cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.1186312
title: Registered Trials Report Less Beneficial Treatment Effects Than Unregistered Ones: A Meta-Epidemiological Study In Orthodontics

description: Dataset and commands for all analyses in the study.
DOI: 10.18112/openneuro.ds004331.v1.0.3
title: The spatiotemporal neural dynamics of object recognition for natural images and line drawings
DOI: 10.18112/openneuro.ds004331.v1.0.4
title: The spatiotemporal neural dynamics of object recognition for natural images and line drawings
DOI: 10.5281/zenodo.7332333
title: Dataset related to article "Multimodal single-cell profiling of intrahepatic cholangiocarcinoma defines hyperactivated Tregs as a potential therapeutic target"

description: This record contains raw data related to article “Multimodal single-cell profiling of intrahepatic cholangiocarcinoma defines hyperactivated Tregs as a potential therapeutic target" Abstract <strong>Background & aims: </strong> The landscape and function of the immune infiltrate of intrahepatic cholangiocarcinoma (iCCA), a rare, yet aggressive tumor of the biliary tract, remains poorly characterized, limiting development of successful immunotherapies. Herein, we aimed to define the molecular characteristics of tumor-infiltrating leukocytes with a special focus on CD4+ regulatory T cells (Tregs). <strong>Methods: </strong> We used high-dimensional single-cell technologies to characterize the T-cell and myeloid compartments of iCCA tissues, comparing these with their tumor-free peritumoral and circulating counterparts. We further used genomics and cellular assays to define the iCCA-specific role of a novel transcription factor, mesenchyme homeobox 1 (MEOX1), in Treg biology. <strong>Results: </strong> We found poor infiltration of putative tumor-specific CD39+ CD8+ T cells accompanied by abundant infiltration of hyperactivated CD4+ Tregs. Single-cell RNA-sequencing identified an altered network of transcription factors in iCCA-infiltrating compared to peritumoral T cells, suggesting reduced effector functions by tumor-infiltrating CD8+ T cells and enhanced immunosuppression by CD4+ Tregs. Specifically, we found that expression of MEOX1 was highly enriched in tumor-infiltrating Tregs, and demonstrated that MEOX1 overexpression is sufficient to reprogram circulating Tregs to acquire the transcriptional and epigenetic landscape of tumor-infiltrating Tregs. Accordingly, enrichment of the MEOX1-dependent gene program in Tregs was strongly associated with poor prognosis in a large cohort of patients with iCCA. <strong>Conclusions: </strong> We observed abundant infiltration of hyperactivated CD4+ Tregs in iCCA tumors along with reduced CD8+ T-cell effector functions. Interfering with hyperactivated Tregs should be explored as an approach to enhance antitumor immunity in iCCA. <strong>Lay summary: </strong> Immune cells have the potential to slow or halt the progression of tumors. However, some tumors, such as intrahepatic cholangiocarcinoma, are associated with very limited immune responses (and infiltration of cancer-targeting immune cells). Herein, we show that a specific population of regulatory T cells (a type of immune cell that actually suppresses the immune response) are hyperactivated in intrahepatic cholangiocarcinoma. Targeting these cells could enable cancer-targeting immune cells to act more effectively and should be looked at as a potential therapeutic approach to this aggressive cancer type.
DOI: 10.5281/zenodo.7332332
title: Dataset related to article "Multimodal single-cell profiling of intrahepatic cholangiocarcinoma defines hyperactivated Tregs as a potential therapeutic target"

