ORCID Profile
0000-0002-9638-5827
Current Organisation
University of Tasmania
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Publisher: Springer Science and Business Media LLC
Date: 19-08-2010
Publisher: University of Chicago Press
Date: 02-2021
DOI: 10.1086/712378
Publisher: Springer Science and Business Media LLC
Date: 06-04-2020
Publisher: Oxford University Press (OUP)
Date: 21-04-2019
Abstract: There is growing empirical evidence around the world demonstrating regime shifts of marine ecosystems. But generalizable criteria to detect and define regime shifts are elusive because of: (i) an incomplete scientific understanding of processes underlying regime shifts (ii) because the baseline state and conditions are ill defined, and (iii) due to an inherent ambiguity in the concept of system identity. We surveyed marine scientists in Tasmania, Australia, and determined the effect of changing conditions (including type of climate impact, species loss, species composition, spatio-temporal extent, and human intervention) on their perception of marine regime shift. We find, there is an objective difficulty in detecting regime shifts that goes beyond scientific uncertainty and there is disagreement on which configurations of change indeed constitute a regime shift. Furthermore, this difference of opinion was not related to the degree of confidence that scientists indicated when identifying regime shifts. This lack of consensus and seemingly unrelated scientific confidence, may be attributable to value ambiguity around people s attitudes, cognitive biases, and baseline shift. When applying evidenced-based reference points in well-reasoned Ecosystem Based Management, there should be scientific consensus on the manifestation and extent of specific regime shifts, and recognition of value ambiguities influencing scientific perceptions.
Publisher: Public Library of Science (PLoS)
Date: 24-05-2019
Publisher: Wiley
Date: 22-07-2001
Publisher: Wiley
Date: 03-2016
DOI: 10.3732/AJB.1500269
Abstract: Pollen on a stigma represents a local population of male gametophytes vying for access to female gametophytes in the associated ovary. As in most populations, density-independent and density-dependent survival depend on intrinsic characteristics of male gametophytes and environmental (pistil) conditions. These characteristics and conditions could differ among flowers, plants, populations, and species, creating erse male-gametophyte population dynamics, which can influence seed siring and production. For nine species, we characterized the relations of both the mean and standard deviation of pollen-tube number at the style base to pollen receipt with nonlinear regression. Models represented asymptotic or peaked relations, providing information about the incidence and magnitude of facilitation and competition, the spatial and temporal characteristics of competition, and the intensity and relative timing of density-independent mortality. We infer that pollen tubes of most species competed sequentially, their tips ceasing growth if earlier tubes had depleted stylar space/resources although two species experienced simultaneous competition. Tube success of three species revealed positive density dependence (facilitation) at low density. For at least four species, density-independent mortality preceded competition. Tube success varied mostly within plants, rather than among plants or conspecific populations. Pollen quality influenced tube success for two of three species affecting density-independent survival in one and density-dependent performance in the other. The erse relations of pollen-tube success to pollen receipt evident among just nine species indicate significant contributions of the processes governing pollen germination and tube growth to the reproductive ersity of angiosperms.
Publisher: Wiley
Date: 21-03-2023
Abstract: Interactions among neighbouring plants are key determinants of plant growth. To characterise the cumulative effect of all neighbours on the growth of a focal plant, neighbourhoods are often described by ‘competition’ indices. Common competition indices calculate the summed size of neighbour plants (focal‐independent index [FII]) whilst others include the summed ratio of the neighbour size relative to focal plant size (focal dependent). A frequently overlooked statistical artefact is that focal‐dependent indices (FDIs) may lead to biased estimates of neighbourhood effects on plant growth when growth is size dependent. Here, we conduct a literature search to determine the most common index types used to explain neighbour effects on tree growth. We then assess the ability of two common index types—focal dependent and focal independent—to correctly infer neighbourhood effects in (1) observations of tree growth in an experimental forest in south‐east Tasmania, Australia, and (2) an artificially created dataset where tree growth is unrelated to the neighbourhood. Both indices detected the competitive neighbourhood effect on tree growth observed in our own dataset but differed in their conclusion regarding neighbour effects in the simulated data. Despite the simulated dataset being generated so there was no relationship between tree growth and their neighbourhood, the FDI detected strong, competitive neighbourhood effects when intrinsic growth was incorrectly related to tree size. In contrast, when we considered the FII as the neighbourhood metric, we correctly did not detect any neighbourhood effects in the simulated data regardless of how size‐dependent growth was described. Synthesis . ‘Competition’ indices are a useful method to characterise the cumulative neighbourhood effect on plant growth however, we demonstrate that indices which include the size of the focal plant in their calculation can be biased by an inherent relationship between tree growth and initial size. Whilst this bias typically overstates the strength of competition in determining focal tree growth, we show that it can be mitigated by correctly describing intrinsic growth. We discuss the limitations of both index types, provide recommendations for performing statistical modelling and outline how to check for accurate neighbour inference.
