cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15121/1991675
title: Laboratory Experiments Examining the Effect of Thermal and Mechanical Processes on Hydraulic Transmissivity Evolution

description: Using laboratory slide-hold-slide experiments, at temperatures from 22 to 200 degrees C, to examine effects of fracture reactivation and quasi-static loading on the evolution of fluid transport properties of simulated fractures in Westerly granite. At all temperatures, the in-plane hydraulic transmissivity consistently decays during hold periods resulting in an overall reduction in transmissivity. During the first three to fifteen hours of an experiment, transmissivity decreases rapidly due to the generation of wear products, development of a sliding surface, and compaction of the resulting gouge. Once the sliding surface has developed, the long-term transmissivity decay rate at 22 and 100 degrees C is significantly lower than the transmissivity decay rate during the initial 3-15 hours of the experiment. However, at 200 degrees C, the decay of hydraulic transmissivity remains high throughout the experiment. The long-term decay of hydraulic transmissivity can be fitted with a power law model with more rapid reduction of hydraulic transmissivity at higher temperature. Periods of sliding on the fracture surface result in transient increases in the transmissivity, due to shear dilation, as is expected for Coulomb materials. These transients are superimposed on the long-term decay. When sliding ceases and a new hold period commences, there is a rapid reduction in transmissivity and return to the long-term rate of transmissivity decay. The rate of decay of the transmissivity transients is inversely correlated with temperature, in contrast to the long-term decay and the expected behavior for processes like subcritical crack growth and indentation creep. The higher decay rates that are observed during the initial 3-15 hours of the tests and following sliding, are associated with times that the porosity of the gouge is expected to be high. The difference in decay rates suggests that when the gouge is driven far from equilibrium by active shearing, densification may be dominated by a different mechanism from long-term compaction.
DOI: 10.5281/zenodo.8174988
title: Chromosome-Level Genome Assembly of the 'Gannanzao' Navel Orange (Citrus sinensis L. Osbeck Gannanzao)

description: Gannanzao navel orange (<em>Citrus sinensis</em> Osbeck cv. Gannanzao) is a variant of the Newhall navel orange (<em>C. sinensis</em> Osbeck cv. Newhall) that exhibits an earlier maturation, making it commercially valuable. However, the underlying mechanism underneath its early maturation remains unknown. To address this question, we conducted genome sequencing and de novo assembly of navel orange cv. Gannanzao. The assembled genome sequence is 334.57 Mb in length with a GC content of 31.48%. It comprises 318 contigs (N50 = 3.23 Mb) and 187 scaffolds (N50 = 31.86 Mb). The BUSCO test demonstrates 94.6% completeness. The annotation revealed 23,037 gene models, 164.95 Mb of repetitive sequences, and 2,554 ncRNA.
DOI: 10.5281/zenodo.8174987
title: Chromosome-Level Genome Assembly of the 'Gannanzao' Navel Orange (Citrus sinensis L. Osbeck Gannanzao)

description: Gannanzao navel orange (<em>Citrus sinensis</em> Osbeck cv. Gannanzao) is a variant of the Newhall navel orange (<em>C. sinensis</em> Osbeck cv. Newhall) that exhibits an earlier maturation, making it commercially valuable. However, the underlying mechanism underneath its early maturation remains unknown. To address this question, we conducted genome sequencing and de novo assembly of navel orange cv. Gannanzao. The assembled genome sequence is 334.57 Mb in length with a GC content of 31.48%. It comprises 318 contigs (N50 = 3.23 Mb) and 187 scaffolds (N50 = 31.86 Mb). The BUSCO test demonstrates 94.6% completeness. The annotation revealed 23,037 gene models, 164.95 Mb of repetitive sequences, and 2,554 ncRNA.
DOI: 10.5519/qd.s83azhhl
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (6531 records)
DOI: 10.6084/m9.figshare.23536374
title: Critical current characterisation of Faraday Factory Japan YBCO 2G HTS superconducting wire

description: Detailed measurements of the critical current of a commercial 2G HTS REBCO wire as a function of temperature, magnetic field, and field angle, performed at the Robinson Research Institute of Victoria University of Wellington. <br>
DOI: 10.6084/m9.figshare.23536374.v3
title: Critical current characterisation of Faraday Factory Japan YBCO 2G HTS superconducting wire

description: Detailed measurements of the critical current of a commercial 2G HTS REBCO wire as a function of temperature, magnetic field, and field angle, performed at the Robinson Research Institute of Victoria University of Wellington. <br>
DOI: 10.6084/m9.figshare.23732883
title: <strong>Massively Parallel Single-Nucleus RNA-Sequencing</strong> <strong>allows</strong> <strong>an Unbiased Assessment</strong> <strong>of Cellular Constituents of the Adult Human Heart and Transcriptional Regulators Involved in Myocardial Remodelling</strong>

