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6,423 results for “BIOMARKER”
Biomarkers in Metastatic Castration-Resistant Prostate Cancer for efficiency of Immune Checkpoint Inhibitors
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Figure 5 in Identification of early biomarkers in proteomic profiles of the phaeophyteSaccharina japonicaproximal to and beneath the front of bryozoan colonies
Figure 5: A close-up view of two-dimensional gels showing the proteins (arrows) that were down-regulated by bryozoan colonization. (A) Distal healthy Saccharina japonica tissue. (B) S. japonica thallus tissue proximal to the bryozoan colony. (C) S. japonica tissue at the bryozoan colony front.
Figure 4 in Identification of early biomarkers in proteomic profiles of the phaeophyteSaccharina japonicaproximal to and beneath the front of bryozoan colonies
Figure 4: A close-up view of two-dimensional gels showing the proteins (arrows) that were up-regulated by bryozoan colonization. (A) Distal healthy Saccharina japonica tissue. (B) S. japonica thallus tissue proximal to the bryozoan colony. (C) S. japonica tissue at the bryozoan colony front.
Figure 3 in Identification of early biomarkers in proteomic profiles of the phaeophyteSaccharina japonicaproximal to and beneath the front of bryozoan colonies
Figure 3: A close-up view of two-dimensional gels showing the proteins (arrows) up-regulated mostly in the thallus tissue proximal to the bryozoan colony and at the colony front, but present at only very low levels in distal healthy tissues. (A) Distal healthy Saccharina japonica tissue. (B) S. japonica thallus tissue proximal to the bryozoan colony. (C) S. japonica tissue at the bryozoan colony front.
Figure 1 in Identification of early biomarkers in proteomic profiles of the phaeophyteSaccharina japonicaproximal to and beneath the front of bryozoan colonies
Figure 1: The Saccharina japonica thallus sections defined as colony-front and thallus tissue proximal to Membranipora membranacea colonies. Colony-front tissues were collected from the narrow zone under the newly formed front of the colony after removing the bryozoans. Thallus tissue proximal to the bryozoan colony was obtained from the 1-cm zone outside the boundary of the colony.
Figure 2 in Identification of early biomarkers in proteomic profiles of the phaeophyteSaccharina japonicaproximal to and beneath the front of bryozoan colonies
Figure 2: Two-dimensional gel electrophoresis profiles of the late-harvested Saccharina japonica. (A) Distal healthy S. japonica tissue. (B) S. japonica thallus tissue proximal to the bryozoan colony. (C) S. japonica tissue at the bryozoan colony front. The separated proteins were visualized by silver staining. Numbers attached to the arrows refer to the spot number listed in Tables 1 and 2.
Systematic analysis identifies CDKN2A as a prognostic biomarker for hepatocellular carcinoma
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Vitellogenins level as a biomarker of the honey bee colony seasonal dynamics
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Endogenous biomarkers reveal diet partitioning among three sympatric species of swallows
<p>Since the early 1990s, aerial insectivorous birds have shown serious population declines in North America, but it is not clear if factors common to all species within this guild account for these declines. Among sympatric swallows, population trends differ, and this may be due to differences in ecology operating throughout the annual cycle. Although these species all feed on aerial insects, prey taxa can differ tremendously in their "aeroecology" and use by swallows. We examined the potential for dietary differences among three species of swallows, Barn Swallow (Hirundo rustica), Cliff Swallow (Petrochelidon pyrrhonota), and Tree Swallow (Tachycineta bicolor), breeding sympatrically in southern Ontario, Canada. Potential interspecific differences in nestling diet were examined using two endogenous biomarkers, DNA barcoding of nestling feces and stable isotope analysis (δ 2H, δ 13C, δ 15N) of nestling feathers. We found evidence for differences in dietary sources of provisioned young where Barn Swallows provisioned more terrestrial-based prey, Cliff Swallows provisioned an intermediate diet, and Tree Swallows the most aquatic-emergent insect diet. We suggest this information may help to identify potential factors contributing to differential declines of aerial insectivores operating on the breeding grounds, including diet quality.</p>
