cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17648680
title: ALD/E Neuro-symbolic Query Dataset over ORKG Comparisons

description: This repository contains the ALD/E Neuro-symbolic Query Dataset over ORKG Comparisons, a curated collection of 33 SPARQL queries (19 for atomic layer deposition, 14 for atomic layer etching) defined over machine-actionable ORKG comparisons of published review tables.

Each query bundle corresponds to a concrete literature table and includes (i) a natural-language question, (ii) the executable SPARQL query, (iii) an example result table (results_example.csv), and (iv) rich metadata (metadata.json) linking to the source paper, DOI, ORKG comparison IDs, and query type (easy/complex, within-table/cross-table).

The dataset is designed to support neurosymbolic evaluation scenarios, LLM-based query generation, and reproducible meta-analysis of ALD/E chemistries and processes. It targets both materials scientists interested in FAIR, queryable representations of ALD/E knowledge and AI researchers developing systems that bridge natural-language questions with knowledge-graph reasoning.
DOI: 10.5281/zenodo.16098019
title: A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq Nanopore long reads data
DOI: 10.5281/zenodo.17632476
title: A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq Nanopore long reads data
DOI: 10.6084/m9.figshare.30656048
title: Support material — “Spatial Profiling of Human Diffuse Cutaneous Leishmaniasis Lesions Reveals Immunosuppressive Microenvironments that Coincide with Parasite Localisation”

description: Diffuse cutaneous leishmaniasis (DCL) is marked by persistent Leishmania amazonensis parasitism and a profoundly immunosuppressive tissue environment. Using multiparametric immunofluorescence, we investigate the immune landscape of DCL skin lesions. We observed large numbers of CD68⁺ phagocytes harbouring intracellular parasites that displayed prominent vacuolated morphology. Spatial mapping demonstrated distinct tissue compartments that were enriched for vacuolated (VA+) or non-vacuolated (VA-) phagocytes. Notably, CD4⁺FOXP3⁺ regulatory T cells were significantly enriched in VA+ regions, in close proximity to CD68⁺ cells, suggesting that macrophages containing parasites were associated with an immunosuppressive microenvironment. Consistent with this, immunofluorescence confirmed a preferential co-localisation of CD68⁺ cells expressing heme oxygenase-1 (HO-1), a key mediator of anti-inflammatory responses, within VA⁺ areas. Strikingly, a strong positive correlation was observed between HO-1⁺ phagocytes and Treg frequencies, supporting the hypothesis of a coordinated immunoregulatory axis contributing to immune evasion and parasite persistence. Collectively, our findings reveal a compartmentalised niches in DCL defined by the co-localisation of parasite engorged vacuolated macrophages and regulatory T cells that may underpin the immunosuppression observed in this severe form of this disease.
DOI: 10.6084/m9.figshare.30656048.v1
title: Support material — “Spatial Profiling of Human Diffuse Cutaneous Leishmaniasis Lesions Reveals Immunosuppressive Microenvironments that Coincide with Parasite Localisation”

description: Diffuse cutaneous leishmaniasis (DCL) is marked by persistent Leishmania amazonensis parasitism and a profoundly immunosuppressive tissue environment. Using multiparametric immunofluorescence, we investigate the immune landscape of DCL skin lesions. We observed large numbers of CD68⁺ phagocytes harbouring intracellular parasites that displayed prominent vacuolated morphology. Spatial mapping demonstrated distinct tissue compartments that were enriched for vacuolated (VA+) or non-vacuolated (VA-) phagocytes. Notably, CD4⁺FOXP3⁺ regulatory T cells were significantly enriched in VA+ regions, in close proximity to CD68⁺ cells, suggesting that macrophages containing parasites were associated with an immunosuppressive microenvironment. Consistent with this, immunofluorescence confirmed a preferential co-localisation of CD68⁺ cells expressing heme oxygenase-1 (HO-1), a key mediator of anti-inflammatory responses, within VA⁺ areas. Strikingly, a strong positive correlation was observed between HO-1⁺ phagocytes and Treg frequencies, supporting the hypothesis of a coordinated immunoregulatory axis contributing to immune evasion and parasite persistence. Collectively, our findings reveal a compartmentalised niches in DCL defined by the co-localisation of parasite engorged vacuolated macrophages and regulatory T cells that may underpin the immunosuppression observed in this severe form of this disease.
DOI: 10.6084/m9.figshare.30656048.v2
title: Support material — “Spatial Profiling of Human Diffuse Cutaneous Leishmaniasis Lesions Reveals Immunosuppressive Microenvironments that Coincide with Parasite Localisation”

