cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8250676
title: Supplementary Files and Data of 'Live-bearing cockroach genome reveals convergent evolutionary mechanisms linked to viviparity in insects and beyond'

description: Live birth (viviparity) has arisen repeatedly and independently among animals. We sequenced the genome and transcriptome of the viviparous Pacific beetle-mimic cockroach and performed comparative analyses with two other viviparous insect lineages, tsetse flies and aphids, to unravel the basis underlying the transition to viviparity in insects. We identified pathways undergoing adaptive evolution for insects, involved in uro-genital remodeling, tracheal system, heart development, and nutrient metabolism. Transcriptomic analysis in the cockroach and tsetse viviparity reveals that uterine remodeling and nutrient production are increased and the immune response is altered during pregnancy, facilitating structural and physiological changes to accommodate and nourish the progeny. These patterns of convergent evolution of viviparity among insects, together with similar adaptive mechanisms identified among vertebrates, highlight that the transition to viviparity requires changes in uro-genital remodeling, enhanced tracheal and heart development (corresponding to angiogenesis in vertebrates), nutrient metabolism, and shifted immunity in all animal systems.
DOI: 10.5281/zenodo.8250553
title: Foliar functional trait maps for six sites along the Western Ghats of India

description: Maps of seven key foliar functional traits for six sites along the Western Ghats of India, derived using field-sampled data and hyperspectral images acquired by NASA's Airborne Visible/ Infrared Imaging Spectrometer-Next Generation (AVIRIS-NG). Traits in this dataset include: Leaf mass per area (LMA) in g/m<sup>2</sup>, foliar nitrogen in % dry mass (%dm), foliar fiber (%dm), foliar lignin (%dm), foliar sugars (%dm), foliar calcium (%dm), and total phenolics (%dm).
description: Funding for this research was provided by NASA grant 80NSSC17K0677
DOI: 10.5281/zenodo.8250552
title: Foliar functional trait maps for six sites along the Western Ghats of India

description: Maps of seven key foliar functional traits for six sites along the Western Ghats of India, derived using field-sampled data and hyperspectral images acquired by NASA's Airborne Visible/ Infrared Imaging Spectrometer-Next Generation (AVIRIS-NG). Traits in this dataset include: Leaf mass per area (LMA) in g/m<sup>2</sup>, foliar nitrogen in % dry mass (%dm), foliar fiber (%dm), foliar lignin (%dm), foliar sugars (%dm), foliar calcium (%dm), and total phenolics (%dm).
description: Funding for this research was provided by NASA grant 80NSSC17K0677
DOI: 10.5517/ccdc.csd.cc280n87
title: CCDC 2085998: Experimental Crystal Structure Determination

description: Related Article: K. Naresh Babu, Fedaa Massarwe, Israa Shioukhi, Ahmad Masarwa|2021|Angew.Chem.,Int.Ed.|60|26199|doi:10.1002/anie.202111164
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.cc28p0gg
title: CCDC 2105565: Experimental Crystal Structure Determination

description: Related Article: K. Naresh Babu, Fedaa Massarwe, Israa Shioukhi, Ahmad Masarwa|2021|Angew.Chem.,Int.Ed.|60|26199|doi:10.1002/anie.202111164
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.6672453
title: PyWGCNA's output example

description: This is an output of running the PyWGCNA package on 5xFAD mice with matching wildtype in four different time points (4,8,12 and 18 months) on the cortex and hippocampus.
DOI: 10.5281/zenodo.6672452
title: PyWGCNA's output example

description: 5xFAD pickle file is an output of running the PyWGCNA package on 5xFAD mice with matching wildtype in four different time points (4,8,12 and 18 months) on the cortex and hippocampus. 3xTgAD pickle file is an output of running the PyWGCNA package on 3xTgAD mice with matching wildtype in three different time points (4, 12 and 18 months) on the hippocampus.
DOI: 10.5281/zenodo.7275097
title: PyWGCNA's output example

