cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r22h4
title: Data from: Lower vocal tract morphologic adjustments are relevant for voice timbre in singing

description: The vocal tract shape is crucial to voice production. Its lower part seems
 particularly relevant for voice timbre. This study analyzes the detailed
 morphology of parts of the epilaryngeal tube and the hypopharynx for the
 sustained German vowels /a/, /e/, /i/, /o/, and /u/ by thirteen male
 singer subjects who were at the beginning of their academic singing
 studies. Analysis was based on two different phonatory conditions: a
 natural, speech-like phonation and a singing phonation, like in classical
 singing. 3D models of the vocal tract were derived from magnetic resonance
 imaging and compared with long-term average spectrum analysis of audio
 recordings from the same subjects. Comparison of singing to the
 speech-like phonation, which served as reference, showed significant
 adjustments of the lower vocal tract: an average lowering of the larynx by
 8 mm and an increase of the hypopharyngeal cross-sectional area (+ 21:9%)
 and volume (+ 16:8%). Changes in the analyzed epilaryngeal portion of the
 vocal tract were not significant. Consequently, lower
 larynx-to-hypopharynx area and volume ratios were found in singing
 compared to the speech-like phonation. All evaluated measures of the lower
 vocal tract varied significantly with vowel quality. Acoustically, an
 increase of high frequency energy in singing correlated with a wider
 hypopharyngeal area. The findings offer an explanation how classical male
 singers might succeed in producing a voice timbre with increased high
 frequency energy, creating a singer`s formant cluster.
description: file format
 DescriptionLTAS
 dataMRI_subject_1MRI subject 1.zipMRI_subject_2MRI subject 2.zipMRI_subject_3MRI subject 3.zipMRI_subject_4MRI subject 4.zipMRI_subject_5MRI subject 5.zipMRI_subject_6MRI subject 6.zipMRI_subject_7MRI subject 7.zipMRI_subject_8MRI subject 8.zipMRI_subject_9MRI subject 9.zipMRI_subject_10MRI subject 10.zipMRI_subject_11MRI subject 11.zipMRI_subject_12MRI subject 12.zipMRI _subject_13MRI subject 13.zip
DOI: 10.5061/dryad.48tj0
title: Data from: More than just two sexes: the neural correlates of voice gender perception in gender dysphoria

description: Gender dysphoria (also known as “transsexualism”) is characterized as a
 discrepancy between anatomical sex and gender identity. Research points
 towards neurobiological influences. Due to the sexually dimorphic
 characteristics of the human voice, voice gender perception provides a
 biologically relevant function, e.g. in the context of mating selection.
 There is evidence for a better recognition of voices of the opposite sex
 and a differentiation of the sexes in its underlying functional cerebral
 correlates, namely the prefrontal and middle temporal areas. This fMRI
 study investigated the neural correlates of voice gender perception in 32
 male-to-female gender dysphoric individuals (MtFs) compared to 20
 non-gender dysphoric men and 19 non-gender dysphoric women. Participants
 indicated the sex of 240 voice stimuli modified in semitone steps in the
 direction to the other gender. Compared to men and women, MtFs showed
 differences in a neural network including the medial prefrontal gyrus, the
 insula, and the precuneus when responding to male vs. female voices. With
 increased voice morphing men recruited more prefrontal areas compared to
 women and MtFs, while MtFs revealed a pattern more similar to women. On a
 behavioral and neuronal level, our results support the feeling of MtFs
 reporting they cannot identify with their assigned sex.
description: fmri data from a voice
 gender perception tasktrage.tgz
DOI: 10.5061/dryad.qp0t3
title: Data from: Extreme heterogeneity of influenza virus infection in single cells

