cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12030663.v1
title: Range-wide snowshoe hare exome SNP genotypes

description: A .ped file containing 10388 unlinked SNP genotypes for snowshoe hares derived from a whole exome capture. SNPs were used to perform a population structure analysis in Admixture v1.3.0. <br>Raw sequence data were first cleaned by trimming adapters and low-quality bases (mean phred-scaled quality score &lt;15 across 4 bp window) using Trimmomatic v0.35 (Bolger et al. 2014). Paired-end reads overlapping more than 10 bp and with lower than 10% mismatched bases were then merged using FLASH2 (Magoč and Salzberg 2011). Cleaned sequence data were then mapped to a snowshoe hare pseudoreference genome (see Jones et al. (2018) for details) using default settings in BWA-MEM v0.7.12 (Li 2013). We used PicardTools to remove duplicate reads with the MarkDuplicates function and assigned read group information with the AddOrReplaceReadGroups function. Using GATK v3.4.046 (McKenna et al. 2010), we then identified poorly aligned genomic regions with RealignerTargetCreator and locally realigned sequence data in these regions with IndelRealigner. We performed multi-sample variant calling for previously defined snowshoe hare populations using default settings with the GATK UnifiedGenotyper and performed variant filtration in VCFtools v0.1.14 (Danecek et al. 2011). We filtered genotypes with individual coverage &lt;5x or &gt;70x or with a phred-scaled quality score &lt;30. Additionally, we removed all indel variants and filtered SNPs with a phred-scaled quality score &lt;30, Hardy-Weinberg P&lt;0.001. We required that sites have no missing data across individuals and that sites were &gt; 10kb apart. We then created a .ped and .map file using the --plink flag in VCFtools.<br>
DOI: 10.6084/m9.figshare.22246096.v1
title: NeuroGravity dataset

description: This is the behavioral and event-related potential data of the Visual and Auditory tasks of the NeuroGravity and its control experiment. The dataset also contains subjects' subjective sleepiness and motion sickness ratings over the experiment sessions.
DOI: 10.6084/m9.figshare.9939770.v1
title: Table S1.xlsx

description: Saline solution composition.
DOI: 10.17632/3kwgxg4stb
title: Papaya Leaf Disease Image Dataset

description: This dataset comprises a comprehensive collection of 3626 raw images and 18,130 augmented images of papaya leaves, capturing a diverse range of diseases and healthy conditions. Originally sourced from Ashulia, Bangladesh, the dataset includes 8 distinct classes: Anthracnose (230 images), Bacterial Spot (214 images), Curl (778 images), Healthy (594 images), Mealybug (182 images), Mite Disease (552 images), Mosaic (546 images), and Ringspot (530 images). This dataset serves as a valuable resource for researchers and practitioners in agricultural science, machine learning, and plant pathology, facilitating the development of automated disease detection and classification systems. Each image is labeled according to its corresponding class, providing a robust foundation for training and validating models aimed at enhancing papaya crop health and management.
DOI: 10.6084/m9.figshare.25036940.v1
title: <b>Plant phylogeny, traits and fungal community composition as drivers of plant-soil feedbacks</b>

description: Data associated with the manuscript:<br>Plant phylogeny, traits and fungal community composition as drivers of plant-soil feedbacks<br>File: 'Supplementary Data File Biomass raw data' contains the biomass data associated with the focal and conditioning plant species within the PSF experiment. This data was used to calculate the PSF values used in this study.File: 'Supplementary Data File Collated Information' contains all of the variables used to try and explain variability in PSFs, including information on plant traits, rhizosphere fungal communities and phylogenetic distance values.
DOI: 10.25446/oxford.28323353.v1
title: Digitised comparative word list derived from von Rosenberg's "Der Malayische Archipel: Land und Leute in Schilderungen, gesammelt während eines driessig-jährigen Aufenhaltes in den Kolonien" from 1878

description: Digitised comparative word list derived from von Rosenberg's "Der Malayische Archipel: Land und Leute in Schilderungen, gesammelt während eines driessig-jährigen Aufenhaltes in den Kolonien" from 1878. The list contains words in Enggano, that are then integrated into <i>EnoLEX</i>.For future updates and versioning, see the Releases on the source GitHub repository.
DOI: 10.6084/m9.figshare.14511630.v2
title: Human-climate coupled changes in vegetation community complexity of China since the 1980s

