cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24190852
title: Lead identification against <i>Mycobacterium tuberculosis</i> using highly enriched active molecules against pantothenate synthetase

description: The Pantothenate synthetase (PS) from the <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) holds a crucial role in the survival and robust proliferation of bacteria through its catalysis of coenzyme A and acyl carrier protein synthesis. The present study undertook the PS drug target in complex with a co-crystallized ligand and subjected it to docking and virtual screening approaches. The experimental design encompassed three discrete datasets: an active dataset featuring 136 compounds, an inactive dataset comprising 56 compounds, and a decoys dataset curated from the zinc library, comprising an extensive compilation of approximately 53,000 compounds. The compounds’ binding energies were observed to be in the range of −5 to ∼−14 kcal/mol. Additionally, binding energy results were further refined through Enrichment Factor analysis (EF). EF is a new statistical approach which uses the scores obtained from docking-based virtual screening and predicts the precision of the scoring function. Remarkably, the Enrichment Factor (EF) analysis produced exceptionally favorable outcomes, attaining an EF of approximately 49% within the uppermost 1% fraction of the compound distribution. Finally, a total of eight compounds, evenly distributed between the active dataset and the decoys dataset, emerged as potent inhibitors of the Pantothenate synthetase (PS) enzyme. The analysis of inhibition constants and binding energy revealed a notable correlation, with an r-squared value (<i>r</i><sup>2</sup>) of 0.912 between the two parameters. Furthermore, the shortlisted compounds were subjected to 100 ns MD simulation to determine their stability and dynamics behavior. The decoy compounds that have been identified, exhibiting properties comparable to the active compounds, are postulated as potential candidates for targeting the Pantothenate synthetase (PS) enzyme to treat <i>Mtb</i> infection. Nevertheless, in the pursuit of a comprehensive investigation, it is advisable to undertake additional experimental validation as a component of the subsequent study. Communicated by Ramaswamy H. Sarma.
DOI: 10.6084/m9.figshare.24204398
title: Genetic polymorphisms in Nrf2 and FoxO1: implications for antioxidant enzyme activity in diabetes

description: In diabetes, persistent hyperglycemia generates excess reactive oxygen species (ROS), leading to oxidative stress (OS). In response to OS, transcription factors (TFs) Nrf2 and FoxO1 get activated, which induce the expression of antioxidant enzymes catalase (CAT) and superoxide dismutase (SOD). It is well documented that the antioxidant response in diabetic individuals is very low. Since Nrf2 and FoxO1 are the major TFs activating these genes, we were interested in determining if single nucleotide polymorphisms (SNPs) in genes for these TFs have any association with lowered antioxidant enzyme activity in diabetic individuals. The activity of CAT and SOD and total antioxidant capacity (TAC) were quantified from the serum samples of diabetic (<i>n</i> = 98) and non-diabetic (<i>n</i> = 90) individuals. Genomic DNA was isolated, and <i>Nrf2</i> and <i>FoxO1</i> were amplified and sequenced by Illumina NextSeq500. Data were screened for SNPs in amplified regions. An independent samples <i>t</i>-test to find an association between CAT, SOD, and TAC and allele frequency of SNP with the diabetic condition was carried out. We found decreased CAT and SOD activity and significantly low TAC in diabetic individuals. Thirty-two and thirty-four SNPs and Single-nucleotide variants (SNVs) were observed in <i>Nrf2</i> and <i>FoxO1</i>, respectively. However, a statistically significant difference in the allele frequency distribution between study groups was observed only in two intronic SNPs, rs17524059:A &gt; C and rs60373589:Indel(A) of <i>Nrf2</i> and <i>FoxO1</i>, respectively. SNPs, rs17524059 in the <i>Nrf2</i> and rs60373589 of <i>FoxO1</i>, were not associated with reduced CAT and SOD activity and level of TAC in Indian diabetic individuals. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24204398.v1
title: Genetic polymorphisms in Nrf2 and FoxO1: implications for antioxidant enzyme activity in diabetes

