cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tk273
title: Data from: Infection reduces anti-predator behaviors in house finches

description: Infectious diseases can cause host mortality through direct or indirect
 mechanisms, including altered behavior. Diminished anti-predator behavior
 is among the most-studied causes of indirect mortality during infection,
 particularly for systems in which a parasite's life-cycle requires
 transmission from prey to predator. Significantly less work has examined
 whether directly-transmitted parasites and pathogens also reduce
 anti-predator behaviors. Here we test whether the directly-transmitted
 bacterial pathogen, Mycoplasma gallisepticum (MG), reduces responses to
 predation-related stimuli in house finches Haemorhous mexicanus. MG causes
 conjunctivitis and reduces survival among free-living finches, but rarely
 causes mortality in captivity, suggesting a role for indirect mechanisms.
 Wild-caught finches were individually housed in captivity and exposed to
 the following treatments: 1) visual presence of a stuffed, mounted
 predator (a Cooper's hawk Accipiter cooperii) or control object (a
 vase or a stuffed, mounted mallard duck Anas platyrhynchos), 2)
 vocalizations of the same predator and non-predator, 3) approach of a
 researcher to enclosures, and 4) simulated predator attack (capture by
 hand). MG infection reduced anti-predator responses during visual exposure
 to a mounted predator and simulated predator attack, even for birds
 without detectable visual obstruction from conjunctivitis. However, MG
 infection did not significantly alter responses during human approach or
 audio playback. These results are consistent with the hypothesis that
 predation plays a role in MG-induced mortality in the wild, with reduced
 locomotion, a common form of sickness behavior for many taxa, as a likely
 mechanism. Our results therefore suggest that additional research on the
 role of sickness behaviors in predation could prove illuminating.
description: Data on cage-side
 preference and latency to move in experiment 1Please see README file
 for variable descriptions.Adelman et al JAB 2016 Exp 1
 Preference and Latency 20160902.csvResponses to audio
 playback of predator vs non-predatorPlease see README file
 for variable descriptions.Adelman et al JAB 2016 Exp 1
 Audio 20160902.csvData on time to capture
 during infection among captive finchesPlease see README file
 for variable descriptions.Adelman et al JAB Capture Speed
 Data 20160905.csv
DOI: 10.5061/dryad.469kf
title: Data from: Species diversity, invasion, and alternative community states in sequentially assembled communities

description: The relationship between resident species diversity and invasion is
 generally negative in experimental studies, but takes various forms in
 observational studies of natural communities. We hypothesized that
 stochastic species colonization, which applies to natural communities but
 not experimental communities generally assembled through simultaneous
 species introduction, may lead to non-negative diversity-invasion
 relationships via incurring priority effects. To test this hypothesis, we
 manipulated both resident species diversity and colonization history in
 sequentially assembled communities of bacterivorous protist species. We
 found that despite a significant effect of assembly history on invader
 abundance, invader abundance declined with diversity. This result was
 largely driven by positive selection effects associated with the dominant
 influence of an invasion-resistant species, which shared the most similar
 resource use pattern with the invader, and by the overall weak priority
 effects observed for the resident communities. Increasing species
 diversity, however, significantly strengthened priority effects, providing
 the first experimental support for the idea that larger species pools
 promote alternative community states. We suggest that elucidating
 mechanisms regulating the strength of priority effects may help understand
 variation in diversity-invasion relationships among natural communities.
description: Protist
 abundanceThe text file (fields
 separated by tabs) containing the population density of each protist
 species (including the invader) on the last sampling day. Figures 1, 2 and
 3 are based on these data. Each resident species is represented by the
 first letter of its genus names, and the invader is represented by the
 first letters of its full species name.bacterial
 abundanceThe population densities
 (CFUs/ml) of the 23 bacterial morphospecies in each of the six protist
 species monocultures plus the bacteria only cultures. These data were
 analyzed to generate Figure 4 in the manuscript.
DOI: 10.5061/dryad.rs467t5
title: Data from: The multiple roles of β–diversity help untangle community assembly processes affecting recovery of temperate rocky shores