Publisher: Wiley
Date: 06-2007
DOI: 10.1890/06-0660
Abstract: To study forest dynamics without relying on the space-for-time substitution, one must be able to follow a population or stand of trees back or forward in time. The method of stand reconstruction looks back in time by aging all the live trees and aging and dating the time of death of dead standing and fallen trees. However, dead trees are lost by decomposition so the record becomes increasingly incomplete with passage of time. Here we present a model of the passage of trees from dead standing to dead decomposed but still datable to completely decomposed and thus undatable or lost. We then generalize a method for calculating the falling rate of dead trees originally proposed in 1985 by A. P. Gore, E. A. Johnson, and H. P. Lo. We do this by removing the assumption that no trees are lost by decomposition, i.e., by using the decomposition rate. Finally, in the most important result, the model allows estimation of how far back a good estimate of the numbers in the population can be made if the decomposition rates are known.
Publisher: Inter-Research Science Center
Date: 1995
DOI: 10.3354/MEPS122059
Publisher: Wiley
Date: 09-2023
DOI: 10.1002/ECE3.10465
Publisher: Wiley
Date: 17-05-2011
DOI: 10.1111/J.1469-8137.2011.03759.X
Abstract: The Arabidopsis protein SENSITIVE TO FREEZING-6 (AtSFR6) is required for cold- and drought-inducible expression of COLD-ON REGULATED (COR) genes and, as a consequence, AtSFR6 is essential for osmotic stress and freezing tolerance in Arabidopsis. Therefore, orthologues of AtSFR6 in crop species represent important candidate targets for future manipulation of stress tolerance. We identified and cloned a homologue of AtSFR6 from rice (Oryza sativa), OsSFR6, and confirmed its orthology in Arabidopsis. OsSFR6 was identified by homology searches, and a full-length coding region isolated using reverse transcription polymerase chain reaction (RT-PCR) from Oryza sativa cDNA. To test for orthology, OsSFR6 was expressed in an Arabidopsis sfr6 loss-of-function mutant background, and restoration of wild-type phenotypes was assessed. Searching the rice genome revealed a single homologue of AtSFR6. Cloning and sequencing the OsSFR6 coding region showed OsSFR6 to have 61.7% identity and 71.1% similarity to AtSFR6 at the predicted protein sequence level. Expression of OsSFR6 in the atsfr6 mutant background restored the wild-type visible phenotype, as well as restoring wild-type levels of COR gene expression and tolerance of osmotic and freezing stresses. OsSFR6 is an orthologue of AtSFR6, and thus a target for future manipulation to improve tolerance to osmotic and other abiotic stresses.
Publisher: The Company of Biologists
Date: 2013
DOI: 10.1242/JCS.133272
Abstract: Nuclear pore complexes (NPCs) mediate nucleocytoplasmic movement. The central channel contains proteins with phenylalanine-glycine (FG) repeats, or variations (GLFG, glycine-leucine-FG). These are “intrinsically disordered” which often represent weak interaction sites that become ordered upon interaction. We investigated this possibility during nuclear transport. Using electron microscopy of S. cerevisiae we show that NPC cytoplasmic filaments form a dome-shaped structure enclosing GLFG domains. GLFG domains extend out of this structure and are part of an “exclusion zone” that may act as a partial barrier to entry of transport inert proteins. The anchor domain of a GLFG nucleoporin locates exclusively to the central channel. Conversely GLFG domains varied between NPCs and could be cytoplasmic, central or nucleoplasmic and could stretch up to 80 nm. These results suggest a dynamic exchange between ordered and disordered states. In contrast to diffusion through the NPC, transport cargoes passed through the exclusion zone and accumulated near the central plane. We also show that movement of cargo through the NPC is accompanied by relocation of GLFG domains, suggesting that binding, restructuring and movement of these domains could constitute part of the translocation mechanism.
Publisher: Springer Science and Business Media LLC
Date: 19-08-2016
Publisher: Wiley
Date: 14-12-2022
DOI: 10.1111/NPH.17888
Abstract: Vulnerability to xylem cavitation is a strong predictor of drought‐induced damage in forest communities. However, biotic features of the community itself can influence water availability at the in idual tree‐level, thereby modifying patterns of drought damage. Using an experimental forest in Tasmania, Australia, we determined the vulnerability to cavitation (leaf P 50 ) of four tree species and assessed the drought‐induced canopy damage of 2944 6‐yr‐old trees after an extreme natural drought episode. We examined how in idual damage was related to their size and the density and species identity of neighbouring trees. The two co‐occurring dominant tree species, Eucalyptus delegatensis and Eucalyptus regnans , were the most vulnerable to drought‐induced xylem cavitation and both species suffered significantly greater damage than neighbouring, subdominant species Pomaderris apetala and Acacia dealbata . While the two eucalypts had similar leaf P 50 values, E. delegatensis suffered significantly greater damage, which was strongly related to the density of neighbouring P. apetala . Damage in E. regnans was less impacted by neighbouring plants and smaller trees of both eucalypts sustained significantly more damage than larger trees. Our findings demonstrate that natural drought damage is influenced by in idual plant physiology as well as the composition, physiology and density of the surrounding stand.
