cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/f9nd3-syg53
title: Hpylori_dFliF_FISE

description: These are H_pylori cells that are lacking FliP protein. In these cells, FliF protein was knocked out  .  to examine its relation to the hat-like complex.
description: <strong>Tilt Series Date:</strong> 2020-10-08</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> The cells were prepared and sent by Carrie Schaffer from the university of Kentucky. The cells were grown at 37C with 5% CO2 on sheep blood agar plates for 2 days from a -80C. No growth was seen . on the plates after 24 hr therefore the plates were kept in the . incubator for another 24Hr.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot . time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100%  humidity. Cu grids. 10 nm . gold</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-235/rawdata/</p>Hpylori_DFliF_FISE_229.mrc,  Tilt Series (Pixel Size 0.452 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-235/rawdata/Hpylori_DFliF_FISE_229.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_DFliF_FISE_229_full.rec,  Reconstruction (Pixel Size 1.808 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-235/3dimage_113954/Hpylori_DFliF_FISE_229_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/xvex3-wfx94
title: P_aeruginosa_PA14_DfliF_Krios

description: Raw data files of P_aeruginosa_PA14_DfliF_Krios
description: <strong>Tilt Series Date:</strong> 2018-09-29</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (50.0°, -50.0°), step: 2°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -9.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> RAPTOR</p>
<strong>Collaborators and Roles:</strong> I (mohammed) obtained the cells from Shannon Park (Dianne Newman lab). The cells are available in their library of Pseudomonas aeruginosa PA14.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I inoculated one colony from an LB agar plate and grew the cells overnight in LB with 100 ug/ml of Gentamycin. Then I concentrated the cells three times and mixed them with gold nanoparticles and added 3 ul on to thick carbon R2 grids and blotted them and plunge froze them (force either 6 or 3, time either 3 or 2 seconds respectively, drain time 1 second).</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-09-29-54/rawdata/</p>Pseudomonas_DfliF51.mrc,  Tilt Series (Pixel Size 0.53 nm), 1.5 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-09-29-54/rawdata/Pseudomonas_DfliF51.mrc"
        > <i class="download icon"></i> Download </a></p>

        Pseudomonas_DfliF51_full.rec,  Reconstruction (Pixel Size 2.12 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-09-29-54/3dimage_97245/Pseudomonas_DfliF51_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.e675qq
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pistacia vera",
 "Country is Croatia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002749-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/dgz3f-1b898
title: JV9082_Janelia42k

description: DotF-sfGFP fusion
description: <strong>Tilt Series Date:</strong> 2018-08-29</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-54.0°, 54.0°), step: 3.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -7.0 μm,  magnification: 42000x. </p>
<strong>Microscope:</strong> Janelia Titan</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> Strain sent to us by Joseph P. Vogel, Washington University School of Medicine. Data collected and processed by Debnath Ghosal. Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine.</p>
<strong>Sample Preparation:</strong> 6 grids were frozen for the JV9082 strain (2x concentrated culture); Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-218/rawdata/</p>JV9082_201808290218.mrc,  Tilt Series (Pixel Size 0.26 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-218/rawdata/JV9082_201808290218.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV9082_201808290218_part37_1.rec,  Reconstruction (Pixel Size 1.04 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2018-08-29-218/3dimage_96832/JV9082_201808290218_part37_1.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/n9j9j-kct02
title: P_aeruginosa_PA14_DfliF_Krios

description: Raw data files of P_aeruginosa_PA14_DfliF_Krios
description: <strong>Tilt Series Date:</strong> 2018-09-29</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (50.0°, -50.0°), step: 2°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -9.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> RAPTOR</p>
<strong>Collaborators and Roles:</strong> I (mohammed) obtained the cells from Shannon Park (Dianne Newman lab). The cells are available in their library of Pseudomonas aeruginosa PA14.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I inoculated one colony from an LB agar plate and grew the cells overnight in LB with 100 ug/ml of Gentamycin. Then I concentrated the cells three times and mixed them with gold nanoparticles and added 3 ul on to thick carbon R2 grids and blotted them and plunge froze them (force either 6 or 3, time either 3 or 2 seconds respectively, drain time 1 second).</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-09-29-15/rawdata/</p>Pseudomonas_DfliF2.mrc,  Tilt Series (Pixel Size 0.53 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-09-29-15/rawdata/Pseudomonas_DfliF2.mrc"
        > <i class="download icon"></i> Download </a></p>

        Pseudomonas_DfliF2_full.rec,  Reconstruction (Pixel Size 2.12 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-09-29-15/3dimage_97154/Pseudomonas_DfliF2_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.7gwe7c
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002748-250827131500795/datasets/export for details.
DOI: 10.15468/dl.796rdd
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is Asia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Carex formosensis"
 ]
}

 The dataset includes 40 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002751-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5pwdy9
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002750-250827131500795/datasets/export for details.
DOI: 10.21335/nmdc-1050781599
title: Havforskningsinstituttet Tråling Postsmolt laks 2025 Boknafjord

description: The dataset includes Institute of Marine Research data from trawl stations in Boknafjord, Norway in 2025. 

