bluuebunny/crossref_metadata_2025_split huggingface dataset:
Under the name of “Lua”: revisiting genetic heterogeneity and population ancestry of Austroasiatic speakers in northern Thailand through genomic analysis
Authors: Kampuansai Jatupol , Seetaraso Tanapon , Dansawan Maneesawan , Sathupak Suwapat , Kutanan Wibhu , Srikummool Metawee , Inta Angkana 
Published: October 2024

Abstract
Background
Austroasiatic (AA)-speaking populations in northern Thailand are of significant interest due to their status as indigenous descendants and their location at the crossroads of AA prehistoric distribution across Southern China, the Indian Subcontinent, and Mainland Southeast Asia. However, the complexity of ethnic identification can result in inaccuracies regarding the origin and migration history of these populations. To address this, we have conducted a genome-wide SNP analysis of 89 individuals from two Lavue and three Lwa-endonym populations. We then combined our outcomes with previously published data to elucidate the genetic diversity and clustering of AA groups in northern Thailand.

Results
Our findings align with existing linguistic classifications, revealing different genetic compositions among the three branches of the Mon-Khmer subfamily within the AA family: Monic, Khmuic, and Palaungic. Although the term “Lua” ethnicity is confusingly used to identify ethnic groups belonging to both Khmuic and Palaungic branches, our genomic data indicate that the Khmuic-speaking Lua living on the eastern side of the region are relatively distant from the Palaungic-speaking Lavue and Lwa populations living on the western side. The Lavue populations, primarily inhabiting mountainous areas, exhibit a genetic makeup unique to the AA family, with a close genetic relationship to the Karenic subgroup of the Sino-Tibetan language family. Conversely, the Lwa and Blang populations, residing in lowland river valleys, display genetic signatures resulting from admixture with Tai-Kadai-speaking ethnic groups.

Conclusion
Utilizing genome-wide SNP markers, our findings indicate genetic heterogeneity among the Lua, Lavue, and Lwa ethnic groups. The intricate interplay of genetics, cultural heritage, and historical influences has shaped these ethnic communities. Our study underscores the importance of accurate ethnic classifications, emphasizing the use of self-identified endonyms, names created and used by the ethnic groups themselves. This approach respects the AA communities in northern Thailand and acknowledges their significant contributions to advancing our understanding of genetic anthropology.
Residual transmission of HIV infection from mother to child in the Atlantic and littoral departments in Benin
Authors: Dagba Gbessin Edwige Hermione , Sina Haziz , Keke René Kpemahouton , Gomgnimbou Michel Kiréopori , Afangnihoun Aldric , Bachabi Moussa , Ouedraogo Abdoul-Salam , Baba-Moussa Lamine 
Published: October 2024

Abstract
Background
The implementation of the WHO’s 2015 recommendations in Benin, requires an assessment of the progress made over time in preventing the transmission of the infection to exposed-infants, and the identification of its determinants.

Methods
This was a retrospective study of HIV-1 exposed-infants who underwent PCR between the 6th and 8th weeks of life. Early diagnostic tests were performed using the Abbott m2000 RealTime platform. Comparison of proportions tests (analysis of the significance of the difference in prevalence) with an error threshold of 5% were used to assess the determinants of the transmission. Statistical analysis was performed using R statistical software, version 4.1.3.0.

Results
A total of 5,312 infants benefited from early diagnosis by PCR between 2016 and 2021. Among them, 52% are males, tritherapy before pregnancy was the majority treatment used by mothers (30.6%) and monotherapy that of newborns (70%). Mixed breastfeeding is the feeding method with the highest prevalence. The overall transmission rate was 3.4% over the six years. The highest prevalence was achieved in 2018 (4.2%) and the lowest in 2021 (2.7%). The prevalence was lower when mothers were on tritherapy before pregnancy. The determinants of transmission were: mixed breastfeeding, lack of treatment in mothers (22.4%), lack of treatment in infants (19.7%), undefined treatments or absence of treatment in the mother-child pair.

