Self-replicating sequences of binary numbers. Foundations II: Strings of length N=4

We study an algorithm which allows sequences of binary numbers (strings) to interact with each other. The simplest system of this kind with a population of 4-bit sequences is considered here. Previously proposed folding methods are used to generate alternative two-dimensional forms of the binary sequences. The interaction of two-dimensional and one-dimensional forms of strings is simulated in a serial computer. The reaction network for the N = 4 system is established. Development of string populations initially generated randomly is observed. Nonlinear rate equations are proposed which provide a model for this simplest system.Dedicated to Professor Hermann Haken on the occasion of his 65th Birthday     

An example of design optimization for high evolvability: string rewriting grammar

As an example of the optimization of an evolutionary system design, a string rewriting system is studied. A set of rewriting rules that defines the growth of a string is experimentarily optimized in terms of maximizing the 'replicative capacity', that is the occurrence ratio of self-replicating strings. It is shown that the most optimized rule set allows many strings to self-replicate by using a special character able to copy an original string sequentially. Then, using various different rewriting rule sets, the connectivity between self-replicating strings is studied. A set of 'hyperblobs' covering the self-replicating strings is extracted and their connectivity is studied. The experimental results show that a large replicative capacity assures strong connectivity between self-replicating genotypes, making the system highly evolvable.     

非人灵长类种群数量调查方法综述

监测估算野生动物的种群数量是保护的核心工作。由于气候变化和人类活动的影响,野生动物种群常处于不稳定的状态。非人灵长类是动物界的高等类群,具有复杂的社会行为、丰富的物种多样性,全球有701种 (含亚种),生活在多种类型的栖息地中,包括热带雨林、沼泽森林、红树林、次生林、落叶林、季雨林、山地森林,和包含孤存林、长廊森林、热带旱生林、山地草甸、地中海灌木林的稀树草原和干草原,以及荒漠、干旱的山地,甚至是雪地。绝大多数非人灵长类处于濒危的状态,长期有效的监测对于灵长类的保护十分重要。物种多样性和栖息地类型的多样性使得灵长类种群数量的调查方法多种多样。本文归纳总结了目前常用的非人灵长类种群数量调查方法的类型、基本原理、适用场景和局限性,并以研究实例加以分析;介绍了无人机、热成像、计算机学习系统等新技术应用在调查方法中的进展,希望为今后的非人灵长类野外数量调查、种群监测提供参考和启发。     

Hexagonal-String Phases in Suspension Flow

Abstract

Investigations of the structure of flowing colloidal suspensions have seen structures of predominantly hexagonal strings moving in layered arrangements in the direction of the velocity gradient. A combination of computer simulation trajectories and computer graphics show that the predominant “hexagonal string phase” is the BCC lattice sheared along its (111) slip plane and, moreover, that all the common cubic lattice types contain “hexagonal strings”.     

Local elongation of endothelial cell-anchored von Willebrand factor strings precedes ADAMTS13 protein-mediated proteolysis

Platelet-decorated von Willebrand factor (VWF) strings anchored to the endothelial surface are rapidly cleaved by ADAMTS13. Individual VWF string characteristics such as number, location, and auxiliary features of the ADAMTS13 cleavage sites were explored here using imaging and computing software. By following changes in VWF string length, we demonstrated that VWF strings are cleaved multiple times, successively shortening string length in the function of time and generating fragments ranging in size from 5 to over 100 μm. These are larger than generally observed in normal plasma, indicating that further proteolysis takes place in circulation. Interestingly, in 89% of all cleavage events, VWF strings elongate precisely at the cleavage site before ADAMTS13 proteolysis. These local elongations are a general characteristic of VWF strings, independent of the presence of ADAMTS13. Furthermore, large elongations, ranging in size from 1.4 to 40 μm, occur at different sites in space and time. In conclusion, ADAMTS13-mediated proteolysis of VWF strings under flow is preceded by large elongations of the string at the cleavage site. These elongations may lead to the simultaneous exposure of many exosites, thereby facilitating ADAMTS13-mediated cleavage.     

