cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8202533.v1
title: Additional file 4: of Time varying causal network reconstruction of a mouse cell cycle

description: Complete list of interactions identified in reconstruction of G1 phase followed by S phase in the {1â 24.5} hour interval. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.8202536.v1
title: Additional file 5: of Time varying causal network reconstruction of a mouse cell cycle

description: Complete list of interactions identified in reconstruction of the G1 and S phases followed by G2/M phases in the {1â 28.5} hour interval. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.8202524.v1
title: Additional file 3: of Time varying causal network reconstruction of a mouse cell cycle

description: Complete list of interactions identified in reconstruction of G1 phase in the {1â 14.5} hour interval. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.8202506
title: Additional file 1: of Time varying causal network reconstruction of a mouse cell cycle

description: List of 63 cell cycle genes and their full names. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8202506.v1
title: Additional file 1: of Time varying causal network reconstruction of a mouse cell cycle

description: List of 63 cell cycle genes and their full names. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8202437
title: MOESM1 of Impact of the rumen microbiome on milk fatty acid composition of Holstein cattle

description: Additional file 1. Annotation of the most abundant bacteria OTU.
DOI: 10.6084/m9.figshare.8202437.v1
title: MOESM1 of Impact of the rumen microbiome on milk fatty acid composition of Holstein cattle

description: Additional file 1. Annotation of the most abundant bacteria OTU.
DOI: 10.6084/m9.figshare.8202410
title: 19-grams number

description: 19-grams
DOI: 10.6084/m9.figshare.8202407
title: 19-grams

description: 19-grams
DOI: 10.6084/m9.figshare.8202410.v1
title: 19-grams number

description: 19-grams
DOI: 10.6084/m9.figshare.8202407.v1
title: 19-grams

description: 19-grams
DOI: 10.21227/n7at-6215
title: VCN

description: Program folder contains all the programs used in the paper. The program is based on tensorflow 2.2.The data folder contains manually generated data and bearing data.
DOI: 10.6084/m9.figshare.8202383.v1
title: Axonal autophagosome maturation defect through failure of ATG9A sorting underpins pathology in AP-4 deficiency syndrome

description: Adaptor protein (AP) complexes mediate key sorting decisions in the cell through selective incorporation of transmembrane proteins into vesicles. Little is known of the roles of AP-4, despite its loss of function leading to a severe early onset neurological disorder, AP-4 deficiency syndrome. Here we demonstrate an AP-4 epsilon subunit knockout mouse model that recapitulates characteristic neuroanatomical phenotypes of AP-4 deficiency patients. We show that ATG9A, critical for autophagosome biogenesis, is an AP-4 cargo, which is retained within the <i>trans</i>-Golgi network (TGN) <i>in vivo</i> and in culture when AP-4 function is lost. TGN retention results in depletion of axonal ATG9A, leading to defective autophagosome generation and aberrant expansions of the distal axon. The reduction in the capacity to generate axonal autophagosomes leads to defective axonal extension and <i>de novo</i> generation of distal axonal swellings containing accumulated ER, underlying the impaired axonal integrity in AP-4 deficiency syndrome. <b>Abbreviations</b>: AP: adaptor protein; AP4B1: adaptor-related protein complex AP-4, beta 1; AP4E1: adaptor-related protein complex AP-4, epsilon 1; ATG: autophagy-related; EBSS: Earle’s balanced salt solution; ER: endoplasmic reticulum; GFAP: glial fibrillary acidic protein; GOLGA1/Golgin-97/GOLG97: golgi autoantigen, golgin subfamily a, 1; GOLGA2/GM130: golgi autoantigen, golgin subfamily a, 2; HSP: hereditary spastic paraplegia; LC3/MAP1LC3B: microtubule-associated protein 1 light chain 3 beta; MAP2: microtubule-associated protein 2; MAPK8IP1/JIP1: mitogen-acitvated protein kinase 8 interacting protein 1; NEFH/NF200: neurofilament, heavy polypeptide; RBFOX3/NeuN (RNA binding protein, fox-1 homolog [C. elegans] 3); SQSTM1/p62: sequestosome 1; TGN: trans-Golgi network; WIPI2: WD repeat domain, phosphoinositide interacting protein 2
DOI: 10.6084/m9.figshare.8202362
title: 18-grams number

description: 18-grams
DOI: 10.6084/m9.figshare.8202314
title: Kinome profiling reveals abnormal activity of kinases in skeletal muscle from adults with obesity and insulin resistance

