bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of the COVID-19 pandemic on regional and national uptake of HIV testing services in Sierra Leone: a descriptive analysis
Authors: Sheriff Hannah , Egesimba Ginika , Molleh Bailah , Tucker Jarieu , Younge Gerald , Tamba Francis K. , Lakoh Sulaiman , Chan Adrienne K. , Mishra Sharmistha , Sevalie Stephen 
Published: January 2025

AbstractBackgroundA key milestone in the reduction of the global HIV burden is reaching the UNAIDS 95-95-95 target by 2025. The COVID-19 pandemic may have affected the ability of countries to achieve this target, but data to describe this impact is limited. This study assessed national HIV testing service uptake in Sierra Leone during three periods of the COVID-19 pandemic.MethodsWe conducted a retrospective cross-sectional study using secondary program data of all patients tested for HIV in all 16 districts of Sierra Leone. Data from March 2019 to February 2020 (pre-COVID-19); March 2020 to February 2021 (during COVID-19); and March 2021 to February 2022 (post-COVID-19) were extracted from DHIS-2 and descriptive analyses were performed using Stata (15.1, StataCorp LLC, College Station, TX).ResultsThe median number of HIV tests was 58,588 (IQR 54,232 to 62,077) in the pre-COVID phase, 55,141 (IQR 52,975 to 57,689) during the COVID-19 phase, and 74,954 (IQR 72,166 to 76,250) in the post-COVID phase. This shows that HIV testing rate decreased by 6.3% during the COVID-19 period and increased substantially by 36.0% in the post-COVID-19 period. Twice more women than men were tested for HIV across all periods—pre-COVID-19 (38,825 vs. 19,789), during COVID-19 (36,923 vs. 17,755), and post-COVID-19 (49,205 vs. 25,472) phases.ConclusionOur study shows that HIV testing was significantly disrupted during the COVID-19 pandemic but recovered quickly after the pandemic. These findings highlight that lessons learned from previous epidemics may influence adaptive strategies to maintain essential health services during public health emergencies.
Baseline associations between exposure to metals and systolic and diastolic blood pressure among women in the Household Air Pollution Intervention Network Trial
Authors: Karakwende Patrick , Barr Dana Boyd , Checkley William , Clasen Thomas , Lovvorn Amy , Contreras Carmen Lucía , Diaz Anaite A. , Dusabimana Ephrem , Las Fuentes Lisa De , Jabbarzadeh Shirin , Johnson Michael , Kalisa Egide , Kirby Miles , McCracken John P. , Ndagijimana Florien , Ndikubwimana Adolphe , Ntakirutimana Theoneste , de Dieu Ntivuguruzwa Jean , Jennifer L , Peel Ajay Pillarisetti , Davila-Roman Victor G. , Rosa Ghislaine , Waller Lance A. , Wang Jiantong , Thompson Lisa , Clark Maggie L. , Young Bonnie N. 
Published: January 2025

AbstractLead (Pb) and cadmium (Cd) are metals that occur naturally in the environment and are present in biomass fuels, such as wood. When these fuels are burned, they can release Pb and Cd into the air, leading to exposure through inhalation. Studies of exposure to metals and health outcomes suggest harmful impacts, including cardiovascular diseases. We assessed baseline associations between Pb and Cd concentrations in dried blood spots with systolic and diastolic blood pressure (SBP, DBP) among women in the Household Air Pollution Intervention Network (HAPIN) trial. We analyzed data from three of the four HAPIN randomized controlled trial sites (Guatemala, Peru, and Rwanda), focusing on women aged 40 to 79 years living in households reliant on biomass cooking. Dried blood spots were collected, processed, and analyzed for Pb and Cd exposure; SBP and DBP were measured following international guidelines. Demographic, socioeconomic, and dietary variables were collected via standardized questionnaires administered by local field staff. Statistical analyses included multivariable linear regression to examine associations between Pb and Cd, separately, and BP, adjusting for covariates informed by a Directed Acyclic Graph. Additional analyses assessed effect modification by age and research site. There was regional variation in BP levels among women, with median SBP and DBP values higher in Rwanda (116.3 mmHg, 73.0 mmHg) and Guatemala (113.3 mmHg, 68.3 mmHg) compared to Peru (106.0 mmHg, 63.3 mmHg). Pb exposure showed positive associations with both SBP and DBP. For each log-unit increase in Pb concentration, we observed increases of 2.36 mmHg SBP (95% CI 0.51, 4.20) and 1.42 mmHg DBP (95% CI 0.16, 2.67). Cd was not associated with SBP or DBP in this analysis. Pb exposure may be an important risk factor for increased SBP and DBP, markers of cardiovascular disease risk.
Applying an Intersectional Approach to Examine the Associations between Sexual Minority Stressors, Resilience, and Substance Misuse Disparities among a National Sample of Sexual Minority Populations
Authors: Zhang Chen , Qiao Shan , Chang Wonkyung , Liu Yu 
Published: January 2025