description: Metacommunity theory highlights the potential of β–diversity as a useful
 link to empirical research, especially in diverse systems where species
 exhibit a range of stage-dependent dispersal characteristics. To
 investigate the importance of different components and scales of
 β–diversity in community assembly we conducted a large-scale disturbance
 experiment and compared relative recovery across multiple sites and among
 plots within sites on the rocky shore. Six sites were spread along 80 km
 of coastline and, at each site, 5 plots were established, matching
 disturbed and undisturbed quadrats. Recovery was not complete at any of
 the sites after 1 year for either epibenthos (mostly composed of
 macroalgae and, locally, mussels) or infauna. Significant differences in
 recovery among sites were observed for epibenthos but not for infauna
 suggesting different community assembly processes were operating. This was
 supported by epibenthos in the recovering plots having higher species
 turnover than in undisturbed sediment, and recovery well predicted by
 local diversity, while infaunal recovery was strongly influenced by the
 epibenthic community’s habitat complexity. However, infaunal community
 recovery did not simply track formation of habitat by recovering
 epibenthos, but appeared to be overlain by within-site and among-site
 aspects of infaunal -diversity. These results suggest that documenting
 changes in the large plants and animals alone will be a poor surrogate for
 rocky shore community assembly processes. No role for ecological
 connectivity (negative effect of among-site β–diversity) in driving
 recovery was observed, suggesting a low risk of effects from multiple
 disturbances propagating along the coast, but a limited resilience at the
 site scale to large-scale disturbances such as landslides or oil spills.
description: datafordryadData on community composition and environmental characterisitics from Ligurian shores
DOI: 10.5061/dryad.6t4f27g
title: Data from: A new fossil marine lizard with soft tissues from the Late Cretaceous of Southern Italy

description: A new marine lizard showing exceptional soft tissue preservation was found
 in Late Cretaceous deposits of the Apulian Platform (Puglia, Italy).
 Primitivus manduriensis gen. et sp. nov. is not only the first evidence of
 the presence of dolichosaurs in a Southern Italian Carbonate Platform,
 filling a paleogeographic gap in the Mediterranean Tethys, but also
 extends the range of this group to the upper Campanian – lower
 Maastrichtian. Our parsimony analysis recover a monophyletic non-ophidian
 pythonomorph clade, including Tetrapodophis amplectus at the stem of
 Mosasauroidea + Dolichosauridae, which together represent the sister group
 of Ophidia (modern and fossil snakes). Based on Bayesian Inference
 instead, Pythonomorpha is monophyletic, with Ophidia representing the more
 deeply nested clade, and the new taxon as basal to all other
 pythonomorphs. Primitivus displays a fairly conservative morphology in
 terms of both axial elongation of the trunk and limb reduction, and the
 coexistence of aquatic adaptations with features hinting at the retention
 of the ability to move on land, suggest a semi-aquatic lifestyle. The
 exceptional preservation of mineralized muscles, portions of the
 integument, cartilages, and gut content provides unique sources of
 information about this extinct group of lizards. The new specimen may
 represent local persistence of a relict dolichosaur population until
 almost the end of the Cretaceous in the Mediterranean Tethys, and
 demonstrates the incompleteness of our knowledge of dolichosaur temporal
 and spatial distributions.
description: Dataset for parsimony
 analysisNexus file containing
 dataset used for the parsimony analysis (equal-weight and
 implied-weight)Paparella-et-al-Suppl.3(parsimony)-RSOS_rev1.nexDataset for Bayesian Inference analysisNexus file containing dataset used for the Bayesian Inference analysisPaparella-et-al-Suppl.4(bayesian)-RSOS_rev1.nex
DOI: 10.5061/dryad.ct17vn7
title: Data from: Before platelets: the production of platelet activating factor during growth and stress in a basal marine organism

