cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15082937
title: tfactivity snp files

description: dbSNP_mm10.bed.gz: file downloaded from https://ftp.ncbi.nih.gov/snp/organisms/archive/mouse_10090/VCF/00-All.vcf.gz and filtered and reformatted

dbSNP_mm19_chr1_1000.bed.gz: same as above but subsetted to the first 1000 entries of chr1

dbSNP_hg38.bed.gz: downloaded from https://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz
DOI: 10.5281/zenodo.15082938
title: tfactivity snp files
DOI: 10.5281/zenodo.15090556
title: tfactivity snp files

description: dbSNP_mm10.bed.gz: file downloaded from https://ftp.ncbi.nih.gov/snp/organisms/archive/mouse_10090/VCF/00-All.vcf.gz and filtered and reformatted

dbSNP_mm19_chr1_1000.bed.gz: same as above but subsetted to the first 1000 entries of chr1

dbSNP_hg38.bed.gz: downloaded from https://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-All.vcf.gz
DOI: 10.15468/dl.autupf
title: Occurrence Download

description: A dataset containing 3684 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "OccurrenceStatus is Present",
 "TaxonKey is Squamata",
 "Year 2001-2020"
 ]
}

 The dataset includes 3684 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002380-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7wzqxh
title: Occurrence Download

description: A dataset containing 44480 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phrygilus patagonicus Lowe, 1923"
 ]
}

 The dataset includes 44480 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052551-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xgqqw2
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Aralia merrillii C.B.Shang, Conocarpus erectus L., Prosopis glandulosa Torr., Prosopis juliflora (Sw.) DC., Leuzea repens (L.) D.J.N.Hind)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Country is one of (Bahrain)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002383-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uwdcu6
title: Occurrence Download

description: A dataset listing the 182 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Sweden",
 "TaxonKey is Leptothecata",
 "Year 1000-2023"
 ]
}

 The dataset's 182 records were derived from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002377-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p849m2
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dromiciops australis F.Philippi, 1893"
 ]
}

 The dataset includes 14 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002381-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4nbrcp
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Hypselotriton yunnanensis (Yang, 1983)"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002384-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34808/bm28-9n17
title: Physicochemical and electrochemical data investigating the properties of electrocatalysts based on borophene and nickel phosphides

description: This dataset contains raw data used in the publication Highly Active and Robust Electrocatalyst Based on Nickel Phosphide Supported by Borophene for Oxygen Evolution Reaction. It includes AFM, Raman, TEM, XPS, XRD, and electrochemical studies. Most of the collected data can be opened using standard tools, while electrochemical data can be accessed with the free EC-Lab software, and XPS results can be viewed in Casa XPS.
DOI: 10.15468/dl.h98c4y
title: Occurrence Download

description: A dataset containing 124 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tympanoctomys barrerae (Lawrence, 1941)"
 ]
}

 The dataset includes 124 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002382-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zdgzaz
title: Occurrence Download

description: A dataset containing 56935 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((11.24503 50.42453,15.11588 50.42453,15.11588 53.03181,11.24503 53.03181,11.24503 50.42453))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Orthoptera",
 "Year 2016-2025"
 ]
}

 The dataset includes 56935 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002376-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14995931
title: Motion of a single particle partially exposed in a simple shear flow

description: The motion of particles over rough surfaces in shear flows is a fundamental problem in fluid mechanics, with applications spanning geophysics, material science, and microfluidics. This study extends Goldman et al.'s theoretical framework for a sphere near a flat surface to rough surfaces, incorporating a correction factor dependent on the effective penetration depth of the fluid flow into the rough substrate. The validity of this approach is assessed through three-dimensional lattice Boltzmann simulations coupled with the discrete element method through momentum exchange. Our results confirm that the theoretical predictions closely match the simulations for particle Reynolds numbers up to two, with deviations increasing at higher particle Reynolds numbers due to inertial effects. We further explore the impact of roughness and friction, demonstrating that surface roughness, defined by the gap distance between substrate spheres, significantly alters hydrodynamic interactions. While friction has a minor influence on the translational velocity, it plays a dominant role in the angular velocity, particularly during particle ascent over roughness-induced hills. A broad range of friction coefficients is covered by the simulations, revealing that deviations from the theory increase as frictional effects become more pronounced. Our findings establish a generalized framework for particle motion over rough surfaces, applicable across various surface geometries and flow conditions.
DOI: 10.5281/zenodo.14995930
title: Motion of a single particle partially exposed in a simple shear flow

