cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.eu82tc
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lamna ditropis Hubbs & Follett, 1947",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007131-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ex95vs
title: Occurrence Download

description: A dataset containing 754 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pristimantis zeuctotylus (Lynch & Hoogmoed, 1977)"
 ]
}

 The dataset includes 754 records from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007132-241126133413365/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.25151693
title: Drosophila_yakuba_mayottensis_rmaverick_MAF20

description: rmaverick population genetic structure analysis of Drosophila yakuba yakuba and D. y. mayottensis populations.
DOI: 10.15468/dl.ak5hgr
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lamna nasus (Bonnaterre, 1788)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007133-241126133413365/datasets/export for details.
DOI: 10.15468/dl.78x43j
title: Occurrence Download

description: A dataset containing 873 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Erythrina edulis Triana ex Micheli"
 ]
}

 The dataset includes 873 records from 74 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007134-241126133413365/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.27931485
title: WebVisualData.zip

description: This file contains screenshots of 300 websites.
DOI: 10.15468/dl.fwh84c
title: Occurrence Download

description: A dataset containing 834 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Puffinus griseus (Gmelin, 1789)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 834 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007135-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.unfser
title: Occurrence Download

description: A dataset containing 1753 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pseudis paradoxa (Linnaeus, 1758)"
 ]
}

 The dataset includes 1753 records from 102 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007136-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rm7r28
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Procellaria grisea Gmelin, 1789",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007137-241126133413365/datasets/export for details.
DOI: 10.15468/dl.9y62wv
title: Occurrence Download

description: A dataset containing 58 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ranitomeya amazonica (Schulte, 1999)"
 ]
}

 The dataset includes 58 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007139-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tp8cys
title: Occurrence Download

description: A dataset containing 429 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ardenna grisea (J.F.Gmelin, 1789)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 429 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007138-241126133413365/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.27931566
title: Drosophila_yakuba_mayottensis_rmaverick_MAF05

description: Population structure of Drosophila yakuba inferred by rmaverick using sites with minor allele frequency of ≥5%.
DOI: 10.15468/dl.8an7jk
title: Occurrence Download

description: A dataset containing 707 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mactra chinensis R.A.Philippi, 1846",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 707 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007140-241126133413365/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.24441276
title: The multi-protein targeting potential of bioactive syringin in inflammatory diseases: using molecular modelling and in-silico analysis of regulatory elements

description: Inflammation plays a crucial role in the onset or progression of a variety of acute and chronic diseases. Non-steroidal anti-inflammatory drugs (NSAIDs) are the only available FDA-approved therapy. The therapeutic outcome of NSAIDs is still finite due to off-target effects and extreme side effects on other vital organs. Bioactive syringin has been manifested to hold anti-osteoporosis, cardiac hypertrophy, alter autophagy, anti-cancer, neuro-preventive effects, etc. However, its multi-protein targeting potential in inflammation mostly remains unexplored. In the present work, we have checked the multi-protein targeting potential of bioactive glycoside syringin in inflammatory diseases. Based on the binding score of protein-ligand complexes, glycoside syringin scored greater than −7 kcal/mol against 12 inflammatory proteins. Our molecular dynamic simulation study (200 ns) confirmed that bioactive syringin remained inside the binding cavity of inflammatory proteins (JAK1, TYK2, and COX1) in a stable conformation. Further, our co-expression analysis suggests that these genes play an essential role in multiple pathways and are regulated by multiple miRNAs. Our study demonstrates that bioactive glycoside syringin might be a multi-protein targeting potential against inflammatory diseases and could be further investigated utilizing different preclinical approaches. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24441276.v1
title: The multi-protein targeting potential of bioactive syringin in inflammatory diseases: using molecular modelling and in-silico analysis of regulatory elements

description: Inflammation plays a crucial role in the onset or progression of a variety of acute and chronic diseases. Non-steroidal anti-inflammatory drugs (NSAIDs) are the only available FDA-approved therapy. The therapeutic outcome of NSAIDs is still finite due to off-target effects and extreme side effects on other vital organs. Bioactive syringin has been manifested to hold anti-osteoporosis, cardiac hypertrophy, alter autophagy, anti-cancer, neuro-preventive effects, etc. However, its multi-protein targeting potential in inflammation mostly remains unexplored. In the present work, we have checked the multi-protein targeting potential of bioactive glycoside syringin in inflammatory diseases. Based on the binding score of protein-ligand complexes, glycoside syringin scored greater than −7 kcal/mol against 12 inflammatory proteins. Our molecular dynamic simulation study (200 ns) confirmed that bioactive syringin remained inside the binding cavity of inflammatory proteins (JAK1, TYK2, and COX1) in a stable conformation. Further, our co-expression analysis suggests that these genes play an essential role in multiple pathways and are regulated by multiple miRNAs. Our study demonstrates that bioactive glycoside syringin might be a multi-protein targeting potential against inflammatory diseases and could be further investigated utilizing different preclinical approaches. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24441274
title: Cheminformatics approach for identification of <i>N-HyMenatPimeMelly</i> as a novel potential ligand against RAS and renal chloride channel

