bluuebunny/crossref_metadata_2025_split huggingface dataset:
The phage shock protein (PSP) envelope stress response: discovery of novel partners and evolutionary history
Authors: Ravi Janani , Anantharaman Vivek , Chen Samuel Zorn , Brenner Evan Pierce , Datta Pratik , Aravind L. , Gennaro Maria Laura 
Published: May 2024

ABSTRACTBacterial phage shock protein (PSP) systems stabilize the bacterial cell membrane and protect against envelope stress. These systems have been associated with virulence, but despite their critical roles, PSP components are not well characterized outside proteobacteria. Using comparative genomics and protein sequence-structure-function analyses, we systematically identified and analyzed PSP homologs, phyletic patterns, domain architectures, and gene neighborhoods. This approach underscored the evolutionary significance of the system, revealing that its core protein PspA (Snf7 in ESCRT outside bacteria) was present in the last universal common ancestor and that this ancestral functionality has since diversified into multiple novel, distinct PSP systems across life. Several novel partners of the PSP system were identified: (i) the Toastrack domain, likely facilitating assembly of sub-membrane stress-sensing and signaling complexes, (ii) the newly defined HTH-associated α-helical signaling domain-PadR-like transcriptional regulator pair system, and (iii) multiple independent associations with ATPase, CesT/Tir-like chaperone, and Band-7 domains in proteins thought to mediate sub-membrane dynamics. Our work also uncovered links between the PSP components and other domains, such as novel variants of SHOCT-like domains, suggesting roles in assembling membrane-associated complexes of proteins with disparate biochemical functions. Results are available at our interactive web app,https://jravilab.org/psp.IMPORTANCEPhage shock proteins (PSP) are virulence-associated, cell membrane stress-protective systems. They have mostly been characterized in Proteobacteria and Firmicutes. We now show that a minimal PSP system was present in the last universal common ancestor that evolved and diversified into newly identified functional contexts. Recognizing the conservation and evolution of PSP systems across bacterial phyla contributes to our understanding of stress response mechanisms in prokaryotes. Moreover, the newly discovered PSP modularity will likely prompt new studies of lineage-specific cell envelope structures, lifestyles, and adaptation mechanisms. Finally, our results validate the use of domain architecture and genetic context for discovery in comparative genomics.
The usefulness of nanopore sequencing in whole-genome sequencing-based genotyping of
Listeria monocytogenes
and
Salmonella enterica
serovar Enteritidis
Authors: Hong Yu-Ping , Chen Bo-Han , Wang You-Wun , Teng Ru-Hsiou , Wei Hsiao-Lun , Chiou Chien-Shun 
Published: May 2024

ABSTRACT

Bacterial genotyping through whole-genome sequencing plays a crucial role in disease surveillance and outbreak investigations in public health laboratories. This study assessed the effectiveness of Oxford Nanopore Technologies (ONT) sequencing in the genotyping of
Listeria monocytogenes
and
Salmonella enterica
serovar Enteritidis. Our results indicated that ONT sequences, generated with the R10.4.1 flow cell and basecalled using the Dorado 0.5.0 Super Accurate 4.3 model, exhibited comparable accuracy to Illumina sequences, effectively discriminating among bacterial strains from outbreaks. These findings suggest that ONT sequencing has the potential to be a promising tool for rapid whole-genome sequencing of bacterial pathogens in public health laboratories for epidemiological investigations.

IMPORTANCE
This study unveils that Oxford Nanopore Technologies sequencing, by itself, holds the potential to serve as a whole-genome sequencing-based genotyping tool in public health laboratories, enabling routine subtyping of bacterial isolates for disease surveillance and outbreak investigations
How Mentors and the State Made a Blind Scientist
Authors: Vermeij Geerat J. 
Published: May 2024

ABSTRACT
As a blind paleobiologist and evolutionary biologist, I have been fortunate to have had highly supportive parents, teachers, and colleagues, whose qualities and insights I discuss. Curiosity, hard work, a willingness to take risks, and a keen ability to observe and to ask questions are critical attributes.
Treating benign paroxysmal positional vertigo in acute traumatic brain injury: a prospective, randomised clinical trial assessing safety, feasibility, and efficacy
Authors: Smith Rebecca M , Burgess Caroline , Beattie Jenna , Newdick Abby , Tahtis Vassilios , Sahu Bithi , Golding John F , Marsden Jonathan , Seemungal Barry M 
Published: May 2024

