cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.428xw2
title: Occurrence Download

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

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002523-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18435500
title: Geometric Confinement from Torsion Flux Tubes: An Algebraic Unification of QCD and Gravity

description: We present a complete geometric-algebraic unification of all fundamental forces and matter fields,originating from a single primordial curvature 2-form valued in an infinite-dimensional associativealgebra. Through spontaneous dimensional reduction and entropic crystallization, the theory natu-rally derives: (i) Einstein-Cartan-Sciama-Kibble gravity with dynamical torsion, (ii) the full Stan-dard Model gauge sector (U(1)×SU(2)×SU(3)) with correct symmetry breaking patterns, (iii) Diracfermions with automatic spin-statistics enforcement, and (iv) the Higgs mechanism with geometricYukawa couplings.The key innovation is an emergent geometric constraint that couples spacetime torsion to non-Abelian gauge fields via contraction operators. In the QCD sector, this constraint generates stabletorsion flux tubes that analytically explain quark confinement, reproduce the Nambu–Goto stringaction, and match all lattice QCD predictions—string tension σ ≈ (440 MeV)2, flux tube radiusrc ≈ 0.5 fm, and Z3 flux quantization.Simultaneously, the framework resolves long-standing theoretical puzzles: the hierarchy problememerges from eigenvalue separation during dimensional reduction; the cosmological constant appears as an integration constant; vacuum energy is geometrically regularized; and charge quantizationfollows from topological properties of the primordial curvature. All coupling constants and symmetry-breaking scales are determined algebraically without fine-tuning.The model makes falsifiable predictions across energy scales: modified gravitational wave spectrawith low-frequency cutoff fΛ ∼ √Λ ≈ 10−18 Hz, black hole echo signals with characteristic spacing,and torsional dark energy contributions. By embedding Perelman entropy functionals into geometric flows, we further demonstrate thermodynamic stabilization of spatial topology.This work establishes a mathematically justified, observationally testable pathway to quantumgravity that naturally incorporates the Standard Model through pure geometric principles
DOI: 10.15468/dl.9stadq
title: Occurrence Download

description: A dataset containing 141 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhinella marina",
 "HasCoordinate is true",
 "Country is Solomon Islands"
 ]
}

 The dataset includes 141 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002524-260129131611470/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.31153243
title: S4B Figure

description: S4B Fig. IFN-β induction during KSHV lytic reactivation requires all three IFN-β enhanceosome transcription factors. BC-3 cells were treated with 20 ng/ml TPA for 48 hours to induce the lytic cycle (“lytic (+TPA)”), 10 μM of the pan-caspase inhibitor IDN-6556 (“casp-i”), and where indicated, 1 μM of the dual AP-1 and NF-κB inhibitor SP100030. A. RNA was extracted and IFN-β mRNA levels were measured by RT-qPCR, normalized to 18S rRNA, and plotted relative to the sample treated with TPA, casp-i, and vehicle control (“(-)”). Cells were stained for KSHV ORF45 and analyzed by flow cytometry. n= 5.
DOI: 10.6084/m9.figshare.31153243.v1
title: S4B Figure

description: S4B Fig. IFN-β induction during KSHV lytic reactivation requires all three IFN-β enhanceosome transcription factors. BC-3 cells were treated with 20 ng/ml TPA for 48 hours to induce the lytic cycle (“lytic (+TPA)”), 10 μM of the pan-caspase inhibitor IDN-6556 (“casp-i”), and where indicated, 1 μM of the dual AP-1 and NF-κB inhibitor SP100030. A. RNA was extracted and IFN-β mRNA levels were measured by RT-qPCR, normalized to 18S rRNA, and plotted relative to the sample treated with TPA, casp-i, and vehicle control (“(-)”). Cells were stained for KSHV ORF45 and analyzed by flow cytometry. n= 5.
DOI: 10.5281/zenodo.18435254
title: labeo_greenii_spades_01.fasta.gz
DOI: 10.5281/zenodo.18435255
title: labeo_greenii_spades_01.fasta.gz
DOI: 10.5281/zenodo.16737648
title: All the Flight We Cannot See Paper data
DOI: 10.5281/zenodo.16737647
title: All the Flight We Cannot See Paper data
DOI: 10.15468/dl.8pja6r
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhinella marina",
 "HasCoordinate is true",
 "Country is Saint Kitts and Nevis"
 ]
}

 The dataset includes 14 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002526-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mvewkp
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhinella marina",
 "HasCoordinate is true",
 "Country is Tuvalu"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002527-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17238549
title: CytokineFindeR data inputs and outputs

description: The following submission are data inputs that are compatible to use with the cytokineFindeR R package.

