cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24101250.v1
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.24212344
title: RAGE acted as a new anti-inflammatory target for Icariin’s treatment against vascular dementia based on network pharmacology-directed verification

description: Vascular dementia (VaD) ranks as the second most prevalent form of dementia and poses a considerable global health challenge. Icariin has been recognized for its robust neuroprotective effects in combating VaD. Nonetheless, the underlying mechanisms have not been fully elucidated. An integrated approach involving network pharmacology, molecular docking, and molecular dynamics simulations (MDS) was employed to systematically investigate the potential pharmacological actions of Icariin in counteracting VaD. The AGE/RAGE pathway was identified as a promising anti-inflammatory pathway. A chronic cerebral hypoperfusion mouse model was utilized to establish VaD. Both Icariin and FP S-ZM1 (a RAGE inhibitor) were administered through oral gavage and intraperitoneal injection, respectively. The Morris water maze (MWZ) was used to evaluate cognitive functions. Moreover, immunofluorescence, RT-qP CR, and Western blot analyses were carried out to evaluate the effects of FP S-ZM1 on neuroinflammation. Network analysis identified 14 crucial targets and highlighted the AGE-RAGE signaling cascade in diabetic complications as the foremost KEGG pathway with potential anti-neuroinflammatory property. MDS results suggested a stable binding of the RAGE-Icariin complex. Remarkably, Icariin was found to effectively mitigate cognitive deficits in VaD mice, which was correlated with the upregulation of the P I3K/AKT pathway and downregulation of the JNK/cJUN signaling cascade. Critically, co-administration of FP S-ZM1 enhanced Icariin’s ameliorative effects on cognitive deficits, owing to bolstered anti-neuroinflammatory action. This study unveils the potential of Icariin in alleviating cognitive dysfunction and neuroinflammation in VaD, which may be attributed to the modulation of the AGE/RAGE pathway. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24212344.v1
title: RAGE acted as a new anti-inflammatory target for Icariin’s treatment against vascular dementia based on network pharmacology-directed verification

description: Vascular dementia (VaD) ranks as the second most prevalent form of dementia and poses a considerable global health challenge. Icariin has been recognized for its robust neuroprotective effects in combating VaD. Nonetheless, the underlying mechanisms have not been fully elucidated. An integrated approach involving network pharmacology, molecular docking, and molecular dynamics simulations (MDS) was employed to systematically investigate the potential pharmacological actions of Icariin in counteracting VaD. The AGE/RAGE pathway was identified as a promising anti-inflammatory pathway. A chronic cerebral hypoperfusion mouse model was utilized to establish VaD. Both Icariin and FP S-ZM1 (a RAGE inhibitor) were administered through oral gavage and intraperitoneal injection, respectively. The Morris water maze (MWZ) was used to evaluate cognitive functions. Moreover, immunofluorescence, RT-qP CR, and Western blot analyses were carried out to evaluate the effects of FP S-ZM1 on neuroinflammation. Network analysis identified 14 crucial targets and highlighted the AGE-RAGE signaling cascade in diabetic complications as the foremost KEGG pathway with potential anti-neuroinflammatory property. MDS results suggested a stable binding of the RAGE-Icariin complex. Remarkably, Icariin was found to effectively mitigate cognitive deficits in VaD mice, which was correlated with the upregulation of the P I3K/AKT pathway and downregulation of the JNK/cJUN signaling cascade. Critically, co-administration of FP S-ZM1 enhanced Icariin’s ameliorative effects on cognitive deficits, owing to bolstered anti-neuroinflammatory action. This study unveils the potential of Icariin in alleviating cognitive dysfunction and neuroinflammation in VaD, which may be attributed to the modulation of the AGE/RAGE pathway. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24117313
title: Embelin targets PI3K/AKT and MAPK in age-related ulcerative colitis: an integrated approach of microarray analysis, network pharmacology, molecular docking, and molecular dynamics

