cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.15b00t8
title: Data from: Effects of breathing movement on the reduction of postural sway during postural-cognitive dual tasking

description: An execution of cognitive processing interferes with postural sway during
 quiet standing. It reduces sway variability in young adults, but the
 mechanism is not clear. To elucidate the mechanisms, we focused on
 breathing in the present study. The purpose of this study was to clarify
 whether a decrease in postural sway amplitude during a postural-cognitive
 task is related to the change in breathing movement. The center of
 pressure (COP) was recorded via a force plate and the motion of leg joints
 (ankle, knee, and hip), and breathing movements were measured with a 3D
 motion capture system in quiet standing and standing with cognitive
 (mental arithmetic) task conditions. The change ratios of each variable
 from the quiet standing condition to the cognitive task were also
 calculated. In the results, the breathing rate was faster and the
 amplitude of breathing movement smaller when subjects performed the
 cognitive task. A significant positive correlation (r = 0.75, p &lt;
 0.01) was found between the change ratio of breathing amplitude and the
 COP amplitude. The present results suggest that reduced standing postural
 sway during a cognitive task is related, at least in part, to a decrease
 in breathing amplitude.
description: Force_dataForce plate (1ch ~ 8ch) dataAngle_dataAngle of Joints (ankle, knee and hip) dataBreath_dataBreath (the distance between the abdominal markers) data
DOI: 10.5061/dryad.m0p56
title: Data from: Evaluation of rockfish conservation area networks in the United States and Canada relative to the dispersal distance for black rockfish (Sebastes melanops)

description: Marine reserves networks are implemented as a way to mitigate the impact
 of fishing on marine ecosystems. Theory suggests that a reserve network
 will function synergistically when connected by dispersal, but the scale
 of dispersal is often unknown. On the Pacific coast of the United States
 and Canada, both countries have recently implemented a number of rockfish
 conservation areas (RCAs) to protect exploited rockfish species, but no
 study has evaluated the connectivity within networks in each country or
 between the two countries. We used isolation-by-distance theory to
 estimate the scale of dispersal from microsatellite data in the black
 rockfish, Sebastes melanops, and compared this estimate with the distance
 between RCAs that would protect this species. Within each country, we
 found that the distance between RCAs was generally within the confidence
 intervals of mean dispersal per generation. The distance between these two
 RCA networks, however, was greater than the average dispersal per
 generation. The data were also consistent with a genetic break between
 southern Oregon and central Oregon. We discuss whether additional
 nearshore RCAs in southern Oregon and Washington would help promote
 connectivity between RCA's for shallow-water rockfishes.
description: All datasets, scripts,
 and resultsThis is a .zip file
 containing the datasets, scripts, and results for the manuscript. In the
 folder, you will find the file named: 0_Metadata_readme.xlsx This file
 contains a list and description of all files included in the .zip
 file.20130831
 DataAndScriptsForDRYAD.zip
DOI: 10.5061/dryad.t297p
title: Data from: Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids

