Dataset includes repeated measures of the National Institute of Standards and Technology Standard Reference Material 2917 (SRM 2917) using an Enterococcus digital PCR (dPCR) assay. “This research dataset has been reviewed in accordance with U.S. Environmental Protection Agency (U.S. EPA), Office of Research and Development, and approved for release. Mention of brand names or vendors does not constitute an endorsement of products or services by the U.S. EPA.”

This data package contains all raw digital PCR (dPCR) data used in the manuscript titled “Clade-specific multiplex digital PCR assay for monkeypox virus detection in wastewater". The study presents the development of a dPCR assay capable of detecting and quantifying the monkeypox virus (MPXV) while simultaneously distinguishing between its clades.

The dataset provides the raw data in support of Tables 1-4 of the paper and include: colony forming unit (CFU) data for each of three replicates of sand, loam, and clay soils; results for the sand/clay and loam/clay soil blend culture experiments; Quibit DNA concentration data; and polymerase chain reaction data. This dataset is associated with the following publication: Griffin, D., J. Lisle, D. Feldhake, and E. Silvestri. Colony-Forming Unit Spreadplate Assay versus Liquid Culture Enrichment-Polymerase Chain Reaction Assay for the Detection of Bacillus Endospores in Soils. Geosciences. MDPI AG, Basel, SWITZERLAND, 10(1): 14, (2020).

After May 3, 2024, this dataset and webpage will no longer be updated because hospitals are no longer required to report data on COVID-19 hospital admissions, and hospital capacity and occupancy data, to HHS through CDC’s National Healthcare Safety Network. Data voluntarily reported to NHSN after May 1, 2024, will be available starting May 10, 2024, at COVID Data Tracker Hospitalizations.

This time series dataset includes viral COVID-19 laboratory test [Polymerase chain reaction (PCR)] results from over 1,000 U.S. laboratories and testing locations including commercial and reference laboratories, public health laboratories, hospital laboratories, and other testing locations. Data are reported to state and jurisdictional health departments in accordance with applicable state or local law and in accordance with the Coronavirus Aid, Relief, and Economic Security (CARES) Act (CARES Act Section 18115).

Data are provisional and subject to change.

Data presented here is representative of diagnostic specimens being tested - not individual people - and excludes serology tests where possible. Data presented might not represent the most current counts for the most recent 3 days due to the time it takes to report testing information. The data may also not include results from all potential testing sites within the jurisdiction (e.g., non-laboratory or point of care test sites) and therefore reflect the majority, but not all, of COVID-19 testing being conducted in the United States.

Sources: CDC COVID-19 Electronic Laboratory Reporting (CELR), Commercial Laboratories, State Public Health Labs, In-House Hospital Labs

Data for each state is sourced from either data submitted directly by the state health department via COVID-19 electronic laboratory reporting (CELR), or a combination of commercial labs, public health labs, and in-house hospital labs. Data is taken from CELR for states that either submit line level data or submit aggregate counts which do not include serology tests.

Adult and neonatal human cardiovacular progenitor cell clonal populations were flown aboard the ISS for 12 days prior to fixation in RNAprotect. Gene expression analysis was performed against clone-, patient-, and passage-matched ground control samples. qPCR gene expression profiling. Human CPCs from three neonates and three adults were individually cultured on the ground or aboard the ISS.

Quantitative PCR targeting Trichodesmium, UCYN-A, UCYN-B, gamma-24774A11, and Het1, based on the nifH gene.

PCRs used for serotype and class identification.

Primer sequences used in q-RT-PCRs assay.

Using real-time reverse transcription PCR ten housekeeping genes from different abundance and functional classes in various human tissues were evaluated. The conventional use of a single gene for normalization leads to relatively large errors in a significant proportion of samples tested.

