cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14914876
title: Plant derived active compounds as potential anti SARS-CoV-2 agents: an <i>in-silico</i> study

description: Plants are a valued potential source of drugs for a variety of diseases and are often considered less toxic to humans. We investigated antiviral compounds that may potentially target SARS-CoV-2 antigenic spike (S) and host proteins; angiotensin-converting enzyme2 (ACE2), and transmembrane serine protease2 (TMPRSS2). We scrutinized 36 phytochemicals from 15 Indian medicinal plants known to be effective against RNA viruses <i>via</i> molecular docking. Besides, the TMPRSS2 structure was modeled and validated using the SWISS-MODEL. Docking was performed using Autodock Vina and 4.2 followed by visualization of the docking poses on Pymol version 2.4.0 and Discovery Studio Visualizer. Molecular docking showed that 12 out of 36 active compounds interacted efficiently with S, ACE2, and TMPRSS2 proteins. The ADMET profile generated using the swissADME and pkCSM server revealed that these compounds were possessed druggable properties. The Amber 12 simulation package was used to carry out energy minimizations and molecular dynamics (MD) simulations. The total simulation time for both S protein: WFA and S protein: WND complexes was 300 ns (100 ns per replica). A total of 120 structures were extracted from the last 60 ns of each MD simulation for further analysis. MM-PBSA and MM-GBSA were employed to assess the binding energy of each ligand and the receptor-binding domain of the viral S-protein. The methods suggested that WND and WFA showed thermodynamically favorable binding energies, and the S protein had a higher affinity with WND. Interestingly, Leu455 hotspot residue in the S protein, also predicted to participate in binding with ACE2, was engaged by WND and WFA. HighlightsPlants' natural active compounds may aid in the development of COVID-19 therapeutics.MD simulation study revealed stable binding of withanolide D and withaferin A with spike proteinWithanolide D and withaferin A could be effective against SARS-CoV-2 spike protein.Discovery of druggable agents that have less or lack of binding affinity with ACE2 to avoid the organs associated with comorbidities.According to ADMET selected phytochemicals may be used as druggable compounds. Plants' natural active compounds may aid in the development of COVID-19 therapeutics. MD simulation study revealed stable binding of withanolide D and withaferin A with spike protein Withanolide D and withaferin A could be effective against SARS-CoV-2 spike protein. Discovery of druggable agents that have less or lack of binding affinity with ACE2 to avoid the organs associated with comorbidities. According to ADMET selected phytochemicals may be used as druggable compounds. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.14390324
title: Transcriptomic analysis of Pinellia ternata (Thunb.) Breit T2 plus line provides insights in host responses resist Pectobacterium carotovorum infection

description: Transcriptome is used to determine the induction response of <i>Pinellia ternata (Thunb.) Breit</i> T2 plus line (abbreviated as <i>PT2P</i> line) infected with <i>Pectobacterium carotovorum</i>. The main objective of the study was to deal with the transcriptome database of <i>PT2P</i> line resistance to soft rot pathogens to provide a new perspective for identifying the resistance-related genes and understanding the molecular mechanism. Results indicated that water soaking and tissue collapse started at 20 h after <i>PT2P</i> line was infected by <i>P. carotovorum</i>. A total of 1360 and 5768 differentially expressed genes (DEGs) were identified at 0 h and 20 h, respectively. After 20 h of infection, growth and development-related pathways were inhibited. Meanwhile, DEGs were promoted the colonization of <i>P. carotovorum</i> pathogens in specific cell wall modification processes at the early infected stage. A shift to a defensive response was triggered at 0 h. A large number of DEGs were mainly up-controlled at 20 h and were substantially used in the pathogen recognition and the introduction of signal transformation cascades, secondary metabolites biosynthesis, pathogenic proteins activation, transcription aspects and numerous transporters. Furthermore, our data provided novel insights into the transcript reprogramming of <i>PT2P</i> line in response to <i>P. carotovorum</i> infestation.
DOI: 10.6084/m9.figshare.14914876.v1
title: Plant derived active compounds as potential anti SARS-CoV-2 agents: an <i>in-silico</i> study

