cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1627969
title: A DDB2 mutant protein unable to interact with PCNA promotes cell cycle progression of human transformed embryonic kidney cells

description: DNA damage binding protein 2 (DDB2) is a protein involved in the early step of DNA damage recognition of the nucleotide excision repair (NER) process. Recently, it has been suggested that DDB2 may play a role in DNA replication, based on its ability to promote cell proliferation. We have previously shown that DDB2 binds PCNA during NER, but also in the absence of DNA damage; however, whether and how this interaction influences cell proliferation is not known. In this study, we have addressed this question by using HEK293 cell clones stably expressing DDB2<sup>Wt</sup> protein, or a mutant form (DDB2<sup>Mut</sup>) unable to interact with PCNA. We report that overexpression of the DDB2<sup>Mut</sup> protein provides a proliferative advantage over the wild type form, by influencing cell cycle progression. In particular, an increase in the number of S-phase cells, together with a reduction in p21<sup>CDKN1A</sup> protein level, and a shorter cell cycle length, has been observed in the DDB2<sup>Mut</sup> cells. These results suggest that DDB2 influences cell cycle progression thanks to its interaction with PCNA.
DOI: 10.6084/m9.figshare.19723405.v1
title: pastclim_beyer2020_v1.0.0

description: Climate reconstructions for the last 120k years from Beyer et al 2020, with icesheets and internal seas masked. To be used in pastclim.
DOI: 10.17632/9x7wn24rrp
title: Water-Energy-Food-Land-Climate Nexus data for the Case Study of Greece: National and River Basin District Scale

description: Complexity science methods applied for policies provide a means of exploring the effects of various types of spatial and temporal drivers and constraints on the behaviour of society and helps scenario-forming and the development of sound policies through stakeholder consultations. In the context of policy-making following a five-component Nexus approach that includes Water, Energy, Food, Land Use and Climate, System Dynamics Modelling is used for the holistic approach, since it presents various advantages, such as integrating different model outputs and handling system complexity via a building-block approach. To this end, the Nexus System Dynamics Model (Nexus_SDM) that establishes and quantifies the interlinkages among all five Nexus components for the national case study of Greece has been built in STELLA Professional (ISEE Systems--https://www.iseesystems.com/store/products/stella-professional.aspx). The methodology of data mapping and linking Nexus components in a complex system is followed, while outputs from thematic models are integrated producing an extensive multi-sectorial data set for the year 2010 that includes an exhaustive list of Water and Energy demands, Agricultural production and resulting agricultural value for 14 different crop types and 8 different animal types and their associated products. Green House Gas emissions from all sectors are presented as well. Data originate from open databases and national sources, such as Eurostat, the Greek National Statistical Authority (ELSTAT), the Hellenic Ministry of the Environment and Climate Change, the Association of Greek Tourism Enterprises and the Independent Power Transmission Operator of Greece are collected. Additional data from thematic models E3ME (https://www.camecon.com/how/e3me-model/) and OSeMOSYS (http://www.osemosys.org/) are also integrated. Advanced disaggregation algorithms are employed in order to disaggregate annual national-scale data to fourteen River Basin Districts in Greece and 12 months of year 2010. The data are used to map and quantify all interlinkages, identifying Nexus hotspots, i.e., which Nexus dimensions strongly affect others and threaten their security and which interlinkages are relatively weak. Mapping multiple Water-Energy-Food-Land Use-Climate Nexus data, analysing and quantifying all interlinkages among its Nexus components is critical in order to assess the Nexus, prioritise expenses and set the agenda for achieving sustainability. Such data sets are necessary to make the Nexus concept operational for policymakers and stakeholders in a participatory process and it is an important step towards achieving the United Nations Sustainable Development Goals. Acknowledgements: The data presented herein have been collected and processed within the project SIM4NEXUS. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under Grant Agreement No. 689150.
DOI: 10.6084/m9.figshare.29045201.v1
title: Data of "Reproducing scattering matrix of black carbon: A comparison of the overlapping and necking models"

