cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12893423.v1
title: Gut microbiome of diabetes

description: Total DNA of microorganisms was extracted from all feces samples using a QIAamp stool DNA minikit (Qiagen, Germany). The extracted genomic DNA was used to construct an amplicon library by amplifying the V3~V4 region of the 16S rRNA gene. An Illumina Miseq high-throughput sequencing platform (Illumina) was used to sequence the PCR products in the 16S RNA V3~V4 region.
DOI: 10.3535/mw9-1gp-04k
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/q42-zzy-nh0
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/0cr-14c-ke3
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/szf-23c-zmq
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.10321298.v1
title: Bioinformatics Code and High Impact Variants for HSRA Rat Model

description: 1. Bioinformatic code supplement for whole genomics sequencing of the HSRA rat model.2. Table S1, genome wide high impact variants queried from whole genome sequencing data.
DOI: 10.6084/m9.figshare.14424386.v1
title: An evolutionary genomic approach reveals both conserved and species-specific genetic elements related to human disease in closely related Aspergillus fungi

description: Aspergillosis is an important opportunistic human disease caused by filamentous fungi in the genus <i>Aspergillus</i>. Roughly 70% of infections are caused by <i>Aspergillus fumigatus</i>, with the rest stemming from approximately a dozen other <i>Aspergillus </i>species. Several of these pathogens are closely related to <i>A. fumigatus </i>and belong in the same taxonomic section, section <i>Fumigati</i>. Pathogenic species are frequently most closely related to non-pathogenic ones, suggesting <i>Aspergillus </i>pathogenicity evolved multiple times independently. To understand the repeated evolution of <i>Aspergillus </i>pathogenicity, we performed comparative genomic analyses on 18 strains from 13 species, including 8 species in<i> </i>section <i>Fumigati</i>, which aimed to identify genes, both ones previously connected to virulence as well as ones never before implicated, whose evolution differs between pathogens and non-pathogens. We found that most genes were present in all species, including approximately half of those previously connected to virulence, but a few genes were section- or species-specific. Evolutionary rate analyses identified over 1,700 genes whose evolutionary rate differed between pathogens and non-pathogens and dozens of genes whose rates differed between specific pathogens and the rest of the taxa. For example, we found 34 genes whose evolutionary rate was uniquely different in <i>A. fumigatus </i>and 85 genes whose rate was uniquely different in the pathogen <i>A. lentulus</i>. Functional testing of deletion mutants of 17 transcription factor-encoding genes whose evolution differed between pathogens and non-pathogens identified eight genes that affect either fungal survival in a model of phagocytic killing, host survival in an animal model of fungal disease, or both. These results suggest that the evolution of pathogenicity in <i>Aspergillus </i>involved both conserved and species-specific genetic elements, illustrating how an evolutionary genomic approach informs the study of fungal disease.<br>These files contain all of the supplementary information for the manuscript.<br>
DOI: 10.6084/m9.figshare.5415241.v2
title: Computationally Efficient Estimation for the Generalized Odds Rate Mixture Cure Model With Interval-Censored Data

description: For semiparametric survival models with interval-censored data and a cure fraction, it is often difficult to derive nonparametric maximum likelihood estimation due to the challenge in maximizing the complex likelihood function. In this article, we propose a computationally efficient EM algorithm, facilitated by a gamma-Poisson data augmentation, for maximum likelihood estimation in a class of generalized odds rate mixture cure (GORMC) models with interval-censored data. The gamma-Poisson data augmentation greatly simplifies the EM estimation and enhances the convergence speed of the EM algorithm. The empirical properties of the proposed method are examined through extensive simulation studies and compared with numerical maximum likelihood estimates. An R package “GORCure” is developed to implement the proposed method and its use is illustrated by an application to the Aerobic Center Longitudinal Study dataset. Supplementary material for this article is available online.
DOI: 10.3535/r5q-qd9-hy7
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/yr7-ajr-xb2
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/d5z-tvr-s1m
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ezq-sjv-682
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.20480346.v1
title: D2 Research data - Qualitative analysis process.docx

description: Qualitative analysis process
DOI: 10.3535/2wc-6jy-dn1
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ce5-zb5-2st
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.24624888.v1
title: Abundance Data for Stephenson et al. 2024

description: Surface abundance data used in Stephenson et al. in prep. Abundance data from 17 fossil surfaces. In this study, we analysed 18 Avalon palaeocommunities to test whether community composition was driven by succession processes.Bed B not included. Only first 100 jack knife subsamples included due to data constraints.<br>Code available: https://github.com/nis38/Morphology_Comm_Dyn<br>DOI: 10.1038/s41559-024-02422-8
DOI: 10.3535/cym-fkw-4qp
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/p1n-29r-p1d
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.14686047.v1
title: ARRIVE checklist

description: This is the ARRIVE checklist for the mouse caecal samples used as a microbiome control sample.<br>
DOI: 10.3535/1qf-qlf-4j0
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/zgw-hmp-e30
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/far-fvr-mla
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/pl1-dtd-24a
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/ghj-3fj-0ml
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/zmv-atl-gst
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.22704571.v2
title: DispersalDiversification_Emberizoidea.zip

