cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/xzz-lzw-a44
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/yrk-bwe-1wh
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/25s-w2m-mhr
title: Hanzawaia boueana (d'Orbigny, 1846)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3qx-8bb-jdm
title: Heterostegina depressa d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/shp-ybp-evb
title: †Catapsydrax dissimilis (Cushman & Bermúdez, 1937)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/f33-53p-jz2
title: †Cyprideis (Cyprideis) Jones, 1856

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mx8-mkr-jtb
title: Bos taurus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/569-rd1-d0p
title: Cnidaria

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8nx-mp6-as5
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.5mr9b6
title: Occurrence Download

description: A dataset containing 84 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Harrimanella stelleriana (Pall.) Coville",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is Japan"
 ]
}

 The dataset includes 84 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002121-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15294454
title: Ontology-based Testing Data Set

description: The ZIP file comprises all files (except ACTS) required for reevaluating the Ontology Browser in combination with the combinatorial testing tool ACTS. In particular, it contains three ontologies used in several research publications, the testing results obtained, and a spreadsheet summarizing the results.

experiment_results.xlsx ... An EXCEL file comprising the experimental results obtainedOntologyBrowser-1.4     ... Ontology browser

+ 3 subdirectories comprising the ontologies and their corresponding information

SUBDIRECTORIES:

Each subdirectory comprises a doc.txt file containing the ACTS tool's output for generating test cases. The CSV files contain the generated test cases in comma-separated-value format of the given strength, ranging from 2 to 4 or 6. The *.txt file comprises the test input model, and the *.json file the ontology that can be loaded into the browser.

Experimental setup:

We conducted the experimental evaluation using an Apple MacBook Pro M1, 16 GB RAM, macOS 15.4, the presented tool for ontology development, and ACTS in version 2.8. During the experiment, the computer ran other software like a Web browser, an email client, etc. For running ACTS, we used the following prompt in the command line shell:

java -Doutput=csv -Ddoi=<k>    -jar <path_to>/acts_cmd_v2_r2.8.jar cmd    <input_model> <output_file>

In this prompt, we set the strength \verb+<k>+, give the path to the ACTS tool \verb+<path_to>+, specify the input model \verb+<input_model>+, and the file to store the test suite \verb+<output_file>+. We used the ontology browser to generate the input model for the ACTS tool and carried out the experiments manually using the given command in a shell.
DOI: 10.5281/zenodo.15294455
title: Ontology-based Testing Data Set

description: The ZIP file comprises all files (except ACTS) required for reevaluating the Ontology Browser in combination with the combinatorial testing tool ACTS. In particular, it contains three ontologies used in several research publications, the testing results obtained, and a spreadsheet summarizing the results.

experiment_results.xlsx ... An EXCEL file comprising the experimental results obtainedOntologyBrowser-1.4     ... Ontology browser

+ 3 subdirectories comprising the ontologies and their corresponding information

SUBDIRECTORIES:

Each subdirectory comprises a doc.txt file containing the ACTS tool's output for generating test cases. The CSV files contain the generated test cases in comma-separated-value format of the given strength, ranging from 2 to 4 or 6. The *.txt file comprises the test input model, and the *.json file the ontology that can be loaded into the browser.

Experimental setup:

We conducted the experimental evaluation using an Apple MacBook Pro M1, 16 GB RAM, macOS 15.4, the presented tool for ontology development, and ACTS in version 2.8. During the experiment, the computer ran other software like a Web browser, an email client, etc. For running ACTS, we used the following prompt in the command line shell:

java -Doutput=csv -Ddoi=<k>    -jar <path_to>/acts_cmd_v2_r2.8.jar cmd    <input_model> <output_file>

