cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4653484.v1
title: Table S11 from Parallel analysis of Arabidopsis circadian clock mutants reveals different scales of transcriptome and proteome regulation

description: The circadian clock regulates physiological processes central to growth and survival. To date, most plant circadian clock studies have relied on diurnal transcriptome changes to elucidate molecular connections between the circadian clock and observable phenotypes in wild-type plants. Here, we have integrated RNA-sequencing and protein mass spectrometry data to comparatively analyse the <i>lhycca1</i>, <i>prr7prr9</i>, <i>gi</i> and <i>toc1</i> circadian clock mutant rosette at the end of day and end of night. Each mutant affects specific sets of genes and proteins, suggesting that the circadian clock regulation is modular. Furthermore, each circadian clock mutant maintains its own dynamically fluctuating transcriptome and proteome profile specific to subcellular compartments. Most of the measured protein levels do not correlate with changes in their corresponding transcripts. Transcripts and proteins that have coordinated changes in abundance are enriched for carbohydrate- and cold-responsive genes. Transcriptome changes in all four circadian clock mutants also affect genes encoding starch degradation enzymes, transcription factors and protein kinases. The comprehensive transcriptome and proteome datasets demonstrate that future system-driven research of the circadian clock requires multi-level experimental approaches. Our work also shows that further work is needed to elucidate the roles of post-translational modifications and protein degradation in the regulation of clock-related processes.
DOI: 10.6084/m9.figshare.5072665.v1
title: Data and code to reproduce Dallas et al. "Estimating parasite host range"

description: This repository contains code and data (only for the Sevilleta LTER) to reproduce the analyses from:<br>&gt; Dallas,T, S Huang, C Nunn, A Park, and JM Drake. 2017. "Estimating parasite host range". Proceedings of the Royal Society B. <br>The Global Mammal Parasite Database is available at https://doi.org/10.1002/ecy.1799
DOI: 10.17632/5bvx4g39dw
title: ECOGEN: An open-source tool for multiphase, compressible, multiphysics flows

description: ECOGEN, a new open-source computational fluid dynamics code is presented. It is a multi-model tool devoted to the simulation of compressible flows. A large range of problems can be solved, from single-phase gas dynamics to multiphase, multiphysics flows including interface problems between pure fluids. This code is suited for strongly unsteady flows. The numerical solver of ECOGEN is implemented in a flexible structure making the code able to compute such complex flows on different kinds of discretization grids. The implemented hyperbolic solver is able to deal with Cartesian geometries as well as unstructured grids. A recent adaptive mesh refinement method is also implemented. Its numerical implementation is presented in detail to help the enthusiastic developer to contribute to this open-source project. Representative test cases are presented to show the tool abilities and to open the gate for future developments.
DOI: 10.17632/dw6y4r7hcr
title: Influence of heat treatment on mRNA expression in PBMCs from healthy donors and ME/CFS patients

description: Our research hypothesis was that heat treatment by water-filtered infrared-A irradiation (wIRA) at 39 °C for 60 minutes would lead to changes in mRNA expression compared to an untreated control. PBMCs from healthy donors and ME/CFS patients were studied. The following files show the calculation of n-fold mRNA expression of the genes AMPK1α, ATG7, Beclin1, FOXO3, HSPA5, IL-10, MAP1LC3B, SIRT1 and ULK1 using the 2-ΔΔCt method, as well as the calculated n-fold mRNA expression values per gene. The data show activation of mRNA gene expression of MAP1LC3B, SIRT1 and HSPA1 by wIRA irradiation.
DOI: 10.6084/m9.figshare.12560567.v1
title: Additional file 7 of Understanding the early cold response mechanism in IR64 indica rice variety through comparative transcriptome analysis

description: Additional file 7. Table containing sequences of primers used for qRT-PCR assays.)
DOI: 10.6084/m9.figshare.12935222.v1
title: Dataset for R analyses v2

description: Supplemental Data for R analyses; each sheet should be saved out as its own .csv for R. This version contains the humerus and femur circumference metrics in sheet 2 (BodyMass_RegMtrx) that were missing in the version 1.
DOI: 10.6084/m9.figshare.22770149.v1
title: yoko_second_forest_dynamic.csv

description: This data was collected along a chronosequence in and around the Yoko forest reserve one the central Congo basin. The data consist of five files behind the manuscript's main figures: "Afrotropical lowland forests exhibit a sustained net carbon sink along succession, despite substantial shifts in allocation, demography and functional composition". You will find in these files plot level AGC for two censuses (2018 and 2020), plot level NPP and NPP allocation, plot level demographic rates, plot level net C sink, NPP partitioning into stem size classes, successional stage partitioning into plant functional groups according to Hawthorne (1995) classification and community weighted mean of plant functional traits and their link to demographic rate.
DOI: 10.6084/m9.figshare.23866962.v47
title: Development of global monthly dataset of CMIP6 climate variables for estimating evapotranspiration

