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30,948 results for “Profile”
Data from: "Steroidal glycoside profile differences among primary roots system and adventitious roots in Solanum dulcamara"
<p>The zip-file contains all chromatograms reported in vendor (.D) and open-source (.mzxml) formats.</p>
A compendium of expression profiles for Corynebacterium glutamicum
<p><em>Corynebacterium glutamicum</em> is the major host for the industrial production of amino acids and has become one of the best studied model organisms in microbial biotechnology. Rational strain construction has led to an improvement of producer strains and to a variety of novel producer strains with a broad substrate and product spectrum. A key factor for the success of these approaches is detailed knowledge of transcriptional regulation in <em>C. glutamicum</em>. Here, we present a large compendium of 927 manually curated microarray-based transcriptional profiles for wild-type and engineered strains detecting genome-wide expression changes of the 3,047 annotated genes in response to various environmental conditions or in response to genetic modifications. The replicates within the 927 experiments were combined to 304 microarray sets ordered into six categories that were used for differential gene expression analysis. Hierarchical clustering confirmed that no outliers were present in the sets. The compendium provides a valuable resource for future fundamental and applied research with <em>C. glutamicum</em> and contributes to a systemic understanding of this microbial cell factory.</p>
Dynamics of the euphotic zone in the Black Sea: The synergy of data from profiling floats, machine learning and numerical modeling
<p>The datasets contain input data and data emulated by Neural networks (NN) used in the study 'Dynamics of the euphotic zone in the Black Sea: The synergy of data from profiling floats, machine learning and numerical modeling'</p> <p>- <strong>NN2018_CMEMS_ARGO.tar.gz</strong>: archive contains Matlab binary files consisting of NN-derived BGC variables (Chlorophyll-a, Oxygen and backscatter at 700nm) along ARGO float paths in 2018 with vertical resolution taken from CMEMS (13 depth levels in the depth range studied here); NN was applied either on CMEMS physics ('C') or on ARGO physics ('A'); additionally, CMEMS BGC model data (Chlorophyll-a and Oxygen) along these paths are included; (filenames follow the names of floats given in Table 1:<em> floatname</em>_2018_NNARGOCMEMS.mat)</p> <p>- <strong>NNalongARGO.tar.gz</strong>: archive contains Matlab binary files consisting of NN-derived BGC variables (Chlorophyll-a, Oxygen and backscatter at 700 nm) along ARGO float paths together with input ARGO data (time, latitude, longitude, salinity, temperature, sigma_T and BGC variables); all variables are mapped with 1m vertical resolution; depth range is [1m 150m] ; additionally, float ogs7 data include NO3, float hzg1 data does not contain Chlorophyll-a and backscatter at 700 nm; (filenames follow the names of floats given in Table 1:<em> floatname</em>_euph_1mRes_150mALLINCLNN.mat)</p> <p>- <strong>NNReconBlackSea.tar.gz</strong>: archive contains Matlab binary files consisting of basin wide NN derived BGC variables (Chlorophyll-a, Oxygen and backscatter at 700nm) for the years 2015-19 and 2010/11 (weekly mean data); additionally CMEMS data (time, latitude, longitude, salinity, temperature, sea surface height) are provided for the photic zone; (filenames are reconNNCMEMS_2015_2019.mat and reconNNCMEMS_2010_2011.mat, respectively)</p>
Machine learning on syngeneic mouse tumor profiles to model clinical immunotherapy response
<p><span>Most cancer patients are refractory to immune checkpoint blockade (ICB) therapy, and proper patient stratification remains an open question. Primary patient data suffer from high heterogeneity, low accessibility, and lack of proper controls. In contrast, syngeneic mouse tumor models enable controlled experiments with ICB treatments. Using transcriptomic and experimental variables from >700 ICB-treated/control syngeneic mouse tumors, we developed a novel machine learning framework to model tumor immunity and identify factors influencing ICB response. Projected on human immunotherapy trial data, we found that the model can predict clinical ICB response. We further applied the model to predicting ICB-responsive/resistant cancer types in TCGA, which agreed well with existing clinical reports. Finally, feature analysis implicated factors associated with ICB response. In summary, our novel computational framework based on mouse tumor data reliably stratified patients regarding ICB response, informed resistance mechanisms, and has the potential for wide applications in disease treatment studies.</span></p>