description: This record contains raw data related to article “Multimodal single-cell profiling of intrahepatic cholangiocarcinoma defines hyperactivated Tregs as a potential therapeutic target" Abstract <strong>Background & aims: </strong> The landscape and function of the immune infiltrate of intrahepatic cholangiocarcinoma (iCCA), a rare, yet aggressive tumor of the biliary tract, remains poorly characterized, limiting development of successful immunotherapies. Herein, we aimed to define the molecular characteristics of tumor-infiltrating leukocytes with a special focus on CD4+ regulatory T cells (Tregs). <strong>Methods: </strong> We used high-dimensional single-cell technologies to characterize the T-cell and myeloid compartments of iCCA tissues, comparing these with their tumor-free peritumoral and circulating counterparts. We further used genomics and cellular assays to define the iCCA-specific role of a novel transcription factor, mesenchyme homeobox 1 (MEOX1), in Treg biology. <strong>Results: </strong> We found poor infiltration of putative tumor-specific CD39+ CD8+ T cells accompanied by abundant infiltration of hyperactivated CD4+ Tregs. Single-cell RNA-sequencing identified an altered network of transcription factors in iCCA-infiltrating compared to peritumoral T cells, suggesting reduced effector functions by tumor-infiltrating CD8+ T cells and enhanced immunosuppression by CD4+ Tregs. Specifically, we found that expression of MEOX1 was highly enriched in tumor-infiltrating Tregs, and demonstrated that MEOX1 overexpression is sufficient to reprogram circulating Tregs to acquire the transcriptional and epigenetic landscape of tumor-infiltrating Tregs. Accordingly, enrichment of the MEOX1-dependent gene program in Tregs was strongly associated with poor prognosis in a large cohort of patients with iCCA. <strong>Conclusions: </strong> We observed abundant infiltration of hyperactivated CD4+ Tregs in iCCA tumors along with reduced CD8+ T-cell effector functions. Interfering with hyperactivated Tregs should be explored as an approach to enhance antitumor immunity in iCCA. <strong>Lay summary: </strong> Immune cells have the potential to slow or halt the progression of tumors. However, some tumors, such as intrahepatic cholangiocarcinoma, are associated with very limited immune responses (and infiltration of cancer-targeting immune cells). Herein, we show that a specific population of regulatory T cells (a type of immune cell that actually suppresses the immune response) are hyperactivated in intrahepatic cholangiocarcinoma. Targeting these cells could enable cancer-targeting immune cells to act more effectively and should be looked at as a potential therapeutic approach to this aggressive cancer type.
DOI: 10.5281/zenodo.7326609
title: Glacial lake outburst flood simulations for Poiqu Basin

description: This zip file contains simulation results (conducted with r.avaflow) for large ice/rock avalanche triggered glacial lake outburst floods in the Poiqu Basin. These results are presented in the paper by Allen et al. 2022, <em>Glacial lake outburst flood hazard under current and future conditions: worst-case scenarios in a transboundary Himalayan basin, </em>Natural Hazards and Earth System Science, https://doi.org/10.5194/nhess-22-1-2022. Raster files of flow height are provided for simulations of Galongco, Jialongco (for the lake volume in 2019, and for the reduced lake volume in 2021), and for the Future Lake. An Excel file provides a time series of flow height and discharge at cross sections measured at the outlet of the lake (moraine), in the town of Nyalam, and in Zhangmu for each simulation.
DOI: 10.34760/637760cac3640
title: Endocrynology
DOI: 10.5519/qd.tqblxiqg
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.5281/zenodo.7334032
title: Dataset Literature Review Online Business AND Customers

description: Data ini digunakan untuk membuat penelitian sesuai dengan tinjauan literatur dengan kata kunci "Online Business" dan "Customers"
DOI: 10.5281/zenodo.7334031
title: Dataset Literature Review Online Business AND Customers

description: Data ini digunakan untuk membuat penelitian sesuai dengan tinjauan literatur dengan kata kunci "Online Business" dan "Customers"
DOI: 10.5281/zenodo.6370336
title: IRIS Multiple Instance Learning Dataset

