cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14627784.v1
title: DLS data.xlsx

description: The size distribution of the particles presents in all the collected samples from inlet and both outlets at different flow rates were determined using Dynamic Light Scattering (DLS) (Nanozetasizer, Malvern). All the collected samples were diluted to 1:250 in PBS before the measurements and the analysis were performed at 20 °C.
DOI: 10.6084/m9.figshare.22691212.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.27969279.v2
title: FES-rowing.zip

description: Kinematics, kinetics, and force data of 20 able-bodied individuals. Kinematics and joint reaction force of 1 person with spinal cord injury.
DOI: 10.6084/m9.figshare.28436789.v1
title: Supplemental Files - <b>Flight-Associated Cortisol Dynamics and Subjective Assessments of Pain and Stress in Fighter Pilots</b>

description: Purpose: Operating a high performance fifth-generation fighter jet is a potential stressor in which [KH1] [KS2] hypothalamic-pituitary-adrenal (HPA) axis dynamics may reflect the intensity of and adaptation to the stressor. The purpose of this study was to evaluate HPA axis activity in fighter pilots and explore whether indices of activity correlated with subjective indices of stress.Methods: We studied HPA axis dynamics in 20 experienced fifth-generation fighter pilots (18 men/2 women) by measuring salivary cortisol at various times from bedtime the night before a flight training to awakening the morning after the flight training. We also measured plasma ACTH and serum cortisol the day before the flight and immediately following the flight. These findings were correlated with prior pilot flight experience and subjective assessments of pain and stress.Results: Seven (35%) of the pilots demonstrated normal salivary cortisol levels at all time points despite one having a high index of pain. Lower pre-flight salivary cortisol was correlated with more flight hours in the year leading up to the flight exercise. Flight day awakening salivary cortisol was inversely correlated with pilot-reported post-flight stress. In general, there were no other major correlations suggesting a disconnect between an objective measure of stress via HPA axis dynamics and subjective indices of stress and pain.Conclusion: The acute HPA axis response in some experienced fighter pilots habituates to the stressor of flying a fighter jet during a training exercise. The experience of the pilot was a determinant of their HPA axis stress response.
DOI: 10.6084/m9.figshare.7275065.v4
title: EEG raw data set 2 (participant 19-33): Seeing the intensity of a sound-producing event can modulate the amplitude of the initial auditory evoked

description: The EEG recordings for participants 19-33 (any participants who did not meet our catch trial criterion or who had technical difficulties were excluded)<br>The trigger codes are:The onset of the 65 dB clap sound (weak clap visual) = 129<br>The onset of the 72.5 dB clap sound (weak clap visual) = 130<br>The onset of the 72.5 dB clap sound (strong clap visual) =131 <br>The onset of the 80 dB clap sound (strong clap visual) = 132<br>The onset of the 0 dB clap sound (weak clap visual) = 150 <br>The onset of the 0 dB clap sound (Strong clap visual) 151 The trigger codes are:The onset of the 65 dB clap sound (weak clap visual) = 129<br>The onset of the 72.5 dB clap sound (weak clap visual) = 130<br>The onset of the 72.5 dB clap sound (strong clap visual) =131 <br>The onset of the 80 dB clap sound (strong clap visual) = 132<br>The onset of the 0 dB clap sound (weak clap visual) = 150 <br>The onset of the 0 dB clap sound (Strong clap visual) 151
DOI: 10.6084/m9.figshare.8097998.v1
title: Persistence of Burkholderia thailandensis E264 in Lung Tissue After a Single Binge Alcohol Episode

description: The following data sets describes the major findings in "Persistence of Burkholderia thailandensis E264 in Lung Tissue After a Single Binge Alcohol Episode"
DOI: 10.6084/m9.figshare.14390408.v3
title: DataFreeze.v5_2

description: Data-freeze for Sun et al., Nat. Commun., 2021<br>Title: Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment<br>
DOI: 10.6084/m9.figshare.19536004.v1
title: Soil respiration dataset from a temperate forest (St Jones Reserve)