The data inputs are RDS files saved as a data frame list containing metadata, gene expression counts matrices, and DEG outputs for the Cytokine Signature Analyzer webtool generated from 6 cytokine treatment and 4 perturbation studies. In our final publication, we did not include TSLP cytokine benchmarking. 

 

For LRI methods, we included all reference databases used.
DOI: 10.5281/zenodo.17238550
title: CytokineFindeR data inputs and outputs

description: The following submission are data inputs that are compatible to use with the cytokineFindeR R package.

The data inputs are RDS files saved as a data frame list containing metadata, gene expression counts matrices, and DEG outputs for the Cytokine Signature Analyzer webtool generated from 6 cytokine treatment and 4 perturbation studies. In our final publication, we did not include TSLP cytokine benchmarking. 

 

For LRI methods, we included all reference databases used.
DOI: 10.15468/pqvnsp
title: Rhacocleis parnassica sp. nov. a new cryptic bush-cricket (katydid) species from Greece (Orthoptera: Tettigoniidae: Tettigoniinae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Willemse, Luc, Odé, Baudewijn, Stefanidis, Apostolis (2025): Rhacocleis parnassica sp. nov. a new cryptic bush-cricket (katydid) species from Greece (Orthoptera: Tettigoniidae: Tettigoniinae). Zootaxa 5723 (3): 401-412, DOI: 10.11646/zootaxa.5723.3.5, URL: https://doi.org/10.11646/zootaxa.5723.3.5AbstractA new species of Rhacocleis, R. parnassica sp.nov. is described. We discovered the species on scree slopes at 1450 m on Mt. Parnassos, central Greece. This bush-cricket is morphologically distinct from all congeners, particularly in male cercal and titillator structures, and differs bioacoustically from closely related taxa. Although superficially resembling the scree-dwelling R. crypta and R. lithoscirtetes, it shows greater morphological affinity with R. distinguenda and R. werneri, and acoustic similarity with R. germanica and R. annulata. The species is currently known only from its type locality within the Natura 2000 site GR2450005. Its restricted range and potential exposure to wildfire and human disturbance highlight the need for further ecological research and conservation assessments. This discovery increases the number of Rhacocleis species in Greece to 17, underscoring the country’s exceptional Orthoptera diversity and the potential for additional undescribed taxa in poorly explored environments.
DOI: 10.5281/zenodo.18435571
title: HiQ-FPAR: a High-Quality and Value-added MODIS Global FPAR Product from 2000 to 2023

description: The High-Quality Fraction of absorbed Photosynthetically Active Radiation (HiQ-FPAR) is derived from the reprocessed MODIS FPAR C6.1 product using the Spatio-Temporal Information Compositing Algorithm (STICA). This method integrates pixel quality information, spatio-temporal correlations, and original observations to enhance raw MODIS FPAR retrievals under poor conditions. HiQ-FPAR covers the period 2000–2023 with global coverage at 500 m and 5 km spatial resolutions and an 8-day temporal resolution. Ground-based validation demonstrates that HiQ-FPAR outperforms the original MOD15A2H C6.1 product, showing reduced anomalous fluctuations and improved alignment with phenological patterns. The dataset is available on Zenodo and a 500 m version is accessible via Google Earth Engine.
DOI: 10.5281/zenodo.18435572
title: HiQ-FPAR: a High-Quality and Value-added MODIS Global FPAR Product from 2000 to 2023

description: The High-Quality Fraction of absorbed Photosynthetically Active Radiation (HiQ-FPAR) is derived from the reprocessed MODIS FPAR C6.1 product using the Spatio-Temporal Information Compositing Algorithm (STICA). This method integrates pixel quality information, spatio-temporal correlations, and original observations to enhance raw MODIS FPAR retrievals under poor conditions. HiQ-FPAR covers the period 2000–2023 with global coverage at 500 m and 5 km spatial resolutions and an 8-day temporal resolution. Ground-based validation demonstrates that HiQ-FPAR outperforms the original MOD15A2H C6.1 product, showing reduced anomalous fluctuations and improved alignment with phenological patterns. The dataset is available on Zenodo and a 500 m version is accessible via Google Earth Engine.
DOI: 10.6084/m9.figshare.31120579
title: S2C Figure

