cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ht79k
title: Data from: Transgenerational effect of infection in Plasmodium-infected mosquitoes

description: Transgenerational effects of infection have a huge potential to influence
 the prevalence and intensity of infections in vectors and, by extension,
 disease epidemiology. These transgenerational effects may increase the
 fitness of offspring through the transfer of protective immune factors.
 Alternatively, however, infected mothers may transfer the costs of
 infection to their offspring. Although transgenerational immune protection
 has been described in a dozen invertebrate species, we still lack a
 complete picture of the incidence and importance of transgenerational
 effects of infection in most invertebrate groups. The existence of
 transgenerational infection effects in mosquito vectors is of particular
 interest because of their potential for influencing parasite prevalence
 and intensity and, by extension, disease transmission. Here we present
 what we believe to be the first study on transgenerational infection
 effects in a mosquito vector infected with malaria parasites. The aim of
 this experiment was to quantify both the benefits and the costs of having
 an infected mother. We find no evidence of transgenerational protection in
 response to a Plasmodium infection. Having an infected mother does,
 however, entail considerable fecundity costs for the offspring: fecundity
 loss is three times higher in infected offspring issued from infected
 mothers than in infected offspring issued from uninfected mothers. We
 discuss the implications of our results and we call for more studies
 looking at transgenerational effects of infection in disease vectors.
description: Transgenerational effect
 of infection in Plasmodium-infected mosquitoesThese data allowed to
 quantify both the benefits and the costs of having an infected mother. We
 have measured : Blood meal size, wing size, number of eggs lay, prevalence
 infection and intensity of infectiondata_18_02.xlsx
DOI: 10.5061/dryad.357vn6p
title: Data from: Study on surface settlement and structural deformation for large span subway station using a new pre-supporting system

description: A new construction pre-supporting system, Steel Tube Slab system (STS), is
 proposed for large underground space excavation with shallow depth. The
 adjacent steel pipes in STS method are connected by a couple of flanges,
 bolt and concrete in order to improve the flexural capacity and lateral
 stiffness of the whole structure. STS method is firstly adopted to
 construct the ultra-shallow buried and large span subway station in China.
 Ground settlement and structural deformation are monitored during the
 construction. A numerical model is established for the subway station, the
 reliability of the numerical model is verified by comparing the numerical
 results with monitored data. The influence of large span underground
 excavation on surrounding soil and existing buildings in soft soils are
 investigated. Results prove that STS method can effectively control and
 reduce the ground settlement during construction. This study can provide a
 strong guidance for application of STS method in soft soils.
description: Supplementary
 File
DOI: 10.5061/dryad.d7g00
title: Data from: Evolutionary optimum for male sexual traits characterized using the multivariate Robertson–Price Identity

description: Phenotypes tend to remain relatively constant in natural populations,
 suggesting a limit to trait evolution. Although stationary phenotypes
 suggest stabilizing selection, directional selection is more commonly
 reported. However, selection on phenotypes will have no evolutionary
 consequence if the traits do not genetically covary with fitness, a
 covariance known as the Robertson–Price Identity. The nature of this
 genetic covariance determines if phenotypes will evolve directionally or
 whether they reside at an evolutionary optimum. Here, we show how a set of
 traits can be shown to be under net stabilizing selection through an
 application of the multivariate Robertson–Price Identity. We characterize
 how a suite of male sexual displays genetically covaries with fitness in a
 population of Drosophila serrata. Despite strong directional sexual
 selection on these phenotypes directly and significant genetic variance in
 them, little genetic covariance was detected with overall fitness.
 Instead, genetic analysis of trait deviations showed substantial
 stabilizing selection on the genetic variance of these traits with respect
 to overall fitness, indicating that they reside at an evolutionary
 optimum. In the presence of widespread pleiotropy, stabilizing selection
 on focal traits will arise through the net effects of selection on other,
 often unmeasured, traits and will tend to be stronger on trait
 combinations than single traits. Such selection may be difficult to detect
 in phenotypic analyses if the environmental covariance between the traits
 and fitness obscures the underlying genetic associations. The genetic
 analysis of trait deviations provides a way of detecting the missing
 stabilizing selection inferred by recent metaanalyses.
description: DELCOURT_fitness_dataPlease see README.txt
DOI: 10.5061/dryad.hg2g312
title: Data from: Impact of confinement housing on study end-points in the calf model of cryptosporidiosis