Gradients4-TN397-LISST-DEEP-Profiles_2022-04-28
<p>Cruise Name: Gradients 4 , TN397</p> <p>Vessel: R/V Thompson</p> <p>Funding: Simons Collaboration on Ocean Processes and Ecology (SCOPE)</p> <p>Dataset description:.</p> <p>This dataset was collected on the R/V Thompson during the Gradients IV cruise which departed from San Diego, CA and ended in Honolulu, HI. A transect was performed on the 140 degree longitude line from roughly 19 degrees N to 2.5 degrees S before heading to Honolulu. A Sequoia Scientific LISST-DEEP instrument was mounted to the R/V Thompson's rosette and ctd system and operated during CTD casts. The data presented here are blank-corrected using a deepwater background scattering calibration, and binned in 2-meter bins from 2 to 200m depths. The summed volume concentration of particles (in uL/L), the standard LISST output, is presented for 3 size ranges: 1.25-2 µm, 2-20 µm, and 20-100 µm. Particle volume concentration can be converted to particle concentration by assuming spherical particles. The total particle concentration (#/L) is calculated for particles with a diameter between 1.25 and 100 um. Larger size classes are excluded due to low detection limits and scattering at density gradients. Note that data have not been processed to remove outliers. </p> <p> </p>
COVID-19-related fatigue: cognitive profiles and multidomain complaints at 12 months follow-up
<p>Cognitive deficits were often reported during the acute and post-acute stages of severe COVID-19 and were often, but not always, associated with signs of brain damage. Population-wide surveys highlighted the need for investigations into the nature, the severity and the evolution of cognitive, behavioural and psychiatric deficits. In this observational study, we describe the outcome at 12 months after severe COVID-19 involving intensive care unit stay and critical chronic illness in six patients, who had no history of prior brain dysfunction. A pervading mental and physical fatigue was consistently reported as well as numerous multidomain complaints, which affect to a certain extent everyday life, and for some of the patients a certain degree of neurobehavioural (apathy) and/or psychiatric (anxiety) dysfunction. Standardized neuropsychological tests revealed for 4 of the 6 patients the occurrence relatively isolated of cognitive dysfunction or performance at the lower limit of the norm in some, but not all attentional, executive and/or working memory tests. Somatic scales highlighted the presence of dyspnoea, muscle weakness, an olfactory disorder and/or minor sleep problems in some but not all patients.</p>
Export for MOdeLINGVis of the Expected Protein Profile of Neurotypical Young Adults
<p>INTRODUCTION: The dataset of the full raw electrophoretic data, named Expected Protein Profile workbook, is treated to be imported to MATLAB. Please refer to https://doi.org/10.5281/zenodo.7054406 to have access to the full dataset and to the preliminary methodology ("EPPStrategyDataExport") used in the electrophoretic data. This treated electrophoretogram was named "ExportForMOdeLINGVis" and can also be consulted at https://tinyurl.com/ExportForMOdeLINGVis.</p> <p>METHODOLOGY: The electrophoretic dataset was treated and imported to MATLAB. First, the section "Present in the following subphenomes" was added, which comprised binary variables (present/absent) to identify in which subgroup the Molecular Bands were present. Secondly, the previously obtained preliminary triple entry table was added to the Molecular Bands Summary for each Subject (ex: D01309). Lastly, the database was implemented into the MODeLING.Vis toolbox and the variables were imported into arrays. Those arrays indexed a linear matrix of the variables: Molecular Bands Subgroups (kDa) and Concentration (ng/µl) of each sample (subject). For the full methodology, please consult https://doi.org/10.5281/zenodo.7041477</p>
Neurotypical young adults' Expected Protein Profile: the EPPStrategyDataExport workbook and strategy applied to the electrophoretic data.
