cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.txvp9v
title: Occurrence Download

description: A dataset containing 1554 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Machine Observation)",
 "Country is Spain",
 "OccurrenceStatus is Present",
 "TaxonKey is Fratercula arctica (Linnaeus, 1758)",
 "Year 2019-2024"
 ]
}

 The dataset includes 1554 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003931-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.adzwr2
title: Occurrence Download

description: A dataset containing 1618 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Machine Observation)",
 "Country is Spain",
 "OccurrenceStatus is Present",
 "TaxonKey is Uria aalge (Pontoppidan, 1763)",
 "Year 2019-2024"
 ]
}

 The dataset includes 1618 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003933-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13382753
title: 2DIR_train_test_data
DOI: 10.15468/dl.n4dnk8
title: Occurrence Download

description: A dataset containing 243 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Pakistan",
 "OccurrenceStatus is Present",
 "TaxonKey is Culex tritaeniorhynchus Giles, 1901"
 ]
}

 The dataset includes 243 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003934-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5519/qd.uvbnh8gw
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (12758 records)
DOI: 10.15468/dl.3nt85z
title: Occurrence Download

description: A dataset containing 1103936 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is DOF/BirdLife Denmark - Observations from DOFbasen",
 "Month is one of (January, March, February, April, May)",
 "Year is 2024"
 ]
}

 The dataset includes 1103936 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003917-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q97gfy
title: Occurrence Download

description: A dataset containing 43471 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Machine Observation)",
 "Country is Spain",
 "OccurrenceStatus is Present",
 "TaxonKey is Charadrius alexandrinus Linnaeus, 1758",
 "Year 2019-2024"
 ]
}

 The dataset includes 43471 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003935-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17172/nomad/2025.02.24-2
title: NOMAD dataset: Kern2023a
DOI: 10.5522/04/28451729
title: Resonant scattering of positronium as a quasi-free electron in collisions with N2 and CO2

description: The present file contains the data supporting the findings of Shipman et al. (2017) [1]. 

Following the observation of the electronlike scattering of positronium (Ps) [2,3] using the positronium beamline at UCL [e.g. 3,5], the total cross sections for Ps + CO2, N2 collisions were measured and observed to display resonant structures in the vicinity of those in the corresponding electron data [4,1]. The measurements for both targets were analyzed by ascribing the energy shifts between the resonance positions for the two projectiles to the energy spent in distorting the Ps atom. The resulting reduced binding energy of Ps was then employed to estimate its Compton profile and used to convolute the electron data before comparing with the Ps measurements. 

The quantitative consistency between the Ps data and the convoluted electron data explains the physical origin of Ps being resonantly scattered like a quasifree electron. Namely, the Ps atom is strongly polarized during the collision with the electron being on average closer to the target and the positron resonantly binding to the resulting temporary negative ion. The findings are in agreement with long-standing theoretical description of the nature of Ps resonances. 

References[1] M. Shipman, S.J. Brawley, L. Sarkadi,and G. Laricchia Phys. Rev. A 95, 032704 (2017). 
[2] S.J. Brawley, S. Armitage, J. Beale, D. Leslie, A. Williams, and G. Laricchia, Science 330, 789 (2010). 
[3] S.J. Brawley, S.E. Fayer, M. Shipman, and G. Laricchia, Phys. Rev. Lett. 115, 223201 (2015). 
[4] S.J. Brawley, A.I. Williams, M. Shipman, and G. Laricchia, Phys. Rev. Lett. 105, 263401 (2010). 
[5] M. Shipman, S. J. Brawley, L. Sarkadi, and G. Laricchia, Eur. Phys. J. D 68, 75 (2014).
DOI: 10.5522/04/28451729.v1
title: Resonant scattering of positronium as a quasi-free electron in collisions with N2 and CO2

description: The present file contains the data supporting the findings of Shipman et al. (2017) [1]. 

Following the observation of the electronlike scattering of positronium (Ps) [2,3] using the positronium beamline at UCL [e.g. 3,5], the total cross sections for Ps + CO2, N2 collisions were measured and observed to display resonant structures in the vicinity of those in the corresponding electron data [4,1]. The measurements for both targets were analyzed by ascribing the energy shifts between the resonance positions for the two projectiles to the energy spent in distorting the Ps atom. The resulting reduced binding energy of Ps was then employed to estimate its Compton profile and used to convolute the electron data before comparing with the Ps measurements. 