description: S2C Fig. Lentivirally established CMV promoter-driven tdTomato expression does not induce IFN-β in BC-3 cells and does not correlate with IFN-β expression. BC3-CMVp-tdTomato cells were treated with 20 ng/mL TPA for 48 hours to induce the lytic cycle (“lytic (+TPA)”). Where indicated, the cells were also treated with 10 μM of the pan-caspase inhibitor IDN-6556 (“casp-i”). Cells were stained for KSHV ORF45 and analyzed by flow cytometry. One-Way ANOVA followed by Dunnett’s post hoc multiple comparisons test. n= 3 for all experiments.
DOI: 10.6084/m9.figshare.31120579.v1
title: S2C Figure

description: S2C Fig. Lentivirally established CMV promoter-driven tdTomato expression does not induce IFN-β in BC-3 cells and does not correlate with IFN-β expression. BC3-CMVp-tdTomato cells were treated with 20 ng/mL TPA for 48 hours to induce the lytic cycle (“lytic (+TPA)”). Where indicated, the cells were also treated with 10 μM of the pan-caspase inhibitor IDN-6556 (“casp-i”). Cells were stained for KSHV ORF45 and analyzed by flow cytometry. One-Way ANOVA followed by Dunnett’s post hoc multiple comparisons test. n= 3 for all experiments.
DOI: 10.15468/dl.txhyjz
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Country is one of (Spain, Portugal, Egypt, France)",
 "MediaType is Image",
 "TaxonKey is Hyalomma lusitanicum"
 ]
}

 The dataset includes 40 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002529-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r2bym5
title: Occurrence Download

description: A dataset containing 394 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "Month is January",
 "TaxonKey is Melanelixia subaurifera",
 "Year 1994-2024"
 ]
}

 The dataset includes 394 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002530-260129131611470/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.31120414
title: S1G Figure

description: S1G Fig. Viral gene expression heterogeneity does not completely explain IFN-β expression. BC3-IFN-βp-tdTomato reporter cells were treated with 20 ng/ml TPA for 48 hours to induce the lytic cycle (“lytic (+TPA)”), 10 μM of the pan-caspase inhibitor IDN-6556 (“casp-i”), and/or a cocktail mix of antibodies against type I IFNs and their receptor (“anti-IFN Abs”) at 1:2000 dilution. Cells from the lytic+casp-i samples were collected both without sorting (“bulk”) and after sorting based on tdTomato expression (tdTomato + and -). RNA was extracted and KSHV ORF59 mRNA levels were measured by RT-qPCR and normalized to 18S rRNA. The fold enrichment of mRNA levels compared to unsorted (“bulk”) samples are plotted in log2 scale. Results in this figure were obtained from the same samples used in Fig 1 and are thus directly comparable to IFN-β enrichment shown in those Figure. ns = p&gt;0.05, ** = p&lt;0.01. One-Way ANOVA followed by Tukey’s post hoc multiple comparisons test. n≥ 4 for all experiments.
DOI: 10.6084/m9.figshare.31120414.v1
title: S1G Figure

description: S1G Fig. Viral gene expression heterogeneity does not completely explain IFN-β expression. BC3-IFN-βp-tdTomato reporter cells were treated with 20 ng/ml TPA for 48 hours to induce the lytic cycle (“lytic (+TPA)”), 10 μM of the pan-caspase inhibitor IDN-6556 (“casp-i”), and/or a cocktail mix of antibodies against type I IFNs and their receptor (“anti-IFN Abs”) at 1:2000 dilution. Cells from the lytic+casp-i samples were collected both without sorting (“bulk”) and after sorting based on tdTomato expression (tdTomato + and -). RNA was extracted and KSHV ORF59 mRNA levels were measured by RT-qPCR and normalized to 18S rRNA. The fold enrichment of mRNA levels compared to unsorted (“bulk”) samples are plotted in log2 scale. Results in this figure were obtained from the same samples used in Fig 1 and are thus directly comparable to IFN-β enrichment shown in those Figure. ns = p&gt;0.05, ** = p&lt;0.01. One-Way ANOVA followed by Tukey’s post hoc multiple comparisons test. n≥ 4 for all experiments.
DOI: 10.5281/zenodo.18435558
title: Geometric Confinement from Torsion Flux Tubes: An Algebraic Unification of QCD and Gravity

