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30,948 results for “Profile”
Neutrophil Profiles of Pediatric COVID-19 and Multisystem Inflammatory Syndrome in Children
<p>Code and data for the manuscript "Neutrophil Profiles of Pediatric COVID-19 and Multisystem Inflammatory Syndrome in Children" to be published in Cell Reports Medicine.</p> <p>Contains all code located at <a href="https://github.com/lasalletj/COVID_Neutrophils">https://github.com/lasalletj/</a><a href="https://github.com/lasalletj/Pediatric_COVID_MISC_Neutrophils">Pediatric_COVID_MISC_Neutrophils</a> as well as additional data files needed to run the code and supplementary materials for the manuscript.</p> <p>Any additional information required to reanalyze the data reported in this work paper is available from the Lead Contact, Lael Yonker (lyonker@mgh.harvard.edu) upon request.</p>
OMPS-NPP L2 LP USask Aerosol Extinction Vertical Profile swath daily V1.2
<p>The USask OMPS-LP L2 2D Aerosol v1.2 product provides stratospheric aerosol extinction retrievals performed at the University of Saskatchewan for the central slit of the Ozone Mapping and Profiler Suite Limb Profiler (OMPS-LP) instrument on the Suomi-NPP satellite. The two-dimensional retrieval algorithm accounts for variation in the along orbital track dimension, retrieving an entire orbit simultaneously instead of treating each image independently. Stratospheric aerosol is retrieved from approximately the thermal tropopause to 30 km on a 1 km grid with a vertical resolution of approximately 2 km, and is assumed to be sulfate aerosol following a log-normal particle size distribution.</p> <p>Each file contains data from the daylight portion of each orbit measured for a full day. Spatial coverage is global (-82 to +82 degrees latitude), and there are about 14.5 orbits per day, each has typically 160 profiles with an along orbital track sampling of 125 km. The files are written using NetCDF4.</p>
Reproductives signature revealed by protein profiling and behavioral bioassays in termite
<p>Proteins are known to be social interaction signals in many species in the animal kingdom. The aim of this project is to explore the potential role of cuticular polar compounds in reproductive recognition on termites. Cuticular polar fractions were extracted from reproductives and workers. These extracts were used for molecular profiling, top-down proteomics and tested in behavioral bioassays to measure behavioral response in termite.</p>
Romanian Higher Education Institutions with a Military Profile Index
<p>OpenAlex data scrape for all the Romanian Higher Education Institutions with a Military Profile, as per https://www.edu.ro/institutii%20inv_superior%20de%20stat%20militare (November 19, 2022 archived version: https://web.archive.org/web/20221119194032/https%3A%2F%2Fwww.edu.ro%2Finstitutii%2520inv_superior%2520de%2520stat%2520militare)</p>
Simultaneous profiling of histone modifications and DNA methylation via nanopore sequencing
<p>Datasets that contain a minimum of nanopore reads sufficient for hidden Markov model training and for evaluating the performance of our computational tool - nanoHiMe at simultaneously calling CpG and/or adenine methylation on individual nanopore reads.<em> Ecoli</em>_PCR_amplicons_100k.tgz, <em>Ecoli</em>_PCR_MSssI_100k.tar.gz and <em>Ecoli</em>_PCR_pA-Hia5_100k.tar.gz are used for training new parameters of the emission distributions of individual <em>k</em>-mers from DNA template without modification, with fully methylated CpGs, and with partially methylated adenines, respectively. nanoHiMe_H3K27me3.fast5.tgz are the nanopore sequencing reads from H3K27me3 nanoHiMe-seq experiments in GM12878 cells and used for evaluating the performance of nanoHiMe at jointly calling CpG and adenine methylation.</p>
Supplementary Data for 'A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA).'
