cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/evjgh-jrr26
title: wt_perfusion

description: There are wt preanaerobically grown perfusion samples.
description: <strong>Tilt Series Date:</strong> 2017-06-30</p>
<strong>Data Taken By:</strong> Poorna Subramanian</p>
<strong>Species / Specimen:</strong> Shewanella oneidensis</p>
<strong>Strain:</strong> MR-1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-55.0°, 55.0°), step: 1.0°, constant angular increment, dosage: 140.0 eV/Å²,  defocus: -10.0 μm,  magnification: 34000x. </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> Sahand and Moh</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2017-06-30-2/rawdata/</p>nano2.mrc,  Tilt Series (Pixel Size 0.32 nm), 3.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2017-06-30-2/rawdata/nano2.mrc"
        > <i class="download icon"></i> Download </a></p>

        nano2_full.rec,  Reconstruction (Pixel Size 1.28 nm), 534.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2017-06-30-2/3dimage_85436/nano2_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.78a5qk
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Uruguay",
 "GadmGid is URY.9_2",
 "OccurrenceStatus is Present",
 "TaxonKey is Phyllomedusa iheringii"
 ]
}

 The dataset includes 18 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047019-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/dgh1y-qaj78
title: Caulobacter crescentus ftsE del

description: Caulobacter crescentus, ftsE, FtsZ, Long cell, PYE
description: <strong>Tilt Series Date:</strong> 2017-01-17</p>
<strong>Data Taken By:</strong> Qing Yao</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 1.0°, constant angular increment, dosage: 190.0 eV/Å²,  defocus: -12.0 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> UCSFTOMO</p>
<strong>Collaborators and Roles:</strong> Goley ED at Johns Hopkins University School of Medicine</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/qya2017-01-17-15/rawdata/</p>montage20005.mrc,  Tilt Series (Pixel Size 0.48 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/qya2017-01-17-15/rawdata/montage20005.mrc"
        > <i class="download icon"></i> Download </a></p>

        montage20005.rec,  Reconstruction (Pixel Size 1.92 nm), 623.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/qya2017-01-17-15/3dimage_81248/montage20005.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/53cb7-vdb92
title: Ecoli+Elastin

description: Raw data files of Ecoli+Elastin
description: <strong>Tilt Series Date:</strong> 2018-10-15</p>
<strong>Data Taken By:</strong> Songye Chen</p>
<strong>Species / Specimen:</strong> Escherichia coli in vitro</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -8.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> SerialEM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Seunghyun Sim from Tirrell Lab provided the sample</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scy2018-10-15-32/rawdata/</p>6N_tilt32.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scy2018-10-15-32/rawdata/6N_tilt32.mrc"
        > <i class="download icon"></i> Download </a></p>

        6N_tilt32_full.rec,  Reconstruction (Pixel Size 1.56 nm), 444.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/scy2018-10-15-32/3dimage_97651/6N_tilt32_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.17632/5wphd7m8bk
title: 3D Shape and Outcomes in Bidirectional Glenn

description: This model illustrates the intermediate anatomical configuration of the superior cavopulmonary connection, derived from the analysis of 29 patients. This anatomical configuration results from the bidirectional Glenn procedure, performed in pediatric patients with congenital heart diseases such as hypoplastic left heart syndrome, tricuspid atresia, right heart hypoplasia, among others. Alongside the STL file, an Excel file is also provided containing anonymized clinical and anatomical data for the 29 patients, allowing further analysis and study.
DOI: 10.17632/5wphd7m8bk.1
title: 3D Shape and Outcomes in Bidirectional Glenn

description: This model illustrates the intermediate anatomical configuration of the superior cavopulmonary connection, derived from the analysis of 29 patients. This anatomical configuration results from the bidirectional Glenn procedure, performed in pediatric patients with congenital heart diseases such as hypoplastic left heart syndrome, tricuspid atresia, right heart hypoplasia, among others. Alongside the STL file, an Excel file is also provided containing anonymized clinical and anatomical data for the 29 patients, allowing further analysis and study.
DOI: 10.22002/v7k90-0gg22
title: Pseudomonas aeruginosa

description: Raw data files of Pseudomonas aeruginosa
description: <strong>Tilt Series Date:</strong> 2018-12-21</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</p>
<strong>Strain:</strong> PA14 flhA::MrT7 (Tn)</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 2°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -10.0 μm,  magnification: 26000x. </p>
<strong>Acquisition Software:</strong> SerialEM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> These cells were obtained from Diana Newman lab (cells given by the lab manager Shannon Park) from the transposon library. This is number (3296) from the non-redundant list (FlhA mutant).</p>
description: Files available via S3 at ttps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-12-21-58/rawdata/</p>Pseudomonas_dflhA24.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/mka2018-12-21-58/rawdata/Pseudomonas_dflhA24.mrc"
        > <i class="download icon"></i> Download </a></p>

