cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25152167.v1
title: Decoding the structural integrity and multifunctional role of Era protein in the survival of <i>Mycobacterium tuberculosis</i> H<sub>37</sub>Rv

description: Era, a widely known GTP binding protein found in many organisms including prokaryotes and eukaryotes and plays a significant role in many fundamental cellular processes like cell growth, differentiation and signaling. In <i>Mycobacterium tuberculosis</i> (Mtb) H<sub>37</sub>Rv, Era protein had been proved as a GTPase protein but its structural and functional insights are still lacking. Through comparative analysis, structural modeling, docking and using various bioinformatic tools, a detailed investigation of Era was carried out to deduce the structure, function and residues involved in the activity of the protein. Intriguingly, docking results revealed high binding affinity of Era not only with GTP but also with ATP. Myristoylation modifications and phosphorylations on Era were predicted to possibly aid in regulating Era activity and localization; and also the role of Era in translation regulation was foreseen by showing its association with 16s rRNA. Moreover, point mutation of Era residues revealed the effect of W288G and K19G in highly destabilizing the protein structure and activity. Additionally, Era protein was docked with 25 GTPase/ATPase inhibitors, where, Dynasore inhibitor showed the highest affinity for the protein’s GTP binding sites and can be used for further drug trials to inhibit growth of mycobacteria. MtEra protein carries five GTP binding motifs (G1, G2, G3, G4 and G5) and one KH domain for RNA binding.Multifunctional role of MtEra predicted in processes like catabolic, metabolic and ribosome biogenesis.Point mutation analysis showed the importance of tryptophan (W) and lysine (K) residues at position 288 and 19 in stability and activity of the protein, respectively.Dynasore inhibitor showed the highest binding energy of −9 kcal/mol for MtEra. MtEra protein carries five GTP binding motifs (G1, G2, G3, G4 and G5) and one KH domain for RNA binding. Multifunctional role of MtEra predicted in processes like catabolic, metabolic and ribosome biogenesis. Point mutation analysis showed the importance of tryptophan (W) and lysine (K) residues at position 288 and 19 in stability and activity of the protein, respectively. Dynasore inhibitor showed the highest binding energy of −9 kcal/mol for MtEra.
DOI: 10.6084/m9.figshare.25152292
title: Identification of potential regulatory mechanisms and therapeutic targets for lung cancer

description: Lung cancer poses a significant health threat globally, especially in regions like India, with 5-year survival rates remain alarmingly low. Our study aimed to uncover key markers for effective treatment and early detection. We identified specific genes related to lung cancer using the BioXpress database and delved into their roles through DAVID enrichment analysis. By employing network theory, we explored the intricate interactions within lung cancer networks, identifying <i>ASPM</i> and MKI67 as crucial regulator genes. Predictions of microRNA and transcription factor interactions provided additional insights. Examining gene expression patterns using GEPIA and KM Plotter revealed the clinical relevance of these key genes. In our pursuit of targeted therapies, Drug Bank pointed to methotrexate as a potential drug for the identified key regulator genes. Confirming this, molecular docking studies through Swiss Dock showed promising binding interactions. To ensure stability, we conducted molecular dynamics simulations using the AMBER 16 suite. In summary, our study pinpoints <i>ASPM</i> and <i>MKI67</i> as vital regulators in lung cancer networks. The identification of hub genes and functional pathways enhances our understanding of molecular processes, offering potential therapeutic targets. Importantly, methotrexate emerged as a promising drug candidate, supported by robust docking and simulation studies. These findings lay a solid foundation for further experimental validations and hold promise for advancing personalized therapeutic strategies in lung cancer.
DOI: 10.6084/m9.figshare.25152292.v1
title: Identification of potential regulatory mechanisms and therapeutic targets for lung cancer

description: Lung cancer poses a significant health threat globally, especially in regions like India, with 5-year survival rates remain alarmingly low. Our study aimed to uncover key markers for effective treatment and early detection. We identified specific genes related to lung cancer using the BioXpress database and delved into their roles through DAVID enrichment analysis. By employing network theory, we explored the intricate interactions within lung cancer networks, identifying <i>ASPM</i> and MKI67 as crucial regulator genes. Predictions of microRNA and transcription factor interactions provided additional insights. Examining gene expression patterns using GEPIA and KM Plotter revealed the clinical relevance of these key genes. In our pursuit of targeted therapies, Drug Bank pointed to methotrexate as a potential drug for the identified key regulator genes. Confirming this, molecular docking studies through Swiss Dock showed promising binding interactions. To ensure stability, we conducted molecular dynamics simulations using the AMBER 16 suite. In summary, our study pinpoints <i>ASPM</i> and <i>MKI67</i> as vital regulators in lung cancer networks. The identification of hub genes and functional pathways enhances our understanding of molecular processes, offering potential therapeutic targets. Importantly, methotrexate emerged as a promising drug candidate, supported by robust docking and simulation studies. These findings lay a solid foundation for further experimental validations and hold promise for advancing personalized therapeutic strategies in lung cancer.
DOI: 10.15468/dl.skjsdv
title: Occurrence Download

description: A dataset containing 602 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Habenaria linearifolia"
 ]
}

