cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24711779
title: Probable targets and mechanism of ginsenoside Rg1 for non-alcoholic fatty liver disease: a study integrating network pharmacology, molecular docking, and molecular dynamics simulation

description: Ginsenoside Rg1 (GRg1), a key bioactive component of medicinal herbs, has shown beneficial effects on non-alcoholic fatty liver disease (NAFLD) and numerous other conditions. Nevertheless, the specific targets that are actively involved and the potential mechanisms underlying NAFLD treatment remain unclear. This study aimed to elucidate the therapeutic effects and mechanism of GRg1 in alleviating NAFLD using a combined approach of network pharmacology and molecular biology validation. The analysis yielded 294 targets for GRg1 and 1293 associated with NAFLD, resulting in 89 overlapping targets. Through protein-protein interactions (PPI) network topology analysis, 10 key targets were identified. Upon evaluating the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) analysis, GRg1 may exert therapeutic effects on NAFLD by negatively regulating the apoptotic process, insulin and endocrine resistance, the AGE-RAGE signaling pathway in diabetic complications, and the Estrogen, PI3K/Akt, and MAPK pathways. The three differential gene targets for Akt1, EGFR, and IGF1 were identified through the compound-target network in conjunction with the aforementioned methods. The molecular docking and molecular dynamics (MD) simulations showed that AKT1 and EGFR had a strong binding affinity with GRg1. Overall, our findings point to a novel therapeutic strategy involving NAFLD, with further <i>in vivo</i> and <i>in vitro</i> studies promising to deepen our comprehension and validate its potential advantages.
DOI: 10.6084/m9.figshare.24721556
title: Network pharmacology and molecular docking to study the potential molecular mechanism of Qi Fu Yin for diabetic encephalopathy

description: Diabetic encephalopathy is a chronic complication of diabetes that lacks an optimized treatment strategy. The present study sought to elucidate the potential molecular mechanism of Qi Fu Yin in improving diabetic encephalopathy through network pharmacology. The active components and target information of Qi Fu Yin were obtained from the TCMSP and Swiss target databases, while the target information of diabetic encephalopathy was sourced from Gene cards, OMIM, and Pharm Gkb databases. Enrichment analyses of KEGG and GO were conducted utilizing drug-disease common targets, while protein-protein interactions were predicted through the utilization of the STRING database platform. Subsequently, molecular docking was executed via Auto Dock Vina to authenticate the interaction between core components and core targets. The findings revealed that Qi Fu Yin exhibited 178 common targets with diabetic encephalopathy, and the enrichment analyses demonstrated that these targets were associated with lipid and atherosclerosis, AGE-RAGE signaling pathways, and other related pathways. The findings of the molecular docking indicated a favorable binding affinity between the active components of drug and the core targets, with EGF and quercetin exhibiting the most notable docking score. Additionally, the molecular dynamics simulation corroborated this high affinity. These results suggested that the active ingredients of Qi Fu Yin, including quercetin and kaempferol, may modulated the expression of genes such as IL10, TNF, EGF, and MMP2, thereby activating the AGE-RAGE signaling pathways and potentially serving as a therapeutic intervention for diabetic encephalopathy.
DOI: 10.6084/m9.figshare.24721556.v1
title: Network pharmacology and molecular docking to study the potential molecular mechanism of Qi Fu Yin for diabetic encephalopathy

description: Diabetic encephalopathy is a chronic complication of diabetes that lacks an optimized treatment strategy. The present study sought to elucidate the potential molecular mechanism of Qi Fu Yin in improving diabetic encephalopathy through network pharmacology. The active components and target information of Qi Fu Yin were obtained from the TCMSP and Swiss target databases, while the target information of diabetic encephalopathy was sourced from Gene cards, OMIM, and Pharm Gkb databases. Enrichment analyses of KEGG and GO were conducted utilizing drug-disease common targets, while protein-protein interactions were predicted through the utilization of the STRING database platform. Subsequently, molecular docking was executed via Auto Dock Vina to authenticate the interaction between core components and core targets. The findings revealed that Qi Fu Yin exhibited 178 common targets with diabetic encephalopathy, and the enrichment analyses demonstrated that these targets were associated with lipid and atherosclerosis, AGE-RAGE signaling pathways, and other related pathways. The findings of the molecular docking indicated a favorable binding affinity between the active components of drug and the core targets, with EGF and quercetin exhibiting the most notable docking score. Additionally, the molecular dynamics simulation corroborated this high affinity. These results suggested that the active ingredients of Qi Fu Yin, including quercetin and kaempferol, may modulated the expression of genes such as IL10, TNF, EGF, and MMP2, thereby activating the AGE-RAGE signaling pathways and potentially serving as a therapeutic intervention for diabetic encephalopathy.
DOI: 10.6084/m9.figshare.24606451
title: <i>In silico</i> exploration and <i>in vitro</i> validation of the filarial thioredoxin reductase inhibitory activity of Scytonemin and its derivatives

