cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20445235.v1
title: Supplementary data from Three-dimensional visualization of the cardiac ryanodine receptor clusters and the molecular-scale fraying of dyads

description: Clusters of ryanodine receptor calcium channels (RyRs) form the primary molecular machinery of intracellular calcium signalling in cardiomyocytes. While a range of optical super-resolution microscopy techniques have revealed the nanoscale structure of these clusters, the three-dimensional (3D) nanoscale topologies of the clusters have remained mostly unresolved. In this paper, we demonstrate the exploitation of molecular-scale resolution in enhanced expansion microscopy (EExM) along with various 2D and 3D visualization strategies to observe the topological complexities, geometries and molecular sub-domains within the RyR clusters. Notably, we observed sub-domains containing RyR-binding protein junctophilin-2 (JPH2) occupying the central regions of RyR clusters in the deeper interior of the myocytes (including dyads), while the poles were typically devoid of JPH2 lending to a looser RyR arrangement. By contrast, peripheral RyR clusters exhibited variable co-clustering patterns and ratios between RyR and JPH2. EExM images of dyadic RyR clusters in right ventricular (RV) myocytes isolated from rats with monocrotaline-induced RV failure revealed hallmarks of RyR cluster fragmentation accompanied by breaches in the JPH2 sub-domains. Frayed RyR patterns observed adjacent to these constitute new evidence that the destabilization of the RyR arrays inside the JPH2 sub-domains may seed the primordial foci of dyad remodelling observed in heart failure.This article is part of the theme issue ‘The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health and disease’.
DOI: 10.6084/m9.figshare.20445235
title: Supplementary data from Three-dimensional visualization of the cardiac ryanodine receptor clusters and the molecular-scale fraying of dyads

description: Clusters of ryanodine receptor calcium channels (RyRs) form the primary molecular machinery of intracellular calcium signalling in cardiomyocytes. While a range of optical super-resolution microscopy techniques have revealed the nanoscale structure of these clusters, the three-dimensional (3D) nanoscale topologies of the clusters have remained mostly unresolved. In this paper, we demonstrate the exploitation of molecular-scale resolution in enhanced expansion microscopy (EExM) along with various 2D and 3D visualization strategies to observe the topological complexities, geometries and molecular sub-domains within the RyR clusters. Notably, we observed sub-domains containing RyR-binding protein junctophilin-2 (JPH2) occupying the central regions of RyR clusters in the deeper interior of the myocytes (including dyads), while the poles were typically devoid of JPH2 lending to a looser RyR arrangement. By contrast, peripheral RyR clusters exhibited variable co-clustering patterns and ratios between RyR and JPH2. EExM images of dyadic RyR clusters in right ventricular (RV) myocytes isolated from rats with monocrotaline-induced RV failure revealed hallmarks of RyR cluster fragmentation accompanied by breaches in the JPH2 sub-domains. Frayed RyR patterns observed adjacent to these constitute new evidence that the destabilization of the RyR arrays inside the JPH2 sub-domains may seed the primordial foci of dyad remodelling observed in heart failure.This article is part of the theme issue ‘The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health and disease’.
DOI: 10.5281/zenodo.6970926
title: Erythroxylum panamense decontaminated gx

description: .
DOI: 10.5281/zenodo.6970925
title: Erythroxylum panamense decontaminated gx

description: .
DOI: 10.21227/2w1j-6d09
title: sEMG signals of ankle movement under different loads

description: This dataset contains the sEMG signals under low, medium, and high loads when 6 subjects performing ankle movements.
DOI: 10.5281/zenodo.6970956
title: Psilopsiagon aymara decontaminated gx

description: .
DOI: 10.5281/zenodo.6970955
title: Psilopsiagon aymara decontaminated gx

description: .
DOI: 10.6084/m9.figshare.20101448
title: Dataset

description: Dataset
DOI: 10.6084/m9.figshare.20101448.v1
title: Dataset for Key Processes and Factors Controlling Climatically Active Gases and Atmospheric Sulfate Aerosols in the Western Pacific.xlsx

description: Dataset for Key Processes and Factors Controlling Climatically Active Gases and Atmospheric Sulfate Aerosols in the Western Pacific
DOI: 10.5281/zenodo.6971006
title: Data for water in lunar grains

