cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3560127.v1
title: Appendix A. Examples of the predator–prey model with logistic growth of prey.

description: Examples of the predator–prey model with logistic growth of prey.
DOI: 10.6084/m9.figshare.24069741.v2
title: QuickClim demonstration input data

description: Pre-curated CMIP5 output required for the demonstration of QuickClim.
DOI: 10.6084/m9.figshare.9114644.v1
title: Data for "Implications of contrasted above- and below-ground biomass responses in a diversity experiment with trees"

description: This database is linked to the IDENT experiment in Montreal. It presents aggregated data for each of the plots that were taken into account in the study named "Implications of contrasted above- and below-ground biomass responses in a diversity experiment with trees". Descriptions for the variables are available in the main text and the Supporting Information.
DOI: 10.15468/dl.y2phjt
title: Occurrence Download

description: A dataset containing 744 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phytophthora ramorum Werres, De Cock & Man"
 ]
}

 The dataset includes 744 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009420-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/94kw2wktyc
title: Solid Phase Condensates In Vitro Imaging Data 2

description: Solid nucleoprotein condensates are modified by different DNA sequences
DOI: 10.6084/m9.figshare.6126641.v1
title: Bird_nest_analysis_code

description: This is code and data used for the bird nest paper
DOI: 10.6084/m9.figshare.28633967.v1
title: SFG Spectrogram

description: Raw data for the sum frequency generation spectrogram [Fig 6 in the manuscript]: SFG Spectrogram.
DOI: 10.6084/m9.figshare.8197565.v1
title: Supplementary Material for: A Common Genetic Variation in Langerin (CD207) Compromises Cellular Uptake of <b><i>Staphylococcus aureus</i></b>

description: Langerhans cells are key sentinel cells of the skin and mucosal lining. They sense microorganisms through their repertoire of pattern-recognition receptors to mount and direct appropriate immune responses. We recently demonstrated that human Langerhans cells interact with the Gram-positive pathogen <i>Staphylococcus aureus</i> through the Langerhans cell-specific receptor langerin (CD207). It was previously hypothesized that two linked single nucleotide polymorphisms (SNPs; N288D and K313I) in the carbohydrate recognition domain of langerin would affect interaction with microorganisms. We show that recognition of <i>S. aureus</i> by recombinant langerin molecules is abrogated in the co-inheriting SNP variant, which is mainly explained by the N288D SNP and further enhanced by K313I. Moreover, introduction of SNP N288D in ectopically-expressed langerin affected cellular distribution of the receptor such that langerin displayed enhanced plasma membrane<i></i>expression. Despite this increased binding of <i>S. aureus</i> by the langerin double SNP variant, uptake of bacteria by this langerin variant was compromised. Our findings indicate that in a proportion of the human population, the recognition and uptake of <i>S. aureus</i> by Langerhans cells may be affected, which could have important consequences for proper immune activation and <i>S. aureus</i>-associated disease.
DOI: 10.6084/m9.figshare.26251148.v1
title: SLogAnalyzer Database [backup.zip]

description: SLogAnalyzer database
DOI: 10.17632/zt93nkrd9y
title: 10.1038/s41598-023-50581-8

description: Raw data of Peripheral blood BDNF and soluble CAM proteins as possible markers of prolonged disorders of consciousness: a pilot study
DOI: 10.6084/m9.figshare.24903249.v1
title: Supplementary Material for: Pattern of expression of microRNA in patients with radiation induced bladder injury