description: Each folder contains the count matrix and cell/gene annotation from a sparse matrix of UMI counts, in the format produced by the CellRanger software suite (matrix.mtx.gz,barcodes.tsv.gz, genes.tsv.gz), and 1 metadata file (meta_data.tsv.gz) for each cell, for example, cell type, sample id, or TNSE/UMAP coordinates. <br> Human1_3_sn_3PV2: single nuclei RNA-seq for Human1_2 with 3'V2 assay Human1_5_sn_5PV2: single nuclei RNA-seq for Human1_5 with 3'V2 assay Human2_sc_3PV2: single-cell RNA-seq for Human2 with 3'V2 assay Human2and3_sn_3PV3: single nuclei RNA-seq for Human2 and Human3 with 3'V3 assay NormalHeart_EC: single nuclei RNA-seq for Human2 and Human3 with 3'V3 assay only for Endothelial NormalHeart_FB: single nuclei RNA-seq for Human2 and Human3 with 3'V3 assay only for Fibroblast NormalHeart_Pericyte: single nuclei RNA-seq for Human2 and Human3 with 3'V3 assay only for Pericyte NormalHeart_SMC: single nuclei RNA-seq for Human2 and Human3 with 3'V3 assay only for Smooth Muscle Cells DCMHeart_FB: single nuclei RNA-seq for DCM heart (3DCM heart and 3 control (normal) Heart) only for Fibroblast <br> <br>
DOI: 10.6084/m9.figshare.23498246
title: <strong>Identification of key responsive genes to some abiotic stresses in Arabidopsis thaliana at the seedling stage based on coupling computational biology methods and Machine learning</strong>

description: Abiotic limitations, like water deficit, high temperature, salinity, and cold are some of the main barrier agents to plant growth throughout the world. To obtain a comprehensive view of a plant’s response to abiotic stresses, we applied the robust bioinformatics approaches that including the integration of meta-analysis, weighted gene co-expression network analysis (WGCNA), and machine learning.
DOI: 10.6084/m9.figshare.23498246.v1
title: <strong>Identification of key responsive genes to some abiotic stresses in Arabidopsis thaliana at the seedling stage based on coupling computational biology methods and Machine learning</strong>

description: Abiotic limitations, like water deficit, high temperature, salinity, and cold are some of the main barrier agents to plant growth throughout the world. To obtain a comprehensive view of a plant’s response to abiotic stresses, we applied the robust bioinformatics approaches that including the integration of meta-analysis, weighted gene co-expression network analysis (WGCNA), and machine learning.
DOI: 10.6084/m9.figshare.23498246.v2
title: <strong>Identification of key responsive genes to some abiotic stresses in Arabidopsis thaliana at the seedling stage based on coupling computational biology methods and Machine learning</strong>

description: Abiotic limitations, like water deficit, high temperature, salinity, and cold are some of the main barrier agents to plant growth throughout the world. To obtain a comprehensive view of a plant’s response to abiotic stresses, we applied the robust bioinformatics approaches that including the integration of meta-analysis, weighted gene co-expression network analysis (WGCNA), and machine learning.
DOI: 10.6084/m9.figshare.22191718
title: Mushrooming GPS-tracks 2015-2017

description: Dataset accompanying our submission <em>Beyond their paths: what do ecological cues reveal about mushroom gatherers’ decision making?</em> <strong>Hunter Gatherer Research</strong> <strong>6(1–2): 169–186</strong>. https://doi.org/10.3828/hgr.2023.5 <br> <strong>clave_id</strong>: character string that uniquely identifies mushrooming trips by date and gatherer. The first section “Ruta” stands for pathway, the second section denotes the last two digits of the year, the month and day (yymmdd), and the third section describes the gatherer by sex (H, hombre – man or M, mujer –, woman) and his/her numeric label. <strong>timeloc</strong>: local time given by date (yyyy-mm-dd) and time (hh:mm:ss). <strong>east</strong>: numeric, indicates displacement in meters (m) to the East from an unknown point of origin. <strong>north</strong>: numeric, indicates displacement in meters (m) to the North from an unknown point of origin. <strong>ele</strong>: numeric, elevation in meters (m) above sea level. <strong>point</strong>: categorical, type of GPS register, either trackpoint (automatically recorded as programmed) or waypoint (manual annotation made while searching). <strong>tipo_encuentro</strong>: categorical, denotes either the type of ecological cue (traces, exploration, or memory) followed by the gatherer or the searching outcome (harvest, failed harvest). <strong>nom_hongo</strong>: categorical, indicates the local name of the mushroom associated with each tipo_encuentro. Not available cases are indicated with NA. See main text for full list of scientific generic and species names. <strong>num_esporoc</strong>: numeric, total carpophores associated with each tipo_encuentro. Not available cases are indicated with NA. <strong>dist</strong>: numeric, Euclidean distance in meters (m) between each consecutive pair of geographic coordinates. <strong>secs</strong>: numeric, time difference in seconds between each consecutive pair of time recordings. EDITING NOTE: we fixed and replaced a former version of "tyw_beyond.csv" where a pathway labeled as <em>Ruta_150823</em> cointained data from a different date and gatherer. All pathways are unique now.
DOI: 10.5281/zenodo.8175027
title: pypsa-usa-data

