cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r5r20
title: Data from: Seawater environmental DNA reflects seasonality of a coastal fish community

description: Coastal marine fish populations are in decline due to overfishing, habitat
 destruction, climate change and invasive species. Seasonal monitoring is
 important for detecting temporal changes in the composition of fish
 communities, but current monitoring is often non-existent or limited to
 annual or semi-annual surveys. In the present study, we investigate the
 potential of using environmental DNA (eDNA) metabarcoding of seawater
 samples to detect the seasonal changes in a coastal marine fish community.
 Water sampling and snorkelling visual census were performed over 1 year
 (from 23rd of August 2013 to 11th of August 2014) at a temperate coastal
 habitat in Denmark (55°45′39″N, 12°35′59″E) and compared to long-term data
 collected over a 7-year period. We used Illumina sequencing of PCR
 products to demonstrate that seawater eDNA showed compositional changes in
 accordance with seasonal changes in the fish community. The vast majority
 of fish diversity observed in the study area by snorkelling was recovered
 from sequencing, although the overlap between methods varied widely among
 sampling events. In total, 24 taxa were detected by both methods, while
 five taxa were only detected using eDNA and three taxa were only detected
 by snorkelling. A limitation of the applied primers was the lack of
 resolution to species level in a few diverse families, and varying
 sequencing depth between samples represents a potential bias. However, our
 study demonstrates the utility of eDNA for recovering seasonal variation
 in marine fish communities, knowledge of which is essential for
 standardised long-term monitoring of marine biodiversity.
description: E4LIllumina MiSeq data from
 PCR amplification of seawater samplesSKH_teleo_MiSeq.zip
DOI: 10.5067/asdc/suborbital/staqs/data001/drone_1
title: STAQS Drone Data
DOI: 10.5061/dryad.2pf38
title: Data from: A new dimension in documenting new species: high-detail imaging for myriapod taxonomy and first 3D cybertype of a new millipede species (Diplopoda, Julida, Julidae)

description: We review the state-of-the-art approaches currently applied in myriapod
 taxonomy, and we describe, for the first time, a new species of millipede
 (Ommatoiulus avatar n. sp., family Julidae) using high-resolution X-ray
 microtomography (microCT) as a substantive adjunct to traditional
 morphological examination. We present 3D models of the holotype and
 paratype specimens and discuss the potential of this non-destructive
 technique in documenting new species of millipedes and other organisms.
 The microCT data have been uploaded to an open repository (Dryad) to serve
 as the first actual millipede cybertypes to be published.
description: O-avatar_holotype_I2E_3-0um_PNGO-avatar_holotype_gonopods_I2E_1-9um_PNGOmmatuoilus_avatar_female_I2E_3-4um_PNGOmma_avatar_cybertypes_metadata
DOI: 10.5067/asdc/suborbital/staqs/data001/instep_1
title: STAQS INSTEP Data
DOI: 10.5067/asdc/suborbital/staqs/data001/ground_1
title: STAQS Ground Data
DOI: 10.5061/dryad.cf472n3
title: Data from: The Chirocopter: a UAV for recording sound and video of bats at altitude

description: 1. Most recordings of bats are conducted with fixed equipment, which
 relies on opportunistic data collection. Unmanned aerial vehicles (such as
 drones) are considered inappropriate for recording bats due to ultrasound
 noise constraints. 2. We developed a UAV system that physically isolates
 UAV noise so we can record, with 3D maneuverability, ultrasonic audio and
 spatial thermal data of bat flight at altitude. 3. We tested the noise of
 our UAV with various payloads and microphone configurations to
 characterize the ultrasonic noise of our system, physically isolate drone
 noise from the microphone, and maximize UAV flight performance. 4. Over 84
 minutes of recordings, we captured 3,847 echolocation signals from bats
 with corresponding thermal data of bat flight. Our system provides a
 feasible mechanism to capture both acoustic and video data of bats aloft
 at flexible locations and altitudes. 5. We include information on how to
 extend our method to apply to acoustic recordings in the audible (20 Hz-20
 kHz) range for recording sounds of other taxa.
description: UAV_Noise_TestingNoise testing files of UAVUAV_Bat_Recordings1UAV recordings from bats aloftUAV_Bat_Recordings2UAV recordings from bats aloftUAV_Bat_Recordings3UAV recordings from bats aloftUAV_Bat_Recordings4Data files from UAV recording bats aloft
DOI: 10.15468/dl.nnfrne
title: Occurrence Download

description: A dataset containing 258 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Uma rufopunctata"
 ]
}

