cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1787f
title: Data from: The role of cell replacement in benthic–pelagic coupling by suspension feeders

description: Benthic–pelagic coupling through suspension feeders and their detrital
 pathways is integral to carbon transport in oceans. In food-poor
 ecosystems however, a novel mechanism of carbon recycling has been
 proposed that involves direct uptake of dissolved carbon by suspension
 feeders followed by shedding of cells as particulate carbon. We studied
 cell replacement rates in a range of cold-water sponge species to
 determine how universal this mechanism might be. We show that cell
 replacement rates of feeding epithelia in explants vary from 30 hours up
 to 7 days, and change during different seasons and life-history stages. We
 also found that feeding epithelia are not replaced through direct
 replication but instead arise from a population of stem cells that
 differentiate and integrate into epithelial tissues. Our results reveal a
 surprising amount of complexity in the control of cell processes in
 sponges, with cell turnover depending on environmental conditions and
 using stem cells as rate-limiting mechanisms. Our results also suggest
 that for species in cold water with high particulate organic matter, cell
 turnover is not the mechanism delivering carbon flux to surrounding
 communities.
description: Cell counts and
 calculationsMicrosoft Excel file
 containing 5 worksheets. Contains raw data (counts of new choanocytes
 labeled with EdU and counts of all choanocytes in a choanocyte chamber;
 counts of cells from the mesohyl), calculations of cell kinetics using the
 one-population steady state model (Nowakowski et al. 1989), and data and
 calculations used to create Figures 3, 4, and supporting tables 2, 3 and
 4.EdU data
 for Dryad.xls
DOI: 10.5061/dryad.km711dm8
title: Data from: Masquerade is associated with polyphagy and larval overwintering in the Lepidoptera

description: Masquerading animals benefit from the difficulty that predators have in
 differentiating them from the inedible objects, such as twigs, that they
 resemble. The function of masquerade has been demonstrated, but how it
 interacts with the life history of organisms has not been studied. Here,
 we report the use of comparative analyses to test hypotheses linking
 masquerade to life-history parameters. We constructed a phylogenetic tree
 of the British species of the lepidoptera families Geometridae and
 Drepanidae and compiled life history and colouration data from the
 literature. We found that masquerade is associated with the exploitation
 of a greater diversity of host plants whether measured by the number of
 families or genera. We found a positive relationship between body size and
 polyphagy among masquerading species, and no relationship among cryptic
 species. Among those species predominantly found on woody host plants,
 masquerading species are more likely to overwinter as larvae while cryptic
 species mostly overwinter as pupae. Polyphenism was associated with
 multivoltinism in masquerading species but not cryptic species. Taken
 together, our results show that masquerade must be viewed as a strategy
 distinct to crypsis and hence may provide insights into the evolution of
 both defensive strategies. Our study further demonstrates the utility of
 broad-scale between-species comparisons in studying associations between
 diverse life-history parameters and sensory aspects of predator-prey
 interactions.
description: Masquerade Appendix
 1Data
 from Porter (1997) and others on the ecological traits of the larvae of
 all of the British Geometridae and Drepanidae, including body length, and
 the number of host plant families, genera, and species.
DOI: 10.5061/dryad.8vd0gf1
title: Data from: Detection for nitrite based on fluorescent carbon dots by hydrothermal method with folic acid

description: A fluorescent carbon dots probe for detection of aqueous nitrite was
 fabricated by a one-pot hydrothermal method and the transmission electron
 microscope, X-ray diffractometer, UV-Vis absorption spectrometer and
 fluorescence spectrophotometer were used to study the property of carbon
 dots. The fluorescent property of carbon dots influenced by concentration
 of aqueous nitrite was studied. The interaction between the
 electron-donating functional groups and the electron-accepting nitrous
 acid could account for the quenching effect on carbon dots by adding
 aqueous nitrite. The products of the hydrolization of aqueous nitrite
 performed stronger quenching effect at lower pH. The relationship between
 the relative fluorescence intensity of carbon dots and the concentration
 of nitrite was described by the Stern-Volmer equation (I0/I-1=0.046[Q])
 with a fine linearity (R2=0.99). The carbon dots-based probe provides a
 convenient method for the detection of nitrite concentration.
description: CDs
 DATA
DOI: 10.5061/dryad.5cg14
title: Data from: Cryptic divergent lineages of Pultenaea pauciflora M.B. Scott (Fabaceae, Mirbelieae) exhibit different evolutionary history

