cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19298423
title: Additional file 2 of Natural killer cell-related gene signature predicts malignancy of glioma and the survival of patients

description: Additional file 2 : Supplement Table 2. NK Cell Related Molecular Signatures in Database.
DOI: 10.6084/m9.figshare.19298423.v1
title: Additional file 2 of Natural killer cell-related gene signature predicts malignancy of glioma and the survival of patients

description: Additional file 2 : Supplement Table 2. NK Cell Related Molecular Signatures in Database.
DOI: 10.6084/m9.figshare.19298447
title: Additional file 2 of Integrative analysis of transcriptomics and metabolomics to reveal the melanogenesis pathway of muscle and related meat characters in Wuliangshan black-boned chickens

description: Additional file 2. Up- and down regulated genes, and genes associated with melanogenesis.
DOI: 10.6084/m9.figshare.19298447.v1
title: Additional file 2 of Integrative analysis of transcriptomics and metabolomics to reveal the melanogenesis pathway of muscle and related meat characters in Wuliangshan black-boned chickens

description: Additional file 2. Up- and down regulated genes, and genes associated with melanogenesis.
DOI: 10.6084/m9.figshare.19298456
title: Additional file 4 of Integrative analysis of transcriptomics and metabolomics to reveal the melanogenesis pathway of muscle and related meat characters in Wuliangshan black-boned chickens

description: Additional file 4. Correlation coefficient between DEGs and SDM (or DMs) – Tables Positive and Negative ion mode.
DOI: 10.6084/m9.figshare.19298456.v1
title: Additional file 4 of Integrative analysis of transcriptomics and metabolomics to reveal the melanogenesis pathway of muscle and related meat characters in Wuliangshan black-boned chickens

description: Additional file 4. Correlation coefficient between DEGs and SDM (or DMs) – Tables Positive and Negative ion mode.
DOI: 10.6084/m9.figshare.13007024
title: Quality Controlled Aerosol Optical Depth Value-Added Product

description: The Quality Control Aerosol Optical Depth (QCAOD) value-added product (VAP) generates sgpqcaodC1.c1 dataset with combined aerosol optical depth (AOD) at two wavelengths (500 and 870 nanometers) with high-quality, enhanced continuity and fine (1-minute) temporal resolution. The tar file sgpqcaodC1.c1.tgz contains the 7965 netCDF files for the sgpqcaodC1.c1 dataset from 1997 to 2018.
DOI: 10.6084/m9.figshare.13007024.v1
title: Quality Controlled Aerosol Optical Depth Value-Added Product

description: The Quality Control Aerosol Optical Depth (QCAOD) value-added product (VAP) generates sgpqcaodC1.c1 dataset with combined aerosol optical depth (AOD) at two wavelengths (500 and 870 nanometers) with high-quality, enhanced continuity and fine (1-minute) temporal resolution. The tar file sgpqcaodC1.c1.tgz contains the 7965 netCDF files for the sgpqcaodC1.c1 dataset from 1997 to 2018.
DOI: 10.6084/m9.figshare.25282360.v1
title: A Deep Dynamic Latent Block Model for Co-clustering of Zero-Inflated Data Matrices

description: The simultaneous clustering of observations and features of data sets (known as co-clustering) has recently emerged as a central machine learning application to summarize massive data sets. However, most existing models focus on continuous and dense data in stationary scenarios, where cluster assignments do not evolve over time. This work introduces a novel latent block model for the dynamic co-clustering of data matrices with high sparsity. To properly model this type of data, we assume that the observations follow a time and block dependent mixture of zero-inflated distributions, thus combining stochastic processes with the time-varying sparsity modeling. To detect abrupt changes in the dynamics of both cluster memberships and data sparsity, the mixing and sparsity proportions are modeled through systems of ordinary differential equations. The inference relies on an original variational procedure whose maximization step trains fully connected neural networks in order to solve the dynamical systems. Numerical experiments on simulated and real world data sets demonstrate the effectiveness of the proposed methodology in the context of count data.
DOI: 10.6084/m9.figshare.25282360
title: A Deep Dynamic Latent Block Model for Co-clustering of Zero-Inflated Data Matrices

