cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16772293.v1
title: Phylogenomic data for Herranz et al.

description: <b>Data for phylotranscriptomic analysis of Kinorhyncha by Herranz et al.</b><br>The repository contains:<br>0_OrthoFinder_MultipleSequenceAlignments.tar.gz: orthogroup alignment files as produced from OrthoFinder.<br>1_OrthoFinder_GeneTrees.tar.gz: gene trees obtained for orthogroup alignments as produced by OrthoFinder using FastTree.<br>2_OrthoFinder_ResolvedGeneTrees.tar.gz: rooted and resolved gene trees as produced by OrthoFinder.<br>3a_PhyloTreePruner_SingleCopyAlignments_GeneTrees.tar.gz: Single copy alignments as generated by PhyloTreePruner from the Resolved Gene trees and the Multiple Sequence Alignments. After pruning, alignments were realigned with MAFFT L-ins-i. Gene trees obtained from the realigned single copy gene trees with IQTREE.<br>3b_ASTRAL_SingleCopySpeciesTree.tar.gz: Input and output files of ASTRAL-III species tree analysis.<br>3c_IQTREE_Supermatrices.tar.gz: Input and output files of concatenated species tree analysis based on the 70% and 80% occupancy matrix analyzed with IQTREE.<br>4_ASTRAL-Pro_MultiCopySpeciesTree.tar.gz: Input and output files of ASTRAL-Pro species tree analysis, which analyzed multi copy gene trees from OrthoFinder (1_OrthoFinder_GeneTrees.tar.gz) to build a species tree. <br>5a_ASTRAL-Pro_noLowQuality.tar.gz: input and output files for ASTRAL-Pro species tree analysis after removing lower quality transcriptomes (E. dujardinii, E. kohni, Pycnophyes sp.).<br>5b_ASTRAL-Pro_noOutgroups.tar.gz: input and output files for ASTRAL-Pro species tree analysis after removing the transcriptomes of the long branched Nematoida and Loricifera.<br><br><br><br>
DOI: 10.6084/m9.figshare.17292410.v3
title: Developer experience metrics

description: Collection of developer experience metrics from the published paper: Metrics to Quantify Software Developer Experience: a Systematic Mapping.
DOI: 10.6084/m9.figshare.25725594.v3
title: Datasets and R code for Hwang, B.C., <i>et al.</i> The impact of insect herbivory on biogeochemical cycling in broadleaved forests varies with temperature. <i>Nature Communications</i><b> </b><b>15</b>, 6011 (2024).

description: We established a global network of 74 plots within 40 mature, undisturbed broadleaved forests located across tropical, temperate, and boreal zones to investigate the impact and drivers of insect herbivory on element cycling. Using standardized methods, we analyzed freshly senesced and green leaves from these plots to estimate foliar production and herbivory, carbon, nitrogen, phosphorus and silica concentrations, and stand-level nutrient fluxes as deposited by insect herbivores. We then compared insect-mediated element fluxes to other sources of labile nutrients such as atmospheric deposition and bedrock weathering. We also investigated abiotic (mean annual temperature, evapotranspiration : mean annual precipitation, soil nutrient concentrations) and biotic (foliar biomass production, leaf-level herbivory, foliar nutrient concentrations) factors as potential drivers of these fluxes. All annual data by litter trap (herblat.xls), by plot means (herblatmeans.xls), and code for analysis (herblatcode.R) found in this folder were used for the following manuscript:Hwang, B.C., Giardina, C.P...Metcalfe, D.B<i>.</i> The impact of insect herbivory on biogeochemical cycling in broadleaved forests varies with temperature. <i>Nature Communications</i> <b>15</b>, 6011 (2024). https://doi.org/10.1038/s41467-024-50245-9<br>V.2 Updated figshare title and citation to corresponding article<br>V.3 Edited plot and means data for GURIA, LAGON1, and SAIRME locations
DOI: 10.6084/m9.figshare.28916324.v2
title: Data and code for wetland plant elemental homeostasis

