cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10849221
title: North Pacific Subtropical Gyre RCLV Atlas (Version 2)

description: This dataset tracks Rotationally Coherent Lagrangian Vortices (RCLVs) at an 8-day resolution in the North Pacific Subtropical Gyre region around Hawai’i. The ‘lat’ and ‘lon’ variables represent the center coordinates of the vortex, or the extremum of integrated relative vorticity. The contour boundaries demark the edge of the RCLV based on 32-day backward-in-time Lagrangian trajectories. In other words, eddies in this dataset represents a fluid mass of substantial size that was coherent for at least 32 days. The fluid masses are tracked through time to assign IDs and RCLV ages. The software used to generate the dataset is publicly available at https://github.com/lexi-jones/RCLVatlas (DOI: 10.5281/ZENODO.7702978).

Version 1 of the dataset (https://simonscmap.com/catalog/datasets/RCLV_atlas; DOI: 10.5281/ZENODO.8139149) only includes contours that represent features of age 32 days or older. Version 2 extends the dataset to include eddy genesis by advecting the particle sets backward-in-time to age 24, 16, and 8 days.
DOI: 10.5281/zenodo.11221599
title: Data and metadata associated with ice-nucleating particles during the 2022 Arctic Cold Air Outbreak Campaign

description: Data and metadata associated with analysis of ice-nucleating particle concentrations and aerosol-size distributions measured during the March 2022 Arctic Cold Air Outbreak campaign.

Contains INP concentrations and aerosol-size normalisations of these, parametrisations of these, SEM data and metadata and backtrajectory modelling inputs and results.
DOI: 10.5281/zenodo.11472769
title: Frost resistance of alkali-activated concrete with different compositions – parametric study

description: Alkali-Activated Materials (AAM) are often considered to be very durable and also frost-resistant. However, there are also contrary experiences. This paper focuses on the frost resistance of AAMs of different compositions – different amounts of activator and different ratios between alkali (R2O) and silicon oxide content. Sodium water glass was used as the activator and its silicate modulus was modified by the addition of KOH. The R2O content was 4 -10 % and the R2O/SiO2 weight ratio was 33/67 (water glass only) up to 100/0 (KOH only). The frost resistance index was tested at the ages of 28, 91 and 365 days. Specimens were cured in foil or water and comparative specimens were also stored in foil or water. The results obtained are inconclusive. Firstly, when the reference specimens are stored in water, their bending strength decreases. This means that the frost resistance index is dependent on the use of the reference specimens – better results of frost resistance index are obtained for water-cured beams as reference specimens as they show lower strengths. The composition has a marginal effect on the frost resistance. Longer curing times also do not increase frost resistance.
DOI: 10.5281/zenodo.13749152
title: Qualitative data from an online survey for "Regional adaptation of Integrated Pest Management to control invasive forest insects"

description: This file contains data from an online global survey of experts working on the Integrated Pest Management of invasive forest insect pests, which we used to inform our largely qualitative synthesis of the issues and challenges surrounding the control of invasive species shared between jurisdictions. It also contains several entries on tree pathogens which we excluded from our paper. Some participants provided more than one response (i.e. case study of a pest species in a given region); each response is included as a separate entry with a unique response ID. Some species are therefore represented by more than one entry (i.e. case studies from different regions).

To comply with the Research Ethics Board that approved this study (REB 2021-100) at the University of New Brunswick, Canada, which hosted the encrypted online survey, we have anonymized the responses, and limited this open data file to short-form (multiple choice) answers. The survey methodology and the full survey questionnaire are available in the Online Appendix with the journal article (in press as of Sept 2024).
DOI: 10.5281/zenodo.13957005
title: The third Met Office Unified Model-JULES Regional Atmosphere and Land configuration, RAL3

description: Supporting data for figures in GMD draft paper: The third Met Office Unified Model-JULES Regional Atmosphere and Land configuration, RAL3
DOI: 10.5281/zenodo.13971280
title: A validated trigonelline-based method for the standardization and quality control of Trigonella foenum-graecum L.
DOI: 10.5281/zenodo.4509372
title: CEDS v_2021_02_05 Release Emission Data