description: <b>ABSTRACT</b><b>Context: Obesity-related insulin resistance (OIR) is one of the main contributors to type 2 diabetes and other metabolic diseases. Protein kinases are implicated in insulin signaling and glucose metabolism. Molecular mechanisms underlying OIR involving global kinase activities remain incompletely understood. Objective: To investigate abnormal kinase activity associated with OIR in human skeletal muscle. Design: Stable isotopic labeling-based quantitative proteomics combined with affinity-based active enzyme probes to profile in vivo kinase activity in skeletal muscle from lean control (Lean) and OIR participants. Participants: Eight Lean and eight OIR non-diabetic human adults who underwent hyperinsulinemic-euglycemic clamp with muscle biopsy. Results: We identified the 1st active kinome comprised of 54 active protein kinases in human skeletal muscle. The activities of 23 kinases were different in OIR compared to Lean muscle (11 hyper- and 12 hypo-active), while their protein abundance was the same between the two groups. The activities of multiple kinases involved in AMPK and p38 signaling were lower in OIR compared to Lean. On the contrary, multiple kinases in the JNK signaling pathway exhibited higher activity in OIR vs. Lean. The kinase-substrate-prediction based on experimental data further confirmed a potential down-regulation of insulin signaling (e.g., inhibited phosphorylation of IRS1 and AKT1/2). Conclusions: These findings provide a global view of the kinome activity in OIR and Lean muscle, pinpoint novel specific impairment in kinase activities in signaling pathways important for skeletal muscle insulin resistance and may provide potential drug targets (i.e., abnormal kinase activities) to prevent and/or reverse skeletal muscle insulin resistance in humans.</b><br>
DOI: 10.6084/m9.figshare.8202356
title: 18-grams

description: 18-grams
DOI: 10.6084/m9.figshare.8202362.v1
title: 18-grams number

description: 18-grams
DOI: 10.6084/m9.figshare.8202356.v1
title: 18-grams

description: 18-grams
DOI: 10.6084/m9.figshare.8202314.v1
title: Global kinome profiling reveals abnormal active kinases in human skeletal muscle from obese insulin resistant participants

description: <b>ABATRACT</b> <b>Context:</b> Obesity-related insulin resistance (OIR) is one of the main contributors to type 2 diabetes and other metabolic diseases. Protein kinases are implicated in key signaling steps including insulin signaling and glucose metabolism. Molecular mechanisms underlying OIR involving global active kinases remain less understood. <b>Objective: </b>To investigate abnormal active kinase responsible for OIR in human skeletal muscle. <b>Design: </b>Stable isotopic labeling-based quantitative proteomics analysis and affinity-based active enzyme probes to profile <i>in vivo</i> active kinases. <b></b> <b>Participants: </b>Eight lean control and eight OIR but non-diabetic human participants who underwent hyperinsulinemic euglycemic clamp with muscle biopsy.<b></b> <b>Results: </b>We identified the 1st active kinome comprised of 54 active protein kinases in human skeletal muscle. The activities of 23 kinases were different in OIR compared to Lean muscle (11 hyper- and 12 hypo-active), while their protein abundance was the same between the two groups. The activities of multiple kinases involved in AMPK and p38 signaling were lower in OIR compared to Lean. On the contrary, multiple kinases in JNK signaling pathway exhibited higher activity in OIR vs. Lean. The kinase-substrate-prediction based on experimental data further confirmed a potential down-regulation of insulin signaling (e.g., inhibited phosphorylation of IRS1 and AKT1/2). <b>Conclusions: </b>These findings provide a global view of the active kinome in OIR and Lean muscle, pinpoint novel specific impairment in kinase activities in multiple signaling pathways important for skeletal muscle insulin resistance and provide potential drug targets (i.e., abnormal active kinase) to prevent and/or reverse skeletal muscle insulin resistance in humans.
DOI: 10.6084/m9.figshare.8202233
title: Ischaemic stroke metaGRS

description: A genomic risk score (metaGRS, a meta-score combining multiple GRSs) for ischaemic stroke, consisting of 3.2 million SNPs that had MAF &gt;1% in the UK Biobank British white subset and imputation INFO &gt;0.4 over the entire UK Biobank dataset.<br><br>Also provided is a version further excluding ambiguous strand SNPs (A/T or G/C), leaving 2.76 million SNPs. This score had very similar performance in the UK Biobank validation set in terms of association with age of ischaemic stroke.<br><br>The rsids, positions, and alleles are with respect to UK Biobank genotyping release 2 (hg19).<br><br>Also included are the SNP weights for each component GRS that contributed to the stroke metaGRS, as well as the weights for the metaGRS itself.<br><br>To apply the metaGRS scores to new data with plink use:<br>plink --bfile your_data \--score metaGRS_stroke_IS_MAF0.01_INFO0.4_exclATGC.txt 2 4 18 header sum<br>
DOI: 10.6084/m9.figshare.8202209
title: 17-grams number

