cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.55f3s
title: Data from: A genome-wide assessment of genetic diversity and population structure of Korean native cattle breeds

description: Background: The native cattle breeds are an important genetic resource for
 meat and milk production throughout Asia. In Asia cattle were domesticated
 around 10,000 years ago and in Korea cattle are being raised since 2000
 B.C. There are three native breeds of cattle in Korea viz. Brown Hanwoo,
 Brindle Hanwoo and Jeju Black. While one of these breeds, Brown Hanwoo, is
 a part of a Food and Agricultural Organization and national genetic
 evaluation plans, others get little attention. This study is an effort to
 understand and provide a detailed insight into the population structure
 and genetic variability of the Korean cattle breeds along with other Asian
 breeds using various methods. In this study we report the genetic
 variation and structure of the Korean cattle breeds and their comparison
 with five other Asian cattle breeds along with a panel of animals from
 European taurine, African taurine and indicine cattle breeds. Results:
 Asian cattle were found to be least differentiated which reflects their
 recent history. Amongst the Asian breeds Hainan, which is an indicine
 breed, had the lowest gene diversity while Yanbian had the highest
 followed by Mongolian and Korean cattle. Amongst the Korean breeds Brown
 Hanwoo had the highest diversity followed by Brindle Hanwoo and Jeju
 Black. The genetic diversity in Asian cattle breeds was found comparable
 to the European taurines and more than the African taurines and Zebu
 cattle. Korean cattle breed, Brown Hanwoo was consistently found to be
 closer to Yanbian, a Chinese cattle breed. We found low divergence and
 moderate levels of genetic diversity among the native Korean breeds.
 Indicine introgression from Hainan was seen in other Asian breeds. From
 Europe, Limousin, Holstein and Hereford introgression was found in Asian
 breeds. Conclusions: In this study we provide a genome-wide insight into
 the genetic history of the native cattle breeds of Korea. The outcomes of
 this study will help in prioritization and designing of the conservation
 plans.
description: A genome-wide assessment
 of genetic diversity and population structure of Korean native cattle
 breedsPlink format Ped and Map
 fileData.zip
DOI: 10.5061/dryad.82c5b
title: Data from: Repetitive flanking sequences challenge SSR marker development: a case study in the lepidopteran Melanargia galathea

description: Microsatellite DNA families (MDF) are stretches of DNA that share similar
 or identical sequences beside nuclear simple-sequence repeat (nSSR)
 motifs, potentially causing problems during nSSR marker development.
 Primers positioned within MDFs can bind several times within the genome
 and might result in multiple banding patterns. It is therefore common
 practice to exclude MDF loci in the course of marker development. Here, we
 propose an approach to deal with multiple primer binding sites by
 purposefully positioning primers within the detected repetitive element.
 We developed a new protocol to determine the family type and the primer
 position in relation to MDFs using the software packages RepARK and
 RepeatMasker together with an in-house R script. We re-evaluated newly
 developed nSSR markers for the lepidopteran Marbled White (Melanargia
 galathea) and explored the implications of our results with regard to
 published data sets of the butterfly Ephydryas aurinia, the grasshopper
 Stethophyma grossum, the conifer Pinus cembra, and the crucifer Arabis
 alpina. For M. galathea, we show that it is not only possible to develop
 reliable nSSR markers for MDF loci, but even to benefit from their
 presence in some cases: We used one unlabeled primer, successfully binding
 within an MDF, for two different loci in a multiplex PCR, combining this
 family primer with uniquely binding and fluorescently labeled primers
 outside of MDFs, respectively. As MDFs are abundant in many taxa, we
 propose to consider these during nSSR marker development in taxa
 concerned. Our new approach might help in reducing the number of tested
 primers during nSSR marker development.
description: ZipArchive of
 Supplementary Material for nSSR detection, including
 ReadMeThis ZipArchive contains
 all files (data, R scripts) required for performing the nSSR search with
 the example data of Melanargia galathea, including a ReadMe for
 explanation.Schmid_etal_MolEcolResour2016.zip
DOI: 10.5061/dryad.1d808
title: Data from: Ocean warming expands habitat of a rich natural resource and benefits a national economy

