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  • Journal article
    Bennett S, Girndt A, Sánchez-Tójar A, Burke T, Simons M, Schroeder Jet al., 2021,

    Evidence of paternal effects on telomere length increases in early-life

  • Journal article
    Zheng JX, Pawar S, Goodman DFM, 2021,

    Further towards unambiguous edge bundling: Investigating power-confluentdrawings for network visualization

    , IEEE Transactions on Visualization and Computer Graphics, Vol: 27, Pages: 2244-2249, ISSN: 1077-2626

    Bach et al. [1] recently presented an algorithm for constructing confluentdrawings, by leveraging power graph decomposition to generate an auxiliaryrouting graph. We identify two problems with their method and offer a singlesolution to solve both. We also classify the exact type of confluent drawingsthat the algorithm can produce as 'power-confluent', and prove that it is asubclass of the previously studied 'strict confluent' drawing. A descriptionand source code of our implementation is also provided, which additionallyincludes an improved method for power graph construction.

  • Journal article
    Weglarz KM, Saunders WC, Van Wagenen A, Pearse WDet al., 2021,

    Phylogenetic diversity efficiently and accurately prioritizes conservation of aquatic macroinvertebrate communities

    , ECOSPHERE, Vol: 12, ISSN: 2150-8925
  • Conference paper
    Abzhanov A, 2021,

    The many faces of evolution: heterochronic developmental mechanisms for adaptive radiations

    , Annual Meeting of the Society-for-Integrative-and-Comparative-Biology (SICB), Publisher: OXFORD UNIV PRESS INC, Pages: E2-E3, ISSN: 1540-7063
  • Journal article
    Willis K, Burt A, 2021,

    Double drives and private alleles for localised population genetic control

    , PLOS GENETICS, Vol: 17, ISSN: 1553-7404
  • Journal article
    Stachewicz JD, Fountain-Jones NM, Koontz A, Woolf H, Pearse WD, Gallinat ASet al., 2021,

    Strong trait correlation and phylogenetic signal in North American ground beetle (Carabidae) morphology

    <jats:title>Abstract</jats:title><jats:p>Functional traits mediate species’ responses to and roles within their environment, and are constrained by evolutionary history. While we have a strong understanding of trait evolution for macro-taxa such as birds and mammals, our understanding of invertebrates is comparatively limited. Here we address this gap in North American beetles with a sample of ground beetles (Carabidae), leveraging a large-scale collection and digitization effort by the National Ecological Observatory Network (NEON). For 154 ground beetle species, we measured seven morphological traits, which we placed into a recently-developed effect-response framework that characterizes traits by how they predict species’ effects on their ecosystems or responses to environmental stressors. We then used cytochrome oxidase one sequences from the same specimens to generate a phylogeny and tested evolutionary tempo and mode of the traits. We found strong phylogenetic signal in, and correlations among, morphological ground beetle traits. These results indicate that, for these species, beetle body shape trait evolution is constrained, and phylogenetic inertia is a stronger driver of beetle traits than (recent) environmental responses. Strong correlations among effect and response traits suggest that future environmental drivers are likely to affect both ecological composition and functioning in these beetles.</jats:p>

  • Journal article
    Russell M, Qureshi A, Wilson C, Cator Let al., 2021,

    Size, not temperature, drives cyclopoid copepod predation of invasive mosquito larvae

    , PLoS One, Vol: 16, ISSN: 1932-6203

    During range expansion, invasive species can experience new thermal regimes. Differences between the thermal performance of local and invasive species can alter species interactions, including predator-prey interactions. The Asian tiger mosquito, Aedes albopictus, is a known vector of several viral diseases of public health importance. It has successfully invaded many regions across the globe and currently threatens to invade regions of the UK where conditions would support seasonal activity. We assessed the functional response and predation efficiency (percentage of prey consumed) of the cyclopoid copepods Macrocyclops albidus and Megacyclops viridis from South East England, UK against newly-hatched French Ae. albopictus larvae across a relevant temperature range (15, 20, and 25°C). Predator-absent controls were included in all experiments to account for background prey mortality. We found that both M. albidus and M. viridis display type II functional response curves, and that both would therefore be suitable biocontrol agents in the event of an Ae. albopictus invasion in the UK. No significant effect of temperature on the predation interaction was detected by either type of analysis. However, the predation efficiency analysis did show differences due to predator species. The results suggest that M. viridis would be a superior predator against invasive Ae. albopictus larvae due to the larger size of this copepod species, relative to M. albidus. Our work highlights the importance of size relationships in predicting interactions between invading prey and local predators.