description: Regridding Global CMIP6 GCMs dataset(0.5 degree)Historical dataset: 14 CMIP6 GCMs (1850-2014)Future dataset: 14 CMIP6 GCMs and 4 SSP scenarios (2015-2100)Code: PET code(Python)Composition of dataset: Average temperature, Maximum temperature, Minimum temperature, Wind speed, Relative humidity, Solar radiation<br>If you are using our codes and dataset, please use the following references:Song, Y.H., Chung, ES., Shahid, S. et al. Development of global monthly dataset of CMIP6 climate variables for estimating evapotranspiration. Sci Data 10, 568 (2023). https://doi.org/10.1038/s41597-023-02475-7
DOI: 10.6084/m9.figshare.13859783.v1
title: Williams etal JEcol Supplemental data files

description: From Williams_etal_JEcol this is the supplemental datasets for root exduates and leachate, including root traits data. A second dataset contains all signficant features and GOLM ids
DOI: 10.6084/m9.figshare.25965397.v3
title: Indentifying materials using Mo isotopes in intraplate alkali basalts from southeastern margin of Tibetan Plateau

description: This study hypothesizes that there are different recycled mantle materials in the deep mantle, which can be identified using molybdenum (Mo) isotope ratios. This dataset comprises analysis data of intraplate alkali basalt samples collected from the southeastern margin of the Tibetan Plateau. These data include Mo isotope ratios, Sr, Nd, and Pb isotope ratios, as well as the major and trace element compositions of the samples. The data analysis reveals significant variations in Mo isotope ratios among the samples, indicating the presence of different types of recycled materials in the mantle source regions of these basalts. This study supports the capability of Mo isotopes to trace different recycled materials in the mantle.embargo period.
DOI: 10.6084/m9.figshare.27934782.v1
title: Raw data of learning style survey for junior doctors

description: Raw data of learning style survey for junior doctors
DOI: 10.17632/8v467h7myg
title: Onion and Garlic Mixture Enhances Performance and Survival in Broiler Chickens Infected with Newcastle Disease Virus and Infectious Bronchitis Virus

description: Vaccines have become less effective due to more virulent antigens, prompting increased recommendations for natural herbs and phytochemicals. This study aimed to evaluate the effects of an onion and garlic mixture (OGM) on performance, carcass composition, liver enzymes, intestinal morphology, and mortality in broiler chickens infected with Newcastle Disease Virus (NDV) and Infectious Bronchitis Virus (IBV). 300 chicks were divided into five treatment groups: the control group (T1) received a basal diet, while groups T2, T3, T4, and T5 were supplemented with 1.5%, 3%, 4.5%, and 6% OGM, respectively. All chicks were infected with NDV on day 7 and IBV on day 25. Results indicated that 3% OGM significantly improved average weight gain (AWG) and feed intake (AFI) during the starter phase (P≤0.05) without affecting performance in the grower phase. OGM supplementation increased AWG, reduced mortality in NDV-infected chicks, and lowered mortality in IBV-infected chickens during the finisher phase. Although there were no significant changes in internal organ weights, intestinal morphology, or NDV antibody levels, OGM reduced liver damage and enhanced immunity against IBV by boosting antibody production (P≤0.05). In conclusion, Including OGM in chicken diets boosts their immune systems, supports growth, and lowers mortality rates. Therefore, adding OGM at 1.5% or 3% in broiler diets can enhance performance and reduce mortality, minimizing economic losses in the poultry sector.
DOI: 10.17632/vy7mxkkgx5
title: Dataset on validation of double U-tube borehole and seasonal solar thermal energy storage system TRNSYS models

description: This dataset includes data from the validation of double U-tube borehole and seasonal solar thermal energy storage system TRNSYS models. The simulated transient temperatures at various points of the systems were compared with the measured ones. To quantify the agreement between each simulated and measured temperature of interest, mean bias error (MBE), root mean square error (RMSE) and correlation coefficient (CC) were applied.
DOI: 10.5281/zenodo.15028927
title: Conjunto de dados da pesquisa: O COMPARTILHAMENTO E O REÚSO DE DADOS DOS PESQUISADORES DE GRUPOS DE PESQUISA NA ÁREA DE ENFERMAGEM DO ESTADO DO RIO DE JANEIRO