description: Geographic redistribution of living natural resources changes access and
 thereby harvesting opportunities between countries. Internationally shared
 fish resources can be sensitive to shifts in the marine environment and
 this may have great impact on the economies of countries and regions that
 rely most heavily on fisheries to provide employment and food supply. Here
 we present a climate change-related biotic expansion of a rich natural
 resource with substantial economic consequences, namely the appearance of
 northeast Atlantic mackerel (Scomber scombrus) in Greenlandic waters. In
 recent years, the summer temperature has reached record highs in the
 Irminger Current, and this development has expanded the available and
 realized mackerel habitat in time and space. Observations in the Irminger
 Current in east Greenland in 2011 of this temperature-sensitive epipelagic
 fish were the first records so far northwest in the Atlantic. This change
 in migration pattern was followed by a rapid development of a large-scale
 fishery of substantial importance for the national economy of Greenland
 (23% of Greenland's export value of all goods in 2014). A pelagic
 trawl survey was conducted in mid-summer 2014 and the results showed that
 the bulk of ~1 million Mg (=t) of mackerel in the Irminger Current in
 southeast Greenland were located in the relatively warm (&gt;8.5°C)
 surface layer. Mackerel was also observed in southwest Greenland. Finally,
 15 CMIP5 Earth System Model projections of future marine climate were used
 to evaluate the epipelagic environment in Greenland. These projections for
 moderate and high CO2 emission scenarios (representative concentration
 pathways [RCP] 4.5 and 8.5) suggest how the available mackerel habitat may
 expand further in space and time. Overall, our results indicate that, if
 the stock remains large, productive, and continues its current migration
 pattern, then climate change has provided Greenland with a new unique
 opportunity for commercial exploitation. However, positive cases like this
 should not be cherry-picked and misused as arguments against timely and
 effective mitigation of climate change.
description: Dryad
 data
DOI: 10.5061/dryad.rt0t0
title: Data from: Laetoli footprints reveal bipedal gait biomechanics different from those of modern humans and chimpanzees

description: Bipedalism is a key adaptation that shaped human evolution, yet the timing
 and nature of its evolution remain unclear. Here we use new experimentally
 based approaches to investigate the locomotor mechanics preserved by the
 famous Pliocene hominin footprints from Laetoli, Tanzania. We conducted
 footprint formation experiments with habitually barefoot humans and with
 chimpanzees to quantitatively compare their footprints to those preserved
 at Laetoli. Our results show that the Laetoli footprints are
 morphologically distinct from those of both chimpanzees and habitually
 barefoot modern humans. By analysing biomechanical data that were
 collected during the human experiments we, for the first time, directly
 link differences between the Laetoli and modern human footprints to
 specific biomechanical variables. We find that the Laetoli hominin
 probably used a more flexed limb posture at foot strike than modern humans
 when walking bipedally. The Laetoli footprints provide a clear snapshot of
 an early hominin bipedal gait that probably involved a limb posture that
 was slightly but significantly different from our own, and these data
 support the hypothesis that important evolutionary changes to hominin
 bipedalism occurred within the past 3.66 Myr.
description: Footprint and kinematic
 data from human experimentsThis file includes a
 non-identifiable version of the human experimental data set. This includes
 measurements of footprint topographies from each experimental trial, along
 with corresponding biomechanical data from those same
 trials.humanFootprintAndKinematicData.xlsxFootprint data from chimpanzee experimentsThis file contains non-identifiable data from the chimpanzee footprint experiments. This includes normalized measurements of the topographies of the footprints created in each experimental trial.chimpanzeeFootprintDepths.xlsxFootprint data from LaetoliThis file contains measurements of footprint topography from the set of Laetoli footprints that were analyzed in this study.laetoliFootprintDepths.xlsxSample human and chimpanzee track modelsSample 3-dimensional models of experimentally-produced human and chimpanzee tracks.Sample track models.zip
DOI: 10.5061/dryad.f1860
title: Data from: Direct effects dominate responses to climate perturbations in grassland plant communities