description: Plants are a valued potential source of drugs for a variety of diseases and are often considered less toxic to humans. We investigated antiviral compounds that may potentially target SARS-CoV-2 antigenic spike (S) and host proteins; angiotensin-converting enzyme2 (ACE2), and transmembrane serine protease2 (TMPRSS2). We scrutinized 36 phytochemicals from 15 Indian medicinal plants known to be effective against RNA viruses <i>via</i> molecular docking. Besides, the TMPRSS2 structure was modeled and validated using the SWISS-MODEL. Docking was performed using Autodock Vina and 4.2 followed by visualization of the docking poses on Pymol version 2.4.0 and Discovery Studio Visualizer. Molecular docking showed that 12 out of 36 active compounds interacted efficiently with S, ACE2, and TMPRSS2 proteins. The ADMET profile generated using the swissADME and pkCSM server revealed that these compounds were possessed druggable properties. The Amber 12 simulation package was used to carry out energy minimizations and molecular dynamics (MD) simulations. The total simulation time for both S protein: WFA and S protein: WND complexes was 300 ns (100 ns per replica). A total of 120 structures were extracted from the last 60 ns of each MD simulation for further analysis. MM-PBSA and MM-GBSA were employed to assess the binding energy of each ligand and the receptor-binding domain of the viral S-protein. The methods suggested that WND and WFA showed thermodynamically favorable binding energies, and the S protein had a higher affinity with WND. Interestingly, Leu455 hotspot residue in the S protein, also predicted to participate in binding with ACE2, was engaged by WND and WFA. HighlightsPlants' natural active compounds may aid in the development of COVID-19 therapeutics.MD simulation study revealed stable binding of withanolide D and withaferin A with spike proteinWithanolide D and withaferin A could be effective against SARS-CoV-2 spike protein.Discovery of druggable agents that have less or lack of binding affinity with ACE2 to avoid the organs associated with comorbidities.According to ADMET selected phytochemicals may be used as druggable compounds. Plants' natural active compounds may aid in the development of COVID-19 therapeutics. MD simulation study revealed stable binding of withanolide D and withaferin A with spike protein Withanolide D and withaferin A could be effective against SARS-CoV-2 spike protein. Discovery of druggable agents that have less or lack of binding affinity with ACE2 to avoid the organs associated with comorbidities. According to ADMET selected phytochemicals may be used as druggable compounds. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12655588.v1
title: Additional file 11 of H3K27ac acetylome signatures reveal the epigenomic reorganization in remodeled non-failing human hearts

description: Additional file 11. Supplementary Table 5. Identified transcription binding motifs from differentially acetylated regions.
DOI: 10.6084/m9.figshare.12655621
title: Additional file 8 of H3K27ac acetylome signatures reveal the epigenomic reorganization in remodeled non-failing human hearts

description: Additional file 8. Supplementary Table 2. a Identified active tandem regulated chromatin domains (TRCDs) in the short range (5Kb–100Kb) in patients when compared with controls. b Identified active TRCDs in the long range (100Kb–1 Mb) in patients when compared with controls. C Identified repressed TRCDs in the short range (5Kb–100Kb) in patients when compared with controls. d Identified repressed TRCDs in the long range (100Kb–1 Mb) in patients when compared with controls. e Randomized TRCDs in the short range (5Kb–100Kb) in patients when compared with controls. f Randomized TRCDs in the long range (100Kb–1 Mb) in patients when compared with controls.
DOI: 10.6084/m9.figshare.12293066.v1
title: Two new Yb(III)-based coordination polymers: structural characterization and treatment effect on femur fracture nonunion combined with PRP and n-HA/PA66