BackgroundBenign paroxysmal positional vertigo (BPPV) affects approximately half of acute, moderate-severe traumatic brain injury (TBI) patients. To date, there have been no rigorous studies of BPPV assessment or treatment in this cohort. We aimed to determine the safety, practicability, and efficacy of therapist-led BPPV management in acute TBI and the feasibility of a larger effectiveness trial.MethodsThis was a multi-centre, three-arm, parallel-groups, randomised, feasibility trial. Recruitment was via convenience sampling. The main inclusion criteria were age over 18 years and a confirmed, non-penetrating, acute TBI. BPPV-positive patients were randomly allocated to one of three interventions (repositioning manoeuvres, Brandt–Daroff exercises or advice) using minimisation criteria. Outcome assessors were blinded to the intervention.ResultsOf 2014 patients screened for inclusion, 180 were assessed for BPPV. Of those assessed, 34% (62/180) had BPPV, and 58 patients received an intervention. Therapist-led interventions were delivered safely and accurately according to intervention monitoring criteria. Resolution of BPPV was observed in 35/58 (60%) patients. The resolution rate was highest following repositioning manoeuvres (78%), followed by the advice (53%) and Brandt–Daroff interventions (42%). 10 patients experienced recurrence. This was observed more frequently in those with skull fractures and bilateral or mixed BPPV.ConclusionsOverall, the results provide strong evidence for the feasibility of a future trial. Therapist-led management of BPPV in acute TBI was safe and practicable. Repositioning manoeuvres seemingly yielded a superior treatment effect. However, given the high recurrence rate of post-traumatic BPPV, the optimal time to treat according to patients’ specific recurrence risk requires further investigation.Trial registrationISRCTN91943864,https://doi.org/10.1186/ISRCTN91943864.
Spontaneous spinal cord infarction: a systematic review
Authors: Gharios Maria , Stenimahitis Vasilios , El-Hajj Victor Gabriel , Mahdi Omar Ali , Fletcher-Sandersjöö Alexander , Jabbour Pascal , Andersson Magnus , Hultling Claes , Elmi-Terander Adrian , Edström Erik 
Published: May 2024

Background and objectivesSpontaneous spinal cord infarction (SCInf) is a rare condition resulting in acute neurological impairment. Consensus on diagnostic criteria is lacking, which may present a challenge for the physician. This review aims to analyse the current literature on spontaneous SCInf, focusing on epidemiology, the diagnostic process, treatment strategies and neurological outcomes.MethodsThe study was performed in accordance with a previously published protocol. PubMed, Web of Science and Embase were searched using the keywords ‘spontaneous’, ‘spinal cord’, ‘infarction’ and ‘ischaemic’. The eligibility of studies was evaluated in two steps by multiple reviewers. Data from eligible studies were extracted and systematically analysed.Results440 patients from 33 studies were included in this systematic review. Analysis of vascular risk factors showed that hypertension was present in 40%, followed by smoking in 30%, dyslipidaemia in 29% and diabetes in 16%. The severity of symptoms at admission according to the American Spinal Injury Association (ASIA) Impairment Scale was score A 19%, score B14%, score C36% and score D32%. The mean follow-up period was 34.8 (±12.2) months. ASIA score at follow-up showed score A 11%, score B 3%, score C 16%, score D 67% and score E 2%. The overall mortality during the follow-up period was 5%. When used, MRI with diffusion-weighted imaging (DWI) supported the diagnosis in 81% of cases. At follow-up, 71% of the patients were able to walk with or without walking aids.ConclusionThe findings suggest a significant role for vascular risk factors in the pathophysiology of spontaneous SCInf. In the diagnostic workup, the use of DWI along with an MRI may help in confirming the diagnosis. The findings at follow-up suggest that neurological recovery is to be expected, with the majority of patients regaining ambulation. This systematic review highlights gaps in the literature and underscores the necessity for further research to establish diagnostic criteria and treatment guidelines.
Identifying characteristics that enable resilient immunisation programmes: a scoping review
Authors: Baxter Luke , Slater Rebeccah , Hermany Lindsay , Bhatti Alexandra , Eiden Amanda L , Mitrovich Rachel , Connolly Mark P , Vanderslott Samantha , Nyaku Mawuli , Bhatt Aomesh 
Published: May 2024