  • Journal article
    Christensen A, Piggott M, Sebille EV, Reeuwijk MV, Pawar Set al., 2021,

    Small-scale convective turbulence constrains microbial patchiness

    <jats:title>Abstract</jats:title> <jats:p>Microbes play a primary role in aquatic ecosystems and biogeochemical cycles. Patchiness is a critical component of these activities, influencing biological productivity, nutrient cycling and dynamics across trophic levels. Incorporating spatial dynamics into microbial models is a long-standing challenge, particularly where small-scale turbulence is involved. Here, we combine a realistic simulation of turbulence with an individual-based microbial model to test the key hypothesis that the coupling of motility and turbulence drives intense microscale patchiness. We find that such patchiness is depth-structured and requires high motility: Near the fluid surface, strong convective turbulence overpowers motility, homogenising motile and non-motile microbes equally. In deeper, thermocline-like conditions, highly motile microbes are up to 1.6-fold more patch-concentrated than non-motile microbes. Our results demonstrate that the delicate balance of turbulence and motility that triggers micro-scale patchiness is not a ubiquitous consequence of motility, and that the intensity of such patchiness in real-world conditions is modest.</jats:p>

  • Software
    Barneche D, Hulatt CJ, Dossena M, Padfield D, Woodward G, Trimmer M, Yvon-Durocher Get al., 2021,

    dbarneche/nature20200508666: Accepted version of paper data and code of manuscript: Warming impairs trophic transfer efficiency in a long-term field experiment (Nature)

    Barneche DR, Hulatt CJ, Dossena M, Padfield D, Woodward G, Trimmer M, Yvon-Durocher G, Warming impairs trophic transfer efficiency in a long-term field experiment. Nature (accepted on 2021-02-11), DOI: 10.1038/s41586-021-03352-2.

  • Journal article
    Gray C, Ma A, McLaughlin O, Petit S, Woodward G, Bohan DAet al., 2021,

    Ecological plasticity governs ecosystem services in multilayer networks

    , Communications Biology, Vol: 4, Pages: 1-7, ISSN: 2399-3642

    Agriculture is under pressure to achieve sustainable development goals for biodiversity and ecosystem services. Services in agro-ecosystems are typically driven by key species, and changes in the community composition and species abundance can have multifaceted effects. Assessment of individual services overlooks co-variance between different, but related, services coupled by a common group of species. This partial view ignores how effects propagate through an ecosystem. We conduct an analysis of 374 agricultural multilayer networks of two related services of weed seed regulation and gastropod mollusc predation delivered by carabid beetles. We found that weed seed regulation increased with the herbivore predation interaction frequency, computed from the network of trophic links between carabids and weed seeds in the herbivore layer. Weed seed regulation and herbivore interaction frequencies declined as the interaction frequencies between carabids and molluscs in the carnivore layer increased. This suggests that carabids can switch to gastropod predation with community change, and that link turnover rewires the herbivore and carnivore network layers affecting seed regulation. Our study reveals that ecosystem services are governed by ecological plasticity in structurally complex, multi-layer networks. Sustainable management therefore needs to go beyond the autecological approaches to ecosystem services that predominate, particularly in agriculture.

  • Journal article
    Simpson EG, Pearse WD, 2021,

    Fractal triads efficiently sample ecological diversity and processes across spatial scales

    <jats:title>Abstract</jats:title><jats:p>The relative influence of ecological assembly processes, such as environmental filtering, competition, and dispersal, vary across spatial scales. Changes in phylogenetic and taxonomic diversity across environments provide insight into these processes, however, it is challenging to assess the effect of spatial scale on these metrics. Here, we outline a nested sampling design that fractally spaces sampling locations to concentrate statistical power across spatial scales in a study area. We test this design in northeast Utah, at a study site with distinct vegetation types (including sagebrush steppe and mixed conifer forest), that vary across environmental gradients. We demonstrate the power of this design to detect changes in community phylogenetic diversity across environmental gradients and assess the spatial scale at which the sampling design captures the most variation in empirical data. We find clear evidence of broad-scale changes in multiple features of phylogenetic and taxonomic diversity across aspect. At finer scales, we find additional variation in phylo-diversity, highlighting the power of our fractal sampling design to efficiently detect patterns across multiple spatial scales. Thus, our fractal sampling design and analysis effectively identify important environmental gradients and spatial scales that drive community phylogenetic structure. We discuss the insights this gives us into the ecological assembly processes that differentiate plant communities found in northeast Utah.</jats:p>