description: Data and code for "Plant elemental homeostasis enhances species performance and community functioning in wetlands: looking beyond nitrogen and phosphorus". figshare. Dataset. https://doi.org/10.6084/m9.figshare.28916324.v2All R scripts use relative paths and assume the working directory is the one where the code is located.Contents:This file contains the dataset and R code used in this study. In this dataset file (Dataset for wetland plant elemental homeostasis), we contain seven sheets.Sheet 1, named "Metadata" contains a detailed description of the abbreviations that appear in the dataset.Sheet 2, named "species-level stoichiometry", we have a 1059*35 matrix, represents the data at the species-level in the analysis of this study;Sheet 3, named "community-level stoichiometry", we have a 225*34 matrix, represents the data at the community-level in the analysis of this study;Sheet 4, named "element_homeostasis_variation ", represents the concentration, coefficient of variation and homeostasis coefficient of 16 elements at the species and community levels;Sheet 5, named "species_H_performance", includes regional abundance, dominance, biomass, stability, elemental concentration and elemental homeostasis coefficient of 12 common species;Sheet 6, named "community biomass-homeostasis", includes community biomass, community-weighted mean (CWM) elemental concentration, elemental homeostasis coefficient and environmental factors at plant community level.Sheet 7, named "site_environment", includes sediment elemental concentrations of 16 elements of this study.Furthermore, we also provide the "Global or regional Plant element database" for comparison with this study.
DOI: 10.6084/m9.figshare.7127267.v1
title: Supplementary Material for: Nitrosonifedipine, a Photodegradation Product of Nifedipine, Suppresses Pharmacologically Induced Aortic Aneurysm Formation

description: <b><i>Background/Aims:</i></b> We have reported that nitrosonifedipine (NO-NIF), a photodegradation product of nifedipine, has strong antioxidant and endothelial protective effects, and can suppress several cardiovascular diseases in animal models. The objective of the present study was to investigate the effects of NO-NIF on aortic aneurysm formation. <b><i>Methods:</i></b> The mice were infused with β-aminopropionitrile for 2 weeks and angiotensin II for 6 weeks to induce aortic aneurysm formation. The oxidative stress was measured by dihydroethidium staining and nitrotyrosine staining. The expressions of inflammation-related genes were assessed by quantitative real-time PCR and immunohistochemical staining. To clarify the mechanisms of how NO-NIF suppresses vascular cell adhesion molecule (VCAM)-1, endothelial cells were used in in vitro system. <b><i>Results:</i></b> NO-NIF suppressed pharmacologically induced the aortic aneurysm formation and aortic expansion without blood pressure changes. NO-NIF suppressed elastin degradation and matrix metalloproteinase-2 mRNA expression. NO-NIF suppressed the reactive oxygen species-cyclophilin A positive feedback loop. Upregulated mRNA expressions of inflammation-related genes and endothelial VCAM-1 were suppressed by NO-NIF co-treatment in aortae. <b><i>Conclusion:</i></b> NO-NIF has the potential to be a new, nifedipine-derived therapeutic drug for suppressing aortic aneurysm formation by directly improving aortic structure with its strong ability to reduce oxidative stress and inflammation.
DOI: 10.17632/ft9rsmtzzv
title: Data for: Assessing Biophilic Design Elements for Ecosystem Service Attributes - A Sub-Tropical Australian Case

description: The sheets within this excel file document participant's scoring of ecosystem function potential of listed Biophilic Design Elements. Based on participant scoring, each listed Biophilic Deisng Element is assessed for ecosystem service attributes
DOI: 10.6084/m9.figshare.7059554.v2
title: CT Scan Files.zip

description: Exemplar CT scan dataset of the femur of the tyrannosaurid <em>Daspletosaurus torosus</em> (specimen number TMP 2001.036.0001).
DOI: 10.17632/b4cg3kyygs
title: Building a Diverse Text-to-Image Generation Dataset

description: In the field of generative artificial intelligence, text-to-image generation makes the tremendous advancements necessary to solve many real-world problems. Data is the key attribute for the model to produce efficient results. This dataset was collected for text-to-image generation research purposes, aiming to train models to generate images based on textual descriptions. It comprises images of 11 classes, with multiple images representing each class. This diverse dataset enables the fine-tuning of text-to-image generation models, enhancing their performance. The collected images are mainly focused on Indian scenarios.
DOI: 10.17632/ps2d37n45h
title: Job performance among prison officers in Slovenia

description: Results of the study among prison officers in the Republic of Slovenia. The survey is based on the following constructs: task performance, job stress, job satisfaction, organizational justice, dangerousness of the job, and job involvement. The survey was conducted on the population of prison officers in Slovenia. Sample size is n=201.
DOI: 10.6084/m9.figshare.1134533.v1
title: Figure 1 full dataset

description: Full dataset for Figure 1 from "Clearance of human IgG1-sensitised red blood cells in vivo in humans relates to the in vitro properties of antibodies from alternative cell lines."
DOI: 10.6084/m9.figshare.15029118.v1
title: Data

