cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28528298.v1
title: Myo et al. Raw Data for Graphs.xlsx

description: Myo et al. Supplemental Materials.pdf from Myo et al., Protocol For Differentiating Primary Human Small Airway Epithelial Cells at the Air-liquid Interface. Am J Physiol: Lung Cell Mol Physiol. 2025.The air-liquid interface (ALI) culture is an important tool in pulmonary research as it models the physiological lung where the epithelium is apically exposed to air and basally to the endothelium and interstitium. While there is an abundance of research that employs primary human bronchial epithelial cells (HBECs) to study larger airways, small airway epithelial cells (SAECs) are an untapped resource in comparison. Primary SAECs are a valuable cell population as they enable the study of pathologies in the bronchioles and are also a favorable surrogate for primary alveolar epithelial cells which are invasive to collect from patients. Currently, there are limited resources on how to culture and differentiate SAECs at the ALI. Here, we provide an optimized detailed protocol to address this knowledge gap. Key culture conditions that determine the quality and uniformity of differentiated SAECs include cell passage number, pH changes caused by media exhaustion and incubator CO2, seeding density and collagen coating of the expansion flask and inserts. We also describe a FITC-dextran permeability assay to measure SAEC barrier integrity both as a pre-test to select uniform wells with strong barrier integrity before an experiment and as a post-test to evaluate treatment effects afterwards. The utility of the differentiated SAEC ALI model to ask biologically relevant questions is demonstrated by increased cytokine (IL-8, MIF, CXCL-10) production and/or epithelial damage following exposure to cigarette smoke, lipopolysaccharide (LPS) or poly(I:C).<br>
DOI: 10.6084/m9.figshare.12594638.v1
title: Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated

description: The archive contains the simulated data used in Barba-Montoya et al. 2020. Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated. <i>Bioinformatics.</i>
DOI: 10.6084/m9.figshare.22041257.v1
title: Alignment S1, Roary – E. chengduensis core-gene alignment

description: For this core-gene alignment, all <em>Enterobacter</em> references from Feng Y. <em>et al.</em> were used in addition to<em> E. chengduensis </em>isolates. <br> <br> Feng Y, Hu Y, Zong Z. Reexamining the Association of AmpC variants with Enterobacter species in the context of updated taxonomy. Antimicrob Agents Chemother. 2021;65(12):e0159621. https://doi.org/10.1128/AAC.01596-21.
DOI: 10.6084/m9.figshare.24999164.v2
title: Navas-Olive, Rubio, et al. (2023). Figure 4 - data

description: <b>Figure 4. Comparison between best performing ML models. a)</b> F1 against threshold from the 10-best models of each architecture as evaluated in the test set, and the 10-best filters of all possible parametric combinations. Each line represents the performance of one trained model, colored by its maximal F1 (mean from all sessions is plotted in dark color). <b>b)</b> F1-scores for the best model of panel A, and ensemble model of panel e). Thresholds used are: 0.4 for XGBoost, 0.5 for SVM, 0.4 for LSTM, 0.1 for CNN2D, 0.5 for CNN1D, 4.5SD for Filter. <b>c)</b> Stability index for the same models as in panel b) (bottom), and the stability index vs the F1 (top). <b>d)</b> Similarity between predicted events of different architectures. Models are the same as in panels b)-c). To measure the similarity, the mean F1 across test sessions have been computed, using detected events in the y-axis as detections, and detected events in the x-axis as ground truth. Note the similarity between LSTM and 1D-CNN (white *), and that by XGBoost against SVM, LSTM and 1D-CNN (white +).<b> e)</b> Ensemble model, trained using the output of the best models of the machine learning architectures. Weights were: w1=-0.11 (XGBOOST); w2=-1.56 (SVM); w3=5.33 (LSTM); w4= 2.03 (2D-CNN); w5= 4.07 (1D-CNN); bias= -4.97. On the right, mean F1 score (line) ±95% confidence interval (shadow) for test sessions. Maximum F1-score and stability index for test sessions has been included in panels b) and c) to facilitate comparison with the rest of the methods.
DOI: 10.6084/m9.figshare.28451804.v1
title: dataset-D0-D5-D6

description: A basic bottleneck dataset and recombination datasets.
DOI: 10.6084/m9.figshare.c.3643793_d23.v1
title: Additional file 2: Table S1. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

description: Rice gene expression data sets. (XLSX 70Â kb) (XLSX 66Â kb)
DOI: 10.6084/m9.figshare.20171240.v1
title: driving force

