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 Acta Biotheoretica   [SJR: 0.419]   [H-I: 25]   [4 followers]  Follow         Hybrid journal (It can contain Open Access articles)    ISSN (Print) 1572-8358 - ISSN (Online) 0001-5342    Published by Springer-Verlag  [2349 journals]
• Quaternion-Based Texture Analysis of Multiband Satellite Images:
Application to the Estimation of Aboveground Biomass in the East Region of
Cameroon
• Authors: Cedrigue Boris Djiongo Kenfack; Olivier Monga; Serge Moto Mpong; René Ndoundam
Abstract: Within the last decade, several approaches using quaternion numbers to handle and model multiband images in a holistic manner were introduced. The quaternion Fourier transform can be efficiently used to model texture in multidimensional data such as color images. For practical application, multispectral satellite data appear as a primary source for measuring past trends and monitoring changes in forest carbon stocks. In this work, we propose a texture-color descriptor based on the quaternion Fourier transform to extract relevant information from multiband satellite images. We propose a new multiband image texture model extraction, called FOTO++, in order to address biomass estimation issues. The first stage consists in removing noise from the multispectral data while preserving the edges of canopies. Afterward, color texture descriptors are extracted thanks to a discrete form of the quaternion Fourier transform, and finally the support vector regression method is used to deduce biomass estimation from texture indices. Our texture features are modeled using a vector composed with the radial spectrum coming from the amplitude of the quaternion Fourier transform. We conduct several experiments in order to study the sensitivity of our model to acquisition parameters. We also assess its performance both on synthetic images and on real multispectral images of Cameroonian forest. The results show that our model is more robust to acquisition parameters than the classical Fourier Texture Ordination model (FOTO). Our scheme is also more accurate for aboveground biomass estimation. We stress that a similar methodology could be implemented using quaternion wavelets. These results highlight the potential of the quaternion-based approach to study multispectral satellite images.
PubDate: 2018-03-21
DOI: 10.1007/s10441-018-9317-z

• A 3D Individual-Based Model to Study Effects of Chemotaxis, Competition
and Diffusion on the Motile-Phytoplankton Aggregation
Abstract: In this paper, we develop a 3D-individual-based model (IBM) to understand effect of various small-scale mechanisms in phytoplankton cells, on the cellular aggregation process. These mechanisms are: spatial interactions between cells due to their chemosensory abilities (chemotaxis), a molecular diffusion and a demographical process. The latter is considered as a branching process with a density-dependent death rate to take into account the local competition on resources. We implement the IBM and simulate various scenarios under real parameter values for phytoplankton cells. To quantify the effects of the different processes quoted above on the spatial and temporal distribution of phytoplankton, we used two spatial statistics: the Clark–Evans index and the group belonging percentage. Our simulation study highlights the role of the branching process with a weak-to-medium competition in reinforcing the aggregating structure that forms from attraction mechanisms (under suitable conditions for diffusion and attraction forces), and shows by contrast that aggregations cannot form when competition is high.
PubDate: 2018-03-15
DOI: 10.1007/s10441-018-9318-y

• Prediction of Apoptosis Protein’s Subcellular Localization by Fusing Two
Different Descriptors Based on Evolutionary Information
• Authors: Yunyun Liang; Shengli Zhang
Abstract: The apoptosis protein has a central role in the development and the homeostasis of an organism. Obtaining information about the subcellular localization of apoptosis protein is very helpful to understand the apoptosis mechanism and the function of this protein. Prediction of apoptosis protein’s subcellular localization is a challenging task, and currently the existing feature extraction methods mainly rely on the protein’s primary sequence. In this paper we develop a feature extraction model based on two different descriptors of evolutionary information, which contains the 192 frequencies of triplet codons (FTC) in the RNA sequence derived from the protein’s primary sequence and the 190 features from a detrended forward moving-average cross-correlation analysis (DFMCA) based on a position-specific scoring matrix (PSSM) generated by the PSI-BLAST program. Hence, this model is called FTC-DFMCA-PSSM. A 382-dimensional (382D) feature vector is constructed on the ZD98, ZW225 and CL317 datasets. Then a support vector machine is adopted as classifier, and the jackknife cross-validation test method is used for evaluating the accuracy. The overall prediction accuracies are further improved by an objective and rigorous jackknife test. Our model not only broadens the source of the feature information, but also provides a more accurate and reliable automated calculation method for the prediction of apoptosis protein’s subcellular localization.
PubDate: 2018-03-12
DOI: 10.1007/s10441-018-9319-x

• In the Future There Will Be No Genes
• Authors: Oren Harman
PubDate: 2018-02-19
DOI: 10.1007/s10441-018-9316-0