description: Lymphatic filariasis (LF) caused by the vector borne parasitic nematode <i>Wuchereria bancrofti</i> is of major concern of the World Health Organization (WHO). Lack of potential drug candidates worsens the situation. Presently available drugs are promising in killing the microfilaria (mf) but are not effective as adulticidal therapeutics. Previous studies have revealed that routine administration of the available drugs (albendazole, ivermectin and albendazole) sometime is associated with severe adverse effects (SAEs) in co-infection state. Therefore, potential and safe therapeutics are still required. Earlier studies on filarial thioredoxin reductase (TrxR) have shown that successful inhibition of it can lead to apoptotic death of the parasites. TrxR in filarial parasites plays a significant role in disease progression and pathogenesis, hence efficient non-reversible inhibition of TrxR can be a good strategy to treat LF. In this research, inhibitory potential of Scytonemin, a cyanobacterial metabolite on filarial TrxR was evaluated <i>via</i> different <i>in silico</i> methods and validated through <i>in vitro</i> experiments. Parasite death upon exposure to Scytonemin can be correlated with the TrxR inhibiting capacity of the compound. Therefore, this cyanobacterial-derived compound may possibly be used further as novel and safe therapeutic candidate against filarial infection.
DOI: 10.6084/m9.figshare.24606451.v1
title: <i>In silico</i> exploration and <i>in vitro</i> validation of the filarial thioredoxin reductase inhibitory activity of Scytonemin and its derivatives

description: Lymphatic filariasis (LF) caused by the vector borne parasitic nematode <i>Wuchereria bancrofti</i> is of major concern of the World Health Organization (WHO). Lack of potential drug candidates worsens the situation. Presently available drugs are promising in killing the microfilaria (mf) but are not effective as adulticidal therapeutics. Previous studies have revealed that routine administration of the available drugs (albendazole, ivermectin and albendazole) sometime is associated with severe adverse effects (SAEs) in co-infection state. Therefore, potential and safe therapeutics are still required. Earlier studies on filarial thioredoxin reductase (TrxR) have shown that successful inhibition of it can lead to apoptotic death of the parasites. TrxR in filarial parasites plays a significant role in disease progression and pathogenesis, hence efficient non-reversible inhibition of TrxR can be a good strategy to treat LF. In this research, inhibitory potential of Scytonemin, a cyanobacterial metabolite on filarial TrxR was evaluated <i>via</i> different <i>in silico</i> methods and validated through <i>in vitro</i> experiments. Parasite death upon exposure to Scytonemin can be correlated with the TrxR inhibiting capacity of the compound. Therefore, this cyanobacterial-derived compound may possibly be used further as novel and safe therapeutic candidate against filarial infection.
DOI: 10.15468/dl.hd2nng
title: Occurrence Download

description: A dataset containing 45255 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Paulownia tomentosa (Thunb.) Steud., Paulownia glabrata Rehder, Paulownia imperialis var. lanata Dode, Paulownia coreana Uyeki, Bignonia tomentosa Thunb., Paulownia grandifolia Wettst., Paulownia lilacina Sprague, Paulownia imperialis Siebold & Zucc., Paulownia tomentosa f. virginea H.Ohashi, Paulownia imperialis var. pallida Dode, Paulownia tomentosa var. japonica Elwes, Paulownia recurva Rehder, Paulownia intermedia T.B.Lee, Paulownia tomentosa var. glabrata (Rehder) S.Z.Qu, Paulownia tomentosa var. lanata (Dode) C.K.Schneid., Incarvillea tomentosa (Thunb.) Spreng., Paulownia tomentosa (Thunb.) Britton, Paulownia tomentosa f. pallida (Dode) Rehder, Paulownia tomentosa var. pallida (Dode) C.K.Schneid.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 45255 records from 301 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000548-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13322617
title: CreatureCast

description: CreatureCast is a collaborative blog produced by members of the Dunn Lab at Brown University, along with assorted friends. This project, which is focussed on zoology in the broad sense, serves as a forum to present original content that we have produced and observations by others that we find interesting and beautiful. Support for some original podcast content is provided by the National Science Foundation (NSF). Mollusc themed podcasts are supported by a collaborative NSF research grant to Casey Dunn, Gonzalo Giribet, and Nerida Wilson. Thanks to Bruce Gellerman for consultation and guidance. Web design graciously provided by Jeremy Ashkenas. Thanks to Erika Edwards for suggesting the name CreatureCast. https://vimeo.com/search?q=creaturecast
DOI: 10.5281/zenodo.13322618
title: CreatureCast