description: As a result of accelerated urbanization, urban fringe areas have become spaces where urban construction conflicts are more prominent. Delineating urban fringe areas and studying the driving forces of their evolution can help optimize resource allocation using spatial planning, improving spatial governance of urban and rural fringes. This paper draws from three time periods of Wuhan land use data from 2000, 2010 and 2020, using moving t-Test，impervious surface ratio and other methods to determine the scope of Wuhan urban fringe areas, and analyze their spatial evolution process. Fifteen driving factors, such as elevation, whether it is within the master plan scope, and distance to the main urban road were brought into a binary logistic model for regression analysis. The results show that from 2000 to 2010, the urban core area and the urban fringe area expanded outward, penetrating the rural hinterland. The urban master plan and transportation facilities play a significant role in enabling the transformation of urban fringe areas to urban core areas and rural hinterlands to urban fringe areas.
DOI: 10.6084/m9.figshare.26564140.v2
title: Global surface ocean fCO2 from CSIR-ML6 (v2024)

description: The CSIR-ML6-v2024 is an update to the original CSIR-ML6 method by Gregor et al. (2019), extending the CO2 data product until 2023-12-15. The following changes have been made:SOCAT-v2024 is used;ERA5 reanalysis wind data and mean sea level pressure (MSLP) are used (instead of ERA-interim);The gas-exchange coefficient (kw) used, is appropriately scaled for the ERA5 wind product as recommended by Fay and Gregor et al. (2021);fCO2, the sea surface fugacity of CO2 is reported as per the Global Carbon Budget recommendation instead of pCO2, the sea surface partial pressure of CO2.<br><b>NETCDF FILE:</b>The dataset is stored in a single netCDF file and it mainly contains the following data variables:sfco2 = surface fugacity of CO2 for the ensemble average (in µatm). Therefgco2 = air-sea CO2 fluxes (in mol m-2 yr-1)area = the ocean area per pixel (in m2) - doubles as mask for the data<br><b>CITATION</b>Please cite the dataset as Djeutchouang et al. (2024), see the DOI: 10.6084/m9.figshare.26564140, as well as the original publication by Gregor et al. (2019), see the DOI: 10.5194/gmd-12-5113-2019.<br><b>HOST</b>CSIR, Southern Ocean Carbon – Climate Observatory (SOCCO)
DOI: 10.6084/m9.figshare.1477893.v1
title: NM14161 v-232.pdf

description: Clinical Study Reports on Orlistat released by EMA
DOI: 10.6084/m9.figshare.24858717.v1
title: Genotype information in VCF format in two populations

description: Preterm birth is the leading cause for neonatal mortality and morbidity worldwide, but its molecular etiologies was limitedly documented and the therapeutical development lacked progress. The only medication to date, progesterone, has been reported to result in discordant treatment effectiveness from clinical trials. To stratify the underlying genetics of preterm birth, we harvested peripheral blood from 48 females with preterm birth history, who received weekly intramuscular injections of Makena from gestational week 16 to 36 for Whole Genome Sequencing. Our downstream analysis identified a panel of genetic variants with myometrium specific functions that significantly result in inferior therapeutical responses on clinical.
DOI: 10.6084/m9.figshare.25241947.v2
title: Why is Wearing Hanfu to Travel Becoming Increasingly Popular? A Mixed Study on the Motivation and Loyalty of Hanfu Tourists

description: This article reveals the motivations of Hanfu tourists and the configurations of "motivation and loyalty". Study 1 involved semistructured interviews with 21 Hanfu tourists and revealed the motivations for tourists to wear Hanfu.Through a two-stage questionnaire survey, Study 2 found that scene consistency is a necessary condition for Hanfu tourists to generate high loyalty.
DOI: 10.4121/uuid:895b26fb-6f25-46eb-9e48-0dca26fcd030
title: BPI Challenge 2020: Request For Payment