description: Light scattering matrix for necking model and overlapping model
DOI: 10.6084/m9.figshare.24492442.v1
title: Young and old mouse EDL muscle

description: We performed metabolomics (together with RNA-seq) to unbiasedly uncover the molecular mechanisms during aging in mouse glycolytic skeletal muscle (EDL).
DOI: 10.17632/4yvtzn7hg6
title: Cancer depends on fatty acid for ATP production: Possible link between cancer and obesity

description: Figure 4. New concept for cancer energy metabolism with FAO. (A) Glucose free condition do not change ATP level in cancer cell. Glucose free DMEM is containing 10% FBS, 1% penicillin/streptomycin and 1 mM sodium pyruvate. X axis denotes A as basal respiration and B as ATP production. Y axis denotes OCR (oxygen consumption rate) as pmol/min/cells.
(B) FAO inhibition by blocking long-chain 3-ketoacyl-CoA thiolase using trimetazidine reduces ATP production in cancer cell. Axes of X and Y denote the same as above. 

Supplementary Figure 1. Oxygen consumption rate (OCR) of cancer cells were performed  using the Seahorse XFe96 Analyzer. (A) OCR in response to normal medium or glucose free medium was measured by the Seahorse XFe96 analyzer. (B) OCR in response to using 5mM trimetazidine as a FAO inhibitor.
DOI: 10.17632/rwgsysdbgz
title: Data-set_ID_2287

description: Data set corresponding to the original study with women in the first trimester of pregnancy. Characterization of both the serological analysis and the exposure to risk factors for T.gondii infection.
DOI: 10.17632/zbdgtt8mmt
title: To fix or not to fix, the Fix: Reassessing the effectiveness of the 4pm Fix. A pre-registered study

description: R code scripts
DOI: 10.6084/m9.figshare.12654728.v1
title: Tabula Muris Senis Data Objects

description: Official data release for Tabula Muris Senis
DOI: 10.17632/fvf2sw6z23
title: A benchmark dataset for the retail multiskilled personnel planning under uncertain demand

description: This dataset is related with the Data in Brief article entitled: “A benchmark dataset for the retail multiskilled personnel planning under uncertain demand”, which was submitted to Data in Brief Journal. This data article describes datasets from a home improvement retail store located in Santiago, Chile. The datasets have been developed to solve a multiskilled personnel assignment problem (MPAP) under uncertain demand. Particularly, this database is related to the published article "Multiskilled personnel assignment problem under uncertain demand: A benchmarking analysis" developed by Henao et al. (2022).

The datasets contain real and simulated data. Regarding the real dataset, it includes information about the store size, number of employees, employment-contract characteristics, mean value of weekly hours demand in each department, and cost parameters. Regarding the simulated datasets, they include information about the random parameter of weekly hours demand in each store department. The simulated data are presented in 18 text files classified by: (i) Sample type (in-sample or out-of-sample). (ii) Truncation-type method (zero-truncated or percentile-truncated). (iii) Coefficient of variation (5, 10, 20, 30, 40, 50%).
DOI: 10.6084/m9.figshare.28483838.v2
title: SAFER study_audit case notes

description: It is easy to overlook risk factors that require specific healthcare actions. This is particularly true in maternity care, which deals with a natural process where risk might be distinguished from normality at many points in the care pathway. Our study describes the effects of clinical decision support, first in the form of paper checklists and then in the form of an electronic checklist to screen for risks of (1) venous thromboembolism (VTE), (2) intrauterine growth restriction (IUGR), (3) high body mass index (BMI), and (4) gestational diabetes mellitus (GDM). Here, we track the effects of different screening algorithms introduced on different media (paper versus computer).
DOI: 10.6084/m9.figshare.11661696.v1
title: Data used to estimate animal abundance from Cunningham et al (2020) Ecology Letters