<p>INTRODUCTION: A dataset of electrophoretic data, named Expected Protein Profile workbook, is published. The dataset corresponds to the full raw electrophoretogram of the Expected Protein Profiles of the 92 neurotypical young adults. The dataset can also be consulted at: https://tinyurl.com/EPPStrategyDataExport.</p> <p>METHODOLOGY: The dataset consist of a workbook comprising 6 worksheets, which demonstrates the preliminary strategy applied to the electrophoretic data – 6 stages were executed. For the full methodology, please consult https://doi.org/10.5281/zenodo.7041477.</p>
Microsatellite profile of Plasmopara viticola isolates collected in Italy
<p class="MsoNormal"><span>Downy mildew, caused by the oomycete <em>Plasmopara viticola</em>, is one of the most serious threat to viticulture. <em>P. viticola </em>is native to North America and causes the most severe damages to the Eurasian grapevine, <em>Vitis vinifera. </em>In this work, we investigated the genetic structure of the pathogen in Italy by collecting 96 <em>P. viticola </em>strains in twelve different regions. Based on microsatellite characterization (19 microsatellites), we confirmed that the Italian population of <em>P. viticola</em> is composed of two separate subpopulations and determined that these two cluster differ for geographic and climatic conditions. These populations could have been originated from the introduction of two separate populations or, more likely, from the evolution of the original population that reached Europe at the end of the XIX century. The pathogen showed a great evolutionary potential, as highlighted by the regular occurrence of sexual reproduction, panmictic structure within cluster and absence of clones. These results confirm that the <em>P. viticola </em>has a strong potential for adaptation and suggest the integration of all the tools (genetic, agronomic and chemical) for achieving a proper disease management.</span></p>
The Community Coevolution Model with application to the study of evolutionary relationships between genes based on phylogenetic profiles
<p>Organismal traits can evolve in a coordinated way, with correlated patterns of gains and losses reflecting important evolutionary associations. Discovering these associations can reveal important information about the functional and ecological linkages among traits. Phylogenetic profiles treat individual genes as traits distributed across sets of genomes and can provide a fine-grained view of the genetic underpinnings of evolutionary processes in a set of genomes. Phylogenetic profiling has been used to identify genes that are functionally linked, and to identify common patterns of lateral gene transfer in microorganisms. However, comparative analysis of phylogenetic profiles and other trait distributions should take into account the phylogenetic relationships among the organisms under consideration.</p> <p>Here we propose the Community Coevolution Model (CCM), a new coevolutionary model to analyze the evolutionary associations among traits, with a focus on phylogenetic profiles. In the CCM, traits are considered to evolve as a community with interactions, and the transition rate for each trait depends on the current states of other traits. Surpassing other comparative methods for pairwise trait analysis, CCM has the additional advantage of being able to examine multiple traits as a community to reveal more dependency relationships. We also develop a simulation procedure to generate phylogenetic profiles with correlated evolutionary patterns that can be used as benchmark data for evaluation purposes.</p> <p>A simulation study demonstrates that CCM is more accurate than other methods including the Jaccard Index and three tree-aware methods. The parameterization of CCM makes the interpretation of the relations between genes more direct, which leads to Darwin's scenario being identified easily based on the estimated parameters. We show that CCM is more efficient and fits real data better than other methods resulting in higher likelihood scores with fewer parameters. An examination of 3786 phylogenetic profiles across a set of 659 bacterial genomes highlights linkages between genes with common functions, including many patterns that would not have been identified under a non-phylogenetic model of common distribution. We also applied the CCM to 44 proteins in the well-studied Mitochondrial Respiratory Complex I and recovered associations that mapped well onto the structural associations that exist in the complex.</p>
