bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomics and evolutionary analysis of
Chlorella variabilis-
infecting viruses demarcate criteria for defining species of giant viruses
Authors: Carvalho João Victor R. P. , Carlson Roger M. , Ghosh Jayadri , Queiroz Victória F. , de Oliveira Ellen G. , Botelho Bruna B. , Filho Clécio A. C. , Agarkova Irina V. , McClung O. William , Van Etten James L. , Dunigan David D. , Rodrigues Rodrigo A. L. 
Published: October 2024

ABSTRACT

Chloroviruses exhibit a close relationship with their hosts with the phenotypic aspect of their ability to form lytic plaques having primarily guided the taxonomy. However, with the isolation of viruses that are only able to complete their replication cycle in one strain of
Chlorella variabilis
, systematic challenges emerged. In this study, we described the genomic features of 53 new chlorovirus isolates and used them to elucidate part of the evolutionary history and taxonomy of this clade. Our analysis revealed new chloroviruses with the largest genomes to date (>400 kbp) and indicated that four genomic features are statistically different in the viruses that only infect the Syngen 2–3 strain of
C. variabilis
(OSy viruses). We found large regions of dissimilarity in the genomes of viruses PBCV-1 and OSy-NE5 when compared with the other genomes. These regions contained genes related to the interaction with the host cell machinery and viral capsid proteins, which provided insights into the evolution of the replicative and structural modules in these giant viruses. Phylogenetic analysis using hallmark genes of
Nucleocytoviricota
revealed that OSy-viruses evolved from the NC64A-viruses, possibly emerging as a result of the strict relationship with their hosts. Merging phylogenetics and nucleotide identity analyses, we propose strategies to demarcate viral species, resulting in seven new species of chloroviruses. Collectively, our results show how genomic data can be used as lines of evidence to demarcate viral species. Using the chloroviruses as a case study, we expect that similar initiatives will emerge using the basis exhibited here.

IMPORTANCE

Chloroviruses are a group of giant viruses with long dsDNA genomes that infect different species of
Chlorella-
like green algae. They are host-specific, and some isolates can only replicate within a single strain of
Chlorella variabilis
. The genomics of these viruses is still poorly explored, and the characterization of new isolates provides important data on their genetic diversity and evolution. In this work, we describe 53 new chlorovirus genomes, including many isolated from alkaline lakes for the first time. Through comparative genomics and molecular phylogeny, we provide evidence of genomic gigantism in chloroviruses and show that a subset of viruses became highly specific for their hosts at a particular point in evolutionary history. We propose criteria to demarcate species of chloroviruses, paving the way for an update in the taxonomy of other groups of viruses. This study is a new and important piece in the complex puzzle of giant algal viruses.
Chlamydia trachomatis
Inc Ct226 is vital for FLI1 and LRRF1 recruitment to the chlamydial inclusion
Authors: Sturd Natalie A. , Knight Lindsey A. , Wood Macy G. , Durham Legacy , Ouellette Scot P. , Rucks Elizabeth A. 
Published: October 2024

ABSTRACT

The obligate intracellular pathogen,
Chlamydia trachomatis
, establishes an intracellular niche within a host membrane-derived vacuole called the chlamydial inclusion. From within this inclusion,
C. trachomatis
orchestrates numerous host-pathogen interactions, in part, by utilizing a family of type III secreted effectors, termed inclusion membrane proteins (Incs). Incs are embedded within the inclusion membrane, and some function to recruit host proteins to the inclusion. Two such recruited host proteins are
l
eucine
r
ich
r
epeat
F
lightless-1
i
nteracting
p
rotein 1 (LRRF1/LRRFIP1) and its binding partner Flightless 1 (FLI1/FLII). Previously, LRRF1 has been shown to interact with Inc protein Ct226/CTL0478. This is the first study to examine interactions of FLI1 with candidate Incs or with LRRF1 during infection. We hypothesized that FLI1 recruitment to the inclusion would be dependent on LRRF1 localization. We demonstrated that FLI1 co-immunoprecipitated with Ct226 but only in the presence of LRRF1. Furthermore, FLI1 localized to the inclusion when LRRF1 was depleted via small interfering RNA, suggesting that FLI1 may have an alternative recruitment mechanism. We further developed a series of CRISPRi knockdown and complementation strains in
C. trachomatis
serovar L2 targeting ct226 and co-transcribed candidate Incs, ct225 and ct224. Simultaneous knockdown of ct226, ct225, and ct224 prevented localization of both FLI1 and LRRF1 to the inclusion, and only complementation of ct226 restored their localization. Thus, we demonstrated Ct226 is critical for FLI1 and LRRF1 localization to the inclusion. Our results also indicate an LRRF1-independent localization mechanism for FLI1, which likely influence their mechanism(s) of action during chlamydial infection.

