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6,423 results for “Biomarkers”
Dataset:Biomarker-based diagnosis of Post COVID-19 Condition
<p>The persistence or development of new symptoms three months after the initial acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection is referred to as post-coronavirus disease (COVID) condition (PCC). The identification of new biomarkers specific for the occurrence of PCC is vital to proceed in the future towards prediction of its evolution.</p> <p>This study was registered with ISRCTN Registry during recruitment (ISRCTN27312680), and it was conducted comparing two parallel groups: individuals diagnosed with PCC versus individuals who completely recovered within 3 months after acute COVID-19.</p> <p>All participants were enrolled between the first semester of 2022 in Primary Health Care Centers (PHCCs) of Zaragoza (Spain). The two parallel groups were matched by age, gender, and date of acute COVID-19 diagnosis. The diagnosis of PCC was determined by a general practitioner, following the WHO criteria [7], before or at the time of inclusion in the study. Recovered individuals were required to have passed acute COVID-19, confirmed by RT-qPCR, antigen test, or SARS-CoV-2 serology.<strong> </strong></p>
Concentrations of methane, sulfate and lipid biomarkers and carbon isotope values oof lipids in the sediments from the outer Laptev Sea
<p>The dataset contains the concentrations of methane, sulfate and microbial lipid biomarkers, and the carbon isotope composition of lipids in the sediment collected from the SWERUS-C3 expedition in 2014. The core sediment samples were from stations 13, 14 and 23 in the outer Laptev Sea. The field investigation reveals it is a methane seep area. </p>
Data from: Fluorescent biomarkers demonstrate prospects for spreadable vaccines to control disease transmission in wild bats
Vaccines that autonomously transfer among individuals have been proposed as a strategy to control infectious diseases within wildlife populations. However, understanding rates of spread and epidemiological efficacy in real world systems remain elusive. Here, we investigated whether topical vaccines that transfer among bats through social contacts can control vampire bat rabies, a medically and economically important zoonosis in Latin America. Field experiments in 3 Peruvian bat colonies which used fluorescent biomarkers as a proxy for the bat-to-bat transfer and ingestion of an oral vaccine revealed that vaccine transfer would increase population-level immunity up to 2.6 times beyond the same effort using conventional, non-spreadable vaccines. Mathematical models demonstrated that observed levels of vaccine transfer would reduce the probability, size, and duration of rabies outbreaks, even at low, but realistically achievable levels of vaccine application. Models further predicted that existing vaccines provide substantial advantages over culling bats, the policy currently implemented in North, Central, and South America. Linking field studies with biomarkers to mathematical models can inform how spreadable vaccines may combat pathogens of health and conservation concern prior to costly investments in vaccine design and testing.
Dataset of clinical biomarkers for prediction of the arboviral infection severity using SIMON analysis
<p>The SISA dataset was used for the identification of clinical biomarkers that can predict the severity of the arboviral infection severity using SIMON analysis, as described (<a href="https://doi.org/10.1101/2020.08.16.252767">https://doi.org/10.1101/2020.08.16.252767</a>). The dataset contains clinical data from 543 individuals hospitalized due to the arboviral infection with Dengue, chikungunya, or Zika viruses from a surveillance study in Ecuador collected from 2013 to 2017 (Suppy et al., 2020, doi: 10.1371/journal.pntd.0007969). In the SISA dataset, we have excluded columns with high level of missing values (pregnancy, <em>WomPreg</em> and complete blood count test which was not performed for all donors and includes columns: <em>PLT_count, Lymphocytes, CBC_N%, WBC_calc </em>and<em> CBC_HCT</em>). Additionally, 9 donors with missing values were removed and SIMON analysis was performed with this final dataset.</p>
Dataset for: Searching for Imaging Biomarkers of Psychotic Dysconnectivity