description: Contains the data used in this work.<br><b>Demographic and clinical:<br></b>- FBC_biochem.txt - full blood counts and blood chemistry<br>- RDW.txt - red blood cell distribution width - smoke.txt - smoking behaviour of a few individuals<br><b>Longitudinal sequencing data:</b>- ALLvariants_exclSynonymous_Xadj.txt - longitudinal sequencing data for all 56 CH genes - Recurrent_sites_finalPhase.txt - data for the 6th timepoint (available for only a few individuals)<br><b>Cross-sectional sequencing data and dN/dS:</b>- dnds_aml_mds.csv - dNdS in AML and MDS for specific sites<br>- dnds_global.txt - global dNdS for this cohort - dnds_genes.txt - gene-wise analysis of dNdS in this cohort<br>- dnds_domains.txt - domain-wise analysis of dNdS in this cohort- dnds_site.txt - site-wise analysis of dNdS in this cohort<br><br><b>Phylogenetic data:</b>- tree_id2259, tree_id3877, tree_id500 - phylogenetic trees for three individuals- details_id2259_CNcorrected, details_id3877, details_id500 - R objects containing information on the phylogenetic trees- Trees_emily.zip - files from Mitchell et al. (2021); must be uncompressed into "Trees_emily"<br><b>Metadata:</b>- excluded_individuals - individuals excluded from this analysis<br>- excluded_individuals_lymphocyte - individuals excluded from this analysis due to abnormal lymphocyte counts- included_genes - genes included in this analysis<br>- variants_bedfile_withDomainAnnotation.xlsx - domain information<br><b>Incidence, AML risk and dN/dS from other studies:</b>- aml_incidence.csv - incidence of acute myeloid leukaemia retrieved from CRUK- aml-risk-coef.csv - coefficients for AML risk from Abelson et al. (2018)- leukaemia_incidence.csv - leukaemia incidence retrieved from CRUK <br><b>Technical replicates:</b>- Replicates_all.txt - technical replicate data for a few individuals<br>- TruQ.txt - sequencing technical replicates
DOI: 10.6084/m9.figshare.27879906.v1
title: PlosOne Data by Ender ŞENEL

description: PlosOne Data by Ender ŞENEL
DOI: 10.6084/m9.figshare.27988568.v1
title: Dataset: Fire and seed dormancy - A global meta-analysis

description: The dataset contains experimental data on fire-related germination cues—such as heat shock, smoke, and smoke-derived chemicals—in plant species worldwide. This data was compiled from published scientific studies.
DOI: 10.6084/m9.figshare.28942752.v1
title: Additional file 1 of Genomic insights into the spread of methicillin-resistant Staphylococcus aureus involved in ear infections

description: Supplementary Material 1
DOI: 10.17632/yj3v4pnd68
title: Data driven multilayer complex networks of Sustainable Development Goals

description: The dataset enables the modeling of countries' sustainable development goals, targets and indicators. It includes the World Bank Open Data database, the own developed MATLAB codes for network formulation, the network files and analyzed networks are also attached.
DOI: 10.6084/m9.figshare.13179947.v1
title: California_Electric_Substation.shp

description: California Electric Substations
DOI: 10.6084/m9.figshare.21994592.v1
title: Trained and Untrained sEMG data

description: Raw data of postural muscles outputed from Delsys during bilateral arm raising movements before and after general fatiguing exercises.
DOI: 10.6084/m9.figshare.24241336.v1
title: RP dataset files

description: Raw and processed alignments and corresponding phylogenetic trees for RP dataset.
DOI: 10.6084/m9.figshare.24786711.v1
title: Container Orchestration Smells in ChaGPT-generated Kubernetes Manifests

description: Dataset and source code used for the paper "Does Generative AI Generate Smells Related to Container Orchestration?: An Exploratory Study with Kubernetes Manifests"
DOI: 10.6084/m9.figshare.26004463.v2
title: Data from: Territorial movements of African lions: can waterholes shape multiple central-place territories?

description: <b>data_trip_to_water.rds</b> contains for each lion used in the analysis (43 individuals) the trajectories (x, y, time) of lion trips between waterholes and the characteristics of these trips (duration, straightness, name of starting and ending waterholes…).<b>IBM_simulation</b>: Here are the trajectories simulated using an integrated step selection function fitted to each lions’ empirical trajectories. For each simulated dataset, one “IBM_returnLION_NAME.rds” is present. The .rds document is a list that contains the simulated coordinates at each time step (x,y,t) (First element of the list) and the coordinates of the territorial borders (Last element of the list).
DOI: 10.17632/7bvnhn5k22
title: Relationship between anemia or RBC transfusion and BPD

