cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9638792.v2
title: Mechanical strain mimicking breathing amplifies alterations in gene expression induced by SiO<sub>2</sub> NPs in lung epithelial cells

description: The effects of engineered nanomaterials on human health are still intensively studied in order to facilitate their safe application. However, relatively little is known how mechanical strain as induced in alveolar epithelial cells by breathing movements modifies biological responses to nanoparticles (NPs). In this study, A549 cells as a model for alveolar epithelial cells were exposed to 25 nm amorphous colloidal silica NPs under dynamic and static culture conditions. Gene array data, qPCR, and ELISA revealed an amplified effect of NPs when cells were mechanically stretched in order to model the physiological mechanical deformation during breathing. In contrast, treatment of cells with either strain or NPs alone only led to minor changes in gene expression or interleukin-8 (IL-8) secretion. Confocal microscopy revealed that stretching does not lead to an increased internalization of NPs, indicating that elevated intracellular NP accumulation is not responsible for the observed effect. Gene expression alterations induced by combined exposure to NPs and mechanical strain showed a high similarity to those known to be induced by TNF-α. This study suggests that the inclusion of mechanical strain into <i>in vitro</i> models of the human lung may have a strong influence on the test results.
DOI: 10.6084/m9.figshare.9638615
title: phylogenomic tree

description: Phylogenomic tree in nexus format<br>
DOI: 10.6084/m9.figshare.9638615.v1
title: phylogenomic tree

description: Phylogenomic tree in nexus format<br>
DOI: 10.6084/m9.figshare.9638549
title: Machine Vision: Creative Works, Sentiments and Genres

description: The Gephi file for a dataset listing creative works (artworks, video games, novels, movies, etc) that use or represent machine vision, connected to the sentiment or general attitude shown towards machine vision in the work. This is an incomplete, in-progress data set, exported from the database we are building as part of the project in August 2019. Works that were not tagged art, game or narrative were not included.<br>Be aware that this is incomplete and tentative data from an early stage of the research.<br><br>The live data from the database is available here: https://machine-vision.no/works---genre-situation
DOI: 10.6084/m9.figshare.9638525
title: Table 1

description: Outcrop data for each formation of the Arroyo Atravesado locality of 103 specimens and its anisotropy of magnetic susceptibility parameters. B. Plane: bedding strike (0º-360º) and dip (90° clockwise, from given strike, 0º-90º). Cleavage: direction (0º-360º) and dip (90° clockwise, from given strike, 0º-90º). S<sub>0</sub> and S<sub>1</sub> foliations measured in thin sections (0°-360°). K<i><sub>max</sub></i>: average orientation of the maximum axe of AMS; K<sub>m</sub> = (K<sub>max</sub>+K<sub>int</sub>+K<sub>min</sub>)/3: average susceptibility volume in SI units; P<sub>j</sub> av: average anisotropy degree (P = K<sub>max</sub>/K<sub>min</sub>: anisotropy degree according to <i>Nagata</i>, 1961); T: average shape parameter of Jelinek (<i>Jelinek</i>, 1981); L = K<sub>max</sub>/K<sub>int</sub>: Average lineation; F = K<sub>int</sub>/K<sub>min</sub>: Average foliation (<i>Flinn</i>, 1962).
DOI: 10.17028/rd.lboro.9638450
title: New functionalised tertiary phosphines : synthesis, coordination and reactivity studies. Additional files.

