cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.wkukr8
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pterorhinus vassali",
 "Country is China",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045740-250811113504898/datasets/export for details.
DOI: 10.22002/k6bfd-21n49
title: Eco 082509 MP15

description: Escherichia coli, 09sep10b_082509MP15_712ly_088, btub filaments,
description: <strong>Tilt Series Date:</strong> 2009-09-10</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> 7.1.2 Martin</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> cultured by Martin Pilhofer; data collected by Martin Pilhofer; processed by Martin Pilhofer</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity, blotting 1/-2/2/0/1/4/200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-09-10-15/rawdata/</p>09sep10b_082509MP15_712ly_088.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09sep10b_082509MP15_712ly_088_part.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/a42ef-0yt69
title: PVA 072309 712

description: Prosthecobacter vanneervenii, 09aug04a_072309_712_Pvastatic30_039,
description: <strong>Tilt Series Date:</strong> 2009-08-04</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter vanneervenii</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> cultured by Martin Pilhofer; data collected by Martin Pilhofer; processed by Martin Pilhofer</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity, blotting 1/-2/2/0/1/4/200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-08-04-12/rawdata/</p>09aug04a_072309_712_Pvastatic30_039.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        39_part.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-08-04-12/3dimage_13943/39_part.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.k7ryc5
title: Occurrence Download

description: A dataset containing 9537 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-29.56447 -6.63652,91.99815 -6.63652,91.99815 75.83716,-29.56447 75.83716,-29.56447 -6.63652))",
 "HasGeospatialIssue is false",
 "TaxonKey is Narcissus triandrus"
 ]
}

 The dataset includes 9537 records from 85 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045739-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/j3t0c-zv860
title: MT310_xyl(+)_AuCl50

description: Raw data files of MT310_xyl(+)_AuCl50
description: <strong>Tilt Series Date:</strong> 2009-06-21</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> RAPTOR, Peach</p>
<strong>Collaborators and Roles:</strong> The MT310 strain was constructed by Martin Thanbichler; cell cultured and treated by Zhuo Li; data collected and processed by Zhuo Li.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> MT310 cells were induced with xylose and treated by 50 uM AuCl for 20 hours. </p>
<strong>Sample Preparation:</strong> 10 nm gold. </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-06-21-50/rawdata/</p>09jun21a_Au50615_058.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jun21a_Au50615_058_part.rec,  Reconstruction (Pixel Size 1.9 nm), 471.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-06-21-50/3dimage_4957/09jun21a_Au50615_058_part.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/t5cnm-hm829
title: Hyphomonas session14 27.5KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-05-22</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Hyphomonas neptunium</p>
<strong>Strain:</strong> ATCC 15444</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -7.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> Cultured by Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in PYE media, overnight at 4degree...</p>
<strong>Sample Preparation:</strong> QF grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-05-22-45/rawdata/</p>09may22b_bx22gr1_020.mrc,  Tilt Series (Pixel Size 0.774 nm), 520.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-05-22-45/rawdata/09may22b_bx22gr1_020.mrc"
        > <i class="download icon"></i> Download </a></p>

        09may22b_bx22gr1_020_1k.rec,  Reconstruction (Pixel Size 1.548 nm), 84.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-05-22-45/3dimage_7662/09may22b_bx22gr1_020_1k.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.16944453
title: Structure of aqueous sodium chloride solutions at concentrations close to crystallisation

description: This repository contains molecular dynamics input and topology files (top and itp), including coordinate (PDB) structures and GROMACS input files (mdp), used in the simulations reported in the associated manuscript.
DOI: 10.5281/zenodo.16944454
title: Structure of aqueous sodium chloride solutions at concentrations close to crystallisation

description: This repository contains molecular dynamics input and topology files (top and itp), including coordinate (PDB) structures and GROMACS input files (mdp), used in the simulations reported in the associated manuscript.
DOI: 10.6084/m9.figshare.29985772
title: Serum metabolomics data

description: These are the raw lipidomics data of mice in the paper "<b><i>Lactobacillus gasseri</i></b><b> B4209 facilitates histamine and 9-cis-retinoic acid as lipolytic regulators to alleviate non-alcoholic fatty liver disease</b>".
DOI: 10.6084/m9.figshare.29985772.v1
title: Serum metabolomics data

