cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/z4fr2xm2ym
title: Pre- and post-harvest factors that affect the quality and commercialization of the Tahiti lime

description: Several factors along the Tahiti lime chain determine the final quality and safety of the fruit. In the pre-harvest, fruit quality is affected by crop location, soil and climate conditions, the rootstock, the cultural activities carried out, and the presence of pests and diseases. Also, post-harvest operations such as conditioning, transportation, and storage affect fruit appearance, quality, and market value. The following data correspond to the subjective assessment of fruits of Tahiti acid limes by visual review of their surface damage. Data are expressed as a percentage of fruits with damage in pre-harvest and post-harvest according to the effect of the location (Lebrija and Villavicencio), the rootstocks (Citromelo, Kryder and Volkameriana), the crop season (dry and rainy seasons) and the storage conditions (temperature and disinfection). In the current study most of the post-harvest diseases of Tahiti lime have their origin in the field. Also, preharvest damage are more frequent during the dry period. Likewise, field temperature and precipitation play a crucial role in Tahiti lime quality. This data can be used for identifying the causes that affect fruit quality in order to generate strategies to minimize fruit damage and maintain its quality.
DOI: 10.6084/m9.figshare.3122734.v3
title: SCS: Self-Compassion Scale, validation of the French version

description: We validated the French version of the Self-Compassion Scale (SCS) on a community sample. Convergent validity was tested with happiness (Bonh), satisfaction with life (LS), depression (BDI), mindfulness (PLC) and affect (PANAS).<br>
DOI: 10.17633/rd.brunel.3452762.v1
title: Usher syndrome study.sav

description: The aim of this study was to determine if psychosocial wellbeing predicts the health-related quality of life (HRQOL) of people with Usher syndrome. Ninety UK-resident adults with Usher syndrome were recruited through deafblind-related charities, support groups and social groups. All participants took part in a survey that measured their physical and mental HRQOL, depressive symptoms, loneliness and social support. Measured confounders included age, sex and health-related characteristics. Hierarchical multiple linear regression analyses examined the association of each psychosocial wellbeing indicator with both physical and mental HRQOL while controlling for confounders in a stepwise manner.
DOI: 10.6084/m9.figshare.21441396.v3
title: Plectropomus leopardus genome

description: <em>Plectropomus leopardus</em>, as known as leopard coral grouper, is a valuable marine fish that has gradually been bred artificially. To promote future conservation, molecular breeding, and comparative studies, we generated an improved high-quality chromosomal-level genome assembly of leopard coral grouper using Nanopore long-reads, Illumina short reads, and the Hi-C sequencing data. The draft genome is 849.74Mb with 45 contigs and N50 of 35.59 Mb. Finally, a total of 846.49 Mb corresponding to 99.6% of the contig sequences was anchored to 24 pseudo-chromosomes using Hi-C technology. A final set of 25,965 genes is annotated after manual curation of the predicted gene models, and BUSCO analysis yielded a completeness score of 99.5%. This study significantly improves the utility of the grouper genome and provided a reference for the study of molecular breeding, genomics and biology in this species.
DOI: 10.6084/m9.figshare.5129791.v1
title: Supplementary Material for: RASopathies: Presentation at the Genome, Interactome, and Phenome Levels

description: Clinical symptoms often reflect molecular correlations between mutated proteins. Alignment between interactome and phenome levels reveals new disease genes and connections between previously unrelated diseases. Despite a great potential for novel discoveries, this approach is still rarely used in genomics. In the present study, we analyzed the data of 6 syndromes belonging to the RASopathy class of disorders (RASopathies) and presented them as a model to study associations between genome, interactome, and phenome levels. Causative genes and clinical symptoms were collected from OMIM and NCBI GeneReviews databases for 6 syndromes: Noonan, Noonan syndrome with multiple lentigines, neurofibromatosis type 1, cardiofaciocutaneous, and Legius and Costello syndrome. The STRING tool was used for the identification of protein interactions. Six RASopathy syndromes were found to be associated with 12 causative genes. We constructed an interactome of RASopathy proteins and their neighbors and developed a database of 328 clinical symptoms. The collected data was presented at genome, interactome, and phenome levels and as an integrated network of all 3 data types. The present study provides a baseline for future studies of associations between interactome and phenome in RASopathies and could serve as a novel approach to analyze phenotypically and genetically related diseases.
DOI: 10.6084/m9.figshare.1209702.v3
title: Positive Semidefinite Rank-Based Correlation Matrix Estimation With Application to Semiparametric Graph Estimation

