cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3689194
title: Monitoring clearcutting and subsequent rapid recovery in Mediterranean coppice forests with Landsat time series

description: This dataset considers information from clear-cut coppice forest occurred between 1999 and 2015 in three different area of Tuscany Region (Italy). The dataset consists in one shape file and two csv files. The shape file contains in 2371 spatial polygons of clear-cut occurred in the three area between 1999 and 2015. The polygons were generated using visual interpretation of the Landsat Time Series and high resolution regional ortomosaic. Photo interpreters delineated the spatial extent of each clear-cut and recorded the year of harvest, adopting a minimum mapping unit of 0.1 hectares. The database associated with shape file report information related with area extent of clear-cut, year of clear-cut and the forest types that is associated with the clear-cut derived by the Tucant Regional Forest Inventory (RFI) data that give information on dominant species. The .csv files reported the temporal characteristic of clear-cut based on Landsat Time Series data and based on Airborne Laser Scanner (ALS) Canopy Height Model (CHM), in order to describe the temporal trend of clear-cut based on remote sensing data.
description: {"references": ["Chirici G., Giannetti F., Mazza E., Francini S., Travaglini D., Pegna R., White J.C. (2020). Monitoring clearcutting and subsequent rapid recovery in Mediterranean coppice forests with Landsat time series, Annals of Forest Science, doi: 10.1007/s13595-020-00936-2"]}
DOI: 10.25386/genetics.11900247
title: Supplemental Material for Funkhouser et al., 2020

description: Supplemental Methods contain additional method details not in manuscript. Figure S1 contains LD decay statistics. Figure S2 contains simulation results for the discovery of any observed causal variant (whether they affect males, females, or both). Figure S3 contains simulation results for the discovery of regions containing masked causal variants (whether they affect males, females, or both). Figure S4 compares local Bayesian regression to single-marker regression for the discovery of gene-by-sex interactions. Figure S5 shows eQTL enrichment as a function of the number of gene-by-sex signals selected, and compares local Bayesian regression to single marker regression. Table S1 contains within-sex phenotype statistics. Table S2 contains a sample of per-replicate simulation results when causal variants are observed. Table S3 contains a sample of per-replicate simulation results when causal variants are masked. Table S4 contains all gene-by-sex interactions discovered using sex-specific window variances.
DOI: 10.25386/genetics.11900247.v1
title: Supplemental Material for Funkhouser et al., 2020

description: Supplemental Methods contain additional method details not in manuscript. Figure S1 contains LD decay statistics. Figure S2 contains simulation results for the discovery of any observed causal variant (whether they affect males, females, or both). Figure S3 contains simulation results for the discovery of regions containing masked causal variants (whether they affect males, females, or both). Figure S4 compares local Bayesian regression to single-marker regression for the discovery of gene-by-sex interactions. Figure S5 shows eQTL enrichment as a function of the number of gene-by-sex signals selected, and compares local Bayesian regression to single marker regression. Table S1 contains within-sex phenotype statistics. Table S2 contains a sample of per-replicate simulation results when causal variants are observed. Table S3 contains a sample of per-replicate simulation results when causal variants are masked. Table S4 contains all gene-by-sex interactions discovered using sex-specific window variances.
DOI: 10.5281/zenodo.3713309
title: Dataset related to article "CXCR3 Identifies Human Naive CD8+ T Cells with Enhanced Effector Differentiation Potential."

