bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenotypic analysis of variousClostridioides difficileribotypes reveals consistency among core processes
Authors: Beebe Merilyn A. , Paredes-Sabja Daniel , Kociolek Larry K. , Rodríguez César , Sorg Joseph A. 
Published: January 2025

AbstractClostridioides difficileinfections (CDI) cause almost 300,000 hospitalizations per year of which ∼15-30% are the result of recurring infections. The prevalence and persistence of CDI in hospital settings has resulted in an extensive collection ofC. difficileclinical isolates and their classification, typically by ribotype. While much of the current literature focuses on one or two prominent ribotypes (e.g., RT027), recent years have seen several other ribotypes dominate the clinical landscape (e.g., RT106 and RT078). Some ribotypes are associated with severe disease and / or increased recurrence rates, but why are certain ribotypes more prominent or harmful than others remains unknown. BecauseC. difficilehas a large, open pan-genome, this observed relationship between ribotype and clinical outcome could be a result of the genetic diversity ofC. difficile. Thus, we hypothesize that core biological processes ofC. difficileare conserved across ribotypes / clades. We tested this hypothesis by observing the growth kinetics, sporulation, germination, bile acid sensitivity, bile salt hydrolase activity, and surface motility of fifteen strains belonging to various ribotypes spanning each knownC. difficileclade. In viewing these phenotypes across each strain, we see that core phenotypes (growth, germination, sporulation, and resistance to bile salt toxicity) are remarkably consistent across clades / ribotypes. This suggests that variations observed in the clinical setting may be due to unidentified factors in the accessory genome or due to unknown host-factors.ImportanceC. difficileinfections impact thousands of individuals every year many of whom experience recurring infections. Clinical studies have reported an unexplained correlation between some clades / ribotypes ofC. difficileand disease severity / recurrence. Here, we demonstrate thatC. difficilestrains across the major clades / ribotypes are consistent in their core phenotypes. This suggests that such phenotypes are not responsible for variations in disease severity / recurrence and are ideal targets for the development of therapeutics meant to treatC. difficilerelated infections.
Effect of Weather and Soil Management on Medicinal Compound Concentration in East African Arid Acacias: A Simulation Study
Authors: Kinyua Esther Wairimu , Pietsch Stephan , Muli Esther , Kungurtsev Vyacheslav , Neru Sospeter , Mugo Kennedy 
Published: January 2025

1AbstractIn African countries various tree spcies are a key part in Non Timber Forest Production (NTFP) economy, be it for fruit, resin collection or medicinal use. Among these species Acacias play an important role in the arid and semi-arid dry-lands over Africa. In this study we explore the potential of BioGeoChemical Modelling techniques to assess growth peformance of Acacia ocurrences within their natural environment, where they only may persist against rain-fed grassland vegetation when having access to seasonally changing groundwater tables. Within this study we assess the applicability of BGC-modeling techonologies to pastoral and AgroForestry settings within a semi-arid region in Kenya. Results show that effects of (i) changing hydrological patterns, (ii) fire and grazing regimes and (iii) plant use for resin production may be captured.
Patterns of population structure and genetic variation within the Saudi Arabian population
Authors: Malomane D.K. , Williams M. P. , Huber C.D. , Mangul S. , Abedalthagafi M. , Chiang C. W. K. 
Published: January 2025

