bluuebunny/crossref_metadata_2025_split huggingface dataset:
Haemovigilance and Trends of Transfusion Transmissible Viral Infections among Asymptomatic Population at Akatsi South Municipal in Volta Region of Ghana from 2014 to 2019
Authors: Hamid Abdul-Wahab Mawuko , Oduro-Mensah Moses , Adase Ishmael , Kwadzokpui Precious Kwablah , Agyemang Kenneth Owusu , Ayivor Pascal , Bonsu Kofi Karikari , Nanga Salifu , Bawah Ahmed Tijani , Alidu Huseini Wiisibie , Agudze Israel Tordzro , Glover-Meni Nathaniel , Jamfaru Ibrahim , Kaba Robert , Ayamba Ali Mahmudu , Kwofie Theophilus Benjamin , Adiku Theophilus , Ofori Eric Kwasi 
Published: December 2022

AbstractBackgroundTracking the changing epidemiology of Transfusion Transmissible Infections (TTIs), including Immunodeficiency virus (HIV), is critical to attaining the Sustainable Development Goals (SDG.3.3) milestones and deadlines. This study assessed the dynamics associated with Blood Donation and TTIs among blood donors at the Akatsi South Municipality in the Volta Region of Ghana.MethodsThis was a haemovigilance study, designed to retrospectively evaluate secondary data on 2,588 blood donors in Akatsi South District Hospital from 2014 to 2019. Data was collected, managed and quality controlled done electronically using Microsoft Visual Basics, and STATA. TTIs’ trends were determined using frequentist and descriptive statistics, and 95% confidence intervals using Clopper Pearson test.ResultsPrevalence of TTIs was 8.0%. The prevalence of HIV as well as HBV and HCV, was 3.8%, 3.2% and 1.0% respectively. For female hosts, the prevalence was 7.4% (HIV), 4.2 % (HBV) and 1.6% (HCV). For Male-host, the rates were 3.1% (HIV), 3.5% (HBV) and 1.0% (HVC). Donors aged 15-19years were most infected at rates of 13.2% (HIV), 4.7% (HBV) and 1.9% (HCV).ConclusionAbout 57(2.4%) and 3(1.2%) of 2380 blood donated were TTIs false negatives and false positives respectively. In addition to being a driver of TTIs among blood donors in this study, the HIV prevalence among teenagers was significantly above the regional and national rates. These rates have ‘programmatic’ and ‘research’ implications. A relatively higher sensitive blood transfusion screening method is urgently needed to prevent the transfusion of TTIs false negative bloods in Akatsi Municipal HospitalWhat is already known about the topic: National and global epidemiology of TTIs, including HIV are known.What this study add?This study serves as baseline data on trends of HIV, HBV and HCV infection among non-sentinel asymptomatic population at Akatsi South Municipality in Volta Region of Ghana.How this study might affect research, practice or policy?Our data shall contribute to understanding on changing epidemiology of Transfusion Transmissible viral infection including HIV after the introduction of the public health sector strategy toward the 2030 deadline to achieve the Sustainable Development Goal 3.3.
Gender-based social norms, psychosocial variation, and power relations during delivery and post natal care: a case study qualitative research in rural Ethiopia
Authors: Ayele Ketema , Kebede Yohannes , Abebe Lakew , Mamo Abebe , Sudakar Morankar 
Published: December 2022

