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2,084 results for “course”
Zebrafish embryos time-course, M&Z 5'UTRs cfl1l
<p>This Zenodo file contains data for the maternal and zygotic 5′ UTR-cfl1l-sfGFP mRNA reporters. Data consists of raw microscopy images of embryos, as well as csv files with quantification of relative sfGFP expression data (normalized to a dextran dye control) and png files depicting ROIs used for quantification presented in Figure 7 of Reimão-Pinto et al., Dev Cell, 2024.</p> <p>Embryos were injected with 1 nL of an injection mix directly into the cell at the 1-cell stage with a microinjection needle (Sutter Instruments) and allowed to develop in standard conditions. For single-reporter injections, 40pg 5′ UTR-sfGFP test reporter were co-injected with 2 ng fluorescent red dextran dye (D1868, Invitrogen) as injection control per embryo. Embryos were collected at the desired developmental stage and placed on a custom-made agarose mold with squared indents for placing and aligning the embryos. For fluorescence intensity quantification, zebrafish embryo images were acquired using an upright ZEISS Axiozoom coupled to an Axiocam 503 color/mono digital camera (14-bit depth) in black & white color mode with fixed laser power (red laser power 85% and 300 ms exposure; green laser power 65% and 300 ms exposure), fixed zoom and fixed exposure time for red mRF12 (590/612) and green AF488 (493/517) channels. Two rounds of single-reporter injections (embryos from two different clutches) were performed for fluorescence intensity quantifications.</p> <p>Images were quantified using Fiji (Image J) using a macro for automated thresholding and channel fluorescence intensity measurement. For each image, the script automatically segments the image based on red channel intensity (control dextran dye) using FIJI’s auto thresholding tool (RenyiEntropy) and outputs csv files with mean fluorescence intensities of red and green channels for that region of interest (and a small invariant region for background correction). The mean fluorescence values outputted were then used for calculating normalized mean intensity ratios (sfGFP/dextran). A total of 25 embryos per injection round were quantified, for a total of 50 embryos per time-point, per reporter. This excel contains normalized fluorescence intensity values calculated. More embryos were quantified than the ones included in the analysis (due to unequal number of embryos imaged per experiment, we decided to consider a fixed number of 25 per reporter injection). Some embryos were not considered for normalized intensity calculations due to improper automatic segmentation (e.g. due to the presence of a background dirt spot that is recognized as "signal"), due to precipitation of the dextran dye in the embryo's chorion or due to improper embryo development resulting from injury from injection. All images acquired are available for inspection. The FIJI macro for automated segmentation and ROI intensity measurements are also provided in the Mendeley Repository associated to the study.</p>
Spectrum, time course, stages, and a proposal for the diagnosis of histamine intolerance in general practice: A Nonrandomized, Quasi-Experimental Study - Supplementary material 1 and supplementary material 2 for "Spectrum, time course, stages, and a proposal for the diagnosis of histamine intolerance in general practice: A Nonrandomized, Quasi-Experimental Study"
<p><span>File name: Supplementary material 1. All data.xls</span></p> <p><span>Title of data: Questionnaire, all patients’ answers. Number of patient-doctor meetings with upper respiratory symptoms in primary care</span></p> <p><span>Description of data: The administered questionnaires (first/initial and second/post-diet). All patients’ answers. Number of patient-doctor meetings 01.09.2021-27.09.2024. with upper respiratory symptoms in primary care.</span></p> <p><span> </span></p> <p><span>File name: Supplementary material 2. Educational material and proposed questionnaire.doc</span></p> <p><span>Title of data: Proposed questionnaire for histamine intolerance in primary care. Educational material for patients with histamine intolerance</span></p> <p><span>Description of data: Proposed questionnaire for HIT in primary care. Educational material for patients to help establish </span><span>cause-and-effect relationships between their meals and their experienced symptoms. Food-symptom diary.<span><br></span></span></p>
Data from "Bending the course of evolution: how mutualistic interactions affect macroevolutionary dynamics of diversification in mimetic Ithomiini butterflies"
<p>Data and codes for the analyses from Chazot et al. "Bending the course of evolution: how mutualistic interactions affect macroevolutionary dynamics of diversification in mimetic Ithomiini butterflies". Check README for more information about the files. </p>
Supplementary material S24: Time course of the loudest Varroa jolting pulse compared to that of a honeybee colony and single bee individual.