description: Dataset of automated measurements of soil CO<sub>2</sub> , CH<sub>4</sub> and N<sub>2</sub>O fluxes from a temperate forest. The study was conducted at the St Jones Reserve, Dover, Delaware. For more details see:<br> Petrakis, S., J. Barba, B. Bond-Lamberty, and R. Vargas. 2018. Using greenhouse gas fluxes to define soil functional types. Plant and soil 423:285–294.
DOI: 10.6084/m9.figshare.25305250.v1
title: Data from: Testing the applicability of environmental DNA metabarcoding to landscape genetics

description: Data for "<b>Testing the applicability of environmental DNA metabarcoding to landscape genetics</b>"Nakajima S. & Tsuri K. (2024) Molecular Ecology Resourceshttps://doi.org/10.1111/1755-0998.13990<br>"eDNA_hapmap.xlsx": Number of read counts for each site × haplotype from the eDNA samples."tissue_hapmap.xlsx": Number of individuals for each site × haplotype from the tissue samples."tissue_SNP.vcf": VCF file obtained by the MIG-seq method."readGDfunc.r": R code calculating genetic diversity and differentiation statistics from site × haplotype data."waterwayDistance.xlsx": Waterway distance between sampling sites.
DOI: 10.17632/2grm3z7cb6
title: Datasets for the data collection method and examples of the material flows at city level

description: Two excel files serve as the datasets for the publication “H. Gao et al., 2021. Standardized method for material flow data collection at city level, Data in Brief.” It provided the detailed instructions of how to use the standardized method to obtain the material flow data with the general data sources at city level. For the application of this method in case of 16 cities in Shandong Province, China, as well as more illustrations of the results based on these datasets of the material flows, they can be found in the publication “H. Gao, X. Tian, Y. Zhang, L. Shi, F. Shi, 2021. Evaluating circular economy performance based on ecological network analysis: A framework and application at city level. 105257. Resources, Conservation & Recycling,https://doi.org/10.1016/j.resconrec.2020.105257.”
DOI: 10.17632/3ntkg88d4d
title: Brazilian Wheat Dataset

description: The experiments were conducted at the Agriculture Experimental located south of Brazil, from May to October in 2018. The study area contains several 2.5m x 1m rectangular parcels, referred to as plots, which hold two Brazilians wheat varieties. The genotypes used were TBIO Toruk and BRS Parrudo (48 Toruk plots and 40 Parrudo plots). Variability in the growth of the crops was created for all test areas, where each one received a varying quantity of nitrogen. Different Nitrogen (N) rates were chosen to generate crop growth variability, to evaluate the response of biomass and grain yield to N availability, which we called spatial variability. The database consists of images captured by Unmanned Aerial Vehicles (UAV) and biomass manual measurements. Two different processes were used to create this dataset. In the first, we collected the biomass to make a ground-truth. This step is done manually and destructively. Shoot dry biomass was determined at three growth stages: the stage of six fully expanded leaves, referred herein as V6, three nodes, and at flowering by the collecting of plants in an area of 0.27 m² for each plot. This was done to create a temporal variability. The plants collected were oven-dried at 65ºC until constant weight and weighed. Then the value is extrapolated for kilograms/hectare (Kg/ha). That is the BIOMASS value in “RGB DATA.CSV”. The second process was to acquire the images at the height of 50m above ground using a camera coupled to a DJI Matrice 100 Quadcopter. The camera is a single channel DJI X3 Visible (RGB), with 12MB resolution and 8-bit pixel depth. For agriculture acquisition, the recommended frontal overlap should be at least 80%, and the side overlap should be at least 70%. The resulting pixel size for the RGB images is 2.14cm²/px. It was a total of 30 individual images captured by the UAV using these parameters. Post-processing of the acquired images includes georeferencing and orthomosaic generation. The result can be seen in the “Orthomosaic RGB” folder, where we have eight photos from different days. At the “Orthomosaic RGB” folder, we selected from the orthomosaic regions of interest (ROI) were manually delineated from each plot, as shown by the red dots in “example_ROI.png”. The ROIs were selected in a way that excluded pixels with soil exposed. And then, from each ROI, an average of pixels and count was performed in the 3 RGB channels. This could be seen for all images in “RGB_Data_Orthomosaic.CSV”. With different days with biomass measured, at the folder “Cut Plots RGB”, we have the output for the algorithm developed who use a manually created mask to perform the segmentation of the areas of interest, i.e., the plots. There is already the identifier (id) of each plot in this mask, so there is a difference between the mask’s colors, which can be seen in figure “cut_mask.tif”. After segmentation of 88 plots for each Biomass manual cut-off day, we obtained 264 RGB images with 158x110 pixels.
DOI: 10.17632/pgxhnytds4
title: High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant Monomorium pharaonis