description: Dataset for PyPSA-USA power systems model. - GEBCO Bathymetry Data for United States: https://www.gebco.net - Copernicus land-use data for the United States: https://zenodo.org/record/3939050
DOI: 10.5281/zenodo.8175026
title: pypsa-usa-data

description: Dataset for PyPSA-USA power systems model. - GEBCO Bathymetry Data for United States: https://www.gebco.net - Copernicus land-use data for the United States: https://zenodo.org/record/3939050
DOI: 10.5281/zenodo.8175051
title: pypsa-usa-data

description: Dataset for PyPSA-USA power systems model. - GEBCO Bathymetry Data for United States: https://www.gebco.net - Copernicus land-use data for the United States: https://zenodo.org/record/3939050
DOI: 10.6084/m9.figshare.22688281
title: Genome assemblies and gene annotation files for Willams 82 and Lee cultivars near-gapless soybean genomes

description: Near gapless genome assemblies of Williams 82 and Lee soybean cultivars
DOI: 10.6084/m9.figshare.22688281.v2
title: Genome assemblies and gene annotation files for Willams 82 and Lee cultivars near-gapless soybean genomes

description: Near gapless genome assemblies of Williams 82 and Lee soybean cultivars
DOI: 10.5066/p9pykoph
title: Mortality, morphology, and water chemistry for 6PPD-quinone exposed coho embryos

description: Understanding evolutionary processes that drive population dynamics is critical in ecology. Measuring the performance-density relationship in long-lived mammalian species demands long-term data, limiting the ability to observe such mechanisms. We tested density-dependent (intrinsic) and density-independent (extrinsic) drivers of body composition of grizzly bears (Ursus arctos) in the Greater Yellowstone Ecosystem over two decades.
DOI: 10.5066/p9ksxagw
title: Native riverine fish occurrences downstream from two hydropower dams with contrasting operations, Georgia, USA

description: Data are fish species occurrences in surveys made by backpack electrofishing and seining in shoal habitats in the Etowah River downstream from Allatoona Dam (n=10 surveys in 2010 and n=5 surveys in 2016; 20 taxa total) and in the Coosawattee River downstream from Carters Dam and re-regulation dam (n=11 surveys in 2010; 32 taxa total), Georgia, USA. Data for the Etowah River include counts of individuals for each species captured; data for the Coosawattee River are observed or not observed for each species in the data set.
DOI: 10.6084/m9.figshare.23733207
title: Nrf2 5'UTR binding protein LC/MS QuantittiveValue AllThree-Keratin-Zero.xlsm

description: In vitro synthesized biotinylated 5'UTR sequence of Nrf2 mRNA was incubated with cell lysate received control or 100 uM hydrogen peroxide treatment for 1 hour before lysis. Synthesized RNA was pulled down and the binding proteins were analyzed by LC/MS
DOI: 10.6084/m9.figshare.23733207.v1
title: Nrf2 5'UTR binding protein LC/MS QuantittiveValue AllThree-Keratin-Zero.xlsm

description: In vitro synthesized biotinylated 5'UTR sequence of Nrf2 mRNA was incubated with cell lysate received control or 100 uM hydrogen peroxide treatment for 1 hour before lysis. Synthesized RNA was pulled down and the binding proteins were analyzed by LC/MS
DOI: 10.5281/zenodo.8174931
title: A first high-quality vector data of buildings in East Asian countries based on a comprehensive large-scale mapping framework

description: We generate a high-quality and complete vector data of buildings in East Asian regions, including China, Japan, North Korea, South Korea and Mongolia, filling the gaps in the existing public buildings data.
DOI: 10.5281/zenodo.8174930
title: A first high-quality vector data of buildings in East Asian countries based on a comprehensive large-scale mapping framework