ObjectivesThe COVID-19 pandemic highlighted the fragility of immunisation programmes and resulted in a significant reduction in vaccination rates, with increasing vaccine-preventable disease outbreaks consequently reported. These vulnerabilities underscore the importance of resilient immunisation programmes to ensure optimal performance during crises. To date, a framework for assessing immunisation programme resilience does not exist. We conducted a scoping review of immunisation programmes during times of crisis to identify factors that characterise resilient immunisation programmes, which may inform an Immunisation Programme Resilience Tool.DesignScoping review design followed the Arksey and O’Malley framework, and manuscript reporting followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses for Scoping Reviews guidelines.Data sourcesCINAHL, CENTRAL, Embase, Google Scholar, MEDLINE, PsycINFO and Web of Science and databases were searched between 1 January 2011 and 2 September 2023. Citation searching of identified studies was also performed.Eligibility criteriaWe included primary empirical peer-reviewed studies that discussed the resilience of immunisation programme to crises, shocks or disruptions.Data extraction and synthesisTwo independent reviewers screened records and performed data extraction. We extracted data on study location and design, crisis description, and resilience characteristics discussed, and identified evidence gaps in the literature. Findings were synthesised using tabulation and an evidence gap map.ResultsThirty-seven studies met the eligibility criteria. These studies captured research conducted across six continents, with most concentrated in Africa, Asia and Europe. One study had a randomised controlled trial design, while 36 studies had observational designs (15 analytical and 21 descriptive). We identified five characteristics of resilient immunisation programmes drawing on the Health System Resilience Index (Integration, Awareness, Resource Availability and Access, Adaptiveness and Self-regulation) and several evidence gaps in the literature.ConclusionsTo our knowledge, no immunisation programme resilience tool exists. We identified factors from the Health System Resilience Index coupled with factors identified through primary empirical evidence, which may inform development of an immunisation programme resilience tool.
Current US prevalence of myocardial injury patterns and clinical outcomes among hospitalised patients with familial hypercholesterolaemia: insight from the National Inpatient Sample—a retrospective cohort study
Authors: Kumi Dennis , Narh Joshua Tetteh , Odoi Samuel Michael , Oduro Anna , Gajjar Rohan , Gwira-Tamattey Edwin , Karki Sadichhya , Abbasi Ayesha , Fugar Setri , Alyousef Tareq 
Published: May 2024

BackgroundFamilial hypercholesterolaemia (FH) increases propensity for premature atherosclerotic disease. Knowledge of inpatient outcomes among patients with FH admitted with acute myocardial injury (AMI) is limited.ObjectivesOur study aimed to identify myocardial injury types, including type 1 myocardial infarction (MI), type 2 MI and takotsubo cardiomyopathy, assess lesion severity and study adverse short-term inpatient outcomes among patients with FH admitted with AMI.SettingOur study retrospectively queried the US National Inpatient Sample from 2018 to 2020.PopulationAdults admitted with AMI and dichotomised based on the presence of FH.Study outcomesWe evaluated myocardial injury types and complexity of coronary revascularisation. Primary outcome of all-cause mortality and other clinical secondary outcomes were studied.ResultsThere were 3 711 765 admissions with AMI including 2360 (0.06%) with FH. FH was associated with higher odds of ST-elevation MI (STEMI) (adjusted OR (aOR): 1.62, p<0.001) and non-ST-elevation MI (NSTEMI) (aOR: 1.29, p<0.001) but lower type 2 MI (aOR: 0.39, p<0.001) and takotsubo cardiomyopathy (aOR: 0.36, p=0.004). FH was associated with higher multistent percutaneous coronary interventions (aOR: 2.36, p<0.001), multivessel coronary artery bypass (aOR: 2.65, p<0.001), higher odds of intracardiac thrombus (aOR: 3.28, p=0.038) and mechanical circulatory support (aOR: 1.79, p<0.001). There was 50% reduction in odds of all-cause mortality (aOR: 0.50, p=0.006) and lower odds of mechanical ventilation (aOR: 0.37, p<0.001). There was no difference in rate of ventricular tachycardia, cardioversion, new implantable cardioverter defibrillator implantation, cardiogenic shock and cardiac arrest.ConclusionAmong patients hospitalised with AMI, FH was associated with higher STEMI and NSTEMI, lower type 2 MI and takotsubo cardiomyopathy, higher number of multiple stents and coronary bypasses, and mechanical circulatory support device but was associated with lower all-cause mortality and rate of mechanical ventilation.
Protocol for a multicentre prospective exploratory mixed-methods study investigating the modifiable psychosocial variables influencing access to and outcomes after kidney transplantation in children and young people in the UK
Authors: Kim Ji Soo , Wray Jo , Ridout Deborah , Plumb Lucy , Nitsch Dorothea , Robb Matthew , Marks Stephen D 
Published: May 2024

