cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.kpjmw8
title: Occurrence Download

description: A dataset containing 27652 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Melampyrum cristatum"
 ]
}

 The dataset includes 27652 records from 443 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031107-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16755946
title: IUPAC names text-mined from patents by SureChEMBL

description: What: This file contains IUPAC names text-mined from patents (US, WIPO, EPO, Chinese, Japanese). 

Who: This file is provided by the SureChEMBL project (https://www.surechembl.org/) under a CC0 license. We are part of the Chemical Biology Services team (https://www.ebi.ac.uk/about/teams/chemical-biology-services/) at EMBL-EBI. Please cite us appropriately if you use this dataset (thanks!).

Format: 

This is a gzipped TSV file with two columns, IUPAC Names and SMILES. The IUPAC Names column may itself contain multiple IUPAC names separated by an exclamation mark (!). Each of these names resolves to the same SMILES and they differ only in casing. They are sorted such that the name with fewer uppercase characters comes first.

Details:

As part of the SureChEMBL text-mining pipeline, we recognise and extract IUPAC names in patents. These are stored in a database at SureChEMBL HQ, and converted to chemical structures which are made available in our downloads. Here we are making available those text-mined IUPAC names, or to be exact, the names after minor corrections (that may involve removing spaces, or fixing parentheses) that enable the name to be interpreted.

How:

We use LeadMine (https://nextmovesoftware.com/leadmine) from NextMove Software to textmine systematic IUPAC names. This incorporates OPSIN (https://www.ebi.ac.uk/opsin/) by Daniel Lowe to resolve IUPAC names to SMILES.

Why:

These names are being made available to support Egon Willighagen's 'One Million IUPAC names' project (https://chem-bla-ics.linkedchemistry.info/2025/03/08/iupac-names.html).
DOI: 10.5281/zenodo.16755947
title: IUPAC names text-mined from patents by SureChEMBL

description: What: This file contains IUPAC names text-mined from patents (US, WIPO, EPO, Chinese, Japanese). 

Who: This file is provided by the SureChEMBL project (https://www.surechembl.org/) under a CC0 license. We are part of the Chemical Biology Services team (https://www.ebi.ac.uk/about/teams/chemical-biology-services/) at EMBL-EBI. Please cite us appropriately if you use this dataset (thanks!).

Format: 

This is a gzipped TSV file with two columns, IUPAC Names and SMILES. The IUPAC Names column may itself contain multiple IUPAC names separated by an exclamation mark (!). Each of these names resolves to the same SMILES and they differ only in casing. They are sorted such that the name with fewer uppercase characters comes first.

Details:

As part of the SureChEMBL text-mining pipeline, we recognise and extract IUPAC names in patents. These are stored in a database at SureChEMBL HQ, and converted to chemical structures which are made available in our downloads. Here we are making available those text-mined IUPAC names, or to be exact, the names after minor corrections (that may involve removing spaces, or fixing parentheses) that enable the name to be interpreted.

How:

We use LeadMine (https://nextmovesoftware.com/leadmine) from NextMove Software to textmine systematic IUPAC names. This incorporates OPSIN (https://www.ebi.ac.uk/opsin/) by Daniel Lowe to resolve IUPAC names to SMILES.

Why:

These names are being made available to support Egon Willighagen's 'One Million IUPAC names' project (https://chem-bla-ics.linkedchemistry.info/2025/03/08/iupac-names.html).
DOI: 10.5281/zenodo.16924563
title: AU-PEMal-2025

description: The AU-PEMal-2025 dataset is created for research purposes, is a malware dataset that was created with proper care. A total of 15,500 benign and 15,500 latest malware samples were collected from VirusTotal, VirusShare, and MalwareBazar and organized into category-wise and family-wise folders. Each sample was run in a dynamic environment to analyze the functionality, and a detailed JavaScript Object Notation (JSON) file was generated against each sample. The sample includes four malware categories (RAT, Ransomware, Info Stealer, and Trojan Horse) and 26 malware families. Details of the malware categories and families as as below:-






Sr. No.



