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6,423 results for “BIOMARKER”
Mode characterization and sensitivity evaluation of an ultra-high-frequency surface acoustic wave (UHF-SAW) resonator biosensor: application to the glial-fibrillary-acidic-protein (GFAP) biomarker detection
<p>Biosensors detect specific bio-analytes by generating a measurable signal from the interaction between the sensing element and the target molecule. Surface acoustic wave (SAW) biosensors offer unique advantages due to their high sensitivity, real-time response capability, and label-free detection. The typical SAW modes are the Rayleigh mode and the shear-horizontal mode. Both present pros and cons for biosensing applications and generally need different substrates and device geometries to be efficiently generated. This study investigates and characterizes ultra-high-frequency (UHF-) SAW resonator biosensors. It reveals the simultaneous presence of the two typical SAW modes, clearly separated in frequency, called slow and fast. The two modes are studied by numerical simulations and biosensing experiments with the glial-fibrillary-acidic-protein (GFAP) biomarker. The slow mode is generally more sensitive to changes in surface properties, such as temperature and mass changes, by a factor of about 1.4 with respect to the fast mode.</p>
Dataset related to article "MiR-146a in ALS: Contribution to Early Peripheral Nerve Degeneration and Relevance as Disease Biomarker"
<p>Raw data supporting results of the study mentioned at title</p>
Code. Midlife proteome-wide analysis identifies plasma biomarkers for 25-year dementia risk linked to diverse pathophysiology
<p>The code used for the analyses for the paper entitled "Midlife proteome-wide analysis identifies plasma biomarkers for 25-year dementia risk linked to diverse pathophysiology". </p>
Immunoassay and proteomics dataset: Identification and validation of urine CXCL-9 as a biomarker for diagnosis of acute interstitial nephritis
<p>Background: Acute tubulointerstitial nephritis (AIN) is one of the few causes of acute kidney injury with diagnosis-specific treatment options. However, due to the need to obtain a kidney biopsy for histological confirmation, AIN diagnosis can be delayed, missed, or incorrectly assumed. Here we identify and validate urine CXCL-9, an interferon-γ-induced chemokine involved in lymphocyte chemotaxis, as a diagnostic biomarker for AIN.</p> <p>Methods: In a prospectively-enrolled cohort with pathologist-adjudicated histological diagnoses (<em>discovery cohort</em>), we tested the association of 180 immune proteins measured by an aptamer-based assay with AIN and validated the top protein, CXCL-9, using sandwich immunoassay. We externally validated these findings in 2 cohorts with biopsy-confirmed diagnoses (<em>validation cohorts</em>) and examined mRNA expression differences in kidney tissue from patients with AIN and controls.</p> <p>Results: In aptamer-based assay, urine CXCL-9 was 7.6-fold higher in AIN than controls (<em>P</em>=1.23·10<sup>-5</sup>). Urine CXCL-9 measured by sandwich immunoassay was associated with AIN in the discovery cohort (n=204; 15% AIN) independently of currently available clinical tests for AIN (adjusted odds ratio for highest vs lowest quartile: 6.0; 95% CI: 1.8-20). Similar findings were noted in external validation cohorts, where CXCL-9 had an AUC of 0.94 (0.86-1.00) for AIN diagnosis. <em>CXCL9</em> mRNA expression was 3.9-fold higher in kidney tissue from patients with AIN (n=19) as compared with controls (n=52; P=5.8·10<sup>-6</sup>).</p> <p>Conclusion: We identified CXCL-9 as a biomarker for AIN diagnosis using aptamer-based urine proteomics, confirmed this association using sandwich immunoassays in discovery and validation cohorts, and observed higher expression of this protein in kidney biopsies with AIN. </p>
BLM overexpression as a predictive biomarker for CHK1 inhibitor response in PARP inhibitor–resistant BRCA-mutant ovarian cancer
<p>PARP inhibitors (PARPis) have changed the treatment paradigm in BRCA-mutant high-grade serous ovarian carcinoma (HGSC). However, most patients eventually develop resistance to PARPis, highlighting an unmet need for novel therapeutic strategies. Using high-throughput drug screens, we identified ATR/CHK1 pathway inhibitors as cytotoxic, and further validated monotherapy activity of the CHK1 inhibitor (CHK1i), prexasertib, in PARPi-resistant BRCA-mutant HGSC cells and animal models. As a proof-of-concept trial, we conducted a phase II study of prexasertib in BRCA-mutant HGSC patients. The treatment was well-tolerated but yielded an objective response rate of 6% (1/17; 1 PR) in patients with prior PARPi treatment. Exploratory biomarker analyses revealed that replication stress and fork stabilization were associated with clinical benefit to CHK1i. In particular, overexpression of BLM, and CCNE1 overexpression or copy number gain/amplification were seen in patients deriving durable benefit from CHK1i. Our findings suggest replication fork–related biomarkers should be further evaluated for CHK1i sensitivity in HGSC.</p>
Saliva and plasma metabolome analysis in mares during anestrus, estrus cycle and early gestation for the identification of salivary biomarkers of reproductive stages.