<p>Supplementary Data for 'Castoldi, M., Schmidt, S., Benes, V., Noerholm, M., Kulozik, A.E., Hentze, M.W. and Muckenthaler, M.U., 2006. A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA). <em>Rna</em>, <em>12</em>(5), pp.913-920.'</p>
CIMMYT spring wheat product profiles 2022
<p>Detailed target product profiles for CIMMYT spring wheat breeding 2022. The product profiles are the trait specifications for selection and release of material from the five CIMMYT spring wheat breeding pipelines: <em>(1) Hard white, optimum environment; (2) Hard white, heat tolerant, early maturity; (3) Hard white, drought tolerant, normal maturity; (4) Hard white, drought tolerant, early maturity </em>and <em>(5) Hard white/red, high rainfall</em>. These five pipelines target eight global market segments in Latin America and the Caribbean, East Africa, Central Asia, West Asia and North Africa and South Asia. Product profiles are defined as in the Excellence in Breeding Toolbox for “product design and management” (https://excellenceinbreeding.org/toolbox/tools/cgiar-seed-product-market-segment-database).</p> <p>Traits include grain and processing traits, nutritional enhancement, agronomic and disease traits. For spring wheat, no specific production, multiplication, or unique product registration traits apply in 2022 so these fields in the product profiles are marked as not applicable (NA). Traits are listed by category and assigned a measurement scale which is used in selection along with a minimum score. The traits are differentiated by requirement: either as “essential” or “nice to have” as well as the requirement for improvement (vs. maintenance). Indication of a trait as a threshold trait indicates it is a requirement for release of material from the breeding pipeline.</p>
CIMMYT winter wheat product profiles 2022
<p>Detailed target product profiles for CIMMYT winter wheat breeding 2022. The product profiles are the trait specifications for selection and release of material from the two CIMMYT winter wheat breeding pipelines: (<em>1) Hard winter, cold tolerant & irrigated, normal maturity</em> (denoted HWW-CTI-NM) and <em>(2) Hard winter, cold tolerant, drought tolerant, normal maturity </em>(denoted HWW-CTD-NM). Product profiles are defined as in the Excellence in Breeding Toolbox for “product design and management” (https://excellenceinbreeding.org/toolbox/tools/cgiar-seed-product-market-segment-database).</p> <p>Traits include grain and processing traits, nutritional enhancement, agronomic and disease traits. For winter wheat, no specific production, multiplication, or unique product registration traits apply in 2022 so these fields in the product profiles are marked as not applicable (NA). Traits are listed by category and assigned a measurement scale which is used in selection along with a minimum score. The traits are differentiated by requirement: either as “must have” or “nice to have” as well as the requirement for improvement (vs. maintenance). Indication of a trait as a threshold trait indicates it is a requirement for release of material from the breeding pipeline.</p>
CIMMYT durum wheat product profiles 2022
<p>Detailed target product profiles for CIMMYT durum wheat breeding 2022. The product profiles are the trait specifications for selection and release of material from the three CIMMYT durum wheat breeding pipelines: (<em>1) Amber durum, optimum environment, normal maturity (AD-OW-NM)</em>; <em>(2) Amber durum, drought tolerant & input-responsive normal maturity (AD-DTIR-NM) </em>and <em>(3) Amber durum, heat tolerant, early maturity (AD-HT-EM). </em>Product profiles are defined as in the Excellence in Breeding Toolbox for “product design and management” (https://excellenceinbreeding.org/toolbox/tools/cgiar-seed-product-market-segment-database).</p> <p>Traits include grain and processing traits, nutritional enhancement, agronomic and disease traits. For winter wheat, no specific production, multiplication, or unique product registration traits apply in 2022 so these fields in the product profiles are marked as not applicable (NA). Traits are listed by category and assigned a measurement scale which is used in selection along with a minimum score. The traits are differentiated by requirement: either as “must have” or “nice to have” as well as the requirement for improvement (vs. maintenance). Indication of a trait as a threshold trait indicates it is a requirement for release of material from the breeding pipeline.</p>