description: This dataset contains the data for the paper 'Using Multiple Instance Learning for Explainable Solar Flare Prediction' (arxiv pre-print) . It comes as a compressed Python Numpy-File and contains the following variables: Name Shape Description data (10'000, 1100, 240) 10'000 Bags of zero-padded spectrograms data_scaled (10'000, 1100, 240) Like data, but standard-scaled masks (10'000, 1100) Masks that indicate where spectrograms have been zero-padded groups (10'000,) Observation group the bag is assigned to obs_ids (10'000,) Observation ID the bag is assigned to obs_classes (10'000,) Observation class (AR/PF) the bag is assigned to raster_pos (10'000,) Raster position number the bag was taken from (always 0 for sit-and-stare) folds (10'000,) Validation fold for the particular observation group To load the e.g. the variable 'data', use Python and Numpy: <pre><code class="language-python">import numpy as np f = np.load("IRISMIL_dataset_10000_bags.npz", allow_pickle=True) f['data']</code></pre>
DOI: 10.5281/zenodo.6370335
title: IRIS Multiple Instance Learning Dataset

description: This dataset contains the data for the paper 'Using Multiple Instance Learning for Explainable Solar Flare Prediction' (arxiv pre-print) . It comes as a compressed Python Numpy-File and contains the following variables: Name Shape Description data (10'000, 1100, 240) 10'000 Bags of zero-padded spectrograms data_scaled (10'000, 1100, 240) Like data, but standard-scaled masks (10'000, 1100) Masks that indicate where spectrograms have been zero-padded groups (10'000,) Observation group the bag is assigned to obs_ids (10'000,) Observation ID the bag is assigned to obs_classes (10'000,) Observation class (AR/PF) the bag is assigned to raster_pos (10'000,) Raster position number the bag was taken from (always 0 for sit-and-stare) folds (10'000,) Validation fold for the particular observation group To load the e.g. the variable 'data', use Python and Numpy: <pre><code class="language-python">import numpy as np f = np.load("IRISMIL_dataset_10000_bags.npz", allow_pickle=True) f['data']</code></pre>
DOI: 10.5281/zenodo.7330573
title: Rescue of lysosomal function as therapeutic strategy for SPG15 hereditary spastic paraplegia

description: Raw data from the research article "Rescue of lysosomal function as therapeutic strategy for SPG15 hereditary spastic paraplegia".
description: This study was supported by the Italian Ministry of Health (RF-2019-12370112 to MTB)
description: {"references": ["Vantaggiato C, Orso G, Guarato G, Brivio F, Napoli B, Panzeri E, Masotti S, Maria Santorelli F, Lamprou M, Gumeni S, Clementi E, Teresa Bassi M. Rescue of lysosomal function as therapeutic strategy for SPG15 hereditary spastic paraplegia. Brain. 2022 Aug 27:awac308. doi: 10.1093/brain/awac308."]}
DOI: 10.5281/zenodo.7330574
title: Rescue of lysosomal function as therapeutic strategy for SPG15 hereditary spastic paraplegia

description: Raw data from the research article "Rescue of lysosomal function as therapeutic strategy for SPG15 hereditary spastic paraplegia".
description: This study was supported by the Italian Ministry of Health (RF-2019-12370112 to MTB)
description: {"references": ["Vantaggiato C, Orso G, Guarato G, Brivio F, Napoli B, Panzeri E, Masotti S, Maria Santorelli F, Lamprou M, Gumeni S, Clementi E, Teresa Bassi M. Rescue of lysosomal function as therapeutic strategy for SPG15 hereditary spastic paraplegia. Brain. 2022 Aug 27:awac308. doi: 10.1093/brain/awac308."]}
DOI: 10.7479/3caa-gq23/09
title: Findbuch K009 Zeitungsausschnittsammlung Adolf Oskrkany

description: Findbuch K009 Zeitungsausschnittsammlung Adolf Oskrkany
DOI: 10.34740/kaggle/dsv/4535935
title: YouTube Daily
DOI: 10.7294/21529440.v1
title: Insect pollinator visitors to ornamental landscape plants data and code to analyze abundance and diversity in experimental gardens

