cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23290892.v4
title: <strong>Prognostic and predictive values of the grading system of lymph node status in patients with advanced-stage gastric cancer</strong>

description: Lymph node metastasis is one of the most important prognostic factors of gastric cancer. However, the effect of germinal centers in lymph nodes on the prognosis of patients with gastric cancer has not been reported. This study aimed to investigate the contribution of germinal center generation to prognostic parameters and clinicopathological significance in gastric cancer.<br>
DOI: 10.34740/kaggle/dsv/5842214
title: Global Genomic Neurofibromatosis Neoplasia
DOI: 10.5281/zenodo.7738602
title: CNN weight data for "Model identification of neural encoding (MINE)" publication - Set 1

description: This dataset contains the weights of fit CNN models generated during the analysis of the zebrafish thermoregulation dataset processed by MINE. This set contains 24/25 fish. The last fish and mouse MINE model weights are contained in Set 2.
description: Funding through NIH grant R01NS123887 and The Ohio State University Wexner Medical Center
DOI: 10.5281/zenodo.7017099
title: Processed data for "Model identification of neural encoding (MINE)" publication

description: This dataset contains mouse and zebrafish data processed by MINE. These datafiles were used to generate the publication figures for the mouse cortical dataset [m<em>usall.hdf5</em>] (Figure 5) and the zebrafish whole-brain [<em>main_analysis.hdf5</em>] (Figures 6 and 7) and reticulospinal datasets [r<em>s_analysis.hdf5</em>] (Figure 6). <em>Musall.hdf5 </em>contains reordered data from "Musall, S., Kaufman, M.T., Juavinett, A.L. <em>et al.</em> Single-trial neural dynamics are dominated by richly varied movements. <em>Nat Neurosci</em> <strong>22</strong>, 1677–1686 (2019)." The contents of each dataset are described in <em>DataContent_xxx.pdf</em>
description: Funding through NIH grant R01NS123887 and The Ohio State University Wexner Medical Center
DOI: 10.5281/zenodo.7741541
title: CNN weight data for "Model identification of neural encoding (MINE)" publication - Set 2

description: This dataset contains the weights of fit CNN models generated during the analysis of the zebrafish thermoregulation dataset and the Musall et al. mouse dataset processed by MINE. This set contains the last fish and the mouse MINE model weights. The other 24 fish are contained in Set 1.
description: Funding through NIH grant R01NS123887 and The Ohio State University Wexner Medical Center
DOI: 10.6084/m9.figshare.23292539
title: Updating germ cell tumor pathogenesis - The ability of seminomas for FOXA2-driven extra-embryonic differentiation

description: Testicular germ cell tumors are the most common solid malignancies in young men of age 14 - 44 years. It is generally accepted that both, seminomas and non-seminomas, arise from a common precursor, the germ cell neoplasia in situ, which itself is the result of a defective (primordial) germ cell development. The stem cell-like population of the non-seminomas, the embryonal carcinoma, is capable of differentiation into cells all three germ layers (teratomas) and extra-embryonic tissues (yolk-sac tumors, choriocarcioma). In contrast, seminoma are thought to have a limited differentiation potential. Nevertheless, several studies pointed at their ability to undergo reprogramming to an embryonal carcinoma or differentiation into other non-seminomatous entities. Here, we demonstrate that in approximately 5 % of seminomas, the yolk-sac tumor driver gene FOXA2 is detectable on protein level, indicative of an occult yolk-sac tumor subpopulation that putatively arose from seminoma cells, since presence of other GCT entities could be excluded. Presence of these subpopulations might render the tumor more aggressive and argue for an adjustment of the therapeutic concept. We used our data to update the model of germ cell tumor pathogenesis, especially regarding the developmental potential of seminomas. Additionally, we suggest to include detection of FOXA2 into standard routine diagnosis of seminomas.
DOI: 10.6084/m9.figshare.23292539.v2
title: Updating germ cell tumor pathogenesis - The ability of seminomas for FOXA2-driven extra-embryonic differentiation