description: This is an output of running the PyWGCNA package on 5xFAD mice with matching wildtype in four different time points (4,8,12 and 18 months) on the cortex and hippocampus.
DOI: 10.5281/zenodo.7759050
title: PyWGCNA's output example

description: This is an output of running the PyWGCNA package on 5xFAD mice with matching wildtype in four different time points (4,8,12 and 18 months) on the cortex and hippocampus.
DOI: 10.5281/zenodo.8067256
title: PyWGCNA's output example

description: 5xFAD pickle file is an output of running the PyWGCNA package on 5xFAD mice with matching wildtype in four different time points (4,8,12 and 18 months) on the cortex and hippocampus. 3xTgAD pickle file is an output of running the PyWGCNA package on 3xTgAD mice with matching wildtype in three different time points (4, 12 and 18 months) on the hippocampus.
DOI: 10.5281/zenodo.7742780
title: Endpoint kinetic assay at variable pH using mouse Acidic Mammalian Chitinase

description: This directory contains all files required to analyze the mouse AMCase enzyme kinetics across pH 2.0 to 8.0 presented in the manuscript Díaz et al., <em>bioRxiv </em>(2023). Enzyme kinetics were performed using a Tecan Spark multimode microplate reader and data was analyzed using Graphpad Prism. Figures were compiled using Adobe Illustrator. Files included in this directory: <strong>20210906 - mAMCase_CatD_6xHis (pmRED006)</strong> - 20210907 - Purification contains FPLC chromatograms and corresponding SDS-PAGE gel stained with InstantBlue. - 202110XX _pHX_100nM contains four replicates performed at that specific pH using 100 nM mAMCase. - 384w_exp.toml contains a 384-well plate layout of the experimental conditions. This file is compatible with wellmap. - 384w_std.toml contains a 384-well plate layout of the 4MU standards. This file is compatible with wellmap. <strong>Figures</strong><br> - contains PDFs of V<sub>max</sub>, <em>k</em><sub>cat, </sub>K<sub>M</sub>, catalytic efficiency, and the initial rate for all pH points tested. <strong>20210906 - mAMCase_CatD_6xHis (pmRED006) - Data.pzfx</strong> - contains all data from <strong>20210906 - mAMCase_CatD_6xHis (pmRED006), </strong>including standard curves, initial time points, and initial rates curves. <strong>20210906 - mAMCase_CatD_6xHis (pmRED006) - Summary.pzfx</strong> - contains summary data of kinetic parameters V<sub>max</sub>, <em>k</em><sub>cat, </sub>K<sub>M</sub>, catalytic efficiency, and initial rates for all pH points tested. Contact:<br> Roberto Efraín Díaz, robertoefrain.diaz@ucsf.edu James Fraser, jfraser@fraserlab.com
DOI: 10.5281/zenodo.7742779
title: Kinetic properties of mAMCase catalytic domain at various pH

