University of South Florida Showcase

Numerical modeling simulation data for Lepas project

The IMPACC cohort, composed of >1,000 hospitalized COVID-19 participants, contains five illness trajectory groups (TGs) during acute infection (first 28 days), ranging from milder (TG1-3) to more severe disease course (TG4) and death (TG5). Here, we report deep immunophenotyping, profiling of >15,000 longitudinal blood and nasal samples from 540 participants of the IMPACC cohort, using 14 distinct assays. These unbiased analyses identify cellular and molecular signatures present within 72 hours of hospital admission that distinguish moderate from severe and fatal COVID-19 disease. Importantly, cellular and molecular states also distinguish participants with more severe disease that recover or stabilize within 28 days from those that progress to fatal outcomes (TG4 vs. TG5). Furthermore, our longitudinal design reveals that these biologic states display distinct temporal patterns associated with clinical outcomes. Characterizing host immune responses in relation to heterogeneity in disease course may inform clinical prognosis and opportunities for intervention.

Specimens were scanned using single propagation distance tomography at the European Synchrotron Radiation Facility (ESRF) in Grenoble, France using the ID19 microtomography beamline. Every specimen used the following scan parameters: 2999 projections collected for a 360° rotation; 0.1 ms exposure time; 360 nm voxel size; 20 mm sample-to-detector distance; x-ray energy of 26.5 keV. Specimen preparation for scanning electron microscopy (SEM) was the same as for synchrotron preparation except that radulae were mounted on stubs with double-sided conductive tape, and coated with Au-Pd for imaging with a Philips XL 30 scanning electron microscope at the Museo Argentino de Ciencias Naturales. Synchrotron *.tif stacks were reconstructed with Paganin phase retrieval, imported into Avizo Lite 9.4 (Thermo Fisher Scientific) and visually explored for mature rachidian teeth that showed no evidence of in vivo wear or post-mortem breaking during sample preparation. The scan volume was then cropped to these sections to facilitate easier data management. Segmentation of one tooth per species was performed semi-automatically: the “Magic Wand” tool was used initially to select the tooth volume based on greyscale intensity and then to manually remove any traces of the supporting radular membrane, mount, or mounting glue remained attached to the teeth. Once segmented, each tooth was exported as an *.stl and brought into Geomagic Wrap 2017 (3D Systems) for smoothing and cleaning of artefacts. In one specimen (Acanthais), damage to the tooth was only apparent after segmentation.

Ridesharing data with 220 samples

This dataset contains measurements of concentrations of MST marker HF183 and fecal indicator microorganisms (fecal coliforms and enterococci). Water samples were collected just outside the river plume in three rivers that impact a Costa Rican beach during the rainy and dry season. Microorganisms were filtered from a 500-mL grab sample onto a 0.45-µm, mixed cellulose ester. Enterococci and fecal coliforms were cultured.HF183 was quantified from nucleic acid using quantitative PCR. We examined microbiological water quality in three rivers that impact a Costa Rican beach.

This file includes the microbial community abundance and community change for the paper titled "Autotrophic denitrification supported sphalerite and oyster shells: Chemical and microbiome analysis."

This dataset contains measurements of concentrations of pathogens, MST markers and fecal indicator microorganisms. Water samples were collected in three rivers that impact a Costa Rican beach during the rainy and dry season. Enterococci and fecal coliforms were filtered from a 500-mL grab sample onto a 0.45-µm, mixed cellulose ester. All other microorganisms were concentrated on site from 50 L of water by ultrafiltration. Enterococci, fecal coliforms, C. perfringens, male specific coliphage, somatic coliphage and Salmonella were cultured. Giardia spp. and Cryptosporidium spp. were enumerated by immunomagnetic separation and microscopy. NoVGI, AdV, HF183 and PMMoV were all quantified from nucleic acid using quantitative PCR. We examined microbiological water quality in three rivers that impact a Costa Rican beach, and the risk of illness from swimming in the rivers.

Amino-acid isotope data associated with publication entitled "Reconstructions of individual fish trophic geographies using isotopic analysis of eye-lens amino acids" by Amy A. Wallace, Greg S. Ellis, and Ernst B. Peebles

This dataset contains integrated red tide (Karenia brevis harmful algal blooms) maps for the West Florida Shelf (24N – 31N, 87W – 81W) every month between 2003 and 2019. The integration is over in situ water sample analysis (which provides K. brevis cell concentration) and satellite data (which provides more frequent and spatial coverage than in situ data) using a practical approach. In situ cell counts data were obtained from a database maintained by the Florida Fish & Wildlife Conservation Commission (https://myfwc.com/research/redtide/monitoring/database/), and satellite data were collected by the Moderate Resolution Imaging Spectroradiometer (MODIS) onboard the Aqua satellite, available through NASA’s OB.DAAC (https://oceancolor.gsfc.nasa.gov). They were integrated to generate monthly maps of K. brevis bloom spatial extent and frequency. Specifically, the maps are expressed as bloom occurrence frequency (BOF) and bloom intensity (BI). The boundary of bloom locations represents the bloom footprint. Both maps are in imagery format (color coded in png files, MODIS_KB_bloom_WFS_images.zip) and binary format (floating point Geotiff files, MODIS_KB_bloom_WFS_binary.zip).

Four hours after plasmid electroporation, we evaluated acute gene expression changes in mouse skeletal muscle to identify regulated genes and genetic pathways. RNA sequencing followed by functional annotation was used to evaluate differentially expressed mRNAs.