Publisher: The Royal Society
Date: 04-2015
DOI: 10.1098/RSOB.150011
Abstract: Elevated cataract risk after radiation exposure was established soon after the discovery of X-rays in 1895. Today, increased cataract incidence among medical imaging practitioners and after nuclear incidents has highlighted how little is still understood about the biological responses of the lens to low-dose ionizing radiation (IR). Here, we show for the first time that in mice, lens epithelial cells (LECs) in the peripheral region repair DNA double strand breaks (DSB) after exposure to 20 and 100 mGy more slowly compared with circulating blood lymphocytes, as demonstrated by counts of γH2AX foci in cell nuclei. LECs in the central region repaired DSBs faster than either LECs in the lens periphery or lymphocytes. Although DSB markers (γH2AX, 53BP1 and RAD51) in both lens regions showed linear dose responses at the 1 h timepoint, nonlinear responses were observed in lenses for EdU (5-ethynyl-2′-deoxy-uridine) incorporation, cyclin D1 staining and cell density after 24 h at 100 and 250 mGy. After 10 months, the lens aspect ratio was also altered, an indicator of the consequences of the altered cell proliferation and cell density changes. A best-fit model demonstrated a dose-response peak at 500 mGy. These data identify specific nonlinear biological responses to low (less than 1000 mGy) dose IR-induced DNA damage in the lens epithelium.
Publisher: Wiley
Date: 26-10-2023
Publisher: Wiley
Date: 30-09-2022
Abstract: There are multiple demands for the development of effective and sustainable disease management practices in wildlife, but solutions are widely lacking. In this perspective, we focus on the need to structure research to support advancement toward enhanced wildlife disease control solutions. We concentrate on the need for improved integration between wildlife disease management undertaken in situ with modelling to guide and assess disease management actions. We recognise that many disease management attempts in wildlife are made in isolation, are not supported by modelling and are not used as a stepping stone to advancement. However, we emphasise that the development of disease control practices in wildlife is greater than any one management attempt, and should be seen and undertaken as a set of systematic steps towards well‐articulated management goals. We describe modelling of disease management and in situ disease management as two complementary phases of investigation, viewed as a feedback loop to support advancements, and highlight established and less established pathways in this loop. We describe how stakeholders engaged in practical management actions can better engage with modellers, and also the need for more fit‐for‐purpose modelling that captures the on‐ground realities of in situ practice to support advancements. The concepts and approaches described in this perspective are captured within a Model Integrated Disease Management for wildlife framework. We illustrate the framework, concepts and challenges proposed in this perspective using a case study for which we have experience: sarcoptic mange (etiologic agent Sarcoptes scabiei ) in bare‐nosed wombats ( Vombatus ursinus ). Synthesis and applications : Effective and sustainable solutions to critical wildlife diseases are needed. Progress can be improved when disease management is guided through iterative and fit‐for‐purpose integration between modelling and in situ practice. We describe and illustrate a Model Integrated Disease Management for wildlife framework. Moving beyond isolated disease management attempts into a structured process of advancement can help overcome barriers to tackling pathogens threatening wildlife.
Publisher: Wiley
Date: 10-03-2002
Publisher: Oxford University Press (OUP)
Date: 05-2002
Publisher: Elsevier BV
Date: 06-2001
Publisher: Oxford University Press (OUP)
Date: 2014
Publisher: Public Library of Science (PLoS)
Date: 25-10-2010
Publisher: Springer Science and Business Media LLC
Date: 05-03-2010
Publisher: University of Chicago Press
Date: 10-2018
DOI: 10.1086/698655
Abstract: Trade-offs in energy allocation between growth, reproduction, and survival are at the core of life-history theory. While age-specific mortality is considered to be the main determinant of the optimal allocation, some life-history strategies, such as delayed or skipped reproduction, may be better understood when also accounting for reproduction costs. Here, we present a two-pool indeterminate grower model that includes survival and energetic costs of reproduction. The energetic cost sets a minimum reserve required for reproduction, while the survival cost reflects increased mortality from low postreproductive body condition. Three life-history parameters determining age-dependent energy allocation to soma, reserve, and reproduction are optimized, and we show that the optimal strategies can reproduce realistic emergent growth trajectories, maturation ages, and reproductive outputs for fish. The model predicts maturation phase shifts along the gradient of condition-related mortality and shows that increased harvesting will select for earlier maturation and higher energy allocation to reproduction. However, since the energetic reproduction cost sets limits on how early an in idual can mature, an increase in fitness at high harvesting can only be achieved by erting most reserves into reproduction. The model presented here can improve predictions of life-history responses to environmental change and human impacts because key life-history traits such as maturation age and size, maximum body size, and size-specific fecundity emerge dynamically.
