cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5142487
title: Datasets-Coated soot particles with tunable, well-controlled properties generated in the laboratory with a miniCAST BC and a micro smog chamber

description: Datasets for manuscript "Coated soot particles with tunable, well-controlled properties generated in the laboratory with a miniCAST BC and a micro smog chamber" by Michaela N. Ess, Michele Berto, Alejandro Keller, Martin Gysel-Beer, Konstantina Vasilatou https://doi.org/10.1016/j.jaerosci.2021.105820
DOI: 10.5281/zenodo.5142486
title: Datasets-Coated soot particles with tunable, well-controlled properties generated in the laboratory with a miniCAST BC and a micro smog chamber

description: Datasets for manuscript "Coated soot particles with tunable, well-controlled properties generated in the laboratory with a miniCAST BC and a micro smog chamber" by Michaela N. Ess, Michele Berto, Alejandro Keller, Martin Gysel-Beer, Konstantina Vasilatou https://doi.org/10.1016/j.jaerosci.2021.105820
DOI: 10.6084/m9.figshare.12844894.v1
title: <i>In silico</i> structure prediction, molecular docking and dynamic simulation studies on G Protein-Coupled Receptor 116: a novel insight into breast cancer therapy

description: G Protein-Coupled Receptor gains more importance in cancer research; because of their key role in several physiologic functions of cells. However, most of the GPCR’s are orphan receptors, this hampers the finding of drugs against GPCR. G Protein-Coupled Receptor 116 is an adhesion orphan receptor that intensifies the invasion of cells in Triple-Negative Breast Cancer. In this study, existing FDA approved anticancer drugs were chosen as ligands and molecular docking was performed using <i>in silico</i> protein model of GPR116. Molecular interaction was analyzed carefully to identify the crucial amino acids present in binding pocket. Molecular dynamics simulations study executed to verify the structural and dynamic properties of Doxorubicin–GPR116 protein complex. The results have shown that Doxorubicin, Neratinib maleate, Epirubicin, and Lapatinib Ditosylate have good interaction with GPR116 binding site. Tyrosine 195 (Y195), Cysteine 196 (C196), Argenine 197 (R197), and Tryptophan 100 (W100) are commonly found in the majority of ligand–target interaction, hence based on the computational studies selective amino acids might be crucial for functional properties. Further to confirm crucial amino acids, computational mutation studies were executed. Molecular docking analysis with mutated GPR116 disclosed that significant variation in <i>G</i> score compared withligand–native protein interaction. Hence, the theoretical confirmatory structural properties changes support to prove selective crucial amino acids play the significant role in ligand binding. Molecular dynamic simulation results reveal that the interaction was stable throughout the MD simulation. To the best of our prognosis, GPR116 could be the best molecular target for breast cancer drug discovery. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12844930
title: Investigation of HDAC8-ligands’ intermolecular forces through molecular dynamics simulations: profiling of non-bonding energies to design potential compounds as new anti-cancer agents

