cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5gd04
title: Data from: Usefulness of fecal calprotectin for the early prediction of short-term outcomes of remission-induction treatments in ulcerative colitis in comparison with two-item patient-reported outcome

description: Background: Fecal calprotectin (FC) is well accepted as a non-invasive
 biomarker which objectively reflects colonic inflammation in ulcerative
 colitis (UC). However, its value as a marker of response during the early
 phase of remission induction treatment has not been well studied. The aim
 of this study is to evaluate the significance of FC for predicting the
 short-term outcomes of remission induction treatment in patients with UC.
 Methods: A prospective observational study was conducted among 31 patients
 with active UC. FC was monitored with two-item patient-reported outcome
 (PRO2), partial Mayo score (PMS), and Lichtiger clinical activity index
 (CAI) during the first 4 weeks of remission induction treatment. Clinical
 response was defined as a decrease in CAI of 3 or more points below
 baseline. Mucosal healing (MH) was defined as Mayo endoscopic subscore 0
 or 1. Within-day and within-stool variability of FC were assessed during
 the first week of treatment. Results: In week 4-clinical responders, PRO2,
 PMS, and CAI significantly decreased from day 3, however, FC did not show
 significant reduction until week 2. Among all markers, the decrease in
 PRO2 at week 4 most accurately predicted MH at week 12. Within-day
 variability of FC was remarkably wide even at the first week in clinical
 responders. Within-stool variability was extremely small. Conclusions:
 PRO2 predicted the short-term outcomes of remission induction treatment
 earlier than FC possibly because of the wide within-day variability of FC
 in active UC.
description: PLOS ONE RAW
 DATARaw data set used in the
 manuscript.
DOI: 10.5061/dryad.5756sg0
title: Data from: Ecology determines how low antibiotic concentration impacts community composition and horizontal transfer of resistance genes

description: Low concentrations of antibiotics have numerous effects on bacteria.
 However, it is unknown whether ecological factors such as trophic
 interactions and spatial structuring influence the effects of low
 concentrations of antibiotics on multispecies microbial communities. Here,
 we address this question by investigating the effects of low antibiotic
 concentration on community composition and horizontal transfer of an
 antibiotic resistance plasmid in a 62-strain bacterial community in
 response to manipulation of the spatial environment and presence of
 predation. The strong effects of antibiotic treatment on community
 composition depend on the presence of predation and spatial structuring
 that have strong community effects on their own. Overall, we find plasmid
 transfer to diverse recipient taxa. Plasmid transfer is likely to occur to
 abundant strains, occurs to a higher number of strains in the presence of
 antibiotic, and also occurs to low-abundance strains in the presence of
 spatial structures. These results fill knowledge gaps concerning the
 effects of low antibiotic concentrations in complex ecological settings.
description: Community
 compositionRelative abundance of
 different taxa in 40 day serial transfer microcosm
 experimentCommunity_composition.txtRP4 recipientsRP4 plasmid recipient taxa at the end-point of 40 day serial transfer microcosm experiment (identified using epicPCR)RP4_recipients.txtRP4 recipients pooled replicatesRP4 recipient taxa based on pooled replicates from end-point of 40-day serial transfer microcosm experimentRP4_recipients_pooled_replicates.txt
DOI: 10.15468/dl.r6d39v
title: Occurrence Download

description: A dataset containing 452 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Salvia miltiorrhiza",
 "Year 1975-2026"
 ]
}