ABSTRACTThe Arabian Peninsula is considered the initial site of historic human migration out of Africa. The modern-day indigenous Arabians are believed to be the descendants who remained from the ancient split of the migrants into Eurasia. Here, we investigated how the population history and cultural practices such as endogamy have shaped the genetic variation of the Saudi Arabians. We genotyped 3,352 individuals and identified twelve genetic sub-clusters that corresponded to the geographical distribution of different tribal regions, differentiated by distinct components of ancestry based on comparisons to modern and ancient DNA references. These sub-clusters also showed variation across ranges of the genome covered in runs of homozygosity, as well as differences in population size changes over time. Using 25,488,981 variants found in whole genome sequencing data (WGS) from 302 individuals, we found that the Saudi tend to show proportionally more deleterious alleles than neutral alleles when compared to Africans/African Americans from gnomAD (e.g. a 13% increase of deleterious alleles annotated by AlphaMissense between 0.5 -5% frequency in Saudi, compared to 7% decrease of the benign alleles; P < 0.001). Saudi sub-clusters with greater inbreeding and lower effective population sizes showed greater enrichment of deleterious alleles as well. Additionally, we found that approximately 10% of the variants discovered in our WGS data are not observed in gnomAD; these variants are also enriched with deleterious annotations. To accelerate studying the population-enriched deleterious alleles and their health consequences in this population, we made available the allele frequency estimates of 25,488,981 variants discovered in our samples. Taken together, our results suggest that Saudi’s population history impacts its pattern of genetic variation with potential consequences to the population health. It further highlights the need to sequence diverse and unique populations so to provide a foundation on which to interpret medical-and pharmaco-genomic findings from these populations.
Cost-effectiveness of tuberculosis infection screening at first reception into English prisons: a model-based analysis
Authors: Mafirakureva Nyashadzaishe , Hunter Rachael , Ferraro Claire F. , Willner Steve , Finnie Thomas , Hayward Andrew , Lee Andrew , Roy Anjana , Edge Chantal , Dodd Peter J. 
Published: January 2025

AbstractBackgroundThe World Health Organization recommends systematic screening for tuberculosis in incarcerated populations, which are consistently at high risk of tuberculosis relative to the general population. In England, new receptions into prisons do not receive screening for tuberculosis infection, and evidence from economic evaluations is lacking.MethodsWe performed a cost-effectiveness analysis of introducing systematic screening for tuberculosis infection at first reception into English prisons from a health systems perspective. We used a tuberculosis transmission model calibrated to public data on prison stocks and flows. We developed decision tree models of prison-specific tuberculosis care pathways and their costs, informed by stakeholders and pilot studies. Sensitivity analyses included eliminating loss to follow-up (LTFU) in care cascades, zeroing extramural escort costs, and targeting screening to those born in countries with higher tuberculosis incidence (over 40 per 100,000 per year).FindingsIn our base case analysis, the intervention had an incremental cost-effectiveness ratio (ICER) of £78,000 per quality-adjusted life-year (QALY) gained. Reducing LTFU and avoiding prison escort costs would substantially improve cost-effectiveness, to ICERs of £70,000 and £54,000 per QALY gained, respectively. Targeting those born in higher incidence countries was predicted to be cost-saving.InterpretationUniversal tuberculosis screening and preventive treatment for new receptions into English prisons is not cost-effective by the usual threshold of £30,000. However, targeting high-risk groups could be cost-saving. Tuberculosis interventions should explore ways to reduce LTFU and extramural healthcare in order to meet the needs of those incarcerated while minimizing costs.FundingUKHSA
Thyroid volume, lobe asymmetry and AP diameter classification - A preliminary study
Authors: Akter Sanjida , Sarker Azmal K , Muttakin Shahriar , Biswas Sanjoy 
Published: January 2025

ABSTRACTObjectiveTo assess the thyroid lobe volumes and the total thyroid volumes across the arbitrary range for AP diameter of thyroid lobes, the age and sex related variation and compare local normal sizes with those in the reference. Because assessment of thyroid gland size by visual comparison with anatomical relations or by an arbitrary category for antero-posterior (AP) diameter precludes use of management guidelines based on thyroid gland volume. Moreover, the international references for AP diameter seem larger for Bangladeshi patients and therefore deemed as inapplicable.MethodsPatients who underwent thyroid ultrasound with thyroid volume measurements from October 2023 to October 2024 were included. The patients were classified into two groups. Group 1 consisted of children aged below 15 years while group 2 consisted of adolescents aged 15 years or more and all adults. Statistical analyses were applied to assess distribution of gland size between sexes and age groups, correlation between gland size and age, and distribution of thyroid lobe volume and total gland volume, across the arbitrary categories of AP diameter.ResultsTotal 110 patients (90 females) with mean (± SD) age of 28.1 ± 13.2 were included. There was no significant difference of gland size between males and females. The AP diameter and right thyroid lobe was significantly larger than the left in group 2 consisting of adolescents and adults (p < 0.05). There was a positive correlation of thyroid size and age in group 1 consisting of pre-adolescents who had normal sized glands (R = 0.91, p < 0.01). Observation of thyroid volumes across the arbitrary AP diameter category showed AP diameter categories of right lobe tended to better classify the normal glands whereas the AP diameter categories of left lobe tended to perform better for classification of the enlarged glands.ConclusionsThis study apart from describing the interaction of age and sex with thyroid size, highlights the importance of considering the natural asymmetry between the thyroid lobes for accurate thyroid volume classification. This study points toward the void for a reference local standard of thyroid volume that can classify not only the different categories of enlargement but also the small volume glands.
Comparison of length of liver among patients with and without fatty change in liver
Authors: Muttakin Shahriar , Sarker Azmal Kabir , Adrita Farzana Rahman , Tamanna Nafisa Kaisar 
Published: January 2025

