cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24063702.v1
title: Supplementary Material for: Effectiveness and factors associated with response to golimumab in Japanese patients with ulcerative colitis in real clinical practice: Phoenix Study

description: Abstract Introduction: There have been limited reports on the clinical efficacy of golimumab (GLM) in Japanese patients with ulcerative colitis (UC) in real clinical practice. This study aimed to explore the real-life effectiveness and factors associated with response to GLM in Japanese patients with UC. Methods: This observational, retrospective, multicenter study was conducted in hospitals with expertise in inflammatory bowel disease treatment. Sixty-three patients treated with GLM and active UC were included in the analysis. Clinical remission (CR) (partial Mayo score ≤2) in the induction and maintenance phases after GLM treatment and associated factors were evaluated. Results: The proportion of patients achieving CR in the induction and maintenance phases was 41.3% (26/63) and 46.0% (29/63, the last observation carried forward method was used for patients who discontinued treatment for reasons other than inadequate response), respectively. The median partial Mayo score was 5 (IQR 4-6) at baseline, 3 (IQR 1-5) in the induction phase, and 1 (IQR 0-3) in the maintenance phase. Hemoglobin, platelet, and C-reactive protein levels changed, consistent with the partial Mayo score. Multivariate logistic analysis revealed that biologic-naive status was an independent factor associated with CR in the induction (p=0.0200) and maintenance (p=0.0459) phases, and a disease duration of &gt;60 months until GLM initiation was associated with CR in the induction phase (p=0.0427). Conclusions: The effectiveness of GLM in daily clinical practice has been confirmed in Japanese patients with active UC. Biologic-naive patients responded more to GLM in the induction and maintenance phases, and patients with a disease duration of &gt;60 months until initiation of GLM were more responsive in the induction phase.
DOI: 10.5517/ccdc.csd.cc2dxq57
title: CCDC 2232129: Experimental Crystal Structure Determination

description: Related Article: Chengmi Huang, Dong Wu, Yangyang Li, Guoyin Yin|2023|J.Am.Chem.Soc.|145|18722|doi:10.1021/jacs.3c05969
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: 10.25345/c5319sd03
title: MassIVE MSV000092800 - Loss of MPC and it's effect on retinal metabolism
title: The mitochondrial pyruvate carrier (MPC) links glycolysis and mitochondrial metabolism. In this study, we knocked out MPC1 gene in rod photoreceptor cells of rhodopsin cre mice to explore the role of MPC1 including vision function and morphology.
DOI: 10.5517/ccdc.csd.cc2g7g7f
title: CCDC 2271284: Experimental Crystal Structure Determination

description: Related Article: Mrittika Roy, Wen Fu, Lilia M. Baldauf, James C. Fettinger, R. David Britt, Alan L. Balch|2023|Inorg.Chem.|62|14055|doi:10.1021/acs.inorgchem.3c02079
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.cc2g7g8g
title: CCDC 2271285: Experimental Crystal Structure Determination

description: Related Article: Mrittika Roy, Wen Fu, Lilia M. Baldauf, James C. Fettinger, R. David Britt, Alan L. Balch|2023|Inorg.Chem.|62|14055|doi:10.1021/acs.inorgchem.3c02079
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.cc2g7g9h
title: CCDC 2271286: Experimental Crystal Structure Determination

description: Related Article: Mrittika Roy, Wen Fu, Lilia M. Baldauf, James C. Fettinger, R. David Britt, Alan L. Balch|2023|Inorg.Chem.|62|14055|doi:10.1021/acs.inorgchem.3c02079
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.cc2g7gbj
title: CCDC 2271287: Experimental Crystal Structure Determination

description: Related Article: Mrittika Roy, Wen Fu, Lilia M. Baldauf, James C. Fettinger, R. David Britt, Alan L. Balch|2023|Inorg.Chem.|62|14055|doi:10.1021/acs.inorgchem.3c02079
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.cc2g7gck
title: CCDC 2271288: Experimental Crystal Structure Determination

description: Related Article: Mrittika Roy, Wen Fu, Lilia M. Baldauf, James C. Fettinger, R. David Britt, Alan L. Balch|2023|Inorg.Chem.|62|14055|doi:10.1021/acs.inorgchem.3c02079
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.cc2fxj63
title: CCDC 2261735: Experimental Crystal Structure Determination

