A5000137125- Gut microbiota and health
- Genomics and Phylogenetic Studies
- Medical History and Innovations
- Metabolomics and Mass Spectrometry Studies
- Marriage and Sexual Relationships
- History of Medical Practice
- Microbial Community Ecology and Physiology
- Diversity and Career in Medicine
- Autoimmune and Inflammatory Disorders
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Medical Research and Practices
- Aortic Thrombus and Embolism
- Health and Conflict Studies
- Molecular Biology Techniques and Applications
- Dental Research and COVID-19
- Homicide, Infanticide, and Child Abuse
- Diverticular Disease and Complications
- Advanced biosensing and bioanalysis techniques
- Primary Care and Health Outcomes
- Research Data Management Practices
- Mycobacterium research and diagnosis
- Diagnosis and treatment of tuberculosis
- Gastrointestinal disorders and treatments
- RNA modifications and cancer
University of California, San Diego
2020-2022
Jacobs (United States)
2020-2022
UC San Diego Health System
2022
Bradford Royal Infirmary
2016
UNSW Sydney
2012
Women's & Children's Health Research Institute
2012
Charles Darwin University
2011
Research for Action
2007
Atrium Health Wake Forest Baptist
2004
Leeds General Infirmary
2002
We introduce the operational genomic unit (OGU) method, a metagenome analysis strategy that directly exploits sequence alignment hits to individual reference genomes as minimum for assessing diversity of microbial communities and their relevance environmental factors. This approach is independent taxonomic classification, granting possibility maximal resolution community composition, organizes features into an accurate hierarchy using phylogenomic tree. The outputs are suitable contemporary...
Microbiome data are sparse and high dimensional, so effective visualization of these requires dimensionality reduction. To date, the most commonly used method for reduction in microbiome is calculation between-sample microbial differences (beta diversity), followed by principal-coordinate analysis (PCoA). Uniform Manifold Approximation Projection (UMAP) an alternative that can reduce beta diversity distance matrices. Here, we demonstrate benefits limitations using UMAP on data. Using real...
SARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Viruses exist in complex microbial environments, and recent studies have revealed both synergistic antagonistic effects of specific bacterial taxa on viral prevalence infectivity. We set out to test whether communities predict occurrence a hospital setting.We collected 972 samples from hospitalized patients with COVID-19, their health care providers, surfaces before, during, after admission. screened...
Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive web tool visualizing trees in context microbiome, metabolome, other community data scalable to with well over 500,000 nodes. EMPress provides novel functionality-including ordination integration animations-alongside many standard tree visualization features thus simplifies exploratory analyses forms 'omic data.IMPORTANCE Phylogenetic are integral...
The number of publicly available microbiome samples is continually growing. As data set size increases, bottlenecks arise in standard analytical pipelines. Faith's phylogenetic diversity (Faith's PD) a highly utilized alpha metric that has thus far failed to effectively scale trees with millions vertices. Stacked (SFPhD) enables calculation this widely adopted at much larger by implementing computationally efficient algorithm. algorithm reduces the amount computational resources required,...
Abstract We introduce Operational Genomic Unit (OGU), a metagenome analysis strategy that directly exploits sequence alignment hits to individual reference genomes as the minimum unit for assessing diversity of microbial communities and their relevance environmental factors. This approach is independent from taxonomic classification, granting possibility maximal resolution community composition, organizes features into an accurate hierarchy using phylogenomic tree. The outputs are suitable...
In shotgun metagenomics studies that seek to relate changes in microbial DNA across samples, processing the data on a computer often takes longer than obtaining from sequencing instrument. Recently developed software packages perform individual steps pipeline of principle offer speed advantages, but practice they may contain pitfalls prevent their use, for example, make approximations introduce unacceptable errors data.
Microbiome data analysis can be difficult because of particular features, some unavoidable and due to technical limitations DNA sequencing instruments. The first step in many analyses that ultimately reveals patterns similarities differences among sets samples (e.g., separating from sick healthy people or seawater versus soil) is calculating the difference between each pair samples.
ABSTRACT The levels of streptococcal antibody titers in populations with or without rheumatic fever from an area a relatively high incidence and low this disease were compared. Streptococcal determined for two populations, each which included children (nonrheumatic children) patients. derived separate geographic areas, one (Grenada) another (central Florida). results revealed absence consistent differences the geometric mean between nonrheumatic subjects patients Grenada. In population...
Synergistic effects of bacteria on viral stability and transmission are widely documented but remain unclear in the context SARS-CoV-2. We collected 972 samples from hospitalized ICU patients with coronavirus disease 2019 (COVID-19), their health care providers, hospital surfaces before, during, after admission. screened for SARS-CoV-2 using RT-qPCR, characterized microbial communities 16S rRNA gene amplicon sequencing, contextualized massive diversity this dataset a meta-analysis over...
Journal Article Deficiency of the mesentery over lower ileum Get access George E Armstrong Montreal Search for other works by this author on: Oxford Academic Google Scholar British Surgery, Volume 9, Issue 34, January 1921, Pages 287–289, https://doi.org/10.1002/bjs.1800093419 Published: 06 December 2005
Between the years 1600 and 1800, vitamin C deficiency probably was responsible for more than one million deaths among seamen—almost certainly total lost during same period in naval battles, shipwrecks, to diseases other scurvy (1). Since then, has become an uncommon condition developed countries with reported cases confined mainly elderly living alone, alcoholics, those on unusual diets (2–4). Thomas Barlow distinguished infantile from rickets late nineteenth century (5). More recently, been...
UniFrac is an important tool in microbiome research that used for phylogenetically comparing profiles to one another (beta diversity). Striped recently added the ability split problem into many independent subproblems, exhibiting nearly linear scaling but suffering from memory contention. Here, we adapt graphics processing units using OpenACC, enabling greater than 1,000× computational improvement, and apply it 307,237 samples, largest 16S rRNA V4 uniformly preprocessed data set analyzed date.
THE FREQUENCY OF PERFORATTON.GENTLEMEN,-It is not often that you hear a lecture on typhoid fever in surgical clinic, but the transference of case requiring aid from medical wards has directed my attention to subject, and I find looking up literature surgeons are directly interested per cent. all cases fever.About 1.2 cent., according statistics, a, e complicated by perforation intestine.About 6 mortality due bowel.The majority occur between ages Ioand 4o, as might be expected, male rather...
ADDRESS OF THE PRESIDENT AT OPENING SESSION AMERICAN SURGICAL ASSOCIATION, JUNE 9, 1915 MONTREAL, CANADA