description: Viral infection can dramatically alter a cell's transcriptome.
 However, these changes have mostly been studied by bulk measurements on
 many cells. Here we use single-cell mRNA sequencing to examine the
 transcriptional consequences of influenza virus infection. We find
 extremely wide cell-to-cell variation in the productivity of viral
 transcription - viral transcripts comprise less than a percent of total
 mRNA in many infected cells, but a few cells derive over half their mRNA
 from virus. Some infected cells fail to express at least one viral gene,
 but this gene absence only partially explains variation in viral
 transcriptional load. Despite variation in viral load, the relative
 abundances of viral mRNAs are fairly consistent across infected cells.
 Activation of innate immune pathways is rare, but some cellular genes
 co-vary in abundance with the amount of viral mRNA. Overall, our results
 highlight the complexity of viral infection at the level of single cells.
description: Supplementary file 2:
 The annotated cell-gene matrix for the single-cell mRNA sequencing of
 influenza virus infected cells.This is the matrix
 generated in ./results/cellgenecounts/ by running the CellRanger analysis
 in align_and_annotate.ipynb in Supplementary file 1 of the
 paper.cellgenecounts.zip
DOI: 10.5061/dryad.qp244
title: Data from: The diversity of floral temperature patterns, and their use by pollinators

description: Pollinating insects utilise various sensory cues to identify and learn
 rewarding flower species. One such cue is floral temperature, created by
 captured sunlight or plant thermogenesis. Bumblebees, honeybees and
 stingless bees can distinguish flowers based on differences in overall
 temperature between flowers. We report here that floral temperature often
 differs between different parts of the flower creating a temperature
 structure or pattern. Temperature patterns are common, with 55% of 118
 plant species thermographed, showing within-flower temperature differences
 greater than the 2°C difference that bees are known to be able to detect.
 Using differential conditioning techniques, we show that bumblebees can
 distinguish artificial flowers differing in temperature patterns
 comparable to those seen in real flowers. Thus, bumblebees are able to
 perceive the shape of these within-flower temperature patterns. Floral
 temperature patterns may therefore represent a new floral cue that could
 assist pollinators in the recognition and learning of rewarding flowers.
description: Infrared thermographs of
 flower speciesThis zipped dataset
 contains 136 folders, corresponding to the 136 species and subspecies
 thermographed as described in Harrap et al. All the files contain three
 .jpg files. Each folder contains two infrared images (which are identical
 to each other, except that the image marked with an ‘m’ has the hottest
 and coldest points identified as described in the text). Each folder also
 contains an accompanying photograph taken in the visible spectrum, taken
 by the thermal camera at the same time as the infrared image. The visible
 spectrum photographs are provided purely to give an indication of the
 floral form, and do not contribute any further data that is used in the
 paper.harrap et al IR
 images.zipRaw and processed data
 for figures 3 and 4A zipped file containing
 nine .csv files. Three of these files each correspond to figures 3a, 3b
 and 4, and contain the raw data and processed versions that relate to the
 final figures. The readme file details the format of these
 filesfigures3and4_data.zip
DOI: 10.5061/dryad.hc5dp
title: Data from: Cell-specific responses to the cytokine TGFβ are determined by variability in protein levels

description: The cytokine TGFβ provides important information during embryonic
 development, adult tissue homeostasis and regeneration. Alterations in the
 cellular response to TGFβ are involved in severe human diseases. To
 understand how cells encode the extracellular input and transmit its
 information to elicit appropriate responses, we acquired quantitative
 time-resolved measurements of pathway activation at the single cell level.
 We established dynamic time warping to quantitatively compare signaling
 dynamics of thousands of individual cells and described heterogeneous
 single-cell responses by mathematical modeling. Our combined experimental
 and theoretical study revealed that the response to a given dose of TGFβ
 is determined cell-specifically by the levels of defined signaling
 proteins. This heterogeneity in signaling protein expression leads to
 decomposition of cells into classes with qualitatively distinct signaling
 dynamics and phenotypic outcome. Negative feedback regulators promote
 heterogeneous signaling, as a SMAD7 knock-out specifically affected the
 signal duration in a subpopulation of cells. Taken together, we propose a
 quantitative framework that allows predicting and testing sources of
 cellular signaling heterogeneity.
description: Live-cell SMAD2/4
 measurementsData from time-resolved
 single-cell measurements of fluorescent SMAD2 or SMAD4 reporter cells
 under different experimental conditions.SMADSignaling_SingleCellData.zip
DOI: 10.5061/dryad.9gn28
title: Data from: Ecological genomics of mutualism decline in nitrogen-fixing bacteria

