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1,647 results for “assay”
A droplet digital polymerase chain reaction assay to detect rare helminth parasites infecting natural host populations (Vancouver Island 2023, University of Wisconsin Madison Laboratory colony 2024)
Helminth infections represent a significant challenge to human, livestock, and wildlife health, yet they remain relatively under-studied, especially in terms of their ecological impacts. Better understanding of how these parasites spread in wildlife populations could improve our ability to predict and manage disease transmission across various species. Traditional detection methods, such as visually identifying parasites in environmental samples or infected hosts, often fall short, especially during the early stages of infection when parasite loads are minimal. In this study, we introduce a highly sensitive and precise droplet digital PCR (ddPCR) assay that quantifies helminth DNA in aquatic habitats, focusing on the 18S rRNA gene as a marker. These data utilize the model host-parasite system between the tapeworm Schistocephalus solidus, and its cyclopoid copepod host, Acanthocyclops robustus. The molecular assays are built around creating an infection standard in the lab, where copepods were singly infected with a single tapeworm parasite. We extracted DNA from 100 infected adults and used this as a standard to translate gene copy numbers from the ddPCR reactions to actual animal values. After creating a known lab standard, we then use the generated probes and primers to detect (and quantify!) infection burdens in field samples, which include both water filter samples (eDNA) and zooplankton tows from several lakes around Vancouver Island, B.C. The data presented here include well-specific data from ddPCR runs (amplitude of individual level oil droplets in the reaction) as well as each ddPCR analysis in its entirety. In order to prove the specificity of probes and probe-primers, we include here ddPCR runs of closely related helminth species, Schistocephalus cotti and Schistocephalus pungitii. We also consider the binding to another genera of copepod, the calanoid Eurytomora. All of the data wrangling, analysis, and data visualization are included as .Rmd files in th
C Concentrations and Characterization Data from DOM Incubation Assay Experiments
This dataset includes (1) original data from a dissolved organic carbon (DOC) incubation experiment and (2) a data synthesis of the DOC incubation experiment literature. Study component (1) was a factorial lab experiment crossing varying dissolved organic matter (DOM) sources (Suwannee River Fulvic Acid, Elliott soil leachate, Chlorella leachate) with varying microbial communities. The objective of this study component was to test the interacting effects of microbial community composition and DOM characteristics on carbon (C) biodegradation. We used a Micro-Oxymax Respirometer (Columbus Instruments, Columbus, Ohio) to measure carbon dioxide and oxygen accumulation at two hour intervals for a period of two weeks, and quantified the initial and final concentrations of dissolved organic carbon and total dissolved nitrogen of each experimental unit. To verify that the three DOM source solutions had differing chemical compositions and potential bioreactivity, we optically characterized each DOM source using mass spectra analysis and excitation-emission matrices (EEMs). Study component (2) is a synthesis of DOC concentrations from the C degradation experiment literature. The criteria for including a study in this synthesis was that (a) incubation DOM was sourced from a river, lake, marine, estuary, or marsh, and (b) that C concentrations were measured at least twice throughout the incubation in addition to an initial measurement. For each study, we extracted initial DOC values, elapsed incubation time, and reported DOC concentrations during the incubation period for each experimental treatment. This data package is completed.