In this prompt, we set the strength \verb+<k>+, give the path to the ACTS tool \verb+<path_to>+, specify the input model \verb+<input_model>+, and the file to store the test suite \verb+<output_file>+. We used the ontology browser to generate the input model for the ACTS tool and carried out the experiments manually using the given command in a shell.
DOI: 10.5281/zenodo.15412142
title: TABLE 1 in The Complete Mitochondrial Genome of the American Palm Cixiid, Haplaxius crudus (Hemiptera: Cixiidae)

description: TABLE 1: Insect taxa used in the phylogenetic analysis based on the entire mitochondrial genome.
SpeciesFamilyOrderGenBank accession no.Nilaparvata lugensDelphacidaeHemipteraNC021748Aphis aurantiiAphidaeHemipteraMN397939Dolycoris baccarumPentatomidaeHemipteraNC020373Magicicada tredecassiniCicadidaeHemipteraNC041654Sitophilus oryzaeCurculionidaeColeopteraKX373615Chauliognathus opacusCantharidaeColeopteraNC013576Nannophya pygmaeaLibellulidaeOdonataNC039410Drosophila melanogasterDrosophilidaeDipteraU37541
description: Published as part of Komondy, Lidia, Huguet-Tapia, Jose, Ascunce, Marina S., Helmick, Ericka E., Goss, Erica M. & Bahder, Brian W., 2021, The Complete Mitochondrial Genome of the American Palm Cixiid, Haplaxius crudus (Hemiptera: Cixiidae), pp. 3 in Psyche: A Journal of Entomology (6625462) 2021 on page 3, DOI: 10.1155/2021/6625462, http://zenodo.org/record/15391578
DOI: 10.5281/zenodo.15412141
title: TABLE 1 in The Complete Mitochondrial Genome of the American Palm Cixiid, Haplaxius crudus (Hemiptera: Cixiidae)

description: TABLE 1: Insect taxa used in the phylogenetic analysis based on the entire mitochondrial genome.
SpeciesFamilyOrderGenBank accession no.Nilaparvata lugensDelphacidaeHemipteraNC021748Aphis aurantiiAphidaeHemipteraMN397939Dolycoris baccarumPentatomidaeHemipteraNC020373Magicicada tredecassiniCicadidaeHemipteraNC041654Sitophilus oryzaeCurculionidaeColeopteraKX373615Chauliognathus opacusCantharidaeColeopteraNC013576Nannophya pygmaeaLibellulidaeOdonataNC039410Drosophila melanogasterDrosophilidaeDipteraU37541
description: Published as part of Komondy, Lidia, Huguet-Tapia, Jose, Ascunce, Marina S., Helmick, Ericka E., Goss, Erica M. & Bahder, Brian W., 2021, The Complete Mitochondrial Genome of the American Palm Cixiid, Haplaxius crudus (Hemiptera: Cixiidae), pp. 3 in Psyche: A Journal of Entomology (6625462) 2021 on page 3, DOI: 10.1155/2021/6625462, http://zenodo.org/record/15391578
DOI: 10.5281/zenodo.15412145
title: TABLE 2 in The Complete Mitochondrial Genome of the American Palm Cixiid, Haplaxius crudus (Hemiptera: Cixiidae)