description: Emissions data files by emission species (SO2, NOx, BC, OC, NH3, NMVOC, CO, CO2, CH4, N2O), country, and sector produced by the Feb-05-2021 release of CEDS. See the CEDS GitHub site for details including journal paper reference information and known issues with this data.
description: {"references": ["Hoesly, R. M., Smith, S. J., Feng, L., Klimont, Z., Janssens-Maenhout, G., Pitkanen, T., Seibert, J. J., Vu, L., Andres, R. J., Bolt, R. M., Bond, T. C., Dawidowski, L., Kholod, N., Kurokawa, J.-I., Li, M., Liu, L., Lu, Z., Moura, M. C. P., O'Rourke, P. R., and Zhang, Q. (2018) Historical (1750\u20132014) anthropogenic emissions of reactive gases and aerosols from the Community Emissions Data System (CEDS), Geosci. Model Dev., 11, 369-408. doi: 10.5194/gmd-11-369-2018.", "Hoesly, R. P. O'Rourke, C. Braun, L. Feng, S. J. Smith, T. Pitkanen, J. J. Seibert, L. Vu, M. Presley, R. Bolt, B. Goldstein. (2019, December 23). JGCRI/CEDS: v-12-23-2019 (Version Dec-23-2019). Zenodo. http://doi.org/10.5281/zenodo.3592073"]}
DOI: 10.5281/zenodo.7851257
title: Stepwise design of pseudosymmetric protein hetero-oligomers; design models

description: Design models for the associated publication
DOI: 10.5281/zenodo.7853171
title: Stepwise design of pseudosymmetric protein hetero-oligomers; experimental data

description: Experimental data presented in the manuscript "Stepwise design of pseudosymmetric protein hetero-oligomers"
DOI: 10.6084/m9.figshare.23631981
title: Exploring immune memory traits in the social immunity of a fungus-growing ant

description: Scripts with all analysis, and raw data used in Goes et al., 2024.Please, check README file for more information.
DOI: 10.6084/m9.figshare.24112548
title: DATA from: Historical dynamics of marginal populations at the leading edge of a temperate species in the boreal-temperate ecotone

description: Data from: Historical dynamics of marginal populations at the leading edge of a temperate species in the boreal-temperate ecotone.A MSExcel spreadsheet including data used to estimate minimal stand age and tree size structure, as well as the identification and radiocarbon dating of wood remains and charcoal particles from 8 marginal red maple stands at the leading edge of the species' range in eastern Canada.## Description of the Data and file structureSheet 1 - Metadata. Provides details about the study sites (Site name, Sampling date, Longitude [decimal degrees north], Latitude [decimal degrees east], and Altitude [m above sea level]), and a glossary for species codes.Sheet 2 - Stand-size structure. At each site, the diameter at breast height (DBH in cm) of each tree (&gt;2 cm DBH) inside a 400 square metre plot was measured with a tree caliper.Sheet 3 - Tree age. At each site, up to 10 of the largest Acer rubrum and Betula payrifera trees were cut down and disks were collected as close to the root collar as possible. Sampled disks were sanded and tree rings were counted. Trees were assigned to their emergence decade.Sheet 4 - Charcoal diversity. At each site, charcoal fragments extracted from 20 soil samples were identified to the highest taxonomic unit possible (TaxonID). For each TaxonID, data from the 20 sampling microsites were aggregated for each stand.Sheet 5 - Radiocarbon dates. Radiocarbon date of charcoal particles and wood remains extracted from forest soil or forest hollow sediments. For each datem, UCIrvine is the reference number at the Keck Carbon Cycle AMS Facility (University of California Irvine); ULaval is the refernce number at the Laboratoire de radiochronologie (Université Laval, Québec); F14C is the is percent modern carbon ± SD ; D14C is the per mille depletion in sample carbon 14 prior to isotopic fractionation correction ± SD ; 14C age is the non-calibrated radiocarbon carbon dates ± SD intervals.
DOI: 10.6084/m9.figshare.25458112
title: <b>Data set of the mineralogical exploration of biotite and </b><b>hornblende</b><b> in Long Valley rhyolite (XI Jaixin, 2024). </b>