description: We generate a high-quality and complete vector data of buildings in East Asian regions, including China, Japan, North Korea, South Korea and Mongolia, filling the gaps in the existing public buildings data.
DOI: 10.15151/esrf-es-1118672762
title: Paris Rive-Gauche BAG: from structure to drug design

description: Our BAG was created in 2006 to federate well-established structural biology laboratories from south Paris. At present, several projects are investigated by different teams from 5 Institutes: (1) I2BC (Institut de Biologie Inte#grative de la Cellule), (2) IBPC (Institut de Biologie Physico-Chimique), (3) INSERM (Institut National de la Sante# et de la Recherche Me#dicale), (4) LBPA (Laboratoire de Biologie et Pharmacologie Applique#e) and (5) CiTCoM (CiblesTherapeutiques et Conception de Medicaments, ex-name LCRB). Our research area focuses on many important biological systems involved in human pathology or infectious diseases, including molecular chaperones, DNA recombination, RNA maturation, ribosome biogenesis, telomerase assembly, bacterial toxins, malaria disease, neurodegenerative disease, drugs resistance and cell-signalling.
DOI: 10.15151/esrf-es-1119937072
title: Austrian Crystallographic Diffraction Consortium

description: This proposed Austrian Crystallographic.... TO BE FILLED IN
DOI: 10.15151/esrf-es-1120143485
title: Structural Biology of Macromolecules and Macromolecular complexes from India

description: Structural biology research groups located in India constitute the INDIA-BAG and will utilize MX & SAXS to study different biological macromolecules. The non-proprietary agreement signed between ESRF and the Department of Biotechnology (DBT) enables studies that provide fundamental mechanistic insight regarding different biological processes. A brief description of over 50 research groups is provided in the global summary and a summary of their research contributions involving data collected at ESRF is provided in the 2 year BAG report. The ESRF-India partnership is supported by a single grant provided to the RCB by the DBT. Please note that a report listing no. of shifts utilized, details of users and the research output from these visits has to be sent to the DBT to obtain release of funds to pay ESRF membership dues. Consequently, all the structural biologists from India are grouped in a single BAG to enable monitoring of progress to collect the required statistics.
DOI: 10.15151/esrf-es-1299161374
title: The Institute of Structural and Molecular Biology (ISMB) application for beam time, comprising groups from Birkbeck College, UCL and the Que

description: The ISMB spans Birkbeck and UCL with researchers in the core Departments at Birkbeck Biological Sciences and several UCL Research Departments. Research groups from Queen Mary University of London (QMUL) and Kingston University (KU) are joint co-applicants as they have strong links and collaborations with groups from ISMB. All groups share common interests in disciplines including structural, chemical, molecular and cell biology; using multidisciplinary andmultiscalar approaches. ISMB, UCL, QMUL and KU investigators, ranging from early-career research fellows to internationally-established senior academics, apply X-ray crystallography carried out mainly at our Wellcome funded facility at Birkbeck, as an essential method enabling: i) description of the atomic-level mechanistic details of macromolecules and macromolecular machines, and ii) structure-based drug discovery, while iii) complementing and supporting cryoelectron microscopy (cryo-EM) projects.
DOI: 10.15151/esrf-es-1208264973
title: A high-resolution 3D map of manganese in the brain of a zebrafish model of manganese neurotoxicity.

description: Manganese (Mn) neurotoxicity causes a disabling movement disorder associated with psychiatric symptoms. We have developed a zebrafish model of Mn neurotoxicity by knockout of the Mn uptake transporter Slc39a14 in order to study the effects of excess Mn on neuronal function. A remaining challenge is to determine the spatial Mn distribution within the zebrafish brain and link functional deficits with regions of Mn accumulation. The ID16A nanoimaging beamline will allow generation of a cellular resolution 3D map of Mn within the zebrafish brain. Combination of the beamline’s MicroXRF, phase contrast imaging, and tomographic approaches will provide an unprecedented improvement in our ability to determine the specific neurons and brain regions in which Mn accumulates, and how that affects brain function and behaviour. Together with our ongoing spatial transcriptomic and behavioural studies, this will further our understanding of the disease pathogenesis underlying Mn neurotoxicity.
DOI: 10.25919/5kqw-ry15
title: Parkes observations for project P1054 semester 2023APRS_09

