cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30182920.v1
title: Supplementary Tables Thesis AMGM Chapter I

description: Supplementary Tables generated for the first chapter of the thesis titled '<b>Novel whole-genome sequencing approaches to study drug resistance, transmission, and evolution of the</b><b><i> Mycobacterium tuberculosis </i></b><b>complex'. </b>Author: Ana María García Marín. Insituto de Biomedicina de Valencia (IBV-CSIC) and Universitat de València. The document, in Excel format, contains:<br>Table S1.1. Phenotypic and genomic drug resistance profiles of MTBC samples collected in the Comunitat Valenciana between 2014 and 2016.Table S1.2. Isoniazid and rifampicin Minimum Inhibitory Concentrations of samples with discrepancies in phenotype-genotype resistance profiles.
DOI: 10.15468/dl.yesmph
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hordeum distichon",
 "Country is Ireland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 16 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006609-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y9nesq
title: Occurrence Download

description: A dataset containing 124 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hordeum distichon",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 124 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006607-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17179872
title: Morpho-Structural Analysis of Impact Craters on Pluto: Implications for the Study of Complex Craters

description: This study investigates the morpho-structural characteristics of impact craters on Pluto, employing high-resolution topographic data and image mosaics from NASA’s Dawn mission. Pluto´craters were classified into three main categories: simple, transitional, and complex, based on the morpho-structural distinctions observed. We introduce a refined classification for Pluto's complex craters, grouping them into three subcategories—Complex I, II, and III—based on their morpho-structural characteristics (such as the presence of central peaks, terraces, flat floors, etc.).
DOI: 10.15468/dl.y3yj75
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hordeum distichon",
 "Country is Czechia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 28 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006608-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rfxss9
title: Occurrence Download

description: A dataset containing 113632 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is one of (Bidens frondosa)"
 ]
}

 The dataset includes 113632 records from 1189 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006588-250920141307145/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.24117295
title: Gene expression analysis reveals GRIN1, SYT1, and SYN2 as significant therapeutic targets and drug repurposing reveals lorazepam and lorediplon as potent inhibitors to manage Alzheimer’s disease

description: Alzheimer’s disease (AD) is a slowly progressive neurodegenerative disease and a leading cause of dementia. We aim to identify key genes for the development of therapeutic targets and biomarkers for potential treatments for AD. Meta-analysis was performed on six microarray datasets and identified the differentially expressed genes between healthy and Alzheimer’s disease samples. Thereafter, we filtered out the common genes which were present in at least four microarray datasets for downstream analysis. We have constructed a gene-gene network for the common genes and identified six hub genes. Furthermore, we investigated the regulatory mechanisms of these hub genes by analysing their interaction with miRNAs and transcription factors. The gene ontology analysis results highlighted the enriched terms significantly associated with hub genes. Through an extensive literature survey, we found that three of the hub genes including GRIN1, SYN2, and SYT1 were critically involved in disease development. To leverage existing drugs for potential repurposing, we predicted drug-gene interaction using the drug-gene interaction database, and performed molecular docking studies. The docking results revealed that the drug compounds had strong interactions and favorable binding with selected hub genes. Lorazepam exhibits a binding energy of −7.3 kcal/mol with GRIN1, Lorediplon exhibits binding energies of −7.7 kcal/mol and −6.3 kcal/mol with the SYT1, and SYN2 respectively. In addition, 100 ns molecular dynamics simulations were carried out for the top complexes and apo protein as well. Furthermore, the MM-PBSA free energy calculations also revealed that these complexes are stable and had favorable energies. According to our study, the identified hub gene could serve as a biomarker as well as a therapeutic target for AD, and the proposed repurposed drug molecules appear to have promising efficacy in treating the disease. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24117295.v1
title: Gene expression analysis reveals GRIN1, SYT1, and SYN2 as significant therapeutic targets and drug repurposing reveals lorazepam and lorediplon as potent inhibitors to manage Alzheimer’s disease