description: This dataset contains the event related to Requests for Payment (should not be travel related): 6,886 cases, 36,796 events. Technically, they should not be linked to travels, but sometimes they can be (this is an unwanted deviation) Parent item: BPI Challenge 2020 The dataset contains events pertaining to two years of travel expense claims. In 2017, events were collected for two departments, in 2018 for the entire university. The various permits and declaration documents (domestic and international declarations, pre-paid travel costs and requests for payment) all follow a similar process flow. After submission by the employee, the request is sent for approval to the travel administration. If approved, the request is then forwarded to the budget owner and after that to the supervisor. If the budget owner and supervisor are the same person, then only one of these steps is taken. In some cases, the director also needs to approve the request.The process finished with either the trip taking place or a payment being requested and payed. On a high level, we distinguish two types of trips, namely domestic and international. For domestic trips, no prior permission is needed, i.e. an employee can undertake these trips and ask for reimbursement of the costs afterwards. For international trips, permission is needed from the supervisor. This permission is obtained by filing a travel-permit and this travel permit should be approved before making any arrangements. To get the costs for a travel reimbursed, a claim is filed. This can be done as soon as costs are actually payed (for example for flights or conference registration fees), or within two months after the trip (for example hotel and food costs which are usually payed on the spot).
DOI: 10.6084/m9.figshare.25981450.v14
title: 2020-2021 Changjiang estuary dissolved oxygen isotopic compositions and results of Monte-Carlo Mixing experiment

description: Understanding the complex processes that lead to oxygen depletion is challenging. The nonlinear relationship between dissolved oxygen (DO) isotopic composition (δ<sup>18</sup>O ) and its concentration makes δ<sup>18</sup>O a unique tracer for studying O2 cycling in oxygen depletion zones. Based on the DO δ<sup>18</sup>O compositions from four cruises conducted from summer 2020 to spring 2021 in the Changjiang Estuary, we identified a dynamic northern oxygen depletion zone (NODZ) with seasonally varying DO δ<sup>18</sup>O values, and a relatively stable southern oxygen depletion zone (SODZ). To quantify the contributions of low oxygen water mixing and respiration to oxygen depletion, we conducted a Monte-Carlo mixing experiment involving high salinity and low oxygen water (HSLO) and mixed layer water (MLW). Our findings indicated that HSLO mixing contributed to 59% to 100% of oxygen deficit in oxygen depletion zones, with SODZ exhibiting a HSLO mixing contribution of more than 78%. Respiration contributed to the remaining oxygen deficit, with water column respiration consuming approximately 1.5 times more oxygen than sediment oxygen consumption. In the NODZ, oxygen depletion was further enhanced by water column stratification, respiration and seafloor topography. Overall, the influx of HSLO was a key trigger for oxygen depletion in the Changjiang Estuary. The spatial and temporal variations of the two oxygen depletion zones were closely linked to the intrusion and retreat of HSLO from summer to autumn. Our findings highlight the importance of utilizing DO δ<sup>18</sup>O to differentiate and quantify biological and physical processes in coastal oxygen depletion zones.File description：Table S1: Data for this study, including latitude and longitude, sampling depth, temperature, salinity, δO<sub>2</sub>/Ar,δ<sup>18</sup>O,[O<sub>2</sub>],[O<sub>2</sub>]/[O<sub>2</sub>]<sub>sat</sub>, densityTable S3: The results of Monte-Carlo mixing experiments in all samples beneath mixed layer: the fraction of HSLO in different water masses, [O<sub>2</sub>] and δ<sup>18</sup>O after mixing from Monte-Carlo mixing experiment. Oxygen depletion caused by mixing and total oxygen depletion. The contribution of mixing and respiration to oxygen deficit. The apparent respiration fractionation factor and the proportion of WCR and SOC to oxygen deficit as well as the observed salinity, [O<sub>2</sub>] and δ<sup>18</sup>O beneath the mixed layer<br><br>
DOI: 10.6084/m9.figshare.19649874.v1
title: Supplementary Material for: Complex Material Properties of Gel-Amin: A Transparent and Ionically Conductive Hydrogel for Neural Tissue Engineering

description: The field of tissue engineering has benefited greatly from the broad development of natural and synthetic polymers. Extensive work in neural engineering has demonstrated the value of conductive materials to improve spontaneous neuron activity as well as lowering the necessary field parameters for exogenous electrical stimulation. Further, cell fate is directly coupled to the mechanical properties of the cell culture substrate. Increasing the conductivity of hydrogel materials often necessitates the addition of dopant materials, organic and inorganic that facilitate electron mobility. However, very little electron transfer is observed in native cell signaling and most of these materials are opaque, severely limiting microscopy applications commonly employed to assess cell culture morphology and function. To overcome these shortcomings, the inclusion of an ionic liquid, Choline Acrylate, into the backbone of a modified collagen polymer increases the bulk conductivity 5-fold at a 1:1 ratio while maintaining optical transmission of visible light. Here, we explore how the inclusion of choline acrylate influences bulk material properties including the mechanical, swelling, and optical properties of our hydrogels, referred to as Gel-Amin hydrogels, as a material for tissue culture. The inclusion of an ionic liquid increases conductivity while maintaining a high degree of optical transmission. Despite an increase in swelling over traditional GelMA materials, the conductive hydrogels support whole dorsal root ganglia encapsulation and outgrowth. Our results indicate that our Gel-Amin system holds potential for neural engineering applications and lowering the required charge injection for the application of exogenous electrical stimulation. This is this first time an ionic liquid-hydrogel system has been used to culture and support primary neurons in vitro.
DOI: 10.6084/m9.figshare.28765568.v1
title: Structural Characterization of SARS-CoV-2 ORF10 via AlphaFold2: Binding Pockets and Conserved Functional Motifs

