cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3622355_d8.v1
title: Additional file 8: Table S7. of A proteomic analysis of chondrogenic, osteogenic and tenogenic constructs from ageing mesenchymal stem cells

description: Presenting upstream log ratio molecule predicted activation p values of target molecules in the dataset. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.c.3622403_d1.v1
title: MOESM1 of Analyzing the Chinese landscape in anti-diabetic drug research: leading knowledge production institutions and thematic communities

description: Additional file 1. Information of 430 institutes. The region information and all centrality measurements of 430 institutes are clearly presented.
DOI: 10.6084/m9.figshare.c.3622403_d2.v1
title: MOESM3 of Analyzing the Chinese landscape in anti-diabetic drug research: leading knowledge production institutions and thematic communities

description: Additional file 3. All keywords in each article. The keywords in different articles are listed, and their Chinese translation are also presented for reference.
DOI: 10.6084/m9.figshare.c.3622403_d3.v1
title: MOESM2 of Analyzing the Chinese landscape in anti-diabetic drug research: leading knowledge production institutions and thematic communities

description: Additional file 2. Tabular data of Fig.Â 3. All keywords in Fig.Â 3 are numbered by their frequency in each community, and the words in italics are research topic relevant to a given community than to other keywords and the bold words are more related to Chinese medicines.
DOI: 10.25378/janelia.24260830
title: Manual organelle segmentations (crop270) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver acinus (jrc_mus-liver-zon-1)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<b>Annotation description</b>: Dense segmentations of mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective in jrc_mus-liver-zon-1 using Amira 3D 2021.1, Classic Segmentation Workroom and the 'Using Amira to manually segment organelles in vEM for machine learning V.3' annotation protocol.<b>Annotation ID</b>: crop270<b>Primary Annotator</b>: Woohyun Park<b>Annotation protocol</b>: Using Amira to manually segment organelles in vEM for machine learning V.3 (http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3)<b>Software</b>: Amira 3D 2021.1, Classic Segmentation Workroom<b>Annotated voxel size (nm)</b>: 8 x 8 x 8 (x, y, z)<b>Annotated data dimensions (µm)</b>: 1.6 x 1.6 x 1.6 (x, y, z)<b>Annotated data offset (nm)</b>: 24616 x 107984 x 207912 (x, y, z)<b>Classes annotated</b>: mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop270<b>Source (EM) dataset ID</b>: jrc_mus-liver-zon-1<b>Source (EM) voxel size (nm)</b>: 8 x 8 x 8 (x, y, z)<b>Source (EM) data dimensions (µm)</b>: 397.16 x 171.61 x 188.81 (x, y, z)<b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.24128700<b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-liver-zon-1<b>Publication:</b> <i>CellMap Segmentation Challenge,</i> 2024.<b>The CellMap Project Team during this time consisted of:</b> David Ackerman, Davis Bennett, Marley Bryant, Hannah Nguyen, Grace Park, Alyson Petruncio, Alannah Post, Jacquelyn Price, Diana Ramirez, Jeff Rhoades, Rebecca Vorimo, Aubrey Weigel, Marwan Zouinkhi, Yurii Zubov.<b>The CellMap Project Team Steering Committee during this time consisted of:</b> Misha Ahrens, Christopher Beck, Teng-Leong Chew, Daniel Feliciano, Jan Funke, Harald Hess, Wyatt Korff, Jennifer Lippincott-Schwartz, Zhe J. Liu, Kayvon Pedram, Stephan Preibisch, Stephan Saalfeld, Ronald Vale, and Aubrey Weigel.
DOI: 10.25378/janelia.24260830.v1
title: Manual organelle segmentations (crop270) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver acinus (jrc_mus-liver-zon-1)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<b>Annotation description</b>: Dense segmentations of mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective in jrc_mus-liver-zon-1 using Amira 3D 2021.1, Classic Segmentation Workroom and the 'Using Amira to manually segment organelles in vEM for machine learning V.3' annotation protocol.<b>Annotation ID</b>: crop270<b>Primary Annotator</b>: Woohyun Park<b>Annotation protocol</b>: Using Amira to manually segment organelles in vEM for machine learning V.3 (http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3)<b>Software</b>: Amira 3D 2021.1, Classic Segmentation Workroom<b>Annotated voxel size (nm)</b>: 8 x 8 x 8 (x, y, z)<b>Annotated data dimensions (µm)</b>: 1.6 x 1.6 x 1.6 (x, y, z)<b>Annotated data offset (nm)</b>: 24616 x 107984 x 207912 (x, y, z)<b>Classes annotated</b>: mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop270<b>Source (EM) dataset ID</b>: jrc_mus-liver-zon-1<b>Source (EM) voxel size (nm)</b>: 8 x 8 x 8 (x, y, z)<b>Source (EM) data dimensions (µm)</b>: 397.16 x 171.61 x 188.81 (x, y, z)<b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.24128700<b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-liver-zon-1<b>Publication:</b> <i>CellMap Segmentation Challenge,</i> 2024.<b>The CellMap Project Team during this time consisted of:</b> David Ackerman, Davis Bennett, Marley Bryant, Hannah Nguyen, Grace Park, Alyson Petruncio, Alannah Post, Jacquelyn Price, Diana Ramirez, Jeff Rhoades, Rebecca Vorimo, Aubrey Weigel, Marwan Zouinkhi, Yurii Zubov.<b>The CellMap Project Team Steering Committee during this time consisted of:</b> Misha Ahrens, Christopher Beck, Teng-Leong Chew, Daniel Feliciano, Jan Funke, Harald Hess, Wyatt Korff, Jennifer Lippincott-Schwartz, Zhe J. Liu, Kayvon Pedram, Stephan Preibisch, Stephan Saalfeld, Ronald Vale, and Aubrey Weigel.
DOI: 10.6084/m9.figshare.c.3622403_d4.v1
title: MOESM4 of Analyzing the Chinese landscape in anti-diabetic drug research: leading knowledge production institutions and thematic communities