<p>1H-NMR spectra of saliva and blood samples collected at seven physiological stages from six pony mares:</p> <ul> <li>in seasonal anestrus,</li> <li>in the follicular phase 3 days, 2 days and 1 day before ovulation, and the day when ovulation was detected,</li> <li>in the luteal phase 6 days after ovulation,</li> <li>in gestation 18 days after ovulation and artificial insemination.</li> </ul> <p> </p> <p>The 42 saliva samples were prepared for <sup>1</sup>H-NMR by precipitation of proteins using methanol. Briefly, 200 µL of saliva was mixed with 400 µL of cold methanol and vortexed. The mixtures were cooled at -20°C for 20 min before centrifugation at 15,000 × g for 15 min at 4°C. The supernatants were recovered and transferred to glass tubes for further evaporation of the solvent. For the 42 plasma samples, a modified Folch’s method (200 µL of plasma, 300 µL of cold methanol and 500 µL of cold chloroform) was preferred to extract metabolites and eliminate proteins and lipids from the plasmas in order to avoid the overlapping of the metabolites of interest with broad lipid and protein signals. The samples were vortexed during 1 min. The polar fractions, containing the metabolites, were separated after centrifugation at 15,000 × g for 15 min at 4°C and 300 µL of the samples were collected in glass tubes. The solvent of saliva supernatants and plasma polar fractions were evaporated in a SpeedVac (Thermo Fisher Scientific, Illkirch-Graffenstaden, France) for 2 h at 35°C followed by another 2 h at room temperature before storage at -20°C until analysis. Five quality control samples for the saliva and plasma experiments were prepared by pooling a fraction of each samples (either saliva or plasma) and were further processed with all the other samples.</p> <p>Before <sup>1</sup>H-NMR analyses, the dried residues were recovered in 210 μL phosphate buffer (pH 7.4, 200 mM) prepared in D<sub>2</sub>O supplemented with 152 µM (final concentration) of 3-trimethylsilylpropionic acid (TSP) as internal reference and transferred to 3 mm NMR tubes.</p> <p><sup>1</sup>H-NMR spectra of the saliva and plasma samples were acquired at 298K on an AVANCE III HD 600 MHz system (Bruker Biospin, Karlsruhe, Germany) equipped with a Bruker 5 mm TCI CryoProbe with Z-gradient. <sup>1</sup>H-NMR spectra were recorded with the «noesypr1d» pulse sequence with a relaxation delay of 20 s, on a sweep width of 12 ppm, 64 k data points, an acquisition time of 4.56 s, with 64 transients, and 8 dummy scans. Sample shimming was performed automatically on the D<sub>2</sub>O signal.</p>
Data for: Lipid biomarkers recording marine microbial community structure changes through the Frasnian‐Famennian mass extinction event
<p>This dataset contains data for a research article published on Geobiology. The article is entitled " <span class="Dummy">Lipid biomarkers recording marine microbial community structure changes through the </span><span class="fc">Frasnian‐Famennian</span><span class="Dummy"> mass extinction event</span>". <span class="Dummy"><span class="Dummy">This study aims to reconstruct changes in the marine microbial community structure through the Late Devonian Frasnian‐Famennian (F‐F) transition. We performed a multiproxy investigation on a drill core of the Upper Devonian New Albany Shale from the Illinois Basin (western Kentucky, USA). </span><span class="Dummy">Detailed information regarding the data collection, analysis, and interpretation can be found in the </span></span><span class="Dummy"><span class="Dummy">following paper:<br></span></span></p> <p class="MsoNormal">Chen J., Hogancamp<sup> </sup>N., Lu<sup> </sup>M., Ikejiri T., Malina N., Ojeda<sup> </sup>A., Sun Y., Lu Y. 2023. Lipid Biomarkers Recording Marine Microbial Community Structure Changes Through the Frasnian‐Famennian Mass Extinction Event. Geobiology <a href="https://doi.org/10.1111/gbi.12568"><span>https://doi.org/10.1111/gbi.12568</span></a></p>