ABSTRACTObjectiveThe retrospective cross-sectional study was done to assess the change of length of liver across the grades of fatty change, across the ages of individual as well as between the male and female sexes.MethodsThe liver length measurement and qualitative visual grading of fatty change (from grade 0 to grade 3), obtained from patients who underwent ultrasound of liver at our institute between July and October of 2024 was retrospectively retrieved. The age of patient, length of liver and the grading of fatty change was used as the variables for the analyses.ResultsThe mean lengths of liver were found to be significantly increasing with increased grades fatty change (grade 0, grade I and grade II), both in males and females (p < 0.01). Male patients were affected by fatty change in liver (both grades I and II), more in comparison to the females (Pearson’s Chi-squared value 4.53, p = 0.033). Being at older age is significantly associated with being affected by fatty change in liver (both grades I and II) in females (p<0.01). Liver with fatty changes (grade I and II combined) were significantly larger than those without fatty change both in males as well as in females (p < 0.01). A weak positive association of length of liver and advancing age was found only among females without fatty change (R 0.29, p = 0.046).ConclusionsFindings from this study is expected to have implications in the clinical and lifestyle management of NAFLD and future research
CRISPR/Cas9-mediated germline mutagenesis in the subsocial parasitoid wasp,Sclerodermus guani
Authors: Ye Zi , Fan Guanzhen , Wei Yun , Li Li , Liu Feng 
Published: January 2025

AbstractThe ectoparasitoid waspSclerodermus guani(Hymenoptera: Bethylidae), as a subsocial insect, is widely applied in biological control against beetle vectors of pine wood nematodes. Despite significant advances in behavioral research, functional genetics inS. guaniremains underdeveloped due to the absence of efficient gene manipulation tools. In this study, we employed CRISPR-mediated mutagenesis to achieve germline gene knockout targeting the eye pigment associated genekynurenine 3-monooxygenase(KMO). Phylogenetic analysis revealed thatS. guaniKMO shares a close relationship with its homolog inProrops nasuta(Hymenoptera: Bethylidae). Two single-guide RNAs (sgRNAs), coupled with Cas9 protein with and without nuclear localization signal (NLS) were tested. Both sgRNAs induced specificin vitroDNA cleavage andin vivoheritable indels at the target genomic loci. Homozygous null mutant females and males exhibit a white-eye phenotype, which was identified during pupal stage. Optimal editing efficiencyin vivowas achieved using the Cas9-NLS variant. Given the complication of germline gene editing in eusocial Hymenopterans, the application of CRISPR in the subsocial parasitoid waspS. guaniprovides an accessible research platform for the molecular evolution of insect sociality.
Identifying Opportunities for Fluid Balance Optimization in Critically Ill Children
Authors: Hasson Denise , Shah Ami , Braun Chloe G. , Kothari Ulka , Drury Steve , Dapul Heda , Fitzgerald Julie C. , Dixon Celeste , Barbera Andrew , Odum James , Terry Nina , Weiss Scott L. , Martin Susan D. , Dziorny Adam C. 
Published: January 2025