description: Histone deacetylases are zinc-dependent isoform enzymes and play important role in cellular homeostasis. Among these, HDAC8 is a potential anticancer drug target. To design new inhibitors using protein-ligand energy profiles, an all atom molecular dynamics (MD) simulations were carried out on nine HDAC8-ligand co-crystals (PDBs: 1T64, 1T69, 1T67, 3F07, 1W22, 1VKG, 5FCW, 3SFF and 3SFH). <b>TSN</b>, <b>SHH</b>, <b>B3N</b>, <b>AGE</b>, <b>NHB</b>, <b>CRI</b>, <b>5YA</b>, <b>0DI</b> and <b>1DI</b> are ligands of PDBs, respectively. For these HDAC8-ligands, relative Gibbs binding free energy (Δ<i>G</i><sub>bind</sub>) from MM/PBSA method and non-bonding energies (NBE) are in agreement with each other (<i>r</i><sup>2</sup>=0.678). Therefore, the NBEs are used to analyze ligands’ sub-structures, namely zinc-binding, linker and CAP groups. For linker/CAP regions, this identified carbonyl, amide, and sulfonamide moieties as desirable and alkyl/aryl moieties as electrostatically unfavourable. Using this information, systematically new compounds were designed and subjected to MD simulations. This resulted in seven compounds (<b>NC-I to NC-VII</b>) with encouraging energy profiles (NBE: −76.25 to −127.09 kcal/mol; Δ<i>G</i><sub>bind</sub>: −17.21 to −57.42 kcal/mol) in comparison to that of the HDAC8 ligands (NBE: −46.25 to −106.29 kcal/mol; Δ<i>G</i><sub>bind</sub>: −14.74 to −49.52 kcal/mol). From these, <b>NC-VI</b> showed best energy profile (NBE = −126.15 kcal/mol; Δ<i>G</i><sub>bind</sub> = −57.42 kcal/mol) suggesting its binding affinity and thermodynamic stability. In addition to this, <b>NC-II</b> and <b>NC-III</b> have shown promising NBE and Δ<i>G</i><sub>bind</sub> profiles. These may serve as lead molecules for exploration against HDAC8 in cancer therapy. This has provided a basis for designing new compounds with improved NBE and ΔG<sub>bind</sub> profiles by modifying the unfavourable or not so favourable regions of ligands. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12844930.v1
title: Investigation of HDAC8-ligands’ intermolecular forces through molecular dynamics simulations: profiling of non-bonding energies to design potential compounds as new anti-cancer agents

description: Histone deacetylases are zinc-dependent isoform enzymes and play important role in cellular homeostasis. Among these, HDAC8 is a potential anticancer drug target. To design new inhibitors using protein-ligand energy profiles, an all atom molecular dynamics (MD) simulations were carried out on nine HDAC8-ligand co-crystals (PDBs: 1T64, 1T69, 1T67, 3F07, 1W22, 1VKG, 5FCW, 3SFF and 3SFH). <b>TSN</b>, <b>SHH</b>, <b>B3N</b>, <b>AGE</b>, <b>NHB</b>, <b>CRI</b>, <b>5YA</b>, <b>0DI</b> and <b>1DI</b> are ligands of PDBs, respectively. For these HDAC8-ligands, relative Gibbs binding free energy (Δ<i>G</i><sub>bind</sub>) from MM/PBSA method and non-bonding energies (NBE) are in agreement with each other (<i>r</i><sup>2</sup>=0.678). Therefore, the NBEs are used to analyze ligands’ sub-structures, namely zinc-binding, linker and CAP groups. For linker/CAP regions, this identified carbonyl, amide, and sulfonamide moieties as desirable and alkyl/aryl moieties as electrostatically unfavourable. Using this information, systematically new compounds were designed and subjected to MD simulations. This resulted in seven compounds (<b>NC-I to NC-VII</b>) with encouraging energy profiles (NBE: −76.25 to −127.09 kcal/mol; Δ<i>G</i><sub>bind</sub>: −17.21 to −57.42 kcal/mol) in comparison to that of the HDAC8 ligands (NBE: −46.25 to −106.29 kcal/mol; Δ<i>G</i><sub>bind</sub>: −14.74 to −49.52 kcal/mol). From these, <b>NC-VI</b> showed best energy profile (NBE = −126.15 kcal/mol; Δ<i>G</i><sub>bind</sub> = −57.42 kcal/mol) suggesting its binding affinity and thermodynamic stability. In addition to this, <b>NC-II</b> and <b>NC-III</b> have shown promising NBE and Δ<i>G</i><sub>bind</sub> profiles. These may serve as lead molecules for exploration against HDAC8 in cancer therapy. This has provided a basis for designing new compounds with improved NBE and ΔG<sub>bind</sub> profiles by modifying the unfavourable or not so favourable regions of ligands. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12844894
title: <i>In silico</i> structure prediction, molecular docking and dynamic simulation studies on G Protein-Coupled Receptor 116: a novel insight into breast cancer therapy

