cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7910/dvn/rcwh9d
title: An exploratory study of social media users’ engagement with COVID-19 vaccine-related contents

description: 1. Data source search strategy Facebook (94.46%) is the most popular social media platform in Bangladesh, compared to YouTube (3.31%) and Twitter (0.3%) (StatCounter, 2020), so I selected it as the source of data for this study. I collected the data from Facebook pages using CrowdTangle, a public insights tool owned and operated by Facebook. It can access the public pages and groups to collect various types of data. However, I excluded groups’ data in this research because Facebook groups and pages are different in terms of users’ interaction patterns, participation rates, and security issues. To collect the data from relevant Facebook posts, I conducted a keyword search. Most of the Facebook users in Bangladesh who write in the Bangla language use the Bangla alphabet. For that reason, I determined the following Bangla keywords: “corona vaccine,” “coronar vaccine,” “corona tika,” “coronar tika,” “corona oshudh,” “coronar oshudh,” “corona protishedhok,” and “coronar protishedhok.” All search terms can be translated as corona vaccine or vaccine of the corona. 2 Data collection analysis I set the timeline from 8 March to 2 December 2020. The first case of coronavirus in Bangladesh was identified on 8 March 2020. As Facebook is an interactive platform, so I collected the data on 17 December 2020 (15 days after the end date of the data collection period) after stabilizing the threads. The search result produced 37,460 Facebook posts relevant to the topic. Of them, I selected the top 10,000 posts for the final analysis based on their total interactions, which was 26.70% of the total search results: These posts were from 1,087 different Facebook pages, on average 9.20 posts from each page. I categorized the contents into six types: link, live video, native video, photo, status, and YouTube video. In Facebook, each of the mentioned contents can usually have the following definitions and modes: a link and a photo can be shared with or without any text; live video can be completed or scheduled; native video is the video that is uploaded directly on Facebook; a status is mainly text-based, often contains other elements, such as tags; YouTube videos are often embedded/shared on Facebook. I measured the users’ engagement based on nine interaction parameters, including six Facebook reactions: comments (M=32.90, SD=140.06), shares (M=145.17, SD=1345.86), like (M=1377.04, SD=4792.64), love (M=74.98, SD=788.35), wow (M=6.50, SD=40.33), haha (M=52.79, SD=408.28), sad (M=16, SD=372.76), angry (M=3.67, SD=55.05), and care (M=5.40, SD=51.67). The numbers and percentages are presented in tables, time-series data are presented in graphs, and a network analysis of the contents’ sources is analyzed using Gephi 0.9.2 and presented in a figure.
DOI: 10.15468/858z7f
title: Checklist of decapod crustaceans from the coast of the São Paulo state (Brazil) supported by integrative molecular and morphological data: III. Infraorder Brachyura Latreille, 1802

description: This dataset contains the digitized treatments in Plazi based on the original journal article Mantelatto, Fernando L., Tamburus, Ana Francisca, Magalhães, Tatiana, Buranelli, Raquel C., Terossi, Mariana, Negri, Mariana, Castilho, Antonio L., Costa, Rogério C., Zara, Fernando J. (2020): Checklist of decapod crustaceans from the coast of the São Paulo state (Brazil) supported by integrative molecular and morphological data: III. Infraorder Brachyura Latreille, 1802. Zootaxa 4872 (1): 1-108, DOI: https://doi.org/10.11646/zootaxa.4872.1.1
DOI: 10.5281/zenodo.4543874
title: Dataset for Single-exposure absorption imaging of ultracold atoms using deep learning

description: Original dataset used in the manuscript <em>Single-Exposure Absorption Imaging of Ultracold Atoms Using Deep Learning</em> Gal Ness, Anastasiya Vainbaum, Constantine Shkedrov, Yanay Florshaim, and Yoav Sagi Phys. Rev. Applied <strong>14</strong>, 014011 – Published 6 July 2020<br> <br> Official code repository is at absDL.github.io/ .
DOI: 10.5281/zenodo.4543873
title: Dataset for Single-exposure absorption imaging of ultracold atoms using deep learning

description: Original dataset used in the manuscript <em>Single-Exposure Absorption Imaging of Ultracold Atoms Using Deep Learning</em> Gal Ness, Anastasiya Vainbaum, Constantine Shkedrov, Yanay Florshaim, and Yoav Sagi Phys. Rev. Applied <strong>14</strong>, 014011 – Published 6 July 2020<br> <br> Official code repository is at absDL.github.io/ .
DOI: 10.6084/m9.figshare.14135066
title: The leaves of Stachytarpheta cayennensis (Rich.) Vahl induce anti-inflamatory and antioxidant activity on in vitro study.