description: In this study, I present a detailed computational analysis of the <b>SARS-CoV-2 ORF10 protein</b>, combining <b>AlphaFold2-predicted structure</b>, <b>binding site characterization</b>, and <b>evolutionary conservation</b> to elucidate its functional potential. Key findings include:<b>1. Structural Prediction & Quality Assessment</b><b>High-confidence PDB model</b> (<code>ORF10PREDICTIONTHB_..._alphafold2_ptm_model_1_seed_000.pdb</code>) with per-residue confidence (pLDDT &gt;90%) and validation plots (<code>plddt.png</code>, <code>pae.png</code>).<b>Two prominent binding pockets (P_0 and P_1)</b>: Comparative metrics (volume, depth, residue types) provided in <code>detailed_comparison_of_p0_and_p1.csv</code>.<b>2. Binding Site Analysis</b><b>10 surface clefts/cavities</b> ranked by volume (largest: 280.97 Å³), annotated with:<b>Accessibility</b> (e.g., Gap 1: 49.48% exposed vertices) and <b>depth</b> (e.g., Gap 3: 6.90 Å average depth).<b>Residue conservation</b>: Highly conserved gaps (e.g., Gap 1, Gap 9) suggest functional importance.<b>Ligand interactions</b>: Non-empty ligand entries highlight potential molecular binding roles.<b>3. Evolutionary Conservation</b><b>BLAST (UniProt)</b>: 100% identity with ORF10 from <i>Betacoronavirus sp. RpYN06</i> (38-residue overlap; E-value: 9e-17), confirming high conservation across SARS-related strains.<b>Conserved motif (cd21597)</b>: Identified via InterPro, implicating ORF10 in viral processes (e.g., protein-protein interactions or immune modulation).<b>4. Functional Implications</b>Larger, deeper, and conserved gaps (e.g., Gap 1, P_0/P_1) are prime candidates for <b>therapeutic targeting</b>.Conserved motif and sequence similarity suggest a <b>shared functional role</b> in viral pathogenesis among coronaviruses.<b>Methods</b><b>Structure Prediction</b>: AlphaFold2 (ColabFold) with pLDDT/PAE validation.<b>Binding Site Detection</b>: Cleft/cavity analysis for volume, depth, residue properties.<b>Evolutionary Analysis</b>: BLAST (UniProt), InterPro motif scanning.<b>Files Included</b><b>PDB</b>: AlphaFold2-predicted ORF10 structure.<b>CSV</b>: Binding pocket comparisons (P_0/P_1) and gap region metrics.<b>Plots</b>: Model quality (pLDDT, PAE, coverage).<b>Supplementary</b>: BLAST/InterPro results in text format.
DOI: 10.6084/m9.figshare.28883453.v1
title: Dataset and Stata Code for "No Research, No Risk? An Empirical Study of the Antecedents of Information Leakage Attacks"

description: This repository contains the dataset and Stata code used for the study "No Research, No Risk? An Empirical Study of the Antecedents of Information Leakage Attacks." <br>The dataset and code are provided for transparency and reproducibility, enabling others to replicate the analysis.
DOI: 10.6084/m9.figshare.24550732.v4
title: Head model collection for mixed reality navigation in neurosurgical intervention for intracranial lesions

description: Mixed Reality Navigation (MRN) technology is emerging as an increasingly significant and interesting topic in neurosurgery. MRN enables neurosurgeons to "see through" the head with an interactive, hybrid visualization environment that merges virtual and physical-world elements. Offering immersive, intuitive, and reliable guidance for preoperative and intraoperative intervention of intracranial lesions, MRN showcases its potential as an economically efficient and user-friendly alternative to standard neuronavigation systems. However, the clinical research and development of MRN systems present challenges: recruiting a sufficient number of patients within a limited timeframe is difficult, and acquiring commercially available, medically significant head or skull models at a low cost is equally challenging. To accelerate the development of novel MRN systems and surmount these obstacles, this study introduces a customized dataset tailored for MRN system development and testing in the neurosurgical domain. It encompasses CT/MRI scan data from 19 patients with intracranial lesions and the corresponding three-dimensional (3D) models of anatomical structures and validation references derived from these data. Models are provided in Wavefront object (OBJ) and Stereolithography (STL) file formats, facilitating the development and evaluation of neurosurgical MRN applications.
DOI: 10.6084/m9.figshare.7932485.v1
title: Insecticide residue database for Africa