Differential gene expression data of commercial compounds used to assess the performance of human TeraTox assay
<p>The dataset supplements the publication `Optimization of the <em>TeraTox</em> assay for preclinical teratogenicity assessment`. </p> <ul> <li>2022-02-18-TeraTox-commercial-logFC.gct: log2FC matrix of genes by compounds (in concentration ranges)</li> <li>2022-02-18-TeraTox-commercial-pScore.gct: p-scores (log 10 transformed p-values with the sign of logFC) of genes by compounds</li> <li>2022-02-18-TeraTox-commercial-featureData.txt: feature annotation in TSV format</li> <li>2022-02-18-TeraTox-commercial-phenoData.txt: sample annotation in TSV format</li> <li>2021-06-10-gcGeneFactorAnno-withPositiveCoefs.tsv: gene membership of germ-layer factors, with germ-layer annotation and average expression in copies per million (cpm).</li> </ul> <p>Citation: Jaklin, Manuela, Jitao David Zhang, Nicole Schäfer, Nicole Clemann, Paul Barrow, Erich Küng, Lisa Sach-Peltason, Claudia McGinnis, Marcel Leist, and Stefan Kustermann. “Optimization of the TeraTox Assay for Preclinical Teratogenicity Assessment.” <em>Toxicological Sciences</em> 188, no. 1 (July 1, 2022): 17–33. <a href="https://doi.org/10.1093/toxsci/kfac046">https://doi.org/10.1093/toxsci/kfac046</a>.</p>
Statistical analysis and dataset for: A high-throughput and sensitive method for food preference assays in walking insects
<p>Linked to the journal article published in bioRxiv (https://doi.org/10.1101/2024.04.10.588882).</p> <p><em><strong>Abstract</strong></em></p> <p>Insects pose significant challenges in both pest management and ecological conservation. Often, the most effective strategy is employing toxicant-laced baits, which must also be designed to specifically attract and be preferred by the targeted species for optimal species-specific effectiveness. However, traditional methods for measuring bait preference are either non-comparative, meaning that most animals only ever taste one bait, or suffer from methodological or conceptual limitations. Here we demonstrate the value of direct comparison food preference assays using the invasive and pest ant <em>Linepithema humile </em>as a model. We compare the food preference sensitivity of non-comparative (one visit to a food source) and sequential comparative (visiting one type of food then another) assays at detecting low levels of aversive quinine in sucrose solution. We then introduce and test a novel dual-choice feeder method for simultaneous comparative evaluation of bait preferences, testing its effectiveness in discerning between foods with varying quinine or sucrose levels. While the non-sequential assay could not detect aversion to 1.25mM quinine in 1M sucrose, the sequential comparative approach detected aversion to quinine levels as low as 0.94mM. The novel dual feeder method approach could detect aversion to quinine levels as low as 0.31mM, and also preference for 1M sucrose over 0.75M sucrose. The dual-feeder method, combines the sensitivity of comparative evaluation with high throughput, ease of use, and avoidance of interpretational issues. This innovative approach offers a promising tool for rapid and effective testing of bait solutions, contributing to the development of targeted control strategies. Moreover, the method can be easily modified for application to a wide range of walking insects, such as cockroaches, crickets, and beetles.</p>
3D and assay data published in "XRF and 3D modelling on a composite Etruscan helmet"
<p>The data presented here are published as part of the publication Emmitt, J.J., McAlister, A., Bawden, N., and J. Armstrong "XRF and 3D modelling on a composite Etruscan helmet" <em>Applied Sciences</em>. <em>11</em>(17): 8026. DOI: 10.3390/app11178026. The methodology for the creation of the photogrammetry model is presented Emmitt et al. (2021a), and further information about the methods used to collect the pXRF data can be found in Emmitt et al. (2021b). The interpolation analysis is done using PyVista by Sullivan and Kaszynski (2019)</p> <p>The model is are published as a .ply file, the assay data is in a csv file with the corresponding location on the model, and a Juypter notebook for running the analysis. The PyVista Python package will be required (Sullivan and Kaszynski 2019). Contained here are:</p> <ul> <li>Negau Helmet, Doug Gold Collection - 1x .ply</li> <li>Helmet assay points and data - 1x .csv</li> <li>Juypter Notebook - 1x .ipynb</li> </ul> <p>Data are published with permission of Museo Nazionale Etrusco di Villa Giulia e Villa Poniatowski di Roma (Director Valentino Nizzo).</p>
BIDS Data for "A Whole-Brain Map and Assay Parameter Analysis of Mouse VTA Dopaminergic Activation"
<p>Base data package for the “"A Whole-Brain Map and Assay Parameter Analysis of Mouse VTA Dopaminergic Activation” article, formatted corresponding to the Brain Imaging Data Structure.</p>