description: Introduction: Bladder cancer (BC) is sensitive to radiation treatment and a subset of patient experiences radiation induced injuries including shrinkage of bladder due to bladder fibrosis. 
Methods: Using a micro-RNA (miRNA) array comparing patient’s samples with, or without radiation induced injuries, we have checked the clustering of miRNA expression. 
Results: Hsa-miR-130a, hsa-miR-200c, hsa-miR-141, and hsa-miR-96 were found to be highly expressed (&gt;50 times) in patients with fibrotic bladder shrinkage (FBS) compared to those with intact bladder (IB) function. In patients with FBS, hsa-miR-6835, hsa-miR-4675, hsa-miR-371a, and hsa-miR-6885 were detected to have lesser than half expression to IB patients. We have analyzed the significance of these genes in relation to overall survival of 409 BC patients retrieved from TCGA data set. We have run combined survival analysis of mean expression of these four miRNAs highly expressed in FBS patients. 175 patients with high expression had longer median survival of 98.47 months than 23.73 months in 233 patients with low expression (HR: 0.53; 0.39 – 0.72, logrank P value: 7.3e-0.5). Combination analysis of all 8 genes including hsa-miR-6835, hsa-miR-4675, hsa-miR-371a, and hsa-miR-6885 showed the same HR for OS. Target scanning for these miRNAs matched specific cytokines known as an early biomarker to develop radiation induced fibrosis.
Conclusions: BC patients with fibrotic radiation injury have specific miRNA expression profile targeting pro-fibrotic cytokines and these miRNAs possibly renders to favorable survival.
DOI: 10.6084/m9.figshare.7370573.v1
title: Supplementary Material for: Integrated Transcriptome Sequencing Analysis Reveals Role of miR-138-5p/ TBL1X in Placenta from Gestational Diabetes Mellitus

description: <b><i>Background/Aims:</i></b> The placenta has been suggested to play a crucial role in the pathology of gestational diabetes mellitus (GDM). Placenta-specific microRNAs (miRNAs) and the corresponding targeting genes involved in the pathology of GDM still remain to be elucidated. We aimed to identify the dysregulated miRNAs and the corresponding mRNA targets through an integrated miRNA and mRNA transcriptomic profiles analysis and investigate the role of differentially expressed miR-138-5p/TBL1X in GDM. <b><i>Methods:</i></b> RNA sequencing (RNA-seq) was performed in 16 placentas from GDM and control group. Differentially expressed mRNAs and miRNAs in GDM were validated by quantitative PCR (qPCR). The wound healing assay and transwell migration assay were used to analyze cell migration ability. The cell proliferation was determined by CCK8 assay. Luciferase assay was used to confirm the direct binding of the targeted <i>TBL1X</i> with miR-138-5p. <b><i>Results:</i></b> Totally, 281 mRNAs and 32 miRNAs were found to be differentially expressed in the GDM placentas. The biological relationships of the miRNA/mRNA pairs were related to cellular development and function and organ morphology. Among the aberrantly expressed molecules, we selected miR-138-5p from the bioinformatics analysis and found that miR-138-5p significantly inhibited the migration and proliferation of trophoblasts (HTR-8/SVneo) by targeting the 3’-UTR of <i>TBL1X</i>. Furthermore, the aberrant expression of miR-138-5p and TBL1X was significantly correlated with the weight of the placenta. <b><i>Conclusion:</i></b> We present the first integrative analysis of miRNA and mRNA expression profiles in GDM placenta and uncover a more detailed role for miR-138-5p, as well as its target <i>TBL1X</i> in the pathology of GDM.
DOI: 10.6084/m9.figshare.13961471.v1
title: Video recording of a mouse face

description: Close up video of a head-fixed mouse face. More details can be found in the README file. Data collected by Mario Dipoppa.
DOI: 10.6084/m9.figshare.21332664.v1
title: Supplementary Material for: Affordability of Alcoholic Beverages in the European Union

description: <b><i>Background:</i></b> From a public health perspective, alcohol taxation should be designed to reduce alcohol affordability and thus alcohol consumption and related harms. <b><i>Objectives:</i></b> In this brief report, we estimate alcohol affordability in European Union Member States and associated countries and investigate whether affordability is related to national alcohol excise duties. <b><i>Method:</i></b> Beverage-specific affordability for beer, wine, and spirits were estimated based on the number of standard drinks a household could purchase based on their median monthly disposable household income in 2020. To determine the pooled affordability of alcohol, the beverage-specific estimates were weighted by the share of the beverage-specific per capita consumption in total recorded consumption. Pearson and Spearman rank correlations were calculated to establish the association between alcohol affordability and alcohol excise duty rates. All data were retrieved from official sources. <b><i>Results:</i></b> On average, a European household can purchase 1,628 standard drinks of alcohol with its monthly income, with affordability being highest in Germany, Austria, France, and Luxembourg. The affordability of spirits, but not that of beer or wine, was inversely correlated with the beverage-specific excise duty rates. <b><i>Conclusions:</i></b> Alcohol is affordable in the Member States of the European Union and associated countries, and low levels of excise duties on beer and wine appear to be unrelated to their affordability. Alcohol taxes should be increased to effectively reduce the affordability of alcoholic beverages in order to lower the alcohol-related health burden in Europe.
DOI: 10.6084/m9.figshare.4689805.v1
title: K–Ar data. Phanerozoic low-temperature evolution of the Uruguayan Shield along the South American passive margin

