Molecular mimicry between viral antigens and host proteins can produce cross-reacting antibodies leading to autoimmunity. The coronavirus SARS-CoV-2 causes COVID-19, a disease curiously resulting in varied symptoms outcomes, ranging from asymptomatic fatal. Autoimmunity due molecular may provide an explanation. Thus, we computationally investigated Spike known epitopes. We discovered hotspots highlight two examples with tentative high autoimmune potential implications for understanding...

Abstract Background While protein-protein docking is fundamental to our understanding of how proteins interact, scoring complex conformations a critical component successful programs. Without accurate and efficient functions differentiate between native non-native binding complexes, the accuracy current tools cannot be guaranteed. Although many innovative have been proposed, good function for remains elusive. Deep learning models offer alternatives using explicit empirical or mathematical...

A strong association between exposure to the common harmful algal bloom toxin microcystin and altered host gut microbiome has been shown. We tested hypothesis that prior cyanotoxin microcystin-LR may alter resistome. show mice exposed had an signature harbored antibiotic resistance genes. Host resistome genotypes such as mefA, msrD, mel, ant6, tet40 increased in diversity relative abundance following exposure. Interestingly, of these genes was traced antibiotics tetracycline, macrolides,...

Upon infection, foreign antigenic proteins stimulate the host's immune system to produce antibodies targeting pathogen. These bind regions on antigen called epitopes. Structural similarity (molecular mimicry) of epitopes between an infecting pathogen and host or other pathogenic has previously encountered can impact response may lead cross-reactive antibodies. The ability identify potential molecular mimicry in a illuminate effects which are especially important treatment vaccine design....

Causal inference in biomedical research allows us to shift the paradigm from investigating associational relationships causal ones. Inferring can help understanding inner workings of biological processes. Association patterns be coincidental and may lead wrong conclusions about causality complex systems. Microbiomes are highly complex, diverse, dynamic environments. Microbes key players human health disease. Hence knowledge critical among entities a microbiome, impact internal external...

Abstract Motivation Epitope-based molecular mimicry occurs when an antibody cross-reacts with two different antigens due to structural and chemical similarities. Molecular between proteins from viruses can lead beneficial cross-protection the antibodies produced by exposure one also react other. On other hand, a protein pathogen human auto-immune disorders if resulting virus end up interacting host proteins. While suggest possible reuse of vaccines developed for pathogens, cross-reaction may...

Abundance profiles from metagenomic sequencing data synthesize information billions of sequenced reads coming thousands microbial genomes. Analyzing and understanding these can be a challenge since the they represent are complex. Particularly challenging is their visualization, as existing techniques inadequate when taxa number in thousands. We present technique, accompanying software, for visualization abundance using space-filling curve that transforms profile into an interactive 2D image....

Bacterial metagenomics profiling for metagenomic whole sequencing (mWGS) usually starts by aligning reads to a collection of reference genomes. Current tools are designed work against small representative genomes, and do not scale very well larger genome collections. However, large collections capable providing more complete accurate profile the bacterial population in dataset. In this paper, we discuss scalable, efficient affordable approach problem, bringing big data solutions within reach...

Summary SARS-CoV-2 causes COVID-19, a disease curiously resulting in varied symptoms and outcomes, ranging from asymptomatic to fatal. Autoimmunity due cross-reacting antibodies molecular mimicry between viral antigens host proteins may provide an explanation. We computationally investigated Spike known epitopes. discovered hotspots highlight two examples with tentative autoimmune potential implications for understanding COVID-19 complications. show that TQLPP motif thrombopoietin shares...

Abstract Inferring causal effects is critically important in biomedical research as it allows us to move from the typical paradigm of associational studies inference, and can impact treatments therapeutics. Association patterns be coincidental may lead wrong inferences complex systems. Microbiomes are highly complex, diverse, dynamic environments. Microbes key players health diseases. Hence knowledge genuine relationships among entities a microbiome, internal external factors on microbial...

Vaginal dysbiosis-induced by an overgrowth of anaerobic bacteria is referred to as bacterial vaginosis (BV). The dysbiosis associated with increased risk for acquisition sexually transmitted infections. Women symptomatic BV are treated oral metronidazole (MET), but its effectiveness remains be elucidated. This study used whole-genome sequencing (WGS) determine the changes in microbiota among women MET. WGS was conducted on DNA obtained from 20 vaginal swabs collected at four time points over...

