Find research datasets worth reusing

opencc-zeroNov 2022View details →

Droplet digital PCR (ddPCR) as a tool for investigating dynamics of cryptic symbionts

Interactions among symbiotic organisms and their hosts are major drivers of ecological and evolutionary processes. Monitoring the infection patterns among natural populations and identifying factors affecting these interactions is critical for understanding symbiont-host relationships. However, many of these interactions remain understudied since the knowledge about the symbiont species is lacking and hinders the development of appropriate tools. In this study, we developed a digital droplet PCR (ddPCR) assay based on apicomplexan COX1 gene to detect an undescribed agamococcidian symbiont. We show that the method gives precise and reproducible results and enables detecting cryptic symbionts in low target concentration. We further exemplify the assay's use to survey seasonally sampled natural host (Pygospio elegans) populations for symbiont infection dynamics. We found that symbiont prevalence differs spatially but does not show seasonal changes. Infection load differed between populations and was low in spring and significantly increased towards fall in all populations. We also found that the symbiont prevalence is affected by host length and population density. Larger hosts were more likely to be infected and high host densities were found to have lower probability of infection. The observed variations could be due to characteristics of both symbiont and host biology, especially the seasonal variation in encounter rates. Our findings show that the developed ddPCR assay is a robust tool for detecting undescribed symbionts that are otherwise difficult to quantify, enabling further insight into the impact cryptic symbionts have on their hosts.

opencc-by-4.0Jan 2023View details →

Dataset related to the article "Extraction-Free Absolute Quantification of Circulating miRNAs by Chip-Based Digital PCR"

This record contains raw data related to the article "Extraction-Free Absolute Quantification of Circulating miRNAs by Chip-Based Digital PCR" Circulating microRNAs (miRNA) have been proposed as specific biomarkers for several diseases. Quantitative Real-Time PCR (RT-qPCR) is the gold standard technique currently used to evaluate miRNAs expression from different sources. In the last few years, digital PCR (dPCR) emerged as a complementary and accurate detection method. When dealing with gene expression, the first and most delicate step is nucleic-acid isolation. However, all currently available protocols for RNA extraction suffer from the variable loss of RNA species due to the chemicals and number of steps involved, from sample lysis to nucleic acid elution. Here, we evaluated a new process for the detection of circulating miRNAs, consisting of sample lysis followed by direct evaluation by dPCR in plasma from healthy donors and in the cardiovascular setting. Our results showed that dPCR is able to detect, with high accuracy, low-copy-number as well as highly expressed miRNAs in human plasma samples without the need for RNA extraction. Moreover, we assessed a known myocardial infarction-related miR-133a in acute myocardial infarct patients vs. healthy subjects. In conclusion, our results show the suitability of the extraction-free quantification of circulating miRNAs as disease markers by direct dPCR.

opencc-by-4.0Feb 2023View details →

Investigation of the diagnostic importance and accuracy of CT in the chest compared to the RT-PCR test for suspected COVID-19 patients in Jordan

As the world continues to battle the COVID-19 pandemic, Jordan is no exception. In order to improve the accuracy of diagnosis, researchers in Jordan have conducted an investigation into the diagnostic importance and accuracy of CT in the chest compared to the RT-PCR test for suspected COVID-19 patients.

opencc-by-4.0Mar 2023View details →

Assessing the prevalence of Female Genital Schistosomiasis and comparing the acceptability and performance of health worker-collected and self-collected cervical-vaginal swabs using PCR testing among women in North-Western Tanzania: the ShWAB study

Female genital schistosomiasis (FGS) is a severe neglected disease, caused by infection with Schistosoma haematobium. The WHO has prioritized the improvement of diagnostics for FGS and previous studies have explored the PCR-based detection of Schistosoma DNA on genital specimens, with encouraging results. We aimed to determine the prevalence of FGS among women living in an endemic district in North-western Tanzania, applying and preliminary comparing self-collected and operator-collected cervical-vaginal swabs followed by PCR, and to assess the acceptability of these sampling procedures.

opencc-zeroJul 2023View details →

Data from: Drop it all: Extraction-free detection of non-indigenous marine species through optimized direct-droplet digital PCR

Molecular biosecurity surveillance programs increasingly use environmental DNA (eDNA) for detecting marine non-indigenous species (NIS). However, the current molecular detection workflow is cumbersome, prone to errors and delays, and is limited in providing knowledge about eDNA beyond the spatial and temporal extent of the sampling. These limitations can hinder management efforts and restrict the "opportunity window" for a rapid response to new marine NIS incursions. Emerging innovative field-deployable digital droplet PCR (ddPCR) systems offer improved workflow efficiency by autonomously analyzing targeted free-floating extra-cellular eDNA (free-eDNA) signals. Despite their potential, these systems have not been tested in marine environments. Thus, an aquarium study was conducted with three distinct marine NIS: the Mediterranean fanworm Sabella spallanzanii, the ascidian clubbed tunicate Styela clava, and the brown bryozoan Bugula neritina to evaluate the detectability of free-eDNA in seawater. The detectability of targeted free-eDNA was assessed by directly analyzing aquarium water samples using an optimized species-specific ddPCR assay, without filtration or DNA extraction, so-called, "direct-ddPCR". The results demonstrated the consistent detection of Sabella spallanzanii and Bugula neritina free-eDNA when these organisms were present in high abundance. Once organisms were removed, the free-eDNA signal exponentially declined, noting that free-eDNA persisted between 24-72 hours. Results indicate that organism biomass, specimen characteristics (e.g., stress and viability), and species-specific biological differences may influence free-eDNA detectability. These results are critical for implementing in-situ nucleic acid automated continuous sensing systems for marine biosurveillance, enabling point-of-need detection and rapid management response to biosecurity threats.