description: In mice, the ability of naive T (T<sub>N</sub>) cells to mount an effector response correlates with TCR sensitivity for self-derived Ags, which can be quantified indirectly by measuring surface expression levels of CD5. Equivalent findings have not been reported previously in humans. We identified two discrete subsets of human CD8<sup>+</sup> T<sub>N</sub> cells, defined by the absence or presence of the chemokine receptor CXCR3. The more abundant CXCR3<sup>+</sup> T<sub>N</sub> cell subset displayed an effector-like transcriptional profile and expressed TCRs with physicochemical characteristics indicative of enhanced interactions with peptide-HLA class I Ags. Moreover, CXCR3<sup>+</sup> T<sub>N</sub> cells frequently produced IL-2 and TNF in response to nonspecific activation directly ex vivo and differentiated readily into Ag-specific effector cells in vitro. Comparative analyses further revealed that human CXCR3<sup>+</sup> T<sub>N</sub> cells were transcriptionally equivalent to murine CXCR3<sup>+</sup> T<sub>N</sub> cells, which expressed high levels of CD5. These findings provide support for the notion that effector differentiation is shaped by heterogeneity in the preimmune repertoire of human CD8<sup>+</sup> T cells.
DOI: 10.5281/zenodo.3712931
title: Auto-tuning Configurable Static Analysis Tools

description: Version 1.1.0 Updates: The new version contains the updated data for the final symbiotic experiments (without filter). Changes: results.tar.xz added seed_2971/log_anneal_symbiotic_false_1.0_2971_base-classification_false.txt added seed_1195/log_anneal_symbiotic_false_1.0_1195_base-classification_false.txt added seed_3928/log_anneal_symbiotic_false_1.0_3928_base-classification_false.txt added seed_5927/log_anneal_symbiotic_false_1.0_5927_base-classification_false.txt experiments.tar.xz added stats/stats-symbiotic-missing-4reps.csv -------- This contains both the executables and the data for our ESEC/FSE 2020 submission, "Auto-tuning Configurable Static Analysis Tools." The results are in results.tar.xz, and the auto-tune source code and experimental environment is is experiments.tar.xz.
DOI: 10.5281/zenodo.3713308
title: Dataset related to article "CXCR3 Identifies Human Naive CD8+ T Cells with Enhanced Effector Differentiation Potential."

description: In mice, the ability of naive T (T<sub>N</sub>) cells to mount an effector response correlates with TCR sensitivity for self-derived Ags, which can be quantified indirectly by measuring surface expression levels of CD5. Equivalent findings have not been reported previously in humans. We identified two discrete subsets of human CD8<sup>+</sup> T<sub>N</sub> cells, defined by the absence or presence of the chemokine receptor CXCR3. The more abundant CXCR3<sup>+</sup> T<sub>N</sub> cell subset displayed an effector-like transcriptional profile and expressed TCRs with physicochemical characteristics indicative of enhanced interactions with peptide-HLA class I Ags. Moreover, CXCR3<sup>+</sup> T<sub>N</sub> cells frequently produced IL-2 and TNF in response to nonspecific activation directly ex vivo and differentiated readily into Ag-specific effector cells in vitro. Comparative analyses further revealed that human CXCR3<sup>+</sup> T<sub>N</sub> cells were transcriptionally equivalent to murine CXCR3<sup>+</sup> T<sub>N</sub> cells, which expressed high levels of CD5. These findings provide support for the notion that effector differentiation is shaped by heterogeneity in the preimmune repertoire of human CD8<sup>+</sup> T cells.
DOI: 10.17632/44fhtn96kw.1
title: Rawdata_4

description: The dataset contains the raw data used for the figure in the manuscript "The UPR sensor IRE1a and the adenovirus E3-19K glycoprotein sustain persistent and lytic infections"
DOI: 10.17632/4d6d2g2kk7.1
title: Rawdata_3

description: The dataset contains the raw data used for the figure in the manuscript "The UPR sensor IRE1a and the adenovirus E3-19K glycoprotein sustain persistent and lytic infections"
DOI: 10.5281/zenodo.3713180
title: Dataset related to article "NKp46-expressing human gut-resident intraepithelial Vδ1 T cell subpopulation exhibits high antitumor activity against colorectal cancer"

