bluuebunny/crossref_metadata_2025_split huggingface dataset:
HIV viral suppression at different thresholds and duration of treatment in the dolutegravir treatment era in Sierra Leone: a nationwide survey
Authors: Song Jin-Wen , Yang Guang , Kamara Matilda N. , Sun Wei , Guan Qun , Barrie Umu , Jiba Darlinda F. , Jalloh Abdulai Tejan , Liu Ming , Tamba Francis K. , Yendewa George A. , Wang Ligui , Zhao Rongtao , Lakoh Sulaiman 
Published: November 2023

Abstract
Introduction
Viral load assessment for people living with HIV is key for monitoring treatment and achieving the 95-95-95. In this study, we aimed to assess the degree of viral suppression at different thresholds and treatment duration after the introduction of dolutegravir-based therapy in ten public hospitals in Sierra Leone.

Methods
We used a cross-sectional study design to recruits patients aged 18 years or older between August 2022 and January 2023. Statistical analyses were performed using R-software. Logistic regression was used to assess factors independently associated with viral suppression. The level of significance was set at P < 0.05.

Results
Of the 2,253 patients recruited, 1,720 (76%) were women and 1,705 (76%) were receiving a fixed dose combination of tenofovir, lamivudine and dolutegravir. The median age and duration of anti-retroviral therapy (ART) was 36.0 (IQR, 28.0–45.0) years and 40.9 (IQR, 14.4–79.6) months, respectively. Using a threshold of HIV RNA < 1000 copies/mL, 1,715 (88.4%) patients on ART for more than 6 months were virally suppressed. Viral suppression rates were higher with dolutegravir-based (1,277, 89.5%) than efavirenz-based (418, 86.2%) ART. HIV RNA was < 200 copies/mL in 1,643 (84.6%) patients or < 50 copies/mL in 1,487 (76.6%) patients or between 50 and 999 copies/mL in 228 (11.7%) patients. Viral suppression rates at different ART durations (months) were as follows: 84.2% (≤ 3), 88.8% (4–6), 90.9% (6–12), and 88.1% (> 12). Viral suppression rates were higher for patients aged 40 or older (40–50 years: aOR 2.05, 95%CI 1.41–3.04, P < 0.01; 50–60 years: aOR 2.51, 95%CI 1.53–4.35, P < 0.01; >60 years: aOR 2.69, 95%CI 1.28–6.63, P = 0.02). Men had 49% lower odds of viral suppression than women (aOR 0.50, 95% CI 0.38–0.67, P < 0.01).

Conclusion
We report a viral suppression rate of 88.4% among patients on treatment for at least 6 months, with higher rate of suppression with dolutegravir than efavirenz. Factors associated with virological suppression were age and gender, emphasizing the need for innovative differentiated ART delivery models to optimize viral suppression and achieve the 95% target.
Identification of potential diagnostic biomarkers for tenosynovial giant cell tumour by integrating microarray and single-cell RNA sequencing data
Authors: Chen Chen , Zheng Linli , Zeng Gang , Chen Yanbo , Liu Wenzhou , Song Weidong 
Published: November 2023

Abstract
Purpose
Tenosynovial giant cell tumour (TGCT) is a benign hyperplastic and inflammatory disease of the joint synovium or tendon sheaths, which may be misdiagnosed due to its atypical symptoms and imaging features. We aimed to identify biomarkers with high sensitivity and specificity to aid in diagnosing TGCT.

Methods
Two scRNA-seq datasets (GSE210750 and GSE152805) and two microarray datasets (GSE3698 and GSE175626) were downloaded from the Gene Expression Omnibus (GEO) database. By integrating the scRNA-seq datasets, we discovered that the osteoclasts are abundant in TGCT in contrast to the control. The single-sample gene set enrichment analysis (ssGSEA) further validated this discovery. Differentially expressed genes (DEGs) of the GSE3698 dataset were screened and the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of DEGs were conducted. Osteoclast-specific up-regulated genes (OCSURGs) were identified by intersecting the osteoclast marker genes in the scRNA-seq and the up-regulated DEGs in the microarray and by the least absolute shrinkage and selection operator (LASSO) regression algorithm. The expression levels of OCSURGs were validated by an external dataset GSE175626. Then, single gene GSEA, protein–protein interaction (PPI) network, and gene-drug network of OCSURGs were performed.