description: <i>Stachytarpheta cayennensis</i> leaves are widely used in folk medicine to treat inflammation syntoms and as an antioxidant agent. However, many of its characteristics are yet to be studied. To evaluate its anti-inflammatory properties we used RAW 264.7 cells estimulated by lipopolysaccharides (LPS) + gamma interferon (IFN-γ), and estimated its effects on nitric oxide (NO) production. We also performed essays using 2,2-difenil-1-picril-hidrazil (DPPH) to evaluate the antioxidant properties of the plant. Anti-inflammatory potencial was shown especially for the hexane (HF) and ethyl acetate (EAF) fractions, and the main antioxidant effect was show for EAF. Both fractions also showed low levels of cytotoxicity (IC<sub>50</sub> above 5000 µg/mL) and high seletivity indexes (SI). The crude extract (CE) and chloroform fraction (CF) however showed low SI due to their high cytotoxicity levels. It becomes evident that the leaves of <i>S. cayennensis</i> are endowed with anti-inflammatory and antioxidant activities and therefore should be further studied. p { margin-bottom: 0.25cm; direction: ltr; font-size: 12pt; line-height: 115%; text-align: left; orphans: 2; widows: 2; background: transparent }
DOI: 10.6084/m9.figshare.14135066.v1
title: The leaves of Stachytarpheta cayennensis (Rich.) Vahl induce anti-inflamatory and antioxidant activity on in vitro study.

description: <i>Stachytarpheta cayennensis</i> leaves are widely used in folk medicine to treat inflammation syntoms and as an antioxidant agent. However, many of its characteristics are yet to be studied. To evaluate its anti-inflammatory properties we used RAW 264.7 cells estimulated by lipopolysaccharides (LPS) + gamma interferon (IFN-γ), and estimated its effects on nitric oxide (NO) production. We also performed essays using 2,2-difenil-1-picril-hidrazil (DPPH) to evaluate the antioxidant properties of the plant. Anti-inflammatory potencial was shown especially for the hexane (HF) and ethyl acetate (EAF) fractions, and the main antioxidant effect was show for EAF. Both fractions also showed low levels of cytotoxicity (IC<sub>50</sub> above 5000 µg/mL) and high seletivity indexes (SI). The crude extract (CE) and chloroform fraction (CF) however showed low SI due to their high cytotoxicity levels. It becomes evident that the leaves of <i>S. cayennensis</i> are endowed with anti-inflammatory and antioxidant activities and therefore should be further studied. p { margin-bottom: 0.25cm; direction: ltr; font-size: 12pt; line-height: 115%; text-align: left; orphans: 2; widows: 2; background: transparent }
DOI: 10.5281/zenodo.4415985
title: 3D Models from La Noira site (Central France)

description: 76 3D models (.pdf) of the handaxes and cleaver-like tools from La Noira sequence (Central France). There are two folders: Lower Levels (stratum a) and Upper Levels (stratum c). The models are unscaled. If you need metrical information, please contact the author. The .xlsx files contains the list of tools (including code and layer information).
DOI: 10.5281/zenodo.4415984
title: 3D Models from La Noira site (Central France)

description: 76 3D models (.pdf) of the handaxes and cleaver-like tools from La Noira sequence (Central France). There are two folders: Lower Levels (stratum a) and Upper Levels (stratum c). The models are unscaled. If you need metrical information, please contact the author. The .xlsx files contains the list of tools (including code and layer information).
DOI: 10.5281/zenodo.4565950
title: Western European Acheulean: 3D models of handaxes and cleavers