AbstractObjectivesOur study aims to investigate the associations between sexual minority stressors, resilience factors, and substance misuse outcomes, using an intersectional framework to examine heterogeneities across sexual minority populations (SMPs). The study hypothesized that resilience factors would mitigate the adverse effects of minority stressors on alcohol and drug misuse risks.DesignThe current study employed a secondary data analysis strategy to analyze a cross-sectional data using Bayesian hierarchical modeling and Multilevel Analysis of Individual Heterogeneity and Discriminatory Accuracy (MAIHDA).SettingData were obtained from the Generation Study (Wave 1), a nationally representative cohort of SMPs in the United States.ParticipantsThe study included 1,518 participants aged 18–59. Combinations of education, birth sex, sexual orientation, income, and race/ethnicity defined intersectional strata. Participants were selected based on self-reported demographic and behavioral data.Primary and Secondary Outcome MeasuresPrimary outcomes were the risks of alcohol use disorder (AUD) and drug use disorder (DUD), measured using validated scales (AUDIT and DUDIT). Explanatory variables included resilience factors (social support, life satisfaction, social well-being, community connectedness) and sexual minority stressors (everyday discrimination, perceived stigma, healthcare stereotype threat, internalized homophobia).ResultsBayesian modeling identified everyday discrimination as the strongest predictor of AUD (Estimate = 0.10, 95% CI [0.01, 0.18]) and DUD (Estimate = 0.23, 95% CI [0.15, 0.32]). Perceived stigma was negatively associated with AUD risk (Estimate = –0.06, 95% CI [-0.12, 0.00]), and social well-being was inversely associated with DUD risk (Estimate = –0.17, 95% CI [-0.23, –0.10]). MAIHDA revealed that intersectional strata contributed to 1.61% of the variance in AUDIT scores and 1.88% in DUDIT scores. Including resilience and stressors in the model explained 93.6% of the strata-level variance for AUDIT and 34.45% for DUDIT, underscoring the significant impact of these factors on substance misuse disparities.ConclusionsThe findings highlight the complex interplay between resilience, stressors, and intersectional identities in substance use behaviors among SMPs. Using an intersectional framework and MAIHDA can enhance understanding of heterogeneities in substance misuse across strata and inform targeted, equity-focused interventions to reduce disparities. Further research should explore longitudinal effects and intervention development.
Real world data analysis of venous thromboembolism, adverse major cardiovascular events, neoplasia and serious infections in ulcerative colitis patients
Authors: de la Oliva Víctor , Esteban-Medina Alberto , Fernández del Valle Patricia , Sánchez Ana , Susin M. Belen , Dopazo Joaquín , Loucera Carlos , Leo-Carnerero Eduardo 
Published: January 2025