description: Related Article: Masahiro Ikeshita, Nobuyuki Hara, Yoshitane Imai, Takeshi Naota|2023|Inorg.Chem.|62|13964|doi:10.1021/acs.inorgchem.3c01935
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.cc2g7gdl
title: CCDC 2271289: Experimental Crystal Structure Determination

description: Related Article: Mrittika Roy, Wen Fu, Lilia M. Baldauf, James C. Fettinger, R. David Britt, Alan L. Balch|2023|Inorg.Chem.|62|14055|doi:10.1021/acs.inorgchem.3c02079
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.8232637
title: Shared genetic factors between stress-related disorders and cardiovascular disease

description: The ultimate goal of this study is to advance our understanding of the biological mechanisms of stress-related disorders and CVD, through demonstrating pleiotropic genes and pathways underlying their comorbidity that are potentially testable as targets of future interventions in experimental investigations.
DOI: 10.5281/zenodo.8232636
title: Shared genetic factors between stress-related disorders and cardiovascular disease

description: The ultimate goal of this study is to advance our understanding of the biological mechanisms of stress-related disorders and CVD, through demonstrating pleiotropic genes and pathways underlying their comorbidity that are potentially testable as targets of future interventions in experimental investigations.
DOI: 10.25345/c5zc7s499
title: MassIVE MSV000092801 - Loss of MPC and its effect on retinal metabolism
title: The mitochondrial pyruvate carrier (MPC) links glycolysis and mitochondrial metabolism. In this study, we knocked out MPC1 gene in rod photoreceptor cells of rhodopsin cre mice to explore the role of MPC1 including vision function and morphology.
DOI: 10.25345/c5tm72b5j
title: MassIVE MSV000092802 - Loss of MPC and it's effect on retinal metabolism
title: The mitochondrial pyruvate carrier (MPC) links glycolysis and mitochondrial metabolism. In this study, we knocked out MPC1 gene in rod photoreceptor cells of rhodopsin cre mice to explore the role of MPC1 including vision function and morphology.
DOI: 10.6084/m9.figshare.23207795
title: PoolData1

description: It contains a training data set for reverberation suppression, a reverberation data set, a noise data set, and a starting point data set.
DOI: 10.6084/m9.figshare.23207795.v1
title: PoolData1

description: It contains a training data set for reverberation suppression, a reverberation data set, a noise data set, and a starting point data set.
DOI: 10.5281/zenodo.8301529
title: TeamTrack Dataset Anonymous Upload

description: TeamTrack Dataset Anonymous Upload. We will be re-uploaded.
DOI: 10.5281/zenodo.8301528
title: TeamTrack Dataset Anonymous Upload

description: TeamTrack Dataset Anonymous Upload. We will be re-uploaded.
DOI: 10.5281/zenodo.8302872
title: TeamTrack Dataset Anonymous Upload

description: TeamTrack Dataset Anonymous Upload. We will be re-uploaded.
DOI: 10.5281/zenodo.8303931
title: TeamTrack Dataset Anonymous Upload

description: TeamTrack Dataset Anonymous Upload. We will be re-uploaded.
DOI: 10.25345/c5pv6bj0x
title: MassIVE MSV000092803 - Loss of MPC and the effect on retinal metabolism
title: The mitochondrial pyruvate carrier (MPC) links glycolysis and mitochondrial metabolism. In this study, we knocked out MPC1 gene in rod photoreceptor cells of rhodopsin cre mice to explore the role of MPC1 including vision function and morphology.
DOI: 10.5281/zenodo.8226441
title: Observation data for pNARA v1.0

description: This dataset includes the observations used to conduct and evaluate the prototype NOAA Aerosol Reanalysis version 1.0 (pNARA v1.0) for 2016. The MODIS NNR AOD data from Terra and Aqua are provided in 2016_MODIS_MOD04.tar and 2016_MODIS_MYD04.tar, respectively. The AOD and Almucantar retrievals from AERONET are provided in 2016_aeronet_alm.tar and 2016_aeronet_aod.tar. The PM2.5 from OpenAQ (2016_openaq.tar) and IMPROVE (2016_improve.tgz) are also included.
DOI: 10.5281/zenodo.8226440
title: Observation data for pNARA v1.0