The quantitative consistency between the Ps data and the convoluted electron data explains the physical origin of Ps being resonantly scattered like a quasifree electron. Namely, the Ps atom is strongly polarized during the collision with the electron being on average closer to the target and the positron resonantly binding to the resulting temporary negative ion. The findings are in agreement with long-standing theoretical description of the nature of Ps resonances. 

References[1] M. Shipman, S.J. Brawley, L. Sarkadi,and G. Laricchia Phys. Rev. A 95, 032704 (2017). 
[2] S.J. Brawley, S. Armitage, J. Beale, D. Leslie, A. Williams, and G. Laricchia, Science 330, 789 (2010). 
[3] S.J. Brawley, S.E. Fayer, M. Shipman, and G. Laricchia, Phys. Rev. Lett. 115, 223201 (2015). 
[4] S.J. Brawley, A.I. Williams, M. Shipman, and G. Laricchia, Phys. Rev. Lett. 105, 263401 (2010). 
[5] M. Shipman, S. J. Brawley, L. Sarkadi, and G. Laricchia, Eur. Phys. J. D 68, 75 (2014).
DOI: 10.15468/dl.mczk58
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Botany Division, Yale Peabody Museum",
 "Country is Croatia"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003382-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xqzdk4
title: Occurrence Download

description: A dataset containing 242 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is AntWeb",
 "Country is Croatia"
 ]
}

 The dataset includes 242 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003378-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4sy4zc
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Bryophyte herbarium, The Arctic University Museum of Norway (TROM)",
 "Country is Croatia"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003379-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.efakfj
title: Occurrence Download

description: A dataset containing 7033 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((3.43422 43.48255,3.52758 43.48255,3.52758 43.53374,3.43422 43.53374,3.43422 43.48255))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Year 2015-2025"
 ]
}

 The dataset includes 7033 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003380-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wc39mk
title: Occurrence Download

description: A dataset containing 8715 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "DatasetKey is 2021_LPO PACA_7",
 "OccurrenceStatus is Present",
 "TaxonKey is Amphibia",
 "Year 2018-2020"
 ]
}

 The dataset includes 8715 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003385-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ruxxyx
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is University of California Museum of Paleontology",
 "Country is Croatia"
 ]
}

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003386-250221090833381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8yr4fb
title: Occurrence Download

description: A dataset containing 101919 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Herbier du Québec (QUE) - Collection de plantes vasculaires"
 ]
}

 The dataset includes 101919 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003383-250221090833381/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.24917681
title: Apigenin exerts anti-cancer effects in colon cancer by targeting HSP90AA1

description: Apigenin, a flavonoid, has shown early promise in colon cancer (CC); thus, exploring potential mechanisms of Apigenin is obligatory. In this study, shared targets of Apigenin and CC were identified through online tools, which were then subjected to functional enrichment analyses, Gene Ontology and KEGG. Further, the protein-protein interaction network of the shared targets was developed (<i>via</i> STRING). The top targets of Apigenin in CC were identified by molecular docking; further investigated for differential gene and protein expression in CC and their influence on CC patient survival (using TCGA data). Out of 13 hub genes, the top 3 targets (<i>HSP90AA1, MMP9, PTGS2</i>) were selected based on docking score. Their expression was significantly elevated and related to poor overall survival in CC (except <i>PTGS2</i>). Molecular dynamics simulation further validated protein-ligand interactions and divulged HSP90AA1 as the best target of Apigenin in CC. Finally, the anti-cancer effects of Apigenin and its major metabolite, luteolin, were investigated in CC, which is involved in the cytotoxicity of CC cells (COLO-205) by reducing <i>HSP90AA1</i> expression revealed by real-time PCR. Thus, HSP90AA1 was identified as one of the prime targets of Apigenin in CC, and Apigenin could be effective against CC.
DOI: 10.6084/m9.figshare.24917681.v1
title: Apigenin exerts anti-cancer effects in colon cancer by targeting HSP90AA1

description: Apigenin, a flavonoid, has shown early promise in colon cancer (CC); thus, exploring potential mechanisms of Apigenin is obligatory. In this study, shared targets of Apigenin and CC were identified through online tools, which were then subjected to functional enrichment analyses, Gene Ontology and KEGG. Further, the protein-protein interaction network of the shared targets was developed (<i>via</i> STRING). The top targets of Apigenin in CC were identified by molecular docking; further investigated for differential gene and protein expression in CC and their influence on CC patient survival (using TCGA data). Out of 13 hub genes, the top 3 targets (<i>HSP90AA1, MMP9, PTGS2</i>) were selected based on docking score. Their expression was significantly elevated and related to poor overall survival in CC (except <i>PTGS2</i>). Molecular dynamics simulation further validated protein-ligand interactions and divulged HSP90AA1 as the best target of Apigenin in CC. Finally, the anti-cancer effects of Apigenin and its major metabolite, luteolin, were investigated in CC, which is involved in the cytotoxicity of CC cells (COLO-205) by reducing <i>HSP90AA1</i> expression revealed by real-time PCR. Thus, HSP90AA1 was identified as one of the prime targets of Apigenin in CC, and Apigenin could be effective against CC.
DOI: 10.6084/m9.figshare.24942178.v1
title: Genetic variants and haplotype structures of miRNA host genes in cancer and obesity

