis and treatment initiation. Although geospatial techniques have been used to map the transmission patterns of drug-resistant TB in South Africa, fewer studies have investigated the accessibility of TB diagnostic services. This study evaluated the accessibility of TB diagnostic services and disease distribution in the eThekwini district of South Africa.MethodsIn this cross-sectional study, population data for 2021 were disaggregated into smaller analysis units and then re-aggregated through the dasymetric mapping technique. Data on notified TB patients, including Global Positioning System coordinates of clinics, were obtained from the District of Health Information System, exported to ArcGIS 10.8.2 and used to calculate distances to the nearest clinics and hospitals.Results92% of the population (3 730 494 people) in eThekwini could access TB diagnostic services within 5 km. Patients travelled an average distance of 4.7 km (range: 0.1–26.9 km). TB diagnostic services were highly accessible in the Northern and Central regions and moderately accessible in the predominately rural Western and Southern regions. The smallest population of eThekwini resides in rural areas; however, 40.7% of its residents live >5 km from a diagnosing facility, with patients in the South having to travel up to 44.5 km. TB incidence was higher in the predominately rural West and South regions compared with the Central and North regions which are mainly comprised of urban and suburban areas. Our findings also showed that 98.4% of the clinics in eThekwini were located within 30 km of a hospital at an average distance of 9.6 km within the district. However, the distribution of these hospitals does not demonstrate equitable access as the majority are located within the Central region, and fewer are found in the other three regions of eThekwini.ConclusionsAddressing the disparities in access to TB diagnostic services is required in the eThekwini district. Leveraging the existing mobile health clinics can assist with this, particularly, in rural areas with inadequate access. Additionally, active-case finding should be intensified in these regions since they had a higher TB burden per population. Prioritising interventions in these areas is crucial for reducing the impact of the disease on affected communities.
Hostel support workers’ experiences navigating healthcare alongside people experiencing homelessness: a qualitative study in the UK
Authors: Muzafar Iman , Cunningham Oliver 
Published: September 2024

ObjectivesThis study aimed to explore how hostel support workers (HSWs) experience navigating healthcare alongside people experiencing homelessness (PEH). PEH experience poor health outcomes, increased mortality and face many barriers when accessing healthcare. HSWs have a dynamic and holistic role, working with PEH to navigate access to health and social care, whilst facilitating independence. HSWs have been described as important in addressing barriers to access and linking healthcare and PEH. However, HSWs’ experiences navigating this role across sectors remains underexplored.DesignIn this qualitative study, semistructured interviews were conducted, and phenomenological thematic analysis was performed.SettingInterviews were conducted with participants from 13 hostels across four UK counties.Participants17 HSWs were interviewed, with experience in their role ranging from 3 months to over 10 years.ResultsThree themes were identified.HSWs feeling stigmatised by healthcare staff (HCS), including power inequalities between HSWs and HCS, and the impact of stigma against PEH in healthcare on HSWs.Working across sectors, including both collaborative and disconnected experiences.In-reach and its role in linking PEH and healthcare. This included the contrasting subthemes of in-reach as an effective link versus in-reach being an impractical and unsustainable solution.ConclusionsCross-sector collaboration has been recognised as an effective way to increase healthcare access and improve outcomes for Inclusion Health Groups, including PEH. This has been further highlighted by the formation of Integrated Care Systems, which strive to bring sectors together to tackle inequalities in outcomes, experience and access. Collaborative relationships between sectors, that is, hostels and healthcare, are vital for increasing healthcare access for PEH. We explored the experiences of HSWs navigating healthcare access for this marginalised population. Recognising and understanding these experiences are the first steps in building collaborative cross-sector relationships to improve healthcare accessibility, experiences and outcomes for PEH.
Cohort profile: the Swiss Mother and Child HIV Cohort Study (MoCHiV)
Authors: Paioni Paolo , Capaul Murezi , Brunner Anja , Traytel Anna , Aebi-Popp Karoline , Crisinel Pierre-Alex , Duppenthaler Andrea , Günthard Huldrych , Martinez De Tejada Begona , Kottanattu Lisa , Stöckle Marcel , Rauch Andri , Wagner Noemie , Hösli Irene , Rudin Christoph , Scherrer Alexandra , Kusejko Katharina , Kahlert Christian R 
Published: September 2024