description: Some angiotensin receptor (AR) blockers interfere with the renal chloride channel (ClC-K), which plays an important role in urine concentration. Identifying ligands targeting this channel, whether activating or blocking, is highly desirable because it could open the way for interventions that modulate their activity. In this study, the Asinex (BioDesign) complete library was screened to identify a compound with favorable physicochemical and pharmacokinetic properties, which have both AR blocking and ClC‐Ka-modulating activities to present it as a novel potential oral candidate which could be useful for treatment of salt-sensitive hypertension without major ClC‐K affection. A compound, N-{[4-Hydroxy-1-(2-methyl-1,6-naphthyridin-4-yl)-4-piperidinyl]methyl}-N-methyl-L-lysinamide (<i>N-HyMenatPimeMelly)</i> (Chem Spider ID 68416221), was identified as a potent potential oral ligand of the renin-angiotensin system (RAS) and ClC-Ka with docking scores ranging from −10.978 to −7.324 with the four selected proteins (4YAY: AR type 1, 2PFI: Cytoplasmic domain of ClC-Ka, 6JOD: AR type 2 and 6M0J: Angiotensin-converting enzyme 2). The protein-ligand complex was used to perform molecular dynamics (MD) simulation for 100 ns. The QikProp and SwissADME tools’ results showed that the compound has ADME/T and drug-likeness properties, which are within the permissible ranges for 95% of known drugs. The density functional theory (DFT) analysis and MD simulation extended the study toward computational validation. Throughout the study, <i>N-HyMenatPimeMelly</i> has shown good interactions and stable performance in MD simulation and DFT analysis. The whole analysis has produced promising results, and <i>N-HyMenatPimeMelly</i> can be treated as a novel potential RAS and ClC-K oral ligand, however, experimental validation is needed before human use. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24441274.v1
title: Cheminformatics approach for identification of <i>N-HyMenatPimeMelly</i> as a novel potential ligand against RAS and renal chloride channel

description: Some angiotensin receptor (AR) blockers interfere with the renal chloride channel (ClC-K), which plays an important role in urine concentration. Identifying ligands targeting this channel, whether activating or blocking, is highly desirable because it could open the way for interventions that modulate their activity. In this study, the Asinex (BioDesign) complete library was screened to identify a compound with favorable physicochemical and pharmacokinetic properties, which have both AR blocking and ClC‐Ka-modulating activities to present it as a novel potential oral candidate which could be useful for treatment of salt-sensitive hypertension without major ClC‐K affection. A compound, N-{[4-Hydroxy-1-(2-methyl-1,6-naphthyridin-4-yl)-4-piperidinyl]methyl}-N-methyl-L-lysinamide (<i>N-HyMenatPimeMelly)</i> (Chem Spider ID 68416221), was identified as a potent potential oral ligand of the renin-angiotensin system (RAS) and ClC-Ka with docking scores ranging from −10.978 to −7.324 with the four selected proteins (4YAY: AR type 1, 2PFI: Cytoplasmic domain of ClC-Ka, 6JOD: AR type 2 and 6M0J: Angiotensin-converting enzyme 2). The protein-ligand complex was used to perform molecular dynamics (MD) simulation for 100 ns. The QikProp and SwissADME tools’ results showed that the compound has ADME/T and drug-likeness properties, which are within the permissible ranges for 95% of known drugs. The density functional theory (DFT) analysis and MD simulation extended the study toward computational validation. Throughout the study, <i>N-HyMenatPimeMelly</i> has shown good interactions and stable performance in MD simulation and DFT analysis. The whole analysis has produced promising results, and <i>N-HyMenatPimeMelly</i> can be treated as a novel potential RAS and ClC-K oral ligand, however, experimental validation is needed before human use. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24420990
title: Integrated molecular modeling and dynamics approaches revealed the mechanism of selective inhibition of HDAC6/8