description: TABLE 2: Annotation of the mitochondrial genome of Haplaxius crudus.
GeneStrandStartEndSizeIntergenic NtStartStopAnticodontRNA-Ile+163640——GATtRNA-Gln−1296070−5——TTGtRNA-Met+12619367−3——CATnad2+19311589650ATTTAA—tRNA-Trp+1156121963−3——TCAtRNA-Cys−1269120961−11——GCAtRNA-Tyr−1329126961−1——GTAcox1+133428721578−5ATTTAA—tRNA-Leu+2867293266−6——TAAcox2+293236016690ATGTAA—tRNA-Lys+3595366773−69——CTTtRNA-Asp+3666371564−2——GTCatp8+3729382496−13ATGTAA—atp6+38234474651−1ATATAA—cox3+44765258782−2ATTTAA—tRNA-Gly+5258531962−3——TCCnad3+531956703510ATATAA—tRNA-Ala+5670572960−1——TGCtRNA-Arg+57395801639——TCGtRNA-Asn+5798586164−4——GTTtRNA-Ser+5857592670−5——GCTtRNA-Glu+59275987610——TTCtRNA-Phe−6050598764−1——GAAnad5−7717605711546ATATAC—tRNA-His−779777336515——GTGnad4−911477771679−21ATTTAA—nad4L−94559105351−10ATTTAA—tRNA- Th r+9383944462−278——TGTtRNA-Pro−9510944368−12——TGGnad6+950310042540−43ATTTAA—Cytb+10008111321125−37ATGTAG—tRNA-Ser+111311119262−52——TGAnad1−1212311143981−50ATGTAA—tRNA-Leu−1218812124650——TAGrRNA-16S−1341012670122214———tRNA-Val−134491338268−402——TACrRNA-12S−1419013445746−5———Control regionN/A147201584811290———
Protein-coding genes � italicized.
description: Published as part of Komondy, Lidia, Huguet-Tapia, Jose, Ascunce, Marina S., Helmick, Ericka E., Goss, Erica M. & Bahder, Brian W., 2021, The Complete Mitochondrial Genome of the American Palm Cixiid, Haplaxius crudus (Hemiptera: Cixiidae), pp. 5 in Psyche: A Journal of Entomology (6625462) 2021 on page 5, DOI: 10.1155/2021/6625462, http://zenodo.org/record/15391578
DOI: 10.5281/zenodo.15412147
title: TABLE 3 in The Complete Mitochondrial Genome of the American Palm Cixiid, Haplaxius crudus (Hemiptera: Cixiidae)

description: TABLE 3: Pairwise comparison of the entire mitochondrial genome of various insect taxa relative to Haplaxius crudus representing percent difference in sequence homology.
1234567891H. crudus—0.40.40.30.40.50.40.40.32N. lugens28.7—0.30.30.40.50.50.40.43A. aurantii30.732.6—0.40.30.40.50.40.34D. baccarum32.235.033.1—0.40.40.40.40.55M. tredecassini33.034.831.832.0—0.30.40.40.36S. oryzae32.734.231.431.932.0—0.40.40.47C. opacus30.733.529.831.030.927.7—0.50.48N. pygmaea32.535.031.930.931.829.729.0—0.49D. melanogaster31.033.729.029.029.026.725.624.5—
description: Published as part of Komondy, Lidia, Huguet-Tapia, Jose, Ascunce, Marina S., Helmick, Ericka E., Goss, Erica M. & Bahder, Brian W., 2021, The Complete Mitochondrial Genome of the American Palm Cixiid, Haplaxius crudus (Hemiptera: Cixiidae), pp. 7 in Psyche: A Journal of Entomology (6625462) 2021 on page 7, DOI: 10.1155/2021/6625462, http://zenodo.org/record/15391578
DOI: 10.15468/dl.39xwd4
title: Occurrence Download

description: A dataset containing 8510 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Quercus shumardii Buckley"
 ]
}

 The dataset includes 8510 records from 189 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030780-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25430/researchdata.cab.unipd.it.00001564
title: Nuclear trafficking of Anelloviridae capsid protein ORF1 reflects modular evolution of subcellular targeting signals

description: This folder contain original Gel Mobility Shift Assays original gels, quantification of Fluorecense Polarization Assays, and single cell data analysis from Confocal Laser Scanning Microscopy.
DOI: 10.15468/dl.2as3nh
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Haplorhus peruviana Engl."
 ]
}

 The dataset's 1 records were derived from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030803-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8vr2ur
title: Occurrence Download

description: A dataset containing 1282 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cavanillesia platanifolia (Humb. & Bonpl.) Kunth"
 ]
}

 The dataset includes 1282 records from 82 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030781-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7274/28792613
title: Scientific Machine Learning for Spatiotemporal Dynamics: Modeling and Control

description: Spatiotemporal dynamics, often governed by partial differential equations (PDEs), underpin many physical processes critical to scientific discovery and engineering innovation. Traditionally, numerical solvers and linearization-based control methods have been widely adopted. However, these first-principle approaches become challenging when (a) the underlying physics is not fully understood, making model construction difficult, or (b) the governing equations are highly nonlinear or stiff, leading to excessive computational costs or ineffective control performance. Deep learning offers a promising alternative, adept at tackling high-dimensional, nonlinear systems through data-driven approaches. However, its reliance on vast datasets, intensive training demands, and poor generalization to unseen scenarios limit its practical utility for modeling and controlling spatiotemporal dynamics.