 The dataset includes 258 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000456-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ch0vn
title: Data from: An assessment of phylogenetic tools for analyzing the interplay between interspecific interactions and phenotypic evolution

description: Much ecological and evolutionary theory predicts that interspecific
 interactions often drive phenotypic diversification and that species
 phenotypes in turn influence species interactions. Several phylogenetic
 comparative methods have been developed to assess the importance of such
 processes in nature; however, the statistical properties of these methods
 have gone largely untested. Focusing mainly on scenarios of competition
 between closely-related species, we assess the performance of available
 comparative approaches for analyzing the interplay between interspecific
 interactions and species phenotypes. We find that many currently used
 statistical methods often fail to detect the impact of interspecific
 interactions on trait evolution, that sister-taxa analyses are
 particularly unreliable in general, and that recently developed
 process-based models have more satisfactory statistical properties.
 Methods for detecting predictors of species interactions are generally
 more reliable than methods for detecting character displacement. In
 weighing the strengths and weaknesses of different approaches, we hope to
 provide a clear guide for empiricists testing hypotheses about the
 reciprocal effect of interspecific interactions and species phenotypes and
 to inspire further development of process-based models.
description: Supplementary
 TablesPhylogenies and
 biogeographies used in simulationsThis .zip file contains
 .RData objects that contain lists of length 100. For the *_tree files,
 each of these list entries contains a simulated phylogeny. For the *_geo
 files, each of these list entries contains a geography object specifying
 sympatry and allopatry through time (see ?CreateGeoObject in the R package
 RPANDA for a description of the contents of geography objects). Together,
 phylogenies and geography objects were used to simulate data under
 character displacement using sim.divergence.geo or sim.convergence.geo in
 RPANDA.Phylogenies_and_Biogeographies.zipSupplementary Material
DOI: 10.5067/asdc/suborbital/staqs/data001/chiwaukee-prairie_1
title: STAQS Chiwaukee Prairie Data
DOI: 10.15468/dl.b839nv
title: Occurrence Download

description: A dataset containing 942 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bursera aptera"
 ]
}

 The dataset includes 942 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000454-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b5ccgz
title: Occurrence Download

description: A dataset containing 2833 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-125.22322 13.10051,-75.77678 13.10051,-75.77678 32.89949,-125.22322 32.89949,-125.22322 13.10051))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Barisia imbricata"
 ]
}

 The dataset includes 2833 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000450-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.s8k81
title: Data from: Integrated metabolomics and metagenomics analysis of plasma and urine identified microbial metabolites associated with coronary heart disease

description: Coronary heart disease (CHD) is top risk factor for health in modern
 society, causing high mortality rate each year. However, there is no
 reliable way for early diagnosis and prevention of CHD so far. So study
 the mechanism of CHD and development of novel biomarkers is urgently
 needed. In this study, metabolomics and metagenomics technology are
 applied to discover new biomarkers from plasma and urine of 59 CHD
 patients and 43 healthy controls and trace their origin. We identify
 GlcNAc-6-P which has good diagnostic capability and can be used as
 potential biomarkers for CHD, together with mannitol and 15 plasma
 cholines. These identified metabolites show significant correlations with
 clinical biochemical indexes. Meanwhile, GlcNAc-6-P and mannitol are
 potential metabolites originated from intestinal microbiota. Association
 analysis on species and function levels between intestinal microbes and
 metabolites suggest a close correlation between Clostridium sp. HGF2 and
 GlcNAc-6-P, Clostridium sp. HGF2, Streptococcus sp. M143, Streptococcus
 sp. M334 and mannitol. These suggest the metabolic abnormality is
 significant and gut microbiota dysbiosis happens in CHD patients.
description: CHD_serum_102samples.tar.gzCHD_serum_102samples.tar.gzCHD_urine_102samples.tar.gzCHD_urine_102samples.tar.gzgut microbe mOTU profilegut microbe mOTU profilemOTU.prof.upload.txt
DOI: 10.5061/dryad.k5m0s
title: Data from: Selective sweeps of mitochondrial DNA can drive the evolution of uniparental inheritance