description: Testicular germ cell tumors are the most common solid malignancies in young men of age 14 - 44 years. It is generally accepted that both, seminomas and non-seminomas, arise from a common precursor, the germ cell neoplasia in situ, which itself is the result of a defective (primordial) germ cell development. The stem cell-like population of the non-seminomas, the embryonal carcinoma, is capable of differentiation into cells all three germ layers (teratomas) and extra-embryonic tissues (yolk-sac tumors, choriocarcioma). In contrast, seminoma are thought to have a limited differentiation potential. Nevertheless, several studies pointed at their ability to undergo reprogramming to an embryonal carcinoma or differentiation into other non-seminomatous entities. Here, we demonstrate that in approximately 5 % of seminomas, the yolk-sac tumor driver gene FOXA2 is detectable on protein level, indicative of an occult yolk-sac tumor subpopulation that putatively arose from seminoma cells, since presence of other GCT entities could be excluded. Presence of these subpopulations might render the tumor more aggressive and argue for an adjustment of the therapeutic concept. We used our data to update the model of germ cell tumor pathogenesis, especially regarding the developmental potential of seminomas. Additionally, we suggest to include detection of FOXA2 into standard routine diagnosis of seminomas.
DOI: 10.6084/m9.figshare.23292539.v1
title: <strong>Updating germ cell tumor pathogenesis -</strong> <strong>The ability of seminomas for FOXA2-driven extra-embryonic differentiation</strong>

description: Testicular germ cell tumors are the most common solid malignancies in young men of age 14 - 44 years. It is generally accepted that both, seminomas and non-seminomas, arise from a common precursor, the germ cell neoplasia in situ, which itself is the result of a defective (primordial) germ cell development. The stem cell-like population of the non-seminomas, the embryonal carcinoma, is capable of differentiation into cells all three germ layers (teratomas) and extra-embryonic tissues (yolk-sac tumors, choriocarcioma). In contrast, seminoma are thought to have a limited differentiation potential. Nevertheless, several studies pointed at their ability to undergo reprogramming to an embryonal carcinoma or differentiation into other non-seminomatous entities. Here, we demonstrate that in approximately 5 % of seminomas, the yolk-sac tumor driver gene FOXA2 is detectable on protein level, indicative of an occult yolk-sac tumor subpopulation that putatively arose from seminoma cells, since presence of other GCT entities could be excluded. Presence of these subpopulations might render the tumor more aggressive and argue for an adjustment of the therapeutic concept. We used our data to update the model of germ cell tumor pathogenesis, especially regarding the developmental potential of seminomas. Additionally, we suggest to include detection of FOXA2 into standard routine diagnosis of seminomas.
DOI: 10.23719/1532182
title: Data from Greenhouse Trials for 11 Enhanced Efficiency Fertilizers (Clark et al.)

description: This is the greenhouse data for Clark et al. "Environmental sustainability of future fertilizers: Tradeoffs between ammonia volatilization and nitrate leaching for 11 enhanced efficiency fertilizers." The data quantifies the environmental performance (NH3 volatilization, N leaching) and agronomic performance (yield) for 11 enhanced efficiency fertilizers on two soil types (Minnesota sandy loam, Iowa clay loam). Yield results are published separately (Dolda et al. in review) but are included here for completeness. See Table S1 in the publication to cross reference brand names with active ingredients.
DOI: 10.15468/dl.3pypra
title: Occurrence Download

description: A dataset containing 202331 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Lathyrus vernus"
 ]
}