description: This dataset includes the observations used to conduct and evaluate the prototype NOAA Aerosol Reanalysis version 1.0 (pNARA v1.0) for 2016. The MODIS NNR AOD data from Terra and Aqua are provided in 2016_MODIS_MOD04.tar and 2016_MODIS_MYD04.tar, respectively. The AOD and Almucantar retrievals from AERONET are provided in 2016_aeronet_alm.tar and 2016_aeronet_aod.tar. The PM2.5 from OpenAQ (2016_openaq.tar) and IMPROVE (2016_improve.tgz) are also included.
DOI: 10.5281/zenodo.8222945
title: Sample data for the evaluation of pNARA v1.0

description: This dataset provides the sample data used in the evaluation of pNARA v1.0. For the AOD evaluation, the pNARA v1.0, MERRA-2, and CAMSRA are NARA-1.0_AOD_2016010100.nc4, MERRA2_400.inst3_2d_gas_Nx.20160101.nc4, and cams_aods_20160101.nc, respectively. The aerosol mass mixing ratios on pressure levels (at 100, 250, 400, 500, 600, 700, 850, 925, and 1000 hPa) for each product are fv3_aeros_2016010100_pll.nc (pNARA v1.0), MERRA2_aeros.20160101.nc4 (MERRA-2), and cams_aeros_20160101.nc (CAMSRA). The aerosol mixing ratios on model level for pNARA v1.0 (NARA-1.0_aero_2016010100.nc4) and MERRA-2 (MERRA2_400.inst3_3d_aer_Nv.20160101.nc4) are also included.
DOI: 10.5281/zenodo.8222944
title: Sample data for the evaluation of pNARA v1.0

description: This dataset provides the sample data used in the evaluation of pNARA v1.0. For the AOD evaluation, the pNARA v1.0, MERRA-2, and CAMSRA are NARA-1.0_AOD_2016010100.nc4, MERRA2_400.inst3_2d_gas_Nx.20160101.nc4, and cams_aods_20160101.nc, respectively. The aerosol mass mixing ratios on pressure levels (at 100, 250, 400, 500, 600, 700, 850, 925, and 1000 hPa) for each product are fv3_aeros_2016010100_pll.nc (pNARA v1.0), MERRA2_aeros.20160101.nc4 (MERRA-2), and cams_aeros_20160101.nc (CAMSRA). The aerosol mixing ratios on model level for pNARA v1.0 (NARA-1.0_aero_2016010100.nc4) and MERRA-2 (MERRA2_400.inst3_3d_aer_Nv.20160101.nc4) are also included.
DOI: 10.5281/zenodo.8226055
title: pNARA v1.0 system (GEFS-Aerosols and JEDI)

description: This includes the source code of GEFS-Aerosols and JEDI used to conduct the aerosol reanalysis product for the prototype NOAA Aerosol Reanalysis version 1.0 (pNARA v1.0).
DOI: 10.5281/zenodo.8226054
title: pNARA v1.0 system (GEFS-Aerosols and JEDI)

description: This includes the source code of GEFS-Aerosols and JEDI used to conduct the aerosol reanalysis product for the prototype NOAA Aerosol Reanalysis version 1.0 (pNARA v1.0).
DOI: 10.25345/c5k35mq6g
title: MassIVE MSV000092804 - More than the clock: distinct regulation of muscle function and metabolism by PER2 and RORalpha
title: Circadian rhythms, governed by the dominant central as well as various peripheral clocks, regulate almost all biological processes, including sleep-wake cycles, hormone secretion, and metabolism. In certain contexts, regulation and function of the peripheral oscillations can be decoupled from the central clock. However, the specific mechanisms underlying muscle-intrinsic clock-dependent modulation of muscle function and metabolism remain unclear. We investigated the outcome of perturbations of the primary and secondary feedback loops of the molecular clock in skeletal muscle by specific gene ablation of Period (Per2) and RAR-related orphan receptor alpha (RORalpha), respectively. In both models, a dampening of core clock gene oscillation was observed, while the phase was preserved. Moreover, both loops seem involved in the homeostasis of amine groups. Very divergent outcomes were seen for overall muscle gene expression, primarily affecting circadian rhythmicity in the Per2, and non-oscillating genes in the RORalpha knockouts, leading to distinct outcomes in terms of metabolome and phenotype. These results highlight the entanglement of the molecular clock and muscle plasticity, and allude to specific functions of different clock components, i.e. the primary and secondary feedback loops, in this context. The reciprocal interaction between muscle contractility and circadian clocks might therefore be instrumental to determine a finely tuned adaptation of muscle tissue to perturbations in health and disease.
DOI: 10.5281/zenodo.8019397
title: Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention: Experiment and simulation data, figures, and notebooks for recreating figures