description: Tables containing crystallographic data for thesis experiments.<b><i>Table A</i></b>.<b><i>1</i></b>.<i> </i>Crystallographic data for <b>2.4</b>, <b>2.14</b>, <b>2.16</b> and <b>2.20</b>. <b><i>Table</i></b> <b><i>A</i></b>.<b><i>2</i></b>. Crystallographic data for <b>2.23</b>,<b> 2.26</b>, <b>2.28 </b>and <b>2.32</b>. <b><i>Table A</i></b>.<b><i>3</i></b>. Crystallographic data for <b>2.47</b>, <b>2.48</b>, <b>2.49 </b>and <b>2.50</b>. <b><i>Table A</i></b>.<b><i>4</i></b>. Crystallographic data for <b>2.53</b>, <b>2.55</b>, <b>2.58</b> and <b>2.64</b>. <b><i>Table A</i></b>.<b><i>5</i></b>. Crystallographic data for <b>2.68</b>, <b>2.69</b>, <b>3.9</b> and <b>3.10</b>. <b><i>Table A</i></b>.<b><i>6</i></b>. Crystallographic data for <b>3.16</b>, <b>3.27</b>, <b>3.28</b> and <b>3.29</b>. <b><i>Table A</i></b>.<b><i>7</i></b>. Crystallographic data for <b>3.30</b>, <b>3.31</b>, <b>3.38</b> and <b>3.45</b>. <b><i>Table A</i></b>.<b><i>8</i></b>. Crystallographic data for <b>3.49</b>, <b>4.1</b>, <b>4.8a</b> and <b>4.8b</b>. <b><i>Table A</i></b>.<b><i>9</i></b>.<b><i> </i></b>Crystallographic data for <b>4.12</b>, <b>4.19</b>, <b>4.30</b> and <b>5.7</b>. <b><i>Table A</i></b>.<b><i>10</i></b>. Crystallographic data for <b>5.8</b>, <b>5.14</b>, <b>5.16</b> and <b>5.22</b>.
DOI: 10.17028/rd.lboro.9638462
title: The supramolecular chemistry of benzene- and pyridinepolycarboxylic acids. Additional files.

description: For all structures in this thesis where a crystal structure diagram is shown, <i>X</i>.rtf and <i>X</i>.res files are included in the directory “Tables and Res Files” within the relevant subdirectory for each chapter, where <i>X</i> is the compound number assigned in the thesis. The .rtf files contain the tabulated output from each determination, including information concerning the data collection strategy and the resulting bond lengths, bond angles and hydrogen bonds. The .res files contain the <i>xyz</i> coordinates for the structures and can be read into a number of crystal structure visualisers (e.g. SHEXTL XP or Mercury) for viewing as required.
DOI: 10.17028/rd.lboro.9638462.v1
title: The supramolecular chemistry of benzene- and pyridinepolycarboxylic acids. Additional files.

description: For all structures in this thesis where a crystal structure diagram is shown, <i>X</i>.rtf and <i>X</i>.res files are included in the directory “Tables and Res Files” within the relevant subdirectory for each chapter, where <i>X</i> is the compound number assigned in the thesis. The .rtf files contain the tabulated output from each determination, including information concerning the data collection strategy and the resulting bond lengths, bond angles and hydrogen bonds. The .res files contain the <i>xyz</i> coordinates for the structures and can be read into a number of crystal structure visualisers (e.g. SHEXTL XP or Mercury) for viewing as required.
DOI: 10.6084/m9.figshare.9638441
title: Virtual identification of novel PPARα/γ dual agonists by 3D-QSAR, molecule docking and molecular dynamics studies