description: G Protein-Coupled Receptor gains more importance in cancer research; because of their key role in several physiologic functions of cells. However, most of the GPCR’s are orphan receptors, this hampers the finding of drugs against GPCR. G Protein-Coupled Receptor 116 is an adhesion orphan receptor that intensifies the invasion of cells in Triple-Negative Breast Cancer. In this study, existing FDA approved anticancer drugs were chosen as ligands and molecular docking was performed using <i>in silico</i> protein model of GPR116. Molecular interaction was analyzed carefully to identify the crucial amino acids present in binding pocket. Molecular dynamics simulations study executed to verify the structural and dynamic properties of Doxorubicin–GPR116 protein complex. The results have shown that Doxorubicin, Neratinib maleate, Epirubicin, and Lapatinib Ditosylate have good interaction with GPR116 binding site. Tyrosine 195 (Y195), Cysteine 196 (C196), Argenine 197 (R197), and Tryptophan 100 (W100) are commonly found in the majority of ligand–target interaction, hence based on the computational studies selective amino acids might be crucial for functional properties. Further to confirm crucial amino acids, computational mutation studies were executed. Molecular docking analysis with mutated GPR116 disclosed that significant variation in <i>G</i> score compared withligand–native protein interaction. Hence, the theoretical confirmatory structural properties changes support to prove selective crucial amino acids play the significant role in ligand binding. Molecular dynamic simulation results reveal that the interaction was stable throughout the MD simulation. To the best of our prognosis, GPR116 could be the best molecular target for breast cancer drug discovery. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12844960.v1
title: <i>In silico</i> identification of natural fungicide from <i>Melia azedarach</i> against isocitrate lyase of <i>Fusarium graminearum</i>

description: Isocitrate Lyase (ICL) is a crucial enzyme involved in the Glyoxylate pathway, essential for the virulence of several fungal pathogens including <i>Fusarium graminearum</i>. ICL is a novel target for the discovery of antifungal compounds and <i>F. graminearum</i> ICL inhibitors can be used to control the growth of this fungus. Although, several inhibitors of ICL have been identified, however, most of these inhibitors are not environment-friendly. Hence there is still a need to discover natural inhibitors of ICL that can be more effective. To identify a potential antifungal compound, we performed a structure‐based screening of phytochemicals of <i>Melia azedarach</i> against the FgICL structure by molecular docking and 104 ligands were found to have a better docking score as compared to the reference molecule. These compounds were assessed for drug-likeness and ADMET prediction. After molecular docking, drug-likeness and toxicity analysis, six potential compounds (Melianoninol (−6.6 kcal/mol), Nimbinene (−7.7 kcal/mol), Vilasinin (−8.1 kcal/mol), Fraxinellone (−6.7 kcal/mol), Gedunin (−7.8 kcal/mol), and Meldenin (−7.8 kcal/mol)) were subjected for rescoring by X-Score. The structural stability and dynamics of screened compounds at the active site of FgICL were examined using MD simulation and MM-PBSA analysis. The result of MM-PBSA revealed that four phytochemicals viz. Melianoninol, Nimbinene, Vilasinin, and Fraxinellone had binding free energy of −17.25 kcal/mol, −59.35 kcal/mol, −64.79 kcal/mol, and −29.86 kcal/mol, respectively. Molecular dynamics simulation and MM-PBSA demonstrated that these four phytochemicals displayed considerable significant structural and pharmacological properties and could be probable antifungal drug candidates against <i>F. graminearum.</i> These phyotchemicals of <i>M. azedarach</i> may be suitable candidates for further experimental analysis. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12844942.v1
title: Unexpected synthesis of novel 2-pyrone derivatives: crystal structures, Hirshfeld surface analysis and computational studies