description: CreatureCast is a collaborative blog produced by members of the Dunn Lab at Brown University, along with assorted friends. This project, which is focussed on zoology in the broad sense, serves as a forum to present original content that we have produced and observations by others that we find interesting and beautiful. Support for some original podcast content is provided by the National Science Foundation (NSF). Mollusc themed podcasts are supported by a collaborative NSF research grant to Casey Dunn, Gonzalo Giribet, and Nerida Wilson. Thanks to Bruce Gellerman for consultation and guidance. Web design graciously provided by Jeremy Ashkenas. Thanks to Erika Edwards for suggesting the name CreatureCast. https://vimeo.com/search?q=creaturecast
DOI: 10.6084/m9.figshare.24788270
title: Phytocompounds from <i>Phyllanthus acidus</i> (L.) Skeels in the management of Monkeypox Virus infections

description: Monkeypox is a communicable disease similar to smallpox, primarily occurring in African countries. However, recently it has spread to countries outside Africa and may arise as the next threat after COVID-pandemic. The causative organism, i.e. Monkeypox Virus (MPV) spreads from one individual to another primarily through inhalation of respiratory droplets or through contact with skin lesions of infected individuals. No known drugs are available specifically for MPV. Due to its similarity with smallpox, treatment of monkeypox is being attempted through the administration of the smallpox vaccine. Therefore, we evaluated the efficacy of the plant <i>Phyllanthus acidus</i> against MPV since it is traditionally used in the treatment of chickenpox and smallpox. Through functional annotation, PASS prediction and Network pharmacology analysis, the effectiveness of these chosen <i>P. acidus</i>-derived phytocompounds against MPV was confirmed. Target prediction of the phytocompounds identified in GC-MS analysis of the plant extract showed them to be associated with 76 human proteins. The compounds also show good binding affinity with selected viral proteins: DNA polymerase (DNApol), Putative Virulence Factor (vPVF) and Cytokine Binding Protein. Prediction of Activity Spectra for Substances (PASS) and functional annotation of the target proteins further support their antiviral nature through interaction with these proteins. The compounds were found to modulate pathways related to symptoms of viral infection and this may help in maintaining homeostasis. Our study demonstrates antiviral activity as well as the therapeutic potential of the plant against MPV infection.
DOI: 10.6084/m9.figshare.24788270.v1
title: Phytocompounds from <i>Phyllanthus acidus</i> (L.) Skeels in the management of Monkeypox Virus infections

description: Monkeypox is a communicable disease similar to smallpox, primarily occurring in African countries. However, recently it has spread to countries outside Africa and may arise as the next threat after COVID-pandemic. The causative organism, i.e. Monkeypox Virus (MPV) spreads from one individual to another primarily through inhalation of respiratory droplets or through contact with skin lesions of infected individuals. No known drugs are available specifically for MPV. Due to its similarity with smallpox, treatment of monkeypox is being attempted through the administration of the smallpox vaccine. Therefore, we evaluated the efficacy of the plant <i>Phyllanthus acidus</i> against MPV since it is traditionally used in the treatment of chickenpox and smallpox. Through functional annotation, PASS prediction and Network pharmacology analysis, the effectiveness of these chosen <i>P. acidus</i>-derived phytocompounds against MPV was confirmed. Target prediction of the phytocompounds identified in GC-MS analysis of the plant extract showed them to be associated with 76 human proteins. The compounds also show good binding affinity with selected viral proteins: DNA polymerase (DNApol), Putative Virulence Factor (vPVF) and Cytokine Binding Protein. Prediction of Activity Spectra for Substances (PASS) and functional annotation of the target proteins further support their antiviral nature through interaction with these proteins. The compounds were found to modulate pathways related to symptoms of viral infection and this may help in maintaining homeostasis. Our study demonstrates antiviral activity as well as the therapeutic potential of the plant against MPV infection.
DOI: 10.6084/m9.figshare.24647979
title: The dynamics of <i>Escherichia coli</i> FtsZ dimer

description: The <i>E. coli</i> FtsZ dimer was studied to gain insights into FtsZ protofilament formation. In the simulation study of the <i>M. janaschii</i> dimer it was found that the monomer-monomer contacts in the GDP bound dimer is lower which results in the high curvature of the GDP bound protofilaments. In this study, the <i>E. coli</i> FtsZ dimer was simulated. The initial structure was obtained from our previous study in which we had simulated the <i>E. coli</i> FtsZ monomer with its C-terminal IDR (Intrinsically Disordered Region). The <i>M. janaschii</i> FtsZ dimer subunit contacts were used as the starting configuration. Simulations of the dimer were performed with GTP and with GDP. It is found that the central helix H5 closes by about 15 degrees in the simulation with GTP than in the simulation with GDP. The C-terminal IDR and the C-terminal domain region between SC2 and HC2 are found to have much high flexibility and hence exhibit domain motion.
DOI: 10.6084/m9.figshare.24647979.v1
title: The dynamics of <i>Escherichia coli</i> FtsZ dimer