Conclusion
This study shows the contribution over time of the PMTCT program to reducing HIV transmission among exposed-infants and also underlines the need for proper conduct of treatment in any women of childbearing age.
The global burden of erectile dysfunction and its associated risk factors in diabetic patients: an umbrella reviews
Authors: kitaw Tegene Atamenta , Abate Biruk Beletew , Tilahun Befkad Derese , Yilak Gizachew , Rede Moges Beriye , Getie Addisu , Haile Ribka Nigatu 
Published: October 2024

Abstract
Background
Erectile dysfunction is no longer a whisper in the shadows; it’s a rising tide threatening the sexual health of millions of men in different regions. In the cases of diabetes, the condition worsens and has a potent cocktail of physical and psychological distress, chipping away at men’s confidence, self-esteem, and mental health. This worrying trend shows no signs of slowing down, with projections claiming a staggering 322 million men globally could be affected in the near future. This urgent issue demands immediate attention and action. Thus, this umbrella review intended to estimate the current burden of erectile dysfunction and associated risk factors among diabetic patients in the global context.

Methods
Following PRISMA guidelines, we searched for relevant studies in PubMed, Embase, Scopus, Web of Science, Cochrane Database of Systematic Reviews, and Google Scholar. These studies reported the prevalence of erectile dysfunction and associated risk factors in diabetic patients. The quality of the included studies was assessed using the Assessment of Multiple Systematic Reviews 2 tool. To estimate the pooled prevalence of erectile dysfunction, we employed a weighted inverse variance random-effects model. We further conducted subgroup analyses, assessed heterogeneity and publication bias, and performed sensitivity analyses to strengthen the robustness of our findings. Prediction intervals were also calculated to estimate the range within which future observations will likely fall. In all statistical analyses, the statistical significance was declared at P- value < 0.05.

Results
In this umbrella review, a total of 108 030 male diabetic patients were included to estimate the global prevalence of erectile dysfunction. The pooled global prevalence of erectile dysfunction in diabetic patients was 65.8% (95CI: 58.3 − 73.3%), while In Africa it was 62.9% (95CI: 46.1–79.7). Age (> 40 years) (AOR = 1.95, 95CI: 1.03–3.24), DM duration (> 10years) (AOR = 1.90,95CI: 1.16–2.65), peripheral vascular disease (AOR = 2.74, 95CI: 1.42–4.06) and BMI (> 30 kg/m2) (AOR = 1.07,95CI: 1.01–1.20) were identified as associated risk factors of erectile dysfunction in diabetic patient.

Conclusion
The high global prevalence of erectile dysfunction (ED) in diabetic patients is alarming, with an estimated two-thirds experiencing the condition. These findings underscore the significant burden of ED faced by diabetic men and emphasize the urgent need for global attention to the issue. This includes promoting early screening for erectile dysfunction in this population and ensuring access to appropriate treatment and support.
Denture microbiome shift and changes of salivary inflammatory markers following insertion of 3D printed removable partial PMMA denture: a pilot study
Authors: Yacob Norlela , Safii Syarida Hasnur , Ahmad Norasmatul Akma , Yunus Norsiah , Razak Fathilah Abdul 
Published: October 2024

Abstract
Background
The aim of this study was to investigate the microbiome shift of denture biofilm formation, the incidence of Candida and changes of salivary inflammatory markers following insertion of 3-dimensional printed PMMA denture.

Methods
This was a pilot study of 6 patients provided with 3D printed (test group) or conventionally heat-cured (control group) removable partial acrylic dentures followed up for 6 weeks. 3 denture swabs were collected at week 1, 3 and 6; and saliva samples were collected at baseline, week 1, 3 and 6 following denture insertion. Microbial DNA was isolated, and the 16S rRNA gene was amplified and sequenced to assess the denture microbiota. The presence of Candida was determined using PCR assay. The levels of salivary biomarkers lactoferrin (LTF) and histatin (HTN) were determined using ELISA.

Results
Denture microbiome of both groups exhibited similar microbial compositions at weeks 1, 3 and 6. However, the percentage of Streptococcus in the test group was significantly lower at week 1 (p < 0.05). Greater bacterial diversity was detected in the test group (p < 0.05; pairwise Wilcoxon) after 6 weeks. The presence of Candida was only detected in one sample of the 3D printed denture (test group) after 6 weeks. The level of LTF biomarkers increased in both groups after 6 weeks, however, the level of HTN increased only in the control group.

Conclusions
Denture microbiome of both groups demonstrated similar microbial compositions. After 6 weeks, 3D printed denture demonstrated higher diversity with delayed microbiome shift compared to conventional heat cure dentures. 3D printed denture may be a viable alternative to conventional denture and it has a potential to delay microbial dysbiosis.

