MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Acta Biotheoretica' source. Thu, 09 Feb 2012 14:07:48 +0100 http://www.medworm.com/index.php?rid=5671439&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22302362%26dopt%3DAbstract Authors: Wennekes PL, Rosindell J, Etienne RS Abstract Ecological communities around the world are under threat while a consensus theory of community structure remains elusive. In the last decade ecologists have struggled with two seemingly opposing theories: niche-based theory that explains diversity with species' differences and the neutral theory of biodiversity that claims that much of the diversity we observe can be explained without explicitly invoking species' differences. Although ecologists are increasingly attempting to reconcile these two theories, there is still much resistance against the neutral theory of biodiversity. Here we argue that the dispute between the two theories is a classic example of the dichotomy between philosophical perspectives, realism and instrumen... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=5671439 Fri, 03 Feb 2012 05:00:00 +0100 5671439 http://www.medworm.com/index.php?rid=5671438&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22302363%26dopt%3DAbstract Authors: Chekhchoukh A, Glade N Abstract Vision substitution by electro-stimulation has been studied since the 60s beginning with P. Bach-y-Rita. Camera pictures or movies encoded in gray levels are displayed using an electro-stimulation display device on the surface of a body part, such as the skin or the tongue. Medical-technical devices have been developed on this principle to compensate for sensory-motor disabilities such as blindness or loss of balance, or to guide specific actions, such as surgery. However, the electrical signals of stationary or moving slowly moving objects, displayed on a Tongue display unit (TDU), are quickly lost due to saturation of receptors undergoing electrostimulation. We propose to add random saccades or sparkle to the displayed visual scene to incr... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=5671438 Fri, 03 Feb 2012 05:00:00 +0100 5671438 http://www.medworm.com/index.php?rid=5671440&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22286946%26dopt%3DAbstract We describe a conceptual model that takes into account these findings. PMID: 22286946 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=5671440 Sun, 29 Jan 2012 05:00:00 +0100 5671440 http://www.medworm.com/index.php?rid=5636559&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22271286%26dopt%3DAbstract Authors: Dao Thi MU, Trocmé C, Montmasson MP, Fanchon E, Toussaint B, Tracqui P Abstract Angiogenesis is a complex morphogenetic process regulated by growth factors, but also by the force balance between endothelial cells (EC) traction stresses and extracellular matrix (ECM) viscoelastic resistance. Studies conducted with in vitro angiogenesis assays demonstrated that decreasing ECM stiffness triggers an angiogenic switch that promotes organization of EC into tubular cords or pseudo-capillaries. Thus, mechano-sensitivity of EC with regard to proteases secretion, and notably matrix metalloproteinases (MMPs), should likely play a pivotal role in this switching mechanism. While most studies analysing strain regulation of MMPs used cell cultured on stretched membranes, this work focus... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=5636559 Tue, 24 Jan 2012 05:00:00 +0100 5636559 http://www.medworm.com/index.php?rid=5557777&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22200989%26dopt%3DAbstract Authors: Baetu TM Abstract Different concepts define species at the pattern-level grouping of organisms into discrete clusters, the level of the processes operating within and between populations leading to the formation and maintenance of these clusters, or the level of the inner-organismic genetic and molecular mechanisms that contribute to species cohesion or promote speciation. I argue that, unlike single-level approaches, a multi-level framework takes into account the complex sequences of cause-effect reinforcements leading to the formation and maintenance of various patterns, and allows for revisions and refinements of pattern-based characterizations in light of the gradual elucidation of the causes and mechanisms contributing to pattern formation and maintenance. PMID: 2... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=5557777 Tue, 27 Dec 2011 05:00:00 +0100 5557777 http://www.medworm.com/index.php?rid=5524914&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22173582%26dopt%3DAbstract Authors: Khaladi M, Lebreton JD, Khermjioui A Abstract In this paper we introduce a stochastic model for a population living and migrating between s sites without distinction in the states between residents and immigrants. The evolutionary stable strategies (ESS) is characterized by the maximization of a stochastic growth rate. We obtain that the expectation of reproductive values, normalized by some random quantity, are constant on all sites and that the expectation of the normalized vector population structure is proportional to eigenvector of the dispersion matrix associated to eigenvalue one, which are, in some way, analogous to the results obtained in the deterministic case. PMID: 22173582 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=5524914 Fri, 16 Dec 2011 05:00:00 +0100 5524914 http://www.medworm.com/index.php?rid=5488534&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22146930%26dopt%3DAbstract Authors: Marvá M, Bravo de la Parra R, Auger P Abstract In this work we deal with a general class of spatially distributed periodic SIS epidemic models with two time scales. We let susceptible and infected individuals migrate between patches with periodic time dependent migration rates. The existence of two time scales in the system allows to describe certain features of the asymptotic behavior of its solutions with the help of a less dimensional, aggregated, system. We derive global reproduction numbers governing the general spatially distributed nonautonomous system through the aggregated system. We apply this result when the mass action law and the frequency dependent transmission law are considered. Comparing these global reproductive numbers to their non spatially distributed... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=5488534 Wed, 07 Dec 2011 05:00:00 +0100 5488534 http://www.medworm.com/index.php?rid=5375935&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22033649%26dopt%3DAbstract Authors: Clairambault J Abstract I will present here a personal point of view on the commitment of mathematicians in medicine. Starting from my personal experience, I will suggest generalisations including favourable signs and caveats to show how mathematicians can be welcome and helpful in medicine, both in a theoretical and in a practical way. PMID: 22033649 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=5375935 Fri, 28 Oct 2011 04:00:00 +0100 5375935 http://www.medworm.com/index.php?rid=5170814&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21863336%26dopt%3DAbstract Authors: Tal O Abstract The presence of gene-environment statistical interaction (GxE) and correlation (rGE) in biological development has led both practitioners and philosophers of science to question the legitimacy of heritability estimates. The paper offers a novel approach to assess the impact of GxE and rGE on the way genetic and environmental causation can be partitioned. A probabilistic framework is developed, based on a quantitative genetic model that incorporates GxE and rGE, offering a rigorous way of interpreting heritability estimates. Specifically, given an estimate of heritability and the variance components associated with estimates of GxE and rGE, I arrive at a probabilistic account of the relative effect of genes and environment. PMID: 21863336 [PubMed - as sup... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=5170814 Tue, 23 Aug 2011 23:00:00 +0100 5170814 http://www.medworm.com/index.php?rid=5088003&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21796418%26dopt%3DAbstract Authors: Gregorius HR Because of their elementary significance in almost all fields of science, measures of association between two variables or traits are abundant and multiform. One aspect of association that is of considerable interest, especially in population genetics and ecology, seems to be widely ignored. This aspect concerns association between complex traits that show variable and arbitrarily defined state differences. Among such traits are genetic characters controlled by many and potentially polyploid loci, species characteristics, and environmental variables, all of which may be mutually and asymmetrically associated. A concept of directed association of one trait with another is developed here that relies solely on difference measures between the states of a trait. Associ... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=5088003 Mon, 27 Jun 2011 23:00:00 +0100 5088003 http://www.medworm.com/index.php?rid=4994461&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21710316%26dopt%3DAbstract Authors: Tahan A, Monajjemi M Quantum mechanical and molecular dynamics methods were used to analyze the structure and stability of neutral and zwitterionic configurations of the extracted active site sequence from a Burkholderia cepacia lipase, histidyl-seryl-glutamin (His86-Ser87-Gln88) and its mutated form, histidyl-cysteyl-glutamin (His86-Cys87-Gln88) in vacuum and different solvents. The effects of solvent dielectric constant, explicit and implicit water molecules and side chain mutation on the structure and stability of this sequence in both neutral and zwitterionic forms are represented. The quantum mechanics computations represent that the relative stability of zwitterionic and neutral configurations depends on the solvent structure and its dielectric constant. Therefore, in va... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=4994461 Mon, 27 Jun 2011 23:00:00 +0100 4994461 http://www.medworm.com/index.php?rid=4896914&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21611886%26dopt%3DAbstract Authors: Mpeshe SC, Haario H, Tchuenche JM Rift Valley Fever is a vector-borne disease mainly transmitted by mosquito. To gain some quantitative insights into its dynamics, a deterministic model with mosquito, livestock, and human host is formulated as a system of nonlinear ordinary differential equations and analyzed. The disease threshold [Formula: see text] is computed and used to investigate the local stability of the equilibria. A sensitivity analysis is performed and the most sensitive model parameters to the measure of initial disease transmission [Formula: see text] and the endemic equilibrium are determined. Both [Formula: see text] and the disease prevalence in mosquitoes are more sensitive to the natural mosquito death rate, d ( m ). The disease prevalence in livestock and h... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=4896914 Wed, 25 May 2011 23:00:00 +0100 4896914 http://www.medworm.com/index.php?rid=4851032&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21559784%26dopt%3DAbstract Authors: Leeb C In organic farming animal welfare is one important aspect included in the internationally agreed organic principles of health, ecology, fairness and care (IFOAM 2006), reflecting expectation of consumers and farmers. The definition of organic animal welfare includes-besides traditional terms of animal welfare-'regeneration' and 'naturalness'. Organic animal welfare assessment needs to reflect this and use complex parameters, include natural behaviour and a systemic view. Furthermore, various parties with seemingly conflicting interests are involved, causing ethical dilemmas, such as the use of nose rings for outdoor sows (impaired animal welfare vs. destruction of humus). Solutions can only be found when foundational concepts are translated and applied to practical situ... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=4851032 Tue, 10 May 2011 23:00:00 +0100 4851032 http://www.medworm.com/index.php?rid=4797686&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21547567%26dopt%3DAbstract Authors: Hagen K, Van den Bos R, de Cock Buning T PMID: 21547567 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=4797686 Thu, 05 May 2011 23:00:00 +0100 4797686 http://www.medworm.com/index.php?rid=4797687&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21528359%26dopt%3DAbstract Authors: Kozusko F, Bourdeau M Sigmoid functions have been applied in many areas to model self limited population growth. The most popular functions; General Logistic (GL), General von Bertalanffy (GV), and Gompertz (G), comprise a family of functions called Theta Logistic ([Formula: see text] L). Previously, we introduced a simple model of tumor cell population dynamics which provided a unifying foundation for these functions. In the model the total population (N) is divided into reproducing (P) and non-reproducing/quiescent (Q) sub-populations. The modes of the rate of change of ratio P/N was shown to produce GL, GV or G growth. We now generalize the population dynamics model and extend the possible modes of the P/N rate of change. We produce a new family of sigmoid growth functions,... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=4797687 Thu, 28 Apr 2011 23:00:00 +0100 4797687 http://www.medworm.com/index.php?rid=4570933&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21347723%26dopt%3DAbstract Authors: Broom DM Human attitudes to animals have changed as non-humans have become more widely incorporated in the category of moral agents who deserve some respect. Parallels between the functioning of humans and non-humans have been made for thousands of years but the idea that the animals that we keep can suffer has spread recently. An improved understanding of motivation, cognition and the complexity of social behaviour in animals has led in the last 30 years to the rapid development of animal welfare science. Early attempts to define welfare referred to individuals being in harmony with nature but the first usable definition incorporated feelings and health as part of attempts to cope with the environment. Others considered that welfare is only about feelings but it is argued th... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=4570933 Thu, 24 Feb 2011 00:00:00 +0100 4570933 http://www.medworm.com/index.php?rid=4517123&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21336941%26dopt%3DAbstract Authors: Swart JA, Keulartz J As a reflection on recent debates on the value of wild animals we examine the question of the intrinsic value of wild animals in both natural and man-made surroundings. We examine the concepts being wild and domesticated. In our approach we consider animals as dependent on their environment, whether it is a human or a natural environment. Stressing this dependence we argue that a distinction can be made between three different interpretations of a wild animal's intrinsic value: a species-specific, a naturalistic, and an individualistic interpretation. According to the species-specific approach, the animal is primarily considered as a member of its species; according to the naturalistic interpretation, the animal is seen as dependent on the natural environm... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=4517123 Sun, 20 Feb 2011 00:00:00 +0100 4517123 http://www.medworm.com/index.php?rid=4517124&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21312052%26dopt%3DAbstract Authors: Schmidt K When animal ethicists deal with welfare they seem to face a dilemma: On the one hand, they recognize the necessity of welfare concepts for their ethical approaches. On the other hand, many animal ethicists do not want to be considered reformist welfarists. Moreover, animal welfare scientists may feel pressed by moral demands for a fundamental change in our attitude towards animals. The analysis of this conflict from the perspective of animal ethics shows that animal welfare science and animal ethics highly depend on each other. Welfare concepts are indispensable in the whole field of animal ethics. Evidence for this can be found by analyzing the structure of theories of animal ethics and the different ways in which these theories employ welfare concepts. Furthermore,... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=4517124 Fri, 11 Feb 2011 00:00:00 +0100 4517124 http://www.medworm.com/index.php?rid=4459494&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21305338%26dopt%3DAbstract Authors: Haynes RP Animal welfare has been conceptualized in such a way that the use of animals in science and for food seems justified. I argue that those who have done this have appropriated the concept of animal welfare, claiming to give a scientific account that is more objective than the "sentimental" account given by animal liberationists. This strategy seems to play a major role in supporting merely limited reform in the use of animals and seems to support the assumption that there are conditions under which animals may be raised and slaughtered for food that are ethically acceptable. Reformists do not need to make this assumption, but they tend to conceptualize animal welfare is such a way that death does not count as harmful to the interests of animals, nor prolonged life a be... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=4459494 Wed, 09 Feb 2011 00:00:00 +0100 4459494 http://www.medworm.com/index.php?rid=4459495&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21298322%26dopt%3DAbstract Authors: Nordenfelt L This paper contains a brief comparative analysis of some philosophical and scientific discourses on human and animal health and welfare, focusing mainly on the welfare of sentient animals. The paper sets forth two kinds of proposals for the analysis of animal welfare which do not appear in the contemporary philosophical discussion of human welfare, viz. the coping theory of welfare and the theory of welfare in terms of natural behaviour. These proposals are scrutinized in the light of some similar theories dealing with human health and quality of life. My conclusion is that the coping theory and the natural behaviour theory are not in themselves adequate for the characterization of welfare, either for humans or for sentient animals. I contend, finally, that, in th... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=4459495 Sat, 05 Feb 2011 00:00:00 +0100 4459495 http://www.medworm.com/index.php?rid=4245899&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21132517%26dopt%3DAbstract Authors: Raerinne J How are scientific explanations possible in ecology, given that there do not appear to be many-if any-ecological laws? To answer this question, I present and defend an account of scientific causal explanation in which ecological generalizations are explanatory if they are invariant rather than lawlike. An invariant generalization continues to hold or be valid under a special change-called an intervention-that changes the value of its variables. According to this account, causes are difference-makers that can be intervened upon to manipulate or control their effects. I apply the account to ecological generalizations to show that invariance under interventions as a criterion of explanatory relevance provides interesting interpretations for the explanatory status of ma... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=4245899 Sun, 05 Dec 2010 00:00:00 +0100 4245899 http://www.medworm.com/index.php?rid=3953813&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20821037%26dopt%3DAbstract Authors: Gaucherel C, Bérard S, Munoz F The issue of whether formal reasoning or a computing-intensive approach is the most efficient manner to address scientific questions is the subject of some considerable debate and pertains not only to the nature of the phenomena and processes investigated by scientists, but also the nature of the equation and algorithm objects they use. Although algorithms and equations both rely on a common background of mathematical language and logic, they nevertheless possess some critical differences. They do not refer to the same level of symbolization, as equations are based on integrated concepts in a denotational manner, while algorithms specifically break down a complex problem into more elementary operations, in an operational manner. They may there... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3953813 Sat, 04 Sep 2010 23:00:00 +0100 3953813 http://www.medworm.com/index.php?rid=3881940&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20711745%26dopt%3DAbstract Authors: Chopard B, Ouared R, Deutsch A, Hatzikirou H, Wolf-Gladrow D Lattice-gas cellular automaton (LGCA) and lattice Boltzmann (LB) models are promising models for studying emergent behaviour of transport and interaction processes in biological systems. In this chapter, we will emphasise the use of LGCA/LB models and the derivation and analysis of LGCA models ranging from the classical example dynamics of fluid flow to clotting phenomena in cerebral aneurysms and the invasion of tumour cells. PMID: 20711745 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3881940 Fri, 13 Aug 2010 23:00:00 +0100 3881940 http://www.medworm.com/index.php?rid=3869311&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20706773%26dopt%3DAbstract Authors: Gaudart J, Ghassani M, Mintsa J, Rachdi M, Waku J, Demongeot J The classical models of epidemics dynamics by Ross and McKendrick have to be revisited in order to incorporate elements coming from the demography (fecundity, mortality and migration) both of host and vector populations and from the diffusion and mutation of infectious agents. The classical approach is indeed dealing with populations supposed to be constant during the epidemic wave, but the presently observed pandemics show duration of their spread during years imposing to take into account the host and vector population changes as well as the transient or permanent migration and diffusion of hosts (susceptible or infected), as well as vectors and infectious agents. Two examples are presented, one concerning the ma... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3869311 Thu, 12 Aug 2010 23:00:00 +0100 3869311 http://www.medworm.com/index.php?rid=3823407&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20683639%26dopt%3DAbstract Authors: Pinto AA, Burroughs NJ, Ferreira M, Oliveira BM We analyse the effect of the regulatory T cells (Tregs) in the local control of the immune responses by T cells. We obtain an explicit formula for the level of antigenic stimulation of T cells as a function of the concentration of T cells and the parameters of the model. The relation between the concentration of the T cells and the antigenic stimulation of T cells is an hysteresis, that is unfold for some parameter values. We study the appearance of autoimmunity from cross-reactivity between a pathogen and a self antigen or from bystander proliferation. We also study an asymmetry in the death rates. With this asymmetry we show that the antigenic stimulation of the Tregs is able to control locally the population size of Tregs. Oth... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3823407 Tue, 03 Aug 2010 23:00:00 +0100 3823407 http://www.medworm.com/index.php?rid=3823406&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20683640%26dopt%3DAbstract Authors: Guillaud F, Hannaert P The renin-angiotensin system (RAS) is critical in sodium and blood pressure (BP) regulation, and in cardiovascular-renal (CVR) diseases and therapeutics. As a contribution to SAPHIR project, we present a realistic computer model of renin production and circulating RAS, integrated into Guyton's circulatory model (GCM). Juxtaglomerular apparatus, JGA, and Plasma modules were implemented in C ++/M2SL (Multi-formalism Multi-resolution Simulation Library) for fusion with GCM. Matlab((c)) optimization toolboxes were used for parameter identification. In JGA, renin production and granular cells recruitment (GCR) are controlled by perfusion pressure (PP), macula densa (MD), angiotensin II (Ang II), and renal sympathetic activity (RSNA). In Plasma, renin and ACE ... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3823406 Tue, 03 Aug 2010 23:00:00 +0100 3823406 http://www.medworm.com/index.php?rid=3823408&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20676732%26dopt%3DAbstract Authors: Geris L, Gerisch A, Schugart RC The processes of wound healing and bone regeneration and problems in tissue engineering have been an active area for mathematical modeling in the last decade. Here we review a selection of recent models which aim at deriving strategies for improved healing. In wound healing, the models have particularly focused on the inflammatory response in order to improve the healing of chronic wound. For bone regeneration, the mathematical models have been applied to design optimal and new treatment strategies for normal and specific cases of impaired fracture healing. For the field of tissue engineering, we focus on mathematical models that analyze the interplay between cells and their biochemical cues within the scaffold to ensure optimal nutrient transpo... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3823408 Fri, 30 Jul 2010 23:00:00 +0100 3823408 http://www.medworm.com/index.php?rid=3823409&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20676731%26dopt%3DAbstract Authors: Doumic M, Maia P, Zubelli JP The aim of this work is twofold. First, we survey the techniques developed in Perthame and Zubelli (Inverse Probl 23(3):1037-1052, 2007), Doumic et al. (Inverse Probl 25, 2009) to reconstruct the division (birth) rate from the cell volume distribution data in certain structured population structured population models. Secondly, we implement such techniques on experimental cell volume distributions available in the literature so as to validate the theoretical and numerical results. As a proof of concept, we use the experimental data experimental data reported in the classical work of Kubitschek (Biophys J 9(6):792-809, 1969) concerning Escherichia coli in vitro experiments measured by means of a Coulter transducer-multichannel analyzer system (Coult... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3823409 Thu, 29 Jul 2010 23:00:00 +0100 3823409 http://www.medworm.com/index.php?rid=3823410&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20668915%26dopt%3DAbstract Authors: Ben Amor H, Glade N, Lobos C, Demongeot J Limit cycles, because they are constituted of a periodic succession of states (discrete or continuous) constitute a good manner to store information. From any points of the state space reached after a perturbation or stimulation of the cognitive system storing this information, one can aim to join through a more or less long return trajectory a precise neighbourhood of the asymptotic trajectory at a specific moment (or a specific place) on the limit cycle, i.e. where the information of interest stands. We propose that the isochronal fibration, initially imagined and described by A. T. Winfree may be an excellent way to connect directly those two locations. Each isochron is indeed the set of points in temporal phase with one single poin... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3823410 Wed, 28 Jul 2010 23:00:00 +0100 3823410 http://www.medworm.com/index.php?rid=3823414&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20665070%26dopt%3DAbstract Authors: Alt W, Byrne H, Deutsch A At the beginning of this special issue of Acta Biotheoretica carrying the above title, we present a brief overview on currently important topics that have been brought up during the last "European Conference on Mathematical and Theoretical Biology" in Edinburgh. After emphasizing the need for a "synthetic biology" also from the side of theory, model building and analysis, we survey most plenary talks of this Conference and a selected series of eigth review articles, which are mainly related to corresponding minisymposia, reflecting the current state of the art and the lively discussion within this interdisciplinary field. PMID: 20665070 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3823414 Tue, 27 Jul 2010 23:00:00 +0100 3823414 http://www.medworm.com/index.php?rid=3823413&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20665071%26dopt%3DAbstract Authors: Houillon A, Bessière P, Droulez J When we perceive the external world, our brain has to deal with the incompleteness and uncertainty associated with sensory inputs, memory and prior knowledge. In theoretical neuroscience probabilistic approaches have received a growing interest recently, as they account for the ability to reason with incomplete knowledge and to efficiently describe perceptive and behavioral tasks. How can the probability distributions that need to be estimated in these models be represented and processed in the brain, in particular at the single cell level? We consider the basic function carried out by photoreceptor cells which consists in detecting the presence or absence of light. We give a system-level understanding of the process of phototransduction ba... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3823413 Tue, 27 Jul 2010 23:00:00 +0100 3823413 http://www.medworm.com/index.php?rid=3823412&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20665072%26dopt%3DAbstract Authors: Chapuisat G, Dronne MA, Grenier E, Hommel M, Boissel JP Ischemic stroke involves numerous and complex pathophysiological mechanisms including blood flow reduction, ionic exchanges, spreading depressions and cell death through necrosis or apoptosis. We used a mathematical model based on these phenomena to study the influences of intensity and duration of ischemia on the final size of the infarcted area. This model relies on a set of ordinary and partial differential equations. After a sensibility study, the model was used to carry out in silico experiments in various ischemic conditions. The simulation results show that the proportion of apoptotic cells increases when the intensity of ischemia decreases, which contributes to the model validation. The simulation results also sho... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3823412 Tue, 27 Jul 2010 23:00:00 +0100 3823412 http://www.medworm.com/index.php?rid=3823411&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20665073%26dopt%3DAbstract This study suggests new tools for analysis and reduction of biological networks. PMID: 20665073 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3823411 Tue, 27 Jul 2010 23:00:00 +0100 3823411 http://www.medworm.com/index.php?rid=3823416&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20661626%26dopt%3DAbstract We present the relation between the SIS stochastic model and the contact process introducing creation and annihilation operators. For the spatial stochastic epidemic reinfection model SIRI, where susceptibles S can become infected I, then recover and remain only partial immune against reinfection R, we present the phase transition lines using the mean field and the pair approximation for the moments. We use a scaling argument that allow us to determine analytically an explicit formula for the phase transition lines in pair approximation. PMID: 20661626 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3823416 Mon, 26 Jul 2010 23:00:00 +0100 3823416 http://www.medworm.com/index.php?rid=3823415&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20661627%26dopt%3DAbstract Authors: Tsaneva-Atanasova K, Osinga HM, Tabak J, Pedersen MG Secretion is a fundamental cellular process involving the regulated release of intracellular products from cells. Physiological functions such as neurotransmission, or the release of hormones and digestive enzymes, are all governed by cell secretion. Anomalies in the processes involved in secretion contribute to the development and progression of diseases such as diabetes and other hormonal disorders. To unravel the mechanisms that govern such diseases, it is essential to understand how hormones, growth factors and neurotransmitters are synthesized and processed, and how their signals are recognized, amplified and transmitted by intracellular signaling pathways in the target cells. Here, we discuss diverse aspects of the det... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3823415 Mon, 26 Jul 2010 23:00:00 +0100 3823415 http://www.medworm.com/index.php?rid=3791514&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20658170%26dopt%3DAbstract Authors: Enderling H, Chaplain MA, Hahnfeldt P Cancer is a complex disease, necessitating research on many different levels; at the subcellular level to identify genes, proteins and signaling pathways associated with the disease; at the cellular level to identify, for example, cell-cell adhesion and communication mechanisms; at the tissue level to investigate disruption of homeostasis and interaction with the tissue of origin or settlement of metastasis; and finally at the systems level to explore its global impact, e.g. through the mechanism of cachexia. Mathematical models have been proposed to identify key mechanisms that underlie dynamics and events at every scale of interest, and increasing effort is now being paid to multi-scale models that bridge the different scales. With more ... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3791514 Fri, 23 Jul 2010 23:00:00 +0100 3791514 http://www.medworm.com/index.php?rid=3791513&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20658171%26dopt%3DAbstract Authors: Pavlic TP, Passino KM Optimal foraging theory has been criticized for underestimating patch exploitation time. However, proper modeling of costs not only answers these criticisms, but it also explains apparently irrational behaviors like the sunk-cost effect. When a forager is sure to experience high initial costs repeatedly, the forager should devote more time to exploitation than searching in order to minimize the accumulation of said costs. Thus, increased recognition or reconnaissance costs lead to increased exploitation times in order to reduce the frequency of future costs, and this result can be used to explain paradoxical human preference for higher costs. In fact, this result also provides an explanation for how continuing a very costly task indefinitely provides the ... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3791513 Fri, 23 Jul 2010 23:00:00 +0100 3791513 http://www.medworm.com/index.php?rid=3791512&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20658172%26dopt%3DAbstract Authors: Viret J In this work, we compare two global approaches which are usually considered as completely unconnected one with the other. The former is Thom's topology and the latter is Jung's psychology. More precisely, it seemed to us interesting to adapt some morphologies of Thom's catastrophe theory to some Jung's notions. Thus, we showed that the swallowtail, which is one of these morphologies, was able to describe geometrically the structural organisation of the psyche according to Jung, with its collective unconscious, personal unconscious and conscious. Moreover, we have correlated this morphology with Jung's evolutive processes like individualisation and individuation. These comparisons incited us to think that some morphologies of Thom's catastrophe theory are the geometrica... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3791512 Fri, 23 Jul 2010 23:00:00 +0100 3791512 http://www.medworm.com/index.php?rid=3791511&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20658173%26dopt%3DAbstract Authors: Ben Miled S, Kebir A, Hbid ML Dusky groupers (Epinephelus marginatus) are characterized by a complex sex allocation strategies and overexploitation of bigger individuals. We developed an individual based model to investigate the long-term effects of density dependence on grouper population dynamics and to analyze the variabilities of extinction probabilities as a result of interacting mortalities at different life stages. We conduct several simulations with different forms of sex allocation functions and different combinations of mortality rates. The model was parametrized using data on dusky grouper populations from the literature. The most important insights produced by this simulation study are that density dependence of sex allocation is an evolutionarily stable strategy, ... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3791511 Fri, 23 Jul 2010 23:00:00 +0100 3791511 http://www.medworm.com/index.php?rid=3791510&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20658174%26dopt%3DAbstract Authors: Lemesle V, Mailleret L, Vaissayre M Toxic plants have been used for years in agriculture to control major crop pests. However, the continuous exposure of targeted pests to toxins dramatically increases the rate of resistance evolution (Gassman et al. in Annu Rev Entomol 54:147-163, 2009a; Tabashnik et al. Nat Biotechnol 26:199-202, 2008). To prevent or delay resistance, non toxic host plants can be used as refuges. Our study considers spatial and temporal refuges that are respectively implemented concurrently or alternatively a toxic crop. A conceptual model based on impulsive differential equations is proposed to describe the dynamics of the susceptible and resistant pest populations over time. The mathematical study enlightens threshold values of the proportion of the spatia... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3791510 Fri, 23 Jul 2010 23:00:00 +0100 3791510 http://www.medworm.com/index.php?rid=3791509&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20658175%26dopt%3DAbstract Authors: Colas F, Diard J, Bessière P How can an incomplete and uncertain model of the environment be used to perceive, infer, decide and act efficiently? This is the challenge that both living and artificial cognitive systems have to face. Symbolic logic is, by its nature, unable to deal with this question. The subjectivist approach to probability is an extension to logic that is designed specifically to face this challenge. In this paper, we review a number of frequently encountered cognitive issues and cast them into a common Bayesian formalism. The concepts we review are ambiguities, fusion, multimodality, conflicts, modularity, hierarchies and loops. First, each of these concepts is introduced briefly using some examples from the neuroscience, psychophysics or robotics literatu... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3791509 Fri, 23 Jul 2010 23:00:00 +0100 3791509 http://www.medworm.com/index.php?rid=3784967&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20652726%26dopt%3DAbstract Authors: Batzel JJ, Bachar M Several key areas in modeling the cardiovascular and respiratory control systems are reviewed and examples are given which reflect the research state of the art in these areas. Attention is given to the interrelated issues of data collection, experimental design, and model application including model development and analysis. Examples are given of current clinical problems which can be examined via modeling, and important issues related to model adaptation to the clinical setting. PMID: 20652726 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3784967 Thu, 22 Jul 2010 23:00:00 +0100 3784967 http://www.medworm.com/index.php?rid=3784966&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20652727%26dopt%3DAbstract Authors: Calabrese P, Baconnier P, Laouani A, Fontecave-Jallon J, Guméry PY, Eberhard A, Benchetrit G To study the interaction of forces that produce chest wall motion, we propose a model based on the lever system of Hillman and Finucane (J Appl Physiol 63(3):951-961, 1987) and introduce some dynamic properties of the respiratory system. The passive elements (rib cage and abdomen) are considered as elastic compartments linked to the open air via a resistive tube, an image of airways. The respiratory muscles (active) force is applied to both compartments. Parameters of the model are identified in using experimental data of airflow signal measured by pneumotachography and rib cage and abdomen signals measured by respiratory inductive plethysmography on eleven healthy volunteers in fiv... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3784966 Thu, 22 Jul 2010 23:00:00 +0100 3784966 http://www.medworm.com/index.php?rid=3784968&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20652367%26dopt%3DAbstract Authors: Calabrese P, Fontecave-Jallon J PMID: 20652367 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3784968 Tue, 20 Jul 2010 23:00:00 +0100 3784968 http://www.medworm.com/index.php?rid=3499460&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20407803%26dopt%3DAbstract Authors: Quintelier K, Van Speybroeck L, Braeckman J The impact of science on ethics forms since long the subject of intense debate. Although there is a growing consensus that science can describe morality and explain its evolutionary origins, there is less consensus about the ability of science to provide input to the normative domain of ethics. Whereas defenders of a scientific normative ethics appeal to naturalism, its critics either see the naturalistic fallacy committed or argue that the relevance of science to normative ethics remains undemonstrated. In this paper, we argue that current scientific normative ethicists commit no fallacy, that criticisms of scientific ethics contradict each other, and that scientific insights are relevant to normative inquiries by informing ethics a... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3499460 Tue, 20 Apr 2010 23:00:00 +0100 3499460 http://www.medworm.com/index.php?rid=3254862&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20140696%26dopt%3DAbstract Authors: Tchuenche JM, Khamis SA, Agusto FB, Mpeshe SC We formulate and analyze the dynamics of an influenza pandemic model with vaccination and treatment using two preventive scenarios: increase and decrease in vaccine uptake. Due to the seasonality of the influenza pandemic, the dynamics is studied in a finite time interval. We focus primarily on controlling the disease with a possible minimal cost and side effects using control theory which is therefore applied via the Pontryagin's maximum principle, and it is observed that full treatment effort should be given while increasing vaccination at the onset of the outbreak. Next, sensitivity analysis and simulations (using the fourth order Runge-Kutta scheme) are carried out in order to determine the relative importance of different fact... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3254862 Sun, 07 Feb 2010 00:00:00 +0100 3254862 http://www.medworm.com/index.php?rid=3031281&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19936626%26dopt%3DAbstract Authors: Bock WJ Variational evolutionary theory as advocated by Darwin is not a single theory, but a bundle of related but independent theories, namely: (a) variational evolution; (b) gradualism rather than large leaps; (c) processes of phyletic evolution and of speciation; (d) causes for the formation of varying individuals in populations and for the action of selective agents; and (e) all organisms evolved from a common ancestor. The first four are nomological-deductive explanations and the fifth is historical-narrative. Therefore evolutionary theory must be divided into nomological and historical theories which are both testable against objective empirical observations. To be scientific, historical evolutionary theories must be based on well corroborated nomological theories, both ... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=3031281 Sat, 21 Nov 2009 00:00:00 +0100 3031281 http://www.medworm.com/index.php?rid=2990093&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19907923%26dopt%3DAbstract Authors: Demongeot J The chronologic age classically used in demography is often unable to give useful information about which exact stage in development or aging processes has reached an organism. Hence, we propose here to explain in some applications for what reason the chronologic age fails in explaining totally the observed state of an organism, which leads to propose a new notion, the biological age. This biological age is essentially determined by the number of divisions before the Hayflick's limit the tissue or mitochondrion in a critical organ (in the sense where its loss causes the death of the whole organism) has already used for its development and adult phases. We give a precise definition of the biological age of an organ based on the Hayflick's limit of its cells and we i... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2990093 Thu, 12 Nov 2009 00:00:00 +0100 2990093 http://www.medworm.com/index.php?rid=2972170&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19894124%26dopt%3DAbstract Authors: López I, Gámez M, Garay J, Standovár T, Varga Z In ecology, if the considered area or space is large, the spatial distribution of individuals of a given plant species is never homogeneous; plants form different patches. The homogeneity change in space or in time (in particular, the related change-point problem) is an important research subject in mathematical statistics. In the paper, for a given data system along a straight line, two areas are considered, where the data of each area come from different discrete distributions, with unknown parameters. In the paper a method is presented for the estimation of the distribution change-point between both areas and an estimate is given for the distributions separated by the obtained change-point. The solution of this ... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2972170 Fri, 06 Nov 2009 00:00:00 +0100 2972170 http://www.medworm.com/index.php?rid=2944001&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19865801%26dopt%3DAbstract Authors: Le Rolle V, Carrault G, Richard PY, Pibarot P, Durand LG, Hernández AI The ventricular pressure profile is characteristic of the cardiac contraction progress and is useful to evaluate the cardiac performance. In this contribution, a tissue-level electromechanical model of the left ventricle is proposed, to assist the interpretation of left ventricular pressure waveforms. The left ventricle has been modeled as an ellipsoid composed of twelve mechano-hydraulic sub-systems. The asynchronous contraction of these twelve myocardial segments has been represented in order to reproduce a realistic pressure profiles. To take into account the different energy domains involved, the tissue-level scale and to facilitate the building of a modular model, multiple formalisms have been use... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2944001 Thu, 29 Oct 2009 00:00:00 +0100 2944001 http://www.medworm.com/index.php?rid=2935198&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19855929%26dopt%3DAbstract Authors: Arino J, Portet S PMID: 19855929 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2935198 Sat, 24 Oct 2009 00:00:00 +0100 2935198 http://www.medworm.com/index.php?rid=2935197&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19855930%26dopt%3DAbstract Ins and Outs of Systems Biology vis-à-vis Molecular Biology: Continuation or Clear Cut? Acta Biotheor. 2009 Oct 24; Authors: De Backer P, De Waele D, Van Speybroeck L The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology 'revolutionizes' molecular biology and 'transcends' its assumed reductionism. The strength of this claim appears to depend on how molecular and systems b... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2935197 Sat, 24 Oct 2009 00:00:00 +0100 2935197 http://www.medworm.com/index.php?rid=2909533&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19842047%26dopt%3DAbstract Authors: Serghini M, Boutayeb A, Auger P, Charouki N, Ramzi A, Ettahiri O, Tchuente M In this paper, we present a deterministic time discrete mathematical model based on multiregional periodic matrices to describe the dynamics of Sardina pilchardus in the Central Atlantic area of the Moroccan coast. This model deals with two stages (immature and mature) and three spatial zones where sardines are supposed to migrate from one zone to another. The population dynamics is described by an autonomous recurrence equation N(t + 1) = A.N(t), where A is a positive matrix whose entries are estimated using data collected during biannual acoustic surveys carried out from 2001 to 2003 onboard the Norwegian research vessel "Dr Fridtjof Nansen". The dominant eigenvalue lambda of A that gives the long-t... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2909533 Mon, 19 Oct 2009 23:00:00 +0100 2909533 http://www.medworm.com/index.php?rid=2909534&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19838808%26dopt%3DAbstract Authors: Farcot E, Gouzé JL This paper concerns periodic solutions of a class of equations that model gene regulatory networks. Unlike the vast majority of previous studies, it is not assumed that all decay rates are identical. To handle this more general situation, we rely on monotonicity properties of these systems. Under an alternative assumption, it is shown that a classical fixed point theorem for monotone, concave operators can be applied to these systems. The required assumption is expressed in geometrical terms as an alignment condition on so-called focal points. As an application, we show the existence and uniqueness of a stable periodic orbit for negative feedback loop systems in dimension 3 or more, and of a unique stable equilibrium point in dimension 2. This extends a... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2909534 Wed, 07 Oct 2009 23:00:00 +0100 2909534 http://www.medworm.com/index.php?rid=2877138&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19809880%26dopt%3DAbstract We present a multitype global model that incorporates the effect of both processes and, making use of the existence of different time scales for demography and migration, build a reduced model in which the variables correspond to the total population in each age class. We extend previous results that relate the behavior of the original and the reduced model showing that, given a large enough separation of time scales between demography and migration, we can obtain information about the behavior of the multitype global model through the study of the simpler reduced model. We concentrate on the case where the two systems are supercritical and therefore the expected number of individuals grows to infinity, and show that we can approximate the asymptotic structure of the population vector and ... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2877138 Tue, 06 Oct 2009 23:00:00 +0100 2877138 http://www.medworm.com/index.php?rid=2829006&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19774465%26dopt%3DAbstract Authors: Dibrov A, Myal Y, Leygue E The prediction of protein-protein interactions based on independently obtained structural information for each interacting partner remains an important challenge in computational chemistry. Procedures where hypothetical interaction models (or decoys) are generated, then ranked using a biochemically relevant scoring function have been garnering interest as an avenue for addressing such challenges. The program PatchDock has been shown to produce reasonable decoys for modeling the association between pig alpha-amylase and the VH-domains of camelide antibody raised against it. We designed a biochemically relevant method by which PatchDock decoys could be ranked in order to separate near-native structures from false positives. Several thousand steps of en... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2829006 Tue, 22 Sep 2009 23:00:00 +0100 2829006 http://www.medworm.com/index.php?rid=2674955&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19653128%26dopt%3DAbstract Authors: Russell MJ PMID: 19653128 [PubMed - in process] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2674955 Thu, 06 Aug 2009 19:20:05 +0100 2674955 http://www.medworm.com/index.php?rid=2546246&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19533376%26dopt%3DAbstract Authors: Zhao LP, Lv YH, Li C, Yao MH, Jin XZ The main idea of S-curve diagram is to assign different angle values (from 0 degrees to 180 degrees ) to different nucleotide acid residues or to different protein amino acids, and then according to cos alpha ( j ) and sin alpha ( j ), the values are accumulated to construct an S-curve diagram, which is in strict one-to-one correspondence with the biological sequence. In addition, the S-curve diagram proves to be without the degeneracy phenomenon, so that both the degeneracy problem represented by diagrams and the problem of visualization for biological sequence data are solved. Meanwhile, a new approach to differentiate the similarity of biological sequences-the degree of similarity-is put forward on the basis of the S-curve diagram. To pu... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2546246 Mon, 15 Jun 2009 23:00:00 +0100 2546246 http://www.medworm.com/index.php?rid=2546248&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19507040%26dopt%3DAbstract Authors: Vergara-Silva F Despite the amount of work that has been produced on the subject over the years, the 'transformation of cladistics' is still a misunderstood episode in the history of comparative biology. Here, I analyze two outstanding, highly contrasting historiographic accounts on the matter, under the perspective of an influential dichotomy in the philosophy of science: the opposition between Scientific Realism and Empiricism. Placing special emphasis on the notion of 'causal grounding' of morphological characters (sensu Olivier Rieppel) in modern developmental biology's (mechanistic) theories, I arrive at the conclusion that a 'new transformation of cladistics' is philosophically plausible. This 'reformed' understanding of 'pattern cladistics' entails retaining the interpr... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2546248 Sun, 31 May 2009 23:00:00 +0100 2546248 http://www.medworm.com/index.php?rid=2546247&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19507041%26dopt%3DAbstract Authors: Vergara-Silva F PMID: 19507041 [PubMed - in process] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2546247 Sun, 31 May 2009 23:00:00 +0100 2546247 http://www.medworm.com/index.php?rid=2323872&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19357968%26dopt%3DAbstract Authors: Bhunu CP, Garira W, Magombedze G A two strain HIV/AIDS model with treatment which allows AIDS patients with sensitive HIV-strain to undergo amelioration is presented as a system of non-linear ordinary differential equations. The disease-free equilibrium is shown to be globally asymptotically stable when the associated epidemic threshold known as the basic reproduction number for the model is less than unity. The centre manifold theory is used to show that the sensitive HIV-strain only and resistant HIV-strain only endemic equilibria are locally asymptotically stable when the associated reproduction numbers are greater than unity. Qualitative analysis of the model including positivity, boundedness and persistence of solutions are presented. The model is numerically analysed to ... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2323872 Thu, 09 Apr 2009 04:00:00 +0100 2323872 http://www.medworm.com/index.php?rid=2323877&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19350210%26dopt%3DAbstract Authors: Schwartz JH I attempt to raise questions regarding elements of systematics-primarily in the realm of phylogenetic reconstruction-in order to provoke discussion on the current state of affairs in this discipline, and also evolutionary biology in general: e.g., conceptions of homology and homoplasy, hypothesis testing, the nature of and objections to Hennigian "phylogenetic systematics", and the schism between (neo)Darwinian descendants of the "modern evolutionary synthesis" and their supposed antagonists, cladists and punctuationalists. PMID: 19350210 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2323877 Tue, 07 Apr 2009 04:00:00 +0100 2323877 http://www.medworm.com/index.php?rid=2323880&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19343507%26dopt%3DAbstract Authors: Vergara-Silva F, Winther RG PMID: 19343507 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2323880 Fri, 03 Apr 2009 04:00:00 +0100 2323880 http://www.medworm.com/index.php?rid=2238076&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19259623%26dopt%3DAbstract Authors: Winther RG PMID: 19259623 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2238076 Wed, 04 Mar 2009 05:00:00 +0100 2238076 http://www.medworm.com/index.php?rid=2203846&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19229636%26dopt%3DAbstract Authors: Winther RG PMID: 19229636 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2203846 Fri, 20 Feb 2009 05:00:00 +0100 2203846 http://www.medworm.com/index.php?rid=2203845&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19229637%26dopt%3DAbstract Authors: Mc Manus FG This paper addresses the general problem of how to rationally choose an algorithm for phylogenetic inference. Specifically, the controversy between maximum likelihood (ML) and maximum parsimony (MP) perspectives is reframed within the philosophical issue of theory choice. A Kuhnian approach in which rationality is bounded and value-laden is offered and construed through the notion of a Style of Modeling. A Style is divided into four stages: collecting remnant models, constructing models of taxonomical identity, implementing modeling algorithms, and finally inferring and confirming evolutionary trees or cladograms. The identification and investigation of styles is useful for exploring sociological and epistemological issues such as individuating scientific communiti... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2203845 Fri, 20 Feb 2009 05:00:00 +0100 2203845 http://www.medworm.com/index.php?rid=2198428&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19224376%26dopt%3DAbstract Authors: Fitzhugh K The formal definition of species as explanatory hypotheses presented by Fitzhugh (Marine Biol 26:155-165, 2005a, b) is emended. A species is an explanatory account of the occurrences of the same character(s) among gonochoristic or cross-fertilizing hermaphroditic individuals by way of character origin and subsequent fixation during tokogeny. In addition to species, biological systematics also employs hypotheses that are ontogenetic, tokogenetic, intraspecific, and phylogenetic, each of which provides explanatory hypotheses for distinctly different classes of causal questions. It is suggested that species hypotheses can not be applied to organisms with obligate asexual, parthenogenetic, and self-fertilizing modes of reproduction. Hypotheses explaining shared characte... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2198428 Wed, 18 Feb 2009 05:00:00 +0100 2198428 http://www.medworm.com/index.php?rid=2162803&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19190984%26dopt%3DAbstract Authors: Kluge AG Deduction leads to causal explanation in phylogenetic inference when the evidence, the systematic character, is conceptualized as a transformation series. Also, the deductive entailment of modus tollens is satisfied when those kinds of events are operationalized as patristic difference. Arguments to the contrary are based largely on the premise that character-states are defined intensionally as objects, in terms of similarity relations. However, such relations leave biologists without epistemological access to the causal explanation and explanatory power of historical statements. Moreover, the prediction-making to which those kinds of relations are limited in practice can lead to a category error-the mental conversion of an abstraction (the classes defined in terms of... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2162803 Wed, 04 Feb 2009 05:00:00 +0100 2162803 http://www.medworm.com/index.php?rid=2155407&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19184455%26dopt%3DAbstract Authors: Imre AR, Rocchini D Different summarized shape indices, like mean shape index (MSI) and area weighted mean shape index (AWMSI) can change over multiple size scales. This variation is important to describe scale heterogeneity of landscapes, but the exact mathematical form of the dependence is rarely known. In this paper, the use of fractal geometry (by the perimeter and area Hausdorff dimensions) made us able to describe the scale dependence of these indices. Moreover, we showed how fractal dimensions can be deducted from existing MSI and AWMSI data. In this way, the equality of a multiscale tabulated MSI and AWMSI dataset and two scale-invariant fractal dimensions has been demonstrated. PMID: 19184455 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2155407 Thu, 29 Jan 2009 05:00:00 +0100 2155407 http://www.medworm.com/index.php?rid=2155406&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19184456%26dopt%3DAbstract This study on the cambium of Pinus sylvestris L. examines the intrusive growth of fusiform cambial initials and its possible contribution to the tangential and radial expansions of the cambial cylinder. The location and extent of intrusive growth of the fusiform initials were determined by microscopic observations and by mathematical modeling. In order to meet the required circumferential expansion of the cambial cylinder, the fusiform initials grow in groups by means of a symplastic rather than intrusive growth, leaving no room for the assumption that intrusive growth of the initials takes place between radial walls and has a direct role in the increase of the cambial circumference. Therefore, it is postulated that the fusiform initials grow intrusively between the tangential walls of the... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2155406 Thu, 29 Jan 2009 05:00:00 +0100 2155406 http://www.medworm.com/index.php?rid=2136747&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19169652%26dopt%3DAbstract Authors: Lin H, Wang H, Ding H, Chen YL, Li QZ Apoptosis proteins play an essential role in regulating a balance between cell proliferation and death. The successful prediction of subcellular localization of apoptosis proteins directly from primary sequence is much benefited to understand programmed cell death and drug discovery. In this paper, by use of Chou's pseudo amino acid composition (PseAAC), a total of 317 apoptosis proteins are predicted by support vector machine (SVM). The jackknife cross-validation is applied to test predictive capability of proposed method. The predictive results show that overall prediction accuracy is 91.1% which is higher than previous methods. Furthermore, another dataset containing 98 apoptosis proteins is examined by proposed method. The overall pred... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2136747 Sat, 24 Jan 2009 05:00:00 +0100 2136747 http://www.medworm.com/index.php?rid=2091736&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19130250%26dopt%3DAbstract Authors: Winther RG The dangers of character reification for cladistic inference are explored. The identification and analysis of characters always involves theory-laden abstraction-there is no theory-free "view from nowhere." Given theory-ladenness, and given a real world with actual objects and processes, how can we separate robustly real biological characters from uncritically reified characters? One way to avoid reification is through the employment of objectivity criteria that give us good methods for identifying robust primary homology statements. I identify six such criteria and explore each with examples. Ultimately, it is important to minimize character reification, because poor character analysis leads to dismal cladograms, even when proper phylogenetic analysis is employed. ... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=2091736 Wed, 07 Jan 2009 05:00:00 +0100 2091736 http://www.medworm.com/index.php?rid=1973379&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19015816%26dopt%3DAbstract Discussion of this "total evidence" approach leads to several interesting conclusions about generating ToL hypotheses. PMID: 19015816 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1973379 Tue, 18 Nov 2008 05:00:00 +0100 1973379 http://www.medworm.com/index.php?rid=1913707&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18953656%26dopt%3DAbstract Authors: Fenlon JS, Faddy MJ, Toussidou M, de Courcy Williams ME A simple numerical procedure is presented for the problem of estimating the parameters of models for the distribution of eggs oviposited in a host. The modelling is extended to incorporate both host density and time dependence to produce a remarkably parsimonious structure with only seven parameters to describe a data set of over 3,000 observations. This is further refined using a mixed model to accommodate several large outliers. Both models show that the level of superparasitism declines with increasing host density, and the rate declines over time. It is proposed that the differing behaviours represented by the mixed model may reflect a balance between behavioural strategies of different selective benefit. PMID: 18... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1913707 Sat, 25 Oct 2008 04:00:00 +0100 1913707 http://www.medworm.com/index.php?rid=1899535&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18941903%26dopt%3DAbstract Authors: Bani-Yaghoub M, Amundsen DE Possible effects of interaction (cross-talk) between signaling pathways is studied in a system of Reaction-Diffusion (RD) equations. Furthermore, the relevance of spontaneous neurite symmetry breaking and Turing instability has been examined through numerical simulations. The interaction between Retinoic Acid (RA) and Notch signaling pathways is considered as a perturbation to RD system of axon-forming potential for N2a neuroblastoma cells. The present work suggests that large increases to the level of RA-Notch interaction can possibly have substantial impacts on neurite outgrowth and on the process of axon formation. This can be observed by the numerical study of the homogeneous system showing that in the absence of RA-Notch interaction the unpertu... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1899535 Wed, 22 Oct 2008 04:00:00 +0100 1899535 http://www.medworm.com/index.php?rid=1867362&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18843538%26dopt%3DAbstract Authors: Aubert M, Badoual M, Grammaticos B We examine the consequences of long-range effects on tumour cell migration. Our starting point are previous results of ours where we have shown that the migration patterns of glioma cells are best interpreted if one assumes attractive interactions between cells. Here we complement the cellular automaton model previously introduced by the assumption of the existence of a chemorepellent produced by the main bulk of large spheroids (in the hypoxic/necrotic areas). Visible effects due to the presence of such a substance can be found in the density profiles of cells migrating out of a single spheroid as well as in the angular distribution of cells coming from two close-lying spheroids. These effects depend crucially on the diffusion speed of the c... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1867362 Thu, 09 Oct 2008 04:00:00 +0100 1867362 http://www.medworm.com/index.php?rid=1847063&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18827974%26dopt%3DAbstract Authors: Love AC The goal of this paper is to encourage a reconfiguration of the discussion about typology in biology away from the metaphysics of essentialism and toward the epistemology of classifying natural phenomena for the purposes of empirical inquiry. First, I briefly review arguments concerning 'typological thinking', essentialism, species, and natural kinds, highlighting their predominantly metaphysical nature. Second, I use a distinction between the aims, strategies, and tactics of science to suggest how a shift from metaphysics to epistemology might be accomplished. Typological thinking can be understood as a scientific tactic that involves representing natural phenomena using idealizations and approximations, which facilitates explanation, investigation, and theorizing via... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1847063 Tue, 30 Sep 2008 04:00:00 +0100 1847063 http://www.medworm.com/index.php?rid=1843402&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18825502%26dopt%3DAbstract Authors: Williams DM, Ebach MC The development of comparative biology (systematics) has been of interest to philosophers and historians. Particular attention has been placed on the 'war' of the 1970s and 1980s, the apparent dispute among those who preferred this or that methodology. In this contribution we examine the history of comparative biology from the perspective of fundamentals rather than methodologies. Our examination is framed within the artificial-natural classification dichotomy, a viewpoint currently lost from view but worth resurrecting. PMID: 18825502 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1843402 Tue, 30 Sep 2008 04:00:00 +0100 1843402 http://www.medworm.com/index.php?rid=1828489&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18813877%26dopt%3DAbstract Authors: Rieppel O Species are generally considered to be the basic units of evolution, and hence to constitute spatio-temporally bounded entities. In addition, it has been argued that species also instantiate a natural kind. Evolution is fundamentally about change. The question then is how species can remain the same through evolutionary change. Proponents of the species qua individuals thesis individuate species through their unique evolutionary origin. Individuals, or spatio-temporally located particulars in general, can be bodies, objects, events, or processes, or a combination of these. It is here argued that species are best understood as open or closed, causally integrated processual systems that also instantiate an historically conditioned homeostatic property cluster natural k... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1828489 Wed, 24 Sep 2008 04:00:00 +0100 1828489 http://www.medworm.com/index.php?rid=1810861&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18802777%26dopt%3DAbstract Authors: Brigandt I Despite the traditional focus on metaphysical issues in discussions of natural kinds in biology, epistemological considerations are at least as important. By revisiting the debate as to whether taxa are kinds or individuals, I argue that both accounts are metaphysically compatible, but that one or the other approach can be pragmatically preferable depending on the epistemic context. Recent objections against construing species as homeostatic property cluster kinds are also addressed. The second part of the paper broadens the perspective by considering homologues as another example of natural kinds, comparing them with analogues as functionally defined kinds. Given that there are various types of natural kinds, I discuss the different theoretical purposes served by d... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1810861 Fri, 19 Sep 2008 04:00:00 +0100 1810861 http://www.medworm.com/index.php?rid=1789755&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18787960%26dopt%3DAbstract Authors: Melkikh AV An analogy between the evolution of organisms and some complex computational problems (cryptosystem cracking, determination of the shortest path in a graph) is considered. It is shown that in the absence of a priori information about possible species of organisms such a problem is complex (is rated in the class NP) and cannot be solved in a polynomial number of steps. This conclusion suggests the need for re-examination of evolution mechanisms. Ideas of a deterministic approach to the evolution are discussed. PMID: 18787960 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1789755 Fri, 12 Sep 2008 04:00:00 +0100 1789755 http://www.medworm.com/index.php?rid=1778115&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18777162%26dopt%3DAbstract Authors: Griffiths PE Dobzhansky argued that biology only makes sense if life on earth has a shared history. But his dictum is often reinterpreted to mean that biology only makes sense in the light of adaptation. Some philosophers of science have argued in this spirit that all work in 'proximal' biosciences such as anatomy, physiology and molecular biology must be framed, at least implicitly, by the selection histories of the organisms under study. Others have denied this and have proposed non-evolutionary ways in which biologists can frame these investigations. This paper argues that an evolutionary perspective is indeed necessary, but that it must be a forward-looking perspective informed by a general understanding of the evolutionary process, not a backward-looking perspective infor... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1778115 Sat, 06 Sep 2008 04:00:00 +0100 1778115 http://www.medworm.com/index.php?rid=1614064&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18618269%26dopt%3DAbstract Authors: Camargo JA The Shannon information function (H) has been extensively used in ecology as a statistic of species diversity. Yet, the use of Shannon diversity index has also been criticized, mainly because of its ambiguous ecological interpretation and because of its relatively great sensitivity to the relative abundances of species in the community. In my opinion, the major shortcoming of the traditional perspective (on the possible relation of species diversity with information theory) is that species need for an external receiver (the scientist or ecologist) to exist and transmit information. Because organisms are self-catalized replicating structures that can transmit genotypic information to offspring, it should be evident that any single species has two possible states or a... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1614064 Fri, 11 Jul 2008 04:00:00 +0100 1614064 http://www.medworm.com/index.php?rid=1506172&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18542843%26dopt%3DAbstract Authors: Soto AM, Sonnenschein C, Miquel PA The dominant position in Philosophy of Science contends that downward causation is an illusion. Instead, we argue that downward causation doesn't introduce vicious circles either in physics or in biology. We also question the metaphysical claim that "physical facts fix all the facts." Downward causation does not imply any contradiction if we reject the assumption of the completeness and the causal closure of the physical world that this assertion contains. We provide an argument for rejecting this assumption. Furthermore, this allows us to reconsider the concept of diachronic emergence. PMID: 18542843 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1506172 Tue, 10 Jun 2008 04:00:00 +0100 1506172 http://www.medworm.com/index.php?rid=1433379&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18465197%26dopt%3DAbstract Authors: Sternberg RV Recently the terms "codes" and "information" as used in the context of molecular biology have been the subject of much discussion. Here I propose that a variety of structural realism can assist us in rethinking the concepts of DNA codes and information apart from semantic criteria. Using the genetic code as a theoretical backdrop, a necessary distinction is made between codes qua symbolic representations and information qua structure that accords with data. Structural attractors are also shown to be entailed by the mapping relation that any DNA code is a part of (as the domain). In this framework, these attractors are higher-order informational structures that obviate any "DNA-centric" reductionism. In addition to the implications that are discussed, this approach... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1433379 Fri, 09 May 2008 04:00:00 +0100 1433379 http://www.medworm.com/index.php?rid=1345657&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18379882%26dopt%3DAbstract Authors: Kasperski A This paper presents an integrated model describing the control of Saccharomyces cerevisiae yeast cells bioenergetics. This model describes the oxidative and respirofermentative metabolism. The model assumes that the mitochondria of the Saccharomyces cerevisiae cells are charged with NADH during the tricarboxylic acid cycle, and NADH is discharged from mitochondria later in the electron transport system. Selected effects observed in the Saccharomyces cerevisiae eucaryotic cells, including the Pasteur's and Crabtree effects, are also modeled. PMID: 18379882 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1345657 Tue, 01 Apr 2008 04:00:00 +0100 1345657 http://www.medworm.com/index.php?rid=1345656&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18379883%26dopt%3DAbstract Authors: Demongeot J, Elena A, Sené S We give in this paper indications about the dynamical impact (as phenotypic changes) coming from the main sources of perturbation in biological regulatory networks. First, we define the boundary of the interaction graph expressing the regulations between the main elements of the network (genes, proteins, metabolites, ...). Then, we search what changes in the state values on the boundary could cause some changes of states in the core of the system (robustness to boundary conditions). After, we analyse the role of the mode of updating (sequential, block sequential or parallel) on the asymptotics of the network, essentially on the occurrence of limit cycles (robustness to updating methods). Finally, we show the influence of some topological chang... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1345656 Tue, 01 Apr 2008 04:00:00 +0100 1345656 http://www.medworm.com/index.php?rid=1342865&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18373070%26dopt%3DAbstract In this study, we address the question of building confidence bounds around the predictions of matrix models due to sampling variability. We focus on a density-dependent Usher model, the maximum likelihood estimator of parameters, and the predicted stationary stage vector. The asymptotic distribution of the stationary stage vector is specified, assuming that the parameters of the model remain in a set of the parameter space where the model admits one unique equilibrium point. Tests for density-dependence are also incidentally provided. The model is applied to a tropical rain forest in French Guiana. PMID: 18373070 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1342865 Sat, 29 Mar 2008 04:00:00 +0100 1342865 http://www.medworm.com/index.php?rid=1313426&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18347755%26dopt%3DAbstract Authors: Gorelick R Extensive empirical work has shown that species richness decreases roughly exponentially or quadratically with latitude. What appears to be a latitudinal gradient in fact may simply be a negative correlation of latitude with area at that latitude, due to convergence of lines of meridian at the poles. There is simply less area at high latitudes, which means fewer niches and fewer opportunities for speciation, hence diminished biodiversity at high latitudes. Similarly, analytic geometry of a cone shows that species number should decrease linearly with altitude on a conical mountain. Here, I provide an explicit mathematical model of the area hypothesis of species richness along latitude and altitude gradients. I re-analyze a previously published latitudinal gradient da... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1313426 Tue, 18 Mar 2008 04:00:00 +0100 1313426 http://www.medworm.com/index.php?rid=1249562&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18288572%26dopt%3DAbstract Authors: Bizzarri M, Cucina A, Conti F, D'Anselmi F In the past decades, an enormous amount of precious information has been collected about molecular and genetic characteristics of cancer. This knowledge is mainly based on a reductionistic approach, meanwhile cancer is widely recognized to be a 'system biology disease'. The behavior of complex physiological processes cannot be understood simply by knowing how the parts work in isolation. There is not solely a matter how to integrate all available knowledge in such a way that we can still deal with complexity, but we must be aware that a deeply transformation of the currently accepted oncologic paradigm is urgently needed. We have to think in terms of biological networks: understanding of complex functions may in fact be impossible wit... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1249562 Thu, 21 Feb 2008 05:00:00 +0100 1249562 http://www.medworm.com/index.php?rid=1236593&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18274863%26dopt%3DAbstract Authors: Forest L, Demongeot J Morphogenesis is a key process in developmental biology. An important issue is the understanding of the generation of shape and cellular organisation in tissues. Despite of their great diversity, morphogenetic processes share common features. This work is an attempt to describe this diversity using the same formalism based on a cellular description. Tissue is seen as a multi-cellular system whose behaviour is the result of all constitutive cells dynamics. Morphogenesis is then considered as a spatiotemporal organization of cells activities. We show how this formalism relies on Reaction-Diffusion/Positional Information approach and how it permits to generalize its modelling possibilities. Three quite different applications for concrete morphogenetic proces... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1236593 Fri, 15 Feb 2008 05:00:00 +0100 1236593 http://www.medworm.com/index.php?rid=1234040&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18273682%26dopt%3DAbstract Authors: Kouokam E, Auger P, Hbid H, Tchuente M We consider a two-patch epidemiological system where individuals can move from one patch to another, and local interactions between the individuals within a patch are governed by the classical SIRS model. When the time-scale associated with migration is much smaller than the time-scale associated with infection, aggregation methods can be used to simplify the initial complete model formulated as a system of ordinary differential equations. Analysis of the aggregated model then shows that the two-patch basic reproduction rate is smaller than the 1 patch one. We extend this result to a linear chain of P patches (P > 2). These results are illustrated by some examples for which numerical integration of the system of ordinary differential e... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1234040 Thu, 14 Feb 2008 05:00:00 +0100 1234040 http://www.medworm.com/index.php?rid=1234039&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18273683%26dopt%3DAbstract Authors: Demongeot J, Glade N, Moreira A The genetic code has evolved from its initial non-degenerate wobble version until reaching its present state of degeneracy. By using the stereochemical hypothesis, we revisit the problem of codon assignations to the synonymy classes of amino-acids. We obtain these classes with a simple classifier based on physico-chemical properties of nucleic bases, like hydrophobicity and molecular weight. Then we propose simple RNA (or more generally XNA, with X for D, P or R) ring structures that present, overlap included, one and only one codon by synonymy class as solutions of a combinatory variational problem. We compare these solutions to sequences of present RNAs considered as relics, with a high interspecific invariance, like invariant parts of (t)RNAs... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1234039 Thu, 14 Feb 2008 05:00:00 +0100 1234039 http://www.medworm.com/index.php?rid=1211465&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18247133%26dopt%3DAbstract Authors: Pischedda L, Poggiale JC, Cuny P, Gilbert F The influence of sediment oxygen heterogeneity, due to bioturbation, on diffusive oxygen flux was investigated. Laboratory experiments were carried out with 3 macrobenthic species presenting different bioturbation behaviour patterns: the polychaetes Nereis diversicolor and Nereis virens, both constructing ventilated galleries in the sediment column, and the gastropod Cyclope neritea, a burrowing species which does not build any structure. Oxygen two-dimensional distribution in sediments was quantified by means of the optical planar optode technique. Diffusive oxygen fluxes (mean and integrated) and a variability index were calculated on the captured oxygen images. All species increased sediment oxygen heterogeneity compared to the co... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1211465 Tue, 05 Feb 2008 05:00:00 +0100 1211465 http://www.medworm.com/index.php?rid=1211464&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18247134%26dopt%3DAbstract Authors: Medkour T, Ferrone F, Galactéros F, Hannaert P Sickle cell haemoglobin (HbS) polymerization reduces erythrocyte deformability, causing deleterous vaso-occlusions. The double-nucleation model states that polymers grow from HbS aggregates, the nuclei, (i) in solution (homogeneous nucleation), (ii) onto existing polymers (heterogeneous nucleation). When linearized at initial HbS concentration, this model predicts early polymerization and its characteristic delay-time (Ferrone et al. J Mol Biol 183(4):591-610, 611-631, 1985). Addressing its relevance for describing complete polymerization, we constructed the full, non-linearized model (Simulink((R)), The MathWorks). Here, we compare the simulated outputs to experimental progress curves (n = 6-8 different [HbS], 3-6 mM range, ... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1211464 Tue, 05 Feb 2008 05:00:00 +0100 1211464 http://www.medworm.com/index.php?rid=1211463&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18247135%26dopt%3DAbstract A Mechanistic Investigation of the Algae Growth "Droop" Model. Acta Biotheor. 2008 Feb 5; Authors: Lemesle V, Mailleret L In this work a mechanistic explanation of the classical algae growth model built by M. R. Droop in the late sixties is proposed. We first recall the history of the construction of the "predictive" variable yield Droop model as well as the meaning of the introduced cell quota. We then introduce some theoretical hypotheses on the biological phenomena involved in nutrient storage by the algae that lead us to a "conceptual" model. Though more complex than Droop's one, our model remains accessible to a complete mathematical study: its confrontation to the Droop model shows both have the same asymptotic behavior. However, while Droop's cell quota comes from experi... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1211463 Tue, 05 Feb 2008 05:00:00 +0100 1211463 http://www.medworm.com/index.php?rid=1190693&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18231864%26dopt%3DAbstract In conclusion, the model reproduces dynamic data as long as oxygen is present. Anticipated improvement by the inclusion of ATP consumption and explicit Krebs cycle are under evaluation. PMID: 18231864 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1190693 Wed, 30 Jan 2008 05:00:00 +0100 1190693 http://www.medworm.com/index.php?rid=1190692&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18231865%26dopt%3DAbstract Authors: Manté C, Nerini D, Viret J PMID: 18231865 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1190692 Wed, 30 Jan 2008 05:00:00 +0100 1190692 http://www.medworm.com/index.php?rid=1002006&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17975732%26dopt%3DAbstract Authors: Stamos DN The primary purpose of this paper is to argue that biologists should stop citing Karl Popper on what a genuinely scientific theory is. Various ways in which biologists cite Popper on this matter are surveyed, including the use of Popper to settle debates on methodology in phylogenetic systematics. It is then argued that the received view on Popper-namely, that a genuinely scientific theory is an empirically falsifiable one-is seriously mistaken, that Popper's real view was that genuinely scientific theories have the form of statements of laws of nature. It is then argued that biology arguably has no genuine laws of its own. In place of Popperian falsifiability, it is suggested that a cluster class epistemic values approach (which subsumes empirical falsifiability) is... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=1002006 Fri, 02 Nov 2007 04:00:00 +0100 1002006 http://www.medworm.com/index.php?rid=981481&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17960483%26dopt%3DAbstract Authors: Hengeveld R, Fedonkin MA This paper suggests that the energy flow on which all living structures depend only started up slowly, the low-energy, initial phase starting up a second, slightly more energetic phase, and so on. In this way, the build up of the energy flow follows a bootstrapping process similar to that found in the development of computers, the first generation making possible the calculations necessary for constructing the second one, etc. In the biogenetic upstart of an energy flow, non-metals in the lower periods of the Periodic Table of Elements would have constituted the most primitive systems, their operation being enhanced and later supplanted by elements in the higher periods that demand more energy. This bootstrapping process would put the development of th... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=981481 Thu, 25 Oct 2007 04:00:00 +0100 981481 http://www.medworm.com/index.php?rid=975741&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17952607%26dopt%3DAbstract Authors: Jax K Sound definitions of its basic concepts are fundamental to every scientific discipline. In some instances, like in the case of the ecosystem concept, the question arises if we can define such concepts at all. And if we can define them, how should we choose from the multiple definitions available? And what are the preconditions for a scientifically sound and useful definition? On the basis of the ecosystem concept, this paper illustrates a major, often neglected distinction in the definition of ecological concepts, namely that between defining criteria and additional descriptive statements connected to those definitions. As is demonstrated by examples from the literature, mixing up these categories leads to false inferences about the properties of physical objects (e.g. a... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=975741 Sat, 20 Oct 2007 04:00:00 +0100 975741 http://www.medworm.com/index.php?rid=946229&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17929173%26dopt%3DAbstract This study represents a historical overview of the development of the homology concept followed by some clues on how to navigate the pluralistic terminology of modern approaches to homology. PMID: 17929173 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=946229 Wed, 10 Oct 2007 04:00:00 +0100 946229 http://www.medworm.com/index.php?rid=892557&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17885808%26dopt%3DAbstract Authors: Pfeifer MA, Henle K, Settele J Biologists studying short-lived organisms have become aware of the need to recognize an explicit temporal extend of a population over a considerable time. In this article we outline the concept and the realm of populations with explicit spatial and temporary boundaries. We call such populations "temporally bounded populations". In the concept, time is of the same importance as space in terms of a dimension to which a population is restricted. Two parameters not available for populations that are only spatially defined characterise temporally bounded populations: total population size, which is the total number of individuals present within the temporal borders, and total residence time, which is the sum of the residence times of all individuals. ... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=892557 Fri, 21 Sep 2007 04:00:00 +0100 892557 http://www.medworm.com/index.php?rid=839895&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17763829%26dopt%3DAbstract Authors: Tsoularis A In this paper I propose a reinforcement learning model for a predator preying upon two types of prey, the unpalatable (noxious) models, and the palatable mimics. The latter type of prey resembles the models in appearance so as to derive some protection from the predator who must avoid the unpalatable models. Essentially the predator is treated as a learning automaton adopting a simple reinforcement learning strategy in order to increase its consumption of palatable prey and reduce the consumption of unpalatable ones. The populations of both mimics and models are assumed to grow logistically. PMID: 17763829 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=839895 Sat, 01 Sep 2007 04:00:00 +0100 839895 http://www.medworm.com/index.php?rid=813292&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17704896%26dopt%3DAbstract Authors: Russell MJ The Earth agglomerates and heats. Convection cells within the planetary interior expedite the cooling process. Volcanoes evolve steam, carbon dioxide, sulfur dioxide and pyrophosphate. An acidulous Hadean ocean condenses from the carbon dioxide atmosphere. Dusts and stratospheric sulfurous smogs absorb a proportion of the Sun's rays. The cooled ocean leaks into the stressed crust and also convects. High temperature acid springs, coupled to magmatic plumes and spreading centers, emit iron, manganese, zinc, cobalt and nickel ions to the ocean. Away from the spreading centers cooler alkaline spring waters emanate from the ocean floor. These bear hydrogen, formate, ammonia, hydrosulfide and minor methane thiol. The thermal potential begins to be dissipated but the chemi... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=813292 Sat, 18 Aug 2007 04:00:00 +0100 813292 http://www.medworm.com/index.php?rid=763862&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17657570%26dopt%3DAbstract Authors: Pisani D, Benton MJ, Wilkinson M When phylogenetic trees constructed from morphological and molecular evidence disagree (i.e. are incongruent) it has been suggested that the differences are spurious or that the molecular results should be preferred a priori. Comparing trees can increase confidence (congruence), or demonstrate that at least one tree is incorrect (incongruence). Statistical analyses of 181 molecular and 49 morphological trees shows that incongruence is greater between than within the morphological and molecular partitions, and this difference is significant for the molecular partition. Because the level of incongruence between a pair of trees gives a minimum bound on how much error is present in the two trees, our results indicate that the level of error may be ... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=763862 Fri, 27 Jul 2007 04:00:00 +0100 763862 http://www.medworm.com/index.php?rid=729218&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17622489%26dopt%3DAbstract Authors: Perovic S Jaegwon Kim's exclusion argument is a general ontological argument, applicable to any properties deemed supervenient on a microproperty basis, including biological properties. It implies that the causal power of any higher-level property must be reducible to the subset of the causal powers of its lower-level properties. Moreover, as Kim's recent version of the argument indicates, a higher-level property can be causally efficient only to the extent of the efficiency of its micro-basis. In response, I argue that the ontology that aims to capture experimentally based explanations of metabolic control systems and morphogenetic systems must involve causally relevant contextual properties. Such an ontology challenges the exclusiveness of micro-based causal efficiency that ... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=729218 Wed, 11 Jul 2007 04:00:00 +0100 729218 http://www.medworm.com/index.php?rid=724019&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17619171%26dopt%3DAbstract Authors: Van Speybroeck L This paper focuses on a running dispute between Werner Callebaut's naturalistic view and Filip Kolen and Gertrudis Van de Vijver's transcendentalist view on the nature of philosophy of biology and the relation of this discipline to biological sciences. It is argued that, despite differences in opinion, both positions agree that philosophy of biology's ultimate goal is to 'move' biology or at least be 'meaningful' to it. In order to make this goal clear and effective, more is needed than a polarizing debate which hardly touches upon biology. Therefore, a redirection in discussion is suggested towards a reflection on the possibilities of incorporating philosophy in interdisciplinary research, and on finding concrete research questions which are of interest both ... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=724019 Sat, 07 Jul 2007 04:00:00 +0100 724019 http://www.medworm.com/index.php?rid=724018&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17619172%26dopt%3DAbstract Authors: Kolen F, Van de Vijver G The aim of this article is to clarify the meaning of a naturalistic position within philosophy of biology, against the background of an alternative view, founded on the basic insights of transcendental philosophy. It is argued that the apparently minimal and neutral constraints naturalism imposes on philosophy of science turn out to involve a quite heavily constraining metaphysics, due to the naturalism's fundamental neglect of its own perspective. Because of its intrinsic sensitivity to perspectivity and historicity, transcendental philosophy can avoid this type of hidden metaphysics. PMID: 17619172 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=724018 Sat, 07 Jul 2007 04:00:00 +0100 724018 http://www.medworm.com/index.php?rid=719169&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17612798%26dopt%3DAbstract Authors: Callebaut W I discuss various reactions to my article "Again, what the philosophy of science is not" [Callebaut (Acta Biotheor 53:92-122 (2005a))], most of which concern the naturalism issue, the place of the philosophy of biology within philosophy of science and philosophy at large, and the proper tasks of the philosophy of biology. PMID: 17612798 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=719169 Fri, 06 Jul 2007 04:00:00 +0100 719169 http://www.medworm.com/index.php?rid=701558&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17594062%26dopt%3DAbstract Authors: Klok C, de Roos AM Many predator species feed on prey that fluctuates in abundance from year to year. Birds of prey can face large fluctuations in food abundance i.e. small mammals, especially voles. These annual changes in prey abundance strongly affect the reproductive success and mortality of the individual predators and thus can be expected to influence their population dynamics and persistence. The barn owl, for example, shows large fluctuations in breeding success that correlate with the dynamics in voles, their main prey species. Analysis of the impact of fluctuations in vole abundance (their amplitude, peaks and lows, cycle length and regularity) with a simple predator prey model parameterized with literature data indicates population persistence is especially affected... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=701558 Wed, 27 Jun 2007 04:00:00 +0100 701558 http://www.medworm.com/index.php?rid=606448&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17486413%26dopt%3DAbstract Authors: Ricotta C Community diversity has been studied extensively in relation to its effects on ecosystem functioning. Testing the consequences of diversity on ecosystem processes will require measures to be available based on a rigorous conceptualization of their very meaning. In the last decades, literally dozens of measures of diversity have been proposed. However, rather than using unrelated metrics, we need to identify their separate components so that possible links between them and ecosystem functioning can be examined using an agreed-upon language. In this paper, first, a short overview on new and old measures of community diversity is presented. Next, I propose a general framework in which most of the existing measures of diversity are sorted into four interrelated semantic ... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=606448 Tue, 08 May 2007 04:00:00 +0100 606448 http://www.medworm.com/index.php?rid=606447&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17486414%26dopt%3DAbstract Authors: Jeune B, Barabé D, Lacroix C In plant morphology, most structures of vascular plants can easily be assigned to pre-established organ categories. However, there are also intermediate structures that do not fit those categories associated with a classical approach to morphology. To integrate the diversity of forms in the same general framework, we constructed a theoretical morphospace based on a variety of modalities where it is possible to calculate the morphological distance between plant organs. This paper gives emphasis on shoot, leaf, leaflet and trichomes while ignoring the root. This will allow us to test the hypothesis that classical morphology (typology) and dynamic morphology occupy the same theoretical morphospace and the relationship between the two approaches remai... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=606447 Tue, 08 May 2007 04:00:00 +0100 606447 http://www.medworm.com/index.php?rid=463535&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17347784%26dopt%3DAbstract Authors: Dubbeldam JL Van der Klaauw was a professor of Descriptive Zoology in the period 1934-1958.This paper presents a concise annotated overview of his publications. In his work three main topics can be recognized: comparative anatomy of the mammalian auditory region, theoretical studies about ecology and ecological morphology, and vertebrate functional morphology. In particular van der Klaauw developed new concepts on functional morphology, based upon a holistic approach. A series of studies in functional morphology of Vertebrates by his students is added. An overview of recent morphological and theoretical studies show that this new approach had a long lasting impact in studies of functional morphology. PMID: 17347784 [PubMed - as supplied by publisher] (Source: Acta Biotheor... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=463535 Fri, 09 Mar 2007 05:00:00 +0100 463535 http://www.medworm.com/index.php?rid=463534&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17347785%26dopt%3DAbstract Authors: Witzany G It is becoming increasingly evident that the driving forces of evolutionary novelty are not randomly derived chance mutations of the genetic text, but a precise genome editing by omnipresent viral agents. These competences integrate the whole toolbox of natural genetic engineering, replication, transcription, translation, genomic imprinting, genomic creativity, enzymatic inventions and all types of genetic repair patterns. Even the non-coding, repetitive DNA sequences which were interpreted as being ancient remnants of former evolutionary stages are now recognized as being of viral descent and crucial for higher-order regulatory and constitutional functions of protein structural vocabulary. In this article I argue that non-randomly derived natural genome editing can ... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=463534 Fri, 09 Mar 2007 05:00:00 +0100 463534 http://www.medworm.com/index.php?rid=449245&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17318328%26dopt%3DAbstract Authors: van der Steen WJ, Ho VK Autoimmune diseases such as rheumatoid arthritis and gastrointestinal disorders such as stomach ulcers are often treated with drugs. NSAIDs, a common treatment in rheumatoid arthritis, may cause stomach ulcers which call for additional medications, notably antacids in the sense of drugs that suppress acid secretion by the stomach. Infection with Helicobacter pylori also plays a role in the ulcers. The infection is typically treated with antibiotics added to antacids. Considering NSAIDs and antacids, we suspect that overmedication is common to the extent that particular diets are a better option. Current research and current treatments with these drugs are also problematic since circadian rhythms are mostly disregarded. All the processes involved in the ... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=449245 Wed, 21 Feb 2007 05:00:00 +0100 449245 http://www.medworm.com/index.php?rid=449244&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17318329%26dopt%3DAbstract Authors: Hemerik L, Hengeveld R, Lippe E This paper distinguishes four recognisably different geographical processes in principle causing species to die out. One of these processes, the one we dub "range eclipse", holds that one range expands at the expense of another one, thereby usurping it. Channell and Lomolino (2000a, Journal of Biogeography 27: 169-179; 2000b, Nature 403: 84-87; see also Lomolino and Channell, 1995, Journal of Mammalogy 76: 335-347) measured the course of this process in terms of the proportion of the total range remaining in its original centre, thereby essentially assuming a homogeneous distribution of animals over the range. However, part of their measure seems mistaken. By giving a general, analytical formulation of eclipsing ranges, we estimate the exact cou... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=449244 Wed, 21 Feb 2007 05:00:00 +0100 449244 http://www.medworm.com/index.php?rid=245452&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17054020%26dopt%3DAbstract Authors: Klok C, Holtkamp R, van Apeldoorn R, Visser ME, Hemerik L The House Sparrow (Passer domesticus), formerly a common bird species, has shown a rapid decline in Western Europe over recent decades. In The Netherlands, its decline is apparent from 1990 onwards. Many causes for this decline have been suggested that all decrease the vital rates, i.e. survival and reproduction, but their actual impact remains unknown. Although the House Sparrow has been dominant in The Netherlands, data on life history characteristics for this bird species are scarce: data on reproduction are non-existent, and here we first present survival estimates based on live encounters and dead recoveries of marked individuals over the period 1976-2003, 14 years before and 14 years during the decline, reported t... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=245452 Sun, 22 Oct 2006 06:36:02 +0100 245452 http://www.medworm.com/index.php?rid=245451&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17054021%26dopt%3DAbstract Authors: Queiroz J, El-Hani CN Any description of the emergence and evolution of different types of meaning processes (semiosis, sensu C.S.Peirce) in living systems must be supported by a theoretical framework which makes it possible to understand the nature and dynamics of such processes. Here we propose that the emergence of semiosis of different kinds can be understood as resulting from fundamental interactions in a triadically-organized hierarchical process. To grasp these interactions, we develop a model grounded on Stanley Salthe's hierarchical structuralism. This model can be applied to establish, in a general sense, a set of theoretical constraints for explaining the instantiation of different kinds of meaning processes (iconic, indexical, symbolic) in semiotic systems. We use ... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=245451 Sun, 22 Oct 2006 06:36:02 +0100 245451 http://www.medworm.com/index.php?rid=245450&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17054022%26dopt%3DAbstract Authors: Viet AF, Fourichon C, Jacob C, Guihenneuc-Jouyaux C, Seegers H Qualitative validation consists in showing that a model is able to mimic available observed data. In population level biological models, the available data frequently represent a group status, such as pool testing, rather than the individual statuses. They are aggregated. Our objective was to explore an approach for qualitative validation of a model with aggregated data and to apply it to validate a stochastic model simulating the bovine viral-diarrhoea virus (BVDV) spread within a dairy cattle herd. Repeated measures of the level of BVDV-specific antibodies in the bulk-tank milk (total milk production of a herd) were used to summarise the BVDV herd status. First, a domain of validation was defined to ensure a comp... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=245450 Sun, 22 Oct 2006 06:36:02 +0100 245450 http://www.medworm.com/index.php?rid=245449&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17054023%26dopt%3DAbstract Authors: Gregorius HR The isolation principle rests on defining internal and external differentiation for each subset of at least two objects. Subsets with larger external than internal differentiation form isolated groups in the sense that they are internally cohesive and externally isolated. Objects that do not belong to any isolated group are termed solitary. The collection of all isolated groups and solitary objects forms a hierarchical (encaptic) structure. This ubiquitous characteristic of biological organization provides the motivation to identify universally applicable practical methods for the detection of such structure, to distinguish primary types of structure, to quantify their distinctiveness, and to simplify interpretation of structural aspects. A method implementing the... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=245449 Sun, 22 Oct 2006 06:36:02 +0100 245449 http://www.medworm.com/index.php?rid=202972&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16988907%26dopt%3DAbstract Authors: Ricotta C This reply paper includes two brief remarks in rejoinder to the commentary papers of Myers and Patil, Podani, and Sarkar. The first observation concerns the fundamental nature of ecological diversity measures, while the second one specifically addresses some interesting mathematical connections between alpha- and beta-diversity. PMID: 16988907 [PubMed - in process] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=202972 Sat, 23 Sep 2006 19:57:02 +0100 202972 http://www.medworm.com/index.php?rid=108094&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16823606%26dopt%3DAbstract Authors: Nams VO It is difficult to watch wild animals while they move, so often biologists analyse characteristics of animal movement paths. One common path characteristic used is tortuousity, measured using the fractal dimension (D). The typical method for estimating fractal D, the divider method, is biased and imprecise. The bias occurs because the path length is truncated. I present a method for minimising the truncation error. The imprecision occurs because sometimes the divider steps land inside the bends of curves, and sometimes they miss the curves. I present three methods for minimising this variation and test the methods with simulated correlated random walks. The traditional divider method significantly overestimates fractal D when paths are short and the range of spatial sc... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=108094 Tue, 18 Jul 2006 20:35:11 +0100 108094 http://www.medworm.com/index.php?rid=108093&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16823607%26dopt%3DAbstract Authors: Schinazi RB We propose a discrete time branching process to model the appearance of drug resistance under treatment. Under our assumptions at every discrete time a pathogen may die with probability 1-p or divide in two with probability p. Each newborn pathogen is drug resistant with probability mu. We start with N drug sensitive pathogens and with no drug resistant pathogens. We declare the treatment successful if all pathogens are eradicated before drug resistance appears. The model predicts that success is possible only if p<1/2. Even in this case the probability of success decreases exponentially with the parameter m=muN. In particular, even with a very potent drug (i.e. p very small) drug resistance is likely if m is large. PMID: 16823607 [PubMed - in process] (Sour... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=108093 Tue, 18 Jul 2006 20:35:11 +0100 108093 http://www.medworm.com/index.php?rid=108092&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16823608%26dopt%3DAbstract Authors: Imre AR In landscape ecology spatial descriptors (or indices) can be used to characterize habitats. Some of these descriptors can be used for habitat's ranking; this ranking is very important for conservation purposes. We would like to show that two traditional descriptors, namely the compactness and interior-to-edge ratio can give contradictory results. Being the second one is a more relevant descriptor, we would like to propose to avoid the further use the compactness in habitat's ranking. PMID: 16823608 [PubMed - in process] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=108092 Tue, 18 Jul 2006 20:35:11 +0100 108092 http://www.medworm.com/index.php?rid=108091&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16823609%26dopt%3DAbstract Authors: Sánchez R, Grau R A novel algebraic structure of the genetic code is proposed. Here, the principal partitions of the genetic code table were obtained as equivalent classes of quotient spaces of the genetic code vector space over the Galois field of the four DNA bases. The new algebraic structure shows strong connections among algebraic relationships, codon assignment and physicochemical properties of amino acids. Moreover, a distance function defined between the codon binary representations in the vector space was demonstrated to have a linear behavior respect to physical variables such as the mean of amino acids interaction energies in proteins. It was also noticed that the distance between wild type and mutant codons approach to smaller values in mutational variants of four... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=108091 Tue, 18 Jul 2006 20:35:11 +0100 108091 http://www.medworm.com/index.php?rid=108090&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16823610%26dopt%3DAbstract Authors: Pawlowski CW The image of a ball rolling along a series of hills and valleys is an effective heuristic by which to communicate stability concepts in ecology. However, the dynamics of this landscape model have little to do with ecological systems. Other landscape representations, however, are possible. These include the particle on an energy landscape, the potential landscape, and the Lyapunov function landscape. I discuss the dynamics that these representations admit, and the application of each to ecological modeling and the analysis and representation of stability. PMID: 16823610 [PubMed - in process] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=108090 Tue, 18 Jul 2006 20:35:11 +0100 108090 http://www.medworm.com/index.php?rid=202977&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16988902%26dopt%3DAbstract Authors: Mamontov E, Koptioug A, Psiuk-Maksymowicz K Oncogenic hyperplasia is the first and inevitable stage of formation of a (solid) tumor. This stage is also the core of many other proliferative diseases. The present work proposes the first minimal model that combines homeorhesis with oncogenic hyperplasia where the latter is regarded as a genotoxically activated homeorhetic dysfunction. This dysfunction is specified as the transitions of the fluid of cells from a fluid, homeorhetic state to a solid, hyperplastic-tumor state, and back. The key part of the model is a nonlinear reaction-diffusion equation (RDE) where the biochemical-reaction rate is generalized to the one in the well-known Schlögl physical theory of the non-equilibrium phase transitions. A rigorous analysis of the st... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=202977 Sun, 01 Jan 2006 07:00:00 +0100 202977 http://www.medworm.com/index.php?rid=202976&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16988903%26dopt%3DAbstract Serial Endosymbiotic Theory (set): the biosemiotic update. Acta Biotheor. 2006;54(2):103-17 Authors: Witzany G The Serial Endosymbiotic Theory explains the origin of nucleated eukaryotic cells by a merging of archaebacterial and eubacterial cells. The paradigmatic change is that the driving force behind evolution is not ramification but merging. Lynn Margulis describes the symbiogenetic processes in the language of mechanistic biology in such terms as "merging", "fusion", and "incorporation". Biosemiotics argues that all cell-cell interactions are (rule-governed) sign-mediated interactions, i.e., communication processes. As the description of plant communication demonstrates, the biosemiotic approach is not limited to the level of molecular biology, but is also helpful in exami... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=202976 Sun, 01 Jan 2006 07:00:00 +0100 202976 http://www.medworm.com/index.php?rid=202975&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16988904%26dopt%3DAbstract Authors: Myers W, Patil GP The multifarious nature of biodiversity is considered in relation to difficulties of definite determination and managerial mandates for monitoring. At a micro scale there is some convergence with the concept of community, but the linkage is largely lost in the spectra of temporal scope, spatial scales, successional seres, and taxonomic trajectories. Practicality points to selecting suitable suites of indicators as surrogates for particular purposes. Domains of partial ordering on multiple indicators constitute comparable collectives, whereas different domains require recognition of special situations. Theoretical treatise and practical process can proceed in parallel, with dialogue and cross-fertilization serving to invigorate and inspire; whereas compulsive ... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=202975 Sun, 01 Jan 2006 07:00:00 +0100 202975 http://www.medworm.com/index.php?rid=202974&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16988905%26dopt%3DAbstract Authors: Podani J This short communication includes comments on a single sentence cited from a recent paper by C. Ricotta. I discuss shortly the relationship between diversity and classification as well as the possibility of expressing diversity for continuous variables. A simple example shows that the notion of diversity can be expanded to situations without an underlying classification. I suggest an evenness formula based on absolute deviations from the perfectly even distribution. If expressed for species data and multiplied by number of species in the community, this becomes an easily interpretable diversity measure. It is stressed that conventional diversity formulae cannot be informative on community structure, but there is a solution. PMID: 16988905 [PubMed - indexed for MED... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=202974 Sun, 01 Jan 2006 07:00:00 +0100 202974 http://www.medworm.com/index.php?rid=202973&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16988906%26dopt%3DAbstract Ecological diversity and biodiversity as concepts for conservation planning: comments on Ricotta. Acta Biotheor. 2006;54(2):133-40; discussion 141-6 Authors: Sarkar S Ricotta argues against the existence of a unique measure of biodiversity by pointing out that no known measure of alpha-diversity satisfies all the adequacy conditions that have traditionally been set for it. While that technical claim is correct, it is not relevant in the context of defining biodiversity which is most usefully measured by beta-diversity. The concept of complementarity provides a closely related family of measures of biodiversity which can be used for systematic conservation planning. Moreover, these measures cannot be replaced by summary statistics but must rely on inventories of biodiversity sur... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=202973 Sun, 01 Jan 2006 07:00:00 +0100 202973 http://www.medworm.com/index.php?rid=158856&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16583269%26dopt%3DAbstract Authors: Seigneuric RG, Chassé JL, Auger P, Bardou A Ventricular Fibrillation is responsible for a majority of sudden cardiac death, but little is known about how ventricular tachycardia (VT) degenerates into ventricular fibrillation. Several clinical studies focused only on preventing VT with a class III antiarrhythmic drug resulted in many deaths. Our simulations investigate the interactions between an antiarrhythmic drug likely to suppress a VT and a Figure 8 reentry. A parameter AAR is introduced to increase the action potential duration and therefore simulate various Class III drugs. Simulations are ran under several conditions (phases of the reentry, values of AAR, durations). They show that a VT can be suppressed whatever the phase of the reentry but it strongly depends on the ... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=158856 Sat, 01 Jan 2005 07:00:00 +0100 158856 http://www.medworm.com/index.php?rid=158855&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16583270%26dopt%3DAbstract Authors: Pustoc'h A, Ohayon J, Usson Y, Kamgoue A, Tracqui P Computational cell models appear as necessary tools for handling the complexity of intracellular cell dynamics, especially calcium dynamics. However, while oscillating intracellular calcium oscillations are well documented and modelled, a simple enough virtual cell taking into account the mechano-chemical coupling between calcium oscillations and cell mechanical properties is still lacking. Considering the spontaneous periodic contraction of isolated cardiac myocytes, we propose here a virtual cardiac cell model in which the cellular contraction is modelled using an hyperelastic description of the cell mechanical behaviour. According to the experimental data, the oscillating cytosolic calcium concentrations trigger the spatio... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=158855 Sat, 01 Jan 2005 07:00:00 +0100 158855 http://www.medworm.com/index.php?rid=158854&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16583271%26dopt%3DAbstract Authors: Le Rolle V, Hernandez AI, Richard PY, Buisson J, Carrault G The study of the autonomic nervous system (ANS) function has shown to provide useful indicators for risk stratification and early detection on a variety of cardiovascular pathologies. However, data gathered during different tests of the ANS are difficult to analyse, mainly due to the complex mechanisms involved in the autonomic regulation of the cardiovascular system (CVS). Although model-based analysis of ANS data has been already proposed as a way to cope with this complexity, only a few models coupling the main elements involved have been presented in the literature. In this paper, a new model of the CVS, representing the ventricles, the circulatory system and the regulation of the CVS activity by the ANS, is prese... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=158854 Sat, 01 Jan 2005 07:00:00 +0100 158854 http://www.medworm.com/index.php?rid=158853&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16583272%26dopt%3DAbstract Authors: Norris V, Cabin A, Zemirline A What is biological complexity? How many sorts exist? Are there levels of complexity? How are they related to one another? How is complexity related to the emergence of new phenotypes? To try to get to grips with these questions, we consider the archetype of a complex biological system, Escherichia coli. We take the position that E. coli has been selected to survive adverse conditions and to grow in favourable ones and that many other complex systems undergo similar selection. We invoke the concept of hyperstructures which constitute a level of organisation intermediate between macromolecules and cells. We also invoke a new concept, competitive coherence, to describe how phenotypes are created by a competition between maintaining a consistent stor... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=158853 Sat, 01 Jan 2005 07:00:00 +0100 158853 http://www.medworm.com/index.php?rid=158852&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16583273%26dopt%3DAbstract Authors: Mchich R, Bergam A, Raïssi N We study the effects of density dependent migrations on the stability of a predator-prey model in a patchy environment which is composed with two sites connected by migration. The two patches are different. On the first patch, preys can find resource but can be captured by predators. The second patch is a refuge for the prey and thus predators do not have access to this patch. We assume a repulsive effect of predator on prey on the resource patch. Therefore, when the predator density is large on that patch, preys are more likely to leave it to return to the refuge. We consider two models. In the first model, preys leave the refuge to go to the resource patch at constant migration rates. In the second model, preys are assumed to be in competition f... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=158852 Sat, 01 Jan 2005 07:00:00 +0100 158852 http://www.medworm.com/index.php?rid=158851&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16583274%26dopt%3DAbstract Authors: Calaud V, Lagadeuc Y A study of stage structured model of fish population is presented. This model focuse on the anchovy population in the Bay of Biscay (Engraulis encrasicolus L.) is presented. The method of study is based on an intermediate complexity mathematical model, taking into account the spatialisation, the environmental conditions and the stage-structure of the fishes. First, to test the model, we show mathematical properties, such as unicity of the solution of structural stability. Then we provide numerical simulations, to validate the model and to test the dynamics according to the variations of the parameters. PMID: 16583274 [PubMed - indexed for MEDLINE] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=158851 Sat, 01 Jan 2005 07:00:00 +0100 158851 http://www.medworm.com/index.php?rid=158850&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16583275%26dopt%3DAbstract Authors: Poggiale JC, Auger P, Nérini D, Manté C, Gilbert F Spatial and temporal heterogeneity are often described as important factors having a strong impact on biodiversity. The effect of heterogeneity is in most cases analyzed by the response of biotic interactions such as competition of predation. It may also modify intrinsic population properties such as growth rate. Most of the studies are theoretic since it is often difficult to manipulate spatial heterogeneity in practice. Despite the large number of studies dealing with this topics, it is still difficult to understand how the heterogeneity affects populations dynamics. On the basis of a very simple model, this paper aims to explicitly provide a simple mechanism which can explain why spatial heterogeneity may be a favorable f... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=158850 Sat, 01 Jan 2005 07:00:00 +0100 158850 http://www.medworm.com/index.php?rid=158849&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16583276%26dopt%3DAbstract Authors: Lagadeuc Y The Influence of turbulence on nutrient fluxes towards phytoplankton cells has been previously estimated, but those studies did not take into account the intermittent nature of turbulent processes. This has been investigated here comparing the nutrient fluxes obtained using both mean and instantaneous turbulent energy dissipation rates. This approach shows that the size of cell potentially influenced by turbulence is lower than previously indicated, and that the spectral average estimate of the turbulence effect overestimates the flux. The capacity of cell to use such intermittent flux is then discussed. PMID: 16583276 [PubMed - indexed for MEDLINE] (Source: Acta Biotheoretica) Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=158849 Sat, 01 Jan 2005 07:00:00 +0100 158849 http://www.medworm.com/index.php?rid=158848&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16583277%26dopt%3DAbstract This article describes new aspects of hysteresis dynamics which have been uncovered through computer experiments. There are several motivations to be interested in fast-slow dynamics. For instance, many physiological or biological systems display different time scales. The bursting oscillations which can be observed in neurons, beta-cells of the pancreas and population dynamics are essentially studied via bifurcation theory and analysis of fast-slow systems (Keener and Sneyd, 1998; Rinzel, 1987). Hysteresis is a possible mechanism to generate bursting oscillations. A first part of this article presents the computer techniques (the dotted-phase portrait, the bifurcation of the fast dynamics and the wave form) we have used to represent several patterns specific to hysteresis dynamics. This f... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=158848 Sat, 01 Jan 2005 07:00:00 +0100 158848 http://www.medworm.com/index.php?rid=158847&cid=s_29926_61_f&fid=29926&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16583278%26dopt%3DAbstract Authors: Viret J A physiological function can be described as a cycle based on a cusp bifurcation set in catastrophe theory. This cycle involves four phases that are successively developed along a functional potential, which is used to perform a given physiological act. The work we present is firstly based on a detailed study of the global function of vision, which covers a vast field extending from the molecular to cerebral scale. We then present other examples of generalised functions by expanding the frame of reference, from the scale of an organ to the scale of a whole organism with predation function, and to the scale of a social group with crisis management. We observed that the criteria remain the same, whether the function is considered on the scale of a cell membrane or a grou... Acta Biotheoretica journals http://www.medworm.com/rss/comments.php?id=158847 Sat, 01 Jan 2005 07:00:00 +0100 158847