description: The motion of particles over rough surfaces in shear flows is a fundamental problem in fluid mechanics, with applications spanning geophysics, material science, and microfluidics. This study extends Goldman et al.'s theoretical framework for a sphere near a flat surface to rough surfaces, incorporating a correction factor dependent on the effective penetration depth of the fluid flow into the rough substrate. The validity of this approach is assessed through three-dimensional lattice Boltzmann simulations coupled with the discrete element method through momentum exchange. Our results confirm that the theoretical predictions closely match the simulations for particle Reynolds numbers up to two, with deviations increasing at higher particle Reynolds numbers due to inertial effects. We further explore the impact of roughness and friction, demonstrating that surface roughness, defined by the gap distance between substrate spheres, significantly alters hydrodynamic interactions. While friction has a minor influence on the translational velocity, it plays a dominant role in the angular velocity, particularly during particle ascent over roughness-induced hills. A broad range of friction coefficients is covered by the simulations, revealing that deviations from the theory increase as frictional effects become more pronounced. Our findings establish a generalized framework for particle motion over rough surfaces, applicable across various surface geometries and flow conditions.
DOI: 10.5281/zenodo.15090017
title: Motion of a single particle partially exposed in a simple shear flow

description: The motion of particles over rough surfaces in shear flows is a fundamental problem in fluid mechanics, with applications spanning geophysics, material science, and microfluidics. This study extends Goldman et al.'s theoretical framework for a sphere near a flat surface to rough surfaces, incorporating a correction factor dependent on the effective penetration depth of the fluid flow into the rough substrate. The validity of this approach is assessed through three-dimensional lattice Boltzmann simulations coupled with the discrete element method through momentum exchange. Our results confirm that the theoretical predictions closely match the simulations for particle Reynolds numbers up to two, with deviations increasing at higher particle Reynolds numbers due to inertial effects. We further explore the impact of roughness and friction, demonstrating that surface roughness, defined by the gap distance between substrate spheres, significantly alters hydrodynamic interactions. While friction has a minor influence on the translational velocity, it plays a dominant role in the angular velocity, particularly during particle ascent over roughness-induced hills. A broad range of friction coefficients is covered by the simulations, revealing that deviations from the theory increase as frictional effects become more pronounced. Our findings establish a generalized framework for particle motion over rough surfaces, applicable across various surface geometries and flow conditions.
DOI: 10.15468/dl.4kbtk9
title: Occurrence Download

description: A dataset containing 327 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Abrus precatorius L., Acacia auriculiformis A.Cunn. ex Benth., Acacia mangium Willd., Aralia merrillii C.B.Shang, Acanthospermum hispidum DC., Achyranthes aspera L., Acrostichum aureum L., Ageratina altissima (L.) R.M.King & H.Rob., Ageratum conyzoides L., Alternanthera ficoidea (L.) R.Br., Alternanthera philoxeroides (Mart.) Griseb., Argemone mexicana L., Arundo donax L., Cajanus scarabaeoides (L.) Thouars, Cardamine flexuosa With., Cestrum diurnum L., Chromolaena odorata (L.) R.M.King & H.Rob., Commelina obliqua Vahl, Convolvulus arvensis L., Croton bonplandianus Baill., Cynodon dactylon (L.) Pers., Cyperus rotundus L., Dalbergia sissoo Roxb. ex DC., Derris trifoliata Lour., Duranta erecta L., Pontederia crassipes Mart., Elaeis guineensis Jacq., Entada rheedei Spreng., Epipremnum pinnatum (L.) Engl., Eucalyptus camaldulensis Denham, Eucalyptus alba Reinw. ex Blume, Falcataria falcata (L.) Greuter & R.Rankin, Heliotropium indicum L., Hygrophila polysperma (Roxb.) T.Anderson, Imperata cylindrica (L.) Raeusch., Ipomoea aquatica Forssk., Ipomoea carnea Jacq., Kalanchoe pinnata (Lam.) Pers., Lantana camara L., Leucaena leucocephala (Lam.) de Wit, Limnocharis flava (L.) Buchenau, Ludwigia adscendens (L.) H.Hara, Malvastrum coromandelianum (L.) Garcke, Mesosphaerum suaveolens (L.) Kuntze, Mikania cordata (Burm.fil.) B.L.Rob., Mikania micrantha Kunth, Mikania scandens (L.) Willd., Mimosa pudica L., Nypa fruticans Wurmb, Opuntia monacantha Haw., Paederia foetida L., Parthenium hysterophorus L., Paspalum distichum L., Persicaria perfoliata (L.) H.Gross, Pistia stratiotes L., Sagittaria sagittifolia L., Salvinia ×molesta D.S.Mitch., Senna occidentalis (L.) Link, Shirakiopsis indica (Willd.) Esser, Syzygium cumini (L.) Skeels, Syzygium samarangense (Blume) Merr. & L.M.Perry, Tamarix indica Willd.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Country is one of (Bangladesh)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 327 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002387-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hxzy2n
title: Occurrence Download