description: Experimental results for the mineralogical investigations of biotite and hornblende in rhyolite from Long Valley, CA.
DOI: 10.6084/m9.figshare.27430458
title: Supplementary Material for: Developing a core outcome set for Netherton syndrome: An international multi-stakeholder e-Delphi consensus study

description: Introduction: Netherton syndrome (NS; OMIM#256500) is a rare and severe disorder of epidermal maturation and keratinization caused by pathogenic variants in the serine protease inhibitor Kazal type 5 (SPINK5), leading to severe skin barrier impairment. Although effective treatment is crucial for NS patients, there is a lack of knowledge on what the best treatment options are for these patients. Large heterogeneity in reported outcomes and measurement instruments hinders accurate comparison of treatment results across studies and the development of a treatment guideline. Therefore, we aimed to develop a core outcome set (COS) for NS that can be used in clinical care and research.

Methods: This study was performed in accordance with the recommendations of the Core Outcome Measures in Effectiveness Trials (COMET) initiative. After identification of outcomes through a literature search and classification based on the International Classification of Functioning and taxonomies published by the COMET initiative, discussion groups were organized at the 2nd International Netherton Congress 2022 to finalize the provisional outcome list. Through a 2-round e-Delphi, 41 stakeholders (patients and family members, professionals, and representatives of industry) from 14 countries rated the importance of the outcomes using a 9-point Likert scale. An online consensus meeting attended by 14 stakeholders finalized the COS.

Results: The core outcome set for NS comprised 21 outcomes in 10 domains. These included four ‘skin’ outcomes, two ‘sensation’ outcomes, two ‘side-effects of treatment’ outcomes, one ‘vitality’ outcome, one ‘emotional functioning’ outcome, two ‘physical development’ outcomes, two ‘nutrition’ outcomes, two ‘infections’ outcomes, two ‘allergies’ outcomes, and three ‘assessment results’ outcomes.

Conclusion: In this study, consensus was reached on 21 outcomes to be included in the COS for NS. The selection of outcomes in the COS underlines that NS not only affects the skin, but is a disease requiring a broad multidisciplinary approach in clinical care and research. International implementation of this COS will lead to more uniform reporting, thereby enabling comparison of study results, which may facilitate future treatment guideline development. The next step is to further conceptually define the outcomes and reach consensus on how the measure these.
DOI: 10.6084/m9.figshare.27732732
title: Supplementary Material for: Hypoxia-treated adipose mesenchymal stem cells derived exosomes enhance the therapeutic effects on unilateral ureteral obstruction mice

description: Introduction: The exosomes from adipose-derived mesenchymal stem cells (AMSCs) had therapeutic effects. However, whether the exosomes derived from hypoxia-treated AMSCs could improve renal functions in unilateral ureteral obstruction (UUO) mice remains unclear. 
Methods: The exosomes were characterized using a transmission electron microscope and Western blot. Its size distribution was determined using the Zetasizer Nano ZS analysis system. The differentiation ability was assessed by alkaline phosphatase and oil red staining. Consequently, the function of exosomes in inhibiting inflammatory factors was evaluated using an enzyme-linked immunosorbent assay, and apoptosis inhibition was evaluated by Western blot. Finally, the function of exosomes to ameliorate kidney fibrosis using qPCR, Western blot, hematoxylin-eosin staining and Masson staining.
Results: The cultured AMSCs could differentiate into osteoblast and adipocyte. Meanwhile, the cultured AMSCs could effectively secrete the exosomes, which were characterized with around 110 nm diameter and surface marker expression. Exosomes derived from hypoxia-treated AMSCs improved renal functions in UUO mice. The mechanism exploration revealed that exosomes could decrease the TNF-α and IL-6 and inhibit cell apoptosis. Finally, the fibrosis-associated protein was reversed, and the renal dysfunctions were ameliorated in UUO mice.
Conclusion: The exosomes derived from the hypoxia-treated AMSCs have a better effect than those from normal AMSCs in ameliorating renal dysfunctions in UUO mice.
DOI: 10.6084/m9.figshare.27851658
title: Supplementary Material for: Functional Role of the Incisive Duct in Neonatal Dogs

