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123 results for “Target detection”
Table S27: Target and identified unknown organic micropollutants detected in surface water samples taken during heavy rain events
<p>In the following table, peak intensities of detected organic micropollutants in water samples are displayed.</p> <p>This data table is part of the appendix of Chapter 4 of the PhD thesis “Novel approaches to identify drivers of chemical stress in small rivers” by Liza-Marie Beckers prepared at RWTH Aachen University and at the Helmholtz Centre for Environmental Research-UFZ. In Chapter 4, precipitation-related pollutant patterns and indicator compounds during heavy rain events were identified in the Holtemme River by nontarget screening and cluster analysis. The table contains peak heights of organic micropollutants detected in water samples taken during heavy rain events in the Holtemme River (Saxony – Anhalt, Germany). The table is structured into the following columns: Compound name, use class of compound (e.g., pharmaceutical or pesticide), distinction between target or identified unknown compounds, mass-to-charge ratio (m/z), retention time (RT), assignment to a pattern identified by cluster analysis (i.e., “Base” or “Quick”), the probability of belonging to the assigned pattern as number between 0 and 1 as well as the peak height of the compound in each sample. The samples are indicated by "B" for "bottle" and a number from 1-16. The use class “NA” indicates that now major use class for this compound could be identified.</p> <p>The sampling was triggered by combined sewer overflow at a wastewater treatment plant upstream of the sampling point. Samples were taken by an automated sampler in 30-min composite samples for 8 hours resulting in 16 samples per rain event. In total, 6 heavy rain events from May to September 2016 were sampled during this study. The table is divided into 6 subtables (i.e., Table S27 A-F). Each subtable displays compounds and their peak heights detected in samples from one heavy rain event. The different rain events are abbreviated by the sampling date:</p> <p>Table S27A displays results from the rain event samples May 29<sup>th</sup> 2016 : E2905</p> <p>Table S27B displays results from the rain event samples June 01<sup>st</sup> 2016 : E0106</p> <p>Table S27C displays results from the rain event samples June 24<sup>th</sup> 2016 : E1306</p> <p>Table S27D displays results from the rain event samples June 13<sup>th</sup> 2016 : E2406</p> <p>Table S27E displays results from the rain event samples July 13<sup>th</sup> 2016 : E1307</p> <p>Table S27F displays results from the rain event samples September 17<sup>th</sup> 2016 : E1709</p> <p>Chemical analysis of the water samples was performed by liquid chromatography (UltiMate 3000 LC system (Thermo Scientific)) coupled to high resolution mass spectrometry (Q Exactive Plus, Thermo Scientific) with a heated electrospray ionization (HESI) source. Nontarget screening was performed as it allows for a comprehensive characterization of the chemical exposure during heavy rain events. However, only annotated target compounds and unknown compounds identified by structure elucidation are presented in the table. Details on data evaluation methods are described in Chapter 4 of the PhD thesis.</p> <p>Beckers, L.M. (2019): Novel approaches to identify drivers of chemical stress in small rivers. RWTH Aachen University, Aachen.</p>
Probiotics reshape the coral microbiome in situ without detectable off-targeted effects in the surrounding environment.
<p>The R code scripts and Supplementary data files from the paper: "Probiotics reshape the coral microbiome in situ without detectable off-targeted effects in the surrounding environment," accepted in Communications Biology. All R code and data necessary to reproduce the published results are available. </p>
Data on the detection of clinically significant prostate cancer by magnetic resonance imaging (MRI)-guided targeted and systematic biopsy
<p>This is a dataset from the original publication “Reasons for missing clinically significant prostate cancer by targeted magnetic resonance imaging/ultrasound fusion-guided biopsy”. From 01/2014 to 04/2019 a sample collective of 785 patients with 3T multiparametric magnetic resonance imaging (mp-MRI) of the prostate and subsequent combined systematic biopsy (SB) and magnetic resonance imaging/ultrasound (US) fusion-guided biopsy (TB) was retrospectively analyzed. Prostate carcinoma (PCa) detection by TB and/or additional SB was analyzed.</p>
Figure 1. Response curves for percent acetyl-coenzyme A in Detecting the effect of ACCase-targeting herbicides on ACCase activity utilizing a malachite green colorimetric functional assay
Figure 1. Response curves for percent acetyl-coenzyme A carboxylase (ACCase) activities of resistant and susceptible Digitaria ciliaris biotypes in response to the increasing concentrations of the ACCase-targeting herbicides, sethoxydim, clethodim,fluazifop-p-butyl, and pinoxaden.The response was modeled based on the log rate of ACCase-targeting herbicides to create equal spacing between rates using least-squares fit regression of ACCase activity to the non-treated check. Means are represented by differing symbols for each biotype, and regression equation models are represented by differing line types for each biotype. Vertical bars represent the standard errors of the means (n = 6). Digitaria ciliaris biotypes: R1 and R2, resistant; S, susceptible. The concentration of ACCase-targeting herbicides required to cause 50% inhibition of ACCase activity (IC50) was calculated from concentration-response curves. CI, confidence interval.