description: The simultaneous clustering of observations and features of data sets (known as co-clustering) has recently emerged as a central machine learning application to summarize massive data sets. However, most existing models focus on continuous and dense data in stationary scenarios, where cluster assignments do not evolve over time. This work introduces a novel latent block model for the dynamic co-clustering of data matrices with high sparsity. To properly model this type of data, we assume that the observations follow a time and block dependent mixture of zero-inflated distributions, thus combining stochastic processes with the time-varying sparsity modeling. To detect abrupt changes in the dynamics of both cluster memberships and data sparsity, the mixing and sparsity proportions are modeled through systems of ordinary differential equations. The inference relies on an original variational procedure whose maximization step trains fully connected neural networks in order to solve the dynamical systems. Numerical experiments on simulated and real world data sets demonstrate the effectiveness of the proposed methodology in the context of count data.
DOI: 10.6084/m9.figshare.19298673
title: Early palaeozoic arc-continent collision in East Kunlun, northern Tibet: evidence from the minerology, geochemistry, and geochronology of the Adatan garnet amphibolites

description: The evolution of the Tethys is one of the key issues in revealing the global ocean-continent transition tectonic process. The East Kunlun Orogenic Belt (E-KOB) in the northern Tibetan Plateau witnessed the subduction-accretion process of the Proto- and Palaeo-Tethyan Oceans formed a trench-arc-back arc basin system. Thus, this back arc basin is a window for exploring the tectonic evolution of the Tethys. In this study, the Adatan garnet amphibolites and the host paragneiss were investigated and used to constrain the evolution of the back arc basin. The mineralogical observations and microstructure of the garnet amphibolite suggest the successive formation of three mineral assemblages: a Hb + Pl + Ilm inclusion assemblage within garnet cores, a Grt + Pl + Hb + Bit + Phe matrix assemblage, and a retrograde assemblage of <i>white-eye</i> coronas around the garnet. The thermobarometric calculations suggest a clockwise <i>P-T</i> path with peak metamorphic conditions of 10.1–12.6 kbar and 715–830°C and a subsequent near-isothermal decompression process. The geochemistry indicates that the protolith of the garnet amphibolites was formed in a subduction-related tectonic setting with enriched mid-ocean ridge basalt (E-MORB) geochemical characteristics. U-Pb zircon dating reveals that the crystallization age of the garnet amphibolite’s protolith is ca. 457–452 Ma. Based on field occurrences, the protolith of the amphibolite was probably mafic dikes that intruded into the paragneiss due to subduction of the back-arc basin. Both the garnet amphibolite and gneissic rocks experienced contemporaneous metamorphism at ca. 420–410 Ma, suggesting that a crustal thickening event occurred due to closure of the back-arc basin and arc-continent collision. Based on the above evidence and the results of previous studies, it can be concluded that the Qimantagh back arc basin involved opening, subduction, and closure tectonic processes at ca. 486 Ma, ca. 460 Ma and ca. 420–410 Ma, respectively.
DOI: 10.6084/m9.figshare.19298673.v1
title: Early palaeozoic arc-continent collision in East Kunlun, northern Tibet: evidence from the minerology, geochemistry, and geochronology of the Adatan garnet amphibolites

description: The evolution of the Tethys is one of the key issues in revealing the global ocean-continent transition tectonic process. The East Kunlun Orogenic Belt (E-KOB) in the northern Tibetan Plateau witnessed the subduction-accretion process of the Proto- and Palaeo-Tethyan Oceans formed a trench-arc-back arc basin system. Thus, this back arc basin is a window for exploring the tectonic evolution of the Tethys. In this study, the Adatan garnet amphibolites and the host paragneiss were investigated and used to constrain the evolution of the back arc basin. The mineralogical observations and microstructure of the garnet amphibolite suggest the successive formation of three mineral assemblages: a Hb + Pl + Ilm inclusion assemblage within garnet cores, a Grt + Pl + Hb + Bit + Phe matrix assemblage, and a retrograde assemblage of <i>white-eye</i> coronas around the garnet. The thermobarometric calculations suggest a clockwise <i>P-T</i> path with peak metamorphic conditions of 10.1–12.6 kbar and 715–830°C and a subsequent near-isothermal decompression process. The geochemistry indicates that the protolith of the garnet amphibolites was formed in a subduction-related tectonic setting with enriched mid-ocean ridge basalt (E-MORB) geochemical characteristics. U-Pb zircon dating reveals that the crystallization age of the garnet amphibolite’s protolith is ca. 457–452 Ma. Based on field occurrences, the protolith of the amphibolite was probably mafic dikes that intruded into the paragneiss due to subduction of the back-arc basin. Both the garnet amphibolite and gneissic rocks experienced contemporaneous metamorphism at ca. 420–410 Ma, suggesting that a crustal thickening event occurred due to closure of the back-arc basin and arc-continent collision. Based on the above evidence and the results of previous studies, it can be concluded that the Qimantagh back arc basin involved opening, subduction, and closure tectonic processes at ca. 486 Ma, ca. 460 Ma and ca. 420–410 Ma, respectively.
DOI: 10.6084/m9.figshare.13531604
title: Additional file 4 of Integrated analysis of the methylome and transcriptome of chickens with fatty liver hemorrhagic syndrome