description: Two novel coordination polymers based on Yb(III) ion as the metal ions have been successfully prepared by using two C<sub>3</sub>-symmetrical ligands via a solvothermal synthesis approach, and their chemical formulae are [Yb<sub>1.5</sub>(TAPB)<sub>1.5</sub>(DMF)]·9DMF}<sub>n</sub> (<b>1</b>, TAPB  =  4,4′,4″-(triazine-2,4,6-triyl-tris-(benzene-4,1-diyl)) tribenzoate) and [Yb(TCBPA)·DMF]<sub>n</sub> (<b>2</b>, H<sub>3</sub>TCBPA = tris(4′-carboxybiphenyl)amine). Furthermore, the two complexes were applicated for the fracture nonunion treatment combined with plate let rich plasma (PRP) and n-HA/Polyamide66 (n-HA/PA66). Firstly, the Rat Femur Fracture Nonunion Model was constructed, and compounds <b>1</b> or <b>2</b> was used for indicated treatment combined with PRP and n-HA/PA66, the enzyme linked immunosorbent assay detection was used for the osteocalcin concentration measurement. The reverse transcription-polymerase chain reaction was carried out to determine <i>alp</i> and <i>Runx2</i> relative expression level.
DOI: 10.6084/m9.figshare.12655621.v1
title: Additional file 8 of H3K27ac acetylome signatures reveal the epigenomic reorganization in remodeled non-failing human hearts

description: Additional file 8. Supplementary Table 2. a Identified active tandem regulated chromatin domains (TRCDs) in the short range (5Kb–100Kb) in patients when compared with controls. b Identified active TRCDs in the long range (100Kb–1 Mb) in patients when compared with controls. C Identified repressed TRCDs in the short range (5Kb–100Kb) in patients when compared with controls. d Identified repressed TRCDs in the long range (100Kb–1 Mb) in patients when compared with controls. e Randomized TRCDs in the short range (5Kb–100Kb) in patients when compared with controls. f Randomized TRCDs in the long range (100Kb–1 Mb) in patients when compared with controls.
DOI: 10.6084/m9.figshare.8099177
title: Additional file 2: of scNPF: an integrative framework assisted by network propagation and network fusion for preprocessing of single-cell RNA-seq data

description: Table S1. Benchmark scRNA-seq data sets. (XLSX 9 kb)
DOI: 10.5281/zenodo.10657457
title: Data for the article "Identifying the domain-wall spin structure in antiferromagnetic NiO/Pt"

description: L.B. acknowledges the European Union’s Horizon 2020 research and innovation program under the Marie SkłodowskaCurie Grant Agreement ARTES No. 793159. L.B., M.F., and M.K. acknowledge support from the Graduate School of Excellence Materials Science in Mainz (MAINZ) DFG 266, the DAAD (Spintronics network, Projects No. 57334897 and 57524834). We acknowledge that this work is funded by the Deutsche Forschungsgemeinschaft (DFG; German Research Foundation), TRR 173-268565370 (Spin+X Projects No. A01and No. B02). This project has received funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 863155 (s-Nebula). We acknowledge Diamond Light Source for time on beamline I06 under Proposal No. MM22448. This work is also supported by ERATO “Spin Quantum Rectification Project” (Grant No. JPMJER1402) and the Grant-in-Aid for Scientific Research on Innovative Area, “Nano Spin Conversion Science” (Grant No. JP26103005), Grant-in-Aid for Scientific Research (S) (Grant No. JP19H05600), and Grant-in-Aid for Scientific Research (C) (Grant No. JP20K05297) from JSPS KAKENHI. R.R. also acknowledges support from the Grant RYC 2019- 026915-I funded by the MCIN/AEI/10.13039/501100011033and by the ESF investing in your future, the Xunta de Galicia (ED431F 2022/04, ED431B 2021/013, Centro Singular de Investigación de Galicia Accreditation 2019-2022, ED431G 2019/03) and the European Union (European Regional Development Fund - ERDF). L.S.T. and G.F. acknowledge financial support from the program “ASSEGNI DI RICERCA 2019” at the University of Messina, the project PRIN 2020LWPKH7 funded by the Italian Ministry of University and Research, and the PETASPIN association [53].
DOI: 10.5281/zenodo.10657458
title: Data for the article "Identifying the domain-wall spin structure in antiferromagnetic NiO/Pt"