This dissertation introduces novel deep learning frameworks to address these limitations. First, it enhances deep reinforcement learning efficiency via (a) large-scale asynchronous parallel training and (b) leveraging physics-informed neural networks as surrogate environments. Second, it proposes two innovative architectures that embed physical principles into deep neural networks, improving generalizability and data efficiency for deterministic spatiotemporal dynamics modeling. Finally, it develops a generative approach based on diffusion models to capture stochastic dynamics, such as turbulence. These advancements collectively enable accurate, efficient, and scalable solutions, bridging the gap between data-driven methods and physics-based algorithms for modeling and controlling spatiotemporal dynamics.
DOI: 10.7274/28792613.v1
title: Scientific Machine Learning for Spatiotemporal Dynamics: Modeling and Control

description: Spatiotemporal dynamics, often governed by partial differential equations (PDEs), underpin many physical processes critical to scientific discovery and engineering innovation. Traditionally, numerical solvers and linearization-based control methods have been widely adopted. However, these first-principle approaches become challenging when (a) the underlying physics is not fully understood, making model construction difficult, or (b) the governing equations are highly nonlinear or stiff, leading to excessive computational costs or ineffective control performance. Deep learning offers a promising alternative, adept at tackling high-dimensional, nonlinear systems through data-driven approaches. However, its reliance on vast datasets, intensive training demands, and poor generalization to unseen scenarios limit its practical utility for modeling and controlling spatiotemporal dynamics.

This dissertation introduces novel deep learning frameworks to address these limitations. First, it enhances deep reinforcement learning efficiency via (a) large-scale asynchronous parallel training and (b) leveraging physics-informed neural networks as surrogate environments. Second, it proposes two innovative architectures that embed physical principles into deep neural networks, improving generalizability and data efficiency for deterministic spatiotemporal dynamics modeling. Finally, it develops a generative approach based on diffusion models to capture stochastic dynamics, such as turbulence. These advancements collectively enable accurate, efficient, and scalable solutions, bridging the gap between data-driven methods and physics-based algorithms for modeling and controlling spatiotemporal dynamics.
DOI: 10.15468/dl.avww9s
title: Occurrence Download

description: A dataset containing 85 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Miconia sastrei"
 ]
}

 The dataset includes 85 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032754-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4wa7aw
title: Occurrence Download

description: A dataset containing 950876 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Senecio glomeratus, Senecio linearifolius, Senecio sylvaticus, Taraxacum erythrospermum, Tragopogon lamottei, Tragopogon porrifolius, Volutaria tubuliflora, Campanula cervicaria, Campanula medium, Nymphoides cristata, Anchusa arvensis, Anchusa azurea, Anchusa officinalis, Buglossoides arvensis, Echium candicans, Myosotis latifolia, Myosotis sylvatica, Alyssum corsicum, Odontarrhena, Aurinia saxatilis, Barbarea verna, Cardamine impatiens, Carrichtera annua, Coincya monensis, Conringia orientalis, Coronopus didymus, Hirschfeldia incana, Draba verna, Iberis amara, Lepidium chalepensis, Lepidium heterophyllum, Lepidium perfoliatum, Lepidium ruderale, Lobularia maritima, Microthlaspi perfoliatum, Nasturtium microphyllum, Sinapis alba, Thlaspi alliaceum, Thlaspi arvense, Reseda alba, Conicosia pugioniformis, Malephora crocea, Tetragonia tetragonioides, Corispermum nitidum, Halogeton glomeratus, Kochia scoparia, Salsola collina, Salsola paulsenii, Salsola ryanii, Salsola soda)",
 "BasisOfRecord is one of (Machine Observation, Human Observation, Observation)",
 "HasCoordinate is true",
 "Year is greater than or equal to 1990"
 ]
}