description: Vegetation community complexity is a critical factor influencing terrestrial ecosystem stability. China, the country leading the world in vegetation greening resulting from human activities, has experienced dramatic changes in vegetation community composition during the past 30 years. However, how China’s vegetation community complexity varies spatially and temporally remains unclear. Here, we provided the datasets and codes used to investigate this issue, as published in "Human-climate coupled changes in vegetation community complexity of China since 1980s" by Su et al.
DOI: 10.6084/m9.figshare.28908959.v1
title: Supplementary Data for: Clinical and Genetic Characteristics of Adult Nonautoimmune Hypothyroidism: A Single-Institution Study

description: This file contains supplementary methods, tables, and data for the above study.
DOI: 10.17632/8z3smmw63p
title: Uppsala University Pressurized water reactor spent nuclear fuel data library

description: The data is extracted from burnup and depletion calculations with the Serpent2 code. The simulations were done with a 2D PWR fuel pin cell geometry, for both initial UO2 and MOX fuel load for a wide range of initial enrichments (IE) or initial plutonium content (IPC), discharge burnup (BU) and cooling time (CT). The fuel library contains the atomic density of 279 nuclides (fission products and actinides), the total spontaneous fission rate, total photon emission rate, activity and decay heat at 789,406 different BU, CT, IE configurations for UO2 fuel and at 531,991 different BU, CT, IPC configurations for MOX fuel. The fuel library is organized in a comma separated value file, thus its further analysis is possible and simple. The file has 288 columns and 1,321,397 rows in addition to the header row. The first column contains an index, the next 8 columns are: - 'BU' (Discharge burnup value in MWd/kgU) - 'CT' (Cooling time in days) - 'IE' (Initial enrichment for UO2 and initial plutonium content (%(Pu + Am) / Heavy metal) for MOX) - 'fuelType' (Description of the fuel type. Takes the value of ‘UOX’ or ‘MOX’ for UO2 and MOX fuel, respectively.) - 'TOT_SF' (Spontaneous fission rate in fissions per second on a per axial length basis) - 'TOT_GSRC' (Photon emission rate in photons per second on a per axial length basis) - 'TOT_A' (Activity in Becquerels on a per axial length basis) - 'TOT_H' (Decay heat in Watts on a per axial length basis) The next 279 columns contain atomic densities in [1E24/cm3] units for 279 different nuclides, each named with their respective chemical element symbol and the mass number concatenated (eg. Cs137 for Cesium-137). When applicable the metastable state is highlighted with “m” at the end of the string.
DOI: 10.6084/m9.figshare.26793190.v3
title: <b>Bridging Genomic Gaps: The Pan-Grass Syntenic Gene Set in Grass Crop Evolution</b>

description: Understanding orthologous and homeologous relationships among genes can inform our understanding of how evolution and artificial selection have shaped the genomes of related species to adapt to different niches and produce different phenotypes. The vast majority of plant genes have not been functionally characterized. High-confidence information on orthologous relationships can also increase the impact of the functional characterization in one species by ensuring this information is available to researchers studying orthologs in other species. The grasses are ecologically and economically critical plants, and many genes are conserved in syntenic blocks between species. Here we leverage that conserved gene order to create and describe the Pan-Grass Syntenic Gene Set (PGSGS), a curated database of orthologous and homeologous relationships among the genes of 17 grass species, including both major and orphan crops as well as wild grasses. As a demonstration of the utility of the PGSGS, the dynamics of chromosome structure and gene content changes after polypoidy in several grass lineages are analyzed. This dataset serves as a critical foundation for improving our understanding of genome evolution subsequent to polyploidy, as well as encouraging and enabling integration of functional genetic and functional genomic information across the grasses, the original promise of the "grasses as a single genetic system" model.
DOI: 10.6084/m9.figshare.29002073.v1
title: Aligning the Facades of Urban Buildings with Sustainable Development Goals