Model 2 assumed that all 1,000 simulated outbreaks had the same value of mean latent and infections periods (estimated using the results of PCR assay), whereas values of R0 were all sampled from the same gamma distribution with parameters κ and ρ at the median value of the posterior distributions. Parameters' meaning: Duration, duration of the epidemic in days; Tpeak, time of the epidemic peak (days after infection); D90%, time interval (days) during which the mid-90% of the cases occur (90% incidence interval); Ipeak, peak number of infective birds; Rpeak, seroprevalence at the epidemic peak; Rfinal, seroprevalence at the end of the outbreak; Tdet50, time by which a serological sample of 10 turkeys would result in detection with 50% probability (days).

Genes, assay ID and c(q) data and corresponding sample list. (XLS)

Validation data for the real-time PCR assays.

A GeXP multiplex, RT-PCR assay was developed and optimized that simultaneously measures expression of a suite of immune-relevant genes in rainbow trout (Oncorhynchus mykiss), concentrating on tumor necrosis factor and interleukin-1 ligand/receptor systems and acute phase response genes. The dataset includes expression values for drpt, il11a, il1b1, il1b2, il1b3, il1r-like-1(e3-5), il1r-like-1(e9-11), il1r1-like-a, il1r1-like-b, il1r2, saa, tnfa1, tnfa2, tnfa3, tnfrsf1a, tnfrsf1a-like-a, tnfrsf1a-like-b, tnfrsf5, and tnfrsf9. Gene expression was measured at four time-points post-challenge in both a resistant line (ARS-Fp-R) and a susceptible line (ARS-Fp-S) of rainbow trout. In addition, fish body weight, spleen index and the Flavobacterium psychrophilum load are reported. These data are an extension of information presented and discussed in the article "Proinflammatory cytokine and cytokine receptor gene expression kinetics following challenge with Flavobacterium psychrophilum in resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss)" (Kutyrev et al., 2016). Resources in this dataset:Resource Title: Dataset of proinflammatory cytokine and cytokine receptor gene expression in rainbow trout (Oncorhynchus mykiss) measured using a novel GeXP multiplex, RT-PCR assay. File Name: Web Page, url: https://www.sciencedirect.com/science/article/pii/S2352340917300331 Data in Brief data article providing expression values for a suite of immune-relevant genes in rainbow trout (Oncorhynchus mykiss), concentrating on tumor necrosis factor and interleukin-1 ligand/receptor systems and acute phase response genes. Data are available for download as Excel spreadsheet.Resource Software Recommended: Microsoft Excel,url: https://office.microsoft.com/excel/

Raw data for RT-PCR,total 44 samples of T, M, D and Zhoumai 18 genotype, wheat actin gene was used as internal control for normalization.

Several layers were examined as part of the highway improvement needs and risk analysis conducted for the 2022 State Transportation Plan. Identifying safety risk for the primary highway systems was analyzed through the use of Safety Performance Functions (SPFs) and the subsequent output of Potential for Crash Reduction (PCR). An SPF is an equation used to predict the average number of crashes per year at a location as a function of exposure and, in some cases, roadway or intersection characteristics. Generally, SPFs more realistically demonstrate the relationship between crashes and traffic volume. SPFs account for the regression to the mean by using an Empirical Bayes statistical method. The advantages of using this method are more accurately calculating the potential for safety improvement and acknowledging the complex, non-linear relationship between crash frequency and volume. For any given segment, the potential for crash reduction (PCR) can be determined by evaluating the predicted number of crashes for the location based on volume. This is based on the functional form of the SPF. The predicted number of crashes for a given site is adjusted by the Empirical Bayes method which adjusts the prediction based on the observed crashes at a site. The difference between the corrected number of crashes with the Empirical Bayes and the predicted number of crashes based on the SPF is considered PCR.For the State Long-Range Transportation Plan SLRTP ten different SPF models (and 29 sub models) based on roadway characteristics were developed to evaluate and predict the number of crashes on Iowa’s primary highways. Subsequently, PCR values were calculated for each segment. The results were aggregated to the defined primary highway corridors established by the Systems Planning Bureau. In evaluating safety risk for the purposes of the SLRTP we normalized the PCR per year by the segment or corridors length.Note: this dataset supersedes SCOPING_MOBILITY_AND_SAFETY_RETIRED, effective with the publication of the State Long Range Transportation Plan (SLRTP) and Freight Plan update in 2022.