description: This data accompanies our 2020 publication in <i>Ecology Letters</i> titled, "<i>A native apex predator limits an invasive mesopredator and protects native prey</i><i>: Tasmanian devils protecting bandicoots from cats.</i>"<br>If you use these datasets, please cite the paper as well as this dataset. Please see the paper for a detailed description of the data and analysis.<br><br>Estimating abundance of feral cats<br>The four files beginning with "cats" are used together to estimate the abudance of feral cats at 28 study sites. <br>"cats_capture history.csv" is the capture history of each uniquely identifiable cat at each study site. <br><br>"cats_marked unidentified.csv" shows the number of detections at each study site of cats with pellage markings that we could not confidently assign to an individual. This usually occurred due to a poor or partial photo. <br><br>"cats_unmarked black cats.csv" shows the number of detections of unmarked cats at each study site. This was usually the case for cats that were completely black in colour. <br>"cats_site covariates.csv" shows site level covariates used in the mark-resight analysis. <br><br>Estimating abundance of other species<br>We estimated the abundance of the other species using either the Royle-Nichols model or the N-mixture model. In each case, we recorded species detections for each camera in five temporal periods. These detection histories are shown in the csv files that begin with the common name of a species. We did this for seven species. <br>The file titled "siteCovariates_nMixture_RoyleNichols.csv" is the site-level covariates used for these models. <br><br>We used two time-varying covariates, one for lure age and one for date: "lureAge.csv" and "dateCovariate.csv"<br>
DOI: 10.6084/m9.figshare.5561881
title: Resolving a phylogenetic hypothesis for parrots: implications from systematics to conservation

description: Advances in sequencing technology and phylogenetics have revolutionised avian biology by providing an evolutionary framework for studying natural groupings. In the parrots (Psittaciformes), DNA-based studies have led to a reclassification of clades, yet substantial gaps remain in the data gleaned from genetic information. Here we provide an overview of published genetic data of parrots, characterise sampling depth across the phylogeny, and evaluate support for existing systematic treatments. We inferred a concatenated tree with 307 species from a 30-gene supermatrix. We recovered well-supported relationships among recently proposed clades. Taxonomic groups were more stable towards the base of the tree and increased sampling will be required to clarify relationships at the tips, particularly below the generic level. Only a third of species have been sampled intraspecifically in population genetic or phylogeographic surveys. Intraspecific sampling has not been geographically or phylogenetically even across Psittaciformes, especially poor in the cockatoos, Southeast Asia, and parts of Australo-Papua. Threatened species are poorly sampled in the Neotropics. We highlight where effort should be focused to improve sampling based on geography and conservation status. In sum, phylogenetic relationships among the major parrot clades are robust, but relationships within and between genera and species provide opportunities for future investigations.
DOI: 10.17632/mt46trxrsk
title: JETSPIN: A specific-purpose open-source software for simulations of nanofiber electrospinning

description: Abstract We present the open-source computer program JETSPIN, specifically designed to simulate the electrospinning process of nanofibers. Its capabilities are shown with proper reference to the underlying model, as well as a description of the relevant input variables and associated test-case simulations. The various interactions included in the electrospinning model implemented in JETSPIN are discussed in detail. The code is designed to exploit different computational architectures, from single to p... Title of program: JETSPIN Catalogue Id: AEXQ_v1_0 Nature of problem Dynamics of the electrospinning process to produce nanofibers Versions of this program held in the CPC repository in Mendeley Data AEXQ_v1_0; JETSPIN; 10.1016/j.cpc.2015.08.013 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.6084/m9.figshare.24001938.v1
title: Wood anatomical traits_TDF_means

description: Wood anatomical trais of six tree species from the mexican tropical dry forest
DOI: 10.6084/m9.figshare.29073710.v1
title: Hisano et al. "<b>Datasets of bird species composition in a land reclamation area of Lake Kahokugata, central Japan, in relation to farmland types</b>"