description: The United Nations Sustainable Development Document outlines a comprehensive framework and encourages countries to take practical steps towards achieving the Sustainable Development Goals. This study assesses adherence to sustainable development criteria by analyzing building materials used in urban façades. Previous research has used different criteria for selecting and evaluating sustainable materials, highlighting inconsistencies in material selection for comparative analyses and decision-making processes. This study aims to advance the field by identifying the most relevant criteria and options for sustainable development while introducing a new and practical approach not previously discussed in the literature. It emphasizes criteria most consistent with the fundamental principles of sustainable development – environmental protection, social equity, and economic sustainability. The selected criteria were prioritized based on a survey of civil engineers, and professional perspectives were considered. Subsequently, the materials used in the façade were ranked using multi-criteria decision-making techniques, specifically the Weighted Sum Product Assessment (WASPAS) method. This method combines the advantages of the Weighted Sum Model (WSM) and the Weighted Product Model (WPM) and provides a complete evaluation of weighted criteria for objective rankings. The WASPAS method is well-suited to the objectives of this study due to its practicality and the lack of specialized software. The results of pairwise comparisons showed that three criteria are critical in the evaluation: acoustic comfort (26%), thermal comfort (22%), and implementation cost (20%). These results indicate the importance of choosing building materials with lower molecular density, as this significantly reduces the transmission coefficient, which is a crucial factor in increasing comfort and energy efficiency in urban buildings. As a result, the materials were ranked as follows: Wood, Brick, Double-Glazed Glass, Cement Boards, Stone, and Aluminum. This ranking represents a move away from conventional choices commonly seen in urban façades towards more sustainable alternatives. By providing a solid framework based on the WASPAS methodology, this study provides valuable insights for project managers, architects, and engineers, promoting sustainable construction practices through careful material selection and emphasizing the importance of the assessed criteria. Ultimately, it contributes to the development of a more sustainable urban environment and contributes to the global mission for responsible and environmentally friendly construction practices.
DOI: 10.6084/m9.figshare.21085486.v2
title: Dataset_for_"Sustainable pest control inspired by prey–predator ultrasound interactions".xlsx

description: This is dataset for all the figures in " Sustainable pest control inspired by prey–predator ultrasound interactions " by Ryo Nakano, Akio Ito and Susumu Tokumaru.
DOI: 10.6084/m9.figshare.25534558.v1
title: The role of demographic traits in explaining the ability of alien tree species to invade subtropical forests

description: Annotated R-NIMBLE script to fit our Bayesian multispecies models to the forest census data from Northern Argentina, and outputs derived from the model. Descriptions of each file:R-NIMBLE-BayesianMultispeciesModel.R: R-NIMBLE code for fitting the Bayesian multispecies model to the tree data from chronosequence permanent plots in Yungas (Argentina).Powelletal-PosteriorEstimatesVitalRates.csv: Posterior estimates of the mean probability of survival, mean recruitment rates, and mean growth rates for 25 species in Northern Argentina. Estimates include mean, standad error, lower 95% credible intervals (‘lowqt_’), and upper 95% credible interval (‘uppqt_)Powelletal-PosteriorCoefficientEstimates.csv: Posterior coefficient estimates obtained from our multispecies model.<br>
DOI: 10.6084/m9.figshare.28787726.v1
title: <b>Facilitation-suppression transitions of plant functional diversity along the density gradient of a native </b><b>poisonous </b><b>plant in degraded alpine grasslands</b>

description: This dataset accompanies the manuscript entitled <i>"Trait-mediated facilitation–suppression dynamics of a native toxic plant in degraded alpine grasslands"</i>, submitted to <i>Functional Ecology</i>. The study explores how the density-dependent expansion of <i>Ligularia virgaurea</i> influences plant community diversity, soil properties, and functional trait structure across alpine grasslands on the Qinghai–Tibet Plateau.
DOI: 10.17632/4pk7zxgshf
title: 68Ga-PSMA and 68Ga-DOTA-RM2 PET/MRI in Recurrent Prostate Cancer: Diagnostic Performance and Association with Clinical and Histopathological Data

description: Raw data to reprlicate the analyses conducted in "68Ga-PSMA and 68Ga-DOTA-RM2 PET/MRI in Recurrent Prostate Cancer: Diagnostic Performance and Association with Clinical and Histopathological Data"
DOI: 10.6084/m9.figshare.25451869.v1
title: Dataset of images of formulations

description: The images are used as part of the formulations dataset analysis and can be used to build classifiers of stability, for example.
DOI: 10.6084/m9.figshare.8259953.v1
title: Post-harvest physicochemical profile and bioactive compounds of 19 bananas and plantains genotypes

description: ABSTRACT Nineteen genotypes of bananas and plantains were analysed in order to differentiate the subgroups and/or groups of consumption or industrial use. Genotypes of banana and plantain from different genomic groups and in three ripening stages (2, 5 and 7) were studied in relation to physical and physicochemical characteristics, including bioactive compounds. Furthermore, with the obtained data analysed by multivariate statistical analyses (Principal Component Analysis) it was possible to relate all analysed characteristic profile of samples with the different genotype. The three ripening stages were differentiate by total soluble solids, titratable acidity, chrome (C*) and the carotenoids contents. ‘Ney Poovan’ contain high total soluble solid content and pulp-to-peel ratio, an interesting result for the promotion of this genotype for in natura consumption. ‘Ney Poovan’, ‘Ouro da Mata’, ‘Pelipita’ and ‘Tiparot’ are sources of antioxidant compounds. The genotypes ‘Pelipita’ and ‘Samurá B’ are promising for the industrial use, mainly for the processing of banana chips, for both green and ripe fruit.
DOI: 10.17632/3g4w8f9vdk
title: Efficient algorithm for representations of U(3) in U(N)

