cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24794577
title: Supplementary files of "<b>Discovery of large eusauropod dinosaur from the earliest Middle Jurassic of Chin</b><b>a</b>"

description: Sauropod dinosaurs were the largest terrestrial animals to have ever lived on Earth. However, in the initial evolutionary stages of sauropod gigantism, few fossils are known. In China, most non-sauropod sauropodomorphs from the Early Jurassic Lufeng Formation of southwestern China do not exceed 10 m in length, while all sauropods from the Middle Jurassic (Bajocian-Bathonian) Dashanpu quarry in the Sichuan Basin do exceed 10 m in length, with its largest member (<i>Omeisaurus</i>) around 16 t and 20 m long. Here, we report two large middle-posterior centra from dorsal vertebrae (the largest and most complete measures 142 mm in length; 201 mm in height, and 230 mm in width at its posterior articular surface) and other associated elements recovered from the earliest Middle Jurassic (Aalenican-earliest Bajocian) Xintiangou Formation in the Sichuan Basin of southwestern China. We perform a cladistic analysis and anatomical study to explore the affinities of the Xintiangou material and the early evolution of sauropod gigantism. The Xintiangou material is most likely an early-diverging eusauropod dinosaur. We recovered the specimen as being a diplodocoid sauropod belonging to the family Dicraeosauridae. This specimen was probably one of the first large-bodied sauropods in China, and may have been one of the largest in the world during the earliest Middle Jurassic. This discovery also provides further support for eusauropod-dominated assemblages that could have existed in China at the beginning of the Middle Jurassic.<br>
DOI: 10.6084/m9.figshare.24794577.v1
title: Supplementary files of "<b>Discovery of large eusauropod dinosaur from the earliest Middle Jurassic of Chin</b><b>a</b>"

description: Sauropod dinosaurs were the largest terrestrial animals to have ever lived on Earth. However, in the initial evolutionary stages of sauropod gigantism, few fossils are known. In China, most non-sauropod sauropodomorphs from the Early Jurassic Lufeng Formation of southwestern China do not exceed 10 m in length, while all sauropods from the Middle Jurassic (Bajocian-Bathonian) Dashanpu quarry in the Sichuan Basin do exceed 10 m in length, with its largest member (<i>Omeisaurus</i>) around 16 t and 20 m long. Here, we report two large middle-posterior centra from dorsal vertebrae (the largest and most complete measures 142 mm in length; 201 mm in height, and 230 mm in width at its posterior articular surface) and other associated elements recovered from the earliest Middle Jurassic (Aalenican-earliest Bajocian) Xintiangou Formation in the Sichuan Basin of southwestern China. We perform a cladistic analysis and anatomical study to explore the affinities of the Xintiangou material and the early evolution of sauropod gigantism. The Xintiangou material is most likely an early-diverging eusauropod dinosaur. We recovered the specimen as being a diplodocoid sauropod belonging to the family Dicraeosauridae. This specimen was probably one of the first large-bodied sauropods in China, and may have been one of the largest in the world during the earliest Middle Jurassic. This discovery also provides further support for eusauropod-dominated assemblages that could have existed in China at the beginning of the Middle Jurassic.<br>
DOI: 10.5281/zenodo.10364310
title: Dataset related to: Sirt3 deficiency promotes endothelial dysfunction and aggravates renal injury

description: The .xlsx file contains raw data related to the article "Sirt3 deficiency promotes endothelial dysfunction and aggravates renal injury. PLOS One. 2023 Oct 10;18(10):e0291909", available at the following link.
 