<p>Time course of the loudest <em>Varroa </em>jolt on brood-comb with the signal from the full colony and a single bee. The signal seen here in each panel is the integral of the magnitude of acceleration with respect to time. The background vibration that is inherent to the room was calculated and subtracted from this data. The loudest jolt (red) is here compared to the signal of a single bee (black) and the vibrations of the full colony at low and high signal (black). High signal is captured when the frame containing the accelerometer is empty of brood. Low signal is captured when the frame is fully loaded with brood and/or honey. The whooping signal (panel a) was captured during a period of high signal.</p>
A novel UPLC-MS metabolomic analysis-based strategy to monitor the course and extent of iPSC differentiation to hepatocytes
<p>ms2 raw data, peak tables generated in Quantitative Analysis Software from Agilent and Matlab functions for QC-SVRC, data clean-up and analysis for the publication with title "Monitoring the differentiation of iPSC to hepatocytes by means of UPLC-MS metabolomics".</p>
Sample ERA5 Climate Reanalysis Data for UW Geospatial Data Analysis Course
<p>Used for Module 09: https://uwgda-jupyterbook.readthedocs.io/en/latest/modules/09_NDarrays_xarray_ERA5/</p> <p>Generated using Copernicus Climate Change Service information [2022]<br> Original license: https://cds.climate.copernicus.eu/api/v2/terms/static/licence-to-use-copernicus-products.pdf</p>
Reproductive strategies affect telomere dynamics across the life course
<p>Because parental care has a heritable basis, the benefits of receiving increased parental provisioning early in life are genetically linked to the costs of providing increased parental provisioning at adulthood. Reproductive strategies thus result in distinct cost-benefit syndromes across the life course that may shape individual health and ageing trajectories. Here we used an artificial selection approach in Japanese quail (<em>Coturnix japonica</em>) to test how reproductive strategies affect telomere length, a biomarker of somatic state, at different life stages. We show that males, but not females, from lines selected for low maternal investment (i.e. developing in a relatively small egg) had shorter telomeres at birth. These patterns were still weakly present at the end of the juvenile growth period. In contrast, significantly shorter telomeres were found in reproductively active adult birds from the high investment lines, suggesting that telomere attrition was accelerated in these individuals once they had become reproductively active. Our study shows that reproductive strategies differentially affect telomere dynamics across the life course, highlighting the role of cross-generational constraints in shaping individual ageing trajectories. </p>
Training course materials: Introduction to Remote Sensing of Water Quality in Lakes
<p>Dataset including ESA Sentinel-2 MSI and Sentinel-3 OLCI L1B scenes (L1B), atmospherically corrected reflectance products (C2RCC), image subsets, and intermediate water quality products from the Copernicus Land Service and ESA Lakes_cci processing chain <em>Calimnos. </em>Data are in support of a recorded course introducing the theoretical and practical basis for water quality observation of lakes through remote sensing. See https://monocle-h2020.eu/Resources/Training</p> <p>The data package contains the following:</p> <p><strong>input_data.zip </strong>- unprocessed (L1B / L1C) satellite scenes of MSI and OLCI instruments over the Razelm/Sinoe lagoon and Black Sea</p> <p><strong>Output_S3_OLCI.zip - </strong>all outputs derived from the Sentinel-3 OLCI scene, including C2RCC and <em>Calimnos </em>(including POLYMER atmospheric correction and biogeochemical estimates as in the Lakes_cci)</p> <p><strong>Output_S2_MSI_Full_Scene_C2RCC.zip</strong> - atmospherically corrected (C2RCC algorithm) full Sentinel-2 MSI scene</p> <p><strong>Output_S2_MSI_Subset_C2RCC.zip </strong>- subset of Sentinel-2 MSI scene and atmospherically corrected results (C2RCC algorithm) </p> <p><strong>Output_S2_MSI_Calimnos_PML.zip </strong>- subset of Sentinel-2 MSI scene atmospherically corrected using POLYMER and biogeochemical estimates, using <em>Calimnos </em>as in the Copernicus Land Service. </p>
