cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7885745
title: Integrated single-cell profiling dissects cell-state-specific enhancer landscapes of human tumor-infiltrating CD8+ T cells_Supplemental_Data

description: Processed Datasets for: EGA Study ID: EGAS00001006141 EGA Dataset ID: EGAD00001008662 Find processed files and arrow files Abstract: Despite extensive studies on the chromatin landscape of exhausted T cells, the transcriptional wiring underlying the heterogeneous functional and dysfunctional states of human tumor-infiltrating lymphocytes (TILs) is incompletely understood. Here, we identify gene-regulatory landscapes in a wide breadth of functional and dysfunctional CD8<sup>+</sup> TIL states covering four cancer entities using single-cell chromatin profiling. We map enhancer-promoter interactions in human TILs by integrating single-cell chromatin accessibility with single-cell RNA-seq data from tumor-entity-matching samples and prioritize cell-state-specific genes by super-enhancer analysis. Besides revealing entity-specific chromatin remodeling in exhausted TILs, our analyses identify a common chromatin trajectory to TIL dysfunction and determine key enhancers, transcriptional regulators, and deregulated genes involved in this process. Finally, we validate enhancer regulation at immunotherapeutically relevant loci by targeting non-coding regulatory elements with potent CRISPR activators and repressors. In summary, our study provides a framework for understanding and manipulating cell-state-specific gene-regulatory cues from human tumor-infiltrating lymphocytes.
description: {"references": ["Mol Cell . 2023 Feb 16;83(4):622-636.e10. doi: 10.1016/j.molcel.2022.12.029. Epub 2023 Jan 18"]}
DOI: 10.5281/zenodo.7885744
title: Integrated single-cell profiling dissects cell-state-specific enhancer landscapes of human tumor-infiltrating CD8+ T cells_Supplemental_Data

description: Processed Datasets for: EGA Study ID: EGAS00001006141 EGA Dataset ID: EGAD00001008662 Find processed files and arrow files Abstract: Despite extensive studies on the chromatin landscape of exhausted T cells, the transcriptional wiring underlying the heterogeneous functional and dysfunctional states of human tumor-infiltrating lymphocytes (TILs) is incompletely understood. Here, we identify gene-regulatory landscapes in a wide breadth of functional and dysfunctional CD8<sup>+</sup> TIL states covering four cancer entities using single-cell chromatin profiling. We map enhancer-promoter interactions in human TILs by integrating single-cell chromatin accessibility with single-cell RNA-seq data from tumor-entity-matching samples and prioritize cell-state-specific genes by super-enhancer analysis. Besides revealing entity-specific chromatin remodeling in exhausted TILs, our analyses identify a common chromatin trajectory to TIL dysfunction and determine key enhancers, transcriptional regulators, and deregulated genes involved in this process. Finally, we validate enhancer regulation at immunotherapeutically relevant loci by targeting non-coding regulatory elements with potent CRISPR activators and repressors. In summary, our study provides a framework for understanding and manipulating cell-state-specific gene-regulatory cues from human tumor-infiltrating lymphocytes.
description: {"references": ["Mol Cell . 2023 Feb 16;83(4):622-636.e10. doi: 10.1016/j.molcel.2022.12.029. Epub 2023 Jan 18"]}
DOI: 10.15151/esrf-es-1106935708
title: Rhenium solubility in chloride-bearing and oxidizing fluids

description: Rhenium (Re) is an extremely rare element with average abundances of 0.7 ppb in the Earth’s crust. It is a ‘critical metal’ due to its strongly limited natural occurrence while it is essential and at present non-replaceable for several industrial applications. The main host phase for Re is molybdenite (100 - 3000 ppm Re) which is mined mainly from porphyry copper deposits (PCDs). Formation of PCDs is based on magmatic-hydrothermal fluids that transport and enrich metals during ascent to shallower levels within the Earth’s crust. While enrichment processes of main metals of PCDs and other magmatic-hydrothermal ore deposits (e.g., Fe, Cu) have been studied in detail, only few works so far focus on secondary metals probably due to challenging experimental setups (detection of extremely high dilution levels of Re at high PT conditions). However, this knowledge is essential particular for ‘critical’ metals to facilitate and support efficient and sustainable exploration of ore deposits.
DOI: 10.6084/m9.figshare.22731545
title: A field recording collected in Zijin Mountain