description: <strong>/Data</strong> Contains all experimental and simulation data used to generate figures in the manuscript. Each folder is labelled with the relevant technique: atomic force microscopy (AFM), dynamic light scattering (DLS), molecular dynamics (MD), small-angle X-ray scattering (SAXS), scanning electron microscopy (SEM), transmission electron microscopy and selected area electron diffraction (TEM-SAED), and ultraviolet-visible light spectroscopy (UV-Vis). Folders may contain subfolders from different experiments and should be unchanged for the notebooks to point to the correct path when loading data. Any file which contains SI in the filename indicates sample information, which includes sample concentration, delay associated with creating the sample (Delay4 is the relevant column name), unique identification (UID), etc. <strong>/Data/AFM</strong> Each filename is labelled with the number of delay associated with the sample or No Z2 Control in the case of the control sample. Each sample contains 3 files, the raw AFM data, a processed image, and an excel file with line profile measurements. <strong>/Data/DLS</strong> Contains exported data from Malvern Nano ZS DLS instrument. <strong>/Data/Images</strong> Images from the colloidal stability experiment. <strong>/Data/MD</strong> Molecular dynamics data and some notebooks for processing peptide and facet combinations. <strong>/Data/SAXS</strong> Reduced SAXS data from time-resolved study of nanoplatelet growth. <strong>/Data/SEM</strong> SEM images of samples prepared with and without dynamic intervention (control). <strong>/Data/TEM_SAED</strong> TEM images of samples prepared with and without dynamic intervention (control), and SAED image of a nanoplatelet. <strong>/Data/UV-Vis</strong> Spectroscopy data from different Z2 variants, the microplate based stability assay, cuvette based stability assay, and the time resolved (kinetics) measurements of particle growth as a result of manual dynamic intervention. <strong>/Notebooks</strong> This folder contains all of the Jupyter notebooks used to plot data and fit SAXS scattering profiles. See <strong>/Notebooks/environment.yml</strong> for packages necessary to execute the notebooks here and in <strong>/Synthesis_Protocol</strong>. We recommend installing this environment by using: Refer to https://github.com/SasView/sasmodels and the first cell of <strong>/Notebooks/SAXS_Fitting.ipynb</strong> for specific instructions on how to complete installation of the sasmodels module (sasmodels will be installed by Pip if you correctly use the shared environment.yml file). <strong>/Figures</strong> Figures presented in the publication
DOI: 10.5281/zenodo.8019398
title: Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention: Experiment and simulation data, figures, and notebooks for recreating figures

