cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13546836.v1
title: Influence of the dimensionality of the periodic boundary conditions on the transport of a drug–peptide complex across model cell membranes

description: Many research efforts are devoted to improving the efficiency of chemotherapy. One of the aspects is to facilitate the transport of drugs across the cell membranes by attaching the therapeutics to a carrier molecule. The current study focuses on computational investigation of such a system with doxorubicin as the model drug, which is covalently bound to a cell-penetrating peptide. The correct description of its membrane translocation at the molecular level requires proper choice of the model membrane and of the simulation parameters. For the purpose, two phospholipid bilayers are built, one containing solely DPPC and another with mixed lipid content mimicking the composition of a human erythrocyte membrane. Atomistic molecular dynamics simulations are carried out in two types of periodic boundary conditions (2D and 3D PBC), in order to assess the effect of the periodicity dimensionality on the intermolecular interactions. The evolution of some basic characteristics of the bilayers and of the drug–peptide complex is tracked: mass density profiles, electrostatic potentials, lateral diffusion coefficients and areas per lipid, lipid-complex radial distribution functions, secondary structure of the peptide and orientation of the drug relative to the membrane. Thus, the influence of the periodic boundary conditions is quantified and it shows that the mixed system in 3D PBC is the most suitable for analysis of the translocation of the transporting moiety across cell membranes. The type of periodic boundary conditions, three-dimensional vs. two-dimensional (3D vs. 2D PBC), causes marked influence on the process of membrane penetration of doxorubicin carried by a cell-penetrating peptide, as evidenced by 1-µs-long atomistic MD simulations. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13536564
title: Utilization of O/S-doped graphene nanoclusters for ultrasensitive detection of flurane derivatives-DFT investigations

description: Nanocluster based drug delivery systems are very useful in modern medical treatment and interaction mechanism of desflurane (DES), isoflurane ISO), sevoflurane (SEV) over carboxyl substituted graphene-doped with O and S atoms were investigated in the present study. Different electronic and chemical properties of adsorbed desflurane, isoflurane and sevoflurane with nanoclusters are analyzed. To track the drugs, SERS is used as an efficient method and drug’s detection was analyzed using SERS. DES’s energy over GQD-S is greater than that over GQD-O nanocluster and for ISO and SEV, adsorption energies over the O/S nanoclusters are same. The title drugs work on the reactives sites and got adsorbed. For ISO, there is an increase in fluorine atom charges and for DES and SEV, the fluorine atom charge decreases due to adsorption in both O/S nanoclusters. Changes in chemical descriptors are identified for the sensing property of drug-nanoclusters. Communicated by Ramaswamy H. Sarma
DOI: 10.23728/b2share.c765674ad42c4a46bc3b0fa780f3329b
title: Post-processing of NWP precipitation forecasts using deep learning data

description: Train and test sets used for the ANNs post processing of NWP to predict precipitation
DOI: 10.6084/m9.figshare.13536564.v1
title: Utilization of O/S-doped graphene nanoclusters for ultrasensitive detection of flurane derivatives-DFT investigations

description: Nanocluster based drug delivery systems are very useful in modern medical treatment and interaction mechanism of desflurane (DES), isoflurane ISO), sevoflurane (SEV) over carboxyl substituted graphene-doped with O and S atoms were investigated in the present study. Different electronic and chemical properties of adsorbed desflurane, isoflurane and sevoflurane with nanoclusters are analyzed. To track the drugs, SERS is used as an efficient method and drug’s detection was analyzed using SERS. DES’s energy over GQD-S is greater than that over GQD-O nanocluster and for ISO and SEV, adsorption energies over the O/S nanoclusters are same. The title drugs work on the reactives sites and got adsorbed. For ISO, there is an increase in fluorine atom charges and for DES and SEV, the fluorine atom charge decreases due to adsorption in both O/S nanoclusters. Changes in chemical descriptors are identified for the sensing property of drug-nanoclusters. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13685860
title: Flavonol morin targets host ACE2, IMP-α, PARP-1 and viral proteins of SARS-CoV-2, SARS-CoV and MERS-CoV critical for infection and survival: a computational analysis

