cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/2kgfz-bwp97
title: mini cells

description: Mini cells (FtsA FtsZ over-expression)
description: <strong>Tilt Series Date:</strong> 2019-11-15</p>
<strong>Data Taken By:</strong> Yuxi Liu</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°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -5.0 μm,  magnification: 33000x. </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> Strain from Craig Roy lab</p>
<strong>Purification / Growth Conditions / Treatment:</strong> FtsA FtsZ over-expression induced by 0.1mM IPTG in liquid culture. O.D. reached 1.8 after ~40 hours. </p>
<strong>Sample Preparation:</strong> Concentrate 600uL of O.D. 1.8 cells, collect supernatant from 500Xg 2min spin, then concentrate again w/ 1000xg 5min spin. Resuspend pellet to 50uL as stock. Vitrobot set to 22 C, 100% humidity. Apply 4uL of 20X diluted stock, blot manually. Quantifoil R2/2 copper.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2019-11-15-61/rawdata/</p>20191115_Lpmini_90.mrc,  Tilt Series (Pixel Size 0.1339 nm), 7.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2019-11-15-61/rawdata/20191115_Lpmini_90.mrc"
        > <i class="download icon"></i> Download </a></p>

        20191115_Lpmini_90_part37_5.rec,  Reconstruction (Pixel Size 1.0712 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2019-11-15-61/3dimage_108645/20191115_Lpmini_90_part37_5.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/yewns-qtd13
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/mka2020-10-08-453/rawdata/</p>Hpylori_DFliF_FISE_458.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/mka2020-10-08-453/rawdata/Hpylori_DFliF_FISE_458.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_DFliF_FISE_458_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/mka2020-10-08-453/3dimage_114347/Hpylori_DFliF_FISE_458_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/drbv8-q0548
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/dga2018-08-29-350/rawdata/</p>JV9082_20180901a0124.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/dga2018-08-29-350/rawdata/JV9082_20180901a0124.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV9082_20180901a0124_full.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/dga2018-08-29-350/3dimage_97059/JV9082_20180901a0124_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/hkjme-g8n30
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/mka2018-09-29-8/rawdata/</p>Pseudomonas_DfliF30.mrc,  Tilt Series (Pixel Size 0.53 nm), 711.6 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-09-29-8/rawdata/Pseudomonas_DfliF30.mrc"
        > <i class="download icon"></i> Download </a></p>

        Pseudomonas_DfliF30_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/mka2018-09-29-8/3dimage_97138/Pseudomonas_DfliF30_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/f2de8-8bq75
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/dga2018-08-29-353/rawdata/</p>JV9082_20180901a0127.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/dga2018-08-29-353/rawdata/JV9082_20180901a0127.mrc"
        > <i class="download icon"></i> Download </a></p>

        JV9082_20180901a0127_full.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/dga2018-08-29-353/3dimage_97060/JV9082_20180901a0127_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15480/336.2879
title: Mechanical properties of zircon for varying degree of amorphization predicted by finite element simulations

description: Die Methode Gauß’scher Zufallsfelder auf der Basis stehender Wellen wurde genutzt, um über einen Schwellwert zweiphasige Mikrostrukturen mit beliebigem Phasenanteil zu generieren. Finite-Elemente Voxelmodelle dieser Mikrostrukturen wurden genutzt, um die mechanischen Eigenschaften von Zirkon (ZrSiO4) für unterschiedliche Amorphisierungsgrade zwischen 0 und 100% mit Perkolationsübergängen bei 15.9 und 84.1% vorherzusagen. Zwischen den Perkolationsschwellen ist die Mikrostruktur bikontinuierlich. Die numerischen Simulationen liefern Werte für die volumetrische Schwellung infolge der Amorphisierung, Dichte, E-Modul, Querkontraktionszahl, Fließspannung und Härte in Abhängigkeit des amorphen Phasenanteils. Um einen Fit der Härte mit Nanoindentationsdaten in der Literatur zu erreichen, berücksichtigt das Modell eine Grenzfläche zwischen der amorphen und kristallinen Phase, deren Dicke angepasst werden kann. Die Fließspannung und Härtedaten wurden für verschiedenen Grenzflächendicken bestimmt. Das Repositorium enthält die Simulationsergebnisse sowie die zum Vergleich herangezogenen Literaturdaten.
description: The level-cut Gaussian random field approach based on standing waves is used to generate bi-phase microstructures of arbitrary phase fraction. Finite Element voxel models based on such microstructures are employed to predict the mechanical properties of zircon (ZrSiO4) for varying degree of amporphization from 0 to 100% with percolation transitions at 15.9 and 84.1%. Between the percolation transitions, the microstructure is bi-continuous. The numerical simulations provide values for the volumetric swelling, density, Young´s modulus, Poisson´s ratio, yield stress, and hardness as function of the amorphous phase fraction. For achieving a fit with nanoindentation hardness data in the literature, the micromechanical model additionally considers an interface between the amorphous and the crystalline phase that can be adjusted in thickness. Yield stress and hardness data are predicted for different values of interface thickness. The repository contains the simulation results as well as the literature data used for comparison.
DOI: 10.5281/zenodo.15597338
title: Twin prime conjecture

