cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5525/gla.researchdata.1488
title: Power and Participation in Aid Assemblages

description: Soundscapes (three), VoiceOver Audio (two), PDF (one)
DOI: 10.5281/zenodo.10669976
title: Dataset: Underestimated land heat uptake alters the global energy distribution in CMIP6 climate models

description: This dataset corresponds to the following publication:Steinert, N., J., et al.: Underestimated land heat uptake alters the global energy distribution in CMIP6 climate models, in review.

Current global warming results in an uptake of heat by the Earth system, which is distributed among the different components of the climate system. However, current-generation climate models deliver heat inventory and partitioning estimates of Earth system components that differ from recent observations. Here we investigate the global heat distribution under warming by using fully-coupled CMIP6 Earth system model experiments, including a version of the MPI-ESM with a deep land model component, accommodating the required space for more realistic terrestrial heat storage. The results show that sufficiently deep land models exert increased subsurface land heat uptake, leading to a heat uptake partitioning among the Earth system components that is closer to observational estimates. The results are relevant for the understanding of Earth's heat partitioning and highlight the importance of the land heat sink in the Earth heat inventory. 

This dataset includes two file archives:MPI-ESM1-2-LR-shallow (modified MPI-ESM shallow experiment output variables required to calculate the Earth heat inventories)MPI-ESM1-2-LR-deep (modified MPI-ESM deep experiment output variables required to calculate the Earth heat inventories)

This dataset represents source data for the following publication. Please refer to this reference for a more detailed description of the use of this dataset:Steinert, N., J., et al.: Underestimated land heat uptake alters the global energy distribution in CMIP6 climate models, in review.

For any questions regarding the dataset, please feel free to contact Norman J. Steinert (norman.steinert@cicero.oslo.no, normanst@ucm.es)
DOI: 10.5281/zenodo.10667163
title: Pskov UFSIN News Crawl Pt.3

description: WARC files produced by a webcrawl of Pskov UFSIN news online resource. WARC reader is necessary to view files.
DOI: 10.5281/zenodo.10667164
title: Pskov UFSIN News Crawl Pt.3

description: WARC files produced by a webcrawl of Pskov UFSIN news online resource. WARC reader is necessary to view files.
DOI: 10.5281/zenodo.10376131
title: Sistan: part 1. Grid Squares

description: Deposit of Grid Squares from the Sistan region (Iran, Afghanistan) maintained within the EAMENA database.

These Grid Squares cover the central region of the Sistan region (Iran, Afghanistan) and represent a subset of the EAMENA grid system. Each square measures 0.25 degrees in both longitude and latitude, spanning the Middle East and North Africa (MENA) region from Afghanistan to Mauritania. These Grid Squares are the one surveyed to create the Sistan: part 1. Heritage Places. Their spatial coverage covers 16,875 km2 with these boundaries:



Northern boundary: + 31.5

Southern boundary: + 30

Eastern boundary: + 62.5

Western boundary: - 60.5


Their geographic centre is the Iranian city of Zabol (زابل)

---























The two repositories (Heritage Places and Grid Squares) both pertain to Part 1 of the Sistan survey. This dataset primarily focuses on the central areas of Sistan, but it can be expanded through future surveys to include the eastern parts of Sistan in Afghanistan and additional undocumented areas in Iran.








 













 
description: EAMENA data entry methodology. Descriptions of Grid Squares field names can be found on the EAMENA website: https://eamena.org/advanced-use
DOI: 10.5281/zenodo.10376132
title: Sistan: part 1. Grid Squares

description: Deposit of Grid Squares from the Sistan region (Iran, Afghanistan) maintained within the EAMENA database.

These Grid Squares cover the central region of the Sistan region (Iran, Afghanistan) and represent a subset of the EAMENA grid system. Each square measures 0.25 degrees in both longitude and latitude, spanning the Middle East and North Africa (MENA) region from Afghanistan to Mauritania. These Grid Squares are the one surveyed to create the Sistan: part 1. Heritage Places. Their spatial coverage covers 16,875 km2 with these boundaries:



Northern boundary: + 31.5

Southern boundary: + 30

Eastern boundary: + 62.5

Western boundary: - 60.5


Their geographic centre is the Iranian city of Zabol (زابل)

---























The two repositories (Heritage Places and Grid Squares) both pertain to Part 1 of the Sistan survey. This dataset primarily focuses on the central areas of Sistan, but it can be expanded through future surveys to include the eastern parts of Sistan in Afghanistan and additional undocumented areas in Iran.