description: The high structural homology of histone deacetylases 6 and 8 (HDAC6/8) poses a challenge in achieving isoform selectivity and has resulted in adverse side effects due to pan-inhibition in clinical applications. Additionally, the rational design of dual-target inhibitors, centered on HDAC6/8, demands a profound understanding of their selectivity mechanisms. Addressing the urgent need for enhanced specificity in the development of inhibitors targeting specific isoforms, we elucidate the mechanism underpinning the selective inhibition of HDAC6/8 inhibitors through <i>in-silico</i> strategies. The hydrogen bonding interaction with Asp101 and Tyr306 is a key factor that enables compound <b>12b</b> to selectively inhibit HDAC8. Its favorable spatial orientation places the Cap group of <b>12b</b> between Tyr306 and Tyr100, resulting in an overall L-shaped conformation. These two factors significantly contribute to the selective inhibitory activity of <b>12b</b> against HDAC8. The zinc binding group (ZBG) of compound <b>NN-390</b> forms a hydrogen bond with His610, a key residue of HDAC6, facilitating stable chelation with zinc ions. In addition, the Cap group of <b>NN-390</b> interacts with Phe620 and Phe680 <i>via</i> van der Waals forces, leading to an overall Y-shaped conformation. The aforementioned factors are the main reasons for the selective inhibition of HDAC6 by <b>NN-390</b>. Furthermore, whether the Cap group is in the para or meta-position will influence the selective inhibition of either HDAC6 or HDAC8. We believe these clues can offer valuable insights for the rational design of selective inhibitors targeting HDAC6/8 and pave the way for rational design of dual-target HDAC6/8-based inhibitors. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24420990.v1
title: Integrated molecular modeling and dynamics approaches revealed the mechanism of selective inhibition of HDAC6/8

description: The high structural homology of histone deacetylases 6 and 8 (HDAC6/8) poses a challenge in achieving isoform selectivity and has resulted in adverse side effects due to pan-inhibition in clinical applications. Additionally, the rational design of dual-target inhibitors, centered on HDAC6/8, demands a profound understanding of their selectivity mechanisms. Addressing the urgent need for enhanced specificity in the development of inhibitors targeting specific isoforms, we elucidate the mechanism underpinning the selective inhibition of HDAC6/8 inhibitors through <i>in-silico</i> strategies. The hydrogen bonding interaction with Asp101 and Tyr306 is a key factor that enables compound <b>12b</b> to selectively inhibit HDAC8. Its favorable spatial orientation places the Cap group of <b>12b</b> between Tyr306 and Tyr100, resulting in an overall L-shaped conformation. These two factors significantly contribute to the selective inhibitory activity of <b>12b</b> against HDAC8. The zinc binding group (ZBG) of compound <b>NN-390</b> forms a hydrogen bond with His610, a key residue of HDAC6, facilitating stable chelation with zinc ions. In addition, the Cap group of <b>NN-390</b> interacts with Phe620 and Phe680 <i>via</i> van der Waals forces, leading to an overall Y-shaped conformation. The aforementioned factors are the main reasons for the selective inhibition of HDAC6 by <b>NN-390</b>. Furthermore, whether the Cap group is in the para or meta-position will influence the selective inhibition of either HDAC6 or HDAC8. We believe these clues can offer valuable insights for the rational design of selective inhibitors targeting HDAC6/8 and pave the way for rational design of dual-target HDAC6/8-based inhibitors. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24496388
title: System pharmacology-based determination of the functional components and mechanisms in chronic heart failure treatment: an example of Zhenwu decoction

description: Chronic heart failure (CHF) is the primary cause of death among patients with cardiovascular diseases, representing the advanced stage in the development of several cardiovascular conditions. Zhenwu decoction (ZWD) has gained widespread recognition as an efficacious remedy for CHF due to its potent therapeutic properties and absence of adverse effects. Nevertheless, the precise molecular mechanisms underlying its actions remain elusive. This study endeavors to unravel the intricate pharmacological underpinnings of five herbs within ZWD concerning CHF through an integrated approach. Initially, pertinent data regarding ZWD and CHF were compiled from established databases, forming the foundation for constructing an intricate network of active component–target interactions. Subsequently, a pioneering method for evaluating node significance was formulated, culminating in the creation of core functional association space (CFAS). To discern vital components, a novel dynamic programming algorithm was devised and used to determine the core component group (CCG) within the CFAS. Enrichment analysis of the CCG targets unveiled the potential coordinated molecular mechanisms of ZWD, illuminating its capacity to ameliorate CHF by modulating genes and related signaling pathways involved in pathological remodeling. Notable pathways encompass PI3K-Akt, diabetic cardiomyopathy, cAMP and MAPK signaling. Concluding the computational analyses, <i>in vitro</i> experiments were executed to assess the effects of vanillic acid, paradol, 10-gingerol and methyl cinnamate. Remarkably, these compounds demonstrated efficacy in reducing the production of ANP and BNP within isoprenaline-induced AC 16 cells, further validating their potential therapeutic utility. This investigation underscores the efficacy of the proposed model in enhancing the precision and reliability of CCG selection within ZWD, thereby presenting a novel avenue for mechanistic inquiries, compound refinement and the secondary development of TCM herbs.
DOI: 10.6084/m9.figshare.24496388.v1
title: System pharmacology-based determination of the functional components and mechanisms in chronic heart failure treatment: an example of Zhenwu decoction