Result
22 seurat clusters were acquired and annotated into 10 cell types based on the scRNA-seq data. TGCT had a larger population of osteoclasts compared to the control. A total of 159 osteoclast marker genes and 104 DEGs (including 61 up-regulated genes and 43 down-regulated genes) were screened from the scRNA-seq analysis and the microarray analysis. Three OCSURGs (MMP9, SPP1, and TYROBP) were finally identified. The AUC of the ROC curve in the training and testing datasets suggested a favourable diagnostic capability. The PPI network results illustrated the protein–protein interaction of each OCSURG. Drugs that potentially target the OCSURGs were predicted by the DGIdb database.

Conclusion
MMP9, SPP1, and TYROBP were identified as osteoclast-specific up-regulated genes of the tenosynovial giant cell tumour via bioinformatic analysis, which had a reasonable diagnostic efficiency and served as potential drug targets.
Performance of DNA methylation analysis in the detection of high-grade cervical intraepithelial neoplasia or worse (CIN3+): a cross-sectional study
Authors: Liu Yuxiang , Chen Yan , Xiong Jing , Zhu Peng , An Yuhang , Li Shu , Chen Puxiang , Li Qing 
Published: November 2023

AbstractIt is commonly accepted that host genes show high methylation in cervical intraepithelial neoplasia 3 (CIN3) or worse (CIN3+). However, study quality varies, as does the clinical performance of markers in different populations. We aimed to validate candidate gene DNA methylation with standardized testing methods in the same batch of samples. We first compared the performance of 16 DNA methylation markers for detecting CIN3+ in the 82-sample training set, including 24 subjects with ≤ CIN1, 10 subjects with CIN2, 23 subjects with CIN3, and 25 subjects with cervical cancer (CC). Then five methylation markers were selected and subsequently validated among an independent set of 74 subjects, including 47 subjects with ≤ CIN1, 13 subjects with CIN2, 6 subjects with CIN3, and 8 subjects with CC. The results in the validation set revealed that methylation analysis of the SOX1 (SOX1m) showed a superior level of clinical performance (AUC = 0.879; sensitivity = 85.7%; specificity = 90.0%). SOX1m had better accuracy than cytology, with a reduced referral rate (23.0% vs. 31.4%) and a lower number of overtreatment (5 vs. 13) cases among high-risk human papillomavirus (hrHPV)-positive women. Importantly, among hrHPV-positive and SOX1m-negative women, only 1 CIN3 patient was at risk for follow-up after 1 year, whereas 1 CIN3 patient and 1 CC patient were at risk among hrHPV-positive and cytology-negative women. In this investigation, we screened 16 reported methylation markers to provide a basis for future studies related to potential precancerous lesion/cancer methylation markers in the Chinese population. The study also revealed that SOX1m has optimal CIN3+ detection performance, suggesting that it may be a promising biomarker for detecting CIN3+ in the Chinese population.
Comparison of diagnostic methods for assessment of Ostertagia ostertagi exposure in Norwegian dairy herds
Authors: Opsal Tonje , Toftaker Ingrid , Robertson Lucy , Woolsey Ian , Hektoen Lisbeth 
Published: November 2023

Abstract
Background
The gastrointestinal nematode (GIN) Ostertagia ostertagi can cause severe disease in first season grazers (FSG) and impaired performance due to subclinical infections in adult cows. Diagnostic methods to assess exposure include faecal egg count and detection of specific antibodies using antibody-ELISAs resulting in an optical density ratio (ODR). Using the ELISA test on bulk tank milk (BTM) allows for a herd level diagnosis. Appropriate use of diagnostic methods for evaluation of O. ostertagi exposure is required to optimize herd parasite surveillance and aid in a sustainable control regime. The aim of this study was to describe the relationship between different diagnostic tests used to assess GIN exposure in Norwegian production systems. A cross-sectional field study was carried out in twenty herds in Norway in the fall of 2020. Serum and faecal samples were taken from 380 individuals, of which 181 were FSG and 199 were cows. In addition, milk was collected from every cow and one BTM sample was taken from each herd. Faecal egg counts were performed. The distribution of ODR values in individual samples within and between herds and the associations between BTM ODR and individual ODR values were described. The data were analysed using visual assessment of scatter plots, Pearson correlation coefficients and linear regression.