description: Here we report synthesis of three new compounds namely, 1-acetyl-1H-benzimidazolo-2(3H)-one (<b>I</b>), <i>N</i>-(5-acetyl-6-methyl-2-oxo-2H-pyran-4-yl)-<i>N</i>-(2-acetamidophenyl)acetamide (<b>II</b>) and <i>N</i>-(2-acetamidophenyl)-<i>N</i>-2-oxo-2H-pyran-4-yl)acetamide (<b>III</b>) have been synthesized and characterized by single crystal X-ray diffraction. Compounds <b>I</b> and <b>II</b> crystallize in the monoclinic space groups P21/n, and P21/c, respectively, while <b>III</b> crystallizes in the triclinic space group P-1. The theoretical parameters of <b>I</b>–<b>III</b> have been calculated through density functional theory (DFT) by using the hybrid functional B3LYP and basis set 6-311++G**. These theoretical parameters have been compared with the experimental ones obtained by XRD. The significant intermolecular interactions arising in crystal packing are rationalized by means of the Hirshfeld surface analysis method. The major intermolecular contacts in the Hirshfeld surfaces of <b>I</b>–<b>III</b> are from H…H contacts. In addition, binding modes of <b>I</b>–<b>III</b> within Tyrosine-protein kinase JAK2 were investigated using molecular docking and molecular dynamics simulation studies. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12844942
title: Unexpected synthesis of novel 2-pyrone derivatives: crystal structures, Hirshfeld surface analysis and computational studies

description: Here we report synthesis of three new compounds namely, 1-acetyl-1H-benzimidazolo-2(3H)-one (<b>I</b>), <i>N</i>-(5-acetyl-6-methyl-2-oxo-2H-pyran-4-yl)-<i>N</i>-(2-acetamidophenyl)acetamide (<b>II</b>) and <i>N</i>-(2-acetamidophenyl)-<i>N</i>-2-oxo-2H-pyran-4-yl)acetamide (<b>III</b>) have been synthesized and characterized by single crystal X-ray diffraction. Compounds <b>I</b> and <b>II</b> crystallize in the monoclinic space groups P21/n, and P21/c, respectively, while <b>III</b> crystallizes in the triclinic space group P-1. The theoretical parameters of <b>I</b>–<b>III</b> have been calculated through density functional theory (DFT) by using the hybrid functional B3LYP and basis set 6-311++G**. These theoretical parameters have been compared with the experimental ones obtained by XRD. The significant intermolecular interactions arising in crystal packing are rationalized by means of the Hirshfeld surface analysis method. The major intermolecular contacts in the Hirshfeld surfaces of <b>I</b>–<b>III</b> are from H…H contacts. In addition, binding modes of <b>I</b>–<b>III</b> within Tyrosine-protein kinase JAK2 were investigated using molecular docking and molecular dynamics simulation studies. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12844960
title: <i>In silico</i> identification of natural fungicide from <i>Melia azedarach</i> against isocitrate lyase of <i>Fusarium graminearum</i>

description: Isocitrate Lyase (ICL) is a crucial enzyme involved in the Glyoxylate pathway, essential for the virulence of several fungal pathogens including <i>Fusarium graminearum</i>. ICL is a novel target for the discovery of antifungal compounds and <i>F. graminearum</i> ICL inhibitors can be used to control the growth of this fungus. Although, several inhibitors of ICL have been identified, however, most of these inhibitors are not environment-friendly. Hence there is still a need to discover natural inhibitors of ICL that can be more effective. To identify a potential antifungal compound, we performed a structure‐based screening of phytochemicals of <i>Melia azedarach</i> against the FgICL structure by molecular docking and 104 ligands were found to have a better docking score as compared to the reference molecule. These compounds were assessed for drug-likeness and ADMET prediction. After molecular docking, drug-likeness and toxicity analysis, six potential compounds (Melianoninol (−6.6 kcal/mol), Nimbinene (−7.7 kcal/mol), Vilasinin (−8.1 kcal/mol), Fraxinellone (−6.7 kcal/mol), Gedunin (−7.8 kcal/mol), and Meldenin (−7.8 kcal/mol)) were subjected for rescoring by X-Score. The structural stability and dynamics of screened compounds at the active site of FgICL were examined using MD simulation and MM-PBSA analysis. The result of MM-PBSA revealed that four phytochemicals viz. Melianoninol, Nimbinene, Vilasinin, and Fraxinellone had binding free energy of −17.25 kcal/mol, −59.35 kcal/mol, −64.79 kcal/mol, and −29.86 kcal/mol, respectively. Molecular dynamics simulation and MM-PBSA demonstrated that these four phytochemicals displayed considerable significant structural and pharmacological properties and could be probable antifungal drug candidates against <i>F. graminearum.</i> These phyotchemicals of <i>M. azedarach</i> may be suitable candidates for further experimental analysis. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.15073125
title: Clinical outcomes and client perception after Postpartum intrauterine device (PPIUD) insertion