AbstractIntroductionFluid overload (FO), a state of pathologic positive cumulative fluid balance (CFB), is common in Pediatric Intensive Care Units (PICU) and associated with morbidity and mortality. Because different PICUs may have unique needs, barriers, and limitations to accurately report fluid balance (FB) and reduce FO, understanding the drivers of positive FB is needed. We hypothesize CFB >5% and >10% is common within initial days of PICU admission, but that reasons for high %CFB will vary across sites, as will barriers to accurate FB recording and opportunities to improve FB recording and management.MethodsConcurrent mixed methods study utilizing a retrospective observational cohort design and prospective interview and survey design performed at four tertiary pediatric ICUs. FB data was extracted from the electronic health record. A federated data collection framework allowed for rapid data aggregation. The primary outcome was %CFB on PICU days 1 and 2, defined as total intake minus total output divided by PICU admission weight. Chi-square test and Wilcoxon rank sum tests compared results across and within sites.ResultsAmongst 3,071 PICU encounters, day 2 CFB >5% varied from 39% to 54% (p=0.03) and day 2 CFB >10% varied from 16% to 25% (p=0.04) across sites. Urine occurrence recordings and patients receiving >100% Holliday-Segar fluids on Day 1 differed across sites (p<0.001). Sites discussed overall FB and specific FB goals on rounds with differing frequency (42-73% and 19-39%, respectively), but they reported similar barriers to accurate FB reporting and achievable opportunities to improve FB measurements.ConclusionDay 2 CFB >5% and >10% was common among PICU encounters but proportion of patients varied significantly across PICUs. Individual ICUs have different drivers of FO that must be targeted to improve FB management.
Longitudinal associations between childhood socioeconomic position and adolescent eating disorder symptoms: findings from the ALSPAC cohort
Authors: Hahn Jane S. , Flouri Eirini , Harrison Amy , Lewis Glyn , Solmi Francesca 
Published: January 2025

AbstractBackgroundThe recorded incidence of eating disorders is elevated in people from higher socioeconomic positions, but self-reported eating disorder symptoms are more common in those from lower socioeconomic positions in cross-sectional studies. Longitudinal studies investigating the role of different socioeconomic indicators in the aetiology of a range of eating disorder symptoms might avoid biases associated with the use of clinical samples but have multiple limitations. We aimed to investigate the association between early childhood socioeconomic indicators and eating disorder symptoms across adolescence.MethodWe used data from the Avon Longitudinal Study of Parents and Children. Parental income, education, occupation, and financial hardship were reported by mothers between 32 weeks of gestation and 47 months postpartum. Area-level deprivation was derived from the Office for National Statistics indicators linked to the participant’s residential post code at 32 weeks gestation. Outcomes were disordered eating (restrictive eating, binge eating, and purging), weight and shape concerns, and body dissatisfaction at age 14, 16, and 18 years. To model these associations, we used univariable and multivariable multilevel logistic and linear regression, and linear regression models.FindingsThe sample included 7,824 participants (48.9% females; 3.8% minoritised ethnic background). Greater financial hardship was associated with increased odds of disordered eating (Odds Ratio= 1·06, 95%CI 1·04 to 1·10) and greater weight and shape concerns (Mean difference[MD] = 0·02, 95%CI 0·01 to 0·04) and body dissatisfaction (MD= 0·22 95%CI 0·06 to 0·37). Lower parental education was associated with 1.80 higher odds of disordered eating (95% CI 1·46 to 2·23).InterpretationOur findings point to potential socioeconomic inequalities in eating disorder identification in clinical settings, which need to be understood and addressed. Reducing population-level socioeconomic inequalities could also aid eating disorder prevention.Funding sourceMental Health Research UK, Wellcome Trust, UK Medical Research Council
COVID-19 Vaccine Uptake and its Determinants in Cameroon: A Systematic Review and Meta-analysis
Authors: Cheuyem Fabrice Zobel Lekeumo , Amani Adidja , Achangwa Chabeja , Ajong Brian Ngongheh , Minkandi Claude Axel , Zeh Myriam Mathilde Mbia Kouda , Ntsek Larissa Linda Eyenga , Essomba Jacques Philippes , Jiogue Rudy Chiozem , Ndagijimana Olivier , Nchanji Ndzi Etienne , Danwang Celestin 
Published: January 2025