description: A sudden outbreak of a novel coronavirus SARS-CoV-2 in 2019 has now emerged as a pandemic threatening to efface the existence of mankind. In absence of any valid and appropriate vaccines to combat this newly evolved agent, there is need of novel resource molecules for treatment and prophylaxis. To this effect, flavonol morin which is found in fruits, vegetables and various medicinal herbs has been evaluated for its antiviral potential in the present study. PASS analysis of morin <i>versus</i> reference antiviral drugs baricitinib, remdesivir and hydroxychloroquine revealed that morin displayed no violations of Lipinski’s rule of five and other druglikeness filters. Morin also displayed no tumorigenic, reproductive or irritant effects and exhibited good absorption and permeation through GI (clogP &lt;5). In principal component analysis, morin appeared closest to baricitinib in 3D space. Morin displayed potent binding to spike glycoprotein, main protease 3CLPro and papain-like protease PLPro of SARS-CoV-2, SARS-CoV and MERS-CoV using molecular docking and significant binding to three viral-specific host proteins <i>viz.</i> human ACE2, importin-α and poly (ADP-ribose) polymerase (PARP)-1, further lending support to its antiviral efficacy. Additionally, morin displayed potent binding to pro-inflammatory cytokines IL-6, 8 and 10 also supporting its anti-inflammatory activity. MD simulation of morin with SARS-CoV-2 3CLPro and PLPro displayed strong stability at 300 K. Both complexes exhibited constant RMSDs of protein side chains and Cα atoms throughout the simulation run time. In conclusion, morin might hold considerable therapeutic potential for the treatment and management of not only COVID-19, but also SARS and MERS if studied further. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13685860.v1
title: Flavonol morin targets host ACE2, IMP-α, PARP-1 and viral proteins of SARS-CoV-2, SARS-CoV and MERS-CoV critical for infection and survival: a computational analysis

description: A sudden outbreak of a novel coronavirus SARS-CoV-2 in 2019 has now emerged as a pandemic threatening to efface the existence of mankind. In absence of any valid and appropriate vaccines to combat this newly evolved agent, there is need of novel resource molecules for treatment and prophylaxis. To this effect, flavonol morin which is found in fruits, vegetables and various medicinal herbs has been evaluated for its antiviral potential in the present study. PASS analysis of morin <i>versus</i> reference antiviral drugs baricitinib, remdesivir and hydroxychloroquine revealed that morin displayed no violations of Lipinski’s rule of five and other druglikeness filters. Morin also displayed no tumorigenic, reproductive or irritant effects and exhibited good absorption and permeation through GI (clogP &lt;5). In principal component analysis, morin appeared closest to baricitinib in 3D space. Morin displayed potent binding to spike glycoprotein, main protease 3CLPro and papain-like protease PLPro of SARS-CoV-2, SARS-CoV and MERS-CoV using molecular docking and significant binding to three viral-specific host proteins <i>viz.</i> human ACE2, importin-α and poly (ADP-ribose) polymerase (PARP)-1, further lending support to its antiviral efficacy. Additionally, morin displayed potent binding to pro-inflammatory cytokines IL-6, 8 and 10 also supporting its anti-inflammatory activity. MD simulation of morin with SARS-CoV-2 3CLPro and PLPro displayed strong stability at 300 K. Both complexes exhibited constant RMSDs of protein side chains and Cα atoms throughout the simulation run time. In conclusion, morin might hold considerable therapeutic potential for the treatment and management of not only COVID-19, but also SARS and MERS if studied further. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13686049
title: Discovery of RTA ricin subunit inhibitors: a computational study using PM7 quantum chemical method and steered molecular dynamics

description: Ricin is a potent toxin derived from the castor bean plant and comprises two subunits, RTA and RTB. Because of its cytotoxicity, ricin has alarmed world authorities for its potential use as a chemical weapon. Ricin also affects castor bean agribusiness, given the risk of animal and human poisoning. Over the years, many groups attempted to propose small-molecules that bind to the RTA active site, the catalytic chain. Despite such efforts, there is still no effective countermeasure against ricin poisoning. The computational study carried out in the present work renews the discussion about small-molecules that may inhibit this toxin. Here, a structure-based virtual screening protocol capable of discerning active RTA inhibitors from inactive ones was performed to screen over 2 million compounds from the ZINC database to find novel scaffolds that strongly bind into the active site of the RTA. Besides, a novel score method based on ligand undocking force profiles and semi-empirical quantum chemical calculations provided insights into the rescore of docking poses. Summing up, the filtering steps pointed out seven main compounds, with the SCF00-451 as a promising candidate to inhibit the killing activity of such potent phytotoxin. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.13686049.v1
title: Discovery of RTA ricin subunit inhibitors: a computational study using PM7 quantum chemical method and steered molecular dynamics

