bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated Hfq-interacting RNAome and transcriptomic analysis reveals complex regulatory networks of nitrogen fixation in root-associated
Pseudomonas stutzeri
A1501
Authors: Lv Fanyang , Zhan Yuhua , Feng Haichao , Sun Wenyue , Yin Changyan , Han Yueyue , Shao Yahui , Xue Wei , Jiang Shanshan , Ma Yiyuan , Hu Haonan , Wei Jinfeng , Yan Yongliang , Lin Min 
Published: May 2024

ABSTRACT

The RNA chaperone Hfq acts as a global regulator of numerous biological processes, such as carbon/nitrogen metabolism and environmental adaptation in plant-associated diazotrophs; however, its target RNAs and the mechanisms underlying nitrogen fixation remain largely unknown. Here, we used enhanced UV cross-linking immunoprecipitation coupled with high-throughput sequencing to identify hundreds of Hfq-binding RNAs probably involved in nitrogen fixation, carbon substrate utilization, biofilm formation, and other functions. Collectively, these processes endow strain A1501 with the requisite capabilities to thrive in the highly competitive rhizosphere. Our findings revealed a previously uncharted landscape of Hfq target genes. Notable among these is
nifM
, encoding an isomerase necessary for nitrogenase reductase solubility;
amtB
, encoding an ammonium transporter;
oprB
, encoding a carbohydrate porin; and
cheZ
, encoding a chemotaxis protein. Furthermore, we identified more than 100 genes of unknown function, which expands the potential direct regulatory targets of Hfq in diazotrophs. Our data showed that Hfq directly interacts with the mRNA of regulatory proteins (RsmA, AlgU, and NifA), regulatory ncRNA RsmY, and other potential targets, thus revealing the mechanistic links in nitrogen fixation and other metabolic pathways.

IMPORTANCE

Numerous experimental approaches often face challenges in distinguishing between direct and indirect effects of Hfq-mediated regulation. New technologies based on high-throughput sequencing are increasingly providing insight into the global regulation of Hfq in gene expression. Here, enhanced UV cross-linking immunoprecipitation coupled with high-throughput sequencing was employed to identify the Hfq-binding sites and potential targets in the root-associated
Pseudomonas stutzeri
A1501 and identify hundreds of novel Hfq-binding RNAs that are predicted to be involved in metabolism, environmental adaptation, and nitrogen fixation. In particular, we have shown Hfq interactions with various regulatory proteins’ mRNA and their potential targets at the posttranscriptional level. This study not only enhances our understanding of Hfq regulation but, importantly, also provides a framework for addressing integrated regulatory network underlying root-associated nitrogen fixation.
Gardnerella
diversity and ecology in pregnancy and preterm birth
Authors: Berman Hanna L. , Goltsman Daniela S. Aliaga , Anderson Megan , Relman David A. , Callahan Benjamin J. 
Published: May 2024

ABSTRACT

The vaginal microbiome has been linked to negative health outcomes including preterm birth. Specific taxa, including
Gardnerella
spp., have been identified as risk factors for these conditions. Historically, microbiome analysis methods have treated all
Gardnerella
spp. as one species, but the broad diversity of
Gardnerella
has become more apparent. We explore the diversity of
Gardnerella
clades and genomic species in the vaginal microbiome of pregnant women and their associations with microbiome composition and preterm birth. Relative abundance of
Gardnerella
clades and genomic species and other taxa was quantified in shotgun metagenomic sequencing data from three distinct cohorts of pregnant women. We also assessed the diversity and abundance of
Gardnerella
variants in 16S rRNA gene amplicon sequencing data from seven previously conducted studies in differing populations. Individual microbiomes often contained multiple
Gardnerella
variants, and the number of clades was associated with increased microbial load, or the ratio of non-human reads to human reads. Taxon co-occurrence patterns were largely consistent across
Gardnerella
clades and among cohorts. Some variants previously described as rare were prevalent in other cohorts, highlighting the importance of surveying a diverse set of populations to fully capture the diversity of
Gardnerella
. The diversity of
Gardnerella
both across populations and within individual vaginal microbiomes has long been unappreciated, as has been the intra-species diversity of many other members of the vaginal microbiome. The broad genomic diversity of
Gardnerella
has led to its reclassification as multiple species; here we demonstrate the diversity of
Gardnerella
found within and between vaginal microbiomes.