description: The <i>E. coli</i> FtsZ dimer was studied to gain insights into FtsZ protofilament formation. In the simulation study of the <i>M. janaschii</i> dimer it was found that the monomer-monomer contacts in the GDP bound dimer is lower which results in the high curvature of the GDP bound protofilaments. In this study, the <i>E. coli</i> FtsZ dimer was simulated. The initial structure was obtained from our previous study in which we had simulated the <i>E. coli</i> FtsZ monomer with its C-terminal IDR (Intrinsically Disordered Region). The <i>M. janaschii</i> FtsZ dimer subunit contacts were used as the starting configuration. Simulations of the dimer were performed with GTP and with GDP. It is found that the central helix H5 closes by about 15 degrees in the simulation with GTP than in the simulation with GDP. The C-terminal IDR and the C-terminal domain region between SC2 and HC2 are found to have much high flexibility and hence exhibit domain motion.
DOI: 10.5281/zenodo.13319101
title: Martin, 2000

description: Martin, R.E. Other Aquatic Life of Economic Significance: Frogs and Frog Legs. In: Roy E. Martin, Emily Paine Carter, George J. Flick, Jr., Lynn M. Davis. 2000. Marine and Freshwater Products Handbook. CRC Press. https://books.google.com/books?id=OFKLk3S0fzgC&pg=PA279&lpg=PA279
DOI: 10.5281/zenodo.13319102
title: Martin, 2000

description: Martin, R.E. Other Aquatic Life of Economic Significance: Frogs and Frog Legs. In: Roy E. Martin, Emily Paine Carter, George J. Flick, Jr., Lynn M. Davis. 2000. Marine and Freshwater Products Handbook. CRC Press. https://books.google.com/books?id=OFKLk3S0fzgC&pg=PA279&lpg=PA279
DOI: 10.5281/zenodo.13318202
title: Phenoscape Catfish Fin Shapes

description: This is where EOL hosts source datasets (archives, dumps, etc.) from EOL content partners (especially partners without a web presence of their own).

This organization will also include the content partner utility files EOL connectors use to generate a particular content partner__s resource EOL archive or XML.

For questions or suggestions please visit the EOL Services forum at http://discuss.eol.org/c/eol-services
DOI: 10.5281/zenodo.13318203
title: Phenoscape Catfish Fin Shapes

description: This is where EOL hosts source datasets (archives, dumps, etc.) from EOL content partners (especially partners without a web presence of their own).

This organization will also include the content partner utility files EOL connectors use to generate a particular content partner__s resource EOL archive or XML.

For questions or suggestions please visit the EOL Services forum at http://discuss.eol.org/c/eol-services
DOI: 10.15468/dl.e38kd7
title: Occurrence Download

description: A dataset containing 247 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Ambystoma mexicanum (Shaw & Nodder, 1798)"
 ]
}

 The dataset includes 247 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000552-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9nkuz9
title: Occurrence Download

description: A dataset containing 1278 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Lactarius indigo (Schwein.) Fr."
 ]
}

 The dataset includes 1278 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000555-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13315704
title: Copepod sizes

description: Measured from specimen photos in EOL with scale bars visible.
DOI: 10.5281/zenodo.13315705
title: Copepod sizes

description: Measured from specimen photos in EOL with scale bars visible.
DOI: 10.15468/dl.39ekz9
title: Occurrence Download

description: A dataset containing 1548 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Panthera onca (Linnaeus, 1758)"
 ]
}

 The dataset includes 1548 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000550-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.at59he
title: Occurrence Download

description: A dataset containing 175 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Cypripedium irapeanum Lex."
 ]
}

 The dataset includes 175 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000556-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fcafft
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eleginus gracilis (Tilesius, 1810)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 38 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000551-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jepa34
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Photinus palaciosi (Zaragoza, 2012)"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000553-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.urpfez
title: Occurrence Download

description: A dataset containing 297 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Romerolagus diazi (Ferrari-Pérez, 1893)"
 ]
}

 The dataset includes 297 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000554-250213122211068/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13318141
title: Deans, Deitz, Wharton et al

description: Collective content from this project is the product of from multiple independent labs (Deans - NCSU, http://evanioidea.info); Deitz et al. - NCSU, 
http://treehoppers.insectmuseum.org; Wharton - TAMU, 
http://paroffit.org) whose data are managed in an instance of mx (
http://mx.phenomix.org).
DOI: 10.5281/zenodo.13318142
title: Deans, Deitz, Wharton et al

description: Collective content from this project is the product of from multiple independent labs (Deans - NCSU, http://evanioidea.info); Deitz et al. - NCSU, 
http://treehoppers.insectmuseum.org; Wharton - TAMU, 
http://paroffit.org) whose data are managed in an instance of mx (
http://mx.phenomix.org).