Dataset on biomarkers for the project "Intermittent hypoxia differentially affects metabolic and oxidative stress responses in two species of cyprinid fish"
<p>The file contains the data for the tissue-level biomarkers evaluating the impact of short-term hypoxia on oxidative stress and metabolic parameters in silver carp <em>Hypophthalmichthys molitrix </em>and gibel carp <em>Carassius gibelio.</em></p>
Association Between Change in The Peripheral Biomarkers of Inflammation, Astrocyte Activation, and Neuroprotection at One Week of Critical Illness and Hospital Mortality in Patients with Delirium: A Prospective Cohort Study
<p>Dataset for the following publication: Association Between Change in The Peripheral Biomarkers of Inflammation, Astrocyte Activation, and Neuroprotection at One Week of Critical Illness and Hospital Mortality in Patients with Delirium: A Prospective Cohort Study</p>
PDB File and MD Simulation results for "The atypical sphingolipid SPB 18:1(14Z);O2 is a biomarker for DEGS1 related hypomyelinating leukodystrophy"
<p>Supplementary structural file for article: "The atypical sphingolipid SPB 18:1(14Z);O2 is a biomarker for DEGS1 related hypomyelinating leukodystrophy":</p> <p>-Predicted Structure of DEGS1 docked to C16 Ceramide in PDB format</p> <p>- 2.5 µsec Molecular Dynamics Simulation of this DEGS1-Ceramide complex embedded in a DPPC membrane and surrounded by TIP3 water and 150 mM NaCl as mp4 (movies) or as original trajectory. In the version with the smaller file size solvent molecules and the membrane are invisible for clarity. </p> <p>Software/Webservices used for generation: AlphaFold, PPM3 web server, CHARM-GUI PDB Manipulator, Maestro/Glide/Ligprep/Desmond (Schrödinger Inc.).</p> <p>Version 1 contained videos in mpeg format that caused error with some players. In Version 2 videos are converted to mp4. </p>
Quantification of multiple environmental controls on lipid biomarkers in common marine diatoms and dinoflagellates
<p>In the monocultures of two algal species, i.e., <em>Phaeodactylum tricornutum</em> (Bacillariophyceae; strain MACC/B254) and <em>Prorocentrum minimum</em> (Dinophyceae; strain HYESL63), we investigated responses of lipid biomarkers (sterols and fatty acids (FAs)) to different temperatures (12, 18 and 24℃), nitrogen and phosphorus concentrations and their molar ratios (N:P ratios) of 10:1, 24:1 and 63:1.</p> <p>Algal cells were counted daily with an improved Neubauer hemacytometer (Glaswarenfabrik Karl Hecht GmbH) under a microscope (Olympus CX41). To analyze particulate organic carbon (POC), sterols and FAs, algal cells at steady-state conditions were harvested on pre-combusted GF/F filters (Whatman) after filtering 15-30 mL of cultures depending on cell density in the culture flask and the parameters to be determined. Samples were kept at − 80℃ after filtration.</p> <p>POC was determined by an elemental analyzer (Thermo Flash 2000) (Sharp 1974, https://doi.org/10.4319/lo.1974.19.6.0984). Sterols and FAs were analyzed according to the methods in Eglinton et al. (1996 https://doi.org/10.1021/ac9508513), Galy et al. (2011, https://doi.org/10.1016/j.epsl.2011.02.003) and Zhao et al. (2006, https://doi.org/10.1016/j.orggeochem.2005.08.022). The trimethylsilyl ether derivatives of sterols and fatty acid methyl esters (FAMEs) were analyzed in a gas chromatograph (Agilent Technologies 8890A) equipped with a flame ionization detector, and a HP-1 column (50 m, 0.32 mm i.d., 0.17 μm film; Agilent J&W) and a SP-2560 column (100 m, 0.25 mm i.d., 0.20 μm film; Supelco) for sterol and FAME analysis, respectively.