description: This recording contained no anthropogenic sounds but mild winds and bird vocalizations.
DOI: 10.6084/m9.figshare.22731545.v1
title: A field recording collected in Zijin Mountain

description: This recording contained no anthropogenic sounds but mild winds and bird vocalizations.
DOI: 10.18112/openneuro.ds004196.v1.0.8
title: FMRI-EEG Prestudy
DOI: 10.5281/zenodo.7826129
title: DIETxPOSOME - Selection of potentially useful papers from literature mining and machine learning protocols

description: DIETxPOSOME database concerning literature selection of potentially useful papers retrieved from PubMed search API, concerning contaminants quantification in food items of worldwide highest supply and using FoodMine code (text matching filter) and machine learning (ML) protocols. A list of 2,442 papers that potentially contained relevant information, covering the period between 2000 and 2022, was compiled from an initial number of 1,932,345 papers.
DOI: 10.5281/zenodo.7826130
title: DIETxPOSOME - Selection of potentially useful papers from literature mining and machine learning protocols

description: DIETxPOSOME database concerning literature selection of potentially useful papers retrieved from PubMed search API, concerning contaminants quantification in food items of worldwide highest supply and using FoodMine code (text matching filter) and machine learning (ML) protocols. A list of 2,442 papers that potentially contained relevant information, covering the period between 2000 and 2022, was compiled from an initial number of 1,932,345 papers.
DOI: 10.6084/m9.figshare.21541723
title: DNA barcodes for Great Salt Lake brine flies establish a baseline for monitoring changes in biodiversity

description: Great Salt Lake (GSL) is the center of a valuable wetland ecosystem in the Great Basin of North America. The lake is an important site for millions of migratory birds that feed on 2 principal invertebrates, brine shrimp and brine flies (Diptera: Ephydridae). Despite their ecological and economic importance, no genetic studies have been published for either resident GSL invertebrate. The family Ephydridae (shore flies and brine flies) is one of the largest in the order Diptera, with nearly 2000 described species. Members of this family are prominent in a variety of aquatic environments and are particularly interesting because of their adaptation to several marginal habitats, including hot springs, oil ponds, highly saline lakes, and inland alkaline pools and marshes. This report provides cytochrome <i>c</i> oxidase I (COI) DNA barcodes for 5 species of GSL shore flies, distributed among 5 genera and 3 subfamilies. The phylogenetic content of these DNA sequences is explored by comparing a molecular phylogeny to those based on morphological features. Over the past decade, urbanization and inflow diversion have reduced the surface area of GSL by nearly 50%, with unknown consequences for the ecosystem. This study establishes a genetic framework to assess changes in GSL invertebrate diversity important in monitoring the effects of anthropogenic and climate pressures on this important natural resource.
DOI: 10.6084/m9.figshare.21541723.v2
title: DNA barcodes for Great Salt Lake brine flies establish a baseline for monitoring changes in biodiversity

description: Great Salt Lake (GSL) is the center of a valuable wetland ecosystem in the Great Basin of North America. The lake is an important site for millions of migratory birds that feed on 2 principal invertebrates, brine shrimp and brine flies (Diptera: Ephydridae). Despite their ecological and economic importance, no genetic studies have been published for either resident GSL invertebrate. The family Ephydridae (shore flies and brine flies) is one of the largest in the order Diptera, with nearly 2000 described species. Members of this family are prominent in a variety of aquatic environments and are particularly interesting because of their adaptation to several marginal habitats, including hot springs, oil ponds, highly saline lakes, and inland alkaline pools and marshes. This report provides cytochrome <i>c</i> oxidase I (COI) DNA barcodes for 5 species of GSL shore flies, distributed among 5 genera and 3 subfamilies. The phylogenetic content of these DNA sequences is explored by comparing a molecular phylogeny to those based on morphological features. Over the past decade, urbanization and inflow diversion have reduced the surface area of GSL by nearly 50%, with unknown consequences for the ecosystem. This study establishes a genetic framework to assess changes in GSL invertebrate diversity important in monitoring the effects of anthropogenic and climate pressures on this important natural resource.
DOI: 10.6084/m9.figshare.20348317
title: The not-so-dead of winter: underwater light climate and primary productivity under snow and ice cover in inland lakes

