cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25452/figshare.plus.22806416.v1
title: Dataset supporting Figure 2: Phylogenomics

description: <br><b>Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Paradigms proposed to explain this variation either invoke trade-offs between performance efficiency and breadth or underlying intrinsic or extrinsic factors. We assembled genomic (1,154 yeast strains from 1,090 species), metabolic (quantitative measures of growth of 843 species in 24 conditions), and ecological (environmental ontology of 1,088 species) data from nearly all known species of the ancient fungal subphylum Saccharomycotina to examine niche breadth evolution. We found large interspecific differences in carbon breadth stem from intrinsic differences in genes encoding specific metabolic pathways but no evidence of trade-offs and a limited role of extrinsic ecological factors. These comprehensive data argue that intrinsic factors driving microbial niche breadth variation</b>.<br>This item includes raw and underlying data associated with Figure # 2 in the manuscript. Input files and results from the construction of the phylogenetic tree of the Saccharomycotina subphylum.<br>Each item contains a README.txt file that gives specific details on the analysis, file structure, and folder structure.<br><b>y1000p_1403_OG_files.tar.gz </b>- The 1403 ortho groups used to construct the phylogeny of the subphylum<b>1154yeasts_1403OGs_ml_timetree.tree</b> - Tree file containing the time tree calibrated phylogeny<b>1154yeasts_1403OGs_ml_timetree_times.txt</b> - File containing the estimated times associated with the time tree<b>1175taxa_1403OGs_iqtree_ML_rooted.nex</b> - Nexus tree file containing the rooted tree file used in Figure 2 and the supplemental tree file<b>1175taxa_1403OGs_astral_length_rooted_lpp_added.tre - </b>Tree file containing the yeast phylogeny estimated using ASTRAL<b>1000_strip*.txt </b>- iTOL (itol.com) files to identify the isolation environment of the strains. <b>itol_color_strip.txt </b> - Add colors to the tree in iTOL<b>ALL_NAMES_FILE.xlsx </b>- The names on the tree have been adjusted to reflect the most recent naming conventions (as of November 2023). This file contains the matching names across the dataset, including earlier versions of the phylogenetic trees which were used for some analyses<br><br>
DOI: 10.6084/m9.figshare.12715490.v1
title: Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome

description: <b>Abstract</b><b><br></b> <b>Background</b> Homeobox-containing genes encode crucial transcription factors in animal and plant development, and changes to these genes have been linked to the evolution of body plans and morphologies. In animals some homeobox genes are clustered in the genome, due to either coordinated gene regulation or as remnants from ancestral genomic arrangements. Analyses of homeobox gene organization across a range of species thus helps to better understand the evolution of genome organization and developmental gene control, and the possible interactions between the two. However, homeobox gene organization in several key animal ancestors, including those of molluscs, lophotrochozoans and bilaterians, remains to be fully elucidated.<br> <b>Results</b> Here, we present a high-quality chromosome-level genome assembly of <i>Magallana hongkongensis</i> (2n = 20), for which 93.2% of the genomic sequences are contained on 10 pseudomolecules (~758Mb, scaffold N50 = 72.3Mb). A total of 46,963 predicted gene models (45,308 protein coding genes) were incorporated for this genome, and genome completeness estimated by BUSCO was 94.6%. Homeobox gene linkages were analysed in detail relative to available data in other mollusc species. Our chromosome-level assembly allows the inference of ancient gene linkages (synteny) for the homeobox-containing genes, even though a number of the homeobox gene clusters, like the Hox/ParaHox clusters, are undergoing dispersal in molluscs such as this oyster. <br> <b>Conclusions</b> The analyses performed in this study and the accompanying genome sequence provide important genetic resources for this economically and culturally valuable oyster species, and offer a platform to improve understanding of animal biology and evolution more generally.<b></b><br>
DOI: 10.6084/m9.figshare.19650957.v1
title: Participants Questionnaires Results

description: The results of three questionnaires (CSAI-2, POMS, PSQI) of all participants.
DOI: 10.6084/m9.figshare.6399965.v1
title: obesity

description: obesity MRI data
DOI: 10.17632/c2h2jf5c54
title: Dataset for: Cross-country Pipeline Inspection Data Analysis and Testing of Probabilistic Degradation Models

description: The present dataset, accompanied by the scripts used to analyze the data and produce the graphics, is available to support the findings presented in "Cross-country Pipeline Inspection Data Analysis and Testing of Probabilistic Degradation Models."