description: Peroxisome proliferator-activated receptors (PPARs) are considered important targets for the treatment of Type 2 diabetes (T2DM). To accelerate the discovery of PPAR α/γ dual agonists, the comparative molecular field analysis (CoMFA) were performed for PPARα and PPARγ, respectively. Based on the molecular alignment, highly predictive CoMFA model for PPARα was obtained with a cross-validated <i>q</i><sup>2</sup> value of 0.741 and a conventional <i>r</i><sup>2</sup> of 0.975 in the non-cross-validated partial least-squares (PLS) analysis, while the CoMFA model for PPARγ with a better predictive ability was shown with <i>q</i><sup>2</sup> and <i>r</i><sup>2</sup> values of 0.557 and 0.996, respectively. Contour maps derived from the 3D-QSAR models provided information on main factors towards the activity. Then, we carried out structural optimization and designed several new compounds to improve the predicted biological activity. To investigate the binding modes of the predicted compounds in the active site of PPARα/γ, a molecular docking simulation was carried out. Molecular dynamic (MD) simulations indicated that the predicted ligands were stable in the active site of PPARα/γ. Therefore, combination of the CoMFA and structure-based drug design results could be used for further structural alteration and synthesis and development of novel and potent dual agonists. AbbreviationsDMdiabetes mellitusT2DMtype 2 diabetesPPARsperoxisome proliferator-activated receptorsLBDDligand based drug design3D-QSARthree-dimensional quantitative structure activity relationshipCoMFAcomparative molecular field analysisPLSpartial least squareLOOleave-one-out<i>q</i><sup>2</sup>cross-validated correlation coefficientONCoptimal number of principal components<i>r</i><sup>2</sup>non-cross-validated correlation coefficientSEEstandard error of estimate<i>F</i>the Fischer ratio<i>r</i><sup>2</sup><sub>pred</sub>predictive correlation coefficientDBDDNA binding domainMDmolecular dynamicsRMSDroot-mean-square deviationRMSFroot mean square fluctuations diabetes mellitus type 2 diabetes peroxisome proliferator-activated receptors ligand based drug design three-dimensional quantitative structure activity relationship comparative molecular field analysis partial least square leave-one-out cross-validated correlation coefficient optimal number of principal components non-cross-validated correlation coefficient standard error of estimate the Fischer ratio predictive correlation coefficient DNA binding domain molecular dynamics root-mean-square deviation root mean square fluctuations Communicated by Ramaswamy H. Sarma In this study, we explored the SARs of zwitterionic derivatives dually targeting PPARα/γ and designed novel PPARα/γ dual agonists, using 3D-QSAR studies. Molecular docking and molecular dynamics simulation served as validation and complement to the SAR results derived from the 3D-QSAR model.
DOI: 10.17028/rd.lboro.9638450.v1
title: New functionalised tertiary phosphines : synthesis, coordination and reactivity studies. Additional files.

description: Tables containing crystallographic data for thesis experiments.<b><i>Table A</i></b>.<b><i>1</i></b>.<i> </i>Crystallographic data for <b>2.4</b>, <b>2.14</b>, <b>2.16</b> and <b>2.20</b>. <b><i>Table</i></b> <b><i>A</i></b>.<b><i>2</i></b>. Crystallographic data for <b>2.23</b>,<b> 2.26</b>, <b>2.28 </b>and <b>2.32</b>. <b><i>Table A</i></b>.<b><i>3</i></b>. Crystallographic data for <b>2.47</b>, <b>2.48</b>, <b>2.49 </b>and <b>2.50</b>. <b><i>Table A</i></b>.<b><i>4</i></b>. Crystallographic data for <b>2.53</b>, <b>2.55</b>, <b>2.58</b> and <b>2.64</b>. <b><i>Table A</i></b>.<b><i>5</i></b>. Crystallographic data for <b>2.68</b>, <b>2.69</b>, <b>3.9</b> and <b>3.10</b>. <b><i>Table A</i></b>.<b><i>6</i></b>. Crystallographic data for <b>3.16</b>, <b>3.27</b>, <b>3.28</b> and <b>3.29</b>. <b><i>Table A</i></b>.<b><i>7</i></b>. Crystallographic data for <b>3.30</b>, <b>3.31</b>, <b>3.38</b> and <b>3.45</b>. <b><i>Table A</i></b>.<b><i>8</i></b>. Crystallographic data for <b>3.49</b>, <b>4.1</b>, <b>4.8a</b> and <b>4.8b</b>. <b><i>Table A</i></b>.<b><i>9</i></b>.<b><i> </i></b>Crystallographic data for <b>4.12</b>, <b>4.19</b>, <b>4.30</b> and <b>5.7</b>. <b><i>Table A</i></b>.<b><i>10</i></b>. Crystallographic data for <b>5.8</b>, <b>5.14</b>, <b>5.16</b> and <b>5.22</b>.
DOI: 10.6084/m9.figshare.9638393
title: PathRacer: benchmarking scripts and datasets

description: The datasets supporting the conclusions of this article "PathRacer: aligning profile HMMs against assembly graphs and long noisy sequences"
DOI: 10.6084/m9.figshare.9638441.v2
title: Virtual identification of novel PPARα/γ dual agonists by 3D-QSAR, molecule docking and molecular dynamics studies