description: Content Summary: Data from experiments in which gold nanoparticles were synthesized in the presence of peptides using a liquid-handling robot. Samples were analyzed using UV-Vis spectroscopy, DLS, SAXS, TEM, SAED, SEM, and MD. Notebooks for loading and plotting data Readme.docx: <strong>/Data</strong> Contains all experimental and simulation data used to generate figures in the manuscript. Each folder is labelled with the relevant technique: atomic force microscopy (AFM), dynamic light scattering (DLS), molecular dynamics (MD), small-angle X-ray scattering (SAXS), scanning electron microscopy (SEM), transmission electron microscopy and selected area electron diffraction (TEM-SAED), and ultraviolet-visible light spectroscopy (UV-Vis). Folders may contain subfolders from different experiments and should be unchanged for the notebooks to point to the correct path when loading data. Any file which contains SI in the filename indicates sample information, which includes sample concentration, delay associated with creating the sample (Delay4 is the relevant column name), unique identification (UID), etc. <strong>/Data/AFM</strong> Each filename is labelled with the number of delay associated with the sample or No Z2 Control in the case of the control sample. Each sample contains 3 files, the raw AFM data, a processed image, and an excel file with line profile measurements. <strong>/Data/DLS</strong> Contains exported data from Malvern Nano ZS DLS instrument. <strong>/Data/Images</strong> Images from the colloidal stability experiment. <strong>/Data/MD</strong> Molecular dynamics data and some notebooks for processing peptide and facet combinations. <strong>/Data/SAXS</strong> Reduced SAXS data from time-resolved study of nanoplatelet growth. <strong>/Data/SEM</strong> SEM images of samples prepared with and without dynamic intervention (control). <strong>/Data/TEM_SAED</strong> TEM images of samples prepared without dynamic intervention (control), and SAED image of a nanoplatelet. <strong>/Data/UV-Vis</strong> Spectroscopy data from different Z2 variants, the microplate based stability assay, cuvette based stability assay, and the time resolved (kinetics) measurements of particle growth as a result of manual dynamic intervention. <strong>/Notebooks</strong> This folder contains all of the Jupyter notebooks used to plot data and fit SAXS scattering profiles. See <strong>/Notebooks/environment.yml</strong> for packages necessary to execute the notebooks here and in <strong>/Synthesis_Protocol</strong>. We recommend installing this environment by using: Refer to https://github.com/SasView/sasmodels and the first cell of <strong>/Notebooks/SAXS_Fitting.ipynb</strong> for specific instructions on how to complete installation of the sasmodels module (sasmodels will be installed by Pip if you correctly use the shared environment.yml file). <strong>/Figures</strong> Figures presented in the publication
DOI: 10.5281/zenodo.8303993
title: Anisotropic Gold Nanomaterial Synthesis Using Peptide Facet Specificity and Timed Intervention: Experiment and simulation data, figures, and notebooks for recreating figures

description: <strong>/Data</strong> Contains all experimental and simulation data used to generate figures in the manuscript. Each folder is labelled with the relevant technique: atomic force microscopy (AFM), dynamic light scattering (DLS), molecular dynamics (MD), small-angle X-ray scattering (SAXS), scanning electron microscopy (SEM), transmission electron microscopy and selected area electron diffraction (TEM-SAED), and ultraviolet-visible light spectroscopy (UV-Vis). Folders may contain subfolders from different experiments and should be unchanged for the notebooks to point to the correct path when loading data. Any file which contains SI in the filename indicates sample information, which includes sample concentration, delay associated with creating the sample (Delay4 is the relevant column name), unique identification (UID), etc. <strong>/Data/AFM</strong> Each filename is labelled with the number of delay associated with the sample or No Z2 Control in the case of the control sample. Each sample contains 3 files, the raw AFM data, a processed image, and an excel file with line profile measurements. <strong>/Data/DLS</strong> Contains exported data from Malvern Nano ZS DLS instrument. <strong>/Data/Images</strong> Images from the colloidal stability experiment. <strong>/Data/MD</strong> Molecular dynamics data and some notebooks for processing peptide and facet combinations. <strong>/Data/SAXS</strong> Reduced SAXS data from time-resolved study of nanoplatelet growth. <strong>/Data/SEM</strong> SEM images of samples prepared with and without dynamic intervention (control). <strong>/Data/TEM_SAED</strong> TEM images of samples prepared with and without dynamic intervention (control), and SAED image of a nanoplatelet. <strong>/Data/UV-Vis</strong> Spectroscopy data from different Z2 variants, the microplate based stability assay, cuvette based stability assay, and the time resolved (kinetics) measurements of particle growth as a result of manual dynamic intervention. <strong>/Notebooks</strong> This folder contains all of the Jupyter notebooks used to plot data and fit SAXS scattering profiles. See <strong>/Notebooks/environment.yml</strong> for packages necessary to execute the notebooks here and in <strong>/Synthesis_Protocol</strong>. We recommend installing this environment by using: Refer to https://github.com/SasView/sasmodels and the first cell of <strong>/Notebooks/SAXS_Fitting.ipynb</strong> for specific instructions on how to complete installation of the sasmodels module (sasmodels will be installed by Pip if you correctly use the shared environment.yml file). <strong>/Figures</strong> Figures presented in the publication
DOI: 10.26182/2p1z-rx18
title: Comprehensive Evaluation of Human Brain Gene Expression Deconvolution Methods