description: With this proposal we ask time to continue our timing follow-up campaign of pulsars discovered with the MeerKAT telescope. Twenty sources have been discovered in targeted observations of Fermi unidentified point sources, one in association with a Supernova Remnant, 13 in the Magellanic Clouds, 71 in Globular Clusters and 74 in a survey of the Galactic plane. A large fraction of the new discoveries are recycled pulsars (including at least one double neutron star system and several 'spider' binaries), or young pulsars. Timing observations have an essential role in exploiting the full potential of any pulsar discovery, allowing the precise measurement of rotational, astrometric and orbital parameters which, in turn, give us powerful tools to improve our understanding of the physics in extreme environments as well as of the population of neutron stars as a whole. The UWL receiver of the Parkes telescope is a sensitive, versatile instrument that is allowing us to successfully time these new sources, in the bright-end of TRAPUM discoveries.
DOI: 10.48366/r602199
title: Large Language Model augmented Knowledge Graph embedding

description: Knowledge graphs are well-known for their ability to organize knowledge in a structured way. They are used in various tasks like question answering, recommendation systems, and web search. However, traditional knowledge graphs often suffer from incompleteness, and existing methods often overlook the incorporation of textual information. To tackle these challenges, recent studies have focused on enhancing knowledge graphs by integrating Language Model-based Models (LLMs). This integration aims to leverage textual information and enhance performance in downstream tasks. In this comparison, there are 8 different models are explored for LLMs as Text Encoders and LLMs for Joint Text and KG Embedding.
DOI: 10.25781/kaust-13udo
title: AlphaFold-predicted Structures Used in the Master's Thesis of Linsheng Zhang
DOI: 10.5281/zenodo.7239205
title: LPHash - datasets

description: These datasets accompany the paper "Locality-Preserving Minimal Perfect Hashing of k-mers", G. E. Pibiri, Y. Shibuya, and A. Limasset, 2023, Bioinformatics DOI: https://doi.org/10.1093/bioinformatics/btad219. We use genomes of increasing size in terms of number of distinct k-mers; namely, the whole- genomes of: Saccharomyces Cerevisiae (Yeast, 11.6 × 10^6 k-mers), Caenorhabditis Elegans (Elegans, 95×10^6 k-mers), Gadus Morhua (Cod, 0.56×10^9 k-mers), Falco Tinnunculus (Kestrel, 1.16×10^9 k-mers), and Homo Sapiens (Human, 2.77 × 10^9 k-mers). For each genome, we obtain the corresponding SPSS (Spectrum-Preserving String Set) by first building the compacted de Bruijn graph using BCALM2 (Chikhi et al., 2016), then running the UST algorithm (Rahman et al., 2020). At our code repository (github.com/jermp/lphash) we provide detailed instructions on how to obtain SPSS datasets like the ones available here from fasta files. <strong>References</strong> Rayan Chikhi, Antoine Limasset, and Paul Medvedev. Compacting de Bruijn graphs from sequenc- ing data quickly and in low memory. Bioinformatics, 32(12):i201–i208, 2016. Amatur Rahman and Paul Medvedev. Representation of k-mer sets using spectrum-preserving string sets. In International Conference on Research in Computational Molecular Biology, pages 152–168. Springer, 2020.
DOI: 10.5281/zenodo.7239204
title: LPHash - datasets

description: These datasets accompany the paper "Locality-Preserving Minimal Perfect Hashing of k-mers", G. E. Pibiri, Y. Shibuya, and A. Limasset, 2023, Bioinformatics DOI: https://doi.org/10.1093/bioinformatics/btad219. We use genomes of increasing size in terms of number of distinct k-mers; namely, the whole- genomes of: Saccharomyces Cerevisiae (Yeast, 11.6 × 10^6 k-mers), Caenorhabditis Elegans (Elegans, 95×10^6 k-mers), Gadus Morhua (Cod, 0.56×10^9 k-mers), Falco Tinnunculus (Kestrel, 1.16×10^9 k-mers), and Homo Sapiens (Human, 2.77 × 10^9 k-mers). For each genome, we obtain the corresponding SPSS (Spectrum-Preserving String Set) by first building the compacted de Bruijn graph using BCALM2 (Chikhi et al., 2016), then running the UST algorithm (Rahman et al., 2020). At our code repository (github.com/jermp/lphash) we provide detailed instructions on how to obtain SPSS datasets like the ones available here from fasta files. <strong>References</strong> Rayan Chikhi, Antoine Limasset, and Paul Medvedev. Compacting de Bruijn graphs from sequenc- ing data quickly and in low memory. Bioinformatics, 32(12):i201–i208, 2016. Amatur Rahman and Paul Medvedev. Representation of k-mer sets using spectrum-preserving string sets. In International Conference on Research in Computational Molecular Biology, pages 152–168. Springer, 2020.