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6,423 results for “BIOMARKER”
Figure 5 in Investigations of the nervous system biomarkers in the brain and muscle of freshwater fish (Oreochromis niloticus) following accumulation of nanoparticles in the tissues
Figure 5. TEM images of brain tissue sample of fish (O. niloticus) exposed to 1 (A and B), 5 (C and D), and 25 (E and F) mg/L of Al2 O 3 NPs for 14 days of uptake and 14 days of depuration periods, respectively.
Figure 9 in Investigations of the nervous system biomarkers in the brain and muscle of freshwater fish (Oreochromis niloticus) following accumulation of nanoparticles in the tissues
Figure 9. The mean Ca-ATPase activity and associated standard errors in the muscle of O. niloticus. See Figure 8 for details.
Figure 3 in Investigations of the nervous system biomarkers in the brain and muscle of freshwater fish (Oreochromis niloticus) following accumulation of nanoparticles in the tissues
Figure 3. TEM images of muscle tissue sample of fish (O. niloticus) exposed to 1 (A and B), 5 (C and D), and 25 (E and F) mg/L of CuO NPs for 14 days of uptake and 14 days of depuration periods, respectively.
Figure 1 in Amphibian and fish eye lens used as biomarker of remote and chronic environmental contamination
Figure 1.The main abnormities of the frog lens in the region of the posterior pole. а – back lens suture is normal; b - "starry sky" picture; c – lesion of the back lens suture.
Fig. 2 in Oxidative stress biomarkers in the African sharptooth catfish, Clarias gariepinus, associated with infections by adult digeneans and water quality
Fig. 2. Monthly variation of physico-chemical parameters during the fish collection period, October 2016–September 2017. A– pH; B– Electrical conductivity; C– Temperature; D– Dissolved oxygen; E– Salinity; F– Turbidity; G– Total dissolved solids.
Fig. 1 in Oxidative stress biomarkers in the African sharptooth catfish, Clarias gariepinus, associated with infections by adult digeneans and water quality
Fig. 1. Various maps of the Incomati River showing the position of the sampling site. A– Mozambique shaded on the African continent; B– shows position of Maputo Province in Mozambique; C– indicates the position of the Incomati River and the sampling site.
Fig. 5 in Oxidative stress biomarkers in the African sharptooth catfish, Clarias gariepinus, associated with infections by adult digeneans and water quality
Fig. 5. Principal Component Analysis (PCA) of physico-chemical variables, biomarkers and parasitism in Clarias gariepinus collected in the Incomati River in Mozambique. Two principal components (PC1 and PC2) explained 45.45% of the total variation between water variables, biomarkers and occurrence of parasites. The EC, TDS and salinity (SAL) are associated with Component 1 while LPX, CAT, SOD, turbidity (TB) and temperature (T) are negatively associated with these variables. CI = co-infection; IM = M. nkomatiensis intensity; IG = G. pedatum intensity, UN = uninfected.
PETM Biomarker data from the NE Peri-Tethys
<p>Biomarker data from three NE Peri-Tethys sites - Guru Fatima, Kheu River and Dzhengutay - spanning the Palaeocene-Eocene Thermal Maximum. Biomarker data include GDGT distributions (including TEX86-derived sea surface temperatures), anoxia indicators (isorenieratane concentrations and lycopane ratios), thermal maturity indicators (hopane indices), and phytane carbon isotopic compositions.</p>
Detection of sepsis biomarkers
<p>Comparison of the working principles, advantages, and disadvantages of different types of sepsis sensors. Summary of the state-of-the-art electrochemical sensors used for the detection of sepsis biomarkers; limit of detection. </p>
Dateset related to article "Cytokines as potential biomarkers of disease clinical course in muscular dystrophies "
<p>This database includes a comprehensive profile of circulating pro- and anti-inflammatory molecules (cytokines, chemokines and growth factors) obtained from a group of 53 patients with muscular laminopathy, 10 with non-muscular laminopathy, 22 with other muscular disorders and 35 healthy controls. Data obtained by Luminex multiple immune-assay identify TGF-b2, IL-17 and G-CSF as potential biomarkers in discriminating between muscle-related laminopathy and healthy subjects. The different expression of IL-1b, IL-4 and IL-8 among the different forms of laminopathy provides a new hint for the understanding of the pathogenic mechanisms underlying the diverse phenotypes caused by <em>LMNA</em> mutations.</p>
Fig. 1 in Oxidative stress biomarkers and aggressive behavior in fish exposed to aquatic cadmium contamination
Fig. 1. Effects of cadmium exposure on aggressiveness parameters of Nile tilapia. Values are means (± SD). * = Statistically different from control.