description: Despite the increasing opportunity to collect large-scale data sets for
 population genomic analyses, the use of high-throughput sequencing to
 study populations of polyploids has seen little application. This is due
 in large part to problems associated with determining allele copy number
 in the genotypes of polyploid individuals (allelic dosage
 uncertainty–ADU), which complicates the calculation of important
 quantities such as allele frequencies. Here, we describe a statistical
 model to estimate biallelic SNP frequencies in a population of
 autopolyploids using high-throughput sequencing data in the form of read
 counts. We bridge the gap from data collection (using restriction enzyme
 based techniques [e.g. GBS, RADseq]) to allele frequency estimation in a
 unified inferential framework using a hierarchical Bayesian model to sum
 over genotype uncertainty. Simulated data sets were generated under
 various conditions for tetraploid, hexaploid and octoploid populations to
 evaluate the model's performance and to help guide the collection of
 empirical data. We also provide an implementation of our model in the R
 package polyfreqs and demonstrate its use with two example analyses that
 investigate (i) levels of expected and observed heterozygosity and (ii)
 model adequacy. Our simulations show that the number of individuals
 sampled from a population has a greater impact on estimation error than
 sequencing coverage. The example analyses also show that our model and
 software can be used to make inferences beyond the estimation of allele
 frequencies for autopolyploids by providing assessments of model adequacy
 and estimates of heterozygosity.
description: Data and code for
 polyfreqs manuscriptThis folder contains all
 of the code and data for the simulation study conducted to evaluate
 polyfreqs. It also contains the empirical data for the potato data set
 analyzed in the manuscript and the supplemental walk through. The code for
 producing all of the figures is also provided. These are all in the
 'code', 'example' or 'supplement' folders.
 Each folder has it's own README file.polyfreqs-dryad.zip
DOI: 10.5061/dryad.q36nr
title: Data from: New SNPs for population genetic analysis reveal possible cryptic speciation of eastern Australian sea mullet (Mugil cephalus)

description: Sustainable management of sea mullet (Mugil cephalus) fisheries needs to
 account for recent observations of regional-scale differentiation.
 Population genetic analysis is sought to assess the situation of this
 ecologically and economically important fish species in eastern Australian
 waters. Here, we report (i) new population genetic markers [single
 nucleotide polymorphisms (SNPs) and potential microsatellites], (ii) first
 estimates of spatial genetic differentiation and (iii) prospective power
 tests for designing more comprehensive studies. Six DNA samples from three
 sampling regions (North Queensland, South Queensland and central New South
 Wales) on the eastern coast of Australia were used to prepare restriction
 site associated DNA (RAD) tag libraries from genomic DNA digested with
 EcoRI and MseI. A pooled sample of regional RAD tag libraries was
 sequenced using the Roche GS-FLX Titanium platform. A total of 172 837 raw
 reads (17.4 Mbp) were retrieved, 95 500 of which were used to discover
 1267 SNPs and 1417 microsatellites. A subset of 161 SNPs was validated
 based on 63 additional DNA samples genotyped using the Sequenom MassArray
 (iPLEX Gold chemistry). Altogether 92 SNPs (57%) were confirmed, with 40%
 of these marking fixed variants between northern and southern sampling
 regions. Our preliminary findings indicate a multispecies fishery stock of
 M. cephalus in eastern Australian waters, but suggest that strong genetic
 differentiation occurs north of major fishing grounds. Low potential
 differentiation within major fishing grounds (e.g. FST = 0.0025) can be
 resolved with a likely power ≥67% by using standard sample sizes of 50 and
 validated subsets of available markers.
description: Mugil_cephalus_RRL_454Roche GS-FLEX SFF files of sequence data generated from sequencing EcoRI/MseI reduced complexity libraries prepared from sea mullet (Mugil cephalus) genomic DNA. Samples were collected from the east coast of Australia.mullet75_assemblydataset-file
DOI: 10.5061/dryad.4r5b8
title: Data from: Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks

description: Multiple sequence aligners typically work by progressively aligning the
 most closely related sequences or group of sequences according to guide
 trees. In PNAS, Boyce et al. report that alignments reconstructed using
 simple chained trees (i.e., comb-like topologies) with random leaf
 assignment performed better in protein structure-based benchmarks than
 those reconstructed using phylogenies estimated from the data as guide
 trees. The authors state that this result could turn decades of research
 in the field on its head. In light of this statement, it is important to
 check immediately whether their result holds under evolutionary criteria:
 recovery of homologous sequence residues and inference of phylogenetic
 trees from the alignments. We have done this and the results are entirely
 opposed to Boyce et al.’s findings.
description: Materials and
 methodsDetailed description of
 the required to reproduce the analysis presented in Figure 1 of the
 letter.guidetree_methods.pdfRaw data of empirical phylogenetic analysesAlignment and trees associated with empirical results.guidetree_empirical.tar.gzRaw data of simulation analysesAlignment and trees associated with simulation-based analysesguidetree_simulation.tar.gz
DOI: 10.5061/dryad.f2v0k
title: Data from: Quantifying post- laser ablation prostate therapy changes on MRI via a domain-specific biomechanical model: preliminary findings