description: A dataset containing 14588 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Switzerland",
 "DatasetKey is Swiss National Mammal Databank",
 "TaxonKey is Cervus elaphus Linnaeus, 1758",
 "Year 2019-2025"
 ]
}

 The dataset includes 14588 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002386-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15090085
title: SpaCross: Deciphering Spatial Domains and Integrating Multiple Slices in Spatially Resolved Transcriptomics

description: Spatially Resolved Transcriptomics (SRT) has revolutionized tissue architecture analysis by integrating gene expression with spatial coordinates. However, existing spatial domain identification methods struggle with unsupervised learning constraints, lack of implicit supervision in latent space, and challenges in balancing local spatial continuity with global semantic consistency, particularly in multi-slice integration. To address these issues, we propose SpaCross, a comprehensive analytical framework for SRT that enhances spatial pattern recognition and cross-slice consistency. SpaCross employs a cross-masked graph autoencoder to reconstruct gene expression features while preserving spatial relationships and mitigating identity mapping issues. A Cross-Masked Latent Consistency module reinforces implicit constraints on latent representations, improving feature robustness. More importantly, an adaptive spatial-semantic graph structure dynamically integrates local and global contextual information, enabling effective multi-slice integration. Extensive evaluations demonstrate that SpaCross outperforms eight state-of-the-art methods on single-slice datasets and achieves robust batch effect correction while preserving biologically meaningful spatial architectures in multi-slice integration. Notably, SpaCross uncovers dynamic spatiotemporal patterns in developing mouse embryos and enables cross-platform integration of mouse olfactory bulb data, detecting shared laminar structures and platform-specific substructures validated by marker gene colocalization. These results highlight its potential to advance spatial transcriptomics analysis in complex tissue systems.
DOI: 10.5281/zenodo.15090086
title: SpaCross: Deciphering Spatial Domains and Integrating Multiple Slices in Spatially Resolved Transcriptomics

description: Spatially Resolved Transcriptomics (SRT) has revolutionized tissue architecture analysis by integrating gene expression with spatial coordinates. However, existing spatial domain identification methods struggle with unsupervised learning constraints, lack of implicit supervision in latent space, and challenges in balancing local spatial continuity with global semantic consistency, particularly in multi-slice integration. To address these issues, we propose SpaCross, a comprehensive analytical framework for SRT that enhances spatial pattern recognition and cross-slice consistency. SpaCross employs a cross-masked graph autoencoder to reconstruct gene expression features while preserving spatial relationships and mitigating identity mapping issues. A Cross-Masked Latent Consistency module reinforces implicit constraints on latent representations, improving feature robustness. More importantly, an adaptive spatial-semantic graph structure dynamically integrates local and global contextual information, enabling effective multi-slice integration. Extensive evaluations demonstrate that SpaCross outperforms eight state-of-the-art methods on single-slice datasets and achieves robust batch effect correction while preserving biologically meaningful spatial architectures in multi-slice integration. Notably, SpaCross uncovers dynamic spatiotemporal patterns in developing mouse embryos and enables cross-platform integration of mouse olfactory bulb data, detecting shared laminar structures and platform-specific substructures validated by marker gene colocalization. These results highlight its potential to advance spatial transcriptomics analysis in complex tissue systems.
DOI: 10.34808/vsnh-4a07
title: Studies on the effect of cellulose on the catalytic activity of nickel phosphide - physicochemical and electrochemical data

description: This dataset contains raw data used in the publication Highly Porous Carbon Flakes Derived from Cellulose and Nickel Phosphide Heterostructure towards Efficient Electrocatalysis of Oxygen Evolution Reaction. It includes AFM, Raman, TEM, XPS, XRD, and electrochemical studies. Most of the collected data can be opened using standard tools, while electrochemical data can be accessed with the free EC-Lab software, and XPS results can be viewed in Casa XPS.
DOI: 10.6084/m9.figshare.25610388
title: Chromosome-scale genome assembly of Phyllanthus emblica L. "Yingyu"