description: As global surface temperatures continue to rise as a result of anthropogenic climate change, effects in temperate lakes are likely to be more pronounced than in other ecosystems. Decreases in snow and ice cover extent and duration and extended periods of summer stratification have been observed in temperate lake systems throughout the Anthropocene. However, the effects of changing snow and ice cover on lacustrine communities remain largely uninvestigated. We examined underwater light climate and associated primary productivity patterns under snow-covered and clear-lake ice in 6 inland lakes in Minnesota, USA, spanning gradients of water column optical properties (blue, green, brown) associated with trophic status and organic material content. In all lakes, snow cover influenced not only the intensity, but also the spectral signature of light penetrating into the water column. Specifically, the wavelength of maximum penetration was shifted towards longer wavelengths under snow cover in green (eutrophic) lakes but was shifted towards shorter wavelengths in blue and brown lakes. Volumetric primary productivity was often higher than anticipated (e.g., ∼1200 mg m<sup>−3</sup> d<sup>−1</sup>; Lake Minnetonka, snow-covered ice). Carbon assimilation rates were lower under snow-covered ice throughout the water column in all lake types except immediately under cleared ice in eutrophic lakes, where phytoplankton were likely photoinhibited because of the penetration of intense, short-wavelength light. These findings suggest that changes to snow and ice cover under ongoing climate change scenarios can affect patterns of phytoplankton primary productivity in sensitive aquatic ecosystems.
DOI: 10.6084/m9.figshare.20348317.v2
title: The not-so-dead of winter: underwater light climate and primary productivity under snow and ice cover in inland lakes

description: As global surface temperatures continue to rise as a result of anthropogenic climate change, effects in temperate lakes are likely to be more pronounced than in other ecosystems. Decreases in snow and ice cover extent and duration and extended periods of summer stratification have been observed in temperate lake systems throughout the Anthropocene. However, the effects of changing snow and ice cover on lacustrine communities remain largely uninvestigated. We examined underwater light climate and associated primary productivity patterns under snow-covered and clear-lake ice in 6 inland lakes in Minnesota, USA, spanning gradients of water column optical properties (blue, green, brown) associated with trophic status and organic material content. In all lakes, snow cover influenced not only the intensity, but also the spectral signature of light penetrating into the water column. Specifically, the wavelength of maximum penetration was shifted towards longer wavelengths under snow cover in green (eutrophic) lakes but was shifted towards shorter wavelengths in blue and brown lakes. Volumetric primary productivity was often higher than anticipated (e.g., ∼1200 mg m<sup>−3</sup> d<sup>−1</sup>; Lake Minnetonka, snow-covered ice). Carbon assimilation rates were lower under snow-covered ice throughout the water column in all lake types except immediately under cleared ice in eutrophic lakes, where phytoplankton were likely photoinhibited because of the penetration of intense, short-wavelength light. These findings suggest that changes to snow and ice cover under ongoing climate change scenarios can affect patterns of phytoplankton primary productivity in sensitive aquatic ecosystems.
DOI: 10.6084/m9.figshare.22586066
title: The first complete chloroplast genome in <i>Engelhardia sensu stricto</i>, <i>Engelhardia hainanensis</i> Chen: genome characterization and its phylogenetic relationships within the family Juglandaceae

description: Trees of <i>Engelhardia</i> are important components of subtropical and tropical forests in South-eastern Asia with great ecological and economic values. However, phylogenetic relationships within Engelhardioideae (Juglandaceae) remains obscure. In this study, we report the first complete chloroplast genome sequences of <i>Engelhardia sensu stricto</i>, <i>Engelhardia hainanensis</i> Chen, a rare species endemic in southern China. Its complete chloroplast genome is 161,574 bp in length, with a typical quadripartite structure that includes a large single-copy region of 91,158 bp, a small single-copy region of 18,790 bp, and its GC content is 35.8%. A total of 128 genes were identified, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Furthermore, a phylogenetic tree of Juglandaceae was constructed based the complete chloroplast genome sequence, which strongly support the three-subfamily classification system in Juglandaceae, and <i>E. hainanensis</i> was resolved sister to two <i>Alfaropsis</i> species. This study provides valuable genomic information for the species identification and phylogenetic study of Juglandaceae.
DOI: 10.6084/m9.figshare.22586066.v1
title: The first complete chloroplast genome in <i>Engelhardia sensu stricto</i>, <i>Engelhardia hainanensis</i> Chen: genome characterization and its phylogenetic relationships within the family Juglandaceae