Results
A high variability of the within-herd individual ODR values in serum and milk in every herd was detected. The ODR in BTM explained a low degree of the variation in the individual serum and milk samples. When plotting the ODR results in milk or serum according to four BTM categories, the distribution of ODR values were notably different in the highest and lowest BTM categories. The correlation between individual milk and serum samples was moderate (r = 0.68), while the highest correlation (r = 0.81) was between the BTM ODR and the group average individual milk samples.

Conclusions
A poor predictive ability for BTM ODR to assess individual ODR values in both FSG and cows was demonstrated. However, the study indicates that the evaluation by ELISA test on BTM to assess exposure to GIN could be useful in herds with a very high or low BTM ODR.
A peer-volunteer led active ageing programme to prevent decline in physical function in older people at risk of mobility disability (Active, Connected, Engaged [ACE]): study protocol for a randomised controlled trial
Authors: Stathi Afroditi , Withall Janet , Crone Diane , Hawley-Hague Helen , Playle Rebecca , Frew Emma , Fenton Sally , Hillsdon Melvyn , Pugh Christopher , Todd Chris , Jolly Kate , Cavill Nick , Western Max , Roche Sarah , Kirby Nigel , Boulton Elisabeth , Thompson Janice , Chatwin Katie , Davies Amy , Szekeres Zsofia , Greaves Colin 
Published: November 2023

Abstract
Background
The Active Connected Engaged [ACE] study is a multi-centre, pragmatic, two-arm, parallel-group randomised controlled trial [RCT] with an internal pilot phase. The ACE study incorporates a multi-level mixed methods process evaluation including a systems mapping approach and an economic evaluation. ACE aims to test the effectiveness and cost-effectiveness of a peer-volunteer led active ageing intervention designed to support older adults at risk of mobility disability to become more physically and socially active within their communities and to reduce or reverse, the progression of functional limitations associated with ageing.

Methods/design
Community-dwelling, older adults aged 65 years and older (n = 515), at risk of mobility disability due to reduced lower limb physical functioning (Short Physical Performance Battery (SPPB) score of 4–9 inclusive) will be recruited. Participants will be randomised to receive either a minimal control intervention or ACE, a 6-month programme underpinned by behaviour change theory, whereby peer volunteers are paired with participants and offer them individually tailored support to engage them in local physical and social activities to improve lower limb mobility and increase their physical activity. Outcome data will be collected at baseline, 6, 12 and 18 months. The primary outcome analysis (difference in SPPB score at 18 months) will be undertaken blinded to group allocation. Primary comparative analyses will be on an intention-to-treat (ITT) basis with due emphasis placed on confidence intervals.

Discussion
ACE is the largest, pragmatic, community-based randomised controlled trial in the UK to target this high-risk segment of the older population by mobilising community resources (peer volunteers). A programme that can successfully engage this population in sufficient activity to improve strength, coordination, balance and social connections would have a major impact on sustaining health and independence.
ACE is also the first study of its kind to conduct a full economic and comprehensive process evaluation of this type of community-based intervention. If effective and cost-effective, the ACE intervention has strong potential to be implemented widely in the UK and elsewhere.

Trial registration
ISRCTN, ISRCTN17660493. Registered on 30 September 2021.
Trial Sponsor: University of Birmingham, Contact: Dr Birgit Whitman, Head of Research Governance and Integrity; Email: researchgovernance@contacts.bham.ac.uk.
Protocol Version 5 22/07/22.
Tolerance of engineered Rhodosporidium toruloides to sorghum hydrolysates during batch and fed-batch lipid production
Authors: Woodruff William , Deshavath Narendra Naik , Susanto Vionna , Rao Christopher V. , Singh Vijay 
Published: November 2023

Abstract
Background
Oleaginous yeasts are a promising candidate for the sustainable conversion of lignocellulosic feedstocks into fuels and chemicals, but their growth on these substrates can be inhibited as a result of upstream pretreatment and enzymatic hydrolysis conditions. Previous studies indicate a high citrate buffer concentration during hydrolysis inhibits downstream cell growth and ethanol fermentation in Saccharomyces cerevisiae. In this study, an engineered Rhodosporidium toruloides strain with enhanced lipid accumulation was grown on sorghum hydrolysate with high and low citrate buffer concentrations.