description: Vaibhdang, an Ayurvedic treatment for Crohn’s and UC, has been used for centuries. The main component of Vaibhdang is embelin derived from <i>Embelia ribes</i>. However, the pharmacological and molecular mechanisms of embelin in UC remain unclear. This study investigated the molecular targets and mechanisms of action of embelin in UC using microarray analysis, network pharmacology, molecular docking, and molecular dynamics simulations. Embelin targets were obtained by Swiss Target, TargetNet, STITCH, ChEMBL, and TCMSP. Ulcerative colitis targets were mapped using DisGenNET, Genecards, TCMSP, Therapeutic targets, and GEO databases (GSE87466). Co-targets between ulcerative colitis and embelin were identified, and a PPI network was constructed using the STRING database. To identify the core targets, we used Cytoscape to analyze the topology of the PPI network. There were 545 effective Embelin targets and 5171 effective ulcerative colitis targets, including 1470 DEG targets. ShinyGo and AutoDock were used to analyze GO and KEGG enrichment pathways and docking studies, respectively. Venn diagram analysis revealed 327 core targets of embelin in UC. An enrichment study showed that embelin is involved in PI3K-AKT, MAPK, RAS, and chemokine signalling. The top ten core targets docked with embelin and AKT1, MAPK1, and SRC complexes were utilized as representations and simulated using GROMACS for 100 ns. A comparison of native proteins and their complex interactions with embelin revealed that embelin might act on various PI3K/AKT and MAPK targets to treat ulcerative colitis. This study provides insights into the molecular targets and mechanisms of action of embelin against ulcerative colitis. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24117313.v1
title: Embelin targets PI3K/AKT and MAPK in age-related ulcerative colitis: an integrated approach of microarray analysis, network pharmacology, molecular docking, and molecular dynamics

description: Vaibhdang, an Ayurvedic treatment for Crohn’s and UC, has been used for centuries. The main component of Vaibhdang is embelin derived from <i>Embelia ribes</i>. However, the pharmacological and molecular mechanisms of embelin in UC remain unclear. This study investigated the molecular targets and mechanisms of action of embelin in UC using microarray analysis, network pharmacology, molecular docking, and molecular dynamics simulations. Embelin targets were obtained by Swiss Target, TargetNet, STITCH, ChEMBL, and TCMSP. Ulcerative colitis targets were mapped using DisGenNET, Genecards, TCMSP, Therapeutic targets, and GEO databases (GSE87466). Co-targets between ulcerative colitis and embelin were identified, and a PPI network was constructed using the STRING database. To identify the core targets, we used Cytoscape to analyze the topology of the PPI network. There were 545 effective Embelin targets and 5171 effective ulcerative colitis targets, including 1470 DEG targets. ShinyGo and AutoDock were used to analyze GO and KEGG enrichment pathways and docking studies, respectively. Venn diagram analysis revealed 327 core targets of embelin in UC. An enrichment study showed that embelin is involved in PI3K-AKT, MAPK, RAS, and chemokine signalling. The top ten core targets docked with embelin and AKT1, MAPK1, and SRC complexes were utilized as representations and simulated using GROMACS for 100 ns. A comparison of native proteins and their complex interactions with embelin revealed that embelin might act on various PI3K/AKT and MAPK targets to treat ulcerative colitis. This study provides insights into the molecular targets and mechanisms of action of embelin against ulcerative colitis. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24168355
title: Decoding the mechanism of andrographolide to combat hepatocellular carcinoma: a network pharmacology integrated molecular docking and dynamics approach

description: HepatoCellular Carcinoma, being one of the most mortally convoluted malignancy with mounting number of occurrences across the world and being classified as the third most prevalent cause of cancer-associated mortalities and sixth most prevalent neoplasia. The active phytoconstituent andrographolide, derived from <i>Andrographis paniculata</i> is conveyed to reconcile a number of human ailments including various oncologies. However, the molecular mechanism underlying the anti-oncogenic effects of Andrographolide on HCC remains skeptical and unclear, emerging as a budding challenge for researchers and oncologists. The present study intends to analyze the underlying pharmacological mechanism of Andrographolide over HCC, established <i>via</i> assimilated approach of network pharmacology. Herein, the Network pharmacology stratagem was instigated to investigate potential HCC targets. The Andrographolide targets along with HCC targets were extracted from multiple databases. A total of 162 potential overlapping targets among HCC and Andrographolide were obtained and further subjected to gene ontology and Pathway enrichment analysis by employing OmicsBox and DAVID database, respectively. Subsequently, Protein–protein interaction network construction by Cytoscape software identified the top 10 hub nodes which were validated by survival and expression analysis. Further, the results derived from molecular docking and dynamic simulations by CB-Dock2 server and Desmond module (Schrodinger software) indicate ALB, CCND1, HIF1A, TNF, and VEGFA as potential Andrographolide related targets with high binding affinity and promising complex stability. Our findings not only reveal the antioncogenic role of andrographolide but also provide novel insights illuminating the identified targets as scientific foundation for anti-oncogenic clinical application of andrographolide in HCC therapeutics. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24168355.v1
title: Decoding the mechanism of andrographolide to combat hepatocellular carcinoma: a network pharmacology integrated molecular docking and dynamics approach

