cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3884601
title: High resolution global industrial and smallholder oil palm map for 2019

description: The dataset contains 634 100x100 km tiles, covering areas where oil palm plantations were detected. The file '<em>grid.shp</em>' contains the grid that covers the potential distribution of oil palm. The file '<em>grid_withOP.shp</em>' shows the 100x100 grid squares with presence of oil palm plantations. The classified images (‘<em>oil_palm_map</em>’ folder, in geotiff format) are the output of the convolutional neural network based on Sentinel-1 and Sentinel-2 half-year composites. The images have a spatial resolution of 10 meters and contain three classes: [1] Industrial closed-canopy oil palm plantations, [2] Smallholder closed-canopy oil palm plantations, and [3] other land covers/uses that are not closed canopy oil palm. The file ‘<em>Validation_points_GlobalOilPalmLayer_2019.shp</em>’ includes the 13,495 points that were used to validate the product. Each point includes the attribute ‘Class’, which is the labelled class assigned by visual interpretation, and the attribute ‘predClass, which reflects the predicted class by the convolutional neural network. The ‘Class’ and ‘predClass’ values are the same as the raster files: [1] Industrial closed-canopy oil palm plantations, [2] Smallholder closed-canopy oil palm plantations, and [3] other land covers/uses that are not closed canopy oil palm. See article for additional information: Descals, Adrià, et al. "High-resolution global map of smallholder and industrial closed-canopy oil palm plantations." <em>Earth System Science Data</em> 13.3 (2021): 1211-1231. Changelog v1: - The analysis was extended to Sri Lanka, South India, and countries in Eastern Africa where oil palm can potentially grow. - The validation dataset only includes the points drawn by simple random sampling and stratified random sampling in the grid cells where the IUCN industrial layer detected oil palm. - The 'Class' and 'predClass' values in the validation dataset were reclassified with the same values as the raster images: [1] Industrial plantations, [2] Smallholder plantations, and [3] Other land covers/uses.
DOI: 10.5281/zenodo.4680896
title: Dataset related to article :"Loss-of-Function Variants in HOPS Complex Genes VPS16 and VPS41 Cause Early Onset Dystonia Associated with Lysosomal Abnormalities"

description: The dataset contains anonymised clinical form of three patients referred at Fondazione Besta included in the study described in the related article
DOI: 10.5281/zenodo.4680895
title: Dataset related to article :"Loss-of-Function Variants in HOPS Complex Genes VPS16 and VPS41 Cause Early Onset Dystonia Associated with Lysosomal Abnormalities"

description: The dataset contains anonymised clinical form of three patients referred at Fondazione Besta included in the study described in the related article
DOI: 10.6084/m9.figshare.14406419
title: Scott et al. Nature Chemistry 2021 Data Figs 1 - 3

description: Raw data from which figures in the manuscript '<i>Constructing ion-channels from water-soluble alpha-helical barrels' </i>were generated.
DOI: 10.6084/m9.figshare.14406419.v1
title: Scott et al. Nature Chemistry 2021 Data Figs 1 - 3

description: Raw data from which figures in the manuscript '<i>Constructing ion-channels from water-soluble alpha-helical barrels' </i>were generated.
DOI: 10.5281/zenodo.4682993
title: Data set Ofertas Kao

description: Este data set es requerido por la materia Tipología de datos.
description: NA
description: {"references": ["PRACTICA 1 TIPOLOG\u00cdA DE DATOS"]}
DOI: 10.5281/zenodo.4682992
title: Data set Ofertas Kao

description: Este data set es requerido por la materia Tipología de datos.
description: NA
description: {"references": ["PRACTICA 1 TIPOLOG\u00cdA DE DATOS"]}
DOI: 10.5281/zenodo.4659924
title: Dataset related to article "Diagnosis of Ventriculoperitoneal Shunt Malfunction: A Practical Algorithm"

