cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21786728.v1
title: IV.2_p0.vcf

description: Somatic mutations observed in single-cell derived colony from fibroblast of individual IV.2 at the start time point of the experiment. Mutations were called using Mutect2. DNA genome sequencing data available from normal tissue (blood, buccal swab or fibroblasts) from the corresponding individual was used as matched normal DNA. Panel of normals (--panel-of-normals Mutect2 argument) was created from all available sequenced blood samples. The population allele frequencies in gnomAD were used as a prior for germline variant detection (--germline-resource Mutect2 argument). Only mutations with vafs between 0.25 and 0.75 were selected for the analysis.
DOI: 10.6084/m9.figshare.21786728
title: IV.2_p0.vcf

description: Somatic mutations observed in single-cell derived colony from fibroblast of individual IV.2 at the start time point of the experiment. Mutations were called using Mutect2. DNA genome sequencing data available from normal tissue (blood, buccal swab or fibroblasts) from the corresponding individual was used as matched normal DNA. Panel of normals (--panel-of-normals Mutect2 argument) was created from all available sequenced blood samples. The population allele frequencies in gnomAD were used as a prior for germline variant detection (--germline-resource Mutect2 argument). Only mutations with vafs between 0.25 and 0.75 were selected for the analysis.
DOI: 10.6084/m9.figshare.21507189.v9
title: CAN5800 & GAN2000 - MODEL WEIGHTS & SAMPLES

description: GAN2000_CAN5800_DEPLOY.zip DATASET/gan2000.csv : url of GAN2000 DATASET/can5800.csv : url of CAN5800 DATASET/download.py : download script Stylegan3-cpu : for generating fakes; not for training <br> PKLs.zip C10000.pkl : Pretrained model; 10000 kimg M500.pkl : GAN20000; melanoma N500.pkl : GAN20000; melanoma MN500.pkl : For morphing; melanoma and nevus <br> mn500.zip : sample images; seed 0~10000 m500.zip : sample images; seed 0~10000 n500.zip : sample images; seed 0~10000 <br> MN500.mp4 : GAN fine-tuning (0 ticks ~ 500 ticks)
DOI: 10.6084/m9.figshare.21786731
title: IV.3_p0.vc

description: Somatic mutations observed in single-cell derived colony from fibroblast of individual IV.3 at the start time point of the experiment. Mutations were called using Mutect2. DNA genome sequencing data available from normal tissue (blood, buccal swab or fibroblasts) from the corresponding individual was used as matched normal DNA. Panel of normals (--panel-of-normals Mutect2 argument) was created from all available sequenced blood samples. The population allele frequencies in gnomAD were used as a prior for germline variant detection (--germline-resource Mutect2 argument). Only mutations with vafs between 0.25 and 0.75 were selected for the analysis.
DOI: 10.6084/m9.figshare.21786731.v1
title: IV.3_p0.vc

description: Somatic mutations observed in single-cell derived colony from fibroblast of individual IV.3 at the start time point of the experiment. Mutations were called using Mutect2. DNA genome sequencing data available from normal tissue (blood, buccal swab or fibroblasts) from the corresponding individual was used as matched normal DNA. Panel of normals (--panel-of-normals Mutect2 argument) was created from all available sequenced blood samples. The population allele frequencies in gnomAD were used as a prior for germline variant detection (--germline-resource Mutect2 argument). Only mutations with vafs between 0.25 and 0.75 were selected for the analysis.
DOI: 10.6084/m9.figshare.21786734
title: IV.4_p0.vcf

description: Somatic mutations observed in single-cell derived colony from fibroblast of individual IV.4 at the start time point of the experiment. Mutations were called using Mutect2. DNA genome sequencing data available from normal tissue (blood, buccal swab or fibroblasts) from the corresponding individual was used as matched normal DNA. Panel of normals (--panel-of-normals Mutect2 argument) was created from all available sequenced blood samples. The population allele frequencies in gnomAD were used as a prior for germline variant detection (--germline-resource Mutect2 argument). Only mutations with vafs between 0.25 and 0.75 were selected for the analysis.
DOI: 10.6084/m9.figshare.21786734.v1
title: IV.4_p0.vcf