description: We present a complete geometric-algebraic unification of all fundamental forces and matter fields,originating from a single primordial curvature 2-form valued in an infinite-dimensional associativealgebra. Through spontaneous dimensional reduction and entropic crystallization, the theory natu-rally derives: (i) Einstein-Cartan-Sciama-Kibble gravity with dynamical torsion, (ii) the full Stan-dard Model gauge sector (U(1)×SU(2)×SU(3)) with correct symmetry breaking patterns, (iii) Diracfermions with automatic spin-statistics enforcement, and (iv) the Higgs mechanism with geometricYukawa couplings.The key innovation is an emergent geometric constraint that couples spacetime torsion to non-Abelian gauge fields via contraction operators. In the QCD sector, this constraint generates stabletorsion flux tubes that analytically explain quark confinement, reproduce the Nambu–Goto stringaction, and match all lattice QCD predictions—string tension σ ≈ (440 MeV)2, flux tube radiusrc ≈ 0.5 fm, and Z3 flux quantization.Simultaneously, the framework resolves long-standing theoretical puzzles: the hierarchy problememerges from eigenvalue separation during dimensional reduction; the cosmological constant appears as an integration constant; vacuum energy is geometrically regularized; and charge quantizationfollows from topological properties of the primordial curvature. All coupling constants and symmetry-breaking scales are determined algebraically without fine-tuning.The model makes falsifiable predictions across energy scales: modified gravitational wave spectrawith low-frequency cutoff fΛ ∼ √Λ ≈ 10−18 Hz, black hole echo signals with characteristic spacing,and torsional dark energy contributions. By embedding Perelman entropy functionals into geometric flows, we further demonstrate thermodynamic stabilization of spatial topology.This work establishes a mathematically justified, observationally testable pathway to quantumgravity that naturally incorporates the Standard Model through pure geometric principles
DOI: 10.5281/zenodo.18248258
title: Geometric Confinement from Torsion Flux Tubes: An Algebraic Unification of QCD and Gravity

description: We present a complete geometric-algebraic unification of all fundamental forces and matter fields,originating from a single primordial curvature 2-form valued in an infinite-dimensional associativealgebra. Through spontaneous dimensional reduction and entropic crystallization, the theory natu-rally derives: (i) Einstein-Cartan-Sciama-Kibble gravity with dynamical torsion, (ii) the full Stan-dard Model gauge sector (U(1)×SU(2)×SU(3)) with correct symmetry breaking patterns, (iii) Diracfermions with automatic spin-statistics enforcement, and (iv) the Higgs mechanism with geometricYukawa couplings.The key innovation is an emergent geometric constraint that couples spacetime torsion to non-Abelian gauge fields via contraction operators. In the QCD sector, this constraint generates stabletorsion flux tubes that analytically explain quark confinement, reproduce the Nambu–Goto stringaction, and match all lattice QCD predictions—string tension σ ≈ (440 MeV)2, flux tube radiusrc ≈ 0.5 fm, and Z3 flux quantization.Simultaneously, the framework resolves long-standing theoretical puzzles: the hierarchy problememerges from eigenvalue separation during dimensional reduction; the cosmological constant appears as an integration constant; vacuum energy is geometrically regularized; and charge quantizationfollows from topological properties of the primordial curvature. All coupling constants and symmetry-breaking scales are determined algebraically without fine-tuning.The model makes falsifiable predictions across energy scales: modified gravitational wave spectrawith low-frequency cutoff fΛ ∼ √Λ ≈ 10−18 Hz, black hole echo signals with characteristic spacing,and torsional dark energy contributions. By embedding Perelman entropy functionals into geometric flows, we further demonstrate thermodynamic stabilization of spatial topology.This work establishes a mathematically justified, observationally testable pathway to quantumgravity that naturally incorporates the Standard Model through pure geometric principles
DOI: 10.6084/m9.figshare.30577139
title: Figure 4C-E primary data