description: database containing anonymised clinical information about a study aimed to present a practical method to accurately diagnose ventriculoperitoneal shunt (VPS) malfunction and to detect the exact level at which the system has failed to tailor VPS revision at that level only.
description: Study received the support of Italian Ministry of Health (program RC2020)
DOI: 10.5281/zenodo.4659923
title: Dataset related to article "Diagnosis of Ventriculoperitoneal Shunt Malfunction: A Practical Algorithm"

description: database containing anonymised clinical information about a study aimed to present a practical method to accurately diagnose ventriculoperitoneal shunt (VPS) malfunction and to detect the exact level at which the system has failed to tailor VPS revision at that level only.
description: Study received the support of Italian Ministry of Health (program RC2020)
DOI: 10.5281/zenodo.4683001
title: Re-evaluation of a riparian restoration experiment in the Western Cape Province: status 8 years down the line

description: In 1998, a study was initiated to assess the relative effectiveness of three different sowing treatments for reducing soil erosion and restoring indigenous vegetation cover after alien clearing in the Western Cape. The study concluded that introducing a mixture of seed to a riparian zone with a history of invasion can increase indigenous vegetation cover and species richness and has a stabilizing effect on eroded riverbanks. We report on a re-assessment of the restoration plots after a period of 8 years (with no follow up control) and a summer fire in 2005. The re-assessment included a survey of all the burnt woody material within the different treatment plots to determine species presence (dead or resprouting) and abundance, as well as a survey of seedlings in a post fire environment. Woody invasive plants dominated all plots, and had survived the burn with the majority re-sprouting, indicating the dire need for follow-up control to justify initial clearing and restoration cost. However the re-assessment revealed that indigenous vegetation cover was considerably higher in the plots that had received sowing treatments, while the control plots were dominated by Acacia mearnsii, the main invader of the tributary. Restoration of riparian areas after alien clearing has potential, but must be coupled with a long term plan for follow-up removal of post clearing alien recruits.
description: To monitor the progress of a riparian restoration experiment.
DOI: 10.5281/zenodo.4683000
title: Re-evaluation of a riparian restoration experiment in the Western Cape Province: status 8 years down the line

description: In 1998, a study was initiated to assess the relative effectiveness of three different sowing treatments for reducing soil erosion and restoring indigenous vegetation cover after alien clearing in the Western Cape. The study concluded that introducing a mixture of seed to a riparian zone with a history of invasion can increase indigenous vegetation cover and species richness and has a stabilizing effect on eroded riverbanks. We report on a re-assessment of the restoration plots after a period of 8 years (with no follow up control) and a summer fire in 2005. The re-assessment included a survey of all the burnt woody material within the different treatment plots to determine species presence (dead or resprouting) and abundance, as well as a survey of seedlings in a post fire environment. Woody invasive plants dominated all plots, and had survived the burn with the majority re-sprouting, indicating the dire need for follow-up control to justify initial clearing and restoration cost. However the re-assessment revealed that indigenous vegetation cover was considerably higher in the plots that had received sowing treatments, while the control plots were dominated by Acacia mearnsii, the main invader of the tributary. Restoration of riparian areas after alien clearing has potential, but must be coupled with a long term plan for follow-up removal of post clearing alien recruits.
description: To monitor the progress of a riparian restoration experiment.
DOI: 10.6084/m9.figshare.14406401
title: Supplementary Material for: Utility of Caudal Angulation for Venous Access under Fluoroscopic Guidance during Cardiovascular Implantable Electronic Device Implantation