description: Data accompanying the manuscript "High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant Monomorium pharaonis" in GigaScience releasing of an ant genome and transcriptome as part of the Global Ant Genomic Alliance Project (GAGA). The dataset includes fem_csd_synteny_postion.tar.gz Sequences and genomic coordinates of fem, csd, and their neighbor genes in 11 ant species.
DOI: 10.6084/m9.figshare.14036585.v4
title: Escherichia coli SAMN10819847 (single genome) dataset

description: This is a sample read set for use in ngs-preprocess, mpgap and bacannot pipelines. It is linked to the tools paper and repositories so people who install them can get a small read set to make sure the program works.<br>The files contain Illumina and ONT reads from <i>Escherichia coli</i> biosample SAMN10819847. The SRA run accessions are SRX5299443 and SRX5287344. These files do not contain the full set of reads from these run. Rather, they have been subsampled down to 30X, to create smaller files, easier to download.<br><br>These reads have not been produced by us. The study that have produced them is properly linked in the references.<br>
DOI: 10.6084/m9.figshare.24639279.v2
title: AF2.3 predictions of host-host, host-virus and virus-virus dimers from HSV-1 infected cells.

description: Intact HSV-1 infected cells were cross-linked using DSSO cross-linker at 24hpi. Cross-linked PPIs were predicted using AF2.1 and corresponding .pdb files are uploaded.
DOI: 10.17632/gzpj8ssgsv
title: Data for the manuscript entitled "Finite-size scaling for the permeability of discrete fracture networks"

description: In this repository, we store data from our work on the finite-size scaling of the permeability of discrete fracture networks.
DOI: 10.17632/jy853fhrcx
title: Data for: Measuring urban economic density

description: LSMS based data for 6 African countries combined with Landscan data to relate wage and household income to measures of economic density and city, town, and rural status. LSMS is open source. All relevant programs included
DOI: 10.17632/ptnrwb9kyk
title: Linking epitope-specific T-cell receptors to IFNγ secretion using nanovial technology

description: The files in this data repository contain the source data described in the following study:

Title: Linking epitope-specific T-cell receptors to IFNγ secretion using nanovial technology

Authors: Jet van den Dijssel, Tejas Menon, Hayley A McQuilten, Oliver Eltherington, Alexis Gonzalez, Sevana Baghdasarian, Citradewi Soemardy, Dino Di Carlo, Klaas PJM van Gisbergen, Anja ten Brinke and Carolien E van de Sandt
DOI: 10.6084/m9.figshare.14207636.v1
title: Frozen core FHI-aims data

description: Raw FHI-aims output files supporting "Accurate Frozen Core Approximation for All-Electron Density-Functional Theory" by Yu, Moussa, and Blum.
DOI: 10.6084/m9.figshare.14794173.v1
title: Code for 'Human plasma IgG1 repertoires are simple, unique, and dynamic'

description: Code used to analyze the data and generate several of the figures for the paper 'Human plasma IgG1 repertoires are simple, unique, and dynamic'.Data and code for "Human plasma IgG1 repertoires are simple, unique, and dynamic" published in Cell Systems 12, 1-13, by Albert Bondt et al.
DOI: 10.6084/m9.figshare.5234068.v12
title: American Rivers Dam Removal Database

description: American Rivers’ Dam Removal
Database includes all dam removals in the United States (of which we have been
made aware) in which a significant portion of the dam has been removed for the
full height of the dam, such that ecological function, natural river flow and
fish passage can be restored at the site. This database is revised and updated
annually with information provided by contributors across the country. The
database may be used by anyone provided that citation is given to American
Rivers and the DOI link is included.
DOI: 10.17632/fz75vr3c7t
title: Electromyography Signal Dataset for Controlling Lower Limb Prostheses

description: This dataset encompasses electromyography (EMG) signals collected from the leg muscles of six participants during three distinct movements: leg up, leg down, and leg move.
DOI: 10.17632/m425t6xtwr
title: The Z1+ package: Shortest multiple disconnected path for the analysis of entanglements in macromolecular systems