description: Additional file 4. Details of 881 publications in 14 thematic communities. This document provides more detailed information of all articles in 14 thematic communities, it contains: article title, author, organization, geographic region and thematic community.
DOI: 10.6084/m9.figshare.27135186
title: FINAL_Sociosexual_data_update_27Sept2024_Figshare.csv

description: Dataset for Snyder et al. Sexual signaling and sociosexual behaviours in relation to rank, parasites and hormones in male vervet monkeys (<i>Chlorocebus pygerythrus</i>) in Uganda
DOI: 10.6084/m9.figshare.27135186.v1
title: FINAL_Sociosexual_data_update_27Sept2024_Figshare.csv

description: Dataset for Snyder et al. Sexual signaling and sociosexual behaviours in relation to rank, parasites and hormones in male vervet monkeys (<i>Chlorocebus pygerythrus</i>) in Uganda
DOI: 10.6084/m9.figshare.c.3622637_d1.v1
title: Additional file 2: of Fab glycosylation of immunoglobulin G does not associate with improvement of rheumatoid arthritis during pregnancy

description: Data used for analysis. Contains the relative abundances of the observed glycans and the calculated glycosylation traits for the RA patients and healthy controls used in the current study. (XLSX 120Â kb)
DOI: 10.25378/janelia.24260824
title: Manual organelle segmentations (crop269) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver acinus (jrc_mus-liver-zon-1)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<b>Annotation description</b>: Dense segmentations of mitochondrial membrane, mitochondrial lumen, vesicle membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, cytosol, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective in jrc_mus-liver-zon-1 using Amira 3D 2021.1, Classic Segmentation Workroom and the 'Using Amira to manually segment organelles in vEM for machine learning V.3' annotation protocol.<b>Annotation ID</b>: crop269<b>Primary Annotator</b>: Rebecca Vorimo<b>Annotation protocol</b>: Using Amira to manually segment organelles in vEM for machine learning V.3 (http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3)<b>Software</b>: Amira 3D 2021.1, Classic Segmentation Workroom<b>Annotated voxel size (nm)</b>: 4 x 4 x 4 (x, y, z)<b>Annotated data dimensions (µm)</b>: 1.6 x 1.6 x 1.6 (x, y, z)<b>Annotated data offset (nm)</b>: 11150 x 95062 x 213310 (x, y, z)<b>Classes annotated</b>: mitochondrial membrane, mitochondrial lumen, vesicle membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, cytosol, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop269<b>Source (EM) dataset ID</b>: jrc_mus-liver-zon-1<b>Source (EM) voxel size (nm)</b>: 8 x 8 x 8 (x, y, z)<b>Source (EM) data dimensions (µm)</b>: 397.16 x 171.61 x 188.81 (x, y, z)<b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.24128700<b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-liver-zon-1<b>Publication:</b> <i>CellMap Segmentation Challenge,</i> 2024.