  • Journal article
    Xu H, Wang H, Prentice IC, Harrison SP, Wang G, Xiangyang Set al., 2021,

    Predictability of leaf traits with climate and elevation: a case study in Gongga Mountain, China

    , Tree Physiology: an international botanical journal, Vol: 41, Pages: 1336-1352, ISSN: 0829-318X

    Leaf mass per area (Ma), nitrogen content per unit leaf area (Narea), maximum carboxylation capacity (Vcmax) and the ratio of leaf-internal to ambient CO2 partial pressure (χ) are important traits related to photosynthetic function, and show systematic variation along climatic and elevational gradients. Separating the effects of air pressure and climate along elevational gradients is challenging due to the covariation of elevation, pressure and climate. However, recently developed models based on optimality theory offer an independent way to predict leaf traits, and thus to separate the contributions of different controls. We apply optimality theory to predict variation in leaf traits across 18 sites in the Gongga Mountain region. We show that the models explain 59% of trait variability on average, without site- or region-specific calibration. Temperature, photosynthetically active radiation, vapor pressure deficit, soil moisture and growing-season length are all necessary to explain the observed patterns. The direct effect of air pressure is shown to have a relatively minor impact. These findings contribute to a growing body of research indicating that leaf-level traits vary with the physical environment in predictable ways, suggesting a promising direction for the improvement for terrestrial ecosystem models.

  • Journal article
    Willis K, Burt A, 2021,

    Double drives and private alleles for localised population genetic control

    <jats:title>Abstract</jats:title><jats:p>Synthetic gene drive constructs could, in principle, provide the basis for highly efficient interventions to control disease vectors and other pest species. This efficiency derives in part from leveraging natural processes of dispersal and gene flow to spread the construct and its impacts from one population to another. However, sometimes (for example, with invasive species) only specific populations are in need of control, and impacts on non-target populations would be undesirable. Many gene drive designs use nucleases that recognise and cleave specific genomic sequences, and one way to restrict their spread would be to exploit sequence differences between target and non-target populations. In this paper we propose and model a series of low threshold double drive designs for population suppression, each consisting of two constructs, one imposing a reproductive load on the population and the other inserted into a differentiated locus and controlling the drive of the first. Simple deterministic, discrete-generation computer simulations are used to assess the alternative designs. We find that the simplest double drive designs are significantly more robust to pre-existing cleavage resistance at the differentiated locus than single drive designs, and that more complex designs incorporating sex ratio distortion can be more efficient still, even allowing for successful control when the differentiated locus is neutral and there is up to 50% pre-existing resistance in the target population. Similar designs can also be used for population replacement, with similar benefits. A population genomic analysis of PAM sites in island and mainland populations of the malaria mosquito<jats:italic>Anopheles gambiae</jats:italic>indicates that the differentiation needed for our methods to work can exist in nature. Double drives should be considered when efficient but localised population genetic control is needed and

  • Journal article
    Kemp L, Aldridge DC, Booy O, Bower H, Browne D, Burgmann M, Burt A, Cunningham AA, Dando M, Dick JTA, Dye C, Evans SW, Gallardo B, Godfray HCJ, Goodfellow I, Gubbins S, Holt LA, Jones KE, Kandil H, Martin P, McCaughan M, McLeish C, Meany T, Millett K, OhEigeartaigh SS, Patron NJ, Rhodes C, Roy HE, Shackelford G, Smith D, Spence N, Steiner H, Sundaram LS, Voeneky S, Walker JR, Watkins H, Whitby S, Wood J, Sutherland WJet al., 2021,

    80 questions for UK biological security

    , PLOS ONE, Vol: 16, ISSN: 1932-6203
  • Journal article
    Turner M, Wei D, Prentice IC, Harrison Set al., 2021,