description: Ricin is a potent toxin derived from the castor bean plant and comprises two subunits, RTA and RTB. Because of its cytotoxicity, ricin has alarmed world authorities for its potential use as a chemical weapon. Ricin also affects castor bean agribusiness, given the risk of animal and human poisoning. Over the years, many groups attempted to propose small-molecules that bind to the RTA active site, the catalytic chain. Despite such efforts, there is still no effective countermeasure against ricin poisoning. The computational study carried out in the present work renews the discussion about small-molecules that may inhibit this toxin. Here, a structure-based virtual screening protocol capable of discerning active RTA inhibitors from inactive ones was performed to screen over 2 million compounds from the ZINC database to find novel scaffolds that strongly bind into the active site of the RTA. Besides, a novel score method based on ligand undocking force profiles and semi-empirical quantum chemical calculations provided insights into the rescore of docking poses. Summing up, the filtering steps pointed out seven main compounds, with the SCF00-451 as a promising candidate to inhibit the killing activity of such potent phytotoxin. Communicated by Ramaswamy H. Sarma
DOI: 10.5281/zenodo.6821240
title: Analyzing the Web: Are Top Websites Lists a Good Choice for Research?

description: Research data associated with the paper "Analyzing the Web: Are Top Websites Lists a Good Choice for Research?"
DOI: 10.5281/zenodo.6821239
title: Analyzing the Web: Are Top Websites Lists a Good Choice for Research?

description: Research data associated with the paper "Analyzing the Web: Are Top Websites Lists a Good Choice for Research?"
DOI: 10.5281/zenodo.6817673
title: Application of adipose-derived Mesenchymal Stem Cells in an in vivo model of peripheral nerve damage

description: The aim of this study is to address this issue by performing a detailed analysis of the therapeutic 29 benefits of two treatment options: adipose tissue derived-mesenchymal stem cells (ASCs) and ASC-30 conditioned medium (CM).
DOI: 10.5281/zenodo.6817672
title: Application of adipose-derived Mesenchymal Stem Cells in an in vivo model of peripheral nerve damage

description: The aim of this study is to address this issue by performing a detailed analysis of the therapeutic 29 benefits of two treatment options: adipose tissue derived-mesenchymal stem cells (ASCs) and ASC-30 conditioned medium (CM).
DOI: 10.34740/kaggle/dsv/3917804
title: Aksara Jawa / Hanacaraka
DOI: 10.6084/m9.figshare.20291325
title: Raw datasets and phylogenetic topology based on BUSCO and exon approaches

description: The raw datasets and phylogenetic topology based on BUSCO and exon approaches in our chondrichthyan Phylogenomics study.
DOI: 10.6084/m9.figshare.20291325.v1
title: Raw datasets and phylogenetic topology based on BUSCO and exon approaches

description: The raw datasets and phylogenetic topology based on BUSCO and exon approaches in our chondrichthyan Phylogenomics study.
DOI: 10.5517/ccdc.csd.cc29y50g
title: CCDC 2143185: Experimental Crystal Structure Determination

description: Related Article: Vladimir O. Gelmboldt, Irina V. Lytvynchuk, Ivan O. Shyshkin, Larysa N. Khromagina, Marina S. Fonari, Victor Ch. Kravtsov|2022|Arch.Pharm.Chem.Life Sci.|355|2200074|doi:10.1002/ardp.202200074
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc29y51h
title: CCDC 2143186: Experimental Crystal Structure Determination

description: Related Article: Vladimir O. Gelmboldt, Irina V. Lytvynchuk, Ivan O. Shyshkin, Larysa N. Khromagina, Marina S. Fonari, Victor Ch. Kravtsov|2022|Arch.Pharm.Chem.Life Sci.|355|2200074|doi:10.1002/ardp.202200074
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc29y52j
title: CCDC 2143187: Experimental Crystal Structure Determination