description: 17-grams
DOI: 10.6084/m9.figshare.8202203
title: 17-grams

description: 17-grams
DOI: 10.6084/m9.figshare.8202203.v1
title: 17-grams

description: 17-grams
DOI: 10.6084/m9.figshare.8202314.v4
title: Kinome profiling reveals abnormal activity of kinases in skeletal muscle from adults with obesity and insulin resistance

description: <b>ABSTRACT</b><b>Context: Obesity-related insulin resistance (OIR) is one of the main contributors to type 2 diabetes and other metabolic diseases. Protein kinases are implicated in insulin signaling and glucose metabolism. Molecular mechanisms underlying OIR involving global kinase activities remain incompletely understood. Objective: To investigate abnormal kinase activity associated with OIR in human skeletal muscle. Design: Stable isotopic labeling-based quantitative proteomics combined with affinity-based active enzyme probes to profile in vivo kinase activity in skeletal muscle from lean control (Lean) and OIR participants. Participants: Eight Lean and eight OIR non-diabetic human adults who underwent hyperinsulinemic-euglycemic clamp with muscle biopsy. Results: We identified the 1st active kinome comprised of 54 active protein kinases in human skeletal muscle. The activities of 23 kinases were different in OIR compared to Lean muscle (11 hyper- and 12 hypo-active), while their protein abundance was the same between the two groups. The activities of multiple kinases involved in AMPK and p38 signaling were lower in OIR compared to Lean. On the contrary, multiple kinases in the JNK signaling pathway exhibited higher activity in OIR vs. Lean. The kinase-substrate-prediction based on experimental data further confirmed a potential down-regulation of insulin signaling (e.g., inhibited phosphorylation of IRS1 and AKT1/2). Conclusions: These findings provide a global view of the kinome activity in OIR and Lean muscle, pinpoint novel specific impairment in kinase activities in signaling pathways important for skeletal muscle insulin resistance and may provide potential drug targets (i.e., abnormal kinase activities) to prevent and/or reverse skeletal muscle insulin resistance in humans.</b><br>
DOI: 10.6084/m9.figshare.8202209.v1
title: 17-grams number

description: 17-grams
DOI: 10.6084/m9.figshare.8202149
title: Molecular Dynamics trajectories of membrane protein YiiP

description: Molecular dynamics (MD) trajectory files of the YiiP membrane protein in a POPE:POPG 4:1 model membrane. The equilibrium simulation was performed in the <i>NPT</i> ensemble at <i>T</i>=300K and<i> P</i>=1 bar. The system was simulated with Gromacs 2018.1, using the CHARMM36 force field, the TIP3P explicit water model, NaCl at approximately 100 mM concentration, and Zinc ions.<br>Trajectory frames were saved every 100 ps for a total of 9 ns and 90ns simulated time. The topology contains the whole system (protein, membrane, water and ions).<br>The topology is contained in the <i>YiiP_system.pdb </i>file. The 9-ns trajectory is contained in the <i>YiiP_system_9ns_center.xtc </i>file. The 90-ns trajectory is contained in the <i>YiiP_system_90ns_center.xtc</i> file.
DOI: 10.6084/m9.figshare.8202137
title: rsEEG eyes closed SPSS file JoN

description: as above<br>
DOI: 10.6084/m9.figshare.8202149.v1
title: Molecular Dynamics trajectories of membrane protein YiiP

description: Molecular dynamics (MD) trajectory files of the YiiP membrane protein in a POPE:POPG 4:1 model membrane. The equilibrium simulation was performed in the <i>NPT</i> ensemble at <i>T</i>=300K and<i> P</i>=1 bar. The system was simulated with Gromacs 2018.1, using the CHARMM36 force field, the TIP3P explicit water model, NaCl at approximately 100 mM concentration, and Zinc ions.<br>Trajectory frames were saved every 100 ps for a total of 9 ns and 90ns simulated time. The topology contains the whole system (protein, membrane, water and ions).<br>The topology is contained in the <i>YiiP_system.pdb </i>file. The 9-ns trajectory is contained in the <i>YiiP_system_9ns_center.xtc </i>file. The 90-ns trajectory is contained in the <i>YiiP_system_90ns_center.xtc</i> file.
DOI: 10.6084/m9.figshare.8202143
title: CCDB_6862.jpg