    The impact of methodological decisions in climate reconstructions using WA- PLS

    , Quaternary Research, Vol: 99, Pages: 341-356, ISSN: 0033-5894

    Most techniques for pollen-based quantitative climate reconstruction use modern assemblages as a reference data set. We examine the implication of methodological choices in the selection and treatment of the reference data set for climate reconstructions using Weighted Averaging Partial Least Squares (WA-PLS) regression, using records of the last glacial period from Europe. We show that the training data set used is important, because it determines the climate space sampled. The range and continuity of sampling along the climate gradient is more important than sampling density. Reconstruction uncertainties are generally reduced when more taxa are included, but combining related taxa that are poorly sampled in the data set to a higher taxonomic level provides more stable reconstructions. Excluding taxa that are climatically insensitive, or systematically over-represented in fossil pollen assemblages because of known biases in pollen production or transport, makes no significant difference to the reconstructions. However, the exclusion of taxa over-represented because of preservation issues does produce an improvement. These findings are relevant not only for WA-PLS reconstructions but also for similar approaches using modern assemblage reference data. There is no universal solution to these issues, but we propose a number of checks to evaluate the robustness of pollen-based reconstructions.

  • Journal article
    Aguirre-Gutierrez J, Rifal S, Shenkin A, Oliveras I, Bentley LP, Svatek M, Girardin CAJ, Both S, Riutta T, Berenguer E, Kissling WD, Bauman D, Raab N, Moore S, Farfan-Rios W, Simoes Figueiredo AE, Reis SM, Ndong JE, Ondo FE, Bengone NN, Mihindou V, Moraes de Seixas MM, Adu-Bredu S, Abemethy K, Asner GP, Barlow J, Burstem DFRP, Coomes DA, Cernusak LA, Dargle GC, Enquist BJ, Ewers RM, Ferreira J, Jeffery KJ, Joly CA, Lewis SL, Marimon-Junior BH, Martin RE, Morandi PS, Phillips OL, Quesada CA, Salinas N, Marimon BS, Silman M, Teh YA, White LJT, Malhi Yet al., 2021,

    Pantropical modelling of canopy functional traits using Sentinel-2 remote sensing data

    , REMOTE SENSING OF ENVIRONMENT, Vol: 252, ISSN: 0034-4257
  • Journal article
    Cavan EL, Kawaguchi S, Boyd PW, 2021,

    Implications for the mesopelagic microbial gardening hypothesis as determined by experimental fragmentation of Antarctic krill fecal pellets

    , ECOLOGY AND EVOLUTION, Vol: 11, Pages: 1023-1036, ISSN: 2045-7758
  • Journal article
    Hammond A, Karlsson X, Morianou I, Kyrou K, Beaghton A, Gribble M, Kranjc N, Galizi R, Burt A, Crisanti A, Nolan Tet al., 2021,

    Regulating the expression of gene drives is key to increasing their invasive potential and the mitigation of resistance

    , PLOS GENETICS, Vol: 17, ISSN: 1553-7404
  • Journal article
    Cornford R, Deinet S, De Palma A, Hill SLL, McRae L, Pettit B, Marconi V, Purvis A, Freeman Ret al., 2021,

    Fast, scalable, and automated identification of articles for biodiversity and macroecological datasets

    , GLOBAL ECOLOGY AND BIOGEOGRAPHY, Vol: 30, Pages: 339-347, ISSN: 1466-822X
  • Journal article
    Schulte To Bühne H, Tobias JA, Durant SM, Pettorelli Net al., 2021,

    Improving predictions of climate change-land use change interactions.

    , Trends in Ecology and Evolution, Vol: 36, Pages: 29-38, ISSN: 0169-5347

    Climate change and land use change often interact, altering biodiversity in unexpected ways. Research into climate change-land use change (CC-LUC) interactions has so far focused on quantifying biodiversity outcomes, rather than identifying the underlying ecological mechanisms, making it difficult to predict interactions and design appropriate conservation responses. We propose a risk-based framework to further our understanding of CC-LUC interactions. By identifying the factors driving the exposure and vulnerability of biodiversity to land use change, and then examining how these factors are altered by climate change (or vice versa), this framework will allow the effects of different interaction mechanisms to be compared across geographic and ecological contexts, supporting efforts to reduce biodiversity loss from interacting stressors.