 The dataset includes 452 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001195-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.466k2sq
title: Data from: High male density favors maintenance over reproduction in a butterfly

description: Environmental factors exert strong effects on phenotypic expression. A
 particularly intriguing factor capable of inducing such plastic responses
 is the social environment experienced by a specific individual. Such
 social effects may alter the fitness of focal individuals if they affect
 the expression of reproductive traits and thus life-history strategies. To
 examine this question, we investigated the effects of individual density
 on morphology, reproduction, and behavior of male Bicyclus anynana
 butterflies. Increasing density significantly increased male body mass and
 the probability to succeed in aggressive interactions, and tended to
 increase abdomen fat content. At the same time, increasing density
 significantly decreased courtship activity and tended to decrease sperm
 number. These results suggest that individual density seemed to induce
 differential strategic investment into survival and somatic maintenance
 versus reproduction in male butterflies. Males kept at high densities
 apparently favored high body mass and storage, which may enable longer
 survival during times of intense intra-specific competition. Moreover,
 their competitiveness was enhanced as suggested by a higher success in
 aggressive interactions. Males kept at low density, in contrast, favored
 reproduction through increased courtship activity and sperm production.
 Our study illustrates that the effects of density on the expression of
 morphological and behavioral traits are complex and difficult to predict,
 owing to resource-allocation trade-offs resulting in prudent strategic
 investment.
description: GeigerFile includes all
 original data relevant to the publication.
DOI: 10.5061/dryad.k48p5h9
title: Data from: Mechanism of anti-remodelling action of treprostinil in human pulmonary arterial smooth muscle cells

description: Treprostinil is applied for pulmonary arterial hypertension (PAH) therapy.
 However, the mechanism by which the drug achieves its beneficial effects
 in PAH vessels is not fully understood. This study investigated the
 effects of treprostinil on PDGF-BB induced remodelling parameters in
 isolated human pulmonary arterial smooth muscle cells (PASMC) of four PAH
 patients. The production of TGF-β1, CTGF, collagen type-I and -IV, and of
 fibronectin were determined by ELISA and PCR. The role of cAMP was
 determined by ELISA and di-deoxyadenosine treatment. Proliferation was
 determined by direct cell count. Treprostinil increased cAMP levels dose
 and time dependently, which was not affected by PDGF-BB. Treprostinil
 significantly reduced PDGF-BB induced secretion of TGF-β1 and CTGF, both
 was counteracted when cAMP generation was blocked. Similarly, the PDGF-BB
 induced proliferation of PASMC was dose dependently reduced by
 treprostinil through signalling via cAMP - C/EBP-α p42 - p21(WAf1/Cip1).
 In regard to extracellular matrix remodelling, treprostinil significantly
 reduced PDGF-BB - TGF-β1 - CTGF induced synthesis and deposition of
 collagen type I and fibronectin, in a cAMP sensitive manner. In contrast,
 the deposition of collagen IV was not affected. The data suggest that this
 action of treprostinil in vessel wall remodelling may benefit patients
 with PAH and may reduce arterial wall remodelling.
description: PONE-D-18-04265_dataPONE-D-18-04265_15_08_2018 (1).xlsx
DOI: 10.5061/dryad.g53d0
title: Data from: Investigating hybridization between the two sibling bat species Myotis myotis and M. blythii from guano in a natural mixed maternity colony

description: Because they can form seasonal mixed-species groups during mating and
 maternal care, bats are exciting models for studying interspecific
 hybridization. Myotis myotis and M. blythii are genetically close and
 morphologically almost identical, but they differ in some aspects of their
 ecology and life-history traits. When they occur in sympatry, they often
 form large mixed maternity colonies, in which their relative abundance can
 vary across time due to a shift in the timing of parturition. For the
 first time, we used non-invasive genetic methods to assess the
 hybridization rate and colony composition in a maternity colony of M.
 myotis and M. blythii located in the French Alps. Bat guano was collected
 on five sampling dates spread across the roost occupancy period and was
 analysed for individual genotype. We investigated whether the presence of
 hybrids followed the pattern of one of the parental species or if it was
 intermediate. We identified 140 M. myotis, 12 M. blythii and 13 hybrids
 among 250 samples. Parental species appeared as genetically
 well-differentiated clusters, with an asymmetrical introgression towards
 M. blythii. By studying colony parameters (effective size, sex ratio and
 proportion of the three bat types) across the sampling dates, we found
 that the abundances of hybrid and M. blythii individuals were positively
 correlated. Our study provides a promising non-invasive method to study
 hybridization in bats and raises questions about the taxonomic status of
 the two Myotis species. We discuss the contribution of this study to the
 knowledge of hybrid ecology, and we make recommendations for possible
 future research to better understand the ecology and behaviour of hybrid
 individuals.
description: Myotis
 genotypesIndividual genotypes
 from 210 samples arising from 165 individuals of a maternity roost located
 in Le Bourg d'Oisans (French Alps), hosting Myotis myotis and Myotis
 blythii individuals. Num = sample identifier, ID = individual identifier,
 Sampling = Sampling date, Type = bat type (Myotis myotis, Myotis blythii
 or hybrid), Sex = F: females and M: males, D15 to H23.M = fragment length
 for each microsatellite locus at each allele (2 alleles by column), NA =
 missing data.Myotis_Dryad_dataset.xlsx
DOI: 10.5061/dryad.7ts20
title: Data from: Topology of tree-mycorrhizal fungus interaction networks in xeric and mesic Douglas-fir forests