The README file provides information on the data source, appended files and describes the dataset variables.
DOI: 10.17632/xf6rggrsn6
title: Eimeria tenella whole genome NGS, unsporulated oocysts and oocysts at 8 hours of sporulation

description: Unsporulated Eimeria tenella oocysts (0 hours of sporulation elapsed): 22-024020-0001_S1_L001_R_001.fasta
Eimeria tenella oocysts at 8 hours of sporulation elapsed: 22-024020-0002_S2_L001_R_001.fasta

Six additional timepoints were sequenced, see:
DOI: 10.17632/547wwd5jfr.1 (Eimeria tenella whole genome NGS, oocysts at 16 hours of sporulation and 24 hours of sporulation)
DOI: 10.17632/962ypgjnmj.1 (Eimeria tenella whole genome NGS, oocysts at 32 hours of sporulation and 64 hours of sporulation)
DOI: 10.17632/frxnm8vyys.1 (Eimeria tenella whole genome NGS, oocysts at 381 hours of sporulation and 835 hours of sporulation)

Relative abundance of each organellar genome was estimated based on the proportion of reads at each time point that mapped to the mitochondrial, apicoplast, and nuclear genomes, see: 
Kruth, P.S. (2024). Molecular Investigation of Exogenous Stages of Eimeria tenella: Expression of Fragmented Mitochondrial rDNA, Organellar Genome Dynamics, and Development of a Transcriptional Activity-Based Assay for Measuring Oocyst Viability. [Doctoral dissertation, University of Guelph, Ontario Veterinary College, Department of Pathobiology]. UofG Atrium, https://hdl.handle.net/10214/28208.
DOI: 10.6084/m9.figshare.28091360.v1
title: Expanding the chicken gut virome: Uncovering viral diversity, host interactions, and regional variations across the intestinal tract

description: This dataset contains 39,380 non-redundant viral genomes of medium quality or higher in the CGVD database.
DOI: 10.6084/m9.figshare.3526742.v1
title: Full Archive

description: Full Archive
DOI: 10.17632/8dxbm7wx5s
title: Propofol inhibition of hepatocellular carcinoma via the prevention of reactive oxygen species-induced Cav1 and HO-1 activation

description: In this study, we showed that Propofol could effectively suppressed the growth of tumor and metastasis derived from metastatic HCC cells, and the growth of HCC patient-derived xenograft. Secondly, we delineated the effect of reactive oxygenase species (ROS) in the activation of Src/caveolin-1 (Cav1). The ROS-induced Cav1 resulted in the upregulation and nuclear translocation of heme oxygenase 1 (HO-1), resulting in HCC aggressive properties. Thirdly, we demonstrated the effect of Propofol in upregulation of mitochondrial antioxidant capacity and suppression of Cav1 expression as well as HO-1 activation in HCC cells. Lastly, we showed that Propofol did not affect the growth of normal hepatocyte, and the exclusive expression of Cav1 and HO-1 in metastatic HCC cells. These findings implicate the potential to develop anti-Cav1 and anti-HO-1 reagents without adverse effects on normal hepatocytes as a new strategy for treating HCC.
DOI: 10.6084/m9.figshare.22126232.v2
title: HSymV2.0: a chromosome-level genome assembly of Hydractinia symbiolongicarpus

description: We constructed the first chromosome-level genome assembly of <em>Hydractinia symbiolongicarpus</em> (the HSymV2.0 assembly) using PacBio HiFi long-read sequencing and Hi-C scaffolding. The HSymV2.0 assembly (NCBI accession number: JARBIS000000000) is 483 Mb in total length with 15 chromosomes, which represent 99.8% of the assembly. We also provide its genome annotation with 25,959 protein-coding genes as well as cDNA/CDS/Protein sequences. Index for cellranger is also provided for single-cell RNA-seq analysis. The HSymV2.0 assembly will be an invaluable resource for the research community performing a wide range of studies with <em>H. symbiolongicarpus.</em>
DOI: 10.6084/m9.figshare.24448393.v1
title: <b>BeSound: A Novel Approach to Manipulate Proprioception and Body Awareness Using Auditory Feedback</b>

description: <b>Background: </b>Movement and physical exercise have been shown to have positive effects on human wellbeing, mental health, and neurorehabilitation. However, little is known about the factors that influence proprioception and body awareness during exercise.<br><b>Method: </b>We designed BeSound, a wearable device that provides continuous real-time auditory feedback on human gestures during exercise and dance. We tested the effects of the device on participants' ratings of bodily awareness, reward, immersion, embodiment, and self-efficacy using a within-subject design.<br><b>Results: </b>The wearable was well received by the participants and had a significant impact on the participants' ratings in all areas.<br><b>Conclusions:</b> The results suggest that auditory feedback can be used to manipulate bodily awareness during exercise and dance. Further research is needed to investigate the potential of auditory proprioceptive feedback for mental health.<br>
DOI: 10.6084/m9.figshare.5682754.v2
title: YUV input PCA dataset.