  • Journal article
    Morris ZS, Abzhanov A, 2021,

    Heading for higher ground: Developmental origins and evolutionary diversification of the amniote face

    , EVOLUTIONARY DEVELOPMENTAL BIOLOGY, Vol: 141, Pages: 241-277, ISSN: 0070-2153
  • Conference paper
    Rizos G, Lawson J, Han Z, Butler D, Rosindell J, Mikolajczyk K, Banks-Leite C, Schuller BWet al., 2021,

    Multi-Attentive Detection of the Spider Monkey Whinny in the (Actual) Wild

    , Interspeech Conference, Publisher: ISCA-INT SPEECH COMMUNICATION ASSOC, Pages: 471-475, ISSN: 2308-457X
  • Journal article
    Tudge SJ, Purvis A, De Palma A, 2020,

    The impacts of biofuel crops on local biodiversity: a global synthesis

    <jats:title>Abstract</jats:title><jats:p>Concerns about the environmental impacts of climate change have led to increased targets for biofuel in the global energy market. First-generation biofuel crops contain oil, sugar or starch and are usually also grown for food, whereas second-generation biofuel is derived from non-food sources, including lignocellulosic crops, fast-growing trees, crop residues and waste. Increasing biofuel production drives land-use change, a major cause of biodiversity loss, but there is limited knowledge of how different first- and second-generation biofuel crops affect local biodiversity. A more detailed understanding could support better decisions about the net environmental impacts of biofuels. We synthesised data from 116 sources where a potential biofuel crop was grown and estimated how two measures of local biodiversity, species richness and total abundance, responded to different crops. Local species richness and abundance were 37% and 49% lower at sites planted with first-generation biofuel crops than in sites with primary vegetation. Soybean, wheat, maize and oil palm had the worst effects; the worst affected regions were Asia and Central and South America; and plant species richness and vertebrate abundance were the worst affected biodiversity measures. Second-generation biofuels had significantly smaller effects: species richness and abundance were 19% and 25%, respectively, lower in such sites than in primary vegetation. Our models suggest that land clearance to generate biofuel results in negative impacts on local biodiversity. However, the geographic and taxonomic variation in effects, and the variation in yields among different crops, are all relevant for making the most sustainable land-use decisions.</jats:p>

  • Journal article
    Koontz A, Brandt B, Dyreson C, Pearse Wet al., 2020,

    SymbiotaR2: An R Package for Accessing Symbiota2 Data

    , Journal of Open Source Software, Vol: 5, Pages: 2917-2917
  • Journal article
    Banks-Leite C, Ewers R, Folkard-Tapp H, Fraser Aet al., 2020,

    Countering the effects of habitat loss, fragmentation, and degradation through habitat restoration

    , One Earth, Vol: 3, Pages: 672-676, ISSN: 2590-3322

    Habitat loss, fragmentation and degradation impacts are the most direct threat to global biodiversity. In this Primer, we discuss how these three forms of habitat transformation are inextricably intertwined, and how their effects on biodiversity and ecosystems are often context-specific. We draw on recent analyses that have explored this context-dependence directly, to discuss how local-scale impacts of habitat transformation are mediated by biogeographic-scale variation in evolutionary histories and species’ geographic ranges. We also discuss how changes to ecosystem functions and services in modified habitats can be just as context-dependent – and how these changes are further obscured by high levels of ecological redundancy in species functions, which can confer resilience to habitat transformation. To avoid the impending extinction of millions of species, it is crucial that the impacts of habitat transformation are mitigated through a combination of preventing further habitat loss while simultaneously extending and repairing the habitats that remain.

  • Working paper
    Joshi J, Stocker BD, Hofhansl F, Zhou S, Dieckmann U, Prentice ICet al., 2020,

    Towards a unified theory of plant photosynthesis and hydraulics

    <jats:title>Abstract</jats:title><jats:p>The global carbon and water cycles are governed by the coupling of CO<jats:sub>2</jats:sub> and water vapour exchanges through the leaves of terrestrial plants, controlled by plant adaptations to balance carbon gains and hydraulic risks. We introduce a trait-based optimality theory that unifies the treatment of stomatal responses and biochemical acclimation of plants to environments changing on multiple timescales. Tested with experimental data from 18 species, our model successfully predicts the simultaneous decline in carbon assimilation rate, stomatal conductance, and photosynthetic capacity during progressive soil drought. It also correctly predicts the dependencies of gas exchange on atmospheric vapour pressure deficit, temperature, and CO<jats:sub>2</jats:sub>. Model predictions are also consistent with widely observed empirical patterns, such as the distribution of hydraulic strategies. Our unified theory opens new avenues for reliably modelling the interactive effects of drying soil and rising atmospheric CO<jats:sub>2</jats:sub> on global photosynthesis and transpiration.</jats:p>