description: Datasets and data keys for Hisano et al. "<b>Datasets of bird species composition in a land reclamation area of Lake Kahokugata, central Japan, in relation to farmland types</b>".“<b>all_data.</b><b>csv</b>”: a bird assemblage dataset, including individuals flying over a plot“<b>ground_data.csv</b>”: a bird assemblage dataset, excluding individuals flying over a plot, only including those observed on the ground or perching on the trees/electric wires, confirming that they utilised the habitat.<b>Data keys</b>: definitions of the columns and units<b>Observed species</b> include:SpeciesCommon name<i>Buteo japonicus</i><i>Eastern buzzard</i><i>Circus spilonotus</i><i>Eastern marsh harrier</i><i>Milvus migrans</i><i>Black kite</i><i>Anas platyrhynchos</i><i>Mallard</i><i>Anas poecilorhyncha</i><i>Spot-billed duck</i><i>Charadrius dubius</i><i>Little ringed plover</i><i>Vanellus cinereus</i><i>Grey-headed lapwing</i><i>Vanellus vanellus</i><i>Northern lapwing</i><i>Gallinago gallinago</i><i>Common snipe</i><i>Ciconia ciconia</i><i>White stork</i><i>Streptopelia orientalis</i><i>Oriental turtle dove</i><i>Columba livia domestica</i><i>Rock dove</i><i>Cuculus canorus</i><i>Common cuckoo</i><i>Phasianus colchicus</i><i>Green pheasant</i><i>Gallinula chloropus</i><i>Common moorhen</i><i>Acrocephalus arundinaceus</i><i>Great reed warbler</i><i>Alauda arvensis</i><i>Eurasian skylark</i><i>Cettia diphone</i><i>Japanese bush warbler</i><i>Corvus corone</i><i>Carrion crow</i><i>Corvus macrorhynchos</i><i>Large-billed crow</i><i>Cyanopica cyanus</i><i>Azure-winged magpie</i><i>Emberiza citrinella</i><i>Meadow bunting</i><i>Emberiza fucata</i><i>Chestnut-eared bunting</i><i>Emberiza rustica</i><i>Rustic bunting</i><i>Chloris sinica</i><i>Oriental greenfinch</i><i>Carpodacus sibiricus</i><i>Long-tailed rosefinch</i><i>Hirundo rustica</i><i>Barn swallow</i><i>Lanius bucephalus</i><i>Bull-headed shrike</i><i>Motacilla alba</i><i>White wagtail</i><i>Motacilla grandis</i><i>Japanese wagtail</i><i>Parus minor</i><i>Japanese tit</i><i>Passer montanus</i><i>Eurasian tree sparrow</i><i>Hypsipetes amaurotis</i><i>Brown-eared bulbul</i><i>Sturnus cineraceus</i><i>White-cheeked starling</i><i>Sturnus vulgaris</i><i>Common starling</i><i>Turdus naumanni</i><i>Dusky thrush</i><i>Zosterops japonicus</i><i>Japanese white-eye</i><i>Ardea alba</i><i>Great egret</i><i>Ardea cinerea</i><i>Grey heron</i><i>Egretta intermedia</i><i>Intermediate egret</i><i>Dendrocopos kizuki</i><i>Japanese pygmy woodpecker</i>
DOI: 10.17632/9zr8vzzt8w
title: Questionnaire Dataset

description: Subject area: Higher Education
More specific subject area: Online learning in EFL 
Type of data: data set, table
How data was acquired: The data were generated through a structured questionnaire
Data format: Raw
Experimental factors: Samples consist of senior students of EFL class in a state university
Experimental features: Student engagement is an essential factor in online learning and represents an essential quality indicator in higher education.
Data source location: State University, Bandung, Indonesia
Data accessibility: Data is available online
DOI: 10.17632/b7f7d28ynd
title: A Python Multiscale Thermochemistry Toolbox (pMuTT) for thermochemical and kinetic parameter estimation

description: Estimating the thermochemical properties of systems is important in many fields such as material science and catalysis. The Python multiscale thermochemistry toolbox (pMuTT) is a Python software library developed to streamline the conversion of ab-initio data to thermochemical properties using statistical mechanics, to perform thermodynamic analysis, and to create input files for kinetic modeling software. Its open-source implementation in Python leverages existing scientific codes, encourages users to write scripts for their needs, and allows the code to be expanded easily. The core classes developed include a statistical mechanical model in which energy modes can be included or excluded to suit the application, empirical models for rapid thermodynamic property estimation, and a reaction model to calculate kinetic parameters or changes in thermodynamic properties. In addition, pMuTT supports other features, such as Brønsted–Evans–Polanyi (BEP) relationships, coverage effects, and ab-initio phase diagrams.
DOI: 10.6084/m9.figshare.28840766.v1
title: Stephania hainanensis genome and annotation