description: Corals and humans represent two extremely disparate metazoan lineages and
 are therefore useful for comparative evolutionary studies. Two lipid-based
 molecules that are central to human immunity, platelet activating factor
 (PAF) and Lyso-PAF were recently identified in scleractinian corals. To
 identify processes in corals that involve these molecules, PAF and
 Lyso-PAF biosynthesis was quantified in conditions known to stimulate PAF
 production in mammals (tissue growth and exposure to elevated levels of
 ultraviolet light) and in conditions unique to corals (competing with
 neighboring colonies over benthic space). Similar to observations in
 mammals, PAF production was higher in regions of active tissue growth and
 increased when corals were exposed to elevated levels of ultraviolet
 light. PAF production also increased when corals were attacked by the
 stinging cells of a neighboring colony, though only the attacked coral
 exhibited an increase in PAF. This reaction was observed in adjacent areas
 of the colony, indicating that this response is coordinated across
 multiple polyps including those not directly subject to the stress. PAF
 and Lyso-PAF are involved in coral stress responses that are both shared
 with mammals and unique to the ecology of cnidarians.
description: Data from: Before
 platelets: the production of platelet activating factor during growth and
 stress in a basal marine organismExcel file containing
 the raw data used for all figures.Dataset_S1.xlsx
DOI: 10.5061/dryad.20md774
title: Data from: Detection of persistent signals and its relation to coherent feedforward loops

description: Many studies have shown that cells use temporal dynamics of signalling
 molecules to encode information. One particular class of temporal dynamics
 is persistent and transient signals, i.e. signals of long and short
 durations respectively. It has been shown that the coherent type-1
 feedforward loop with an AND logic at the output (or C1-FFL for short) can
 be used to discriminate a persistent input signal from a transient one.
 This has been done by modelling the C1-FFL, and then use the model to show
 that persistent and transient input signals give, respectively, a non-zero
 and zero output. The aim of this paper is to make a connection between the
 statistical detection of a persistent signals and the C1-FFL. We begin by
 first formulating a statistical detection problem of distinguishing
 persistent signals from transient ones. The solution of the detection
 problem is to compute the log-likelihood ratio of observing a persistent
 signal to a transient signal. We show that, if this log-likelihood ratio
 is positive, which happens when the signal is likely to be persistent,
 then it can be approximately computed by a C1-FFL. Although the capability
 of C1-FFL to discriminate persistent signals is known, this paper adds an
 information processing interpretation on how a C1-FFL works as a detector
 of persistent signals.
description: Zip file of matlab
 codeZip files of the matlab
 code used to generate the results in the paperC1FFL-matlab.zip
DOI: 10.5061/dryad.6r5j8
title: Data from: "Size" and "shape" in the measurement of multivariate proximity

description: 1. Ordination and clustering methods are widely applied to ecological data
 that are nonnegative, for example species abundances or biomasses. These
 methods rely on a measure of multivariate proximity that quantifies
 differences between the sampling units (e.g. individuals, stations, time
 points), leading to results such as: (i) ordinations of the units, where
 interpoint distances optimally display the measured differences; (ii)
 clustering the units into homogeneous clusters; or (iii) assessing
 differences between pre-specified groups of units (e.g., regions, periods,
 treatment-control groups). 2. These methods all conceal a fundamental
 question: To what extent are the differences between the sampling units,
 computed according to the chosen proximity function, capturing the
 "size" in the multivariate observations, or their
 "shape"? "Size" means the overall level of the
 measurements: for example, some samples contain higher total abundances or
 more biomass, others less. "Shape" means the relative levels of
 the measurements: for example, some samples have different relative
 abundances, i.e. different compositions. To answer this question, several
 well-known proximity measures are considered and applied to two data sets,
 one of which is used in a simulation exercise where "shape"
 differences have been eliminated by randomization. For any data set and
 any proximity measure, a quantification is achieved of the proportion of
 "size" variance and "shape" variance that the measure
 is capturing, as well as the proportion of variance that confounds
 "size" and "shape" together. 3. The results
 consistently show that the Bray-Curtis coefficient incorporates both
 "size" and "shape" differences, to varying degrees.
 These two components are thus always confounded by this proximity measure
 in the determination of ordinations, clusters, group comparisons and
 relations to environmental variables. 4. There are several implications of
 these results, the main one being that researchers should be aware of this
 issue when they choose a proximity measure. They should compute the
 "size" and "shape" components for their particular
 data sets, since this can radically affect the interpretation of their
 results. It is recommended to separate these components: analysing total
 abundances or other measures of "size" by univariate methods,
 and using multivariate analysis on the relative abundances where size has
 been specifically excluded.
description: Barents Sea fish
 abundancesAbundance counts of 41
 fish species at 158 stations in the Barents Sea. This is a subset of a
 larger data set that spans more stations and years.fish.txtExperimental dataThree samples of size n=10 each, one from a control and two from two treatments. Each sample unit consists of abundances of 45 marine species.experiment.txt
DOI: 10.5061/dryad.6kp2n
title: Data from: Decay rates of leaf litters from arbuscular mycorrhizal trees are more sensitive to soil effects than litters from ectomycorrhizal trees