description: We performed a descriptive cross-sectional study as a telephone survey in Galle, Sri Lanka. All the Postpartum intrauterine device (PPIUD) insertions carried out at Teaching Hospital, Mahamodara, Galle, Sri Lanka were included into the study. This study evaluated its long-term impact and clinical outcomes few years after the insertion of PPIUD (from 2014 to 2019) at the Teaching Hospital, Mahamodara, Galle, Sri Lanka. These data generated during the above study.
DOI: 10.6084/m9.figshare.15073125.v1
title: Clinical outcomes and client perception after Postpartum intrauterine device (PPIUD) insertion

description: We performed a descriptive cross-sectional study as a telephone survey in Galle, Sri Lanka. All the Postpartum intrauterine device (PPIUD) insertions carried out at Teaching Hospital, Mahamodara, Galle, Sri Lanka were included into the study. This study evaluated its long-term impact and clinical outcomes few years after the insertion of PPIUD (from 2014 to 2019) at the Teaching Hospital, Mahamodara, Galle, Sri Lanka. These data generated during the above study.
DOI: 10.5281/zenodo.5118651
title: Leone Allemandes Corpus

description: The corpus we present is comprised of twenty-four allemandes (dance music originating from Germany, usually possessing even meter), written in 1768 by Gabriele Leone (sometimes referred to as Pietro Leone), a mandolin virtuoso from Naples. These pieces were originally included in a method for teaching mandolin to violin players (in particular, the method was dedicated to Louis Philippe II, later known as Philippe Égalité, at the time when he was Duke of Chartres). As such, despite the great technical ability of the author, the pieces are extremely simple and can be played by a novice. All of the allemandes are written for a mandolin duo, ideally having the first part played by the student and the second by the teacher, so all these pieces are polyphonic. In addition, a single instrument often plays chords, so either part may polyphonic on its own. Since the Neapolitan mandolin has only four strings, neither part ever has more than four simultaneous notes.<br> <br> These pieces are released here in MusicXML format, with added chord annotations. We propose this corpus as a tool for the study of musical structure, as these simple pieces have strong formal regularities. More information can be found on the paper below. <br> <br> _________________<br> <br> If you use this corpus for an academic publication, please cite the following paper: <br> <br> Filippo Carnovalini, Antonio Rodà, Nicholas Harley, Steven T. Homer, and Geraint A. Wiggins. 2021. A New Corpus for Computational Music Research and A Novel Method for Musical Structure Analysis. In Audio Mostly 2021 (AM ’21), September 1–3, 2021, virtual/Trento, Italy. ACM, New York, NY, USA, 4 pages. https://doi.org/10.1145/3478384.3478402
description: The original method is in the public domain and can be found at https://imslp.org/wiki/Méthode_raisonnée_pour_passer_du_Violon_à_la_Mandoline_(Leone%2C_Gabriele) The additional work done to that corpus to release it in MusicXML format with chord annotations is released here under Creative Commons license.
description: {"references": ["Filippo Carnovalini, Antonio Rod\u00e0, Nicholas Harley, Steven T. Homer, and Geraint A. Wiggins. 2021. A New Corpus for Computational Music Research and A Novel Method for Musical Structure Analysis. In Audio Mostly 2021 (AM '21), September 1\u20133, 2021, virtual/Trento, Italy. ACM, New York, NY, USA, 4 pages. https://doi.org/10.1145/3478384.3478402"]}
DOI: 10.5281/zenodo.5144878
title: User Study Data for "Enhancing Ultrasound Haptics with Parametric Audio Effects"