Dataset used for the study of "Validation of Aeolus wind profiles using ground-based lidar and radiosonde observations at La Réunion Island and the Observatoire de Haute Provence"
<p>Datasets used to create the figures and statistical study in "Validation of Aeolus wind profiles using ground-based lidar and radiosonde observations at La Réunion Island and the Observatoire de Haute Provence" </p>
Datasets of the manuscript "Rational design of profile HMMs for sensitive and specific sequence detection with case studies applied to viruses, bacteriophages, and casposons"
<p><strong>DATASETS</strong></p> <p>Rational design of profile HMMs for sensitive and specific sequence detection with case studies applied to viruses, bacteriophages, and casposons</p> <p>Liliane S. Oliveira, Alejandro Reyes, Bas E. Dutilh and Arthur Gruber<sup>*</sup></p> <p>* Correspondence: <a href="mailto:argruber@usp.br">argruber@usp.br</a> (AG); Tel. +55 11 3091 7274</p> <p> </p> <p>Here we provide different data of <em>Microviridae</em>, <em>Flavivirus</em> and casposons used throughout the work:</p> <ul> <li>Microviridae folder <ul> <li>conserved_HMMs – profile HMMs constructed with TABAJARA in Conservation mode for <em>Microviridae</em></li> <li>discriminative_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for <em>Microviridae</em></li> <li>sequences – different sequence datasets and respective multiple sequence alignments <ul> <li>Microviridae_113-seq_training_set.fasta - 113 VP1 sequences covering diversity of the <em>Microviridae</em> family</li> <li>Microviridae_113-seq.aln – multiple sequence alignment of the 113-protein dataset</li> <li>Microviridae_1836-seq_testset.fasta - 1,836 sequence dataset covering 1,836 sequences of the major capsid protein (VP1) comprising 501 <em>Alpavirinae</em> sequences, 1,040 <em>Gokushovirinae</em> sequences and 295 <em>Pichovirinae</em> sequences</li> <li>Microviridae_1866-seq.aln - multiple sequence alignment of the 1,866-protein <em>Microviridae</em> dataset used in the experiment of Figure 4</li> </ul> </li> </ul> </li> <li>Flavivirus folder <ul> <li>conserved_HMMs – profile HMMs constructed with TABAJARA in Conservation mode for <em>Flavivirus</em></li> <li>discriminative_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for <em>Flavivirus</em> <ul> <li>full-length – models constructed from full-length protein sequences</li> <li>short - models constructed from selected short alignment blocks of the protein sequences</li> </ul> </li> <li>sequences – different sequence datasets and respective multiple sequence alignments <ul> <li>Flavivirus_127-seq_training_set.fasta - 127 polyprotein sequences covering species diversity of the genus <em>Flavivirus</em></li> <li>Flavivirus_127-seq.aln – multiple sequence alignment of the 127-protein dataset</li> <li>Flavivirus_6364-seq_testset.fasta - 6,364 sequence dataset covering species diversity of <em>Flavivirus</em>, including 3,919 of dengue virus (DENV), 327 of Zika virus (ZIKV), 63 of yellow fever virus (YFV), and the remaining 2,055 sequences covering other available flaviviruses</li> <li>Flavivirus_6364-seq.aln - multiple sequence alignment of the 6,364-protein <em>Flavivirus</em> dataset</li> </ul> </li> </ul> </li> <li>Casposons folder <ul> <li>casposon_generic_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for the generic detection of all casposons and discrimination from CRISPRs.</li> <li>casposon_family_discriminative_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for the specific discrimination among casposon families and from CRISPRs.</li> <li>sequences – different sequence datasets and respective multiple sequence alignments <ul> <li>casposons_crisprs.fasta – 106 Cas1 <em>bona fide</em> sequences derived from 52 CRISPRs and 54 casposons</li> <li>casposon_family_discrimination.aln - multiple sequence alignment of 52 <em>bona fide</em> CRISPR and 54 casposon sequences, with appropriate nomenclature to run TABAJARA for the discrimination of each casposon family.</li> <li>casposons_crisprs_discrimination.aln - multiple sequence alignment of 52 <em>bona fide</em> CRISPR and 54 casposon sequences, with appropriate nomenclature to run TABAJARA for discrimination of CRISPRs and casposons.</li> </ul> </li> </ul> </li> </ul>