description: A retrospective study was conducted to investigate the association of anemia，especially severe anemia, with the development of BPD in preterm Infants. We also investigated whether the rate, number and volume of red blood cell transfusion are related to the risk and of BPD and its severity.
DOI: 10.6084/m9.figshare.10252949.v1
title: List of predicted secreted proteins of M. enterolobii (genome V1, INRA/JKI)

description: Predicted Secretome of M. enterolobii genome (V1, INRA/JKI)<br><br>Strategy:<br>1. Use SignalP 4.0 that better discriminate between SP and N-terminal TM<br>Put the -m 'file' option to produce a FASTA with cleaved SP<br><br>signalp -f short -m MentV1-cleaved.fa -t euk MentV1.pep.fa &gt; MentV1.SP<br><br>--&gt; there are 6,065 proteins with a predicted SP.<br><br>2. Use TMHMM-2.0 to predict TMs on the cleaved FASTA sequences.<br><br>tmhmm --short MentV1-cleaved.fa &gt; MentV1-cleaved-TM-short.txt<br><br>--&gt; there are 1,092 proteins with a SP and at least one TM (that is not included within the SP).<br>Thus 4,973 proteins with SP and no TM.<br><br>3. Generate a list of sequences with predicted SP an no predicted TM<br>The accession numbers for the 4,973 proteins with SP and no TM is saved in MentV1.SP-no-TM.acc<br>
DOI: 10.6084/m9.figshare.22014317.v1
title: Cytotoxicity detection for infrared fluorescent proteins

description: Cytotoxicity detection for infrared fluorescent proteins
DOI: 10.6084/m9.figshare.23912082.v1
title: Raw Data M Zahid Dogan.rar

description: Raw data of the research study
DOI: 10.6084/m9.figshare.24161226.v5
title: Data and codes of "Uncovering widespread Anthropocene dietary shifts in Chinese large mammalian herbivores".

description: This is the original data used in the ecological paper titled "Uncovering widespread Anthropocene dietary shifts in Chinese large mammalian herbivores". There are a total of five Excel files and one txt file:Code for microwear diversity. txt. The code of calculating microwear diversity with the package "FD" (functional diversity).a_e.csv & a_w.csv. The matrices "a" of eastern & western China respectively for calculating the microwear diversity by the package "FD". #Abbreviation Reference: e1 = east-early; e2 = east-late; w1 = west-early; w2 = west-late; The capital letters represent the acronyms of the latin names of species, except: CA = Capra sibirica, CL = Cervus elaphus.microwear_e.csv & microwear_w.csv. a_e.csv & a_w.csv. The matrices "x" of eastern & western China respectively for calculating the microwear diversity by the package "FD".code-regression.txt. The code of regression analysis (linear model), including the summary of results, the visualizations of normality and the test of heteroscedasticity.lm-all.csv. The matrices containing all factors for the linear regression. #Abbreviation reference of each column: countdif = specimen number differences between periods; geo = geo-distance between periods; landuse = human-dominated land expansion; MDis = microwear dispersion; MDiv = microwear divergence; MEve = microwear evenness.
DOI: 10.6084/m9.figshare.27195843.v1
title: Surface Reflectance Study Spectral Data

description: Luminaire spectral power distribution and effective spectral irradiance at standard observer location accounting for surface reflectance in the built environment
DOI: 10.17632/5ssjb87t97
title: Data for: An Arbitrary Lagrangian-Eulerian, coupled neutronics-shock physics model for the analysis of shockwave implosion of solid fissile materials

description: For more information, please contact: eric.cervi@polimi.it
DOI: 10.17632/g79w8wxpr7
title: Differences in male Aedes aegypti and Aedes albopictus hearing systems facilitate recognition of conspecific female flight tones

description: Raw data and analysed values used for the study 'Differences in male Aedes aegypti and Aedes albopictus hearing systems facilitate recognition of conspecific female flight tones'.
DOI: 10.6084/m9.figshare.27144723.v1
title: Diaporthe species on palms

