cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24955524.v1
title: vOTU sequences assembled from the underground anchialine estuary, Bundera Sinkhole, Australia

description: <i>Background</i>Viruses play important roles in modulating microbial communities and influencing global biogeochemistry. There is now growing interest in characterising their ecological roles across diverse biomes. However, little is known about viral ecology in low-nutrient, chemotrophic-based environments. In such ecosystems, virus-driven manipulation of nutrient cycles might have profound impacts across trophic levels. In particular, anchialine environments, which are low-energy underground estuaries sustained by chemotrophic processes, represent ideal model systems to study novel virus-host-environment interactions.<i>Results</i>Here, we employ metagenomic sequencing to investigate the viral community in Bundera Sinkhole, an anchialine ecosystem rich in endemic species supported by microbial chemosynthesis. We find that the viruses are highly novel, with less than 2% representing described viruses, and are hugely abundant, making up as much as 12% of microbial intracellular DNA. These highly abundant viruses largely infect important prokaryotic taxa that drive key metabolic processes in the sinkhole. Further, the abundance of viral auxiliary metabolic genes (AMGs) involved in nucleotide and protein synthesis was strongly correlated with declines in environmental phosphate and sulphate concentrations. These AMGs encoded key enzymes needed to produce sulphur-containing amino acids, and phosphorus metabolic enzymes involved in purine and pyrimidine nucleotide synthesis. We hypothesise that this correlation is either due to selection of these AMGs under low phosphate and sulphate concentrations, highlighting the dynamic interactions between viruses, their hosts, and the environment; or, that these AMGs are driving increased viral nucleotide and protein synthesis via manipulation of host phosphorus and sulphur metabolism, consequently driving nutrient depletion in the surrounding water.<i>Conclusion</i>This study represents the first metagenomic investigation of viruses in anchialine ecosystems, and provides new hypotheses and insights into virus-host-environment interactions in such ‘dark’, low-energy environments. This is particularly important since anchialine ecosystems are characterised by diverse endemic species, both in their microbial and faunal assemblages, which are primarily supported by microbial chemosynthesis. Thus, virus-host-environment interactions could have profound effects cascading through all trophic levels.
DOI: 10.5281/zenodo.8259941
title: Single-cell Spatial Transcriptomics Data with Paired RNAseq for TISSUE spatial gene expression prediction

description: Dataset folders from "TISSUE: uncertainty-calibrated prediction of single-cell spatial transcriptomics improves downstream analyses". If using the processed data or TISSUE algorithm, please cite: https://doi.org/10.1101/2023.04.25.538326.

The directory of datasets are compressed in tar gzip format. The top level contains folders with dataset names and within each of those folders, there are the relevant data files which include:

- Spatial_count.txt --- a tab-delimited file containing spatial transcriptomics counts matrix

- scRNA_count.txt --- a tab-delimited file containing RNAseq counts matrix

- Locations.txt --- a tab-delimited file containing the (x,y) spatial coordinates of cells in the spatial transcriptomics data

- Metadata.txt --- for some datasets, this is a comma-separated file containing the metadata table for the spatial transcriptomics data

These files are formatted and organized to be read into AnnData objects using the native loading functions in the TISSUE package (https://github.com/sunericd/TISSUE). Some folders will also have additional accessory files such as gene lists corresponding to some experiments present in our manuscript and/or adjacency matrix objects.

Also included are the two simulated spatial transcriptomics datasets that we generated using SRTsim.

The SVZ folders contain our processed MERFISH spatial transcriptomics dataset on the adult mouse subventricular zone. Refer to the SVZFullFinal folder for the full dataset with TISSUE-informed cell labels. All other folders are processed data accessed from publicly available sources. The identity of numbered folders can be found in the Data Availability statement of the benchmarking paper from which they were retrieved: https://doi.org/10.1038/s41592-022-01480-9

"svz_merfish_data.zip" includes the raw MERFISH dataset on the adult mouse subventricular zone.
DOI: 10.5281/zenodo.8259942
title: Single-cell Spatial Transcriptomics Data with Paired RNAseq for TISSUE spatial gene expression prediction

description: Dataset folders from "TISSUE: uncertainty-calibrated prediction of single-cell spatial transcriptomics improves downstream analyses". If using the processed data or TISSUE algorithm, please cite: https://doi.org/10.1101/2023.04.25.538326.