description: Many statistical methods gain robustness and flexibility by sacrificing convenient computational structures. In this article, we illustrate this fundamental tradeoff by studying a semiparametric graph estimation problem in high dimensions. We explain how novel computational techniques help to solve this type of problem. In particular, we propose a nonparanormal neighborhood pursuit algorithm to estimate high-dimensional semiparametric graphical models with theoretical guarantees. Moreover, we provide an alternative view to analyze the tradeoff between computational efficiency and statistical error under a smoothing optimization framework. Though this article focuses on the problem of graph estimation, the proposed methodology is widely applicable to other problems with similar structures. We also report thorough experimental results on text, stock, and genomic datasets.
DOI: 10.6084/m9.figshare.14914896.v1
title: Results of Monte Carlo modelling

description: Output of Monte Carlo modelling. Results shown here are the summary data of the 10,000 simulations run to estimate P supply from the GICE, HICE and the weathering of terrestrial tephra deposits.<br>Used in Figure 4 of "Late Ordovician climate change and extinctions driven by elevated volcanic nutrient supply" by Longman et al., Nat. Geosci. (2021) <br>
DOI: 10.6084/m9.figshare.25377439.v1
title: Data for: Phylogenomic Profiles of Whole-Genome Duplications in Poaceae and Landscape of Differential Duplicate Retention and Losses among Major Poaceae Lineages

description: Here, we present sequence alignments and gene tree files of orthogroups and their reconciliations as described in our publication titled “Phylogenomic Profiles of Whole-Genome Duplications in Poaceae and Landscape of Differential Duplicate Retention and Losses among Major Poaceae Lineages”.The ‘Grass Phylogenomics’ folder includes datasets for estimation of retention/loss patterns of the rho-derived duplicates, which were used for our custom scripts in GitHub and the online tool in Code Ocean (10.24433/CO.1170454.v1).The “Bayesian divergence time estimation” folder consists of datasets for dating Poaceae time-tree. The folder of Alignments includes nuclear gene alignments of 166 single-copy gene families. The DatedTrees folder comprises 166 dated trees. Grass.time.tree is the dated tree summarized from 166 dated trees and corresponds to our Supplementary Figure 2.Datasets for phylogenomic analyses using Tree2GD, corresponding to our Supplementary Figures 3-16, are available in folders of “Phylogenomic analyses for Poaceae and other Poales”, “Phylogenomic analyses for Poaceae”, “Phylogenomic analysis for Bambusoideae”, “Phylogenomic analyses for Oryzoideae”, “Phylogenomic analyses for Pooideae”, “Phylogenomic analyses for Poeae”, “Phylogenomic analyses for Agrostidodinae and Poodinae”, “Phylogenomic analyses for Triticodae”, “Phylogenomic analysis for Panicoideae”, “Phylogenomic analyses for Panicodae”, “Phylogenomic analyses for Andropogoneae”, “Phylogenomic analyses for Chloridoideae”, “Phylogenomic analyses for Boutelouodinae”, and “Phylogenomic analyses for Gouiniodinae and Eragrostideae”.Datasets for MAPS analyses are available in the folder of ‘MAPS’. Datasets for Supplementary Figure 32 are available in the folder of “Bamboo Genome Analyses”. Datasets for ASTRAL analyses of pruned subtrees for <i>Oryza</i> are available in the folder of “ASTRAL analyses of pruned subtrees for <i>Oryza</i>” (Supplementary Figure 43).In addition, the code of species used in our study can be found in the PDF file of “WGD”.
DOI: 10.6084/m9.figshare.25696266.v1
title: Transcriptomic Changes in Oxidative Stress, Immunity and Cancer Pathways Caused by Cannabis Vapor on Alveolar Epithelial Cells

description: RNA-seq Tables
DOI: 10.6084/m9.figshare.3381073.v2
title: Jaric et al., Data mining in conservation research using Latin and vernacular species names. Peerj - Supplementary material