description: Conjunto de dados gerados durante a pesquisa de tese O COMPARTILHAMENTO E O REÚSO DE DADOS DOS PESQUISADORES DE GRUPOS DE PESQUISA NA ÁREA DE ENFERMAGEM DO ESTADO DO RIO DE JANEIRO
DOI: 10.6084/m9.figshare.17206589.v1
title: A Proteogenomic Atlas of Clear Cell Renal Cell Carcinoma in a Chinese Population

description: Clear cell renal cell carcinoma (ccRCC) is a majority and aggressive subtype of renal cancer. Here we conduct a comprehensive proteogenomic analysis of 232 tumor and adjacent non-tumor tissue pairs from Chinese ccRCC patients. By comparing with tumor adjacent tissues, we find that ccRCC shows extensive metabolic dysregulation and intensive immune response. Molecular subtyping classifies ccRCC tumors into three subtypes (GP1–3), among which the most aggressive GP1 exhibit dominant immune response, metastasis, and metabolic imbalance, linking the proteomic features, transcription factor activities, genomic alterations, and clinical outcomes of ccRCC. Nicotinamide N-methyltransferase (NNMT), a one-carbon metabolic enzyme, is identified as a potential marker of ccRCC and a drug target for GP1. We demonstrate that NNMT induces DNA-dependent protein kinase catalytic subunit (DNA-PKcs) homocysteinylation, increases DNA repair, and promotes tumor growth in ccRCC. This study provides valuable insights into the biological underpinnings and prognosis assessment of ccRCC, revealing targetable metabolic vulnerabilities.
DOI: 10.6084/m9.figshare.26242157.v1
title: SupplementaryTable1.xlsx

description: Excel spreadsheet containing ophiolite isotopic and trace element data
DOI: 10.6084/m9.figshare.28547030.v1
title: Supplementary Files 3: 50p_AA_MC

description: Supplementary Files 3: 50p_AA_MC
DOI: 10.6084/m9.figshare.4042407.v1
title: Larval zebrafish electrical heart model

description: COMSOL electrical model of larval zebrafish and associated geometry files (.step) and COMSOL geometry.
DOI: 10.17632/kwjfn96d6z
title: Analyzing Recycling Infrastructure Disparities in Costa Rica Through Geospatial Analysis and Monte Carlo Simulations

description: Python Code Files (.py):
These Python scripts were used for Monte Carlo simulations and statistical analyses of recycling infrastructure disparities in different regions of Costa Rica, specifically focusing on Limon and San Jose. The scripts generate simulation models to assess the variability of recycling rates, simulate the financial costs associated with recycling infrastructure, and produce relevant visualizations such as recycling rate figures. The simulations and analyses support the research paper by providing detailed statistical insights and graphical representations of recycling performance.

PDF Files (.pdf):
The uploaded PDF files include both infographics and reference materials:

Infographics for Limon, Puntarenas, and San Jose present regional data on population and housing estimates, which were used as input for the recycling rate and infrastructure simulations.
Reference documents on solid waste management in Latin America and the Caribbean provide context on regional waste management practices, while documents on tariffs and costs for January 2024 supply financial data used in the simulations for evaluating the cost efficiency of recycling infrastructure.
DOI: 10.17632/rsdgtkphsb
title: Data for: Modelling the optimal target age group for seasonal influenza vaccination in Japan

description: The data for analysis in "Modelling the optimal target age group for seasonal influenza vaccination in Japan" Population data: "age_sizes_japan.rda" Contact data: "jpoly2.rda" Influenza incidence data: "jpinci2.rda", "jpswab20XX.rda" Vaccination data: "jpvac20XX.rda" Virological data: "jpvir.rda", "jpvir20XX.rda" Virological data other than influenza virus: "vir20XX.csv" (just for reference, not entered in the model) R codes for SEIR model: "flu_model.R", "run_model.R", and "vac_model.R"
DOI: 10.17632/scy82bdkh4
title: Is US Trade Policy Reshaping Global Supply Chains?