description: While the uniparental (or maternal) inheritance of mitochondrial DNA
 (mtDNA) is widespread, the reasons for its evolution remain unclear. Two
 main hypotheses have been proposed: selection against individuals
 containing different mtDNAs (heteroplasmy) and selection against “selfish”
 mtDNA mutations. Recently, uniparental inheritance was shown to promote
 adaptive evolution in mtDNA, potentially providing a third hypothesis for
 its evolution. Here we explore this hypothesis theoretically and ask if
 the accumulation of beneficial mutations provides a sufficient fitness
 advantage for uniparental inheritance to invade a population in which
 mtDNA is inherited biparentally. In a deterministic model, uniparental
 inheritance increases in frequency but cannot replace biparental
 inheritance if only a single beneficial mtDNA mutation sweeps through the
 population. When we allow successive selective sweeps of mtDNA, however,
 uniparental inheritance can replace biparental inheritance. Using a
 stochastic model, we show that a combination of selection and drift
 facilitates the fixation of uniparental inheritance (compared to a neutral
 trait) when there is only a single selective mtDNA sweep. When we consider
 multiple mtDNA sweeps in a stochastic model, uniparental inheritance
 becomes even more likely to replace biparental inheritance. Our findings
 thus suggest that selective sweeps of beneficial mtDNA haplotypes can
 drive the evolution of uniparental inheritance.
description: ChristieEvolution2017DataScripts and data to generate Figs 1-3 and Table 1
DOI: 10.15468/dl.g75us4
title: Occurrence Download

description: A dataset containing 36141 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cervus canadensis"
 ]
}

 The dataset includes 36141 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000453-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.vh0qt
title: Data from: Assessing canalisation of intraspecific variation on a macroevolutionary scale: the case of crinoid arms through the Phanerozoic

description: [No abstract entered]
description: Pictures of Crinoid
 Specimens 1Pictures of species with
 names that start with the letters A-Ccrinoids_1.zipPictures of Crinoid Specimens 2Pictures of species with names that start with the letters D-Ocrinoids_2.zipPictures of Crinoid Specimens 3Pictures of species with names that start with the letter Pcrinoids_3.zipPictures of Crinoid Specimens 4Pictures of species with names that start with the letters S-Zcrinoids_4.zip
DOI: 10.15468/dl.5rdkat
title: Occurrence Download

description: A dataset containing 78347 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Aedes aegypti"
 ]
}

 The dataset includes 78347 records from 111 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000407-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.54bg04m
title: Data from: Aerodynamics of manoeuvring flight in brown long-eared bats (Plecotus auritus)

description: In this study, we explicitly examine the aerodynamics of manoeuvring
 flight in animals. We studied brown long-eared bats flying in a wind
 tunnel while performing basic sideways manoeuvres. We used particle image
 velocimetry in combination with high-speed filming to link aerodynamics
 and kinematics to understand the mechanistic basis of manoeuvres. We
 predicted that the bats would primarily use the downstroke to generate the
 asymmetries for the manoeuvre since it has been shown previously that the
 majority of forces are generated during this phase of the wingbeat. We
 found instead that the bats more often used the upstroke than they used
 the downstroke for this. We also found that the bats used both
 drag/thrust-based and lift-based asymmetries to perform the manoeuvre and
 that they even frequently switch between these within the course of a
 manoeuvre. We conclude that the bats used three main modes: lift
 asymmetries during downstroke, thrust/drag asymmetries during downstroke
 and thrust/drag asymmetries during upstroke. For future studies, we
 hypothesize that lift asymmetries are used for fast turns and thrust/drag
 for slow turns and that the choice between up- and downstroke depends on
 the timing of when the bat needs to generate asymmetries.
description: Data for Henningsson et
 al 2018-J R Soc Interface-Part 1Sequences 1 to 4 of the
 dataData for Henningsson et
 al 2018-J R Soc Interface-Part 2Sequences 5 to 7 of the
 dataData for Henningsson et
 al 2018-J R Soc Interface-Part 3Sequences 8 to 10 of the
 data
DOI: 10.5061/dryad.3k8g5
title: Data from: An upper bound for accuracy of prediction using GBLUP