description: In diabetes, persistent hyperglycemia generates excess reactive oxygen species (ROS), leading to oxidative stress (OS). In response to OS, transcription factors (TFs) Nrf2 and FoxO1 get activated, which induce the expression of antioxidant enzymes catalase (CAT) and superoxide dismutase (SOD). It is well documented that the antioxidant response in diabetic individuals is very low. Since Nrf2 and FoxO1 are the major TFs activating these genes, we were interested in determining if single nucleotide polymorphisms (SNPs) in genes for these TFs have any association with lowered antioxidant enzyme activity in diabetic individuals. The activity of CAT and SOD and total antioxidant capacity (TAC) were quantified from the serum samples of diabetic (<i>n</i> = 98) and non-diabetic (<i>n</i> = 90) individuals. Genomic DNA was isolated, and <i>Nrf2</i> and <i>FoxO1</i> were amplified and sequenced by Illumina NextSeq500. Data were screened for SNPs in amplified regions. An independent samples <i>t</i>-test to find an association between CAT, SOD, and TAC and allele frequency of SNP with the diabetic condition was carried out. We found decreased CAT and SOD activity and significantly low TAC in diabetic individuals. Thirty-two and thirty-four SNPs and Single-nucleotide variants (SNVs) were observed in <i>Nrf2</i> and <i>FoxO1</i>, respectively. However, a statistically significant difference in the allele frequency distribution between study groups was observed only in two intronic SNPs, rs17524059:A &gt; C and rs60373589:Indel(A) of <i>Nrf2</i> and <i>FoxO1</i>, respectively. SNPs, rs17524059 in the <i>Nrf2</i> and rs60373589 of <i>FoxO1</i>, were not associated with reduced CAT and SOD activity and level of TAC in Indian diabetic individuals. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24137431.v1
title: Comprehensive examination on codon usage bias pattern of the Bovine Ephemeral fever virus

description: Bovine Ephemeral Fever Virus (BEFV) is a non-contagious virus that commonly infects cattle and water buffalo, reduces milk productivity, decreases the quality of beef, and causes an adverse economic impact on the global livestock industry. However, the evolution of BEFV is unclear, and uncertainty exists regarding its global geodynamics. Consequently, this study aims to comprehend the pattern of viral evolution and gene expression in the BEFV genes G, M, N, and P, including synonymous codons. Additionally, we performed recombination analyses, which exclusively detected recombination signals in the G- and P-genes. Subsequently, a phylogenetic tree was constructed to validate and support these findings. The codon usage bias results showed that the BEFV-selected genes were influenced by both natural and mutation pressure. Furthermore, nucleotide A is more abundant in all the selected genes. The eNC values, ranging from 42.99 to 47.10, revealed the presence of moderate codon usage bias, where gene P exhibited the highest and gene G had the lowest codon usage bias. The neutrality and PR-2 plots, specified codon usage patterns of the genes, are also being shaped by strong selectional pressure. This comprehensive analysis of BEFV genes (G, M, N, and P) sheds light on the molecular evolutionary patterns, co-adaptation, and different genes expression in diverse regions, facilitating the development of preventative programs and insights into viral pathogenesis and vaccine design. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24137431
title: Comprehensive examination on codon usage bias pattern of the Bovine Ephemeral fever virus

description: Bovine Ephemeral Fever Virus (BEFV) is a non-contagious virus that commonly infects cattle and water buffalo, reduces milk productivity, decreases the quality of beef, and causes an adverse economic impact on the global livestock industry. However, the evolution of BEFV is unclear, and uncertainty exists regarding its global geodynamics. Consequently, this study aims to comprehend the pattern of viral evolution and gene expression in the BEFV genes G, M, N, and P, including synonymous codons. Additionally, we performed recombination analyses, which exclusively detected recombination signals in the G- and P-genes. Subsequently, a phylogenetic tree was constructed to validate and support these findings. The codon usage bias results showed that the BEFV-selected genes were influenced by both natural and mutation pressure. Furthermore, nucleotide A is more abundant in all the selected genes. The eNC values, ranging from 42.99 to 47.10, revealed the presence of moderate codon usage bias, where gene P exhibited the highest and gene G had the lowest codon usage bias. The neutrality and PR-2 plots, specified codon usage patterns of the genes, are also being shaped by strong selectional pressure. This comprehensive analysis of BEFV genes (G, M, N, and P) sheds light on the molecular evolutionary patterns, co-adaptation, and different genes expression in diverse regions, facilitating the development of preventative programs and insights into viral pathogenesis and vaccine design. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.27637936
title: <i>In silico</i> studies of alkaloids and their derivatives against N-acetyltransferase EIS protein from <i>Mycobacterium tuberculosis</i>