description: Replication files for "Is US Trade Policy Reshaping Global Supply Chains?" 
Caroline Freund, Aaditya Mattoo, Alen Mulabdic, Michele Ruta
DOI: 10.6084/m9.figshare.20693128.v1
title: BCC-CSM2-MR

description: This archive contains downscaled daily data from the BCC-CSM2-MR model for the historical (1980–2014) and future (2015–2099) periods. The compressed tar file can be expanded using the following command: tar zxvf BCC-CSM2-MR.tar.gz Data availability: - Variables: pr, tas, tasmax, tasmin - Historical period: 1980–2014 - Future period: 2015–2099 - Scenarios: SSP1-2.6, SSP2-4.5, SSP3-7.0, SSP5-8.5
DOI: 10.6084/m9.figshare.20709391.v1
title: Supplementary Material for: Suggestive evidence for an antidepressant effect of metreleptin treatment in patients with lipodystrophy

description: Introduction: Lipodystrophy (LD) syndromes are rare heterogeneous disorders characterized by reduction or absence of subcutaneous fat, low or non-detectable leptin concentrations in blood and impaired hunger/satiety regulation. Metreleptin treatment reverses metabolic complications and improves eating behavior in LD. Because depression in anorexia nervosa (AN), which is also characterized by hypoleptinemia, improves substantially upon treatment with metreleptin, we hypothesized, that metreleptin substitution may be associated with an antidepressant effect in patients with LD, too. Methods: In this ancillary study ten adult patients with LD were treated with metreleptin. To assess depressive symptoms, the self-rating questionnaire Beck’s Depression Inventory (BDI) was filled in at pre-established time points prior (T1) and after initiation of metreleptin (T2: 1 week; T3: 4 weeks; T4: 12 weeks) dosing. The differences between time points were tested with nonparametric Friedman's analysis of variance. Sensitivity analyses were performed upon exclusion of the BDI items addressing appetite and weight changes. Results: According to their BDI scores, four patients had mild depression and two had moderate depression at baseline. Friedman’s test revealed significant differences in BDI scores between the four time points. Post-hoc analyses revealed that the difference between T1 and T3 was significant upon Bonferroni correction (p=0.034, effect size r=0.88). The sensitivity analyses upon exclusion of the appetite and weight change items again revealed a significant Friedman’s test and significant Bonferroni corrected differences in the revised BDI scores between T1 vs. T2 (p=0.002, r=0.99) and T1 vs. T3 (p=0.007, r=0.79). Discussion/Conclusion: Our study for the first time revealed suggestive evidence for an antidepressant effect of metreleptin in patients with LD. Metreleptin caused a rapid drop in depression scores within one week of treatment. A reduction of the depression score was also observed in two of the three LD patients whose BDI scores were in the normal range before start of the treatment. The reduction in total scores of BDI were still apparent after three months (T4) of dosing. This observation matches findings obtained in clinical case studies of AN patients, in whom depression scores also dropped during the first week of metreleptin treatment.
DOI: 10.6084/m9.figshare.26973085.v1
title: 3D Mask R-CNN data

description: Image repository of the paper 3D Mask R-CNN Benchmarks in Controlled Environment and Morphogenesis StudyThis repository contains the test set of the Phallusia mammillata dataset and used in the paper to train and validate the 3D Mask R-CNN. The test set is composed of the PM1 embryo images and ground truth. In details:<br>the 3D input image of Phallusia mammillata PM1 embryo (Inputs.zip)the ground truth ASTEC instance segmentation of these input images (ASTEC_Ground_truth.zip)the predictions infered by the trained 3D Mask R-CNN (3D_Mask_R_CNN.zip)the predictions infered by the state-of-the-art network for cell instance segmentation Cellpose (Cellpose.zip)the resulting weights of the 3D Mask R-CNN trained over the Phallusia mammillata dataset. These data can be used to reproduce the 3D Mask R-CNN inference over the Phallusia mammillata test set and to evaluate the predictions against the ASTEC ground truth.The 3D Mask R-CNN code is available here: https://github.com/gdavid57/3d-mask-r-cnnSee the "morphogenesis" branch for the Phallusia mammillata dataset.
DOI: 10.6084/m9.figshare.5226328.v1
title: EnergyPlus Input Data Files used to test HVAC systems in two buildings in eight different climate regions of Portugal

description: This is a set of EnergyPlus v8.7.0 Input Data Files (IDFs) used to test several HVAC systems in two buildings in eight different climate regions of Portugal.
DOI: 10.15468/dl.b5ej49
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Nycticebus javanicus É.Geoffroy Saint-Hilaire, 1812"
 ]
}