description: This data set accompanies the article MC Palmersheim, R Schürch, ME O’Rourke, J Slezak, & MJ Couvillon (2022) “If You Grow It, They Will Come: Ornamental Plants Impact the Abundance and Diversity of Pollinators and Other Flower-Visiting Insects in Gardens”, <em>Horticulturae</em>. https://doi.org/10.3390/horticulturae8111068
DOI: 10.7294/21529440
title: Insect pollinator visitors to ornamental landscape plants data and code to analyze abundance and diversity in experimental gardens

description: This data set accompanies the article MC Palmersheim, R Schürch, ME O’Rourke, J Slezak, & MJ Couvillon (2022) “If You Grow It, They Will Come: Ornamental Plants Impact the Abundance and Diversity of Pollinators and Other Flower-Visiting Insects in Gardens”, <em>Horticulturae</em>. https://doi.org/10.3390/horticulturae8111068
DOI: 10.6084/m9.figshare.21581670
title: 4-Spatio-temporal Evolution Law and Prevention of Spontaneous Combustion Danger Area in “110 Method” Goaf

description: <strong>Spatio-temporal Evolution Law and Prevention of Spontaneous Combustion Danger Area in “110 Method” Goaf</strong>
DOI: 10.6084/m9.figshare.21581670.v1
title: 4-Spatio-temporal Evolution Law and Prevention of Spontaneous Combustion Danger Area in “110 Method” Goaf

description: <strong>Spatio-temporal Evolution Law and Prevention of Spontaneous Combustion Danger Area in “110 Method” Goaf</strong>
DOI: 10.6084/m9.figshare.21581358
title: Cenfind datasets

description: Datasets used to train and test cenfind with annotations for centriole markers and nuclei. Dataset names RPE1wt_CEP63+CETN2+PCNT_1 RPE1wt_CP110+GTU88+PCNT_2 RPE1wt_CEP152+GTU88+PCNT_1 RPE1p53+Cnone_CEP63+CETN2+PCNT_1 U2OS_CEP63+SAS6+PCNT_1 Dataset structure projections/ annotations/ fields.txt test.txt train.txt
DOI: 10.6084/m9.figshare.21581358.v2
title: Cenfind datasets

description: Datasets used to train and test cenfind with annotations for centriole markers and nuclei. Dataset names RPE1wt_CEP63+CETN2+PCNT_1 RPE1wt_CP110+GTU88+PCNT_2 RPE1wt_CEP152+GTU88+PCNT_1 RPE1p53+Cnone_CEP63+CETN2+PCNT_1 U2OS_CEP63+SAS6+PCNT_1 Dataset structure projections/ annotations/ fields.txt test.txt train.txt
DOI: 10.6084/m9.figshare.21581358.v3
title: Cenfind datasets

description: Datasets used to train and test cenfind with annotations for centriole markers and nuclei. Dataset names RPE1wt_CEP63+CETN2+PCNT_1 RPE1wt_CP110+GTU88+PCNT_2 RPE1wt_CEP152+GTU88+PCNT_1 RPE1p53+Cnone_CEP63+CETN2+PCNT_1 U2OS_CEP63+SAS6+PCNT_1 Dataset structure projections/ annotations/ fields.txt test.txt train.txt
DOI: 10.6084/m9.figshare.21581718
title: Supplementary Material for: Genomically stable gastric cancer characterized by hypomethylation in Wnt signal cascade