description: This study aims at characterizing the asymptotic behavior of genomic
 prediction R2 as the size of the reference population increases for common
 or rare QTL alleles through simulations. Haplotypes derived from
 whole-genome sequence of 85 Caucasian individuals from the 1,000 Genomes
 Project were used to simulate random mating in a population of 10,000
 individuals for at least 100 generations to create the LD structure in
 humans for a large number of individuals. To reduce computational demands,
 only SNPs within a 0.1M region of each of the first 5 chromosomes were
 used in simulations, and therefore, the total genome length simulated was
 0.5M. When the genome length is 30M, to get the same genomic prediction R2
 as with a 0.5M genome would require a reference population 60 fold larger.
 Three scenarios were considered varying in minor allele frequency
 distributions of markers and QTL, for h2 = 0.8 resembling height in
 humans. Total number of markers was 4,200 and QTL were 70 for each
 scenario. In this study, we considered the prediction accuracy in terms of
 an estimability problem, and thereby provided an upper bound for
 reliability of prediction, and thus, for prediction R2. Genomic prediction
 methods GBLUP, BayesB and BayesC were compared. Our results imply that for
 human height variable selection methods BayesB and BayesC applied to a 30M
 genome have no advantage over GBLUP when the size of reference population
 was small (&lt;6,000 individuals), but are superior as more
 individuals are included in the reference population. All methods become
 asymptotically equivalent in terms of prediction R2, which approaches
 genomic heritability when the size of the reference population reaches
 480,000 individuals.
description: Simulated
 genotypesSimulated genotypes
 based on haplotypes of 85 Caucasian individuals from the 1,000 Genome
 Project. Only SNPs with known positions within a 0.1M region of each of
 the first 5 chromosomes were used for simulations.genoData.csv
DOI: 10.5061/dryad.rh97t
title: Data from: A well-defined readily releasable pool with fixed capacity for storing vesicles at calyx of held

description: The readily releasable pool (RRP) of vesicles is a core concept in studies
 of presynaptic function. However, operating principles lack consensus
 definition and the utility for quantitative analysis has been questioned.
 Here we confirm that RRPs at calyces of Held from 14 to 21 day old mice
 have a fixed capacity for storing vesicles that is not modulated by Ca2+.
 Discrepancies with previous studies are explained by a dynamic
 flow-through pool, established during heavy use, containing vesicles that
 are released with low probability despite being immediately releasable.
 Quantitative analysis ruled out a posteriori explanations for the vesicles
 with low release probability, such as Ca2+-channel inactivation, and
 established unexpected boundary conditions for remaining alternatives.
 Vesicles in the flow-through pool could be incompletely primed, in which
 case the full sequence of priming steps downstream of recruitment to the
 RRP would have an average unitary rate of at least 9/s during heavy use.
 Alternatively, vesicles with low and high release probability could be
 recruited to distinct types of release sites; in this case the timing of
 recruitment would be similar at the two types, and the downstream
 transition from recruited to fully primed would be much faster. In either
 case, further analysis showed that activity accelerates the upstream step
 where vesicles are initially recruited to the RRP. Overall, our results
 show that the RRP can be well defined in the mathematical sense, and
 support the concept that the defining mechanism is a stable group of
 autonomous release sites.
description: KeysContains information
 about which data archives go with which experiments. Download this archive
 first, untar, and read the ReadMe.txt file within.A020513Data archiveA071014Data archiveA090613Data archiveA120713Data archiveA160413Data archiveA190413Data archiveA190913Data archiveA200613Data archiveA220713Data archiveA230713Data archiveA230913Data archiveA250413Data archiveA250613Data archiveA260413Data archiveA290413Data archiveA301014Data archiveA300413Data archiveA311014Data archiveB071014Data archiveB080613Data archiveB081014Data archiveB160713Data archiveB190913Data archiveB230913Data archiveB250613Data archiveB311014Data archiveC071014Data archiveC160713Data archiveC250613Data archiveD180413Data archive
DOI: 10.5061/dryad.jg6tc
title: Data from: Stalk formation of Brevundimonas and how it compares to Caulobacter crescentus