description: Figure 4C-E legend. BC3-IFN-βp-tdTomato reporter cells were treated with 20 ng/ml TPA for 48 hours to induce the lytic cycle (“lytic (+TPA)”). Where indicated, the cells were also treated with 10 μM of the pan-caspase inhibitor IDN-6556 (“casp-i”) and/or a cocktail of antibodies against type I IFNs and their receptor (“anti-IFN Abs”) at 1:2000 dilution. Protein lysates were probed for phosphorylated IRF3 (Ser386), total IRF3, phosphorylated TBK1 (Ser172), total TBK1, and β-actin as a loading control. As a positive control for IRF3 and TBK1 activation/phosphorylation, A549 cells were treated with poly(I:C) for 6 and 48 hours before protein lysates were collected. Protein was isolated from treated BC3-IFN-βp-tdTomato reporter cells without sorting (“bulk”), or after sorting the lytic+casp-i sample based on tdTomato expression. Western blot for phosphorylated TBK1 and phosphorylated IRF3 for bulk lytic+casp-i or lytic+casp-i+anti-IFN Abs treated samples and sorted tdTomato+ and tdTomato- samples were quantified by normalizing the density of phosphorylated protein to unphosphorylated protein bands. Phosphorylation levels are plotted relative to the bulk lytic+casp-i or lytic+casp-i+anti-IFN Abs treated samples.
DOI: 10.6084/m9.figshare.30577139.v1
title: Figure 4C-E primary data

description: Figure 4C-E legend. BC3-IFN-βp-tdTomato reporter cells were treated with 20 ng/ml TPA for 48 hours to induce the lytic cycle (“lytic (+TPA)”). Where indicated, the cells were also treated with 10 μM of the pan-caspase inhibitor IDN-6556 (“casp-i”) and/or a cocktail of antibodies against type I IFNs and their receptor (“anti-IFN Abs”) at 1:2000 dilution. Protein lysates were probed for phosphorylated IRF3 (Ser386), total IRF3, phosphorylated TBK1 (Ser172), total TBK1, and β-actin as a loading control. As a positive control for IRF3 and TBK1 activation/phosphorylation, A549 cells were treated with poly(I:C) for 6 and 48 hours before protein lysates were collected. Protein was isolated from treated BC3-IFN-βp-tdTomato reporter cells without sorting (“bulk”), or after sorting the lytic+casp-i sample based on tdTomato expression. Western blot for phosphorylated TBK1 and phosphorylated IRF3 for bulk lytic+casp-i or lytic+casp-i+anti-IFN Abs treated samples and sorted tdTomato+ and tdTomato- samples were quantified by normalizing the density of phosphorylated protein to unphosphorylated protein bands. Phosphorylation levels are plotted relative to the bulk lytic+casp-i or lytic+casp-i+anti-IFN Abs treated samples.
DOI: 10.6084/m9.figshare.31153408
title: Figure 4F-G primary data

description: Fig 4. TBK1 and IRF3 are necessary but not sufficient to direct IFN-β expression, as they are activated even in cells with low IFN-β expression. BC3-IFN-βp-tdTomato reporter cells were treated with 20 ng/ml TPA for 48 hours to induce the lytic cycle (“lytic (+TPA)”). Where indicated, the cells were also treated with 10 μM of the pan-caspase inhibitor IDN-6556 (“casp-i”), 10 μM of the TBK1 inhibitor MRT76307 (“TBK1i”), 10 μM of the cGAS inhibitor G140 (“cGASi”), and/or a cocktail of antibodies against type I IFNs and their receptor (“anti-IFN Abs”) at 1:2000 dilution. Protein lysates were probed for phosphorylated IRF3 (Ser396), and β-actin as a loading control. Protein was isolated from treated BC3-IFN-βp-tdTomato reporter cells without sorting (“bulk”), or after sorting the lytic+casp-i sample based on tdTomato expression. Western blot for phosphorylated IRF3 for bulk lytic+casp-i treated samples and sorted tdTomato+ and tdTomato- samples were quantified by normalizing the density of phosphorylated protein to unphosphorylated protein bands. Phosphorylation levels are plotted relative to the bulk lytic+casp-i or lytic+casp-i+anti-IFN Abs treated samples. Images shown are representative of 3 replicates. One-Way ANOVA followed by Tukey’s post hoc multiple comparisons test.