cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c1b54
title: Data from: Monitoring chicken flock behaviour provides early warning of infection by human pathogen Campylobacter

description: Campylobacter is the commonest bacterial cause of gastrointestinal
 infection in humans and chicken meat is the major source of infection
 throughout the world. Strict and expensive on-farm biosecurity measures
 have been largely unsuccessful in controlling infection and are hampered
 by the time needed to analyze faecal samples with the result that
 Campylobacter status is often known only after a flock has been processed.
 Our data demonstrate an alternative approach that monitors the behaviour
 of live chickens with cameras and analyses the ‘optical flow’ patterns
 made by flock movements. Campylobacter-free chicken flocks have higher
 mean and lower kurtosis of optical flow than those testing positive for
 Campylobacter by microbiological methods. We show that by monitoring
 behaviour in this way, flocks likely to become positive can be identified
 within the first 7-10 days of life, much earlier than conventional on-farm
 microbiological methods. This early warning has the potential to lead to a
 more targeted approach to Campylobacter control and also provides new
 insights into possible sources of infection that could transform the
 control of this globally important foodborne pathogen.
description: FARMTABLE1Farm informationFARMTABLE2Flock data: optical flow, Campylobacter status and temperature
DOI: 10.5061/dryad.7h766
title: Data from: A new mechanistic approach for the further development of a population with established size bimodality

description: Usually, the origin of a within-cohort bimodal size distribution is
 assumed to be caused by initial size differences or by one discrete period
 of accelerated growth for one part of the population. The aim of this
 study was to determine if more continuous pathways exist allowing shifts
 from the small to the large fraction within a bimodal age-cohort.
 Therefore, a Eurasian perch population, which had already developed a
 bimodal size-distribution and had differential resource use of the two
 size-cohorts, was examined. Results revealed that formation of a bimodal
 size-distribution can be a continuous process. Perch from the small
 size-cohort were able to grow into the large size-cohort by feeding on
 macroinvertebrates not used by their conspecifics. The diet shifts were
 accompanied by morphological shape changes. Intra-specific competition
 seemed to trigger the development towards an increasing number of large
 individuals. A stage-structured matrix model confirmed these assumptions.
 The fact that bimodality can be a continuous process is important to
 consider for the understanding of ecological processes and links within
 ecosystems.
description: Heermann et
 al_PLOSONEIn this file, data on
 food resources (zooplankton and macroinvertebrates) of perch can be found.
 Also given is total length of fish used in the analyses as well as the
 percentage composition of diet items and where available information about
 sex and maturation state of perch. Further, data derived from Procrustes
 superimposition describing shape of perch is shown.
DOI: 10.5061/dryad.n9f8j
title: Data from: Highly diverse nirK genes comprise two major clades that harbour ammonium-producing denitrifiers

description: Background: Copper dependent nitrite reductase, NirK, catalyses the key
 step in denitrification, i.e. nitrite reduction to nitric oxide. Distinct
 structural NirK classes and phylogenetic clades of NirK-type denitrifiers
 have previously been observed based on a limited set of NirK sequences,
 however, their environmental distribution or ecological strategies are
 currently unknown. In addition, environmental nirK-type denitrifiers are
 currently underestimated in PCR-dependent surveys due to primer coverage
 limitations that can be attributed to their broad taxonomic diversity and
 enormous nirK sequence divergence. Therefore, we revisited reported
 analyses on partial NirK sequences using a taxonomically diverse,
 full-length NirK sequence dataset. Results: Division of NirK sequences
 into two phylogenetically distinct clades was confirmed, with Clade I
 mainly comprising Alphaproteobacteria (plus some Gamma- and
 Betaproteobacteria) and Clade II harbouring more diverse taxonomic groups
 like Archaea, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Nitrospirae,
 Firmicutes, Actinobacteria, Planctomycetes and Proteobacteria (mainly Beta
 and Gamma). Failure of currently available primer sets to target diverse
 NirK-type denitrifiers in environmental surveys could be attributed to
 mismatches over the whole length of the primer binding regions including
 the 3′ site, with Clade II sequences containing higher sequence divergence
 than Clade I sequences. Simultaneous presence of both the denitrification
 and DNRA pathway could be observed in 67 % of all NirK-type denitrifiers.
 Conclusion: The previously reported division of NirK into two distinct
 phylogenetic clades was confirmed using a taxonomically diverse set of
 full-length NirK sequences. Enormous sequence divergence of nirK gene
 sequences, probably due to variable nirK evolutionary trajectories, will
 remain an issue for covering diverse NirK-type denitrifiers in
 amplicon-based environmental surveys. The potential of a single organism
 to partition nitrate to either denitrification or dissimilatory nitrate
 reduction to ammonium appeared to be more widespread than originally
 anticipated as more than half of all NirK-type denitrifiers were shown to
 contain both pathways in their genome.
description: Align_NirK_267NirK amino acid alignment used for tree building
DOI: 10.5061/dryad.2r107
title: Data from: Ex situ conservation of underutilised fruit tree species: establishment of a core collection for Ficus carica L. using microsatellite markers (SSRs)