Clinical Relevance
Among wearers, 3D printed denture can potentially reduce the risk of denture stomatitis. A greater diversity may delay or slow the transition of denture microbiome to dysbiosis.
Role of mast cells in the pathogenesis of oral submucous fibrosis: a systematic review and meta-analysis
Authors: Bijai Laliytha Kumar , Aboalela Ali A. , Albalawi Farraj , Khanagar Sanjeev B , Iyer Kiran 
Published: October 2024

Abstract
Background
Oral Submucous Fibrosis (OSMF) is an oral potentially malignant disorder (OPMD) that commonly occurs in the South Asian population as there is high usage of areca nut. There has been extensive research on the pathogenesis and treatment of this condition. It is well-established in the scientific literature that mast cells (MC) have a definitive role in several inflammatory disorders. OSMF being a chronic inflammatory disorder, is also expected to have increased MCs. Hence, this review aims to evaluate the role of MCs in the pathogenesis of OSMF.

Methods
A systematic search of articles was performed by two of the authors independently in PubMed, Scopus, Embase, Web of Science, and Google Scholar using the appropriate keywords and Boolean terms. The risk of bias was assessed using the Modified Newcastle-Ottawa Scale. The meta-analysis was performed with R studio software (Version: 4.4.0, Year: 2024, Company: The R foundation for statistical computing).

Results
The search retrieved 36 studies, of which 16 were suitable for the review. There is evidence for a marked increase in the number of MCs in OSMF than the normal mucosa upon analyzing the retrieved articles. However, when comparing the grades of OSMF, there are variations in the reports. As all the retrieved articles were case-control studies, the risk of bias was analyzed using the Modified New Castle Ottawa Scale. All the studies scored in the good category (Score 6–9). The pooled effect size shows the Standard Mean Deviation (SMD) to be 0.09, 95% confidence interval (CI) [-0.18;0.37] to lie on either side of no effect. Hence the role of MCs in OSMF has not been established because of homogeneity and consistent sampling error.

Conclusion
Our systematic review does suggest a definitive role of mast cells in the progression of OSMF. However, there is a lack of methodological rigor in the included studies. This may contribute to diluting the results.
COVID-19 vaccination and lethality reduction: a prospective observational study in Venezuela during the last two waves
Authors: Forero-Peña David A. , Leyva Jéssica L. , Valenzuela María V. , Omaña-Ávila Óscar D. , Regalado-Gutiérrez Oriana A. , Mendoza-Millán Daniela L. , Sánchez-Ytriago Elisanny A. , Lahoud-El Hachem Andrea C. , Farro Katherine R. , Maita Ana K. , González Romina del C. , Rodriguez-Saavedra Carlis M. , Hernández-Medina Fernando , Camejo-Ávila Natasha A. , Freitas-de Nobrega Diana C. , Celis Rodrigo T. , Forero-Peña José L. , Martínez Alfonso , Grillet María E. , Landaeta María E. , Carrión-Nessi Fhabián S. 
Published: October 2024

Abstract
Background
In Venezuela, the predominant vaccines administered are BBIBP-CorV and Gam-COVID-Vac. Despite robust evidence from randomized clinical trials validating the effectiveness of COVID-19 vaccines in mitigating hospitalization and mortality, there is still a lack of post-authorization safety studies conducted within this demographic population.

Methods
A prospective observational study from October 5, 2021 to March 31, 2022 encompassed COVID-19 vaccinated and unvaccinated patients from four sentinel hospitals in Venezuela. Patient lethality was predicted using Charlson Comorbidity index. Clinical outcomes were assessed through WHO’s COVID-19 Clinical Progression Scale.

Results
Out of the 175 patients assessed, 85 (48.6%) were vaccinated. The median Charlson Comorbidity index was 3 points, with no statistically significant differences observed between the groups (p = 0.2). A total of 50 (28.6%) patients died during the study period, with higher proportion of deaths in unvaccinated patients (35.6% vs. 21.2%, p = 0.035). Advanced age (OR = 1.043, 95% CI = 1.015–1.071, p = 0.002) was associated with increased death risk, whereas vaccination against COVID-19 (OR = 0.428, 95% CI = 0.185–0.99, p = 0.047), high oxygen saturation (OR = 0.964, 95% CI = 0.934–0.995, p = 0.024), and enoxaparin administration (OR = 0.292, 95% CI = 0.093–0.917, p = 0.035) were associated with decreased death risk.

