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ShareScore release 0.9.0
Dataset results
73 results for “pathogen detection”
Detection of Bloodstream Pathogens in Hematological Malignancies
ClinicalTrials.gov study NCT03896880. IPD Sharing: UNDECIDED. Countries: 1. Publications: 4.
Pneumonia in the ImmunoCompromised - Use of the Karius Test for the Detection of Undiagnosed Pathogens
ClinicalTrials.gov study NCT04047719. IPD Sharing: UNDECIDED. Countries: 1. Publications: 9.
Bio-reconfigurable Electronic Platform for Multiplex Detection of Viral Respiratory Pathogens
ClinicalTrials.gov study NCT06702540. IPD Sharing: NO. Countries: 1. Publications: 4.
Urine Gene Analysis for Pathogen Detection
ClinicalTrials.gov study NCT05591911. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: Using the wax moth larva Galleria mellonella infection model to detect emerging bacterial pathogens
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Data from: Evolution of Drosophila resistance against different pathogens and infection routes entails no detectable maintenance costs
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Data from: A comparison between transcriptome sequencing and 16S metagenomics for detection of bacterial pathogens in wildlife
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On-site plant pathogen detection methods and introduction to microfluidics
<p>On June 24, 2020, IPANEMA organized the fourth Scientific online lecture (SOL4). The lesson was held by Dr. Cor Schoen from <a href="https://www.wur.nl/">Wageningen University & Research</a>, who brought us closer to different possible approaches for pathogen detection on the field.</p>
Validation of an eDNA-based method for the detection of wildlife pathogens in water
<p>Monitoring the occurrence and density of parasites and pathogens can identify high infection-risk areas and facilitates disease control and eradication measures. Environmental DNA (eDNA) techniques are increasingly used for pathogen detection due to their relative ease of application. Since many factors affect the reliability and efficacy of eDNA-based detection, rigorous validation and assessment of method limitations is a crucial first step. We evaluated an eDNA detection method using in-situ filtration of large volume water samples, developed to detect and quantify aquatic wildlife parasites by qPCR. We assessed method reliability using Batrachochytrium dendrobatidis, a pathogenic fungus of amphibians and the myxozoan Tetracapsuloides bryosalmonae, causative agent of salmonid proliferative kidney disease, in a controlled experimental setup. Different amounts of parasite spores were added to tanks containing either clean tap water or water from a semi-natural mesocosm community. Overall detection rates were higher than 80 %, but detection was not consistent among replicate samples. Within tank variation in detection emphasises the need for increased site-level replication when dealing with parasites and pathogens. Estimated parasite DNA concentrations in water samples were highly variable and significant increase with higher spore concentrations was observed only for B. dendrobatidis. Despite evidence for PCR inhibition in DNA extractions from mesocosm water samples, the type of water did not affect detection rates significantly. Direct spiking controls revealed that the filtration step reduced detection sensitivity. Our study identifies sensitive quantification and sufficient replication as major remaining challenges of eDNA-based methods for detection of parasites in water.</p>
Data from: DNA extraction method affects the detection of a fungal pathogen in formalin-fixed specimens using qPCR
Museum collections provide indispensable repositories for obtaining information about the historical presence of disease in wildlife populations. The pathogenic amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has played a significant role in global amphibian declines, and examining preserved specimens for Bd can improve our understanding of its emergence and spread. Quantitative PCR (qPCR) enables Bd detection with minimal disturbance to amphibian skin and is significantly more sensitive to detecting Bd than histology; therefore, developing effective qPCR methodologies for detecting Bd DNA in formalin-fixed specimens can provide an efficient and effective approach to examining historical Bd emergence and prevalence. Techniques for detecting Bd in museum specimens have not been evaluated for their effectiveness in control specimens that mimic the conditions of animals most likely to be encountered in museums, including those with low pathogen loads. We used American bullfrogs (Lithobates catesbeianus) of known infection status to evaluate the success of qPCR to detect Bd in formalin-fixed specimens after three years of ethanol storage. Our objectives were to compare the most commonly used DNA extraction method for Bd (PrepMan, PM) to Macherey-Nagel DNA FFPE (MN), test optimizations for Bd detection with PM, and provide recommendations for maximizing Bd detection. We found that successful detection is relatively high (80–90%) when Bd loads before formalin fixation are high, regardless of the extraction method used; however, at lower infection levels, detection probabilities were significantly reduced. The MN DNA extraction method increased Bd detection by as much as 50% at moderate infection levels. Our results indicate that, for animals characterized by lower pathogen loads (i.e., those most commonly encountered in museum collections), current methods may underestimate the proportion of Bd-infected amphibians. Those extracting DNA from archived museum specimens should ensure that the techniques they are using are known to provide high-quality throughput DNA for later analysis.