description: γδ T cells account for a large fraction of human intestinal intraepithelial lymphocytes (IELs) endowed with potent antitumor activities. However, little is known about their origin, phenotype, and clinical relevance in colorectal cancer (CRC). To determine γδ IEL gut specificity, homing, and functions, γδ T cells were purified from human healthy blood, lymph nodes, liver, skin, and intestine, either disease-free, affected by CRC, or generated from thymic precursors. The constitutive expression of NKp46 specifically identifies a subset of cytotoxic Vδ1 T cells representing the largest fraction of gut-resident IELs. The ontogeny and gut-tropism of NKp46+/Vδ1 IELs depends both on distinctive features of Vδ1 thymic precursors and gut-environmental factors. Either the constitutive presence of NKp46 on tissue-resident Vδ1 intestinal IELs or its induced expression on IL-2/IL-15-activated Vδ1 thymocytes are associated with antitumor functions. Higher frequencies of NKp46+/Vδ1 IELs in tumor-free specimens from CRC patients correlate with a lower risk of developing metastatic III/IV disease stages. Additionally, our in vitro settings reproducing CRC tumor microenvironment inhibited the expansion of NKp46+/Vδ1 cells from activated thymic precursors. These results parallel the very low frequencies of NKp46+/Vδ1 IELs able to infiltrate CRC, thus providing insights to either follow-up cancer progression or to develop adoptive cellular therapies. This dataset is created with fcs files form, in order to guarantee the access we attach a pdf information about
DOI: 10.5281/zenodo.3713181
title: Dataset related to article "NKp46-expressing human gut-resident intraepithelial Vδ1 T cell subpopulation exhibits high antitumor activity against colorectal cancer"

description: γδ T cells account for a large fraction of human intestinal intraepithelial lymphocytes (IELs) endowed with potent antitumor activities. However, little is known about their origin, phenotype, and clinical relevance in colorectal cancer (CRC). To determine γδ IEL gut specificity, homing, and functions, γδ T cells were purified from human healthy blood, lymph nodes, liver, skin, and intestine, either disease-free, affected by CRC, or generated from thymic precursors. The constitutive expression of NKp46 specifically identifies a subset of cytotoxic Vδ1 T cells representing the largest fraction of gut-resident IELs. The ontogeny and gut-tropism of NKp46+/Vδ1 IELs depends both on distinctive features of Vδ1 thymic precursors and gut-environmental factors. Either the constitutive presence of NKp46 on tissue-resident Vδ1 intestinal IELs or its induced expression on IL-2/IL-15-activated Vδ1 thymocytes are associated with antitumor functions. Higher frequencies of NKp46+/Vδ1 IELs in tumor-free specimens from CRC patients correlate with a lower risk of developing metastatic III/IV disease stages. Additionally, our in vitro settings reproducing CRC tumor microenvironment inhibited the expansion of NKp46+/Vδ1 cells from activated thymic precursors. These results parallel the very low frequencies of NKp46+/Vδ1 IELs able to infiltrate CRC, thus providing insights to either follow-up cancer progression or to develop adoptive cellular therapies. This dataset is created with fcs files form, in order to guarantee the access we attach a pdf information about
DOI: 10.17632/vzsw4r33dg.1
title: Rawdata_2

description: The dataset contains the raw data used for the figure in the manuscript "The UPR sensor IRE1a and the adenovirus E3-19K glycoprotein sustain persistent and lytic infections"
DOI: 10.5281/zenodo.3713241
title: The Turing Change Point Dataset

description: This is the first complete release of the Turing Change Point Dataset, a dataset created specifically for the evaluation and development of change point detection algorithms. For more information, see: https://arxiv.org/abs/2003.06222
description: {"references": ["Van den Burg, G.J.J. and Williams, C.K.I. (2020). An Evaluation of Change Point Detection Algorithms. arxiv:2003.06222"]}
DOI: 10.5281/zenodo.3713242
title: The Turing Change Point Dataset

description: This is the first complete release of the Turing Change Point Dataset, a dataset created specifically for the evaluation and development of change point detection algorithms. For more information, see: https://arxiv.org/abs/2003.06222
description: {"references": ["Van den Burg, G.J.J. and Williams, C.K.I. (2020). An Evaluation of Change Point Detection Algorithms. arxiv:2003.06222"]}
DOI: 10.5281/zenodo.3713331
title: Dataset related to article "Antitumor Activity of a Novel Fibroblast Growth Factor Receptor Inhibitor for Intrahepatic Cholangiocarcinoma."