description: Somatic mutations observed in single-cell derived colony from fibroblast of individual IV.4 at the start time point of the experiment. Mutations were called using Mutect2. DNA genome sequencing data available from normal tissue (blood, buccal swab or fibroblasts) from the corresponding individual was used as matched normal DNA. Panel of normals (--panel-of-normals Mutect2 argument) was created from all available sequenced blood samples. The population allele frequencies in gnomAD were used as a prior for germline variant detection (--germline-resource Mutect2 argument). Only mutations with vafs between 0.25 and 0.75 were selected for the analysis.
DOI: 10.6084/m9.figshare.21786740
title: IV.6_p0.vcf

description: Somatic mutations observed in single-cell derived colony from fibroblast of individual IV.6 at the start time point of the experiment. Mutations were called using Mutect2. DNA genome sequencing data available from normal tissue (blood, buccal swab or fibroblasts) from the corresponding individual was used as matched normal DNA. Panel of normals (--panel-of-normals Mutect2 argument) was created from all available sequenced blood samples. The population allele frequencies in gnomAD were used as a prior for germline variant detection (--germline-resource Mutect2 argument). Only mutations with vafs between 0.25 and 0.75 were selected for the analysis.
DOI: 10.6084/m9.figshare.21786740.v1
title: IV.6_p0.vcf

description: Somatic mutations observed in single-cell derived colony from fibroblast of individual IV.6 at the start time point of the experiment. Mutations were called using Mutect2. DNA genome sequencing data available from normal tissue (blood, buccal swab or fibroblasts) from the corresponding individual was used as matched normal DNA. Panel of normals (--panel-of-normals Mutect2 argument) was created from all available sequenced blood samples. The population allele frequencies in gnomAD were used as a prior for germline variant detection (--germline-resource Mutect2 argument). Only mutations with vafs between 0.25 and 0.75 were selected for the analysis.
DOI: 10.6084/m9.figshare.21786644
title: Data of Cervical Cancer HPV 16 oncogen E6 or E7 with Cyclin D1 expression.xlsx

description: Data contains a dataset about cervical cancer with HPV type 16 infection cases from Prof. Dr. I.G.N.G. Ngoerah Hospital, Bali, Indonesia. It contains data of 31 samples: HPV Positive (%), Category based on percentage, Mutation/wild oncogene, oncogene mutation, and immunoreactive score of cyclin D1.
DOI: 10.6084/m9.figshare.21786737
title: IV.5_p0.vcf

description: Somatic mutations observed in single-cell derived colony from fibroblast of individual IV.5 at the start time point of the experiment. Mutations were called using Mutect2. DNA genome sequencing data available from normal tissue (blood, buccal swab or fibroblasts) from the corresponding individual was used as matched normal DNA. Panel of normals (--panel-of-normals Mutect2 argument) was created from all available sequenced blood samples. The population allele frequencies in gnomAD were used as a prior for germline variant detection (--germline-resource Mutect2 argument). Only mutations with vafs between 0.25 and 0.75 were selected for the analysis.
DOI: 10.6084/m9.figshare.21786737.v2
title: IV.5_p0.vcf

description: Somatic mutations observed in single-cell derived colony from fibroblast of individual IV.5 at the start time point of the experiment. Mutations were called using Mutect2. DNA genome sequencing data available from normal tissue (blood, buccal swab or fibroblasts) from the corresponding individual was used as matched normal DNA. Panel of normals (--panel-of-normals Mutect2 argument) was created from all available sequenced blood samples. The population allele frequencies in gnomAD were used as a prior for germline variant detection (--germline-resource Mutect2 argument). Only mutations with vafs between 0.25 and 0.75 were selected for the analysis.
DOI: 10.6084/m9.figshare.21786737.v1
title: IV.5_p0

description: Somatic mutations observed in single-cell derived colony from fibroblast of individual IV.5 at the start time point of the experiment. Mutations were called using Mutect2. DNA genome sequencing data available from normal tissue (blood, buccal swab or fibroblasts) from the corresponding individual was used as matched normal DNA. Panel of normals (--panel-of-normals Mutect2 argument) was created from all available sequenced blood samples. The population allele frequencies in gnomAD were used as a prior for germline variant detection (--germline-resource Mutect2 argument). Only mutations with vafs between 0.25 and 0.75 were selected for the analysis.
DOI: 10.6084/m9.figshare.14397854
title: Elucidation of the inhibitory activity of ivermectin with host nuclear importin α and several SARS-CoV-2 targets