Supplementary material 1 from: Roques A, Ren L, Rassati D, Shi J, Akulov E, Audsley N, Auger-Rozenberg M-A, Avtzis D, Battisti A, Bellanger R, Bernard A, Bernadinelli I, Branco M, Cavaletto G, Cocquempot C, Contarini M, Courtial B, Courtin C, Denux O, Dvořák M, Fan J-t, Feddern N, Francese J, Franzen EKL, Garcia A, Georgiev G, Georgieva M, Giarruzzo F, Gossner M, Gross L, Guarneri D, Hoch G, Hölling D, Jonsell M, Kirichenko N, Loomans A, Luo Y-q, McCullough D, Maddox C, Magnoux E, Marchioro M, Martinek P, Mas H, Mériguet B, Pan Y-z, Phélut R, Pineau P, Ray AM, Roques O, Ruiz M-C, Sarto i Monteys V, Speranza S, Sun J-h, Sweeney JD, Touroult J, Valladares L, Veillat L, Yuan Y, Zalucki MP, Zou Y, Žunič-Kosi A, Hanks LM, Millar JG (2023) Worldwide tests of generic attractants, a promising tool for early detection of non-native cerambycid species. In: Jactel H, Orazio C, Robinet C, Douma JC, Santini A, Battisti A, Branco M, Seehausen L, Kenis M (Eds) Conceptual and technical innovations to better manage invasions of alien pests and pathogens in forests. NeoBiota 84: 169-209. https://doi.org/10.3897/neobiota.84.91096
Total trapping network
Supplementary material 2 from: Green S, Dehnen-Schmutz K, Drakulic J, Eschen R, Orazio C, Douma JC, Lundén K, Colombari F, Jactel H (2023) Awareness, detection and management of new and emerging tree pests and pathogens in Europe: stakeholders' perspectives. In: Jactel H, Orazio C, Robinet C, Douma JC, Santini A, Battisti A, Branco M, Seehausen L, Kenis M (Eds) Conceptual and technical innovations to better manage invasions of alien pests and pathogens in forests. NeoBiota 84: 9-40. https://doi.org/10.3897/neobiota.84.95761
Supplementary tables and figures
Supplementary material 3 from: Colombari F, Battisti A (2023) Citizen science at school increases awareness of biological invasions and contributes to the detection of exotic ambrosia beetles. In: Jactel H, Orazio C, Robinet C, Douma JC, Santini A, Battisti A, Branco M, Seehausen L, Kenis M (Eds) Conceptual and technical innovations to better manage invasions of alien pests and pathogens in forests. NeoBiota 84: 211-229. https://doi.org/10.3897/neobiota.84.95177
Number of individuals of each species captured at each school
Supplementary material 1 from: Garcia A, Samalens J-C, Grillet A, Soares P, Branco M, van Halder I, Jactel H, Battisti A (2023) Testing early detection of pine processionary moth Thaumetopoea pityocampa nests using UAV-based methods. In: Jactel H, Orazio C, Robinet C, Douma JC, Santini A, Battisti A, Branco M, Seehausen L, Kenis M (Eds) Conceptual and technical innovations to better manage invasions of alien pests and pathogens in forests. NeoBiota 84: 267-279. https://doi.org/10.3897/neobiota.84.95692
Supplementary images
Supplementary material 1 from: Green S, Dehnen-Schmutz K, Drakulic J, Eschen R, Orazio C, Douma JC, Lundén K, Colombari F, Jactel H (2023) Awareness, detection and management of new and emerging tree pests and pathogens in Europe: stakeholders' perspectives. In: Jactel H, Orazio C, Robinet C, Douma JC, Santini A, Battisti A, Branco M, Seehausen L, Kenis M (Eds) Conceptual and technical innovations to better manage invasions of alien pests and pathogens in forests. NeoBiota 84: 9-40. https://doi.org/10.3897/neobiota.84.95761
HOMED stakeholder survey
Supplementary material 1 from: Colombari F, Battisti A (2023) Citizen science at school increases awareness of biological invasions and contributes to the detection of exotic ambrosia beetles. In: Jactel H, Orazio C, Robinet C, Douma JC, Santini A, Battisti A, Branco M, Seehausen L, Kenis M (Eds) Conceptual and technical innovations to better manage invasions of alien pests and pathogens in forests. NeoBiota 84: 211-229. https://doi.org/10.3897/neobiota.84.95177
Lecture questionnaires
Pathogen Identification of Bacterial Pneumonia Via DNA Detection
ClinicalTrials.gov study NCT00567827. IPD Sharing: Not stated. Countries: 0. Publications: 1.
Next-Generation Sequencing for Pathogen Detection and Quantification in Children With Musculoskeletal Infections
ClinicalTrials.gov study NCT03846804. IPD Sharing: NO. Countries: 1. Publications: 0.
Detection of Pathogen and Antibiotic Resistance Genes by Targeted Next-Generation Sequencing in ICU Patients.
ClinicalTrials.gov study NCT06157372. IPD Sharing: NO. Countries: 0. Publications: 6.
Data from: DNA extraction method affects the detection of a fungal pathogen in formalin-fixed specimens using qPCR
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.