description: Single computed slice through a tomographic reconstruction of a protoplasmic astrocyte in a 0.5 um thick section from the hippocampus of a 1 month old male mouse, imaged with intermediate voltage electron microscopy. This reconstruction is the 26th in a series of 26 serial reconstructions through the cell soma. The complete reconstruction can be viewed under MP7503.
DOI: 10.6084/m9.figshare.8202134
title: rsEEG eyes open SPSS file JoN

description: as above<br>
DOI: 10.6084/m9.figshare.8202143.v1
title: CCDB_6862.jpg

description: Single computed slice through a tomographic reconstruction of a protoplasmic astrocyte in a 0.5 um thick section from the hippocampus of a 1 month old male mouse, imaged with intermediate voltage electron microscopy. This reconstruction is the 26th in a series of 26 serial reconstructions through the cell soma. The complete reconstruction can be viewed under MP7503.
DOI: 10.6084/m9.figshare.8202119
title: CCDB_6861.jpg

description: Single computed slice through a tomographic reconstruction of a protoplasmic astrocyte in a 0.5 um thick section from the hippocampus of a 1 month old male mouse, imaged with intermediate voltage electron microscopy. This reconstruction is the 6th in a series of 26 serial reconstructions through the cell soma. The complete reconstruction can be viewed under MP7503.
DOI: 10.6084/m9.figshare.8202116
title: Coherence data SPSS file

description: as above<br>
DOI: 10.6084/m9.figshare.8202119.v1
title: CCDB_6861.jpg

description: Single computed slice through a tomographic reconstruction of a protoplasmic astrocyte in a 0.5 um thick section from the hippocampus of a 1 month old male mouse, imaged with intermediate voltage electron microscopy. This reconstruction is the 6th in a series of 26 serial reconstructions through the cell soma. The complete reconstruction can be viewed under MP7503.
DOI: 10.6084/m9.figshare.8202116.v1
title: Coherence data SPSS file

description: as above<br>
DOI: 10.6084/m9.figshare.8202092
title: 16-grams number

description: 16-grams
DOI: 10.6084/m9.figshare.8202092.v1
title: 16-grams number

description: 16-grams
DOI: 10.6084/m9.figshare.8202089
title: 16-grams

description: 16-grams
DOI: 10.6084/m9.figshare.8202077
title: CCDB_6859.jpg

description: Single computed slice through a tomographic reconstruction of a protoplasmic astrocyte in a 0.5 um thick section from the hippocampus of a 1 month old male mouse, imaged with intermediate voltage electron microscopy. This reconstruction is the 4th in a series of 26 serial reconstructions through the cell soma. The complete reconstruction can be viewed under MP7503.
DOI: 10.6084/m9.figshare.8202041
title: Figshare-ACP-VOCtrendpaper.xlsx

description: NMVOC emissions of China by sectors, speciated results, and ozone formation potentials during 1990-2017. <br>Detailed data of figures presented in Li et al. (2019):<br><i>Li, M., Zhang, Q., Zheng, B., Tong, D., Lei, Y., Liu, F., Hong, C., Kang, S., Yan, L., Zhang, Y., Bo, Y., Su, H., Cheng, Y., and He, K.: Persistent growth of anthropogenic NMVOC emissions in China during 1990-2017: dynamics, speciation, and ozone formation potentials, Atmos. Chem. Phys. Discuss., 2019, 1-29, 10.5194/acp-2019-125, 2019.</i><br>
DOI: 10.6084/m9.figshare.8202086
title: CCDB_6860.jpg

description: Single computed slice through a tomographic reconstruction of a protoplasmic astrocyte in a 0.5 um thick section from the hippocampus of a 1 month old male mouse, imaged with intermediate voltage electron microscopy. This reconstruction is the 5th in a series of 26 serial reconstructions through the cell soma. The complete reconstruction can be viewed under MP7503.
DOI: 10.6084/m9.figshare.8202089.v1
title: 16-grams

description: 16-grams
DOI: 10.6084/m9.figshare.8202077.v1
title: CCDB_6859.jpg

description: Single computed slice through a tomographic reconstruction of a protoplasmic astrocyte in a 0.5 um thick section from the hippocampus of a 1 month old male mouse, imaged with intermediate voltage electron microscopy. This reconstruction is the 4th in a series of 26 serial reconstructions through the cell soma. The complete reconstruction can be viewed under MP7503.
DOI: 10.6084/m9.figshare.8201942
title: 15-grams