description: 3D models (.pdf) of handaxes and cleavers from 10 sites along UK, France and Spain: - UK: Brandon Fields, Boxgrove, Elveden, Swanscombe-UMG - FR: La Noira stratum a and c, Cagny-la-Garenne I, Menez Dregan, Saint-Pierre-lés-Elbeuf -SP: Atapuerca (Galería and Gran Dolina-TD10.1) The models are unscaled. If you need metrical information, please contact the author. The .xlsx file contains a general list of tools (sites, level and piece code).
DOI: 10.5281/zenodo.4565949
title: Western European Acheulean: 3D models of handaxes and cleavers

description: 3D models (.pdf) of handaxes and cleavers from 10 sites along UK, France and Spain: - UK: Brandon Fields, Boxgrove, Elveden, Swanscombe-UMG - FR: La Noira stratum a and c, Cagny-la-Garenne I, Menez Dregan, Saint-Pierre-lés-Elbeuf -SP: Atapuerca (Galería and Gran Dolina-TD10.1) The models are unscaled. If you need metrical information, please contact the author. The .xlsx file contains a general list of tools (sites, level and piece code).
DOI: 10.6084/m9.figshare.11938746
title: Probing the fibrillation of lysozyme by nanoscale-infrared spectroscopy

description: Amyloid fibrillation is the root cause of several neuro as well as non-neurological disorders. Understanding the molecular basis of amyloid aggregate formation is crucial for deciphering various neurodegenerative diseases. In our study, we have examined the lysozyme fibrillation process using nano-infrared spectroscopy (nanoIR). NanoIR enabled us to investigate both structural and chemical characteristics of lysozyme fibrillar species concurrently. The spectroscopic results indicate that lysozyme transformed into a fibrillar structure having mainly parallel β-sheets, with almost no antiparallel β-sheets. Features such as protein stiffness have a good correlation with obtained secondary structural information showing the state of the protein within the fibrillation state. The structural and chemical details were compared with transmission electron microscopy (TEM) and circular dichroism (CD). We have utilized nanoIR and measured infrared spectra to characterize lysozyme amyloid fibril structures in terms of morphology, molecular structure, secondary structure content, stability, and size of the cross-β core. We have shown that the use of nanoIR can complement other biophysical studies to analyze the aggregation process and is particularly useful for studying proteins involved in aggregation to help in designing molecules against amyloid aggregation. Specifically, the nanoIR spectra afford higher resolution information and a characteristic fingerprint for determining states of aggregation. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11938746.v2
title: Probing the fibrillation of lysozyme by nanoscale-infrared spectroscopy

description: Amyloid fibrillation is the root cause of several neuro as well as non-neurological disorders. Understanding the molecular basis of amyloid aggregate formation is crucial for deciphering various neurodegenerative diseases. In our study, we have examined the lysozyme fibrillation process using nano-infrared spectroscopy (nanoIR). NanoIR enabled us to investigate both structural and chemical characteristics of lysozyme fibrillar species concurrently. The spectroscopic results indicate that lysozyme transformed into a fibrillar structure having mainly parallel β-sheets, with almost no antiparallel β-sheets. Features such as protein stiffness have a good correlation with obtained secondary structural information showing the state of the protein within the fibrillation state. The structural and chemical details were compared with transmission electron microscopy (TEM) and circular dichroism (CD). We have utilized nanoIR and measured infrared spectra to characterize lysozyme amyloid fibril structures in terms of morphology, molecular structure, secondary structure content, stability, and size of the cross-β core. We have shown that the use of nanoIR can complement other biophysical studies to analyze the aggregation process and is particularly useful for studying proteins involved in aggregation to help in designing molecules against amyloid aggregation. Specifically, the nanoIR spectra afford higher resolution information and a characteristic fingerprint for determining states of aggregation. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11829669.v2
title: Computational identification of natural product leads that inhibit mast cell chymase: an exclusive plausible treatment for Japanese encephalitis