description: K–Ar data
DOI: 10.6084/m9.figshare.16834633.v1
title: Appendix I GSEA, Hallmark, REACTOME.zip

description: GSEA, Hallmark, REACTOME data for study "HIV-1 provirus transcription and translation in macrophages differs from macrophages containing pre-integrated cDNA complexes and requires E2F transcriptional programs"
DOI: 10.17632/sfvcsfz4sb
title: COCHASE, a code for coupled channel Schrödinger equations

description: Title of program: COCHASE Catalogue Id: ABIC_v1_0 Nature of problem The computer code COCHASE is designed to calculate the S-matrix in the form of a real phase shift and inelasticity for the interaction of two particles coupled to the possible production of five other two particle channels. The production cross section for each secondary channel is also easily obtained. Versions of this program held in the CPC repository in Mendeley Data ABIC_v1_0; COCHASE; 10.1016/0010-4655(75)90053-3 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2019)
DOI: 10.6084/m9.figshare.3544469.v1
title: Appendix A. Rank–biomass diagrams for ants in each of the 12 study sites.

description: Rank–biomass diagrams for ants in each of the 12 study sites.
DOI: 10.17632/fw52ydz3gg
title: Green Official Development Aid, Concessional External Debt and Green Growth in East African Community Countries

description: According to United Nations (2023), green growth can be measured through Gross National Domestic Product which can be achieved by deducting environmental emissions and degradation from the GDP growth. The carbon emissions (CO2), emission damage (EmD), energy depletion (EnD), natural forest depletion (NfD) and mineral depletion (MD) were used in the current study to derive GNDP as a percentage of GDP growth. GNDP as a percentage of GDP growth was used as the dependent variable while Green Official Development Aid (GODA) and external concessional debt (CoD) were the independent variables for the study. GODA data was extracted from the Organization for Economic Co-operation and Development (OECD) Credit Reporting System database. External concessional debt data was extracted from the World Bank data base. Control variables for the study include debt service for external debt, inflation, real interest rate and corruption estimate all extracted from the World Bank database. The data analyzed was from1980 to 2022 for six East African Community (EAC) states, Democratic Republic of Congo (DRC), Kenya, Burundi, Tanzania, Rwanda, and Uganda. Attached is the analyzed data set using the Stata 15 software.
DOI: 10.6084/m9.figshare.19499303.v1
title: patches and local annotations, slide 177, zoom 248x248 um2

description: patches and local annotations: data for slide with ID of the last 3 characters of the file name: local annotations in csv format and a folder with patches at zoom level indicated at the 6th character of the file name
DOI: 10.6084/m9.figshare.21740177.v1
title: Carbon stress anticipates the budbreak timing in shade-tolerant species and delays it in shade-intolerant species

description: File Budbreak DRYAD: Budbreak dynamics in saplings of temperate tree species expressed as the cumulative number of plants showing broken buds and as the cumulative number of plants showing broken buds relative to the final number of plants showing broken buds. Budbreak was recorded weekly in an outdoor experiment using saplings of five species of the temperate forest of southern Chile and the exotic temperate species <em>Acer pseudoplatanus. Saplings were expsoed </em>to two experimental light conditions (open and shade conditions); budbreak was evaluated after one year under the light conditions. <br> <br> The open light condition was represented by full light availability, whereas the severe shade condition was achieved by placing the pots on the ground beneath a sparse shade of <em>Alnus glutinosa</em> (Betulaceae) trees, and by completely covering the lateral sides and the top with frames of a black raschel mesh 80% of shade. Each block contained 6 individual saplings per species and light condition. The photosynthetic photon flux density (PPFD, mean ± SE, n = 4 blocks) was 888 ± 169 and 85 ± 199 μmol·m −2·s −1 for the full light and severe shade conditions, respectively. Saplings were regularly watered during the growing seasons. By August 2014 (late winter), i.e., eleven months after the light treatment application, we started to record sapling’s budbreak. Budbreak was defined as the bud stage when at least one small new leaflet was visible. This budbreak monitoring was completed by late November 2014 when all individuals showed leaves. <br> <br> File NSC DRYAD: <br> Mean whole-sapling concentrations of non-structural carbohydrates (NSC), total soluble sugars (TSS), starch, and the TSS/NSC ratio, of saplings of five species of the temperate forest of southern Chile and the exotic temperate species <em>Acer pseudoplatanus</em> under two experimental light conditions. In late April 2015, two living saplings per light treatment and block were harvested for biomass and non-structural carbohydrates (NSC) determination. Each sapling was separated into roots, stems (including branches and twigs), and leaves. Tissue samples were dried and then ground into a fine powder and analyzed for biomass and carbohydrates concentrations.
DOI: 10.25946/25856284.v1
title: Fermentation data, raw material analysis

