bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systemic inflammation during fasting and postprandial states: a comprehensive study of key determinants in a deeply characterized cohort of young adults
Authors: Ebrahimi Parvaneh , Horner David , Burgner David , Brustad Nicklas , Wang Tingting , Ali Mina , Chen Liang , Schoos Ann-Marie M , Bønnelykke Klaus , Stokholm Jakob , Acar Evrim , Vahman Nilo , Chawes Bo , Rasmussen Morten A. 
Published: August 2024

AbstractSystemic inflammation contributes to the pathogenesis of many noncommunicable diseases. Additionally, postprandial inflammation can exacerbate systemic inflammation. These emphasize the need to examine inflammation in both fasting and postprandial states, to identify modifiable factors to alleviate inflammation. This study investigated a comprehensive list of factors spanning from foetal stage to young-adulthood against inflammation levels at fasting (chronic inflammation) and postprandial states (meal-induced transient inflammation). A meal challenge was undertaken in 18-year-olds(n= 298), and inflammation was assessed using the robust GlycA biomarker. Associations between inflammation and various factors were observed, some of which were sex-specific; e.g. the associations of alcohol consumption and smoking with inflammation were significantly stronger in females. Moreover, novel associations from gestation and early life (e.g. pregnancy smoking) were identified. Our findings highlight factors that should inform dietary and lifestyle interventions for reducing systemic inflammation and highlight the importance of considering inflammation in precision nutrition practices.
Estimating optimal therapeutic drug levels of anti-tuberculosis medications based on treatment safety and effectiveness
Authors: Amorim Gustavo , Haas David W. , Cordeiro-Santos Marcelo , Kritski Afrânio L. , Figueiredo Marina C. , Staats Cody , Hachey Brian , Turner Megan , Andrade Bruno B. , Rolla Valeria C. , Sterling Timothy R. ,   the Regional Prospective Observational Research in Tuberculosis (RePORT)-Brazil network
Published: August 2024

BackgroundTherapeutic drug ranges (TDR) for standard anti-tuberculosis (TB) treatment have been determined based on expected drug levels at least 2 hours after taking the dose. In this study we constructed TDR for TB drug levels based on minimizing drug toxicity and maximizing treatment effectiveness.MethodsParticipants were followed prospectively in the Regional Prospective Observational Research in Tuberculosis (RePORT)-Brazil observational cohort study. We focused on participants with culture-confirmed drug-susceptible pulmonary TB who underwent standard TB therapy. TDR were estimated for each TB drug separately: isoniazid (INH), rifampin (RIF), ethambutol (EMB), and pyrazinamide (PZA). TDR were defined as drug concentrations that were both safe and effective: safety was defined as the probability of having an ADR of at most 5%, while effectiveness was defined as a probability of at least 95% of not having either TB treatment failure or recurrence.ResultsThere were 765 plasma samples from 448 patients; 110 (24.6%) were people with HIV, 9 (2.0%) had a grade 3 or higher ADR, and 15 (3.3%) had treatment failure/recurrence. Higher drug concentrations of INH, RIF and EMB were associated with increased odds of having ADR. High concentrations of INH suggested protection against treatment failure/recurrence. Estimated therapeutic drug range for INH (2.3-8.2 µg/ml) and for RIF (0.5-7.5 µg/ml) differed from the currently recommended drug ranges (3-5 µg/ml and 8-24 µg/ml, respectively). Estimates for PZA and EMB were similar to the currently recommended values.ConclusionsOur estimated upper end TDR were higher for INH and lower for RIF compared to currently recommended ranges.
Open Access Data Repository and Common Data Model for Pulse Oximeter Performance Data
Authors: Fong Nicholas , Lipnick Michael S. , Behnke Ella , Chou Yu , Elmankabadi Seif , Ortiz Lily , Almond Christopher S. , Auchus Isabella , Burnett Garrett W. , Bisegerwa Ronald , Conrad Desireé R , Hendrickson Carolyn M. , Hooli Shubhada , Kopotic Robert , Leeb Gregory , Martin Daniel , McCollum Eric D. , Monk Ellis P. , Moore Kelvin L. , Shmuylovich Leonid , Scott J. Brady , Wong An-Kwok Ian , Zhou Tianyue , Pirracchio Romain , Bickler Philip E. , Feiner John , Law Tyler 
Published: August 2024