description: A recent research has identified chymase, a mast cell-specific protease as an exclusive novel therapeutic target to prevent Japanese encephalitis virus (JEV) induced encephalitis. Interestingly, JEV activates mast cell specific chymase during its penetration through blood brain barrier (BBB) which eventually guide to viral encephalitis. Hence, in this study, natural chemical entities (NCE) from multiple databases (MPD3, TIPDB and MTDP) were virtually screened for their binding affinity as chymase inhibitors, a promising negotiator for prolong survival against JEV tempted encephalitis. Merged computational programs, Maestro software, QikProp, ProTox and Gromacs were applied to screen the NCEs against target receptor (PDB: 4KP0). Three hits (C00008437, C00014417 and 8141903) were identified after employing a series of sieves such as High Throughput Virtual Screening (HTVS), Standard precision (SP) and Xtra precision (XP) molecular docking simulations followed by desired pharmacokinetic-toxicity profile predictions and molecular dynamics (MD) examinations. Maestro simulations resulted in best three binding energy scores as −11.992 kcal/mol (first ranked; C00008437), −11.673 kcal/mol (second ranked; C00014417) and −11.456 kcal/mol (third ranked; 8141903), respectively. The top three hits revealed an ideal range of pharmacokinetic and toxicity descriptors values. In addition, MD simulations enabled us to confirm top hits higher selectivity toward chymase receptor. In conclusion, this might potentially represent remarkable novel classes with an effective chymase mediated treatment to combat JEV induced encephalitis, which need to justify with further detail studies. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11829669
title: Computational identification of natural product leads that inhibit mast cell chymase: an exclusive plausible treatment for Japanese encephalitis

description: A recent research has identified chymase, a mast cell-specific protease as an exclusive novel therapeutic target to prevent Japanese encephalitis virus (JEV) induced encephalitis. Interestingly, JEV activates mast cell specific chymase during its penetration through blood brain barrier (BBB) which eventually guide to viral encephalitis. Hence, in this study, natural chemical entities (NCE) from multiple databases (MPD3, TIPDB and MTDP) were virtually screened for their binding affinity as chymase inhibitors, a promising negotiator for prolong survival against JEV tempted encephalitis. Merged computational programs, Maestro software, QikProp, ProTox and Gromacs were applied to screen the NCEs against target receptor (PDB: 4KP0). Three hits (C00008437, C00014417 and 8141903) were identified after employing a series of sieves such as High Throughput Virtual Screening (HTVS), Standard precision (SP) and Xtra precision (XP) molecular docking simulations followed by desired pharmacokinetic-toxicity profile predictions and molecular dynamics (MD) examinations. Maestro simulations resulted in best three binding energy scores as −11.992 kcal/mol (first ranked; C00008437), −11.673 kcal/mol (second ranked; C00014417) and −11.456 kcal/mol (third ranked; 8141903), respectively. The top three hits revealed an ideal range of pharmacokinetic and toxicity descriptors values. In addition, MD simulations enabled us to confirm top hits higher selectivity toward chymase receptor. In conclusion, this might potentially represent remarkable novel classes with an effective chymase mediated treatment to combat JEV induced encephalitis, which need to justify with further detail studies. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11871195
title: Enhanced metastable state models of TAM kinase binding to cabozantinib explains the dynamic nature of receptor tyrosine kinases

description: Receptor tyrosine kinases (RTKs) are essential proteins in the regulation of cell signaling. Tyro3, Axl and Mer are members of TAM RTKs and are overexpressed in several cancer forms. Kinase inhibitors such as cabozantinib, foretinib are reported to inhibit TAM kinases at nanomolar concentrations. The atomistic details of structure and mechanism of functional regulation is required to understand their normal physiological process and when bound to an inhibitor. The docking of cabozantinib into the active state conformations of TAM kinases (crystal structure and computational models) revealed the best binding pose and the complex formation that is mediated through non-bonding interactions involving the hinge region residues. The alterations in the conformations and the regions of flexibility in apo and complexed TAM kinases as a course of time are studied using 250 ns molecular dynamics (MD) simulations. The post-MD trajectory analysis using Python libraries like ProDy, MDTraj and PyEMMA revealed encrypted protein dynamic motions in active kinetic metastable states. Comparison between Principal component analysis and Anisotropic mode analysis deciphered structural residue interactions and salt bridge contacts between apo and inhibitor bound TAM kinases. Various structural changes occurred in αC-helix and activation loop involving hydrogen bonding between residues from Lys-(β3 sheet), Glu-(αC-helix) and Asp-(DFG-motif) resulting in higher RMSD. Mechanical stiffness plots revealed that similar regions in apo and cabozantinib bound Axl fluctuated during MD simulations whereas different regions in Tyro3 and Mer kinases. The residue interaction network plots revealed important salt bridges that lead to constrained domain motions in the TAM kinases. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11829531.v2
title: Extensive immunoinformatics study for the prediction of novel peptide-based epitope vaccine with docking confirmation against envelope protein of Chikungunya virus: a computational biology approach