opencc-zeroAug 2023View details →

Multiplexing PCR allows the identification of within-species genetic diversity in ancient eDNA

Sedimentary ancient DNA (sedaDNA) has rarely been used to obtain population-level data due to either a lack of taxonomic resolution for the molecular method used, limitations in the reference material or inefficient methods. Here, we present the potential of multiplexing different PCR primers to retrieve population-level genetic data from sedaDNA samples. Vaccinium uliginosum (Ericaceae) is a widespread species with a circumpolar distribution and three lineages for present-day populations. We searched 18 plastid genomes for intraspecific variable regions and developed 61 primers to target these. Initial multiplex PCR testing resulted in a final set of 38 primers. These primers were used to analyse 20 lake sedaDNA samples (11,200 cal. yr BP to present) from five different localities in northern Norway, the Alps and the Polar Urals. All known V. uliginosum lineages in these regions and all primers could be recovered from the sedaDNA data, where for each sample 28.1 primers containing 34.15 variant sequences were obtained on average. All sediment samples were dominated by a single lineage, except three alpine samples which had co-occurrence of two different lineages. Furthermore, lineage turnover was observed in the Alps and northern Norway, suggesting that present-day phylogeographical studies may overlook past genetic patterns. Multiplexing primers is a promising tool for generating population-level genetic information from sedaDNA. The relatively simple method, combined with high sensitivity, provides a scalable method that will allow researchers to track populations through time and space using environmental DNA.

opencc-zeroSep 2023View details →

BBB permeability, sleep and qRT-PCR data for: The Drosophila blood-brain barrier regulates sleep via moody GPCR signaling

Sleep is vital for most animals, yet its mechanism and function remain unclear. We found that permeability of the BBB–the organ required for maintenance of homeostatic levels of nutrients, ions, and other molecules in the brain–is modulated by sleep deprivation and can cell-autonomously effect sleep changes. We observed increased BBB permeability in known sleep mutants as well as in acutely sleep deprived animals. In addition to molecular tracers, sleep deprivation-induced BBB changes also increased penetration of drugs used in the treatment of brain pathologies. After chronic/ genetic or acute sleep deprivation, rebound sleep or administration of the sleeping aid gaboxadol normalized BBB permeability, showing that sleep deprivation effects on the BBB are reversible. Along with BBB permeability, RNA levels of the BBB master regulator moody are modulated by sleep. Conversely, altering BBB permeability alone through glia-specific modulation of moody, gαo, loco, lachesin, or neuroglian – each a well-studied regulator of BBB function – was sufficient to induce robust sleep phenotypes. These studies demonstrate a tight link between BBB permeability and sleep and indicate a novel role for the BBB in the regulation of sleep.

opencc-by-4.0Oct 2023View details →

ATUAÇÃO DO ENFERMEIRO LÍDER FRENTE A UMA PCR NO PRONTO SOCORRO

O presente estudo demonstra Atuação do enfermeiro líder frente a uma PCR em ambiente intra-hospitalar. Metodologia: Baseado em um estudo de revisão da literatura do tipo bibliográfica integrativa, descritiva e retrospectiva com fontes de informação bibliográfica e análise qualitativa e quantitativa. Resultados: Os principais cuidados e intervenções da assistência de enfermagem, frente ao diagnóstico de PCR, inserem a Sistematização da Enfermagem nas tomadas de decisões de toda equipe multidisciplinar. Concretiza que o papel do enfermeiro é essencial e indispensável. Conclusão: Torna-se fundamental a atuação do enfermeiro em aspecto de alta complexidade e demonstra a necessidade dessa assistência perante o protocolo e sobrevida do paciente.

restrictedIPD-UNDECIDEDFeb 2026View details →

Trial of Eribulin in Patients Who Do Not Achieve Pathologic Complete Response (pCR) Following Neoadjuvant Chemotherapy

ClinicalTrials.gov study NCT01401959. IPD Sharing: Not stated. Countries: 1. Publications: 3.

closedIPD-NOFeb 2026View details →

KCNA3 and OTOP2 Gene Methylation Combined Detection Kit (Fluorescent PCR Method)

ClinicalTrials.gov study NCT05680077. IPD Sharing: NO. Countries: 1. Publications: 8.

restrictedIPD-UNDECIDEDFeb 2026View details →

Evaluation of the Artus® CMV PCR Test

ClinicalTrials.gov study NCT01034709. IPD Sharing: Not stated. Countries: 1. Publications: 11.

closedIPD-NOFeb 2026View details →

Efficacy of a Multiplex BangasureTM RT-PCR Kit for the Detection of COVID-19

ClinicalTrials.gov study NCT05190016. IPD Sharing: NO. Countries: 1. Publications: 14.

restrictedIPD-UNDECIDEDFeb 2026View details →

Posterior Cruciate Retaining (PCR) Versus Posterior Cruciate Substituting (PCS) Total Knee Arthroplasty (TKA)

ClinicalTrials.gov study NCT02429856. IPD Sharing: Not stated. Countries: 1. Publications: 1.

closedIPD-NOFeb 2026View details →

Improvements Through the Use of a Rapid Multiplex PCR Enteric Pathogen Detection Kit in Children With Hematochezia

ClinicalTrials.gov study NCT03362970. IPD Sharing: NO. Countries: 1. Publications: 5.

controlledIPD-YESFeb 2026View details →

A Study of an Ad26.RSV.preF-based Regimen in the Prevention of Reverse Transcriptase Polymerase Chain Reaction (RT-PCR)-Confirmed Respiratory Syncytial Virus (RSV)-Mediated Lower Respiratory Tract Dis

ClinicalTrials.gov study NCT03982199. IPD Sharing: YES. Countries: 1. Publications: 2.