CEPHIA Evaluation Panel data for Maxim and Sedia Limiting Antigen Avidity assays
<p>CEPHIA Evaluation Panel dataset containing final ODn values for each assay. The first file contains results on all standard panel samples, and the second contains results on blinded control samples tested in replicate.</p>
Spectrophotometric Assay for the Detection of 2,5-Diformylfuran and Its Validation through Laccase-Mediated Oxidation of 5-Hydroxymethylfurfural
<p>Modern biocatalysis requires fast, sensitive, and efficient high-throughput screening methods to screen enzyme libraries in order to seek out novel biocatalysts or enhanced variants for the production of chemicals. For instance, the synthesis of bio-based furan compounds like 2,5-diformylfuran (DFF) from 5-hydroxymethylfurfural (HMF) via aerobic oxidation is a crucial process in industrial chemistry. Laccases, known for their mild operating conditions, independence from cofactors, and versatility with various substrates, thanks to the use of chemical mediators, are appealing candidates for catalyzing HMF oxidation. Herein, Schiff-based polymers based on the coupling of DFF and 1,4-phenylenediamine (PPD) have been used in the set-up of a novel colorimetric assay for detecting the presence of DFF in different reaction mixtures. This method may be employed for the fast screening of enzymes (Z' values ranging from 0.68 to 0.72). The sensitivity of the method has been proved, and detection (8.4 μM) and quantification (25.5 μM) limits have been calculated. Notably, the assay displayed selectivity for DFF and enabled the measurement of kinetics in DFF production from HMF using three distinct laccase–mediator systems.</p>
Exploring the Exclusive Isolation of Pseudomonas syringae in Peltigera Lichens via metabolite analysis and growth assays - Appendix
<p>Lichen samples from Iceland were collected from the genera Peltigera, Cladonia, and Stereocaulon in March 2023 at Heidmork forest, Oskjuhlid hill, and the shores of Ellidaa in Arbaejarstifla. All specimens underwent morphological analysis, and corresponding vouchers have been deposited at the Icelandic Institute of Natural History.</p>
Raw images from: Detecting life by behavior, the overlooked sensitivity of behavioral assays
<p>Raw images of the manuscript entitle: "Detecting life by behavior, the overlooked sensitivity of behavioral assays"</p> <p>Description: Using a magnetotactic bacterial species,<em> Magnetospirillum magneticum</em>, we conduct a lab sensitivity experiment comparing PCR with the hanging drop behavioral assay, using a dilution series.</p> <p>Data:</p> <p>1.-Gel image resulted from the <em>Magnetospirillum magneticum </em>PCR assays. </p> <p>2.-Microphotographs of <em>Magnetospirillum magneticum </em>obtained using the hanging drop technique and serial dilution. </p> <p>3.-Videos 1 to 4.Environmental samples were taken from Agmon Hula lake, (33° 10′ N 35° 60′ E). We used the HDT (see main MS) to morphologically identify magnetotactic bacterial species.</p>
Development of ferret immune repertoire reference resources and single-cell-based high- throughput profiling assays
<p>We performed long read transcriptome sequencing of ferret splenocyte and lymph node samples full-length, non-chimeric circular consensus sequencing (CCS) reads to obtain over 120,000 high-quality immunoglobin (Ig) and T cell receptor (TCR) transcripts.</p>
The importance of geometry in the corneal micropocket angiogenesis assay
<p>Dataset and software supporting the submitted and revised manuscript for the study: "The importance of geometry in the corneal angiogenesis micropocket assay." See the enclosed README and manuscript for further information.</p>
Data and R script for 'Evaluating the cyclic ratio schedule as an assay of feeding behaviour in the European starling (Sturnus vulgaris)'
<p>Data files and R script for Dunn et al. "Evaluating the cyclic ratio schedule as an assay of feeding behaviour in the European starling (<em>Sturnus vulgaris</em>)"</p> <p>Includes a single R script that produces all the analyses in the paper. The script makes use of three different .csv data files.</p>
Arena assay and gene expression of stingless bees
<p>The dataset includes behavioral data collected from arena experiments with workers of stingless bee species <em>Scaptotrigona postica</em>, <em>Frieseomelitta varia</em>, and <em>Melipona quadrifasciata</em>. Additionally, it contains gene expression data (CT values) for these species across different life stages and tissues.</p>
Literature Curated PPIs from "Accurate and Sensitive Interactome Profiling Using a Quantitative Protein-Fragment Complementation Assay"
<p>This dataset includes the literature curated protein-protein interactions supporting the manuscript titled 'Accurate and Sensitive Interactome Profiling Using a Quantitative Protein-Fragment Complementation Assay'.</p>