description: HepatoCellular Carcinoma, being one of the most mortally convoluted malignancy with mounting number of occurrences across the world and being classified as the third most prevalent cause of cancer-associated mortalities and sixth most prevalent neoplasia. The active phytoconstituent andrographolide, derived from <i>Andrographis paniculata</i> is conveyed to reconcile a number of human ailments including various oncologies. However, the molecular mechanism underlying the anti-oncogenic effects of Andrographolide on HCC remains skeptical and unclear, emerging as a budding challenge for researchers and oncologists. The present study intends to analyze the underlying pharmacological mechanism of Andrographolide over HCC, established <i>via</i> assimilated approach of network pharmacology. Herein, the Network pharmacology stratagem was instigated to investigate potential HCC targets. The Andrographolide targets along with HCC targets were extracted from multiple databases. A total of 162 potential overlapping targets among HCC and Andrographolide were obtained and further subjected to gene ontology and Pathway enrichment analysis by employing OmicsBox and DAVID database, respectively. Subsequently, Protein–protein interaction network construction by Cytoscape software identified the top 10 hub nodes which were validated by survival and expression analysis. Further, the results derived from molecular docking and dynamic simulations by CB-Dock2 server and Desmond module (Schrodinger software) indicate ALB, CCND1, HIF1A, TNF, and VEGFA as potential Andrographolide related targets with high binding affinity and promising complex stability. Our findings not only reveal the antioncogenic role of andrographolide but also provide novel insights illuminating the identified targets as scientific foundation for anti-oncogenic clinical application of andrographolide in HCC therapeutics. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24137480
title: Antitumor activities of a novel fluorinated small molecule (A1) in CT26 colorectal cancer cells: molecular docking and in vitro studies

description: Chemotherapeutic treatment of colorectal cancer (CRC) has not been satisfactory until now; therefore, the discovery of more efficient medications is of great significance. Based on available knowledge, the CXCL12/CXCR4 axis plays a significant role in tumorigenesis, and inhibition of CXCR4 chemokine receptor with AMD3100 is one of the most known therapeutic modalities in cancer therapy. Herein, N, N''-thiocarbonylbis(N'-(3,4-dimethylphenyl)-2,2,2-trifluoroacetimidamide) (<b>A1</b>) was synthesized as a potent CXCR4 inhibitor. <b>A1</b> inhibitory activity was first evaluated employing Molecular Docking simulations in comparison with the most potent CXCR4 inhibitors. Then, the antiproliferative and cytotoxic effect of <b>A1</b> on CT26 mouse CRC cells was investigated by MTT assay technique and compared with those of the control molecule, AMD3100. The impact of the target compounds IC<sub>50</sub> on apoptosis, cell cycle arrest, and CXCR4 expression was determined by flow cytometry technique. Our finding demonstrated that <b>A1</b> induces a cytotoxic effect on CT26 cells at 60 μg/mL concentration within 72 h and provokes cell apoptosis and G2/M cell cycle arrest in comparison with the untreated cells, while AMD3100 did not show a cytotoxic effect up to 800 μg/mL dose. The obtained results show that <b>A1</b> (at a concentration of 40 μg/mL) significantly reduced the proliferation of CT26 cells treated with 100 ng/mL of CXCL12 in 72 h. Moreover, treatment with 60 μg/mL of <b>A1</b> and 100 ng/mL of CXCL12 for 72 h significantly decreased the number of cells expressing the CXCR4 receptor compared to the control group treated with CXCL12. Eventually, the obtained results indicate that <b>A1</b>, as a dual-function fluorinated small molecule, may benefit CRC treatment through inhibition of CXCR4 and exert a cytotoxic effect on tumor cells. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24137480.v1
title: Antitumor activities of a novel fluorinated small molecule (A1) in CT26 colorectal cancer cells: molecular docking and in vitro studies

description: Chemotherapeutic treatment of colorectal cancer (CRC) has not been satisfactory until now; therefore, the discovery of more efficient medications is of great significance. Based on available knowledge, the CXCL12/CXCR4 axis plays a significant role in tumorigenesis, and inhibition of CXCR4 chemokine receptor with AMD3100 is one of the most known therapeutic modalities in cancer therapy. Herein, N, N''-thiocarbonylbis(N'-(3,4-dimethylphenyl)-2,2,2-trifluoroacetimidamide) (<b>A1</b>) was synthesized as a potent CXCR4 inhibitor. <b>A1</b> inhibitory activity was first evaluated employing Molecular Docking simulations in comparison with the most potent CXCR4 inhibitors. Then, the antiproliferative and cytotoxic effect of <b>A1</b> on CT26 mouse CRC cells was investigated by MTT assay technique and compared with those of the control molecule, AMD3100. The impact of the target compounds IC<sub>50</sub> on apoptosis, cell cycle arrest, and CXCR4 expression was determined by flow cytometry technique. Our finding demonstrated that <b>A1</b> induces a cytotoxic effect on CT26 cells at 60 μg/mL concentration within 72 h and provokes cell apoptosis and G2/M cell cycle arrest in comparison with the untreated cells, while AMD3100 did not show a cytotoxic effect up to 800 μg/mL dose. The obtained results show that <b>A1</b> (at a concentration of 40 μg/mL) significantly reduced the proliferation of CT26 cells treated with 100 ng/mL of CXCL12 in 72 h. Moreover, treatment with 60 μg/mL of <b>A1</b> and 100 ng/mL of CXCL12 for 72 h significantly decreased the number of cells expressing the CXCR4 receptor compared to the control group treated with CXCL12. Eventually, the obtained results indicate that <b>A1</b>, as a dual-function fluorinated small molecule, may benefit CRC treatment through inhibition of CXCR4 and exert a cytotoxic effect on tumor cells. Communicated by Ramaswamy H. Sarma
DOI: 10.15468/dl.w37yxw
title: Occurrence Download