description: Cancer and obesity are two important public health problems. This study aimed to investigate the role of genetic variants and haplotypes of miRNA host genes in cancer and obesity. Data from the catalog of genome-wide association studies (GWAS) were used to find significant variants (index). Then, 1000-genome phase 3 data were used to find haplotypic variants (proxy) associated with these diseases. The candidate variants and haplotypes were identified from proxy and index variants. Finally, SNP function analysis was performed. All GWAS-significant cancer-associated miRNA host gene variants, including MIR4713HG, MIR663AHG, MIR99AHG and MIR4435-2HG, were also significantly associated with obesity. The rs703764 variant was common between cutaneous melanoma and obesity traits in the European population (P ≤ 5E−8). The rs2414098 variant was associated with endometrial cancer (P ≤ 5E-13), and the rs7173595 variant was associated with waist-hip ratio (P ≤ 5E-13) and new CGGCATCA haplotypic located at MIR4713HG was identified in the European population. In addition, the ATCTTGTT haplotype for rs17041868 in MIR4435-2HG was identified to be associated with obesity traits (waist-hip ratio and BMI) in the European population (P ≤ 5E−8). This study found that rs703764 is a common genetic marker between cancer and obesity. The CGGCATCA haplotype is common between endometrial cancer and waist-hip ratio. Also, ATCTTGTT haplotype is associated with obesity traits. These results indicate that the variants and haplotypes of miRNAs host genes play an important role between cancer and obesity in the European population. It is suggested to investigate the effect of these structures in other populations.
DOI: 10.6084/m9.figshare.24907827
title: Network pharmacology, molecular docking and molecular dynamics simulation of chalcone scaffold-based compounds targeting breast cancer receptors

description: Compounds with a chalcone scaffold-based structure have demonstrated promising anticancer biological activity. However, the molecular interactions between chalcone scaffold-based compounds and breast cancer-associated proteins remain unclear. Through network pharmacology, molecular docking, and molecular dynamics (MD) simulation analyses, compounds with a chalcone scaffold-based structure were evaluated for their interaction with potential breast cancer targets. The compounds were retrieved from the ASINEX database, resulting in 575,302 compounds. A total of 342 compounds with chalcone scaffold-based structures were discovered. From the 342 compounds that was analysed, ten were chosen due to their adherence to Lipinski’s rule, having an appropriate range of lipophilicity (LOGP), and topological polar surface area (TPSA), and absence of any toxicity. Based on target intersection, 50 target genes were found and subjected to protein-protein interaction (PPI), gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Four target genes were found to be involved in the breast cancer pathway. Consequently, molecular docking was utilised to analyse the molecular interactions between the compounds and four target protein receptors. Compound <b>211</b> exhibited the highest binding affinities for the epidermal growth factor receptor (EGFR), fibroblast growth factor receptor 1 (FGFR1), oestrogen receptor (ESR1), and cyclin dependent kinase 6 (CDK6) with values of −8.95 kcal/mol, −8.60 kcal/mol, −10.33 kcal/mol, and −9.90 kcal/mol, respectively. During MD simulation, compound <b>211</b> and its respective proteins were stable, compact, and had minimal flexibility. The findings provide foundations for future studies into the interaction underlying the anti-breast cancer potential of compounds with chalcone-based scaffold structures.
DOI: 10.6084/m9.figshare.24942178
title: Genetic variants and haplotype structures of miRNA host genes in cancer and obesity