IntroductionKidney transplantation is the preferred therapy for children with stage 5 chronic kidney disease (CKD-5). However, there is a wide variation in access to kidney transplantation across the UK for children. This study aims to explore the psychosocial factors that influence access to and outcomes after kidney transplantation in children in the UK using a mixed-methods prospective longitudinal design.MethodsQualitative data will be collected through semistructured interviews with children affected by CKD-5, their carers and paediatric renal multidisciplinary team. Recruitment for interviews will continue till data saturation. These interviews will inform the choice of existing validated questionnaires, which will be distributed to a larger national cohort of children with pretransplant CKD-5 (n=180) and their carers. Follow-up questionnaires will be sent at protocolised time points regardless of whether they receive a kidney transplant or not. Coexisting health data from hospital, UK renal registry and National Health Service Blood and Transplant registry records will be mapped to each questionnaire time point. An integrative analysis of the mixed qualitative and quantitative data will define psychosocial aspects of care for potential intervention to improve transplant access.AnalysisQualitative data will be analysed using thematic analysis. Quantitative data will be analysed using appropriate statistical methods to understand how these factors influence access to transplantation, as well as the distribution of psychosocial factors pretransplantation and post-transplantation.Ethics and disseminationThis study protocol has been reviewed by the National Institute for Health Research Academy and approved by the Wales Research Ethics Committee 4 (IRAS number 270493/ref: 20/WA/0285) and the Scotland A Research Ethics Committee (ref: 21/SS/0038). Results from this study will be disseminated across media platforms accessed by affected families, presented at conferences and published in peer-reviewed journals.
Does the effect of adolescent health behaviours on adult cardiometabolic health differ by socioeconomic background? Protocol for a population-based cohort study
Authors: Jackisch Josephine , Noor Nazihah , Raitakari Olli T , Lehtimäki Terho , Kähönen Mika , Cullati Stéphane , Delpierre Cyrille , Kivimäki Mika , Carmeli Cristian 
Published: May 2024

IntroductionAdolescence is a sensitive period for cardiometabolic health. Yet, it remains unknown if adolescent health behaviours, such as alcohol use, smoking, diet and physical activity, have differential effects across socioeconomic strata. Adopting a life-course perspective and a causal inference framework, we aim to assess whether the effects of adolescent health behaviours on adult cardiometabolic health differ by levels of neighbourhood deprivation, parental education and occupational class. Gaining a better understanding of these social disparities in susceptibility to health behaviours can inform policy initiatives that aim to improve population health and reduce socioeconomic inequalities in cardiometabolic health.Methods and analysisWe will conduct a secondary analysis of the Young Finns Study, which is a longitudinal population-based cohort study. We will use measures of health behaviours—smoking, alcohol use, fruit and vegetable consumption, and physical activity—as exposure and parental education, occupational class and neighbourhood deprivation as effect modifiers during adolescence (ages 12–18 years). Eight biomarkers of cardiometabolic health (outcomes)—waist circumference, body mass index, blood pressure, low-density lipoprotein cholesterol, apolipoprotein B, plasma glucose and insulin resistance—will be measured when participants were aged 33–40. A descriptive analysis will investigate the clustering of health behaviours. Informed by this, we will conduct a causal analysis to estimate effects of single or clustered adolescent health behaviours on cardiometabolic health conditional on socioeconomic background. This analysis will be based on a causal model implemented via a directed acyclic graph and inverse probability-weighted marginal structural models to estimate effect modification.Ethics and disseminationThe Young Finns study was conducted according to the guidelines of the Declaration of Helsinki, and the protocol was approved by ethics committees of University of Helsinki, Kuopio, Oulu, Tampere and Turku. We will disseminate findings at international conferences and a manuscript in an open-access peer-reviewed journal.
Design of the multicentre randomised controlled BENTO trial to demonstrate patient-relevant benefit of bronchoscopic lung volume reduction using thermal vapour ablation in the German healthcare system for patients with upper lobe emphysema: a study protocol
Authors: Kontogianni Konstantina , Darwiche Kaid , Huebner Ralf Harto , Hassinger Fathema , Riemer Thomas , Herth Felix JF , Brock Judith 
Published: May 2024