Computer experiments on the evolution of sex: the haploid case

We have conducted a set of computer experiments that investigate the conditions under which sexual reproduction can evolve. In these experiments, haploid genomes are treated as integer strings able to undergo mutation and, in the case of sexual strings, recombination, with string sequence (the genotype) determining fitness. Our results indicate that the likelihood of a rare sexual mutant spreading through an otherwise asexual population is small when sexual reproduction entails the classical two-fold cost of males. However, our results indicate that when mutation rates are not excessively high, sexual reproduction constitutes a more efficient fitness optimization algorithm, allowing a sexual population to adapt more quickly to its environment than an asexual population.     

Primate Seed Dispersal: Old and New Challenges

Primate seed dispersal plays crucial roles in many ecological processes at various levels of biological organization: from plant population genetics and demography to community assembly and ecosystem function. Although research on primate seed dispersal has advanced significantly in the last 20–30 years, many aspects are still poorly understood. Here, we discuss some new challenges that we need to address, as well as some old ones that still need our attention, highlighting examples from the Neotropics. Despite new analytical tools from network theory, research on primate seed dispersal rarely takes a community-wide approach, thus limiting our understanding of its evolutionary, ecological, and conservation implications. Of particular relevance for conservation are changes caused by landscape-scale processes (e.g., forest loss and fragmentation), but these effects need to be assessed using a landscape approach, which is currently absent in primate seed dispersal research. Agroecosystems can play a key role in maintaining primate seed dispersal in anthropogenic landscapes, but this topic remains poorly studied. Primate seed dispersal research will need to play a role in refaunation projects aimed at restoring plant–animal interactions. Old challenges that we still need to address include the long-term effects of primate declines on plant populations and communities, and the role of primate seed dispersal in the regeneration of degraded habitats. If we take advantage of all tools provided by modern science, from powerful methods of data analyses to molecular techniques, and combine them with strong multidisciplinary collaborations, the future of primate seed dispersal research will indeed be exciting.     

Stochastic models of neuronal dynamics

Cortical activity is the product of interactions among neuronal populations. Macroscopic electrophysiological phenomena are generated by these interactions. In principle, the mechanisms of these interactions afford constraints on biologically plausible models of electrophysiological responses. In other words, the macroscopic features of cortical activity can be modelled in terms of the microscopic behaviour of neurons. An evoked response potential (ERP) is the mean electrical potential measured from an electrode on the scalp, in response to some event. The purpose of this paper is to outline a population density approach to modelling ERPs.We propose a biologically plausible model of neuronal activity that enables the estimation of physiologically meaningful parameters from electrophysiological data. The model encompasses four basic characteristics of neuronal activity and organization: (i) neurons are dynamic units, (ii) driven by stochastic forces, (iii) organized into populations with similar biophysical properties and response characteristics and (iv) multiple populations interact to form functional networks. This leads to a formulation of population dynamics in terms of the Fokker-Planck equation. The solution of this equation is the temporal evolution of a probability density over state-space, representing the distribution of an ensemble of trajectories. Each trajectory corresponds to the changing state of a neuron. Measurements can be modelled by taking expectations over this density, e.g. mean membrane potential, firing rate or energy consumption per neuron. The key motivation behind our approach is that ERPs represent an average response over many neurons. This means it is sufficient to model the probability density over neurons, because this implicitly models their average state. Although the dynamics of each neuron can be highly stochastic, the dynamics of the density is not. This means we can use Bayesian inference and estimation tools that have already been established for deterministic systems. The potential importance of modelling density dynamics (as opposed to more conventional neural mass models) is that they include interactions among the moments of neuronal states (e.g. the mean depolarization may depend on the variance of synaptic currents through nonlinear mechanisms).Here, we formulate a population model, based on biologically informed model-neurons with spike-rate adaptation and synaptic dynamics. Neuronal sub-populations are coupled to form an observation model, with the aim of estimating and making inferences about coupling among sub-populations using real data. We approximate the time-dependent solution of the system using a bi-orthogonal set and first-order perturbation expansion. For didactic purposes, the model is developed first in the context of deterministic input, and then extended to include stochastic effects. The approach is demonstrated using synthetic data, where model parameters are identified using a Bayesian estimation scheme we have described previously.     