description: <b>Abstract: </b>The application of traditional morphological and ecological species concepts to closely related, asexual fungal taxa is challenging due to the lack of distinctive morphological characters and frequent cosmopolitan and plurivorous behaviour. As a result, multilocus sequence analysis (MLSA) has become a powerful and widely used tool to recognise and delimit independent evolutionary lineages (IEL) in fungi. However, MLSA can mask discordances in individual gene trees and lead to misinterpretation of speciation events. This phenomenon has been extensively documented in <i>Diaporthe</i>, and species identifications in this genus remains an ongoing challenge. However, the accurate delimitation of <i>Diaporthe</i> species is critical as the genus encompasses several cosmopolitan pathogens that cause serious diseases on many economically important plant hosts. In this regard, following a survey of palm leaf spotting fungi in Lisbon, Portugal, <i>Diaporthe</i> species occurring on <i>Arecaceae</i> hosts were used as a case study to implement an integrative taxonomic approach for a reliable species identification in the genus. Molecular analyses based on the genealogical concordance phylogenetic species recognition (GCPSR) and DNA-based species delimitation methods revealed that speciation events in the genus have been highly overestimated. Most IEL identified by the GCPSR were also recognised by Poisson tree processes (PTP) coalescent-based methods, which indicated that phylogenetic lineages in <i>Diaporthe </i>are likely influenced by incomplete lineage sorting (ILS) and reticulation events. Furthermore, the recognition of genetic recombination signals and the evaluation of genetic variability based on sequence polymorphisms reinforced these hypotheses. New clues towards the intraspecific variation in the common loci used for phylogenetic inference of <i>Diaporthe</i> species are discussed. These results demonstrate that intraspecific variability has often been used as an indicator to introduce new species in <i>Diaporthe</i>, which has led to a proliferation of species names in the genus. Based on these data, 53 species are reduced to synonymy with 18 existing <i>Diaporthe </i>species, and a new species, <i>D. pygmaeae</i>, is introduced. Thirteen new plant host-fungus associations are reported, all of which represent new host family records for <i>Arecaceae</i>. This study has recognised and resolved a total of 14 valid <i>Diaporthe</i> species associated with <i>Arecaceae</i> hosts worldwide, some of which are associated with disease symptoms. This illustrates the need for more systematic research to examine the complex of <i>Diaporthe</i> taxa associated with palms and determine their potential pathogenicity. By implementing a more rational framework for future studies on species delimitation in <i>Diaporthe</i>, this study provides a solid foundation to stabilise the taxonomy of species in the genus. Guidelines for species recognition, definition and identification in <i>Diaporthe</i> are included.
DOI: 10.6084/m9.figshare.c.3918607_d2.v1
title: Additional file 2: Table S1. of Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection

description: Antisense transcripts. (XLSX 1601 kb)
DOI: 10.17632/435dz52wxw
title: SEM image

description: SEM image data shown in Fig. 3.
DOI: 10.17632/mngdrjm8gv
title: Digitalization and unphysicalization of relationships in business systems

description: The purposes of this article are to clarify and supplement the theory and methodology of digitalization and unphysicalization of relationship management of business system links, as well as to create theoretical and methodological prerequisites for the creation of its digital twin.
Descriptive and faceted classification methods, methods of analysis and synthesis, induc-tion and deduction were chosen as research methods, and binary matrices formed on the basis of qualitative attributes and dichotomies of objects and components of relationship management of business system links were used as tools.
Based on a systematic approach, the article substantiates the basic components that allow identifying, describing (measuring) and digitizing the relationships of business system links; de-termines a set of actual qualitative attributes and dichotomies of these components; develops an end-to-end (hierarchically ordered) classification of relationships of business system links, as well as an algorithm for justifying management decisions using digitized standards (virtual objects) of these relationships.
The value of research lies in the creation of theoretical and methodological prerequisites for the digitalization of non-physical objects and components of business system relationship management in order to develop rational management decisions using a digital twin aggregate containing the following blocks: consumer value; management system; business system in statics; business system in dynamics; environmental factors; management decision; and the organizational structure of management.
DOI: 10.17632/vnpjbfstg7
title: JGRA_KNakazawa2024

description: Data for K. Nakazawa et al. manuscript "On-ground Detection of An Upward Multi-pulse TGF Distant from an Ascending Stepped Leader".
DOI: 10.6084/m9.figshare.12950531.v10
title: probability density data.xls

description: The frequency distribution of collision results between sand and gravel( crust)
DOI: 10.6084/m9.figshare.23552964.v3
title: The raw data of resting EEG of patients with prolonged disorders of consciousness

description: The dataset consists of resting-state electroencephalogram (EEG) data in dat format from 32 healthy individuals and 59 patients with consciousness disorders. Each data segment comprises 60 epochs, with each epoch lasting 2 seconds. There are 62 electrode points, and the sampling rate is 250 Hz.
DOI: 10.6084/m9.figshare.26485030.v1
title: Uncovering Avalanche Sources via Acceleration Measurements

description: The source data files that accompany the manuscript "Uncovering Avalanche Sources via Acceleration Measurements"
DOI: 10.6084/m9.figshare.29196176.v1
title: Chemeleon-dng

description: Chemeleon-dng checkpoints