description: Cancer and obesity are two important public health problems. This study aimed to investigate the role of genetic variants and haplotypes of miRNA host genes in cancer and obesity. Data from the catalog of genome-wide association studies (GWAS) were used to find significant variants (index). Then, 1000-genome phase 3 data were used to find haplotypic variants (proxy) associated with these diseases. The candidate variants and haplotypes were identified from proxy and index variants. Finally, SNP function analysis was performed. All GWAS-significant cancer-associated miRNA host gene variants, including MIR4713HG, MIR663AHG, MIR99AHG and MIR4435-2HG, were also significantly associated with obesity. The rs703764 variant was common between cutaneous melanoma and obesity traits in the European population (P ≤ 5E−8). The rs2414098 variant was associated with endometrial cancer (P ≤ 5E-13), and the rs7173595 variant was associated with waist-hip ratio (P ≤ 5E-13) and new CGGCATCA haplotypic located at MIR4713HG was identified in the European population. In addition, the ATCTTGTT haplotype for rs17041868 in MIR4435-2HG was identified to be associated with obesity traits (waist-hip ratio and BMI) in the European population (P ≤ 5E−8). This study found that rs703764 is a common genetic marker between cancer and obesity. The CGGCATCA haplotype is common between endometrial cancer and waist-hip ratio. Also, ATCTTGTT haplotype is associated with obesity traits. These results indicate that the variants and haplotypes of miRNAs host genes play an important role between cancer and obesity in the European population. It is suggested to investigate the effect of these structures in other populations.
DOI: 10.6084/m9.figshare.24895259
title: A computational investigation of potential plant-based bioactive compounds against drug-resistant <i>Staphylococcus aureus</i> of multiple target proteins

description: Drug-resistant <i>Staphylococcus aureus</i> (DRSA) poses a significant global health threat, like bacteremia, endocarditis, skin, soft tissue, bone, and joint infections. Nowadays, the resistance against conventional drugs has been a prompt and focused medical concern. The present study aimed to explore the inhibitory potential of plant-based bioactive compounds (PBBCs) against effective target proteins using a computational approach. We retrieved and verified 22 target proteins associated with DRSA and conducted a screening process that involved testing 87 PBBCs. Molecular docking was performed between screened PBBCs and reference drugs with selected target proteins via AutoDock. Subsequently, we filtered the target proteins and top PBBCs based on their binding affinity scores. Furthermore, molecular dynamic simulation was carried out through GROMACS for a duration of 100 ns, and the binding free energy was calculated using the gmx_MMPBSA. The result showed consistent hydrogen bonding interactions among the amino acid residues Ser 149, Arg 151, Thr 165, Thr 216, Glu 239, Ser 240, Ile 14, as well as Asn 18, Gln 19, Lys 45, Thr 46, Tyr 109, with their respective target proteins of the penicillin-binding protein and dihydrofolate reductase complex. Additionally, we assessed the pharmacokinetic properties of screened PBBCs <i>via</i> SwissADME and AdmetSAR. The findings suggest that β-amyrin, oleanolic acid, kaempferol, quercetin, and friedelin have the potential to inhibit the selected target proteins. In future research, both <i>in vitro</i> and <i>in vivo</i>, experiments will be needed to establish these PBBCs as potent antimicrobial drugs for DRSA.
DOI: 10.6084/m9.figshare.24907827.v1
title: Network pharmacology, molecular docking and molecular dynamics simulation of chalcone scaffold-based compounds targeting breast cancer receptors

description: Compounds with a chalcone scaffold-based structure have demonstrated promising anticancer biological activity. However, the molecular interactions between chalcone scaffold-based compounds and breast cancer-associated proteins remain unclear. Through network pharmacology, molecular docking, and molecular dynamics (MD) simulation analyses, compounds with a chalcone scaffold-based structure were evaluated for their interaction with potential breast cancer targets. The compounds were retrieved from the ASINEX database, resulting in 575,302 compounds. A total of 342 compounds with chalcone scaffold-based structures were discovered. From the 342 compounds that was analysed, ten were chosen due to their adherence to Lipinski’s rule, having an appropriate range of lipophilicity (LOGP), and topological polar surface area (TPSA), and absence of any toxicity. Based on target intersection, 50 target genes were found and subjected to protein-protein interaction (PPI), gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Four target genes were found to be involved in the breast cancer pathway. Consequently, molecular docking was utilised to analyse the molecular interactions between the compounds and four target protein receptors. Compound <b>211</b> exhibited the highest binding affinities for the epidermal growth factor receptor (EGFR), fibroblast growth factor receptor 1 (FGFR1), oestrogen receptor (ESR1), and cyclin dependent kinase 6 (CDK6) with values of −8.95 kcal/mol, −8.60 kcal/mol, −10.33 kcal/mol, and −9.90 kcal/mol, respectively. During MD simulation, compound <b>211</b> and its respective proteins were stable, compact, and had minimal flexibility. The findings provide foundations for future studies into the interaction underlying the anti-breast cancer potential of compounds with chalcone-based scaffold structures.