description: Theory predicts that strong indirect effects of environmental change will
 impact communities when niche differences between competitors are small
 and variation in the direct effects experienced by competitors is large,
 but empirical tests are lacking. Here we estimate negative frequency
 dependence, a proxy for niche differences, and quantify the direct and
 indirect effects of climate change on each species. Consistent with
 theory, in four of five communities indirect effects are strongest for
 species showing weak negative frequency dependence. Indirect effects are
 also stronger in communities where there is greater variation in direct
 effects. Overall responses to climate perturbations are driven primarily
 by direct effects, suggesting that single species models may be adequate
 for forecasting the impacts of climate change in these communities.
description: Data & Scripts for
 Chu et al. (2016) Nature CommunicationsThis data file includes
 data and R scripts used to fit the vital rates models and to run
 simulations (IBM and IPM) for Chu et al. (2016) Nature
 Communications.Data &
 Scripts.rar
DOI: 10.5061/dryad.h846r
title: Data from: Preferred gait and walk–run transition speeds in ostriches measured using GPS-IMU sensors

description: The ostrich (Struthio camelus) is widely appreciated as a fast and agile
 bipedal athlete, and is a useful comparative bipedal model for human
 locomotion. Here, we used GPS-IMU sensors to measure naturally selected
 gait dynamics of ostriches roaming freely over a wide range of speeds in
 an open field and developed a quantitative method for distinguishing
 walking and running using accelerometry. We compared freely selected
 gait–speed distributions with previous laboratory measures of gait
 dynamics and energetics. We also measured the walk–run and run–walk
 transition speeds and compared them with those reported for humans. We
 found that ostriches prefer to walk remarkably slowly, with a narrow
 walking speed distribution consistent with minimizing cost of transport
 (CoT) according to a rigid-legged walking model. The dimensionless speeds
 of the walk–run and run–walk transitions are slower than those observed in
 humans. Unlike humans, ostriches transition to a run well below the
 mechanical limit necessitating an aerial phase, as predicted by a
 compass-gait walking model. When running, ostriches use a broad speed
 distribution, consistent with previous observations that ostriches are
 relatively economical runners and have a flat curve for CoT against speed.
 In contrast, horses exhibit U-shaped curves for CoT against speed, with a
 narrow speed range within each gait for minimizing CoT. Overall, the gait
 dynamics of ostriches moving freely over natural terrain are consistent
 with previous lab-based measures of locomotion. Nonetheless, ostriches,
 like humans, exhibit a gait-transition hysteresis that is not explained by
 steady-state locomotor dynamics and energetics. Further study is required
 to understand the dynamics of gait transitions.
description: Ostrich Overground Gait
 DataFile containing bird ID,
 hip height, body mass, time of each step, position, gait ID, relative
 speed (vel_norm), relative step frequency (stepFreq_Norm), relative step
 length (stepLength_Norm) and energy phase for all recorded steady steps,
 walk to run transitions and run to walk transitions. (Note the
 'gait_ID' column is only in the steady data, not the gait
 transitions. 1=walk and 2 = run, based on the gait metric described and
 used in the manuscript).OstrichGaitData_Daley_etal_R1.xls
DOI: 10.5061/dryad.n2g31
title: Data from: Characterization and analysis of a de novo transcriptome from the pygmy grasshopper Tetrix japonica