description: L.B. acknowledges the European Union’s Horizon 2020 research and innovation program under the Marie SkłodowskaCurie Grant Agreement ARTES No. 793159. L.B., M.F., and M.K. acknowledge support from the Graduate School of Excellence Materials Science in Mainz (MAINZ) DFG 266, the DAAD (Spintronics network, Projects No. 57334897 and 57524834). We acknowledge that this work is funded by the Deutsche Forschungsgemeinschaft (DFG; German Research Foundation), TRR 173-268565370 (Spin+X Projects No. A01and No. B02). This project has received funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 863155 (s-Nebula). We acknowledge Diamond Light Source for time on beamline I06 under Proposal No. MM22448. This work is also supported by ERATO “Spin Quantum Rectification Project” (Grant No. JPMJER1402) and the Grant-in-Aid for Scientific Research on Innovative Area, “Nano Spin Conversion Science” (Grant No. JP26103005), Grant-in-Aid for Scientific Research (S) (Grant No. JP19H05600), and Grant-in-Aid for Scientific Research (C) (Grant No. JP20K05297) from JSPS KAKENHI. R.R. also acknowledges support from the Grant RYC 2019- 026915-I funded by the MCIN/AEI/10.13039/501100011033and by the ESF investing in your future, the Xunta de Galicia (ED431F 2022/04, ED431B 2021/013, Centro Singular de Investigación de Galicia Accreditation 2019-2022, ED431G 2019/03) and the European Union (European Regional Development Fund - ERDF). L.S.T. and G.F. acknowledge financial support from the program “ASSEGNI DI RICERCA 2019” at the University of Messina, the project PRIN 2020LWPKH7 funded by the Italian Ministry of University and Research, and the PETASPIN association [53].
DOI: 10.6084/m9.figshare.8099177.v1
title: Additional file 2: of scNPF: an integrative framework assisted by network propagation and network fusion for preprocessing of single-cell RNA-seq data

description: Table S1. Benchmark scRNA-seq data sets. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.12655618.v1
title: Additional file 7 of H3K27ac acetylome signatures reveal the epigenomic reorganization in remodeled non-failing human hearts

description: Additional file 7 Supplementary Table 1. Regions with different H3K27ac occupancy in patients compared with the control group (adjusted p value &lt; 0.05).
DOI: 10.6084/m9.figshare.12285224.v1
title: Additional file 1 of Two old drugs, NVP-AEW541 and GSK-J4, repurposed against the Toxoplasma gondii RH strain

description: Additional file 1: Table S1. Summarized information of inhibition of Toxoplasma gondii growth and host cell viability by all 666 compounds.
DOI: 10.6084/m9.figshare.12293324.v1
title: The Rs12569232 SNP Association with Vogt-Koyanagi-Harada Disease and Behcet’s Disease is Probably Mediated by Regulation of Linc00467 Expression

description: <b>Purpose</b>: To investigate whether the rs12569232 SNP association with Vogt-Koyanagi-Harada disease and Behcet’s disease is mediated by regulation of Linc00467 expression. <b>Methods</b>: The expression of linc00467 was detected by real-time PCR. Adenovirus carrying the linc00467 was transduced into CD4<sup>+</sup>T cells and the effect on cell viability was measured by the CCK-8 test. Human proteome microarray and starBase 2.0 were used to identify the binding proteins of linc00467 and RNA Immunoprecipitation (RIP) was used to confirm the identity of bound proteins. <b>Results</b>: The rs12569232 was associated with the expression of linc00467. The expression of linc00467 was up-regulated in PBMCs and CD4<sup>+</sup>T cells from VKH disease and BD patients. Over-expression of linc00467 increased cell viability of CD4<sup>+</sup>T cells. HUR was the common binding protein identified by the two methods and confirmed by RIP. <b>Conclusions</b>: The rs12569232 association with VKH disease and BD may be mediated via regulating the expression of linc00467.
DOI: 10.6084/m9.figshare.12285080.v1
title: Additional file 2 of Characterization of the interleukin-17 effect on articular cartilage in a translational model: an explorative study

description: Additional file 2: Table S1. 199 proteins selected for differential expression analysis sorted by PEP score. Table S2. Mean log2 abundances of 199 proteins selected for differential expression analysis.
DOI: 10.6084/m9.figshare.8099318
title: Additional file 3: of Initial function of microRNAs as a defence mechanism against invading organisms

description: The predicted domains of all ago and ago-like protein of the 17 species investigated. The domain IDs along with the p values of the predicted domains were listed in this file. (XLSX 23 kb)
DOI: 10.5281/zenodo.10657405
title: Processed tracking data of Southern Giant Petrels during breeding activity in Harmony Point, Nelson Island, between 2021 and 2023

description: Processed GPS data for 36 Southern Giant Petrels (Macronectes giganteus) in December and January of 2021/22 and 2022/23 breeding season in Harmony Point (62°17′60″ S, 59°10′60″ W), Nelson Island, Maritime Antarctic Peninusula. All individuals had active nests. Bill size and tarsus length for 50 southern giant petrels ringed in the area.