description: Peroxisome proliferator-activated receptors (PPARs) are considered important targets for the treatment of Type 2 diabetes (T2DM). To accelerate the discovery of PPAR α/γ dual agonists, the comparative molecular field analysis (CoMFA) were performed for PPARα and PPARγ, respectively. Based on the molecular alignment, highly predictive CoMFA model for PPARα was obtained with a cross-validated <i>q</i><sup>2</sup> value of 0.741 and a conventional <i>r</i><sup>2</sup> of 0.975 in the non-cross-validated partial least-squares (PLS) analysis, while the CoMFA model for PPARγ with a better predictive ability was shown with <i>q</i><sup>2</sup> and <i>r</i><sup>2</sup> values of 0.557 and 0.996, respectively. Contour maps derived from the 3D-QSAR models provided information on main factors towards the activity. Then, we carried out structural optimization and designed several new compounds to improve the predicted biological activity. To investigate the binding modes of the predicted compounds in the active site of PPARα/γ, a molecular docking simulation was carried out. Molecular dynamic (MD) simulations indicated that the predicted ligands were stable in the active site of PPARα/γ. Therefore, combination of the CoMFA and structure-based drug design results could be used for further structural alteration and synthesis and development of novel and potent dual agonists. AbbreviationsDMdiabetes mellitusT2DMtype 2 diabetesPPARsperoxisome proliferator-activated receptorsLBDDligand based drug design3D-QSARthree-dimensional quantitative structure activity relationshipCoMFAcomparative molecular field analysisPLSpartial least squareLOOleave-one-out<i>q</i><sup>2</sup>cross-validated correlation coefficientONCoptimal number of principal components<i>r</i><sup>2</sup>non-cross-validated correlation coefficientSEEstandard error of estimate<i>F</i>the Fischer ratio<i>r</i><sup>2</sup><sub>pred</sub>predictive correlation coefficientDBDDNA binding domainMDmolecular dynamicsRMSDroot-mean-square deviationRMSFroot mean square fluctuations diabetes mellitus type 2 diabetes peroxisome proliferator-activated receptors ligand based drug design three-dimensional quantitative structure activity relationship comparative molecular field analysis partial least square leave-one-out cross-validated correlation coefficient optimal number of principal components non-cross-validated correlation coefficient standard error of estimate the Fischer ratio predictive correlation coefficient DNA binding domain molecular dynamics root-mean-square deviation root mean square fluctuations Communicated by Ramaswamy H. Sarma In this study, we explored the SARs of zwitterionic derivatives dually targeting PPARα/γ and designed novel PPARα/γ dual agonists, using 3D-QSAR studies. Molecular docking and molecular dynamics simulation served as validation and complement to the SAR results derived from the 3D-QSAR model.
DOI: 10.6084/m9.figshare.9638393.v1
title: PathRacer: benchmarking scripts and datasets

description: The datasets supporting the conclusions of this article "PathRacer: aligning profile HMMs against assembly graphs and long noisy sequences"
DOI: 10.17028/rd.lboro.9638285
title: Integrable equations of the dispersionless Hirota type. Additional files

description: Additional files to support thesis. Contains:Integrability_conds - Mathematica program for the derivation of integrability conditions of the equations u_tt = f (u_xx, u_xy, u_yy, u_xt, u_yt).The main result of this computation is stored in the file "conditions.txt". Integrability_test - this program can be used to test <br>conditions.txt - integrability conditions.<br>For full details see read me file.<br>
DOI: 10.17028/rd.lboro.9638279
title: Understanding sorting algorithms using music and spatial distribution. Additional files.

description: Additional files to support thesis. Including audio files used in experiments and documentation for SIMBAA.
DOI: 10.17028/rd.lboro.9638285.v1
title: Integrable equations of the dispersionless Hirota type. Additional files

description: Additional files to support thesis. Contains:Integrability_conds - Mathematica program for the derivation of integrability conditions of the equations u_tt = f (u_xx, u_xy, u_yy, u_xt, u_yt).The main result of this computation is stored in the file "conditions.txt". Integrability_test - this program can be used to test <br>conditions.txt - integrability conditions.<br>For full details see read me file.<br>
DOI: 10.17028/rd.lboro.9638279.v1
title: Understanding sorting algorithms using music and spatial distribution. Additional files.