description: Introduction Gastric cancer is divided into four subtypes by their molecular features linked with genetic alterations, e.g., Epstein-Barr virus (EBV), microsatellite instability-high (MSI-high), chromosomal instability (CIN), and genomically stable (GS), called as TCGA classification. In this study, we tried to clarify the epigenetic features of the four GC subtypes according to aberrant methylation status in 23 loci. Methods A total of 98 gastric cancers and their normal gastric mucosa samples were included in this study. We divided gastric cancers into TCGA subtypes which were determined in line with MSI-high, EBV, CIN, to GS by their molecular features. The 13 loci of polymorphic microsatellite sequences were used to determine loss of heterogeneity (LOH) for the detection of CIN. The MSI status was determined by three mononucleotide repeat markers. Infection of EBV was determined by recovering EBV BNRF1 sequence from genomic DNA collected from gastric cancers. Methylation status of 23 loci was investigated by the combined bisulfite restriction analysis (COBRA). Status of other findings, e.g., KRAS mutations, HER2 expression status and infection of helicobacter pylori were confirmed. Results Gastric cancers were divided into MSI (13%), EBV (7%), CIN (53%), and GS (27%). By histological classification, poorly differentiated adenocarcinoma (por) was more in tumors categorized in MSI-high, and GS and signet-ring cell carcinoma (sig) was more in GS. Among the 23 loci investigated their methylation status, 18 loci were significantly hypermethylated in caner tissues. A unsupervised clustering divided gastric cancers into two clusters, and revealed that most GS tumors clustered together in a cluster that exhibited lower methylation levels, distinct from the other subtypes. The inter-variable clustering revealed that a cluster contained the three loci (SFRP2-region 1/2 and APC) belonging to the Wnt signal cascade (Wnt-associated loci). The mean methylation score of Wnt-associated loci was the lowest in GS tumors (MSI-high: 2.7 [95% confidence interval (CI), 2.3-2.9]; EBV:2.1[1.2-3.1]; CIN: 2.4 [2.2-2.7]; GS: 1.3 [0.8-0.7]). In contrast, the mean methylation score of the other 15 loci was significantly higher in MSI-high, while that in GS was as same as that in EBV or CIN (MSI- high: 10.4 [8.3-12.4]; EBV:5.7 [1.7-9.7]; CIN: 4.4 [3.6-5.1]; GS: 3.4 [2.2-4.6]). Additionally, the lower methylation score of Wnt-associated loci was observed only in sig tumors. Conclusions GS subtype tumors have the potential to possess distinct signatures in DNA hypomethylation profiles in Wnt signaling pathway, especially in signet-ring cell carcinoma.
DOI: 10.6084/m9.figshare.21581718.v1
title: Supplementary Material for: Genomically stable gastric cancer characterized by hypomethylation in Wnt signal cascade

description: Introduction Gastric cancer is divided into four subtypes by their molecular features linked with genetic alterations, e.g., Epstein-Barr virus (EBV), microsatellite instability-high (MSI-high), chromosomal instability (CIN), and genomically stable (GS), called as TCGA classification. In this study, we tried to clarify the epigenetic features of the four GC subtypes according to aberrant methylation status in 23 loci. Methods A total of 98 gastric cancers and their normal gastric mucosa samples were included in this study. We divided gastric cancers into TCGA subtypes which were determined in line with MSI-high, EBV, CIN, to GS by their molecular features. The 13 loci of polymorphic microsatellite sequences were used to determine loss of heterogeneity (LOH) for the detection of CIN. The MSI status was determined by three mononucleotide repeat markers. Infection of EBV was determined by recovering EBV BNRF1 sequence from genomic DNA collected from gastric cancers. Methylation status of 23 loci was investigated by the combined bisulfite restriction analysis (COBRA). Status of other findings, e.g., KRAS mutations, HER2 expression status and infection of helicobacter pylori were confirmed. Results Gastric cancers were divided into MSI (13%), EBV (7%), CIN (53%), and GS (27%). By histological classification, poorly differentiated adenocarcinoma (por) was more in tumors categorized in MSI-high, and GS and signet-ring cell carcinoma (sig) was more in GS. Among the 23 loci investigated their methylation status, 18 loci were significantly hypermethylated in caner tissues. A unsupervised clustering divided gastric cancers into two clusters, and revealed that most GS tumors clustered together in a cluster that exhibited lower methylation levels, distinct from the other subtypes. The inter-variable clustering revealed that a cluster contained the three loci (SFRP2-region 1/2 and APC) belonging to the Wnt signal cascade (Wnt-associated loci). The mean methylation score of Wnt-associated loci was the lowest in GS tumors (MSI-high: 2.7 [95% confidence interval (CI), 2.3-2.9]; EBV:2.1[1.2-3.1]; CIN: 2.4 [2.2-2.7]; GS: 1.3 [0.8-0.7]). In contrast, the mean methylation score of the other 15 loci was significantly higher in MSI-high, while that in GS was as same as that in EBV or CIN (MSI- high: 10.4 [8.3-12.4]; EBV:5.7 [1.7-9.7]; CIN: 4.4 [3.6-5.1]; GS: 3.4 [2.2-4.6]). Additionally, the lower methylation score of Wnt-associated loci was observed only in sig tumors. Conclusions GS subtype tumors have the potential to possess distinct signatures in DNA hypomethylation profiles in Wnt signaling pathway, especially in signet-ring cell carcinoma.
DOI: 10.6084/m9.figshare.21581727
title: Supplementary Material for: Genomically stable gastric cancer characterized by hypomethylation in Wnt signal cascade