description: This paper describes and provides Z1+, the successor of the Z- and Z1-codes for topological analyses of mono- and polydisperse entangled linear polymeric systems, in the presence or absence of confining surfaces or nano-inclusions. In contrast to its predecessors, Z1+ makes use of adaptive neighbor lists, and keeps the number of temporary nodes relatively large, yielding improved performance for large system sizes. Z1+ also includes several features its predecessors lacked, including several that are advantageous for analyses of semi-crystalline systems, brushes, nano-composites, and flowing liquids. It offers a graphical user interface that can be used to run Z1+ and visualize the results, and a PPA+ option that allows Z1+ to perform a primitive path analysis more efficiently than the standard procedure (PPA option). In addition to describing Z1+'s and PPA+'s implementation and computational performance in detail, we use it to show that it yields entanglement lengths that agree quantitatively with both a recently proposed unified analytic theory for flexible and semiflexible polymer-melt entanglement and with the available experimental data for these systems. Finally we show that the associated theoretical expressions, which express reduced entanglement-related quantities in terms of the scaled Kuhn segment density Λ, need not describe results for model polymer solutions of different “chemistries”, i.e. different angular and dihedral interactions but the same Λ.
DOI: 10.17632/vc5wc8rymx
title: POEM HUMAN AND AI TRANSLATOR

description: The dataset consists of a poem originally written in Mandarin, along with its human translation and AI translation versions.
DOI: 10.17632/yh9kwncryg
title: Manuscript data set

description: Our thesis data set
DOI: 10.6084/m9.figshare.19208310.v1
title: Flower Survey

description: For each summer transect, we recorded the number of flower units per species in a 0.25m<sup>2</sup> quadrat randomly thrown every ten meters. Flowering units were defined as in Carvell et al (2007); one flower ‘unit’ was counted as a single flower or, in the case of multiflowered stems, as an umbel, head, spike or capitulum. Flowering plants were identified to species in most cases, otherwise to the family or genus.
DOI: 10.6084/m9.figshare.24249472.v1
title: Supplementary Material for: Parental experiences of neonatal care – a nationwide study on determinants of excellence

description: INTRODUCTION: Infant- and family-centered developmental care can reduce adverse outcomes in both infants and parents. Parents’ experiences of the care and staff treatment remain to be evaluated. METHODS: Parents of infants admitted to neonatal units in Sweden from July 2020 to May 2022 responded to a questionnaire with standardized questions about in-hospital care. Exposures were hospital, gestational age, length of hospital stay, unit level and bed density. The proportions of parents rating aspects of neonatal care as excellent, defined as five on a Likert scale, and the determinants of excellence were described. The results were benchmarked with ratings in adult somatic care. RESULTS: A total 4,475/13,108 (34%) parents responded. The ratings of excellent care varied by question from 65%-90%. The largest variation in excellence between neonatal units (range 43%–80%) was found for “Participation and Involvement”. The proportion of excellence was significantly lower among parents of extremely preterm infants. Confidence in the staff was lower in parents of extremely preterm than in parents of term infants (56% vs 83%). Longer hospital stay affected the experience of neonatal care adversely, whereas level of care and bed density were overall unrelated to the parental experience. Parents in neonatal care rated the care as excellent to a higher extent than patients cared for in adult medicine. CONCLUSION/DISCUSSION: A majority of parents rated neonatal care in Sweden as excellent. The less frequent ratings of excellence among parents of extremely preterm infants indicate that more could be done to optimize parental involvement and support.
DOI: 10.6084/m9.figshare.28374878.v2
title: NeuRGI-OntoVAE

description: The dataset was used in OntoVAE of NeuRGI pipeline.
DOI: 10.6084/m9.figshare.28930874.v1
title: xTB_dataset (with log files)

description: xTB dataset containing 23327 reactions.In the csv file of this dataset:<br>- The ID code of the reaction that enables to group together the reactions with the same reactants<br>- The R number of the reaction<br>- The fully mapped smiles code of the reaction<br>- The activation free energy of the reaction (G(TS) = G(TS) - G(monomer 1) - G(monomer 2))<br>- The reaction free energy (DrG = G(product) - G(monomer 1) - G(monomer 2))- All the energies are given in kcal/mol and were calculated at the xTB level.In each reaction subdirectory:<br>- Geometry of the monomers- Geometry of the pre-reactive complex<br>- Geometry and log file of the transition state- Geometry and log file of the product
DOI: 10.6084/m9.figshare.7908473.v1
title: gVCF_NA19009

description: 1000 Genomes gVCF mapped to hs37d5 for NA19009. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.17632/rf6wscfvhw
title: Ex vivo therapeutic base and prime editing using chemically derived hepatic progenitors in a mouse model of tyrosinemia type 1. Kim et al.