description: Title: Resolution of the Twin Prime Conjecture

Description:This paper presents a formal resolution to the Twin Prime Conjecture, one of the most enduring questions in number theory. The conjecture asserts that there are infinitely many pairs of prime numbers (p, p+2) such that both numbers are prime. Building upon the framework of analytic number theory, sieve methods, and prime gap distributions, this work introduces a structured approach that models the distribution of twin primes through a novel coherence field lens. The argument is rigorously constructed, adhering to modern standards of proof, and integrates both classical techniques and innovative theoretical constructs. This resolution not only supports the infinitude of twin primes but also offers a broader perspective on the underlying order governing prime number pairs. The paper has been prepared in alignment with peer-review criteria suitable for submission to academic mathematics journals and recognition by the Clay Mathematics Institute.
DOI: 10.5281/zenodo.15597339
title: Twin prime conjecture

description: Title: Resolution of the Twin Prime Conjecture

Description:This paper presents a formal resolution to the Twin Prime Conjecture, one of the most enduring questions in number theory. The conjecture asserts that there are infinitely many pairs of prime numbers (p, p+2) such that both numbers are prime. Building upon the framework of analytic number theory, sieve methods, and prime gap distributions, this work introduces a structured approach that models the distribution of twin primes through a novel coherence field lens. The argument is rigorously constructed, adhering to modern standards of proof, and integrates both classical techniques and innovative theoretical constructs. This resolution not only supports the infinitude of twin primes but also offers a broader perspective on the underlying order governing prime number pairs. The paper has been prepared in alignment with peer-review criteria suitable for submission to academic mathematics journals and recognition by the Clay Mathematics Institute.
DOI: 10.5066/p136qhp9
title: Particle size analysis results from the VA-Clarke-03 core, Cherry Hill quadrangle, Dinwiddie County, Virginia (ver. 1.1, May 2025)

description: The dataset documents results from particle size analysis conducted on a suite of sediment samples from the VA-Clarke-03 core, Cherry Hill quadrangle, Dinwiddie county, Virginia [36.931926, -77.566802]. The 44-foot-long core was collected on 05/16/2023 using the North Carolina Geological Survey Geoprobe. The core was collected from sands and gravels of the uppermost coastal plain that host the Old Hickory heavy mineral deposit. Because host sediments are non-fossiliferous, there is little consensus as to their age, stratigraphic position, or nomenclature. Current mapping assigns host sands and gravels to two units in the upper part of the Pliocene to Pleistocene Chesapeake Group.

In the lab, the core was analyzed using the USGS GeoTek multi-sensor core logger system housed in the Florence Bascom Geoscience Center, Reston, VA. After Geotek analysis (Carter and others, 2024), sediment samples were collected from the core for particle size analysis, detrital zircon analysis, and 26Al/10Be cosmogenic burial dating.  Particle size analysis was conducted using the Beckman Coulter LS 13 320 XR analyzer housed in the Bascom Laser Diffraction Sedimentology Laboratory in Reston, VA.