description: 15-grams
DOI: 10.6084/m9.figshare.8202086.v1
title: CCDB_6860.jpg

description: Single computed slice through a tomographic reconstruction of a protoplasmic astrocyte in a 0.5 um thick section from the hippocampus of a 1 month old male mouse, imaged with intermediate voltage electron microscopy. This reconstruction is the 5th in a series of 26 serial reconstructions through the cell soma. The complete reconstruction can be viewed under MP7503.
DOI: 10.6084/m9.figshare.8201945
title: 15-grams number

description: 15-grams
DOI: 10.6084/m9.figshare.8201945.v1
title: 15-grams number

description: 15-grams
DOI: 10.6084/m9.figshare.8201942.v1
title: 15-grams

description: 15-grams
DOI: 10.6084/m9.figshare.8201939
title: Grycz et al 2019 repository

description: Tables with data, materials, reagents and devices used to prepare the manuscript
DOI: 10.6084/m9.figshare.8201930
title: CCDB_6858.jpg

description: Electron micrograph of the soma of a protoplasmic astrocyte in a 0.5 um thick section from the hippocampus of a 1 month old male mouse, imaged with intermediate voltage electron microscopy at zero degrees tilt. This section is the 3rd in a series of 26 serial semi-thick sections through the astrocyte soma used for a serial tomographic reconstruction (MP7503).
DOI: 10.6084/m9.figshare.8201939.v2
title: Grycz et al 2019 repository

description: Tables with data, materials, reagents and devices used to prepare the manuscript
DOI: 10.6084/m9.figshare.8201930.v1
title: CCDB_6858.jpg

description: Electron micrograph of the soma of a protoplasmic astrocyte in a 0.5 um thick section from the hippocampus of a 1 month old male mouse, imaged with intermediate voltage electron microscopy at zero degrees tilt. This section is the 3rd in a series of 26 serial semi-thick sections through the astrocyte soma used for a serial tomographic reconstruction (MP7503).
DOI: 10.6084/m9.figshare.8201912
title: CCDB_6857.jpg

description: Electron micrograph of the soma of a protoplasmic astrocyte in a 0.5 um thick section from the hippocampus of a 1 month old male mouse, imaged with intermediate voltage electron microscopy at zero degrees tilt. This section is the 2nd in a series of 26 serial semi-thick sections through the astrocyte soma used for a serial tomographic reconstruction (MP7503).
DOI: 10.6084/m9.figshare.8201939.v1
title: Grycz et al 2019 repository

description: Tables with data, materials, reagents and devices used to prepare the manuscript
DOI: 10.6084/m9.figshare.8201912.v1
title: CCDB_6857.jpg

description: Electron micrograph of the soma of a protoplasmic astrocyte in a 0.5 um thick section from the hippocampus of a 1 month old male mouse, imaged with intermediate voltage electron microscopy at zero degrees tilt. This section is the 2nd in a series of 26 serial semi-thick sections through the astrocyte soma used for a serial tomographic reconstruction (MP7503).
DOI: 10.1184/r1/8201834
title: Data and Analysis Code for Kantzos 2019: Design of Interpretable CNN. . .

description: This dataset is from the paper: "Design of an Interpretable Convolutional Neural Network for Stress Concentration Prediction in Rough Surfaces" by Kantzos et. al. (2019)<br>Paper Abstract: We present the application of a Convolutional Neural Network (CNN) to relate stress concentrations to surface roughness. Stress concentrations at the low points of rough surfaces are one of the primary causes of fatigue crack initiation but there is no generally accepted way to analyze rough surfaces to predict crack initiation. Synthetically generated rough surfaces, instantiated in a mechanical model allow for the simulation of stress concentrations, creating a database of surface images and corresponding mechanical data. In this work, the CNN is designed and trained to interpret a height map of a surface and, from that data, to predict the stress concentrations created by the surface. Using a simple architecture, the CNN achieved R2 = 0.75 in prediction for test images, i.e., those not used in training. This CNN can be adapted for experimental surfaces thus creating a new and straightforward tool for prediction of crack initiation. Considerable work was taken to minimize the complexity of the CNN architecture and to make it interpretable via viewports.<br><br>Herein are 4 files that can be downloaded to analyze the data, reproduce figures from the paper, and train new CNNs. The files are compressed directories. <br><br>
DOI: 10.6084/m9.figshare.8201852
title: SPIROPLASMA PANGENOME FROM YEOMAN ET AL

description: This archive contains the necessary data files to visualize, update, and edit the Spiroplasma pangenome publish in Yeoman et al study titled "Genome-resolved insights into a novel Spiroplasma symbiont of the Wheat Stem Sawfly (Cephus cinctus)".<br>For more information, visit http://merenlab.org/data/spiroplasma-pangenome/