The directory of datasets are compressed in tar gzip format. The top level contains folders with dataset names and within each of those folders, there are the relevant data files which include:

- Spatial_count.txt --- a tab-delimited file containing spatial transcriptomics counts matrix

- scRNA_count.txt --- a tab-delimited file containing RNAseq counts matrix

- Locations.txt --- a tab-delimited file containing the (x,y) spatial coordinates of cells in the spatial transcriptomics data

- Metadata.txt --- for some datasets, this is a comma-separated file containing the metadata table for the spatial transcriptomics data

These files are formatted and organized to be read into AnnData objects using the native loading functions in the TISSUE package (https://github.com/sunericd/TISSUE). Some folders will also have additional accessory files such as gene lists corresponding to some experiments present in our manuscript and/or adjacency matrix objects.

Also included are the two simulated spatial transcriptomics datasets that we generated using SRTsim.

The SVZ folders contain our processed MERFISH spatial transcriptomics dataset on the adult mouse subventricular zone. Refer to the SVZFullFinal folder for the full dataset with TISSUE-informed cell labels. All other folders are processed data accessed from publicly available sources. The identity of numbered folders can be found in the Data Availability statement of the benchmarking paper from which they were retrieved: https://doi.org/10.1038/s41592-022-01480-9

"svz_merfish_data.zip" includes the raw MERFISH dataset on the adult mouse subventricular zone.
DOI: 10.6084/m9.figshare.22802341
title: Metasomatized mantle under the Eastern Mexican Alkaline Province: evidence from the Oligocene Rincón Murillo Gabbro, Sierra de San Carlos-Cruillas, NE México

description: The Cenozoic Sierra de San Carlos-Cruillas (SSCC) magmatic complex belongs to the Eastern Mexican Alkaline Province (EMAP). The SSCC mainly consists of plutonic and subvolcanic bodies displaying diverse lithological compositions. These rocks exhibit both OIB- and arc-like geochemical characteristics. In this contribution, we present new petrographic, geochemical, isotopic, and geochronological data of the Rincón Murillo Gabbro (RMG), situated in the southern part of the SSCC. The RMG is nepheline normative and displays an OIB-like intraplate character. Laser ablation ICP-MS U-Pb analyses on titanites yielded Oligocene (Rupelian) crystallization ages of 31.8 ± 1.8 and 31.0 ± 1.7 Ma. The <sup>87</sup>Sr/<sup>86</sup>Sr<sub>(i)</sub> (0.703400–0.704159) and <sup>143</sup>Nd/<sup>144</sup>Nd<sub>(i)</sub> (0.512732–0.512815) ratios indicate a mantle origin. Trace element data indicate the participation of different enriched mantle components in the source. One component is related to previous subduction processes, generating the HFSE-depleted arc-like magmas of San José Gabbro in the northern part of SSCC. The second component is related to deep mantle melts with a slightly carbonatitic signal and HFSE-enriched fluids derived from the subducted Hess conjugate plateau generating different enriched sources in the upper mantle under the SSCC. The passage, eclogitization, detachment and foundering of the Hess plateau gave rise to an asthenospheric upwelling that triggered the low to moderate partial melting degrees (3–15%) of an amphibole-bearing garnet peridotite, generating the OIB-like parental magmas of RMG, located in the southern part of SSCC. Two-component mixing, and AFC models indicate that variable degrees of crystal fractionation and minor crustal assimilation are involved in the evolution of Rincón Murillo Gabbro.
DOI: 10.6084/m9.figshare.22726876
title: Reworked Neoproterozoic sub-arc lithosphere beneath the Eastern Desert (Egypt): Evidence from geochemistry and geochronology of metabasites and granitoid gneisses, Gabal Um Gunud area

description: High-grade granitoid gneisses (740–710 Ma) and elongate bodies of amphibolite and hornblende schist with cm-scale layers of garnet pyroxenite form an overturned fold in the Gabal Um Gunud area, South Eastern Desert of Egypt. Whole-rock geochemical data combined with zircon U-Pb-Hf isotope data suggest that the metabasites represent relics of oceanic crust with an N-MORB affinity, which has been derived from partial melting (2.0–1.4 GPa; ~65- ~ 45 km depth) of a depleted mantle source beneath an intra-oceanic, spreading forearc basin. Such increment of melting degree resulted in small basaltic melt batches with transitional tholeiitic to boninitic affinities. Progressive slab subduction and partial melting of the tholeiitic amphibolite produced high-Al and low HREE melts for trondhjemite at av. <i>T</i> = 854°C and low-Al and high HREE melts for tonalite at higher temperatures (av. 949°C). The low Mg# of the trondhjemite-tonalite rocks may be attributed to limited contamination of subduction components, as evidenced by the weak lanthanide tetrad effects (TE<sub>1,3</sub>~1) and near-chondritic Zr/Hf, Nb/Ta, and Y/Ho ratios, while the garnet pyroxenite was the residuum produced in equilibrium with the trondhjemite-tonalite melts.
DOI: 10.6084/m9.figshare.22802341.v1
title: Metasomatized mantle under the Eastern Mexican Alkaline Province: evidence from the Oligocene Rincón Murillo Gabbro, Sierra de San Carlos-Cruillas, NE México

