Statistical inference for serial dilution assay data

Serial dilution assays are widely employed for estimating substance concentrations and minimum inhibitory concentrations. The Poisson-Bernoulli model for such assays is appropriate for count data but not for continuous measurements that are encountered in applications involving substance concentrations. This paper presents practical inference methods based on a log-normal model and illustrates these methods using a case application involving bacterial toxins.     

Trends in single trait dispersion between early-mid successional stages: the importance of species pool extension and habitat scale

Aims Are there trends of increasing/decreasing dispersion of single, categorical traits related to early/late-successional species between stages of community development? If yes, are these trends dependent on species pool extension and habitat scale? Is there a consistent reduction in single trait convergence or divergence in any seral stage when scaling down from ecological to local species pool?Methods Presence of all vascular species rooted within plots of 5 × 5 m was recorded in assemblages of exposed mining spoils (EMS) and heathlands (HTL), which form a chronosequence on two abandoned ore tailing heaps located close to each other in the south-eastern Carpathians (Romania). Fifteen nominal, trait attributes of plant species co-occurring in the two seral assemblages were collected from available databases and subsequently classified as either successionally 'pioneer' or 'mature'. The strength of single trait convergence or divergence was estimated by comparison with null plant assemblages at patch type (meta-community) level by reference to the ecological or local species pool, and at community level.Important findings At patch type level, all pioneer and mature trait attributes (apart from short life span), with significant variation between the two seral stages, increased and, respectively, decreased in dispersion irrespective of species pool extension. However, these trends were more conspicuous when using the ecological species pool, very likely due to relaxation in abiotic filtering and dispersal limitation. At community level, no consistent trends were observed between EMS and HTL assemblages, probably because most trait attributes were sorted by microenvironmental filters displaying high variation, like topography or habitat patch geometry. In both seral stages, there was a general weakening of trait convergence or divergence at patch type level when scaling down from the ecological to the local species pool, which was due to niche space contraction. At community level, there was a trend of rise in dispersion of pioneer attributes along the observed chronosequence, presumably imputable to increasing competition for light and underground water, but an opposite trend of dispersion drop in mature attributes was not so evident. Based on these findings, we proposed two rules of thumb concerning the expected changes in dispersion of trait attributes at patch level along successions and between levels of species pool extension. In conclusion, trends in the successional dynamics of pioneer and mature trait dispersion are clearly detectable at meta-community level, especially by reference to the ecological species pool. Habitat scale and species pool extension are key factors to consider and report when estimating the magnitude of single trait dispersion.     

Immunomic Identification of Malaria Antigens Associated With Protection in Mice

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Highlights

• •Production of sera with different levels of protection against rodent Plasmodium.
• •Generation of immunomic and proteomic data sets enriched in protective antigens.
• •Prediction of the most likely protective antigens using a weighted scoring system.

     

Performance of the marginal structural models under various scenarios of incomplete marker's values: A simulation study

Marginal structural models (MSMs) have been proposed for estimating a treatment's effect, in the presence of time‐dependent confounding. We aimed to evaluate the performance of the Cox MSM in the presence of missing data and to explore methods to adjust for missingness. We simulated data with a continuous time‐dependent confounder and a binary treatment. We explored two classes of missing data: (i) missed visits, which resemble clinical cohort studies; (ii) missing confounder's values, which correspond to interval cohort studies. Missing data were generated under various mechanisms. In the first class, the source of the bias was the extreme treatment weights. Truncation or normalization improved estimation. Therefore, particular attention must be paid to the distribution of weights, and truncation or normalization should be applied if extreme weights are noticed. In the second case, bias was due to the misspecification of the treatment model. Last observation carried forward (LOCF), multiple imputation (MI), and inverse probability of missingness weighting (IPMW) were used to correct for the missingness. We found that alternatives, especially the IPMW method, perform better than the classic LOCF method. Nevertheless, in situations with high marker's variance and rarely recorded measurements none of the examined method adequately corrected the bias.     

Seamounts: centres of endemism or species richness for ophiuroids?

Aim To test the hypotheses that seamounts exhibit high rates of endemism and/or species richness compared to surrounding areas of the continental slope and oceanic ridges. Location The south‐west Pacific Ocean from 19–57° S to 143–171° E. Methods Presence/absence museum data were compiled for seamount and non‐seamount areas at depths between 100 and 1500 m for the Ophiuroidea (brittle‐stars), an abundant and speciose group of benthic invertebrates. Large‐scale biogeographical gradients were examined through multivariate analyses at two spatial scales, at the scale of seamounts (< 1° of latitude/longitude) and regions (5–9°). The robustness of these patterns to spatially inconsistent sampling effort was tested using Monte Carlo‐style simulations. Levels of local endemism and species richness over numbers of samples were compared for seamount and non‐seamount areas using linear regressions. Non‐seamount populations were randomly generated from areas and depth ranges that reflected the typical sampling profile of seamounts. Results Seamount ophiuroid assemblages did not exhibit elevated levels of species richness or narrow‐range endemism compared with non‐seamount areas. Seamounts can exhibit high overall species richness for low numbers of samples, particularly on seamounts supporting a dense coral matrix, but this does not increase with additional sampling at the rates found in non‐seamount areas. There were relatively few identifiable seamount specialists. In general, seamount faunas reflected those found at similar depths in surrounding areas, including the continental slope. Seamount and non‐seamount faunas within the study area exhibited congruent latitudinal and bathymetric species turnover. Main conclusions Seamount faunas were variable for ophiuroid faunal composition, species richness and narrow‐range endemism, reflecting their environmental diversity and complex history. The continental slope was also variable, with some areas being particularly species rich. Broad geomorphological habitat categories such as ‘seamounts’ or ‘continental slope’ may be at the wrong scale to be useful for conservation planning.     