description: Ex situ germ plasm collections of woody crops are necessary to ensure the
 optimal use of plant genetic resources. The fig tree (Ficus carica L.)
 germ plasm bank, consisting of 229 accessions, is located in Centro de
 Investigación ‘La Orden’. Despite great progress in conservation, ex situ
 collections face size and organization problems. Core collections obtained
 from structured samples of bigger collections are a useful tool to improve
 germ plasm management. In this work, we used simple sequence repeat (SSR)
 markers to establish a core collection in this underutilised Mediterranean
 fruit tree species. Four approaches have been carried out (random
 sampling, maximization, simulated annealing and stepwise clustering) to
 determine the best method to develop a core collection in this woody
 plant. The genetic diversity obtained with each subset was compared with
 that of the complete collection. It was found that the most efficient way
 to achieve the maximum diversity was the maximization strategy, which,
 with 30 accessions, recovers all the SSR alleles and does not show
 significant differences in allele frequency distribution in any of the
 loci or in the variability parameters (H O, H E) between the whole and
 core collections. Thus, this core collection, a representative of most fig
 diversity conserved in the germ plasm bank, could be used as a basis for
 plant material exchange among researchers and breeders.
description: Fig Core Collection
 MetadataDetailed 9 simple
 sequence repeats used in this work, developed by Giraldo et al. 2005. SSR
 matrix of all accessions. Fig tree Germplasm Bank dendrogram. Summary of
 all genetic parameters obtained with 4 approaches.
DOI: 10.5061/dryad.r7r01
title: Data from: Preterm birth prevention post-conization: a model of cervical length screening with targeted cerclage

description: Women with a history of excisional treatment (conization) for cervical
 intra-epithelial neoplasia (CIN) are at increased risk of preterm birth,
 perinatal morbidity and mortality in subsequent pregnancy. We aimed to
 develop a screening model to effectively differentiate pregnancies
 post-conization into low- and high-risk for preterm birth, and to evaluate
 the impact of suture material on the efficacy of ultrasound indicated
 cervical cerclage. We analysed longitudinal cervical length (CL) data from
 725 pregnant women post-conization attending preterm surveillance clinics
 at three London university Hospitals over a ten year period (2004–2014).
 Rates of preterm birth &lt;37 weeks after targeted cerclage for
 CL&lt;25mm were compared with local and national background rates and
 expected rates for this cohort. Rates for cerclage using monofilament or
 braided suture material were also compared. Of 725 women post-conization
 13.5% (98/725) received an ultrasound indicated cerclage and 9.7% (70/725)
 delivered prematurely, &lt;37weeks; 24.5% (24/98) of these despite
 insertion of cerclage. The preterm birth rate was lower for those that had
 monofilament (9/60, 15%) versus braided (15/38, 40%) cerclage (RR 0.7, 95%
 CI 0.54 to 0.94, P = 0.008). Accuracy parameters of interval reduction in
 CL between longitudinal second trimester screenings were calculated to
 identify women at low risk of preterm birth, who could safely discontinue
 surveillance. A reduction of CL &lt;10% between screening timepoints
 predicts term birth, &gt;37weeks. Our triage model enables timely
 discharge of low risk women, eliminating 36% of unnecessary follow-up CL
 scans. We demonstrate that preterm birth in women post-conization may be
 reduced by targeted cervical cerclage. Cerclage efficacy is however suture
 material-dependant: monofilament is preferable to braided suture. The
 introduction of triage prediction models has the potential to reduce the
 number of unnecessary CL scan for women at low risk of preterm birth.
description: Kindinger data_Uploaded
 PlosOneAnonymised individual
 cervical length and outcome data of pregnant women who had been treated by
 excision cervical cervical treatment for cervical intraepithelial
 neoplasia, pre-pregnancy.
DOI: 10.5061/dryad.716hk
title: Data from: Frequency-dependent selection acting on the widely fluctuating sex ratio of the aphid Prociphilus oriens