description: Antibiotic resistance against <i>Mycobacterium tuberculosis</i> (<i>M.tb.</i>) has been a significant cause of death worldwide. The Enhanced intracellular survival (EIS) protein of the bacteria is an acetyltransferase that multiacetylates aminoglycoside antibiotics, preventing them from binding to the bacterial ribosome. To overcome the EIS-mediated antibiotics resistance of <i>M.tb</i>., we compiled 888 alkaloids and derivatives from five different databases and virtually screened them against the EIS receptor. The compound library was filtered down to 87 compounds, which underwent additional analysis and filtration. Moreover, the top 15 most prominent phytocompounds were obtained after the drug-likeness prediction and ADMET screening. Out of 15, nine compounds confirmed the maximum number of hydrogen bond interactions and reliable binding energies during molecular docking. Additionally, the Molecular dynamics (MD) simulation of nine compounds showed the three most stable complexes, further verified by re-docking with mutated protein. The density functional theory (DFT) calculation was performed to identify the HOMO-LUMO energy gaps of the selected three potential compounds. Finally, our selected top lead compounds i.e., Alkaloid AQC2 (PubChem85634496), Nobilisitine A (ChEbi68116), and N-methylcheilanthifoline (ChEbi140673) demonstrated more favourable outcomes when compared with reference compounds (i.e., 39b and 2i) in all parameters used in this study. Therefore, we anticipate that our findings will help to explore and develop natural compound therapy against multi and extensively drug-resistant strains of <i>M.tb</i>. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.27637936.v1
title: <i>In silico</i> studies of alkaloids and their derivatives against N-acetyltransferase EIS protein from <i>Mycobacterium tuberculosis</i>

description: Antibiotic resistance against <i>Mycobacterium tuberculosis</i> (<i>M.tb.</i>) has been a significant cause of death worldwide. The Enhanced intracellular survival (EIS) protein of the bacteria is an acetyltransferase that multiacetylates aminoglycoside antibiotics, preventing them from binding to the bacterial ribosome. To overcome the EIS-mediated antibiotics resistance of <i>M.tb</i>., we compiled 888 alkaloids and derivatives from five different databases and virtually screened them against the EIS receptor. The compound library was filtered down to 87 compounds, which underwent additional analysis and filtration. Moreover, the top 15 most prominent phytocompounds were obtained after the drug-likeness prediction and ADMET screening. Out of 15, nine compounds confirmed the maximum number of hydrogen bond interactions and reliable binding energies during molecular docking. Additionally, the Molecular dynamics (MD) simulation of nine compounds showed the three most stable complexes, further verified by re-docking with mutated protein. The density functional theory (DFT) calculation was performed to identify the HOMO-LUMO energy gaps of the selected three potential compounds. Finally, our selected top lead compounds i.e., Alkaloid AQC2 (PubChem85634496), Nobilisitine A (ChEbi68116), and N-methylcheilanthifoline (ChEbi140673) demonstrated more favourable outcomes when compared with reference compounds (i.e., 39b and 2i) in all parameters used in this study. Therefore, we anticipate that our findings will help to explore and develop natural compound therapy against multi and extensively drug-resistant strains of <i>M.tb</i>. Communicated by Ramaswamy H. Sarma
DOI: 10.15468/dl.44ks9g
title: Occurrence Download

description: A dataset containing 301 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lithobates capito (LeConte, 1855)",
 "Year 1970-2020"
 ]
}

 The dataset includes 301 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003496-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14057081
title: Estimates for US foreign-born population size and immigration flows, 2000-2019

description: Detailed results files for "Bayesian evidence synthesis to infer unobserved population dynamics: an application to international migration into the United States, 2000-2019"
DOI: 10.5281/zenodo.14057082
title: Estimates for US foreign-born population size and immigration flows, 2000-2019

description: Detailed results files for "Bayesian evidence synthesis to infer unobserved population dynamics: an application to international migration into the United States, 2000-2019"
DOI: 10.17613/d3gz7-jfk98
title: Collation of the Epistle of Jude from 563 MSS (XML)

description: This collation is in XML format and TEI-compliant. It is based on 563 continuous-text MSS of the Epistle of Jude (This includes the NA28 and the Robinson-Pierpont Majority Text). This is machine-readable format.
DOI: 10.17613/fxx9-0453
title: Collation of the Epistle of Jude from 563 MSS (XML)

description: This collation is in XML format and TEI-compliant. It is based on 563 continuous-text MSS of the Epistle of Jude (This includes the NA28 and the Robinson-Pierpont Majority Text). This is machine-readable format.
DOI: 10.6084/m9.figshare.27638031
title: us-states.json

description: Us Map .json data from OSU CSE 5544 class
DOI: 10.15468/dl.mh2yg3
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Drymarchon couperi (Holbrook, 1842)",
 "Year 1970-2020"
 ]
}