description: 1. From the phytocentric perspective, a mycorrhizal network (MN) is formed
 when the roots of two or more plants are colonized by the same fungal
 genet. MNs can be modelled as interaction networks with plants as nodes
 and fungal genets as links. The potential effects of MNs on facilitation
 or competition between plants are increasingly recognized, but their
 network topologies remain largely unknown. This information is needed to
 understand the ecological significance of MN functional traits. 2. The
 objectives of this study were to describe the interaction network
 topologies of MNs formed between two ectomycorrhizal fungal species,
 Rhizopogon vesiculosus and R. vinicolor, and interior Douglas-fir trees at
 the forest stand scale, identify factors leading to this structure and to
 contrast MN structures between forest plots with xeric versus mesic soil
 moisture regimes. 3. Tuberculate mycorrhizas were sampled in six 10 × 10 m
 plots with either xeric or mesic soil moisture regimes. Microsatellite DNA
 markers were used to identify tree and fungal genotypes isolated from
 mycorrhizas and for comparison with reference tree boles above-ground. 4.
 In all six plots, trees and fungal genets were highly interconnected. Size
 asymmetries between different tree cohorts led to non-random MN
 topologies, while differences in size and connectivity between Rhizopogon
 species-specific subnetwork components contributed towards MN nestedness.
 Large mature trees acted as network hubs with a significantly higher node
 degree compared to smaller trees. MNs representing trees linked by R.
 vinicolor genets were mostly nested within larger, more highly connected
 R. vesiculosus-linked MNs. 5. Attributes of network nodes showed that hub
 trees were more important to MN topology on xeric than mesic sites, but
 the emergent structures of MNs were similar in the two soil moisture
 regimes. 6. Synthesis. This study suggests MNs formed between interior
 Douglas-fir trees and R. vesiculosus and R. vinicolor genets are resilient
 to the random loss of participants, and to soil water stress, but may be
 susceptible to the loss of large trees or fungal genets. Our results
 regarding the topology of MNs contribute to the understanding of forest
 stand dynamics and the resilience of forests to stress or disturbance.
description: Beiler,etal_Datapack_JEcol-2014-0405.R2Sample location and genetic data from: Topology of tree-mycorrhizal fungus interaction networks in xeric and mesic Douglas-fir forests
DOI: 10.15468/dl.d82ksh
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is Kazakhstan",
 "Geometry POLYGON((13.88120 20.83435,117.11880 20.83435,117.11880 62.16565,13.88120 62.16565,13.88120 20.83435))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ferula caspica"
 ]
}

