Analysis of covariance: an alternative to nutritional indices

Some statistical problems are added to the growing list of cautionary tales regarding the use of the conventional, ratio-based nutritional indices (RCR, RGR, ECI, AD and ECD). Analysis of ratios is based on the, probably unrealistic, assumption of an isometric relationship between denominator and numerator variables. Analysis of covariance (ANCOVA) makes less restrictive assumptions, and additionally provides important information about the data which is lost by using ratio variables. We demonstrate, using computer-generated data sets, some of the pitfalls of statistical analysis of ratios and illustrate how these may be avoided using ANCOVA. Some possible consequences of such statistical iniquities for biological interpretations are discussed.     

Factor analysis models for structuring covariance matrices of additive genetic effects: a Bayesian implementation

Multivariate linear models are increasingly important in quantitative genetics. In high dimensional specifications, factor analysis (FA) may provide an avenue for structuring (co)variance matrices, thus reducing the number of parameters needed for describing (co)dispersion. We describe how FA can be used to model genetic effects in the context of a multivariate linear mixed model. An orthogonal common factor structure is used to model genetic effects under Gaussian assumption, so that the marginal likelihood is multivariate normal with a structured genetic (co)variance matrix. Under standard prior assumptions, all fully conditional distributions have closed form, and samples from the joint posterior distribution can be obtained via Gibbs sampling. The model and the algorithm developed for its Bayesian implementation were used to describe five repeated records of milk yield in dairy cattle, and a one common FA model was compared with a standard multiple trait model. The Bayesian Information Criterion favored the FA model.     

Application of a self-organizing map to select representative species in multivariate analysis: A case study determining diatom distribution patterns across France

Ecological communities consist of a large number of species. Most species are rare or have low abundance, and only a few are abundant and/or frequent. In quantitative community analysis, abundant species are commonly used to interpret patterns of habitat disturbance or ecosystem degradation. Rare species cause many difficulties in quantitative analysis by introducing noises and bulking datasets, which is worsened by the fact that large datasets suffer from difficulties of data handling. In this study we propose a method to reduce the size of large datasets by selecting the most ecologically representative species using a self organizing map (SOM) and structuring index (SI). As an example, we used diatom community data sampled at 836 sites with 941 species throughout the French hydrosystem. Out of the 941 species, 353 were selected. The selected dataset was effectively classified according to the similarities of community assemblages in the SOM map. Compared to the SOM map generated with the original dataset, the community pattern gave a very similar representation of ecological conditions of the sampling sites, displaying clear gradients of environmental factors between different clusters. Our results showed that this computational technique can be applied to preprocessing data in multivariate analysis. It could be useful for ecosystem assessment and management, helping to reduce both the list of species for identification and the size of datasets to be processed for diagnosing the ecological status of water courses.     

Mathematical hazard models of mortality: an alternative to model life tables

A five-parameter competing hazard model of the age pattern of mortality is described, and methods of fitting it to survivorship, death rate, and age structure data are developed and presented. The methods are then applied to published life table and census data to construct life tables for a Late Woodland population, a Christian period Nubian population, and the Yanomama. The advantage of this approach over the use of model life tables is that the hazard model facilitates life-table construction without imposing a particular age pattern of mortality on the data. This development makes it possible to use anthropological data to extend the study of human variation in mortality patterns to small populations.     

Dynamical entropy via entropy of non-random matrices: Application to stability and complexity in modelling ecosystems

In the present paper we have first introduced a measure of dynamical entropy of an ecosystem on the basis of the dynamical model of the system. The dynamical entropy which depends on the eigenvalues of the community matrix of the system leads to a consistent measure of complexity of the ecosystem to characterize the dynamical behaviours such as the stability, instability and periodicity around the stationary states of the system. We have illustrated the theory with some model ecosystems.     

An evolutionary account of science: A response to Rosenberg's critical notice

In his critical notice, Rosenberg (1991) raises three objections to my evolutionary account of science: whether it is more than a week metaphor, the compatibility of my past objections to reduction and my current advocacy of viewing selection in terms of replication and interaction, and finally, the feasibility of identifying appropriate replicators and interactors in biological evolution, let alone conceptual evolution. I discuss each of these objections in turn.     