Post-smolts were collected in the outer parts of the fjord systems in late spring and early summer with a specialized surface trawl for live fish sampling, towed behind a suitable fishing vessel (15-25 m). The trawl is 5 m deep and up to 35 m wide depending on speed through water.
The trawl is mounted to a system where smaller catch, such as post-smolts are separated from other catch, and remain free swimming in low turbulence in a hydrodynamic aquarium. The separation takes place when the current flow through a net tunnel and over two 45 degrees racks. The first rack (10 mm between bars) lifts the catch to the next (20 mm between bars) where the separation is done. Everything wider than 20 mm will continue to the cod end of the trawl. Details of the post-smolt trawl are described in Holst and McDonald (2000), Fisheries Research 48, pp 87-91. The standard trawling speed is 2–3 knots (STW), with an average duration of approximately 45 minutes per haul. 

Lice counts on post-smolts were performed on the ship as soon as possible after they were captured. The fish were killed using an overdose of Benzocaine 200 mg/ml. Lice counts were performed with the fish submerged in a white plastic tub (5-10 l) using a strong headlamp (&gt;500 lumen). The counts were only performed by personnel with special training in identification of all salmon lice stages. The following categories were recorded: copepodite, chalimus 1, chalimus 2, pre-adult, adult male and adult female. Fish length in mm and mass in gram were recorded. All post-smolts were then frozen for subsequent analysis.
DOI: 10.71724/7m2n-b474
title: Dataset for Tuning physical properties of GelMA Hydrogels through Microarchitecture for Engineering Osteoid Tissue

description: <p><span style="font-size:12.04px">Dataset supporting the publication: Tuning Physical Properties of GelMA </span><span style="font-size:12.04px">Hydrogels through Microarchitecture for Engineering Osteoid Tissue </span><span style="font-size:12.04px">(PubMed link: https://pubmed.ncbi.nlm.nih.gov/38102990/)</span></p><p><span style="font-size:12.04px">Funding: This research was financially supported by the National Science </span><span style="font-size:12.04px">Centre (Poland), PRELUDIUM project UMO-2021/41/N/ST5/04220.</span></p><p><span style="font-size:12.04px">Description: This dataset contains the experimental data underlying the </span><span style="font-size:12.04px">publication. It includes: </span><span style="font-size:12.04px">rheological measurements and gelation kinetics, </span><span style="font-size:12.04px">crosslinking efficiency data, </span><span style="font-size:12.04px">cell proliferation in GelMA hydrogels, </span><span style="font-size:12.04px">mechanical properties (compressive modulus), </span><span style="font-size:12.04px">swelling ratio and water uptake analysis, </span><span style="font-size:12.04px">TGA and FTiR analysis of PEO removal.</span></p><p><br /></p>
DOI: 10.15468/dl.9r6vg4
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002752-250827131500795/datasets/export for details.
DOI: 10.21335/nmdc-1784250263
title: Havforskningsinstituttet Tråling Postsmolt laks 2025 Hardangerfjord

description: The dataset includes Institute of Marine Research data from trawl stations in Hardangerfjord, Norway in 2025. 

Post-smolts were collected in the outer parts of the fjord systems in late spring and early summer with a specialized surface trawl for live fish sampling, towed behind a suitable fishing vessel (15-25 m). The trawl is 5 m deep and up to 35 m wide depending on speed through water.
The trawl is mounted to a system where smaller catch, such as post-smolts are separated from other catch, and remain free swimming in low turbulence in a hydrodynamic aquarium. The separation takes place when the current flow through a net tunnel and over two 45 degrees racks. The first rack (10 mm between bars) lifts the catch to the next (20 mm between bars) where the separation is done. Everything wider than 20 mm will continue to the cod end of the trawl. Details of the post-smolt trawl are described in Holst and McDonald (2000), Fisheries Research 48, pp 87-91. The standard trawling speed is 2–3 knots (STW), with an average duration of approximately 45 minutes per haul. 

Lice counts on post-smolts were performed on the ship as soon as possible after they were captured. The fish were killed using an overdose of Benzocaine 200 mg/ml. Lice counts were performed with the fish submerged in a white plastic tub (5-10 l) using a strong headlamp (&gt;500 lumen). The counts were only performed by personnel with special training in identification of all salmon lice stages. The following categories were recorded: copepodite, chalimus 1, chalimus 2, pre-adult, adult male and adult female. Fish length in mm and mass in gram were recorded. All post-smolts were then frozen for subsequent analysis.
DOI: 10.15468/dl.5rahg3
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhus typhina",
 "Country is Armenia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002753-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jfj6pu
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhus typhina",
 "Country is Australia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 7 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002754-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tqqpdj
title: Occurrence Download

description: A dataset containing 1087 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhus typhina",
 "Country is Austria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1087 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002755-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ypf9hn
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is Asia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Carex hypochlora"
 ]
}

 The dataset includes 47 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002756-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21335/nmdc-1547478502
title: Havforskningsinstituttet Tråling Postsmolt laks 2025 Romsdalsfjord

description: The dataset includes Institute of Marine Research data from trawl stations in Romsdalsfjord, Norway in 2025. 

