bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Binge Drinking During College on Resting State Functional Connectivity
Authors: Tong Tien T. , Vaidya Jatin G. , Kramer John R. , Kuperman Samuel , Langbehn Douglas R. , O’Leary Daniel S. 
Published: February 2021

AbstractAimThe current study aimed to examine the longitudinal effects of standard binge drinking (4+/5+ drinks for females/males in 2 hours) and extreme binge drinking (8+/10+ drinks for females/males in 2 hours) on resting state functional connectivity.Method119 college students with distinct alcohol bingeing patterns (35 non-bingeing controls, 44 standard bingers, and 40 extreme bingers) were recruited to ensure variability in bingeing frequency. Resting state fMRI scans were obtained at time 1 when participants were college freshmen and sophomores and again approximately two years later. On four occasions during the 2-year period between scans, participants reported monthly standard and extreme binge drinking for the past 6 months. Association between bingeing and change in functional connectivity was studied using both network-level and edge-level analysis. Network connectivity was calculated by aggregating multiple edges (a functional connection between any two brain regions) affiliated with the same network. The network-level analysis used mixed-effects models to assess the association between standard/extreme binge drinking and change in network connectivity, focusing on canonical networks often implicated in substance misuse. On the other hand, the edge-level analysis tested the relationship between bingeing and change in whole-brain connectivity edges using connectome-based predictive modeling (CPM).ResultsFor network-level analysis, higher standard bingeing was associated with a decrease in connectivity between Default Mode Network-Ventral Attention Network (DMN-VAN) from time 1 to time 2, controlling for the initial binge groups at time 1, longitudinal network changes, in-scanner motion and other demographic covariates. For edge-level analysis, the CPM failed to identify a generalizable predictive model of cumulative standard/extreme bingeing from change in connectivity edges.ConclusionsOur findings suggest that binge drinking is associated with abnormality in networks implicated in attention allocation and self-focused processes, which, in turn, have been implicated in rumination, craving, and relapse. More extensive alterations in functional connectivity might be observed with heavier or longer binge drinking pattern.
Deep learning models for COVID-19 chest x-ray classification: Preventing shortcut learning using feature disentanglement
Authors: Robinson Caleb , Trivedi Anusua , Blazes Marian , Ortiz Anthony , Desbiens Jocelyn , Gupta Sunil , Dodhia Rahul , Bhatraju Pavan K. , Liles W. Conrad , Lee Aaron , Kalpathy-Cramer Jayashree , Ferres Juan M. Lavista 
Published: February 2021

ABSTRACTIn response to the COVID-19 global pandemic, recent research has proposed creating deep learning based models that use chest radiographs (CXRs) in a variety of clinical tasks to help manage the crisis. However, the size of existing datasets of CXRs from COVID-19+ patients are relatively small, and researchers often pool CXR data from multiple sources, for example, using different x-ray machines in various patient populations under different clinical scenarios. Deep learning models trained on such datasets have been shown to overfit to erroneous features instead of learning pulmonary characteristics – a phenomenon known as shortcut learning. We propose adding feature disentanglement to the training process, forcing the models to identify pulmonary features from the images while penalizing them for learning features that can discriminate between the original datasets that the images come from. We find that models trained in this way indeed have better generalization performance on unseen data; in the best case we found that it improved AUC by 0.13 on held out data. We further find that this outperforms masking out non-lung parts of the CXRs and performing histogram equalization, both of which are recently proposed methods for removing biases in CXR datasets.
Evaluation of the Knowledge of University Students in the Health Area About Sexually Transmitted Infections: A Cross-Sectional Study
Authors: Filho Carlos Izaias Sartorão , Neto Carlos Izaias Sartorão , Guazelli Carla Fabiana Souza , Avello Camila Rodrigues , Rodrigues Ivana Geraldeli Neiva , Alvarez Luana Durante , de Souza Reis Fabiana Vieira Duarte , Patrícia Fagundes Vanessa , Takano Luiz , Prudêncio Caroline Baldini , Barbosa Angélica Mércia Pascon , Rudge Marilza Vieira Cunha 
Published: February 2021