description: Trees of <i>Engelhardia</i> are important components of subtropical and tropical forests in South-eastern Asia with great ecological and economic values. However, phylogenetic relationships within Engelhardioideae (Juglandaceae) remains obscure. In this study, we report the first complete chloroplast genome sequences of <i>Engelhardia sensu stricto</i>, <i>Engelhardia hainanensis</i> Chen, a rare species endemic in southern China. Its complete chloroplast genome is 161,574 bp in length, with a typical quadripartite structure that includes a large single-copy region of 91,158 bp, a small single-copy region of 18,790 bp, and its GC content is 35.8%. A total of 128 genes were identified, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Furthermore, a phylogenetic tree of Juglandaceae was constructed based the complete chloroplast genome sequence, which strongly support the three-subfamily classification system in Juglandaceae, and <i>E. hainanensis</i> was resolved sister to two <i>Alfaropsis</i> species. This study provides valuable genomic information for the species identification and phylogenetic study of Juglandaceae.
DOI: 10.6084/m9.figshare.22643444
title: The characteristics of the complete chloroplast genome of <i>Staurogyne concinnula</i> (Hance) O. Kuntze (Acanthaceae)

description: <i>Staurogyne concinnula</i> (Hance) O. Kuntze (Acanthaceae) is an important ornamental herb mainly distributed in the southern region of China, including Fujian, Guangdong, Hainan, and Taiwan provinces. However, the complete chloroplast genome of <i>S. concinnula</i>, which could serve as a genetic resource for studies on its taxonomy and evolution, is poorly studied at present. In this study, we reported the complete chloroplast genome of <i>S. concinnula</i> that was assembled using high-throughput sequencing data. The chloroplast genome was 153,783 bp long, with a typical quadripartite structure containing a small single-copy region (SSC; 17,855 bp), a large single-copy region (LSC; 84,636 bp) and a pair of inverted repeats (IRs; each 25,646 bp). The overall GC content of the chloroplast genome was 38.04%. A total of 86 protein-coding genes (PCGs), 8 rRNA genes, and 37 tRNA genes were predicted. Phylogenetic analysis based on the combined sequences of 86 PCGs with the other 16 closely related species of Acanthaceae indicated that <i>S. concinnula</i> is closely related to <i>Avicennia marina</i>. The genomic data and finding from the phylogenetic studies of <i>S. concinnula</i> could provide useful information and give light to in-depth studies on the evolution pattern of the understudied species, as well as Staurogyne.
DOI: 10.6084/m9.figshare.22643444.v1
title: The characteristics of the complete chloroplast genome of <i>Staurogyne concinnula</i> (Hance) O. Kuntze (Acanthaceae)

description: <i>Staurogyne concinnula</i> (Hance) O. Kuntze (Acanthaceae) is an important ornamental herb mainly distributed in the southern region of China, including Fujian, Guangdong, Hainan, and Taiwan provinces. However, the complete chloroplast genome of <i>S. concinnula</i>, which could serve as a genetic resource for studies on its taxonomy and evolution, is poorly studied at present. In this study, we reported the complete chloroplast genome of <i>S. concinnula</i> that was assembled using high-throughput sequencing data. The chloroplast genome was 153,783 bp long, with a typical quadripartite structure containing a small single-copy region (SSC; 17,855 bp), a large single-copy region (LSC; 84,636 bp) and a pair of inverted repeats (IRs; each 25,646 bp). The overall GC content of the chloroplast genome was 38.04%. A total of 86 protein-coding genes (PCGs), 8 rRNA genes, and 37 tRNA genes were predicted. Phylogenetic analysis based on the combined sequences of 86 PCGs with the other 16 closely related species of Acanthaceae indicated that <i>S. concinnula</i> is closely related to <i>Avicennia marina</i>. The genomic data and finding from the phylogenetic studies of <i>S. concinnula</i> could provide useful information and give light to in-depth studies on the evolution pattern of the understudied species, as well as Staurogyne.
DOI: 10.5281/zenodo.7886113
title: DIETxPOSOME - Summary statistics from papers obtained from literature mining and machine learning protocols

description: DIETxPOSOME database concerning literature selection of potentially useful papers retrieved from PubMed search API, concerning contaminants quantification in food items of worldwide highest supply and using FoodMine code (text matching filter) and machine learning (ML) protocols. 11,723 data points were collected from 254 papers from the last two decades in 72 foods to obtain relevant information on 96 contaminants, including heavy metals, polychlorinated biphenyls, dioxins, furans, polycyclic aromatic hydrocarbons (PAHs), pesticides, mycotoxins, and heterocyclic aromatic amines (HAAs).
DOI: 10.5281/zenodo.7886112
title: DIETxPOSOME - Summary statistics from papers obtained from literature mining and machine learning protocols