description: Fibroblast growth factor receptor 2 (FGFR2) might have an important role in the pathogenesis and biology of cholangiocarcinoma (CCA). We examined FGFR expression in CCA tumor specimens obtained from patients and CCA cell lines, and then determined the effects of the novel FGFR inhibitor, derazantinib (DZB; formally, ARQ 087), which is currently in clinical phase 2 trials for intrahepatic CCA. DZB inhibited the growth of CCA cell lines in a dose-dependent manner, and extracellular signal-regulated kinase 1/2 and AKT. It also activated apoptotic and cell growth arrest signaling. DZB reduced the in vitro invasiveness and the expression of key epithelial-mesenchymal transition genes. The in vitro data correlated with the expression of FGFRs in human CCA specimens by immunohistochemistry (FGFR1, 30% positive; and FGFR2, 65% positive) and the CCA cell lines assayed by Western blot analysis. These correlated in vitro studies suggest that FGFR may play an important role in the pathogenesis and biology of CCA. Our findings support the notion that FGFR inhibitors, like DZB, should be further evaluated at the clinical stage as targeted therapy for CCA treatment.
DOI: 10.5281/zenodo.3713332
title: Dataset related to article "Antitumor Activity of a Novel Fibroblast Growth Factor Receptor Inhibitor for Intrahepatic Cholangiocarcinoma."

description: Fibroblast growth factor receptor 2 (FGFR2) might have an important role in the pathogenesis and biology of cholangiocarcinoma (CCA). We examined FGFR expression in CCA tumor specimens obtained from patients and CCA cell lines, and then determined the effects of the novel FGFR inhibitor, derazantinib (DZB; formally, ARQ 087), which is currently in clinical phase 2 trials for intrahepatic CCA. DZB inhibited the growth of CCA cell lines in a dose-dependent manner, and extracellular signal-regulated kinase 1/2 and AKT. It also activated apoptotic and cell growth arrest signaling. DZB reduced the in vitro invasiveness and the expression of key epithelial-mesenchymal transition genes. The in vitro data correlated with the expression of FGFRs in human CCA specimens by immunohistochemistry (FGFR1, 30% positive; and FGFR2, 65% positive) and the CCA cell lines assayed by Western blot analysis. These correlated in vitro studies suggest that FGFR may play an important role in the pathogenesis and biology of CCA. Our findings support the notion that FGFR inhibitors, like DZB, should be further evaluated at the clinical stage as targeted therapy for CCA treatment.
DOI: 10.17632/fr78yy63zz.1
title: Rawdata_1

description: The dataset contains the raw data used for the figure in the manuscript "The UPR sensor IRE1a and the adenovirus E3-19K glycoprotein sustain persistent and lytic infections"
DOI: 10.21223/p3/2l9h6y/bhtl4d
title: PTPVS112018_HUANUCO_CANCHAN.tab

description: :unav
DOI: 10.21223/p3/2l9h6y/robanm
title: Data_dictionary.xls

description: :unav
DOI: 10.17632/7pfhksrd4v.1
title: Scripts and Workflow

description: The dataset contains the CellProfiler Scripts and KNIME workflow for the manuscript "The UPR sensor IRE1a and the adenovirus E3-19K glycoprotein sustain persistent and lytic infections"
DOI: 10.5281/zenodo.3713336
title: ZeroCostDL4Mic - CARE (3D) example training and test dataset