description: Anthropogenic changes can influence mutualism evolution; however, the
 genomic regions underpinning mutualism that are most affected by
 environmental change are generally unknown, even in well-studied model
 mutualisms like the interaction between legumes and their nitrogen
 (N)-fixing rhizobia. Such genomic information can shed light on the agents
 and targets of selection maintaining cooperation in nature. We recently
 demonstrated that N-fertilization has caused an evolutionary decline in
 mutualistic partner quality in the rhizobia that form symbiosis with
 clover. Here population genomic analyses of N-fertilized versus control
 rhizobium populations indicate that evolutionary differentiation at a key
 symbiosis gene region on the symbiotic plasmid (pSym) contributes to
 partner quality decline. Moreover patterns of genetic variation at
 selected loci were consistent with recent positive selection within
 N-fertilized environments, suggesting that N-rich environments might
 select for less-beneficial rhizobia. By studying the molecular population
 genomics of a natural bacterial population within a long-term ecological
 field experiment, we find that: 1) the N environment is indeed a potent
 selective force mediating mutualism evolution in this symbiosis, 2)
 natural variation in rhizobium partner quality is mediated in part by key
 symbiosis genes on the symbiotic plasmid, and 3) differentiation at
 selected genes occurred in the context of otherwise recombining genomes,
 resembling eukaryotic models of adaptation.
description: R. leguminosarum de novo
 assembliesDe novo assemblies for
 62 strains of R. leguminosarum using the A5 pipeline with a portion of
 gaps filled in silico with GapFiller v. 1.11. A strain key is included as
 a ReadMe file.Gapfilled_Assemblies_KlingerLauHeath.zipR. leguminosarum whole genome raw sequence readsPaired-end raw sequencing reads from Illumina HiSeq2000 sequencer. Libraries prepared with Illumina Nextera XT.
DOI: 10.5061/dryad.kp905
title: Data from: Seven common mistakes in population genetics and how to avoid them

description: As the data resulting from modern genotyping tools are astoundingly
 complex, genotyping studies require great care in the sampling design,
 genotyping, data analysis and interpretation. Such care is necessary
 because, with data sets containing thousands of loci, small biases can
 easily become strongly significant patterns. Such biases may already be
 present in routine tasks that are present in almost every genotyping
 study. Here, I discuss seven common mistakes that can be frequently
 encountered in the genotyping literature: (i) giving more attention to
 genotyping than to sampling, (ii) failing to perform or report
 experimental randomization in the laboratory, (iii) equating geopolitical
 borders with biological borders, (iv) testing significance of clustering
 output, (v) misinterpreting Mantel's r statistic, (vi) only
 interpreting a single value of k and (vii) forgetting that only a small
 portion of the genome will be associated with climate. For every of those
 issues, I give some suggestions how to avoid the mistake. Overall, I argue
 that genotyping studies would benefit from establishing a more rigorous
 experimental design, involving proper sampling design, randomization and
 better distinction of a priori hypotheses and exploratory analyses.
description: Simulated genetic
 dataGenetic marker data
 simulated under a stepping stone migration model and a tree-like migration
 model. See the attached ReadMe file for information regarding the used
 program, simulation settings, and data analysis.Dryad
 data.zip
DOI: 10.5061/dryad.1975
title: Data from: Species recognition and patterns of population variation in the reproductive structures of a damselfly genus

description: The selection pressures imposed by mate choice for species identity should
 impose strong stabilizing selection on traits that confer species identity
 to mates. Thus, we expect that such traits should show non-overlapping
 distributions among closely related species, but show little to no
 variance among populations within a species. We tested these predictions
 by comparing levels of population differentiation in the sizes and shapes
 of male cerci (i.e., the clasper structures used for species identity
 during mating) of six Enallagma damselfly species. Cerci shapes were
 non-overlapping among Enallagma species, and five of six Enallagma species
 showed no population variation across their entire species ranges. In
 contrast, cerci sizes overlapped among species and varied substantially
 among populations within species. These results, taken with previous
 studies, suggest that cerci shape is a primary feature used in species
 recognition used to discriminate conspecific from heterospecifics during
 mating.
description: Enallagma Cerci
 ModelsThis zip file contains
 the original triangualr mesh models of all specimens analyzed in this
 paper, and the registered spherical harmonic (SPHARM) models that were
 derived from these models. The triangular mesh files are ASCII files, and
 each has a corresponding file (same file name but with an LandmarkAscii
 file extension) that contains seven landmarks used to spatially register
 them to one another. The SPHARM models are in a directory, and are in
 Matlab .MAT format.
DOI: 10.5061/dryad.81ps2
title: Data from: Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany

description: Knowledge of the range and chronology of historic trade and long-distance
 transport of natural resources is essential for determining the impacts of
 past human activities on marine environments. However, the specific
 biological sources of imported fauna are often difficult to identify, in
 particular if species have a wide spatial distribution and lack clear
 osteological or isotopic differentiation between populations. Here, we
 report that ancient fish-bone remains, despite being porous, brittle, and
 light, provide an excellent source of endogenous DNA (15–46%) of
 sufficient quality for whole-genome reconstruction. By comparing ancient
 sequence data to that of modern specimens, we determine the biological
 origin of 15 Viking Age (800–1066 CE) and subsequent medieval (1066–1280
 CE) Atlantic cod (Gadus morhua) specimens from excavation sites in
 Germany, Norway, and the United Kingdom. Archaeological context indicates
 that one of these sites was a fishing settlement for the procurement of
 local catches, whereas the other localities were centers of trade. Fish
 from the trade sites show a mixed ancestry and are statistically
 differentiated from local fish populations. Moreover, Viking Age samples
 from Haithabu, Germany, are traced back to the North East Arctic Atlantic
 cod population that has supported the Lofoten fisheries of Norway for
 centuries. Our results resolve a long-standing controversial hypothesis
 and indicate that the marine resources of the North Atlantic Ocean were
 used to sustain an international demand for protein as far back as the
 Viking Age.
description: PNAS.201710186.vcf
DOI: 10.5061/dryad.h862n
title: Data from: Development of an intravascular ultrasound elastography based on a dual-element transducer

description: The ability to measure the elastic properties of plaques and vessels would
 be useful in clinical diagnoses, particularly for detecting a vulnerable
 plaque. This study demonstrates the feasibility of combination of
 intravascular ultrasound (IVUS) and acoustic radiation force (ARF)
 elasticity imaging for detecting the distribution of stiffness within
 atherosclerotic arteries ex vivo. A dual-frequency IVUS transducer with
 two elements was used to induce the propagation of shear wave (by the
 8.5-MHz pushing element) which could be simultaneously monitored by the
 31-MHz imaging element. The wave-amplitude image and the wave-velocity
 image was reconstructed by measuring the peak displacement and wave
 velocity of shear wave propagation, respectively. System performance was
 verified using gelatin phantoms. The phantom results demonstrate that the
 stiffness differences of shear modulus of 1.6 kPa can be distinguished
 through the wave-amplitude and wave-velocity images. Moreover, the
 stiffness distributions of the atherosclerotic aorta from a rabbit were
 obtained, for which the peak displacement and the shear-wave velocity were
 averaged to be 3.7 μm and 0.38 m/s, respectively, in the lipid-rich
 plaques, and 1.0 μm and 3.45 m/s in the arterial walls. These results
 indicate that IVUS elasticity imaging can be used to distinguish the
 elastic properties of plaques and vessels.
description: Data from Shih et al
 2018 for Royal society science open-curvesmeasurement of acoustic
 radiation force induced intensities, displacements, and velocities by a
 dual-frequency ultrasound IVUS transducer.curves_data.xlsxData from Shih et al 2018 for Royal society science open-elastographic mapselastographic map of wave-amplitude, wave-velocity and their corresponding B-mode images for gelatin phantoms and an artery sample. All the files are ".mat", and should be loaded by Matlab Software. Please find the "README file" for displaying each elastographic map in Matlab.elastographic map.zip
DOI: 10.15468/dl.jshx3w
title: Occurrence Download

description: A dataset containing 258 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-77.79732 2.1968,-81.48266 -14.61296,-51.53697 -9.44091,-45.23418 -11.3505,-50.05074 5.89246,-59.01464 7.15657,-66.76648 0.02623,-77.79732 2.1968))",
 "HasCoordinate is true",
 "TaxonKey is Osteoglossum bicirrhosum"
 ]
}