 













 
description: EAMENA data entry methodology. Descriptions of Grid Squares field names can be found on the EAMENA website: https://eamena.org/advanced-use
DOI: 10.5281/zenodo.10375901
title: Sistan: part 1. Heritage Places

description: Deposit of Heritage Places from the Sistan region (Iran, Afghanistan) maintained within the EAMENA database.

This dataset is an exported subset of the Endangered Archaeology in the Middle East and North Africa (EAMENA) database. It includes archaeological and cultural heritage places, such as ancient settlements, historical structures, traditional villages, and irrigation systemswithin the central areas of the historical landscape of Sistan (سیستان), located in eastern Iran and southwestern Afghanistan. The data was gathered by the visual inspection of 16,875 km2 of open-access satellite imagery accessible on Google Earth covering the period from 2001 to 2022, utilising the EAMENA methodology for archaeological and condition assessment. It is stored in the EAMENA web-based open-access database, hosted by the University of Oxford. The primary objective of compiling this dataset is to evaluate the impact of recent climate and environmental changes, as well as other disturbance factors, such as agriculture, building and development, and infrastructure, on the cultural heritage places of this historical region.

---

The two repositories (Heritage Places and Grid Squares) both pertain to Part 1 of the Sistan survey. This dataset primarily focuses on the central areas of Sistan, but it can be expanded through future surveys to include the eastern parts of Sistan in Afghanistan and additional undocumented areas in Iran.
description: EAMENA data entry methodology. Descriptions of Heritage Places field names can be found on the EAMENA website: https://eamena.org/advanced-use
DOI: 10.5281/zenodo.10375902
title: Sistan: part 1. Heritage Places

description: Deposit of Heritage Places from the Sistan region (Iran, Afghanistan) maintained within the EAMENA database.

This dataset is an exported subset of the Endangered Archaeology in the Middle East and North Africa (EAMENA) database. It includes archaeological and cultural heritage places, such as ancient settlements, historical structures, traditional villages, and irrigation systemswithin the central areas of the historical landscape of Sistan (سیستان), located in eastern Iran and southwestern Afghanistan. The data was gathered by the visual inspection of 16,875 km2 of open-access satellite imagery accessible on Google Earth covering the period from 2001 to 2022, utilising the EAMENA methodology for archaeological and condition assessment. It is stored in the EAMENA web-based open-access database, hosted by the University of Oxford. The primary objective of compiling this dataset is to evaluate the impact of recent climate and environmental changes, as well as other disturbance factors, such as agriculture, building and development, and infrastructure, on the cultural heritage places of this historical region.

---

The two repositories (Heritage Places and Grid Squares) both pertain to Part 1 of the Sistan survey. This dataset primarily focuses on the central areas of Sistan, but it can be expanded through future surveys to include the eastern parts of Sistan in Afghanistan and additional undocumented areas in Iran.
description: EAMENA data entry methodology. Descriptions of Heritage Places field names can be found on the EAMENA website: https://eamena.org/advanced-use
DOI: 10.5281/zenodo.10670325
title: Pskov UFSIN News Crawl Pt.4

description: WARC files produced by a webcrawl of Pskov UFSIN news online resource. WARC reader is necessary to view files.
DOI: 10.5281/zenodo.10670221
title: GPR dataset_San Segundo Hermitage (Ávila, Spain)
title: Raw data
DOI: 10.5281/zenodo.10670222
title: GPR dataset_San Segundo Hermitage (Ávila, Spain)
title: Raw data
DOI: 10.6084/m9.figshare.25232896
title: RPKM and TPM values for each AR gene and sample (ed.)

description: Normalized AR gene coverage depth calculated for each AR gene in each sample as RPKM (Reads Per Kilobase per Million mapped reads) and TPM (Transcripts Per Million mapped reads) values.
DOI: 10.6084/m9.figshare.25232896.v1
title: RPKM and TPM values for each AR gene and sample (ed.)

description: Normalized AR gene coverage depth calculated for each AR gene in each sample as RPKM (Reads Per Kilobase per Million mapped reads) and TPM (Transcripts Per Million mapped reads) values.
DOI: 10.6084/m9.figshare.17079301
title: Additional file 7 of Identification of a novel metabolism-related gene signature associated with the survival of bladder cancer

description: Additional file 7: Table S6. The survival analysis between mutated and nonmutated samples of each mutated gene among the 27 metabolism-related DEGs.
DOI: 10.6084/m9.figshare.17079301.v1
title: Additional file 7 of Identification of a novel metabolism-related gene signature associated with the survival of bladder cancer

description: Additional file 7: Table S6. The survival analysis between mutated and nonmutated samples of each mutated gene among the 27 metabolism-related DEGs.
DOI: 10.5281/zenodo.10670326
title: Pskov UFSIN News Crawl Pt.4