Results
Both hydrolysis conditions resulted in similar sugar recovery rates and concentrations. No significant differences in cell growth, sugar utilization rates, or lipid production rates were observed between the two citrate buffer conditions during batch fermentation of R. toruloides. Under fed-batch growth on low-citrate hydrolysate a lipid titer of 16.7 g/L was obtained.

Conclusions
Citrate buffer was not found to inhibit growth or lipid production in this engineered R. toruloides strain, nor did reducing the citrate buffer concentration negatively affect sugar yields in the hydrolysate. As this process is scaled-up, $131 per ton of hydrothermally pretreated biomass can be saved by use of the lower citrate buffer concentration during enzymatic hydrolysis.

Graphical Abstract
Differential associations of horizontally and vertically transmitted symbionts on Ixodes ricinus behaviour and physiology
Authors: Bakker Julian W. , Begemann Hannah L. M. , Fonville Manoj , Esser Helen J. , de Boer Willem F. , Sprong Hein , Koenraadt Constantianus J. M. 
Published: November 2023

Abstract
Background
Ixodes ricinus ticks are infected with a large diversity of vertically and horizontally transmitted symbionts. While horizontally transmitted symbionts rely on a vertebrate host for their transmission, vertically transmitted symbionts rely more on the survival of their invertebrate host for transmission. We therefore hypothesized horizontally transmitted symbionts to be associated with increased tick activity to increase host contact rate and vertically transmitted symbionts to be associated with higher tick weight and lipid fraction to promote tick survival.

Methods
We used a behavioural assay to record the questing activity of I. ricinus ticks. In addition, we measured weight and lipid fraction and determined the presence of ten symbiont species in these ticks using qPCR, of which six were vertically transmitted and four horizontally transmitted.

Results
Vertically transmitted symbionts (e.g. Midichloria mitochondrii) were associated with an increase in tick weight, whereas horizontally transmitted symbionts (e.g. Borrelia burgdorferi sensu lato) were often associated with lower weight and lipid fraction of ticks. Moreover, horizontally transmitted symbionts (e.g. B. burgdorferi s.l.) were associated with increased tick activity, which may benefit pathogen transmission and increases tick-borne disease hazard.

Conclusions
Our study shows that horizontally and vertically transmitted symbionts differentially influence the behaviour and physiology of I. ricinus and warrants future research to study the underlying mechanisms and effects on transmission dynamics of tick-borne pathogens.

Graphical abstract
Impact of thermodynamical rotational flow of cerebrospinal fluid in the presence of elasticity
Authors: Balasundaram Hemalatha 
Published: November 2023

AbstractObjectiveTo explore the experimental justification of cerebrospinal fluid (CSF) amplitude and elastic fluctuations of ventricles, we extend our previous computational study to models with rotational flow and suitable boundary conditions. In the present study, we include an elastic effect due to the interaction with the thermal solutal model which accounts for CSF motion which flows rotationally due to hydrocephalus flows within the spinal canal.MethodsUsing an analytical pertubation method, we have attempted a new model to justify CSF flow movement using the influences of wall temperature difference.ResultsThis paper presents results from a computational study of the biomechanics of hydrocephalus, with special emphasis on a reassessment of the parenchymal elastic module. CSF amplitude in hydrocephalus patients is 2.7 times greater than that of normal subjects.ConclusionsThis finding suggests a non-linear mechanical system to present the hydrocephalic condition using a numerical model. The results can be useful to relieve the complexities in the mechanism of hydrocephalus and can shed light to support clinically for a convincing simulation.
Determinants of adoption of female headed household in microfinance program: a case study on Oromia Credit and Saving Share Company (OCSSCO) in Guto Gida district, Ethiopia
Authors: Hinkosa Bonsa 
Published: November 2023