Conclusion
During the third and fourth waves of the pandemic, COVID-19 vaccination was associated with a 57% reduction in lethality among patients in four public hospitals in Venezuela.
Yiqihuoxue decoction (GSC) inhibits mitochondrial fission through the AMPK pathway to ameliorate EPCs senescence and optimize vascular aging transplantation regimens
Authors: Liu Yinan , Niu Zenghui , Wang Xue , Xiu Chengkui , Hu Yanhong , Wang Jiali , Lei Yan , Yang Jing 
Published: October 2024

Abstract
Background
During the aging process, the number and functional activity of endothelial progenitor cells (EPCs) are impaired, leading to the unsatisfactory efficacy of transplantation. Previous studies demonstrated that Yiqihuoxue decoction (Ginseng-Sanqi-Chuanxiong, GSC) exerts anti-vascular aging effects. The purpose of this study is to evaluated the effects of GSC on D-galactose (D-gal)induced senescence and the underlying mechanisms.

Methods
The levels of cellular senescence-related markers P16, P21, P53, AMPK and p-AMPK were detected by Western blot analysis (WB). SA-β-gal staining was used to evaluate cell senescence. EPCs function was measured by CCK-8, Transwell cell migration and cell adhesion assay. The morphological changes of mitochondria were detected by confocal microscopy. The protein and mRNA expression of mitochondrial fusion fission Drp1, Mff, Fis1, Mfn1, Mfn2 and Opa1 in mitochondria were detect using WB and RT–qPCR. Mitochondrial membrane potential, mtROS and ATP of EPCs were measured using IF. H&E staining was used to observe the pathological changes and IMT of the aorta. The expressions of AGEs, MMP-2 and VEGF in aorta were measured using Immunohistochemical (IHC). The levels of SOD, MDA, NO and ET-1 in serum were detected by SOD, MDA and NO kits.

Results
In vitro, GSC ameliorated the senescence of EPCs induced by D-gal and reduced the expression of P16, P21 and P53. The mitochondrial morphology of EPCs was restored, the expression of mitochondrial Drp1, Mff and Fis1 protein was decreased, the levels of mtROS and ATP were decreased, and mitochondrial function was improved. Meanwhile, the expression of AMPK and p-AMPK increased. The improvement effects of GSC on aging and mitochondrial morphology and function were were hindered after adding AMPK inhibitor. In vivo, GSC improved EPCs efficiency, ameliorated aortic structural disorder and decreased IMT in aging mice. The serum SOD level increased and MDA level decreased, indicating the improvement of antioxidant capacity. Increased NO content and ET-1 content suggested improvement of vascular endothelial function. The changes observed in SOD and MMP-2 suggested a reduction in vascular stiffness and the degree of vascular damage. The decreased expression of P21 and P53 indicates the delay of vascular senescence.
Adolescent mental health services in West Africa: a comparative analysis of Burkina Faso, Ghana, and Niger
Authors: Amenah Michel Adurayi , Ibrahim Nassirou , Tapsoba Ludovic Deo Gracias , Novignon Jacob , Fenny Ama Pokuaa , Agyepong Irene A. , da Silva Roxane Borges , Ensor Tim 
Published: October 2024

Abstract
Background
Adolescent mental health (AMH) is a critical issue worldwide, particularly in West Africa, where it is intensified by socio-economic, cultural, and security challenges. Insecurity and the presence of mining sites expose adolescents to hazardous environments, substance abuse, and adulterated alcohol, further aggravating their mental health. Despite these severe issues, research on AMH in this region remains limited. This study aims to analyze the provision of AMH services in Burkina Faso, Ghana, and Niger, highlighting the unique challenges these countries face within the broader West African healthcare context.

Methods
The study adopted a multi-stage, stratified sampling design to collect data from primary healthcare centers (PHCs) in the three countries. Using STATA.17, Descriptive analysis was conducted on the data related to availability of AMH services, types of mental health disorders treated, resources available, and OPD attendance rates. The analysis also incorporated factors such as the rural-urban divide and the presence of national guidelines for AMH services.

Results
The findings reveal a significant shortfall in the provision of AMH services across the region, with less than 30% of PHCs across all the countries offering these services. The study also highlights a pronounced rural-urban disparity in AMH service availability, a general absence of national guidelines for AMH care, and low OPD attendance rates.