description: The research seeks to assess the feasibility of obtaining a higher ethanol yield in the fermentation of molasses to produce rum. It will be an industry-based project, associated with Bundaberg Distilling Company, a subsidiary of Diageo Australia. Evaluation of their current production process has revealed a financially significant inefficiency with an ethanol yield of 85 % obtained from the fermentable sugars present in molasses, the feedstock of rum fermentations. For any industrial fermentation process, the fermentation medium and fermentation process conditions play a critical role because they affect the formation, concentration and yield of a particular fermentation product thus affecting the overall process economics. The research will therefore investigate processes that influence fermentation and assess whether a higher ethanol yield can be obtained to optimize the fermentation process. Further to that, the study will seek to understand the reasons of the observed inconsistencies in the fermentation outputs of various batches. The impact of molasses and other raw materials on the fermentation process will be investigated, seeking to understand the optimum parameters for use in fermentation. Focused studies on chemical, physical, and microbiological parameters will provide a clear depiction of the raw material composition and processes influencing and leading up to fermentation in a way to explore and establish methods of fermentation optimization during the production of Bundaberg rum product.
DOI: 10.6084/m9.figshare.6110282.v1
title: Consumer Decision Making Style

description: Data relates to exploring CDMS in Online shooping Context for Purpose of EFA & CFA.<br><br>First file relates to EFa and Second file for CFA<br>
DOI: 10.6084/m9.figshare.11916162.v1
title: Bourque PLOS one

description: Nerve conduction studies of median and ulnar nerves at time of cast removal and 6 weeks subsequentlyPublication submitted to PLOS one
DOI: 10.6084/m9.figshare.24758709.v1
title: Drive Through Study

description: Test images for each test kit are organized within a tar file accordingly.
DOI: 10.17632/ggywzpf8mf
title: Karst Depression Dataset

description: The dataset consists of images and corresponding labels designed to study karst landscapes. Each image in the dataset is a composite patch composed of multiple layers or spectral bands, encapsulating a wealth of geographical and topographical information. These patches have dimensions of 128 pixels by 128 pixels, with each pixel representing a specific area on the ground. The dataset contains a total of 55 spectral bands, organized as follows:

- SRTM (Shuttle Radar Topography Mission) Bands (0-10): These bands are derived from the SRTM mission and provide elevation data, crucial for identifying karst features such as sinkholes and ridges. The SRTM data offers a foundational layer for understanding the surface topography.

- ASTER GDEM (Advanced Spaceborne Thermal Emission and Reflection Radiometer Global Digital Elevation Model) Bands (11-21): These bands offer additional elevation data with a focus on thermal emissions and reflection, which helps in differentiating between various landforms and can be particularly useful in karst terrain analysis.

- AW3D30 (ALOS World 3D - 30m) Bands (22-32): Derived from the ALOS (Advanced Land Observing Satellite), these bands provide high-resolution elevation data, enhancing the detail with which karst features can be identified and analyzed.

- GLO-30 (Global Digital Elevation Model - 30m) Bands (33-43): GLO-30 bands offer a global perspective on elevation, sourced from a compilation of high-resolution satellite images, aiding in a comprehensive understanding of karst landscapes on a broader scale.

- NASADEM (NASA Digital Elevation Model) Bands (44-54): These bands are the latest in elevation modeling from NASA, offering refined elevation data that incorporates data from previous missions like SRTM, but with improved accuracy and resolution.