 The dataset includes 602 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032147-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tfhuyx
title: Occurrence Download

description: A dataset containing 56556 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Plethodon cinereus)",
 "Country is one of (Bermuda, Canada, Greenland, Saint Pierre and Miquelon, United States of America)"
 ]
}

 The dataset includes 56556 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032135-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xk3m5d
title: Occurrence Download

description: A dataset containing 272453 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gymnadenia conopsea"
 ]
}

 The dataset includes 272453 records from 1109 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032064-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3aqqkr
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arundo donax",
 "Country is Nicaragua",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032150-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tvt2pj
title: Occurrence Download

description: A dataset containing 23120 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((25.41845 43.43395,62.28041 43.43395,62.28041 67.97940,25.41845 67.97940,25.41845 43.43395))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Erigeron canadensis"
 ]
}

 The dataset includes 23120 records from 180 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032149-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m8etqf
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rumex ruwenzoriensis",
 "HasCoordinate is true",
 "Geometry POLYGON ((-17.66889 -35.11691, 51.34702 -35.11691, 51.34702 37.62, -17.66889 37.62, -17.66889 -35.11691))"
 ]
}

 The dataset includes 27 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032148-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.audydz
title: Occurrence Download

description: A dataset containing 1052 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Palicourea amethystina"
 ]
}

 The dataset includes 1052 records from 70 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032151-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qnz5pz
title: Occurrence Download

description: A dataset containing 1052 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Palicourea amethystina"
 ]
}

 The dataset includes 1052 records from 70 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032152-250717081556266/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.28636028
title: [Artifact Respository] Quantum Program Linting with LLMs: Emerging Results from a Comparative Study

description: This page contains the artifacts of our paper, entitled "Quantum Program Linting with LLMs: Emerging Results from a Comparative Study". In particular, this pape provides the experiment package to increase the reproducibility of our experiments.<b>Datasets</b>In our experiments, we used real-world Qiskit source code files and the annotated dataset from the LintQ repository, which is available at https://github.com/sola-st/LintQ.<b>Files</b>LintQ-LLM.py: A Python script that generates prompts and executes them.results.txt: The results produced by LintQ-LLM in the experiments presented in our paper.<b>LintQ-LLM Usage Instruction</b>Update line 18 in LintQ-LLM.py with a valid OpenAI API key.Create a ./files_selected directory and place Qiskit source code files in it.Run "python LintQ-LLM.py", which will output results.txt<b>License</b>This software is licensed under the Apache License 2.0, which permits use, modification, and distribution under open source terms. However, please be aware of the following: Access to and use of the OpenAI API is governed by OpenAI’s Terms of Use and Usage Policies, which include but are not limited to:Requirements for account registration and a valid API key.Restrictions on prohibited use cases (e.g., illegal, harmful, or misleading content generation).Usage limits, pricing, and billing terms defined by OpenAI.By running this software with OpenAI API integration, you (the user) are responsible for complying with OpenAI’s terms and policies. This project does not provide, include, or distribute access to OpenAI’s services, nor does it accept liability for how those services are used.
DOI: 10.6084/m9.figshare.28636028.v1
title: [Artifact Respository] Quantum Program Linting with LLMs: Emerging Results from a Comparative Study