description: WARC files produced by a webcrawl of Pskov UFSIN news online resource. WARC reader is necessary to view files.
DOI: 10.6084/m9.figshare.20474064
title: Data supporting the paper "<b>COVID-19 pandemic-related drugs and microplastics from mask fibers jointly affect soil functions and processes</b>"

description: Results from the combined effects of pharamceuticals and mask microplastic experiment on soil processes and functions.
DOI: 10.6084/m9.figshare.9745955
title: Additional file 1: of Prim-O-glucosylcimifugin enhances the antitumour effect of PD-1 inhibition by targeting myeloid-derived suppressor cells

description: The structures of the traditional Chinese medicines from TCM Database@Taiwan. (SDF 93000 kb)
DOI: 10.6084/m9.figshare.9745955.v1
title: Additional file 1: of Prim-O-glucosylcimifugin enhances the antitumour effect of PD-1 inhibition by targeting myeloid-derived suppressor cells

description: The structures of the traditional Chinese medicines from TCM Database@Taiwan. (SDF 93000 kb)
DOI: 10.6084/m9.figshare.7648814
title: Integrative analysis identifies potential DNA methylation biomarkers for pan-cancer diagnosis and prognosis

description: DNA methylation status is closely associated with diverse diseases, and is generally more stable than gene expression, thus abnormal DNA methylation could be important biomarkers for tumor diagnosis, treatment and prognosis. However, the signatures regarding DNA methylation changes for pan-cancer diagnosis and prognosis are less explored. Here we systematically analyzed the genome-wide DNA methylation patterns in diverse TCGA cancers with machine learning. We identified seven CpG sites that could effectively discriminate tumor samples from adjacent normal tissue samples for 12 main cancers of TCGA (1216 samples, AUC &gt; 0.99). Those seven potential diagnostic biomarkers were further validated in the other 9 different TCGA cancers and 4 independent datasets (AUC &gt; 0.92). Three out of the seven CpG sites were correlated with cell division, DNA replication and cell cycle. We also identified 12 CpG sites that can effectively distinguish 26 different cancers (7605 samples), and the result was repeatable in independent datasets as well as two disparate tumors with metastases (micro-average AUC &gt; 0.89). Furthermore, a series of potential signatures that could significantly predict the prognosis of tumor patients for 7 different cancer were identified via survival analysis (<i>p</i>-value &lt; 1e-4). Collectively, DNA methylation patterns vary greatly between tumor and adjacent normal tissues, as well as among different types of cancers. Our identified signatures may aid the decision of clinical diagnosis and prognosis for pan-cancer and the potential cancer-specific biomarkers could be used to predict the primary site of metastatic breast and prostate cancers.
DOI: 10.6084/m9.figshare.7648814.v1
title: Integrative analysis identifies potential DNA methylation biomarkers for pan-cancer diagnosis and prognosis

description: DNA methylation status is closely associated with diverse diseases, and is generally more stable than gene expression, thus abnormal DNA methylation could be important biomarkers for tumor diagnosis, treatment and prognosis. However, the signatures regarding DNA methylation changes for pan-cancer diagnosis and prognosis are less explored. Here we systematically analyzed the genome-wide DNA methylation patterns in diverse TCGA cancers with machine learning. We identified seven CpG sites that could effectively discriminate tumor samples from adjacent normal tissue samples for 12 main cancers of TCGA (1216 samples, AUC &gt; 0.99). Those seven potential diagnostic biomarkers were further validated in the other 9 different TCGA cancers and 4 independent datasets (AUC &gt; 0.92). Three out of the seven CpG sites were correlated with cell division, DNA replication and cell cycle. We also identified 12 CpG sites that can effectively distinguish 26 different cancers (7605 samples), and the result was repeatable in independent datasets as well as two disparate tumors with metastases (micro-average AUC &gt; 0.89). Furthermore, a series of potential signatures that could significantly predict the prognosis of tumor patients for 7 different cancer were identified via survival analysis (<i>p</i>-value &lt; 1e-4). Collectively, DNA methylation patterns vary greatly between tumor and adjacent normal tissues, as well as among different types of cancers. Our identified signatures may aid the decision of clinical diagnosis and prognosis for pan-cancer and the potential cancer-specific biomarkers could be used to predict the primary site of metastatic breast and prostate cancers.
DOI: 10.6084/m9.figshare.10270352
title: MOESM2 of Silicon dioxide nanoparticles induce insulin resistance through endoplasmic reticulum stress and generation of reactive oxygen species