AbstractThe OpenOximetry Repository is a structured database storing clinical and lab pulse oximetry data, serving as a centralized repository and data model for pulse oximetry initiatives. It supports measurements of arterial oxygen saturation (SaO2) by arterial blood gas co-oximetry and pulse oximetry (SpO2), alongside processed and unprocessed photoplethysmography (PPG) data and other metadata. This includes skin color measurements, finger diameter, vital signs (e.g., arterial blood pressure, end-tidal carbon dioxide), and arterial blood gas parameters (e.g., acid-base balance, hemoglobin concentration).Data contributions are encouraged. All data, from desaturation studies to clinical trials, are collected prospectively to ensure accuracy. A common data model and standardized protocols for consistent archival and interpretation ensure consistent data archival and interpretation. The dataset aims to facilitate research on pulse oximeter performance across diverse human characteristics, addressing performance issues and promoting accurate pulse oximeters.The initial release includes controlled lab desaturation studies (CLDS), with ongoing updates planned as further data from clinical trials and CLDS become available.
Routine Testing for Chlamydia and Gonorrhea in an HIV Pre-Exposure Prophylaxis Program in Hanoi, Vietnam: Implications for Low- and Middle-Income Countries
Authors: Adamson Paul C. , Bui Hao T.M. , Pham Loc Q. , Truong Phuong T. , Le Ngan T. , Le Giang M. , Klausner Jeffrey D. 
Published: August 2024

AbstractObjectivesTo assess the prevalence, anatomical distribution, and correlates ofNeisseria gonorrhoeae(NG) andChlamydia trachomatis(CT) infections within an HIV pre-exposure prophylaxis (PrEP) program in Hanoi, Vietnam.DesignCross-sectional, observational studyMethodsBetween January-December 2022, HIV PrEP program clients who were male at birth, ≥16 years old, reported ≥1 male sex partner in the prior 12 months, were enrolled. A questionnaire collected sociodemographics, sexual behaviors, and clinical data. CT/NG testing was performed on self-collected urine, rectal, and pharyngeal specimens. Multivariate logistic regression was used to identify factors associated with infections.ResultsAmong 529 participants, the prevalence of CT or NG was 28.9% (153/529). The prevalence of NG was 14.4% (76/529) and highest for pharyngeal infections (11.7%; 62/528), while for CT, the prevalence was 20.4% (108/529) and highest for rectal infections (15.0%; 74/493). Symptoms in the prior week were reported by 45.8% (70/153) of those with CT or NG infections. Among asymptomatic participants, there was a low prevalence of urethral CT (3.1%; 14/457) and NG (0.9%; 4/457). Condomless anal sex (aOR= 1.98; 95% CI: 1.27, 3.09) and sexualized drug use in the prior 6 months (aOR= 1.71; 95% CI: 1.09, 2.69) were associated with CT/NG infections.ConclusionsThe study found a high prevalence of CT/NG infections, particularly pharyngeal and rectal infections, within an HIV PrEP program in Hanoi, Vietnam. The findings suggest testing for urethral infections among asymptomatic individuals is of limited value. Further research is needed for STI prevention strategies and updated guidelines for CT/NG screening in HIV PrEP programs in low- and middle-income countries.
BrainGT: Multifunctional Brain Graph Transformer for Brain Disorder Diagnosis
Authors: Shehzad Ahsan , Yu Shuo , Zhang Dongyu , Abid Shagufta , Cheng Xinrui , Zhou Jingjing , Xia Feng 
Published: August 2024