description: <strong>Name</strong>: ZeroCostDL4Mic - CARE (3D) example training and test dataset (see our Wiki for details) <strong>Data type</strong>: 3D paired microscopy images (fluorescence) of low and high signal-to-noise ratio <strong>Microscopy data type</strong>: Fluorescence microscopy (Lifeact-RFP) <strong>Microscope</strong>: Structured Illumination Microscopy (SIM) with a 60x 1.42 NA objective <strong>Cell type</strong>: DCIS.COM Lifeact-RFP <strong>File format</strong>: .tif (32-bit) <strong>Image size</strong>: 1024x1024x33 (Pixel size: x,y: 40 nm, z: 125 nm) <strong>Author(s)</strong>: Guillaume Jacquemet<sup>1,2</sup> <strong>Contact email</strong>: guillaume.jacquemet@abo.fi <strong>Affiliation</strong>: 1) Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland 2) Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland <strong>Associated publications</strong>: Unpublished <strong>Funding bodies</strong>: G.J. was supported by grants awarded by the Academy of Finland, the Sigrid Juselius Foundation and Åbo Akademi University Research Foundation (CoE CellMech) and by Drug Discovery and Diagnostics strategic funding to Åbo Akademi University.
DOI: 10.5281/zenodo.3713337
title: ZeroCostDL4Mic - CARE (3D) example training and test dataset

description: <strong>Name</strong>: ZeroCostDL4Mic - CARE (3D) example training and test dataset (see our Wiki for details) <strong>Data type</strong>: 3D paired microscopy images (fluorescence) of low and high signal-to-noise ratio <strong>Microscopy data type</strong>: Fluorescence microscopy (Lifeact-RFP) <strong>Microscope</strong>: Structured Illumination Microscopy (SIM) with a 60x 1.42 NA objective <strong>Cell type</strong>: DCIS.COM Lifeact-RFP <strong>File format</strong>: .tif (32-bit) <strong>Image size</strong>: 1024x1024x33 (Pixel size: x,y: 40 nm, z: 125 nm) <strong>Author(s)</strong>: Guillaume Jacquemet<sup>1,2</sup> <strong>Contact email</strong>: guillaume.jacquemet@abo.fi <strong>Affiliation</strong>: 1) Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, 20520 Turku, Finland 2) Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland <strong>Associated publications</strong>: Unpublished <strong>Funding bodies</strong>: G.J. was supported by grants awarded by the Academy of Finland, the Sigrid Juselius Foundation and Åbo Akademi University Research Foundation (CoE CellMech) and by Drug Discovery and Diagnostics strategic funding to Åbo Akademi University.
DOI: 10.5519/qd.jdpmmk7k
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (744414 records)
DOI: 10.17632/bs4hx7cgmc.1
title: Processed data

description: Processed data
DOI: 10.17632/wkxbx2k5r5.1
title: Raw data

description: Raw data
DOI: 10.14469/hpc/6994
title: Reverse-phase chromatography mass-spectrometry (positive mode) in serum

description: lipid-targeted reverse-phase chromatography (denoted L in NPC assays) provides maximal resolution of fatty acids,triglycerides, and phospholipids, ionised in positive mode
DOI: 10.5281/zenodo.3713299
title: Dataset related to article "Pretransplant active disease status and HLA class II mismatching are associated with increased incidence and severity of cytokine release syndrome after haploidentical transplantation with posttransplant cyclophosphamide."