 The dataset includes 39 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003497-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9cqb4a
title: Occurrence Download

description: A dataset containing 2748 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Montia linearis (Douglas ex Hook.) Greene"
 ]
}

 The dataset includes 2748 records from 137 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003498-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2ak9vf
title: Occurrence Download

description: A dataset containing 59 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Drosophila suzukii (Matsumura, 1931)",
 "Country is Italy",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 59 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003499-241107131044228/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.27637434
title: Appendix 1: Summary of descriptive statistics

description: The descriptive statistics of the data.
DOI: 10.6084/m9.figshare.27637434.v2
title: Appendix 1: Summary of descriptive statistics

description: The descriptive statistics of the data.
DOI: 10.15468/dl.83twy2
title: Occurrence Download

description: A dataset containing 7408 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Mahonia bealei (Fortune) Carrière"
 ]
}

 The dataset includes 7408 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003501-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14057117
title: Effect of an alkaline reactive on the thermochemical process (pyrolytic) of HIPS
DOI: 10.5281/zenodo.14057118
title: Effect of an alkaline reactive on the thermochemical process (pyrolytic) of HIPS
DOI: 10.15468/dl.5ef69q
title: Occurrence Download

description: A dataset containing 46844 species occurrences available in GBIF matching the query:
{
 "and" : [
 "ScientificName is one of (Bucorvus abyssinicus (Boddaert, 1783), Bucorvus leadbeateri (Vigors, 1825))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 46844 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003502-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mbp4rv
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "OccurrenceStatus is Present",
 "TaxonKey is Ambrosia trifida L."
 ]
}

 The dataset includes 30 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003503-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s92k2g
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-9.8187 38.20743,-8.44312 38.20743,-8.44312 39.21415,-9.8187 39.21415,-9.8187 38.20743))",
 "HasGeospatialIssue is false",
 "TaxonKey is Syngnathus typhle Linnaeus, 1758"
 ]
}

 The dataset includes 20 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003504-241107131044228/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.27637989
title: Metagenomics of the Iberian Margin: the deep subsurface at IODP Site U1385. Metabolism data for metagenomes and metagenome-assembled genomes (MAGs).

description: Subsurface sediment collected from IODP Site U1385 of the Iberian Margin was examined via metagenomics.
DOI: 10.6084/m9.figshare.27637989.v1
title: Metagenomics of the Iberian Margin: the deep subsurface at IODP Site U1385. Metabolism data for metagenomes and metagenome-assembled genomes (MAGs).

description: Subsurface sediment collected from IODP Site U1385 of the Iberian Margin was examined via metagenomics.
DOI: 10.5281/zenodo.14057097
title: Enhanced_Precipitation_of_energetic_protons_due_to_Uranus_asymmetric_magnetic_field

description: The dataset pertaining to Figures 1-4 in the academic paper titled: "Enhanced Precipitation of energetic protons due to Uranus asymmetric magnetic field" by Matthew Acevski and Adam Masters
DOI: 10.15468/dl.7ndb9n
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is North America",
 "TaxonKey is Vicia bithynica (L.) L."
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003506-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u4fsca
title: Occurrence Download

description: A dataset containing 191108 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "TaxonKey is Amphibia"
 ]
}

 The dataset includes 191108 records from 100 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003495-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dvk5fq
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((84.77958 56.08814,85.49154 56.08814,85.49154 56.4075,84.77958 56.4075,84.77958 56.08814))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Podiceps cristatus (Linnaeus, 1758)"
 ]
}

 The dataset includes 38 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003507-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8vvv5s
title: Occurrence Download

description: A dataset containing 5164 species occurrences available in GBIF matching the query:
{
 "and" : [
 "ScientificName is one of (Pterocles gutturalis A.Smith, 1836)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5164 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003508-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yqeuh8
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((84.77958 56.08814,85.49154 56.08814,85.49154 56.4075,84.77958 56.4075,84.77958 56.08814))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Podiceps auritus (Linnaeus, 1758)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003510-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fy6efk
title: Occurrence Download

description: A dataset containing 3548 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eschweilera ovata (Cambess.) Mart. ex Miers"
 ]
}

 The dataset includes 3548 records from 137 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003509-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.