description: While it is well established that leaf litter decomposition is controlled
 by climate and substrate quality at broad spatial scales, conceptual
 frameworks that consider how local-scale factors affect litter decay in
 heterogeneous landscapes are generally lacking. A critical challenge in
 disentangling the relative impacts of and interactions among local-scale
 factors is that these factors frequently covary due to feedbacks between
 plant and soil communities. For example, forest plots dominated by trees
 that associate with ectomycorrhizal (ECM) fungi often differ from those
 dominated by trees that associate with arbuscular mycorrhizal (AM) fungi
 in terms of their litter quality, microbial community structure and
 inorganic nutrient availability. Here, we evaluate the extent to which
 such factors alter leaf litter decomposition rates. To characterize
 variations in decomposition rates, we compared decay rates of high-quality
 litter (maple; AM) and low-quality litter (oak; ECM) across forest plots
 representing a gradient in litter matrix quality and nitrogen (N)
 availability driven by the relative proportions of AM and ECM trees in
 each plot. In experiment two, we added litter from two AM and three ECM
 tree species to forest plots with either a high-quality litter matrix and
 high N availability (i.e. AM-dominated plots) or a low-quality litter
 matrix and low N availability (i.e. ECM-dominated plots). In both
 experiments, we found that AM litter decomposed more rapidly than ECM
 litter, and this effect was enhanced in AM-dominated plots. Then, to
 separate the contributions of litter matrix effects from N availability
 effects, we added N fertilizer to a subset of plots from experiment two.
 Nitrogen addition increased decay rates of high-quality litter across all
 sites, but had no effect on low-quality litter, suggesting that low N
 availability, not litter matrix quality, constrains decomposition of
 high-quality litters. Hence, N availability appears to alter litter
 decomposition patterns independently of litter matrix properties.
 Synthesis. Our results indicate that shifts in the relative abundance of
 ECM- and AM-associated trees in a plot or stand have the potential to
 affect litter decay rates through both changes in litter quality as well
 as through alterations of the local-scale soil environment.
description: JEcol-Midgley et
 al.Litter quality and
 decomposition ratesDryad
 file.xlsx
DOI: 10.5061/dryad.66t00
title: Data from: Diabetes mellitus and prediabetes on kidney transplant waiting list- prevalence, metabolic phenotyping and risk stratification approach

description: Background: Despite a significant prognostic impact, little is known about
 disturbances in glucose metabolism among kidney transplant candidates. We
 assess the prevalence of diabetes mellitus (DM) and prediabetes on kidney
 transplant waiting list, its underlying pathophysiology and propose an
 approach for individual risk stratification. Methods: All patients on
 active kidney transplant waiting list of a large European university
 hospital transplant center were metabolically phenotyped. Results: Of 138
 patients, 76 (55%) had disturbances in glucose metabolism. 22% of patients
 had known DM, 3% were newly diagnosed. 30% were detected to have
 prediabetes. Insulin sensitivity and -secretion indices allowed for
 identification of underlying pathophysiology and risk factors. Age
 independently affected insulin secretion, resulting in a relative risk for
 prediabetes of 2.95 (95%CI 1.38-4.83) with a cut-off at 48 years. Body
 mass index independently affected insulin sensitivity as a continuous
 variable. Conclusions: The prevalence of DM or prediabetes on kidney
 transplant waiting list is as high as 55%, with more than one third of
 patients previously undiagnosed. Oral glucose tolerance test is mandatory
 to detect all patients at risk. Metabolic phenotyping allows for
 differentiation of underlying pathophysiology and provides a basis for
 early individual risk stratification and specific intervention to improve
 patient and allograft outcome.
description: WL_file basic
 databasic data file of
 investigated patients
DOI: 10.5061/dryad.3nb53
title: Data from: Duration of the parasitic phase determines subsequent performance in juvenile freshwater pearl mussels (Margaritifera margaritifera)

