Mating,births, and transitions: a flexible two-sex matrix model for evolutionary demography

Models of sexually-reproducing populations that consider only a single sex cannot capture the effects of sex-specific demographic differences and mate availability. We present a new framework for two-sex demographic models that implements and extends the birth-matrix mating-rule approach of Pollak. The model is a continuous-time matrix model that explicitly includes the processes of mating (which is nonlinear but homogeneous), offspring production, and demographic transitions and survival. The resulting nonlinear model converges to exponential growth with an equilibrium population composition. The model can incorporate age- or stage-structured life histories and flexible mating functions. As an example, we apply the model to analyze the effects of mating strategies (polygamy or monogamy, and mated unions composed of males and females, of variable duration) on the response to sex-biased harvesting. The combination of demographic complexity with the interaction of the sexes can have major population dynamic effects and can change the outcome of evolution on sex-related characters.     

Presynaptic learning and memory with a persistent firing neuron and a habituating synapse: a model of short term persistent habituation

Our paper explores the interaction of persistent firing axonal and presynaptic processes in the generation of short term memory for habituation. We first propose a model of a sensory neuron whose axon is able to switch between passive conduction and persistent firing states, thereby triggering short term retention to the stimulus. Then we propose a model of a habituating synapse and explore all nine of the behavioral characteristics of short term habituation in a two neuron circuit. We couple the persistent firing neuron to the habituation synapse and investigate the behavior of short term retention of habituating response. Simulations show that, depending on the amount of synaptic resources, persistent firing either results in continued habituation or maintains the response, both leading to longer recovery times. The effectiveness of the model as an element in a bio-inspired memory system is discussed.     

A multivariate generalization of the FRIEDMAN rank test with application to a problem in molecular biology

A series of experiments was recently undertaken at the National Institutes of Health to ascertain whether tRNA populations are determined by or adapted to the major proteins synthesized by tumor cells. Dissimilarity indices between chromatographic profiles of animoacyl-tRNAs from 11 mouse plasmacytomas and from normal adult mouse liver and brain were calculated and then compared using a multivariate generalization of the FRIEDMAN rank test. This test is described herein, and its use is illustrated with data from the experiments.     

Population differentiation and migration: coalescence times in a two-sex island model for autosomal and X-linked loci

Evolutionists have debated whether population-genetic parameters, such as effective population size and migration rate, differ between males and females. In humans, most analyses of this problem have focused on the Y chromosome and the mitochondrial genome, while the X chromosome has largely been omitted from the discussion. Past studies have compared F_ST values for the Y chromosome and mitochondrion under a model with migration rates that differ between the sexes but with equal male and female population sizes. In this study we investigate rates of coalescence for X-linked and autosomal lineages in an island model with different population sizes and migration rates for males and females, obtaining the mean time to coalescence for pairs of lineages from the same deme and for pairs of lineages from different demes. We apply our results to microsatellite data from the Human Genome Diversity Panel, and we examine the male and female migration rates implied by observed F_ST values.     

Optimal control of a rabies epidemic model with a birth pulse

A system of ordinary differential equations describes the population dynamics of a rabies epidemic in raccoons. The model accounts for the dynamics of a vaccine, including loss of vaccine due to animal consumption and loss from factors other than racoon uptake. A control method to reduce the spread of disease is introduced through temporal distribution of vaccine packets. This work incorporates the effect of the seasonal birth pulse in the racoon population and the attendant increase in new-borns which are susceptible to the diseases, analysing the impact of the timing and length of this pulse on the optimal distribution of vaccine packets. The optimization criterion is to minimize the number of infected raccoons while minimizing the cost of distributing the vaccine. Using an optimal control setting, numerical results illustrate strategies for distributing the vaccine depending on the timing of the infection outbreak with respect to the birth pulse.     

The Catch model: a solution to the problem of saliency in facial features

The goal of the present paper is to propose a solution to the 'saliency problem' which has been raised in regard to Rakover and Cahlon's (1989) Catch model for identifying a previously seen target face (Ft). In contrast to real life situations, the Catch model assigned the same weight to different facial dimensions and values. Mathematical proofs, reanalyses of the results of three experiments reported in Rakover and Cahlon, and the analysis of the results of a new experiment show that this proposal expands and improves the Catch model.     

Who underreports smoking on birth records: a Monte Carlo predictive model with validation

Background

Research has shown that self-reports of smoking during pregnancy may underestimate true prevalence. However, little is known about which populations have higher rates of underreporting. Availability of more accurate measures of smoking during pregnancy could greatly enhance the usefulness of existing studies on the effects of maternal smoking offspring, especially in those populations where underreporting may lead to underestimation of the impact of smoking during pregnancy.

Methods and Findings

In this paper, we develop a statistical Monte Carlo model to estimate patterns of underreporting of smoking during pregnancy, and apply it to analyze the smoking self-report data from birth certificates in the state of Massachusetts. Our results illustrate non-uniform patterns of underreporting of smoking during pregnancy among different populations. Estimates of likely underreporting of smoking during pregnancy were highest among mothers who were college-educated, married, aged 30 years or older, employed full-time, and planning to breastfeed. The model''s findings are validated and compared to an existing underreporting adjustment approach in the Maternal and Infant Smoking Study of East Boston (MISSEB).

Conclusions

The validation results show that when biological assays are not available, the Monte Carlo method proposed can provide a more accurate estimate of the smoking status during pregnancy than self-reports alone. Such methods hold promise for providing a better assessment of the impact of smoking during pregnancy.     

Towards the development of a minimal cell model by generalization of a model of Escherichia coli: use of dimensionless rate parameters.