description: the data of water content and hydrogen isotope compositions in lunar soil grains
DOI: 10.5281/zenodo.6971005
title: Data for water in lunar grains

description: the data of water content and hydrogen isotope compositions in lunar soil grains
DOI: 10.6084/m9.figshare.20445261
title: Untitled Item

description: Complete data abstraction table and study protocol.
DOI: 10.6084/m9.figshare.20445261.v1
title: Untitled Item

description: Complete data abstraction table and study protocol.
DOI: 10.5281/zenodo.6971038
title: Erythroxylum confusum zanfona 1

description: .
DOI: 10.5281/zenodo.6971037
title: Erythroxylum confusum zanfona 1

description: .
DOI: 10.6084/m9.figshare.20445279
title: Does surgical position affect infective complications in percutaneous nephrolithotomy?

description: The dataset of the manuscript of "Does surgical position affect infective complications in percutaneous nephrolithotomy?"
DOI: 10.6084/m9.figshare.14813121
title: Parameters and load data

description: " <strong>Parameters and load data1.xlsx</strong>": The parameters and load data of the modified Barry Island HE-IES and an industrial park HE-IES. The original data is refered from "X. Qin, X. Shen, Y. Guo, Z. Pan, and Q. Guo, “Combined electric and heat system testbeds for power flow analysis and economic dispatch,” CSEE J. Power Energy Syst., vol. 7, no. 1, pp. 34–44, Jan. 2021.". " <strong>Case-data of large-scale EH-IES.xlsx</strong>": The parameters and load data of a large-scale EH-IES modified from "X. Qin, X. Shen, Y. Guo, Z. Pan, and Q. Guo, “S. Yao, W. Gu, S. Lu, S. Zhou, Z. Wu, G. Pan, and Di He, “Dynamic optimal energy flow in the heat and electricity integrated energy system,”IEEE Trans. Sustain. Energy, vol. 12, no. 1, pp. 179–190, Aug. 2021.".
DOI: 10.5281/zenodo.6647024
title: Data for manuscript "rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data"

description: Output files generated by rMATS-turbo for the two example datasets described in the manuscript titled "rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data". File Description Cell lines BioProject PC3E-GS689.tar.gz Compressed folder containing all 36 rMATS-turbo output files for Example 1 described in the manuscript PC3E and GS689 cell lines PRJNA438990 CCLE.tar.gz Compressed folder containing all 36 rMATS-turbo output files for Example 2 described in the manuscript 1,019 CCLE human cancer cell lines PRJNA523380 A detailed description of the output files is available in the manuscript and the rMATS-turbo software GitHub repository (https://github.com/Xinglab/rmats-turbo).
DOI: 10.5281/zenodo.6647023
title: Data for manuscript "rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data"

description: Output files generated by rMATS-turbo for the two example datasets described in the manuscript titled "rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data". File Description Cell lines BioProject PC3E-GS689.tar.gz Compressed folder containing all 36 rMATS-turbo output files for Example 1 described in the manuscript PC3E and GS689 cell lines PRJNA438990 CCLE.tar.gz Compressed folder containing all 36 rMATS-turbo output files for Example 2 described in the manuscript 1,019 CCLE human cancer cell lines PRJNA523380 A detailed description of the output files is available in the manuscript and the rMATS-turbo software GitHub repository (https://github.com/Xinglab/rmats-turbo).
DOI: 10.34740/kaggle/dsv/4040530
title: 3d Nodules Segmentation Data Pfe 2
DOI: 10.6084/m9.figshare.20445355.v1
title: Additional file 4 of ELIMINATOR: essentiality analysis using multisystem networks and integer programming

description: Additional file 4: Table S3. BRCA essentiality results (BRCA vs healthy) complete list.
DOI: 10.6084/m9.figshare.20445358.v1
title: Additional file 5 of ELIMINATOR: essentiality analysis using multisystem networks and integer programming

description: Additional file 5: Table S4. BRCA group-specific essentiality results (complete list).
DOI: 10.6084/m9.figshare.20445352.v1
title: Additional file 3 of ELIMINATOR: essentiality analysis using multisystem networks and integer programming

description: Additional file 3: Table S2. BRCA group-specific essentiality results (top 10).
DOI: 10.6084/m9.figshare.20445349.v1
title: Additional file 2 of ELIMINATOR: essentiality analysis using multisystem networks and integer programming