AbstractBackgroundCOVID-19 vaccination is crucial for mitigating the pandemic’s impact. However, vaccine hesitancy and access challenges have hindered global vaccination efforts. This meta-analysis aimed to estimate the pooled COVID-19 vaccine uptake proportion and identify associated determinants in Cameroon.MethodsThis review, conducted according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, identified articles through searches of electronic databases, including PubMed, Scopus, Web of Science, ScienceDirect, and Google Scholar, as well as through gray literature. The search encompassed published and unpublished studies from 2021 to 2024 reporting on COVID-19 vaccine uptake and/or acceptance in Cameroon. Extracted data were compiled in a Microsoft Excel spreadsheet and analyzed using R statistical software (version 4.4.2). A random-effects model was employed when heterogeneity exceeded 50%. Publication bias was assessed using funnel plots, Egger’s test, and Begg’s test. Meta-regression was used to explore the influence of study characteristics.ResultsTwenty-two studies, encompassing 24,130 participants, were included. The pooled vaccine uptake proportion was 37.14% (95% CI: 29.24-45.05), with substantial heterogeneity (I² = 98.2%,p<0.001). Subgroup analyses revealed lower uptake among the general population (23.18%; 95% CI: 10.11-36.25) and in community settings (16.0%; 95% CI: 0.97-31.04) compared with healthcare workers (42.12%; 95% CI: 34.14-50.09). Younger age (OR = 0.53; 95% CI: 0.42-0.67) was inversely associated with vaccine uptake, while being in a partnership (OR = 1.59; 95% CI: 1.11-2.27) was positively associated. Higher levels of education (OR = 1.75; 95% CI: 1.56-1.97), urban residence (OR = 1.66; 95% CI: 1.21-2.29).ConclusionThis meta-analysis revealed a suboptimal pooled COVID-19 vaccine uptake required to ensure a herd immunity. The results of this meta-analysis underline the crucial need to step up efforts to improve vaccination coverage, particularly among the most vulnerable populations. Identifying and addressing the factors underlying this low coverage is imperative if public health objectives are to be met. Public health interventions should be tailored to address the specific concerns and needs of different age groups and marital statuses.
Temporal Dynamics of Microbial Communities in Anaerobic Digestion: Influence of Temperature and Feedstock Composition on Reactor Performance and Stability
Authors: Piercy Ellen , Sun Xinyang , Ellis Peter R. , Taylor Mark , Guo Miao 
Published: January 2025

AbstractAnaerobic digestion (AD) offers a sustainable biotechnology to recover resources from carbon- and nutrient-rich wastewater streams, such as food-processing wastewater. Despite the wide adoption of crude wastewater characterisation, the impact of detailed chemical fingerprinting on AD remains underexplored. This study investigated the influence of fermentation-wastewater composition and operational parameters on AD over time to identify critical parameters influencing microbiome diversity and reactor performance. Eighteen bioreactors were operated under various operational conditions using mycoprotein fermentation wastewater. Detailed chemical analysis fingerprinted the molecules in the fermentation-wastewater throughout the AD process including sugars, sugar alcohols and volatile fatty acids (VFAs). High-throughput sequencing revealed distinct microbiome profiles linked to temperature and reactor configuration, with mesophilic conditions supporting a more diverse and densely connected microbiome. Importantly, significant elevations inMethanomassiliicoccuswere correlated to high butyric acid concentrations and decreased biogas production, further elucidating the role of this newly discovered methanogen in AD. Reactors from different experimental runs had distinct VFA profiles, which impacted microbial taxonomy and diversity. Dissimilarity analysis demonstrated the importance of individual VFAs, sugars and sugar alcohols on microbiome diversity, highlighting the need for detailed chemical fingerprinting in AD studies of microbial trends. Furthermore, machine learning models predicting reactor performance achieved high accuracy based on operational parameters and microbial taxonomy. Operational parameters were found to have the most substantial influence on chemical oxygen demand removal, whilstOscillibacterand twoClostridiumspecies were highlighted as key factors in biogas production. By integrating detailed chemical and biological fingerprinting with explainable machine learning models this research presents a novel approach to advance our understanding of AD microbial ecology, offering insights for industrial applications of sustainable waste-to-energy systems.