Stochastic Time Models of Syllable Structure

Drawing on phonology research within the generative linguistics tradition, stochastic methods, and notions from complex systems, we develop a modelling paradigm linking phonological structure, expressed in terms of syllables, to speech movement data acquired with 3D electromagnetic articulography and X-ray microbeam methods. The essential variable in the models is syllable structure. When mapped to discrete coordination topologies, syllabic organization imposes systematic patterns of variability on the temporal dynamics of speech articulation. We simulated these dynamics under different syllabic parses and evaluated simulations against experimental data from Arabic and English, two languages claimed to parse similar strings of segments into different syllabic structures. Model simulations replicated several key experimental results, including the fallibility of past phonetic heuristics for syllable structure, and exposed the range of conditions under which such heuristics remain valid. More importantly, the modelling approach consistently diagnosed syllable structure proving resilient to multiple sources of variability in experimental data including measurement variability, speaker variability, and contextual variability. Prospects for extensions of our modelling paradigm to acoustic data are also discussed.     

Birth, growth and death as structuring operators in bacterial population dynamics

A new model is presented that describes microbial population dynamics that emerge from complex interactions among birth, growth and death as oriented, discrete events. Specifically, birth and death act as structuring operators for individual organisms within the population, which become synchronised as age clusters (called cell generations that are structured in age classes) that are born at the same time and die in concert; a pattern very consistent with recent experimental data that show bacterial group death correlates with temporal population dynamics in chemostats operating at carrying capacity. Although the model only assumes “natural death” (i.e., no death from predation or antimicrobial exposure), it indicates that short-term non-linear dynamic behaviour can exist in a bacterial population growing under longer term pseudo-steady-state conditions (a confined dynamic equilibrium). After summarizing traditional assumptions about bacterial aging, simulations of batch, continuous-flow, and bioreactors with recycle are used to show how population dynamics vary as function of hydraulic retention time, microbial kinetics, substrate level, and other factors that cause differential changes in the distribution of living and dead cells within the system. In summary, we show that population structures induced by birth and death (as discrete and delayed events) intrinsically create a non-linear dynamic system, implying that a true steady state can never exist in growing bacterial populations. This conclusion is discussed within the context of process stability in biotechnology.     

Infanticide as an alternative male reproductive strategy in langurs: A mathematical model

This paper makes explicit some of the assumptions underlying the view that infanticide is one of two (or more) alternative reproductive strategies utilized by adult male langur monkeys (genus Presbytis). A mathematical model has been developed from these assumptions, and formulae derived which give the equilibrium proportion of infanticidal males expected in langur populations under any given set of reproductive and demographic conditions. Together with estimates of adult male reproductive success obtained from a previous analysis of langur infanticide, these formulae were then used to calculate the precise proportion of infanticidal males expected in natural populations of langurs characterized by specific average male tenures. Further, the number of generations required for such populations to reach their predicted equilibrium was estimated using a simple computer model of langur population dynamics. The present work has thus produced several quantitative predictions which are directly falsifiable with observational data obtainable from wild populations of langur monkeys. With only slight modification, the present model may also be applied to the numerous other primate and non-primate species whose mating systems include many of the same general features as that of langurs.     

Non-linear feedback processes and a latitudinal gradient in the climatic effects determine green spruce aphid outbreaks in the UK

The role of climatic fluctuations in determining the dynamics of insect populations has been a classical problem in population ecology. Here, we use long-term annual data on green spruce aphid populations at nine localities in the UK for determining the importance of endogenous processes, local weather and large-scale climatic factors. We rely on diagnostic and modelling tools from population dynamic theory to analyse these long-term data and to determine the role of the North Atlantic Oscillation (NAO) and local weather as exogenous factors influencing aphid dynamics. Our modelling suggests that the key elements determining population fluctuations in green spruce aphid populations in the UK are the strong non-linear feedback structure, the high potential for population growth and the effects of winter and spring weather. The results indicate that the main effect of the NAO on green spruce aphid populations is operating through the effect of winter temperatures on the maximum per capita growth rate (R_m). In particular, we can predict quite accurately the occurrence of an outbreak by using a simple logistic model with weather as a perturbation effect. However, model predictions using different climatic variables showed a clear geographical signature. The NAO and winter temperature were best for predicting observed dynamics toward the southern localities, while spring temperature was a much better predictor of aphid dynamics at northern localities. Although aphid species are characterized by complex life-cycles, we emphasize the value of simple and general population dynamic models in predicting their dynamics.     