IMPORTANCE

The present study shows that single microbiomes can contain all currently known species of
Gardnerella
and that multiple similar species can exist within the same environment. Furthermore, surveys of demographically distinct populations suggest that some species appear more commonly in certain populations. Further studies in broad and diverse populations will be necessary to fully understand the ecological roles of each
Gardnerella
sp., how they can co-exist, and their distinct impacts on microbial communities, preterm birth, and other health outcomes.
Origin of the Site U1504 alkaline basalts in the South China Sea continental margin: Insights on deep mantle diversity and subduction dynamics under continental arcs
Authors: Sun Liheng , Zhang Yunying , Sun Zhen , Miao Xiuquan , Li Ruilong , Zhang Wanfeng 
Published: May 2024

Abstract
Alkaline basalts produced in continental arcs should contain information different from the arc tholeiite-calc-alkaline-series magmas, and their origin could provide unique constraints on deep mantle composition and material cycling. However, due to their sparse occurrence, alkaline basalts in continental arcs have not been studied thoroughly, which hinders our understanding of the mantle diversity and subduction dynamics under continental arcs. In this study, we present new 40Ar/39Ar ages, major and trace elements, and Sr-Nd-Hf isotopic data for the International Ocean Discovery Program Site U1504 alkaline basalts in the continental arc developed on the South China Block (SCB). These alkaline basalts were generated at ca. 121 Ma and display typical oceanic-island basalt geochemical characteristics. Their relatively high εNd(t) (3.5–3.7) and low (87Sr/86Sr)i (0.7034–0.7040) and La/Nb (0.5–1.0) values suggest that they were mainly derived from an asthenosphere mantle source. Compared to alkaline basalts in the SCB inland, U1504 alkaline basalts exhibit lower K2O/Na2O, Zr/Sm, Zr/Y, εNd(t), and εHf(t) values, indicating the addition of minor sub-continental lithospheric mantle. The enrichment of Nb, Ta, light rare earth elements, and slight depletion of Zr, Hf, and Ti, as well as elevated Fe/Mn and Sm/Yb and low CaO, indicate that their mantle lithology was mainly garnet pyroxenite. Based upon these findings and previous studies, the garnet pyroxenite was probably formed by the interaction of upwelling asthenosphere with slab edges in the scenario of break-off of the Paleo-Pacific Plate, and such interaction diversified the mantle chemistry beneath continental arcs. In conjunction with other reported alkaline basalt data, it is proposed that the enriched asthenosphere mantle beneath the SCB had formed sequentially from inland to coastal since the late Mesozoic, and this may be related to lateral and vertical flow in the deep asthenosphere controlled by the break-off of subducted plates.
Long-term healthcare utilisation, costs and quality of life after invasive group BStreptococcusdisease: a cohort study in five low-income and middle-income countries
Authors: Seedat Farah , Procter Simon R , Dangor Ziyaad , Leahy Shannon , Santhanam Sridhar , John Hima B , Bassat Quique , Aerts Celine , Abubakar Amina , Nasambu Carophine , Libster Romina , Yanotti Clara Sánchez , Paul Proma , Chanda Jaya , Gonçalves Bronner P , Horváth-Puhó Erzsébet , Lawn Joy E ,   the GBS Long-Term Outcomes LMIC Collaborative Group, Jit Mark 
Published: May 2024