description: Additional file 4: Supplementary Table 1. Identification and annotation of DMRs and DMGs between two groups.
DOI: 10.6084/m9.figshare.13531604.v1
title: Additional file 4 of Integrated analysis of the methylome and transcriptome of chickens with fatty liver hemorrhagic syndrome

description: Additional file 4: Supplementary Table 1. Identification and annotation of DMRs and DMGs between two groups.
DOI: 10.5281/zenodo.10699275
title: GODEEEP Generator Hourly Emissions

description: Preliminary hourly plant emissions data from the GODEEEP project produced using the proprietary GridView modeling software.

Currently available:



2020, the initial conditions year for all GODEEEP scenarios


Updated data and better data description to follow; results are preliminary.

Notes:



Datetimes are in Mountain Time (MT)

Emissions are reported in pounds (lbs)

Some generators do not have an associated EIA PlantID; reasoning to follow later

Multiple generators can be associated to the same EIA PlantID

Generator names are from a backcast study and are not always meaningful; citation to follow later

Coordinates are provided in EPSG:4326 datum in the lat and lon columns


Known Issues:



Datetimes are reported as the year 2030 even though they represent the hours in the year 2020


 

Acknowledgement

This research was supported by the Grid Operations, Decarbonization, Environmental and Energy Equity Platform (GODEEEP) Investment, under the Laboratory Directed Research and Development (LDRD) Program at Pacific Northwest National Laboratory (PNNL).

PNNL is a multi-program national laboratory operated for the U.S. Department of Energy (DOE) by Battelle Memorial Institute under Contract No. DE-AC05-76RL01830.
DOI: 10.5281/zenodo.10699276
title: GODEEEP Generator Hourly Emissions

description: Preliminary hourly plant emissions data from the GODEEEP project produced using the proprietary GridView modeling software.

Currently available:



2020, the initial conditions year for all GODEEEP scenarios


Updated data and better data description to follow; results are preliminary.

Notes:



Datetimes are in Mountain Time (MT)

Emissions are reported in pounds (lbs)

Some generators do not have an associated EIA PlantID; reasoning to follow later

Multiple generators can be associated to the same EIA PlantID

Generator names are from a backcast study and are not always meaningful; citation to follow later

Coordinates are provided in EPSG:4326 datum in the lat and lon columns


Known Issues:



Datetimes are reported as the year 2030 even though they represent the hours in the year 2020


 

Acknowledgement

This research was supported by the Grid Operations, Decarbonization, Environmental and Energy Equity Platform (GODEEEP) Investment, under the Laboratory Directed Research and Development (LDRD) Program at Pacific Northwest National Laboratory (PNNL).

PNNL is a multi-program national laboratory operated for the U.S. Department of Energy (DOE) by Battelle Memorial Institute under Contract No. DE-AC05-76RL01830.
DOI: 10.6084/m9.figshare.13531607
title: Additional file 5 of Integrated analysis of the methylome and transcriptome of chickens with fatty liver hemorrhagic syndrome

description: Additional file 5: Supplementary Table 2. Identification and annotation of DEGs between two groups.
DOI: 10.6084/m9.figshare.13531607.v1
title: Additional file 5 of Integrated analysis of the methylome and transcriptome of chickens with fatty liver hemorrhagic syndrome

description: Additional file 5: Supplementary Table 2. Identification and annotation of DEGs between two groups.
DOI: 10.6084/m9.figshare.13531610
title: Additional file 6 of Integrated analysis of the methylome and transcriptome of chickens with fatty liver hemorrhagic syndrome

description: Additional file 6: Supplementary Table 3. Overlapping genes between DMGs and DEGs.
DOI: 10.6084/m9.figshare.13531610.v1
title: Additional file 6 of Integrated analysis of the methylome and transcriptome of chickens with fatty liver hemorrhagic syndrome