description: Cytokine release syndrome (CRS) represents a life-threatening side effect after haploidentical stem cell transplantation (Haplo-SCT) with posttransplant cyclophosphamide (PT-Cy). Factors predictive of CRS development is still a matter of debate. We retrospectively analyzed 102 consecutive patients receiving a bone marrow (BM) (n = 42) or peripheral blood stem cells (PBSC) (n = 60) Haplo-SCT with PT-Cy. The two cohorts were similar in main patients' characteristics besides disease type (P = .02). Cumulative incidence of grades 1, 2, and ≥3 CRS was 80%, 52%, and 15% at a median of 2, 4, and 7 days, respectively. Moderate/High-grade fever (39°-41°), grade 1 and grade ≥3 CRS occurred more frequently after PBSC relative to BM grafts (68% vs 33%, P = .0005; 87% vs 71%, P = .009; 20% vs 7%, P = .07). Only patients experiencing grade ≥3 CRS had a worse outcome in terms of 1-year overall survival (OS) and nonrelapse mortality (NRM): 39% vs 80% (P = .002) and 40% vs 8% (P = .005), respectively. By univariate analysis the only factors associated with the increased risk of ≥3 CRS were pretransplant disease status (8% for complete remission, 11% for partial remission, and 38% for active disease, P = .002), HLA-DRB1 mismatching (57% vs 14%, P = .007), and PBSC graft (P = .07). By multivariable analysis, only pretransplant disease status (hazard ratio, HR: 6.84, P = .005) and HLA-DRB1 mismatching (HR: 17.19, P = .003) remained independent predictors of grade ≥3 CRS. Only grade ≥3 CRS is clinically relevant for the final outcome of patients receiving Haplo-SCT with PT-Cy, is more frequent after a PBSC graft and is associated with pretransplant active disease and HLA-DRB1 mismatching.
DOI: 10.5281/zenodo.3713300
title: Dataset related to article "Pretransplant active disease status and HLA class II mismatching are associated with increased incidence and severity of cytokine release syndrome after haploidentical transplantation with posttransplant cyclophosphamide."

description: Cytokine release syndrome (CRS) represents a life-threatening side effect after haploidentical stem cell transplantation (Haplo-SCT) with posttransplant cyclophosphamide (PT-Cy). Factors predictive of CRS development is still a matter of debate. We retrospectively analyzed 102 consecutive patients receiving a bone marrow (BM) (n = 42) or peripheral blood stem cells (PBSC) (n = 60) Haplo-SCT with PT-Cy. The two cohorts were similar in main patients' characteristics besides disease type (P = .02). Cumulative incidence of grades 1, 2, and ≥3 CRS was 80%, 52%, and 15% at a median of 2, 4, and 7 days, respectively. Moderate/High-grade fever (39°-41°), grade 1 and grade ≥3 CRS occurred more frequently after PBSC relative to BM grafts (68% vs 33%, P = .0005; 87% vs 71%, P = .009; 20% vs 7%, P = .07). Only patients experiencing grade ≥3 CRS had a worse outcome in terms of 1-year overall survival (OS) and nonrelapse mortality (NRM): 39% vs 80% (P = .002) and 40% vs 8% (P = .005), respectively. By univariate analysis the only factors associated with the increased risk of ≥3 CRS were pretransplant disease status (8% for complete remission, 11% for partial remission, and 38% for active disease, P = .002), HLA-DRB1 mismatching (57% vs 14%, P = .007), and PBSC graft (P = .07). By multivariable analysis, only pretransplant disease status (hazard ratio, HR: 6.84, P = .005) and HLA-DRB1 mismatching (HR: 17.19, P = .003) remained independent predictors of grade ≥3 CRS. Only grade ≥3 CRS is clinically relevant for the final outcome of patients receiving Haplo-SCT with PT-Cy, is more frequent after a PBSC graft and is associated with pretransplant active disease and HLA-DRB1 mismatching.
DOI: 10.25387/g3.10058657
title: Supplemental Material for Tanaka et al., 2020

description: Table S1. Annotation data of possible missing genes in IR64 genome. Figure S1. Genome alignment between IRGSP-1.0 genome and IR64 scaffolds. Red and blue dots represent forward and reverse alignments, respectively. Figure S2. Chromosome alignments between R498 and IR64 v.1.0. Figure S3. Chromosome alignments between IRGSP-1.0 and IR64 v.1.0. Figure S4. Chromosome alignments of chromosome 6 from 13 Mbp to 19 Mbp. Figure S5. Chromosomal distribution of genes mapped on IR64 v.1.0 unanchored sequences. Figure S6. Fraction of missing genic regions in IR64 covered by paired-end reads obtained from linked-read sequencing of IR64 genome. Figure S7. Distribution of gene ontologies.