ABSTRACTBackgroundThe World Health Organization (WHO) strongly encouraged men to support women to use maternal health care services. However, especially in developing countries, maternal health care has traditionally been viewed as a women’s issue, men making little or no contribution, despite the fact that sexuality and children are shared products. The study’s goal was to understand how gender-based norms, psychosocial variation, power relations, and community social support are related to child delivery and post-natal care services.MethodThe study took place in three rural districts of Ethiopia’s Oromia regional state, Jimma Zone. An in-depth interview and focus group discussion were held with a group of carefully chosen health professionals, community health development armies, and religious leaders. The data was collected, translated, and transcribed by men and women with experience in qualitative research. For data analysis, Atlas ti version 9 was used. Gender-based delivery and postnatal care service utilization were investigated using gender-based categories.ResultIndependent and shared gender-based roles were identified as a means to improve maternal health-care services delivery. Men have the ability to persuade pregnant women to use delivery services and post-natal care. The place of delivery is determined by the levels of gender power relations at the household level, but women are usually the last decision-makers. Furthermore, the community’s belief that giving birth in a health facility makes women look clean and neat, as opposed to home delivery, increases their intention to use maternal health care services..ConclusionUnderstanding men’s and women’s roles, knowledge levels, beliefs, decision-making, and social support significantly improves maternal health care service utilization, allowing pregnant women to receive delivery services at a health facility. Pregnant women were the last to make a decision about using maternal health care services. There are still gaps in knowledge and negative beliefs about maternal health care that limit delivery and postnatal service utilization.RecommendationIncreasing community-level social support can significantly improve maternal health care service delivery. Men’s concern about institutional delivery is increased when they are viewed as the primary audience during maternal health education. Researchers should focus on the mechanisms through which men participate in delivery in the future, and postnatal services will fully address men’s involvement in maternal health care services.
Predicting preterm births from electrohysterogram recordings via deep learning
Authors: Goldsztejn Uri , Nehorai Arye 
Published: December 2022

AbstractAbout one in ten babies is born preterm, i.e., before completing 37 weeks of gestation, which can result in permanent neurologic deficit and is a leading cause of child mortality. Although imminent preterm labor can be detected, predicting preterm births more than one week in advance remains elusive. Here, we develop a deep learning method to predict preterm births directly from electrohysterogram (EHG) recordings of pregnant mothers without symptoms of preterm labor. We developed a prediction model, which includes a recurrent neural network, to predict preterm births using short-time Fourier transforms of EHG recordings and clinical information from two public datasets. We predicted preterm births with an area under the receiver-operating characteristic curve (AUC) of 0.80 (95% confidence interval: 0.79-0.82). Moreover, we found that the spectral patterns of the measurements were more predictive than the temporal patterns, suggesting that preterm births can be predicted from short EHG recordings in an automated process. We show that, even without symptoms of preterm labor, preterm births can be predicted for pregnant mothers around their 31st week of gestation, prompting beneficial treatments to reduce the incidence of preterm births and improve their outcomes.
Parkinson’s disease-associated genetic variants synergistically shape brain networks
Authors: Chen Zhichun , Wu Bin , Li Guanglu , Zhou Liche , Zhang Lina , Liu Jun 
Published: December 2022

SummaryBackgroundOver 90 genetic variants have been found to be associated with Parkinson’s disease (PD) in genome-wide association studies, however, the neural mechanisms of previously identified risk variants in PD were largely unexplored. The objective of this study was to evaluate the associations between PD-associated genetic variants and brain gene expressions, clinical features, and brain networks.MethodsPD patients (n = 198) receiving magnetic resonance imaging examinations from Parkinson’s Progression Markers Initiative (PPMI) database were included in the analysis. The effects of PD-associated genetic variants assayed in PPMI database on clinical manifestations and brain networks of PD patients were systematically evaluated.FindingsMost associations between 14 PD-associated risk variants and clinical manifestations of PD patients failed to reach the stringentp-value threshold of 0.00026 (0.05/14 clinical variables x 14 variants). Shared and distinct brain network metrics were significantly shaped by PD-associated genetic variants. Small-worldness properties at the global level and nodal metrics in caudate and putamen of basal ganglia network were preferentially modified. Small-worldness properties in gray matter covariance network mediated the effects ofOGFOD2/CCDC62rs11060180 on motor assessments of PD patients.InterpretationOur findings support that both shared and distinct brain network metrics are shaped by PD-associated risk variants. Small-worldness properties modified byOGFOD2/CCDC62rs11060180 in gray matter covariance network are associated with motor severity of PD patients. Future studies are encouraged to explore the underlying mechanisms of PD-associated risk variants in PD pathogenesis.FundingThis work was supported by grants from the National Key Research and Development Program (2016YFC1306505) and the National Natural Science Foundation of China (81471287, 81071024, 81171202).
PanCanSurvPlot: A Large-scale Pan-cancer Survival Analysis Web Application
Authors: Lin Anqi , Yang Hong , Shi Ying , Cheng Quan , Liu Zaoqu , Zhang Jian , Luo Peng 
Published: December 2022

