Find research datasets worth reusing

opencc-by-4.0Apr 2020View details →

NEMO ORCA05 FOCI Test Data

This is nine years of monthly NEMO data that is very similar to data written by the Ocean component of FOCI from GEOMAR. Feel free to use it for development and testing but be aware that these data are in no way suitable for scientific use. Data prepared by Jan Harlaß and Willi Rath (2020)

opencc-by-4.0Aug 2022View details →

Image data for bioRxiv article named: mtFociCounter - Reproducible, open source and quantitative single-cell analysis of mitochondrial nucleoids and other foci

Raw imaging data to reproduce and test the findings of the bioRxiv article: mtFociCounter - Reproducible, open source and quantitative single-cell analysis of mitochondrial nucleoids and other foci. It contains data from three imaging days and 2 or three technical replicates on each day.

opencc-by-4.0Jun 2021View details →

FOCI model output used in the study by Ivanciu et al. - Twenty-first century Southern Hemisphere impacts of ozone recovery and climate change from the stratosphere to the ocean

This dataset comprises the output from simulations with the coupled climate model FOCI (Flexible Ocean and Climate Infrastructure, Matthes et al., 2020) used in the analysis presented in the study by Ivanciu et al., 2021 “Twenty-first century Southern Hemisphere impacts of ozone recovery and climate change from the stratosphere to the ocean”. Four ensembles of three simulations each were performed: FixODS (II012, II014, II016), FixGHG (II013, II015, II017), INTERACT_O3 (SW128, II010, II011) and PRESC_O3 (JH027, II037, JH039). A detailed description of the simulations can be found in the above-mentioned manuscript.

opencc-by-4.0Sep 2022View details →

CESM and FOCI model data as supplementary data for Climate Index Collection based on model data (CICMoD)

The Community Earth System Model (CESM) and the Flexible Ocean and Climate Infrastructure (FOCI) are both fully-coupled, global climate models that provide state-of-the-art computer simulations of the Earth's past, present, and future climate states. This dataset contains results from control runs with conditions of year 1850 without additional external forcing for 1000 years and 999 years for FOCI and CESM, respectively. Included features are: <ul> <li>sea surface temperature</li> <li>surface air temperature</li> <li>sea level pressure</li> <li>sea surface salinity</li> <li>geopotential height (500mb)</li> <li>precipitation</li> </ul>

opencc-by-4.0May 2022View details →

FOCI model output used in the study by Ivanciu et al. - On the ridging of the South Atlantic Anticyclone over South Africa: the impact of Rossby wave breaking and of climate change

This dataset contains the model output used in the analysis presented in the study by Ivanciu et al., 2022 - On the ridging of the South Atlantic Anticyclone over South Africa: the impact of Rossby wave breaking and of climate change. Four ensembles of three simulations each were performed with the global coupled climate model FOCI (Flexible Ocean and Climate Infrastructure, Matthes et al., 2020). Details about the ensembles can be found in the above-mentioned publication. The files containing "past" in their name belong to the ensemble "PAST", the files containing "future" in their name belong to the ensemble "FUTURE", the files containing "future_GHG" in their name belong to the ensemble "GHG" and the files containing "future_Ozone" in their name belong to the ensemble "OZONE" from the publication.

opencc-by-4.0Feb 2019View details →

Confocal microscopy of gH2AX and 53BP1 DNA repair foci of cells exposed to gamma-irradiation, pt. 2/3