description: <b><i>Background:</i></b> Axillary venous access is preferred for CIED implantation. The procedure is usually performed under fluoroscopic guidance in anteroposterior (A-P) view. However, there is a lack of perception of depth in this view with a fear of creating complications. Caudal fluoroscopy (adding 30°–35° caudal angulation to A-P projection) has been proposed to circumvent this problem. <b><i>Objective:</i></b> The aim of this study was to elucidate the advantages of caudal fluoroscopy using fluoroscopic images, contrast venograms, and CT angiography images of axillary vein. <b><i>Methods:</i></b> The fluoroscopic images and contrast venograms obtained in the A-P view were compared with caudal fluoroscopy in patients undergoing CIED implantation at our centre. Also, the CT angiography images of axillary vein were reconstructed to understand the relative anatomy of the vein and the underlying lung parenchyma, simulating these 2 projections. <b><i>Results:</i></b> The CT angiography images, contrast venograms, and fluoroscopic images confirmed that caudal fluoroscopy allows better visualization of the vein in relation to the lung parenchyma and rib cage. Analysis of fluoroscopic images revealed that the bend of the first rib formed a conical prominence in caudal fluoroscopy. This served as an important bony landmark for successful venous access, which was usually obtained while the needle was being directed towards this prominence in caudal fluoroscopy. <b><i>Conclusions:</i></b> The proposed advantages of caudal fluoroscopy for CIED implantation have been elucidated by analysis of CT angiography images, contrast venograms, and fluoroscopic images.
DOI: 10.6084/m9.figshare.14406401.v1
title: Supplementary Material for: Utility of Caudal Angulation for Venous Access under Fluoroscopic Guidance during Cardiovascular Implantable Electronic Device Implantation

description: <b><i>Background:</i></b> Axillary venous access is preferred for CIED implantation. The procedure is usually performed under fluoroscopic guidance in anteroposterior (A-P) view. However, there is a lack of perception of depth in this view with a fear of creating complications. Caudal fluoroscopy (adding 30°–35° caudal angulation to A-P projection) has been proposed to circumvent this problem. <b><i>Objective:</i></b> The aim of this study was to elucidate the advantages of caudal fluoroscopy using fluoroscopic images, contrast venograms, and CT angiography images of axillary vein. <b><i>Methods:</i></b> The fluoroscopic images and contrast venograms obtained in the A-P view were compared with caudal fluoroscopy in patients undergoing CIED implantation at our centre. Also, the CT angiography images of axillary vein were reconstructed to understand the relative anatomy of the vein and the underlying lung parenchyma, simulating these 2 projections. <b><i>Results:</i></b> The CT angiography images, contrast venograms, and fluoroscopic images confirmed that caudal fluoroscopy allows better visualization of the vein in relation to the lung parenchyma and rib cage. Analysis of fluoroscopic images revealed that the bend of the first rib formed a conical prominence in caudal fluoroscopy. This served as an important bony landmark for successful venous access, which was usually obtained while the needle was being directed towards this prominence in caudal fluoroscopy. <b><i>Conclusions:</i></b> The proposed advantages of caudal fluoroscopy for CIED implantation have been elucidated by analysis of CT angiography images, contrast venograms, and fluoroscopic images.
DOI: 10.5281/zenodo.4682403
title: On the Discoverability of npm Package Vulnerabilities in Node.js Projects

description: This package contains the scripts used for our approach in the manuscript "On the Discoverability of npm Package Vulnerabilities in Node.js Projects." For more information on how to understand the folder structure, please read the README.md.
DOI: 10.15161/oar.it/73659
title: CovidStat project data

description: This record contains the daily updated data of the CovidStat project. CovidStat is a project carried out by the CovidStat Working Group at INFN, whose creation was promoted within the Italian National Institute of Nuclear Physics with the aim of making a statistical analysis of the data provided daily by the Civil Protection on the spread of the pandemic in Italy. CovidStat data can interactively be browsed at https://covid19.infn.it.
description: The software to process this Root TTree is in the related identifier. Be sure to use the right corresponding version, based on the data in which Root TTree was generated.
DOI: 10.17632/n6s22hpj56.1
title: Renal agenesis

description: Magnetic resonance imaging (MRI) shows renal agenesis in a 6-year-old girl.
DOI: 10.17632/hxk7pzfk26.1
title: Dopamine Signaling Impairs ROS Modulation by Mitochondrial Hexokinase and leads to high H2O2 release by Human Neural Progenitor Cells