description: Phyllanthus emblica L. is an edible plant with medicinal properties native to the dry-hot valley of Yunnan, China. Here, we report a de novo chromosome-scale genome of P. emblica wild type “Yingyu”. “Yingyu” is an octopoid plant with a total of 104 chromosomes. In total, we assembled and clustered 480 Mb of the genome and constructed 26 pseudochromosomes (haplotypes) of P. emblica wild type “Yingyu” that encompass 97.9% of the genome and demonstrate to have relatively high integrity. We annotated 31,111 genes found in the genome of P. emblica. We screened five different tissues for searching the tissue-specific expression candidate genes. Four unknown function candidate genes were expressed at high levels in the flowers while genes relating to the biosynthesis of gibberellins and cellulose were specifically expressed in the fruits. The ascorbate biosynthesis related genes were screened on P. emblica “Yingyu” genome. The high expression level of two GDP-mannose epimerases and one L-galactono-1,4- lactone dehydrogenases in the fruit may be related to the active of absorbate biosynthesis in the fruit. The chromosome-level genomic data for P. emblica we report will be important for the development of molecular markers to facilitate the selection of superior cultivars for the processing and pharmaceuticals.
DOI: 10.15468/dl.rxuz2x
title: Occurrence Download

description: A dataset containing 7607 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Macaca mulatta (Zimmermann, 1780)"
 ]
}

 The dataset includes 7607 records from 92 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002389-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48597/v9dr-bzem
title: Measurement of Inorganics in air and particle phase at Zarra

description: Measurement of Inorganics in air and particle phase at Zarra
DOI: 10.48597/wdq3-7pga
title: Inorganics in air and particle phase at Zarra

description: Measurement of Inorganics in air and particle phase at Zarra
DOI: 10.48597/3xak-t5th
title: Measurement of Inorganics in air and particle phase at Zarra

description: Measurement of Inorganics in air and particle phase at Zarra
DOI: 10.15468/dl.55d2bf
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Occurrence evidence, Human Observation, Machine Observation)",
 "Continent is South America",
 "DatasetKey is Avistajes de espcies de valor especial en áreas protegidas del noreste de Argentina",
 "Geometry POLYGON((-70.74741 -16.71543,-78.34611 -50.65487,-71.40846 -58.92628,-54.59798 -50.4854,-66.0718 -50.31532,-63.93713 -44.54738,-59.93464 -40.62012,-54.06432 -38.14568,-52.99699 -31.12895,-43.78724 -24.7022,-39.15589 -16.71543,-49.53062 -14.03906,-59.42989 -13.72325,-70.74741 -16.71543))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Cebus apella (Linnaeus, 1758)"
 ]
}

 The dataset includes 44 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002391-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fkz6hx
title: Occurrence Download

description: A dataset containing 128805 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Netherlands",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sorbus aucuparia L.",
 "Year 1880-2025"
 ]
}

 The dataset includes 128805 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002385-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15085638
title: Berenike trench BE24-165 documentation

description: Dokumentacja wytworzona w ramach projektu badawczego finansowanego ze środków Narodowego Centrum Nauki nr 2021/43/D/HS3/00248 pt. Kulturowe, demograficzne i biologiczne profile postrzymskich (IV-VI w. n.e.) mieszkańców portu w Berenike (Egipt), na podstawie nieinwazyjnych, wykopaliskowych i bioarcheologicznych badań dwóch miejskich nekropolii.
DOI: 10.5281/zenodo.15085639
title: Berenike trench BE24-165 documentation

description: Dokumentacja wytworzona w ramach projektu badawczego finansowanego ze środków Narodowego Centrum Nauki nr 2021/43/D/HS3/00248 pt. Kulturowe, demograficzne i biologiczne profile postrzymskich (IV-VI w. n.e.) mieszkańców portu w Berenike (Egipt), na podstawie nieinwazyjnych, wykopaliskowych i bioarcheologicznych badań dwóch miejskich nekropolii.
DOI: 10.15468/dl.9nebzf
title: Occurrence Download

description: A dataset containing 834 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Zaedyus pichiy (Desmarest, 1804)"
 ]
}

 The dataset includes 834 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002392-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.