description: Genetic structure among disjunct population groups of Pultenaea pauciflora
 was assessed to determine the evolutionary history of this species as a
 basis for conservation management strategies. Analysis of individuals from
 all extant populations using 1737 amplified length polymorphism markers
 revealed two highly divergent genetic entities with strong geographical
 structuring. Populations located at Narrogin and Brookton clustered
 together in Bayesian assignment analysis with every individual optimally
 placed in a single cluster with complete membership. Genetic
 differentiation between populations in these two areas was very low.
 Populations at Boddington were highly divergent from those located at
 Narrogin and Brookton. All individuals from Boddington populations were
 optimally placed into a second cluster with complete membership.
 Populations located at Boddington maintain lower levels of allelic
 diversity, yet greater levels of mean heterozygosity than populations
 located at Narrogin and Brookton. The degree of genetic differentiation
 and different patterns of genetic diversity strongly suggest historical
 divergence and separate evolutionary influences on the two lineages that
 occur in different ecological habitat. These Evolutionary Significant
 Units are likely to represent two cryptic sister taxa in the extant
 populations currently recognized as P. pauciflora, and the reassessment of
 taxonomic and conservation status of both lineages is required.
description: MillarPultenaeaAFLPScoresThis file contains AFLP scores for 142 individuals of Pultenaea pauciflora at 1737 loci. The data file was created using the software 'TextPad'. Further details can be found in the ReadMe file.
DOI: 10.5061/dryad.mf7qb0c
title: Data from: Niclosamide activates the NLRP3 inflammasome by intracellular acidification and mitochondrial inhibition

description: The NLRP3 inflammasome is unique among pattern recognition receptors in
 using changes in cellular physiology as a mechanism for sensing host
 danger. To dissect the physiological network controlling inflammasome
 activation, we screened for small-molecule activators and suppressors of
 IL-1β release in macrophages. Here we identified niclosamide, a
 mitochondrial uncoupler, as an activator of NLRP3 inflammasome. We find
 that niclosamide inhibits mitochondria and induces intracellular
 acidification, both of which are necessary for inflammasome activation.
 Intracellular acidification, by inhibiting glycolysis, works together with
 mitochondrial inhibition to induce intracellular ATP loss, which
 compromises intracellular potassium maintenance, a key event to NLRP3
 inflammasome activation. A modest decline in intracellular ATP or pH
 within an optimal range induces maximum IL-1β release while their
 excessive decline suppresses IL-1β release. Our work illustrates how
 energy metabolism converges upon intracellular potassium to activate NLRP3
 inflammasome and highlights a biphasic relationship between cellular
 physiology and IL-1β release.
description: CellProfiler
 pipelineCellProfiler pipeline
 for counting the number of nuclei in Hoechst stained image (4x
 image).CellCount4x.cppipeCOMMSBIO-18-0553-SupplementaryData1Activator and suppressor screens in THP-1 macrophages.COMMSBIO-18-0553-SupplementaryData2Activator and suppressor screens in LPS-primed bone marrow derived macrophages (BMDMs).Description of dataDescription of data contained within the Excel sheets (Supplementary Data 1 and Supplementary Data 2).COMMSBIO-18-0553_Description.pdf
DOI: 10.5061/dryad.dh439
title: Data from: Long-term changes in liana loads and tree dynamics in a Malaysian forest