Category



Families



Total Samples





1



Trojan Horse



1.     AgentTesla (337)

2.     Emotet (345)

3.     Guloader (444)

4.     Qbot (320)



1446





2



Info Stealer



1.     Formbook (473)

2.     Raccoon (518)

3.     RedLine (500)

4.     Snake (527)



2018





3



Ransomware



1.     Cerber (332)

2.     DarkSide (335)

3.     Dharma (505)

4.     Gandcrab (382)

5.     LockBit (438)

6.     Maze (290)

7.     Phobos (550)

8.     Ragnar (133)

9.     Revil (347)

10.  Ryuk (449)

11.  Shade (504)

12.  WannaCry (496)



4761





4



RAT



1.     Gh0st (446)

2.     Glupteba (346)

3.     NanoCore (520)

4.     njRat (506)

5.     Remcos (512)

6.     Ursnif (309)



2639





5



Benign



1.     Benign (10839)



10839





 

Selected features in the dataset are selected after a thorough analysis and by applying different techniques. The dataset is validated by training Machine Learning-based as well as Deep Learning-based models.



AU-PEMal-2025-V1 contains original data in categorical form.

AU-PEMal-2025-V2 contains numerical data with only target columns with categorical data.
DOI: 10.5281/zenodo.16924564
title: AU-PEMal-2025

description: The AU-PEMal-2025 dataset is created for research purposes, is a malware dataset that was created with proper care. A total of 15,500 benign and 15,500 latest malware samples were collected from VirusTotal, VirusShare, and MalwareBazar and organized into category-wise and family-wise folders. Each sample was run in a dynamic environment to analyze the functionality, and a detailed JavaScript Object Notation (JSON) file was generated against each sample. The sample includes four malware categories (RAT, Ransomware, Info Stealer, and Trojan Horse) and 26 malware families. Details of the malware categories and families as as below:-






Sr. No.



Category



Families



Total Samples





1



Trojan Horse



1.     AgentTesla (337)

2.     Emotet (345)

3.     Guloader (444)

4.     Qbot (320)



1446





2



Info Stealer



1.     Formbook (473)

2.     Raccoon (518)

3.     RedLine (500)

4.     Snake (527)



2018





3



Ransomware



1.     Cerber (332)

2.     DarkSide (335)

3.     Dharma (505)

4.     Gandcrab (382)

5.     LockBit (438)

6.     Maze (290)

7.     Phobos (550)

8.     Ragnar (133)

9.     Revil (347)

10.  Ryuk (449)

11.  Shade (504)

12.  WannaCry (496)



4761





4



RAT



1.     Gh0st (446)

2.     Glupteba (346)

3.     NanoCore (520)

4.     njRat (506)

5.     Remcos (512)

6.     Ursnif (309)



2639





5



Benign



1.     Benign (10839)



10839





 

Selected features in the dataset are selected after a thorough analysis and by applying different techniques. The dataset is validated by training Machine Learning-based as well as Deep Learning-based models.



AU-PEMal-2025-V1 contains original data in categorical form.

AU-PEMal-2025-V2 contains numerical data with only target columns with categorical data.
DOI: 10.18150/pmlr3b
title: Dataset for All-Optical 3D Blue Phase Photonic Crystal Switch with Photosensitive Dopants