 The dataset includes 50 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013188-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.16745896.v1
title: Raw sequencing data

description: Sequencing data from healthy volunteers
DOI: 10.6084/m9.figshare.28440581.v1
title: Data from:<i> </i><i>Lerista karichigara </i>sp. nov. (Scincidae; Sphenomorphini), a new fossorial skink from Australia's underexplored Gulf Plains Bioregion

description: Data from: Zozaya S.M., Vanderduys, E., Macor, S.A., Read, W.J. & Amey, A.P. (2025) <i>Lerista karichigara </i>sp. nov. (Scincidae; Sphenomorphini), a new fossorial skink from Australia's underexplored Gulf Plains Bioregion. <i>Zootaxa</i>, 5613 (2): 262–278.Files include:(i) karichigara_raw_mophology.csv — Raw morphological data and geographic coordinates for the type series of <i>Lerista karichigara</i>.(ii) morphology_definitions.csv — Definitions for columns in karichigara_raw_mophology.csv.(iii) Lerista-karichigara_ND4.fasta — Sequence alignment in FASTA format, comprising 849 bp of mitochondrial DNA (mtDNA), including 738 bp of the NADH dehydrogenase 4 (ND4) protein-coding gene and 111 bp of the 3'-end tRNA region. Note that 'N' was added to the first two sites to ensure the sequence is in the correct reading frame.(iv) Lerista-karichigara_ND4_partitions.txt — Partition file for Lerista-karichigara_ND4.fasta.(v) p-distances_wilkinsi-clade.csv — Pairwise sequence dissimilarity among the respective <i>Lerista</i> species, calculated from Lerista-karichigara_ND4.fasta.
DOI: 10.17632/9ktv578p59
title: Emotional Instability and Behavior Difficulties Scale (EIBDS)
DOI: 10.6084/m9.figshare.12547574.v1
title: PMOA-CITE dataset

description: The dataset used in the experiments on the paper "Modeling citation worthiness by using attention‑based bidirectional long short‑term memory networks and interpretable models"<br>There are one million sentences in total, and further splitted into trainning, validation and testing by 60%, 20% and 20%, respectively.<br>For the pre-processing of the dataset, please refer to the paper.<br>The data are stored in jsonl format (each row is an json object), we list a couple of rows as example:{"sec_name":"introduction","cur_sent_id":"12213838@0#3$0","next_sent_id":"12213838@0#3$1","cur_sent":"All three spectrin subunits are essential for normal development.","next_sent":"βH, encoded by the karst locus, is an essential protein that is required for epithelial morphogenesis .","cur_scaled_len_features":{"type":1,"values":[0.17716535433070865,0.13513513513513514]},"next_scaled_len_features":{"type":1,"values":[0.32677165354330706,0.35135135135135137]},"cur_has_citation":0,"next_has_citation":1}{"sec_name":"results","prev_sent_id":"12230634@1@1#0$2","cur_sent_id":"12230634@1@1#0$3","next_sent_id":"12230634@1@1#0$4","prev_sent":"μIU/ml at the 2.0-h postprandial time point.","cur_sent":"Statistically significant differences between the mean plasma insulin levels of dogs treated with 50 mg/kg of GSNO, and those treated with 50 mg/kg GSNO and vitamin C (50 mg/kg) were observed at the 1.0-h and 1.5-h time points (P &lt; 0.05).","next_sent":"The mean plasma insulin concentrations in the dogs treated with 50 mg/kg of vitamin C and 50 mg/kg of GSNO, or 50 mg/kg of GSNO was significantly altered compared to those of controls or captopril-treated dogs (P &lt; 0.05).","prev_scaled_len_features":{"type":1,"values":[0.09448818897637795,0.08108108108108109]},"cur_scaled_len_features":{"type":1,"values":[0.8582677165354331,1.0]},"next_scaled_len_features":{"type":1,"values":[0.7913385826771654,0.9459459459459459]},"prev_has_citation":0,"cur_has_citation":0,"next_has_citation":0}<br><br>{"sec_name":"results","prev_sent_id":"12213837@1@0#3$3","cur_sent_id":"12213837@1@0#3$4","next_sent_id":"12213837@1@0#3$5","prev_sent":"Cleavage of VAMP2 by BoNT/D releases the NH2-terminal 59 amino acids from the protein and eliminates exocytosis.","cur_sent":"However, in this case, exocytosis cannot be recovered by addition of the cleaved fragment .","next_sent":"Peptides that exactly correspond to the BoNT/D cleavage site (VAMP2 aa 25–59 and 60–94-cys) were equally efficient at mediating liposome fusion (unpublished data).","prev_scaled_len_features":{"type":1,"values":[0.36220472440944884,0.35135135135135137]},"cur_scaled_len_features":{"type":1,"values":[0.2795275590551181,0.2972972972972973]},"next_scaled_len_features":{"type":1,"values":[0.562992125984252,0.5135135135135135]},"prev_has_citation":0,"cur_has_citation":1,"next_has_citation":0}<br>For the code using this dataset to modeling citation worthiness, please refer to https://github.com/sciosci/cite-worthiness<br><br><br><br><br>