IntroductionThere are no published data on the long-term impact of invasive group BStreptococcusdisease (iGBS) on economic costs or health-related quality of life (HRQoL) in low-income and middle-income countries. We assessed the impact of iGBS on healthcare utilisation, costs and HRQoL in Argentina, India, Kenya, Mozambique and South Africa.MethodsInpatient and outpatient visits, out-of-pocket (OOP) healthcare payments in the 12 months before study enrolment, and health-state utility of children and caregivers (using the EuroQol 5-Dimensions-3-Level) were collected from iGBS survivors and an unexposed cohort matched on site, age at recruitment and sex. We used logistic or Poisson regression for analysing healthcare utilisation and zero-inflated gamma regression models for family and health system costs. For HRQoL, we used a zero-inflated beta model of disutility pooled data.Results161 iGBS-exposed and 439 unexposed children and young adults (age 1–20) were included in the analysis. Compared with unexposed participants, iGBS was associated with increased odds of any healthcare utilisation in India (adjusted OR 11.2, 95% CI 2.9 to 43.1) and Mozambique (6.8, 95% CI 2.2 to 21.1) and more frequent healthcare visits (adjusted incidence rate ratio (IRR) for India 1.7 (95% CI 1.4 to 2.2) and for Mozambique 6.0 (95% CI 3.2 to 11.2)). iGBS was also associated with more frequent days in inpatient care in India (adjusted IRR 4.0 (95% CI 2.3 to 6.8) and Kenya 6.4 (95% CI 2.9 to 14.3)). OOP payments were higher in the iGBS cohort in India (adjusted mean: Int$682.22 (95% CI Int$364.28 to Int$1000.16) vs Int$133.95 (95% CI Int$72.83 to Int$195.06)) and Argentina (Int$244.86 (95% CI Int$47.38 to Int$442.33) vs Int$52.38 (95% CI Int$−1.39 to Int$106.1)). For all remaining sites, differences were in the same direction but not statistically significant for almost all outcomes. Health-state disutility was higher in iGBS survivors (0.08, 0.04–0.13 vs 0.06, 0.02–0.10).ConclusionThe iGBS health and economic burden may persist for years after acute disease. Larger studies are needed for more robust estimates to inform the cost-effectiveness of iGBS prevention.
Improving the impact of clinical documentation through patient-driven co-design: experiences with cancer pathology reports
Authors: Austin Elizabeth J , Lee Jenney R , Ko Cynthia W , Kilgore Mark R , Parker Elizabeth U , Bergstedt Brandelyn , Mitchell Anita I , Javid Sara H , Gore John L 
Published: May 2024

ObjectiveWith the unprecedented rise of patient access to clinical documentation through electronic health records, there is a need for health systems to understand best practices for redesigning clinical documentation to support patient needs. This study used an experience-based co-design approach to inform the redesign of cancer pathology reports to improve their patient-centeredness and impact on patient engagement.Materials and methodsMultiple methods for data collection and stakeholder engagement were used, including Delphi prioritisation with breast and colorectal cancer experts (n=78) and focus groups with patients with cancer (n=23) in the Seattle area. Iterative rounds of consensus generation and reflection were used to elicit themes and design recommendations for the development of patient-centred pathology reports on cancer care.ResultsAlthough each cancer type had nuanced elements to consider, common design requirements emerged around two key themes: (1) clinical documentation language should be framed in a way that informs and engages patients, and (2) clinical documentation format should be leveraged to enhance readability and information flow. Study activities illuminated detailed recommendations to improve the patient-centeredness of pathology reports based on patients’ and clinicians’ lived experience.DiscussionThe design requirements that emerged from this study provide a framework that can guide the rapid development of patient-centred pathology reports for all cancer types. Even further, health systems can replicate these methods to guide experience-based co-design of clinical documentation for contexts beyond cancer care.ConclusionThis work offers practice-based learnings that can more effectively guide health systems in their clinical documentation redesign efforts.
Educational attainment, severity and short-term prognosis of intracerebral haemorrhage
Authors: Yechoor Nirupama , Rist Pamela , Ganbold Alena , Kourkoulis Christina , Mora Samantha , Mayerhofer Ernst , Parodi Livia , Rosenfeld Lindsay , Anderson Christopher D , Rosand Jonathan 
Published: May 2024

