Boehm Research Group at Stanford Collection in SearchWorks catalog (2024)

Concentrations of Candida auris nucleic acids in wastewater solids across the Untied States fall 2023-Spring 2024

Study results described in the corresponding manuscript.

This deposit contains three elements: 1. data analysis code (.ipynb file); 2. code input files (data); and 3. code output files (figures and tables). The .ipynb file and dataset reproduce analysis, figures, and tables for the manuscript titled "You can bring plankton to fecal indicator organisms, but you cannot make them graze: particle contribution to E. coli and MS2 inactivation in surface waters." The experiments are described in the manuscript.1. The data analysis code "2024_grazing_MS2_ecoli.ipynb" is a Jupyter Notebook in R and requires installation of an R kernel (installation instructions are available at: https://irkernel.github.io/installation/). To generate the figures and tables in the manuscript, place input files in a folder named "Data," create an empty folder named "Figures_and_tables", and execute the code in the same directory as the two created folders. These files are also available in github where the .ipynb file can be viewed directly (see "Links to related content" section).2. The dataset includes eight code input files: a. MS2 in experimental samples and controls quantified via plaque assay ("ms2.tsv")b. E. coli in experimental samples and controls quantified via spread plate method ("ecoli.tsv")c. absorbance spectra of water samples ("abs.csv"), d. DAPI cell counts in raw water (DAPI.csv) e. field data for water samples (i.e., date, time, temperature, salinity, pH, turbidity), the amount of raw water filtered to enumerate plankton, the volume of ethanol used to preserve plankton, the amount of raw water filtered for ~500% concentration ("c1"), and the amount of raw water filtered for ~1000% concentration ("c2") ("field.csv)f. total solids data in the raw water ("solids.csv")g. zooplankton enumeration in undiluted ethanol (zoo1.csv)h. zooplankton enumeration in diluted ethanol (zoo2.csv)3. The dataset contains figures and tables generated by the code and referenced in the manuscript (.jpg and .doc files).

Contains data on HIV nucleic acids and PMMoV RNA in wastewater solids over 26 months in two bay area wastewater treatment plants

Concentrations of the influenza A M and H5 genes in select wastewater treatment plants

Concentrations of rotavirus, human adenovirus, enteroviruses, and human noroviruses in wastewater solids at two wastewater treatment plants in the Bay Area of California

Concentrations of nucleic-acid markers of the targets mentioned in the title in wastewater solids measured by digital droplet (RT-)PCR

Data and documentation for the Cowell Circulation Study (2021). Drifter and benthic instrument deployments in late 2021 at Cowell Beach, Santa Cruz, CA. PIs: Stephen Monismith, Alexandria Boehm

Data and R code associated with the corresponding manuscript. Refer to the README file for variable descriptions and an overview of each R code file. Download and save all files in the same directory.

Date used for work described in paper Bayesian sequential approach to monitor COVID-19 variants through positivity rate from wastewater

Data to support the manuscript: Community occurrence of metapneumovirus, influenza A, and respiratory syncytial virus (RSV) inferred from wastewater monitoring during the winter 2022-2023 tripledemic

Data used in the manuscript entitled Respiratory virus concentrations in human excretions that contribute to wastewater: A systematic review

Data on concentrations of Dengue virus RNA in wastewater solids from three wastewater plants in Miami-Dade county Florida

Systematic review results described in the corresponding manuscript.

The goal of the present study is to investigate the solar photoinactivation of enveloped viruses in clear water. We measured endogenous, direct photoinactivation rate constants for Phi6 and murine hepatitis virus (MHV), surrogate enveloped viruses that have been used extensively as biosafety level 1 and 2 alternatives, respectively, to enveloped human viruses like avian influenza22 and human coronaviruses23 in experimental studies. We included MS2, an F+ coliphage whose solar photoinactivation has been thoroughly characterized as a model non-enveloped virus. MS2 will serve as a biological reference point to which we could compare the decay rate constants of the enveloped viruses. We used different solar spectrums generated by a solar simulator and passed through filters to investigate the role of different wavelengths in promoting photoinactivation. The experiments herein provide some of the first estimates of solar photoinactivation rate constants for enveloped viruses in clear water while providing insight into the mechanisms of photoinactivation for each virus.

This deposit contains four elements: 1. data analysis code (.ipynb files); 2. code input files original to this study (data); 3. code input files from a previous study that the .ipynb file pulls from to generate comparison figures (data), and 4. code output files (data). The .ipynb file and dataset reproduce analysis, figures, and tables for the manuscript titled "Temperature and particle content interact to affect human norovirus and MS2 persistence in surface water." The experiments are described in the manuscript.1. The data analysis code "HuNoV_MS2_persistence_data_analysis.ipynb" is a Jupyter Notebook in R and requires installation of an R kernel (installation instructions are available at: https://irkernel.github.io/installation/). To generate the figures and tables in the manuscript, place input files in a folder named "Data," create an empty folder named "Figures_and_tables", and execute the code in the same directory as the two created folders. These files are also available in github where the .ipynb file can be viewed directly (see "Links to related content" section).2. The dataset includes three original code input files: human norovirus and MS2 in experimental samples and controls quantified via RT-qPCR as threshold cycle values to assess intact capsids, long genome segments (>30 bp), and short genome segments (89 bp) ("expt_5_unk_ntc.csv"), MS2 in experimental samples and controls quantified via plaque assay ("ms2.csv"), and RT-qPCR standard curves ("expt_5_std.csv")3. The dataset includes two code input files that include previously published data [DOI: 10.25740/tr061rz9792 ] that the ipynb file pulls from to generate comparison figures: absorbance spectra for the raw and filter-sterilized water used in the experiments ("absorbance.csv") and ("kobs_import.csv")4. The dataset contains code output files: human norovirus and MS2 in experimental samples and controls quantified via RT-qPCR and converted to units of gene copies per mL in the code ("hunov_MS2_qpcr_gcperml.csv") as well as the figures and tables generated by the code.Columns labeled "quantity" (RT-qPCR standard curve files) are in units of gene copies per reaction and columns labeled "CT" are unitless RT-qPCR threshold cycle values.

The EMMI guideline checklist is provided as an excel file and link for a google sheet.

Human Norovirus GII RNA concentrations in wastewater solids from 145 wastewater treatment plants across the United States, as well as PMMoV RNA concentrations

We measured concentrations of SARS-CoV-2, influenza A and B virus, respiratory syncytial virus (RSV), mpox virus, human metapneumovirus, norovirus GII, and pepper mild mottle virus nucleic acids in wastewater solids at twelve wastewater treatment plants in Central California, USA. Measurements were made daily for up to two years, depending on the wastewater treatment plant. Measurements were made using digital droplet (reverse-transcription–) polymerase chain reaction (RT-PCR) following best practices for making environmental molecular biology measurements. These data can be used to better understand disease occurrence in communities contributing to the wastewater.

Data for paper on influenza A and PMMoV RNA in wastewater solids across the United States 2022-2023