description: Introduction Gastric cancer is divided into four subtypes by their molecular features linked with genetic alterations, e.g., Epstein-Barr virus (EBV), microsatellite instability-high (MSI-high), chromosomal instability (CIN), and genomically stable (GS), called as TCGA classification. In this study, we tried to clarify the epigenetic features of the four GC subtypes according to aberrant methylation status in 23 loci. Methods A total of 98 gastric cancers and their normal gastric mucosa samples were included in this study. We divided gastric cancers into TCGA subtypes which were determined in line with MSI-high, EBV, CIN, to GS by their molecular features. The 13 loci of polymorphic microsatellite sequences were used to determine loss of heterogeneity (LOH) for the detection of CIN. The MSI status was determined by three mononucleotide repeat markers. Infection of EBV was determined by recovering EBV BNRF1 sequence from genomic DNA collected from gastric cancers. Methylation status of 23 loci was investigated by the combined bisulfite restriction analysis (COBRA). Status of other findings, e.g., KRAS mutations, HER2 expression status and infection of helicobacter pylori were confirmed. Results Gastric cancers were divided into MSI (13%), EBV (7%), CIN (53%), and GS (27%). By histological classification, poorly differentiated adenocarcinoma (por) was more in tumors categorized in MSI-high, and GS and signet-ring cell carcinoma (sig) was more in GS. Among the 23 loci investigated their methylation status, 18 loci were significantly hypermethylated in caner tissues. A unsupervised clustering divided gastric cancers into two clusters, and revealed that most GS tumors clustered together in a cluster that exhibited lower methylation levels, distinct from the other subtypes. The inter-variable clustering revealed that a cluster contained the three loci (SFRP2-region 1/2 and APC) belonging to the Wnt signal cascade (Wnt-associated loci). The mean methylation score of Wnt-associated loci was the lowest in GS tumors (MSI-high: 2.7 [95% confidence interval (CI), 2.3-2.9]; EBV:2.1[1.2-3.1]; CIN: 2.4 [2.2-2.7]; GS: 1.3 [0.8-0.7]). In contrast, the mean methylation score of the other 15 loci was significantly higher in MSI-high, while that in GS was as same as that in EBV or CIN (MSI- high: 10.4 [8.3-12.4]; EBV:5.7 [1.7-9.7]; CIN: 4.4 [3.6-5.1]; GS: 3.4 [2.2-4.6]). Additionally, the lower methylation score of Wnt-associated loci was observed only in sig tumors. Conclusions GS subtype tumors have the potential to possess distinct signatures in DNA hypomethylation profiles in Wnt signaling pathway, especially in signet-ring cell carcinoma.