ABSTRACTIntroductionSexually transmitted infections (STI) have consequences that negatively affect the population’s quality of life and health. Young adults are susceptible to low access to preventive measures and a greater risk behavior risk. The objective was to evaluate and compare STI’ Knowledge in university students from health courses, a public institution, and a private institution of higher education in Brazil.Methodsa cross-sectional study conducted in 2019 in Brazil at the FEMA School of Medicine in Assis-SP and the University of the State of São Paulo (UNESP) in Marília in the courses of Physiotherapy, Speech Therapy, and Occupational Therapy, in undergraduate students, over 18 years of age, through a self-applied questionnaire translated and adapted to the Brazilian Portuguese from the STD-KQ – Transmitted Disease Knowledge Questionnaire.Results462/700 students participated (66.66%) 18-46 years of age (mean 21.46 years, +/− 3.61), 99 men and 363 women. In the private institution, 262/340 (77.06%), and in the public institution, 200/360 (55.55%). The mean age was 22.21 (+/− 4.21) years among men and 21.25 (+/− 3.41) years among women. The mean percentage of the 28 test questions’ correct answers was 52.07%. The average number of correct responses per student was 17.49 out of 28 possible, 62% (+/− 4.97). The distribution between the groups was normal. In the multiple linear regression model for the percentage of correct answers, adjusted for the confounding variables, the intercept was 55.2. The students of the private institution answered 19,655 questions more than the public one (P<.001), and for each semester of graduation, the students answered 1,628 more questions (P<.001). There were no relevant differences regarding the gender and age of the students.Conclusionthere are gaps in STI knowledge among university students in the health area. The students of the first semesters of the courses, and, in particular, students from a public educational institution, had a significantly lower performance of the right in the questionnaire applied. Thus, actions to promote STI knowledge and preventive attitudes are necessary among university students.
SearcHPV: a novel approach to identify and assemble human papillomavirus-host genomic integration events in cancer
Authors: Pinatti Lisa M. , Gu Wenjin , Wang Yifan , El Hossiny Ahmed , Bhangale Apurva D. , Brummel Collin V. , Carey Thomas E. , Mills Ryan E. , Brenner J. Chad 
Published: February 2021

ABSTRACTBackgroundHuman papillomavirus (HPV) is a well-established driver of malignant transformation in a number of sites including head and neck, cervical, vulvar, anorectal and penile squamous cell carcinomas; however, the impact of HPV integration into the host human genome on this process remains largely unresolved. This is due to the technical challenge of identifying HPV integration sites, which includes limitations of existing informatics approaches to discover viral-host breakpoints from low read coverage sequencing data.MethodsTo overcome this limitation, we developed a new HPV detection pipeline called SearcHPV based on targeted capture technology and applied the algorithm to targeted capture data. We performed an integrated analysis of SearcHPV-defined breakpoints with genome-wide linked read sequencing to identify potential HPV-related structural variations.ResultsThrough analysis of HPV+ models, we show that SearcHPV detects HPV-host integration sites with a higher sensitivity and specificity than two other commonly used HPV detection callers. SearcHPV uncovered HPV integration sites adjacent to known cancer-related genes includingTP63andMYC, as well as near regions of large structural variation. We further validated the junction contig assembly feature of SearcHPV, which helped to accurately identify viral-host junction breakpoint sequences. We found that viral integration occurred through a variety of DNA repair mechanisms including non-homologous end joining, alternative end joining and microhomology mediated repair.ConclusionsIn summary, we show that SearcHPV is a new optimized tool for the accurate detection of HPV-human integration sites from targeted capture DNA sequencing data.
Animal soundscapes reveal key markers of Amazon forest degradation from fire and logging
Authors: Rappaport Danielle I. , Swain Anshuman , Fagan William F. , Dubayah Ralph , Morton Douglas C. 
Published: February 2021