description: Objectives: To evaluate the behavior of Blue Phase liquid crystals when doped with photosensitive dopants.Methods: Several photosensitive dopants were synthesized and added to Blue Phase liquid crystal precursor mixtures. After the Blue Phases were formed, the isomerization of said photosensitive dopants was tested by illuminating the samples switching back and forth at different wavelegths.Results: Two switching modes have been achieved, one where the BP reversibly migrates between two Blue Phase phases, (BPI and BPII, two different cubic crystal systems) while maintaining the monocrystallinity of the whole system. The second mode, again reversible, switches between BPI and isotropic state. None of these modes are related to the regular thermal transitions between liquid crystal phases; switching is triggered by light pulses of different wavelengths.The dataset includes the synthetic procedures and mesomorphic behavior of the new photosensitive dopants.File list: File 1. General synthetic experimentalSynthethic procedures for:(E)-1-(4-Ethoxy-2,6-dimethylphenyl)-2-[4-(hexyloxy)phenyl]diazene (MCF526)Ethyl (E)-4-((4-amino-2,6-dimethylphenyl)diazenyl)benzoate (3) Ethyl (E)-4-((4-cyano-2,6-dimethylphenyl)diazenyl)benzoate (4) (E)-4-((4-Cyano-2,6-dimethylphenyl)diazenyl)benzoate (MCF528) (E)-3,5-difluoro-4-{[4-(hexyloxy)phenyl]diazenyl}phenol (1b) (E)-3,5-Difluoro-4-{[4-(hexyloxy)phenyl]diazenyl}phenyl 4-butoxybenzoate (MCF613)(E)-4-{[4-(Hexyloxy)phenyl]diazenyl}-3,5-dimethylphenyl 4-butoxybenzoate (MCF619)File 2. Mesomorphic behavior of new photosensitive dopantsPhases and phase transition temperatures of new photosensitive dopantsPhotos of characteristic textures obtained on cooling for new photosensitive dopantsThe second heating and cooling DSC runs (10 Kmin-1) for photosensitive dopantsFile 3: UV-Vis spectral data for PDsUV-Vis absorption maxima and corresponding absorption coefficientsUV-Vis absorption coefficients of PDs at the used illumination wavelengths, measured in 1,2-dichloroethane.File 4 - FIGURE 1 - Synthetic pathway for the designed PDs. - relates to File 1.File 5 - FIGURE 2 - Photos of characteristic textures obtained on cooling for new photosensitive dopants - relates to File 2File 6 - FIGURE 3 - Second heating (red) and cooling (blue) DSC runs (10 Kmin-1) for photosensitive dopants: relates File 2
DOI: 10.34740/kaggle/dsv/12833838
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.j9z65q
title: Occurrence Download

description: A dataset containing 628 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Glaucidium sanchezi"
 ]
}

 The dataset includes 628 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031110-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21979/n9/smr703
title: FunQA: Towards Surprising Video Comprehension

description: Surprising videos, e.g., funny clips, creative performances, or visual illusions, attract significant attention. Enjoyment of these videos is not simply a response to visual stimuli; rather, it hinges on the human capacity to understand (and appreciate) commonsense violations depicted in these videos. We introduce FunQA, a challenging video question answering (QA) dataset specifically designed to evaluate and enhance the depth of video reasoning based on counter-intuitive and fun videos. Unlike most video QA benchmarks which focus on less surprising contexts, e.g., cooking or instructional videos, FunQA covers three previously unexplored types of surprising videos: 1) HumorQA , 2) CreativeQA, and 3) MagicQA. For each subset, we establish rigorous QA tasks designed to assess the model's capability in counter-intuitive timestamp localization, detailed video description, and reasoning around counter-intuitiveness. We also pose higher-level tasks, such as attributing a fitting and vivid title to the video, and scoring the video creativity. In total, the FunQA benchmark consists of 312K free-text QA pairs derived from 4.3K video clips, spanning a total of 24 video hours. Extensive experiments with existing VideoQA models reveal significant performance gaps for the FunQA videos across spatial-temporal reasoning, visual-centered reasoning, and free-text generation.
DOI: 10.15468/dl.4ayc3h
title: Occurrence Download

description: A dataset containing 42058 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Columba livia",
 "Country is Peru",
 "HasCoordinate is true"
 ]
}