 The dataset includes 34 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001194-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.71mh5
title: Data from: Low-quality birds do not display high-quality signals: the cysteine-pheomelanin mechanism of honesty

description: The mechanisms that make that the costs of producing high-quality signals
 are unaffordable to low-quality signalers are a current issue in animal
 communication. The size of the melanin-based bib of male house sparrows
 Passer domesticus honestly signals quality. We induced the development of
 new bibs while treating males with buthionine-sulfoximine (BSO), a
 substance that depletes the levels of the antioxidant glutathione and the
 amino acid cysteine, two elements that switch melanogenesis from eumelanin
 to pheomelanin. Final bib size is negatively related to pheomelanin levels
 in the bib feathers. BSO reduced cysteine and glutathione levels in all
 birds, but improved phenotypes (bibs larger than controls) were only
 expressed by high-quality birds (BSO-birds with largest bibs initially).
 Negative associations between final bib size and cysteine levels in
 erythrocytes, and between pheomelanin and cysteine levels, were observed
 in high-quality birds only. These findings suggest that a mechanism
 uncoupling pheomelanin and cysteine levels may have evolved in low-quality
 birds to avoid producing bibs of size not corresponding to their quality
 and greater relative costs. Indeed, greater oxidative stress in cells was
 not observed in low-quality birds. This may represent the first mechanism
 maintaining signal honesty without producing greater relative costs on
 low-quality signalers.
description: Evolution-BSO_sparrows-Dryad
DOI: 10.5061/dryad.dv164
title: Data from: A geography aware reconciliation method to investigate diversification patterns in host/parasite cospeciation interactions

description: Cospeciation studies aim at investigating whether hosts and symbionts
 speciate simultaneously or whether the associations diversify through host
 shifts. This problem is often tackled through reconciliation analyses that
 map the symbiont phylogeny onto the host phylogeny by mixing different
 types of diversification events. These reconciliations can be difficult to
 interpret and not always biologically realistic. Researchers have
 underlined that the biogeographic histories of both hosts and symbionts
 influence the probability of cospeciation and host switches, but up to now
 no reconciliation software integrates geographic data. We present a new
 functionality in the Mowgli software that bridges this gap. The user can
 provide geographic information on both the host and symbiont extant and
 ancestral taxa. Constraints in the reconciliation algorithm have been
 implemented to generate biologically realistic codiversification
 scenarios.. We apply our method to the fig/fig wasp association and infer
 diversification scenarios that differ from reconciliations ignoring
 geographic information. In addition, we updated the reconciliation viewer
 SylvX in order to visualize ancestral characters states on the
 phylogenetic trees and highlight zones that are geographically
 inconsistent in reconciliations computed without geographic constraintse.
 We suggest that the comparison of reconciliations obtained with and
 without geographic constraints can sometimes help solving ambiguities in
 the biogeographic histories of the partners. With the development of
 robust methods in historical biogeography and the advent of
 next-generation sequencing that leads to better-resolved trees, a
 geography aware reconciliation method represents a substantial advance
 that is likely to be useful to researchers studying the evolution of
 biotic interactions and biogeography.
description: geoRecHelperPerl Script to edit input files for MowgliExample filesData files used in "A geography aware reconciliation method to investigate diversification patterns in host/parasite cospeciation interactions "dataFiles.zip
DOI: 10.5061/dryad.1989
title: Data from: Selection on signal-reward correlation: limits and opportunities to the evolution of deceit in Turnera ulmifolia L.

description: Because pollinators are unable to directly assess the amount of rewards
 offered by flowers, they rely on the information provided by advertising
 floral traits. Thus, having a lower intra-individual correlation between
 signal and reward (signal accuracy) than other plants in the population
 provides the opportunity to reduce investment in rewards and cheat
 pollinators. However, pollinators' cognitive capacities can impose a
 limit to the evolution of this plant cheating strategy if they can punish
 those plants with low signal accuracy. In this study we examined the
 opportunity for cheating in the perennial weed Turnera ulmifolia L.
 evaluating the selective value of signal accuracy, floral display and
 reward production in a natural population. We found that plant
 reproductive success was positively related to signal accuracy and floral
 display, but not to nectar production. The intensity of selection on
 floral display was more than three times higher than on signal accuracy.
 The pattern of selection indicated that pollinators can select for signal
 accuracy provided by plants, and suggest that learning abilities of
 pollinators can limit the evolution of deceptive strategies in T.
 ulmifolia.
description: measurements in Turnera
 flowersInclude petal legth and
 nectar production data from 319 flowers (57 plants), used to estimate
 signal accuracy for each individual plants.selection in Turnera
 ulmifoliaInclude morphological
 and reproductive success data from 57 Turnera ulmifolia plants used to
 estimate phenotypic selection on flower number, mean nectar production
 rate, mean petal lenght and signal accuracy.
DOI: 10.5061/dryad.6r2p226
title: Data from: Frequency of virus-resistant hosts determines experimental community dynamics