description: The importance of lianas through time and their effect on tree
 reproduction are evaluated for the first time in a Southeast Asian
 Dipterocarp forest. We quantified flower and seed production by lianas and
 trees for 13 years, assessed liana loads in the crowns of all trees larger
 than 30 cm in diameter at breast height (1.3 m) in 2002 and 2014, and
 assessed levels of reproduction for the same trees during a strong general
 flowering event in 2014 for the 50-ha forest dynamics plot at the Pasoh
 Forest Reserve, Malaysia. General flowering refers to synchronous
 reproduction by hundreds of plant species at irregular, multiyear
 intervals and only occurs in Southeast Asian Dipterocarp forests. Overall,
 lianas were present in 50% of tree crowns and comprised 31% of flower
 production and 46% of seed production. Lianas reduced growth, survival,
 and reproduction by their host trees. Lianas were less frequent in
 canopy-emergent trees, Dipterocarps comprised a disproportionately large
 proportion of canopy emergents, and, as a consequence, lianas were less
 frequent in Dipterocarps than in trees from other plant families. Lianas
 infested the crowns of significantly fewer trees in 2014 (47.9%) than in
 2002 (52.3%); however, the decrease was restricted to trees with the
 lightest liana loads and sample sizes and statistical power were enormous.
 Lianas comprised a stable proportion of flower production and a highly
 variable proportion of seed production from 2002 through 2013. We conclude
 lianas have a huge impact on trees in this forest and were a stable
 component of the forest between 2002 and 2014. The emergent habit and
 associated ability to avoid lianas might contribute to the success of the
 Dipterocarpaceae.
description: Survey of lianas and
 reproduction for large trees in the Pasoh Research Forest,
 MalaysiaWe surveyed all trees
 larger than 30 cm in diameter at breast height in the Pasoh 50-ha plot for
 crown exposure to light and level of liana infestation in 2002 and for
 crown exposure, liana infestation and reproductive status in 2014. The
 2014 survey took place during a strong general flowering
 event.Dryad.txt
DOI: 10.5061/dryad.8078
title: Data from: What invasive species reveal about the rate and form of contemporary phenotypic change in nature

description: Biological invasions represent opportunities to gain insight into
 fundamental evolutionary questions as reproductive isolation and sudden
 changes in selection pressures are likely to lead to rapid evolutionary
 change. Here I investigate the role of invasive species in revealing the
 rate and form of contemporary phenotypic change in wild populations by
 expanding a database of over 5,500 rates of phenotypic change from 90
 species of plants and animals. Invasive species are widely used as model
 organisms and thus contribute disproportionately to available rates of
 phenotypic change. However, the preponderance of these rates is the
 consequence of extensive study in a small number of species. I found mixed
 evidence to support the hypothesis that phenotypic change is associated
 with time depending on the metric of choice (i.e. darwins or haldanes).
 Insights from invasive and native species both provide evidence for abrupt
 phenotypic change and suggest a potentially important role of the
 environment to drive trait change in wild populations, though the
 environmental influence on the observed trajectories remains unclear. Thus
 future work should continue to seek an understanding of the mechanistic
 underpinnings –both genetic and environmental– of how phenotypic variation
 allows populations to adapt to rapidly changing global environments.
description: Appendix
 AEvolutionary rates
 database
DOI: 10.5061/dryad.t86145r
title: Data from: Impacts of species richness on productivity in a large-scale subtropical forest experiment

description: Biodiversity experiments have shown that species loss reduces ecosystem
 functioning in grassland. To test whether this result can be extrapolated
 to forests, the main contributors to terrestrial primary productivity,
 requires large-scale experiments. We manipulated tree species richness by
 planting more than 150,000 trees in plots with 1 to 16 species. Simulating
 multiple extinction scenarios, we found that richness strongly increased
 stand-level productivity. After 8 years, 16-species mixtures had
 accumulated over twice the amount of carbon found in average monocultures
 and similar amounts as those of two commercial monocultures. Species
 richness effects were strongly associated with functional and phylogenetic
 diversity. A shrub addition treatment reduced tree productivity, but this
 reduction was smaller at high shrub species richness. Our results
 encourage multispecies afforestation strategies to restore biodiversity
 and mitigate climate change.
description: aat6405_dataPlot-level aboveground productivity indicators underlying published analyses.aat6405R script with statistical models presented in article.
DOI: 10.5061/dryad.2d7b0
title: Data from: Fast life history traits promote invasion success in amphibians and reptiles