Abstract
Sirtuin 3 (SIRT3), the main deacetylase of mitochondria, modulates the acetylation levels of substrates governing metabolism and oxidative stress. In the kidney, we showed that SIRT3 affects the proper functioning of high energy-demanding cells, such as tubular cells and podocytes. Less is known about the role of SIRT3 in regulating endothelial cell function and its impact on the progression of kidney disease. Here, we found that whole body Sirt3-deficient mice exhibited reduced renal capillary density, reflecting endothelial dysfunction, and VEGFA expression compared to wild-type mice. This was paralleled by activation of hypoxia signaling, upregulation of HIF-1α and Angiopietin-2, and oxidative stress increase. These alterations did not result in kidney disease. However, when Sirt3-deficient mice were exposed to the nephrotoxic stimulus Adriamycin (ADR) they developed aggravated endothelial rarefaction, altered VEGFA signaling, and higher oxidative stress compared to wild-type mice receiving ADR. As a result, ADR-treated Sirt3-deficient mice experienced a more severe injury with exacerbated albuminuria, podocyte loss and fibrotic lesions. These data suggest that SIRT3 is a crucial regulator of renal vascular homeostasis and its dysregulation is a predisposing factor for kidney disease. By extension, our findings indicate SIRT3 as a pharmacologic target in progressive renal disease whose treatments are still imperfect.
DOI: 10.5281/zenodo.10364311
title: Dataset related to: Sirt3 deficiency promotes endothelial dysfunction and aggravates renal injury

description: The .xlsx file contains raw data related to the article "Sirt3 deficiency promotes endothelial dysfunction and aggravates renal injury. PLOS One. 2023 Oct 10;18(10):e0291909", available at the following link.
 
Abstract
Sirtuin 3 (SIRT3), the main deacetylase of mitochondria, modulates the acetylation levels of substrates governing metabolism and oxidative stress. In the kidney, we showed that SIRT3 affects the proper functioning of high energy-demanding cells, such as tubular cells and podocytes. Less is known about the role of SIRT3 in regulating endothelial cell function and its impact on the progression of kidney disease. Here, we found that whole body Sirt3-deficient mice exhibited reduced renal capillary density, reflecting endothelial dysfunction, and VEGFA expression compared to wild-type mice. This was paralleled by activation of hypoxia signaling, upregulation of HIF-1α and Angiopietin-2, and oxidative stress increase. These alterations did not result in kidney disease. However, when Sirt3-deficient mice were exposed to the nephrotoxic stimulus Adriamycin (ADR) they developed aggravated endothelial rarefaction, altered VEGFA signaling, and higher oxidative stress compared to wild-type mice receiving ADR. As a result, ADR-treated Sirt3-deficient mice experienced a more severe injury with exacerbated albuminuria, podocyte loss and fibrotic lesions. These data suggest that SIRT3 is a crucial regulator of renal vascular homeostasis and its dysregulation is a predisposing factor for kidney disease. By extension, our findings indicate SIRT3 as a pharmacologic target in progressive renal disease whose treatments are still imperfect.
DOI: 10.6073/pasta/c8fca3b945b010900593fc58262c7305
title: PhenoCam Images and Canopy Phenology at the Harvard Forest Farm since 2015

description: The PhenoCam Network uses imagery from digital cameras to track vegetation phenology and seasonal changes in vegetation activity in diverse ecosystems across North America and around the world. Imagery is uploaded to the PhenoCam server at the University of New Hampshire, where it is made publicly available in near-real time, every 30 minutes from sunrise to sunset, 365 days a year.
 The data are processed using simple image analysis tools to yield a measure of canopy greenness, from which phenological metrics are extracted, characterizing the start and end of the growing season. These transition dates have been shown to align well with on-the-ground observations of tree phenology at Harvard Forest (HF003). Long-term PhenoCam data can be used to track the impact of climate variability and change on the rhythm of the seasons.
 This dataset contains one mid-day image for each camera. Please see the PhenoCam Network website (https://phenocam.nau.edu/webcam/) for more information and additional images.
DOI: 10.5281/zenodo.10364537
title: 3D printed electrolyte-supported Solid Oxide Cells based on scandia-stabilized zirconia co-doped with ytterbia
DOI: 10.5281/zenodo.10364538
title: 3D printed electrolyte-supported Solid Oxide Cells based on scandia-stabilized zirconia co-doped with ytterbia
DOI: 10.5281/zenodo.10364693
title: 3D printed electrolyte-supported Solid Oxide Cells based on scandia-stabilized zirconia co-doped with ytterbia
DOI: 10.5519/qd.ghptngi4
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (69 records)
DOI: 10.5517/ccdc.csd.cc2fmzxz
title: CCDC 2253542: Experimental Crystal Structure Determination