description: Each column represents a vector of 25600 elements that were obtained from the calculation of 30 PCA for the Y component 10 for the U componet and 10 for the V component ofthe YUV color matrix, to the image dataset.
DOI: 10.6084/m9.figshare.24407812.v3
title: Identified Arabidopsis secondary metabolites in extended darkness treatment

description: Table 1 Identified metabolites in the present study
DOI: 10.6084/m9.figshare.26712709.v2
title: A Global Terrestrial Precipitable Water Vapor Dataset from 2012 to 2020 Based on Microwave Radiation Imager Measurements from Three Fengyun Satellites

description: A global terrestrial precipitable water vapor (PWV) dataset has been developed using observations from the MicroWave Radiation Imager (MWRI) aboard the FY-3 satellite series (FY-3B, FY-3C and FY-3D) spanning 2012 to 2020. The dataset offers twice-daily PWV records at a spatial resolution of 0.25° × 0.25°, aligned with the ascending and descending orbits of the FY-3 satellites. The dataset was generated using an automated machine learning (ML) model that leverages MWRI-based features characterizing surface conditions and an enhanced Global Position System (GPS) PWV dataset as a reference. Trained on over one million sampling points from more than ten thousand stations worldwide, the model ensures a robust representation of global PWV variations. Independent evaluations against SuomiNet GPS and Integrated Global Radiosonde Archive Version 2 (IGRA2) PWV products yielded root mean square error (RMSE) of 4.47 mm and 3.89 mm, respectively, with RMSE values ranging from 2.90 to 5.49 mm across various surface conditions. The dataset effectively captures both spatial and temporal PWV variations, allowing for precise examination of localized and abrupt changes in water vapor induced by extreme weather events. Representing a significant advancement in global terrestrial PWV monitoring, the MWRI PWV dataset provides an all-weather, high-precision data record that bridges gaps in global coverage of passive microwave-based terrestrial PWV observations. It is a valuable resource for atmospheric research, climate modeling, water cycle studies, and beyond.
DOI: 10.6084/m9.figshare.28608278.v1
title: PONE-D-24-48304.rar

description: 数据和代码
DOI: 10.17632/6cybtznx22
title: bd oxidase force field parameters

description: Amber force field parameters for E. coli cytochrome bd oxidase (PDB: 6RKO)
DOI: 10.17632/ny39z7w5wc
title: Effectiveness of quality improvement strategies for type 1 diabetes in children and adolescents: a systematic review search strategy

description: A search strategy for systematic review assessing effectiveness of quality improvement strategies in children with type 1 diabetes. The results of this review will be disseminated through peer-reviewed publication in order to inform invested partners (e.g., Paediatric Endocrinologists) on the potential of QI strategies to improve glycaemic management and other related health outcomes in children with T1D, thereby guiding best practices in the outpatient management of the disorder.
DOI: 10.6084/m9.figshare.21953795.v2
title: Data-Research on emergency material demand based on urgency and satisfaction under public health emergencies.xlsx

description: In recent years, the frequent occurrence of public health emergencies has had a significant impact on people's life. The study of emergency logistics has also attracted scholars’ attention. Therefore, matching emergency materials’ supply and demand quickly, which meets urgency and satisfaction, is the purpose of this paper. This paper used <strong>the Metabolism Grey Model (1,1) </strong>(GM (1,1)) and the material demand prediction model to predict the number of infections and material demand. Besides, we established <strong>a double objective optimization model</strong> by constructing<strong> a profit and loss matrix and a comprehensive utility perception matrix</strong>. The results show that the method is helpful in matching the optimal supply and demand decision quickly on the basis of meeting urgency and satisfaction. The method is helpful in improving the fairness of emergency material distribution, which could better protect people's livelihoods. <br> <br> The data of infected people comes from the Hebei Provincial Health Commission (2022.04.05–04.11, http://wsjkw.hebei.gov.cn/ ). <br> The voting weight of the 5 demanders on the index attribute comes from a questionnaire. <br> The voting weight of the 5 suppliers on the index attribute comes from a questionnaire. <br> The evaluation value of the index attribute by suppliers comes from a questionnaire. <br> The evaluation value of the index attribute by demanders comes from a questionnaire. <br> <br>
DOI: 10.6084/m9.figshare.23805075.v1
title: Untitled Item