description: Additional file 2: Table S1. Significant differently expressed genes of RNA-seq (XLS 599 kb)
DOI: 10.6084/m9.figshare.10270352.v1
title: MOESM2 of Silicon dioxide nanoparticles induce insulin resistance through endoplasmic reticulum stress and generation of reactive oxygen species

description: Additional file 2: Table S1. Significant differently expressed genes of RNA-seq (XLS 599 kb)
DOI: 10.6084/m9.figshare.10270358
title: MOESM3 of Silicon dioxide nanoparticles induce insulin resistance through endoplasmic reticulum stress and generation of reactive oxygen species

description: Additional file 3: Table S2. GO terms Table S1 (XLS 150 kb)
DOI: 10.6084/m9.figshare.10270358.v1
title: MOESM3 of Silicon dioxide nanoparticles induce insulin resistance through endoplasmic reticulum stress and generation of reactive oxygen species

description: Additional file 3: Table S2. GO terms Table S1 (XLS 150 kb)
DOI: 10.6084/m9.figshare.9746078
title: Copper associates with differential methylation in placentae from two US birth cohorts

description: Copper is an essential trace nutrient and an enzymatic cofactor necessary for diverse physiological and biological processes. Copper metabolism is uniquely controlled in the placenta and changes to copper metabolism have been linked with adverse birth outcomes. We investigated associations between patterns of DNA methylation (DNAm; measured at &gt;485 k CpG sites) and copper concentration measured from placentae in two independent mother-infant cohorts: the New Hampshire Birth Cohort Study (NHBCS, n = 306) and the Rhode Island Child Health Study (RICHS, n = 141). We identified nine copper-associated differentially methylated regions (DMRs; adjusted P &lt; 0.05) and 15 suggestive CpGs (raw P &lt; 1e-5). One of the most robust variably methylated CpGs associated with the expression of the antioxidant, GSTP1. Our most robust DMR negatively associates with the expression of the zinc-finger gene, <i>ZNF197</i> (FDR = 4.5e-11). Genes co-expressed with <i>ZNF197</i>, a transcription factor, are enriched for genes that associate with birth weight in RICHS (OR = 2.9, P = 2.6e-6, N = 194), genes that are near a ZNF197 consensus binding motif (OR = 1.34, P = 0.01, N = 194), and for those classified in GO biological processes <i>growth hormone secretion</i> (P = 3.4e-4), <i>multicellular organism growth</i> (P = 3.8e-4), and <i>molecular functions related to lipid biosynthesis</i> (P = 1.9e-4). Further, putative transcriptional targets for ZNF197 include genes involved in copper metabolism and placentation. Our results suggest that copper metabolism is tied to DNAm in the placenta and that copper-associated patterns in DNAm may mediate normal placentation and foetal development.
DOI: 10.6084/m9.figshare.9746078.v2
title: Copper associates with differential methylation in placentae from two US birth cohorts

description: Copper is an essential trace nutrient and an enzymatic cofactor necessary for diverse physiological and biological processes. Copper metabolism is uniquely controlled in the placenta and changes to copper metabolism have been linked with adverse birth outcomes. We investigated associations between patterns of DNA methylation (DNAm; measured at &gt;485 k CpG sites) and copper concentration measured from placentae in two independent mother-infant cohorts: the New Hampshire Birth Cohort Study (NHBCS, n = 306) and the Rhode Island Child Health Study (RICHS, n = 141). We identified nine copper-associated differentially methylated regions (DMRs; adjusted P &lt; 0.05) and 15 suggestive CpGs (raw P &lt; 1e-5). One of the most robust variably methylated CpGs associated with the expression of the antioxidant, GSTP1. Our most robust DMR negatively associates with the expression of the zinc-finger gene, <i>ZNF197</i> (FDR = 4.5e-11). Genes co-expressed with <i>ZNF197</i>, a transcription factor, are enriched for genes that associate with birth weight in RICHS (OR = 2.9, P = 2.6e-6, N = 194), genes that are near a ZNF197 consensus binding motif (OR = 1.34, P = 0.01, N = 194), and for those classified in GO biological processes <i>growth hormone secretion</i> (P = 3.4e-4), <i>multicellular organism growth</i> (P = 3.8e-4), and <i>molecular functions related to lipid biosynthesis</i> (P = 1.9e-4). Further, putative transcriptional targets for ZNF197 include genes involved in copper metabolism and placentation. Our results suggest that copper metabolism is tied to DNAm in the placenta and that copper-associated patterns in DNAm may mediate normal placentation and foetal development.
DOI: 10.6084/m9.figshare.9746078.v1
title: Copper Associates with Differential Methylation in Placentae from Two US Birth Cohorts