Publisher: Oxford University Press (OUP)
Date: 21-05-2016
Publisher: University of Chicago Press
Date: 12-2012
DOI: 10.1086/668082
Abstract: Age-dependent reproductive timing has been observed in females of a number of species older females often breed earlier in the season and experience higher reproductive success as a result. However, to date, evidence for within-season variation in reproductive effort (RE) for males has been relatively weak. Males are expected to time RE in light of intraseasonal variations in the availability of receptive females and competition with other males. Young males, which are typically smaller and less experienced, might benefit from breeding later in the season, when male-male competition is less intense. Using a long-term data set of Alpine chamois Rupicapra rupicapra, we sought to evaluate the hypothesis that younger males allocate highest RE late in the breeding season, at a time when older male RE has decreased substantially. Our results support this hypothesis, which suggests that intraseasonal variation in RE may be an adaptive life-history trait for males as well as females.
Publisher: Oxford University Press (OUP)
Date: 1996
Publisher: Wiley
Date: 24-11-2023
Abstract: Interventions against infectious diseases in wildlife are increasingly necessary but remain problematic. Dissimilar to public and domestic animal health, pharmacological interventions (PIs) are rarely used against disease in wildlife populations. However, drugs can combat a range of pathogen types while aligning with positive ethical, epidemiological, evolutionary and socio‐economic outcomes. We discuss how recent conceptual and technological advances could overcome barriers, improve safety and begin a new era of contemporary wildlife management that embraces PIs. We then provide a framework that supports an objective comparison of intervention suitability, including PIs. We find numerous directions for PI optimisation through innovation and transdisciplinary collaboration and demonstrate the utility of the framework for judging the appropriateness of a PI. Synthesis and applications : Interrogating how and when pharmacological interventions can be used to the greatest effect reduces risks and improves outcomes for wildlife, while empowering decision makers to draw from the full suite of intervention methods to find the most appropriate disease management solutions.
Publisher: Public Library of Science (PLoS)
Date: 10-09-2013
Publisher: The Royal Society
Date: 10-2014
Abstract: Understanding the relationship between disease transmission and host density is essential for predicting disease spread and control. Using long-term data on sarcoptic mange in a red fox Vulpes vulpes population, we tested long-held assumptions of density- and frequency-dependent direct disease transmission. We also assessed the role of indirect transmission. Contrary to assumptions typical of epidemiological models, mange dynamics are better explained by frequency-dependent disease transmission than by density-dependent transmission in this canid. We found no support for indirect transmission. We present the first estimates of R 0 and age-specific transmission coefficients for mange in foxes. These parameters are important for managing this poorly understood but highly contagious and economically damaging disease.
Publisher: Wiley
Date: 17-10-2007
DOI: 10.1111/J.1558-5646.2007.00272.X
Abstract: Hermaphroditism allows considerable scope for contributing genes to subsequent generations through various mixtures of selfed and outcrossed offspring. The fitness consequences of different family compositions determine the evolutionarily stable mating strategy and depend on the interplay of genetic features, the nature of mating, and factors that govern offspring development. This theoretical article considers the relative contributions of these influences and their interacting effects on mating-system evolution, given a fixed genetic load within a population. Strong inbreeding depression after offspring gain independence selects for exclusive outcrossing, regardless of the intensity of predispersal inbreeding depression, unless insufficient mating limits offspring production. The extent to which selfing evolves under weak postdispersal inbreeding depression depends on predispersal inbreeding depression and the opportunity for resource limitation of offspring production. Mixed selfing and outcrossing is an evolutionarily stable strategy (ESS) if selfed zygotes survive poorly, but selfed offspring survive well, and maternal in iduals produce enough "extra" eggs that deaths of unviable outcrossed embryos do not impact offspring production (reproductive compensation). Mixed mating can also be an ESS, despite weak lifetime inbreeding depression, if self-mating reduces the number of male gametes available for outcrossing (male-gamete discounting). Reproductive compensation and male-gamete discounting act largely independently on mating-system evolution. ESS mating systems always involve either complete fertilization or fertilization of enough eggs to induce resource competition among embryos, so although reproductive assurance is adaptive with insufficient mating, it is never an ESS. Our results illustrate the theoretical importance of different constraints on offspring production (availability of male gametes, egg production, and maternal resources) for both the course and outcome of mating-system evolution, whereas unequal competition between selfed and outcrossed embryos has limited effect. These results also underscore the significance of heterogeneity in the nature and intensity of inbreeding depression during the life cycle for the evolution of hermaphrodite mating systems.