AbstractThe identification of reliable tumor prognostic markers can help clinicians and researchers predict tumor development and patient survival outcomes more accurately, which plays a vital role in clinical diagnosis, treatment effectiveness assessment, and prognostic evaluation. Existing web tools supporting online survival analysis are gradually failing to meet the increasing demands of researchers in terms of the dataset size, richness of survival analysis methods, and diversity of customization features. Therefore, there is an urgent need for a large-scale, one-stop pan-cancer survival analysis web server. We developed PanCanSurvPlot (https://smuonco.shinyapps.io/PanCanSurvPlot/), a Shiny web tool that has incorporated a total of 215 cancer-related datasets from the GEO and TCGA databases, covering nearly 100,000 genes (mRNAs, miRNAs, and lncRNAs), approximately 45,000 samples, 51 different cancer types, and 13 different survival outcomes. The website also provides two cutoff methods based on median and optimal cutpoints. All survival analysis results from the log-rank test and univariate Cox regression are presented in a clear and straightforward summary table. Finally, users can customize color schemes and cutpoint levels to quickly obtain high-quality Kaplan-Meier survival plots that meet publication requirements.
The Effect of COVID-19 on Distracted Driving: A Survey Study
Authors: Javid Ramina , Sadeghvaziri Eazaz , Jeihani Mansoureh 
Published: December 2022

AbstractThe COVID-19 pandemic caused a significant shift in people’s travel behaviors and distractions while driving. This paper aims to investigate the impacts of the COVID-19 pandemic on distracted driving by comparing their behavior before and during the pandemic (from 3/1/2019 to 3/1/2021) in the state of Maryland using a stated preference online survey. Some 158 people were recruited for the survey. Participants were asked about their risky driving behaviors and self-reported distraction both before and during the pandemic. To analyze the results, the Chi-square and posthoc tests with the Bonferroni adjustment were applied. The results showed that during the pandemic, distraction dropped from 25% to 21%. The highest reported distracted driving behavior during the pandemic was using hands-free cell phones (64%), using GPS (75%), and eating or drinking (57%). The respondents’ daily trips have significantly decreased - about 44% below prepandemic rates. Moreover, using a binary logistic regression, it was revealed that the odds of becoming distracted among participants who used a handheld cell phone before and during the pandemic were 4.5 and 6.6 times higher than others, respectively. The findings of this study shed light on the causes of distraction before and during the pandemic.
Interaction between myelodysplasia-related gene mutations and ontogeny in acute myeloid leukemia: an appraisal of the new WHO and IC classifications and ELN risk stratification
Authors: McCarter Joseph GW. , Nemirovsky David , Famulare Christopher A. , Farnoud Noushin , Mohanty Abhinita S. , Stone-Molloy Zoe S. , Chervin Jordan , Ball Brian J. , Epstein-Peterson Zachary D. , Arcila Maria E. , Stonestrom Aaron J. , Dunbar Andrew , Cai Sheng F. , Glass Jacob L. , Geyer Mark B. , Rampal Raajit K. , Berman Ellin , Abdel-Wahab Omar I. , Stein Eytan M. , Tallman Martin S. , Levine Ross L. , Goldberg Aaron D. , Papaemmanuil Elli , Zhang Yanming , Roshal Mikhail , Derkach Andriy , Xiao Wenbin 
Published: December 2022