The role of cerebral regulatory structures in the formation of human EEG

This article generalizes the results of many years’ studies of the EEG of patients with tumorous lesions in the diencephalic, brainstem, and limbic structures, which fulfill the regulatory function in ensuring integral brain activity. The specific features of the inclusion of individual structures under investigation in the organization of the intra- and interhemispheric relations of cortical biopotentials were demonstrated against the background of diffuse changes in the biopotentials that reflect the systemic character of neurodynamic reorganizations when the regulatory brain structures are involved in the pathological process. This study expands the idea of the predominant functional connection of the diencephalic structures with the right hemisphere and brainstem structures with the left one with determination of the regional specific features of changes in the intrahemispheric EEG coherences. The distinguishing features of intercentral relations when the limbic structures are involved in the pathological process show similarity with the neurodynamic reorganizations in patients with lesions in both diencephalic and (even more so) brainstem structures. Universal elements were detected in the formation of integral adaptive reactions of the brain with lesions in its regulatory structures, which reflects their close functional interaction and makes it possible to consider them the individual links of an integral regulatory system. The study revealed reciprocal changes in various forms of electrical activity, which reflects reciprocation of interaction of individual regulatory structures. This is one of the EEG equivalents of the formation of adaptive-compensatory cerebral reactions. The specificity of influence of the studied regulatory structures are clearly seen in situations of their morphofunctional isolation observed during cerebral coma. In these conditions, when the cortex is functionally inactive, the authors demonstrated the dynamic character of changes in interhemispheric asymmetry, which reflects the dominance of individual links of the regulatory system playing the role of supreme regulator of life support of the body in critical states.     

Controlled synthesis of target strings in a class of splicing systems

This article presents an approach for synthesizing target strings in a class of computational models of DNA recombination. The computational models are formalized as splicing systems in the context of formal languages. Given a splicing system (of a restricted type) and a target string to be synthesized, we construct (i) a rule-embedded splicing automaton that recognizes languages containing strings embedded with symbols representing splicing rules, and (ii) an automaton that implicitly recognizes the target string. By manipulating these two automata, we extract all rule sequences that lead to the production of the target string (if that string belongs to the splicing language). An algorithm for synthesizing a certain type of target strings based on such rule sequences is presented.     

Primates and Cameras

Field-based primate studies often make population inferences using count-based indices (e.g., individuals/plot) or distance sampling; the first does not account for the probability of detection and thus can be biased, while the second requires large sample sizes to obtain precise estimates, which is difficult for many primate studies. We discuss photographic sampling and occupancy modeling to correct for imperfect detection when estimating system states and dynamics at the landscape level, specifically in relation to primate ecology. We highlight the flexibility of the occupancy framework and its many applications to studying low-density primate populations or species that are difficult to detect. We discuss relevant sampling and estimation procedures with special attention to data collection via photographic sampling. To provide tangible meaning to terminology and clarify subtleties, we use illustrative examples. Photographic sampling can have many advantages over observer-based sampling, especially when studying rare or elusive species. Combining photographic sampling with an occupancy framework allows inference to larger scales than is common in primate studies, addresses uncertainty due to the observation process, and allows researchers to examine questions of how landscape-level anthropogenic changes affect primate distributions.     

Reducing the dimensionality of the protein-folding search problem

How does a folding protein negotiate a vast, featureless conformational landscape and adopt its native structure in biological real time? Motivated by this search problem, we developed a novel algorithm to compare protein structures. Procedures to identify structural analogs are typically conducted in three-dimensional space: the tertiary structure of a target protein is matched against each candidate in a database of structures, and goodness of fit is evaluated by a distance-based measure, such as the root-mean-square distance between target and candidate. This is an expensive approach because three-dimensional space is complex. Here, we transform the problem into a simpler one-dimensional procedure. Specifically, we identify and label the 11 most populated residue basins in a database of high-resolution protein structures. Using this 11-letter alphabet, any protein''s three-dimensional structure can be transformed into a one-dimensional string by mapping each residue onto its corresponding basin. Similarity between the resultant basin strings can then be evaluated by conventional sequence-based comparison. The disorder → order folding transition is abridged on both sides. At the onset, folding conditions necessitate formation of hydrogen-bonded scaffold elements on which proteins are assembled, severely restricting the magnitude of accessible conformational space. Near the end, chain topology is established prior to emergence of the close-packed native state. At this latter stage of folding, the chain remains molten, and residues populate natural basins that are approximated by the 11 basins derived here. In essence, our algorithm reduces the protein-folding search problem to mapping the amino acid sequence onto a restricted basin string.     