Biomarker Signatures of Quality for Engineering Nasal Chondrocyte-Derived Cartilage
<p>Data underlying the figures in the publication “Biomarker Signatures of Quality for Engineering Nasal Chondrocyte-Derived Cartilage”, published in <em>Front Bioeng Biotechnol., </em><strong>2020</strong>, 8: 283. (DOI: 10.3389/fbioe.2020.00283).</p> <p>Table of contents:</p> <p><strong>1. biochem_summary</strong>; Biochemistry data and MBS of pellets made from NC and PC mixtures in the titration experiment.</p> <p><strong>2. dirty-clean-biochem</strong>; Biochemistry data and MBS of pellets made from passage 2 cells from dirty/clean biopsies.</p> <p><strong>3. identity_all</strong>; All passage 1 and passage 2 cells of type pure NC and pure PC from the titration and dirty/clean datasets. All PCR data included.</p> <p><strong>4. identity_titration</strong>; Passage 1 and 2 and pellets made from pure NC and PC populations in the titration experiment. All PCR data included. Average (avg) refers to the average of the biologicsl replicates (which are already the average of the experimental replicates of Data 5).</p> <p><strong>5. identity_titration_avg</strong>; Passage 1 and 2 and pellets made from pure NC and PC populations in the titration experiment. All PCR data included. All experimental replicate information is included (which are the average of the technical replicates).</p> <p><strong>6. PCR_cells_summary</strong>; For the purity and potency assays, mixtures of increasing NC to PC cell ratios were created. The PCR data from those mixtures are here for passage 2 and for the pure populations as passage 1.</p> <p><strong>7. PCR_pellet_summary</strong>; For the purity and potency assays, mixtures of increasing NC to PC cell ratios were created. PCR data from engineered pellets are here included.</p> <p><strong>8. PCRdirty-clean</strong>; PCR data of cells obtained from dirty/clean biopsies at passage 0,1, and 2.</p> <p><strong>9. PCRsummary_all</strong>; Combined Data 5, 7, and 8.</p> <p><strong>10. Proliferation_TOT</strong>; Proliferation rates of cells from clean and dirty biopsies. </p>
Metastability as a neuromechanistic biomarker of schizophrenia pathology
<p>Matlab files for Human Connectome Project - Early Psychosis (HCPEP) and COBRE in AAL116 parcellation.</p> <p>HCPEP files contain data for 4 runs of resting-state fMRI for healthy controls and non-affective psychosis groups.</p> <p>COBRE files contain data for 1 run of resting-state fMRI for healthy controls and established schizophrenia groups.</p>
dataset related to article: " Cerebrospinal fluid neuropathological biomarkers in beta-propeller protein-associated neurodegeneration, with complicated parkinsonian phenotype"
<p>analysis sanger electropherograms in the patient's in .abi format and segregation in the family (mother; father and sister</p>
In vitro genotoxicity testing using γH2AX biomarker, Microscopy Dataset
<p>The Dataset was used and is supplementary to the paper "<em>In vitro genotoxicity testing using γH2AX biomarker, microscopy and automatic image analysis in ImageJ - a pilot study with valinomycin</em>". It contains both RAW single-channel images and numerical results obtained with BioImage Analysis and evaluation available through the GitHub repository: <a href="https://github.com/martinschatz-cz/genotoxicity-bia">https://github.com/martinschatz-cz/genotoxicity-bia</a>.</p> <p><strong>Naming Convention for images</strong><br> ChannelName_YYYYMMD_Well_PossitionInWell_AcqRun.tiff</p> <p><strong>Naming Convention for results</strong><br> Well_AllResults_YYYY-MM-DD_Results.csv</p> <p>The csv are ‘,’ separated, and automatically named by analysis script.</p> <p><br> </p> <p><strong>Folder Structure</strong></p> <ul> <li> <p>Images (1069 files, as Images.zip)</p> <ul> <li> <p>4H - all images for all wells</p> </li> <li> <p>24H - all images for all wells</p> </li> </ul> </li> <li> <p>Results (36 files)</p> <ul> <li> <p>Results_4H (as Results_4h.zip)</p> </li> <li> <p>Results_24H (as Results_24h.zip)</p> </li> </ul> </li> </ul> <p> </p> <p><strong>Measurement Settings</strong></p> <ul> <li> <p>Manufacturer and model of microscope: Olympus IX83 P2ZF</p> </li> <li> <p>Objective lens magnification, NA: 10x Olympus IX3 Nosepiece, LensNA=0.3</p> </li> <li> <p>Excitation filters (mounted in the light source)</p> <ul> <li> <p>Violet: 395/25nm LED module 1, DAPI</p> </li> <li> <p>Green: 555/28nm LED module 5, Cy3</p> </li> </ul> </li> <li> <p>Quad band filter set for DAPI/FITC/Cy3/Cy5</p> </li> <li> <p>Quad band polychroic mirror (mounted in the filter turret):</p> <ul> <li> <p>BP 411-454nm,</p> </li> <li> <p>BP 495-536nm,</p> </li> <li> <p>BP 577-617nm</p> </li> <li> <p>BP 655-810nm</p> </li> </ul> </li> <li> <p>Emission filters (mounted in the fast emission