description: Ivermectin (IVM) is an FDA-approved drug that has shown antiviral activity against a wide variety of viruses in recent years. IVM inhibits the formation of the importin-α/β1 heterodimeric complex responsible for the translocation and replication of various viral species proteins. Also, IVM hampers SARS-CoV-2 replication in vitro; however, the molecular mechanism through which IVM inhibits SARS-CoV-2 is not well understood. Previous studies have explored the molecular mechanism through which IVM inhibits importin-α and several potential targets associated with COVID-19 by using docking approaches and MD simulations to corroborate the docked complexes. This study explores the energetic and structural properties through which IVM inhibits importin-α and five targets associated with COVID-19 by using docking and MD simulations combined with the molecular mechanics generalized Born surface area (MMGBSA) approach. Energetic and structural analysis showed that the main protease 3CL<sup>pro</sup> reached the most favorable affinity, followed by importin-α and Nsp9, which shared a similar relationship. Therefore, in vitro activity of IVM can be explained by acting as an inhibitor of importin-α, dimeric 3CL<sup>pro</sup>, and Nsp9, but mainly over dimeric 3CL<sup>pro</sup>. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.14397854.v1
title: Elucidation of the inhibitory activity of ivermectin with host nuclear importin α and several SARS-CoV-2 targets

description: Ivermectin (IVM) is an FDA-approved drug that has shown antiviral activity against a wide variety of viruses in recent years. IVM inhibits the formation of the importin-α/β1 heterodimeric complex responsible for the translocation and replication of various viral species proteins. Also, IVM hampers SARS-CoV-2 replication in vitro; however, the molecular mechanism through which IVM inhibits SARS-CoV-2 is not well understood. Previous studies have explored the molecular mechanism through which IVM inhibits importin-α and several potential targets associated with COVID-19 by using docking approaches and MD simulations to corroborate the docked complexes. This study explores the energetic and structural properties through which IVM inhibits importin-α and five targets associated with COVID-19 by using docking and MD simulations combined with the molecular mechanics generalized Born surface area (MMGBSA) approach. Energetic and structural analysis showed that the main protease 3CL<sup>pro</sup> reached the most favorable affinity, followed by importin-α and Nsp9, which shared a similar relationship. Therefore, in vitro activity of IVM can be explained by acting as an inhibitor of importin-α, dimeric 3CL<sup>pro</sup>, and Nsp9, but mainly over dimeric 3CL<sup>pro</sup>. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.14384205
title: Identification of novel multitarget antitubercular inhibitors against mycobacterial peptidoglycan biosynthetic Mur enzymes by structure-based virtual screening

description: Current therapeutic strategies for several diseases, including <i>Mycobacterium tuberculosis</i> infection, have evolved from an initial single-target treatment to a multitarget one. A multitarget antitubercular drugs targeting different mycobacterial proteins are more effective at suppressing bacterial growth. In this study, a high throughput virtual screening was performed to identify hits to the potential antitubercular multitarget: murA, murB, murC, murD, murE, murF, murG and murI from <i>M. tuberculosis</i> that is involved in peptidoglycan biosynthesis. In the virtual screening, we were docked 56,400 compounds of the ChEMBL antimycobacterial library and re-scored and identified the top 10 ranked compounds as antitubercular drug candidates. Further, the best common docked complex CHEMBL446262 was subjected to molecular dynamics simulation to understand the molecule's stability in the presence of an active site environment. After that, we have calculated binding free energy the top-ranked docked complexes using the MM/PBSA method. These ligands exhibited the highest binding affinity; find out novel drug-likeness might show the <i>M. tuberculosis</i> effect's inhibitor by interacting with multitarget Mur enzymes. New antitubercular therapies that include multitarget drugs may have higher efficacy than single-target medicines and provide a more straightforward antitubercular therapy regimen. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.14384205.v1
title: Identification of novel multitarget antitubercular inhibitors against mycobacterial peptidoglycan biosynthetic Mur enzymes by structure-based virtual screening