description: Alzheimer’s disease (AD) is a slowly progressive neurodegenerative disease and a leading cause of dementia. We aim to identify key genes for the development of therapeutic targets and biomarkers for potential treatments for AD. Meta-analysis was performed on six microarray datasets and identified the differentially expressed genes between healthy and Alzheimer’s disease samples. Thereafter, we filtered out the common genes which were present in at least four microarray datasets for downstream analysis. We have constructed a gene-gene network for the common genes and identified six hub genes. Furthermore, we investigated the regulatory mechanisms of these hub genes by analysing their interaction with miRNAs and transcription factors. The gene ontology analysis results highlighted the enriched terms significantly associated with hub genes. Through an extensive literature survey, we found that three of the hub genes including GRIN1, SYN2, and SYT1 were critically involved in disease development. To leverage existing drugs for potential repurposing, we predicted drug-gene interaction using the drug-gene interaction database, and performed molecular docking studies. The docking results revealed that the drug compounds had strong interactions and favorable binding with selected hub genes. Lorazepam exhibits a binding energy of −7.3 kcal/mol with GRIN1, Lorediplon exhibits binding energies of −7.7 kcal/mol and −6.3 kcal/mol with the SYT1, and SYN2 respectively. In addition, 100 ns molecular dynamics simulations were carried out for the top complexes and apo protein as well. Furthermore, the MM-PBSA free energy calculations also revealed that these complexes are stable and had favorable energies. According to our study, the identified hub gene could serve as a biomarker as well as a therapeutic target for AD, and the proposed repurposed drug molecules appear to have promising efficacy in treating the disease. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24119572
title: Curcumin-sulfobutyl-ether beta cyclodextrin inclusion complex: preparation, spectral characterization, molecular modeling, and antimicrobial activity

description: Urinary tract infections (UTIs) caused by Gram-negative bacteria <i>E. coli</i> is responsible for 80–90% of uncomplicated cases in women. The increased prevalence of antibiotic resistance has made the management of UTIs more challenging. Plant-derived compounds have long been used to treat various diseases, and constitute an alternative to antibiotic resistance. Curcumin (CUR), a naturally occurring polyphenolic phytoconstituent obtained from <i>Curcuma longa</i> is endowed with diverse medicinal properties. The present study aims to form a complex of CUR with Sulfobutyl ether-β-cyclodextrin (SBEβCD) to overcome the poor solubility and bioavailability of CUR and to evaluate the antimicrobial activity of CUR-SBEβCD. Phase solubility studies and spectral characterization showed the entrapment of CUR in the SBEβCD cavity. In silico docking studies performed to investigate the complexation process of CUR with SBEβCD, revealed that the methoxy group and OH group of CUR interacted with SBEβCD. The cytotoxicity and HET-CAM assays confirmed that CUR-SBEβCD was non-irritant. The prepared complex investigated with the disc diffusion method showed antimicrobial activity with a zone of inhibition (ZOI) of 13 mm against Escherichia coli (<i>E. coli)</i> and 11.5 mm against Staphylococcus aureus (<i>S. aureus)</i> whereas CUR alone did not show any ZOI. It can be concluded that prepared CUR-SBEβCD demonstrated superior antimicrobial activity and therefore can be a promising alternative for the treatment of UTIs. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24119572.v1
title: Curcumin-sulfobutyl-ether beta cyclodextrin inclusion complex: preparation, spectral characterization, molecular modeling, and antimicrobial activity

description: Urinary tract infections (UTIs) caused by Gram-negative bacteria <i>E. coli</i> is responsible for 80–90% of uncomplicated cases in women. The increased prevalence of antibiotic resistance has made the management of UTIs more challenging. Plant-derived compounds have long been used to treat various diseases, and constitute an alternative to antibiotic resistance. Curcumin (CUR), a naturally occurring polyphenolic phytoconstituent obtained from <i>Curcuma longa</i> is endowed with diverse medicinal properties. The present study aims to form a complex of CUR with Sulfobutyl ether-β-cyclodextrin (SBEβCD) to overcome the poor solubility and bioavailability of CUR and to evaluate the antimicrobial activity of CUR-SBEβCD. Phase solubility studies and spectral characterization showed the entrapment of CUR in the SBEβCD cavity. In silico docking studies performed to investigate the complexation process of CUR with SBEβCD, revealed that the methoxy group and OH group of CUR interacted with SBEβCD. The cytotoxicity and HET-CAM assays confirmed that CUR-SBEβCD was non-irritant. The prepared complex investigated with the disc diffusion method showed antimicrobial activity with a zone of inhibition (ZOI) of 13 mm against Escherichia coli (<i>E. coli)</i> and 11.5 mm against Staphylococcus aureus (<i>S. aureus)</i> whereas CUR alone did not show any ZOI. It can be concluded that prepared CUR-SBEβCD demonstrated superior antimicrobial activity and therefore can be a promising alternative for the treatment of UTIs. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24092246
title: SBS 3.1, a novel natural product small molecule regulates TNF-α-induced NF-κB activation and key signals of inflammation to promote apoptosis in lung cancer tumour microenvironment