IntroductionApplication of vapour ablation as a novel approach to lung volume reduction has positive effects in patients with severe emphysema. The BENTO study is a randomised, controlled, open, multicentre trial, to assess the effects of bronchoscopic thermal vapour ablation (BTVA) in the German healthcare system.Methods and analysisPatients with bilateral heterogeneous emphysema of the upper lobes in Global Initiative for Chronic Obstructive Lung Disease (GOLD) stage 3/4 will be enrolled in this trial and will receive either standard medical management alone (according to GOLD guidelines) or BTVA treatment with the InterVapor system together with standard medical management. Patients will be randomised in a 2:1 ratio (treatment group:control group). A total of 224 patients will be enrolled at 15 study sites. The primary endpoint is the change in patient-reported disease-specific quality of life, as measured by the St George’s Respiratory Questionnaire for chronic obstructive pulmonary disease patients between randomisation and the 9-month follow-up visit. Secondary endpoints include adverse events, mortality, vital status, changes in lung function parameters, exercise capacity and other efficacy measures at 3, 9 and 12 months.The BENTO trial was commissioned by the German Federal Joint Committee, to demonstrate that this approach is an efficient and safe treatment option in the German healthcare system.Ethics and disseminationThe protocol has been approved by the lead ethics committee in Germany (Ethics Committee of the Medical Faculty of Heidelberg) and until present also by the following ethics committees: Ethics Committee of the Medical Faculty of Duisburg-Essen, Ethics Committee of the Medical Faculty of Martin-Luther-University Halle-Wittenberg, Ethics Committee of the State Medical Association of Hessen, Ethics Commission of the State Office for Health and Social Affairs of the State of Berlin, Ethics Committee of the Medical Faculty of Greifswald. The results will be published in a peer-reviewed journal.Trial registration numberNCT05717192.
Cross-sectional study of prevalence and correlates of fear of falling in the older people in residential care in India: the Hyderabad Ocular Morbidity in Elderly Study (HOMES)
Authors: Marmamula Srinivas , Kumbham Thirupathi Reddy , Modepalli Satya Brahmanandam , Barrenkala Navya Rekha , Keeffe Jill Elizabeth , Friedman David S 
Published: May 2024

ObjectiveTo report the prevalence and risk factors for the fear of falling (FOF) among older individuals living in residential care facilities in India.DesignCross-sectional study.SettingHomes for the aged centres in Hyderabad, India.ParticipantsThe study included individuals aged ≥60 years from homes for the aged centres. The participants underwent a comprehensive eye examination in make-shift clinics setup in homes. Trained investigators collected the personal and demographic information of the participants and administered the Patient Health Questionnaire-9 and Hearing Handicap Inventory for Elderly questionnaire in the vernacular language. FOF was assessed using the Short Falls Efficacy Scale. The presence of hearing and visual impairment in the same individual was considered dual sensory impairment (DSI). A multiple logistic regression analysis was done to assess the factors associated with FOF.Primary outcome measureFOF.ResultsIn total, 867 participants were included from 41 homes for the aged centres in the analyses. The mean (±SD) age of the participants was 74.2 (±8.3) years (range 60–96 years). The prevalence of FOF was 56.1% (95% CI 52.7% to 59.4%; n=486). The multivariate analysis showed that those with DSI had eleven times higher odds of reporting FOF than those with no impairment (OR 11.14; 95% CI 3.15 to 41.4.) Similarly, those with moderate depression had seven times higher odds (OR 6.85; 95% CI 3.70 to 12.70), and those with severe depression had eight times higher odds (OR 8.13; 95% CI 3.50 to 18.90) of reporting FOF. A history of falls in the last year was also associated with increased odds for FOF (OR 1.52; 95% CI 1.03 to 2.26).ConclusionFOF is common among older individuals in residential care in India. Depression, falling in the previous year and DSI were strongly associated with FOF. A cross-disciplinary approach may be required to address FOF among the older people in residential care in India.