description: Additional file 2: Table S1. manual curation of the NCI-PID pathway list.
DOI: 10.6084/m9.figshare.20445366
title: Additional file 1 of Proteomics analysis of chronic skin injuries caused by mustard gas

description: Additional file 1. The list of diffrentially abundant proteins.
DOI: 10.6084/m9.figshare.20445366.v1
title: Additional file 1 of Proteomics analysis of chronic skin injuries caused by mustard gas

description: Additional file 1. The list of diffrentially abundant proteins.
DOI: 10.6084/m9.figshare.20445369
title: Additional file 2 of Proteomics analysis of chronic skin injuries caused by mustard gas

description: Additional file 2. The list of GO analysis and the KEGG pathway.
DOI: 10.6084/m9.figshare.20445369.v1
title: Additional file 2 of Proteomics analysis of chronic skin injuries caused by mustard gas

description: Additional file 2. The list of GO analysis and the KEGG pathway.
DOI: 10.6084/m9.figshare.20445391
title: Additional file 1 of Neuropathology in chronic traumatic encephalopathy: a systematic review of comparative post-mortem histology literature

description: Additional file 1. Summary of data acquired from all studies examined in this review.
DOI: 10.6084/m9.figshare.20445391.v1
title: Additional file 1 of Neuropathology in chronic traumatic encephalopathy: a systematic review of comparative post-mortem histology literature

description: Additional file 1. Summary of data acquired from all studies examined in this review.
DOI: 10.6084/m9.figshare.20445358
title: Additional file 5 of ELIMINATOR: essentiality analysis using multisystem networks and integer programming

description: Additional file 5: Table S4. BRCA group-specific essentiality results (complete list).
DOI: 10.6084/m9.figshare.20445355
title: Additional file 4 of ELIMINATOR: essentiality analysis using multisystem networks and integer programming

description: Additional file 4: Table S3. BRCA essentiality results (BRCA vs healthy) complete list.
DOI: 10.6084/m9.figshare.20445352
title: Additional file 3 of ELIMINATOR: essentiality analysis using multisystem networks and integer programming

description: Additional file 3: Table S2. BRCA group-specific essentiality results (top 10).
DOI: 10.6084/m9.figshare.20445349
title: Additional file 2 of ELIMINATOR: essentiality analysis using multisystem networks and integer programming

description: Additional file 2: Table S1. manual curation of the NCI-PID pathway list.
DOI: 10.6084/m9.figshare.20445438
title: Additional file 3 of DeLTa-Seq: direct-lysate targeted RNA-Seq from crude tissue lysate

description: Additional file 3: Table S1 List of the RT primers harboring 1st indexes. Table S2 List of the gene-specific primers for gene set 1 (Tradict target gene set). Table S3. List of the PCR primers harboring 2nd indexes. Table S4. List of the gene-specific primers for gene set 2 (JA- and SA-related genes).
DOI: 10.6084/m9.figshare.20445438.v1
title: Additional file 3 of DeLTa-Seq: direct-lysate targeted RNA-Seq from crude tissue lysate

description: Additional file 3: Table S1 List of the RT primers harboring 1st indexes. Table S2 List of the gene-specific primers for gene set 1 (Tradict target gene set). Table S3. List of the PCR primers harboring 2nd indexes. Table S4. List of the gene-specific primers for gene set 2 (JA- and SA-related genes).
DOI: 10.6084/m9.figshare.20445451
title: Additional file 10 of Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs

description: Additional file 10: Table S10. Intersection of human orthologues genes detected in ROHRs with NCBI gene lists for phenotype-related terms.
DOI: 10.6084/m9.figshare.20445451.v1
title: Additional file 10 of Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs

description: Additional file 10: Table S10. Intersection of human orthologues genes detected in ROHRs with NCBI gene lists for phenotype-related terms.
DOI: 10.6084/m9.figshare.20445454.v1
title: Additional file 11 of Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs

description: Additional file 11: Table S11. ROH regions identified for disease resistance and ear phenotypes using PLINK_A, PLINK_B and RZooRoH.
DOI: 10.6084/m9.figshare.20445457
title: Additional file 12 of Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs

description: Additional file 12: Table S12. Overlap of ROH regions (ROHRs) identified for lop and prick ear phenotypes.
DOI: 10.6084/m9.figshare.20445454
title: Additional file 11 of Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs

description: Additional file 11: Table S11. ROH regions identified for disease resistance and ear phenotypes using PLINK_A, PLINK_B and RZooRoH.
DOI: 10.6084/m9.figshare.20445457.v1
title: Additional file 12 of Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs

description: Additional file 12: Table S12. Overlap of ROH regions (ROHRs) identified for lop and prick ear phenotypes.
DOI: 10.6084/m9.figshare.20445472
title: Additional file 4 of Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs

description: Additional file 4: Table S4. Number of ROHs detected using PLINK parameters defining a ROH segment.
DOI: 10.6084/m9.figshare.20445472.v1
title: Additional file 4 of Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs

description: Additional file 4: Table S4. Number of ROHs detected using PLINK parameters defining a ROH segment.
DOI: 10.6084/m9.figshare.20445478
title: Additional file 6 of Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs

description: Additional file 6: Table S6. Number of ROHs overlapping between RZooRoH, PLINK_A and PLINK_B.
DOI: 10.6084/m9.figshare.20445478.v1
title: Additional file 6 of Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs

description: Additional file 6: Table S6. Number of ROHs overlapping between RZooRoH, PLINK_A and PLINK_B.
DOI: 10.6084/m9.figshare.20445481
title: Additional file 7 of Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs

description: Additional file 7: Table S7. Overlap of ROHs between RZooRoH, PLINK_A and PLINK_B datasets in base pairs (bp).
DOI: 10.6084/m9.figshare.20445481.v1
title: Additional file 7 of Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs

description: Additional file 7: Table S7. Overlap of ROHs between RZooRoH, PLINK_A and PLINK_B datasets in base pairs (bp).
DOI: 10.6084/m9.figshare.20445484
title: Additional file 8 of Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs

description: Additional file 8: Table S8. ROH regions identified for heritage pigs using PLINK_A and PLINK_B and RZooRoH.
DOI: 10.6084/m9.figshare.20445484.v1
title: Additional file 8 of Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs

description: Additional file 8: Table S8. ROH regions identified for heritage pigs using PLINK_A and PLINK_B and RZooRoH.
DOI: 10.6084/m9.figshare.20445487
title: Additional file 9 of Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs

description: Additional file 9: Table S9. Functional PANTHER gene enrichment analysis for annotated pig genes identified in ROHRs.
DOI: 10.6084/m9.figshare.20445487.v1
title: Additional file 9 of Simultaneous testing of rule- and model-based approaches for runs of homozygosity detection opens up a window into genomic footprints of selection in pigs

description: Additional file 9: Table S9. Functional PANTHER gene enrichment analysis for annotated pig genes identified in ROHRs.
DOI: 10.6084/m9.figshare.20445492
title: Additional file 2 of Prevalence of Plasmodium spp. in Anopheles mosquitoes in Thailand: a systematic review and meta-analysis

description: Additional file 2: Table S2. Details of the included studies
DOI: 10.6084/m9.figshare.20445495
title: Additional file 3 of Prevalence of Plasmodium spp. in Anopheles mosquitoes in Thailand: a systematic review and meta-analysis

description: Additional file 3: Table S3. Quality of the included studies
DOI: 10.6084/m9.figshare.20445492.v1
title: Additional file 2 of Prevalence of Plasmodium spp. in Anopheles mosquitoes in Thailand: a systematic review and meta-analysis

description: Additional file 2: Table S2. Details of the included studies
DOI: 10.6084/m9.figshare.20445495.v1
title: Additional file 3 of Prevalence of Plasmodium spp. in Anopheles mosquitoes in Thailand: a systematic review and meta-analysis

description: Additional file 3: Table S3. Quality of the included studies
DOI: 10.5281/zenodo.6971295
title: Ara severus decontaminated FSCR

description: .
DOI: 10.5281/zenodo.6971294
title: Ara severus decontaminated FSCR

description: .
DOI: 10.5281/zenodo.6969670
title: Modelled basal melt rate underneath the Antarctic Lambert–Amery glacial system