description: Focal laser ablation destroys cancerous cells via thermal destruction of
 tissue by a laser. Heat is absorbed, causing thermal necrosis of the
 target region. It combines the aggressive benefits of radiation treatment
 (destroying cancer cells) without the harmful side effects (due to its
 precise localization). MRI is typically used pre-treatment to determine
 the targeted area, and post-treatment to determine efficacy by detecting
 necrotic tissue, or tumor recurrence. However, no system exists to
 quantitatively evaluate the post-treatment effects on the morphology and
 structure via MRI. To quantify these changes, the pre- and post-treatment
 MR images must first be spatially aligned. The goal is to quantify (a)
 laser-induced shape-based changes, and (b) changes in MRI parameters
 post-treatment. The shape-based changes may be correlated with treatment
 efficacy, and the quantitative effects of laser treatment over time is
 currently poorly understood. This work attempts to model changes in gland
 morphology following laser treatment due to (1) patient alignment, (2)
 changes due to surrounding organs such as the bladder and rectum, and (3)
 changes due to the treatment itself. To isolate the treatment-induced
 shape-based changes, the changes from (1) and (2) are first modeled and
 removed using a finite element model (FEM). A FEM models the physical
 properties of tissue. The use of a physical biomechanical model is
 important since a stated goal of this work is to determine the physical
 shape-based changes to the prostate from the treatment, and therefore only
 physical real deformations are to be allowed. A second FEM is then used to
 isolate the physical, shape-based, treatment-induced changes. We applied
 and evaluated our model in capturing the laser induced changes to the
 prostate morphology on eight patients with 3.0 Tesla, T2-weighted MRI,
 acquired approximately six months following treatment. Our results suggest
 the laser treatment causes a decrease in prostate volume, which appears to
 manifest predominantly at the site of ablation. After spatially aligning
 the images, changes to MRI intensity values are clearly visible at the
 site of ablation. Our results suggest that our new methodology is able to
 capture and quantify the degree of laser-induced changes to the prostate.
 The quantitative measurements reflecting of the deformation changes can be
 used to track treatment response over time.
description: Pre- and post-LITT MRI
 acquisitionsThis dataset comprises a
 total of 9 patients who underwent LITT therapy. For each patient, at least
 one pre-treatment acquisition and one post-treatment acquisition is
 available. Some patients have an acquisition from "during"
 therapy. Further details in paper and README file.fem_data.zip
DOI: 10.5061/dryad.t4k7h
title: Data from: Genome sequencing of a single tardigrade Hypsibius dujardini individual

description: Tardigrades are ubiquitous microscopic animals that play an important role
 in the study of metazoan phylogeny. Most terrestrial tardigrades can
 withstand extreme environments by entering an ametabolic desiccated state
 termed anhydrobiosis. Due to their small size and the non-axenic nature of
 laboratory cultures, molecular studies of tardigrades are prone to
 contamination. To minimize the possibility of microbial contaminations and
 to obtain high-quality genomic information, we have developed an ultra-low
 input library sequencing protocol to enable the genome sequencing of a
 single tardigrade Hypsibius dujardini individual. Here, we describe the
 details of our sequencing data and the ultra-low input library preparation
 methodologies.
description: Hypsibius dujardini
 genome assemblyGenome sequence assembly
 of a single individual of Hypsibius dujardini Z151 sequencing reads
 (Illumina MiSeq 300bp paired end), using MaSuR-CA 3.1.3
 software.genome.scf.fasta
DOI: 10.15468/dl.4wyqu7
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Glyptodon clavipes"
 ]
}