PurposeProspective, multicentric observational cohort study in Switzerland investigating measures to prevent mother-to-child transmission in pregnant women with HIV (WWH) and assessing health and development of their exposed children as well as of children with HIV (CWH) in general.ParticipantsBetween January 1986 and December 2022, a total of 1446 mother–child pairs were enrolled. During the same period, the study also registered 187 CWH and 521 HIV-exposed but uninfected children (HEU), for whom detailed maternal information was not available. Consequently, the cohort comprises a total of 2154 children.Findings to dateDuring these 37 years, research by the Swiss Mother and Child HIV Cohort Study (MoCHiV) and its international collaborators has strongly influenced the prevention of vertical transmission of HIV (eg, introduction and discontinuation of elective caesarean section, neonatal postexposure prophylaxis and breastfeeding). Contributions have also been made to the management of diagnostics (eg, p24 antigen assay) and the effects of antiretroviral treatment (eg, prematurity, growth) in HEU and CWH.Future plansMost children present within the cohort are now HEU, highlighting the need to investigate other vertically transmitted pathogens such as hepatitis B and C viruses, cytomegalovirus orTreponema pallidum. In addition, analyses are planned on the longitudinal health status of CWH (eg, resistance and prolonged exposure to antiretroviral therapy), on social aspects including stigma in CWH and HEU, and on interventions to further optimise antenatal and postpartum care in WWH.
Acustimulation combined with pharmacological prophylaxis versus pharmacological prophylaxis alone in postoperative nausea and vomiting (PONV) prophylaxis among patients undergoing laparoscopy abdominal surgery: a research protocol for a randomised controlled trial
Authors: Chen Junjie , Che Lu , Cui Quexuan , Lang Jiaxin , Zhang Yuelun , Zhu Bo , Huang Yuguang 
Published: September 2024

IntroductionThis study evaluates the efficacy of integrating percutaneous electrical nerve stimulation at the pericardium 6 (PC6) acupuncture point through a wearable acustimulation device with standard pharmacological prophylaxis to prevent postoperative nausea and vomiting (PONV) compared with pharmacological prophylaxis alone in patients undergoing laparoscopic abdominal surgery.Method and analysisThis prospective study will enrol 302 patients scheduled for elective laparoscopic surgery. Participants will be randomly allocated to one of two groups: acustimulation combined with pharmacological prophylaxis or sham stimulation combined with pharmacological prophylaxis. Randomisation will involve a computer-generated sequence, with allocation concealment implemented through sealed envelopes. The acustimulation group will receive electrical stimulation at the PC6 point starting 30 min before surgery and continuing until discharge from the postanaesthesia care unit. Sham group will wear a wristband that does not provide stimulation. The primary outcome is the incidence of PONV. Secondary outcomes include the severity of PONV, incidence rates of nausea and vomiting at different postoperative intervals and indices of gastrointestinal functional recovery. Exploratory outcomes will assess haemodynamic parameters, baroreflex sensitivity, hospital stay duration, costs and both short-term and long-term postoperative recovery.Ethics and disseminationAll participants will provide written informed consent. The study has been approved by the Ethics Committee of Peking Union Medical Hospital (approval number: I-23PJ1712). Results will be published open access.Trial registration numberNCT06241547.
Frailty is independently associated with subclinical cardiovascular disease in patients with systemic lupus erythematosus
Authors: Pappa Maria , Keramiotou Kyriaki , Sfikakis Petros P , Tektonidou Maria G 
Published: September 2024

ObjectivesCardiovascular disease is a leading cause of mortality in systemic lupus erythematosus (SLE). Frailty has been associated with an increased cardiovascular disease risk (CVR) in the general population. We aimed to examine the association between frailty and subclinical cardiovascular disease in patients with SLE.MethodsIn this cross-sectional study, we included all patients with SLE who underwent carotid/femoral artery ultrasound in our unit between 2016 and 2018. Clinical and laboratory data were collected at the time of ultrasound testing. Frailty was measured using the Systemic Lupus International Collaborating Clinics-Frailty Index (SLICC-FI). CVR (low, moderate, high, very high) was evaluated by the Systematic COronary Risk Evaluation (SCORE) model. Determinants of atherosclerotic plaque presence were assessed by logistic regression analyses, adjusting for potential confounders.Results202 patients were included in the study. Atherosclerotic plaques (20.8% carotid, 17.3% femoral) were observed in 52/202 (25.7%) patients (89.1% women, mean (±SD) age 46.7±12.6). Median (IQR) SLICC-FI was 0.08 (0.04–0.10). 39 (19.3%) patients were classified as robust, 91 (45%) as relatively less fit, 59 (29.2%) as least fit and 13 (6.4%) as frail. In univariate analysis, plaque presence was significantly associated with age, disease duration, smoking, hypertension, systolic blood pressure, dyslipidaemia, SCORE, CVR class and SLICC-FI. CVR class (OR 5.16, p=0.000) and SLICC-FI (OR 1.34, p=0.03 per 0.05 point increase) remained significant in multivariate analysis after adjustment for traditional and disease-related CVR factors.ConclusionsSLICC-FI is independently associated with plaque presence. Further studies are warranted to determine whether frailty-specific interventions can reduce CVR in patients with SLE.