</p> <p>The identification of sterols was performed by gas chromatography-mass spectrometry (GC-MS) analysis at 70 eV using an Agilent 7890B GC (HP-5MS column; 30 m, 0.25 mm i.d., 0.25 μm film; Agilent J&W) connected to an Agilent MSD 5977B mass selective detector (ion source temperature 230℃). Sterols were identified be comparison of the mass spectra of their trimethylsilyl ether derivatives to those of published GC-MS values (Lisboa et al. 1982, https://doi.org/10.1016/0305-0491(82)90281-4; Taipale et al. 2016, https://doi.org/10.3389/fpls.2016.00212), based on the molecular ion and prominent ions. The following sterols were identified: brassicasterol/epi-brassicasterol,and dinosterol. FAs were identified with reference to the standard Supelco 37 component FAME mixture. C-normalized (on a per POC basis; μg mg C-1) and per-cell (pg cell-1) contents of sterols and FAs were presented, and FA proportions (% of total fatty acids (TFAs)) were also reported in the dataset.</p>
Original dataset of the study entitled Molecular biomarkers of zebrafish exposed to trabectedin
<p><strong>Original data set_Spreadsheet ZFL cells - enzymes activity</strong></p> <p>Activity of the acetylcholinesterase, Glutathione-<em>S</em>-transferase, Catalase, Glutathione reductase, and Lactate dehydrogenase in zebrafish embryos measured by spectrophotometry.</p> <p><strong>Original data set_Spreadsheet </strong><strong>ZF larvae - enzymes activity</strong></p> <p>Activity of the acetylcholinesterase, Glutathione-<em>S</em>-transferase, Catalase, Glutathione reductase, and Lactate dehydrogenase in zebrafish liver (ZFL) cells measured by spectrophotometry.</p> <p><strong>Original data set_Spreadsheet ZF larvae - genotoxicity</strong></p> <p>DNA in tail percentage in zebrafish embryos measured by comet assay.</p> <p><strong>Original data set_Spreadsheet </strong><strong>ZFL cells - Cell cycle</strong></p> <p>Number of cells en each cell cycle phase measured by flow cytometry.</p> <p><strong>Original data set_Spreadsheet </strong><strong>ZFL cells - qPCR</strong></p> <p>Expression of genes associated to cell proliferation and survival in ZFL cells.</p>
Novel Biomarkers of Thrombotic Risk
ClinicalTrials.gov study NCT02505217. IPD Sharing: Not stated. Countries: 1. Publications: 3.
The Effect of RNS60 on ALS Biomarkers
ClinicalTrials.gov study NCT03456882. IPD Sharing: NO. Countries: 2. Publications: 1.
PH 1 Biomarker Study of Nivolumab and Ipilimumab and Nivolumab in Combination With Ipilimumab in Advanced Melanoma
ClinicalTrials.gov study NCT01621490. IPD Sharing: Not stated. Countries: 3. Publications: 3.
Motivational Negative Symptoms in Schizophrenia: Intervention and Biomarkers
ClinicalTrials.gov study NCT02386605. IPD Sharing: NO. Countries: 1. Publications: 1.
Biomarkers in Repetitive Transcranial Magnetic Stimulation (rTMS) for Adolescent Depression
ClinicalTrials.gov study NCT03363919. IPD Sharing: NO. Countries: 1. Publications: 9.
Chronic Obstructive Pulmonary Disease (COPD) Biomarker Identification Study
ClinicalTrials.gov study NCT01780298. IPD Sharing: YES. Countries: 1. Publications: 4.
Bridging Pediatric and Adult Biomarkers in Graft-Versus-Host Disease
ClinicalTrials.gov study NCT02194439. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Serum Biomarkers to Predict Response to Angiotensin II in Septic Shock
ClinicalTrials.gov study NCT05824767. IPD Sharing: NO. Countries: 1. Publications: 17.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.