description: Background: Diarrhea is the second leading cause of death in children
 &lt; 5 years globally and the parasite genus Cryptosporidium is a
 leading cause of that diarrhea. The global disease burden attributable to
 cryptosporidiosis is substantial and the only approved chemotherapeutic,
 nitazoxanide, has poor efficacy in HIV positive children. Chemotherapeutic
 development is dependent on the calf model of cryptosporidiosis, which is
 the best approximation of human disease. However, the model is not
 consistently applied across research studies. Data collection commonly
 occurs using two different methods: Complete Fecal Collection (CFC), which
 requires use of confinement housing, and Interval Collection (IC), which
 permits use of box stalls. CFC mimics human challenge model methodology
 but it is unknown if confinement housing impacts study end-points and if
 data gathered via this method is suitable for generalization to human
 populations. Methods: Using a modified crossover study design we compared
 CFC and IC and evaluated the impact of housing on study end-points. At
 birth, calves were randomly assigned to confinement (n = 14) or box stall
 housing (n = 9), or were challenged with 5 x 107 C. parvum oocysts, and
 followed for 10 days. Study end-points included fecal oocyst shedding,
 severity of diarrhea, degree of dehydration, and plasma cortisol.
 Findings: Calves in confinement had no significant differences in mean log
 oocysts enumerated per gram of fecal dry matter between CFC and IC samples
 (P = 0.6), nor were there diurnal variations in oocyst shedding (P = 0.1).
 Confinement housed calves shed significantly more oocysts (P = 0.05), had
 higher plasma cortisol (P = 0.001), and required more supportive care (P =
 0.0009) than calves in box stalls. Conclusion: Housing method confounds
 study end-points in the calf model of cryptosporidiosis. Due to increased
 stress data collected from calves in confinement housing may not
 accurately estimate the efficacy of chemotherapeutics targeting C. parvum.
description: Calf Clinical
 DataSheet S1: Fecal oocyst
 shedding and severity of diarrhea for infected calves, including data on
 housing system, sample type, and sample time for days 0-10 post-infection.
 Sheet S2: Clinical outcomes for days 0-10 post-infection. Sheet S3: Calf
 body weights and calculation of average daily weight gain. Sheet S4:
 Frequency and type of morbidities and treatments for each calf. Sheet S5:
 Data DictionaryGraef&Zambriski_Dryad_Data_PLoSNTD_2018.xls
DOI: 10.5061/dryad.38s8g
title: Data from: Elevation and latitude interact to drive life-history variation in precocial birds: a comparative analysis using Galliformes