The gut–liver axis has been recognized as a potential pathway in which dietary factors may contribute to liver disease people living with HIV (PLWH). objective of this study was explore associations between quality, the fecal microbiome, metabolome, and health PLWH from Miami Adult Studies on (MASH) cohort. We performed cross-sectional analysis 50 MASH cohort utilized USDA Healthy Eating Index (HEI)–2015 measure diet quality. A Fibrosis-4 (FIB-4) score < 1.45 used strong indication that...

The pathophysiology of Gulf War Illness (GWI) remains elusive even after three decades. persistence multiple complex symptoms along with metabolic disorders such as obesity worsens the health present (GW) Veterans often by interactions host gut microbiome and inflammatory mediators. In this study, we hypothesized that administration a Western diet might alter metabolomic profile, which is likely associated altered bacterial species. Using five-month symptom GWI model in mice whole-genome...

Abstract The computational studies of protein binding are widely used to investigate fundamental biological processes and facilitate the development modern drugs, vaccines, therapeutics. Scoring functions aim predict complexes that would be formed by two biomolecules assess rank strength at interface. Despite past efforts, accurate prediction scoring interfaces remain a challenge. physics-based methods computationally intensive often have trade accuracy for cost. possible limitations current...

Motivation: Metagenomics sequencing data can be used to compute not just the relative abundance profile, but also replication rates of every taxon in microbiome sample. We investigate how dynamics implied by understand antibiotic response microbiomes, given significant variation types antibiotics and different taxa. The analysis is further expanded factoring resistome which readily profiled from metagenomic sequence data. fact that some such as β -lactams target replicating cells makes it...

Abstract Upon infection, foreign antigenic proteins stimulate the host’s immune system to produce antibodies targeting pathogen. These bind regions on antibody called epitopes. Structural similarity (molecular mimicry) of epitopes between an infecting pathogen and host or other pathogenic has previously encountered can impact response may lead cross-reactive antibodies. The ability identify potential molecular mimicry in a illuminate effects which are especially important treatment vaccine...

Over 19 million individuals globally have a cocaine use disorder, significant public health crisis. Cocaine has also been associated with pro-inflammatory state and recently imbalances in the intestinal microbiota as compared to nonuse. The objective of this pilot study was characterize gut plasma metabolites people HIV (PWH) who those do not.Cross-sectional study.A PWH conducted on 25 users nonusers from Miami Adult Studies cohort. Stool samples blood were collected. Bacterial composition...

The use of whole metagenomic data to infer the relative abundance all its microbes is well established. same can be used determine replication rate eubacterial taxa with circular chromosomes. Despite their availability, profiles (metareplicome) have not been fully exploited in microbiome analyses. Another relatively new approach application causal inferencing analyse that goes beyond correlational studies. A novel scalable pipeline called MeRRCI (Metagenome, metaResistome, and metaReplicome...

Abstract While the vaccination efforts against SARS-CoV-2 infections are ongoing worldwide, new genetic variants of virus emerging and spreading. Following initial surges Alpha (B.1.1.7) Beta (B.1.351) variants, a more infectious Delta variant (B.1.617.2) is now surging, further deepening health crises caused by pandemic. The sharp rise in cases attributed to has made it especially disturbing concern. Fortunately, current vaccines offer protection known concern, including variant. However,...

<title>Abstract</title> Background: While protein-protein docking is fundamental to our understanding of how proteins interact, scoring complex conformations a critical component successful programs. Without accurate and efficient functions differentiate between native non-native binding complexes, the accuracy current tools cannot be guaranteed. Although many innovative have been proposed, good function for remains elusive. Deep learning models offer alternatives using explicit empirical or...

Floods can cause horrific harm to life and property. However, they be mitigated or even avoided by the effective use of hydraulic structures such as dams, gates, pumps. By pre-releasing water via these in advance extreme weather events, levels are sufficiently lowered prevent floods. In this work, we propose FIDLAR, a Forecast Informed Deep Learning Architecture, achieving flood management watersheds with an optimal manner balancing out mitigation unnecessary wastage pre-releases. We perform...

Floods can be very destructive causing heavy damage to life, property, and livelihoods. Global climate change the consequent sea-level rise have increased occurrence of extreme weather events, resulting in elevated frequent flood risk. Therefore, accurate timely forecasting coastal river systems is critical facilitate good management. However, computational tools currently used are either slow or inaccurate. In this paper, we propose a Flood prediction tool using Graph Transformer Network...