filter wheel, infront the camera):</p> <ul> <li> <p>DAPI: BP 421-445nm</p> </li> <li> <p>Cy3: BP 581-619nm</p> </li> </ul> </li> <li> <p>Illumination light source: Lumencor Lumencor Spectra X Lamp</p> </li> <li> <p>Pixel size: 650nm x 650nm</p> </li> <li> <p>Camera manufacturer and model: Hamamatsu ORCA-Flash4.0</p> </li> <li> <p>Software program(s) and version: OLYMPUS cellSens Dimension 3.2 (Build 23706)</p> </li> <li> <p>Image acquisition settings </p> <ul> <li> <p>expposure 500 ms</p> </li> <li> <p>gain: 0</p> </li> <li> <p>binning: 4 x 4</p> </li> </ul> </li> <li> <p>Experiment manager: ZDC + autofocus, two channels: DAPI and Cy3</p> </li> </ul> <p> </p> <p><strong>Image Processing and Analysis</strong><br> The data analysis workflow consists of several stages, each of which was executed by a specific script. Firstly, the raw data were manually cleaned and automatically sorted and organized using <em>sort_wells.ijm</em> in FIJI. Secondly, image analysis was performed using <em>Process_WFolder_macro_v1.ijm</em> in FIJI, which processed the image data and extracted the relevant features. Finally, the results were further processed using S<em>F_dataVis_and_statistics_mean_XYh.ipynb</em> in Python (Jupyter Notebook), which generated the final output in the form of a CSV file.</p> <p> </p> <p>In this repository, you can access the resulting CSV file, which contains the final results of our analysis. Additionally, we have provided the scripts used to process the data, which are available on our GitHub repository (LINK). You will find instruction how to create local Jupyter Hub for Python scripts. These scripts are accompanied by a short manual that provides an overview of the data analysis workflow and helps users navigate through the code. By making our scripts available, we hope to facilitate transparency and reproducibility of our research. If you encounter any issues, please report them through the GitHub repository: <a href="https://github.com/martinschatz-cz/genotoxicity-bia">https://github.com/martinschatz-cz/genotoxicity-bia</a>.</p> <p>We believe that our work can be useful for other researchers and analysts who are interested in studying similar datasets. We invite you to explore the contents of this repository and use the data and scripts provided here to further your research.</p> <p> </p> <p><strong>Cell lines and culture conditions</strong><br> Human cervical adenocarcinoma (HeLa) and a Chinese hamster ovary (CHO-K1) cell lines were obtained from American Type Culture Collection (ATCC). The HeLa cells were grown MEM supplemented with 10 % FBS and NEAA. CHO-K1 cells were cultivated with DMEM supplemented with L-proline (final concentration 35 mg/l). The cell incubation took place in a humidified atmosphere of 5% CO2 at 37 °C.</p> <p> </p> <p><strong>Direct measurement of DNA DSBs</strong><br> The cells were seeded in concentration 0,5 × 105 cells/ml into the 96-well plate (VWR, 10062-900). The cells were rinsed by phosphate buffered saline (PBS;) after 24h incubation, and medium with reduced FBS content (5 %) was added. Valinomycin was dissolved in DMSO and added to cells in two final concentrations (30 and 15 𝞵M). After 4h/24h incubation the visualization was done using and following protocol of HCS DNA Damage Kit. The cells were fixed by 4% paraformaldehyde solution for 15 min at room temperature. The cells were rinsed once by PBS and the permeabilization was performed using Triton® X-100 () solution by incubation for 15 min at room temperature. The wells were rinsed with PBS once and the plate was blocked by 1% BSA blocking solution. After 1 hour incubation at room temperature the blocking solution was removed and 100 𝞵l of pH2AX mouse monoclonal antibody solution (1:1000 in BSA) was pipetted into each well incubated for 1 hour at room temperature. After three times rinsing by PBS the 100 𝞵l of Alexa Fluor® 555 goat anti-mouse IgG (H+L; 1:2000) and Hoechst 33342 (1:6000) solution was incubated for 1 hour at room temperature protected from light. After the incubation the wells were rinsed three times by PBS. The plate was stored with 100 𝞵l in the refrigerator (4 °C) until the image analysis was performed.</p>
Data set used in "Effect of turbulence and viscosity models on wall shear stress derived biomarkers for aorta simulations"
<p>Data set used in "Effect of turbulence and viscosity models on wall shear stress derived biomarkers for aorta simulations"</p> <p>Includes the data for 20 heartbeats. Divided into external and internal walls regions. </p>
A more accurate risk biomarkers recognition for Progressive Multifocal Leukoencephalopathy (PML) caused by Polyomavirus JC in patients with multiple sclerosis during treatment with disease-modifying therapies (DMTs): an ongoing clinical challenge.