Coral physiology datasets (health/condition, biomarkers, IBR) under combined ocean warming and predation
<p>These datasets were obtained following an experiment testing the combined effects of gradual warming scenarios and predation wounds in coral condition (paleness, bleaching and mortality), cellular stress responses (heat shock protein Hsp70, total ubiquitin Ub, and total antioxidant capacity TAC) and physiological state (integrated biomarker response index, IBR) of seven Scleractinian coral species (<em>Acropora tenuis, Echinopora lamellosa, Montipora capricornis B - </em>brown and G - green<em> </em>morphotypes<em>, Galaxea fascicularis, Psammocora contigua </em>and<em> Turbinaria reniformis</em>) after being exposed for 60 days.</p>
Supplemental material: Astrocyte biomarkers in Alzheimer's disease: a systematic review and meta-analysis
<p><span><span><span><span><span><span><span><span><span><span><span><b>Objective:</b> To perform a systematic review and meta-analysis to determine whether fluid and imaging astrocyte biomarkers are altered in Alzheimer's disease (AD).</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Methods:</b> PubMed and Web of Science databases were searched for articles reporting fluid or imaging astrocyte biomarkers in AD. Pooled effect sizes were determined with mean differences (SMD) using the Hedge's G method with random-effects to determine biomarker performance. Adapted questions from QUADAS-2 were applied for quality assessment. A protocol for this study has been previously registered in PROSPERO (registration number: CRD42020192304).</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Results:</b> The initial search identified 1,425 articles. After exclusion criteria were applied, 33 articles (a total of 3,204 individuals) measuring levels of GFAP, S100B, YKL-40 and AQP4 in the blood and cerebrospinal fluid (CSF), as well as MAO-B, indexed by positron emission tomography <sup>11</sup>C-deuterium-L-deprenyl ([<sup>11</sup>C]-DED), were included. GFAP (SMD = 0.94; 95% CI = 0.71-1.18) and YKL-40 (SMD = 0.76; CI 95% = 0.63-0.89) levels in the CSF, S100B levels in the blood (SMD = 2.91; CI 95% = 1.01-4.8) were found significantly increased in AD patients. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Conclusions:</b> Despite significant progress, applications of astrocyte biomarkers in AD remain in their early days. The meta-analysis demonstrated that astrocyte biomarkers are consistently altered in AD and supports further investigation for their inclusion in the AD clinical research framework for observational and interventional studies.</span></span></span></span></span></span></span></span></span></span></span></p>
Urine uromodulin as a biomarker of kidney tubulointerstitial fibrosis
Background and objectives <p> </p> <p class="MsoNormal">Uromodulin, produced exclusively in the kidney's thick ascending limb, is a biomarker of kidney tubular health. However, the relationship between urine uromodulin and histological changes in kidney tubulointerstitium has not been characterized. In this study, we test the association of urine uromodulin with kidney histological findings in humans and mice. </p> Design, setting, participants, and measurements <p> </p> <p class="MsoNormal">We investigated the independent association of urine uromodulin measured at the time of kidney biopsy with histological features in 364 participants at two