description: Additional file 6: Supplementary Table 3. Overlapping genes between DMGs and DEGs.
DOI: 10.7284/158384
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise FKt231024 using a Hawaii UHDAS instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158385
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise FKt231024 using a SeaBird SBE-911+ instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158407
title: Expendable Probe data collected during research cruise FKt231024 using a Turo Quoll instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158397
title: Fluorometer data collected during research cruise FKt231024 using a WETLabs ECO-FL instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158398
title: Fluorometer data collected during research cruise FKt231024 using a WETLabs ECO-FL instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158388
title: Gyrocompass data collected during research cruise FKt231024 using a Sperry NAVIGAT X MK 1 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158389
title: Gyrocompass data collected during research cruise FKt231024 using a Sperry NAVIGAT X MK 1 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158390
title: Gyrocompass data collected during research cruise FKt231024 using a Sperry NAVIGAT X MK 1 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158386
title: INS (Inertial Navigation System) data collected during research cruise FKt231024 using a Kongsberg Seapath 330+ instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158387
title: INS (Inertial Navigation System) data collected during research cruise FKt231024 using a Kongsberg DPS122 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158409
title: INS (Inertial Navigation System) data collected during research cruise FKt231024 using a Applanix POS/MV-320 V5 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158410
title: INS (Inertial Navigation System) data collected during research cruise FKt231024 using a Applanix POS/MV-320 V5 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158403
title: Meteorological Station data collected during research cruise FKt231024 using a Paroscientific MET4A instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158404
title: Meteorological Station data collected during research cruise FKt231024 using a Gill MetPak Pro instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158391
title: Multibeam Echosounder data collected during research cruise FKt231024 using a Kongsberg EM124 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158392
title: Multibeam Echosounder data collected during research cruise FKt231024 using a Kongsberg EM712 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158393
title: Multibeam Echosounder data collected during research cruise FKt231024 using a Kongsberg EM712 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158394
title: Multibeam Echosounder data collected during research cruise FKt231024 using a Kongsberg EM124 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158395
title: Multibeam Echosounder data collected during research cruise FKt231024 using a Kongsberg EM2040 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158396
title: Multibeam Echosounder data collected during research cruise FKt231024 using a Kongsberg EM2040 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158408
title: Singlebeam Echosounder data collected during research cruise FKt231024 using a Kongsberg SBP-29 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158405
title: SSV (Sound Speed Velocimeter) data collected during research cruise FKt231024 using a Valeport MiniSVS instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158406
title: SSV (Sound Speed Velocimeter) data collected during research cruise FKt231024 using a Valeport MiniSVS instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158400
title: Transmissometer data collected during research cruise FKt231024 using a SeaBird C-Star instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.25066010
title: Three <i>de novo</i> assembled wild cacao genomes from the Upper Amazon region

description: <i>Theobroma cacao</i>, the chocolate tree, is indigenous to the Amazon basin, the greatest biodiversity hotspot on earth. In this study, we constructed three high-quality chromosome-level genomes,<i>de novo</i>assembled using long reads sequencing and scaffolded using a reference-free strategy. These genomes represent the three most important genetic clusters of wild cacao trees from the Upper Amazon region. The three wild cacao genomes were compared with two reference genomes of domesticated cacao. We found that the five cacao genetic clusters diverged in the early and middle Pleistocene period, approximately 1.83 – 0.69 million years ago. This finding challenges the existing Pleistocene refugia hypothesis that suggests a more recent cacao intra-specific diversification. We also found significantly higher percentages of transposable elements and lower numbers of disease resistance genes in the wild cacao genomes than in the domesticated reference genomes. Our results serve as an example of understanding how the Amazonian biodiversity was developed. The three wild cacao genomes provide valuable resources for studying cacao genetic diversity.
DOI: 10.7284/158401
title: TSG (Thermosalinograph) data collected during research cruise FKt231024 using a SeaBird SBE-45 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/158402
title: TSG (Thermosalinograph) data collected during research cruise FKt231024 using a SeaBird SBE-45 instrument system onboard the platform RV Falkor (too)

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.13531699
title: Additional file 6 of Model based on five tumour immune microenvironment-related genes for predicting hepatocellular carcinoma immunotherapy outcomes

description: Additional file 6. Additional material.
DOI: 10.6084/m9.figshare.13531699.v1
title: Additional file 6 of Model based on five tumour immune microenvironment-related genes for predicting hepatocellular carcinoma immunotherapy outcomes

description: Additional file 6. Additional material.