AbstractVenous thromboembolism (VTE), major adverse cardiovascular events (MACE), neoplasia, and serious infections are significant complications associated with Immune-mediated inflammatory diseases. Actually, the occurrence of such complications in these patients has been observed to be higher than that anticipated from classical risk factors alone. Additionally, the administration of anti-inflammatory treatments, such as corticosteroids, associated to inflammatory diseases is recognized to further elevate this risk. In Spain, data on the prevalence of risk of cardiovascular events, neoplasia or serious infections, particularly among individuals with ulcerative colitis are scarce. This study leverages real-world data from the Andalusian Health Population Database (BPS) to analyze the incidence and risk factors of these complications among ulcerative colitis patients. A cohort of 23,518 patients, aged 18 years or older, with an ulcerative colitis diagnosis between 2010 and 2019, was used in the study. The objective was to assess the incidence of VTE, MACE, neoplasms, and serious infections and to evaluate the impact of age and other factors related to ulcerative colitis on these outcomes.The study revealed a notably higher incidence of VTE and MACE in ulcerative colitis patients compared to the incidence described for the general population, particularly among those over 60 years of age. Specifically, the incidence of VTE was significantly elevated post-diagnosis, with deep vein thrombosis (DVT) and pulmonary embolism, being the most common manifestations. MACE, including myocardial infarction and stroke, also presented a higher risk, especially in older patients. Also, a significant portion of patients developed various malignancies. Also remarkable is the significant higher incidence of VTE, malignancies and serious infections as the severity of ulcerative colitis increases. The use of immunosuppressive therapies was associated with an increased risk of infections, and likely with VTE and malignancies, further complicating the management of these patients.The findings of this study underscore the need for heightened vigilance in the management of ulcerative colitis patients, particularly those at advanced ages. Preventive strategies, such as thromboprophylaxis during hospitalization and regular monitoring for cardiovascular and neoplastic complications, are essential. The study contributes valuable insights into the burden of comorbidities in ulcerative colitis and highlights the importance of tailored treatment and monitoring strategies to improve patient outcomes.
Host environment shapes filarial parasite fitness andWolbachiaendosymbionts dynamics
Authors: Fercoq Frédéric , Cormerais Clément , Remion Estelle , Gal Joséphine , Plisson Julien , Fall Arame , Alonso Joy , Lhermitte-Vallarino Nathaly , Hübner Marc P. , Kohl Linda , Landmann Frédéric , Martin Coralie 
Published: January 2025

SummaryFilarial nematodes, responsible for diseases like lymphatic filariasis and onchocerciasis, depend on symbioticWolbachiabacteria for reproduction and development. Using theLitomosoides sigmodontisrodent model, we investigated how host type-2 immunity influencesWolbachiadynamics and parasite development. Type-2 immune environments selectively reduce germlineWolbachiain female filariae from wild-type mice, a change associated with disrupted oogenesis, embryogenesis, and microfilarial production, while somaticWolbachiaremain unaffected. Antibiotic treatments achieving systemicWolbachiaclearance result in similar reproductive impairments. Notably,Wolbachia-free microfilariae are observed shortly afterWolbachiadepletion, suggesting that early-stage embryogenesis can proceed temporarily before progressive germline dysfunction ensues.Wolbachia-free microfilariae develop into infective larvae in the vector, but stall beyond the L4 stage in vertebrate hosts, showing arrested growth and reproductive organ maturation defects in both male and female larvae. These findings highlight the variable dependency onWolbachiaacross life stages and provide insights into host-parasite-endosymbiont interactions shaped by environmental pressures.Graphical abstract.
Multicilia dynamically transduce Shh signaling to regulate choroid plexus functions
Authors: Mao Suifang , Song Rui , Jin Shibo , Pang Song , Jovanovic Aleksandra , Zimmerman Adam , Li Peng , Wu Xinying , Wendland Michael F. , Lin Kerry , Chen Wei-Chi , Choksi Semil P. , Chen Gang , Holtzman Michael J. , Reiter Jeremy F. , Wan Ying , Xuan Zhenyu , Xiang Yang K. , Xu C Shan , Upadhyayula Srigokul , Hess Harald F. , He Lin 
Published: January 2025

