bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between post-infection COVID-19 vaccination and symptom severity of post COVID-19 condition among patients on Bonaire, Caribbean Netherlands: a retrospective cohort study
Authors: Berry D.S.F. , Dalhuisen T. , Marchena G. , Tiemessen I. , Geubbels E. , Jaspers L. 
Published: June 2023

ABSTRACTObjectivesIn this retrospective cohort study, we aimed to investigate symptom severity change following COVID-19 vaccination among post COVID-19 condition (PCC) patients on Bonaire.MethodsSymptomatic cases who tested positive for SARS-CoV-2 between the start of the pandemic and 1 October 2021, were unrecovered on the interview day and unvaccinated prior to infection were identified from the national case registry. Patients were interviewed by telephone between 15 November and 4 December 2021 about sociodemographic factors, pre-pandemic health, COVID-19 symptoms and vaccination status. We compared symptom severity change between the acute and post-acute disease phase (>4 weeks after disease onset) of 14 symptoms on a five-point Likert scale for 36 PCC patients having received at least one dose of the BNT162 (BioNTech/Pfizer) vaccine and 11 patients who remained unvaccinated, using separate multiple linear regression models.ResultsMost common post-acute symptoms included fatigue (81%), reduced physical endurance (79%), and reduced muscle strength (64%). Post-infection vaccination was significantly associated with reduced severity of heart palpitations, after adjusting for acute phase severity and duration of illness (β 0.60, 95% CI 0.18-1.02). We did not find a statistically significant association with symptom severity change for other, more prevalent symptoms.ConclusionsLarger prospective studies are needed to confirm our observation in a small study population that post-infection COVID-19 vaccination was associated with reduced severity of heart palpitations among those with this symptom self-attributed to SARS-CoV-2 infection.
Risk screening tools could potentially miss out HIV positive individuals who seek testing services: A secondary program data analysis on the performance characteristics of an adolescent and adult HIV risk screening tool in Uganda
Authors: Lubega Marvin , Guerra Katherine , Ginivan Megan , Kamuntu Yewande , Senyama George , Musoke Andrew , Geoffrey Taasi , Nalubega Sylivia , Khan Shaukat , John Bosco Junior Matovu 
Published: June 2023

AbstractIntroductionImproving HIV testing efficiency has been documented to save financial and material resources for health. In October 2019, the Ministry of health Uganda deployed an HIV risk screening tool for use in 24 health facilities targeting clients aged 15 years and above in both outpatient and Voluntary Counselling and Testing departments.MethodsWe conducted a retrospective secondary data analysis of routinely collected HIV risk screening program data in Uganda, collected from October to November 2019, to determine the performance characteristics of the adolescent and adult HIV risk screening tool in public health facility settings. Statistical measures for the risk screening tool performance included sensitivity, specificity, positive and negative predictive values, and a cost analysis.ResultsA total of 19,854 clients were screened for HIV testing eligibility; we excluded 150 records with incomplete testing information. The overall positivity rate (cluster weighted prevalence of HIV) among those screened was 4.5% (95% CI: 4.1%-4.8%) versus 3.71% (95% CI: 3.06-4.50) among those not screened. The sensitivity and specificity of the risk screening tool were found to be 90.7% (95% CI: 88.4%, 92.7%) and 75.8%, (75.2-76.4) respectively. With screening, the number needed to test to identify one PLHIV reduced from 27 to 22. Although risk screening would have led to 24.5% (4,825/19,704) reduction in testing volume, 9.3% (68/732) of PLHIV would have been missed as they were misclassified as not eligible for testing. The cost per PLHIV identified fell by 3% from $69 without screening to $66.9 with implementation of the screening tool.ConclusionsThe use of HIV risk screening tool in OPD settings in Uganda demonstrated improved HIV testing efficiency by reducing testing volumes but resulted in screening out of a significant number of people living with HIV. The team recommends that scientifically validated HIV risk screening tools be considered for use by countries.
Correlates of the Post-Stroke cognitive impairment among patients with first-ever stroke admitted at tertiary hospitals in Dodoma, Tanzania: a prospective longitudinal study
Authors: Alphonce Baraka , Meda John , Nyundo Azan 
Published: June 2023