 The dataset includes 24 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000411-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.42gp897
title: Data from: Integrating vital rates explains optimal worker size for resource return by bumble bee workers

description: 1. Size-number trade-offs in reproduction are commonly observed in nature.
 Bumble bee (Bombus spp.) colonies produce workers that vary considerably
 in size. This variation suggests that colonies face potential size-number
 trade-offs when producing workers. 2. Here, we estimated size-based vital
 rates of Bombus vosnesenskii workers using colonies reared from wild
 caught queens. We conducted a mark-recapture study to estimate worker
 survival as a function of body size. We also collected data on pollen and
 nectar loads as well as foraging trips using a radio-frequency
 identification system to estimate daily resource return as a function of
 body size. We integrated survival and daily resource return to estimate
 lifetime resource collection and offset these estimates by the size-based
 worker production costs. 3. We found size-based trade-offs among workers
 of different sizes. Smaller workers had higher survival, but larger
 workers returned with more resources per day. The largest workers made
 slightly fewer foraging trips per day. 4. Overall, larger workers made the
 greatest lifetime contribution to both nectar and pollen collection.
 However, once the benefits of larger workers are offset by their higher
 production costs, intermediate-sized workers were the optimal for net
 resource contribution according to our models. Many previous studies have
 found that larger workers outperformed smaller workers with foraging and
 in-nest tasks, yet these studies have not integrated multiple fitness
 components or worker production costs to quantify net resource
 contribution towards colony growth. 5. Accounting for tradeoffs between
 costs and performance changed our conclusions about optimal body size from
 being large to being near the observed average. Similar approaches of
 integrating multiple vital rates may resolve apparently suboptimal life
 histories in other taxa.
description: BeeSurv_MarkRecaptureResourceReturnRFID_RawDataRFID_ProcessedData
DOI: 10.5061/dryad.5n481
title: Data from: Testing hypotheses of element loss and instability in the apparatus composition of complex conodonts: articulated skeletons of Hindeodus

description: Knowledge of the conodont skeleton, in terms of the morphology of the
 elements and the positions they occupy, provides the foundation for
 understanding of homology, taxonomy and evolutionary relationships in
 conodonts. This knowledge also underpins analyses of conodont functional
 morphology and feeding. Direct evidence of skeletal anatomy and apparatus
 architecture comes from natural assemblages: fossils that preserve
 together the articulated remains of the conodont apparatus, either
 collapsed onto a bedding plane or as clusters of elements in which
 juxtaposed and overlapping elements have been fused together by diagenetic
 minerals. Here we describe six clusters of the biostratigraphically
 important conodont Hindeodus parvus from the Lower Triassic Shangsi
 section, Sichuan Province, South China. Five of these clusters represent
 the partial remains of articulated skeletons, providing direct evidence of
 the number and arrangement of elements in the apparatus. Combined with
 data from previously published natural assemblages this provides a test of
 the hypothesis that Triassic conodonts had a reduced dentition. Hindeodus
 parvus possessed a complete raptorial array of two M and nine S elements
 (unpaired S0; symmetrically paired S1, S2, S3, S4); the paired P1
 locations were occupied by carminiscaphate elements, but the apparatus
 lacked P2 elements. This is consistent with broader evidence for a
 particularly high degree of integration and constraint operating on the
 S–M array of morphologically complex conodonts, leading to conserved
 architecture of the array over a period of more than 250 million years.
 The loss of elements from the P domain implies a change in food processing
 ability and, given the predominance of data from P elements in conodont
 taxonomy and biostratigraphy, the hypothesis of element loss from the P
 domain has significant implications for the broader understanding of
 conodont diversity and evolutionary patterns.
description: WinRAR file for clusters
 1-6 of ShangsiSix zip
 filesWinRAR_file_for_clusters_1-6_of_Shangsi.rarFig.3-Cluster 1-video of 3dfig3-flash-3d.aviFig.4-Cluster 2-video of 3dfig4-flash-3d.aviFig.5-Cluster 3-video of 3dfig5-flash-3d.aviFig.6-Cluster 4-video of 3dfig6-flash-3d.aviFig.7-Cluster 5-video of 3dfig7-flash-3d.aviFig.8-Cluster 6-video of 3dfig8-flash-3d.avi
DOI: 10.5061/dryad.3pm63
title: Data from: Defining functional biomes and monitoring their change globally