        Pseudomonas_dflhA24_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/mka2018-12-21-58/3dimage_99907/Pseudomonas_dflhA24_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.6084/m9.figshare.29988670
title: DMG bulk regulatory network

description: To avoid technical artifacts resulting from batch effects across datasets as well as transcriptional bias between autopsy versus biopsy specimens, we generated a consensus network across 120 DMG gene expression profiles containing autopsy vs. biopsy information, integrating individual ARACNe3 networks reverse engineered from the following sample sets: CBTTC_Autopsy_Network (15 samples), CBTTC_Biopsy_Network (30 samples), PNOC_Biopsy_Network (31 samples), StJude_Autopsy_Network (28 samples), StJude_Biopsy_Network (16 samples). We accounted for the small sample size in each individual network by setting a higher FDR threshold and integrating the results weighted by the number of samples per network so that only the most robust interactions remained. As such, each network was pruned with a mutual information threshold calculated to control the FDR at 0.50 and subsequently by MaxEnt pruning (<i>i.e.,</i> DPI pruning). Regulons from each network were integrated using a consensus scoring approach where Association Weight (<i>i.e.</i> likelihood) and Association Mode (<i>i.e.</i> tfmode) values were averaged for each target over all networks, and each networks’ data was weighted according to the number of gene expression profiles used to reverse engineer the network.The final network comprised regulons with 50 targets for 6,138 regulatory proteins, with 7,002,347 interactions, allowing inference of accurate regulons for proteins whose expression was too low to be detected at the single-cell level.
DOI: 10.6084/m9.figshare.29988670.v2
title: DMG bulk regulatory network

description: To avoid technical artifacts resulting from batch effects across datasets as well as transcriptional bias between autopsy versus biopsy specimens, we generated a consensus network across 120 DMG gene expression profiles containing autopsy vs. biopsy information, integrating individual ARACNe3 networks reverse engineered from the following sample sets: CBTTC_Autopsy_Network (15 samples), CBTTC_Biopsy_Network (30 samples), PNOC_Biopsy_Network (31 samples), StJude_Autopsy_Network (28 samples), StJude_Biopsy_Network (16 samples). We accounted for the small sample size in each individual network by setting a higher FDR threshold and integrating the results weighted by the number of samples per network so that only the most robust interactions remained. As such, each network was pruned with a mutual information threshold calculated to control the FDR at 0.50 and subsequently by MaxEnt pruning (<i>i.e.,</i> DPI pruning). Regulons from each network were integrated using a consensus scoring approach where Association Weight (<i>i.e.</i> likelihood) and Association Mode (<i>i.e.</i> tfmode) values were averaged for each target over all networks, and each networks’ data was weighted according to the number of gene expression profiles used to reverse engineer the network.The final network comprised regulons with 50 targets for 6,138 regulatory proteins, with 7,002,347 interactions, allowing inference of accurate regulons for proteins whose expression was too low to be detected at the single-cell level.
DOI: 10.6084/m9.figshare.29988670.v1
title: <b>DMG bulk regulatory network</b>

description: To avoid technical artifacts resulting from batch effects across datasets as well as transcriptional bias between autopsy versus biopsy specimens, we generated a consensus network across 120 DMG gene expression profiles containing autopsy vs. biopsy information, integrating individual ARACNe3 networks reverse engineered from the following sample sets: CBTTC_Autopsy_Network (15 samples), CBTTC_Biopsy_Network (30 samples), PNOC_Biopsy_Network (31 samples), StJude_Autopsy_Network (28 samples), StJude_Biopsy_Network (16 samples). We accounted for the small sample size in each individual network by setting a higher FDR threshold and integrating the results weighted by the number of samples per network so that only the most robust interactions remained. As such, each network was pruned with a mutual information threshold calculated to control the FDR at 0.50 and subsequently by MaxEnt pruning (<i>i.e.,</i> DPI pruning). Regulons from each network were integrated using a consensus scoring approach where Association Weight (<i>i.e.</i> likelihood) and Association Mode (<i>i.e.</i> tfmode) values were averaged for each target over all networks, and each networks’ data was weighted according to the number of gene expression profiles used to reverse engineer the network.The final network comprised regulons with ³ 50 targets for 6,138 regulatory proteins, with 7,002,347 interactions, allowing inference of accurate regulons for proteins whose expression was too low to be detected at the single-cell level.
DOI: 10.17632/k8kv2t8kby
title: Data for: Brachinites and ungrouped achondrites with brachinite-affinity: sampling a single heterogeneous parent body

description: Raw data that were used for the mineralogical and geochemical analyses throughout the main text and supplementary material. In red, brachinites; in yellow, ungrouped brachinites like achondrites
DOI: 10.22002/j0ab7-5rv65
title: Native EC93 Cells Cdi-

description: These are native cells that are Cdi- imaged as a negative control
description: <strong>Tilt Series Date:</strong> 2018-06-23</p>
<strong>Data Taken By:</strong> Poorna Subramanian</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.5°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -8.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</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> Chris Hayes and Zach Ruhe</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Sample was frozen in BI Vitrobot. -5 ,4 freezing condition</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2018-06-23-41/rawdata/</p>T5NativeCellsCdi-116.mrc,  Tilt Series (Pixel Size 0.538 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2018-06-23-41/rawdata/T5NativeCellsCdi-116.mrc"
        > <i class="download icon"></i> Download </a></p>