description: Elevational gradients provide a powerful laboratory for understanding the
 environmental and ecological drivers of geographic variation in avian
 life-history strategies. Environmental variation across elevational
 gradients is hypothesized to select for a trade-off of reduced fecundity
 (lower clutch size and/or fewer broods) for higher offspring quality
 (larger eggs and/or increased parental care) in higher elevation species
 and populations. In birds, a focus on altricial species from north
 temperate latitudes has prevented an evaluation of the generality of this
 trade-off, and how it is affected by latitude and intrinsic factors
 (development mode). We performed a comparative analysis controlling for
 body size and phylogenetic relationships on a global data set of 135
 galliform species to test (i) whether higher elevation precocial species
 have lower fecundity (smaller clutch and/or fewer broods) and invest more
 in offspring quality (greater egg mass) and (ii) whether latitude
 influences the traits involved and/or the trade-off, and (iii) to identify
 ecological and environmental drivers of life-history variation along
 elevational gradients. Life-history traits showed significant interaction
 effects across elevation and latitude: temperate higher elevation species
 had smaller clutches and clutch mass, larger eggs and shorter incubation
 periods, whereas more tropical species had larger clutches, eggs and
 clutch mass, and longer incubation periods as elevation increased. Number
 of broods and body mass did not vary with elevation or latitude.
 Latitudinal gradient in clutch size was observed only for low-elevation
 species. Significantly, an overlooked latitude-by-elevation interaction
 confounds our traditional view of clutch size variation across a
 tropical-to-temperate gradient. Across all latitudes, higher elevation
 species invested in offspring quality via larger eggs but support for
 reduced fecundity resulting from smaller clutches was found only along
 temperate elevational gradients; contrary to expectations, tropical
 high-elevation species showed increased fecundity. Variation in nest
 predation risk could explain differences between temperate and tropical
 elevational gradients, but we lack a consistent mechanism to explain why
 predation risk should vary in this manner. Alternatively, a resource
 availability hypothesis based on physical attributes that globally differ
 between elevation and latitude (seasonality in day length and temperature)
 seems more plausible.
description: GalliformDataGalliformDataSourcesGalliformPhylogenyPhylogeneticStandardization
DOI: 10.5061/dryad.h58qc
title: Data from: NOS: a software suite to compute node overlap and segregation in ecological networks

description: Investigating the structure of ecological networks can help unravel the
 mechanisms promoting and maintaining biodiversity. Recently, Strona and
 Veech (10.1111/2041-210X.12395) introduced a new metric (Ɲ ̅, pronounced
 ‘nos’), that allows assessment of structural patterns in networks ranging
 from complete node segregation to perfect nestedness, and that also
 provides a visual and quantitative assessment of the degree of network
 modularity. The Ɲ ̅ metric permits testing of a wide range of hypotheses
 regarding the tendency for species to share interacting partners by taking
 into account ecologically plausible species interactions based on
 constraints such as trophic levels and habitat preference. Here we
 introduce NOS, a software suite (including a web interface freely
 accessible at http://nos.alwaysdata.net, an executable program, and Python
 and R packages) that makes it possible to exploit the full potential of
 this method. Besides computing node overlap and segregation (Ɲ ̅), the
 software provides different functions to automatically identify a set of
 possible resource-consumer interactions in food webs based on trophic
 levels. As an example of application, we analyzed two well-resolved
 high-latitude marine food webs, showing that an explicit a priori
 consideration of trophic levels is fundamental for a proper assessment of
 food web structure.
description: User manual for static
 NOS softwareThe manual provides
 detailed instructions to use the Python NOS package, and the Windows
 executable program.static_NOS_user_manual.pdfNOS python packageThe file includes an implementation of NOS in Python programming language. Detailed instructions about how to use the package are provided in the NOS user manual. The Executable version of NOS for Windows available for download at http://nos.alwaysdata.net, and a NOS R package is available for download from CRAN https://CRAN.R-project.org/package=nosnos.pyMarine Arctic food-webSample food web for the NOS software suite. Data from: Kortsch, S. et al. 2015. Climate change alters the structure of arctic marine food webs due to poleward shifts of boreal generalists. Proc. R. Soc. B 282: 20151546.arctic.csvMarine Boreal food-webSample food web for the NOS software suite. Data from: Kortsch, S. et al. 2015. Climate change alters the structure of arctic marine food webs due to poleward shifts of boreal generalists. Proc. R. Soc. B 282: 20151546.boreal.csv
DOI: 10.5061/dryad.7c93n5s
title: Data from: Incidence of influenza A(H3N2) virus infections in Hong Kong in a longitudinal sero-epidemiological study, 2009-2015