description: The "Database of Densely Populated‒Informal Settlements (DPIS)" is a comprehensive repository of geospatial data and analysis results related to densely populated‒informal settlements in urban areas. This database aims to contribute to the understanding of informal housing and its implications for sustainable urban development in various regions.The dataset contains valuable information on DPISs, which are typically characterized by high population densities, dilapidated structures, and disorganized urbanization. The database includes shapefiles and associated attributes, derived through machine-learning methods and geospatial analysis.Researchers and urban planners can access and utilize this database to investigate the spatial distribution, characteristics, and dynamics of DPISs in different cities and regions. The data can be utilized for sustainable urban planning, social welfare programs, and policy-making to address the challenges posed by informal settlements and promote inclusive and resilient urban development.
DOI: 10.6084/m9.figshare.27629901.v2
title: Data from El Zamuro and Camburito

description: 3D digitisation of pre-Columbian skulls from Camburito and El Zamuro recovered by Alfredo Jahn Hartman in Lake Valencia basin in Venezuela in 1903.
DOI: 10.6084/m9.figshare.5471941.v1
title: PredictTrophicMode_Tool

description: tool for predicting trophic mode, given whole genome or transcriptome predicted protein sequences
DOI: 10.6084/m9.figshare.871529.v1
title: Refleksje na temat pracy Analiza finansowa ekonomicznej kondycji na przykładzie polskich instytucji autorstwa Isztwan M., Kozub K., Pietrusiak O., Frącala J., Kawecki D.

description: Praca ocenia artykuł studentów Uniwersytetu Ekonomicznego we Wrocławiu, którzy analizują kondycje finansową polskich instytucji. Praca oparta jest na modelu J. Zieltowa, a obiektem badań są 3 polskie instytucje: non profit, instytucji finansowej i przedsiębiorstwa.
DOI: 10.6084/m9.figshare.9927632.v3
title: Ground Star Observation Data

description: This data is the gray scale, number and apparent magnitude data of stars observed by KAI-4021 on the ground. 1. StarMap1 refers to the data when the optical axis points to point to 101.636°for the right ascension, 31.054°for the declination. 2. StarMap2 refers to the data when the optical axis points to point to 106.778°for the right ascension, 31.068°for the declination. 3. StarMap3 refers to the data when the optical axis points to point to 112.501°for the right ascension, 31.069°for the declination. 4. StarMapi.track_num refers to the number of navigation stars in the image. 5. StarMapi.Mag refers to the apparent magnitude. 6. StarMapi.win_info refers to the 8*8 gray data of each star in the image. 7. StarMapi.ID_frm refers refers to the number of each star in our catalogue.
DOI: 10.17632/nczyy8rhfk
title: Bengali Text Classification Corpora

description: The corpora are gathered through the specified research efforts and standardized by the same. The copyright policy is reserved by the originating source.
IndicNLP: https://arxiv.org/abs/2005.00085
ProthomAlo: https://www.kaggle.com/datasets/twintyone/prothomalo
OSBC: https://www.kaggle.com/datasets/ratulcse10/open-source-autonomous-bengali-corpus
BARD: https://ieeexplore.ieee.org/document/8554382 
BTCC11: https://doi.org/10.1016/j.engappai.2023.106586
DOI: 10.6084/m9.figshare.14005130.v1
title: Supplementary Files

description: Supplementary Files 1,2,3,4,8,9,10
DOI: 10.6084/m9.figshare.5427181
title: Analysis of the small non-protein-coding RNA profile of mouse spermatozoa reveals specific enrichment of piRNAs within mature spermatozoa