Publisher: Wiley
Date: 11-03-2016
DOI: 10.1111/ELE.12596
Abstract: The fate of male gametophytes after pollen reaches stigmas links pollination to ovule fertilisation, governing subsequent siring success and seed production. Although male gametophyte performance primarily involves cellular processes, an ecological analogy may expose insights into the nature and implications of male gametophyte success. We elaborate this analogy theoretically and present empirical ex les that illustrate associated insights. Specifically, we consider pollen loads on stigmas as localised populations subject to density-independent mortality and density-dependent processes as they traverse complex stylar environments. Different combinations of the timing of pollen-tube access to limiting stylar resources (simultaneous or sequential), the tube distribution among resources (repulsed or random) and the timing of density-independent mortality relative to competition (before or after) create signature relations of mean pollen-tube success and its variation among pistils to pollen receipt. Using novel nonlinear regression analyses (two-moment regression), we illustrate contrasting relations for two species, demonstrating that variety in these relations is a feature of reproductive ersity among angiosperms, rather than merely a theoretical curiosity. Thus, the details of male gametophyte ecology should shape sporophyte reproductive success and hence the dynamics and structure of angiosperm populations.
Publisher: Laser Pages Publishing Ltd.
Date: 02-2004
Publisher: Wiley
Date: 11-2003
DOI: 10.1890/02-0020
Publisher: Wiley
Date: 05-2000
Publisher: American Physical Society (APS)
Date: 29-03-2001
Publisher: The Royal Society
Date: 10-2023
Publisher: University of Chicago Press
Date: 2000
DOI: 10.1086/303297
Abstract: A general consumer-resource model assuming discrete consumers and a continuously structured resource is examined. We study two foraging behaviors, which lead to fixed and flexible patch residence times, in conjunction with a simple consumer energetics model linking resource consumption, foraging behavior, and metabolic costs. Results indicate a single, evolutionarily stable foraging strategy for fixed and flexible foraging in a nonspatial environment, but flexible foraging in a spatial environment leads to consumer grouping, which affects the resource distribution such that no single foraging strategy can exclude all other strategies. This evolutionarily stable coexistence of multiple foraging strategies may help explain a dichotomous pattern observed in a wide variety of natural systems.
Publisher: Wiley
Date: 02-10-2012
Publisher: Public Library of Science (PLoS)
Date: 16-11-2012
Publisher: Springer Science and Business Media LLC
Date: 06-01-2021
DOI: 10.1186/S13071-020-04500-9
Abstract: Sarcoptic mange causes significant animal welfare and occasional conservation concerns for bare-nosed wombats ( Vombatus ursinus ) throughout their range. To date, in situ chemotherapeutic interventions have involved macrocytic lactones, but their short duration of action and need for frequent re-administration has limited treatment success. Fluralaner (Bravecto® MSD Animal Health), a novel isoxazoline class ectoparasiticide, has several advantageous properties that may overcome such limitations. Fluralaner was administered topically at 25 mg/kg ( n = 5) and 85 mg/kg ( n = 2) to healthy captive bare-nosed wombats. Safety was assessed over 12 weeks by clinical observation and monitoring of haematological and biochemical parameters. Fluralaner plasma pharmacokinetics were quantified using ultra-performance liquid chromatography and tandem mass spectrometry. Efficacy was evaluated through clinical assessment of response to treatment, including mange and body condition scoring, for 15 weeks after topical administration of 25 mg/kg fluralaner to sarcoptic mange-affected wild bare-nosed wombats ( n = 3). Duration of action was determined through analysis of pharmacokinetic parameters and visual inspection of study subjects for ticks during the monitoring period. Methods for diluting fluralaner to enable ‘pour-on’ application were compared, and an economic and treatment effort analysis of fluralaner relative to moxidectin was undertaken. No deleterious health impacts were detected following fluralaner administration. Fluralaner was absorbed and remained quantifiable in plasma throughout the monitoring period. For the 25 mg/kg and 85 mg/kg treatment groups, the respective means for maximum recorded plasma concentrations (C max ) were 6.2 and 16.4 ng/ml for maximum recorded times to C max , 3.0 and 37.5 days and for plasma elimination half-lives, 40.1 and 166.5 days. Clinical resolution of sarcoptic mange was observed in all study animals within 3–4 weeks of treatment, and all wombats remained tick-free for 15 weeks. A suitable product for diluting fluralaner into a ‘pour-on’ was found. Treatment costs were competitive, and predicted treatment effort was substantially lower relative to moxidectin. Fluralaner appears to be a safe and efficacious treatment for sarcoptic mange in the bare-nosed wombat, with a single dose lasting over 1–3 months. It has economic and treatment-effort-related advantages over moxidectin, the most commonly used alternative. We recommend a dose of 25 mg/kg fluralaner and, based on the conservative assumption that at least 50% of a dose makes dermal contact, Bravecto Spot-On for Large Dogs as the most appropriate formulation for adult bare-nosed wombats.