Relationships among recent models for insect population dynamics with variable rates of development

A classification scheme for those population models which allow variation in development rates is proposed, based on two ways of modifying standard age-structured models. The resulting classes of models are termed development index models and sojourn time models. General formulations for the two classes of models are developed from two basic balance equations, and numerous specific models from the literature are shown to fit into the scheme. Concepts from competing risks theory are shown to be important in understanding the interplay between mortality and maturation. Relationships among the classes are investigated both for the most general forms of the models and for the simpler forms often used. The scheme can provide guidance in developing appropriate insect population models for specific modelling situations.Contribution 3878871     

Diurnal water storage in the stems of Picea sitchensis (Bong.) Carr.

Abstract. Two models of the relationship between diurnal variation in shoot water potential and transpiration in 14-year-old Picea sitchensis (Bong.) Carr. were compared. The first model was a physiologically based resistance-capacitance (R-C) analogue with its associated differential equations. The second was a non-physiological discrete-difference (D-D) or stochastic transfer function model. The RC model included only the effect of water storage in the phloem and bark while the D-D model implicity included all storage mechanisms. The R-C and D-D models explained similar fractions (62% and 68% respectively) of the variation in shoot water potential due to diurnal changes in transpiration rate. However, the D-D model had fewer parameters than the R-C model. The results from the D-D model showed that the resistance to flow from soil to shoots along the trunk, (RT), was 5 × 10³ MPa kg^-1s and the capacitance of the phloem and bark treated as a single store, (C_s), was 1.6 kg MPa^-1. It is suggested that the resistance to flow into storage (R_s) is much greater than R_T and can be disregarded. A non-linear version of the D-D model suggested [hat resistance to flow in the trunk increases with increasing transpiration rate.     

Risk-Based Approaches to Managing Contaminants in Catchments

Risk-based methods promise improved decision-making for managing of contaminants, such as salinity, sediments, nutrients, and toxicants, that can adversely affect the ecological condition of aquatic ecosystems. Two aspects of ecological risk assessment (ERA) and management—stakeholder involvement and more quantitative approaches to risk analysis—are particularly challenging. Stakeholder involvement is crucial both in the risk assessment process and the development, acceptance, and implementation of a risk management plan. Additionally, a number of quantitative approaches (particularly Bayesian approaches and multi-criteria decision-making) have been identified as having the potential to include expert-based inputs into risk-based decision-making. These offer promise for better inclusion of stakeholder knowledge and preferences into the decision-making process, and for improving the links between stakeholder inputs and potential risks to the ecological condition of the system. A major challenge for ecologists and natural resource managers is to make the ERA process more quantitative. Most ERAs conducted to date have been qualitative assessments that suffer from a number of deficiencies, the most serious being the lack of transparency and a reliance on subjective judgments. This article argues that the most productive way forward may be to use Bayesian methods to couple existing process-based models, empirical relationships based on good data, and expert opinion, to make the analysis of ecological risks more robust, consistent, and repeatable.     

Resistance to change and vulnerability to stress: autistic‐like features of GAP43‐deficient mice

There is an urgent need for animal models of autism spectrum disorder (ASD) to understand the underlying pathology and facilitate development and testing of new treatments. The synaptic growth‐associated protein‐43 (GAP43) has recently been identified as an autism candidate gene of interest. Our previous studies show many brain abnormalities in mice lacking one allele for GAP43 [GAP43 (+/?)] that are consistent with the disordered connectivity theory of ASD. Thus, we hypothesized that GAP43 (+/?) mice would show at least some autistic‐like behaviors. We found that GAP43 (+/?) mice, relative to wild‐type (+/+) littermates, displayed resistance to change, consistent with one of the diagnostic criteria for ASD. GAP43 (+/?) mice also displayed stress‐induced behavioral withdrawal and anxiety, as seen in many autistic individuals. In addition, both GAP43 (+/?) mice and (+/+) littermates showed low social approach and lack of preference for social novelty, consistent with another diagnostic criterion for ASD. This low sociability is likely because of the mixed C57BL/6J 129S3/SvImJ background. We conclude that GAP43 deficiency leads to the development of a subset of autistic‐like behaviors. As these behaviors occur in a mouse that displays disordered connectivity, we propose that future anatomical and functional studies in this mouse may help uncover underlying mechanisms for these specific behaviors. Strain‐specific low sociability may be advantageous in these studies, creating a more autistic‐like environment for study of the GAP43‐mediated deficits of resistance to change and vulnerability to stress.