AbstractSince its introduction in the 1970, the word microfinance is being used very often in the development vocabulary today. It is taken as a strategy to overcome the constraints of conventional bank in reaching the poor and seen as one of the most efficient instruments for livelihood improvement. However, empirically the effectiveness of these programs on the livelihood of household is still inconclusive and debatable. Additionally, the relationships between socio-economic, demographic factors and participation in microfinance program are not seen in the study area and this motivated the researcher to undertake the study. The objectives of this study were identifying the factors that affect female headed household participation in microfinance program. Multi-stage sampling technique was used to draw representative sample and used cross-sectional survey. Cross-sectional survey data were collected from randomly selected 169 female headed household using interview/survey schedules. Descriptive and econometric methods were used to analyze the data. The results of descriptive statistics indicate that the majority of client household use microcredit to purchase agricultural input. Logit results indicate that program participation was significantly affected by seven explanatory variables. Among the variable’s family size of the household, livestock ownership and land size affected household participation in the program positively, whereas age of household head, distance of household home from microfinance office, wealth status of the household and household perception of risk have negative effect. Finally, the study recommends that microfinance institutions should broaden their outreach and expand its access in to large.
Development of an amperometric sensor for epinephrine determination using an Azure A/silver nanocluster modified electrode
Authors: Priya C. , Anuja S. , Babu R. Suresh , Narayanan S. Sriman 
Published: November 2023

AbstractA novel electrochemical sensor was developed for the detection of Epinephrine (EP) utilizing Azure A (AzA), a phenothiazine dye, and citrate-capped silver nanoparticles. The interaction between Azure A and silver nanoparticles facilitated the formation of AzA/silver nanoclusters through a self-assembled approach. The morphological analysis of AzA/silver nanoclusters was conducted using field-emission scanning electron microscopy (FESEM). The nanoclusters were then immobilized on a graphite electrode via a simple drop-casting method, resulting in a modified electrode. The electrochemical properties of the modified electrode were investigated using cyclic voltammetry and linear sweep voltammetry techniques. The modified electrode exhibited enhanced electrocatalytic oxidation of EP at a lower oxidation potential of 0.27 V. The electrochemical analysis demonstrated that the modified electrode functioned as an amperometric sensor, enabling the detection of EP within a concentration range of 4.6 × 10–7 to 3.6 × 10–3 M, with a correlation coefficient of 0.9950 and a detection limit of 2.2 × 10–7 M (S/N = 3). The modified electrode exhibited excellent selectivity, sensitivity, and a remarkably low detection limit, making it highly suitable for EP determination. Its ease of preparation further adds to the practicality and potential applications of this electrode.
Child maltreatment among victims of violent death: an analysis of national violent death reporting system data, 2014–2018
Authors: Barrett Nicole M. , Michaels Nichole L. , Kistamgari Sandhya , Smith Gary A. , Brink Farah W. 
Published: November 2023

Abstract
Background
Limited information is known about the impact of childhood maltreatment on lifetime risk of violent death. This study aimed to compare manner of death, demographics, age at time of death, and the presence of a mental health or substance use disorder among decedents of violent deaths with a history of child maltreatment to those without.

Methods
This cross-sectional study compared characteristics of pediatric and adult violent deaths with and without a history of child maltreatment that were captured in the National Violent Death Reporting System from 2014 through 2018.

Results
Decedents who were male, multiracial, and had adulthood substance or mental health disorders were more likely to have a history of maltreatment. All-age decedents with a history of maltreatment were more likely to die by homicide. Adult decedents with a history of maltreatment were more likely to die by suicide. Maltreated decedents died significantly younger than non-maltreated decedents.

Conclusions
Among victims of violent deaths, an identified history of child maltreatment was associated with increased risk of homicide across the lifespan, adult suicide, and earlier death. A history of child maltreatment was also associated with mental health and substance use disorders, which may reflect one of the pathways through which the child maltreatment-to-death association functions.