description: Related Article: Chaoyang Li, Xinyue Niu, Wan Xu, Zhanwei Bu, Wenjing Zhang, Qilin Wang|2023|Green Chemistry|25|10587|doi:10.1039/D3GC03165A
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.cc2fyblb
title: CCDC 2262522: Experimental Crystal Structure Determination

description: Related Article: Yuming Zhao, Rudie Zhang, Cheng Xiao, Dan Yue, Bowen Qin, Jinhui Liu, Zhenling Wang, Yu Fu|2023|CrystEngComm|25|6528|doi:10.1039/D3CE00902E
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: 10.6073/pasta/7b497b4aa98559b43c0730bed7164a8b
title: PhenoCam Images and Canopy Phenology at the Harvard Forest Hemlock Tower since 2010

description: The PhenoCam Network uses imagery from digital cameras to track vegetation phenology and seasonal changes in vegetation activity in diverse ecosystems across North America and around the world. Imagery is uploaded to the PhenoCam server at the University of New Hampshire, where it is made publicly available in near-real time, every 30 minutes from sunrise to sunset, 365 days a year.
 The data are processed using simple image analysis tools to yield a measure of canopy greenness, from which phenological metrics are extracted, characterizing the start and end of the growing season. These transition dates have been shown to align well with on-the-ground observations of tree phenology at Harvard Forest (HF003). Long-term PhenoCam data can be used to track the impact of climate variability and change on the rhythm of the seasons.
 This dataset contains one mid-day image for each camera. Please see the PhenoCam Network website (https://phenocam.nau.edu/webcam/) for more information and additional images.
DOI: 10.5517/ccdc.csd.cc2h5gfl
title: CCDC 2299159: Experimental Crystal Structure Determination

description: Related Article: Isabelle M. Jones, Gemma F. Turner, Kari Pitts, Rees Powell, Alan Riboldi-Tunnicliffe, Rachel Williamson, Stephanie Boer, Lauren Allen, Stephen A. Moggach|2023|CrystEngComm|25|6533|doi:10.1039/D3CE00979C
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.cc2h5ggm
title: CCDC 2299160: Experimental Crystal Structure Determination

description: Related Article: Isabelle M. Jones, Gemma F. Turner, Kari Pitts, Rees Powell, Alan Riboldi-Tunnicliffe, Rachel Williamson, Stephanie Boer, Lauren Allen, Stephen A. Moggach|2023|CrystEngComm|25|6533|doi:10.1039/D3CE00979C
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.cc2h5ghn
title: CCDC 2299161: Experimental Crystal Structure Determination

description: Related Article: Isabelle M. Jones, Gemma F. Turner, Kari Pitts, Rees Powell, Alan Riboldi-Tunnicliffe, Rachel Williamson, Stephanie Boer, Lauren Allen, Stephen A. Moggach|2023|CrystEngComm|25|6533|doi:10.1039/D3CE00979C
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: 10.6073/pasta/a899edd42aaff9c22ef226f11279be12
title: PhenoCam Images and Canopy Phenology at the Harvard Forest Witness Tree since 2014

description: The PhenoCam Network uses imagery from digital cameras to track vegetation phenology and seasonal changes in vegetation activity in diverse ecosystems across North America and around the world. Imagery is uploaded to the PhenoCam server at the University of New Hampshire, where it is made publicly available in near-real time, every 30 minutes from sunrise to sunset, 365 days a year.
 The data are processed using simple image analysis tools to yield a measure of canopy greenness, from which phenological metrics are extracted, characterizing the start and end of the growing season. These transition dates have been shown to align well with on-the-ground observations of tree phenology at Harvard Forest (HF003). Long-term PhenoCam data can be used to track the impact of climate variability and change on the rhythm of the seasons.
 This dataset contains one mid-day image for each camera. Please see the PhenoCam Network website (https://phenocam.nau.edu/webcam/) for more information and additional images.
DOI: 10.6073/pasta/844df90f5aee5a6c604068370bc062e9
title: Quantifying Growth and Structure along Forest Edges in the Northeastern USA 2010-2021