<p>This dataset contains features used in analyses for the following manuscript:</p> <p>Rodrigue, AL, et al. (2021). Searching for Imaging Biomarkers of Psychotic Dysconnectivity. <em>Biological Psychiatry: Cognitive Neuroscience and Neuroimaging,</em> in press.</p> <p>Contents:</p> <p><br> - 4 Demographic csv files. Each dataset has a csv for covariates of interest- Age, Sex, and Site (BSNIP1 only)<br> site coding: 1=Hartford,CT, 2=Baltimore,MD<br> DIAG coding: SZ=Schizophrenia, SAD=Schizoaffective Disorder, BPP=Bipolar Disorder I with Psychosis, MDD=Major Depressive Disorder with Psychosis,OTH=Other Psychotic Disorder</p> <p>- 16 feature csv files. Each dataset has a .csv for raw and residualized DTI and rsfMRI features<br> ISMMS_DTI_raw_Features.csv<br> Olin_DTI_raw_Features.csv<br> BSNIP1_DTI_raw_Features.csv<br> BSNIP2_DTI_raw_Features.csv<br> ISMMS_rsfMRI_raw_Features.csv<br> Olin_rsfMRI_raw_Features.csv<br> BSNIP1_rsfMRI_raw_Features.csv<br> BSNIP2_rsfMRI_raw_Features.csv</p> <p>Residualized (age, sex, site (BNIP1 only))<br> ISMMS_DTI_res_Features.csv<br> Olin_DTI_res_Features.csv<br> BSNIP1_DTI_res_Features.csv<br> BSNIP2_DTI_res_Features.csv<br> ISMMS_rsfMRI_res_Features.csv<br> Olin_rsfMRI_res_Features.csv<br> BSNIP1_rsfMRI_res_Features.csv<br> BSNIP2_rsfMRI_res_Features.csv</p>
Metabolomics Analysis for the Identification of Biomarkers in Small Cell Lung Cancer
<p>Small cell lung cancer (SCLC), a highly aggressive malignancy with a poor prognosis is usually detected at the extensive stage of the disease. The demand for early diagnostic methods and reliable biomarkers is increasing, although a number of tumor markers such as NSE and NCAM have already been utilized in clinics. Here, we conducted untargeted metabolomics in 54 plasma samples from 34 patients with SCLC and 20 healthy controls.</p>
Fecal-bbu-genes-quantification-predicts-L-carnitine-mediated-TMAO-production-and-serves-as-a-biomarker-for-precision-nutrition-code-20231201
<p>Custom code related to the original research article "Fecal bbu genes quantification predicts L-carnitine-mediated TMAO production and serves as a biomarker for precision nutrition"</p>
Title: Health-Related Quality of Life and DNA Methylation-Based Aging Biomarkers among Survivors of Childhood Cancer
<p><strong><span>Abstract</span></strong></p> <p><strong><span>Background: </span></strong><span>Childhood cancer survivors are at high risk for morbidity and mortality and poor patient-reported outcomes, typically health-related-quality-of-life (HRQOL). However, </span><span>associations between DNA methylation (DNAm)-based aging biomarkers and HRQOL have not been evaluated.</span></p> <p><strong><span>Methods: </span></strong><span>DNAm was generated with Infinium EPIC BeadChip on blood-derived DNA (median[range] for age at blood draw=34.5[18.5-66.6] years) and HRQOL was assessed with age at survey (32.3[18.4-64.5] years) from 2,206 survivors in the St. Jude Lifetime Cohort. DNAm-based aging biomarkers, including epigenetic age using multiple clocks (e.g., <span>GrimAge</span>) and others (e.g., DNAmB2M: beta-2-microglobulin; DNAmADM: adrenomedullin), were derived from the DNAm Age Calculator (https://dnamage.genetics.ucla.edu). HRQOL was assessed using the Medical Outcomes Study 36-Item Short-Form Health Survey to capture eight domains, and physical and mental component summaries (PCS and MCS). General linear models evaluated associations between HRQOL and epigenetic age acceleration (EAA, e.g., EAA_GrimAge) or other age-adjusted DNAm-based biomarkers (e.g., ageadj_DNAmB2M) after adjusting for age at blood draw, sex, cancer treatments, and DNAm-based surrogate for smoking pack-years. All P values were 2-sided.</span></p> <p><strong><span>Results: </span></strong><span>Worse HRQOL was associated with greater EAA_GrimAge (</span><span>PCS: β[95%CI]=-0.18[-0.251,-0.11] years, P=1.85×10<sup>-5</sup>; and four individual HRQOL domains), followed by ageadj_DNAmB2M (PCS: -0.08[-0.124,-0.037], P=0.003; and three individual HRQOL domains), and ageadj_DNAmADM (PCS: -0.082[-0.125,-0.039], P=0.002; and two HRQOL domains). EAA_Hannum (Hannum clock) was not associated with any HRQOL.</span></p> <p><strong>Conclustion: </strong>Overall and domain-specific measures of HRQOL are associated with DNAm measures of biological aging. Future longitudinal studies should test biological aging as a potential mechanism.</p>
THE ROLE OF HOMOCYSTEINE AS A BIOMARKER OF CYTOKINE STORM IN IMMUNOONCOLOGY AND THERAPY OF COVID-19
<p>Homocysteine is a sulfur-containing amino acid that can act as an important biomarker of inflammatory processes, including cytokine storm, observed in various pathological conditions such as cancer and COVID-19. In the conditions of the cytokine storm characteristic of severe forms of COVID-19 and progressive stages of cancer, elevated homocysteine levels can increase oxidative stress and inflammatory reactions, which, in turn, exacerbates tissue and organ damage. Studies show that homocysteine can play a significant role in the pathogenesis of these conditions, affecting the vascular and immune systems. Thus, monitoring of homocysteine levels is important for the diagnosis, prognosis and development of new therapeutic strategies in the field of immuno-oncology and treatment of COVID-19.</p>
Selected articles from the scoping review of biomarker discovery studies for the EU project on "Personalised Medicine Trials" (PERMIT)