description: Supplementary material for: Jaric et al., Data mining in conservation research using Latin and vernacular species names. Peerj<br><br>Abstract - In conservation science, assessments of trends and priorities often focus on species as the management unit. Studies on species coverage in online media are commonly conducted by using species vernacular names. However, use of species vernacular names for web-based data search is problematic due to high risk of mismatches in results. While the use of Latin names may produce more consistent results, it is uncertain whether a search using Latin names will produce unbiased results as compared to vernacular names. We assessed the potential of Latin names to be used as an alternative to vernacular names for the data mining within the field of conservation science. By using Latin and vernacular names, we searched for species from four species groups: diurnal birds of prey, Carnivora, Primates and marine mammals. We assessed the relationship of the results obtained within different online sources, such as Internet pages, newspapers and social media networks. Results indicated that the search results based on Latin and vernacular names were highly correlated, and confirmed that one can be used as an alternative for the other. We also demonstrated the potential of the number of images posted on the Internet to be used as an indication of the public attention towards different species. <br> <br>
DOI: 10.17632/b3fkfhh867
title: Brothers or Invaders? How Crisis-Driven Migrants Shape Voting Behavior

description: Replication files and data for the paper: "Brothers or Invaders? How Crisis-Driven Migrants Shape Voting Behavior" Authors: Sandra V. Rozo and Juan F. Vargas Journal: Journal of Development Economics, Forthcoming
DOI: 10.6084/m9.figshare.11110361.v1
title: FE47_1990.zip

description: This document describes the design process, definitions, and algorithmic implementation for the pan-European Assessment of Forest Fragmentation. This study is a preceding presentation of the indicator 4.7 in the State of Europe’s Forests 2020 report, published by FOREST EUROPE. The spatial forest coverage is assessed from the Copernicus CORINE Land Cover dataset (CLC, version 20, downloaded in July 2019) for the years 1990, 2000, 2006, 2012, 2018. Spatially explicit maps and statistical summaries are derived at three reporting levels: CLC (entire CLC coverage), EU28 and at country level. The status product consists of maps and summary statistics for each year and assessment level. The change product highlights areas where non-forest and forest fragmentation classes changed over time. The change product is provided for the time frame 2000 to 2018, which is the longest time span with comparable data coverage.
DOI: 10.6084/m9.figshare.1224307.v3
title: Week 6-Experimental design

description: This experiment was designed to examine which of the treatments were more attractant to insects with respect the weather conditions at York University grassland. There were 3 sets; each had all four treatments (water, sugar, salt, and perfume). The stations were placed randomly, where the first set was placed where the T.A. stopped at. The second station was placed 8 meters to the right of the first station and the third was 8 meters to the right of the second station. All the treatments were dissolved with water at 5% concentration, but the perfume was 10 buffs on the grass bundle. Each grass bundle treatment was placed on white sheet. The stations were about 2 meter square with additional 50cm of human free zoon to eliminate disturbance. Insects’ abundance was collected every 20 minutes from each set for every treatment allowing the researchers to obtain 3 trials on 20 minutes intervals. Thus, in 120 minutes, there were 18 replicated trials collected for each treatment. The same experiment was conducted on another day; the only change was that the sheets of paper were changed from white to brown and the weather condition. On day “1” there were showers, gentle breeze (7-9 mph), with 12°C temperature. Further, day “2” was sunny and the soil was lightly wet with temperature 15°C. Day “1” was 15/10/2014 while day “2” was on 22/10/2014 and the experiments timing was 3:00pm-4:45pm for both days. The limitation for this experiment was the used paper sheets, they may alternate the readings since the white or brown color may alternate in insects’ attention. Thus, that may violate the data collection from the both days. Further, the change in weather condition between day “1” and day “2” as rain may reduce the number of flying insects and heat may alternate insects’ behaviour from looking for food to looking for water. Thus, to overcome those limitations, the weather conditions need to be controlled (i.e. in lab experiment). Further, the experiment needs to have a uniform in terms of the color of the paper sheets used.
DOI: 10.6084/m9.figshare.12464687.v1
title: Hammouda 2020

description: X-Ray diffraction patterns
DOI: 10.6084/m9.figshare.19808818.v1
title: scRNA_seq_CoronaVac.cloupe

description: CoronaVac, a promising inactivated SARS-CoV-2 vaccine, may induce gene expression changes in peripheral blood mononuclear cells (PBMC) at early stages of vaccination. We used single cell RNA sequencing (scRNA-seq) to analyze the PBMC transcriptomics of CoronaVac-vaccinated participants (the vaccination group, two individuals, various timepoints at 0, 14, 28, 35 days) and COVID-19-recovered patients (the recovery group, three individuals, 8 months after recovery). The h5 file is the merged-barcode-feature-matrix file processed by the Cell Ranger (version 5).The cloupe file can be viewed using the Loupe Browser (version 5).
DOI: 10.6084/m9.figshare.28490204.v1
title: ISA-1: AI-Empowered Super-Resolution Mapping 1-m Impervious Surface Area in the Yangtze River Economic Belt