description: Fragmentation transforms the environment along forest edges. The prevailing narrative, driven by tropical research, suggests that edge environments increase tree mortality and structural degradation resulting in net decreases in ecosystem productivity. We show that temperate forest edges exhibit increased forest growth (basal area increment; BAI) and biomass (basal area; BA) with no change in total mortality relative to the forest interior. To assess forest edges, we analyzed more than 48,000 forest inventory plots (USDA FIA) across the north-eastern US using a quasi-experimental matching design. At forest edges adjacent to anthropogenic land covers, we report increases of 36.3% and 24.1% in forest growth and biomass, respectively. We then scale the edge impacts on growth (along anthropogenic edges only) across our study area using maps of land-cover and forest type. We find large variability in the effect of including edges on estimates of total forest growth, largely driven by differences in the prevalence of fragmentation. Estimated increases in forest growth range from a 23% increase in the agricultural-dominated western areas, a 2% increase in the least-fragmented northern regions, and a 15% increase within the metropolitan east coast. Finally, we also quantify forest fragmentation globally, at 30-m resolution, showing that temperate forests contain 52% more edge forest area than tropical forests.
 We provide two tables containing the post-matched dataset of FIA subplots, including subplot BA, BAI, and edge status. We include the associated environmental covariates, extracted from gridded raster data, and used in our matching and statistical analyses. Due to plot confidentiality restrictions we do not provide spatial locations of the FIA subplots, but we do provide unique plot identifiers that allow users to link each record to the publically-available data provided by the USDA FIA database (https://apps.fs.usda.gov/fia/datamart/). This dataset can be used to recreate our regression modelling results and regional estimates of forest growth.
 We also provide two polygon shapefile layers: EPA Level IV Ecoregion boundaries with spatially-aggregated estimates of edge and total BAI (m2 yr-1) as well as total forest area and edge forest area (forest less than 30 m from a non-forest pixel)and global terrestrial ecoregions boundaries with spatially-aggregated estimates of total forest area and edge forest area (forest less than 30 m from a non-forest pixel).
DOI: 10.6073/pasta/823727f64e32ad7d0be2c5dc69b0e52f
title: Land Conservation and Human Demographics by Census Tract in New England 2014-2018

description: This dataset summarizes land protection, conservation prioritization layer scores, and human demographics within New England communities, defined as census tracts. This dataset was created to identify disparities in land protection according to metrics of social marginalization and assess how incorporating environmental justice criteria into land conservation prioritization systems might change conservation priorities.
DOI: 10.6084/m9.figshare.24794592.v1
title: Untitled Item

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DOI: 10.6084/m9.figshare.24794592
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DOI: 10.6073/pasta/6a45cf16a9593a12370c251ae40369b1
title: Impacts of Phloem Chilling on Mature Red Maples at Harvard Forest 2019

description: Whether tree growth is limited by carbon supply or demand is a crucial question due to wide-ranging repercussions for projections of carbon sequestration on land. By temporarily restricting phloem transport using stem chilling, which increases phloem sap viscosity to create local bottlenecks to phloem transport, we created gradients of carbon supply in stems of mature red maples during the first half of the growing season. These carbon supply gradients had clear effects on tree physiology with radial growth in particular varying up to almost seven-fold with carbon supply. Local bulk nonstructural carbon concentrations in stems and roots remained relatively stable, suggesting that they are not rapidly modulated in response to changes in supply and demand. However, phloem and leaf nonstructural carbon accumulated above chilling-induced bottlenecks and were associated with reductions in photosynthetic capacity as well as the advancement of leaf coloration and fall, supporting the idea of within-tree feedbacks reducing carbon supply when supply exceeds demand. Most strikingly, radial growth varied systematically with carbon supply up to almost seven-fold, indicating that growth of red maple during the early growing season is strongly carbon-supply limited.
 The code to process these data and reproduce our results is available at https://github.com/TTRademacher/Exp2019Analysis. For more details pertaining to the methods see Rademacher et al. (2021) and contact the investigator.
DOI: 10.5281/zenodo.10361474
title: Heterogeneity of synaptic connectivity in the fly visual system

