Genetics of Early Neurological InStability after Ischemic Stroke (GENISIS) - USA

The Genetics of Early Neurological InStability after Ischemic Stroke (GENISIS) project is a multi-center, prospective cohort study aimed at identifying genetic contributors to neurological changes occurring within the first 24 hours after acute ischemic stroke. For each enrolled participant, NIH Stroke Scale (NIHSS) scores were recorded both within six hours of symptom onset and again at the 24-hour mark to capture early neurological dynamics. This dataset represents the GENISIS-USA cohort, consisting of 871 participants enrolled at U.S. sites as part of a larger international effort spanning seven countries. Prior to release, all data were thoroughly de-identified in accordance with best practices. Measures included application of the mri_reface tool to obscure facial features in imaging, removal of direct identifiers, recoding of sensitive clinical variables, and date shifting of scan timestamps to preserve participant privacy. The shared imaging dataset includes 1,821 CT scans and 57 MR scans, available in both DICOM and NIfTI file formats. The complete dataset occupies approximately 142.6 GB. This dataset is hosted on the Imaging Cerebrovascular Disease Knowledge Portal (iCDKP), which is supported in part by the National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), under Grant No. 1U24NS132940-01. Users are required to acknowledge both iCDKP and its federal funding source in any presentations or publications that utilize the dataset, following the citation guidelines provided on the dataset’s iCDKP page. To request access, users must register for an account and complete a Data Request License Agreement available via the iCDKP request portal: https://sites.wustl.edu/icdkp/request_data/

Scripts and data for: Emergent predictability in microbial ecosystems

Raw data, Matlab analysis scripts and simulation code reproducing all figures in Moran, Graham & Tikhonov (2025), "Emergent predictability in microbial ecosystems." Optional pre-computed simulation data included to speed-up figure plotting -- remove or rename any data file to rerun the corresponding analysis or simulations from scratch

Dataset for "A trivalent mucosal vaccine encoding phylogenetically inferred ancestral RBD sequences confers pan-Sarbecovirus protection in mice"

This dataset contains the raw data supporting all main and supplementary figures used in the manuscript "A trivalent mucosal vaccine encoding phylogenetically inferred ancestral RBD sequences confers pan-Sarbecovirus protection in mice" published in Cell Host & Microbe. The data contains viral and antibody titers and T cell responses in mice not-vaccinated, intramuscularly and/or mucosally vaccinated, and then infected with SARS-CoV-1, SARS-CoV-2, or other pre-emergent bat coronaviruses

Dataset for 'Barcoded SARS-CoV-2 viruses define the impact of duration and route of exposure on the transmission bottleneck in a hamster model'

SARS-CoV-2’s transmission bottleneck remains poorly characterized, in part due to a lack of quantitative measurement tools. To address this, we adapted a SARS-CoV-2 reverse genetics system to generate a pool of >200 isogenic SARS-CoV-2 viruses harboring specific 6-nucleotide barcodes inserted in ORF10, a non-translated ORF. We directly inoculated donor Syrian hamsters intranasally with this barcoded virus pool and exposed a paired naïve contact hamster to each donor. Following exposure, the nasal turbinates, trachea, and lungs were collected, viral titers were measured, and the number of barcodes in each tissue were enumerated to quantify the transmission bottleneck. The duration and route (airborne, direct contact, and fomite) of exposure were varied to assess their impact on the transmission bottleneck. Primarily, the dataset contains (1) fastq files from next-generation sequencing of a small amplicon that contains the barcode of our barcoded viruses and (2) associated count matrices showing how many of each barcode are present in each sample. Secondarily, RT-qPCR results measuring viral titers in various respiratory tissues are also included

Dataset for the manuscript titled 'Serosurveillance identifies Bourbon virus neutralizing antibodies in bobcats, coyotes, and red foxes in Missouri'

Bourbon virus (BRBV) is an emerging pathogen that can cause severe and fatal disease in humans. BRBV is vectored by Amblyomma americanum (lone star ticks), which are widely distributed across the central, southern, and eastern United States. This dataset describes wild animal species captured in two locations close to St. Louis Metro area and their corresponding BRBV neutralizing activity in serum illustrated by IC50 and IC90 values and their capture sites

Dataset for "MRN-CtIP, EXO1, and DNA2-WRN/BLM act bidirectionally to process DNA gaps in PARPi-treated cells without strand cleavage"