academic medical centers from 2015-2018 using multivariable linear regression models. This relationship was further examined by comparison of uromodulin staining in murine models of kidney fibrosis and repair. </p> <p> </p> Results <p> </p> <p class="MsoNormal">We found urine uromodulin to be correlated with serum creatinine (rho = -0.43, P<0.001), bicarbonate (0.20, P<0.001) and hemoglobin (0.11, P=0.03) at the time of biopsy, but not with urine albumin (-0.07, P=0.34). Multivariable models controlling for pre-biopsy glomerular filtration rate, serum creatinine at biopsy, and urine albumin showed higher uromodulin to be associated with lower severity of interstitial fibrosis/tubular atrophy (IF/TA) and glomerulosclerosis [IF/TA -3.5 (-5.7, -1.2)% and glomerulosclerosis -3.3 (-5.9, -0.6)% per 2-fold difference in uromodulin]. However, when both IF/TA and glomerulosclerosis were included in multivariable analysis, only IF/TA was independently associated with uromodulin [IF/TA -2.5 (-4.6, -0.4)% and glomerulosclerosis -0.9 (-3.4, 1.5)% per 2-fold difference in uromodulin]. In mouse kidneys, uromodulin staining was found to be lower in the fibrotic model than in normal or repaired models. </p> Conclusions <p><span>Higher urine uromodulin is independently associated with lower tubulointerstitial fibrosis in both human kidney biopsies and a mouse model of fibrosis. </span></p>
Identification of biomarkers for the earlier detection of lung cancer: a systematic review and meta-analysis
<p>All data analysed during this study are included in this excel sheet showing the steps in this systematic literature review process.</p>
Learning about Learning: Mining Human Brain Sub-Network Biomarkers from fMRI Data
<p>These are coherence matrices originally described in: Dynamic reconfiguration of human brain networks during learning. Bassett DS, Wymbs NF, Porter MA, Mucha PJ, Carlson JM, Grafton ST. Proc Natl Acad Sci U S A. 2011 May 3;108(18):7641-6. doi:10.1073/pnas.1018985108. Epub 2011 Apr 18. Later the matrices were also studied in Cohesive network reconfiguration accompanies extended training. Telesford QK, Ashourvan A, Wymbs NF, Grafton ST, Vettel JM, BassettDS. Hum Brain Mapp. 2017 Sep;38(9):4744-4759. doi: 10.1002/hbm.23699. Epub 2017 Jun 24.</p>
Multi-omics data for ischemic stroke etiology biomarker discovery
<p>Multi-omics data for ischemic stroke etiology biomarker discovery</p>
Data from: Pilot study demonstrating potential association between breast cancer image-based risk phenotypes and genomic biomarkers.
<p>Genotype data from</p> <p>Li H, Giger ML, Sun C, Ponsukcharoen U, Huo D, Lan L, Olopade OI, Jamieson AR, Brown JB, Di Rienzo A. (2014) Pilot study demonstrating potential association between breast cancer image-based risk phenotypes and genomic biomarkers. Med Phys. 41(3)</p>
Excess 210Pb, 137C, total organic carbon content, HBI biomarkers (IPSO25, HBI III) and biogenic silica of marine deposits from sediment core 2018_R2_2F from Sheldon Cove, Antarctic Peninsula
<p><strong>Description</strong>: Sediment core 2018_R2_2F was collected from Sheldon Cove, Antarctic Peninsula (67.55°S 68.27°W) from a water depth of 177 m, in December 2018 as part of expedition JR18003 by the British Antarctic Survey aboard RV James Clark Ross (Sands et al. 2019). Total core length was 25 cm. The dataset presented here consists of: gamma spectrometry measurements of excess 210Pb (calculated as a difference between the total 210Pb and the average of 214Pb and 214Bi) and 137Cs; total organic carbon (TOC) content; biogenic silica (BSi) content; and HBI biomarker (IPSO25, HBI III) concentrations. The excess 210Pb and 137Cs were measured at the Institute of Geology at Adam Mickiewicz University in Poznań, Poland, using a gamma detector Canberra BE3830, cooled with cryostat Cryo-Pulse®5 plus. The detector is placed in 10 cm thick lead shield walls and is equipped with a remote detector chamber option (RDC-6 inches) for low energy background