description: Introduction: The detection of chemical signals by the vomeronasal organ (VNO) is critical for mammals from an early age, influencing behaviors such as suckling and recognition of the mother. Located at the base of the nasal cavity, the VNO features a duct covered with a sensory epithelium. A critical aspect of VNO functionality is the efficient access of stimuli from the nasal and oral cavities to the receptors. In adult dogs, it has been demonstrated how the VNO duct (VD) communicates to the environment through the incisive duct (ID). In newborn puppies, the existence of functional communication between the ID and the VD has not been confirmed to date, raising doubts about the potential physiological obliteration of the ID. Determining this aspect is necessary to evaluate the role played by chemocommunication in the survival and socialization of puppies. Methods: This study employs serial histological staining to examine the presence and functionality of the ID in neonatal dogs. Additionally, a histochemical study was conducted using PAS and Alcian Blue staining, along with labelling with six lectins to characterize the expression of glycoconjugates in the incisive papilla and in the area between the ID and the VD. Results: The histological study has confirmed both the existence of functional communication between both ducts in perinatal puppies, and the dual functional communication of the ID with the oral and nasal cavities. The ID is associated with a sophisticated cartilaginous complex that prevents its collapse, as well as erectile tissue that acts as a cushion, facilitating its action under pressure induced by sampling behaviors such as tonguing. Lectin labelling has allowed for the characterization of the glycoconjugate expression profile in the papilla and ID, showing significant differences between lectins . Discussion: This investigation demonstrates the communicative capabilities of the VNO during the perinatal stage in dogs.
DOI: 10.6084/m9.figshare.28051433
title: Supplementary Material for: Analysis of Fibroblast Growth Factor 2 Impact and Mechanism on Broncho-Pulmonary Dysplasia

description: Objective:Epithelial-mesenchymal transition (EMT) of alveolar epithelial cells is an important mechanism for the onset and development of broncho-pulmonary dysplasia (BPD).The role of FGF-2 in BPD is currently unclear. The aim of our study is to investigate the expression of FGF-2 in lung tissue of BPD mice, to further clarify the effect of FGF-2 on EMT in alveolar epithelial cells and to actively search for possible signaling pathways. Methods: The BPD model was induced by exposure to hyperoxia. Lung tissue samples were collected and Hematoxylin and eosin (HE) staining was used to determine the modelling effect. Quantitative Real-time Polymerase Chain Reaction (QRT-PCR), immunohistochemistry were used to detect FGF-2 expression in BPD mice. To further investigate the effect of FGF-2 supplementation and deficiency on EMT in alveolar epithelial cells, A549 cells were cryopreserved, resuspended, cultured and passaged. Transforming growth factor-β1 (TGFβ1) was used to induce EMT. FGF-2 small interfering RNA fragments were synthesised and screened. Fbroblast growth factor receptor1 (FGFR1) expression was inhibited by BGJ398.  (3-(4, 5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H tetrazolium) (MTS) assay was used to detect the effect of FGF-2 and Infigratinib (BGJ398) on cell proliferation. We used qRT-PCR and Western blot to detect the expression of epithelial cell markers, mesenchymal cell markers and EMT-related signaling pathway proteins. Results: Our results showed that the successful established hyperoxia mice model were characteristic by BPD. Hyperoxia decreased FGF-2 on day 4, upregulated FGF-2 on day 21, which resulted in EMT. In vitro, we found that FGF-2 alone increased the expression of mesenchymal markers, decreased the expression of epithelial markers and activated Phosphatidylinositol 3-kinase/Protein kinase B (PI3K/AKT), Small mother against decapentaplegic (Smad), mitogen-activated protein kinase (P38) and extracellular signal-regulated kinase (ERK) signaling pathways. FGF-2 could not reverse but synergistically promote TGF-β1-induced EMT of alveolar epithelial cells. Silencing FGF-2 increased the expression of epithelial marker E-cadherin, inhibited the PI3K/AKT, Smad, and P38 signaling pathways activated by TGF-β1, but activated ERK signaling. FGF-2 receptor inhibitor BGJ398 reversed TGF-β1-induced EMT, decreased the expression of FGFR1, and inhibited ERK signaling pathway activation. Conclusions: FGF2 was closely associated with EMT in BPD mice. Both high and low levels of FGF2 promoted EMT in A549. The FGF-2 receptor inhibitor BGJ398 reversed TGF-β1-induced EMT in A549 by inhibiting the FGFR1/P-ERK signaling pathway.
DOI: 10.6084/m9.figshare.28053497
title: Supplementary Material for: Plasma transcriptome profile associated with CKD progression