Between 2021 and 2023 50 breeding individuals were captured on the nest, following methods and protocols previously approved (https://zenodo.org/doi/10.5281/zenodo.10640094). For capture, one researcher approached the colony, while the others remained at a distance, preferentially out of sight of the birds. Response behavior to the approaching researcher was used as a proxy for capture selection, for instance, animals that regurgitate or stand on the nest exposing the eggs when the researcher approaches are more likely to leave the nest or might take longer to return to the nest after releasing, increasing the risk of breeding failure (Krüger et al. in prep). Therefore, animals displaying those behaviors were not captured. Before capture, the egg was gently removed from below the bird, covered in thermal tissue and put inside a box, for protection from cold and predation. Then the bird was captured by hand and taken to the site where other two researchers were waiting. Animals had their eyes covered with a head hood. All captured animals were ringed with stainless steel bands (rings), preferentially both animals from the same nest each season. All captured animals had bill and tarsus measured with calipers. Bill was used to determine sex, since males have larger bills with no overlap of measures with females. After release back to the nest, behavioral status of the animal was observed, and after the animal remained sat at the nest, the egg was placed back.

GPSs were deployed on the back of the birds using 3M Extreme Hold Duct Tape 2835-B (1.88 inches) and Loctite glue.  In 2021/22 and 2022/2023 seasons 30 and 20 birds were tagged with GPSs, respectively. In 2021/22, 4 females lost the GPS, and in 2022/23 one male and one female lost the GPS. Therefore there was tracking data for 26 and 18 animals, respectively.  Eight animals were repeated in both seasons, totalizing 36 animals tracked in the two seasons. CatLog-P Gen 2 epoxy cased GPSs loggers (Perthold Technology, 50g) and Sputnik XAIS GPSs (Sextant technology, 70g) were used. Southern Giant Petrel weight varies between 4 kg and 6 kg, therefore the heavier instrumentation on the lighter birds would represent less than 2% of body weight, percentage which is accepted to have no significant effect on large procellariforms . Loggers were configurated to record one geographical fix each 5 minutes, and were recovered from the birds after 2 to 4 weeks.

See https://github.com/drlucaskruger/SouthernGiantPetrel_Movements_and_Individual_Size for codes.

This study was funded by INACH (Programa Áreas Marinas Protegidas 24 03 052) and ANID – Programa Iniciativa Milenio – ICN2021_002 (BASE).
DOI: 10.6084/m9.figshare.12285080
title: Additional file 2 of Characterization of the interleukin-17 effect on articular cartilage in a translational model: an explorative study

description: Additional file 2: Table S1. 199 proteins selected for differential expression analysis sorted by PEP score. Table S2. Mean log2 abundances of 199 proteins selected for differential expression analysis.
DOI: 10.6084/m9.figshare.8099393.v1
title: Additional file 4: of Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube

description: KEGG pathway enrichment for DEGs (Level3) at DAT1. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.12285224
title: Additional file 1 of Two old drugs, NVP-AEW541 and GSK-J4, repurposed against the Toxoplasma gondii RH strain

description: Additional file 1: Table S1. Summarized information of inhibition of Toxoplasma gondii growth and host cell viability by all 666 compounds.
DOI: 10.6084/m9.figshare.8099399
title: Additional file 5: of Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube

description: DEGs related to metabolism pathways by MapMan. (XLSX 68 kb)
DOI: 10.6084/m9.figshare.8099384
title: Additional file 3: of Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube

description: GO enrichment for DEGs at DAT1. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.8099399.v1
title: Additional file 5: of Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube

description: DEGs related to metabolism pathways by MapMan. (XLSX 68 kb)