The hidden matrilineal structure of a solitary lemur: implications for primate social evolution

Kin selection affects many aspects of social behaviour, especially in gregarious animals in which relatives are permanently associated. In most group-living primates with complex social behaviour, females are philopatric and organized into matrilines. Models of primate social evolution assume that females in solitary primates are also organized into matrilines. We examined the genetic structure and the mating system of a population of Coquerel's dwarf lemur (Mirza coquereli), a solitary primate from Madagascar, to test this assumption. Our genetic and behavioural analyses revealed that this population of solitary individuals is indeed structured into matrilines, even though this pattern was not predicted by behavioural data. Specifically, females sharing a mitochondrial DNA haplotype were significantly clustered in space and the average genetic and geographical distances among them were negatively correlated. Not all females were philopatric, but there is no evidence for the successful settlement of dispersing females. Although not all adult males dispersed from their natal range, they were not significantly clustered in space and all of them roamed widely in search of oestrous females. As a result, paternity was widely spread among males and mixed paternities existed, indicating that scramble competition polygyny is the mating system of this species. Our data therefore revealed facultative dispersal in both sexes with a strong bias towards female philopatry in this primitive primate. We further conclude that complex kinship structures also exist in non-gregarious species, where their consequences for social behaviour are not obvious.     

The determinant role of temporary proglacial drainages on the genetic structure of fishes

Phylogeographic studies have shed light on Pleistocene glaciations as a key factor in shaping present-day genetic structure of many organisms. In formerly glaciated regions, the combined action of several factors such as refuges origin, physiological capacities and demographic parameters have contributed importantly to this process but specifically for each species. Therefore, a fine-scale genetic structure is not expected to be similar for different species, unless it has been modulated by the action of a strong environmental pressure. The aim of this study is to investigate the effects of postglacial environment on the genetic structure of fishes. To achieve this objective, three fish species (northern pike, lake whitefish and yellow perch) commonly found in sympatry in Laurentian Shield lakes but displaying different ecological and physiological characteristics were analysed. The comparison of these unrelated species was performed to identify the factors determining the organization of their genetic structure. Populations of all species mostly originated from the Mississippian refuge. Low genetic differentiation was observed among populations but significant structures were detected for the three species. Despite marked differences among species, these structures presented common characteristics: a lack of congruence with drainage and a longitudinal organization. This suggested that the dispersion of species occurred independently, leading to a species-specific structure. However, the settling of populations appeared to be mediated by a dynamic system of proglacial meltwater streams associated to the glacial Lake Ojibway-Barlow, providing such similarities among species.     

The ups and downs of protein topology; rapid comparison of protein structure

Protein topology can be described at different levels. At the most fundamental level, it is a sequence of secondary structure elements (a "primary topology string"). Searching predicted primary topology strings against a library of strings from known protein structures is the basis of some protein fold recognition methods. Here a method known as TOPSCAN is presented for rapid comparison of protein structures. Rather than a simple two-letter alphabet (encoding strand and helix), more complex alphabets are used encoding direction, proximity, accessibility and length of secondary elements and loops in addition to secondary structure. Comparisons are made between the structural information content of primary topology strings and encodings which contain additional information ("secondary topology strings"). The algorithm is extremely fast, with a scan of a large domain against a library of more than 2000 secondary structure strings completing in approximately 30 s. Analysis of protein fold similarity using TOPSCAN at primary and secondary topology levels is presented.     

A new design of stochastic partnership models for epidemics of sexually transmitted diseases with stages

A problem of importance in modelling epidemics of sexually transmitted diseases is the development of mathematical structures accommodating sexual and other contacts among members of a population. Because these models may be complex, it is often necessary to use computer intensive methods in their analysis, which raises questions on the design of computer models. In this paper a new approach to designing models sexual contacts is presented within the context of a stochastic model accommodating the formation and dissolution of partnerships in heterosexual populations. Emphasis will be placed on the development of algorithms with a view towards developing software to implement computer intensive methods. Unlike previous formulations, rather than using rejection methods in Monte Carlo simulations to impose necessary constraints on random functions describing partnership formation, in the new formulation all constraints are satisfied with probability one.