<p>This dataset provides the data extracted for the scoping review of the literature on biomarker discovery studies for patient stratification using machine learning analysis of omics data, as part of the EU project on “Personalised Medicine Trials” (PERMIT). It covers the references for all articles selected as part of the scoping review, as well as information on the study type and methodology, the outcome measures, the validation type, and representative sentences extracted from each article on the main results and key findings of the corresponding biomarker study.</p>
Urinary biomarkers for the non-invasive diagnosis of endometriosis: a systematic literature review
<p>Raw dataset from a systematic literature review performed until August 2021 in which the research question was 'Are there urine biomarkers sensitive and specific enough for endometriosis detection?' and the Medical Subject Heading (MeSH) terms were (endometrios*) AND (urin*). </p>
Summary Statistics from "Genetically regulated gene expression and proteins revealed discordant effects" (LWAS of biomarker)
<p>Summary statistics of 92 blood protein levels. The corresponding publication is currently under revision.</p> <p> The zipped txt file is tab-delimited and contains the following columns:</p> <ul> <li>protein: protein name abbreviation</li> <li>cytoband: genomic region</li> <li>gene: gene name abbreviation</li> <li>setting: either "combined" (adj. for sex & age) or sex-stratified ("males", "females"; adj. for age)</li> <li>variant_id_hg19: SNP ID according to hg19</li> <li>variant_id_hg38: SNP ID according to hg19</li> <li>chr: chromosome</li> <li>pos_hg19: base position according to hg19</li> <li>pos_hg38: base position according to hg19</li> <li>effect_allele: also known as counted allele in additive model</li> <li>other_allele: not-counted allele</li> <li>eaf: effect allele frequency</li> <li>maf: minor allele frequency</li> <li>info: imputation info score</li> <li>n_samples: number of samples</li> <li>beta: effect estimate</li> <li>se: standard error</li> <li>zscore: Z-statistic</li> <li>pvalue: p-value</li> <li>FDR: FDR by gene and setting</li> <li>BBFDR: hierarchical FDR by setting</li> <li>hierFDR: TRUE if SNP is significant after hierarchical FDR</li> </ul>
Comparative host transcriptomics as a tool to identify candidate biomarkers for immune reactions in leprosy: A meta-analysis study
<p>The dataset consists of R source code for the individual dataset analysis of the studies and their meta-analysis. It also contains supplementary tables and figure.</p>
Evaluation of selected semen parameters and biomarkers of male infertility – preliminary study
<p>Data base and statistics for publication entitled: Evaluation of selected semen parameters and biomarkers of male infertility – preliminary study.</p>
A dataset of anonymised hospitalised COVID-19 patient data: outcomes, demographics and biomarker measurements for two New York hospitals
<p>These datasets are for a cohort of n=1540 anonymised hospitalised COVID-19 patients, and the data provide information on outcomes (i.e. patient death or discharge), demographics and biomarker measurements for two New York hospitals: State<br> University of New York (SUNY) Downstate Health Sciences University and Maimonides<br> Medical Center.</p> <p>The file "demographics_both_hospitals.csv" contains the ultimate outcomes of hospitalisation (whether a patient was discharged or died), demographic information and known comorbidities for each of the patients.</p> <p>The file "dynamics_clean_both_hospitals.csv" contains cleaned dynamic biomarker measurements for the n=1233 patients where this information was available and the data passed our various checks (see https://doi.org/10.1101/2021.11.12.21266248 for information of these checks and the cleaning process). Patients can be matched to demographic data via the "id" column.</p> <p><strong>Study approval and data collection</strong></p> <p>Study approval was obtained from the State University of New York (SUNY) Downstate Health Sciences University Institutional Review Board (IRB\#1595271-1) and Maimonides Medical Center Institutional Review Board/Research Committee (IRB\#2020-05-07). A retrospective query was performed among the patients who were admitted to SUNY Downstate Medical Center and Maimonides Medical Center with COVID-19-related symptoms, which was subsequently confirmed by RT PCR, from the beginning of February 2020 until the end of May 2020. Stratified randomization was used to select at least 500 patients who were discharged and 500 patients who died due to the complications of COVID-19. Patient outcome was recorded as a binary choice of “discharged” versus “COVID-19 related mortality”. Patients whose outcome was unknown were excluded. Demographic, clinical history and laboratory data was extracted from the hospital’s electronic health records.</p>
The Upper-Airway Microbiome as a Biomarker of Asthma Exacerbations despite Inhaled Corticosteroid Treatment