IMPORTANCE

Chlamydia trachomatis
is a leading cause of both bacterial sexually transmitted infections and preventable infectious blindness worldwide. As an obligate intracellular pathogen,
C. trachomatis
has evolved multiple ways of manipulating the host to establish a successful infection. As such, it is important to understand host-chlamydial protein-protein interactions as these reveal strategies that
C. trachomatis
uses to shape its intracellular environment. This study looks in detail at interactions of two host proteins, FLI1 and LRRF1, during chlamydial infection. Importantly, the series of CRISPR inference knockdown and complement strains developed in this study suggest these proteins have both independent and overlapping mechanisms for localization, which ultimately will dictate how these proteins function during chlamydial infection.
Late Paleozoic slab rollback events in the southeastern part of the Central Asian orogenic belt: Implications for Paleo-Asian Ocean subduction and continental crust growth
Authors: Gao Qiang , Yan Mao-Qiang , Huizenga Jan Marten , Lai Lian-Xin , Li Bin , Zeng Hong-Hong , Moritz Robert , Wei Jun-Hao 
Published: October 2024

Abstract
The Central Asian orogenic belt is considered to be the largest Phanerozoic accretive orogenic belt on Earth. The late Paleozoic magmatic rocks in central Inner Mongolia are crucial for understanding continental crust growth and the tectonic evolution of the southeastern part of the Central Asian orogenic belt. We present comprehensive geochemical, isotopic, and geochronological data from three late Paleozoic magmatic units in the Mandula area, west of the Solonker suture zone. Zircon U-Pb dating indicates that these rocks formed during the late Carboniferous (316–304 Ma). The Mandula high-Mg diorites exhibit high MgO (3.9–6.5 wt%), high Mg# (61–69), and depleted Nd-Hf isotopic compositions, generated through interaction between a metasomatized mantle and slab melts with the overlying sediments. The Mandula granodiorites display adakite geochemical characteristics with high Sr/Y mass ratios (29–52), high MgO (1.7–2.2 wt%), and high Mg# (52–54), formed by partial melting of the oceanic slab with the addition of overlying sediment. Mafic microgranular enclaves have consistent ages, Sr-Nd-Hf isotope compositions, and hornblende crystallization temperature-pressure conditions with their host granodiorite, formed from a cognate magma associated with the host granodiorites through cumulate. We propose that two phases of slab rollback took place during the late Paleozoic southward subduction-accretion of the Paleo-Asian Ocean. The first phase corresponded to the transformation of low- to medium-angle slab subduction, while the second phase led to subduction-related extension. Considering the tectonic-magmatic evolution, crustal maturity, and thickness variations in the late Paleozoic southeastern part of the Central Asian orogenic belt, we propose that prolonged subduction and slab rollback promoted continental crust growth. The Central Asian orogenic belt coincides temporally and spatially with the Phanerozoic Pangea cycle, suggesting that continuous subduction and supercontinent amalgamation significantly contributed to continental crust growth.
Prescribing strength training for stroke recovery: a systematic review and meta-analysis of randomised controlled trials
Authors: Noguchi Kenneth S , Moncion Kevin , Wiley Elise , Morgan Ashley , Huynh Eric , Balbim Guilherme Moraes , Elliott Brad , Harris-Blake Carlene , Krysa Brent , Koetsier Barb , Pinili Karolyn , Beauchamp Marla K , Phillips Stuart M , Thabane Lehana , Tang Ada 
Published: October 2024