description: Parasites, such as bacterial viruses (phages), can have large effects on
 host populations both at the ecological and evolutionary levels. In the
 case of cyanobacteria, phages can reduce primary production and infected
 hosts release intracellular nutrients influencing planktonic food web
 structure, community dynamics and biogeochemical cycles. Cyanophages may
 be of great importance in aquatic food webs during large cyanobacterial
 blooms unless the host population becomes resistant to phage infection.
 The consequences on plankton community dynamics of the evolution of phage
 resistance in bloom forming cyanobacterial populations is still poorly
 studied. Here we examined the effect of different frequencies of a
 phage-resistant genotype within a filamentous nitrogen-fixing Nodularia
 spumigena population on an experimental plankton community. Three
 Nodularia populations with different initial frequencies (0%, 5% and 50%)
 of phage-resistant genotypes were inoculated in separate treatments with
 the phage 2AV2, the green alga Chlorella vulgaris and the rotifer
 Brachionus plicatilis which formed the experimental plankton community
 subjected to either nitrogen-limited or nitrogen-rich conditions. We found
 that the frequency of the phage-resistant Nodularia genotype determined
 experimental community dynamics. Cyanobacterial populations with a high
 frequency (50%) of the phage-resistant genotype dominated the cultures
 despite the presence of phages, retaining most of the intracellular
 nitrogen in the plankton community. In contrast, populations with low
 frequencies (0% and 5%) of the phage-resistant genotype were lysed and
 reduced to extinction by the phage, transferring the intracellular
 nitrogen held by Nodularia to Chlorella and rotifers, and allowing
 Chlorella to dominate the communities and rotifers to survive. This study
 shows that even though phages represent minuscule biomass, they can have
 key effects on community composition and eco-evolutionary feedbacks in
 plankton communities.
description: Coloma
 DATAPopulation data from the
 community experiment. Units are individuals / ml and time units are
 weeks
DOI: 10.5061/dryad.81r60
title: Data from: State-dependent judgement bias in Drosophila: evidence for evolutionarily primitive affective processes

description: Affective states influence decision-making under ambiguity in humans and
 other animals. Individuals in a negative state tend to interpret ambiguous
 cues more negatively than individuals in a positive state. We demonstrate
 that the fruit fly, Drosophila melanogaster, also exhibits state-dependent
 changes in cue interpretation. Drosophila were trained on a Go/Go task to
 approach a positive (P) odour associated with a sugar reward and actively
 avoid a negative (N) odour associated with shock. Trained flies were then
 either shaken to induce a purported negative state or left undisturbed
 (control), and given a choice between: air or P; air or N; air or
 ambiguous odour (1:1 blend of P:N). Shaken flies were significantly less
 likely to approach the ambiguous odour than control flies. This ‘judgement
 bias’ may be mediated by changes in neural activity that reflect
 evolutionarily primitive affective states. We cannot say whether such
 states are consciously experienced, but utilisation of this model
 organism’s versatile experimental tool kit may facilitate elucidation of
 their neural and genetic basis.
description: Data from:
 State-dependent judgement bias in Drosophila: evidence for evolutionarily
 primitive affective processesDrosophila judgement bias
 Biology Letters.xlsx