This dataset supports the publication titled “MRN-CtIP, EXO1, and DNA2-WRN/BLM act bidirectionally to process DNA gaps in PARPi-treated cells without strand cleavage,” published in Genes & Development. It contains data from a range of experimental approaches, including single-molecule DNA fiber analysis, immunofluorescence, flow cytometry, electron microscopy, metaphase spread assays, and biochemical analyses. All cellular assays were conducted in human cell lines, while biochemical experiments used purified proteins from both human and yeast sources. The complete dataset is approximately 88 GB in size and includes 66,960 files organized into two main folders. The Figures folder contains 44,103 files across 1,651 subfolders and is 69.4 GB in size. The Supplemental Figures folder contains 22,805 files across 880 subfolders and is 18.7 GB

Shortwave imaginary refractive index of alumina aerosols.

This repository contains the following datasets and supporting materials: 1) Alumina_Refractive_Index_1nm.csv Description: Complex refractive index (n and k) at 1 nm resolution. Wavelength Range: 10–100,000 nm. Refractive indices between 120–6500 nm are derived from Urbach-tail fits of photoacoustic spectrometry (PAS) data; values outside this range are from Tropf and Thomas (1997). Columns: • wavelength (nm) • k — imaginary part of refractive index • k_25 — 25th percentile of k from PAS-derived fits • k_75 — 75th percentile of k from PAS-derived fits 2) Alumina_Refractive_Index_PAS.csv Description: Imaginary refractive index (k) retrieved from in situ measurements and Mie theory inversions (Sumlin et al., 2016). Absorption and scattering coefficients were measured with integrated photoacoustic spectrometers (Upadhyay et al., 2025), and particle number size distributions with a scanning mobility particle sizer and an aerodynamic aerosol classifier. Columns: • particle_type — spherical α-phase, irregular α-phase, irregular γ-phase • wavelength (nm) — 375, 405, 532, 721, and 1047 nm. • N — number of data points • k_25 — 25th percentile • k_median — median value • k_75 — 75th percentile 3) Alumina_Refractive_Index_EELS.csv Description: Imaginary refractive index (k) measured for individual particles using STEM–EELS (Scanning Transmission Electron Microscopy–Electron Energy Loss Spectroscopy) of spherical α-phase alumina particles. Columns: • wavelength (nm) • k_1 to k_10 — k values for ten individual particles 4) EELS_Anlysis (folder) • Contains raw EELS spectra (subfolder: particles) and processed data (subfolder: data). • A PowerPoint presentation (EELS_SI.pptx) provides a comprehensive analysis of the EELS measurements, including an exemplar particle with a corresponding HAADF image, the extraction of the refractive index (k) via Kramers–Kronig analysis (KKA), an assessment of the influence of zero-loss peak (ZLP) tail cutoff on the derived optical constants, and the identification of oxygen-vacancy defects through the evaluation of the imaginary component of the refractive index. • A separate codes folder includes the analysis scripts used to process the EELS data and generate figures

Replication package for "Entrepreneurship and the Gig Economy: Evidence from U.S. Tax Returns"

Replication package for "Entrepreneurship and the Gig Economy: Evidence from U.S. Tax Returns

Data and Code for "Late adverse event reporting from medical device manufacturers to the FDA: cross sectional study"

These files represent the needed data and code to reconstruct all figures presented in "Late adverse event reporting from medical device manufacturers to the FDA: cross sectional study." In order to recreate the figures and tables, users should first run "everhart_et_al_bmj_cohort_construction.do" followed by "everhart_et_al_bmj_analysis.do". Users will need to extract certain zip files and change directory names within the STATA do-files as appropriate. Please see the included read-me file to understand how the code and files are related, as well as the original sources for data. Some files are in ZIP files due to their size

Dataset for 'A multivalent capsule vaccine protects against Klebsiella pneumoniae bloodstream infections in healthy and immunocompromised mice'

In the accompanying publication, we reported on the production and characterization of the broadest K. pneumoniae capsule bioconjugate vaccine to date. We tested this vaccine for its immunogenicity, functionality, efficacy, and antibody durability against a variety of K. pneumoniae isolates in a murine bacteremia model. We also established an immunocompromised murine model of bacteremia to better recapitulate human infection and tested our vaccine’s efficacy in this background. The data included in the metadata set includes ELISAs, serum bactericidal assay, opsonophagocytosis assay, and survival curves. All data was generated in mice. GraphPad Prism is needed to open the data files. To view the data, use the free viewer mode of the software