description: The Cenozoic Sierra de San Carlos-Cruillas (SSCC) magmatic complex belongs to the Eastern Mexican Alkaline Province (EMAP). The SSCC mainly consists of plutonic and subvolcanic bodies displaying diverse lithological compositions. These rocks exhibit both OIB- and arc-like geochemical characteristics. In this contribution, we present new petrographic, geochemical, isotopic, and geochronological data of the Rincón Murillo Gabbro (RMG), situated in the southern part of the SSCC. The RMG is nepheline normative and displays an OIB-like intraplate character. Laser ablation ICP-MS U-Pb analyses on titanites yielded Oligocene (Rupelian) crystallization ages of 31.8 ± 1.8 and 31.0 ± 1.7 Ma. The <sup>87</sup>Sr/<sup>86</sup>Sr<sub>(i)</sub> (0.703400–0.704159) and <sup>143</sup>Nd/<sup>144</sup>Nd<sub>(i)</sub> (0.512732–0.512815) ratios indicate a mantle origin. Trace element data indicate the participation of different enriched mantle components in the source. One component is related to previous subduction processes, generating the HFSE-depleted arc-like magmas of San José Gabbro in the northern part of SSCC. The second component is related to deep mantle melts with a slightly carbonatitic signal and HFSE-enriched fluids derived from the subducted Hess conjugate plateau generating different enriched sources in the upper mantle under the SSCC. The passage, eclogitization, detachment and foundering of the Hess plateau gave rise to an asthenospheric upwelling that triggered the low to moderate partial melting degrees (3–15%) of an amphibole-bearing garnet peridotite, generating the OIB-like parental magmas of RMG, located in the southern part of SSCC. Two-component mixing, and AFC models indicate that variable degrees of crystal fractionation and minor crustal assimilation are involved in the evolution of Rincón Murillo Gabbro.
DOI: 10.6084/m9.figshare.22726876.v1
title: Reworked Neoproterozoic sub-arc lithosphere beneath the Eastern Desert (Egypt): Evidence from geochemistry and geochronology of metabasites and granitoid gneisses, Gabal Um Gunud area

description: High-grade granitoid gneisses (740–710 Ma) and elongate bodies of amphibolite and hornblende schist with cm-scale layers of garnet pyroxenite form an overturned fold in the Gabal Um Gunud area, South Eastern Desert of Egypt. Whole-rock geochemical data combined with zircon U-Pb-Hf isotope data suggest that the metabasites represent relics of oceanic crust with an N-MORB affinity, which has been derived from partial melting (2.0–1.4 GPa; ~65- ~ 45 km depth) of a depleted mantle source beneath an intra-oceanic, spreading forearc basin. Such increment of melting degree resulted in small basaltic melt batches with transitional tholeiitic to boninitic affinities. Progressive slab subduction and partial melting of the tholeiitic amphibolite produced high-Al and low HREE melts for trondhjemite at av. <i>T</i> = 854°C and low-Al and high HREE melts for tonalite at higher temperatures (av. 949°C). The low Mg# of the trondhjemite-tonalite rocks may be attributed to limited contamination of subduction components, as evidenced by the weak lanthanide tetrad effects (TE<sub>1,3</sub>~1) and near-chondritic Zr/Hf, Nb/Ta, and Y/Ho ratios, while the garnet pyroxenite was the residuum produced in equilibrium with the trondhjemite-tonalite melts.
DOI: 10.6084/m9.figshare.24804912
title: ERG11 CNV

description: Copy number variants of <i>ERG11</i> in <i>C. tropicalis</i>
DOI: 10.6084/m9.figshare.24804912.v1
title: ERG11 CNV

description: Copy number variants of <i>ERG11</i> in <i>C. tropicalis</i>
DOI: 10.6084/m9.figshare.24804951
title: Whole genome sequence