description: Chronic heart failure (CHF) is the primary cause of death among patients with cardiovascular diseases, representing the advanced stage in the development of several cardiovascular conditions. Zhenwu decoction (ZWD) has gained widespread recognition as an efficacious remedy for CHF due to its potent therapeutic properties and absence of adverse effects. Nevertheless, the precise molecular mechanisms underlying its actions remain elusive. This study endeavors to unravel the intricate pharmacological underpinnings of five herbs within ZWD concerning CHF through an integrated approach. Initially, pertinent data regarding ZWD and CHF were compiled from established databases, forming the foundation for constructing an intricate network of active component–target interactions. Subsequently, a pioneering method for evaluating node significance was formulated, culminating in the creation of core functional association space (CFAS). To discern vital components, a novel dynamic programming algorithm was devised and used to determine the core component group (CCG) within the CFAS. Enrichment analysis of the CCG targets unveiled the potential coordinated molecular mechanisms of ZWD, illuminating its capacity to ameliorate CHF by modulating genes and related signaling pathways involved in pathological remodeling. Notable pathways encompass PI3K-Akt, diabetic cardiomyopathy, cAMP and MAPK signaling. Concluding the computational analyses, <i>in vitro</i> experiments were executed to assess the effects of vanillic acid, paradol, 10-gingerol and methyl cinnamate. Remarkably, these compounds demonstrated efficacy in reducing the production of ANP and BNP within isoprenaline-induced AC 16 cells, further validating their potential therapeutic utility. This investigation underscores the efficacy of the proposed model in enhancing the precision and reliability of CCG selection within ZWD, thereby presenting a novel avenue for mechanistic inquiries, compound refinement and the secondary development of TCM herbs.
DOI: 10.6084/m9.figshare.27931569
title: Diáspora Venezolana - RRSS (+tiktok)

description: Data Set - TikTok #DisporaVenezolana
DOI: 10.6084/m9.figshare.24465493
title: The cytotoxic potential of sinapic acid on luminal A breast cancer; a computational and experimental pharmacology approach

description: Breast cancer is a highly concerning and prevalent disease that impacts a significant proportion of women worldwide, whose repeated exposure to therapies leads to resistance for drugs; making it alarming to identify novel chemotherapeutic agents. Sinapic acid is a phenolic acid that occurs naturally and is known to exhibit cytotoxic action in a variety of cancer cell types. In the present study, we utilized cell cytotoxicity assays to assess the cytotoxic potential of sinapic acid on various breast cancer subtypes. In addition, we assessed the cell migration rate, cell apoptosis, and cell cycle phases. Moreover, we utilized multiple system biology tools to predict the potential targets, and molecular docking was performed on the hub targets followed by molecular dynamic (MD) simulations. Cytotoxicity assay was performed on cell lines MCF7, T47D, MDA-MB-468, and SKBR3 at different time exposures of 24, 48, and 96 h. Our results revealed sinapic acid to be potent on MCF7 and T47D cell lines. The cell cycle analysis and cell apoptotic assays revealed sinapic acid to cause cell death by apoptosis majorly in the G0/G1 phase. Computational biology revealed <i>KIF18B</i> and <i>VKORC1</i> to possess the highest binding affinity of −6.5 and −7.5 kcal/mol; displayed stable trajectories on MD run. The cytotoxicity of sinapic acid on luminal A cell lines may be due to the modulation of <i>VKORC1</i> and <i>KIF18B</i> with major cell death in the G0/G1 phase. However, the mechanism has been proposed <i>via in silico</i> tools, which need further validation using wet lab protocols. Communicated by Ramaswamy H. Sarma