 The dataset includes 42058 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031109-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xcumw6
title: Occurrence Download

description: A dataset containing 57842 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Paralichthys lethostigma",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 57842 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031092-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.svmmjs
title: Occurrence Download

description: A dataset containing 323 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Columba livia",
 "Country is Seychelles",
 "HasCoordinate is true"
 ]
}

 The dataset includes 323 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031113-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17172/nomad/2025.08.22-1
title: NOMAD dataset: CsTiO
DOI: 10.15468/dl.ufywng
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coregonus artedi",
 "Country is China",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031117-250811113504898/datasets/export for details.
DOI: 10.15468/dl.euxxpu
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Columba livia",
 "Country is South Sudan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 14 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031119-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tyynrn
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Gekko hulk"
 ]
}

 The dataset includes 30 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031120-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p4b4df
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Nepal",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Viruses"
 ]
}

 The dataset includes 33 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031116-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pf8zba
title: Occurrence Download

description: A dataset containing 6715 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coregonus artedi",
 "Country is United States of America",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6715 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031118-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vydcqq
title: Occurrence Download

description: A dataset containing 87661 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "TaxonKey is Oxalis pes-caprae",
 "Year 1950-2025",
 "HasCoordinate is true"
 ]
}

 The dataset includes 87661 records from 131 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031081-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15826759
title: DATA: Comparison of Amorphous and Crystalline Ni-MOFs for Environmental Applications

description: Dataset contains data related to Amorphous and Crystalline Ni-MOFs . Dataset consists of spredsheets in csv format and XRD data.
description: Both amorphous (Ni-MOF-A) and crystalline (Ni-MOF-C) Ni-MOFs were synthesized via a one-pot method at RT. For the preparation of Ni-MOF-A, 4.00 mmol of nickel(II) nitrate hexahydrate was dissolved in 50 mL of methanol, and 8.00 mmol of 2-MIM was dissolved in a separate 50 mL of methanol. The two solutions were stirred individually and then combined by pouring the nickel solution into the ligand solution under continuous stirring. The mixture was stirred for 24 h at RT. The resulting precipitate was collected by centrifugation, washed several times with methanol, and dried in an oven at 80 °C overnight.

Ni-MOF-C was prepared using the same molar amounts of precursors, but with a reduced total solvent volume of 15 mL. Specifically, 4.00 mmol of nickel salt and 8.00 mmol of 2-MIM were each dissolved in 7.5 mL of methanol. After mixing under identical conditions, the resulting precipitate was washed several times with acetone and dried as described above.
description: The authors acknowledge the assistance provided by the Advanced Multiscale Materials for Key Enabling Technologies project (AMULET), supported by the Ministry of Education, Youth, and Sports of the Czech Republic. Project No. CZ.02.01.01/00/22_008/0004558, Co-funded by the European Union and by the Czech Science Foundation (GAČR) under project no. 23-05197S.
DOI: 10.5281/zenodo.15826760
title: DATA: Comparison of Amorphous and Crystalline Ni-MOFs for Environmental Applications

description: Dataset contains data related to Amorphous and Crystalline Ni-MOFs . Dataset consists of spredsheets in csv format and XRD data.
description: Both amorphous (Ni-MOF-A) and crystalline (Ni-MOF-C) Ni-MOFs were synthesized via a one-pot method at RT. For the preparation of Ni-MOF-A, 4.00 mmol of nickel(II) nitrate hexahydrate was dissolved in 50 mL of methanol, and 8.00 mmol of 2-MIM was dissolved in a separate 50 mL of methanol. The two solutions were stirred individually and then combined by pouring the nickel solution into the ligand solution under continuous stirring. The mixture was stirred for 24 h at RT. The resulting precipitate was collected by centrifugation, washed several times with methanol, and dried in an oven at 80 °C overnight.