AbstractChoroid plexus is a major site for cerebrospinal fluid (CSF) production, characterized by a multiciliated epithelial monolayer that regulates CSF production. We demonstrate that defective choroid plexus ciliogenesis or Intraflagellar transport yields neonatal hydrocephalus, at least in part, due to increased water channel Aqp1 and ion transporter Atp1a2 expression. We demonstrate choroid plexus multicilia as sensory cilia, transducing both canonical and non-canonical Shh signaling. Interestingly, it is the non-canonical Shh signaling that represses Aqp1 and Atp1a2 expression by Smo/Gαi/cAMP pathway. Choroid plexus multicilia exhibit unique ciliary ultrastructure, carrying features of both primary and motile cilia. Unlike most cilia that elongate during maturation, choroid plexus ciliary length decreases during development, causing a decline of Shh signaling intensity in developing choroid plexus, a derepression of Aqp1 and Atp1a2, and ultimately, an increased CSF production. Hence, developmental dynamics of choroid plexus multicilia dampens the Shh signaling intensity to promote CSF production.
Single-cell spatial transcriptome reveals pathological features of human hippocampus with sclerosis
Authors: Wang Lifang , Li Xingjie , Liu Yuyang , Jin Bufan , Wei Yanrong , He Youzhe , Ma Yaru , Wu Zihan , Gong Xue , An Yanru , Kong Xueying , Xing Yanan , Ye Ruixi , Tao Quyuan , Li Aiqing , Chang Mingkai , Pu Li , Li Jinmei , Pang Li , Zhou Dong , Song Cai , Liu Shiping , Xu Xun , Liu Longqi , Han Lei , Hong Zhen 
Published: January 2025

AbstractMore than half of epileptic patients ultimately turned to intractable epilepsy. Mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE-HS), the most common type of intractable epilepsies, whose pathological mechanism remains elusive. Here, using 42 human hippocampal samples from surgical donors of MTLE (32 with and 10 without HS) through single-cell resolution Stereo-seq and histologcial experiments, we revealed spatially pathological changes of gene expression and cell type composition with HS systematically. After precise parcellation of hippocampal subregions and differentially expressed gene (DEG) analysis between each region with and without sclerosis, we found Cornu Ammonis (CA) subregions with higher number of DEGs were vulnerable to sclerosis, especially CA1 and CA3. Within CA1, we found that CA1-superficial and proximal areas were more vulnerable than CA1-deep and distal areas in sclerosis. Meanwhile, after analyzing 350,795 segmented cells from Stereo-seq, we found dramatically increasing density of astrocyte accompanied with significantly decreasing density of excitatory neurons in CA1, especially superficial and proximal CA1, and CA3 in sclerosis. In these two vulnerable subregions, proliferative astrocyte (P_astrocyte) and reactive astrocyte (R_astrocyte) were found to be enriched whereas apoptotic subtype of astrocyte (A_astrocyte), related with apoptotic pathway, was mainly located in alveus, which strengthened cell communication with reactive microglia (R_microglia) in HS, revealing the novel pathological feature in our work. The pseudotime analysis indicated that CA excitatory neurons underwent synaptic impairment, energy dysfunction, aging, and finally losing cell identity until death through autophagy or apoptosis. Besides, we also found a resilient subtype, EX_CA2-4.3, highly expressed extracellular matrix related genes includingPDYN, and was increasing the interaction of BDNF-NTRK, NFASC-CNTN1 to withstand the damage from sclerosis. Together, our study provided a reference of human hippocampus with and without HS caused by MTLE, and highlighted the potential pathological mechanism on molecular and cellular level of MTLE-HS.
Peptide Design through Binding Interface Mimicry
Authors: Kong Xiangzhe , Jiao Rui , Lin Haowei , Guo Ruihan , Huang Wenbing , Ma Wei-Ying , Wang Zihua , Liu Yang , Ma Jianzhu 
Published: January 2025

ABSTRACTPeptides offer distinct advantages for targeted therapy, including oral bioavailability, cellular permeability, and high specificity, which set them apart from conventional small molecules and biologics. In this work, we developed an AI algorithm, named PepMimic, to transform a known protein receptor or an existing antibody of a target into a short peptide drug by mimicking the binding interfaces between targets and known binders. The structural root mean square deviation and interface DockQ with reference binders were 61% and 75% better than the best existing methods on the PepBench datasets. We then applied this novel peptide-design methodology to five drug targets: PD-L1, CD38, BCMA, HER2, and CD4. SPRi results show that 8% of the peptides exhibited dissociation constant (KD) values at the 10-8M level, and 26 peptides achieving KDvalues as low as 10-9M. This success rate was 20,000 times higher than that observed in a random library screening conducted under identical conditions. PepMimic was applied to target proteins lacking available binders by first utilizing AI algorithms to design protein binders, followed by the generation of peptides through simulation of these artificial interfaces. The top-ranked peptides underwent extensive cellular validation andin vivotesting through tail vein injections in breast, myeloma, and lung tumor mouse models. Experimental results demonstrated effective membrane binding and highlighted the strong potential of these peptides for clinical diagnostic imaging and targeted therapeutic applications.
Characterising ongoing brain aging from cross-sectional data
Authors: Smith Stephen M. , Miller Karla L. , Nichols Thomas E. 
Published: January 2025