 The dataset includes 202331 records from 515 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011838-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/nfj56-1b176
title: MEF cells - Dynamin2 knockdown

description: Dynamin2 knocked down with retroviral delivery of shRNA to study mitochondrial division. grid info - DG2_grid1.
description: <strong>Tilt Series Date:</strong> 2018-11-27</p>
<strong>Data Taken By:</strong> Shrawan kumar Mageswaran</p>
<strong>Species / Specimen:</strong> MEF cells</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -8.0 μm,  magnification: 33000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> SerialEM</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> IMOD, tomo3D</p>
<strong>Collaborators and Roles:</strong> Chun Shik from Chan lab helped design shRNA and provided protocols for viral transduction into Chan lab's MEF cells. Shrawan and Danielle made the cell line. Shrawan FIB-milled and performed ECT.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown on R2/2 quantifoil gold grids treated with 0.1 mg/mL fibronectin (10min)</p>
<strong>Sample Preparation:</strong> Cells were treated with 10 µM FCCP, plunge frozen and FIB-milled.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/smk2018-11-27-20/rawdata/</p>TS12.mrc,  Tilt Series (Pixel Size 0.432 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/smk2018-11-27-20/rawdata/TS12.mrc"
        > <i class="download icon"></i> Download </a></p>

        TS12_4bin_SIRTl20_rotx.rec,  Reconstruction (Pixel Size 0.0 nm), 819.6 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.23719/1532410
title: Including dispersive shear stress in urban environments for single column dispersion models

description: The data files consist of measurements gathered from EPA's Meteorological Wind Tunnel Laboratory and Large Eddy Simulations (LES).  Comparisons are made to the existing formulations in AERMOD, the EPA’s preferred Gaussian dispersion model. A data dictionary for each figure is provided in the zipped file package.
DOI: 10.23719/1532463
title: 2022 Grand Lake St. Marys qPCR data for microcystin producers

description: This data set includes qPCR data for the microcystin producing planktothrix (mcyApla) gene and the microcystin producing cyanobacteria (Hep) gene for samples collected from Grand Lake St. Marys and downstream waterways in 2022.
DOI: 10.22002/vrydn-e2m83
title: Lp02-fixed

description: WT Lp02 cells were fixed with GA and re-suspended in  PBS.
description: <strong>Tilt Series Date:</strong> 2017-11-20</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: (-60.0°, 60.0°), step: 1.5°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -7.0 μm,  magnification: 27500x. </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> Joelle Gabay and Howard Shuman prepared samples, Debnath Ghosal collected data.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Shuman Lab</p>
<strong>Sample Preparation:</strong> 6 grids were frozen, cell density was increased to 2x by centrifugation. 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. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-11-20-23/rawdata/</p>Legionella_fixed_201711200029.mrc,  Tilt Series (Pixel Size 0.39 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-11-20-23/rawdata/Legionella_fixed_201711200029.mrc"
        > <i class="download icon"></i> Download </a></p>

        Legionella_fixed_201711200029.rec,  Reconstruction (Pixel Size 1.56 nm), 889.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-11-20-23/3dimage_90344/Legionella_fixed_201711200029.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.23719/1532470
title: Model Code Associated with "Challenges for extrapolation of risk from ingestion to inhalation exposure for per- and polyfluorinated alkyl acids and their precursors"

description: This ScienceHub entry contains a zip file with the pharmacokinetic modeling code used for the linked publication, "Challenges for extrapolation of risk from ingestion to inhalation exposure for per- and polyfluorinated alkyl acids and their precursors." The model code is written in R with a .model file written in the MCSim language. The inhalation pharmacokinetic model builds on a previous publication of Bernstein et al., "A Model Template Approach for Rapid Evaluation and Application of Physiologically Based Pharmacokinetic Models for Use in Human Health Risk Assessments: A Case Study on Per- and Polyfluoroalkyl Substances" https://doi.org/10.1093/toxsci/kfab063
DOI: 10.23719/1532472
title: Gray 2025 Phthalate transcriptomic and apical points of departure dataset

description: Dataset includes all endpoint measurements from studies described in the manuscript and SAS code for statistical analyses of data.
DOI: 10.23719/1532471
title: Conley 2025 Maternal and neonatal effects of PFHxS dataset