description: This directory contains all files required to analyze the mouse AMCase enzyme kinetics across pH 2.0 to 8.0 presented in <strong>Figure 1</strong> and <strong>Supplemental Figures 1 and 2</strong> the manuscript Díaz et al., <em>bioRxiv </em>(2023). Enzyme kinetics were performed using a Tecan Spark multimode microplate reader and data was analyzed using Graphpad Prism. Figures were compiled using Adobe Illustrator. Files included in this directory: <strong>20210906 - mAMCase_CatD_6xHis (pmRED006)</strong> - 20210907 - Purification contains FPLC chromatograms and corresponding SDS-PAGE gel stained with InstantBlue. - 202110XX _pHX_100nM contains four replicates performed at that specific pH using 100 nM mAMCase. - 384w_exp.toml contains a 384-well plate layout of the experimental conditions. This file is compatible with wellmap. - 384w_std.toml contains a 384-well plate layout of the 4MU standards. This file is compatible with wellmap. <strong>Figures</strong><br> - contains PDFs of V<sub>max</sub>, <em>k</em><sub>cat, </sub>K<sub>M</sub>, catalytic efficiency, and the initial rate for all pH points tested. <strong>20210906 - mAMCase_CatD_6xHis (pmRED006) - Data.pzfx</strong> - contains all data from <strong>20210906 - mAMCase_CatD_6xHis (pmRED006), </strong>including standard curves, initial time points, and initial rates curves. <strong>20210906 - mAMCase_CatD_6xHis (pmRED006) - Summary.pzfx</strong> - contains summary data of kinetic parameters V<sub>max</sub>, <em>k</em><sub>cat, </sub>K<sub>M</sub>, catalytic efficiency, and initial rates for all pH points tested. Contact:<br> Roberto Efraín Díaz, robertoefrain.diaz@ucsf.edu James Fraser, jfraser@fraserlab.com
description: {"references": ["D\u00edaz, Roberto Efra\u00edn et al. (2023). Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase."]}
DOI: 10.5281/zenodo.7968293
title: Kinetic properties of mAMCase catalytic domain at various pH

description: This directory contains all files required to analyze the mouse AMCase enzyme kinetics across pH 2.0 to 8.0 presented in <strong>Figure 1</strong> and <strong>Supplemental Figures 1 and 2</strong> the manuscript Díaz et al., <em>bioRxiv </em>(2023). Enzyme kinetics were performed using a Tecan Spark multimode microplate reader and data was analyzed using Graphpad Prism. Figures were compiled using Adobe Illustrator. Files included in this directory: <strong>20210906 - mAMCase_CatD_6xHis (pmRED006)</strong> - 20210907 - Purification contains FPLC chromatograms and corresponding SDS-PAGE gel stained with InstantBlue. - 202110XX _pHX_100nM contains four replicates performed at that specific pH using 100 nM mAMCase. - 384w_exp.toml contains a 384-well plate layout of the experimental conditions. This file is compatible with wellmap. - 384w_std.toml contains a 384-well plate layout of the 4MU standards. This file is compatible with wellmap. <strong>Figures</strong><br> - contains PDFs of V<sub>max</sub>, <em>k</em><sub>cat, </sub>K<sub>M</sub>, catalytic efficiency, and the initial rate for all pH points tested. <strong>20210906 - mAMCase_CatD_6xHis (pmRED006) - Data.pzfx</strong> - contains all data from <strong>20210906 - mAMCase_CatD_6xHis (pmRED006), </strong>including standard curves, initial time points, and initial rates curves. <strong>20210906 - mAMCase_CatD_6xHis (pmRED006) - Summary.pzfx</strong> - contains summary data of kinetic parameters V<sub>max</sub>, <em>k</em><sub>cat, </sub>K<sub>M</sub>, catalytic efficiency, and initial rates for all pH points tested. Contact:<br> Roberto Efraín Díaz, robertoefrain.diaz@ucsf.edu James Fraser, jfraser@fraserlab.com
description: {"references": ["D\u00edaz, Roberto Efra\u00edn et al. (2023). Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase."]}
DOI: 10.5281/zenodo.8250616
title: Kinetic properties of mAMCase catalytic domain at various pH