description: Competing theoretical models make different predictions on which life
 history strategies facilitate growth of small populations. While ‘fast’
 strategies allow for rapid increase in population size and limit
 vulnerability to stochastic events, ‘slow’ strategies and bet-hedging may
 reduce variance in vital rates in response to stochasticity. We test these
 predictions using biological invasions since founder alien populations
 start small, compiling the largest dataset yet of global herpetological
 introductions and life history traits. Using state-of-the-art phylogenetic
 comparative methods, we show that successful invaders have fast traits,
 such as large and frequent clutches, at both establishment and spread
 stages. These results, together with recent findings in mammals and
 plants, support ‘fast advantage’ models and the importance of high
 potential population growth rate. Conversely, successful alien birds are
 bet-hedgers. We propose that transient population dynamics and differences
 in longevity and behavioural flexibility can help reconcile apparently
 contrasting results across terrestrial vertebrate classes.
description: Allen et
 al17EL_Amphibian_reptile_invasion_&_life_historyThe data file contains
 data on the status of alien (non-native) amphibian and reptile species at
 the global scale and their life history traits. In the ReadMe file we
 provide the basic details on the variables in the datafile. Full details
 on the protocol for the extraction of the data from the literature,
 classification of the species, and references underling the data can be
 found in the Supplementary Information of the Ecology Letters paper (Data
 collection: SI, Section 1.1; Data references: SI, 4.2 and
 4.3).
DOI: 10.5061/dryad.5jg7f
title: Data from: The interrelationship among economic activities, environmental degradation, material consumption, and population health in low-income countries: a longitudinal ecological study

description: Objectives: The theory of ecological unequal exchange explains how trade
 and various forms of economic activity create the problem of environmental
 degradation, and lead to the deterioration of population health. Based on
 this theory, our study examined the inter-relationship among economic
 characteristics, ecological footprints, CO2 emissions, infant mortality
 rates and under-5 mortality rates in low-income countries. Design: A
 longitudinal ecological study design. Setting: Sixty-six low-income
 countries from 1980 to 2010 were included in the analyses. Data for each
 country represented an average of 23 years (N=1497). Data sources: Data
 were from the World Development Indicators, UN Commodity Trade Statistics
 Database, Global Footprint Network and Polity IV Project. Analyses: Linear
 mixed models with a spatial power covariance structure and a correlation
 that decreased over time were constructed to accommodate the repeated
 measures. Statistical analyses were conducted separately by sub-Saharan
 Africa, Latin America and other regions. Results: After controlling for
 country-level sociodemographic characteristics, debt and manufacturing,
 economic activities were positively associated with infant mortality rates
 and under-5 mortality rates in sub-Saharan Africa. By contrast, export
 intensity and foreign investment were beneficial for reducing infant and
 under-5 mortality rates in Latin America and other regions. Although the
 ecological footprints and CO2 emissions did not mediate the relationship
 between economic characteristics and health outcomes, export intensity
 increased CO2 emissions, but reduced the ecological footprints in
 sub-Saharan Africa. By contrast, in Asia, the Middle East and North
 Africa, although export intensity was positively associated with the
 ecological footprints and also CO2 emissions, the percentage of exports to
 high-income countries was negatively associated with the ecological
 footprints. Conclusions: This study suggested that environmental
 protection and economic development are important for reducing infant and
 under-5 mortality rates in low-income countries.
description: data
DOI: 10.5061/dryad.v66p0
title: Data from: The loci of repeated evolution: a catalogue of genetic hotspots of phenotypic variation