description: This .zip contains the necessary tools to recreate the analyses performed in the study: "Broad geographic dispersal is not a driver for diversification in Emberizoidea", along with some extra analyses.<br>Includes a Readme explaining all contained data.
DOI: 10.6084/m9.figshare.23197985.v1
title: Source data and uncropped blots corresponding to "Sympathetic tone dictates the impact of lipolysis on FABP4 secretion"

description: Source data and uncropped blots corresponding to article: Prentice KJ, Lee A, Cedillo P, Inouye KE, Ertunc ME, Riveros JK, Lee GY, Hotamisligil GS. Sympathetic tone dictates the impact of lipolysis on FABP4 secretion. J Lipid Res. 2023 May 10:100386. doi: 10.1016/j.jlr.2023.100386. Epub ahead of print. PMID: 37172691
DOI: 10.3535/b03-fcb-5wy
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/c4j-rqw-m17
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/vn5-jfs-h8g
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/4s2-elr-jrn
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/wts-wra-cpn
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/grf-wkr-kfa
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/vrw-1fe-713
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/g34-422-jyk
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/m1k-9k7-tvp
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.28665608.v1
title: Soil microbial properties and mineral protection drive carbon use efficiency along elevation gradient

description: Understanding the elevational variation of soil microbial carbon use efﬁciency (CUE) can provide a better understanding for soil C-climate change feedback. Here, we used the 18O-H2O tracer method to quantify microbial CUE along an elevation gradient ranging from 840 m to 3400 m in the Eastern Himalaya. We found that soil microbial CUE first increases and then decreases along elevation gradient and reaches a peak in the mid-altitude area, indicating that the environmental conditions at mid-altitude are more conducive to the efficient utilization of C by microorganisms. Climate was the primary factor that affected elevational variations of CUE by altering microbial properties and mineral protection. In areas with relatively climate-adaptive conditions, soils with lower microbial alpha diversity instead provide higher CUE, and fungal phyla, in contrast with bacterial phyla, has more effects on CUE. Also, soil mineral protection indirectly regulates CUE by altering microbial properties, and both of which consequently determine the changes of SOC along elevation gradient. Particularly, the positive correlation between the fraction of particulate organic carbon and microbial CUE indicated that soil microbes tend to utilize and transform more labile C sources along elevation gradient. Overall, the complex interactions between mineral protection and microbial attributes lead to a more complex soil C climate-feedback.
DOI: 10.3535/c69-2ak-8vw
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/q3g-xyg-p1k
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/xsn-ep5-jwz
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/4p5-9sl-pt4
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/x5y-rkg-zpe
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.7777226.v3
title: Estimation and Inference for Generalized Geoadditive Models

description: In many application areas, data are collected on a count or binary response with spatial covariate information. In this article, we introduce a new class of generalized geoadditive models (GGAMs) for spatial data distributed over complex domains. Through a link function, the proposed GGAM assumes that the mean of the discrete response variable depends on additive univariate functions of explanatory variables and a bivariate function to adjust for the spatial effect. We propose a two-stage approach for estimating and making inferences of the components in the GGAM. In the first stage, the univariate components and the geographical component in the model are approximated via univariate polynomial splines and bivariate penalized splines over triangulation, respectively. In the second stage, local polynomial smoothing is applied to the cleaned univariate data to average out the variation of the first-stage estimators. We investigate the consistency of the proposed estimators and the asymptotic normality of the univariate components. We also establish the simultaneous confidence band for each of the univariate components. The performance of the proposed method is evaluated by two simulation studies. We apply the proposed method to analyze the crash counts data in the Tampa-St. Petersburg urbanized area in Florida. Supplementary materials for this article are available online.
DOI: 10.3535/3v2-5td-hb9
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/wkf-zs3-5fl
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/5nv-ndh-p8w
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/jx3-352-gqt
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.12326288.v1
title: To click, or not to click?

description: New game technologies seem to permeate every area of daily life. Therefore, it is not surprising that, in addition to the incorporation of entertaining gaming features into otherwise dull or tedious activities, the positive influence of user experience and user engagement has also been on the rise in recent years. It is all part of gamification. Individual differences in response to gamification deserve attention. Specifically, the objective of this experimental study was to investigate how perfectionism and gender affect behavior under two conditions — free play and competition — during a logic video game played by 155 gifted high school students. Game points monitoring frequency (GPMF) and game completion time (GCT) were measured. Functional perfectionists showed significantly higher GPMF than dysfunctional perfectionists. Furthermore, the competitive condition increased GPMF significantly more in functional perfectionists (compared to dysfunctional perfectionists) and girls tended to show higher GCT across the conditions. The results indicate that, in a competitive environment, the effectiveness of employing points for feedback is influenced by both a perfectionistic personality style and gender. Our study supports the notion that gamification elements can affect individuals differently, supporting the motivation of some students, yet being ignored by others.
DOI: 10.3535/dzk-jxp-l9p
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/krs-amq-r7j
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.9121751.v1
title: gTRCA_SciRep.zip