<p>The response to inhaled corticosteroids (ICS) in asthma is affected by the interplay of several factors. Among these, the role of the upper-airway microbiome has been scarcely investigated. We aimed to evaluate the association between the salivary, pharyngeal, and nasal microbiome with asthma exacerbations despite ICS use. Samples from 250 asthma patients from the Genomics and Metagenomics of Asthma Severity (GEMAS) study treated with ICS were analyzed. Controls/cases were defined by the absence/presence of asthma exacerbations in the past six months despite being treated with ICS. The bacterial microbiota was profiled by sequencing the V3-V4 region of the 16S rRNA gene. Differences between groups were assessed by PERMANOVA and regression models adjusted for potential confounders. A false discovery rate (FDR) of 5% was used to correct for multiple comparisons. Classification models of asthma exacerbations despite ICS treatment were built with machine learning approaches based on clinical, genetic, and microbiome data. In nasal and saliva samples, cases had lower bacterial diversity (Richness, Shannon, and Faith indexes) than controls (0.007≤p≤0.037). Asthma exacerbations accounted for 8-9% of the interindividual variation of the salivary and nasal microbiomes (0.003≤p≤0.046). Three, four, and eleven bacterial genera from the salivary, pharyngeal, and nasal microbiomes were differentially abundant between groups (4.09x10<sup>-12</sup>≤FDR≤0.047). Integrating clinical, genetic, and microbiome data showed good discrimination for the development of asthma exacerbations despite ICS use (AUC<sub>training</sub>:0.82 and AUC<sub>validation</sub>:0.77). The diversity and composition of the upper-airway microbiome are associated with asthma exacerbations despite ICS treatment. The salivary microbiome has a potential application as a biomarker of asthma exacerbations despite ICS use.</p> <p>The summary results of the association between bacterial genera and asthma exacerbations despite ICS use are published in this repository. Analyses were conducted using the DESeq2 package adjusting for potential confounders (see more details in the manuscript). The submitted summary tables contains the following columns:</p> <ul> <li>Kingdom: Taxonomic classification at Kingdom level</li> <li>Phylum: Taxonomic classification at Phylum level</li> <li>Class: Taxonomic classification at Class level</li> <li>Order: Taxonomic classification at Order level</li> <li>Family: Taxonomic classification at Family level</li> <li>Genus: Taxonomic classification at Genus level</li> <li>log2FC: log<sub>2</sub>(fold-change). Positive values indicate higher abundance in cases and negative values in controls</li> <li>SE: standard error of log<sub>2</sub>(fold-change)</li> <li>P.Value: p-value of the regression model</li> <li>FDR: adjusted p-value by false discovery rate (Benjamin-Hochberg method)</li> </ul>
Pre-processed ex vivo MRI data for manuscript titled "Neuroanatomical and cognitive biomarkers of alpha-synuclein propagation in a mouse model of synucleinopathy prior to onset of motor symptoms""
<p>Repository for <em>ex vivo</em> magnetic resonance imaging data from the project titled "Presymptomatic neuroanatomical and cognitive biomarkers of alpha-synuclein propagation in a mouse model of synucleinopathy"</p> <p>Contains the pre-processed <em>ex vivo</em> T1-weighted images (Bruker 7T; 70 micron isotropic voxel resolution) for M83 alpha-synuclein A53T hemizygous mice that received either a phosphate buffered saline (PBS) or alpha-synuclein pre-formed fibrils (PFF) injection in the right dorsal striatum. Full subject list can be viewed with the "subject_list.csv" file. More details are available in the manuscript. </p>
Figure 3 in Multiple metals and agricultural use affects oxidative stress biomarkers in freshwater Aegla crabs
Figure 3. Biomarkers grouped by hydrographic basin (Suzana River basin, Ligeirinho-Leãozinho River basin, Dourado River basin). Different letters indicate significant differences (p <0.05), as compared by one-way ANOVA plus Tukey post-test (between basins).
Figure 2 in Multiple metals and agricultural use affects oxidative stress biomarkers in freshwater Aegla crabs
Figure 2. Biplot of PCA ordination for the metal concentration in sediment of the three studied basins. Suzana River basin (S); Ligeirinho-Leãozinho River basin (L); Dourado River basin (D).
Figure 1 in Multiple metals and agricultural use affects oxidative stress biomarkers in freshwater Aegla crabs
Figure 1. Map of the sampling sites. (A) Suzana River basin (between 27°35'38" and 27°36'16"S; 52°11'11" and 52°13'41"W); (B) Ligeirinho-Leãozinho River basin (between 27°40'15" and 27°36'16"S; 52°16'03" and 52°13'41"W); (C) Dourado River basin (between 27°33'59" and 27°37'13"S; 52°17'46" and 52°19'36"W). The circles (•) indicate the sampled streams. The numbered boxes indicate the areas of land uses analysis.
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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.