AbstractAccurate classification and risk stratification is critical for clinical decision making in AML patients. In the newly proposed World Health Organization (WHO) and International Consensus classifications (ICC) of hematolymphoid neoplasms, the presence of myelodysplasia-related (MR) gene mutations is included as one of the diagnostic criteria of AML, myelodysplasia-related (AML-MR), largely based on the assumption that these mutations are specific for AML with an antecedent myelodysplastic syndrome. ICC also prioritizes MR gene mutations over ontogeny (as defined by clinical history). Furthermore, European LeukemiaNet (ELN) 2022 stratifies these MR gene mutations to the adverse-risk group. By thoroughly annotating a cohort of 344 newly diagnosed AML patients treated at Memorial Sloan Kettering Cancer Center (MSKCC), we show that ontogeny assignment based on database registry lacks accuracy. MR gene mutations are frequently seen inde novoAML. Among MR gene mutations, onlyEZH2andSF3B1were associated with an inferior outcome in a univariate analysis. In a multivariate analysis, AML ontogeny had independent prognostic values even after adjusting for age, treatment, allo-transplant and genomic classes or ELN risks. Ontogeny also stratified the outcome of AML with MR gene mutations. Finally,de novoAML with MR gene mutations did not show an adverse outcome. In summary, our study emphasizes the importance of accurate ontogeny designation in clinical studies, demonstrates the independent prognostic value of AML ontogeny and questions the current classification and risk stratification of AML with MR gene mutations.Key pointsBoth ontogeny and genomics show independent prognostic values in AML.The newly proposed myelodysplasia-related gene mutations are neither specific to AML-MRCWHO2016nor predictive for adverse outcomes.Ontogeny stratifies the outcome of AML with myelodysplasia-related gene mutations.
The role of stimulus periodicity on spinal cord stimulation-induced artificial sensations in rodents
Authors: Slack Jacob C. , Zeiser Sidnee L. , Yadav Amol P. 
Published: December 2022

AbstractSensory feedback is critical for effectively controlling brain-machine interfaces (BMIs) and neuroprosthetic devices. Spinal cord stimulation (SCS) is proposed as a technique to induce artificial sensory perceptions in rodents, monkeys, and humans. However, to realize the full potential of SCS as a sensory neuroprosthetic technology, a better understanding of the effect of SCS pulse train parameter changes on sensory detection and discrimination thresholds is necessary. Here we investigated whether stimulation periodicity impacts rats’ ability to detect and discriminate SCS-induced perceptions at different frequencies. By varying the coefficient of variation (CV) of interstimulus pulse interval, we showed that at lower frequencies, rats could detect highly aperiodic SCS pulse trains at lower amplitudes (i.e., decreased detection thresholds). Furthermore, rats learned to discriminate stimuli with subtle differences in periodicity, and the just-noticeable differences (JNDs) from a highly aperiodic stimulus were smaller than those from a periodic stimulus. These results demonstrate that the temporal structure of an SCS pulse train is an integral parameter for modulating sensory feedback in neuroprosthetic applications.
Principles of assembly and regulation of condensates of Polycomb repressive complex 1 through phase separation
Authors: Brown Kyle , Chew Pin Yu , Ingersoll Steven , Espinosa Jorge R , Aguirre Anne , Kutateladze Tatiana , Guevara Rosana Collepardo , Ren Xiaojun 
Published: December 2022

SUMMARYPRC1 (Polycomb repressive complex 1) plays a significant role in cellular differentiation and development by repressing lineage-inappropriate genes. PRC1 proteins phase separate to form Polycomb condensates (bodies) that are multi-component hubs for silencing Polycomb target genes; however, the molecular principles that underpin the condensate assembly and biophysical properties remain unknown. Here, by using biochemical reconstitution, cellular imaging, and multiscale molecular simulations, we show that PRC1 condensates are assembled via a scaffold-client liquid–liquid phase separation (LLPS) model by which Chromobox 2 (CBX2) is the scaffold and other subunits of the CBX2-PRC1 complex act as clients. The clients induce a reentrant phase transition of CBX2 condensates in a concentration-dependent manner. The composition of the multi-component, heterotypic LLPS systems directs the assembly and biophysical properties of CBX2-PRC1 condensates and selectively promotes the formation of CBX4-PRC1 condensates, but specifically dissolves condensates of CBX6-, CBX7-, and CBX8-PRC1. Additionally, the composition of CBX2-PRC1 condensates controls the enrichment of CBX4-, CBX7-, and CBX8-PRC1 into condensates but the exclusion of CBX6-PRC1 from condensates. Our results show the composition- and stoichiometry-dependent scaffold-client assembly of multi-component PRC1 condensates and supply a conceptual framework underlying the molecular basis and dynamics of Polycomb condensate assembly.
Enhanced antibody-antigen structure prediction from molecular docking using AlphaFold2
Authors: Gaudreault Francis , Corbeil Christopher R. , Sulea Traian 
Published: December 2022