description: Related Article: Vladimir O. Gelmboldt, Irina V. Lytvynchuk, Ivan O. Shyshkin, Larysa N. Khromagina, Marina S. Fonari, Victor Ch. Kravtsov|2022|Arch.Pharm.Chem.Life Sci.|355|2200074|doi:10.1002/ardp.202200074
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.6821462
title: Therapeutic effect of herbal infusion on Abnormal Uterine Bleeding Extended data

description: This project contains the following extended data
DOI: 10.5281/zenodo.6671603
title: Therapeutic effect of herbal infusion on Abnormal Uterine Bleeding Extended data

description: This project contains the following extended data
DOI: 10.34740/kaggle/dsv/3933229
title: YouTube Daily
DOI: 10.5281/zenodo.6814620
title: The appendix for dynamic model of respiratory infectious disease transmission by population mobility based on city network

description: First, a scale-free city network was established, and the shortest path between any two nodes was determined. Second, the movement path of tourists was designed based on the shortest path. Subsequently, every infected person's information, such as the city, infection time, onset, and hospitalisation, was confirmed based on their movement path. Third, the features of the transmission path and time distribution of the epidemic were characterised after summarising the information. Finally, the reliability of the model was verified.
DOI: 10.5281/zenodo.6814619
title: The appendix for dynamic model of respiratory infectious disease transmission by population mobility based on city network

description: First, a scale-free city network was established, and the shortest path between any two nodes was determined. Second, the movement path of tourists was designed based on the shortest path. Subsequently, every infected person's information, such as the city, infection time, onset, and hospitalisation, was confirmed based on their movement path. Third, the features of the transmission path and time distribution of the epidemic were characterised after summarising the information. Finally, the reliability of the model was verified.
DOI: 10.5281/zenodo.6799940
title: Distance matrix for UNITE sequences

description: Flattened and compressed version of 2 pairwise distance matrices corresponding to this UNITE release. Can be imported in a pipeline for building an overarching fungal phylogeny for UNITE (Github source code). Importing might take up to an hour, but this is still much quicker than the 36-hours pairwise distance calculation. The 6-mer Google distance is way more accurate than the w-metric, so we highly recommend using the 6-mer Google distance. More documentation can be found here.
DOI: 10.5281/zenodo.6799939
title: Distance matrix for UNITE sequences

description: Flattened and compressed version of 2 pairwise distance matrices corresponding to this UNITE release. Can be imported in a pipeline for building an overarching fungal phylogeny for UNITE (Github source code). Importing might take up to an hour, but this is still much quicker than the 36-hours pairwise distance calculation. The 6-mer Google distance is way more accurate than the w-metric, so we highly recommend using the 6-mer Google distance. More documentation can be found here.
DOI: 10.5281/zenodo.6787347
title: Tomogram of SARS-CoV-2

description: Tomogram of SARS-CoV-2 purified using Capto Core
description: associated with submission to "Viruses"
DOI: 10.5281/zenodo.6787346
title: Tomogram of SARS-CoV-2

description: Tomogram of SARS-CoV-2 purified using Capto Core
description: associated with submission to "Viruses"
DOI: 10.5281/zenodo.6798184
title: Energy System Analysis Dataset_HS Offenburg

description: Energy System Analysis Dataset_HS Offenburg
DOI: 10.5281/zenodo.6798183
title: Energy System Analysis Dataset_HS Offenburg

description: Energy System Analysis Dataset_HS Offenburg
DOI: 10.6084/m9.figshare.20237976
title: Climatic legacy effects on the drought response of the Amazon rainforest