<b>The CellMap Project Team during this time consisted of:</b> David Ackerman, Davis Bennett, Marley Bryant, Hannah Nguyen, Grace Park, Alyson Petruncio, Alannah Post, Jacquelyn Price, Diana Ramirez, Jeff Rhoades, Rebecca Vorimo, Aubrey Weigel, Marwan Zouinkhi, Yurii Zubov.<b>The CellMap Project Team Steering Committee during this time consisted of:</b> Misha Ahrens, Christopher Beck, Teng-Leong Chew, Daniel Feliciano, Jan Funke, Harald Hess, Wyatt Korff, Jennifer Lippincott-Schwartz, Zhe J. Liu, Kayvon Pedram, Stephan Preibisch, Stephan Saalfeld, Ronald Vale, and Aubrey Weigel.
DOI: 10.25378/janelia.24260824.v1
title: Manual organelle segmentations (crop269) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver acinus (jrc_mus-liver-zon-1)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<b>Annotation description</b>: Dense segmentations of mitochondrial membrane, mitochondrial lumen, vesicle membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, cytosol, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective in jrc_mus-liver-zon-1 using Amira 3D 2021.1, Classic Segmentation Workroom and the 'Using Amira to manually segment organelles in vEM for machine learning V.3' annotation protocol.<b>Annotation ID</b>: crop269<b>Primary Annotator</b>: Rebecca Vorimo<b>Annotation protocol</b>: Using Amira to manually segment organelles in vEM for machine learning V.3 (http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3)<b>Software</b>: Amira 3D 2021.1, Classic Segmentation Workroom<b>Annotated voxel size (nm)</b>: 4 x 4 x 4 (x, y, z)<b>Annotated data dimensions (µm)</b>: 1.6 x 1.6 x 1.6 (x, y, z)<b>Annotated data offset (nm)</b>: 11150 x 95062 x 213310 (x, y, z)<b>Classes annotated</b>: mitochondrial membrane, mitochondrial lumen, vesicle membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, cytosol, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop269<b>Source (EM) dataset ID</b>: jrc_mus-liver-zon-1<b>Source (EM) voxel size (nm)</b>: 8 x 8 x 8 (x, y, z)<b>Source (EM) data dimensions (µm)</b>: 397.16 x 171.61 x 188.81 (x, y, z)<b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.24128700<b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-liver-zon-1<b>Publication:</b> <i>CellMap Segmentation Challenge,</i> 2024.<b>The CellMap Project Team during this time consisted of:</b> David Ackerman, Davis Bennett, Marley Bryant, Hannah Nguyen, Grace Park, Alyson Petruncio, Alannah Post, Jacquelyn Price, Diana Ramirez, Jeff Rhoades, Rebecca Vorimo, Aubrey Weigel, Marwan Zouinkhi, Yurii Zubov.<b>The CellMap Project Team Steering Committee during this time consisted of:</b> Misha Ahrens, Christopher Beck, Teng-Leong Chew, Daniel Feliciano, Jan Funke, Harald Hess, Wyatt Korff, Jennifer Lippincott-Schwartz, Zhe J. Liu, Kayvon Pedram, Stephan Preibisch, Stephan Saalfeld, Ronald Vale, and Aubrey Weigel.
DOI: 10.6084/m9.figshare.c.3622634_d2.v1
title: MOESM2 of Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion

description: Additional file 2.
DOI: 10.25378/janelia.24260821
title: Manual organelle segmentations (crop268) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver acinus (jrc_mus-liver-zon-1)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<b>Annotation description</b>: Dense segmentations of mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective in jrc_mus-liver-zon-1 using Amira 3D 2021.1, Classic Segmentation Workroom and the 'Using Amira to manually segment organelles in vEM for machine learning V.3' annotation protocol.<b>Annotation ID</b>: crop268<b>Primary Annotator</b>: Woohyun Park<b>Annotation protocol</b>: Using Amira to manually segment organelles in vEM for machine learning V.3 (http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3)<b>Software</b>: Amira 3D 2021.1, Classic Segmentation Workroom<b>Annotated voxel size (nm)</b>: 4 x 4 x 4 (x, y, z)<b>Annotated data dimensions (µm)</b>: 1.6 x 1.6 x 1.6 (x, y, z)<b>Annotated data offset (nm)</b>: 50174 x 99382 x 211294 (x, y, z)<b>Classes annotated</b>: mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop268<b>Source (EM) dataset ID</b>: jrc_mus-liver-zon-1<b>Source (EM) voxel size (nm)</b>: 8 x 8 x 8 (x, y, z)<b>Source (EM) data dimensions (µm)</b>: 397.16 x 171.61 x 188.81 (x, y, z)<b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.24128700<b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-liver-zon-1<b>Publication:</b> <i>CellMap Segmentation Challenge,</i> 2024.<b>The CellMap Project Team during this time consisted of:</b> David Ackerman, Davis Bennett, Marley Bryant, Hannah Nguyen, Grace Park, Alyson Petruncio, Alannah Post, Jacquelyn Price, Diana Ramirez, Jeff Rhoades, Rebecca Vorimo, Aubrey Weigel, Marwan Zouinkhi, Yurii Zubov.<b>The CellMap Project Team Steering Committee during this time consisted of:</b> Misha Ahrens, Christopher Beck, Teng-Leong Chew, Daniel Feliciano, Jan Funke, Harald Hess, Wyatt Korff, Jennifer Lippincott-Schwartz, Zhe J. Liu, Kayvon Pedram, Stephan Preibisch, Stephan Saalfeld, Ronald Vale, and Aubrey Weigel.
DOI: 10.25378/janelia.24260821.v1
title: Manual organelle segmentations (crop268) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse liver acinus (jrc_mus-liver-zon-1)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<b>Annotation description</b>: Dense segmentations of mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective in jrc_mus-liver-zon-1 using Amira 3D 2021.1, Classic Segmentation Workroom and the 'Using Amira to manually segment organelles in vEM for machine learning V.3' annotation protocol.<b>Annotation ID</b>: crop268<b>Primary Annotator</b>: Woohyun Park<b>Annotation protocol</b>: Using Amira to manually segment organelles in vEM for machine learning V.3 (http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3)<b>Software</b>: Amira 3D 2021.1, Classic Segmentation Workroom<b>Annotated voxel size (nm)</b>: 4 x 4 x 4 (x, y, z)<b>Annotated data dimensions (µm)</b>: 1.6 x 1.6 x 1.6 (x, y, z)<b>Annotated data offset (nm)</b>: 50174 x 99382 x 211294 (x, y, z)<b>Classes annotated</b>: mitochondrial membrane, mitochondrial lumen, vesicle membrane, endosome membrane, vesicle lumen, mitochondrial ribosome, endoplasmic reticulum lumen, endoplasmic reticulum membrane, endosome lumen, cytosol, endosome, vesicle, peroxisome membrane, peroxisome, peroxisome lumen, mitochondria, endoplasmic reticulum, cell, endoplasmic reticulum membrane collective<b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_mus-liver-zon-1/jrc_mus-liver-zon-1.zarr/recon-1/labels/groundtruth/crop268<b>Source (EM) dataset ID</b>: jrc_mus-liver-zon-1<b>Source (EM) voxel size (nm)</b>: 8 x 8 x 8 (x, y, z)<b>Source (EM) data dimensions (µm)</b>: 397.16 x 171.61 x 188.81 (x, y, z)<b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.24128700<b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-liver-zon-1<b>Publication:</b> <i>CellMap Segmentation Challenge,</i> 2024.<b>The CellMap Project Team during this time consisted of:</b> David Ackerman, Davis Bennett, Marley Bryant, Hannah Nguyen, Grace Park, Alyson Petruncio, Alannah Post, Jacquelyn Price, Diana Ramirez, Jeff Rhoades, Rebecca Vorimo, Aubrey Weigel, Marwan Zouinkhi, Yurii Zubov.<b>The CellMap Project Team Steering Committee during this time consisted of:</b> Misha Ahrens, Christopher Beck, Teng-Leong Chew, Daniel Feliciano, Jan Funke, Harald Hess, Wyatt Korff, Jennifer Lippincott-Schwartz, Zhe J. Liu, Kayvon Pedram, Stephan Preibisch, Stephan Saalfeld, Ronald Vale, and Aubrey Weigel.
DOI: 10.6084/m9.figshare.c.3622883_d4.v1
title: Additional file 4: of Metagenome-assembled genomes uncover a global brackish microbiome