description: we characterized whole genome sequences of 36 <i>C.</i> <i>tropicalis</i> isolates, of which 34 causing infections in human collected from Taiwan Surveillance of Antimicrobial Resistance of Yeasts (TSARY)
DOI: 10.6084/m9.figshare.24804951.v1
title: Whole genome sequence

description: we characterized whole genome sequences of 36 <i>C.</i> <i>tropicalis</i> isolates, of which 34 causing infections in human collected from Taiwan Surveillance of Antimicrobial Resistance of Yeasts (TSARY)
DOI: 10.6084/m9.figshare.24955560
title: Prokaryote MAG sequences assembled from the underground anchialine estuary, Bundera Sinkhole, Australia

description: BackgroundAnchialine environments, in which oceanic water mixes with freshwater in coastal aquifers, are characterised by stratified water columns with complex physicochemical profiles. These environments, also known as subterranean estuaries, support an abundance of endemic macro and microorganisms. There is now growing interest in characterising the metabolisms of anchialine microbial communities, which is essential for understanding how complex ecosystems are supported in extreme environments, and assessing their vulnerability to environmental change. However, the diversity of metabolic strategies that are utilised in anchialine ecosystems remains poorly understood.ResultsHere, we employ shotgun metagenomics to elucidate the key microorganisms and their dominant metabolisms along a physicochemical profile in Bundera Sinkhole, the only known continental subterranean estuary in the Southern Hemisphere. Genome-resolved metagenomics suggests that the communities are largely represented by novel taxonomic lineages, with 75% of metagenome-assembled genomes assigned to entirely new or uncharacterised families. These diverse and novel taxa displayed depth-dependent metabolisms, reflecting distinct phases along dissolved oxygen and salinity gradients. In particular, the communities appear to drive nutrient feedback loops involving nitrification, nitrate ammonification, and sulphate cycling. Genomic analysis of the most highly abundant members in this system suggests that an important source of chemotrophic energy is generated via the metabolic coupling of nitrogen and sulphur cycling.ConclusionThese findings substantially contribute to our understanding of the novel and specialised microbial communities in anchialine ecosystems, and highlight key chemosynthetic pathways that appear to be important in these energy-limited environments. Such knowledge is essential for the conservation of anchialine ecosystems, and sheds light on adaptive processes in extreme environments.
DOI: 10.6084/m9.figshare.24955560.v1
title: Prokaryote MAG sequences assembled from the underground anchialine estuary, Bundera Sinkhole, Australia

description: BackgroundAnchialine environments, in which oceanic water mixes with freshwater in coastal aquifers, are characterised by stratified water columns with complex physicochemical profiles. These environments, also known as subterranean estuaries, support an abundance of endemic macro and microorganisms. There is now growing interest in characterising the metabolisms of anchialine microbial communities, which is essential for understanding how complex ecosystems are supported in extreme environments, and assessing their vulnerability to environmental change. However, the diversity of metabolic strategies that are utilised in anchialine ecosystems remains poorly understood.ResultsHere, we employ shotgun metagenomics to elucidate the key microorganisms and their dominant metabolisms along a physicochemical profile in Bundera Sinkhole, the only known continental subterranean estuary in the Southern Hemisphere. Genome-resolved metagenomics suggests that the communities are largely represented by novel taxonomic lineages, with 75% of metagenome-assembled genomes assigned to entirely new or uncharacterised families. These diverse and novel taxa displayed depth-dependent metabolisms, reflecting distinct phases along dissolved oxygen and salinity gradients. In particular, the communities appear to drive nutrient feedback loops involving nitrification, nitrate ammonification, and sulphate cycling. Genomic analysis of the most highly abundant members in this system suggests that an important source of chemotrophic energy is generated via the metabolic coupling of nitrogen and sulphur cycling.ConclusionThese findings substantially contribute to our understanding of the novel and specialised microbial communities in anchialine ecosystems, and highlight key chemosynthetic pathways that appear to be important in these energy-limited environments. Such knowledge is essential for the conservation of anchialine ecosystems, and sheds light on adaptive processes in extreme environments.
DOI: 10.34740/kaggle/dsv/7358806
title: BBC News
DOI: 10.34740/kaggle/dsv/7358848
title: Polish-Ukrainian translations from Tatoeba
DOI: 10.5281/zenodo.10467506
title: Effects of fluid saturation and viscosity on seismic dispersion characteristics in Berea sandstone