description: Current therapeutic strategies for several diseases, including <i>Mycobacterium tuberculosis</i> infection, have evolved from an initial single-target treatment to a multitarget one. A multitarget antitubercular drugs targeting different mycobacterial proteins are more effective at suppressing bacterial growth. In this study, a high throughput virtual screening was performed to identify hits to the potential antitubercular multitarget: murA, murB, murC, murD, murE, murF, murG and murI from <i>M. tuberculosis</i> that is involved in peptidoglycan biosynthesis. In the virtual screening, we were docked 56,400 compounds of the ChEMBL antimycobacterial library and re-scored and identified the top 10 ranked compounds as antitubercular drug candidates. Further, the best common docked complex CHEMBL446262 was subjected to molecular dynamics simulation to understand the molecule's stability in the presence of an active site environment. After that, we have calculated binding free energy the top-ranked docked complexes using the MM/PBSA method. These ligands exhibited the highest binding affinity; find out novel drug-likeness might show the <i>M. tuberculosis</i> effect's inhibitor by interacting with multitarget Mur enzymes. New antitubercular therapies that include multitarget drugs may have higher efficacy than single-target medicines and provide a more straightforward antitubercular therapy regimen. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.14406657
title: Docking and molecular dynamics predicted B-DNA and dihydropyrimidinone selenoesters interactions elucidating antiproliferative effects on breast adenocarcinoma cells

description: Dihydropyrimidinones have demonstrated different biological activities including anticancer properties. Cytotoxic potential and antiproliferative potential of new dihydropyrimidinone-derived selenoesters (Se-DHPM) compounds were assessed <i>in vitro</i> against the breast adenocarcinoma cells (MCF-7). Among the eight Se-DHPM compounds tested just 49A and 49F were the most cytotoxic for MCF-7 and the most selective for the non-tumor strain (McCoy) and reduced cell viability in a time- and concentration-dependent manner. Compounds 49A and 49F increased the rate of cell death due to apoptosis and necrosis comparatively to the control, however only the 49F showed antiproliferative potential, reducing the number of colonies formed. In the molecular assay 49A interacts with CT-DNA and caused hyperchromism while 49F caused a hypochromic effect. The intercalation test revealed that the two compounds caused destabilization in the CT-DNA molecule. This effect was evidenced by the loss of fluorescence when the compounds competed and caused the displacement of propidium iodide. Simulations (docking and molecular dynamics) using B-DNA brought a greater understanding of ligand–B-DNA interactions. Furthermore, they predicted that the compounds act as minor groove ligands that are stabilized through hydrogen bonds and hydrophobic interactions. However, the form of interaction foreseen for 49A was more energetically favorable and had more stable hydrogen bonds during the simulation time. Despite some violations foreseen in the ADMET for 49F, the set of other results point to this Se-DHPM as a promising <i>leader</i> compound with anti-tumor potential for breast cancer. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.14406657.v1
title: Docking and molecular dynamics predicted B-DNA and dihydropyrimidinone selenoesters interactions elucidating antiproliferative effects on breast adenocarcinoma cells

description: Dihydropyrimidinones have demonstrated different biological activities including anticancer properties. Cytotoxic potential and antiproliferative potential of new dihydropyrimidinone-derived selenoesters (Se-DHPM) compounds were assessed <i>in vitro</i> against the breast adenocarcinoma cells (MCF-7). Among the eight Se-DHPM compounds tested just 49A and 49F were the most cytotoxic for MCF-7 and the most selective for the non-tumor strain (McCoy) and reduced cell viability in a time- and concentration-dependent manner. Compounds 49A and 49F increased the rate of cell death due to apoptosis and necrosis comparatively to the control, however only the 49F showed antiproliferative potential, reducing the number of colonies formed. In the molecular assay 49A interacts with CT-DNA and caused hyperchromism while 49F caused a hypochromic effect. The intercalation test revealed that the two compounds caused destabilization in the CT-DNA molecule. This effect was evidenced by the loss of fluorescence when the compounds competed and caused the displacement of propidium iodide. Simulations (docking and molecular dynamics) using B-DNA brought a greater understanding of ligand–B-DNA interactions. Furthermore, they predicted that the compounds act as minor groove ligands that are stabilized through hydrogen bonds and hydrophobic interactions. However, the form of interaction foreseen for 49A was more energetically favorable and had more stable hydrogen bonds during the simulation time. Despite some violations foreseen in the ADMET for 49F, the set of other results point to this Se-DHPM as a promising <i>leader</i> compound with anti-tumor potential for breast cancer. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.21371076
title: Green mechanochemical route for the synthesis of carboxy-rich polyaniline/multiwalled carbon nanotubes composite as a competent adsorbent for cationic dyes