This work is a collaboration with the Virginia Department of Energy, Geology and Mineral Resources Program and the North Carolina Geological Survey through the USGS National Cooperative Geologic Mapping Program, southeastern Atlantic Coastal Plain Working Group, and the USGS Earth MRI Program.

Citation: Carter, M., Seidenstein, J., Farrell, K., Nelson, M., Rodysill, J., Odom, W., Holm-Denoma, C., Occhi, M., and Hawkins, D., 2024, Using the U.S. Geological Survey Geotek Multi-Sensor Core Logger System to analyze and preserve core from the Old Hickory Heavy Mineral deposit, southeastern Virginia: Geological Society of America Abstracts with Programs, Vol. 56, No. 2, doi: 10.1130/abs/2024SE-398116

This Data Release was revised to v1.1 in May 2025 to include updated statistics data for laser diffractometry results contained therein. No other changes to the data release were made for v1.1.
 
First release: 2024
Revised: May 2025 (ver. 1.1)
DOI: 10.5517/ccdc.csd.cc1q0dgl
title: CCDC 1579309: Experimental Crystal Structure Determination

description: Related Article: Xingyu Xu, Linfeng Li, Zengyu Zhang, Xiaoyu Yan|2018|Tetrahedron|74|6846|doi:10.1016/j.tet.2018.10.009
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.5zfce6
title: Occurrence Download

description: A dataset containing 327386 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Turdus merula",
 "Country is New Zealand",
 "HasCoordinate is true"
 ]
}

 The dataset includes 327386 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006907-250827131500795/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.29995102
title: Web of Science search query for tropical and subtropical ancient environmental DNA research

description: Search terms used in the WoS literature research
DOI: 10.6084/m9.figshare.29995102.v1
title: Web of Science search query for tropical and subtropical ancient environmental DNA research

description: Search terms used in the WoS literature research
DOI: 10.22002/76s2y-hqq27
title: E. Coli delta53

description: Mutant MreB with sfGFP in sandwich position. WT MreB is replaced at the original locus with this fusion.
description: <strong>Tilt Series Date:</strong> 2014-04-01</p>
<strong>Data Taken By:</strong> Matt Swulius</p>
<strong>Species / Specimen:</strong> Escherichia Coli </p>
<strong>Strain:</strong> delta53</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-64.0°, 64.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 26000x. </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> Josh Schaevitz</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 37 celsius to OD 600 ~ 0.3</p>
<strong>Sample Preparation:</strong> Blotted manually from rear in vitrobot at 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mst2014-04-01-51/rawdata/</p>040114_delta53_0019.mrc,  Tilt Series (Pixel Size 0.42 nm), 3.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mst2014-04-01-51/rawdata/040114_delta53_0019.mrc"
        > <i class="download icon"></i> Download </a></p>

        040114_delta53_0019_part131_3.rec,  Reconstruction (Pixel Size 1.68 nm), 861.2 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mst2014-04-01-51/3dimage_41599/040114_delta53_0019_part131_3.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/09dtp-0kq52
title: HUVECs infx pNLGFP

description: pNLGFP obtained from Irvin Chen (UCLA)
description: <strong>Tilt Series Date:</strong> 2013-10-22</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> HUVECs</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: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 26000x. </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> pNLGFP obtained from Irvin Chen (UCLA)</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Whole cells were grown on Au finder grids and infected with pNLGFP- VSVG. Sample frozen 36h post infection</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at ://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2013-10-22-3/rawdata/</p>C169-2_HUVECs_pNL36h_atlas3_0002.mrc,  Tilt Series (Pixel Size 0.42 nm), 3.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2013-10-22-3/rawdata/C169-2_HUVECs_pNL36h_atlas3_0002.mrc"
        > <i class="download icon"></i> Download </a></p>

        C169-2_HUVECs_pNL36h_atlas3_0002_part121_12.rec,  Reconstruction (Pixel Size 1.68 nm), 516.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2013-10-22-3/3dimage_33629/C169-2_HUVECs_pNL36h_atlas3_0002_part121_12.rec"
        > <i class="download icon"></i> Download </a></p>