Selecting models to predict the timing of flowering of temperate trees: implications for tree phenology modelling

Classical budburst models (Spring Warming, Sequential, Parallel and Alternating) are unable to fully predict external data, partly because of the methods of optimization used to adjust them. The purpose of this study was to examine different assumptions of budburst models and select those which are best supported by the data, defining new models able to predict external data. Eight models, each differing in one assumption, were fitted and tested using external data. The dataset used to test the models was deduced from aeropalynological data at two stations in France. The results show that some of the models proposed are able to accurately predict external dates of flowering of most of the studied species. The assumptions of those models have been individually tested and shown to improve the models accuracy. Robust estimates of the best predictor models of 12 tree species are presented. The analysis of hypothetical provenance transfer of two species, Buxus sempervirens and Platanus acerifolia, between the two study sites, shows that P. acerifolia estimates are similar in both environments whereas B. sempervirens estimates are variable. This result, which agrees with the genetic characteristics of both species, shows that local adaptation of phenology can also be studied through modelling approaches.     

Prediction of biogas potentials using quick laboratory analyses: Upgrading previous models for application to heterogeneous organic matrices

This study presents an upgrading of the mathematical models to predict anaerobic biogasification potential (ABP) through quick laboratory analyses that have been presented in an earlier study. The aim is to widen the applicability of the models to heterogeneous organic substrates and to improve their reliability through a deeper statistical approach.Three multiple-step linear regressions were obtained using biomass oxygen demand in 20 h (OD₂₀) plus the volatile solids content (VS) of 23 new samples of heterogeneous organic matrices, of 46 samples presented in the earlier work and of the data set comprising all the 69 samples. The two variables chosen were found to be suitable for very heterogeneous materials. To judge the prediction quality, a validation procedure was performed with 12 new samples using model efficiency indexes. The proposed model had good prediction ability for a large variety of organic substrates, and allows the calculation of the ABP value within only 2-day’s laboratory work instead of the 60–90 days required to obtain ABP by anaerobic test.     

The multifactor pelvis: An alternative to the adaptationist approach of the obstetrical dilemma

The obstetrical dilemma describes the competing demands that a bipedally adapted pelvis and a large-brained neonate place on human childbirth and is the predominant model within which hypotheses about the evolution of the pelvis are framed. I argue the obstetrical dilemma follows the adaptationist program outlined by Gould and Lewontin in 1979 and should be replaced with a new model, the multifactor pelvis. This change will allow thorough consideration of nonadaptive explanations for the evolution of the human pelvis and avoid negative social impacts from considering human childbirth inherently dangerous. First, the atomization of the pelvis into discrete traits is discussed, after which current evidence for both adaptive and nonadaptive hypotheses is evaluated, including childbirth, locomotion, shared genetics with other traits under selection, evolutionary history, genetic drift, and environmental and epigenetic influences on the pelvis.     

An alternative pathway to eusociality: Exploring the molecular and functional basis of fortress defense

Some animals express a form of eusociality known as “fortress defense,” in which defense rather than brood care is the primary social act. Aphids are small plant‐feeding insects, but like termites, some species express division of labor and castes of aggressive juvenile “soldiers.” What is the functional basis of fortress defense eusociality in aphids? Previous work showed that the acquisition of venoms might be a key innovation in aphid social evolution. We show that the lethality of aphid soldiers derives in part from the induction of exaggerated immune responses in insects they attack. Comparisons between closely related social and nonsocial species identified a number of secreted effector molecules that are candidates for immune modulation, including a convergently recruited protease described in unrelated aphid species with venom‐like functions. These results suggest that aphids are capable of antagonizing conserved features of the insect immune response, and provide new insights into the mechanisms underlying the evolution of fortress defense eusociality in aphids.     