description: <b>Chromosome-level genome assembly of the </b><b><i>Stephania hainanensis</i></b>
DOI: 10.6084/m9.figshare.21524481.v1
title: 70 hour locomotor, feeding and drinking behavioral time series of female Japanese quail

description: Adult female quails were individually housed in 40 x 40 x 40cm (width × length × height, respectively) boxes with 3 solid white walls and one wire mesh wall that allowed visual contact with the female located in the contiguous box. Nylon monofilament line was extended over the top of the boxes with a 1 cm separation to prevent the birds from escaping without interfering with their visualization. A 14 light: 10 dark cycle was used. A video camera connected to a computer was suspended 1.5 m above the box. These cameras have built-in, infrared LED lighting, automatically switching to infrared recording after lights were turned off. Boxes had feeder, automatic nipple drinker, and floor with wood shavings. A period of at least 30 days acclimatization was taken before the actual 70 hora long recordings were performed. Locomotor activity data was obtained using ANY-maze video tracking system, at 0.5s sampling interval. Feeding and Drinking behavior was registered through visual observation of video-recording using customized software in Matlab, allowing high resolution data acquisition. Data from 2 animals are shown. Data was integrated in either 6min or 1min time intervals. <br> Analysis was presented in Kembro et al (2023) A dynamically coherent pattern of rhythms that matches between distant species across the evolutionary scale. Sci Rep. https://doi.org/10.1038/s41598-023-32286-0
DOI: 10.6084/m9.figshare.3761562.v3041
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.6084/m9.figshare.889718.v3
title: On-screen movie kill counts for hundreds of actors

description: This file contains the on-screen kill counts for roughly 200 actors. The data in this file were scraped from www.MovieBodyCounts.com and tallied according to the web site's counting guidelines: http://moviebodycounts.proboards.com/index.cgi?board=general&action=display&thread=6 All of the actors and the details of the tallies are at: http://www.moviebodycounts.com/actors.htm If you would like to update an entry in this list, please email Randy Olson at olsonran@msu.edu A blog post describing the data in more detail is linked below.
DOI: 10.17632/ky9gd9vrhn
title: Patients’ perceptions of nurse caring behaviors at referral hospitals in Ethiopia: Cross-sectional data

description: Nurse caring behaviors play a significant role in clinical practice. The extent to which patients’ feeling cared for derives from their perceptions of nurse caring behaviors. Several factors have been reported to be associated with patients’ perceptions of nurse caring behaviors. Patients’ perceptions of nurse caring behaviors were measured using the Caring Behaviors Inventory-16 Ethiopian Amharic version. This study aimed to determine patients’ perceptions of nurse caring behaviors and to identify factors associated with these perceptions. Data are presented in Stata DTA File and Microsoft Excel 97-2003 Worksheet formats.
DOI: 10.6084/m9.figshare.12581402.v1
title: Supplementary Material for: Differential Impact of Cognitive Impairment in MCI Patients: A Case-Based Report

description: Mild cognitive impairment (MCI) traditionally refers to an intermediate stage between healthy individuals and early Alzheimer disease. Evidence shows grey and white matter volume changes and decrease in several executive functions, albeit the relation between cognitive performance and brain volume remains unclear. Here, we discuss 3 individual cases of MCI by investigating their MRI scans and cognitive test performance. We also recruited age-matched healthy older adults serving as gold standard for both grey and white matter volume and cognitive test outcomes. Our results show the impact of cognitive impairment on cognitive test performance and grey and white matter volumes, and the role played by cognitive and brain reserve on mitigating cognitive decline. Furthermore, we add evidence to previous studies by showing an increase in white matter volume compared to healthy controls, in all 3 patients. This pattern of increased white matter volume might help us to better understand the pathological mechanisms underlying MCI which in turn could contribute to future investigations.