reduction. The detector was commercially characterized by ISOCS (In-Situ Object Calibration Software) and LabSOCS (Laboratory Sourceless Object Calibration Software). Efficiencies for measured geometries were determined using LabSOCS code applying all corrections for sample geometry, matrix, and container type, and were verified with IAEA standards measurements. The results (spectra) were analyzed in Canberra GENIE-2000 v. 3.3 gamma spectrometry software and are presented with 2-sigma uncertainty ranges (Szczuciński, submitted). TOC concentrations (given in %) were measured at the Faculty of Earth Sciences, University of Silesia, Poland, using an Eltra CS-500 IRanalyzer with a Total Inorganic Carbon module according to the procedure described in Racka et al. (2010). TOC was calculated as the difference between TC (total carbon) and TIC (total inorganic carbon). Each TOC sample was analysed in duplicate. Analytical precision and accuracy were better than ±2% for TC and ±3% for TIC. HBI biomarker preparation and analysis followed slightly modified (Pieńkowski et al. 2021) standard protocols (Belt 2012). HBI concentrations are given per weight of sediment (ng/g sed), and organic carbon content (μg/g OC) (Belt et al. 2012). Biogenic (opaline) silica (BSi) analysis on dried, homogenised samples followed Heiri et al. (2001) and Bechtel et al. (2007). Each BSi and TOC sample was analysed in duplicate; values are given in %. BSi and TOC standard deviation calculations are based on data from the replication.</p> <p><strong>References</strong> <br><br>* Bechtel, A., Woszczyk, M., Reischenbacher, D., Sachsenhoffer, R., Gratzer, R., Püttmann, W. Spychalski, W., 2007: Biomarkers and geochemical indicators of Holocene environmental changes in Lake Sarbsko (Poland). Org. Geoch. 38, 1112–1131. <br>* Belt, S.T., Brown, T.A., Navarro Rodriguez, A., Cabedo Sanz, P., Tonkin, A., Ingle, R. 2012. A reproducible method for the extraction, identification and quantification of the Arctic sea ice proxy IP25 from marine sediments. Anal. Methods 4, 705-713. <br>* Heiri, O., Lotter, A. F., Lemcke, G., 2001. Loss on ignition as a method for estimating organic and carbonate content in sediments: reproducibility and comparability of results. J. Paleolimnol. 25, 101-110. <br>* Pieńkowski, A.J., Husum, K., Belt, S.T., Ninnemann, U., Köseoğlu, D., Divine, D.V., Smik, L., Knies, J., Hogan, K., Noormets, R. 2021. Seasonal sea ice persisted through the Holocene Thermal Maximum at 80°N. Commun. Earth Environ. 2, 124. <br>* Racka, M., Marynowski, L., Filipiak, P., Sobstel, M., Pisarzowska, A., Bond, D.P.G., 2010: Anoxic Annulata events in the Late Famennian of the Holy Cross Mountains (Southern Poland): geochemical and palaeontological record. Palaeogeography, Palaeoclimatology, Palaeoecology 297(3-4), 549-575. <br>* Sands, C.J., Annett, A., Apeland, B., Barnes, D.K.A, Bascur, M., Bruning, P., Costa, M., Dadd, G., De Lecea, A., Ensor, N., Featherstone, A., Flint, G., Goodger, D., Guzzi, A., Howard, F., Hunter, D., Jenkins, S., Kender, S., Lincoln, B., Munoz-Ramirez C., Pienkowski, A., Retallick, K., Roman-Gonzalez, A., Scourse, J., Sheen, K., Whitaker, T., Williams, J., Zhao, L., Zwerschke, N., 2019: JR18003 Cruise Report. British Antarctic Survey, 132 pp. <br>* Szczuciński, W. (submitted): Applications of gamma-emitting isotopes (210Pb and 137Cs) for assessment of sedimentary processes – insights from studies of lake, deltaic and continental shelf deposits. <br><br><strong>Projects</strong> <br><br>* CHARME: CHanging AntaRctic Marine Environments, <strong>Web</strong>: <a title="Follow link" href="https://charme.amu.edu.pl/" target="_blank" rel="nofollow noopener">https://charme.amu.edu.pl/</a>, <strong>Award</strong>: Norwegian Financial Mechanism 2014-2021, UMO-2020/37/K/ST10/04127 <br><br><strong>File descriptions</strong>: Excel file with all data, as well as core details (coordinates and water depth).</p> <p><strong>Comment</strong>: This dataset is related to the following article which has been accepted for publication:</p> <p>Pieńkowski, Anna J.; Szczuciński, Witold; Breszka, Agnieszka; Chyleński, Maciej; Juras, Anna; Romel, Paulina; Rozwalak, Piotr; Trzebny, Artur; Dabert, Mirosława; Belt, Simon; Jagodziński, Robert; Smik, Lukas; Włodarski, Wojciech. Sedimentary ancient DNA and HBI biomarkers as sea-ice indicators: a complementary approach in Antarctic fjord environments. Limnology Oceanography Letters. doi: 10.1002/lol2.10395</p>