description: The Caulobacter crescentus cell extension known as a stalk represents an
 unusual bacterial morphology. C. crescentus produces stalks under multiple
 nutrient conditions, but the length of the stalk is increased in response
 to phosphate starvation. However, the exact function of the stalk is not
 known, nor is it known how much stalk biogenesis or function is conserved
 with other stalked bacteria. Work presented here shows that many organisms
 in the Caulobacter genus and the next closest genus (Brevundimonas)
 generally do not synthesize stalks in the relatively-rich PYE growth
 medium, suggesting that the synthesis of a stalk under nutrient-rich
 conditions by C. crescentus may be the exception instead of the norm among
 its phylogenetic group. Brevundimonas subvibrioides can be induced to
 synthesize stalks by genetically mimicking phosphate starvation
 conditions, indicating stalk synthesis in this organism may be performed
 on an as-need basis. This mutation, however, does not appear to increase
 the incidence of holdfast synthesis. While B. subvibrioides stalks appear
 to be synthesized with the same polarity with respect to holdfast as C.
 crescentus stalks, evidence is presented that suggests B. subvibrioides
 may disassemble stalks when they are no longer needed. Many homologs of C.
 crescentus genes encoding stalk-associated proteins are absent in the B.
 subvibrioides genome, and B. subvibrioides PstA-GFP as well as C.
 crescentus StpX-GFP are able to enter the B. subvibrioides stalk
 compartment, calling into question the level of compartmentalization of
 the B. subvibrioides stalk. In summary, this work begins to address how
 much the C. crescentus model for this unusual morphological adaptation can
 be extended to related organisms.
description: Stalk Quantification
 (Phase Contrast)Stalk Quantification
 (TEM)Holdfast
 QuantificationFluorescence
 Quantification
DOI: 10.5061/dryad.1bv87
title: Data from: An experimental study on the manufacture and characterisation of in-plane fibre-waviness defects in composites

description: A new method has been developed for creating localised in-plane
 fibre-waviness in composite coupons and used to create a large batch of
 specimens. This method could be used by manufacturers to experimentally
 explore the effect of fibre-waviness on composite structures both directly
 and indirectly to develop and validate computational models. The specimens
 were assessed using ultrasound, digital image correlation and a novel
 inspection technique capable of measuring residual strain fields. To
 explore how the defect affects the performance of composite structures,
 the specimens were then loaded to failure. Predictions of remnant strength
 were made using a simple ultrasound damage metric and a new residual
 strain-based damage metric. The predictions made using residual strain
 measurements were found to be substantially more effective at
 characterising ultimate strength than ultrasound measurements. This
 suggests that residual strains have a significant effect on the failure of
 laminates containing fibre-waviness and that these strains could be
 incorporated into computational models to improve their ability to
 simulate the defect.
description: DIC Data (0% Nominal
 Waviness)DIC Data for the 0%
 nominal waviness specimens. Data is exported from Istra-4D in a
 standardized file type.DIC_Data_0_nw.tarDIC Data (10% Nominal Waviness)DIC Data for the 10% nominal waviness specimens. Data is exported from Istra-4D in a standardized file type.DIC_Data_10_nw.tarDIC Data (15% and 17.5% Nominal Waviness)DIC Data for the 15% and 17.5% nominal waviness specimens. Data is exported from Istra-4D in a standardized file type.DIC_Data_15_and_17.5_nw.tarDIC Data (20% and 25% Nominal Waviness)DIC Data for the 15% and 17.5% nominal waviness specimens. Data is exported from Istra-4D in a standardized file type.DIC_Data_20_and_25_nw.tarLoad Data, Microscopy Images, and Ultrasound ImagesArchive containing: The load-displacement data for all specimens, recorded during load to failure. The raw microscopy images captured for sectioned specimens. The ultrasound images for all specimens. All file types are standardized.Load_Microscopy_Ultrasound.tar