AbstractSafeguarding tropical forest biodiversity requires solutions for monitoring ecosystem composition over time. In the Amazon, logging and fire reduce forest carbon stocks and alter tree species diversity, but the long-term consequences for wildlife remain unclear, especially for lesser-known taxa. Here, we combined data from multi-day acoustic surveys, airborne lidar, and satellite timeseries covering logged and burned forests (n=39) in the southern Brazilian Amazon to identify acoustic markers of degradation. Our findings contradict theoretical expectations from the Acoustic Niche Hypothesis that animal communities in more degraded habitats occupy fewer ‘acoustic niches.’ Instead, we found that habitat structure (e.g., aboveground biomass) was not a consistent proxy for biodiversity based on divergent patterns of acoustic space occupancy (ASO) in logged and burned forests. Full 24-hr soundscapes highlighted a stark and sustained reorganization in community structure after multiple fires; animal communication networks were quieter, more homogenous, and less acoustically integrated in forests burned multiple times than in logged or once-burned forests. These findings demonstrate strong biodiversity co-benefits from protecting Amazon forests from recurrent fire activity. By contrast, soundscape changes after logging were subtle and more consistent with community recovery than reassembly. In both logged and burned forests, insects were the dominant acoustic markers of degradation, particularly during midday and nighttime hours that are not typically sampled by traditional field surveys of biodiversity. The acoustic fingerprints of degradation history were conserved across replicate recording locations at each site, indicating that soundscapes offer a robust, taxonomically inclusive solution for tracking changes in community composition over time.Significance StatementFire and logging reduce the carbon stored in Amazon forests, but little is known about how human degradation alters animal communities. We recorded thousands of hours of ecosystem sounds to investigate animal community assembly and the associations between biodiversity and biomass following Amazon forest degradation over time. 24-hr patterns of acoustic activity differed between logged and burned forests, and we observed large and sustained breakpoints in community structure after multiple burns. Soundscape differences among degraded forests were clearest during insect-dominated hours rarely sampled in field studies of biodiversity. These findings demonstrate that acoustic monitoring holds promise for routine biodiversity accounting, even by non-experts, to capture a holistic measure of animal communities in degraded tropical forests and benchmark change over time.
Neural indicators of human gut feelings
Authors: Mayeli Ahmad , Al Zoubi Obada , White Evan J. , Chappelle Sheridan , Kuplicki Rayus , Smith Ryan , Feinstein Justin S. , Bodurka Jerzy , Paulus Martin P. , Khalsa Sahib S. 
Published: February 2021

AbstractUnderstanding the neural processes governing the human gut-brain connection has been challenging due to the inaccessibility of the body’s interior. Here, we investigated neural responses to gastrointestinal sensation using a minimally invasive mechanosensory probe by quantifying brain, stomach, and perceptual responses following the ingestion of a vibrating capsule. Participants successfully perceived capsule stimulation under two vibration conditions (normal and enhanced), as evidenced by above chance accuracy scores. Perceptual accuracy improved significantly during the enhanced relative to normal stimulation, which was associated with a more rapid detection of the stimulation and reduced reaction time variability. Stomach stimulation induced early and late neural responses in parieto-occipital leads near the midline. Moreover, these ‘gastric evoked potentials’ showed intensity-dependent increases in amplitude and were significantly correlated with perceptual accuracy. These findings highlight a unique form of enterically-focused sensory monitoring within the human brain, with implications for understanding gut-brain interactions in healthy and clinical populations.
Mesenchymal stem cells carry and transport clusters of cancer cells
Authors: Zarubova Jana , Hasani-Sadrabadi Mohammad Mahdi , Norris Sam CP , Kasko Andrea M , Li Song 
Published: February 2021