AbstractBrain networks play a crucial role in the diagnosis of brain disorders by enabling the identification of abnormal patterns and connections in brain activities. Previous studies exploit the Pearson’s correlation coefficient to construct functional brain networks from fMRI data and use graph learning to diagnose brain diseases. However, correlation-based brain networks are overly dense (often fully connected), which obscures meaningful connections and complicates subsequent analyses. This dense connectivity poses substantial performance challenges to traditional graph transformers, which are primarily designed for sparse graphs. Consequently, this results in a notable reduction in diagnostic accuracy. To address this challenging issue, we propose a multifunctional brain graph transformer model for brain disorders diagnosis, namely BrainGT, which is capable of constructing multifunctional brain networks rather than a dense brain network from fMRI data. It utilizes the fusion of self-attention and cross-attention mechanisms to learn important features within and across multiple functional brain networks. Classification (diagnosis) experiments conducted on three real fMRI datasets (i.e., ADNI, PPMI, and ABIDE) demonstrate the superiority of the proposed BrainGT over state-of-the-art methods.Impact StatementThe proposed BrainGT model represents a substantial advancement in computational neuroscience, offering a promising tool for more accurate and efficient diagnosis of brain disorders. By constructing multifunctional brain networks from fMRI data, BrainGT overcomes the limitations of traditional graph transformers and correlation-based brain networks. This innovation has profound implications across social, economic, and technological dimensions. Socially, BrainGT can enhance the quality of life for individuals with brain disorders by enabling more accurate diagnoses, leading to more effective treatments and better patient outcomes. Economically, BrainGT has the potential to reduce healthcare costs by streamlining the diagnostic process and potentially reducing the need for more expensive or invasive procedures. Technologically, BrainGT pushes the boundaries of AI and neuroscience, opening new avenues for research and development. It demonstrates the potential of AI to handle complex and dense data structures, with applications that could extend to other fields.
Evaluation of a One Health public health program based on minimum inputs to control Taenia solium in Madagascar
Authors: ANDRIA-MANANJARA Diana Edithe , Raliniaina Modestine , Rakotoarinoro Mihaja , Nely José A , Razafindraibe Nivohanitra , Ramiandrasoa Sylvia Noromanana , Ramahefasoa Betthelhein , Rakotoarison Valisoa Claude , Torgerson Paul R. , Cardinale Eric , Rasamoelina Harena Andriamanivo , Edosoa Glenn , Fleury Agnès , Mwape Kabemba E. , Abela Bernadette , Lightowlers Marshall W. , Donadeu Meritxell 
Published: August 2024

Cysticercosis in humans caused by the parasite Taenia solium is one of the World Health Organization’s Neglected Tropical Diseases. The parasite is transmitted between the human host and pigs. Efforts to prevent the disease have relied mainly on treatment of people with anthelmintics. However to date there is no practical and effective control method that has been delivered as a public health program. Here we describe a large-scale, minimum inputs T. solium control program implemented as a public health program in Madagascar. Initially pigs were vaccinated for porcine cysticercosis and medicated with oxfendazole, after which only young piglets and pigs imported into the program area were targeted for interventions. After piglet interventions were in place and on-going, a single mass drug administration (MDA) was delivered to the human population with a taeniacide. The outcomes were assessed one year after the human treatment, by comparing pre-and post-intervention levels of human T. solium taeniasis and porcine cysticercosis caused by T. solium. Over a twenty-two-month period, 96,735 pig vaccinations were delivered and during the MDA, 117,216 people received taeniacide. Ninety percent of the pig population were receiving vaccination and medication at the end of the intervention period. Coverage of the eligible human population by the MDA was 62.5%. Human taeniasis was found to be 1.25% prior to the MDA and 0.6% one year after the MDA. Prior to the intervention 30.8% of slaughter-age pigs had viable T. solium infection whereas no viable infection was detected in any pig treated in the program. The program successfully demonstrated effective control of T. solium transmission using minimum inputs and delivered as a public health program. Sustained control and expansion of the program could potentially lead to the elimination of the disease being a public health problem in Madagascar.
Deciphering causal relationships between cell type-specific genetic factors and brain imaging-derived phenotypes and disorders
Authors: Yang Anyi , Zhao Xingzhong , Yang Yucheng T. , Zhao Xing-Ming 
Published: August 2024