Does the tail show when the nose knows? AI-enhanced analysis of tail kinematics outperforms human experts at predicting when detection dogs find their target odor
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Fluorescence‐based detection of field targets using an autonomous unmanned aerial vehicle system
<p>This dataset comprises of the IDL code referenced in the 'Open Research' section of the Kaye and Pittman (2020) study 'Fluorescence‐based detection of field targets using an autonomous unmanned aerial vehicle system' published in <em>Methods in Ecology and Evolution</em> (<a href="https://doi.org/10.1111/2041-210X.13402">https://doi.org/10.1111/2041-210X.13402</a>).</p> <p>This study describes a proof‐of‐concept autonomous unmanned aerial vehicle (UAV) system that utilizes the fluorescence characteristics unique to different materials to scan and acquire targets in the field e.g. fossils, rocks and minerals, organisms and archaeological artefacts. This is possible because these targets are often highly fluorescent against lower fluorescence backgrounds and may exhibit different colours. Fluorescence is stimulated by a near‐UV laser that is projected across the ground as a horizontal line directly below the UAV. The IDL code is for laser line and colour extractions in the laser scan strip. The raw .jpeg data for the IDL code is not provided here as this depends on what target is being scanned. All image data are made available in the paper. Additional contextual information is provided in the '2 MATERIALS AND METHODS' section of the paper, especially in Figure 3.</p>
Data from: Development and validation of targeted environmental DNA (eDNA) metabarcoding for early detection of 69 invasive fishes and aquatic invertebrates
<p>Invasive species are of concern due to their impacts on ecosystems and economies, but they pose significant control challenges. Environmental DNA (eDNA) is a powerful tool in the detection of aquatic organisms at low densities due to high sensitivity and ease of collection. Aquatic eDNA analyses have increased worldwide and are generally either applied to a few target species (quantitative PCR) or for broad taxonomic applications (metabarcoding). Here we describe the development and testing of a hybrid approach that utilized high sensitivity PCR primer sets and high-throughput sequencing (HTS), referred to as <em>targeted metabarcoding</em>, to detect 69 fishes and invertebrates. We identified target species based on reports of globally important invasive species and developed two independent PCR primers for each species (CO1 and a second mtDNA region). We assessed sensitivity and eDNA interference for all 138 primers (2 per species, 69 species) using standard end-point PCR and tested them on 10 eDNA samples spiked with various amounts of one or more of the target species' DNA. The sensitivity of the 138 primer sets ranged between 1.5×10<sup>-5</sup> and 2.64 ng template DNA (mean = 0.069 ng). Primers were also tested for interference effects using plankton eDNA to simulate field conditions. The inclusion of interfering plankton DNA reduced the sensitivity for most primer sets by one or more orders of magnitude (range 0 to 3). Overall, our targeted metabarcoding resulted in the detection of ~ 98% of species in the DNA spiked samples, and, perhaps more importantly, the HTS read count was positively related to the quantity of spiked DNA (P < 0.002). We envision this technique being particularly useful for the early detection of species at low population densities; however, there are diverse applications of targeted metabarcoding for monitoring aquatic community composition and quantifying ecosystem change and health.</p>
BIOMETSCO progress presentation 2022: Identification of Novel Biomarkers and Drug Targets for the Detection and Elimination of Occult Metastases in Colon Cancer
<p>This is a recorded talk with head of the BIOMETSCO project - Lasse Sommer Kristensen - where he presents the latest project progress.</p> <p>The talk was given at one of ODIN's (the Open Discovery Innovation Network) Knowledge Sharing Events in May 2022.</p> <p> </p> <p> </p>
NGS data from: Detection of unintended on-target effects in CRISPR genome editing by DNA donors carrying diagnostic mutations
<p>We developed a method to detect copy number variation and loss of heterozygosity in genome-edited cell lines by only sequencing the edited site. We introduced different substitutions on both chromosomes of diploid H9 human embryonic stem cells using CRISPR/Cas9 and a mixture of homology-directed repair donor DNAs carrying different substitutions. Here, we deposit the associated sequencing data (BAM-files) generated by extracting genomic DNA from genome-edited H9 cells, PCR amplifying the region of interest and sequencing on a MiSeq platform. We sequenced the edited site of cell bulks to investigate the editing efficiencies of individual donors from the donor mixtures. For proof of concept, we isolated over 850 cellular clones from the edited cell bulks and sequenced the edited site and heterozygous positions flanking the edited site to determine the number of alleles at the edited site and detect copy-neutral loss of heterozygosity. Additionally, we sequenced the DNA donors to assess, the distribution of individual donors in the mixtures.</p>
Detection of Clinically Significant Prostate Cancer Using Transperineal Targeted Biopsy Compared to Standard Transrectal Biopsy
ClinicalTrials.gov study NCT03044197. IPD Sharing: NO. Countries: 1. Publications: 1.