ObjectiveTo examine the effects of strength training on patient-important outcomes of stroke recovery and to quantify the influence of the exercise prescription on treatment effects.DesignSystematic review and meta-analysis.Data sourcesEight electronic databases (MEDLINE, EMBASE, EMCARE, AMED, PsycINFO, CINAHL, SPORTDiscus, and Web of Science) and two clinical trial registries (ClinicalTrials.gov and WHO International Clinical Trials Registry Platform) were searched from inception to 19 June 2024.Eligibility criteriaRandomised controlled trials were eligible if they examined the effects of strength training compared with no exercise or usual care and reported at least one exercise prescription parameter. An advisory group of community members with lived experience of stroke helped inform outcomes most relevant to stroke recovery.ResultsForty-two randomised trials (N=2204) were included. Overall risk of bias was high across most outcomes. Strength training improved outcomes rated as ‘critical for decision-making’ by the advisory group, including walking capacity (standardised mean difference (SMD)=0.95 (95% CI 0.34–1.56)), balance (SMD=1.13 (0.51–1.75)), functional ability and mobility (SMD=0.61 (0.09–1.14)), and habitual (mean difference (MD)=0.05 m/s (0.02–0.09)) and fast-paced walking speed (MD=0.09 m/s (0.01–0.17)), with very low to moderate certainty of evidence, mainly due to risk of bias and inconsistency. More frequent strength training, traditional strength training programmes and power-focused intensities (ie, emphasis on movement velocity) were positively associated with walking capacity, health-related quality of life and fast-paced walking speed.ConclusionStrength training alone or combined with usual care improves stroke recovery outcomes that are important for decision-making. More frequent strength training, power-focused intensities and traditional programme designs may best support stroke recovery.PROSPERO registration numberCRD42023414077.
Exploration of the relationship between general health-related problems and subclinical coronary artery disease: a cross-sectional study in a general population
Authors: Koopman Moniek Y , van der Ende M Yldau , Reijnders Jorn J W , Willemsen Robert T A , van Bruggen Rykel , Gratama Jan Willem C , Kietselaer Bastiaan L J H , van der Harst Pim , Vliegenthart Rozemarijn 
Published: October 2024

ObjectiveTo explore associations between general health-related problems and subclinical coronary artery disease (CAD), determined by CT coronary calcium score (CT-CCS), in a general population.DesignA cross-sectional design.SettingThis study was performed in a prospective population-based cohort, examining the health and health-related behaviour of individuals living in the Northern Netherlands.ParticipantsThe initial cohort comprised 6763 participants ≥45 years of age who underwent CT-scanning. Participants were included for the current analysis if they filled in three validated questionnaires (Symptomatic Checklist-90, Research and Development Survey-36 and Reviving the Early Diagnosis of CardioVascular Diseases questionnaire (RED-CVD)) and did not have a history of cardiovascular disease. The final analysis included 6530 participants.Primary outcome measureBackward-stepwise and forward-stepwise logistic regression analyses were performed to determine associations between general health-related problems and subclinical CAD (CCS≥100 and ≥300).ResultsThe median age was 53 years (25th, 75th percentile: 48, 58); 57% were women. CRCS≥100 was found in 1236 (19%) participants, 437 (12%) in women and 799 (29%) men and CCS≥300 in 643 (9.9%) participants of which 180 (4.8%) were women and 463 (16.6%) men. In univariate analysis, in women the expectation of health to worsen (OR=1.13, 95% CI: 1.05 to 1.21), and in men reduced exercise intolerance (OR=1.14, 95% CI: 1.06 to 1.23) were associated with CCS≥100. The total RED-CVD score in women (OR=1.06, (95% CI: 1.05 to 1.08) and men (OR=1.07, 95% CI: 1.06 to 1.09), and in men also reduced exercise intolerance (OR=1.15, 95% CI: 1.06 to 1.25) and headache (OR=0.55, 95% CI: 0.38 to 0.79) were associated with CCS≥300. In multivariate analyses, only general health expectation in women was still significantly associated with subclinical CAD (CCS≥300) (OR=1.92, 95% CI: 1.56 to 2.37).ConclusionOnly a few general health-related problems were associated with the presence of subclinical CAD in the general population, however, these problems showed no strong association. Therefore, using health-related symptoms does not seem useful to pre-select for CT-CCS.Trial registration numberCCMO Register, NL17981.042.07 and NL58592.042.16.
Clean intermittent catheterisation determinants and caregiver adherence in paediatric patients with spinal dysraphism and spinal cord injury in a paediatric spinal differences clinic: a mixed methods study protocol
Authors: Wickham Azadeh , Russell Cynthia L , Gatti John M 
Published: October 2024