Conclusion
The study highlights the urgent need for comprehensive policy reform and targeted interventions to enhance AMH services in West Africa. Key policy reforms should include the development and implementation of national guidelines for AMH care and integration of AMH services into primary healthcare. Additionally, efforts should focus on capacity building through the training of mental health professionals, increasing public awareness to reduce stigma, and ensuring equitable resource allocation across rural and urban areas. Improving AMH care is essential not only for the well-being of adolescents but also for driving broader socio-economic development in the region.
A validated heart-specific model for splice-disrupting variants in childhood heart disease
Authors: Lesurf Robert , Breckpot Jeroen , Bouwmeester Jade , Hanafi Nour , Jain Anjali , Liang Yijing , Papaz Tanya , Lougheed Jane , Mondal Tapas , Alsalehi Mahmoud , Altamirano-Diaz Luis , Oechslin Erwin , Audain Enrique , Dombrowsky Gregor , Postma Alex V. , Woudstra Odilia I. , Bouma Berto J. , Hitz Marc-Phillip , Bezzina Connie R. , Blue Gillian M. , Winlaw David S. , Mital Seema 
Published: October 2024

Abstract
Background
Congenital heart disease (CHD) is the most common congenital anomaly. Almost 90% of isolated cases have an unexplained genetic etiology after clinical testing. Non-canonical splice variants that disrupt mRNA splicing through the loss or creation of exon boundaries are not routinely captured and/or evaluated by standard clinical genetic tests. Recent computational algorithms such as SpliceAI have shown an ability to predict such variants, but are not specific to cardiac-expressed genes and transcriptional isoforms.

Methods
We used genome sequencing (GS) (n = 1101 CHD probands) and myocardial RNA-Sequencing (RNA-Seq) (n = 154 CHD and n = 43 cardiomyopathy probands) to identify and validate splice disrupting variants, and to develop a heart-specific model for canonical and non-canonical splice variants that can be applied to patients with CHD and cardiomyopathy. Two thousand five hundred seventy GS samples from the Medical Genome Reference Bank were analyzed as healthy controls.

Results
Of 8583 rare DNA splice-disrupting variants initially identified using SpliceAI, 100 were associated with altered splice junctions in the corresponding patient myocardium affecting 95 genes. Using strength of myocardial gene expression and genome-wide DNA variant features that were confirmed to affect splicing in myocardial RNA, we trained a machine learning model for predicting cardiac-specific splice-disrupting variants (AUC 0.86 on internal validation). In a validation set of 48 CHD probands, the cardiac-specific model outperformed a SpliceAI model alone (AUC 0.94 vs 0.67 respectively). Application of this model to an additional 947 CHD probands with only GS data identified 1% patients with canonical and 11% patients with non-canonical splice-disrupting variants in CHD genes. Forty-nine percent of predicted splice-disrupting variants were intronic and > 10 bp from existing splice junctions. The burden of high-confidence splice-disrupting variants in CHD genes was 1.28-fold higher in CHD cases compared with healthy controls.

Conclusions
A new cardiac-specific in silico model was developed using complementary GS and RNA-Seq data that improved genetic yield by identifying a significant burden of non-canonical splice variants associated with CHD that would not be detectable through panel or exome sequencing.
Recommendations for the creation of benchmark datasets for reproducible artificial intelligence in radiology
Authors: Sourlos Nikos , Vliegenthart Rozemarijn , Santinha Joao , Klontzas Michail E. , Cuocolo Renato , Huisman Merel , van Ooijen Peter 
Published: October 2024

Abstract
Various healthcare domains have witnessed successful preliminary implementation of artificial intelligence (AI) solutions, including radiology, though limited generalizability hinders their widespread adoption. Currently, most research groups and industry have limited access to the data needed for external validation studies. The creation and accessibility of benchmark datasets to validate such solutions represents a critical step towards generalizability, for which an array of aspects ranging from preprocessing to regulatory issues and biostatistical principles come into play. In this article, the authors provide recommendations for the creation of benchmark datasets in radiology, explain current limitations in this realm, and explore potential new approaches.

Clinical relevance statement
Benchmark datasets, facilitating validation of AI software performance can contribute to the adoption of AI in clinical practice.

Key Points

Benchmark datasets are essential for the validation of AI software performance.

Factors like image quality and representativeness of cases should be considered.

Benchmark datasets can help adoption by increasing the trustworthiness and robustness of AI.

Graphical Abstract