description: Data from an experiment investigation the perception of ultrasound haptic and parametric audio stimuli, as described in a paper at ACM ICMI 2021.
DOI: 10.5281/zenodo.5144877
title: User Study Data for "Enhancing Ultrasound Haptics with Parametric Audio Effects"

description: Data from an experiment investigation the perception of ultrasound haptic and parametric audio stimuli, as described in a paper at ACM ICMI 2021.
DOI: 10.5281/zenodo.4638884
title: Pharmacological Therapies in Non-Alcoholic steatohepatitis Disease: Identifying Highly Cited Papers via H-Classics (Citation Report and WoS Dataset)

description: Pharmacological Therapies in Non-Alcoholic steatohepatitis Disease: Identifying Highly Cited Papers via H-Classics (Citation Report and WoS Dataset)
DOI: 10.5281/zenodo.4638883
title: Pharmacological Therapies in Non-Alcoholic steatohepatitis Disease: Identifying Highly Cited Papers via H-Classics (Citation Report and WoS Dataset)

description: Pharmacological Therapies in Non-Alcoholic steatohepatitis Disease: Identifying Highly Cited Papers via H-Classics (Citation Report and WoS Dataset)
DOI: 10.5281/zenodo.5055755
title: Obtaining Better Static Word Embeddings Using Contextual Embedding Models

description: <strong>Obtaining Better Static Word Embeddings Using Contextual Embedding Models</strong> This repository contains the dataset of pretrained word embeddings as well as datasets used to train them, released with the following paper. “Obtaining Better Static Word Embeddings Using Contextual Embedding Models” <em>ACL</em> (2021). The wikipedia datasets were preprocessed from the wikipedia dump downloaded from dumps.wikimedia.org under Creative Commons Attribution-Share-Alike 3.0 License . If you found the provided resources useful, please cite the above paper. Here's a BibTeX entry you may use: @inproceedings{Gupta2021ObtainingPC,<br> title={Obtaining Better Static Word Embeddings Using Contextual Embedding Models},<br> author={Prakhar Gupta and Martin Jaggi},<br> booktitle={ACL},<br> year={2021}<br> }
DOI: 10.5281/zenodo.5055754
title: Obtaining Better Static Word Embeddings Using Contextual Embedding Models

description: <strong>Obtaining Better Static Word Embeddings Using Contextual Embedding Models</strong> This repository contains the dataset of pretrained word embeddings as well as datasets used to train them, released with the following paper. “Obtaining Better Static Word Embeddings Using Contextual Embedding Models” <em>ACL</em> (2021). The wikipedia datasets were preprocessed from the wikipedia dump downloaded from dumps.wikimedia.org under Creative Commons Attribution-Share-Alike 3.0 License . If you found the provided resources useful, please cite the above paper. Here's a BibTeX entry you may use: @inproceedings{Gupta2021ObtainingPC,<br> title={Obtaining Better Static Word Embeddings Using Contextual Embedding Models},<br> author={Prakhar Gupta and Martin Jaggi},<br> booktitle={ACL},<br> year={2021}<br> }
DOI: 10.5281/zenodo.4812962
title: Long document similarity dataset, Wikipedia excerptions for video games collections

description: Video games-related articles extracted from Wikipedia. For all articles, the figures and tables have been filtered out, as well as the categories and "see also" sections. The article structure, and particularly the sub-titles and paragraphs are kept in these datasets <strong>Video games</strong> The Wikipedia video games dataset consists of 21,935 articles reviewing video games from all genres and consoles. Each article may consist of a different combination of sections, including summary, gameplay, plot, production, etc. Examples for ground-truth expert-based recommendations are: Grand Theft Auto - Mafia Burnout Paradise - Forza Horizon 3