description: These are the raw lipidomics data of mice in the paper "<b><i>Lactobacillus gasseri</i></b><b> B4209 facilitates histamine and 9-cis-retinoic acid as lipolytic regulators to alleviate non-alcoholic fatty liver disease</b>".
DOI: 10.22002/knhvq-ts943
title: Rhodobacter 1558 cryosections

description: Cryosections by MArk Ladinsky
description: <strong>Tilt Series Date:</strong> 2010-10-07</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Rhodobacter sphaeroides</p>
<strong>Strain:</strong> ATCC 17023</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-61.0°, 64.0°), step: 2°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -10.0 μm,  magnification: 34000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Collaborators and Roles:</strong> Judy Armitage</p>
<strong>Purification / Growth Conditions / Treatment:</strong> grown in SUX media</p>
<strong>Sample Preparation:</strong> prepared for cryosectioning (gold prep see JWIKI)</p>
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2010-10-07-20/rawdata/</p>10oct07a_rhcryosections_1_020.st,  Tilt Series (Pixel Size 0.0 nm), 528.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        10oct07a_rhcryosections_1_020.rec,  Reconstruction (Pixel Size 0.0 nm), 159.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/qdvrf-vn704
title: B. subtilis 3267

description: Raw data files of B. subtilis 3267
description: <strong>Tilt Series Date:</strong> 2011-12-08</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Bacillus subtilis </p>
<strong>Strain:</strong> AD3267, ponA null, Alp7A-GFP</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Joe Pogliano</p>
<strong>Purification / Growth Conditions / Treatment:</strong> cells were grown in LB</p>
<strong>Sample Preparation:</strong> Vitrobot</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-12-08-41/rawdata/</p>3267a0041.mrc,  Tilt Series (Pixel Size 1.9 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-12-08-41/rawdata/3267a0041.mrc"
        > <i class="download icon"></i> Download </a></p>

        3267a0041_part.rec,  Reconstruction (Pixel Size 3.8 nm), 825.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-12-08-41/3dimage_16048/3267a0041_part.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/81xwk-07k36
title: GFP-MreB fusion methanol control

description: Raw data files of GFP-MreB fusion methanol control
description: <strong>Tilt Series Date:</strong> 2009-08-01</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> RAPTOR, REACH</p>
<strong>Collaborators and Roles:</strong> Experiments were done by Zhuo Li.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The GFP-MreB-expressing NA1000 cells were cultured to exponential phase and treated with methanol as a control.</p>
<strong>Sample Preparation:</strong> 10 nm gold.</p>
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-08-01-76/rawdata/</p>09aug01a_methanolgfmr1_076.mrc,  Tilt Series (Pixel Size 1.2 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09aug01a_methanolgfmr1_076_full.rec,  Reconstruction (Pixel Size 2.4 nm), 367.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.346mt9
title: Occurrence Download

description: A dataset containing 163 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "Geometry POLYGON((93 29,112 29,112 43,93 43,93 29))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Artemisia giraldii"
 ]
}

 The dataset includes 163 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045743-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ph9yxm
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pareutropius longifilis)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 7 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045744-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/kzwc5-18e10
title: E. coli (pLE7, 20 uM IPTG)

description: Cells contain WT MreB in the chromosome plus an N-terminal YFP fusion to MreB (YFP-MreB) on the plasmid pLe7. pLE7 also confers a resistance to ampicillin.
description: <strong>Tilt Series Date:</strong> 2011-06-02</p>
<strong>Data Taken By:</strong> Matt Swulius</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: None μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> UCSFTomo</p>
<strong>Collaborators and Roles:</strong> Gift from Larry Rothfield</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grown at 37 degrees celsius to OD600=0.2 then 20 uM IPTG was added for 2 hours of growth before freezing.</p>
<strong>Sample Preparation:</strong> Vitrobot plunge freezing</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mst2011-06-02-22/rawdata/</p>20110602_PLE7_27.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        20110602_PLE7_27_part122_8.rec,  Reconstruction (Pixel Size 1.9 nm), 825.8 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.57745/f9qe5d
title: Données de recharge potentielle des aquifères par MESO en France hexagonale - modèle RECHARGE