description: Chronic inflammation leads to many maladies in lung cancer. Tumor necrosis factor-alpha (T NF- α), a pleiotropic proinflammatory cytokine regulates the activation of the nuclear factor-κB (NF-κB) to drive many physiological and pathological signaling pathways in inflammation and cancer apoptosis. This study identified a novel natural product to inhibit T NF-α induced NF-κB activation. Virtual docking of ZINC natural product library and computational modeling analysis showed compounds that target crucial amino acid residues on p50 protein involved in DNA binding. Molecular dynamic simulation showed, compound SBS-3.1, as the best lead compound that binds efficiently and stably with p50 protein. MMP BSA analysis of the lead compound predicted a favorable binding free energy. The compound inhibited the proliferations of T NF-α induced A-549 with a GI50 value of 30.53 μM. SBS-3.1 decreased the percentage of T NF-α induced NF-κB-65, p38 and ERK1/2 positive lung cancer cells, while the apoptosis in these cells were elevated. In summary, SBS-3.1, a natural product, was identified as the lead compound targeting Rel-homology region of p50. Inhibition of NF-κB and inflammatory signals by SBS 3.1 promoted apoptosis in lung cancer. Further research can bring new therapeutic strategies for treating inflammation associated T ME of lung cancer cells. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24092246.v1
title: SBS 3.1, a novel natural product small molecule regulates TNF-α-induced NF-κB activation and key signals of inflammation to promote apoptosis in lung cancer tumour microenvironment

description: Chronic inflammation leads to many maladies in lung cancer. Tumor necrosis factor-alpha (T NF- α), a pleiotropic proinflammatory cytokine regulates the activation of the nuclear factor-κB (NF-κB) to drive many physiological and pathological signaling pathways in inflammation and cancer apoptosis. This study identified a novel natural product to inhibit T NF-α induced NF-κB activation. Virtual docking of ZINC natural product library and computational modeling analysis showed compounds that target crucial amino acid residues on p50 protein involved in DNA binding. Molecular dynamic simulation showed, compound SBS-3.1, as the best lead compound that binds efficiently and stably with p50 protein. MMP BSA analysis of the lead compound predicted a favorable binding free energy. The compound inhibited the proliferations of T NF-α induced A-549 with a GI50 value of 30.53 μM. SBS-3.1 decreased the percentage of T NF-α induced NF-κB-65, p38 and ERK1/2 positive lung cancer cells, while the apoptosis in these cells were elevated. In summary, SBS-3.1, a natural product, was identified as the lead compound targeting Rel-homology region of p50. Inhibition of NF-κB and inflammatory signals by SBS 3.1 promoted apoptosis in lung cancer. Further research can bring new therapeutic strategies for treating inflammation associated T ME of lung cancer cells. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24131789
title: Structural insight into G2019S mutated LRRK2 kinase and brain-penetrant type I inhibitor complex: a molecular dynamics approach

description: More than 40 mutations in the multidomain leucine-rich repeat kinase 2 (LRRK2) are found and mutation G2019S in the kinase domain is the most concerned with Parkinson’s disease (PD). The discovery of the various types of inhibitors has largely emerged recently. However, the comparative study on molecular insight in WT and G2019S LRRK2 kinase domain upon binding of the inhibitors has not yet been explored in detail. This work considered five ATP-competitive Type I inhibitors complexed with WT and mutated LRRK2 kinase. Three reported potent and brain-penetrant inhibitors, GNE-7915, PF-06447475 and MLi-2 (comp1, comp2 and comp3 respectively) and also, another two inhibitors, Pyrrolo[2,3-b] pyridine derivative (comp4) and Pyrrolo[2,3-d] pyrimidine derivative (comp5), were used. In this work, classical and accelerated molecular dynamics (cMD and aMD) simulations were performed for a total of 12 systems (apo and holo). This study found structural and thermodynamic stability for all the inhibitors. Comparatively larger molecules (size 15.3 − 15.4 Å), comp1, comp3 and comp5, showed more selectivity towards mutated LRRK2 kinase in terms of flexibility of residues, compactness and dynamics of kinase, the stability inside the binding-pocket. Also, inhibitors comp3 and comp5 showed higher binding affinity towards G2019S LRRK2 among the five. Residues, E1948 and A1950 (in hinge region) were observed mainly to form hydrogen bonds with inhibitors. Finally, MLi-2 showed a conformational rearrangement by dihedral flipping in both WT and mutated systems but got stability in G2019S LRRK2. This work could potentially help design more improved and effective Type I inhibitors for G2019S LRRK2 kinase. Among five Type-I inhibitor molecules, comp1 (GNE-7915), comp2 (PF-06447475), comp3 (MLi-2), comp4 (Pyrrolo[2,3-b]pyridine derivative), comp5 (Pyrrolo[2,3-d]pyrimidine derivative), comparatively larger molecules (comp1, comp3 and comp5) showed selectivity towards G2019S LRRK2 and a stable conformation for MLi-2 (after dihedral flipping of the molecule) was found in the mutated system. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24101250
title: Normal mode analysis and comparative study of intrinsic dynamics of alcohol oxidase enzymes from GMC protein family