description: Background: Many serologic studies were done during and after the 2009
 influenza pandemic, to estimate the cumulative incidence of influenza
 A(H1N1)pdm09 virus infections, but there are few comparative estimates of
 the incidence of influenza A(H3N2) virus infections during epidemics.
 Methods: We conducted a longitudinal serologic study in Hong Kong. We
 collected sera annually and tested samples from 2009-13 by HAI against the
 A/Perth/16/2009(H3N2) virus, and samples from 2013-15 against the
 A/Victoria/361/2011(H3N2) virus using the hemagglutination inhibition
 (HAI) assay. We estimated the cumulative incidence of infections based on
 4-fold or greater rises in HAI titers in consecutive sera. Results: There
 were four major H3N2 epidemics: (1) Aug-Oct 2010; (2) Mar-Jun 2012; (3)
 Jul-Oct 2013; and (4) Jun-Jul 2014. Between 514 516 and 614 619 relevant
 pairs of sera were available for each epidemic. We estimated that 98%,
 2019%, 57% and 7% of the population were infected in each epidemic,
 respectively, with higher incidence in children in epidemics 1 and 4.
 Conclusions: We estimatedfound that around 5% to 20% of the Hong Kong
 population were infectedre-infections in each of the four H3N2 epidemics
 that occurred from 2010 through 2014 were rare. The largest H3N2 epidemic
 occurred with the lowest level of pre-epidemic immunity.
description: Read me (data file
 explanations)Epidemic 1
 dataThis data file contains
 Epidemic 1 information from the serologic study in Hong
 Kong.titer.epi1.csvEpidemic 2 dataThis data file contains Epidemic 2 information from the serologic study in Hong Kong.titer.epi2.csvEpidemic 3 dataThis data file contains Epidemic 3 information from the serologic study in Hong Kong.titer.epi3.csvEpidemic 4 dataThis data file contains Epidemic 4 information from the serologic study in Hong Kong.titer.epi4.csvInfluenza proxy dataThe influenza proxy used in the analysis.ILILAB.csvTable 1 scriptsR syntax to reproduce results in Table 1.Table1.RTable 2 scriptsR syntax to reproduce results in Table 2.Table2.RFigure 1 scriptsR syntax to reproduce Figure 1.Figure1.RFigure 2 scriptsR syntax to reproduce Figure 2.Figure2.RFigure 3 scriptsR syntax to reproduce Figure 3.Figure3.RFigure 4 scriptsR syntax to reproduce Figure 4.Figure4.RMain text result scriptsR syntax to reproduce re-infection results (shown in main text).reinfection.R
DOI: 10.5061/dryad.60g61
title: Data from: Experimental evidence that even minor livestock trampling has severe effects on land snail communities in forest remnants

description: 1. Land-use intensification is increasing dramatically in production
 systems world-wide. Livestock production is an important component of
 production land use, and increases in livestock densities have had a wide
 range of negative consequences. The off-site effects of livestock grazing
 and trampling on native vegetation adjacent to pastoral land have received
 less attention than on-farm effects. Moreover, where significant
 ecological effects of livestock spillover have been identified, the
 mechanistic determinants of these effects have not typically been
 investigated. 2. Here, we tested the mechanistic drivers of livestock
 trampling effects on land snail communities in forest remnants using
 simulated trampling under field conditions. We used a factorial
 combination of leaf-litter manipulation and trampling treatments to
 partition different causal drivers of livestock impacts on land snail
 communities and related them to five environmental variables that are
 altered by livestock. 3. We show that even very low frequency trampling
 caused severe changes to land snail communities. Land snail density, even
 under the lowest trampling frequency, declined by an average of 42
 individuals m−2 and land snail species richness decreased by an average of
 10 species per plot compared with control plots. 4. The underlying drivers
 of changes in land snail communities varied, but were primarily linked to
 leaf-litter mass, rather than soil compaction. 5. Synthesis and
 applications. Overall, these results suggest that even minimal disturbance
 by livestock has large effects on land snail communities, but the
 underlying drivers of these effects require further investigation in
 longer duration and more intensive studies. Our results provide strong
 support for livestock exclusion as an important management tool for native
 forest remnants embedded within production landscapes.
description: Predictor
 variablesValues of habitat
 structure and microclimatic variables (‘endogenous’ predictors in SEM
 models) measured in each experimental plotSpecies
 abundanceTotal number of each
 land snail species identified in each leaf-litter sample collected from
 the experimental plots pre- and post treatment.
DOI: 10.5061/dryad.n4g25
title: Data from: Multi-generational response to artificial selection for biased clutch sex ratios in Tigriopus californicus populations