Abstract“Brain age delta” is the difference between age estimated from brain imaging data and actual age. Positive delta in adults is normally interpreted as implying that an individual is aging (or has aged) faster than the population norm, an indicator of unhealthy aging. Unfortunately, from cross-sectional (single timepoint) imaging data, it is impossible to know whether a single individual’s positive delta reflects a state of faster ongoing aging, or an unvarying trait (in other words, a “historical baseline effect” in the context of the population being studied). However, for a cross-sectional dataset comprising many individuals, one could attempt to disambiguate the overall relative contributions of varying aging rates vs. fixed baseline effects. We present a method for doing this, and show that for the most common approaches, which estimate a single delta per subject, baseline effects are likely to dominate. If instead one estimates multiple biologically distinct modes of brain aging, we find that some modes do reflect aging rates varying strongly across subjects. We demonstrate this, and verify our modelling, using longitudinal (two timepoint) data from 4,400 participants in UK Biobank. In addition, whereas previous work found incompatibility between cross-sectional and longitudinal brain aging, we show that careful data processing does show consistency between cross-sectional and longitudinal results.
Defining the cell and molecular origins of the primate ovarian reserve
Authors: Wamaitha Sissy E. , Rojas Ernesto J. , Monticolo Francesco , Hsu Fei-man , Sosa Enrique , Mackie Amanda M. , Oyama Kiana , Custer Maggie , Murphy Melinda , Laird Diana J. , Shu Jian , Hennebold Jon D. , Clark Amander T. 
Published: January 2025

AbstractThe primate ovarian reserve is established during late fetal development and consists of quiescent primordial follicles in the ovarian cortex, each composed of granulosa cells surrounding an oocyte in dictate. As late stages of fetal development are not routinely accessible for study with human tissue, we exploited the evolutionary proximity of the rhesus macaque to investigate primate follicle formation. Similar to human prenatal ovaries, the rhesus also develops multiple types of pre-granulosa (PG) cells, with the majority of primordial follicles derived from PG2 with small variable contributions from PG1. We observed that activated medullary follicles recruit fetal theca cells to establish a two-cell system for sex-steroid hormone production prior to birth, providing a cell-based explanation for mini puberty.
Meta all the way down: An overview of neuroimaging meta-analyses
Authors: Oudyk Kendra , Dockès Jérôme , Peraza Julio , Kent James , Torabi Mohammad , Wang Michelle , McPherson Brent , Mirhakimi Niusha , de la Vega Alejandro , Laird Angela R. , Poline JB 
Published: January 2025

AbstractMeta-analyses are invaluable tools for navigating the rapidly expanding scientific literature. Given their high value, ensuring the quality of meta-analyses is paramount. We conducted a multifaceted overview, examining each step in a manual neuroimaging meta-analysis on a large scale. We used four novel datasets comprising over 14,000 papers, including fMRI meta-analyses, fMRI studies, studies included in meta-analyses, and studies associated with image data on NeuroVault.Regarding successes, two-thirds of meta-analyses stated that they followed PRISMA guidelines, and 65% included a flowchart describing their inclusion process.We point out several areas for improvement. Pre-registration was fairly rare (20%), and only half listed their exact search strategy. There could be a location bias in which papers are included, and many did not include enough studies to be robust against publication bias (68% of meta analyses have less than 30 studies included).We also offer ideas for future directions. As image based meta-analysis is the gold standard, we have indicated which topics have the most image data available. The potential redundancy of topics can be visualized in our paper, and we recommend future meta-analyses be in conversation with past ones by citing and discussing previous similar work. By addressing these findings, the neuroimaging community can collectively improve the field of neuroimaging meta-analyses.