Taking up and terminating leisure-time physical activity over the life course: The role of life events in the familial and occupational life domains
<p>Dataset used for the analyses in the following publication:</p> <p>Lenze, L., Klostermann, C., Lamprecht, M. & Nagel, S. (2021). Taking up and terminating leisure-time physical activity over the life course: The role of life events in the familial and occupational life domains. <em>International Journal of Environmental Research and Public Health</em>, <em>18</em>, 9809. https://doi.org/10.3390/ijerph18189809</p>
EMBL-EBI scRNA Bioinformatics T cell course 2022 (RESULTS)
<p>Repository: Final results for the projects developed during the 'Bioinformatics for T-Cell immunology' course (11-15/07/2022) at EMBL-EBI: [https://www.ebi.ac.uk/training/events/bioinformatics-t-cell-immunology-2022](https://www.ebi.ac.uk/training/events/bioinformatics-t-cell-immunology-2022)</p> <p>Official website: [https://elolab.github.io/Bioinfo_Tcell_projects_22](https://elolab.github.io/Bioinfo_Tcell_projects_22)</p> <p>Maintainer: [Elo lab](https://elolab.utu.fi)</p> <p>Contact: **António Sousa** ([ENLIGHT-TEN+](http://www.enlight-ten.eu) PhD student at the [Medical Bioinformatics Centre](https://elolab.utu.fi), TBC, University of Turku & Åbo Akademi)</p> <p>Last update: 07/07/2022</p> <p> </p> <p><br></p> <p> </p> <p>---</p> <p> </p> <p><br></p> <p> </p> <p>### Projects</p> <p> </p> <p>This repository hosts the results related with three standalone/independent data analysis projects examples using publicly available data generated and published elsewhere properly referenced below:</p> <p> 1. _Integration of single-cell data from patients developing arthritis arAE under ICI_<br> <br> + _publication_: [Kim et al., 2022](https://www.nature.com/articles/s41467-022-29539-3)<br> <br> + _data_: GEO [GSE173303](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE173303)<br> <br> + _R markdown notebook_: `01_integration_arthritis_arAE_ICI.Rmd`<br> <br> + _vignette_: [01_integration_arthritis_arAE_ICI.html](https://elolab.github.io/Bioinfo_Tcell_projects_22/pages/01_integration_arthritis_arAE_ICI.html)<br> <br> + _results_ (_in this repository_): GSE173303.tar.gz<br> <br> 2. _Fine-grained clustering of single-cell data of melanoma immune/stroma cells_<br> <br> + _publication_: [Jerby-Arnon et al., 2018](https://www.sciencedirect.com/science/article/pii/S0092867418311784?via%3Dihub)<br> <br> + _data_: GEO [GSE115978](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE115978)<br> <br> + _R markdown notebook_: `02_clustering_seurat_vs_iloreg.Rmd`<br> <br> + _vignette_: [02_clustering_seurat_vs_iloreg.html](https://elolab.github.io/Bioinfo_Tcell_projects_22/pages/02_clustering_seurat_vs_iloreg.html)</p> <p> + _results_ (_in this repository_): GSE115978.tar.gz</p> <p> 3. _Differential gene expression of stimulated CD4+ T single-cell data with single-cell and pseudobulk methods_<br> <br> + _publication_: [Cano-Gamez et al., 2020](https://www.nature.com/articles/s41467-020-15543-y)<br> <br> + _data_: [www.opentargets.org](https://www.opentargets.org/projects/effectorness)<br> <br> + _R markdown notebook_: `03_pseudobulks_dge_rots_cd4_act.Rmd`<br> <br> + _vignette_: [03_pseudobulks_dge_rots_cd4_act.html](https://elolab.github.io/Bioinfo_Tcell_projects_22/pages/03_pseudobulks_dge_rots_cd4_act.html)</p> <p> + _results_ (_in this repository_): CanoGamez_et_al_2020.tar.gz</p> <p> </p> <p><br></p> <p> </p> <p>---</p> <p> </p> <p><br></p> <p> </p> <p>### Disclaimer</p> <p> </p> <p>>All the data used along each project notebook was made public elsewhere by the respective authors and it has been properly referenced in each project (proper links were provided along each project notebook). The data and tools chosen to address the topic(s) of each project notebook reflect only my personal experience/knowledge and they were chosen to highlight particular aspects that I consider important. The results generated and explored within each project notebook have just the general purpose of give a brief introduction to the topics addressed in each project and do not aim, at any point, to reproduce or question neither the approaches taken nor the main findings published along with the data sets used herein.</p> <p> </p>