description: Polygenic sex determination (PSD) is relatively rare and theoretically
 evolutionary unstable, yet has been reported across a range of taxa.
 Evidence for multilocus PSD is provided by (i) large between-family
 variance in sex ratio, (ii) paternal and maternal effects on family sex
 ratio and (iii) response to selection for family sex ratio. This study
 tests the polygenic hypothesis of sex determination in the harpacticoid
 copepod Tigriopus californicus using the criterion of response to
 selection. We report the first multigenerational quantitative evidence
 that clutch sex ratio responds to artificial selection in both directions
 (selection for male- and female-biased families) and in multiple
 populations of T. californicus. In the five of six lines that showed a
 response to selection, realized heritability estimated by
 multigenerational analysis ranged from 0.24 to 0.58. Divergence of clutch
 sex ratio between selection lines is rapid, with response to selection
 detectable within the first four generations of selection.
description: Tigriopus sex ratio
 selectionRaw data on clutch sex
 ratio from females. Tigriopus californicus were collected from two
 populations (British Columbia coast and San Diego, California coast) and
 three selection lines were established for each
 population.Tigriopus_SRselection.csv
DOI: 10.5061/dryad.c3648g4
title: Data from: Plant competition alters the temporal dynamics of plant-soil feedbacks

description: 1. Most studies on plant-soil feedback (PSF) and plant competition measure
 the feedback response at one moment only. However, PSFs and competition
 may both change over time, and how PSF and competition interact over time
 is unclear. 2. We tested the temporal dynamics of PSF and interspecific
 competition for the forb Jacobaea vulgaris and the grass Holcus lanatus.
 We grew both species individually and in interspecific competition in soil
 that was first conditioned in the greenhouse by J. vulgaris, by H. lanatus
 or without plant growth. For a period of 11 weeks, we harvested plants
 twice a week and analyzed the fungal and chemical composition of the
 different soils at the end of the first and second growth phase. 3. During
 the second growth phase, when grown in isolation, both species produced
 more biomass in heterospecific conditioned soil than in conspecific
 conditioned soil. Young J. vulgaris exhibited a strong negative
 conspecific feedback, but this effect diminished over time and became
 neutral in older plants. In contrast, when grown in competition, the
 negative conspecific feedback of J. vulgaris exacerbated over time. Older
 H. lanatus plants benefited more from heterospecific conditioning when
 competing with J. vulgaris, then when grown isolated. 4. Fungal community
 composition and soil chemistry differed significantly between soils but
 this was mainly driven by differences between plant-conditioned and
 unconditioned soils. Remarkably, at the end of the second growth phase,
 fungal community composition was not explained by the legacy of the
 species that had been grown in the soil most recently, but still reflected
 the legacy of the first growth phase. We reexamined plant growth during a
 third growth phase. Biomass of J. vulgaris was still influenced by the
 treatments imposed during the first phase, while H. lanatus responded only
 to the plant growth treatments imposed during the second phase. 5.
 Synthesis: Our study shows that the direction and magnitude of PSF depends
 on plant age and competition but also on soil legacy effects of earlier
 plant growth. These results highlight the need to incorporate dynamic PSFs
 in research on plant populations and communities.
description: dataset belonging to
 Bezemer et al. Journal of Ecologydata from a greenhouse
 study. data include plant biomass, soil chemistry, fungal composition
 (TRFLP) and calculated plant growth parameters. explanations are in the
 filedryad
 dataset.xlsx