description: Additional files to support thesis. Including audio files used in experiments and documentation for SIMBAA.
DOI: 10.6084/m9.figshare.9638234
title: Extended Data - Biological Effects of Nicotine Exposure: A narrative review of the scientific literature

description: Search methods, criteria and results for a non-systematic literature review
DOI: 10.6084/m9.figshare.9638228
title: Data for "Paleo-ocean destratification triggered by the subduction of the Oyashio water into the Sea of Japan after the Last Glacial Maximum"

description: Data and fortran90 code for "Paleo-ocean destratification triggered by the subduction of the Oyashio water into the Sea of Japan after the Last Glacial Maximum" submitted to Paleoceanography and paleoclimatology (Isobe, in revision)
DOI: 10.6084/m9.figshare.9638228.v1
title: Data for "Paleo-ocean destratification triggered by the subduction of the Oyashio water into the Sea of Japan after the Last Glacial Maximum"

description: Data and fortran90 code for "Paleo-ocean destratification triggered by the subduction of the Oyashio water into the Sea of Japan after the Last Glacial Maximum" submitted to Paleoceanography and paleoclimatology (Isobe, in revision)
DOI: 10.6084/m9.figshare.9638093
title: QM-sym-database

description: 188 kilo molecules together with properties. Please read the 'readme' file for more description before using it.
DOI: 10.6084/m9.figshare.9638093.v1
title: QM-sym-database

description: 135 kilo molecules together with properties. Please read the 'readme' file for more description before using it.
DOI: 10.6084/m9.figshare.9638093.v2
title: QM-sym-database

description: 188 kilo molecules together with properties. Please read the 'readme' file for more description before using it.
DOI: 10.6084/m9.figshare.9638093.v3
title: QM-sym-database

description: 188 kilo molecules together with properties. Please read the 'readme' file for more description before using it.
DOI: 10.6084/m9.figshare.9638093.v4
title: QM-sym-database

description: 188 kilo molecules together with properties. Please read the 'readme' file for more description before using it.
DOI: 10.6084/m9.figshare.9638093.v5
title: QM-sym-database

description: 188 kilo molecules together with properties. Please read the 'readme' file for more description before using it.
DOI: 10.6084/m9.figshare.9638093.v6
title: QM-sym-database

description: 188 kilo molecules together with properties. Please read the 'readme' file for more description before using it.
DOI: 10.6084/m9.figshare.9638024
title: Supplementary data_Effect of Meditative Movement on affect and flow in qigong practitioners

description: Supplementary data from PANAS, FSS and open questionnaires
DOI: 10.6084/m9.figshare.9638024.v1
title: Supplementary data_Effect of Meditative Movement on affect and flow in qigong practitioners

description: Supplementary data from PANAS, FSS and open questionnaires
DOI: 10.6084/m9.figshare.9638093.v7
title: QM-sym-database

description: 188 kilo molecules together with properties. Please read the 'readme' file for more description before using it.
DOI: 10.6084/m9.figshare.9637886
title: ONT-only assemblies

description: Results of ONT-only assemblies of nine NG isolates using Unicycler.
DOI: 10.6084/m9.figshare.9637886.v1
title: ONT-only assemblies

description: Results of ONT-only assemblies of nine NG isolates using Unicycler.
DOI: 10.6084/m9.figshare.9637859
title: hybrid_assembly.rar

description: Results of hybrid assemblies of nine NG isolates using Unicycler.
DOI: 10.6084/m9.figshare.9637859.v1
title: hybrid_assembly.rar

description: Results of hybrid assemblies of nine NG isolates using Unicycler.
DOI: 10.6084/m9.figshare.9637634
title: user survey data

description: Suntae Kim created on 16th August, 2019. This suvey document was created for collecting users' preference about the local representative library in Jeonbuk provicne, Korea.
DOI: 10.6084/m9.figshare.9637634.v1
title: user survey data