Summary Dataset of confocal microscopy data of cells exposed to gamma-irradiation and immunostained with gH2AX and 53BP1. <ul> <li>Part 1/3: Head and neck primocultures immunostained with gH2AX/53BP1, Testing dataset. DOI <a href="https://doi.org/10.5281/zenodo.2564980">10.5281/zenodo.2564980</a></li> <li>Part 2/3 (this dataset): U-87 and NHDF Cells exposed to 1-4 Gy confocal microscopy data of head and neck tumor primocultures immunostained with gH2AX/53BP1. Testing dataset. DOI <a href="https://doi.org/10.5281/zenodo.2572450">10.5281/zenodo.2572450</a>. 174 TIFFs</li> <li>Part 3/3: training dataset for nuclei and gH2AX foci with ground truth annotation masks, head and neck primocultures (head and neck non-tumor and spinocellular tumor cells). DOI <a href="https://doi.org/10.5281/zenodo.2576241">10.5281/zenodo.2576241</a>. 150 TIFFs for nuclei learning incl 150 png nuclei masks + 99 TIFFs for DNA repair foci training</li> <li>Code: the code is available at <a href="https://github.com/tomasvicar/LearnFoci">https://github.com/tomasvicar/LearnFoci</a></li> </ul> Materials and methods Dataset Following cells were used: (1) patient primocultures of patients with  spinocellular head and neck tumors (histologically verified tumor and tumor-adjacent tissues), isolation protocol descibed in Svobodova et al, 2017, (2) primary glioblastoma cell line U-87 (ATCC HTB-14, LGC Standards, United Kingdom), (3) primary normal human dermal fibroblasts (NHDF, PromoCell, Hedelberg, Germany) isolated from the dermis of juvenile foreskin or adult skin. The study was conducted in accord with the Helsinki Declaration of 1964 and all subsequent revisions thereof. It was approved by the ethical committee of St. Anne’s Faculty Hospital, Brno. Primoculture cells were cultivated in Pen/Strep antibiotic solution (PAA Laboratories GmbH, Austria) in RPMI-1640 medium with 10% FBS (Biochrom, USA) at 37 °C and 50% CO2 in humidified atmosphere up to 50% confluence. U-87 were grown in Eagle's MEM with 10% FBS. Gamma irradiation The cells were irradiated at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic in a following schemes: (a) patient-derived primoculture was irradiated with a single dose of 2 Gy (D = 1 Gy/min) of gamma-rays (60Co, Chisostat, Chirana, CR) , (b) U-87 and NHDF cells were irradiated with doses 1, 2, and 4 Gy (D = 1 Gy/min). Cells were irradiated in RPMI 1640 medium (37 °C, normal atmosphere). Confocal microscopy of gammaH2AX and 53BP1 foci immunodetection was consequently performed. Fluorescent staining DNA double strand breaks (DSBs) were quantified in different periods of time post-irradiation (30 min, 8h and 24h post irradiation) by means of $\gamma$H2AX and 53BP1 foci immunodetection combined with  confocal microscopy. For details see \cite{falk2007chromatin}. Confocal microscopy The microscopy of samples was performed at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic. Leica DM RXA microscope (equipped with DMSTC motorized stage, Piezzo z-movement, MicroMax CCD camera, CSU-10 confocal unit and 488, 562, and 714 nm laser diodes with AOTF) was used for acquiring detailed cell images (100× oil immersion Plan Fluotar lens, NA 1.3). Total 50 Z slices was captured with Z step size 0.3 μm. File description all files are compressed hyperstack tiffs (50 Z slices and 3 fluorescent channels, XYCZ order), 100x magnification <ul> <li>Confocal_NHDF_cells_IR_1-4Gy.zip: Human fibroblast NHDF cell line, exposed to gamma irradiation doses 1, 2, and 4 Gy, 64 TIFFs</li> <li>Confocal_U-87_cells_IR_1-4Gy.zip: Human glioblastoma U-87 cell line, exposed to gamma irradiation doses 1, 2, and 4 Gy, 108 TIFFs</li> </ul>

opencc-by-4.0Feb 2019View details →

Confocal microscopy of gH2AX and 53BP1 DNA repair foci of cells exposed to gamma-irradiation, pt. 1/3