description: This material includes Matlab demo scripts, functions and sample data of group task-related component analysis (gTRCA).<br>
DOI: 10.3535/v5c-ymt-ber
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/zpt-0ah-nmq
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/4pg-7fp-pca
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/j2q-m83-4w3
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/n9n-8qg-32z
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.12594746.v2
title: Code: A survey of the aerodynamic efficiency of gliding birds vs. modern UAVs

description: The codes used to create the figures in the article
DOI: 10.3535/07c-2yq-xkk
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/1js-ldy-w9j
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.14618235.v5
title: ForestTemp: sub-canopy microclimate temperatures of European forests

description: Combining more than 1,200 time series of <em>in situ</em> near-surface forest temperatures with topographical, biological and macroclimatic variables in a machine learning model, we predicted the monthly offset for minimum, mean and maximum temperature between sub-canopy temperature at 15 cm above the surface and free-air temperature over the period 2000-2020 at a spatial resolution of 25 x 25 m² across Europe.
When using any of these layers, please cite: 

 Haesen et al. (2021). ForestTemp –Sub-canopy microclimate temperatures of European forests. Global Change Biology, <em>27</em>(23), 6307–6319. https://doi.org/10.1111/gcb.15892

To mask pixels by the proportion of extrapolation, the file 'extrapolation.tif' can be used. All layers are projected in epsg:3035.
<br>
Version history:

 v1: original layers (DO NOT USE)
 v2: corrigendum layers
 v3: added layers for maximum temperature offsets
 v4: added layers for minimum temperature offsets
DOI: 10.3535/ecz-rz4-lce
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/hef-lj4-nd7
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/hgd-f5m-tkg
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/k5h-r1n-274
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/tq0-zw8-wkc
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/wej-05s-eh3
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/1zj-q8m-ps7
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/a6k-8ef-546
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.14394596.v2
title: Underwater acoustic wave gauge and ADCP measurements

description: This is the Underwater acoustic wave gauge measurements and comparison with ADCP measurements. Experiment conducted on the Gelendzhik test site, February 1-10, 2021. Data for the paper in the journal "Journal of Geophysical Research: Oceans"
DOI: 10.3535/zxy-fmz-fwf
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.1608313.v1
title: Tables 01 to 04 - PloS One - Ayo et al 2015

description: Table 1 - General characteristics of patients with and without ocular toxoplasmosis and its manifestation as primary or recurrent<br><br> Table 2 - Distribution of MICA alleles in patients with and without ocular toxoplasmosis and its manifestation as primary or recurrent<br><br> Table 3 - Genotype and allele frequencies of the MICA-129 polymorphism (rs1051792) in patients with and without ocular toxoplasmosis and its manifestation as primary or recurrent<br><br> Table 4 - Haplotype frequencies of MICA, HLA-B and HLA-C in patients with and without ocular toxoplasmosis and its manifestation as primary or recurrent
DOI: 10.6084/m9.figshare.25199528.v1
title: S4 GPOC Survey Results.xlsx

description: S4 GPOC Survey Results.
DOI: 10.3535/1z5-vfb-kb8
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/asy-lvd-pcx
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.6084/m9.figshare.23193842.v1
title: Data and analysis: Spring migration patterns of red knots in the Southeast United States disentangled using automated telemetry

description: This repository contains the data and code necessary to reproduce the analysis and figures in the manuscript " Spring migration patterns of red knots in the Southeast United States disentangled using automated telemetry " by Smith et al. (Scientific Reports 13:11138).<br>Authors (affiliation):Adam D. Smith (U.S. Fish and Wildlife Service, National Wildlife Refuge System, Inventory and Monitoring Branch; Current address: American Bird Conservancy)Felicia J. Sanders (South Carolina Department of Natural Resources)Kara L. Lefevre (Florida Gulf Coast University; Current address: Thompson River University)Janet M. Thibault (South Carolina Department of Natural Resources)Kevin S. Kalasz (U.S. Fish and Wildlife Service, Florida Ecological Services Field Office)Deborah L. Carter (University of Georgia, College of Veterinary Medicine, Southeastern Cooperative Wildlife Disease Study)Maina C. Handmaker (Department of Environmental Conservation, University of Massachusetts)Fletcher M. Smith (Georgia Department of Natural Resources)Tim Keyes (Georgia Department of Natural Resources)<br>To run the analysis:Download this repository; all code and data is available in this repositoryExtract the zipped `REKN-main` directory to the desired location on your local machine.Within the `REKN-main` directory, open the REKN.Rproj file in RStudio on a computer with internet access. Note that RStudio requires R to be installed. This opens the RStudio project associated with the data, code, and analysis.All of the code necessary to process, analyze, and generate figures is located in the Code directory. Open and begin by running the code within 00_Process_REKN_Motus_data.R. Proceed sequentially through other similarly-named files. If interested only in the figures, these are provided as a convenience in the Output directory.
DOI: 10.3535/6kx-pzg-wj1
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/n17-v7q-gap
title: Brachiopoda Duméril, 1805

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.