description: Suntae Kim created on 16th August, 2019. This suvey document was created for collecting users' preference about the local representative library in Jeonbuk provicne, Korea.
DOI: 10.6084/m9.figshare.9637595
title: Additional file 2: of Identification and potential mechanisms of a 4-lncRNA signature that predicts prognosis in patients with laryngeal cancer

description: R language code. R language code of Multivariate Cox regression analysis to develop a 4-lncRNA signature. (TXT 1 kb)
DOI: 10.6084/m9.figshare.9637595.v1
title: Additional file 2: of Identification and potential mechanisms of a 4-lncRNA signature that predicts prognosis in patients with laryngeal cancer

description: R language code. R language code of Multivariate Cox regression analysis to develop a 4-lncRNA signature. (TXT 1 kb)
DOI: 10.6084/m9.figshare.9637571
title: Additional file 9: of Evaluation of novel rapid detection kits for dengue virus NS1 antigen in Dhaka, Bangladesh, in 2017

description: Sequences of NS1 region from GenBank used in phylogenetic analysis. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.9637571.v1
title: Additional file 9: of Evaluation of novel rapid detection kits for dengue virus NS1 antigen in Dhaka, Bangladesh, in 2017

description: Sequences of NS1 region from GenBank used in phylogenetic analysis. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.9637547
title: Additional file 5: of Evaluation of novel rapid detection kits for dengue virus NS1 antigen in Dhaka, Bangladesh, in 2017

description: Results of RDT evaluation in all DENV RT-PCR-negative samples. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.9637544
title: Additional file 4: of Evaluation of novel rapid detection kits for dengue virus NS1 antigen in Dhaka, Bangladesh, in 2017

description: Results of RDT evaluation in all DENV RT-PCR-positive samples. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.9637547.v1
title: Additional file 5: of Evaluation of novel rapid detection kits for dengue virus NS1 antigen in Dhaka, Bangladesh, in 2017

description: Results of RDT evaluation in all DENV RT-PCR-negative samples. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.9637541
title: Additional file 6: of The transcriptome of peripheral blood mononuclear cells in patients with clinical subtypes of late age-related macular degeneration

description: List of significantly differentially expressed genes between neovascular AMD with and without subretinal fibrosis. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.9637544.v1
title: Additional file 4: of Evaluation of novel rapid detection kits for dengue virus NS1 antigen in Dhaka, Bangladesh, in 2017

description: Results of RDT evaluation in all DENV RT-PCR-positive samples. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.9637541.v1
title: Additional file 6: of The transcriptome of peripheral blood mononuclear cells in patients with clinical subtypes of late age-related macular degeneration

description: List of significantly differentially expressed genes between neovascular AMD with and without subretinal fibrosis. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.9637526
title: Additional file 4: of The transcriptome of peripheral blood mononuclear cells in patients with clinical subtypes of late age-related macular degeneration

description: Complete data of gene expression comparison between neovascular AMD with and without subretinal fibrosis. (XLSX 1443 kb)
DOI: 10.6084/m9.figshare.9637526.v1
title: Additional file 4: of The transcriptome of peripheral blood mononuclear cells in patients with clinical subtypes of late age-related macular degeneration

description: Complete data of gene expression comparison between neovascular AMD with and without subretinal fibrosis. (XLSX 1443 kb)
DOI: 10.6084/m9.figshare.9637499
title: Additional file 1: of The transcriptome of peripheral blood mononuclear cells in patients with clinical subtypes of late age-related macular degeneration

description: Gene annotation list. (XLSX 1932 kb)
DOI: 10.6084/m9.figshare.9637502
title: MOESM3 of Wavelet-based verification of a relative paleointensity record from the North Pacific

description: Additional file 3: Table S2. The relative paleointensity data of NPGP1401-2A.
DOI: 10.6084/m9.figshare.9637505
title: Additional file 10: of Evaluation of novel rapid detection kits for dengue virus NS1 antigen in Dhaka, Bangladesh, in 2017

description: Sequences of NS1 region obtained in this study. (XLSX 11 kb)