description: An efficient algorithm for enumerating representations of U(3) that occur in a representation of the unitary group U(N) is introduced. The algorithm is applicable to U(N) representations associated with a system of identical fermions (protons, neutrons, electrons, etc.) distributed among the $N=(\eta+1)(\eta+2)/2$ degenerate eigenstates of the $\eta$th level of the three-dimensional harmonic oscillator. A C++ implementation of the algorithm is provided and its performance is evaluated. The implementation can employ OpenMP threading for use in parallel applications.
DOI: 10.17632/zjmcrjcx8p
title: Weighing geophysical data with trans-dimensional algorithms: An earthquake location case study

description: THIS REPOSITORY CONTAINS THE SOURCE CODE for publication: AUTHORS: Piana Agostinetti, N., A. Malinverno, T. Bodin, C. Dahner, S. Dineva and E. Kissling TITLE: Weighing geophysical data with trans-dimensional algorithms: An earthquake location case study JOURNAL: Geophysical Research Letters YEAR: 2023 The repository contains a FORTRAN source code which implements the algorithm presented in the publication, namely the trans-dimensional sampling of the Data Space for the location of a seismic event. All innovation, formulas and details are given in the publication. The code can be used to reproduce all the results obtained in the paper, for one of the real-world cases presented in the manuscript, the "blast" event, i. e. a man-made controlled explosion occurred in a well-known position of a mine (for which the data and all necessary information are given).
DOI: 10.6084/m9.figshare.14046385.v1
title: Vitamin D status, vitamin D intake, and sunlight exposure in adults adhering or not to periodic religious fasting for decades

description: We investigated whether periodic abstinence from foods of animal origin and a conservative lifestyle, with reduced sunlight exposure, affect vitamin D status. In a cross-sectional design, we measured the serum 25-hydroxyvitamin D concentration and assessed dietary vitamin D intake and sunlight exposure in 200 adults adhering to religious fasting for decades and in 200 non-fasters, with no differences between groups in bone mineral density. Fasters showed lower 25-hydroxyvitamin D concentration than non-fasters in winter and spring. Vitamin D intake and some indices of sunlight exposure (including two related to winter and spring) were lower in fasters, and 378 of the 400 participants exhibited vitamin D insufficiency or deficiency. In conclusion, individuals following a religious lifestyle had lower vitamin D intake, sunlight exposure and, at times, serum 25-hydroxyvitamin D concentration than controls, although these differences did not impact bone health.
DOI: 10.6084/m9.figshare.22691425.v2
title: Untitled Item

description: The MIDOG++ dataset represents an extension of the data set used in the MIDOG 2021 and 2022 challenges. We provide region of interest images from 503 histological specimens of seven different tumor types with variable morphology: breast carcinoma, lung carcinoma, lymphosarcoma, neuroendocrine tumor, cutaneous mast cell tumor, cutaneous melanoma, and (sub)cutaneous soft tissue sarcoma. The human and canine samples were processed and stained at different human and veterinary pathology laboratories with standard H&E dye and digitized with different digital whole slide image scanners. We provide labels for 11,937 mitotic figures that have been differentiated against 14,351 imposter cells in a blinded consensus by two pathologists and a final decision by a third pathologist for disagreed labels.
DOI: 10.6084/m9.figshare.23607669.v1
title: patient53.rar

description: A Patient with fundus images that taken by Ret-cam.
DOI: 10.17632/hy9ykhsj3y
title: An observational study of abrocitinib in adults with moderate-to-severe atopic dermatitis after switching from dupilumab.  Mendeley Supplements.