description: This directory contains all files required to analyze the mouse AMCase enzyme kinetics across pH 2.0 to 8.0 presented in <strong>Figure 1</strong> and <strong>Supplemental Figures 1 and 2</strong> the manuscript Díaz et al., <em>bioRxiv </em>(2023). Enzyme kinetics were performed using a Tecan Spark multimode microplate reader and data was analyzed using Graphpad Prism. Figures were compiled using Adobe Illustrator. Files included in this directory: <strong>20210906 - mAMCase_CatD_6xHis (pmRED006)</strong> - 20210907 - Purification contains FPLC chromatograms and corresponding SDS-PAGE gel stained with InstantBlue. - 202110XX _pHX_100nM contains four replicates performed at that specific pH using 100 nM mAMCase. - 384w_exp.toml contains a 384-well plate layout of the experimental conditions. This file is compatible with wellmap. - 384w_std.toml contains a 384-well plate layout of the 4MU standards. This file is compatible with wellmap. <strong>Figures</strong><br> - contains PDFs of V<sub>max</sub>, <em>k</em><sub>cat, </sub>K<sub>M</sub>, catalytic efficiency, and the initial rate for all pH points tested. <strong>20210906 - mAMCase_CatD_6xHis (pmRED006) - Data.pzfx</strong> - contains all data from <strong>20210906 - mAMCase_CatD_6xHis (pmRED006), </strong>including standard curves, initial time points, and initial rates curves. <strong>20210906 - mAMCase_CatD_6xHis (pmRED006) - Summary.pzfx</strong> - contains summary data of kinetic parameters V<sub>max</sub>, <em>k</em><sub>cat, </sub>K<sub>M</sub>, catalytic efficiency, and initial rates for all pH points tested. Contact:<br> Roberto Efraín Díaz, robertoefrain.diaz@ucsf.edu James Fraser, jfraser@fraserlab.com
description: {"references": ["D\u00edaz, Roberto Efra\u00edn et al. (2023). Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase."]}
DOI: 10.5281/zenodo.8250581
title: Analyse statistique de la méthode Feulgen-Acropora sp.-TFE

description: <em> </em>Travail de fin d’étude portant sur « Mesure des tailles de génomes de coraux du genre<em> Acropora</em> sp. par la méthode Feulgen », analyse statistique et résultats.
DOI: 10.5281/zenodo.8250580
title: Analyse statistique de la méthode Feulgen-Acropora sp.-TFE

description: <em> </em>Travail de fin d’étude portant sur « Mesure des tailles de génomes de coraux du genre<em> Acropora</em> sp. par la méthode Feulgen », analyse statistique et résultats.
DOI: 10.6084/m9.figshare.23961015
title: qPCR metabolism data

description: qpcr data for nutrient starvation experiment in the griddient
DOI: 10.6084/m9.figshare.23961015.v1
title: qPCR metabolism data

description: qpcr data for nutrient starvation experiment in the griddient
DOI: 10.5281/zenodo.8051337
title: Martian crustal models at the InSight landing site from joint inversion of ellipticity, P-to-s RFs and autocorrelations times

description: - Preferred models resulting from the joint inversion of three local-scale measurements: Rayleigh-wave ellipticity, P-to-s Receiver functions (Joshi et al., 2023) and P-wave lag times from autocorrelation (Schimmel et al., 2021). - Scripts and observables to perform joint inversion.
DOI: 10.5281/zenodo.8051336
title: Martian crustal models at the InSight landing site from joint inversion of ellipticity, P-to-s RFs and autocorrelations times

description: - Preferred models resulting from the joint inversion of three local-scale measurements: Rayleigh-wave ellipticity, P-to-s Receiver functions (Joshi et al., 2023) and P-wave lag times from autocorrelation (Schimmel et al., 2021). - Scripts and observables to perform joint inversion.
DOI: 10.5519/qd.oyh6jclq
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (27 records)
DOI: 10.6084/m9.figshare.23961033
title: Diffusion experiment

description: Diffusion of dextran in the griddient device
DOI: 10.6084/m9.figshare.23961039
title: Cell viability over time in the Griddient

description: Cell viability over time in the griddient device
DOI: 10.6084/m9.figshare.23961039.v1
title: Cell viability over time in the Griddient

description: Cell viability over time in the griddient device
DOI: 10.6084/m9.figshare.23961045
title: OMI experiment