<p>The therapeutic scenario for the treatment of MS has recently been characterized by a veritable revolution, which has included the introduction, for the first time, of drug treatment guidelines and the entry, in the therapeutic landscape of the last decade, of numerous new drugs that, in varying but significantly relevant ways, have proven capable of modifying the course of the disease (Disease-Modifying Therapies - DMTs). <br> While the arsenal of available drugs has resulted in advances in efficacy and selectivity, it has also exposed them to the danger of side effects, potentially serious and in some cases even fatal. Among the most important side effects, complications of infectious origin, characterized by cases of viral infection/reactivation, as in the case of JCPyV, the etiologic agent of PML, are the most represented. This study, based on the follow-up of MS patients treated with different DMTs, contributes to implementing the data in the literature regarding a greater understanding of the risks related to the administration of these drugs and more appropriate monitoring of MS treatment. The risk of JCPyV reactivation with Fingolimod and Dimethyl fumarate is lower than the risk of viral reactivation associated with natalizumab.<br> In light of the data obtained, it is possible to conclude that, in the case of natalizumab, testing for JC viruria would seem to be more useful in identifying those patients with a JCPyV-specific humoral response that is not yet detectable. In addition, our results, draw attention to the importance of analyzing the NCCR rearrangements of JCPyV. Indeed, the particular rearrangements found in plasma and PBMCs of patients with RRMS treated with natalizumab could represent an alert of neuroinvasiveness in order to detect early those patients with a higher risk of developing PML. In the case of dimethyl fumarate, it seems likely that monitoring of lymphopenia would identify a higher risk group of patients in whom alternative therapy should be sought. Prolonged lymphopenia, with absolute lymphocyte counts less than 750 lymphocytes/mL, might be the major risk factor for PML although, a greater risk might lie in the loss of CD8+ cells that are crucial for JCPyV control.<br> For fingolimod, this strategy cannot be applied because the number of circulating lymphocytes decreases while the actual lymphocyte function appears largely normal therefore, monitoring viruria and viremia along with identification of the neurotrophic variant of the virus seems a more exploitable means for risk stratification.</p> <p>In conclusion, the results of this study can be considered directly transferable to the National Health System in that, both the monitoring of JCPyV reactivation by viruria and the sequence analysis of viral NCCR and host immune set-up could play the role of translatable biomarkers in clinical practice in order to assess the risk of PML onset. In addition to improving risk stratification of this disease, these biomarkers of viral reactivation and pathogenicity could facilitate timely diagnosis, optimizing the use of health care resources and contributing to the reduction of direct and indirect costs of MS disease.</p> <p>Prezioso Carla was supported by the Italian Ministry of Health (Starting Grant: SG-2018-12366194).</p>
Discovery of sparse, reliable omic biomarkers with Stabl
<p><span>Adoption of high-content omic technologies in clinical studies, coupled with computational </span><span>methods, have yielded an abundance of candidate biomarkers. However, translating such find</span><span>ings into bona fide clinical biomarkers remains challenging.</span> <span>To facilitate this process, we </span><span>introduce Stabl, a general machine learning framework that identifies a sparse, reliable set </span><span>of biomarkers by integrating noise injection and a data-driven signal-to-noise threshold into </span><span>multivariable predictive modeling.</span> <span>Evaluation of Stabl on synthetic datasets and five inde</span><span>pendent clinical studies demonstrates improved biomarker sparsity and reliability compared to </span><span>commonly used sparsity-promoting regularization methods while maintaining predictive per</span><span>formance; it distills datasets containing 1,400 to 35,000 features down to 4 to 34 candidate </span><span>biomarkers. Stabl extends to multi-omic integration tasks, enabling biological interpretation of </span><span>complex predictive models, as it hones in on a shortlist of proteomic, metabolomic, and cyto</span><span>metric events predicting labor onset, microbial biomarkers of preterm birth, and a pre-operative </span><span>immune signature of post-surgical infections.</span></p>
Study of Innovative Multimodal Imaging Biomarkers to Predict Anatomical Outcome in Naive Patients With wAMD Treated With Brolucizumab.
ClinicalTrials.gov study NCT04774926. IPD Sharing: YES. Countries: 1. Publications: 1.
Study of Relationship Between Vedolizumab Therapeutic Drug Monitoring, Biomarkers of Inflammation and Clinical Outcomes
ClinicalTrials.gov study NCT04567628. IPD Sharing: YES. Countries: 1. Publications: 1.
ScienceDex guides
Understand access before you commit
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.