IODP Expedition 376 Laser height profile (section half)
<p>Height profile data were measured on the Section Half Multisensor Logger (SHMSL) by a rangefinding laser and recorded in uncorrected height units in millimeters in CSV files.</p>
Single-cell profiling identifies ACE+ granuloma macrophages as a non-permissive niche for intracellular bacteria during persistent Salmonella infection
<p>Macrophages mediate key antimicrobial responses against intracellular bacterial pathogens, such as <em>Salmonella enterica</em>. Yet, they can also act as a permissive niche for these pathogens to persist in infected tissues within granulomas, which are immunological structures comprised of macrophages and other immune cells. We apply single-cell transcriptomics to investigate macrophage functional diversity during persistent <em>Salmonella</em> <em>enterica</em> serovar Typhimurium (<em>S</em>Tm) infection in mice. We identify determinants of macrophage heterogeneity in infected spleens and describe populations of distinct phenotypes, functional programming, and spatial localization. Using a <em>S</em>Tm mutant with impaired ability to polarize macrophage phenotypes, we find that angiotensin converting enzyme (ACE) defines a granuloma macrophage population that is non-permissive for intracellular bacteria and their abundance anticorrelates with tissue bacterial burden. Disruption of pathogen control by neutralizing TNF is linked to preferential depletion of ACE<sup>+</sup> macrophages in infected tissues. Thus ACE<em><sup>+</sup></em> macrophages have limited capacity to serve as cellular niche for intracellular bacteria to establish persistent infection.</p>
Expression Profile of CD157 Reveals Functional Heterogeneity of Capillaries in Human Dermal Skin
<p>CD157 acts as a receptor, regulating leukocyte trafficking and the binding of extracellular matrix components. However, the expression pattern and the role of CD157 in human blood (BEC) and the lymphatic endothelial cells (LEC) of human dermal microvascular cells (HDMEC), remain elusive. We demonstrated constitutive expression of CD157 on BEC and LEC, in fetal and juvenile/adult skin, in situ, as well as in isolated HDMEC. Interestingly, CD157 epitopes were mostly localized on BEC, co-expressing high levels of CD31 (CD31<sup>High</sup>), as compared to CD31<sup>Low</sup> BEC, whereas the podoplanin expression level on LEC did not affect CD157. Cultured HDMEC exhibited significantly higher numbers of CD157-positive LEC, as compared to BEC. Interestingly, separated CD157<sup>-</sup> and CD157<sup>+</sup> HDMEC demonstrated no significant differences in clonal expansion in vitro, but they showed distinct expression levels of cell adhesion molecules, before and after cytokine stimulation in vitro. In particular, we proved the enhanced and specific adherence of CD11b-expressing human blood myeloid cells to CD157<sup>+</sup> HDMEC fraction, using an in vitro immune-binding assay. Indeed, CD157 was also involved in chemotaxis and adhesion of CD11b/c monocytes/neutrophils in prevascularized dermo-epidermal skin substitutes (vascDESS) in vivo. Thus, our data attribute specific roles to endothelial CD157, in the regulation of innate immunity during inflammation.</p> <p> </p>
Data for: High-throughput profiling of sequence recognition by tyrosine kinases and SH2 domains using bacterial peptide display