description: This page contains the artifacts of our paper, entitled "Quantum Program Linting with LLMs: Emerging Results from a Comparative Study". In particular, this pape provides the experiment package to increase the reproducibility of our experiments.<b>Datasets</b>In our experiments, we used real-world Qiskit source code files and the annotated dataset from the LintQ repository, which is available at https://github.com/sola-st/LintQ.<b>Files</b>LintQ-LLM.py: A Python script that generates prompts and executes them.results.txt: The results produced by LintQ-LLM in the experiments presented in our paper.<b>LintQ-LLM Usage Instruction</b>Update line 18 in LintQ-LLM.py with a valid OpenAI API key.Create a ./files_selected directory and place Qiskit source code files in it.Run "python LintQ-LLM.py", which will output results.txt<b>License</b>This software is licensed under the Apache License 2.0, which permits use, modification, and distribution under open source terms. However, please be aware of the following: Access to and use of the OpenAI API is governed by OpenAI’s Terms of Use and Usage Policies, which include but are not limited to:Requirements for account registration and a valid API key.Restrictions on prohibited use cases (e.g., illegal, harmful, or misleading content generation).Usage limits, pricing, and billing terms defined by OpenAI.By running this software with OpenAI API integration, you (the user) are responsible for complying with OpenAI’s terms and policies. This project does not provide, include, or distribute access to OpenAI’s services, nor does it accept liability for how those services are used.
DOI: 10.15468/dl.8ye7t4
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Plethodon cinereus)",
 "Country is one of (American Samoa, Australia, Christmas Island, Cocos (Keeling) Islands, Cook Islands, Fiji, French Polynesia, Guam, Heard Island and McDonald Islands, Kiribati, Marshall Islands, Micronesia (Federated States of), Nauru, New Caledonia, New Zealand, Niue, Norfolk Island, Northern Mariana Islands, Palau, Papua New Guinea, Pitcairn, Samoa, Solomon Islands, Tokelau, Tonga, Tuvalu, United States Minor Outlying Islands, Vanuatu, Wallis and Futuna)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032153-250717081556266/datasets/export for details.
DOI: 10.15468/dl.378bdt
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Plethodon cinereus)",
 "Country is one of (Algeria, Angola, Benin, Botswana, British Indian Ocean Territory, Burkina Faso, Burundi, Cabo Verde, Cameroon, Central African Republic, Chad, Comoros, Congo, Congo, Democratic Republic of the, Côte d’Ivoire, Djibouti, Egypt, Equatorial Guinea, Eritrea, Eswatini, Ethiopia, French Southern Territories, Gabon, Gambia, Ghana, Guinea, Guinea-Bissau, Kenya, Lesotho, Liberia, Libya, Madagascar, Malawi, Mali, Mauritania, Mauritius, Mayotte, Morocco, Mozambique, Namibia, Niger, Nigeria, Réunion, Rwanda, Saint Helena, Ascension and Tristan da Cunha, Sao Tome and Principe, Senegal, Seychelles, Sierra Leone, Somalia, South Africa, South Sudan, Sudan, Tanzania, United Republic of, Togo, Tunisia, Uganda, Western Sahara, Zambia, Zimbabwe)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032155-250717081556266/datasets/export for details.
DOI: 10.15468/dl.uqtmw3
title: Occurrence Download

description: A dataset containing 124 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Echium vulgare",
 "Country is South Africa",
 "HasCoordinate is true"
 ]
}

 The dataset includes 124 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032154-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rqsw8w
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arundo donax",
 "Country is North Macedonia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032156-250717081556266/datasets/export for details.
DOI: 10.15468/dl.8wzbkj
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Serpula lacrymans",
 "Country is Slovenia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032157-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8evd4q
title: Occurrence Download

description: A dataset containing 45 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arundo donax",
 "Country is Pakistan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 45 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032159-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hxeksm
title: Occurrence Download

description: A dataset containing 854 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Habenaria dentata"
 ]
}

 The dataset includes 854 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032160-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh0169596.10fu
title: SH0169596.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15468/dl.jqgbv4
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((74.89763499999999 20.602305, 74.822605 20.596729, 74.749439 20.580139, 74.679951 20.552946, 74.615866 20.515827, 74.558767 20.4697, 74.510063 20.41571, 74.470951 20.355194, 74.442385 20.289647, 74.42505800000001 20.220689, 74.419383 20.150022, 74.425483 20.079385, 74.44319299999999 20.010518, 74.47206300000001 19.945112, 74.511371 19.884774, 74.560142 19.830981, 74.61717400000001 19.785052, 74.68106400000001 19.74811, 74.750247 19.721058, 74.82303 19.704559, 74.89763499999999 19.699014, 74.97224 19.704559, 75.045023 19.721058, 75.114206 19.74811, 75.178096 19.785052, 75.235128 19.830981, 75.28389900000001 19.884774, 75.323207 19.945112, 75.35207699999999 20.010518, 75.369787 20.079385, 75.37588700000001 20.150022, 75.370212 20.220689, 75.352885 20.289647, 75.324319 20.355194, 75.285207 20.41571, 75.236503 20.4697, 75.17940400000001 20.515827, 75.115319 20.552946, 75.04583100000001 20.580139, 74.97266500000001 20.596729, 74.89763499999999 20.602305))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 8 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001358-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh0169597.10fu
title: SH0169597.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0169598.10fu
title: SH0169598.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.