The problem of bone lamellation: An attempt to explain different proposed models

Collagen texture and osteocyte distribution were analyzed in human woven‐ and lamellar‐bone using scanning and transmission electron microscopy. We provide data substantiating the concept that lamellar bone is made up of an alternation of dense‐acellular lamellae and loose‐cellular lamellae, all exhibiting an interwoven texture of collagen fibers. An attempt is also made to explain how the present findings might conform to those of authors whose models propose orderly, geometric arrangements of collagen fibers inside bony lamellae. Such a comparison is possible because the present investigation analyzes split loose lamellae and tangentially‐sectioned dense lamellae. It emerged that only loose lamellae can be dissected, revealing a loose interwoven collagen texture and halved osteocyte lacunae. Dense lamellae cannot be split because of their compactness. The analysis of tangentially sectioned dense lamellae demonstrates that they consist of a network of interwoven collagen fiber bundles. Inside each bundle, collagen fibers run parallel to each other but change direction where they enter adjacent bundles, at angles as described by other authors whose TEM investigations were performed at a much higher magnification than those of the present study. Consequently, what these authors consider to be a lamella are, instead, bundles of collagen fibers inside a lamella. There is discussion of the role played by the manner of osteocyte‐recruitment in the deposition of lamellar‐ and woven‐bone and how the presence of these cells is crucial for collagen spatial arrangement in bone tissues. J. Morphol., 2013. © 2013 Wiley Periodicals, Inc.     

Wrapping Up Greenhouse Gas Emissions An Assessment of GHG Emission Reduction Related to Efficient Packaging Use: An Assessment of GHG Emission Reduction Related to Efficient Packaging Use

The use of packaging materials results in greenhouse gas (GHG) emissions through production and transport of materials and packaging and through end-of-life management. In this article, we investigate the potential reduction of GHGs that are related to packaging. For this purpose, we use the dynamic MATTER-MARKAL model in which the western European energy and materials system is modeled. The results show that GHGs related to packaging can technically be reduced by up to 58% in the period 1995–2030. Current European packaging directives will result in a 10% emission reduction. Cost-effective improved material management 1 that includes lightweighting, reusable packages, material recycling, and related strategies can contribute a 22% GHG emission reduction. An additional 13% reduction becomes cost effective when a GHG emission penalty of 100 euros per metric ton 2 (EUR/ton) is introduced (1 EUR 0.9 USD). Generally speaking, improved material management dominates the gains that can be achieved without a penalty or with low GHG emission penalties (up to 100 EUR/ton CO2 equivalent). By contrast, the reduction of emissions in materials production and waste handling dominate when high GHG penalties are applied (between 100 and 500 EUR/ton CO2 equivalent). Given the significant technical potential and the low costs, more attention should be paid to material efficiency improvement in GHG emission reduction strategies.     

Infection of organotypic slice cultures from rat central nervous tissue with Neospora caninum: an alternative approach to study host-parasite interactions

Neospora caninum is an apicomplexan parasite which has emerged as an important cause of bovine abortion worldwide. Abortion is usually triggered by reactivation of dormant bradyzoites during pregnancy and subsequent congenital infection of the foetus, where the central nervous system appears to be most frequently affected. We here report on an organotypic tissue culture model for Neospora infection which can be used to study certain aspects of the cerebral phase of neosporosis within the context of a three-dimensionally organised neuronal network. Organotypic slice cultures of rat cortical tissue were infected with N. caninum tachyzoites, and the kinetics of parasite proliferation, as well as the proliferation-inhibitory effect of interferon-gamma (IFN-gamma), were monitored by either immunofluorescence, transmission electron microscopy, and a quantitative PCR-assay using the LightCycler instrument, respectively. In addition, the neuronal cytoskeletal elements, namely glial acidic protein filaments as well as actin microfilament bundles were shown to be largely colocalising with the pseudocyst periphery. This organotypic culture model for cerebral neosporosis provides a system, which is useful to study the proliferation, ultrastructural characteristics, development, and the interactions of N. caninum within the context of neuronal tissue, which at the same time can be modulated and influenced under controlled conditions, and will be useful in the future to gain more information on the cerebral phase of neosporosis.     

An inexpensive alternative to routine section adhesives for histology: the mucilaginous substance of the Assyrian plum

We found that the mucilaginous substance of the Assyrian plum, Cordia myxa, can be used as an adhesive for attaching sections of animal tissues to slides. Unlike Mayer's albumen, this material left no stainable residue and had no noticeable effect on the histological structure of the tissue sections. The mucilaginous substance of C. myxa is a useful and inexpensive alternative to standard adhesives.