AbstractThe integration of expression quantitative trait loci (eQTLs) and genome-wide association study (GWAS) findings to identify causal genes aids in elucidating the biological mechanisms and the discovery of potential drug targets underlying complex traits. This can be achieved by Mendelian randomization (MR), but to date, most MR studies investigating the contribution of genes to brain phenotypes have been conducted on heterogeneous brain tissues and not on specific cell types, thus limiting our knowledge at the cellular level. In this study, we employ a MR framework to infer cell type-specific causal relationships between gene expression and brain-associated complex traits, using eQTL data from eight cell types and large-scale GWASs of 123 imaging-derived phenotypes (IDPs) and 26 brain disorders and behaviors (DBs). Our analysis constructs a cell type-specific causal gene atlas for IDPs and DBs, which include 254 and 217 potential causal cell type-specific eQTL target genes (eGenes) for IDPs and DBs, respectively. The identified results exhibit high cell type specificity, with over 90% of gene-IDP and 80% of gene-DB associations being unique to a single cell type. We highlight shared cell type-specific patterns between IDPs and DBs, characterize the putative causal pathways among cell type-specific causal eGenes, DBs and IDPs, and reveal the spatiotemporal expression patterns of these cell type-specific causal eGenes. We also demonstrate that cell type-specific causal eGenes can characterize the associations between IDPs and DBs. In summary, our study provides novel insights into the genetic foundations at the cellular level that influence brain structures, disorders and behaviors, which reveals important implications for therapeutic targets and brain health management.
Patient-Reported Characteristics of Pernicious Anaemia:A first step to initiate James Lind Alliance Priority Setting Partnership Driven Research
Authors: Thain Alfie , Visser Petra , Hart Kathryn , Nexo Ebba , McCaddon Andrew , Hannibal Luciana , Wolffenbuttel Bruce HR , Green Ralph , Ward Nicola , Seage Catherine Heidi , Owen Julian , Burchell Katrina , Dib Marie-Joe , Ahmadi Kourosh R 
Published: August 2024

AbstractObjectivePernicious anaemia (PA) is characterised by vitamin B12 deficiency due to autoimmune-mediated loss of gastric parietal cells and intrinsic factor. The Pernicious Anaemia Society (PAS) identified 10 research priorities for PA through a James-Lind Alliance Priority Setting Partnership (JLA-PSP). This study aimed to survey PAS members to identify and characterise a cohort of patients to form a PA research repository.MethodsAn online survey was designed using SurveyMonkey, comprising 21 questions on diagnosis, comorbidities, family history, and management. The survey was sent to 3,482 PAS members (April-September 2022) via the PAS website and email.ResultsAtotal of 1,191 PAS members completed the survey. Among individuals with a probable (n=471) or suspected PA (n=500) diagnosis, 84% were UK-based, and 81% were female, with an age range of 23-93 years. Diagnosis was predominantly based on low serum B12 (50%), positive intrinsic factor (38%), and/or parietal cell autoantibodies (15%). Diagnostic delays were common, with 37% waiting ≥3 years for a diagnosis. Nearly half had one or more other autoimmune diseases. One-third reported having at least 2 and up to 7 family members with PA or other autoimmune diseases. Vitamin B12 treatment frequency varied widely, ranging from daily to 3-monthly injections.ConclusionThis study highlights gaps in current diagnostic and management approaches for PA, paving the way for future work in line with the JLA-PSP research priorities. By characterising a cohort of PA patients and compiling baseline data, we provide a foundation for research to develop more effective diagnostic and management strategies.
Modeling the drivers of differential Typhoid Conjugate Vaccine (TCV) impact in Pakistan: force of infection and age-specific duration of protection
Authors: Kraay Alicia N.M. , Yousafzai Mohammad T. , Qureshi Sonia , Gauld Jillian , Qamar Farah N. 
Published: August 2024