A model of a minimal cell would be a valuable tool in identifying the organizing principles that relate the static sequence information of the genome to the dynamic functioning of the living cell. Our approach for developing a minimal cell model is to first generalize an existing model of Escherichia coli by expressing reaction rates as ratios to a set of reference parameters. This generalized model is a prototype minimal cell model that will be developed by adding detail to explicitly include each chemical species. We tested the concept of a generalized model by testing the effect of scaling all enzyme-catalyzed reactions in the E. coli model. The scaling has little effect on cellular function for a wide range of kinetic ratios, where the kinetic ratio is defined as the rate of all enzyme-catalyzed reactions in a given model relative to those in the E. coli model.     

When the exception becomes the rule: The disappearance of limiting similarity in the Lotka-Volterra model

We investigate the transition between limiting similarity and coexistence of a continuum in the competitive Lotka-Volterra model. It is known that there exist exceptional cases in which, contrary to the limiting similarity expectation, all phenotypes coexist along a trait axis. Earlier studies established that the distance between surviving phenotypes is in the magnitude of the niche width 2σ provided that the carrying capacity curve differs from the exceptional one significantly enough. In this paper we studied the outcome of competition for small perturbations of the exceptional (Gaussian) carrying capacity. We found that the average distance between the surviving phenotypes goes to zero when the perturbation vanishes. The number of coexisting species in equilibrium is proportional to the negative logarithm of the perturbation. Nevertheless, the niche width provides a good order of magnitude for the distance between survivors if the perturbations are larger than 10%. Therefore, we conclude that limiting similarity is a good framework of biological thinking despite the lack of an absolute lower bound of similarity.     

The three-for-one model for Gram-negative wall growth: a problem and a possible solution

The murein wall in Gram-negative bacteria is so thin that the mechanism of growth is necessarily complicated. From analytical data of murein components, Höltje suggested a model for the growth mechanism that would lead to safe wall enlargement. The model depended on the formation of trimers of peptidoglycan disaccharides linked via their pentapeptides. In the `three-for-one' model three oligopeptidoglycan chains are linked to each other in the usual linkages between the carboxyl group of d-alanine residues and the ϵ-amino group of diaminopimelic acid residues; these are designated `tail-to-tail' linkages. This three-chained raft is then linked to the stress-bearing wall via the formation of trimers, defined as three peptide chains linked together by tail-to-tail linkages. Then by autolyzing the oldest bonds in each trimer, the old chain is excised and the raft becomes part of the stress-bearing wall and the wall is enlarged. There is a problem with the three-for-one model in that it demands a precise fitting of the prefabricated raft of three crosslinked chains to a stress-bearing chain in the wall fabric to allow the series of trimer linkages to form. Because the wall, when bearing stress, must be pulled into a `honeycomb' structure, the end-to-end distance would be shortened. The possibility is raised here that the glycan chains in the stress-bearing wall are stretched to a sufficient degree by the cell's turgor pressure to compensate for its zig-zag structure; this could allow the model to function. A calculation is presented that assumes that the area of the pores in the fabric, called tessera, is maximized by the cell's turgor pressure. In this case the glycan chain must stretch 10% (and the end-to-end distance of peptide strands stretch 28%) so that the end-to-end distance of a glycan chain in the stress-bearing wall and the unstretched nascent wall can be the same and permit indefinite stable growth.     

A persistent model of the reptation movement of a DNA molecule

By using a persistent model of the movement of a DNA molecule, the penetration of the DNA molecule into a cell has been described. The method enables one to estimate the time and the rate of passage of the DNA molecule into the cell nucleus. The effect of the curvature of the molecule on its longitudinal movement has been studied. The results obtained can be applied to characterize long chain molecules.     

The problem with the species problem

When Charles Darwin convinced the scientific community that species evolve, the long-held essentialist view of each species as fixed was rejected and a clear conceptual understanding of the term was lost. For the next century, a real species problem existed that became culturally entrenched within the scientific community. Although largely solved decades ago, the species problem remains entrenched today due to a suite of factors. Most of the factors that help maintain its perceived intractability have been revealed and logically dismissed; yet this is not widely known so those factors continue to be influential. It is time to recognize this false foundation and relegate the species problem to history.     

Asymptotic and explicit formulae for a non-markovian model with linear transition rule

Asymptotic and explicit formulae are obtained for the n-step stochastic kernel of a special class of non-MARKOVIAN models with linear transition rule which occur in learning theory, adaption theory, control theory, and biological research.     

The standardization–generalization dilemma: a way out

Recently, a debate has emerged on the use and necessity of standardization in experimental testing using animal subjects. The difficulties encountered when trying to reconcile standardization and generalization largely underlie this debate. The more specific the testing procedures are, the less one can generalize to more naturalistic situations, including to human clinical populations. If the goal of a study is to generalize to a larger population, there may be a higher risk attached to false‐positive than false‐negative results; thus the balance sways toward generalization. Heterogenization of housing conditions and of genetic makeup of experimental animals has been suggested as a possible method to increase the generalizability of results. It is important to remain cognizant, however, of situations in which false negatives can be counterproductive or even dangerous, such as when the goal is to elucidate a physiological mechanism, when expected effect sizes are small, in toxicological studies and in drug safety testing. In such cases, experiments based on standardization may provide more useful information. We pose that it is essential that the goal of the specific experiment conducted is clearly defined and that the decision to balance between standardization and generalization must be made based on the specific needs to meet the intended goal. In this light, we discuss a multi‐tiered approach to animal experimentation, in which standardization and generalizability are each given precedence during different phases of a project, depending upon the goal of the experiment.