Ni-MOF-C was prepared using the same molar amounts of precursors, but with a reduced total solvent volume of 15 mL. Specifically, 4.00 mmol of nickel salt and 8.00 mmol of 2-MIM were each dissolved in 7.5 mL of methanol. After mixing under identical conditions, the resulting precipitate was washed several times with acetone and dried as described above.
description: The authors acknowledge the assistance provided by the Advanced Multiscale Materials for Key Enabling Technologies project (AMULET), supported by the Ministry of Education, Youth, and Sports of the Czech Republic. Project No. CZ.02.01.01/00/22_008/0004558, Co-funded by the European Union and by the Czech Science Foundation (GAČR) under project no. 23-05197S.
DOI: 10.15468/dl.jnex9g
title: Occurrence Download

description: A dataset containing 98032 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ciconia nigra)",
 "Year is one of (2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023, 2024)",
 "DecimalLatitude is greater than or equal to 44.95782311925129",
 "DecimalLatitude is less than or equal to 58.30331634439415",
 "DecimalLongitude is greater than or equal to -10.001896207643075",
 "DecimalLongitude is less than or equal to 30.31691447027875",
 "Year is not null",
 "HasCoordinate is TRUE",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is FALSE"
 ]
}

 The dataset includes 98032 records from 527 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031099-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15151/esrf-es-2228385958
title: To study the functional mechanism of AAA+ metalloprotease from Aquifex aeolicus

description: AAA+ (ATPases Associated with diverse cellular Activities) proteins undergo complex conformational changes driven by ATP binding and hydrolysis. Cryo-electron microscopy (cryo-EM), combined with nucleotide analogues such as ATPγS, ADP, or AMP-PNP, allows the capture of these dynamic proteins in distinct mechanochemical states. By comparing these snapshots, cryo-EM provides mechanistic insight into how nucleotide state coordinates structural transitions, substrate engagement, and force generation, shedding light on the core principles of AAA+ protein function. We have chosen the AAA+ protein from Aquifex aeolicus. Furthermore we would like to study the structure of this protein with a nanobody to stabilize the flexibility observed in the ATPase part of the protein.
DOI: 10.15151/esrf-es-2228429625
title: E9A20D4

description: Vaccine polymerase
DOI: 10.6084/m9.figshare.28927964.v3
title: Bioinformatics analyses of lignin peroxidases from the smoky bracket fungi <i>Bjerkandera adusta</i> for endocrine disrupting chemical bioremediation

description: Lignin peroxidases (LiP; EC 1.11.1.14) are important oxidative enzymes involved in lignin biodegradation, a key constituent of plant cell walls. Despite their environmental and industrial potential, fungal LiPs are difficult to express and purify. <i>Bjerkandera adusta</i> is a white-rot fungus that secretes LiPs, the three-dimensional structure of which remains unknown. In this study, two LiPs from <i>B. adusta</i> were subjected to various bioinformatics tools to determine their physio-chemical, structural, and functional properties. Their 3D structure was modeled and molecular dynamic simulations were performed to assess their binding to endocrine disrupting chemicals (EDCs). Moreover, molecular docking analysis revealed that among the model lignin compounds, the dimer guaiacyl 4-O-5 guaiacyl exhibited the lowest binding energy with the EDC ligands, estrone (E1) and bisphenol A showing the strongest binding affinity for LiP 588479560 and LiP 444058, respectively. Molecular dynamics simulations further confirmed the stability of these complexes, with bisphenol A exhibiting particularly high stability as indicated by its low RMSD (≤2 Å) and favorable RoG values, reflecting a strong fit within the enzyme’s active site. Additionally, the binding free energy calculations showed the substrate dimer had the most favorable binding energy, driven primarily by Van der Waals and lipophilic interactions, suggesting its intrinsic compatibility with <i>B. adusta</i> LiPs. This in silico characterization advances the understanding of LiP structure-function relationships and bioremediation potential. <i>B. adusta</i> LiPs demonstrate promising capacity to target persistent EDCs, offering solutions for environmental pollution mitigation.