description: DIETxPOSOME database concerning literature selection of potentially useful papers retrieved from PubMed search API, concerning contaminants quantification in food items of worldwide highest supply and using FoodMine code (text matching filter) and machine learning (ML) protocols. 11,723 data points were collected from 254 papers from the last two decades in 72 foods to obtain relevant information on 96 contaminants, including heavy metals, polychlorinated biphenyls, dioxins, furans, polycyclic aromatic hydrocarbons (PAHs), pesticides, mycotoxins, and heterocyclic aromatic amines (HAAs).
DOI: 10.5281/zenodo.7866103
title: PolyMed: A Medical Dataset Addressing Disease Imbalance for Robust Automatic Diagnosis Systems

description: We introduce the PolyMed dataset, designed to address the limitations of existing medical case data for Automatic Diagnosis Systems (ADS). ADS assists doctors by predicting diseases based on patients' basic information, such as age, gender, and symptoms. However, these systems face challenges due to imbalanced disease label data and difficulties in accessing or collecting medical data. To tackle these issues, the PolyMed dataset has been developed to improve the evaluation of ADS by incorporating medical knowledge graph data and diagnosis case data. The dataset aims to provide comprehensive evaluation, include diverse disease information, effectively utilize external knowledge, and perform tasks closer to real-world scenarios. We have also made the data collection tools publicly available to enable researchers and other interested parties to contribute additional data in a standardized format. These tools feature a range of customizable input fields that can be selectively utilized according to the user's specific requirements, ensuring consistency and professionalism in the data collection process. All train and test code of our data available in https://github.com/krchanyang/PolyMed
DOI: 10.5281/zenodo.7866102
title: PolyMed: A Medical Dataset Addressing Disease Imbalance for Robust Automatic Diagnosis Systems

description: We introduce the PolyMed dataset, designed to address the limitations of existing medical case data for Automatic Diagnosis Systems (ADS). ADS assists doctors by predicting diseases based on patients' basic information, such as age, gender, and symptoms. However, these systems face challenges due to imbalanced disease label data and difficulties in accessing or collecting medical data. To tackle these issues, the PolyMed dataset has been developed to improve the evaluation of ADS by incorporating medical knowledge graph data and diagnosis case data. The dataset aims to provide comprehensive evaluation, include diverse disease information, effectively utilize external knowledge, and perform tasks closer to real-world scenarios. We have also made the data collection tools publicly available to enable researchers and other interested parties to contribute additional data in a standardized format. These tools feature a range of customizable input fields that can be selectively utilized according to the user's specific requirements, ensuring consistency and professionalism in the data collection process. All train and test code of our data available in https://github.com/krchanyang/PolyMed
DOI: 10.6084/m9.figshare.22731662
title: No consistent correlation of behavioral laterality with cognitive ability of scatter-hoarding rodents

description: No consistent correlation of behavioral laterality with cognitive ability of scatter-hoarding rodents
DOI: 10.6084/m9.figshare.22731662.v1
title: No consistent correlation of behavioral laterality with cognitive ability of scatter-hoarding rodents

description: No consistent correlation of behavioral laterality with cognitive ability of scatter-hoarding rodents
DOI: 10.25345/c59p2wg8v
title: MassIVE MSV000091835 - A region-resolved proteomic map of the human brain enabled by high-throughput proteomics
title: High-throughput proteomics by micro-flow LC timsTOF-HT maps the human brain proteome in a region-resolved manner
DOI: 10.22008/fk2/lvbp1d/kopsj1
title: G100_Uiffaq_69V1_ S_400dpi.tif
DOI: 10.22008/fk2/lvbp1d
title: Geological map of Greenland, 1:100 000, Uiffaq 69 V.1 Syd

description: Geologisk kort over Grønland / Geological map of Greenland - 1:100 000, central West Greenland, Disko/Qeqertarsuaq
DOI: 10.22008/fk2/lvbp1d/y97ktg
title: G100_Uiffaq_69V1_ S_400dpi.pdf
DOI: 10.57745/5z7lie
title: yolov8l-640.pt

description: pytorch format of yolov8