description: Source data of the paper Cornean, Molina-Obando et al. 2024, Nature Communications. This work contains an analysis of synaptic connectivity in the Drosophila system, focusing on the presynaptic circuitry of three medulla interneurons, Tm9, Tm1, and Tm2.Synaptic connectivity was analyzed using the FAFB dataset (Zheng et al. 2018 Cell) and the Flywire connectome (Schlegel et al. 2023 bioRxiv, Dorkenwald et al. 2023 bioRxiv), as well as expansion microscopy. This analysis is supplement by some functional analysis using in vivo 2-photon calcium imaging. Connectomics data used for this study are provided as .xlsx and .text files containing raw and processed data. Expansion microscopy are uploaded as .tiff files containing raw data, as well as .nrrd and .csv files containing processed data.Calcium imaging data are provided at .mat files containing both raw and processed data, as well as .xml files with information about the experimental protocol.
Please find all relevant information to use the code in the README files.
The code to analyze the data, either written in Matlab or Python, is found at https://github.com/silieslab/Cornean_Molina-Obando_etal_2024.git
DOI: 10.5281/zenodo.10361475
title: Heterogeneity of synaptic connectivity in the fly visual system

description: Source data of the paper Cornean, Molina-Obando et al. 2024, Nature Communications. This work contains an analysis of synaptic connectivity in the Drosophila system, focusing on the presynaptic circuitry of three medulla interneurons, Tm9, Tm1, and Tm2.Synaptic connectivity was analyzed using the FAFB dataset (Zheng et al. 2018 Cell) and the Flywire connectome (Schlegel et al. 2023 bioRxiv, Dorkenwald et al. 2023 bioRxiv), as well as expansion microscopy. This analysis is supplement by some functional analysis using in vivo 2-photon calcium imaging. Connectomics data used for this study are provided as .xlsx and .text files containing raw and processed data. Expansion microscopy are uploaded as .tiff files containing raw data, as well as .nrrd and .csv files containing processed data.Calcium imaging data are provided at .mat files containing both raw and processed data, as well as .xml files with information about the experimental protocol.
Please find all relevant information to use the code in the README files.
The code to analyze the data, either written in Matlab or Python, is found at https://github.com/silieslab/Cornean_Molina-Obando_etal_2024.git
DOI: 10.6073/pasta/fb84f49e1234c06855b27564f89795aa
title: Impacts of Phloem Chilling and Compression on Mature White Pine at Harvard Forest 2018

description: Wood formation is a crucial process for carbon sequestration on land, yet how variations in phloem-transported carbon and temperature affect wood formation, respiration and nonstructural carbon pools remains poorly understood.
 To better understand the role of carbon supply on allocation to wood formation, we constrained phloem transport using compression and chilling around the stem of 15 mature white pines to monitor the effects of contrasting carbon supply (enriched above and reduced below the manipulations) on local wood formation and respiration, as well as on nonstructural carbon pools in stems and roots.
 This data set contains all data measured during the experiment. This includes wood anatomical, xylogenetic, dendrochronological, stem CO2 efflux, and nonstructural carbon measurements in coarse roots and stems, as well as pre-dawn water potential measurements of needles and branches. Furthermore, we provide basic allometric measurements for all trees. The code to process these data and reproduce our results is available at https://github.com/TTRademacher/Exp2018Analysis. For more details pertaining to the methods see Rademacher et al. (2021) and contact the investigator.
DOI: 10.5281/zenodo.10363777
title: Quantitative proteomic dataset of  the spring wheat (Triticum aestivum L.) at drought stress

description: We presented the proteomic datasets of spring wheat (Triticum aestivum L.) leaves and roots under drought stress conditions. Using isobaric tags for relative and absolute quantitation (iTRAQ), we identified differentially expressed proteins involved in photosynthesis, primary metabolism, antioxidant defense, and translation.
DOI: 10.5281/zenodo.10363778
title: Quantitative proteomic dataset of  the spring wheat (Triticum aestivum L.) at drought stress

description: We presented the proteomic datasets of spring wheat (Triticum aestivum L.) leaves and roots under drought stress conditions. Using isobaric tags for relative and absolute quantitation (iTRAQ), we identified differentially expressed proteins involved in photosynthesis, primary metabolism, antioxidant defense, and translation.