ABSTRACTPredicting the structure of antibody-antigen complexes has tremendous value in biomedical research but unfortunately suffers from a poor performance in real-life applications. AlphaFold2 (AF2) has provided renewed hope for improvements in the field of protein-protein docking but has shown limited success for the medically relevant class of antibody-antigen complexes due to the lack of co-evolutionary constraints. Some research groups have demonstrated the usefulness of the AF2 confidence metrics for assessing the plausibility of protein folding models. In this study, we used physics-based protein docking methods for building decoy sets consisting of low-energy docking solutions that were either geometrically close to the native structure (positives) or not (negatives). The docking models were then fed into AF2 to assess their confidence with a novel composite score based on the pLDDT and pTMscore metrics. We show benefits of the AF2 composite score for rescoring docking poses in two scenarios: (1) a more trivial experiment based on the bound conformations of the antibody and antigen backbone structures, and (2) a more realistic test employing the unbound backbone conformations of the binding partners. Docking success rates improved after AF2 rescoring with particular emphasis on early enrichment of positives at the very top of the re-ranked list of decoys. The AF2 rescoring markedly improved classification of positives and negatives in most systems. Docking models of at least medium quality present in the decoy set, but not necessarily highly ranked by docking methods, benefitted most from AF2 rescoring by experiencing large advances towards the top of the reranked list of models. These improvements, obtained without any calibration or novel methodologies, led to a notable level of performance in antibody-antigen unbound docking that was never achieved previously.
Simultaneous visualization of cells and marker genes from scRNA-seq studies
Authors: Bhattacharya Namrata , Chakraborti Swagatam , Gupta Krishan , Mittal Aayushi , Sinha Debajyoti , Nelson Colleen , Chakraborty Tanmoy , Ahuja Gaurav , Sengupta Debarka 
Published: December 2022

ABSTRACTThe complexity of scRNA-sequencing datasets highlights the urgent need for enhanced clustering and visualization methods. Here, we propose Stardust, an iterative, force-directed graph layouting algorithm that enables the simultaneous embedding of cells and marker genes. Stardust, for the first time, allows a single-stop visualization of cells and marker genes on a single 2D map. While Stardust provides its own visualization pipeline, it can be plugged in with state-of-the-art methods such as Uniform Manifold Approximation and Projection (UMAP) and t-Distributed Stochastic Neighbor Embedding (tSNE). We benchmarked Stardust against popular visualization and clustering tools on both scRNA-seq and spatial transcriptomics datasets. In all cases, Stardust performs competitively in identifying and visualizing cell types in an accurate and spatially coherent manner.
Calcium signals tune AMPK activity and mitochondrial homeostasis in dendrites of developing neurons
Authors: Hatsuda Akane , Kurisu Junko , Fujishima Kazuto , Kawaguchi Ayano , Ohno Nobuhiko , Kengaku Mineko 
Published: December 2022

AbstractThe growth of dendritic arbors in developing neurons is known to be regulated by neuronal activity, which is thought as one of the mechanisms of neural circuit optimization. Here we demonstrate that activity-dependent calcium signaling controls mitochondrial homeostasis and dendritic outgrowth via AMP-activated protein kinase (AMPK) in developing hippocampal neurons. AMPK deficiency phenocopies the inhibition of neuronal activity, inducing dendritic hypotrophy with abnormally elongated mitochondria. In growing dendrites, AMPK is activated by neuronal activity and dynamically oscillates in synchrony with calcium spikes, and this AMPK oscillation is inhibited by CaMKK2 knockdown. AMPK activation leads to phosphorylation of MFF and ULK1, which initiate mitochondrial fission and mitophagy, respectively. Dendritic mitochondria in AMPK-depleted neurons exhibit impaired fission and mitophagy and display multiple signs of dysfunction. Thus, AMPK activity is finely tuned by the calcium-CaMKK2 pathway and regulates mitochondrial homeostasis by facilitating removal of damaged components in rapidly growing neurons during normal brain development.