AbstractIntroductionStroke patients develop cognitive impairment that, significantly impacting their quality of life, their families, and the community as a whole, but they are not given attention. This study aims to determine the prevalence and predictors of post-stroke cognitive impairment (PSCI) among adult stroke patients admitted to a tertiary hospital in Dodoma, Tanzania.MethodologyA prospective longitudinal study was conducted at tertiary hospitals in the Dodoma region, central Tanzania. A sample size of 158 participants with the first stroke confirmed by CT/MRI brain aged ≥ 18 years met the criteria. At baseline, social-demographic, cardiovascular risks and stroke characteristics were acquired and then at 30 days, participants were evaluated for depression and apathy.. Descriptive statistics were summarised as continuous data reported as Mean (SD) or Median (IQR), and categorical data were summarised using proportions and frequencies. Univariate and multivariable logistic regression analysis were computed to determine predictors of PSCIResultsOf 158 participants, the mean age was 58.7 years, 57.6% were female, and 80.4% of participants met the criteria for post-stroke cognitive impairment. After multivariable logistic regression, left hemisphere stroke (AOR: 5.798, CI: 1.030 – 32.623,p= 0.046), a unit cm3increase in infarct volume (AOR: 1.064, 95% CI: 1.018 – 1.113,p= 0.007), and apathy symptoms (AOR: 12.259, CI: 1.112 – 89.173,p= 0.041) had a significant association with PSCI.ConclusionThe study showed a high prevalence of PSCI; profiling at-risk stroke survivors in a timely intervention may improve their prognosis. Future studies in the area would inform future interventions and policies.
ETIOLOGY OF PRIMARY CEREBELLAR INTRACEREBRAL HEMORRHAGE BASED ON TOPOGRAPHIC LOCALIZATION
Authors: Incontri Diego , Marchina Sarah , Andreev Alexander , Wilson Mitchell , Wang Jia-Yi , Lin David , Heistand Elizabeth C. , Carvalho Filipa , Selim Magdy , Lioutas Vasileios-Arsenios 
Published: June 2023

AbstractBackgroundCerebellar intracerebral hemorrhage (cICH) is often attributed to hypertension or cerebral amyloid angiopathy (CAA). However, deciphering the exact etiology can be challenging. A recent study reported a topographic etiologic relationship with superficial cICH secondary to CAA. We aimed to re-examine this relationship between topography and etiology in a separate cohort of patients and using the most recent Boston criteria version 2.0.MethodsRetrospective analysis of consecutive patients with primary cICH admitted to a tertiary academic center between 2000-2022. cICH location on brain CT/MRI scan(s) was divided into strictly superficial (cortex, surrounding white matter, vermis), vs deep (cerebellar nuclei, deep white matter) or mixed (both regions). MRIs were rated for markers of cerebral small vessel disease. We assigned possible/probable vs absent CAA using Boston criteria 2.0.ResultsWe included 197 patients; 106 (53.8%) females, median age 74 (63-82) years. Fifty-six (28%) patients had superficial cICH and 141 (72%) deep/mixed cICH. MRI was available for 112 (57%) patients [30(26.8%) with superficial and 82(73.2%) with deep/mixed cICH]. Superficial cICH patients were more likely to have possible/probable CAA (48.3% vs 8.6%; OR 11.43, 95%CI 3.26-40.05; p<0.001), strictly lobar cerebral microbleeds (CMBs) (51.7% vs 6.2%; OR 14.18, 95%CI 3.98-50.50; p<0.001), and cortical superficial siderosis (13.8% vs 1.2%; OR 7.70, 95%CI 0.73-80.49; p=0.08). Patients with deep/mixed cICH patients were more likely to have deep/mixed CMBs (59.2% vs 3.4%; OR 41.39, 95% CI 5.01-341.68; p=0.001), lacunes (54.9% vs 17.2%; OR 6.14, 95% CI 1.89-19.91; p=0.002), severe basal ganglia enlarged perivascular spaces (36.6% vs 7.1%; OR 7.63, 95% CI 1.58-36.73; p=0.01), hypertension (84.4% vs 62.5%; OR 3.43, 95% CI 1.61,-7.30; p=0.001), and higher admission systolic blood pressure (172 [146-200] vs 146 [124-158] mmHg, p<0.001).ConclusionsOur results suggest that superficial cICH is strongly associated with CAA whereas deep/mixed cICH is almost exclusively linked to hypertensive arteriopathy.
Diagnostic test accuracy of artificial intelligence in screening for referable diabetic retinopathy in real-world settings: A systematic review and meta-analysis
Authors: Uy Holijah , Fielding Christopher , Hohlfeld Ameer , Ochodo Eleanor , Opare Abraham , Mukonda Elton , Minnies Deon , Engel Mark E 
Published: June 2023