description: 1. Supplemental Materials including:
    Supplementary Figure 1: Flow diagram of study;
    Supplementary Figure 2: Numbers of AD patients achieving EASI 25/50/75 at week 2, 4, 8 and week 12.
    Supplementary Figure 3: Numbers of AD patients achieving SCORAD 25/50/75 at week 2, 4, 8 and week 12.
    Supplementary Figure 4: Clinical photographs and the EASI score of two typical patients during the follow-up. 
    Supplemental Table 1: Demographic and clinical characteristics of 16 patients.
    Supplemental Table 2: Laboratory parameters before and during abrocitinib treatment.
2.Supplemental Methods
DOI: 10.17632/mhghzmyvrn
title: Data for: Reply to “Comments on Density, viscosity, surface tension and intermolecular interaction of triethylene glycol and 1,2-diaminopropane binary solution & its potential downstream usage for bioplastic production”

description: These data were available as supplementary materials to the short communication entitiled "Reply to “Comments on Density, viscosity, surface tension and intermolecular interaction of triethylene glycol and 1,2-diaminopropane binary solution & its potential downstream usage for bioplastic production”. These data were used to replace the Table S4 and Table S5 that found incorrect in the original published paper entitled " Density, viscosity, surface tension and intermolecular interaction of triethylene glycol and 1,2-diaminopropane binary solution & its potential downstream usage for bioplastic production".
DOI: 10.17632/x6xr4vptn6
title: research data for H isotope fractionation at high P-T conditions

description: Raw data for all figures in the manuscript by Gao and Liu to be published by Geochimica et Cosmochimica Acta as "Path-integral molecular dynamics predictions of H isotope fractionation between brucite and water at elevated temperatures and pressures".
DOI: 10.6084/m9.figshare.13502001.v1
title: Hamamelis virginiana reference genome and annotation

description: This project contains the <i>Hamamelis virginiana</i> reference genome and annotation (GFF) associated with the publication "A novel family of secreted insect proteins linked to plant gall development" by Korgaonkar <i>et al.</i> (2021).<br>Please contact Clair Han at hanc@janelia.hhmi.org with questions. <br>
DOI: 10.6084/m9.figshare.14068106.v5
title: Vocalization of marine mammals

description: Audio files, spectrograms images and details of experimental protocols used in the paper "On the Importance of Passive Acoustic Monitoring Filters".The audio files were collected from the website Watkins Marine Mammal Sound Database, Woods Hole Oceanographic Institution.
DOI: 10.6084/m9.figshare.9092045.v3
title: Autoencoder trained on transcriptomic signals

description: (A) Microarray normalised gene expression data used in reverse training to define the disease modules: MicroarrayDataForDiseaseGene.zip<br><br>(B) 3 layer with 512 nodes in first, second and third layer deep autoencoder trained on the 20K microarray data samples: MicroarrayDeep512_512_512_AE20K.h5<br>(C) 3 layer with 256 nodes in first, second and third layer deep autoencoder trained on the 20K microarray data samples: MicroarrayDeep256_256_256_AE20K.h5<br>(D) 3 layer with 1024 nodes in first, second and third layer deep autoencoder trained on the 20K microarray data samples: MicroarrayDeep1024_1024_1024_AE20K.h5<br>(E) 1 layer shallow autoencoder trained on the 20K microarray data samples: MicroarrayShallow512AE20K.h5<br>(F) 3 layer sparsified deep autoencoder trained on the 20K micro-array data samples: MicroarrayDeep512_512_512_AE_Regularised20K.h5<br>(G) 3 layer denoised deep autoencoder trained on 20K micro-array data samples: MicroarrayDeep512_512_512_AE_Denoised20K.h5<br>(H) 5 layer funnel shaped deep autoencoder trained on 20K microarray data samples: MicroarrayDeep512_256_128_256_512_AE20K.h5<br>(I) 3 layer funnel shaped deep autoencoder trained on 20K microarray data samples: MicroarrayDeep512_128_512_AE20K.h5<br>(J) RNA seq normalised gene expression data used in reverse training to define the disease modules: RNAseqDataForDiseaseGene.zip<br><br>(K) 3 layer deep autoencoder trained on the 50K samples: RNAseqDeep512_512_512_AE50K.h5<br><br>(L) 3 layer deep autoencoder trained on the 20K samples as a first realisation: RNAseqDeep512_512_512_AE20K1.h5<br><br>(M) 3 layer deep autoencoder trained on the 20K samples as a second realisation: RNAseqDeep512_512_512_AE20K2.h5<br><br>(N) 3 layer deep autoencoder trained on the 20K samples as a third realisation: RNAseqDeep512_512_512_AE20K3.h5
DOI: 10.6084/m9.figshare.14497947.v1
title: Liu_etal_GRL_manuscript - Re-gridded monthly model output

description: This repository contains MOM6-COBALTv2 model outputs as monthly means (1961-2010, thus 600 time steps) remapped onto a standard 1-deg grid (r360x180).