description: Dopamine signaling has numerous roles during brain development. In addition, alterations in dopamine may be also involved in the pathophysiology of psychiatric disorders. Neurodevelopment is modulated in multiple steps by reactive oxygen species (ROS), byproducts of oxidative metabolism which are signaling factors involved in proliferation, differentiation and migration. Hexokinase (HK), when associated with the mitochondria (mt-HK), is a potent modulator of the generation of mitochondrial ROS in the brain. In this study we investigated whether dopamine could affect both the activity and redox function of mt-HK in human neural progenitor cells (NPCs). We found that dopamine signaling via D1R decreases mt-HK activity and impairs ROS modulation, which is followed by an expressive release of H2O2 and impairment in calcium handling by the mitochondria. Accordingly, dopamine-exposed NPCs showed a significant decrease in the protein content of HKI. Nevertheless, mitochondrial respiration is not affected, suggesting specificity for dopamine on mt-HK function. In neural stem cells (NSCs) derived from iPSCs of schizophrenic patients, mt-HK is unable to modulate mitochondrial ROS, in contrast to NSCs derived from healthy individuals. Our data point to mitochondrial hexokinase as a novel target of dopaminergic signaling, as well as a redox modulator in human neural progenitor cells, which may be relevant to the pathophysiology of neurodevelopmental disorders such as schizophrenia.
DOI: 10.17632/k8d386ndz6.2
title: HNF4A is required to specify glucocorticoid action in the liver

description: The glucocorticoid receptor (GR) is a nuclear hormone receptor critical to the regulation of energy metabolism and the inflammatory response. The actions of GR are highly dependent on cell type and environmental context. Here, we demonstrate the necessity for liver lineage-determining factor hepatocyte nuclear factor 4A (HNF4A) in defining liver-specificity of GR action. In normal mouse liver, the HNF4 motif lies adjacent to the glucocorticoid response element (GRE) at GR binding sites found within regions of open chromatin. In the absence of HNF4A, the liver GR cistrome is remodelled, with both loss and gain of GR recruitment evident. Lost sites are characterised by HNF4 motifs and weak GRE motifs. Gained sites are characterised by strong GRE motifs, and typically show GR recruitment in non-liver tissues. The functional importance of these HNF4A-regulated GR sites is further demonstrated by evidence of an altered transcriptional response to glucocorticoid treatment in the Hnf4a-null liver. This Mendeley Data repository contains supportive data and code for our bioRxiv preprint. Methods are described in the preprint text. All experiments conducted on mouse (Mus musculus) liver, all processed data derived from raw sequencing data aligned to the mm10 genome. Differential GR binding analysis incorporated spike-in normalisation (spiked-in Drosophila melanogaster chromatin; reads aligned to dm6 genome). The "MACS2 GR ChIP-seq peaks, wildtype liver" folder contains the BED files for GR ChIP-seq peaks called in dexamethasone- or vehicle-treated mouse liver (Figures 1 & S1). The "Output of differential binding and differential expression analyses" folder contains the edgeR, stageR and csaw output, following the methods described in the text, using the code in the "Code for differential binding and differential expression analyses" folder (Figures 2, 4, S3). The "HOMER motif discovery" folder contains screenshots of the output from HOMER (http://homer.ucsd.edu/homer/ngs/peakMotifs.html) motif discovery analysis of GR binding sites (Figures 1, S1, 2). The "GIGGLE output" folder contains the output (csv) from GIGGLE analysis of GR binding sites, run through the Cistrome DB Toolkit portal (http://dbtoolkit.cistrome.org/) (Figure 3).
DOI: 10.17632/7yctt99gmv.1
title: Data of Storage capacity threshold as a function of rainfall rate for saturation overland flow over shallow sloping aquifers

description: Simulated TSO, T and h on twenty-five hillslopes by kinematic wave analytical solutions (KW) and Boussinesq numerical solutions (BS) under rainfall rates from 1mm/h to 20mm/h.The critical state terms of 25 hillslopes simulated by the two methods are also given.
DOI: 10.17632/v59gnk2rs6.1
title: Hydrous wadsleyite crystal structure and symmetric hydrogen bonding in the mantle