description: <b>Cell metabolism in response to nutrient gradients</b>. A. Schematic representation of the experimental settings. HCT-116 cells were seeded at 30 million cells/mL in a collagen hydrogel. After 12h media was replaced by PBS following the described configuration. After 30h, OMI images were obtained. Then PBS was replaced with media again. Cells were cultured under media for another 20h (50 h post initial PBS change) before cells were imaged again. Cells were culture for 20 additional hours (70 and 40 h post initial PBS change and subsequent return to media). B-C OMI images (B) and quantification (C) of the ORR (Optical Redox Ratio) after 30 min in PBS/media, and at 20 and 40h after PBS was replaced by media. D-E OMI images (D) and quantification (E) of of NAD(P)H τ<sub>m </sub>(mean lifetime) after 30 min in PBS/media, and at 20 and 40h after PBS was replaced by media. Significant main effects of different medias at the same time point are denotated by asterisks (*), significant comparisons between different time points are denotated by a hash (#) for the interface and a dagger (†) for PBS. For all symbols conferring statistical significance: single symbol p&lt;0.05, double symbol p&lt;0.01, triple symbol using One-Way ANOVA. For each condition a total of at least 40 cells from two independent experiments were analyzed with 3 Griddient plates per experiment.
DOI: 10.6084/m9.figshare.23961045.v1
title: OMI experiment

description: <b>Cell metabolism in response to nutrient gradients</b>. A. Schematic representation of the experimental settings. HCT-116 cells were seeded at 30 million cells/mL in a collagen hydrogel. After 12h media was replaced by PBS following the described configuration. After 30h, OMI images were obtained. Then PBS was replaced with media again. Cells were cultured under media for another 20h (50 h post initial PBS change) before cells were imaged again. Cells were culture for 20 additional hours (70 and 40 h post initial PBS change and subsequent return to media). B-C OMI images (B) and quantification (C) of the ORR (Optical Redox Ratio) after 30 min in PBS/media, and at 20 and 40h after PBS was replaced by media. D-E OMI images (D) and quantification (E) of of NAD(P)H τ<sub>m </sub>(mean lifetime) after 30 min in PBS/media, and at 20 and 40h after PBS was replaced by media. Significant main effects of different medias at the same time point are denotated by asterisks (*), significant comparisons between different time points are denotated by a hash (#) for the interface and a dagger (†) for PBS. For all symbols conferring statistical significance: single symbol p&lt;0.05, double symbol p&lt;0.01, triple symbol using One-Way ANOVA. For each condition a total of at least 40 cells from two independent experiments were analyzed with 3 Griddient plates per experiment.
DOI: 10.6084/m9.figshare.23961054
title: HUVEC with and w/o INFa

description: Different types of cell co-culture in the Griddient. A. Collagen gel was added in the main chamber. After polymerization, HUVEC cells, stained with CellTracker™ Green CMFDA, were seeded in the collagen interface. Cells were treated with vehicle or 20ng/mL TNF-α for 24 hours. Cells were stained with phalloidin and visualized on a fluorescence microscope. Area covered by cells was analyzed and plot as mean ±SEM, n=
DOI: 10.6084/m9.figshare.23961054.v1
title: HUVEC with and w/o INFa

description: Different types of cell co-culture in the Griddient. A. Collagen gel was added in the main chamber. After polymerization, HUVEC cells, stained with CellTracker™ Green CMFDA, were seeded in the collagen interface. Cells were treated with vehicle or 20ng/mL TNF-α for 24 hours. Cells were stained with phalloidin and visualized on a fluorescence microscope. Area covered by cells was analyzed and plot as mean ±SEM, n=
DOI: 10.6084/m9.figshare.23961057
title: NK cell analysis in the griddient

description: HCT-116 cells (blue) were seeded at 30 million cells/mL in a collagen solution. A biopsy of the gel was isolated, and the cavity was filled with a hydrogel containing NK-92 cells (green). IP was added into the media to visualize dead cells. Images was obtained in a fluorescence microscope at day 0 and 15 after the addition of NK-92 cells. Quantification of the NK cell number and area covered by NK cell at day 0 and 15. Data was normalized by area covered at day 0 and plot as as mean ±SEM, n=3 . .
DOI: 10.6084/m9.figshare.23961057.v1
title: NK cell analysis in the griddient