description: <i>Currently, only the results of a few example cities have been released. All results will be made available once the paper is accepted.</i><br>The Yangtze River Economic Belt (YREB) is a critical region for the ecological and economic sustainability in China, which faces significant challenges from rapid urbanization, particularly the expansion of artificial impervious surfaces area (ISA). While existing many well-known ISA products (e.g., ESA-10m) offer foundational insights, their coarse spatial resolution limits accuracy, especially in fragmented landscapes and complex terrains. To this end, we map a 1-m very-high-resolution ISA product by means of AI techniques, called ISA-1, covering 36 cities in YREB, contributing to the community. ISA-1 is generated by integrating 10-m Sentinel-2 images with a generative adversarial network (GAN)-based super-resolution segmentation framework. Our approach overcomes the limitations of traditional methods, achieving a 10× spatial enhancement to resolve fine-grained urban structures and dispersed rural ISA features. Validation across 36 municipal-level administrative regions along the main stream of the Yangtze River shows that ISA-1 reduces ISA overestimation in densely urbanized areas (e.g., Shanghai, Suzhou) by 0.04%–36.15% compared with ESA-10m, while detecting 5.00% –81.74% more ISA in mountainous regions (e.g., Garzê, Liangshan), demonstrating superior capability in capturing small-scale artificial impervious surfaces. The model achieved an overall accuracy of 94.42%, with F1 scores of 96.64% (non-ISA) and 83.61% (ISA), outperforming existing mid-resolution products in both geometric precision and semantic consistency. This advancement not only enhances the monitoring of urbanization’s ecological impacts, such as altered hydrological cycles and biodiversity loss, but also provides a scalable, cost-effective solution for high-resolution ISA mapping
DOI: 10.6084/m9.figshare.28658807.v1
title: New Phylogenetic Markers with Enhanced Phylogenetic Resolution for Cladoniaceae and Parmeliaceae

description: Taxonomic revisions of fungi have traditionally relied on molecular phylogenies using universal markers such as nuclear and mitochondrial rRNA, cytochrome oxidase, RNA polymerase II, minichromosome maintenance complex component 7, and elongation factor 1. However, these markers often fail to resolve the phylogenetic relationships of closely related fungal species, and further development of fungal universal markers for classification is limited. To address this, the study attempted to develop semi-universal markers targeting specific fungal families rather than the entire kingdom, assessing their potential for taxonomic purposes. Cladoniaceae and Parmeliaceae were selected due to their high species diversity and significant taxonomic challenges. High-resolution phylogenetic markers for single-copy genes with high substitution rates were developed for these families. In this study, primer sequences for nine newly developed phylogenetic markers are presented: cell division control protein 12 (CDC12), histone acetyltransferase esa1 (ESA1), GPI-anchor transamidase (GPITA), the intergenic spacer between hypothetical protein and elongation factor 3 (HYP2-EF3), isocitrate dehydrogenase (ICDH), mitochondrial-processing peptidase-like protein subunit beta (MPP2), SNF7 family protein (SNF7), zf-C2HC5-domain-containing protein (ZFCP), and V-type ATP synthase subunit B (VATPS). These markers exhibited substitution rates at least three times and up to seven times higher than the ITS domain. The phylogeny of Cladonia gracilis (Cladoniaceae), reconstructed using concatenated sequences of ten markers (ITS, CDC12, ESA1, GPITA, HYP2-EF3, ICDH, MPP2, SNF7, VATPS, and ZFCP), displayed well-resolved branches with high bootstrap support. These markers are expected to provide sufficient resolution for the phylogenetic analysis of closely related species in Cladoniaceae and Parmeliaceae. Experimental conditions and bioinformatic tools for multiplex PCR with barcode primers and sequencing on the MiSeq platform were established, ensuring labor- and cost-effective sequencing performance. This approach demonstrates that semi-universal phylogenetic markers targeting the family level can be used to draw taxonomic conclusions for problematic taxa and potentially be applied to other taxonomic groups.
DOI: 10.6084/m9.figshare.5126353.v1
title: Supplementary Material for: Efficacy of Cognitive Behaviour Therapy versus Anxiety Management for Body Dysmorphic Disorder: A Randomised Controlled Trial