description: Chikungunya virus (CHIKV) instigating Chikungunya fever is a global infective menace resulting in high fever, weakened joint-muscle pain, and brain inflammation. Inaccessibility and unavailability of effective drugs have led us to an uncertain arena when it comes to providing proper medical treatment to the affected people. In this study, authentic encroachment has been made concerning the peptide-based epitope vaccine designing against CHIKV. A Proteome-wide search was performed to locate a conserved portion among the accessible viral outer membrane proteins which showcase a remarkable immune response using specific immunoinformatics and docking simulation tools. Primarily, the most probable immunogenic envelope glycoproteins E1 and E2 were identified from the UniProt database depending on their antigenicity scores. Subsequently, we selected two distinctive sequences “SEDVYANTQLVLQRP” and “IMLLYPDHPTLLSYR” in both E1 and E2 glycoproteins respectively. These two sequences identified as the most potent T and B cell epitope-based peptides as they interacted with 6 and 7 HLA-I and 5 HLA-II molecules with an extremely low IC50 score that was verified by molecular docking. Moreover, the sequences possess no allergenicity and are certainly located outside the transmembrane region. In addition, the sequences exhibited 88.46% and 100.00% Conservancy, covering high population coverage of 89.49% to 94.74% and 60.51% to 88.87% respectively in endemic countries. The identified peptide SEDVYANTQLVLQRP and IMLLYPDHPTLLSYR can be utilized next for the development of peptide-based epitope vaccine contrary to CHIKV, so further documentations and experimentations like Antigen testing, Antigen production, Clinical trials are needed to prove the validity of it. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.11871195.v2
title: Enhanced metastable state models of TAM kinase binding to cabozantinib explains the dynamic nature of receptor tyrosine kinases

description: Receptor tyrosine kinases (RTKs) are essential proteins in the regulation of cell signaling. Tyro3, Axl and Mer are members of TAM RTKs and are overexpressed in several cancer forms. Kinase inhibitors such as cabozantinib, foretinib are reported to inhibit TAM kinases at nanomolar concentrations. The atomistic details of structure and mechanism of functional regulation is required to understand their normal physiological process and when bound to an inhibitor. The docking of cabozantinib into the active state conformations of TAM kinases (crystal structure and computational models) revealed the best binding pose and the complex formation that is mediated through non-bonding interactions involving the hinge region residues. The alterations in the conformations and the regions of flexibility in apo and complexed TAM kinases as a course of time are studied using 250 ns molecular dynamics (MD) simulations. The post-MD trajectory analysis using Python libraries like ProDy, MDTraj and PyEMMA revealed encrypted protein dynamic motions in active kinetic metastable states. Comparison between Principal component analysis and Anisotropic mode analysis deciphered structural residue interactions and salt bridge contacts between apo and inhibitor bound TAM kinases. Various structural changes occurred in αC-helix and activation loop involving hydrogen bonding between residues from Lys-(β3 sheet), Glu-(αC-helix) and Asp-(DFG-motif) resulting in higher RMSD. Mechanical stiffness plots revealed that similar regions in apo and cabozantinib bound Axl fluctuated during MD simulations whereas different regions in Tyro3 and Mer kinases. The residue interaction network plots revealed important salt bridges that lead to constrained domain motions in the TAM kinases. Communicated by Ramaswamy H. Sarma