description: In the present investigation, we describe a rapid and eco-friendly mechanochemical method that completely avoids the use of corrosive acids for the synthesis of carboxy-rich-polyaniline decorated MCNTs composite (cPANI@MCNTs) at room temperature as an efficient adsorbent for the removal of cationic methylene blue (MB) and methyl violet (MV) dyes from water. The intrinsic physico-chemical properties of newly synthesized materials were characterized by using FTIR, XRD, SEM, and EDX analytical techniques. To ascertain the effects of adsorbent dose, contact time, and pH of the medium on the adsorption process, batch adsorption studies were conducted. It was discovered that pH values of 7 and above are the most favorable for cationic dye adsorption onto cPANI@MCNTs. The adsorption equilibrium data for the dye adsorption process fitted well with the Langmuir model of adsorption and adsorption kinetics disclosed that the data are in excellent agreement with R<sup>2</sup> values of 1 (MB) and 0.99996 (MV) for the pseudo-second-order. The adsorption of dyes on cPANI@MCNTs from thermodynamic data was found to be spontaneous and endothermic in nature. The results indicate that the composite demonstrated admirable maximum adsorption capacity toward both MB (194.9 mg g <sup>−1</sup>) and MV (122.5 mg g <sup>−1</sup>) signifying cPANI@MCNTs as an efficient cationic-dye adsorbent.
DOI: 10.6084/m9.figshare.21371076.v1
title: Green mechanochemical route for the synthesis of carboxy-rich polyaniline/multiwalled carbon nanotubes composite as a competent adsorbent for cationic dyes

description: In the present investigation, we describe a rapid and eco-friendly mechanochemical method that completely avoids the use of corrosive acids for the synthesis of carboxy-rich-polyaniline decorated MCNTs composite (cPANI@MCNTs) at room temperature as an efficient adsorbent for the removal of cationic methylene blue (MB) and methyl violet (MV) dyes from water. The intrinsic physico-chemical properties of newly synthesized materials were characterized by using FTIR, XRD, SEM, and EDX analytical techniques. To ascertain the effects of adsorbent dose, contact time, and pH of the medium on the adsorption process, batch adsorption studies were conducted. It was discovered that pH values of 7 and above are the most favorable for cationic dye adsorption onto cPANI@MCNTs. The adsorption equilibrium data for the dye adsorption process fitted well with the Langmuir model of adsorption and adsorption kinetics disclosed that the data are in excellent agreement with R<sup>2</sup> values of 1 (MB) and 0.99996 (MV) for the pseudo-second-order. The adsorption of dyes on cPANI@MCNTs from thermodynamic data was found to be spontaneous and endothermic in nature. The results indicate that the composite demonstrated admirable maximum adsorption capacity toward both MB (194.9 mg g <sup>−1</sup>) and MV (122.5 mg g <sup>−1</sup>) signifying cPANI@MCNTs as an efficient cationic-dye adsorbent.
DOI: 10.6084/m9.figshare.21766859.v4
title: Data: Spatial habitat structure assembles willow-dependent communities across the primary successional watersheds of Mount St. Helens

description: All data and code for the analyses in "Spatial habitat structure assembles willow-dependent communities across the primary successional watersheds of Mount St. Helens" by Minsavage-Davis et al. 2023.
DOI: 10.6084/m9.figshare.19666488
title: All data and analyses

description: All analyses for "Simple machine learning with aerial imagery reveals severe loss of a salt marsh foundation species."
DOI: 10.6084/m9.figshare.19666488.v6
title: All data and analyses

description: All analyses for "Simple machine learning with aerial imagery reveals severe loss of a salt marsh foundation species."
DOI: 10.6084/m9.figshare.19666488.v5
title: Data: Simple machine learning with aerial imagery reveals severe loss of a salt marsh foundation species

description: All analyses for "Simple machine learning with aerial imagery reveals severe loss of a salt marsh foundation species."