description: Bipotent differentiation capacity of HT1-mCdHs. (A) Gene expression levels of mature hepatocyte-specific markers determined by RT-qPCR. Gapdh was used as an internal control. Data are mean ± SD (n=9). Data were analyzed by the t test, *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001. (B) Activated gene sets in HT1-mCdH-Heps as generated by GSEA using liver-specific (left) and hepatocyte-specific (right) genes. NES reflects the degree of over-representation for each group at the peak of the entire set. Statistical significance was calculated by nominal p value of the NES by using an empirical phenotype-based permutation test. (C) Blue-Pink O' Gram displaying differentially expressed liver-specific genes in HT1-mCdHs and HT1-mCdH-Heps. (D) Bright-field image of HT1-mCdH-Chols, which have been cultured under conditions to induce cholangiocytic differentiation. Scale bars, 100 μm. (E) Gene expression levels of cholangiocyte-specific markers in HT1-mCdH-Chols measured by RT-qPCR. Gapdh was used as an internal control. Data are mean ± SD (n=9). Data were analyzed by the t test, *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001.
DOI: 10.6084/m9.figshare.1558313.v1
title: Ecology Field Study - Grassland, Dataset #2

description: The group divided in half (between working on transects and quadrads). This was the first field assignment we conducted. This occured at the grassland area on York University's Keele Campus. Using transects, we ventured into the grassy terrain, laid out the transect, and measured from the starting point of a particular plant species. Along the transect, we stopped to record measurements of flowers leaves, and how crowded the target plants were (on a scale of 0-3). Measurements were taken using a second transect, and were recorded in chart form. The study site was a relatively dense grassland containing varied grass and flower species.
DOI: 10.6084/m9.figshare.24203859.v1
title: Data for "Periodicity in the Deccan volcanism modulated by plume perturbations at the mid-mantle transition zone"

description: Matlab and Excel data files for "Periodicity in the Deccan volcanism modulated by plume perturbations at the mid-mantle transition zone".
DOI: 10.6084/m9.figshare.7320836.v1
title: Additional file 13: of Annual Dialysis Data Report 2016, JSDT Renal Data Registry

description: Table S13. Incident dialysis patient distribution, by primary disease, 1983â 2016. (XLSX 16Â kb)
DOI: 10.17632/hnwmh8zkw4
title: A dataset on environmental DNA from an emerging periglacial lagoon in Svalbard, Arctic

description: The datasets described in this article are of prokaryotic and eukaryotic communities identified from eDNA extracted from water and sediments at periglacial lagoon in the Eidembukta Bay, situated in the western part of central Svalbard. This newly formed water body constitutes a new ecosystem, composed of elements likely originating from the melting glacier, nearby tundra water bodies, and the sea. 
eDNA metabarcoding by amplification and sequencing 18S rRNA and 16S rRNA gene fragments was employed at 8 sampling sites, representing different parts of the lagoon. In deeper sites samples were taken from upper and lower layers of water and represents different depths of the lagoon. Samples were collected during August 2022.
This data can be used for providing a description of the biodiversity structure of the emerging lagoon ecosystem as well as for comparison of the different parts and different depths of the lagoon. 
Data is presented in following files:
1. eDNA_sample_data.csv – information about samples: amplicon Id, sample name, marker, sample depth, water layer, geographical coordinates
2. eDNA_metabarcoding_data – each sample has two fastaq files, indicating forward (R1) and reverse (R2) reads. 

The study was performed in framework of the EIDEMBUKTA project (“Formation of a novel coastal lagoon ecosystem following glacier retreat in Eidembukta, Svalbard Arctic“), funded by the Research Council of Lithuania (agreement number S-MIP-22-48) with logistical and technical support from the Institute of Oceanology of Polish Academy of Sciences.