description: Ce dépôt comporte les données spatialisées de recharge potentielle obtenues en mettant en œuvre le modèle RECHARGE sur l’ensemble du territoire hexagonal avec, pour données d’entrée, les évolutions climatiques projetées par l’ensemble élaboré et corrigées avec la méthode ADAMONT dans le cadre du projet Explore2. Les résultats sont présentés dans un rapport dédié (Lanini et al., 2024). La méthodologie associée est décrite par Robelin et al., 2024 (soumis). Le dépôt comporte un répertoire associé à chaque RCP (RCP26 ; RCP 45 ; RCP85) contenant lui-même un répertoire par horizon temporel (H0 : 1976-2005 ; H1 : 2021-2050 ; H2 : 2041-2070 ; H3 2071-2100). Pour chaque horizon temporel, se trouvent 5 fichiers ".shp" et son sous-ensemble de fichiers associés : 1 fichier par saison hydrologique (JJA ; SON ; DJF ; MAM) et 1 fichier à l'année (YEAR). Les données sont fournies sur les masses d'eau souterraines (MESO). Les attributs des fichiers sont les suivants : - CdEuMasseD : identifiant européen de la MESO ; - ID_MESO : identifiant numérique de la MESO ; - Altitud : altitude moyenne de la MESO ; - NomMasseDE : dénomination de la MESO ; - Non_Aqfr : pourcentage de la MESO considérée comme non aquifère ; - gcmrcm : la médiane de recharge potentielle interannuelle sur l'horizon donné pour chaque projection climatique "gcmrcm" ; - indiceNRe : des indicateurs (matérialisés par "indice") pour l'analyse multi-modèles ("N" modèles) de la recharge potentielle interannuelle (moyenne, médiane, min, max, Q5 et Q95 de l'ensemble) ; - ANgcmrcm : l'anomalie de recharge potentielle interannuelle sur l'horizon donné pour chaque projection climatique (liste des projections climatiques) "gcmrcm" (sauf pour H0) par rapport à la période de référence H0 ; - ANindiceNRe : des indicateurs (matérialisés par "indice") pour l'analyse multi-modèles ("N" modèles) de l'anomalie de recharge potentielle interannuelle (moyenne, médiane, min, max, Q5 et Q95 de l'ensemble). - COUNT_SEIL : Nombre de modèles dans l'ensemble dont le signal du changement sort de la variabilité interne. - COUNT_SIGN : Nombre de modèles dans l'ensemble dont le signe du changement est en accord avec la médiane multi-modèles. La recharge potentielle n'est pas pertinente pour les entités non-aquifères (pourcenatge exprimé dans le champ "Non_Aqfr"). Concernant les MESO en zone de montagne, il est conseillé d'utiliser la recharge annuelle pour s'affranchir de la fonte de la neige dont la dynamique est parfois mal reproduite par le modèle RECHARGE (altitude moyenne de la MESO est renseignée dans le champ "Altitud").
DOI: 10.22002/znnt7-9na36
title: Hyphomonas chq session18 41KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-06-24</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Hyphomonas neptunium</p>
<strong>Strain:</strong> ATCC 15444</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-61.0°, 61.0°), step: 2°, constant angular increment, dosage: 75.0 eV/Å²,  defocus: -7.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> Cultured by Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in PYE media, chloroquine 1.0mg/ml, 4degree...</p>
<strong>Sample Preparation:</strong> QF grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-06-24-18/rawdata/</p>09jun24a_bx217c_042.mrc,  Tilt Series (Pixel Size 0.512 nm), 520.1 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jun24a_bx217c_042_full.rec,  Reconstruction (Pixel Size 1.024 nm), 419.4 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/8qwd0-rqx81
title: HIV gag session12 41KX

description: Opti-prep HIV gag shell
description: <strong>Tilt Series Date:</strong> 2009-04-13</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> HIV cores</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: 2°, constant angular increment, dosage: 72.0 eV/Å²,  defocus: -7.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> Cultured by Virgine; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Opti-prep</p>
<strong>Sample Preparation:</strong> QF grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-04-13-3/rawdata/</p>09apr13a_b19a_003.mrc,  Tilt Series (Pixel Size 0.512 nm), 570.4 MB  
        
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        09apr13a_b19a_003_part.rec,  Reconstruction (Pixel Size 1.024 nm), 293.6 MB  
        
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