Multimodel inference in ecology and evolution: challenges and solutions

Information theoretic approaches and model averaging are increasing in popularity, but this approach can be difficult to apply to the realistic, complex models that typify many ecological and evolutionary analyses. This is especially true for those researchers without a formal background in information theory. Here, we highlight a number of practical obstacles to model averaging complex models. Although not meant to be an exhaustive review, we identify several important issues with tentative solutions where they exist (e.g. dealing with collinearity amongst predictors; how to compute model-averaged parameters) and highlight areas for future research where solutions are not clear (e.g. when to use random intercepts or slopes; which information criteria to use when random factors are involved). We also provide a worked example of a mixed model analysis of inbreeding depression in a wild population. By providing an overview of these issues, we hope that this approach will become more accessible to those investigating any process where multiple variables impact an evolutionary or ecological response.     

On the evolution of homochirality

This work reconsiders recent ideas on the origin of biological homochirality by formally invoking the standard groupoid approach to stereochemistry in a thermodynamic context that generalizes Landau's spontaneous symmetry breaking arguments. On Earth, limited metabolic free energy density may have served as a low temperature-analog to 'freeze' the system in the lowest energy state, i.e., the set of simplest homochiral transitive groupoids representing reproductive chemistries. These engaged in Darwinian competition until a single configuration survived. Subsequent path-dependent evolutionary process locked-in this initial condition. Astrobiological outcomes, in the presence of higher initial metabolic free energy densities, could well be considerably richer, for example, of mixed chirality. One result would be a complicated distribution of biological chirality across a statistically large sample of extraterrestrial stereochemistry, in marked contrast with recent published analyses predicting a racemic average.     

灾难及突发事件住院信息管理系统研究现状及趋势

信息工作是决策的依据和先导,如何准确、及时、高效地收集、整理、分析灾难及突发事件信息、伤病员基本信息、救治信息等,已成为医院管理信息学的研究热点问题,也是医院在灾难和突发事件大量伤员信息管理中面临的难点问题。本文就灾难及突发事件住院信息管理系统研究现状及趋势进行综述。     

Profiling cytogenetic diversity with entropy-based karyotypic analysis

Regardless the high degree of variation observed in solid tumor karyotypes, the use of diversity as a measurable phenomenon remains unexplored. Here we present a systematic cytogenetic analysis using Shannon's entropy as a measure for karyotypic diversity. Karyotypes from 14 epithelial tumor types (n = 1232) have the aneuploidy status scored, resulting in highly asymmetrical sample distribution, for which we determine the index of diversity (Shannon H') of structural and numerical chromosomal aberrations. Since karyotypic diversity is tissue-specific, this approach may give rise to new insights into the processes that may account for aneuploidy progression and solid tumor outcomes.     

Fourier shell correlation threshold criteria

The resolution value claimed for an electron microscopical three-dimensional reconstruction indicates the overall quality of the experiment. The Fourier shell correlation (FSC) criterion has now become the standard quality measure. However, what has continued to be controversial is the issue of the FSC threshold level at which one defines the reproducible resolution. Here, we discuss the theoretical behaviour of the FSC in conjunction with the various factors which influence it: the number of "voxels" in a given Fourier shell, the symmetry of the structure, and the size of the structure within the reconstruction volume. Both the theoretical considerations and our model experiments show that fixed-valued FSC threshold (like "0.5") may never be used in a reproducible criterion. Fixed threshold values are-as we show here-simply the result of incorrect assumptions in the basic statistics. Two families of FSC threshold curves are discussed: the sigma-factor curves and the new family of bit-based information threshold curves. Whereas sigma-factor curves indicate the resolution level at which one has collected information significantly above the noise level, the information curves indicate the resolution level at which enough information has been collected for interpretation.     

Pathway information for systems biology

Pathway information is vital for successful quantitative modeling of biological systems. The almost 170 online pathway databases vary widely in coverage and representation of biological processes, making their use extremely difficult. Future pathway information systems for querying, visualization and analysis must support standard exchange formats to successfully integrate data on a large scale. Such integrated systems will greatly facilitate the constructive cycle of computational model building and experimental verification that lies at the heart of systems biology.     

Low level lead (Pb) exposure during gestation and lactation: assessment of effects on pubertal development in Fisher 344 and Sprague-Dawley female rats

Studies using both Fisher 344 and Sprague-Dawley (SD) rat lines have shown that gestational and/or lactational maternal lead (Pb) exposure causes delayed reproductive maturation in their respective female offspring. Because these studies utilized different experimental regimens for dosing and for monitoring Pb levels, it has not been possible to determine which rat line provides the best model for low level Pb toxicity studies. This study was designed to address this issue. Adult Fisher and SD female rats were dosed with either a solution of PbAc containing 12 mg of Pb/ml or sodium acetate (NaAc) for controls. Dosing began 30 days prior to breeding and continued until their pups were weaned at 21 days of age. At the time of breeding and through weaning the blood lead (BPb) levels in the Fisher dams averaged 37.3 microg/dl and the SD dams averaged 29.9 microg/dl. Pb delayed the timing of puberty (p < 0.01) in Fisher offspring, and suppressed serum levels of luteinizing hormone (LH, p < 0.001) and estradiol (E2, p < 0.01). These effects did not occur in the SD offspring. Doubling the dose given to the SD rats increased their BPb levels to 62.6 microg/dl, yet there were still no effects noted. These results indicate that Fisher offspring are more sensitive to maternal Pb exposure with regard to puberty related insults than are SD rats, suggesting that the Fisher line may be a more reliable rodent model to study the effects of low level Pb toxicity.     

Evolutionary dynamics, epistatic interactions, and biological information

We investigate a definition of biological information that connects population genetics with the tools of information theory by focusing on the distribution of genotypes found in a population. Previous research has treated loci as non-interacting by making specific approximations in the calculation of information-theoretic quantities. We expand earlier mathematical forms to include epistasis, or interactions between mutations at all pairs of loci. Application of our improved measure of biological information to evolution on two-locus, two-allele fitness landscapes demonstrates that mutual information between loci reflects epistatic interaction of mutations. Finally, we consider four-locus, two-allele fitness landscapes with modular structure. As modular interactions are inherently epistatic, we demonstrate that our refined approximation provides insight into the underlying structure of these non-trivial fitness landscapes.