AbstractStudies on artificial intelligence (AI) in screening for diabetic retinopathy (DR) have shown promising results in addressing the mismatch between the capacity to implement DR screening and the increasing DR incidence; however, most of these studies were done retrospectively. This review sought to evaluate the diagnostic test accuracy (DTA) of AI in screening for referable diabetic retinopathy (RDR) in real-world settings. We searched CENTRAL, PubMed, CINAHL, Scopus, and Web of Science on 9 February 2023. We included prospective DTA studies assessing AI against trained human graders (HGs) in screening for RDR in patients living with diabetes. synthesis Two reviewers independently extracted data and assessed methodological quality against QUADAS-2 criteria. We used the hierarchical summary receiver operating characteristics (HSROC) model to pool estimates of sensitivity and specificity and, forest plots and SROC plots to visually examine heterogeneity in accuracy estimates. Finally, we conducted sensitivity analyses to explore the effects of studies deemed to possibly affect the quality of the studies. We included 15 studies (17 datasets: 10 patient-level analysis (N=45,785), and 7 eye-level analysis (N=15,390). Meta-analyses revealed a pooled sensitivity of 95.33%(95% CI: 90.60-100%) and specificity of 92.01%(95% CI: 87.61-96.42%) for patient-level analysis; for the eye-level analysis, pooled sensitivity was 91.24% (95% CI: 79.15-100%) and specificity, 93.90% (95% CI: 90.63-97.16%). Subgroup analyses did not provide variations in the diagnostic accuracy of country classification and DR classification criteria; however, a moderate increase was observed in diagnostic accuracy at the primary-level and, a minimal decrease in the tertiary-level healthcare settings. Sensitivity analyses did not show any variations in studies that included diabetic macular edema in the RDR definition, nor in studies with ≥3 HGs. This review provides evidence, for the first time from prospective studies, for the effectiveness of AI in screening for RDR, in real-world settings.
Evaluating the buffering role of perceived social support and coping resources against the adult mental health impacts of COVID-19 psychosocial stress: a cross-sectional study in South Africa
Authors: Kim Andrew Wooyoung , Swana Someleze , Sarma Mallika S. 
Published: June 2023

ABSTRACTObjectiveswGrowing evidence has highlighted the global mental health impacts of the COVID- 19 pandemic and lockdown, particularly in societies with pre-existing socioeconomic adversities and public health concerns. Despite the sudden and prolonged nature of many psychosocial stressors during the pandemic, recent studies have shown that communities utilized several coping mechanisms to buffer the mental health consequences of COVID-related stress. This paper examines the extent to which coping resources and social support buffered against the mental health effects of COVID-19 psychosocial stress among adults in South Africa.Materials & MethodsAdult participants (n=117) completed an online survey during the second and third waves of the COVID-19 pandemic in South Africa (January-July 2021), which assessed experiences of stress, coping resources, social support, and four mental health outcomes: depression, anxiety, post-traumatic stress disorder, and bipolar disorder. Moderation analyses examined the potential buffering role of coping resources and social support against the mental health effects of COVID-19 stress.ResultsAdults reported elevated rates of psychiatric symptoms. Coping resources buffered against the poor mental health effects of COVID-19 psychosocial stress, whereas perceived social support did not significantly moderate the association between COVID-19 stress and adult mental health.DiscussionThese results suggest that adults in our sample utilized a variety of coping resources to protect their mental health against psychosocial stress experienced during the COVID-19 lockdown and pandemic in South Africa. Additionally, existing mental health conditions and strained social relationships may have attenuated the potential stress-buffering effect of perceived social support on adult mental health.
Metagenomics for pathogen detection during a wildlife mortality event in songbirds
Authors: Mwakibete Lusajo , Greening Sabrina S. , Kalantar Katrina , Ahyong Vida , Anis Eman , Miller Erica A. , Needle David B. , Oglesbee Michael , Thomas W. Kelley , Sevigny Joseph L. , Gordon Lawrence M. , Nemeth Nicole M. , Ogbunugafor C. Brandon , Ayala Andrea J. , Faith Seth A. , Neff Norma , Detweiler Angela M. , Baillargeon Tessa , Tanguay Stacy , Simpson Stephen D. , Murphy Lisa A. , Ellis Julie C. , Tato Cristina M. , Gagne Roderick B. 
Published: June 2023