description: The pygmy grasshopper Tetrix japonica is a common insect distributed
 throughout the world, and it has the potential for use in studies of body
 colour polymorphism, genomics and the biology of Tetrigoidea (Insecta:
 Orthoptera). However, limited biological information is available for this
 insect. Here, we conducted a de novo transcriptome study of adult and
 larval T. japonica to provide a better understanding of its gene
 expression and develop genomic resources for future work. We sequenced and
 explored the characteristics of the de novo transcriptome of T. japonica
 using Illumina HiSeq 2000 platform. A total of 107 608 206 paired-end
 clean reads were assembled into 61 141 unigenes using the trinity
 software; the mean unigene size was 771 bp, and the N50 length was 1238
 bp. A total of 29 225 unigenes were functionally annotated to the NCBI
 nonredundant protein sequences (Nr), NCBI nonredundant nucleotide
 sequences (Nt), a manually annotated and reviewed protein sequence
 database (Swiss-Prot), Gene Ontology (GO) and Kyoto Encyclopedia of Genes
 and Genomes (KEGG) databases. A large number of putative genes that are
 potentially involved in pigment pathways, juvenile hormone (JH) metabolism
 and signalling pathways were identified in the T. japonica transcriptome.
 Additionally, 165 769 and 156 796 putative single nucleotide polymorphisms
 occurred in the adult and larvae transcriptomes, respectively, and a total
 of 3162 simple sequence repeats were detected in this assembly. This
 comprehensive transcriptomic data for T. japonica will provide a usable
 resource for gene predictions, signalling pathway investigations and
 molecular marker development for this species and other pygmy
 grasshoppers.
description: The unigenes of the
 Tetrix japoncia assembly"TjA-Unigene.fa" represents all the unigenes of the adult samples from Tetrix japonica. "TjL-Unigene.fa" represents all the unigenes of the larval samples from T.japonica. "TjATjL-Unigene.fa" represents allthe unigenes of the merged assembly of adult and larval samples from T.japoncia.read me.txtTjA-UnigeneThe unigenes of the larval samples from Tetrix japonicaTjL-Unigene.zipAllthe unigenes of the merged assembly of adult and larval samples from Tetrix japonica.TjATjL-Unigene.zip
DOI: 10.5061/dryad.15m0d
title: Data from: Increasing compliance with low tidal volume ventilation in the ICU with two nudge-based interventions: evaluation through intervention time-series analyses

description: Objectives: Low tidal volume (TVe) ventilation improves outcomes for
 ventilated patients, and the majority of clinicians state they implement
 it. Unfortunately, most patients never receive low TVes. ‘Nudges’
 influence decision-making with subtle cognitive mechanisms and are
 effective in many contexts. There have been few studies examining their
 impact on clinical decision-making. We investigated the impact of 2
 interventions designed using principles from behavioural science on the
 deployment of low TVe ventilation in the intensive care unit (ICU).
 Setting: University Hospitals Bristol, a tertiary, mixed medical and
 surgical ICU with 20 beds, admitting over 1300 patients per year.
 Participants: Data were collected from 2144 consecutive patients receiving
 controlled mechanical ventilation for more than 1 hour between October
 2010 and September 2014. Patients on controlled mechanical ventilation for
 more than 20 hours were included in the final analysis. Interventions: (1)
 Default ventilator settings were adjusted to comply with low TVe targets
 from the initiation of ventilation unless actively changed by a clinician.
 (2) A large dashboard was deployed displaying TVes in the format mL/kg
 ideal body weight (IBW) with alerts when TVes were excessive. Primary
 outcome measure: TVe in mL/kg IBW. Findings: TVe was significantly lower
 in the defaults group. In the dashboard intervention, TVe fell more
 quickly and by a greater amount after a TVe of 8 mL/kg IBW was breached
 when compared with controls. This effect improved in each subsequent year
 for 3 years. Conclusions: This study has demonstrated that adjustment of
 default ventilator settings and a dashboard with alerts for excessive TVe
 can significantly influence clinical decision-making. This offers a
 promising strategy to improve compliance with low TVe ventilation, and
 suggests that using insights from behavioural science has potential to
 improve the translation of evidence into practice.
description: newalldata_corrected
DOI: 10.5061/dryad.gv1dq
title: Data from: Does hunting or hiking affect wildlife communities in protected areas?