 The dataset includes 950876 records from 2411 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032719-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3wrh3e
title: Occurrence Download

description: A dataset containing 25870 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ailanthus altissima (Mill.) Swingle)",
 "BasisOfRecord is one of (Observation, Human Observation, Material sample, Specimen, Unknown evidence, Machine Observation, Occurrence evidence)",
 "Year is greater than or equal to 1971",
 "Year is less than or equal to 2010",
 "HasCoordinate is true"
 ]
}

 The dataset includes 25870 records from 474 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003271-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5jwshn
title: Occurrence Download

description: A dataset containing 164709 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Quercus rubra L.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 164709 records from 1034 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003263-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tkvyqu
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Human Observation, Material sample, Material citation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Channa melasoma (Bleeker, 1851)"
 ]
}

 The dataset includes 49 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003273-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.69ftg6
title: Occurrence Download

description: A dataset containing 955 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Zanthoxylum acanthopodium DC."
 ]
}

 The dataset includes 955 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003275-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7266/n7862dd2
title: Dataset for: Competitive Adsorption Between PEO-Containing Block Copolymers and Homopolymers at Silica
DOI: 10.15468/dl.mm3yne
title: Occurrence Download

description: A dataset containing 13539 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Quercus serrata Murray)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 13539 records from 146 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003276-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13363823
title: An Online Paleoclimate Data Assimilation with a Deep Learning-based Network

description: OnlinePDA_zenodo.rar (files compressed with RAR compression) includes:

1. Directory 'Code' contains the LIM.m and NET.m for the examination of predictive skills of the surrogate models; the Exp_LIM.m and Exp_NET.m for the reconstruction of SAT during the preindustrial period (851-1850 CE) and the instrumental period(1880-2000CE), for both pseudoproxy experiments and real proxy experiments; 

2. Directory 'Data' contains the necessary data in the model, prior, proxy, and obs directory used to perform the resconstruction. e.g. surrogate models, prior samples, pseudoproxy and real proxy, and instrumental data; Figure*.m and CERMSE*.mat provide the necessary code and data for plotting Figures 3-10
DOI: 10.5281/zenodo.15532124
title: An Online Paleoclimate Data Assimilation with a Deep Learning-based Network

description: OnlinePDA_zenodo.rar (files compressed with RAR compression) includes:

1. Directory 'Code' contains the LIM.m and NET.m for the examination of predictive skills of the surrogate models; the Exp_LIM.m and Exp_NET.m for the reconstruction of SAT during the preindustrial period (851-1850 CE) and the instrumental period(1880-2000CE), for both pseudoproxy experiments and real proxy experiments; 

2. Directory 'Data' contains the necessary data in the model, prior, proxy, and obs directory used to perform the resconstruction. e.g. surrogate models, prior samples, pseudoproxy and real proxy, and instrumental data; Figure*.m and CERMSE*.mat provide the necessary code and data for plotting Figures 3-10
DOI: 10.5281/zenodo.17618011
title: Climate projections and renewable energy UKESM1-0-LL SSP370 China
DOI: 10.25345/c56h4d40t
title: MassIVE MSV000099920 - Single-Islet Proteomics Maps Pseudo-Temporal Islet Immune Responses and Dysfunction in Stage 1 Type 1 Diabetes
title: Global proteomic profiling of LMD-isolated single islet sections from matched non-diabetic and stage 1 type 1 diabetic donors (n=3). Samples were processed using a nanoPOTS-based proteomics workflow. Peptides were identified using FragPipe.
DOI: 10.15468/dl.tmknv7
title: Occurrence Download

description: A dataset containing 81 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((-113.5188 29.69913, -113.3688 29.69913, -113.3688 29.84913, -113.5188 29.84913, -113.5188 29.69913))"
 ]
}

 The dataset includes 81 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036999-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.