ABSTRACTMass mortality events in wildlife can be indications of an emerging infectious disease. During the spring and summer of 2021, hundreds of dead passerines were reported across the eastern US. Birds exhibited a range of clinical signs including swollen conjunctiva, ocular discharge, ataxia, and nystagmus. As part of the diagnostic investigation, high-throughput metagenomic next-generation sequencing was performed across three molecular laboratories on samples from affected birds. Many potentially pathogenic microbes were detected, with bacteria comprising the largest proportion; however, no singular agent was consistently identified, with many of the detected microbes also found in unaffected (control) birds, and thus considered to be subclinical infections. Congruent results across laboratories have helped drive further investigation into alternative causes including environmental contaminants and nutritional deficiencies. This work highlights the utility of metagenomic approaches in investigations of emerging diseases and provides a framework for future wildlife mortality events.Article Summary LineThe causative agent of a mass mortality event in passerines remains inconclusive after metagenomic high-throughput sequencing with results prompting further investigation into non-pathogenic causes.
Improved characterization of soil organic matter by integrating FTICR-MS, liquid chromatography tandem mass spectrometry and molecular networking: a case study of root litter decay under drought conditions
Authors: DiDonato Nicole , Rivas-Ubach Albert , Kew William , Clendinen Chaevien , Sokol Noah , Kyle Jennifer E. , Martínez Carmen E. , Foley Megan M. , Tolić Nikola , Pett-Ridge Jennifer , Paša-Tolić Ljiljana 
Published: June 2023

AbstractKnowledge of the type of carbon contained in soils is important for predicting carbon fluxes in a warming climate, yet most soil organic matter (SOM) components are unknown. We used an integrated three-part approach to characterize SOM from decaying root-detritus microcosms subject to either drought or normal conditions. To observe broad differences in SOM compositions we employed direct infusion Fourier transform ion cyclotron resonance mass spectrometry (DI-FTICR-MS). We complemented this with liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify components by library matching. Since libraries contain only a small fraction of SOM components, we also used fragment spectra cosine similarity scores to relate unknowns and library matches through molecular networks. This approach allowed us to corroborate DI-FTICR-MS molecular formulas using library matches and infer structures of unknowns from molecular networks to improve SOM annotation. We found matches to fungal metabolites, and under drought conditions, greater relative amounts of lignin-like vs condensed aromatic polyphenol formulas, and lower average nominal oxidation state of SOM carbon, suggesting reduced decomposition of carbon and/or microbes under stress. We propose this integrated approach as more comprehensive than individual analyses in parallel, with the potential to improve knowledge of the chemical composition and persistence of SOM.SynopsisStructural characterization and identifications are lacking for soil organic matter components. This study integrates molecular formula assignments and structural information from fragment ion spectra into molecular networks to better characterize unknown soil organic matter components.For Table of Contents Only
Bayesian analysis dissects kinetic modulation during non-stationary gene expression
Authors: Wildner Christian , Mehta Gunjan D. , Ball David A. , Karpova Tatiana S. , Koeppl Heinz 
Published: June 2023

ABSTRACTLabelling of nascent stem loops with fluorescent proteins has fostered the visualization of transcription in living cells. Quantitative analysis of recorded fluorescence traces can shed light on kinetic transcription parameters and regulatory mechanisms. However, existing methods typically focus on steady state dynamics. Here, we combine a stochastic process transcription model with a hierarchical Bayesian method to infer global as well locally shared parameters for groups of cells and recover unobserved quantities such as initiation times and polymerase loading of the gene. We apply our approach to the cyclic response of the yeastCUP1locus to heavy metal stress. Within the previously described slow cycle of transcriptional activity on the scale of minutes, we discover fast time-modulated bursting on the scale of seconds. Model comparison suggests that slow oscillations of transcriptional output are regulated by the amplitude of the bursts. Several polymerases may initiate during a burst.
GeNNius: An ultrafast drug-target interaction inference method based on graph neural networks
Authors: Veleiro Uxía , de la Fuente Jesús , Serrano Guillemo , Pizurica Marija , Casals Mikel , Pineda-Lucena Antonio , Vicent Silve , Ochoa Idoia , Gevaert Olivier , Hernáez Mikel 
Published: June 2023