description: A dataset containing 16212 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rubus bifrons Vest ex Tratt."
 ]
}

 The dataset includes 16212 records from 234 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017408-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.unttqv
title: Occurrence Download

description: A dataset listing the 100 species recorded in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON((45.14408 53.19985,45.12681 53.19108,45.14815 53.17444,45.15851 53.17977,45.15204 53.18574,45.14928 53.18714,45.14973 53.19591,45.14408 53.19985))"
 ]
}

 The dataset's 100 records were derived from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017406-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5258/soton/d3173
title: Dataset in support of the thesis 'Reputational risk management in the social media age: an evaluation of reputation management in the service industry of an emerging economy'

description: The data consists of two Excel files. The first file is the first paper data, which was harvested from Twitter platforms for six insurance firms in Saudi Arabia. In addition, the second file is the data for the third study, which was collected using a questionnaire from Saudi/resident customers who had experienced purchasing motor insurance from Saudi insurers.
DOI: 10.23729/be058a47-4418-4e4c-b17c-d35de1a9f60b
title: Data for Kotilainen et al.: "Detecting consistent patterns in pseudorange residuals in GNSS timing data"

description: CGGTTS data analyzed in Kotilainen et al.: "Detecting consistent patterns in pseudorange residuals in GNSS timing data". CGGTTS is currently used by over 70 laboratories to compute the Coordinated Universal Time (UTC) together with Precise Point Positioning.
DOI: 10.15468/dl.qq9vnj
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Grewia hierniana Exell & Mendonça",
 "Continent is Africa"
 ]
}

 The dataset includes 44 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017410-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3x2u4f
title: Occurrence Download

description: A dataset containing 714 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Abildgaardia ovata (Burm.f.) Kral",
 "Continent is Africa"
 ]
}

 The dataset includes 714 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017411-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.345mvb
title: Occurrence Download

description: A dataset containing 555 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acroceras macrum Stapf",
 "Continent is Africa"
 ]
}

 The dataset includes 555 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017412-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wcpa8p
title: Occurrence Download

description: A dataset containing 13734 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bubalus bubalis (Linnaeus, 1758)"
 ]
}

 The dataset includes 13734 records from 98 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017413-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14024635
title: dictionaria/diidxaza: La Ventosa Diidxazá Lexico-Botanical Dictionary

description: Pérez Báez, Gabriela and Kaufman, Terrence. 2018. La Ventosa Diidxazá Lexico-Botanical Dictionary. Dictionaria 5. 1-952 (Available online at https://dictionaria.clld.org/contributions/diidxaza)
DOI: 10.5281/zenodo.4675104
title: dictionaria/diidxaza: La Ventosa Diidxazá Lexico-Botanical Dictionary

description: Pérez Báez, Gabriela and Kaufman, Terrence. 2018. La Ventosa Diidxazá Lexico-Botanical Dictionary. Dictionaria 5. 1-952 (Available online at https://dictionaria.clld.org/contributions/diidxaza)
DOI: 10.5281/zenodo.5526305
title: dictionaria/diidxaza: La Ventosa Diidxazá Lexico-Botanical Dictionary

description: Pérez Báez, Gabriela and Kaufman, Terrence. 2018. La Ventosa Diidxazá Lexico-Botanical Dictionary. Dictionaria 5. 1-952 (Available online at https://dictionaria.clld.org/contributions/diidxaza)
DOI: 10.5281/zenodo.3451856
title: dictionaria/diidxaza: La Ventosa Diidxazá Lexico-Botanical Dictionary

description: Pérez Báez, Gabriela and Kaufman, Terrence. 2018. La Ventosa Diidxazá Lexico-Botanical Dictionary. Dictionaria 5. 1-952 (Available online at https://dictionaria.clld.org/contributions/diidxaza)
DOI: 10.15468/dl.txrx3r
title: Occurrence Download

description: A dataset containing 199 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Adenochloa adenophora (K.Schum.) Zuloaga",
 "Continent is Africa"
 ]
}

 The dataset includes 199 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017414-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.