        T5NativeCellsCdi-116_full.rec,  Reconstruction (Pixel Size 2.152 nm), 712.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2018-06-23-41/3dimage_93140/T5NativeCellsCdi-116_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.3dres2
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Uruguay",
 "OccurrenceStatus is Present",
 "TaxonKey is Xanthopsar flavus"
 ]
}

 The dataset includes 50 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047018-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/k8kv2t8kby.2
title: Data for: Brachinites and ungrouped achondrites with brachinite-affinity: sampling a single heterogeneous parent body

description: Raw data that were used for the mineralogical and geochemical analyses throughout the main text and supplementary material. In red, brachinites; in yellow, ungrouped brachinites like achondrites
DOI: 10.22002/vyw65-nfj49
title: insulin granules

description: Raw data files of insulin granules
description: <strong>Tilt Series Date:</strong> 2018-10-08</p>
<strong>Data Taken By:</strong> Xianjun Zhang</p>
<strong>Species / Specimen:</strong> Rat INS-1E pancreatic beta cells</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: °, constant angular increment, dosage: 53.0 eV/Å²,  defocus: -10.0 μm,  magnification: 33000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Sample Preparation:</strong> 25mM glucose treatment for 30mins</p>
description: Files available via S3 at s://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/xzj2018-10-08-9/rawdata/</p>tomography9.mrc,  Tilt Series (Pixel Size 0.429 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/xzj2018-10-08-9/rawdata/tomography9.mrc"
        > <i class="download icon"></i> Download </a></p>

        tomography9.rec,  Reconstruction (Pixel Size 1.728 nm), 280.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/xzj2018-10-08-9/3dimage_105408/tomography9.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.jy62w9
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pungitius hellenicus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-6.6 29.26705, -6.6 50.94, 40.81373 50.94, 40.81373 29.26705, -6.6 29.26705))",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation, Material sample)"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047020-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/p2hk1-2be85
title: P. gingivalis wild type

description: Raw data files of P. gingivalis wild type
description: <strong>Tilt Series Date:</strong> 2020-11-06</p>
<strong>Data Taken By:</strong> Georges Chreifi</p>
<strong>Species / Specimen:</strong> Porphyromonas gingivalis</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 170.0 eV/Å²,  defocus: -6.0 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> Eric Reynolds</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grown and harvested from plates</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/gca2020-11-06-195/rawdata/</p>PginWT9_194.mrc,  Tilt Series (Pixel Size 0.333 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/gca2020-11-06-195/rawdata/PginWT9_194.mrc"
        > <i class="download icon"></i> Download </a></p>

        PginWT9_194_full.rec,  Reconstruction (Pixel Size 1.332 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/gca2020-11-06-195/3dimage_115361/PginWT9_194_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.17632/jm8c2vn28s.1
title: pork adulteration in e nose dataset(7 levels of adulteration)

description: Abstract
Electronic noses (E-noses) are increasingly utilized for food authentication and adulteration detection. In the context of halal compliance, pork adulteration in beef remains a significant concern. This study presents an E-nose system developed using eight MQ series gas sensors (MQ2, MQ3, MQ4, MQ5, MQ135, MQ136, MQ137, and MQ138) alongside a DHT22 sensor for temperature and humidity monitoring. These sensors were integrated with an ESP32-WROOM microcontroller, with each sensor connected to an analog input pin. The system transmits raw analog-to-digital converter (ADC) values wirelessly to a web server hosted at iotwebserver.com. The web server is configured to hold a maximum of 50 data entries, after which older entries are overwritten. To preserve the full dataset, raw readings are periodically downloaded and merged after every 50 updates.

Instructions:
Fresh ground beef and pork were procured from the same source on the same date. A total of seven sample compositions (each 250 g) were prepared:

250 g beef (100% beef)-class 1

225 g beef + 25 g pork (90% beef, 10% pork)-class 2

175 g beef + 75 g pork (70% beef, 30% pork)-class 3

125 g beef + 125 g pork (50% beef, 50% pork)-class 4

75 g beef + 175 g pork (30% beef, 70% pork)-class 5

25 g beef + 225 g pork (10% beef, 90% pork)-class 6

250 g pork (100% pork)-class 7

The procedure for each combination was as follows:

Sensors were preheated for 20 minutes before data acquisition.

The prepared sample was placed in the E-nose sampling chamber.

Sensor outputs were recorded every 1 minute for a duration of 124 minutes per sample.

After each trial, the chamber was ventilated using a fan for 4 minutes to prevent residual gas interference.

The dataset comprises exclusively raw ADC values. Each sample's data was saved in a .csv format, labeled according to its composition. Each record contains readings from the eight MQ sensors, followed by temperature and humidity values.
DOI: 10.15468/dl.jgkvmt
title: Occurrence Download

description: A dataset containing 45498 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 "DatasetKey is Royal Ontario Museum - Ichthyology",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 45498 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047021-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3xn3y3
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Meleagris gallopavo",
 "Country is China",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047023-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.