Multi-Target Colorectal Cancer Screening Test for the Detection of Colorectal Advanced Adenomatous Polyps and Cancer
ClinicalTrials.gov study NCT01397747. IPD Sharing: Not stated. Countries: 2. Publications: 3.
Targeted Melanoma Detection With Skin Self-Examination During COVID-19 Restricted Physician Access
ClinicalTrials.gov study NCT04420273. IPD Sharing: NO. Countries: 1. Publications: 2.
DETECT: Target Volume for Rectal Endoluminal Radiation Boosting
ClinicalTrials.gov study NCT04927897. IPD Sharing: NO. Countries: 1. Publications: 23.
Combining High-frequency Micro-ultrasound and Multiparametric MRI Target Biopsy for Detecting Prostate Cancer
ClinicalTrials.gov study NCT06579911. IPD Sharing: NO. Countries: 1. Publications: 10.
Data from: Detecting aquatic invasive species in bait and pond stores with targeted environmental (e) DNA high-throughput sequencing metabarcode assays: angler, retailer, and manager implications
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NGS data from: Detection of unintended on-target effects in CRISPR genome editing by DNA donors carrying diagnostic mutations
Open the record for dataset details and reuse information.
Fluorescence‐based detection of field targets using an autonomous unmanned aerial vehicle system
Open the record for dataset details and reuse information.
Data from: Development and validation of targeted environmental DNA (eDNA) metabarcoding for early detection of 69 invasive fishes and aquatic invertebrates
Open the record for dataset details and reuse information.
Targeted indication of imaging for detection of vesicoureteric reflux after pediatric febrile urinary tract infections based on a multiparametric computational tool
<p>This is the original data used for our study on differentiated indication of a voiding cystourethrography after pediatric febrile urinary tract infections. </p>
Data from: D quantification of tumor vasculature in lymphoma xenografts in NOD/SCID mice allows to detect differences among vascular-targeted therapies
Quantitative characterization of the in vivo effects of vascular-targeted therapies on tumor vessels is hampered by the absence of useful 3D vascular network descriptors aside from microvessel density. In this study, we extended the quantification of planar vessel distribution to the analysis of vascular volumes by studying the effects of antiangiogenic (sorafenib and sunitinib) or antivascular (combretastatin A4 phosphate) treatments on the quantity and spatial distributions of thin microvessels. These observations were restricted to perinecrotic areas of treated human multiple myeloma tumors xenografted in immunodeficient mice and to microvessels with an approximate cross-sectional area lower than 75 µm2. Finally, vessel skeletonization minimized artifacts due to possible differential wall staining and allowed a comparison of the various treatment effects. Antiangiogenic drug treatment reduced the number of vessels of every caliber (at least 2-fold fewer vessels vs. controls; p<0.001, n = 8) and caused a heterogeneous distribution of the remaining vessels. In contrast, the effects of combretastatin A4 phosphate mainly appeared to be restricted to a homogeneous reduction in the number of thin microvessels (not more than 2-fold less vs. controls; p<0.001, n = 8) with marginal effects on spatial distribution. Unexpectedly, these results also highlighted a strict relationship between microvessel quantity, distribution and cross-sectional area. Treatment-specific changes in the curves describing this relationship were consistent with the effects ascribed to the different drugs. This finding suggests that our results can highlight differences among vascular-targeted therapies, providing hints on the processes underlying sample vascularization together with the detailed characterization of a pathological vascular tree.
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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.