<p>Tyrosine kinases and SH2 (phosphotyrosine recognition) domains have binding specificities that depend on the amino acid sequence surrounding the target (phospho)tyrosine residue. Although the preferred recognition motifs of many kinases and SH2 domains are known, we lack a quantitative description of sequence specificity that could guide predictions about signaling pathways or be used to design sequences for biomedical applications. Here, we present a platform that combines genetically-encoded peptide libraries and deep sequencing to profile sequence recognition by tyrosine kinases and SH2 domains. We screened several tyrosine kinases against a million-peptide random library and used the resulting profiles to design high-activity sequences. We also screened several kinases against a library containing thousands of human proteome-derived peptides and their naturally-occurring variants. These screens recapitulated independently measured phosphorylation rates and revealed hundreds of phosphosite-proximal mutations that impact phosphosite recognition by tyrosine kinases. We extended this platform to the analysis of SH2 domains and showed that screens could predict relative binding affinities. Finally, we expanded our method to assess the impact of non-canonical and post-translationally modified amino acids on sequence recognition. This specificity profiling platform will shed new light on phosphotyrosine signaling and could readily be adapted to other protein modification/recognition domains.</p>
Dissolved trace metal depth profile concentrations from the North Pacific Ocean Gradients 3 (KM1906) spring 2019 cruise
<p>This dataset contains dissolved trace metal depth profiles collected in the North Pacific Ocean in spring of 2019 on the KM1906 Gradients 3 cruise (Chief Scientist E. Virginia Armbrust). The project was funded by the Simons Collaboration on Ocean Processes and Ecology Gradients program (SCOPE award 426570SP to SGJ). The samples were collected by trace metal clean rosette. Data were produced at the University of Southern California Marine Trace Elements Lab run by Prof. Seth G. John. Briefly, the metals were preconcentrated using an Elemental Scientific Inc. SeaFast automated robot, detected by Element 2 ICP-MS and quantified using isotope dilution as described in Hawco et al. 2020. <em>GCA</em> <a href="https://doi.org/10.1016/j.gca.2020.05.005">https://doi.org/10.1016/j.gca.2020.05.005</a>. All concentrations are dissolved (<0.2um SUPOR filter) and reported as nmol/L. </p>
dATASET RELATED TO ARTICLE "Complement Activation Profile in Myasthenia Gravis Patients: Perspectives for Tailoring Anti-Complement Therapy"
<p><strong>raw data derived by quantification of complement components and activation products in plasma samples of myasthenia gravis (MG) patients positive for anti-achr and anti-musk autoantibodies and healthy controls, using multiplex immunoassays and elisa</strong></p>
Fig. 2 in Eco-taxonomic profile of an iconic vermicomposter - the 'African Nightcrawler' earthworm, Eudrilus eugeniae (Kinberg, 1867)
Fig. 2. Eudrilus eugeniae: (a) ventral view of Qld specimen, (b) vasa deferentia unite to form the muscular euprostates ducting to the centre of the copulatory chamber (characteristic Y-shaped gland on rhs ducts to lhs), (c) 'spermathecal' aperture and combined oviduct (unravelled) to ovisac opposite saccular gland at junction of duct and 'ampulla' (ovary not shown), (d) prostomium, (e) calciferous glands, hearts and dorsal vessel, (f) dorso-lateral view of caudal segments narrowing to pygomere, (g) cocoon. BoXed are: Perrier's (1872: figs 27, 28, 30) figures of male organs – with penis both retracted and everted – plus an enlargement of a seta (his fig. 29 differs somewhat in its internal organ details); Michaelsen's (1892: fig. 10) figure of female organs also showing ovary "ov" (or ovisac?) on 12/13; plus Beddard's (1895: fig. 30) figure of male organs with glandular appendices to bursa copulatriX sometimes fused to form a "single horseshoe-shaped" appendiX neXt to what Eisen (1900: fig. 44) called the silk-producing "Y-shaped gland" (indicated as "Y-sg").
Fig. 3 in Eco-taxonomic profile of an iconic vermicomposter - the 'African Nightcrawler' earthworm, Eudrilus eugeniae (Kinberg, 1867)
Fig. 3. Distribution map from Michaelsen (1903: chart 1) (hash marks family distribution). Note that New Zealand was in error but other records outside its West African homeland are due mainly to human transportation and the worm's acclimatisation; early Caribbean and Latin American introductions possibly relate to the 16th – 19th century Atlantic slave trade.