 The dataset includes 258 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000410-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.d1d1m
title: Data from: Statistical analysis of the individual variability of 1D protein profiles as a tool in ecology: an application to parasitoid venom

description: Understanding the forces that shape eco-evolutionary patterns often
 requires linking phenotypes to genotypes, allowing characterization of
 these patterns at the molecular level. DNA-based markers are less
 informative in this aim compared to markers associated with gene
 expression and, more specifically, with protein quantities. The
 characterization of eco-evolutionary patterns also usually requires the
 analysis of large sample sizes to accurately estimate interindividual
 variability. However, the methods used to characterize and compare protein
 samples are generally expensive and time-consuming, which constrains the
 size of the produced data sets to few individuals. We present here a
 method that estimates the interindividual variability of protein
 quantities based on a global, semi-automatic analysis of 1D
 electrophoretic profiles, opening the way to rapid analysis and comparison
 of hundreds of individuals. The main original features of the method are
 the in silico normalization of sample protein quantities using pictures of
 electrophoresis gels at different staining levels, as well as a new method
 of analysis of electrophoretic profiles based on a median profile. We
 demonstrate that this method can accurately discriminate between species
 and between geographically distant or close populations, based on
 interindividual variation in venom protein profiles from three
 endoparasitoid wasps of two different genera (Psyttalia concolor,
 Psyttalia lounsburyi and Leptopilina boulardi). Finally, we discuss the
 experimental designs that would benefit from the use of this method.
description: Data used in the paper
 -Statistical analysis of the individual variability of 1D protein profiles
 as a tool in ecology-In this folder, their
 are the data used in the paper "Statistical analysis of the
 individual variability of 1D protein profiles as a tool in ecology: an
 application to parasitoid venom".Dataset.zip
DOI: 10.5061/dryad.4m402
title: Data from: Phylogenomic analyses reveal novel relationships among snake families

description: Snakes are a diverse and important group of vertebrates. However,
 relationships among the major groups of snakes have remained highly
 uncertain, with recent studies hypothesizing very different (and typically
 weakly supported) relationships. Here, we address family-level snake
 relationships with new phylogenomic data from 3,776 nuclear loci from
 ultraconserved elements (1.34 million aligned base pairs, 52% missing data
 overall) sampled from 29 snake species that together represent almost all
 families, a dataset ∼100 times larger than used in previous studies. We
 found relatively strong support from species-tree analyses (NJst) for most
 relationships, including three largely novel clades: (1) a clade uniting
 the boas, pythons and their relatives, (2) a clade placing cylindrophiids
 and uropeltids with this clade, and (3) a clade uniting bolyeriids (Round
 Island boas) with pythonids and their relatives (xenopeltids and
 loxocemids). Relationships among families of advanced snakes
 (caenophidians) were also strongly supported. The results show the
 potential for phylogenomic analyses to resolve difficult groups, but also
 show a surprising sensitivity of the analyses to the inclusion or
 exclusion of outgroups.
description: Species-tree analysis
 (NJst) dataset with outgroups (Fig. 2)Bootstrap tree files
 used to infer tree and support values in Fig. 2.NJst_outgroups_3776_bs.zipSpecies-tree analysis (NJst) dataset (Fig. 4, B)Bootstrap tree files used to infer tree and support values in Fig. 4, B.snakes_only_NJst.zipConcatenated analysis (RAxML) dataset used in Fig. 3.PHYLIP file used to infer tree and support values depicted in Fig. 3.snakes_RAxML_outgroups.phy.txtConcatenated analysis (RAxML) dataset used in Fig. 4, A.PHYLIP file used to infer tree and support values depicted in Fig. 4, A.snakes_only_RAxML.phyConcatenated analysis (RAxML) dataset used in Fig. S1.PHYLIP file used to infer tree and support values depicted in Fig. S1.snakes_S1_0.75.phyConcatenated analysis (RAxML) dataset used in Fig. S2.PHYLIP file used to infer tree and support values depicted in Fig. S2.snakes_S2_0.60.phy