Post-smolts were collected in the outer parts of the fjord systems in late spring and early summer with a specialized surface trawl for live fish sampling, towed behind a suitable fishing vessel (15-25 m). The trawl is 5 m deep and up to 35 m wide depending on speed through water.
The trawl is mounted to a system where smaller catch, such as post-smolts are separated from other catch, and remain free swimming in low turbulence in a hydrodynamic aquarium. The separation takes place when the current flow through a net tunnel and over two 45 degrees racks. The first rack (10 mm between bars) lifts the catch to the next (20 mm between bars) where the separation is done. Everything wider than 20 mm will continue to the cod end of the trawl. Details of the post-smolt trawl are described in Holst and McDonald (2000), Fisheries Research 48, pp 87-91. The standard trawling speed is 2–3 knots (STW), with an average duration of approximately 45 minutes per haul. 

Lice counts on post-smolts were performed on the ship as soon as possible after they were captured. The fish were killed using an overdose of Benzocaine 200 mg/ml. Lice counts were performed with the fish submerged in a white plastic tub (5-10 l) using a strong headlamp (&gt;500 lumen). The counts were only performed by personnel with special training in identification of all salmon lice stages. The following categories were recorded: copepodite, chalimus 1, chalimus 2, pre-adult, adult male and adult female. Fish length in mm and mass in gram were recorded. All post-smolts were then frozen for subsequent analysis.
DOI: 10.15468/dl.bequyp
title: Occurrence Download

description: A dataset containing 132867 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Scrophularia auriculata"
 ]
}

 The dataset includes 132867 records from 1006 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002676-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gbfhhn
title: Occurrence Download

description: A dataset containing 3447 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhus typhina",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3447 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002758-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7u5w8g
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhus typhina",
 "Country is Bosnia and Herzegovina",
 "HasCoordinate is true"
 ]
}

 The dataset includes 49 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002759-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.29958301
title: Characteristics and phylogenetic analysis of the complete chloroplast genome of <i>Gardneria multiflora</i> Makino 1901 from the family Loganiaceae

description: <i>Gardneria multiflora</i> Makino is an important medicinal plant endemic to China, with its roots and leaves traditionally used for therapeutic purposes. In this study, we report the complete chloroplast genome of <i>G. multiflora</i>. The 144,920 bp genome (GC 37.82%) has a typical circular quadripartite structure: 98,036 bp LSC, 18,382 bp SSC, and two 14,251 bp IRs. It has 125 unique genes, comprising 82 protein-coding, 35 tRNA, and 8 rRNA genes. Phylogenetic analysis revealed that G. multiflora is closely related to G. ovata. The data presented in this study can guide future research on the evolutionary history of this species.
DOI: 10.6084/m9.figshare.29958301.v1
title: Characteristics and phylogenetic analysis of the complete chloroplast genome of <i>Gardneria multiflora</i> Makino 1901 from the family Loganiaceae

description: <i>Gardneria multiflora</i> Makino is an important medicinal plant endemic to China, with its roots and leaves traditionally used for therapeutic purposes. In this study, we report the complete chloroplast genome of <i>G. multiflora</i>. The 144,920 bp genome (GC 37.82%) has a typical circular quadripartite structure: 98,036 bp LSC, 18,382 bp SSC, and two 14,251 bp IRs. It has 125 unique genes, comprising 82 protein-coding, 35 tRNA, and 8 rRNA genes. Phylogenetic analysis revealed that G. multiflora is closely related to G. ovata. The data presented in this study can guide future research on the evolutionary history of this species.
DOI: 10.6084/m9.figshare.29949742
title: Complete chloroplast genome of a coastal herb, <i>Linaria japonica</i> Miquel 1865 (Plantaginaceae)

description: <i>Linaria japonica</i> Miquel 1865 (Plantaginaceae) is a perennial herb found in coastal areas of north-east China, Japan, Korea, and the Far East Russia. Here, we report the complete chloroplast genome of <i>L. japonica</i> and determine its systematic position in 11 tribes of Plantaginaceae. The size of complete chloroplast genome was 150,660 bp, consisting of a pair of inverted repeats (25,647 bp each) separated by a large single-copy region (81,766 bp) and a small single-copy region (17,600 bp). Our phylogenomic analyses using 78 protein-coding genes show that <i>Linaria</i> belongs to the tribe Antirrhineae. Within <i>Linaria</i>, <i>L. japonica</i> is sister to <i>L. buriatica</i> Turcz.