Thallium(I) exposure perturbs the gut microbiota and metabolic profile as well as the regional immune function of C57BL/6 J mice
<p><span>Intestinal microbes</span><span> regulate the development of diseases induced by environmental exposure. Thallium (Tl) is a highly toxic heavy metal</span><span>, </span><span>and its toxicity is rarely discussed in relation to gut microbes. Herein, we showed that Tl(I) exposure (10 ppm for two weeks) affected the alpha diversity of bacteria in </span><span>the ileum, colon, and </span><span>feces, but had little effect on the beta diversity of bacteria through 16S rRNA sequencing. LEfSe analysis revealed that Tl(I) exposure changed the abundance of intestinal microbiota along the digestive tract. Cecum metabolomic detection and analysis showed that Tl(I) exposure altered the abundance and composition of metabolites. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that Tl(I) exposure impaired amino acid, lipid, purine metabolism, and G protein-coupled receptor signalling pathways. A consistency test revealed a strong correlation, and a Pearson's correlation analysis showed an extensive interaction, between microorganisms and metabolites. Analysis of the intestinal immunity revealed that Tl(I) exposure suppressed the immune responses, which also had regional differences. These results identify the perturbation of the intestinal microenvironment by Tl exposure and provide a new explanation for Tl toxicity.</span></p>
Bayesian Estimation on Microbial Electrochemical Time Profiles obtained by a High-Throughput Bioelectrochemical Device
<p>Bioelectrochemical systems (BESs) are attracting much attention, but the mechanisms are not yet fully clarified. One of the issues for the BESs research is the lack of a high-quality database that is developed through well-controlled experiments with a high-throughput data-collecting system. Here, we developed a new high-throughput potentiostat with 96 well plates with silk-screen-printed electrodes. With this potentiostat, we obtained 576 time-profiles of microbial current production for viewing the complex landscape of the parameters, namely, the redox mediator concentration and the electrode potential. This dataset contains the following materials:</p> <ul> <li>Current production profiles for <em>Shewanella </em>(Data with average of four data sets for impact of mediators.zip)</li> <li>Summary of the calculated values (statistics summary.csv)</li> <li>Python code for calculating the maximum slope (Slope EF.py)</li> <li>Python codes for Bayesian estimation (2D Bayesian Optimization mapping.py and 2D Bayesian Optimization_slice.py)</li> </ul>
Reproduction package for the paper "Constraining planetary mass-loss rates by simulating Parker wind profiles with Cloudy"
<p>This is a basic reproduction package for the paper "Constraining planetary mass-loss rates by simulating Parker wind profiles with Cloudy" by Linssen et al. (2022). It provides the data products necessary to reproduce the figures of the paper.</p>
Normalized linear counts from NanoString autoimmune profiling panel and summary of statistical analyses
<p>Though dependent on genetic anomalies, clinical manifestations of the human autoimmune disease systemic lupus erythematosus (lupus) can be triggered by environmental exposures including inhalation toxicants such as crystalline silica dust (cSiO<sub>2</sub>), tobacco smoke, and ambient air particles. Prednisone, a glucocorticoid (GC), is a keystone therapy for managing lupus flaring and progression, however, long-term use is associated with many adverse side effects. Here, we characterized the dose-dependent immunomodulation and toxicity of prednisone in a preclinical model that emulates onset and progression of cSiO<sub>2</sub>-triggered lupus. Two cohorts of 6-wk-old female NZBWF1 mice were fed either control AIN-93G diet or one of three AIN-93G diets containing prednisone at 5, 15, or 50 mg/kg diet which span human equivalent oral doses (HED) currently considered to be low (PL; 5 mg/d HED), moderate (PM; 14 mg/d HED), or high (PH; 46 mg/d HED), respectively. At 8 wk of age, mice were intranasally instilled with either saline vehicle or 1 mg cSiO<sub>2</sub> once weekly