description: Host–parasite systems have been useful in understanding coevolutionary
 patterns in sympatric species. Based on the exceptional interaction of the
 long-lived and highly host-specific freshwater pearl mussel (FPM;
 Margaritifera margaritifera) with its much shorter-lived host fish (Salmo
 trutta or Salmo salar), we tested the hypotheses that a longer duration of
 the parasitic phase increases fitness-related performance of mussels in
 their subsequent post parasitic phase, and that temperature is the main
 factor governing the duration of the parasitic phase. We collected
 juvenile mussels from naturally and artificially infested fish from eight
 rivers in Norway. Excysted juvenile mussels were maintained separately for
 each collection day, under similar temperature and food regimes, for up to
 56 days. We recorded size at excystment, post excystment growth, and
 survival as indicators of juvenile fitness in relation to the duration of
 the parasitic phase. We also recorded the daily average temperatures for
 the entire excystment period. We observed strong positive relationships
 between the length of the parasitic phase and the post parasitic growth
 rate, size at excystment and post parasitic survival. Temperature was
 identified as an important factor governing excystment, with higher
 temperatures decreasing the duration of the parasitic phase. Our results
 indicate that juvenile mussels with the longest parasitic phase have
 better resources (larger size and better growth rate) to start their
 benthic developmental phase and therefore to survive their first winter.
 Consequently, the parasitic phase is crucial in determining subsequent
 survival. The temperature dependence of this interaction suggests that
 climate change may affect the sensitive relationship between endangered
 FPMs and their fish hosts.
description: MarMa_datasetSize and survival data collected from juvenile mussels (Margaritifera margaritifera) from 8 river populations from southern Norway.
DOI: 10.15468/dl.9fsuue
title: Occurrence Download

description: A dataset containing 144 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is one of (China, Chinese Taipei)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Bretschneidera sinensis"
 ]
}

 The dataset includes 144 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001279-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.sc14n
title: Data from: Octopamine and cooperation: octopamine regulates the disappearance of cooperative behaviours between genetically unrelated founding queens in the ant

description: We investigated whether octopamine (OA) is associated with the
 disappearance of cooperation in Polyrhachis moesta ant queens. Queens of
 P. moesta facultatively found the colony with genetically unrelated
 queens. The founding queens perform frequent food exchange with these
 non-related queens and partake in cooperative brood rearing, whereas
 single colony queens exclude non-related queens via aggressive behaviour.
 Thus, aggression is a factor that reduces cooperation. Given that
 aggression is generally associated with brain OA in insects, we
 hypothesized that OA controls the behavioural change in cooperation in the
 ant queen, via an increase in aggression. To test this hypothesis, we
 compared the amounts of OA and related substances in the brain between
 founding and colony queens, and observed the interaction of founding
 queens following oral OA administration. The brain OA levels in colony
 queens were significantly higher than those in founding queens. Oral
 administration of OA to founding queens caused significantly less
 trophallaxis and allogrooming behaviour than in the control founding
 queens, but with no significant increase in aggression. These results
 suggest that OA promotes the disappearance of cooperation in founding
 queens of P. moesta. This is the first study to reveal the neuroendocrine
 mechanism of cooperation in ant queens.
description: original
 dataFrom Table S2-4: Table
 S2. Data of the brain amine levels (pmol/brain) in founding and colony
 queens, Table S3. Data of the behavioural observation in control and
 OA-fed queens, Table S4. Data of the brain amine levels (pmol/brain) in
 control and OA-fed queens.