A label with dimensions of 128x128 accompanies each image patch. These labels are crucial for supervised learning tasks, as they provide the ground truth for the presence or absence of karst features within each patch. The labels are designed to facilitate the training of machine learning models that can automatically detect and classify karst phenomena from the spectral data provided.
DOI: 10.6084/m9.figshare.9034184.v4
title: Secondary structures of the training set of eukatyotic group II introns

description: Secondary structures of the training set of eukaryotic group II introns
DOI: 10.6084/m9.figshare.12016209.v1
title: revised article data.rar

description: data
DOI: 10.6084/m9.figshare.8092682.v1
title: DETERMINATION OF METALS PRESENT IN MAKE-UP SHADOWS BY UV-VIS SPECTROPHOTOMETRY: A CONTEXTUAL EXPERIMENT IN HIGHER EDUCATION

description: Metallic oxides are used in cosmetic shadows formulations in order to highlight the area around the eyes, with different colors. Due to the close proximity to the eye mucosa, these products are a potential source of metal intoxication in human body. Based in this fact, several analytical methods to quantify metals in cosmetic shadows have been proposed in the literature. This paper, propose a contextual experiment to investigated the presence of Al3+, Fe3+ and Cu2+ using UV-VIS spectrophotometric and complexation reactions in solvent mixtures to generate cromophore species. These experiments have the potential to insert a contextual discussion in chemistry and pharmaceutical graduation courses, making a meaningful experimentation in the formative attribute of these courses.
DOI: 10.6084/m9.figshare.28761773.v1
title: Rossetta Stone for Change.pdf

description: Without any reference to gravity, the moon's orbit is offered mechanics. Implications directly offer an association to the cause of change.
DOI: 10.17632/sfbh738spb
title: Reconstructed individual patient-level survival data for CheckMate 649 and ORIENT-16

description: Reconstructed individual patient-level survival data for CheckMate 649 and ORIENT-16
DOI: 10.6084/m9.figshare.19298963.v1
title: Source Data for figures in this Article:

description: This dataset contains: <br> · Supplementary Data 1-5 files, include the information for the 5 main figures of the Article entitled "Environmental and health impacts of atmospheric CO<sub>2</sub> removal by enhanced rock weathering depend on nations' energy mix" Supplementary Data 6 file, contains 6 spreadsheets corresponding to Figs 3-8 of the Supplementary references <br> ·
DOI: 10.6084/m9.figshare.21220436.v1
title: Supplementary Material for: Hepatocyte Growth Factor Promotes Differentiation Potential and Stress Response of Human Stem Cells from Apical Papilla

description: Harsh local microenvironment, such as hypoxia and lack of instructive clues for transplanted stem cells, presents the serious obstacle for stem cell therapies’ efficacy. Therefore, continued efforts have been taken to improve stem cells’ viability and plasticity. Hepatocyte growth factor (HGF) have previously been reported to mitigate complications of various human diseases in animal model studies and in some clinical trials. Besides, human stem cells from root apical papilla (SCAP) are deemed a better resource of mesenchymal stem cells due to derived stem cells holding greater amplification ability in vitro compared with those from other dental resources. To move forward, evaluating effects and understanding underlying molecular mechanisms of HGF on SCAP for periodontal regeneration are needed. In this study, HGF was transgenic expressed in SCAP, and it was found that HGF enhanced osteo/dentinogenic differentiation capacity of SCAP compared with those non-treated control in an ectopic mineralization model. Moreover, HGF reduced apoptosis of SCAP under both normoxia and hypoxia condition, whereas combination of HGF and hypoxia exposure had inhibitory effects on cell proliferation during an eight-day in vitro culture period. Transcriptome analysis further revealed that suppressed cell cycle progression and activated BMP/ TGFβ, Hedgehog, WNT, FGF, HOX and other morphogen family members upon HGF overexpression, which may render SCAP recapitulate part of neural crest stem cells characteristics. Moreover, strengthened stress-response modulation such as unfolded protein response, macroautophagy and anti-apoptotic molecules might explain increased viability of SCAP. In all, our results imply that these potential mechanisms underlying HGF promoting SCAP differentiation could be further elucidated and harnessed to improve dental tissue regeneration.
DOI: 10.17632/xm8v7d5fwh
title: MIRROR Code