Summary Dataset of confocal microscopy data of cells exposed to gamma-irradiation and immunostained with gH2AX and 53BP1. <ul> <li>Part 1/3 (this dataset): Head and neck primocultures immunostained with gH2AX/53BP1, Testing dataset. DOI <a href="https://doi.org/10.5281/zenodo.2564980">10.5281/zenodo.2564980</a></li> <li>Part 2/3: U-87 and NHDF Cells exposed to 1-4 Gy confocal microscopy data of head and neck tumor primocultures immunostained with gH2AX/53BP1. Testing dataset. DOI <a href="https://doi.org/10.5281/zenodo.2572450">10.5281/zenodo.2572450</a>. 174 TIFFs</li> <li>Part 3/3: training dataset for nuclei and gH2AX foci with ground truth annotation masks, head and neck primocultures (head and neck non-tumor and spinocellular tumor cells). DOI <a href="https://doi.org/10.5281/zenodo.2576241">10.5281/zenodo.2576241</a>. 150 TIFFs for nuclei learning incl 150 png nuclei masks + 99 TIFFs for DNA repair foci training</li> <li>Code: the code is available at <a href="https://github.com/tomasvicar/LearnFoci">https://github.com/tomasvicar/LearnFoci</a></li> </ul> Materials and methods Dataset Following cells were used: (1) patient primocultures of patients with  spinocellular head and neck tumors (histologically verified tumor and tumor-adjacent tissues), isolation protocol descibed in Svobodova et al, 2017, (2) primary glioblastoma cell line U-87 (ATCC HTB-14, LGC Standards, United Kingdom), (3) primary normal human dermal fibroblasts (NHDF, PromoCell, Hedelberg, Germany) isolated from the dermis of juvenile foreskin or adult skin. The study was conducted in accord with the Helsinki Declaration of 1964 and all subsequent revisions thereof. It was approved by the ethical committee of St. Anne’s Faculty Hospital, Brno. Primoculture cells were cultivated in Pen/Strep antibiotic solution (PAA Laboratories GmbH, Austria) in RPMI-1640 medium with 10% FBS (Biochrom, USA) at 37 °C and 50% CO2 in humidified atmosphere up to 50% confluence. U-87 were grown in Eagle's MEM with 10% FBS. Gamma irradiation The cells were irradiated at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic in a following schemes: (a) patient-derived primoculture was irradiated with a single dose of 2 Gy (D = 1 Gy/min) of gamma-rays (60Co, Chisostat, Chirana, CR) , (b) U-87 and NHDF cells were irradiated with doses 1, 2, and 4 Gy (D = 1 Gy/min). Cells were irradiated in RPMI 1640 medium (37 °C, normal atmosphere). Confocal microscopy of gammaH2AX and 53BP1 foci immunodetection was consequently performed. Fluorescent staining DNA double strand breaks (DSBs) were quantified in different periods of time post-irradiation (30 min, 8h and 24h post irradiation) by means of $\gamma$H2AX and 53BP1 foci immunodetection combined with  confocal microscopy. For details see \cite{falk2007chromatin}. Confocal microscopy The microscopy of samples was performed at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic. Leica DM RXA microscope (equipped with DMSTC motorized stage, Piezzo z-movement, MicroMax CCD camera, CSU-10 confocal unit and 488, 562, and 714 nm laser diodes with AOTF) was used for acquiring detailed cell images (100× oil immersion Plan Fluotar lens, NA 1.3). Total 50 Z slices was captured with Z step size 0.3 μm. File description all files are compressed hyperstack tiffs (50 Z slices and 3 fluorescent channels, XYCZ order), 100x magnification <ul> <li>Confocal_HN_tumor_primocultures.zip: dataset of patient-derived primocultures (gamma-irradiated with 2 Gy and controls), for description see file below, 100 FOVs,</li> <li>Confocal_HN_tumor_primocultures_description.xlsx: description of confocal dataset files and patient tumor characteristics</li> <li>Confocal_HN_tumor_primocultures_train_nuclei.zip: annotated training subset 1 of dataset of patient-derived primocultures (gamma-irradiated with 2 Gy and controls) used for nuclei segmentation training, 150 FOVs, includes TIFF and manually annotated binary mask for nuclei (data_###.tif and respective mask_###.png)</li> <li>Confocal_HN_tumor_primocultures_train_nuclei_description.xlsx: description of above-mentioned files (tissue type, TNM stage, grade, time post irradiation)</li> </ul>

opencc-by-4.0Mar 2019View details →

Supplemental Figures S1-S8: Direct CD137 costimulation of CD8 T cells promotes retention and innate-like function within nascent atherogenic foci