BackgroundEducational attainment is a critical social determinant of health that impacts the risk and severity of incident ischaemic stroke, but less is known of its impact on intracerebral haemorrhage (ICH). The objective of this study is to determine whether educational attainment is associated with ICH severity and short-term prognosis.MethodsSubjects were enrolled in a prospectively ascertained cohort with primary ICH from 1994 to 2020 at Massachusetts General Hospital. Educational attainment, medical history of ICH risk factors, ICH volume and ICH score were obtained on admission. The primary outcomes were ICH volume and the ICH score.ResultsOf 2539 eligible patients eligible, the median age of the sample was 74 (IQR 64–82) and 2159 (85%) had high school-only education. 1655 (65%) presented with an ICH volume less than or equal to 30 mL and 1744 (69%) presented with an ICH score less than 3. In multivariable logistic regression analyses controlling for age, income, employment history and prestroke diagnoses of hypertension and coronary artery disease, patients with high school-only education were more likely to have an ICH volume greater than 30 mL compared with college diplomates (OR 1.58, 95% CI 1.24 to 2.08) and more likely to have an ICH score of 3 or greater compared with college diplomates (OR 2.37, 95% CI 1.77 to 3.19).DiscussionPrestroke educational attainment is independently associated with ICH severity and short-term prognosis, with lower educational attainment associated with larger ICH volumes and higher ICH scores. Future studies should examine how educational attainment impacts exposure to traditional clinical risk factors.
Population-based assessment of prevalence and causes of visual impairment in the state of Telangana, India: a cross-sectional study using the Rapid Assessment of Visual Impairment (RAVI) methodology
Authors: Marmamula Srinivas , Khanna Rohit C , Kunkunu Eswararao , Rao Gullapalli N 
Published: May 2024

ObjectiveTo assess the prevalence and causes of visual impairment (VI) among a rural population aged 40 years and older in the state of Telangana in India.DesignPopulation-based cross-sectional study.SettingDistricts of Adilabad and Mahbubnagar in south Indian state of Telangana, India.ParticipantsA sample of 6150 people was selected using cluster random sampling methodology. A team comprising a trained vision technician and a field worker visited the households and conducted the eye examination. Presenting, pinhole and aided visual acuity were assessed. Anterior segment was examined using a torchlight. Lens was examined using distant direct ophthalmoscopy in a semidark room. In all, 5881 (95.6%) participants were examined from 123 study clusters. Among those examined, 2723 (46.3%) were men, 4824 (82%) had no education, 2974 (50.6%) were from Adilabad district and 1694 (28.8%) of them were using spectacles at the time of eye examination.Primary outcome measureVI was defined as presenting visual acuity <6/18 in the better eye and it included moderate VI (<6/18 to 6/60) and blindness (<6/60).ResultsThe age-adjusted and gender-adjusted prevalence of VI was 15.0% (95% CI 14.1% to 15.9%). On applying binary logistic regression analysis, VI was associated with older age groups. The odds of having VI were higher among women (OR 1.2; 95% CI 1.0 to 1.4). Having any education (OR 0.4; 95% CI 0.3 to 0.6) and current use of glasses (OR 0.19; 95% CI 0.1 to 0.2) were protective. VI was also higher in Mahbubnagar (OR 1.0 to 1.5) district. Cataract (54.7%) was the leading cause of VI followed by uncorrected refractive errors (38.6%).ConclusionsVI continues to remain a challenge in rural Telangana. As over 90% of the VI is avoidable, massive eye care programmes are required to address the burden of VI in Telangana.
Effectiveness of the HuCare Quality Improvement Strategy on health-related quality of life in patients with cancer: study protocol of a stepped-wedge cluster randomised controlled trial (HuCare2 study)
Authors: Caminiti Caterina , Iezzi Elisa , Passalacqua Rodolfo 
Published: May 2024

IntroductionOur group previously demonstrated the feasibility of the HuCare Quality Improvement Strategy (HQIS), aimed at integrating into practice six psychosocial interventions recommended by international guidelines. This trial will assess whether the introduction of the strategy in oncology wards improves patient’s health-related quality of life (HRQoL).Methods and analysisMulticentre, incomplete stepped-wedge cluster randomised controlled trial, conducted in three clusters of five centres each, in three equally spaced time epochs. The study also includes an initial epoch when none of the centres are exposed to the intervention, and a final epoch when all centres will have implemented the strategy. The intervention is applied at a cluster level, and assessed at an individual level with cross-sectional model. A total of 720 patients who received a cancer diagnosis in the previous 2 months and about to start medical treatment will be enrolled. The primary aim is to evaluate the effectiveness of the HQIS versus standard care in terms of improvement of at least one of two domains (emotional and social functions) of HRQoL using the EORTC QLQ-C30 (European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire-Core 30 items) questionnaire, at baseline and at 3 months. This outcome was chosen because patients with cancer generally exhibit low HRQoL, particularly at certain stages of care, and because it allows to assess the strategy’s impact as perceived by patients themselves. The HQIS comprises three phases: (1) clinician training—to improve communication-relational skills and instruct on the project; (2) centre support—four on-site visits by experts of the project team, aimed to boost motivation, help with context analysis and identification of solutions; (3) implementation of Evidence-Based Medicine (EBM) recommendations at the centre.Ethics and disseminationEthics committee review approval has been obtained from the Ethics Committee of Parma. Results will be disseminated at conferences, and in peer-reviewed and professional journals intended for policymakers and managers.Trial registration numberNCT03008993; Pre-results.
Study protocol for a randomised controlled trial of ultrasound-guided pulsed radiofrequency of the genicular nerves in the treatment of patients with osteoarthritis knee pain
Authors: Mata Javier , Valentí Pedro , Hernández Beatriz , Mir Bartolome , Aguilar Jose Luis 
Published: May 2024