Raw NanoLuc and NanoBiT Data from "Accurate and Sensitive Interactome Profiling Using a Quantitative Protein-Fragment Complementation Assay"
<p>This dataset includes raw NanoLuc and NanoBiT data supporting the manuscript titled 'Accurate and Sensitive Interactome Profiling Using a Quantitative Protein-Fragment Complementation Assay'.</p>
Analyzed NanoBiT Data from "Accurate and Sensitive Interactome Profiling Using a Quantitative Protein-Fragment Complementation Assay"
<p>This dataset includes analyzed NanoBiT data supporting the manuscript titled 'Accurate and Sensitive Interactome Profiling Using a Quantitative Protein-Fragment Complementation Assay'.</p>
Comparison of conventional IgE assay and measurement of specific IgE to hemocyanin for the diagnosis of adult crab allergy (Running tile: Utility of crab extracts and hemocyanin in diagnosing crab allergy)
<p><span>Summary: </span></p> <p><span><span> </span>Specific IgE to hemocyanin was elevated in crab-allergic as compared to crab-tolerant patients.</span></p> <p><span><span> </span>The combination of specific IgE to hemocyanin and conventional IgE assays improved specificity.</span></p>
Comparison of conventional IgE assay and measurement of specific IgE to hemocyanin for the diagnosis of adult crab allergy (Running tile: Utility of crab extracts and hemocyanin in diagnosing crab allergy)
<p>Summary:</p> <p> Specific IgE to hemocyanin was elevated in crab-allergic as compared to crab-tolerant patients.</p> <p> The combination of specific IgE to hemocyanin and conventional IgE assays improved specificity.</p>
Dataset related to article "Molecular Studies and ex vivo Complement assay on Endothelium Highlight the Genetic Complexity of Atypical Hemolytic Uremic Syndrome: The Case of a Pedigree With a Null CD46 Variant".
<p><em>The files contain raw data related to the article "Molecular Studies and ex vivo Complement assay on Endothelium Highlight the Genetic Complexity of Atypical Hemolytic Uremic Syndrome: The Case of a Pedigree With a Null CD46 Variant", available from <a href="https://www.frontiersin.org/articles/10.3389/fmed.2020.579418/full">https://www.frontiersin.org/articles/10.3389/fmed.2020.579418/ful</a>l.</em></p> <p>File <strong>"Genetic and clinical data"</strong>:</p> <ul> <li>In the sheet "485 aHUS patients" are reported data obtained from the screening of 485 unrelated patients with aHUS including rare variants (RVs) in complement disease-associated genes (<em>CFH, CD46, CFI, C3, CFB </em>and <em>THBD</em>), the presence of <em>CFH-CFHR</em> genomic rearrangements and/or anti-FH antibodies.</li> <li>In the sheet "Pedigrees with c.286+2T>G" are listed all pedigrees carrying the c.286+2T>G variant, the diseases status of all subjects and the age of disease onset of patients. In bold are indicated pedigrees (n=7) used to study the penetrance of aHUS in c.286+2T>G carriers.</li> <li>In the sheet "Haplotypes" are reported genotypes used to evaluate the association between the presence of <em>CFH-H3</em> and <em>CD46<sub>GGAAC</sub></em> risk haplotypes and aHUS. Results of this analysis are reported in Table 3 of the published paper.</li> <li>In the sheet "Raw data Fig.2" are reported data of "platelet count" and "serum creatinine" of the proband used to elaborate Figure 2.</li> </ul> <p>In the file <strong>"C3 and C5b-9 deposition"</strong> is reported the quantification of serum-induced C3 and C5b-9 deposition on human microvascular endothelial cell line (HMEC-1). The fluorescent staining was evaluated with Image J and expressed as pixel<sup>2 </sup>per field analyzed. The fields with the lowest and highest values were excluded from calculation. These values were used to elaborate data included in Table 2 and in Figure 5.</p> <p>In the file <strong>"CD46 protein expression"</strong> are reported data of CD46 expression on peripheral blood mononuclear cells (PBMCs) isolated from the proband, his relatives and healthy volunteers. Data of specific expression of CD46 (evaluated for SCR1 or for SCR4 as reported in the materials and methods section) are indicated as median fluorescence intensity (MFI) percentage compared with the control.</p> <p>In the ppt file <strong>"cDNA amplification and sequencing results"</strong> is reported:</p> <ul> <li>the agarose gel image of the amplified cDNA from the control (ctr), the proband (IV-8) and his healthy father (III-7).</li> <li>Electropherograms obtained from the cDNA sequencing of the control (ctr), the proband (IV-8) and his healthy father (III-7).</li> </ul> <p>Additional data will be made available by the authors, without undue reservation, to any qualified researcher. </p>
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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.