description: What is the nature of the genetic changes underlying phenotypic evolution?
 We have catalogued 1008 alleles described in the literature that cause
 phenotypic differences among animals, plants and yeasts. Surprisingly,
 evolution of similar traits in distinct lineages often involves mutations
 in the same gene (“gene reuse”). This compilation yields three important
 qualitative implications about repeated evolution. First, the apparent
 evolution of similar traits by gene reuse can be traced back to two
 alternatives, either several independent causative mutations or a single
 original mutational event followed by sorting processes. Second, hotspots
 of evolution – defined as the repeated occurrence of de novo mutations at
 orthologous loci and causing similar phenotypic variation – are
 omnipresent in the literature with more than 100 examples covering various
 levels of analysis, including numerous gain-of-function events. Third,
 several alleles of large effect have been shown to result from the
 aggregation of multiple small-effect mutations at the same hotspot locus,
 thus reconciling micro-mutationist theories of adaptation with the
 empirical observation of large-effect variants. While data heterogeneity
 and experimental biases prevented us from extracting quantitative trends,
 our synthesis highlights the existence of genetic paths of least
 resistance leading to viable evolutionary change.
description: The Loci of Evolution
 catalogSee readme file for
 description of spreadsheetMartin&Orgogozo_DATASET
 DRYAD.xls
DOI: 10.5061/dryad.c520h
title: Data from: Extraction of lotus fibres from lotus stems under microwave irradiation

description: An efficient technology for preparing lotus fibres under microwave
 irradiation was developed. The lotus fibres were characterized by scanning
 electron microscopy, Fourier transform infrared spectrometry, X-ray
 diffraction and thermogravimetry. Lotus fibres prepared are a kind of
 hollow fibres which are composed of a superfine fibre and an external
 shell. The effect of the treatment time with hydrogen peroxide under
 microwave irradiation on components, whiteness, moisture regain, removal
 rate of impurities, fineness, tensile strength and breaking elongation of
 lotus fibres was investigated. The results show that the cellulose content
 in lotus fibres increases with increase in treatment time. Whiteness and
 moisture regain of lotus fibres increase with increase in treatment time
 with hydrogen peroxide. The removal rate of impurities and the fineness of
 lotus fibres are improved after they are treated with hydrogen peroxide.
 Microwave irradiation is supposed to be an efficient method for producing
 lotus fibres.
description: Supplementary Material
 for RSC Open Science 23.6.2017XRD data of raw lotus
 fibers and lotus fibers after being treated with hydrogen
 peroxide
DOI: 10.5061/dryad.23gq5
title: Data from: Biodiversity-ecosystem functioning relationships in long-term time series and palaeoecological records: deep sea as a test bed

description: The link between biodiversity and ecosystem functioning (BEF) over long
 temporal scales is poorly understood. Here, we investigate biological
 monitoring and palaeoecological records on decadal, centennial and
 millennial time scales from a BEF framework, by using deep-sea,
 soft-sediment environments as a test bed. Results generally show positive
 BEF relationships, in agreement with BEF studies based on present-day
 spatial analyses and short-term manipulative experiments. However, the
 deep-sea BEF relationship is much noisier across longer time scales
 compared with modern observational studies. We also demonstrate with
 palaeoecological time-series data that a larger species pool does not
 enhance ecosystem stability through time, whereas abundance, as an
 indicator of higher ecosystem functioning, may enhance ecosystem
 stability. These results suggest that BEF relationships are potentially
 timescale-dependent. Environmental impacts on biodiversity and ecosystem
 functioning may be much stronger than biodiversity impacts on ecosystem
 functioning at long, decadal–millennial, time scales. Longer time-scale
 perspectives, including palaeoecological and ecosystem monitoring data,
 are critical for predicting future BEF relationships on a rapidly changing
 planet.
description: 23GGC ostracode
 functional diversity dataData used for 23GGC
 ostracode functional diversity calculation. Please see the paper for more
 details.FD_Datamatrix.xlsx23GGC ostracode biovolume dataData used for 23GGC ostracode biovolume calculation. Please see the paper for more details.Biovolume.xlsxReferencesReferences for biovolume and functional diversity Dryad data files.Dryad_refs.docxTable S1 in Excel formatTable S1 List of functional and morphological traits for ostracode speciesYasuhara_TransB_TableS1.xlsx