description: Dataset includes summary statistics (mean, standard error, sample size) for all endpoints measured and reported from the the experiments described in the published manuscript.
DOI: 10.22002/vg2s4-n0m86
title: Thermococcus koakarensis

description: Imaging Thermococcus koakarensis flagella
description: <strong>Tilt Series Date:</strong> 2016-09-20</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Thermococcus kodakarensis</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: 140.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </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> Strain sent to us by Robert Gunsalus, UCLA. Data collected and processed by Kiwoo and Debnath Ghosal</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Standard Tk medium with starch and sulfur</p>
<strong>Sample Preparation:</strong> 8 grids were frozen for the this strain. Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 3.5 sec. Wait time 8 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-09-20-24/3dimage_79367/</p>atlas10023_full.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-09-20-24/3dimage_79367/atlas10023_full.rec"
        > <i class="download icon"></i> Download </a></p>

        atlas10023.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-09-20-24/rawdata/atlas10023.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.23719/1531787
title: FTIR Datasets

description: FTIR Data
DOI: 10.23719/1523148
title: Influence of Volumetric Water Content Sensor Configuration in Evaluating Bioretention Planter Retention and Evaporation Dataset 

description: This dataset includes volumetric water content data from 8 or 14 sensors in two bioretention planters and the relevant previous storm size.
DOI: 10.22002/4gg1p-7qe20
title: M. xanthus PilQ delete AA25-300

description: Grid box YWC126SA6808: delta-pilQ_AA25~300
description: <strong>Tilt Series Date:</strong> 2015-04-23</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Myxococcus xanthus</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: -6.0 μm,  magnification: 27500x. </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> Strain form Lotte Sogaard-Andersen</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown 2 days in 220 rpm shaking CTT medium at 30 degrees without antibiotics. OD600=0.8</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. Blot force 6, blot time 2.5 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/ycw2015-04-23-42/rawdata/</p>20150423_YWC126_10044.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-04-23-42/rawdata/20150423_YWC126_10044.mrc"
        > <i class="download icon"></i> Download </a></p>

        20150423_YWC126_10044_part121_3.rec,  Reconstruction (Pixel Size 1.56 nm), 534.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/9pfwj-bdj56
title: V. cholerae RT4236 (stationary)

description: Classical strain with ctxA deletion.Cell harbors pMT5 plasmid (inducible toxT).
description: <strong>Tilt Series Date:</strong> 2015-05-11</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> O395-N1</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: -6.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> SIRT</p>
<strong>Collaborators and Roles:</strong> Strain from Ronald K. Taylor</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Overnight cultures of Vibrio cholerae O395 NI pMT5 grown in LB pH 6.5, 1 mM IPTG and 100 ug/mL ampicilin</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. Blot force 6, blot time 2.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 finder.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-05-11-32/3dimage_73308/</p>20150511_AK07_10032_SIRT_2K.rec,  Reconstruction (Pixel Size 0.0 nm), 5.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-05-11-32/3dimage_73308/20150511_AK07_10032_SIRT_2K.rec"
        > <i class="download icon"></i> Download </a></p>

        20150511_AK07_10032.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2015-05-11-32/rawdata/20150511_AK07_10032.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/9nv08-zp312
title: V. cholerae RT4236 (stationary)

description: Classical strain with ctxA deletion.Cell harbors pMT5 plasmid (inducible toxT).
description: <strong>Tilt Series Date:</strong> 2015-04-09</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> O395-N1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </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> Strain from Ronald K. Taylor</p>
<strong>Purification / Growth Conditions / Treatment:</strong> ON cultures of Vibrio cholerae O395 NI pMT5 grown in LB pH 6.5, 1 mM IPTG and 100 ug/mL ampicilin</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 4µl sample, 10 mg/ml BSA treated gold. Blot force 6, blot time 2.5 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/ycw2015-04-09-16/rawdata/</p>20150409_AK005_10016.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        20150409_AK005_10016.rec,  Reconstruction (Pixel Size 1.56 nm), 1.1 GB  
        
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