Supplemental Figures and Table S1-S8 for "Direct CD137 costimulation of CD8 T cells promotes retention and innate-like function within nascent atherogenic foci" H-00088-2019, to the American Journal of Physiology-Heart and Circulatory Physiology.

opencc-by-4.0Feb 2019View details →

Annotated DNA Double Strand Break Ionizing Radiation-Induced Foci (gH2AX 53BP1) Confocal Microscopy, pt. 2

Summary Dataset of confocal microscopy data of cells exposed to gamma-irradiation and immunostained with gH2AX and 53BP1. <ul> <li>Nuclei segmentation Head and neck primocultures immunostained with gH2AX/53BP1, Training/Testing/Validation dataset (nucleus_segmentation.zip) (available in part 1, <a href="https://dx.doi.org/10.5281/zenodo.4067741">https://dx.doi.org/10.5281/zenodo.4067741</a>) </li> <li>IRIF Foci: Head and neck primocultures immunostained with gH2AX/53BP1, Training/Testing/Validation dataset. (foci_detection.zip) (available in part 1, <a href="https://dx.doi.org/10.5281/zenodo.4067741">https://dx.doi.org/10.5281/zenodo.4067741</a>)</li> <li>Cell lines: U-87 and NHDF Cells exposed to 0.5-8 Gy 30 min and 8h post irradiation - confocal microscopy data of gH2AX/53BP1/DAPI annotated for gH2AX, 53BP1 and colocalized foci separately (cell_lines_U87.zip and cell_lines_NHDF.zip, this part of dataset) </li> <li>Code: the code is available at <a href="https://github.com/tomasvicar/DeepFoci">https://github.com/tomasvicar/DeepFoci</a></li> <li>Preprint: Vicar et al, DeepFoci: Deep Learning-Based Algorithm for Fast Automatic Analysis of DNA Double Strand Break Ionizing Radiation-Induced Foci, <a href="https://doi.org/10.1101/2020.10.07.321927">10.1101/2020.10.07.321927</a></li> <li>Publication: Vicar et al, TBA</li> </ul> Materials and methods Dataset Following cells were used: 1) The training/validation/testing datasets was based on patient-derived primary cell cultures prepared from spinocellular tumors and morphologically normal tissues adjacent to the tumor taken from patients suffering from head and neck cancer. The dataset was divided into two subsets: one for training, validation and testing the nucleus segmentation (237/10/30 fields of view (FOVs), respectively) and one for training, validation and testing the focus segmentation (239/60/100 FOVs). The dataset consisted of several cell types: a) tumor cells, b) tumor-associated fibroblasts, and c) cells from morphologically normal tissues. All cell types were fixed at different periods of time (0 (non-irradiated control), 0.5, 8 or 24 h PI) after exposure to 2 Gy of gamma-rays. The representation of cells in two subsets with respect to the cell type and post-irradiation time (i.e., DSB repair duration) was random. 2) The evaluation dataset was used to assess the robustness of segmentation procedures. It was composed of multiple types of differently treated cells in order to represent a highly challenging dataset maximally reflecting high biological and technical variability between samples, as it may appear in research or clinical practice. The dataset contained  a) mesenchymal NHDF fibroblasts coming from a standard permanent cell line, b) radioresistant U-87 glioblastoma cells coming from a standard permanent cell line, c) tumor cells (CD90-) and tumor-associated fibroblasts (CD90+) prepared as a primary culture from a spinocellular tumors of patients (different from dataset 1) suffering from a head and neck cancer, and d) cells prepared as primary cultures from morphologically normal tissue adjacent to tumors of involved head and neck cancer patients. NHDF and U-87 cells received 0.5, 0, 1, 2,  4 and 8 Gy of gamma-rays and were fixed at 30 min and 8 h post-irradiation, while the primary cultures were only exposed to the dose of 2 Gy (for a limited