Publisher: Wiley
Date: 18-10-2007
Publisher: Elsevier BV
Date: 12-2021
DOI: 10.1016/J.EXER.2021.108808
Abstract: Human lens regeneration and the Bag-in-the-Lens (BIL) surgical treatment for cataract both depend upon lens capsule closure for their success. Our studies suggest that the first three days after surgery are critical to their long-term outcomes. Using a rat model of lens regeneration, we evidenced lens epithelial cell (LEC) proliferation increased some 50 fold in the first day before rapidly declining to rates observed in the germinative zone of the contra-lateral, un-operated lens. Cell multi-layering at the lens equator occurred on days 1 and 2, but then reorganised into two discrete layers by day 3. E- and N-cadherin expression preceded cell polarity being re-established during the first week. Aquaporin 0 (AQP0) was first detected in the elongated cells at the lens equator at day 7. Cells at the capsulotomy site, however, behaved very differently expressing the epithelial mesenchymal transition (EMT) markers fibronectin and alpha-smooth muscle actin (SMA) from day 3 onwards. The physical interaction between the apical surfaces of the anterior and posterior LECs from day 3 after surgery preceded cell elongation. In the human BIL s le fibre cell formation was confirmed by both histological and proteome analyses, but the cellular response is less ordered and variable culminating in Soemmerring's ring (SR) formation and sometimes Elschnig's pearls. This we evidence for lenses from a single patient. No bow region or recognisable epithelial-fibre cell interface (EFI) was evident and consequently the fibre cells were disorganised. We conclude that lens cells require spatial and cellular cues to initiate, sustain and produce an optically functional tissue in addition to capsule integrity and the EFI.
Publisher: Wiley
Date: 03-01-2023
DOI: 10.1002/ECM.1557
Abstract: Specifying, assessing, and selecting among candidate statistical models is fundamental to ecological research. Commonly used approaches to model selection are based on predictive scores and include information criteria such as Akaike's information criterion, and cross validation. Based on data splitting, cross validation is particularly versatile because it can be used even when it is not possible to derive a likelihood (e.g., many forms of machine learning) or count parameters precisely (e.g., mixed‐effects models). However, much of the literature on cross validation is technical and spread across statistical journals, making it difficult for ecological analysts to assess and choose among the wide range of options. Here we provide a comprehensive, accessible review that explains important—but often overlooked—technical aspects of cross validation for model selection, such as: bias correction, estimation uncertainty, choice of scores, and selection rules to mitigate overfitting. We synthesize the relevant statistical advances to make recommendations for the choice of cross‐validation technique and we present two ecological case studies to illustrate their application. In most instances, we recommend using exact or approximate leave‐one‐out cross validation to minimize bias, or otherwise k ‐fold with bias correction if k 10. To mitigate overfitting when using cross validation, we recommend calibrated selection via our recently introduced modified one‐standard‐error rule. We advocate for the use of predictive scores in model selection across a range of typical modeling goals, such as exploration, hypothesis testing, and prediction, provided that models are specified in accordance with the stated goal. We also emphasize, as others have done, that inference on parameter estimates is biased if preceded by model selection and instead requires a carefully specified single model or further technical adjustments.
Publisher: Resilience Alliance, Inc.
Date: 2018
Publisher: Wiley
Date: 23-07-2019
Abstract: Long‐term pathogen control or eradication in wildlife is rare and represents a major challenge in conservation. Control is particularly difficult for environmentally transmitted pathogens, including some of the most conservation‐critical wildlife diseases. We undertook a treatment programme aimed at population‐scale eradication of the environmentally transmitted Sarcoptes scabiei mite (causative agent of sarcoptic mange) during an epizootic in bare‐nosed wombats ( Vombatus ursinus ). Field trial results were used to parameterize a mechanistic host‐disease model that explicitly described indirect transmission, host behaviour and viable disease intervention methods. Model analysis shows that elimination of S. scabiei in the wild is most sensitive to the success of treatment delivery, and duration of the programme. In addition, we found the frequency that wombats switch burrows was an important positive driver of mite persistence. Synthesis and applications . This research emphasizes the utility of applying model‐guided management techniques in order to achieve practical solutions for controlling disease in the field. We find that control efforts of Sarcoptes scabiei are most successful when simultaneous improvements are made to the current best‐practice protocol, specifically the implementation of better treatment application methods in combination with a longer lasting treatment. These suggested management changes may also reduce the resources and field effort required to implement a successful regime. Furthermore, our approach and findings have applicability to other species affected by S. scabiei (e.g. wolves, red foxes, Spanish ibex and American black bear), as well as other conservation‐critical systems involving environmental transmission (e.g. bat white‐nose syndrome and hibian chytridiomycosis).