description: <b><i>Background:</i></b> The evidence base for the efficacy of cognitive behaviour therapy (CBT) for treating body dysmorphic disorder (BDD) is weak. <b><i>Aims:</i></b> To determine whether CBT is more effective than anxiety management (AM) in an outpatient setting. <b><i>Method:</i></b> This was a single-blind stratified parallel-group randomised controlled trial. The primary endpoint was at 12 weeks, and the Yale-Brown Obsessive Compulsive Scale for BDD (BDD-YBOCS) was the primary outcome measure. Secondary measures for BDD included the Brown Assessment of Beliefs Scale (BABS), the Appearance Anxiety Inventory (AAI) and the Body Image Quality of Life Inventory (BIQLI). The outcome measures were collected at baseline and week 12. The CBT group, unlike the AM group, had 4 further weekly sessions that were analysed for their added value. Both groups then completed measures at their 1-month follow-up. Forty-six participants with a DSM-IV diagnosis of BDD, including those with delusional BDD, were randomly allocated to either CBT or AM. <b><i>Results:</i></b> At 12 weeks, CBT was found to be significantly superior to AM on the BDD-YBOCS [β = -7.19; SE (β) = 2.61; p &lt; 0.01; 95% CI = -12.31 to -2.07; d = 0.99] as well as the secondary outcome measures of the BABS, AAI and BIQLI. Further benefits occurred by week 16 within the CBT group. There were no differences in outcome for those with delusional BDD or depression. <b><i>Conclusions:</i></b> CBT is an effective intervention for people with BDD even with delusional beliefs or depression and is more effective than AM over 12 weeks.
DOI: 10.6084/m9.figshare.6406475.v1
title: Genotypes of 50 Spar tetrads

description: 50 genotype files are deposited here, each including the genotypes of 4 meiotic spores from a tetrad and their parents. "1" indicates same genotype as N17, "2" indicates same genotype as N44.
DOI: 10.17632/s4pw3hx7vy
title: Data for: Zircon U-Pb ages constraints on the provenance of the Upper Oligocene to Upper Miocene sandstones in the western area of the Qiongdongnan Basin, South China Sea

description: Zircon ages of the sediments in the Qiongdongnan Basin, South China Sea.
DOI: 10.6084/m9.figshare.1026223.v2
title: 3 to 1 strength ratio

description: Current source density reconstructions for two sources of different strengths (one three times the strength of the other).
DOI: 10.6084/m9.figshare.25330354.v1
title: Photogrammetric 3D models and sitemaps for Amzil et al. 2024: New records of Dinosaur tracks from Middle Jurassic red beds in the Middle Atlas, Morocco: Application of Photogrammetry to Ichnology and Conservation of Geological Heritage

description: Dataset for: Amzil et al. (submitted): New records of Dinosaur tracks from Middle Jurassic red beds in the Middle Atlas, Morocco: Application of Photogrammetry to Ichnology and Conservation of Geological Heritage.Authors: Mustapha Amzil, Mostafa Oukassou, Jens Lallensack, Hendrik Klein, Omar Zafaty, Hafid Saber, André Charrière, Christian Meyer, Gerard D. GierlińskiThe dataset contains the following zip files:Inzar-Oufounas.zip: Photogrammetric 3D models (.ply) with textures (.jpg) of the Inzar O’Founass siteTasra.zip: Photogrammetric 3D models (.ply) with textures (.jpg) of the Tasra siteEl_Mers_Center.zip: Photogrammetric 3D model of the El Mers Center site. Note: A single high resolution model, 1.6 GB.Laach-O-Medda.zip: Photogrammetric 3D models (.ply) with textures (.jpg) of the Laach O'Medda site.Tassmante-O-Moche.zip: Photogrammetric 3D models (.ply) with textures (.jpg) of the Tassmante-O-Moche site.Infri-N-Tfrane.zip: Photogrammetric 3D models (.ply) with textures (.jpg) of the Infri-N'Tfrane site.Heightmaps_and_orthofotos: Height maps and orthophotos (all as .png) of all sitesMaps.zip: Interpretive sitemaps<br>
DOI: 10.6084/m9.figshare.11323289.v1
title: Time-to-target simplifies optimal control of visuomotor feedback responses

description: This is the dataset, analysis and figure scripts for the article entitled "Time-to-target simplifies optimal control of visuomotor feedback responses". We provide the behavioural data (kinematics and forces) for point-to-point reaches to a target, where lateral cursor jumps are introduced during the reach. We also include various OFC models to normatively model our data: finite, infinite and receding horizon models, as well as a time-to-target dependent model