description: Biomes are important constructs for organizing understanding of how the
 worlds’ major terrestrial ecosystems differ from one another and for
 monitoring change in these ecosystems. Yet existing biome schemes have
 been criticized for being overly subjective and for explicitly or
 implicitly invoking climate. We propose a new biome map and classification
 scheme that uses information on (i) an index of vegetation productivity,
 (ii) whether the minimum of vegetation activity is in the driest or
 coldest part of the year, and (iii) vegetation height. Although biomes
 produced on the basis of this classification show a strong spatial
 coherence, they show little congruence with existing biome classification
 schemes. Our biome map provides an alternative classification scheme for
 synthesizing data of the biogeochemical rates of terrestrial ecosystems.
 We use this new biome classification scheme to analyse the patterns of
 biome change observed over recent decades. Overall, 13 - 14% of analysed
 pixels shifted in biome state over the 30-year study period. A wide range
 of biome transitions were observed. For example, biomes with tall
 vegetation and seasonality associated with cold in the unfavourable
 growing period shifted to higher productivity biome states. Sites
 dominated by biomes characterized by short vegetation and low seasonality
 shifted to seasonally moisture-limited biome states. Our findings and
 method provide a new source of data for rigorously monitoring global
 vegetation change, analysing drivers of vegetation change and for
 benchmarking models of terrestrial ecosystem function.
description: NetCDFs of a functional
 biome map and the underlying data structures used to create
 it.Tar archive containing
 netcdf files. See readme file for further detailsHiggins_etal_GCB_FunctionalBiomes.tar
DOI: 10.5061/dryad.8tk11
title: Data from: How to find home backwards? Navigation during rearward homing of Cataglyphis fortis desert ants

description: Cataglyphis ants are renowned for their impressive navigation skills,
 which have been studied in numerous experiments during forward locomotion.
 However, the ants' navigational performance during backward homing
 when dragging large food loads has not been investigated until now. During
 backward locomotion, the odometer has to deal with unsteady motion and
 irregularities in inter-leg coordination. The legs' sensory feedback
 during backward walking is not just a simple reversal of the forward
 stepping movements: compared with forward homing, ants are facing towards
 the opposite direction during backward dragging. Hence, the compass system
 has to cope with a flipped celestial view (in terms of the polarization
 pattern and the position of the sun) and an inverted retinotopic image of
 the visual panorama and landmark environment. The same is true for wind
 and olfactory cues. In this study we analyze for the first time
 backward-homing ants and evaluate their navigational performance in
 channel and open field experiments. Backward-homing Cataglyphis fortis
 desert ants show remarkable similarities in the performance of homing
 compared with forward-walking ants. Despite the numerous challenges
 emerging for the navigational system during backward walking, we show that
 ants perform quite well in our experiments. Direction and distance gauging
 was comparable to that of the forward-walking control groups.
 Interestingly, we found that backward-homing ants often put down the food
 item and performed foodless search loops around the left food item. These
 search loops were mainly centred around the drop-off position (and not
 around the nest position), and increased in length the closer the ants
 came to their fictive nest site.
description: supplementary video V1
 (backward homing)Shown is an ant that is
 presented a large food item. It grasps immediately the booty and starts
 its homing journey in backward locomotion. The ant also drops the load and
 performs foodless search loops that are directed towards the fictive nest
 site. Note that the early performed foodless search loops tend to be even
 much shorter in length and time than the two foodless search loops seen in
 this video.