description: We evaluated the Amazon forest stability (resistance and resilience) to drought in the context of past dry and wet climatic events using MODIS EVI satellite imagery and cumulative water deficit and excess anomalies. <br> The layers included are (1) monthly MODIS EVI time series from 2001 to 2019, masked for outliers, burnt areas and missing values due to clouds and low quality pixels; (2) montly cumulative water deficit (CWD) time series from 1980 to 2019; and (3) monthly cumulative water excess (CWE) time series from 1980 to 2019. All layers have a spatial resolution of 0.05° and their spatial extent is the Amazon basin. <br> When using any of these layers, please cite: Van Passel et al. (2022). Climatic legacy effects on the drought response of the Amazon rainforest. Global Change Biology. https://doi.org/10.1111/gcb.16336
DOI: 10.6084/m9.figshare.20237976.v1
title: Climatic legacy effects on the drought response of the Amazon rainforest

description: We evaluated the Amazon forest stability (resistance and resilience) to drought in the context of past dry and wet climatic events using MODIS EVI satellite imagery and cumulative water deficit and excess anomalies. <br> The layers included are (1) monthly MODIS EVI time series from 2001 to 2019, masked for outliers, burnt areas and missing values due to clouds and low quality pixels; (2) montly cumulative water deficit (CWD) time series from 1980 to 2019; and (3) monthly cumulative water excess (CWE) time series from 1980 to 2019. All layers have a spatial resolution of 0.05° and their spatial extent is the Amazon basin. <br> When using any of these layers, please cite: Van Passel et al. (2022). Climatic legacy effects on the drought response of the Amazon rainforest. Global Change Biology. https://doi.org/10.1111/gcb.16336
DOI: 10.5281/zenodo.6821054
title: Data and codes for peer review

description: For peer review purpose only. Thank you very much.
DOI: 10.5281/zenodo.6821053
title: Data and codes for peer review

description: For peer review purpose only. Thank you very much.
DOI: 10.5517/ccdc.csd.cc21lh49
title: CCDC 1894600: Experimental Crystal Structure Determination

description: Related Article: Yuangang Xu, Ze Xu, Xiaopeng Zhang, Tianyang Hou, Ming Lu|2022|CrystEngComm|24|4853|doi:10.1039/D2CE00713D
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc24yrhc
title: CCDC 1994803: Experimental Crystal Structure Determination

description: Related Article: W. Clegg, M.R.J. Elsegood|2020|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.34740/kaggle/dsv/3512475
title: Natural Language to Python Code
DOI: 10.57760/sciencedb.01970
title: test
title: 流程测试

description: Please describe the process of data set generation, processing methods or steps, equipment and tools used, etc; • please specify the temporal and spatial information, temporal and spatial resolution and other information involved in the data set (if applicable); • table data, please describe the number of records in the table data, the meaning of row labels and column labels in the data table, and the related UOM information (if applicable); • if there is missing data, please clearly point out the missing data and explain it (if applicable); • whether there is error in the data, the error range or the reason for introducing the error, if necessary, please explain appropriately (if applicable); • the content of each data file and its descriptive information (if applicable); • if the format of the data file you submitted is relatively small, please explain the applicable software, the official download address of the software and other information (if applicable). The above suggestions are for reference only. If there is any omission, please supplement and improve your data set introduction by yourself. Your data set profile should be organized and submitted in the form of one or more natural segments. Please do not reply to the above questions one by one in the form of questions and answers.
description: 请具体描述数据集产生的过程、处理方法或处理步骤、使用设备及工具等信息；• 请具体说明数据集内容涉及的时间、空间信息，时间、空间分辨率等信息（如适用）；• 表格数据，请说明表格数据中的记录条数信息，数据表中行标签及列标签的含义，以及涉及的计量单位信息（如适用）；• 若数据存在缺失情况，请明确指出数据的缺失情况并做以说明（如适用）；• 数据是否存在误差，误差范围或引入误差的原因等情况如有必要请适当说明（如适用）；• 每个数据文件的内容及其描述信息（如适用）；• 若您提交的数据文件格式较为小众，请您说明适用软件情况、软件的官方下载地址等信息（如适用）。以上建议仅供参考，如有遗漏还请作者自行补充完善您的数据集简介。您的数据集简介应整理为一个或多个自然段的形式组织进行提交，请不要以问答的形式逐一回复上述问题。
DOI: 10.6084/m9.figshare.20291442
title: Signature sequence Chlorella genus

description: SIGNATURE SEQUENCE: A NOVEL TOOL TO IDENTIFY <em>CHLORELLA</em> SPECIES (Chlorophyta)