Identification of novel biomarkers related to pathogenesis and treatment of psoriasis
<p><span> Table S1.txt</span></p> <p><span>Differentially</span> <span>expressed genes</span><span> in the NL/LS cohort.</span></p> <p><span> </span><span> Table S2.txt</span></p> <p><span>Differentially</span> <span>expressed genes</span><span> in the pre/post treatment cohort.</span></p> <p><span> </span><span> Figure S1.pdf</span></p> <p><span>The heat map of differentially expressed genes.</span></p> <p><span>A: The heat map of the 50 most differentially expressed genes in NL/LS cohort.</span></p> <p><span>B: The heat map of the 50 most differentially expressed genes in pre/post treatment cohort.</span></p> <p><span> </span><span> </span><span>Figure S2.pdf</span></p> <p><span>Cluster outlier detection of NL/LS cohort.</span></p> <p><span>Figure S3.pdf</span></p> <p><span>Cluster outlier detection of pre/post treatment cohort.</span></p> <p><span> </span><span>Table S3.txt</span></p> <p><span>The results of GO enrichment analysis in </span><span>NL/LS cohort.</span></p> <p><span> </span><span>Figure S4</span><span>.pdf</span></p> <p><span>Chord diagram</span><span>: Go analysis of the key module in NL/LS cohort (Biological process).</span></p> <p><span> </span><span>Figure S5.pdf</span></p> <p><span>Chord diagram</span><span>: Go analysis of the key module in NL/LS cohort (Cellular component).</span></p> <p><span> </span><span>Figure S6.pdf</span></p> <p><span>Chord diagram</span><span>: Go analysis of the key module in NL/LS cohort (Molecular function).</span></p> <p><span> </span><span>Table S4.txt</span></p> <p><span>The results of KEGG enrichment analysis in </span><span>NL/LS cohort.</span></p> <p><span> </span><span>Table S5.txt</span></p> <p><span>The results of GO enrichment analysis in </span><span>pre/post treatment cohort.</span></p> <p><span> </span><span> Figure S7.pdf</span></p> <p><span>Chord diagram</span><span>: Go analysis of the key module in pre/post treatment cohort (Biological process).</span></p> <p><span> </span><span> Figure S8.pdf</span></p> <p><span>Chord diagram</span><span>: Go analysis of the key module in pre/post treatment cohort (Cellular component).</span></p> <p><span> </span><span> Figure S9.pdf</span></p> <p><span>Chord diagram</span><span>: Go analysis of the key module in pre/post treatment cohort (Molecular function).</span></p> <p><span> </span><span> Table S6.txt</span></p> <p><span>The results of KEGG enrichment analysis </span><span>in pre/post treatment cohort.</span></p> <p><span> Figure S10.pdf</span></p> <p><span>LASSO model</span></p> <p><span>A: </span><span>LASSO model of NL/LS cohort.</span></p> <p><span>B: LASSO model of </span><span>pre/post treatment cohort.</span></p>
Data for: High-throughput micro-CT analysis identifies sex-dependent biomarkers of erosive arthritis in TNF-Tg mice and differential response to anti-TNF therapy
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MRI Dataset: Diffusion MRI as a potential non-invasive biomarker of neuroinflammation following intracerebral haemorrhage
<p>Raw MRI dataset of T2 and NODDI scans.</p> <p>Subjects: Adult male Sprague-Dawley rats, aged 10-12 weeks, 300-450g. Subjected to intracerebral haemorrhage induction by intracranial injection of 0.2 Type VII collagenase, recovered for 7 days prior to these MRI scans being performed. Further methodological information available upon request.</p>
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.