AbstractCell clusters that collectively migrate from primary tumors appear to be far more potent in forming distant metastases than single cancer cells. A better understanding of collective cell migration phenomenon and the involvement of different cell types during this process is needed. Here, we utilize a micropatterned surface composed of a thousand of low-adhesive microwells to screen motility of spheroids containing different cell types by analyzing their ability to move from the bottom to the top of the microwells. Mesenchymal stem cells (MSCs) spheroid migration was efficient in contrast to cancer cell only spheroids. In spheroids with both cell types mixed together, MSCs were able to carry the low-motile cancer cells during migration. As the percentage of MSCs increased in the spheroids, more migrating spheroids were detected. Extracellular vesicles secreted by MSCs also contributed to the pro-migratory effect exerted by MSCs. However, the transport of cancer cells was more efficient when MSCs were physically present in the cluster. Similar results were obtained when cell clusters were encapsulated within a micropatterned hydrogel, where collective migration was guided by micropatterned matrix stiffness. These results suggest that stromal cells facilitate the migration of cancer cell clusters, which is contrary to the general belief that malignant cells metastasize independently.SignificanceDuring metastasis, tumor cells may migrate as a cluster, which exhibit higher metastatic capacity compared to single cells. However, whether and how non-cancer cells contained in tumor cluster regulate it’s migration is not clear. Here, we utilize two unique approaches to study collective tumor cell migration in vitro: first, in low-adhesive microwells and second, in micropatterned hydrogels to analyze migration in 3D microenvironment. Our results indicate that MSCs in tumor cell clusters could play an important role in the dissemination of cancer cells by actively transporting low-motile cancer cells. In addition, MSC-released paracrine factors also increase the motility of tumor cells. These findings reveal a new mechanism of cancer cell migration and may lead to new approaches to suppress metastases.
Natural Mucosal Barriers and COVID-19 in Children
Authors: Pierce Carl A. , Sy Sharlene , Galen Benjamin , Goldstein Doctor Y , Orner Erika , Keller Marla J. , Herold Kevan C. , Herold Betsy C. 
Published: February 2021

AbstractCOVID-19 is more benign in children compared to adults for unknown reasons. This contrasts with other respiratory viruses where disease manifestations are often more severe in children. We hypothesized that a more robust early innate immune response to SARS-CoV-2 may protect against severe disease and compared clinical outcomes, viral copies and cellular gene and protein expression in nasopharyngeal swabs from 12 children and 27 adults upon presentation to the Emergency Department. SARS-CoV-2 copies were similar, but compared to adults, children displayed higher expression of genes associated with interferon signaling, NLRP3 inflammasome, and other innate pathways. Higher levels of IFN-α2, IFN-γ, IP-10, IL-8, and IL-1β protein were detected in nasal fluid in children versus adults. Anti-SARS-CoV-2 IgA and IgG were detected in nasal fluid from both groups and correlated negatively with mucosal IL-18. These findings suggest that a vigorous mucosal immune response in children compared to adults contributes to favorable clinical outcomes.
Sub-diagnostic effects of genetic variants associated with autism
Authors: Rolland Thomas , Cliquet Freddy , Anney Richard J.L. , Moreau Clara , Traut Nicolas , Mathieu Alexandre , Huguet Guillaume , Duan Jinjie , Warrier Varun , Portalier Swan , Dry Louise , Leblond Claire S. , Douard Elise , Amsellem Frédérique , Malesys Simon , Maruani Anna , Toro Roberto , Børglum Anders D. , Grove Jakob , Baron-Cohen Simon , Packer Alan , Chung Wendy K. , Jacquemont Sébastien , Delorme Richard , Bourgeron Thomas 
Published: February 2021

ABSTRACTWhile over a hundred genes are significantly associated with autism, little is known about the prevalence of variants affecting them in the general population. Nor do we fully appreciate the phenotypic diversity beyond the formal autism diagnosis. Using data from more than 13,000 autistic individuals and 210,000 undiagnosed individuals, we provide a gene-level map of the odds ratio for autism associated to rare loss-of-function (LoF) variants in 185 genes robustly associated with autism, alongside 2,492 genes displaying intolerance to LoF variants. In contrast to autism-centric approaches, we investigated the phenotype of undiagnosed individuals heterozygous for such variants and show that they exhibit a decrease in fluid intelligence, qualification level and income, and an increase in material deprivation. These effects were larger for LoFs in autism-associated genes than in other LoF-intolerant genes and appeared largely independent of sex and polygenic scores for autism. Using brain imaging data from 21,049 UK-Biobank individuals, we provide evidence for smaller cortical surface area and volume among carriers of LoFs in genes with high odds ratios for autism. Our gene-level map is a key resource to distinguish genes with high and low odds ratio for autism, and highlights the importance of including quantitative data on both diagnosed and undiagnosed individuals to better delineate the effect of genetic variants beyond the categorical diagnosis. Data are available athttps://genetrek.pasteur.fr/.
Performance of SARS-CoV-2 rapid antigen test compared with real-time RT-PCR in asymptomatic individuals
Authors: Peña Mónica , Ampuero Manuel , Garcés Carlos , Gaggero Aldo , García Patricia , Velasquez María Soledad , Luza Ricardo , Alvarez Pía , Paredes Fabio , Acevedo Johanna , Farfán Mauricio J. , Solari Sandra , Soto-Rifo Ricardo , Valiente-Echeverría y Fernando 
Published: February 2021