amount of the cell material) and fixed at 0 (non-irradiated control), 0.5, 8 or 24 h post-irradiation times. Gamma irradiation The cells were irradiated at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic in a following schemes: (a) patient-derived primoculture was irradiated with a single dose of 2 Gy (D = 1 Gy/min) of gamma-rays (60Co, Chisostat, Chirana, CR) , (b) U-87 and NHDF cells were irradiated with doses 0.5-8 Gy (D = 1 Gy/min). Cells were irradiated in RPMI 1640 medium (37 °C, normal atmosphere). Confocal microscopy of gammaH2AX and 53BP1 foci immunodetection was consequently performed. Fluorescent staining DNA double strand breaks (DSBs) were quantified in different periods of time post-irradiation (30 min, 8h and 24h post irradiation) by means of $\gamma$H2AX and 53BP1 foci immunodetection combined with  confocal microscopy. For details see \cite{falk2007chromatin}. Confocal microscopy The microscopy of samples was performed at the Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic. Leica DM RXA microscope (equipped with DMSTC motorized stage, Piezzo z-movement, MicroMax CCD camera, CSU-10 confocal unit and 488, 562, and 714 nm laser diodes with AOTF) was used for acquiring detailed cell images (100× oil immersion Plan Fluotar lens, NA 1.3). Total 50 Z slices was captured with Z step size 0.3 μm. File description all files are compressed hyperstack tiffs (50 Z slices and 3 fluorescent channels, XYCZ order), 100x magnification <ul> <li>foci_detection.zip: IRIF Foci (available in part 1, <a href="https://dx.doi.org/10.5281/zenodo.4067741">https://dx.doi.org/10.5281/zenodo.4067741</a>): Head and neck primocultures immunostained with gH2AX/53BP1, Training/Testing/Validation dataset: FOVs 240/100/120 files for training, testing, and validation, organisation: <ul> <li>data_001.tif – 3channel Z.stack tiff</li> <li>mask_001.tif – respective Z stack mask with single points per IRIF focus (manual annotation, training and testing subsets only)</li> <li>data_description.xlsx – description of sample type (2Gy post irradiation times and characteristics of primary culture of squamous cell cancer of patients)</li> <li>data_001_pos.csv – manual annotation of gH2AX/53BPI IRIF foci by two experts – cordinates file (in 2D, validation only)</li> </ul> </li> <li>nucleus_segmentation.zip (available in part 1, <a href="https://dx.doi.org/10.5281/zenodo.4067741">https://dx.doi.org/10.5281/zenodo.4067741</a>) Nuclei segmentation Head and neck primocultures immunostained with gH2AX/53BP1, FOVs 237 Training/ 30 Testing/ 10 Validation dataset <ul> <li>data_001.tif – 3channel Z.stack tiff</li> <li>mask_001.tif – respective Z stack mask with manually annotated nucleus mask (manual annotation, training and testing subsets only)</li> <li>data_description.xlsx – description of sample type (2Gy post irradiation times and characteristics of primary culture of squamous cell cancer of patients)</li> </ul> </li> <li>U87.zip and NHDF.zip: Annotated gH2AX/53BP1 foci in cell lines exposed to increasing dose, annotations performed for gH2AX, 53BP1 and colocalized focus separatelly. 679 annotated FOVs for both cell lines. <ul> <li>control.png - RGB control figure showing merge and annotated overlay</li> <li>data_53BP1.tif - TIFF Z-stack, confocal microcopy, 53BP1 channel</li> <li>data_DAPI.tif -  TIFF Z-stack, confocal microcopy, DAPI channel</li> <li>data_gH2AX.tif  - TIFF Z-stack, confocal microcopy, gH2AX channel</li> <li>labels.json - foci labels for individual channel</li> <li>mask.tif - generated Z-stack of nucleus mask</li> </ul> </li> </ul>

opencc-by-4.0Jul 2023View details →

Datasets from: A Worldwide View of Nation-state Internet Censorship, Free and Open Communications on the Internet (FOCI), 2023