description: An insecticide residue database was compiled for Africa from a literature review in Web of Knowledge to identify studies that measured insecticide residues in soil, sediment, water and air. The search terms that were used for the extraction of the literature are available as additional file in the manuscript. The database extracted the following data systematically from the individual papers: year and month(s) of sampling, sample collection methods and depth, insecticide extraction method, insecticide quantification method, quantification and detection limits, insecticide and insecticide class, the measured insecticide concentration and geographical coordinates.
DOI: 10.6084/m9.figshare.1320834.v1
title: Figshare Public Metadata until 02/12/2014

description: This dataset contains metadata of publicly available items on figshare up until (excluding) 2 December 2014. The data was retrieved via the figshare API (http://api.figshare.com). The format is one item per line, encoded with JSON. There are two files in this dataset: 1. basic-metadata.json contains basic metadata for all publicly available items on figshare up until (excluding) 2 December 2014 (n=1,092,808 items). The data was retrieved using a wildcard search (see http://api.figshare.com/docs/howto.html#q-search for details). Basic metadata fields are:<br>* article_id<br>* title<br>* DOI<br>* description<br>* type<br>* defined_type<br>* published_date<br>* modified_date<br>* url<br>* authors<br>* links<br>* page_nr: The page the item is returned on in the search results. 2. full-metadata-datasets-filesets-unique-doi.json contains extended metadata for all items of defined_type "dataset" or "fileset" with a unique DOI (n=266,961 items). The data was retrieved using the listing functionality (see http://api.figshare.com/docs/howto.html#q-listing for details). Extended metadata fields are:<br>* article_id<br>* title<br>* doi<br>* description<br>* defined_type<br>* published_date<br>* url<br>* authors<br>* links<br>* figshare_url<br>* views<br>* downloads<br>* shares<br>* publisher_doi<br>* publisher_citation<br>* master_publisher_id<br>* status<br>* version<br>* total_size<br>* owner<br>* tags<br>* categories<br>* files
DOI: 10.6084/m9.figshare.20372529.v1
title: Data Set for The Nutritive and Anti-Nutritive Components in the Red Cabbage Vegetable and Extracts.

description: The inclusion of red cabbage vegetables in locally prepared meals is gradually becoming popular and quickly gaining acceptability within the regions, Africa inclusive, owing to the number of bioactive compounds in the vegetable in higher amounts than the more popular white specie. The study, therefore, seeks to quantify the nutrients, estimate the phytochemicals, and determine the antioxidant capacity of the red cabbage vegetable. The analyses were executed in line with accepted standard procedures. On analysis, the vegetable was shown to contain more carbohydrate (45.72±1.96), moisture (23.23 ±0.29), and proteins (15.05 ± 0.35), compared to the ash content (5.01±0.04), lipids (7.23±0.98) and fibre (3.77±0.32). The vitamin content ranged from 60.43±0.05 for vitamin C to 0.02± 0.15 for vitamin B2, occurring in the order: C&gt;E&gt;A&gt;B12&gt;B9&gt;D&gt;B3&gt;B6&gt;B1 and B2. While potassium recorded the highest concentration (6.89±1.24), nickel and chromium had the lowest concentration (0.01± 0.10 and 0.01±0.92). A total of 35 phytochemical compounds were identified in the GC-MS analysis of the red cabbage aqueous extract: such as alkaloids, anthocyanin, sterols, phenolic compounds, etc., with appreciable levels of antioxidant capacity demonstrated as portrayed by the 1, 1-Diphenyl-2-picyrylhydrazyl (DPPH) free radical scavenging activity and ferric reducing antioxidant capacity (FRAC) assay. Therefore, this study provides evidence that the red cabbage vegetable grown in Nigeria is compact with nutrients which can be included in daily meals to meet dietary needs when anti-nutrients are minimized.
DOI: 10.6084/m9.figshare.4902140.v1
title: RNA-seq raw data of maize CMS-C line

description: RNA-seq raw data of biological replicate 1 of cytoplasmic male sterility line C48-2 spikelets at mononuclear stage