description: Glucose-Methanol-Choline (GMC) family enzymes are very important in catalyzing the oxidation of a wide range of structurally diverse substrates. Enzymes that constitute the GMC family, share a common tertiary fold but &lt; 25% sequence identity. Cofactor FAD, FAD binding signature motif, and similar structural scaffold of the active site are common features of oxidoreductase enzymes of the GMC family. Protein functionality mainly depends on protein three-dimensional structures and dynamics. In this study, we used the normal mode analysis method to search the intrinsic dynamics of GMC family enzymes. We have explored the dynamical behavior of enzymes with unique substrate catabolism and active site characteristics from different classes of the GMC family. Analysis of individual enzymes and comparative ensemble analysis of enzymes from different classes has shown conserved dynamic motion at FAD binding sites. The present study revealed that GMC enzymes share a strong dynamic similarity (Bhattacharyya coefficient &gt;90% and root mean squared inner product &gt;52%) despite low sequence identity across the GMC family enzymes. The study predicts that local deformation energy between atoms of the enzyme may be responsible for the catalysis of different substrates. This study may help that intrinsic dynamics can be used to make meaningful classifications of proteins or enzymes from different organisms. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24119555
title: Designing a novel chimeric multi-epitope vaccine subunit against <i>Staphylococcus argenteus</i> through artificial intelligence approach integrating pan-genome analysis, <i>in vitro</i> identification, and immunogenicity profiling

description: <i>Staphylococcus argenteus</i> is a newly identified pathogen that causes respiratory tract infections, skin infections, such as cellulitis, abscesses, and impetigo, and currently, there is no licensed vaccine available against it. To develop a vaccine against <i>S. argenteus</i>, a bacterial pan-genome analysis was applied to identify potential vaccine candidates. A total of 4908 core proteins were retrieved and utilized for identifying four proteins, including SG38 Panton-Valentine leukocidin LukS-PV protein, SG62 staphylococcal enterotoxin type A protein, SG39 enterotoxin B protein, and SG43 enterotoxin type C3 protein as potential vaccine candidates. Epitopes were predicted for these proteins using different types of B and T-cell epitope prediction tools, and only those with a non-toxic profile, antigenic, non-allergenic, and immunogenic were selected. The selected epitopes were linked to each other to form a multi-epitope vaccine construct, which was further linked to the PADRE sequence (AKFVAAWTLKAAA) and 50s ribosomal L7/L12 protein to enhance the vaccine’s antigenicity. The three-dimensional structure of the vaccine construct was assessed to determine its binding affinity with key Toll-like receptor 9 (TLR-9) and Toll-like receptor 5 (TLR-5) immune cell receptors. Our findings demonstrate that the vaccine exhibits favorable binding interactions with these immune cell receptors, indicating its potential efficacy. Molecular dynamic simulations further confirmed the accessibility of vaccine epitopes to the host immune system, substantiating its ability to elicit protective immune responses. Taken together, this study highlights the promising candidacy of the modeled vaccine construct for future <i>in vivo</i> and <i>in vitro</i> experimental investigations. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24119555.v1
title: Designing a novel chimeric multi-epitope vaccine subunit against <i>Staphylococcus argenteus</i> through artificial intelligence approach integrating pan-genome analysis, <i>in vitro</i> identification, and immunogenicity profiling

description: <i>Staphylococcus argenteus</i> is a newly identified pathogen that causes respiratory tract infections, skin infections, such as cellulitis, abscesses, and impetigo, and currently, there is no licensed vaccine available against it. To develop a vaccine against <i>S. argenteus</i>, a bacterial pan-genome analysis was applied to identify potential vaccine candidates. A total of 4908 core proteins were retrieved and utilized for identifying four proteins, including SG38 Panton-Valentine leukocidin LukS-PV protein, SG62 staphylococcal enterotoxin type A protein, SG39 enterotoxin B protein, and SG43 enterotoxin type C3 protein as potential vaccine candidates. Epitopes were predicted for these proteins using different types of B and T-cell epitope prediction tools, and only those with a non-toxic profile, antigenic, non-allergenic, and immunogenic were selected. The selected epitopes were linked to each other to form a multi-epitope vaccine construct, which was further linked to the PADRE sequence (AKFVAAWTLKAAA) and 50s ribosomal L7/L12 protein to enhance the vaccine’s antigenicity. The three-dimensional structure of the vaccine construct was assessed to determine its binding affinity with key Toll-like receptor 9 (TLR-9) and Toll-like receptor 5 (TLR-5) immune cell receptors. Our findings demonstrate that the vaccine exhibits favorable binding interactions with these immune cell receptors, indicating its potential efficacy. Molecular dynamic simulations further confirmed the accessibility of vaccine epitopes to the host immune system, substantiating its ability to elicit protective immune responses. Taken together, this study highlights the promising candidacy of the modeled vaccine construct for future <i>in vivo</i> and <i>in vitro</i> experimental investigations. Communicated by Ramaswamy H. Sarma