Drug-target interaction (DTI) prediction is a relevant but challenging task in the drug repurposing field. In-silico approaches have drawn particular attention as they can reduce associated costs and time commitment of traditional methodologies. Yet, current state-of-the-art methods present several limitations: existing DTI prediction approaches are computationally expensive, thereby hindering the ability to use large networks and exploit available datasets and, the generalization to unseen datasets of DTI prediction methods remains unexplored, which could potentially improve the development processes of DTI inferring approaches in terms of accuracy and robustness. In this work, we introduce Gennius(Graph Embedding Neural Network Interaction Uncovering System), a Graph Neural Network (GNN)-based method that outperforms state-of-the-art models in terms of both accuracy and time efficiency across a variety of datasets. We also demonstrated its prediction power to uncover new interactions by evaluating not previously known DTIs for each dataset. We further assessed the generalization capability of Genniusby training and testing it on different datasets, showing that this framework can potentially improve the DTI prediction task by training on large datasets and testing on smaller ones. Finally, we investigated qualitatively the embeddings generated by Gennius, revealing that the GNN encoder maintains biological information after the graph convolutions while diffusing this information through nodes, eventually distinguishing protein families in the node embedding space.Code Availabilityhttps://github.com/ubioinformat/GeNNius
Modeling Molecular Pathogenesis of Idiopathic Pulmonary Fibrosis-Associated Lung Cancer in Mice
Authors: Barravecchia Ivana , Lee Jennifer M. , Manassa Jason , Magnuson Brian , Cavanaugh Sophia , Steele Nina G. , Espinoza Carlos , Galban Craig J. , Ramnath Nithya , Frankel Timothy L. , di Magliano Marina Pasca , Galban Stefanie 
Published: June 2023

AbstractIdiopathic Pulmonary Fibrosis (IPF) is characterized by progressive, often fatal loss of lung function due to overactive collagen production and tissue scarring. IPF patients have a sevenfold-increased risk of developing lung cancer. The COVID-19 pandemic has increased the number of patients with lung diseases, and infection can worsen prognoses for those with chronic lung diseases and disease-associated cancer. Understanding the molecular pathogenesis of IPF-associated lung cancer is imperative for identifying diagnostic biomarkers and targeted therapies that will facilitate prevention of IPF and progression to lung cancer. To understand how IPF-associated fibroblast activation, matrix remodeling, epithelial-mesenchymal transition, and immune modulation influences lung cancer predisposition, we developed a mouse model to recapitulate the molecular pathogenesis of pulmonary fibrosis-associated lung cancer using the bleomycin and the Lewis Lung Carcinoma models. Models of pulmonary fibrosis, particularly bleomycin-induced fibrosis, do not recapitulate all aspects of human disease; however, to simplify nomenclature, we refer to our bleomycin-induced fibrosis model as IPF. We demonstrate that development of pulmonary fibrosis-associated lung cancer is linked to increased recruitment or reprogramming of tumor-associated macrophages and a unique gene signature that supports an immune-suppressive microenvironment through secreted factors. Not surprisingly, pre-existing fibrosis provides a pre-metastatic niche and results in augmented tumor growth. Tumors associated with bleomycin-induced fibrosis are characterized by an epithelial-to-mesenchymal transition characterized by dramatic loss of cytokeratin expression.ImplicationsWe provide new therapeutic targets that may aid the characterization of tumors associated with lung diseases and development of treatment paradigms for lung cancer patients with pre-existing pulmonary diseases.
The increase of Cyclin A/cdk activity and of FAM122A-dependent inhibition of PP2A-B55 are the key events triggering mitosis
Authors: Lacroix Benjamin , Vigneron Suzanne , Labbé Jean Claude , Pintard Lionel , Labesse Gilles , Castro Anna , Lorca Thierry 
Published: June 2023

ABSTRACTEntry into mitosis has been classically attributed to the activation of cyclin B/cdk1 amplification loop by a partial pool of this kinase that becomes active at the end of G2. However, how this pool is activated is still unknown. Here we discovered a new role of the recently identified PP2A-B55 inhibitor FAM122A in triggering mitotic entry. Accordingly, the depletion of the orthologue of FAM122A inC. elegans, prevents entry into mitosis in germline stem cells. Moreover, our data in Xenopus egg extract strongly supports that FAM122A-dependent inhibition of PP2A-B55 could be the initial event promoting mitotic entry. The inhibition of this phosphatase allows the subsequent phosphorylation of first mitotic substrates by cyclin A/cdk resulting in cyclin B/cdk1 and Greatwall (Gwl) activation. However, interestingly, from Gwl activation, Arpp19/ENSA become phosphorylated and compete with FAM122A promoting its dissociation from PP2A-B55 and taking over its inhibition until the end of mitosis.