description: Introduction: Understanding the molecular signals associated with the progression of kidney disease is vital for risk stratification and targeted treatment. Recent advances in RNA-sequencing technique has enabled us to characterize extracellular transcriptome profiles for precision diagnostics. 
Method: We evaluated the plasma mRNA profile of participants exhibiting slow (n=119) and fast (n=119) decline in estimated glomerular filtration rate (eGFR) among the Chronic Renal Insufficiency Cohort (CRIC) in a nested case control study. The two groups were matched for age, sex, race, baseline eGFR, proteinuria and diabetes status. The next generation sequencing data was analyzed using edgeR to identify differentially expressed genes (DEGs) and Ingenuity Pathway Analysis (IPA) was done to identify the associated pathways. We also compared the top plasma DEGs with gene expression in microdissected human CKD kidney.
Results: We identified fragments from ~28,000 annotated genes, of which 783 transcripts exhibited differential expression between slow and fast CKD progressors. Among 629 protein coding genes, 469 were overexpressed in slow progressors, while 157 showed increased expression in fast progressors. Expression of GLI2, CUX1, NOTCH1 and LRP1 transcripts were amplified in slow progressors. Pathway analysis linked these differentially expressed genes to WNT/β-catenin signaling, IL-12 signaling and production in macrophages, Netrin-1 Signaling and Epithelial-Mesenchymal Transition pathways. Many of the plasma differentially expressed genes were also upregulated in microdissected human CKD kidney. 
Conclusion: Warranting further validation, circulating levels of aberrantly expressed transcripts hold potential to be used as biomarkers for fast CKD progression.
DOI: 10.5281/zenodo.13951878
title: Energy and cost calculations for retrofitting packages based on Tabula building archetypes in the Netherlands

description: The dataset contains detailed energy and cost calculations for various retrofitting packages applied to different Tabula building archetypes in the Netherlands. The energy balance calculations are structured by building type and age categories, such as DH (detached house) and SD (semi-detached house) from different time periods (e.g., 1965-1974). The sheets include calculations of existing building performance, proposed retrofit scenarios, and associated energy savings. Cost breakdowns are provided for each retrofit option, detailing specific construction costs, taxes, and subsidies available for each scenario. This comprehensive dataset integrates both the technical (energy savings and U-values) and financial (costs and subsidies) aspects of retrofitting to provide a holistic view of retrofitting strategies in the Netherlands.
DOI: 10.5281/zenodo.14177307
title: An Integrated Machine Learning Approach Delineates an Entropic Expansion Mechanism for the Binding of a Small Molecule to α-Synuclein

description: The TRAJECTORY.zip contains two trajectories. One for the apo simulation (traj_mw_c4.xtc) and the other for the water simulation in .gro format (traj.gro). The  run1.tpr is the binary file for running the apo simulation in gromacs. For water simulation, the raw DOSPT files are also included to calculate the entropy.

The figure_raw_data.zip file contains the raw data that was used for plotting the figures in the main text and in the supplementary material.

For any further inquiries or requests for additional data, please contact jmondal@tifrh.res.in.
DOI: 10.15468/dl.zvgrms
title: Occurrence Download

description: A dataset containing 125 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Squalus blainville (Risso, 1827)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 125 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043329-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aycdug
title: Occurrence Download

description: A dataset containing 143339 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Arbutus unedo L."
 ]
}

 The dataset includes 143339 records from 707 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043313-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2df55v
title: Occurrence Download

description: A dataset containing 268 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Busseola fusca Fuller, 1901"
 ]
}

 The dataset includes 268 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043330-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.24432/c5h911
title: CAN-MIRGU
DOI: 10.15468/dl.7ayzsm
title: Occurrence Download

description: A dataset containing 186 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Squalus suckleyi (Girard, 1855)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 186 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043332-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.