description: Managed public wild areas have dual mandates to protect biodiversity and
 provide recreational opportunities for people. These goals could be at
 odds if recreation, ranging from hiking to legal hunting, disrupts
 wildlife enough to alter their space use or community structure. We
 evaluated the effect of managed hunting and recreation on 12 terrestrial
 wildlife species by employing a large citizen science camera trapping
 survey at 1947 sites stratified across different levels of human
 activities in 32 protected forests in the eastern USA. Habitat covariates,
 especially the amount of large continuous forest and local housing
 density, were more important than recreation for affecting the
 distribution of most species. The four most hunted species (white-tailed
 deer, raccoons, eastern grey and fox squirrels) were commonly detected
 throughout the region, but relatively less so at hunted sites. Recreation
 was most important for affecting the distribution of coyotes, which used
 hunted areas more compared with unhunted control areas, and did not avoid
 areas used by hikers. Most species did not avoid human-made trails, and
 many predators positively selected them. Bears and bobcats were more
 likely to avoid people in hunted areas than unhunted preserves, suggesting
 that they perceive the risk of humans differently depending on local
 hunting regulations. However, this effect was not found for the most
 heavily hunted species, suggesting that human hunters are not broadly
 creating ‘fear’ effects to the wildlife community as would be expected for
 apex predators. Synthesis and applications. Although we found that hiking
 and managed hunting have measureable effects on the distribution of some
 species, these were relatively minor in comparison with the importance of
 habitat covariates associated with land use and habitat fragmentation.
 These patterns of wildlife distribution suggest that the present practices
 for regulating recreation in the region are sustainable and in balance
 with the goal of protecting wildlife populations and may be facilitated by
 decades of animal habituation to humans. The citizen science monitoring
 approach we developed could offer a long-term monitoring protocol for
 protected areas, which would help managers to detect where and when the
 balance between recreation and wildlife has tipped.
description: eMammal detections
 datasetThis file contains the
 raw species detections from camera-trap data across 33 protected areas in
 the Southeastern United States from 2012-2013. Each row represents one
 detection and the associated location, time and
 species.Raw
 Data.xlsxCamera-level
 covariatesThis file contains
 spatial and temporal covariates for the camera-trap dataset collected
 across 33 protected areas in the Southeastern United States from
 2012-2013. Each row represents one camera site.Covariates.xlsx
DOI: 10.5061/dryad.vd156
title: Data from: State-space reduction and equivalence class sampling for a molecular self-assembly model

description: Direct simulation of a model with a large state space will generate
 enormous volumes of data, much of which is not relevant to the questions
 under study. In this paper, we consider a molecular self-assembly model as
 a typical example of a large state-space model, and present a method for
 selectively retrieving ‘target information’ from this model. This method
 partitions the state space into equivalence classes, as identified by an
 appropriate equivalence relation. The set of equivalence classes H, which
 serves as a reduced state space, contains none of the superfluous
 information of the original model. After construction and characterization
 of a Markov chain with state space H, the target information is
 efficiently retrieved via Markov chain Monte Carlo sampling. This approach
 represents a new breed of simulation techniques which are highly optimized
 for studying molecular self-assembly and, moreover, serves as a valuable
 guideline for analysis of other large state-space models.
description: Supporting data for the
 paper 'State Space Reduction and Equivalence Class Sampling for a
 Molecular Self-Assembly Model'The equivalence class
 sample used to generate Figure 5 as an .Rdata workspace file for R. Upon
 loading this data into the R environment, one should type “Message” to
 receive an explanation of the data structure.Supporting_Information.Rdata