Trypanosoma (Herpetosoma) lewisi is a trypanosome of the sub-genus Herpetosoma (Stercoraria section), parasite of rats (Rattus rattus and Rattus norvegicus) transmitted by fleas. T. lewisi has a stringent species specificity and cannot grow in other rodents such as mice. Rats are infected principally by oral route, through contamination by flea faeces or ingestion of fleas. Trypanosoma lewisi infections in rat colonies can interfere with research protocols and fleas of wild rats are often the source of such infections. Currently, diagnosis of T. lewisi in rats is performed by microscopic observation of stained blood smears. In the course of a research project at CIRDES, a T. lewisi infection was detected in the rat colony. In this study we evaluated PCR primer sets for their ability to diagnose multiple species of trypanosomes with a single amplification. We show that the use of ITS1 sequence of ribosomal DNA provides an efficient and sensitive assay for detection and identification of T. lewisi infection in rats and recommend the use of this assay for monitoring of T. lewisi infections in rat colonies.

These data contain sample information and locality and quantitative polymerase chain reaction (qPCR) results from extraction and testing of individual tape strips within Passive Environmental Samplers (PES). Samplers were placed at 5 locations on Hawaii Island between 2016 and 2017.

PCR

## Overview

PCR is a dataset for object detection tasks - it contains Dsitresses annotations for 7,052 images.

## Getting Started

You can download this dataset for use within your own projects, or fork it into a workspace on Roboflow to create your own model.

  ## License

  This dataset is available under the [CC BY 4.0 license](https://creativecommons.org/licenses/CC BY 4.0).

Background Chlamydia pneumoniae infection has been detected by serological methods, but PCR is gaining more interest. A number of different PCR assays have been developed and some are used in combination with serology for diagnosis. Real-time PCR could be an attractive new PCR method; therefore it must be evaluated and compared to conventional PCR methods.

   Results
   We compared the performance of a newly developed real-time PCR with a conventional PCR method for detection of C. pneumoniae. The PCR methods were tested on reference samples containing C. pneumoniae DNA and on 136 nasopharyngeal samples from patients with a chronic cough. We found the same detection limit for the two methods and that clinical performance was equal for the real-time PCR and for the conventional PCR method, although only three samples tested positive. To investigate whether the low prevalence of C. pneumoniae among patients with a chronic cough was caused by suboptimal PCR efficiency in the samples, PCR efficiency was determined based on the real-time PCR. Seventeen of twenty randomly selected clinical samples had a similar PCR efficiency to samples containing pure genomic C. pneumoniae DNA.


   Conclusions
   These results indicate that the performance of real-time PCR is comparable to that of conventional PCR, but that needs to be confirmed further. Real-time PCR can be used to investigate the PCR efficiency which gives a rough estimate of how well the real-time PCR assay works in a specific sample type. Suboptimal PCR efficiency of PCR is not a likely explanation for the low positivity rate of C. pneumoniae in patients with a chronic cough.

Background Suppression Subtractive Hybridization PCR (SSH PCR) is a sophisticated cDNA subtraction method to enrich and isolate differentially expressed genes. Despite its popularity, the method has not been thoroughly studied for its practical efficacy and potential limitations.

   Results
   To determine the factors that influence the efficacy of SSH PCR, a theoretical model, under the assumption that cDNA hybridization follows the ideal second kinetic order, is proposed. The theoretical model suggests that the critical factor influencing the efficacy of SSH PCR is the concentration ratio (R) of a target gene between two cDNA preparations. It preferentially enriches "all or nothing" differentially expressed genes, of which R is infinite, and strongly favors the genes with large R. The theoretical predictions were validated by our experiments. In addition, the experiments revealed some practical limitations that are not obvious from the theoretical model. For effective enrichment of differentially expressed genes, it requires fractional concentration of a target gene to be more than 0.01% and concentration ratio to be more than 5 folds between two cDNA preparations.


   Conclusion
   Our research demonstrated theoretical and practical limitations of SSH PCR, which could be useful for its experimental design and interpretation.