Publisher: The Royal Society
Date: 07-12-1999
Publisher: Wiley
Date: 28-09-2020
Publisher: Public Library of Science (PLoS)
Date: 28-02-2013
Publisher: Worldwide Protein Data Bank
Date: 22-07-2015
DOI: 10.2210/PDB4R8H/PDB
Publisher: Wiley
Date: 10-2005
DOI: 10.1890/05-0074
Publisher: Wiley
Date: 10-10-2016
Publisher: University of Chicago Press
Date: 09-2009
DOI: 10.1086/603626
Abstract: Pollen dispersal by animals varies extensively because of differences in pollinator visitation rates among plants, dissimilar pollination by the various pollinators that visit in idual plants, and stochastic variation in deposition as an in idual pollinator disperses a plant's pollen to subsequently visited recipient flowers. Such variation reduces expected female and male success if seed production decelerates with increasing pollen receipt, because less than average receipt diminishes mean seed production more than copious pollination increases it (Jensen's inequality). We report empirical studies of the nature and magnitude of pollen dispersal variance, which provide the basis for a numerical model of the consequences of dispersal for expected seed production. Model fitting revealed that dispersal of Brassica napus pollen by bumblebees and especially butterflies exhibited much more variation than is expected of a binomial process and was best modeled as a beta-binomial process with a constant mean. Overdispersion arose primarily during pollen dispersal by in idual insects, since differences between in iduals of the same pollinator type were limited. Our model revealed variance limitation as a previously unrecognized, substantial, and ubiquitous component of pollen limitation of seed production. Variance limitation should select for floral traits that increase pollinator visitation, reduce dispersal variance, or reduce the postpollination nonlinearities that cause Jensen's inequality.
Publisher: The Company of Biologists
Date: 15-08-2010
DOI: 10.1242/JCS.070730
Abstract: Transport across the nuclear envelope is regulated by nuclear pore complexes (NPCs). Much is understood about the factors that shuttle and control the movement of cargos through the NPC, but less has been resolved about the translocation process itself. Various models predict how cargos move through the channel however, direct observation of the process is missing. Therefore, we have developed methods to accurately determine cargo positions within the NPC. Cargos were instantly trapped in transit by high-pressure freezing, optimally preserved by low-temperature fixation and then localized by immunoelectron microscopy. A statistical modelling approach was used to identify cargo distribution. We found import cargos localized surprisingly close to the edge of the channel, whereas mRNA export factors were at the very centre of the NPC. On the other hand, diffusion of GFP was randomly distributed. Thus, we suggest that spatially distinguished pathways exist within the NPC. Deletion of specific FG domains of particular NPC proteins resulted in collapse of the peripheral localization and transport defects specific to a certain karyopherin pathway. This further confirms that constraints on the route of travel are biochemical rather than structural and that the peripheral route of travel is essential for facilitated import.
Publisher: Wiley
Date: 08-12-2013
Publisher: University of Chicago Press
Date: 10-2022
DOI: 10.1086/722027
Publisher: Elsevier BV
Date: 02-2016
Publisher: Elsevier BV
Date: 06-2000
Publisher: Oxford University PressOxford
Date: 29-01-2015
DOI: 10.1093/ACPROF:OSO/9780199672547.003.0004
Abstract: Ecologists study systems in which the biological patterns of interest are usually the result of complex webs of interactions. In such cases, many hypotheses may be proposed that might account for the patterns observed, and the problem is to determine which hypotheses are indeed consistent with the data. This chapter introduces the concept of a likelihood function, which is a way of formalizing a biological hypothesis as a mathematical model and linking it to a s ling design. It then explains how likelihood functions can be used to select among competing models, focusing on the information-theoretic approach to model selection. Ex les are provided that illustrate key concepts, and demonstrate good practice when performing model selection.
Publisher: Cambridge University Press (CUP)
Date: 21-05-2018
DOI: 10.1017/S0030605317001727
Abstract: Non-lethal mitigation of crop use by elephants Loxodonta africana is an increasingly important part of protected area management across Africa and Asia. Recently, beehive fences have been suggested as a potential mitigation strategy. We tested the effectiveness of this method in a farming community adjacent to Udzungwa Mountains National Park in southern Tanzania. Over a 5.5-year period (2010–2016) a beehive fence was introduced and subsequently extended along the Park boundary. The probability that one or more farms experienced crop loss from elephants on a given day was reduced in the presence of the fence and was reduced further as the fence was extended. The number of hives occupied by bees along the fence was the best predictor of elephants’ visits to farms. Farms closest to the fence experienced a greater likelihood of damage, particularly during the initial period when the fence was shorter. The number of farms affected by elephants declined when the fence was extended. There was a higher probability of damage on farms that were closer to the Park boundary and further from a road. Our mixed results suggest that the shape, length and location of fences need to be carefully planned because changes in a farm's long-term susceptibility to elephant damage vary between in idual farms fences need to be long enough to be effective and ensure that decreasing crop loss frequency is not outweighed by an increasing number of farms damaged per visit.