AbstractScreening, testing and contact tracing plays a pivotal role in the control of COVID-19 pandemic. To carry out this strategy it is necessary to increase the testing capacity. Here, we compared a SARS CoV-2 rapid antigen test (RAT) and RT-PCR in 842 asymptomatic individuals from Tarapacá, Chile. We report a sensibility of 69.86%, a specificity of 99.61%, PPV of 94.44% and NPP of 97.22% with Ct values (Ct > 27) that were significantly higher among individuals with false-negative RAT. These results support the fact that RAT might have a significant impact in the identification of asymptomatic carriers in areas that lack well-equipped laboratories to perform SARS-CoV-2 real -time RT-PCR diagnostics or the results take more than 24-48 hours, as well as zones with high traffic of individuals, such as border/customs, airports, interregional bus, train stations or in any mass testing campaign requiring rapid results.
Memory of split-belt walking endures weeks in young children and younger adults but less so in older adults
Authors: Lissinna Brittany , Smith Allison , La Kaylie , Yang Jaynie F 
Published: February 2021

AbstractAdults and children modify how they move to accommodate persistent changes in their surroundings, called motor adaptation. Walking-related motor adaption can be seen when one walks on a treadmill with two belts running at different speeds, a split-belt treadmill, where a new walking pattern is slowly adopted with practice. This has been suggested as a way to improve left-right symmetry in walking after a stroke. Central to using split-belt walking for rehabilitation is whether the adapted motor pattern is retained over days and weeks, and whether this motor memory is a function of the person’s age. When first exposed to split-belt walking, the walking is asymmetric (initial error), resembling a limp. With subsequent exposure, the error is smaller than the initial error, indicating the adaptation was remembered. Here, we explored the persistence of this memory over 24 hours, one week, and two weeks, in young children (3-6 yr old), younger adults (20-30 yr old) and older adults (50-70 yr old). We found that the motor memory declines with the interval duration, but was still evident up to 2 weeks after initial exposure. Retention of the motor memory in children and younger adults was better than older adults. Further, forgetting between trials was seen on the first day of split-belt walking especially in children and older adults, but this forgetting diminished with repeated trials. The results indicate that long-term memory of motor adaptation on the split-belt treadmill is affected by age, but it may be possible to enhance the memory by more frequent and repeated exposure. This suggests that when using split-belt adaptation in rehabilitation, the sessions should ideally be less than one week apart.
Experimental Control of a Reaction Occurring during the Interaction between Chicken Anemia Virus (CAV) and Its Corresponding Antibodies
Authors: Ivanov Ognyan , Todorov Petar , Simeonov Konstantin , Vaseashta Ashok 
Published: February 2021

AbstractIn our ongoing investigations, we have studied a specific interaction between electromagnetic fields and matter – the so-called Electromagnetic echo effect (EMEE). It enables rapid and contactless investigations of gases, liquids and solids to be performed, since the signal generated as a result of the effect is quite sensitive to all kinds of changes occurring within the studied samples. The effect can be considered universal for all matter and provides analysis in real time. We use this phenomenon to demonstrate the practical possibility to control reactions, occurring between Chicken anemia virus (CAV) and the corresponding antibodies. This methodology can be used for simple but reliable control of similar, otherwise hard to detect, antigen-antibody reactions, in order to confirm the presence of a certain viral species. The approach offers a high level of safety, since it enables measurements to be taken remotely, thus limiting exposure to contagion. We further discuss the possibility to register the presence of SARS-nCoV-2 in an attempt to address current global pandemic.