description: HCT-116 cells (blue) were seeded at 30 million cells/mL in a collagen solution. A biopsy of the gel was isolated, and the cavity was filled with a hydrogel containing NK-92 cells (green). IP was added into the media to visualize dead cells. Images was obtained in a fluorescence microscope at day 0 and 15 after the addition of NK-92 cells. Quantification of the NK cell number and area covered by NK cell at day 0 and 15. Data was normalized by area covered at day 0 and plot as as mean ±SEM, n=3 . .
DOI: 10.5281/zenodo.8069429
title: The catalytic role of glutathione transferases in heterologous anthocyanin biosynthesis

description: Electronic energies, entropies, enthalpies, Gibbs free energies, and lowest frequencies of the QM-calculated structures (<em>QM_Energies.xlsx</em>). Gaussian 16 input and output files, and optimized geometries in MOL2 format, for all QM-calculated structures <em>(QM_calculations.zip</em>). Input coordinates, topology file (in Amber and PDB formats) and output geometries (in PDB format) for the Molecular Dynamics equilibration of the GST-GSH-flav-3-on-4-ol (<strong>7</strong>) ternary complex (<em>MD_equilibration.zip</em>). Optimized geometries for the PtGSTF8-catalyzed deprotonation-protonation reaction: flavan-3-on-4-ol (<strong>7</strong>), transition state for deprotonation (<strong>7-TS</strong>), deprotonation product (<strong>8-enolate</strong>) and cyanidin (<strong>8-B4</strong>) bound to the wildtype enzyme and the C13S variant (<em>QMMM_optimized_structures.zip</em>).
DOI: 10.5281/zenodo.8069428
title: The catalytic role of glutathione transferases in heterologous anthocyanin biosynthesis

description: Electronic energies, entropies, enthalpies, Gibbs free energies, and lowest frequencies of the QM-calculated structures (<em>QM_Energies.xlsx</em>). Gaussian 16 input and output files, and optimized geometries in MOL2 format, for all QM-calculated structures <em>(QM_calculations.zip</em>). Input coordinates, topology file (in Amber and PDB formats) and output geometries (in PDB format) for the Molecular Dynamics equilibration of the GST-GSH-flav-3-on-4-ol (<strong>7</strong>) ternary complex (<em>MD_equilibration.zip</em>). Optimized geometries for the PtGSTF8-catalyzed deprotonation-protonation reaction: flavan-3-on-4-ol (<strong>7</strong>), transition state for deprotonation (<strong>7-TS</strong>), deprotonation product (<strong>8-enolate</strong>) and cyanidin (<strong>8-B4</strong>) bound to the wildtype enzyme and the C13S variant (<em>QMMM_optimized_structures.zip</em>).
DOI: 10.34943/91d7184b-1317-4bca-9bc8-e51aa9fb161e
title: Fraser River Delta Upper Slope Video Camera Deployed 2023-03-16

description: The Axis P1378 Camera SN ACCC8EFCEDDE was deployed on 2023-03-16 at Fraser River Delta Upper Slope. This site is located on the upper slope of the Fraser River delta, where depth is approximately 100 metres. This device is a Video Camera. Video cameras record video of characteristics of the surrounding environments and can be deployed on fixed and mobile platforms. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.34943/8a514742-deed-4cc7-913c-4f0be0c9994a
title: Fraser River Delta Upper Slope Video Camera Deployed 2023-03-16

description: The Axis P1378 Camera SN ACCC8EFCEDDE was deployed on 2023-03-16 at Fraser River Delta Upper Slope. This site is located on the upper slope of the Fraser River delta, where depth is approximately 100 metres. This device is a Video Camera. Video cameras record video of characteristics of the surrounding environments and can be deployed on fixed and mobile platforms. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.