Publisher: Wiley
Date: 11-2006
DOI: 10.1577/M06-035.1
Publisher: Wiley
Date: 16-12-2011
DOI: 10.1111/J.1558-5646.2011.01515.X
Abstract: Inbreeding depression can reduce the performance of offspring produced by mating between relatives, with consequences for population dynamics and sexual-system evolution. In flowering plants, inbreeding depression commonly acts most intensely during seed development. This predispersal component is typically estimated by comparing seed production following exclusive self- and cross-pollination, but such estimates are unbiased only if seed production is limited by ovule availability, rather than by pollen receipt or seed-development resources. To overcome this problem, we propose experimental and statistical methods based on a model of ovule fertilization and seed development that accounts for differential fertilization by self- and cross-pollen, limited ovule viability or receptivity, differential survival of self- and cross-zygotes and limited resource availability. Simulations illustrate that the proposed methods eliminate bias in estimated predispersal inbreeding depression caused by pollen limitation and can improve estimates under resource limitation. Application of these methods to two orchid species further demonstrates their utility in identifying and estimating erse influences on reproductive performance under typical conditions. Although our theoretical results raise questions about the reported intensity of predispersal inbreeding depression, our proposed methods guard against bias while also providing insight into plant reproduction.
Publisher: Wiley
Date: 29-11-2019
DOI: 10.1002/ECY.2906
Publisher: University of Chicago Press
Date: 02-2000
DOI: 10.1086/303316
Abstract: A mathematical model is presented that describes a system where two consumer species compete exploitatively for a single renewable resource. The resource is distributed in a patchy but homogeneous environment that is, all patches are intrinsically identical. The two consumer species are referred to as diggers and grazers, where diggers deplete the resource within a patch to lower densities than grazers. We show that the two distinct feeding strategies can produce a heterogeneous resource distribution that enables their coexistence. Coexistence requires that grazers must either move faster than diggers between patches or convert the resources to population growth much more efficiently than diggers. The model shows that the functional form of resource renewal within a patch is also important for coexistence. These results contrast with theory that considers exploitation competition for a single resource when the resource is assumed to be well mixed throughout the system.
Publisher: Wiley
Date: 09-11-2020
DOI: 10.1002/ECE3.6954
Publisher: Wiley
Date: 09-2021
DOI: 10.1002/ECY.3475
Abstract: Information‐theoretic approaches to model selection, such as Akaike's information criterion (AIC) and cross validation, provide a rigorous framework to select among candidate hypotheses in ecology, yet the persistent concern of overfitting undermines the interpretation of inferred processes. A common misconception is that overfitting is due to the choice of criterion or model score, despite research demonstrating that selection uncertainty associated with score estimation is the predominant influence. Here we introduce a novel selection rule that identifies a parsimonious model by directly accounting for estimation uncertainty, while still retaining an information‐theoretic interpretation. The new rule, which is a modification of the existing one‐standard‐error rule, mitigates overfitting and reduces the likelihood that spurious effects will be included in the selected model, thereby improving its inferential properties. We present the rule and illustrative ex les in the context of maximum‐likelihood estimation and Kullback‐Leibler discrepancy, although the rule is applicable in a more general setting, including Bayesian model selection and other types of discrepancy.
Publisher: Public Library of Science (PLoS)
Date: 18-11-2011
Publisher: Oxford University Press (OUP)
Date: 08-2011
DOI: 10.1093/HMG/DDR327
Abstract: Fibroblasts from patients with the severe laminopathy diseases, restrictive dermopathy (RD) and Hutchinson Gilford progeria syndrome (HGPS), are characterized by poor growth in culture, the presence of abnormally shaped nuclei and the accumulation of DNA double-strand breaks (DSB). Here we show that the accumulation of DSB and poor growth of the fibroblasts but not the presence of abnormally shaped nuclei are caused by elevated levels of reactive oxygen species (ROS) and greater sensitivity to oxidative stress. Basal levels of ROS and sensitivity to H(2)O(2) were compared in fibroblasts from normal, RD and HGPS in iduals using fluorescence activated cell sorting-based assays. Basal levels of ROS and stimulated levels of ROS were both 5-fold higher in the progeria fibroblasts. Elevated levels of ROS were correlated with lower proliferation indices but not with the presence of abnormally shaped nuclei. DSB induced by etoposide were repaired efficiently in normal, RD and HGPS fibroblasts. In contrast, DSB induced by ROS were repaired efficiently in normal fibroblasts, but in RD and HGPS fibroblasts many ROS-induced DSB were un-repairable. The accumulation of ROS-induced DSB appeared to cause the poor growth of RD and HGPS fibroblasts, since culture in the presence of the ROS scavenger N-acetyl cysteine (NAC) reduced the basal levels of DSB, eliminated un-repairable ROS-induced DSB and greatly improved population-doubling times. Our findings suggest that un-repaired ROS-induced DSB contribute significantly to the RD and HGPS phenotypes and that inclusion of NAC in a combinatorial therapy might prove beneficial to HGPS patients.
Publisher: Oxford University Press (OUP)
Date: 05-07-2016
No related grants have been discovered for Shane Richards.