IntroductionClean intermittent catheterisation (CIC) is the standard of care for treating neurogenic lower urinary tract dysfunction (NLUTD), the most common bladder dysfunction in children diagnosed with spinal dysraphism (SD) and spinal cord injury (SCI). Failure to follow the prescribed CIC regimen results in urinary tract infections, incontinence and renal insufficiency. Adherence to CIC is suboptimal, with reported non-adherence rates of 18%–66%. Despite the efficacy of CIC, the research on CIC adherence is not well defined in the literature and even less for caregivers of children on CIC protocols.MethodsThis proposed study aims to identify caregiver CIC adherence and determinants while exploring the personal experiences of performing CIC from the perspective of caregivers of children with NLUTD due to SD and SCI. This cross-sectional, correlational, convergent mixed methods study design in which qualitative and quantitative data will be collected simultaneously will be used to study the level of adherence and the relationship of caregiver determinants to CIC in children with SD and SCI and adherence to the CIC protocol. Convenience sampling will be used to identify 60 adult caregivers who can read and write English or Spanish and have a child diagnosed with SD and SCI who is currently prescribed CIC by a urology provider.AnalysisThe adherence data will be reported as frequency and percentages. A correlation analysis will be computed to assess the association between determinants measured by the Clean Intermittent Catheterization-Caregiver Questionnaire and adherence levels measured with the Intermittent Catheterization Adherence Scale. Thematic analysis will be used to analyse and interpret the interview data. A comparison joint display will be developed to compare quantitative and qualitative data results.Ethical and disseminationInstitutional review board approval was obtained from the Children’s Mercy Kansas City (Study00003003) and the University of Missouri-Kansas City (#2100185). The study’s main results will be disseminated to caregiver participants, published in peer-reviewed journals and presented at conferences.
Reference equations for DLNO and DLCO in Mexican Hispanics: influence of altitude and race
Authors: Gochicoa-Rangel Laura , De-Los-Santos-Martínez Ada , Reyes-García Alejandro , Martínez-Briseño David , Vargas Mario H , Lechuga-Trejo Irma , Guzmán-Valderrábano Carlos , Torre-Bouscoulet Luis , Zavorsky Gerald Stanley 
Published: October 2024

ObjectivesThis study aimed to evaluate pulmonary diffusing capacity for nitric oxide (DLNO) and pulmonary diffusing capacity for carbon monoxide (DLCO) in Mexican Hispanics born and raised at 2240 m altitude (midlanders) compared with those born and raised at sea level (lowlanders). It also aimed to assess the effectiveness of race-specific reference equations for pulmonary diffusing capacity (white people vs Mexican Hispanics) in minimising root mean square errors (RMSE) compared with race-neutral equations.MethodsDLNO, DLCO, alveolar volume (VA) and gas transfer coefficients (KNO and KCO) were measured in 392 Mexican Hispanics (5 to 78 years) and compared with 1056 white subjects (5 to 95 years). Reference equations were developed using segmented linear regression (DLNO, DLCO and VA) and multiple linear regression (KNO and KCO) and validated with Least Absolute Shrinkage and Selection Operator. RMSE comparisons between race-specific and race-neutral models were conducted using repeated k-fold cross-validation and random forests.ResultsMidlanders exhibited higher DLCO (mean difference: +4 mL/min/mm Hg), DLNO (mean difference: +7 mL/min/mm Hg) and VA (mean difference: +0.17 L) compared with lowlanders. The Bayesian information criterion favoured race-specific models and excluding race as a covariate increased RMSE by 61% (DLNO), 18% (DLCO) and 4% (KNO). RMSE values for VA and KCO were comparable between race-specific and race-neutral models. For DLCO and DLNO, race-neutral equations resulted in 3% to 6% false positive rates (FPRs) in Mexican Hispanics and 20% to 49% false negative rates (FNRs) in white subjects compared with race-specific equations.ConclusionsMexican Hispanics born and raised at 2240 m exhibit higher DLCO and DLNO compared with lowlanders. Including race as a covariate in reference equations lowers the RMSE for DLNO, DLCO and KNO and reduces FPR and FNR compared with race-neutral models. This study highlights the need for altitude-specific and race-specific reference equations to improve pulmonary function assessments across diverse populations.
‘Downhill race for a rainbow jersey’: the epidemiology of injuries in downhill mountain biking at the 2023 UCI cycling world championships—a prospective cohort study of 230 elite cyclists
Authors: Fallon Thomas , Palmer Debbie , Bigard Xavier , Elliott Niall , Lunan Emma , Heron Neil 
Published: October 2024