These data were used to perform the cross-sectional study, systematic literature review, and analysis presented in the research framework from the paper, A Worldwide View of Nation-state Internet Censorship - presented at the FOCI workshop as part of the 23rd Privacy Enhancing Technologies Symposium in Lausanne, Switzerland.

opencc-by-4.0Aug 2023View details →

Data for "Reducing Southern Ocean biases in the FOCI climate model"

Jupyter notebooks and time-averaged data needed to reproduce all plots in "Reducing Southern Ocean biases in the FOCI climate model" submitted to JAMES. Source code modifications needed to compile and run the model is also included. See attached README for more information.

zenodo32/100

Single molecule microscopy reveals key physical features of repair foci in living cells

Single Particle Tracking data of repair proteins in budding yeast, described in the manuscript entitled 'Single molecule microscopy reveals key physical features of repair foci in living cells'.

opencc-by-4.0Feb 2021View details →

dryad32/100

Data from: Genetic diversity and population structure of Glossina morsitans morsitans in the active foci of human African trypanosomiasis in Zambia and Malawi

The tsetse fly, Glossina morsitans morsitans, is a significant problem in Zambia and Malawi. It is the vector for the human infective parasite Trypanosoma brucei rhodesiense, which causes human African trypanosomiasis, and various Trypanosoma species, which cause African animal trypanosomiasis. Understanding the genetic diversity and population structure of G. m. morsitans is the basis of elucidating the connectivity of the tsetse fly populations, information that is essential in implementing successful tsetse fly control activities. This study conducted a population genetic study using partial mitochondrial cytochrome oxidase gene 1 (CO1) and 10 microsatellite loci to investigate the genetic diversity and population structure of G. m. morsitans captured in the major HAT foci in Zambia and Malawi. We have included 108 and 99 G. m. morsitans samples for CO1 and microsatellite analyses respectively. Our results suggest the presence of two different genetic clusters of G. m. morsitans, existing East and West of the escarpment of the Great Rift Valley. We have also revealed genetic similarity between the G. m. morsitans in Kasungu National Park and those in the Luangwa river basin in Zambia, indicating that this population should also be included in this historical tsetse belt. Although further investigation is necessary to illustrate the whole picture in East and Southern Africa, this study has extended our knowledge of the population structure of G. m. morsitans in Southern Africa.

opencc-zeroAug 2019View details →

zenodo32/100

Supplemental Figures S1-S8: Direct CD137 costimulation of CD8 T cells promotes retention and innate-like function within nascent atherogenic foci

opencc-by-4.0Mar 2019View details →

restrictedIPD-UNDECIDEDFeb 2026View details →

Colonoscopic Removal of Aberrant Crypt Foci: a Prospective, Randomized, Blinded Trial

ClinicalTrials.gov study NCT00623883. IPD Sharing: Not stated. Countries: 1. Publications: 2.

closedIPD-NOFeb 2026View details →

Postnatal Managemant of Prenetal Cardiac Echogenic Foci in Hillel Yaffe Medical Center

ClinicalTrials.gov study NCT04265352. IPD Sharing: NO. Countries: 1. Publications: 1.

closedIPD-NOFeb 2026View details →

Exploring the Characteristics of Epileptogenic Foci in Drug-Resistant Epilepsy Based on Multimodal Imaging Technology

ClinicalTrials.gov study NCT06557720. IPD Sharing: NO. Countries: 1. Publications: 6.

closedIPD-NOFeb 2026View details →

Changes in Inflammatory Biomarkers Including Soluble CD14 and Hyperreflective Foci in DME Patients Treated With Aflibercept (FORESIGHT)

ClinicalTrials.gov study NCT03780361. IPD Sharing: NO. Countries: 1. Publications: 1.