Questionnaire Response About Weight Of Criteria For Selecting Online Course Using Weighted Product Method
<p>This dataset is a response to a questionnaire that we already delivered to some Institut Teknologi Sepuluh Nopember Surabaya students. In this questionnaire, they chose which criteria are important for selecting an online course, and by that data, we can get the weights of each criteria and we use that data to do our Weighted Product selection.</p>
The time course of acclimation to the stress of triose phosphate use limitation
<p>Triose-phosphate utilization (TPU) limits the maximum rate at which plants can photosynthesize. However, TPU is almost never found to be limiting photosynthesis under ambient conditions for plants. This, along with previous results showing adaptability of TPU at low temperature, suggest that TPU capacity is regulated to be just above the photosynthetic rate achievable under the prevailing conditions. A set of experiments were performed to study the adaptability of TPU capacity when plants are acclimated to elevated CO<sub>2</sub> concentrations. Plants held at 1500 ppm CO<sub>2</sub> were initially TPU-limited. After 30 hours, they no longer exhibited TPU limitations, but they did not elevate their TPU capacity. Instead, the maximum rates of carboxylation and electron transport declined. A time course of regulatory responses was established. A step increase of CO<sub>2</sub> first caused PSI to be oxidized, but after 40 s, both PSI and PSII had excess electrons as a result of acceptor-side limitations. Electron flow to PSI slowed, and the proton motive force increased. Eventually, non-photochemical quenching reduced electron flow sufficiently to balance the TPU limitation. Over several minutes rubisco deactivated contributing to regulation of metabolism to overcome the TPU limitation.</p>
2d and 3d Drawing in Field Archeology Course
This exercise of photogrammetry was the base for the drawing of my final project for the online course taken at "Koré Formación Online en Patrimonio y Tecnología". The aim was to learn profesional techniques of graphic documentation used at an archeological excavation site. All materials for this exercise were provided at the online platform for the course. Source: Objaverse 1.0 / Sketchfab
Storyboard "Courses"
<p>This storyboard is inyended for elicitation of emphatic coordination</p>
Fig. 14 in On The Study Of Fauna (Macroinvertebrates, Fish, Amphibians, Reptiles, Birds And Mammals) Of The Lower Course Of Shokhdara River Valley In Pamir, Mountain Bodakhshan, Tajikistan
Fig. 14. Grey draft hamster.
Fig. 9 in On The Study Of Fauna (Macroinvertebrates, Fish, Amphibians, Reptiles, Birds And Mammals) Of The Lower Course Of Shokhdara River Valley In Pamir, Mountain Bodakhshan, Tajikistan
Fig. 9. Young individual of spotted whip snake, road kill, Sebzor village.
Fig. 8. N in On The Study Of Fauna (Macroinvertebrates, Fish, Amphibians, Reptiles, Birds And Mammals) Of The Lower Course Of Shokhdara River Valley In Pamir, Mountain Bodakhshan, Tajikistan
Fig. 8. N. tessellata specimen found near Shokhdara River.
Fig. 5. Caught Tibetian stone loach N in On The Study Of Fauna (Macroinvertebrates, Fish, Amphibians, Reptiles, Birds And Mammals) Of The Lower Course Of Shokhdara River Valley In Pamir, Mountain Bodakhshan, Tajikistan
Fig. 5. Caught Tibetian stone loach N. stoliczkai.
Fig. 11 in On The Study Of Fauna (Macroinvertebrates, Fish, Amphibians, Reptiles, Birds And Mammals) Of The Lower Course Of Shokhdara River Valley In Pamir, Mountain Bodakhshan, Tajikistan
Fig. 11. Grey thin-toed geckos registered within the study area.
Fig. 15 in On The Study Of Fauna (Macroinvertebrates, Fish, Amphibians, Reptiles, Birds And Mammals) Of The Lower Course Of Shokhdara River Valley In Pamir, Mountain Bodakhshan, Tajikistan
Fig. 15. Dr. Abdulnazarov with female of snow leopard in Pamir biological institute.
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.