description: Post-testicular sperm maturation and storage within the epididymis is a key determinant of gamete quality and fertilization competence. Here we demonstrate that mouse spermatozoa possess a complex small non-protein-coding RNA (sRNA) profile, the composition of which is markedly influenced by their epididymal transit. Thus, although microRNAs (miRNAs) are highly represented in the spermatozoa of the proximal epididymis, this sRNA class is largely diminished in mature spermatozoa of the distal epididymis. Coincident with this, a substantial enrichment in Piwi-interacting RNA (piRNA) abundance in cauda spermatozoa was detected. Further, features of cauda piRNAs, including; predominantly 29–31 nts in length; preference for uracil at their 5' terminus; no adenine enrichment at piRNA nt 10, and; predominantly mapping to intergenic regions of the mouse genome, indicate that these piRNAs are generated by the PIWIL1-directed primary piRNA production pathway. Accordingly, PIWIL1 was detected via immunoblotting and mass spectrometry in epididymal spermatozoa. These data provide insight into the complexity and dynamic nature of the sRNA profile of spermatozoa and raise the intriguing prospect that piRNAs are generated <i>in situ</i> in maturing spermatozoa. Such information is of particular interest in view of the potential role for paternal sRNAs in influencing conception, embryo development and intergenerational inheritance.
DOI: 10.17632/2cnv329v9w
title: Fine Dining Choice Descrete Choice Experiment

description: A quantitative research approach–choice-based conjoint analysis–was adopted to assess consumer preferences. Data were collected from 492 respondents and attributes such as food quality, service quality, price, online reviews, ambience, location, quality of ingredients, menu style, and restaurant type were analysed. The analysis was conducted using a full-factorial discrete choice experiment (DCE) on an online platform.
DOI: 10.6084/m9.figshare.19165670.v1
title: An examination of the stochastic distribution of spatial accessibility to intensive care unit (ICU) beds during the COVID-19 pandemic: a case study of the Greater Houston area of Texas

description: This dataset and code are presented to explain a manuscript entitled "An examination of the stochastic distribution of spatial accessibility to intensive care unit (ICU) beds during the COVID-19 pandemic: a case study of the Greater Houston area of Texas", which is under review in Geographical Analysis. To run this code properly, two zip files (data and result) should be unzipped in the same directory with the other files (*.ipynb, *.py, and *.jpg).<br>
DOI: 10.6084/m9.figshare.19291166.v1
title: Infrared Colorization.zip

description: Dataset used in Browne, Deyneka, Ceccarelli, Chen, To, Tang, Vu, Baldi 'Deep Learning to Enable Color Vision in the Dark' <br>Description of the dataset:Labeled Faces in the Wild: A Database for Studying Face Recognition in Unconstrained Environments, illuminated with diffuse uniform illumination by 6 different LED wavelengths spanning the visible and near-infrared spectrum (center wavelengths: 447, 529, 604, 718, 777, 807nm)Number of samples: 200Illuminations: 447, 529, 604, 718, 777, 807 nm + merged-colour RGB imageImage size: (2056, 2464)<br><br>Photographs of each printed image under multispectral illumination were acquired using a monochromatic camera (Zeiss Axiocam 305, CarlZeiss) mounted on a dissection microscope focused on the image. To account for diminishing camera quantum efficiency in the red and infrared spectrum, each image channel was normalized to the white background of the paper upon which the images were printed. <br>The dataset was used for the development of machine learning models to predict RGB color images from individual or combinations of wavelength illuminations.<br>
DOI: 10.6084/m9.figshare.15070554.v2
title: MDA-MB-231-MATRIGEL-SERIES-1-CONTROL

description: -Triple Negative Breast Cancer (mda-mb-231) cells (transfected with GFP) were cultured in 3D matrigel scaffolds for 15 days (Time-points: 0, 2, 5, 7, 9, 12, 14 days). <br> -File format: tif, nd2<br> <br> -Number of datasets in this file: 6 <br> -Series: 1/2 <br> -References: Dimitriou, N. M., Flores-Torres, S., Kinsella, J. M., & Mitsis, G. D. (2022). Quantifying the Morphology and Mechanisms of Cancer Progression in 3D in-vitro environments: Integrating Experiments and Multiscale Models. <em>IEEE Transactions on Biomedical Engineering</em>, 1–12. https://doi.org/10.1109/TBME.2022.3216231 Dimitriou, N. M., Flores-Torres, S., Kinsella, J. M., & Mitsis, G. D. (2022). Detection and Spatiotemporal Analysis of In-vitro 3D Migratory Triple-Negative Breast Cancer Cells. <em>Annals of Biomedical Engineering</em>. https://doi.org/10.1007/s10439-022-03022-y
DOI: 10.6084/m9.figshare.16702471.v1
title: Comparative genomic and metabolomic analysis of Termitomyces sp. provides insights into the terpenome of the fungal cultivar and the characteristic odour of the fungus garden of Macrotermes natalensis termites

description: Supporting data