description: This is the modelled basal melt rates in six experiments using different geothermal heat flux (GHF) maps as forcing for an offline coupling between a forward model and an inverse model. The forward model consists of a thermomechanical steady state model using an improved shallow ice approximation in equilibrium with the subglacial hydrological system. The inverse model is solved using 3D full Stokes model. The six GHF maps are from Martos et al. (2017), Shen et al. (2020), An et al. (2015), Shapiro and Ritzwoller (2004), Purucker (2012) and Li et al. (2021). Each filename includes the family name of the first author of the GHF map that is used. For instance, basal_meltrate_an.nc provides the modelled basal melt rates using An et al. (2015) GHF. Files are provided in netcdf format. The netcdf files have 2D grids only. The unit of modelled basal melt rate is mm/yr. The value outside our modelled domain is given as 9.96921e36. The positive value inside our modelled domain represents basal melt rate, while negative represents basal freeze rate. For more information, please see the following paper that is currently accepted by The Cryosphere: H. Kang et al.: Evaluation of six geothermal heat flux maps for the Antarctic Lambert–Amery glacial system, The Cryosphere, 2022.
DOI: 10.6069/g80d-zw25
title: Absolute quantification of influenza virus proteins

description: SWATH- mass spectrometry coupled with isotope labelled standard peptides for absolute quantification (AQUA) of proteins is a relatively new technique for the characterization of proteins. In this study, a mass spectrometry-based method for absolute quantification of selected influenza A virus proteins (hemagglutinin, neuraminidase, nucleoprotein, matrix protein 1) is presented.
DOI: 10.34740/kaggle/dsv/4040644
title: Mahanagar Yatayat Dataset
DOI: 10.5281/zenodo.6971487
title: Ara severus decontaminated gx

description: .
DOI: 10.5281/zenodo.6971486
title: Ara severus decontaminated gx

description: .
DOI: 10.6084/m9.figshare.20445093
title: MLSA data

description: MLSA gene sequences derived from respective genomes.
DOI: 10.6084/m9.figshare.20445093.v1
title: MLSA data

description: MLSA gene sequences derived from respective genomes.
DOI: 10.6084/m9.figshare.20445528
title: Reynoutria

description: Reynoutria
DOI: 10.6084/m9.figshare.20445528.v1
title: Reynoutria

description: Reynoutria
DOI: 10.18112/openneuro.ds003498.v1.1.0
title: interictal iEEG during slow-wave sleep with HFO markings
DOI: 10.6084/m9.figshare.14744331
title: Dengue Comorbid Study.dta

description: Data set for research Case-control study
DOI: 10.6084/m9.figshare.14744331.v1
title: Dengue Comorbid Study.dta

description: Data set for research Case-control study
DOI: 10.6084/m9.figshare.16593020
title: Data Repository of the manuscript entitled "The release of inflammatory mediators from acid-stimulated mesenchymal stromal cells favours tumour invasiveness and metastasis in osteosarcoma" from Avnet S. et al.

description: Row data associated with the manuscript entitled "The release of inflammatory mediators from by acid-stimulated mesenchymal stromal cells favours tumour invasiveness and metastasis in osteosarcoma" from Avnet et al.
DOI: 10.6084/m9.figshare.16593020.v1
title: Data Repository of the manuscript entitled "The release of inflammatory mediators from acid-stimulated mesenchymal stromal cells favours tumour invasiveness and metastasis in osteosarcoma" from Avnet S. et al.

description: Row data associated with the manuscript entitled "The release of inflammatory mediators from by acid-stimulated mesenchymal stromal cells favours tumour invasiveness and metastasis in osteosarcoma" from Avnet et al.
DOI: 10.5519/qd.csll7mg6
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.5519/qd.10ccvkin
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (16 records)
DOI: 10.6084/m9.figshare.20444460
title: Imaging data from Warriner et al., 2022

description: Neural (calcium imaging recording of corticospinal neurons) and behavioral (EMG) data from alternation and cocontraction paradigm for two mice, with corresponding tagging of GAD2+ CSN subtype.
DOI: 10.6084/m9.figshare.20444460.v1
title: Imaging data from Warriner et al., 2022

description: Neural (calcium imaging recording of corticospinal neurons) and behavioral (EMG) data from alternation and cocontraction paradigm for two mice, with corresponding tagging of GAD2+ CSN subtype.