description: Diffuse cutaneous leishmaniasis (DCL) is marked by persistent Leishmania amazonensis parasitism and a profoundly immunosuppressive tissue environment. Using multiparametric immunofluorescence, we investigate the immune landscape of DCL skin lesions. We observed large numbers of CD68⁺ phagocytes harbouring intracellular parasites that displayed prominent vacuolated morphology. Spatial mapping demonstrated distinct tissue compartments that were enriched for vacuolated (VA+) or non-vacuolated (VA-) phagocytes. Notably, CD4⁺FOXP3⁺ regulatory T cells were significantly enriched in VA+ regions, in close proximity to CD68⁺ cells, suggesting that macrophages containing parasites were associated with an immunosuppressive microenvironment. Consistent with this, immunofluorescence confirmed a preferential co-localisation of CD68⁺ cells expressing heme oxygenase-1 (HO-1), a key mediator of anti-inflammatory responses, within VA⁺ areas. Strikingly, a strong positive correlation was observed between HO-1⁺ phagocytes and Treg frequencies, supporting the hypothesis of a coordinated immunoregulatory axis contributing to immune evasion and parasite persistence. Collectively, our findings reveal a compartmentalised niches in DCL defined by the co-localisation of parasite engorged vacuolated macrophages and regulatory T cells that may underpin the immunosuppression observed in this severe form of this disease.
DOI: 10.15468/dl.w7sp3z
title: Occurrence Download

description: A dataset containing 1262 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Trifolium bifidum",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1262 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044910-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yz374c
title: Occurrence Download

description: A dataset containing 100219 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Momotus aequatorialis",
 "Country is Colombia"
 ]
}

 The dataset includes 100219 records from 159 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044864-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21227/40cv-tz15
title: "Data files for testing entropy coding software"

description: "This series of raw data contains two types of data:a) synthetically generated data: each file comprises 10^8 bytes, while each byte represents a single symbol drawn from an alphabet with K different symbols. The distribution of theses symbols is either uniform or geometrically (truncated). For K &gt; 256, the files contain 2 bytes per symbol.b) real-life data (3 files): one screen shot 1785 x 1225 px and two prediction-error images of same size."
DOI: 10.15468/dl.sv4sc8
title: Occurrence Download

description: A dataset containing 324536 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Quercus petraea"
 ]
}

 The dataset includes 324536 records from 1690 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044861-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/71vj3-8n798
title: MEF cells - Dynamin2 knockdown

description: Dyn2 knocked down using retroviral delivery of shRNA.
description: <strong>Tilt Series Date:</strong> 2019-01-04</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> tomo3D</p>
<strong>Collaborators and Roles:</strong> Chun-Shik Chin from Chan lab helped design shRNA for Dyn2 knockdown. Shrawan and Danielle made retrovirus for transduction and froze cells. FIB milled by Danielle and Tilt series collected by Shrawan and Danielle</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown on R2/2 quantifoil gold grids coated with 0.1 mg/mL fibronectin</p>
<strong>Sample Preparation:</strong> 10uM FCCP, plunge frozen and FIB milled.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/smk2019-01-04-15/rawdata/</p>TS14.mrc,  Tilt Series (Pixel Size 0.432 nm), 1.8 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/smk2019-01-04-15/rawdata/TS14.mrc"
        > <i class="download icon"></i> Download </a></p>

        TS14_4bin_SIRTl20_rotx.rec,  Reconstruction (Pixel Size 0.0 nm), 1.2 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.jevw3e
title: Occurrence Download

description: A dataset containing 303 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 "TaxonKey is one of (Strabomantis anomalus [GBIF Backbone Taxonomy])"
 ]
}

 The dataset includes 303 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048083-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/ny5yp-axk52
title: M. xanthus pilA - pilY1.3-flag

description: Raw data files of M. xanthus pilA - pilY1.3-flag
description: <strong>Tilt Series Date:</strong> 2020-01-31</p>
<strong>Data Taken By:</strong> Georges Chreifi</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°, constant angular increment, dosage: 150.0 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> Yi-Wei Chang, Anke Treuner-Lange, Lotte Sogaard-Andersen</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Inoculated 15 mL 1% CTT with 1mL previously frozen glycerol stock. . Incubated at 32C/225rpm for 2 days.</p>
<strong>Sample Preparation:</strong> Harvested, mixed 40uL cells with 10nm Au fiducials, plunge froze 4uL . (bf 6, bt 6s, d 1s)</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/gca2020-01-31-1/rawdata/</p>pilY13_001_af.mrc,  Tilt Series (Pixel Size 0.336 nm), 5.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/gca2020-01-31-1/rawdata/pilY13_001_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        pilY13_001_af_full.rec,  Reconstruction (Pixel Size 1.344 nm), 737.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/08720-ptk82
title: Pseudomonas aeruinosa

description: This is from the transposon mutant library of Pseudomonas aeruginosa PAO1. The aim is to check for the presence of PL sub complexes in the absence of FliF protein.
description: <strong>Tilt Series Date:</strong> 2018-10-03</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: 150.0 eV/Å²,  defocus: -9.0 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> Serial EM</p>
<strong>Collaborators and Roles:</strong> I obtained these cells from Dianne Newmann lab (Shannon Park)</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The cells were grown overnight at 37 C in LB with 100 ug/ml gentamicin</p>
<strong>Sample Preparation:</strong> Samples from the overnight culture were used to prepare the grids.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-10-03-20/rawdata/</p>Test_Pseudomonas_dfliF_98.mrc,  Tilt Series (Pixel Size 0.37 nm), 1.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-10-03-20/rawdata/Test_Pseudomonas_dfliF_98.mrc"
        > <i class="download icon"></i> Download </a></p>