description: Copper is an essential trace nutrient and an enzymatic cofactor necessary for diverse physiological and biological processes. Copper metabolism is uniquely controlled in the placenta and changes to copper metabolism have been linked with adverse birth outcomes. We investigated associations between patterns of DNA methylation (DNAm; measured at &gt;485k CpG sites) and copper concentration measured from placentae in two independent mother-infant cohorts: the New Hampshire Birth Cohort Study (NHBCS, n = 306) and the Rhode Island Child Health Study (RICHS, n = 141). We identified nine copper-associated differentially methylated regions (DMRs; adjusted P &lt; 0.05) and 15 suggestive CpGs (raw P&lt;1e-5). One of the most robust variably methylated CpGs associated with the expression of the antioxidant, GSTP1. Our most robust DMR negatively associates with expression of the zinc finger gene, <i>ZNF197</i> (FDR=4.5e-11). Genes co-expressed with <i>ZNF197</i>, a transcription factor, are enriched for genes that associate with birth weight in RICHS (OR= 2.9, P= 2.6e-6, N=194), genes that are near a ZNF197 consensus binding motif (OR= 1.34, P= 0.01, N=194), and for those classified in GO biological processes <i>growth hormone secretion</i> (P=3.4e-4), <i>multicellular organism growth</i> (P=3.8e-4), and <i>molecular functions related to lipid biosynthesis</i> (P=1.9e-4). Further, putative transcriptional targets for ZNF197 include genes involved in copper metabolism and placentation. Our results suggest that copper metabolism is tied to DNAm in the placenta and that copper-associated patterns in DNAm may mediate normal placentation and fetal development.
DOI: 10.6084/m9.figshare.10270367
title: MOESM4 of Silicon dioxide nanoparticles induce insulin resistance through endoplasmic reticulum stress and generation of reactive oxygen species

description: Additional file 4: Table S3. List of primer sequences (XLS 28 kb)
DOI: 10.6084/m9.figshare.10270367.v1
title: MOESM4 of Silicon dioxide nanoparticles induce insulin resistance through endoplasmic reticulum stress and generation of reactive oxygen species

description: Additional file 4: Table S3. List of primer sequences (XLS 28 kb)
DOI: 10.6084/m9.figshare.14464677
title: Output files(part10)

description: The output files of MIP3D.
DOI: 10.6084/m9.figshare.10270373
title: MOESM1 of DNA methylation profiles capturing breast cancer heterogeneity

description: Additional file 1: Table S1. Annotations of prognostic CpGs. Table S2. Annotations of prognostic DMGs. Table S3. Correlation between the methylation and expression of pDMGs. Table S4. Learning matrix of the 313 CpG (with gene attribution) and outcome variables.
DOI: 10.6084/m9.figshare.14464677.v1
title: Output files(part10)

description: The output files of MIP3D.
DOI: 10.6084/m9.figshare.10270373.v1
title: MOESM1 of DNA methylation profiles capturing breast cancer heterogeneity

description: Additional file 1: Table S1. Annotations of prognostic CpGs. Table S2. Annotations of prognostic DMGs. Table S3. Correlation between the methylation and expression of pDMGs. Table S4. Learning matrix of the 313 CpG (with gene attribution) and outcome variables.
DOI: 10.6084/m9.figshare.10270388
title: MOESM1 of Dysregulation of neuron differentiation in an autistic savant with exceptional memory

description: Additional file 1: Table S1. Exome sequencing of family members and control _ CNVs and SNPs. Related to Fig. 1.
DOI: 10.6084/m9.figshare.10270388.v1
title: MOESM1 of Dysregulation of neuron differentiation in an autistic savant with exceptional memory

description: Additional file 1: Table S1. Exome sequencing of family members and control _ CNVs and SNPs. Related to Fig. 1.
DOI: 10.6084/m9.figshare.10270394
title: MOESM2 of Dysregulation of neuron differentiation in an autistic savant with exceptional memory

description: Additional file 2: Table S2. Secondary RNA sequencing _ differentially expressed genes _ significant. Related to Fig. 2.
DOI: 10.6084/m9.figshare.10270394.v1
title: MOESM2 of Dysregulation of neuron differentiation in an autistic savant with exceptional memory

description: Additional file 2: Table S2. Secondary RNA sequencing _ differentially expressed genes _ significant. Related to Fig. 2.
DOI: 10.6084/m9.figshare.6600380
title: Additional file 8: of Characterization of the Populus Rab family genes and the function of PtRabE1b in salt tolerance

description: Table S3. Expression data of 27 PtRab paralogous pairs used for correlation analysis. (XLSX 22 kb)