  • Working paper
    Joshi J, Stocker B, Hofhansl F, Zhou S, Dieckmann U, Prentice ICet al., 2020,

    Towards a unified theory of plant photosynthesis and hydraulics

    , Publisher: Cold Spring Harbor Laboratory

    The global carbon and water cycles are strongly governed by the simultaneous diffusion of CO2 and water vapour through the leaves of terrestrial plants. These diffusive fluxes are controlled by plants’ adaptations to balance carbon gains and hydraulic risks. We introduce a trait-based optimality theory that unifies the treatment of stomatal responses and biochemical acclimation of plants to changing environments. Tested with experimental data from eighteen species, our model successfully predicts the simultaneous decline in carbon assimilation rate, stomatal conductance, and photosynthetic capacity during progressive soil drought. It also correctly predicts the dependencies of gas exchange on atmospheric vapour pressure deficit, temperature, and CO2. Consistent with widely observed patterns, inferred trait values for the analysed species display a spectrum of stomatal strategies, a safety-efficiency trade-off, and a convergence towards low hydraulic safety margins. Our unifying theory opens new avenues for reliably modelling the interactive effects of drying soil and air and rising atmospheric CO2 on global photosynthesis and transpiration.

  • Journal article
    Prentice IC, Cai W, 2020,

    Recent trends in gross primary production and their drivers: analysis and modelling at flux-site and global scales

    , Environmental Research Letters, Vol: 15, ISSN: 1748-9326

    Gross primary production (GPP) by terrestrial ecosystems is the largest flux in the global carbon cycle, and its continuing increase in response to environmental changes is key to land ecosystems' capacity to offset anthropogenic CO2 emissions. However, the CO2- and climate-sensitivities of GPP vary among models. We applied the 'P model'—a parameter-sparse and extensively tested light use efficiency (LUE) model, driven by CO2, climate and remotely sensed greenness data—at 29 sites with multi-year eddy-covariance flux measurements. Observed (both positive and negative) GPP trends at these sites were predicted, albeit with some bias. Increasing LUE (due to rising atmospheric CO2 concentration) and green vegetation cover were the primary controls of modelled GPP trends across sites. Global GPP simulated by the same model increased by 0.46 ± 0.09 Pg C yr–2 during 1982–2016. This increase falls in the mid-range rate of simulated increase by the TRENDY v8 ensemble of state-of-the-art ecosystem models. The modelled LUE increase during 1900–2013 was 15%, similar to a published estimate based on deuterium isotopomers. Rising CO2 was the largest contributor to the modelled GPP increase. Greening, which may in part be caused by rising CO2, ranked second but dominated the modelled GPP change over large areas, including semi-arid vegetation on all continents. Warming caused a small net reduction in modelled global GPP, but dominated the modelled GPP increase in high northern latitudes. These findings strengthen the evidence that rising LUE due to rising CO2 level and increased green vegetation cover (fAPAR) are the main causes of increasing GPP, and thereby, the terrestrial carbon sink.

  • Journal article
    Sanchez-Ortiz K, Taylor KJM, De Palma A, Essl F, Dawson W, Kreft H, Pergl J, Pysek P, van Kleunen M, Weigelt P, Purvis Aet al., 2020,

    Effects of land-use change and related pressures on alien and native subsets of island communities

    , PLOS ONE, Vol: 15, ISSN: 1932-6203
  • Software
    Pearse WD, 2020,

    ropensci/SymbiotaR2: SymbiotaR2 Initial Release

    Symbiota is an open-source content management system designed to integrate virtual biodiversity databases. This R package, SymbiotaR2, allows users to access and download specimen- and observation-based data from a published portal of Symbiota2--the refactored and improved version of the original Symbiota framework. SymbiotaR2 is released through rOpenSci.

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