description: Phylogenetic tree in Newick format including all complete prokaryotic genomes in NCBI [ 112 ], all approved reconstructed bins (MAGs), and selected single amplified genomes, metagenome bins and isolate genomes from previous studies. (NWK 191 kb)
DOI: 10.6084/m9.figshare.c.3622883_d5.v1
title: Additional file 2: of Metagenome-assembled genomes uncover a global brackish microbiome

description: Summary statistics of MAGs. For each MAG, the number of bases, number of contigs, N50, N50 length, N90, N90 length, length of longest contig, coverage, taxonomy and copy number of single-copy core and phylum-specific COGs are reported. Universal single-copy genes are defined here as present in &gt;97 % of relevant genomes with an average copy number &lt;1.03. The name of each MAG has the format yymmdd-bin##, where yymmdd is the date of sample collection and ## is a unique numerical identifier assigned by CONCOCT. (XLSX 99 kb)
DOI: 10.6084/m9.figshare.c.3622880_d3.v1
title: MOESM1 of N-glycosylation proteome enrichment analysis in kidney reveals differences between diabetic mouse models

description: Additional file 1. Additional file 1 includes additional excel sheets 1a-f where 1a shows shotgun peptide data from the STZ mouse model, formerly N-glycosylated peptides for the 153 common proteins, 1b shows shotgun peptide data from the db/db mouse model, formerly N-glycosylated peptides for the common 153 proteins, 1c shows the relative mean intensities, SD, Mascot score, peptide count and number of unique peptides used in the identification of the shared proteins of importance in the multivariate analyses and the proteins where insulin had an effect on the abundances. 1d shows proteins identified in both mouse models with significant protein abundances in the db/db mouse model but not in the STZ mouse model, 1e show protein characteristics in relation to diabetes or kidney damage for a selection of the proteins with significantly changed protein abundances and 1f shows a conversion table of Proteome Exchange filenames and the corresponding kidney sample name and mouse group.
DOI: 10.6084/m9.figshare.c.3622862_d7.v1
title: Additional file 8: of The impact of taphonomic data on phylogenetic resolution: Helenodora inopinata (Carboniferous, Mazon Creek LagerstĂ¤tte) and the onychophoran stem lineage

description: Character matrix and TNT search parameters. Based on data presented by Yang et al. [4], with the addition of our new coding for Helenodora inopinata and our â  conservativeâ   coding ignoring taphonomic data. Changes described in the text. (TXT 6 kb)
DOI: 10.6084/m9.figshare.c.3622883_d6.v1
title: Additional file 5: of Metagenome-assembled genomes uncover a global brackish microbiome

description: Counts of COGs, PFAMs, TIGRFAMs and enzymes in each MAG. (XLSX 2595 kb)