description: Frequency-dependent selection is a fundamental principle of adaptive
 sex-ratio evolution in all sex ratio theories but has rarely been detected
 in the wild. Through long-term censuses, we confirmed large fluctuations
 in the population sex ratio of the aphid Prociphilus oriens and detected
 frequency-dependent selection acting on these fluctuations. Fluctuations
 in the population sex ratio were partly attributable to climatic factors
 during the growing season. Climatic factors likely affected the growth
 conditions of host plants, which in turn led to yearly fluctuations in
 maternal conditions and sex ratios. In the process of frequency-dependent
 selection, female proportion higher or lower than ca. 60% was associated
 with a reduction or increase in female proportion, respectively, the next
 year. The rearing of aphid clones in the laboratory indicated that mothers
 of each clone produced an increasing number of females as maternal size
 increased. However, the mean male number was not related to maternal size,
 but varied largely among clones. Given genetic variance in the ability to
 produce males among clones, selection should favor clones that can produce
 more numerous males in years with a high female proportion.
 Population-level sex allocation to females was on average 71%–73% for
 three localities and more female-biased when maternal conditions were
 better. This tendency was accounted for by the hypothesis of competition
 among foundresses rather than the hypothesis of local mate competition. We
 conclude that despite consistent operation of frequency-dependent
 selection, the sex ratio continues to fluctuate because environmental
 conditions always push it away from equilibrium.
description: Sex ratio and
 climateThis table describes %
 females, % of all-female sexuparae, and the total investment of sexuparae
 in each locality and year. Climatic factors are precipitation in July,
 August, and September, and mean temperature in July, August, and
 September.sex ratio and
 climate.csvThe sex ratio of each
 autumnal winged femaleThis file shows the
 numbers of male and female embryos that autumnal winged females of
 Prociphilus oriens have in their abdomen. The localities and collection
 years of the females are also shown. The embryos are fully grown, and they
 sexually mature without taking food after birth.Total sex
 ratio.csv
DOI: 10.5061/dryad.8j27n
title: Data from: A method for detecting characteristic patterns in social interactions with an application to handover interactions

description: Social interactions are a defining behavioural trait of social animals.
 Discovering characteristic patterns in the display of such behaviour is
 one of the fundamental endeavours in behavioural biology and psychology,
 as this promises to facilitate the general understanding, classification,
 prediction and even automation of social interactions. We present a novel
 approach to study characteristic patterns, including both sequential and
 synchronous actions in social interactions. The key concept in our
 analysis is to represent social interactions as sequences of behavioural
 states and to focus on changes in behavioural states shown by individuals
 rather than on the duration for which they are displayed. We extend
 techniques from data mining and bioinformatics to detect frequent patterns
 in these sequences and to assess how these patterns vary across
 individuals or changes in interaction tasks. To illustrate our approach
 and to demonstrate its potential, we apply it to novel data on a simple
 physical interaction, where one person hands a cup to another person. Our
 findings advance the understanding of handover interactions, a benchmark
 scenario for social interactions. More generally, we suggest that our
 approach permits a general perspective for studying social interactions.
description: Data and
 algorithmsData and algorithms for
 analysis associated with manuscript. See 'readme.txt' for
 further detail.alldata.zip
DOI: 10.5061/dryad.sm72f
title: Data from: Controlled fluorescence in a beetle's photonic structure and its sensitivity to environmentally induced changes