description: The transition zone acts as a geochemical filter to mantle material passing through the 410 and 660 km seismic discontinuities. The high water storage capacity of wadsleyite, Mg2SiO4, an abundant transition zone mineral, therefore plays an important role in the global water cycle. Hydration of wadsleyite by (OH)- associated with cation defects is well known to influence its physical and mechanical properties, however an atomic-scale understanding of the structure and hydrogen bonding at high pressures is needed to interpret the influence of water on the behavior of wadsleyite in the mantle transition zone. We have determined the pressure evolution of the wadsleyite crystal structure, lattice symmetry, and hydrogen-bond distances up to 35 GPa using single-crystal X-ray diffraction on well-characterized, Fe-bearing samples containing ~0.25 and ~2.0 wt.% H2O. Both compositions undergo a linear increase in the monoclinic distortion from orthorhombic symmetry above 10 GPa, with the less hydrous sample showing a greater increase in distortion on further compression. Although the proton positions cannot be modeled from the experimental data, the evolution of the primary hydrogen bond in the structure was monitored by the behavior of the O1–H…O4 hydrogen bond lengths along the M3 octahedron during compression. Above about 25 GPa, the hydrogen bond undergoes a transition to being completely incompressible, which is not observed in other O-O interatomic distances. We interpret this change in compression behavior as resulting from symmetrization of the hydrogen bond in wadsleyite. The observed strengthening of the hydrogen bond in wadsleyite has implications for the partitioning of hydrogen isotopes in the mantle transition zone.
DOI: 10.17632/6wkmndk4ss.1
title: Disruption of model-based decision making by silencing of serotonin neurons in the dorsal raphe nucleus

description: Each Excel file contains the data corresponding to each figure.
DOI: 10.17632/krd7t69ydw.1
title: twin dataset

description: Dataset for twin deficit hypothesis in India
DOI: 10.17632/hs2nbsw5vy.1
title: Directional tuning in the hippocampal formation of birds. Ben-Yishai et al.,

description: This data set contains spike trains, position and head direction trajectories of 2140 single units and additional information and results about each unit. The work in-which this data set was collected and analysed is published in Ben-Yishai et al., Directional tuning in the hippocampal formation of birds. Current Biology (2021). In-press. The study is summarized below: Birds strongly rely on spatial memory and navigation. Therefore, it is of utmost interest to reveal how space is represented in the avian brain. Here we used tetrodes to record neurons from the hippocampal formation of Japanese quails – a ground-dwelling species – while the quails roamed in an open-field arena. Whereas spatially-modulated cells (place-cells, grid cells, border-cells) were generally not encountered, the firing-rate of about 12% of the neurons was unimodally and significantly modulated by the head-azimuth – i.e. these were head-direction cells (HD cells). Typically, HD cells were maximally active at one preferred-direction and minimally at the opposite null-direction, with preferred-directions spanning all 360o across the population. The preferred-direction was independent of the animal’s position and speed, and was stable during the recording session. The HD tuning was broader compared to that of HD cells in rodents, and most cells had non-zero baseline firing in all directions. However, similarly to findings in rodents, the HD tuning usually rotated with the rotation of a salient visual cue in the arena. Thus, these findings support the existence of an allocentric head-direction representation in the quail hippocampal formation, and provide the first demonstration of head-direction cells in birds.
DOI: 10.17632/zgxmxnn82w.1
title: Magnesium isotope constraints on contributions of recycled oceanic crust and lithospheric mantle to generation of intraplate basalts in a big mantle wedge

description: Data for the manuscript entitled Magnesium isotope constraints on contributions of recycled oceanic crust and lithospheric mantle to generation of intraplate basalts in a big mantle wedge. The dataset include major, trace and Sr-Nd isotopic data, and parameters and results for modelling
DOI: 10.6084/m9.figshare.14374616
title: Risk factors for groin pain in male high school soccer players: a cluster-randomised controlled trial

description: Groin pain is one of the most common pain conditions reported by soccer players, especially adductor muscle-related pain. However, there are no reports of risk factors in high school soccer players. In order to establish a preventive method for groin pain, it is important to understand the physical characteristics of people with groin pain. The purpose of this study was to investigate the risk factors associated with having groin pain in order to establish a preventive exercise for groin pain in high school soccer players.