AbstractBackgroundWhile trials have demonstrated high efficacy of typhoid conjugate vaccine (TCV), data on effectiveness are limited. We report initial impacts and predict future benefits of TCV from two provinces in Pakistan.MethodsWe used blood culture-confirmed typhoid cases from the Surveillance for Enteric Fever in Asia Project (SEAP) and Impact assessment of Typhoid conjugate vaccine following introduction in Routine Immunization Program of Pakistan (ITRIPP) to estimate the population-level impact of vaccination (2018-2023). We used regression models to estimate initial impacts and an agent-based model to predict future benefits.FindingsIn Sindh, typhoid incidence was higher and cases were younger compared with Punjab. TCV reduced incidence by 48.9% in Sindh (95% CI: 47.3-50.3%) and 66.2% in Punjab (95% CI: 64.7%, 67.6%) over the first 2 years after vaccine rollout but declined each year. In Sindh, waning was quicker and models predicted that population incidence would stabilize near pre-vaccine levels in 2024. An additional campaign could provide short-term, but not long-term, benefits. In contrast, in Punjab, incidence is projected to remain low for several years, and the standard vaccine program may be sufficient. However, follow up data from Punjab are needed to better characterize waning immunity.InterpretationTCV has reduced incidence in Pakistan, but protection varies by site. Standard vaccine policy may be sufficient to control incidence in settings with moderate transmission. However, in settings with particularly high incidence and/or short duration of protection, alternative strategies to reduce the force of infection may be needed.FundingBill & Melinda Gates Foundation
Unpacking sources of transmission in HIV prevention trials with deep-sequence pathogen data – BCPP/ Ya Tsie study
Authors: Magosi Lerato E. , Tchetgen Tchetgen Eric , Novitsky Vlad , Pretorius Holme Molly , Moore Janet , Bachanas Pam , Lebelonyane Refeletswe , Fraser Christophe , Moyo Sikhulile , Hurwitz Kathleen E. , Gaolathe Tendani , Goyal Ravi , Makhema Joseph , Lockman Shahin , Essex Max , De Gruttola Victor , Lipsitch Marc 
Published: August 2024

AbstractTo develop effective HIV prevention strategies that can guide public health policy it is important to identify the main sources of infection in HIV prevention studies. Accordingly, we devised a statistical approach that leverages deep- (or next generation) sequenced pathogen data to estimate the relative contribution of different sources of infection in community-randomized trials of infectious disease prevention. We applied this approach to the Botswana Combination Prevention Project (BCPP) and estimated that 90% [95% Confidence Interval (CI): 81 – 93] of new infections that occurred in individuals in communities that received combination prevention (including universal HIV test-and-treat) originated from individuals residing in communities outside of the trial area. We estimate that the relative impact of the intervention was greater in rural geographically isolated communities with limited opportunity for imported infections compared to communities neighboring major urban centers. Treating people with HIV limits the spread of infection to uninfected individuals; accordingly, counterfactual modeling scenarios estimated that a nationwide application of the intervention could have reduced transmissions to recipients in trial communities by 59% [3 – 87], much higher than the observed 30% reduction. Our results suggest that the impact of the BCPP trial intervention was substantially limited by sources of transmission outside the trial area, and that the impact of the intervention could be considerably larger if applied nationally. We recommend that studies of infectious disease prevention consider the impact of sources of transmission beyond the reach of the intervention when designing and evaluating interventions to inform public health programs.
Temporal and interaction dynamics of dengue cases, entomological and meteorological variables in Melaka, Malaysia: A multivariate time series analysis
Authors: Alipitchay Shazelin , Alias Muhammad Aswad , Hamid Sharifah Nur Shahirah Syed Abdul , Hamzah Rabizah , Mansor Norain , Ab. Hamid Nurulhusna , Othman Hidayatulfathi 
Published: August 2024

AbstractThe interaction between dengue cases, entomological and meteorological variables has remained intricate for decades. Validated facts are important to form robust decision making with the adoption of safer and sustainable efforts. This study aims to elucidate the relationship between the variables in the long run and short-term dynamic focusing in Melaka, Malaysia, in an attempt to improve the understanding of the variables and their temporal associations. This study quantifies the variables on their temporal associations, potential time lags, and dynamic interplays between all the variable data sets. The research applies a Johansen Cointegration Test and Vector Error Correction Model to validate long term run and examine short-term deviations among dengue cases, temperature, ovitrap and sticky ovitrap data from 2020-2022. Empirical findings prove that temperature, sticky ovitrap index (SOI) and ovitrap index (OI) has a significant and unique long-run equilibrium relationship with dengue cases. The short-term equilibrium results display a robust causality between variables. The model fit elucidates 74.2% of the dynamics. The VECM model provides an excellent trade-off between goodness of fit and complexity in describing the variables examined. Previous dengue occurrences predicted a surge of new dengue cases while preserving the cyclical pattern. The model predicts the utility and efficacy of sticky ovitraps. It also validates ovitrap use as a surveillance tool and offers substantiation of the influence of temperature on the progression of dengue cases.