description: Data contains two forced-oscillation measurements in partially saturated sandstone with varying fluid viscosities (e.g., water, glycerin) at seismic frequencies (2~400 Hz)
DOI: 10.5281/zenodo.10467507
title: Effects of fluid saturation and viscosity on seismic dispersion characteristics in Berea sandstone

description: Data contains two forced-oscillation measurements in partially saturated sandstone with varying fluid viscosities (e.g., water, glycerin) at seismic frequencies (2~400 Hz)
DOI: 10.34740/kaggle/dsv/7359092
title: WallStreetBets 2022
DOI: 10.34740/kaggle/dsv/7358691
title: Brand Sentiment Analysis Dataset (Twitter)
DOI: 10.6084/m9.figshare.24021591
title: C3RO demographics analysis

description: For secondary analysis of C3RO data. These CSV files were generated for each disease site separately which can then be used to regression modeling. More information on this data can be found in the accompanying preprint: https://www.medrxiv.org/content/10.1101/2023.08.30.23294786v2.Original C3RO data can be found here: https://figshare.com/articles/dataset/Large-scale_crowdsourced_radiotherapy_segmentations_across_a_variety_of_cancer_sites/21074182.Version history:v2: Jan 7, 2023. Included additional column for HD95 binary data.
DOI: 10.6084/m9.figshare.24021591.v1
title: C3RO demographics analysis

description: For secondary analysis of C3RO data. These CSV files were generated for each disease site separately which can then be used to regression modeling. More information on this data can be found in the accompanying preprint: LINK TO BE INSERTED. Original C3RO data can be found here: https://figshare.com/articles/dataset/Large-scale_crowdsourced_radiotherapy_segmentations_across_a_variety_of_cancer_sites/21074182.
DOI: 10.6084/m9.figshare.24955719
title: Identification and Description of Emotions by Current Large Language Models - Dataset

description: The assertion that artificial intelligence (AI) cannot grasp the complexities of human emotions has been a long-standing debate. However, recent advancements in large language models (LLMs) challenge this notion by demonstrating an increased capacity for understanding and generating human-like text. In this study, we evaluated the empathy levels and the identification and description of emotions by three current language models: Bard, GPT 3.5, and GPT 4. We used the Toronto Alexithymia Scale (TAS-20) and the 60-question Empathy Quotient (EQ-60) questions to prompt these models and score the responses. The models' performance was contrasted with human benchmarks of neurotypical controls and clinical populations. We found that the less sophisticated models (Bard and GPT 3.5) performed inferiorly on TAS-20, aligning close to alexithymia, a condition with significant difficulties in recognizing, expressing, and describing one's or others' experienced emotions. However, GPT 4 achieved performance close to the human level. These results demonstrated that LLMs are comparable in their ability to identify and describe emotions and may be able to surpass humans in their capacity for emotional intelligence. Our novel insights provide alignment research benchmarks and a methodology for aligning AI with human values, leading toward an empathetic AI that mitigates risk.
DOI: 10.5281/zenodo.10433294
title: Can Conversational Artificial Intelligence Identify Red Flags of Low Back Pain? A Comparative Analysis of ChatGPT and GoogleBard.

description: This study evaluated the effectiveness of two conversational artificial intelligence systems, ChatGPT and GoogleBard, in providing correct, complete and relevant answers to questions related to red flags (RFs) associated with low back pain (LBP). RFs are important indicators of serious medical conditions in LBP cases. The study involved 70 English questions based on the symptoms outlined in LBP guidelines, with 58 focusing on single symptoms and 12 involving multiple symptoms in addition to LBP. Both ChatGPT and GoogleBard demonstrated strong performance in terms of correctness, completeness, and relevance of their responses. The severity of the conditions was effectively conveyed in the majority of responses, and there were no statistically significant differences between the two systems. This research highlights the potential of AI systems like ChatGPT and GoogleBard in providing reliable health information, which is particularly valuable as more individuals turn to online sources for medical guidance.
DOI: 10.25959/83qe-ng09
title: 2009-2019 data from Tasmania: grape botrytis bunch rot

description: Data files for field studies of botrytis bunch rot (BBR) in wine grapes, caused by Botrytis cinerea.  Studies were conducted in  Riesling or Sauvignon Blanc vines in commercial vineyards in Tasmania.
DOI: 10.5281/zenodo.10467505
title: Characteristics, Origins, and Atmospheric Processes of Amines in Fine Aerosol Particles in Winter in China

description: data
DOI: 10.5281/zenodo.7943433
title: Characteristics, Origins, and Atmospheric Processes of Amines in Fine Aerosol Particles in Winter in China

description: data