description: The scales covering the elytra of the male Hoplia coerulea beetle contain
 fluorophores embedded within a porous photonic structure. The photonic
 structure controls both insect colour (reflected light) and fluorescence
 emission. Herein, the effects of water-induced changes on the fluorescence
 emission from the beetle were investigated. The fluorescence emission peak
 wavelength was observed to blue-shift on water immersion of the elytra
 whereas its reflectance peak wavelength was observed to red-shift.
 Time-resolved fluorescence measurements, together with optical
 simulations, confirmed that the radiative emission is controlled by a
 naturally engineered photonic bandgap while the elytra are in the dry
 state, whereas non-radiative relaxation pathways dominate the emission
 response of wet elytra.
description: Mouchet et al., 2016,
 Proc. R. Soc. B, Primary DataReflectance spectra;
 Excitation spectra; Emission spectra; Time-resolved Fluorescence Intensity
 - Further information: see related article.Primary_data.xlsx
DOI: 10.5061/dryad.gm700
title: Data from: Contralateral noise stimulation delays P300 latency in school-aged children

description: Background and objective: The auditory cortex modulates auditory afferents
 through the olivocochlear system, which innervates the outer hair cells
 and the afferent neurons under the inner hair cells in the cochlea. Most
 of the studies that investigated the efferent activity in humans focused
 on evaluating the suppression of the otoacoustic emissions by stimulating
 the contralateral ear with noise, which assesses the activation of the
 medial olivocochlear bundle. The neurophysiology and the mechanisms
 involving efferent activity on higher regions of the auditory pathway,
 however, are still unknown. Also, the lack of studies investigating the
 effects of noise on human auditory cortex, especially in peadiatric
 population, points to the need for recording the late auditory potentials
 in noise conditions. Assessing the auditory efferents in schoolaged
 children is highly important due to some of its attributed functions such
 as selective attention and signal detection in noise, which are important
 abilities related to the development of language and academic skills. For
 this reason, the aim of the present study was to evaluate the effects of
 noise on P300 responses of children with normal hearing. Methods: P300 was
 recorded in 27 children aged from 8 to 14 years with normal hearing in two
 conditions: with and whitout contralateral white noise stimulation.
 Results: P300 latencies were significantly longer at the presence of
 contralateral noise. No significant changes were observed for the
 amplitude values. Conclusion: Contralateral white noise stimulation
 delayed P300 latency in a group of school-aged children with normal
 hearing. These results suggest a possible influence of the medial
 olivocochlear activation on P300 responses under noise condition.
description: Demographics_ParticipantsDemographics of the participantsP300_LatencyP300 latency (ms) obtained in two assessment conditions ("without noise" and "with noise") and the values of the difference between conditions ("with noise" minus "without noise").P300_AmplitudeP300 amplitude (mV) obtained in two assessment conditions ("without noise" and "with noise") and the values of the difference between conditions ("with noise" minus "without noise").
DOI: 10.5061/dryad.2m667
title: Data from: Complete species phylogeny of the marine midge Pontomyia (Diptera: Chironomidae) reveals a cosmopolitan species and a new synonym

description: Pontomyia (Diptera: Chironomidae) is an exclusively marine and flightless
 insect genus with four described species from the Indo-Pacific and one
 undescribed taxon known only by its larvae, pupal skins and females from
 the western Atlantic. A previous study of relationships among three of the
 Indo-Pacific species reported each of them to be monophyletic, with high
 genetic diversity within P. natans Edwards, the type species, and P.
 pacifica Tokunaga. The evolutionary affinities of the Australian endemic
 P. cottoni Womersley that resembles P. natans, as well as the putative
 Atlantic species are hitherto undetermined. A complete molecular phylogeny
 of the genus based on two nuclear and two mitochondrial DNA markers
 indicates that P. cottoni and a Puerto Rican (Atlantic) larval population
 are nested within the P. natans clade. Furthermore, P. natans and P.
 cottoni are inseparable in all morphological characters used previously to
 distinguish them. Therefore, we synonymize P. cottoni with P. natans, syn.
 nov., whose known range now encompasses all three ocean basins after
 including the Puerto Rican population. This distribution warrants further
 investigation into the life history of Pontomyia, a midge with one of the
 shortest known adult lifespans among insects.
description: Pontomyia phylogenetic
 datasets and treesNEXUS file for Mesquite:
 A Modular System for Evolutionary Analysis (Maddison and Maddison 2011),
 containing the datasets subjected to phylogenetic analyses and the
 resulting trees.Pontomyia.nex
DOI: 10.5061/dryad.088qv
title: Data from: Genetically distinct populations of northern shrimp, Pandalus borealis, in the North Atlantic: adaptation to different temperatures as an isolation factor