ObjectivesThis study aims to understand the prevalence, incidence rate, anatomical sites, injury severity and main medical actions carried out during official training and racing by elite downhill mountain biking (DHMTB) riders during the 2023 Union Cycliste Internationale (UCI) Cycling World Championships.MethodsThe participants of this prospective, observational study were elite male and female cyclists competing at the UCI DHMTB World Championships located in the Nevis range in Fort William, Scotland, in 2023. This study followed the injury reporting guidelines established by the International Olympic Committee, which include the Strengthening the Reporting of Observational Studies in Epidemiology—Sports Injury and Illness Surveillance (SIIS) and the cycling-specific extension. Injuries were defined as ‘tissue damage or other derangement of normal physical function due to participation in sports, resulting from rapid or repetitive transfer of kinetic energy requiring medical attention’. All epidemiological data were collected by the local organising committee medical professionals working at the event through an online survey. All data inputted were screened daily by the lead event physician and UCI medical delegate.ResultsThroughout 5 days of the championships, 10.4% of the 230 cyclists sustained at least one injury. The overall injury incidence rate was 3.3 (95% CI 3.1 to 3.5) per 100 rides. The incidence rates were higher in the training 4.3 (95% CI 4.0 to 4.6)/100 rides than in the racing 2.2 (95% CI 2.1 to 2.3)/100 rides. There was a greater incidence of injury in female cyclists in the training 5.8 (95% CI 5.0 to 6.6)/100 rides and racing 4.5 (95% CI 3.9 to 4.9)/100 rides compared with male cyclists. Female cyclists experienced more severe injuries, with an average of 12.6 (±14, 95% CI 5.66 to 19.54) days lost to injury compared with 5.5 (±1.6 95% CI 1.89 to 9.11) seen in male cyclists. The main event medical actions were lifting, immobilisation and helmet removal.ConclusionThis study provides insights into the risk of injury to athletes within DHMTB. Our findings suggest more focus should be placed on the female DHMTB athlete. Additionally, this study provides unique information about common medical actions required of medical professionals working at DHMTB events and the importance of pre-event scenario training.
Culture of safety in an adult and paediatric emergency department before and after the COVID-19 pandemic
Authors: Beteta Fernández Dolores , Pereda Mas Arturo , Perez Canovas Carlos , Navarro Egea Ana Patricia , Pardo Rios Manuel , Alcaraz-Martinez Julian 
Published: October 2024

BackgroundThe WHO recognises patient safety as a serious public health problem. The COVID-19 pandemic affected adult EDs (AEDs) and paediatric EDs (PEDs) differently. We compared the culture of safety in the adult AED and PED before and after the COVID-19 pandemic.MethodsA quasi-experimental study was performed. In 2019, we conducted a survey using the Spanish-adapted Hospital Survey on Patient Safety Culture open to all staff (doctors, nurses and paediatric residents) in AED and PED. This survey provides scores for 12 separate domains and a global assessment of safety (scale 0–10). The survey was repeated in 2021 after the first wave of the COVID-19 pandemic. After the second survey, the researchers constructed a Pareto Chart (based on the responses from the surveys), demonstrating the most important problems to develop improvement proposals.ResultsThe 2019 questionnaire was completed by 125 AED workers and 65 PED workers. The 2021 questionnaire was completed by 79 AED workers and 50 PED workers. The global assessment of safety in the AED was 6.13 points at baseline and increased to 7.58 points (p<0.001) after COVID-19. The global assessment for the PED was 6.8 points at baseline and increased to 7.62 points after COVID-19 (p<0.001). In both services, the dimension that was most favourably assessed was ‘Teamwork in the Service’ while ‘Provision of Staff’ was least favourably assessed. The Pareto charts showed four dimensions contributing more than 50% of negative responses: ‘Provision of staff’ and ‘Hospital Management support for patient safety’ coincided in both services.ConclusionThe baseline perception of the culture of safety was higher in the PED but improved in both services during the COVID-19 pandemic. Adverse situations can provide an opportunity to improve patient safety culture.