IntroductionThe goals for the management of patients with osteoarthritis (OA) of the knee are to control pain and to minimise disability. Because the number of patients will increase as the population ages, alternative approaches to alleviate their joint pain other than conventional treatments are necessary. The purpose of this article is to present a refined protocol to determine if there is long-term improvement in pain and function after ultrasound-guided pulsed radiofrequency treatment of the genicular nerves (GNs) in patients with chronic painful knee OA.Methods and analysisThis study is a randomised, double-blind, placebo-controlled, parallel design trial. One hundred and forty-two outpatients with OA of the knee will be recruited from Mallorca, Spain. Participants will be randomly allocated into two groups: ultrasound-guided sham GN pulsed radiofrequency without active treatment and ultrasound-guided real GN pulsed radiofrequency. The primary outcome measures will be the observed changes from baseline pain intensity based on visual analogue scale (VAS). The possible changes in the secondary efficacy variables from the baseline as assessed by the Goldberg Anxiety and Depression Scale, pain medication use, Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC subscales) and VAS pain intensity are also to be included in the study. These variables will be assessed at baseline, 1 month, 3 months, 6 months and 1 year after treatment.Ethics and disseminationThe protocol was approved by the Research Ethic Committee of the Balearic Islands (IB 3223/16 PI). The results will be disseminated in peer-reviewed journals and at scientific conferences.Trial registrationTrial registration numberNCT02915120; Pre-results
Study protocol for statin web-based investigation of side effects (StatinWISE): a series of randomised controlled N-of-1 trials comparing atorvastatin and placebo in UK primary care
Authors: Herrett Emily , Williamson Elizabeth , Beaumont Danielle , Prowse Danielle , Youssouf Nabila , Brack Kieran , Armitage Jane , Goldacre Ben , MacDonald Thomas , Staa Tjeerd van , Roberts Ian , Shakur-Still Haleema , Smeeth Liam 
Published: May 2024

IntroductionStatins are effective at preventing cardiovascular disease, widely prescribed and their use is growing. Uncertainty persists about whether they cause symptomatic muscle adverse effects, such as pain and weakness, in the absence of statin myopathy. Discrepancies between data from observational studies, which suggest statins are associated with excess muscle symptoms, and from randomised trials, which suggest no such excess, have caused confusion. N-of-1 trials offer the opportunity to establish whether muscle symptoms during statin use are caused by statins in particular individuals.Methods and analysisThis series of 200 randomised, double-blinded N-of-1 trials in primary care will determine (1) the effect of statins on all muscle symptoms and (2) the effect of statins on muscle pain that is perceived to be statin related. Patients who are considering discontinuing statin use due to muscle symptoms and those who have discontinued in the last 3 years due to such symptoms will be recruited. Participants will be randomised to a sequence of six 2-month treatment periods during which they will receive atorvastatin 20 mg per day or matched placebo. On each of the last 7 days of each treatment period, participants will rate their muscle symptoms on a Visual Analogue Scale (VAS).At the end of their trial, participants will be shown numerical and graphical summaries of their own symptom data during statin and placebo periods. The primary analysis on the aggregate data from all participants will be a linear mixed model for VAS muscle symptom score, comparing scores during treatment with statin and placebo.Ethics and disseminationThis trial received a favourable opinion from South Central-Hampshire A Research Ethics Committee. Results will be published in a peer-reviewed medical journal. Dissemination of results to patients will take place via the media, website (statinwise.lshtm.ac.uk) and patient organisations.Trial registration numberISRCTN30952488.