An archive of net community production estimates derived from autonomous profiler observations at Ocean Station Papa
<p>This dataset contains an archive of marine net community production estimates for Ocean Station Papa, derived using autonomous profilers, including BGC-Argo floats and sea gliders. The archive contains data from the following original publications:</p> <ol> <li>Haskell, W. Z., Fassbender, A. J., Long, J. S., and Plant, J. N.: Annual Net Community Production of Particulate and Dissolved Organic Carbon From a Decade of Biogeochemical Profiling Float Observations in the Northeast Pacific, Global Biogeochemical Cycles, 34, 1–22, <a href="https://doi.org/10.1029/2020GB006599">https://doi.org/10.1029/2020GB006599</a>, 2020.</li> <li>Huang, Y., Fassbender, A. J., Long, J. S., Johannessen, S., and Bernardi Bif, M.: Partitioning the Export of Distinct Biogenic Carbon Pools in the Northeast Pacific Ocean Using a Biogeochemical Profiling Float, Global Biogeochemical Cycles, 36, <a href="https://doi.org/10.1029/2021gb007178">https://doi.org/10.1029/2021gb007178</a>, 2022.</li> <li>Pelland, N. A., Eriksen, C. C., Emerson, S. R., and Cronin, M. F.: Seaglider Surveys at Ocean Station Papa: Oxygen Kinematics and Upper-Ocean Metabolism, Journal of Geophysical Research: Oceans, 123, 6408–6427, <a href="https://doi.org/10.1029/2018JC014091">https://doi.org/10.1029/2018JC014091</a>, 2018.</li> <li>Plant, J. N., Johnson, K. S., Sakamoto, C. M., Jannasch, H. W., Coletti, L. J., Riser, S. C., and Swift, D. D.: Net community production at Ocean Station Papa observed with nitrate and oxygen sensors on profiling floats, Global Biogeochemical Cycles, 30, 859–879, <a href="https://doi.org/10.1002/2015GB005349">https://doi.org/10.1002/2015GB005349</a>, 2016.</li> <li>Yang, B., Emerson, S. R., and Bushinsky, S. M.: Annual net community production in the subtropical Pacific Ocean from in-situ oxygen measurements on profiling floats, Global Biogeochemical Cycles, 31, 728–744, <a href="https://doi.org/10.1002/2016GB005545">https://doi.org/10.1002/2016GB005545</a>, 2017.</li> </ol> <p> </p> <p><strong>Dataset description:</strong></p> <p>Separate Matlab (.mat) and NetCDF (.nc) files are provided for each original publication dataset. At minimum, each contains time (recorded as absolute days since 01 Jan 2000, 00:00:00), and time-explicit depth-integrated NCP. Additional fields include depth-resolved NCP, and water column depth (Plant et al., 2016; Pelland et al., 2018).</p> <p>Note that the Haskell et al. (2020) dataset (haskell20.mat, haskell20.nc) contains climatological NCP estimates. Accordingly, the time field represents the Year-day only. </p> <p>All NCP units are recorded in units of mmol O2/m2/d (depth-integrated) or mmol O2/m3/d (depth-resolved).</p> <p>Additional information on each dataset is contained within the data files. Additional processing information is contained in Izett et al. (under review).</p> <p> </p> <p><strong>The data were compiled in: </strong></p> <p>Izett, R. W., Fennel, K., Stoer, A. C., and Nicholson, D. P. Reviews and syntheses: Expanding the global coverage of gross primary production and net community production measurements using BGC-Argo floats, <em>Submitted to Biogeosciences. 2023</em>.</p> <p> </p> <p><strong>Please cite as:</strong></p> <p>Izett, R., Haskell, W., Huang, Y., Pelland, N., Plant, J., and Yang, B. 2023. An archive of net community production estimates derived from autonomous profiler observations at Ocean Station Papa. Database. Zenodo. doi: 10.5281/zenodo.7667521. Accessed on <em>DATE</em>. </p>
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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.