description: The large-scale population genetic structure of northern shrimp, Pandalus
 borealis, was investigated over the species’ range in the North Atlantic,
 identifying multiple genetically distinct groups. Genetic divergence among
 sample localities varied among 10 microsatellite loci (range: FST =
 −0.0002 to 0.0475) with a highly significant average (FST = 0.0149; P
 &lt; 0.0001). In contrast, little or no genetic differences were
 observed among temporal replicates from the same localities (FST = 0.0004;
 P = 0.33). Spatial genetic patterns were compared to geographic distances,
 patterns of larval drift obtained through oceanographic modelling, and
 temperature differences, within a multiple linear regression framework.
 The best-fit model included all three factors and explained approximately
 29% of all spatial genetic divergence. However, geographic distance and
 larval drift alone had only minor effects (2.5–4.7%) on large-scale
 genetic differentiation patterns, whereas bottom temperature differences
 explained most (26%). Larval drift was found to promote genetic
 homogeneity in parts of the study area with strong currents, but appeared
 ineffective across large temperature gradients. These findings highlight
 the breakdown of gene flow in a species with a long pelagic larval phase
 (up to 3 months) and indicate a role for local adaptation to temperature
 conditions in promoting evolutionary diversification and speciation in the
 marine environment.
description: Pandalus borealis
 microsatellite dataMicrosatellite data (10
 loci) for northern shrimp, Pandalus borealis: 2053 individuals,
 representing 21 samples and 16 geographic localities throughout the
 species' range in the North Atlantic.popborealis.zip
DOI: 10.5061/dryad.ts8fd6m
title: Data from: Animal-mediated organic matter transformation: aquatic insects as a source of microbially bioavailable organic nutrients and energy

description: 1. Animal communities are essential drivers of energy and elemental flow
 in ecosystems. However, few studies have investigated the functional role
 of animals as sources of dissolved organic matter (DOM) and the subsequent
 utilization of that DOM by the microbial community. 2. In a small forested
 headwater stream, we tested the effects of taxonomy, feeding traits, and
 body size on the quality and quantity of dissolved organic carbon (DOC)
 and dissolved organic nitrogen (DON) excreted by aquatic insects. In
 addition, we conducted steady-state solute additions to estimate instream
 demand for labile C and compared it to the C excreted by invertebrates. 3.
 Individual excretion rates and excretion composition varied with body
 size, taxonomy, and feeding guild. The estimated average community
 excretion rate was 1.31 μg DOC· per mg insect dry weight (DW)-1·h-1 and
 0.33 μg DON·mg DW-1·h-1 and individuals excreted DON at nearly twice the
 rate of 〖"NH" 〗_"4" ^"+" . This DOM was 2-5
 times more bioavailable to microbial heterotrophs than ambient stream
 water DOM. 4. We estimated that the insect community, conservatively,
 excreted 1.62 mg of bioavailable DOC·m-2·h-1 and through steady-state
 additions measured an ambient labile C demand as 3.97±0.67 mg C·m-2·h-1.
 This suggests that insect-mediated transformation and excretion of labile
 DOC could satisfy a significant fraction (40±7%) of labile C demand in
 this small stream. 5. Collectively, our results suggest that animal
 excretion plays an essential functional role in transforming organic
 matter into microbially bioavailable forms and may satisfy a variable but
 significant portion of microbial demand for labile C and N.
description: FE-2018-00549R2
 dataData used in
 FE-2018-00549R2. Data covers all figures. Excel workbook contains readme
 and detailed key to all column headers/variables.Dryad
 Data.xlsx