for 4 wk. The experimental plan was to 1) terminate one cohort of mice (n=8/group) 14 wk after the last cSiO<sub>2</sub> instillation for pathology and autoimmunity assessment and 2) to maintain a second cohort (n=9/group) to monitor glomerulonephritis development and survival. Mean blood concentrations of prednisone's chief active metabolite, prednisolone, in mice fed PL, PM, and PH diets were 27, 105, 151 ng/ml, respectively, which are consistent with levels observed in human blood ≤ 12 h after single bolus treatments with equivalent prednisone doses. Results from the first cohort revealed that consumption of PM but not PL diet significantly reduced cSiO<sub>2</sub>-induced pulmonary ectopic lymphoid structure formation, nuclear-specific AAb production, and inflammation/autoimmune gene expression in the lung, splenomegaly, and glomerulonephritis in the kidney. Relative to GC-associated toxicity, PM but not PL diet elicited muscle wasting, but these diets did not affect bone density or cause glucosuria. Importantly, neither PM nor PL diet influenced latency of cSiO<sub>2</sub>-accelerated death. PH-fed mice in both cohorts displayed robust GC-associated toxicity including body weight loss, reduced muscle mass, and hyperglycemia 7 wk after the final cSiO<sub>2</sub> instillation requiring their early removal from the study. Taken together, our results demonstrate that while moderate doses of prednisone can reduce certain pathological endpoints of cSiO<sub>2</sub>-induced autoimmunity in lupus-prone mice, these ameliorative effects come with unwanted GC toxicity and, crucially, none of these three doses extended survival time.</p>
IAA/CSIC Temperature and CO2 density profiles in Mars Year 34 retrieved from the 1st year of NOMAD/TGO solar occultation observations [dataset]
<p>Dataset associated to manuscript 2022JE007278, "Martian atmospheric temperature and density profiles during the 1st year of NOMAD/TGO solar occultation measurements", submitted on Feb 28th, 2022, to Journal of Geophysical Research - Planets (AGU) for the Special Issue "ExoMars Trace Gas Orbiter: One Martian Year of Science".</p> <p>Format and Number of datafiles: 1 README.txt and 1 tar file containing 325 ASCII files, one for each retrieved NOMAD scan. Each of these files contains one vertical profile of 7 parameters: altitude (km), Temperature in the last iteration (K), atmospheric pressure (mb), Temperature of First Guess (K), pressure of First Guess (mb), Temperature retrieval error (K) and diagonal element fo the Averaging Kernel matrix at that tangent altitude (normalized to 0-1). Also, the header of each file contains extra info, like the NOMAD "internal" data filename, and the ranges in latitude, longitude, Local time, Solar Longitude, tangent heights observed, and Line-of-Sight shift needed to obtain a good fit, together with the number of altitudes in the retrieval vector (usually around 100 km). See README file for more details.<br> </p>
Data for: Connecting voice profiling to genomics
<p>This dataset contains a graph-based path-finding algorithm to detect chainlink genes for voice chains that connect the genes in chromosomal microdeletion regions to the FOXP2 gene. Instructions are within multiple README files included with the package. The code is set up to be used on Linux platforms.</p>
Search Strategies for Gene Expression Profiling Tests
<p>The dataset includes the complete, reproducible search strategies for all literature databases searched during this project. The Endnote file contain all citations considered for inclusion in the review.</p>
Rapid pathogen identification in aqueous humor samples by combining Fc-MBL@Fe3O4 enrichment and MALDI-TOF MS profiling
<p>Prompt clinical diagnosis and antimicrobial therapy are key to managing infective endophthalmitis. The small volume of aqueous humor, low bacterial counts, and empirical medication by physicians make existing diagnostic methods time-consuming and imprecise. Here, we investigated the feasibility of combining Fc-MBL@Fe3O4 enrichment with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling to identify pathogens in aqueous humor. Aqueous humor aspirated from freshly enucleated porcine eyes was inoculated with different inocula of <em>Staphylococcus aureus</em> (<em>S. aureus</em>), <em>Staphylococcus </em><em>epidermidis</em> (<em>S. epidermidis</em>), and <em>Klebsiella pneumoniae</em> (<em>K. pneumoniae</em>). We performed identification directly in aqueous humor samples and after short-term culture of micro-LB broth. Aqueous humor endophthalmitis samples were enriched with Fc-MBL@Fe3O4 and analyzed with MALDI-TOF MS. The identification time and minimum bacterial concentration required for identification were determined. The enrichment efficiency of Fc-MBL@Fe3O4 for different bacteria was > (87.5±5.0)%. The objects of direct identification include live bacteria and bacteria treated with antibiotics, which can be completed within 1.5 hours. The minimum number of bacteria needed for positive identification was 2.20×10<sup>6 </sup>CFU. For micro-LB broth culture, the identification of bacteria can be completed within 6.5-9.5 h for aqueous humor samples with an initial bacterial count of tens to hundreds.</p>
Clustering of psychological profiles of primary school pupils
<p>Traditionally, arbitrary psychological research on different types of student activities uses certain sets of tests that reflect different states of students. These states are defined on the basis of certain criteria, the values of which are usually reflected by numerical scales with different intervals. Table 1 provides a list of these profiles and their factors, evaluation criteria with corresponding scales. Table 2 presents generalized results of testing of primary school pupils of the 2nd grade. <br> Due to the fact that the whole study is implemented on the basis of certain psychological profiles, which we also interpret as hyperproperties, in our case they are the receptors. <br> So the psychological profile of school motivation as a hyper-property defines five receptors, namely: <br> school motivation_high level <br> school motivation_good school motivation <br> school motivation_positive attitude to school<br> school motivation_low school motivation <br> school motivation_negative attitude to school<br> The protocol of cluster formation with receptor names is given in the file result of clustering.rtf</p> <p>Традиційно довільне психологічне дослідження різних видів діяльності учнів використовує певні набори тестів, які відображають різні стани учнів. Ці стани визначаються на основі певних критеріїв, значення яких звичайно відображаються числовими шкалами з різними інтервалами. вказані критерії оцінювання можуть бути проінтерпретовані як відповідні властивості учнів, що мають різні рівні прояву в їх діяльності. У табл. 1 наведено перелік цих профілів та їх фактори, означено критерії їх оцінювання з відповідними шкалами. У табл.2 наведені узагальнені результати тестування молодших учнів 2-го класу. <br> У зв’язку з тим, що усе дослідження реалізується на основі певних психологічних профілів, які ми ще й інтерпретуємо як гіпервластивості, у нашому випадку рецепторами є саме вони. <br> Так психологічний профіль school motivation, як гіпервластивість визначає п’ять рецепторів, а саме: <br> school motivation_high level <br> school motivation_good school motivation <br> school motivation_positive attitude to school<br> school motivation_low school motivation <br> school motivation_negative attitude to school<br> Протокол утворення кластерів з іменами рецепторів наведено в файлі result of clustering.rtf</p> <p> </p> <p> </p>
Gut metabolome and cytokine profiling of MSM prior to and following HIV seroconversion
<p>Alterations in the gut microbiome have been associated with HIV infection, but the relative impact of HIV versus other factors on the gut microbiome has been difficult to determine in cross-sectional studies. To address this, we examined the gut microbiome, serum metabolome, and cytokines longitudinally within individuals before and after HIV seroconversion. We identified few changes in the microbiome following HIV infection, but greater differences including decreased Bacteroides were seen between pre-HIV infection visits compared to matched controls. Those who acquired HIV also had elevated inflammatory cytokines and bioactive lipids prior to HIV acquisition compared to matched controls. Following HIV seroconversion, alterations in serum metabolites involving secondary bile acid metabolism and amino acid metabolism were observed. These data highlight the importance of understanding the role of the microbiome in HIV susceptibility.</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.