        Test_Pseudomonas_dfliF_98_part50_3.rec,  Reconstruction (Pixel Size 1.48 nm), 444.5 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/q9ygt-31q29
title: bio3-1_lam1_cell1

description: BIO3-1 - 1.2s - Phase plate
description: <strong>Tilt Series Date:</strong> 2018-10-31</p>
<strong>Data Taken By:</strong> William Nicolas</p>
<strong>Species / Specimen:</strong> Gluconacetobacter hansenii</p>
<strong>Strain:</strong> ATCC 23769</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (60.0°, 60.0°), step: 1°, constant angular increment, dosage: 86.0 eV/Å²,  defocus: -2.0 μm,  magnification: 26000x. </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>Purification / Growth Conditions / Treatment:</strong> 1mL of SH+carb inoculated with cellulose mat in little Petri dish with 4  Quantifoil gold grids R 2/2 Au 200 at 8:30am</p>
<strong>Sample Preparation:</strong> Freezing started at 3:45pm (7:15h of incubation)Manual backblotting 5sHum 70% - 30C</p>
  wnj2018-10-31-1_slicer19944.jpg: ACS machinery?
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2018-10-31-1/rawdata/</p>bio3-1_lam1_cell1.st,  Tilt Series (Pixel Size 5.41 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/wnj2018-10-31-1/rawdata/bio3-1_lam1_cell1.st"
        > <i class="download icon"></i> Download </a></p>

        bio3-1_lam1_cell1.rec,  Reconstruction (Pixel Size 21.64 nm), 136.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/1a312-jaq57
title: JV9298

description: DotF-sfGFP DotB E191K
description: <strong>Tilt Series Date:</strong> 2019-10-14</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> PNCC Krios 3</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 Joe Vogel</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Late exponential/Early stationary</p>
<strong>Sample Preparation:</strong> Quantifoil R2/2 copper. Vitrobot 22 deg C, 100% humidity, 4uL of 2X concentrated culture, blot force 6, blot time 3 sec, drain time 1 sec, wait time 0 sec.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2019-10-14-135/rawdata/</p>JV9298_85_A4.mrc,  Tilt Series (Pixel Size 0.1323 nm), 14.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2019-10-14-135/rawdata/JV9298_85_A4.mrc"
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        JV9298_85_A4_part37_1.rec,  Reconstruction (Pixel Size 1.0584 nm), 737.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/evegg-4s834
title: JV9298

description: DotF-sfGFP DotB E191K
description: <strong>Tilt Series Date:</strong> 2019-10-14</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> PNCC Krios 3</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 Joe Vogel</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Late exponential/Early stationary</p>
<strong>Sample Preparation:</strong> Quantifoil R2/2 copper. Vitrobot 22 deg C, 100% humidity, 4uL of 2X concentrated culture, blot force 6, blot time 3 sec, drain time 1 sec, wait time 0 sec.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2019-10-14-177/rawdata/</p>JV9298_79_B3.mrc,  Tilt Series (Pixel Size 0.1323 nm), 14.0 GB  
        
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        JV9298_79_B3_part37_8.rec,  Reconstruction (Pixel Size 1.0584 nm), 737.3 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/ycwgk-fpp78
title: RalF-Ub V76

description: Lp02 pCyaA::RalF-Ub V76 free from U937
description: <strong>Tilt Series Date:</strong> 2020-07-31</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: 110.0 eV/Å²,  defocus: -6.0 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> Stephen Carter</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 1h infection, 1-2 washes, fibronectin/vitronectin/no matrix. Legionella: 2.5 O.D, 3h after 200mM  IPTG induction, at O.D. 3</p>
<strong>Sample Preparation:</strong> 200mesh Gold quantifoil,  10nm gold, 37deg C, 80-90% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2020-07-31-78/rawdata/</p>RalFUbV76_215.mrc,  Tilt Series (Pixel Size 0.265 nm), 1.7 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        RalFUbV76_215_full.rec,  Reconstruction (Pixel Size 1.06 nm), 516.1 MB  
        
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DOI: 10.22002/g2erf-ebw04
title: JV9082

description: DotF-GFP, defocus range -3 to 6
description: <strong>Tilt Series Date:</strong> 2019-12-05</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> Janelia Titan</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 Joe Vogel lab</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Late exponential phase, early stationary phase</p>
<strong>Sample Preparation:</strong> 10nm gold, Quantifoil R2/2 copper mesh 200 Finder grid, Vitrobot 22 deg C, 100% humidity, blot . time 3 sec, blot force 6, drain 1 sec, wait 0 sec.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2019-12-05-94/rawdata/</p>9082_box1_No1_223.mrc,  Tilt Series (Pixel Size 0.2612 nm), 1.7 GB  
        
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        9082_box1_No1_223_part37_3.rec,  Reconstruction (Pixel Size 1.0448 nm), 516.1 MB  
        
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        > <i class="download icon"></i> Download </a></p>