• R 0 : Host Longevity Matters
• Authors: L. M. Viljoen; L. Hemerik; J. Molenaar
Abstract: The basic reproduction ratio, R0, is a fundamental concept in epidemiology. It is defined as the total number of secondary infections brought on by a single primary infection, in a totally susceptible population. The value of R0 indicates whether a starting epidemic reaches a considerable part of the population and causes a lot of damage, or whether it remains restricted to a relatively small number of individuals. To calculate R0 one has to evaluate an integral that ranges over the duration of the infection of the host. This duration is, of course, limited by remaining host longevity. So, R0 depends on remaining host longevity and in this paper we show that for long-lived hosts this aspect may not be ignored for long-lasting infections. We investigate in particular how this epidemiological measure of pathogen fitness depends on host longevity. For our analyses we adopt and combine a generic within- and between-host model from the literature. To find the optimal strategy for a pathogen from an evolutionary point of view, we focus on the indicator $$R_0^{{opt}}$$ , i.e., the optimum of R0 as a function of its replication and mutation rates. These are the within-host parameters that the pathogen has at its disposal to optimize its strategy. We show that $$R_0^{{opt}}$$ is highly influenced by remaining host longevity in combination with the contact rate between hosts in a susceptible population. In addition, these two parameters determine whether a killer-like or a milker-like strategy is optimal for a given pathogen. In the killer-like strategy the pathogen has a high rate of reproduction within the host in a short time span causing a relatively short disease, whereas in the milker-like strategy the pathogen multiplies relatively slowly, producing a continuous small amount of offspring over time with a small effect on host health. The present research allows for the determination of a bifurcation line in the plane of host longevity versus contact rate that forms the boundary between the milker-like and killer-like regions. This plot shows that for short remaining host longevities the killer-like strategy is optimal, whereas for very long remaining host longevities the milker-like strategy is advantageous. For in-between values of host longevity, the contact rate determines which of both strategies is optimal.
PubDate: 2018-02-19
DOI: 10.1007/s10441-018-9315-1

• A Model of Isotope Separation in Plants
• Authors: A. V. Melkikh; A. O. Bokunyaeva
Pages: 271 - 284
Abstract: A model representing isotope separation during water evaporation in plants was constructed. The model accounts for substance diffusion, convective transfer and evaporation from the surface of the leaves. The dependence of the system’s separation and enrichment coefficients on various parameters (liquid velocity, diffusion coefficient, and potential barriers for molecules and their thermal velocities) was determined. A comparison was made between the enrichment coefficients calculated from experimental data from different plants and those based on the model. Qualitative agreement between the experimental and theoretical values was obtained for the case of $$\frac{uh}{D} {\gg} 1$$ , where u is the average velocity of water in the plant, h is the height of the plant, and D is the diffusion coefficient of the substance.
PubDate: 2017-11-24
DOI: 10.1007/s10441-017-9314-7
Issue No: Vol. 65, No. 4 (2017)

• The Role of Hyalomma Truncatum on the Dynamics of Rift Valley Fever:
Insights from a Mathematical Epidemic Model
• Authors: Sansao A. Pedro; Shirley Abelman; Henri E. Z. Tonnang
Pages: 1 - 36
Abstract: To date, our knowledge of Rift Valley fever (RVF) disease spread and maintenance is still limited, as flooding, humid weather and presence of biting insects such as mosquitoes, have not completely explained RVF outbreaks. We propose a model that includes livestock, mosquitoes and ticks compartments structured according to their questing and feeding behaviour in order to study the possible role of ticks on the dynamics of RVF. To quantify disease transmission at the initial stage of the epidemic, we derive an explicit formula of the basic reproductive number, $$R_0$$ . Using the concept of Metzler matrix, we state necessary conditions for global asymptotic stability of the disease-free equilibrium. Results suggest that although host-ticks interactions may serve as disease reservoirs or disease amplifiers, the Aedes reproductive number should be kept under unity if disease post-epizootics activities are to be controlled. Results of both local and global sensitivity analysis of selected model parameters indicate that $$R_0$$ is more sensitive to the ticks attachment and detachment rates, probability of transmission from ticks to host and from host to ticks, length of infection in livestock and ticks death rate. Furthermore, when comparing the mean value of $$R_0$$ with that from previous studies which did not include ticks we found that our $$R_0$$ is very much larger resulting in an increase in the exponential phase of an outbreak. These findings suggest that if ticks are capable of transmitting the virus, they may be contributing to disease outbreaks and endemicity.
PubDate: 2017-03-01
DOI: 10.1007/s10441-016-9285-0
Issue No: Vol. 65, No. 1 (2017)

• SMT and TOFT Integrable After All: A Reply to Bizzarri and Cucina
• Authors: Baptiste Bedessem; Stphanie Ruphy
Pages: 81 - 85
Abstract: In a previous paper recently published in this journal, we argue that the two main theories of carcinogenesis (SMT and TOFT) should be considered as compatible, at the metaphysical, epistemological and biological levels. In a reply to our contribution, Bizzarri and Cucina claim we are wrong since SMT and TOFT are opposite and incompatible paradigms. Here, we show that their arguments are not satisfactory. Indeed, the authors go through the same mistakes that we already addressed. In particular, they confuse reductionism, as an ontological frame, and genetic determinism, as a causal pathway. Beside, they make an inadequate use of the Kuhnian notion of paradigm shift. Finally, we confirm our previous conclusion: there is no strong argument to totally abandon the somatic mutation theory. It describes a partial causal pathway, compatible with the one proposed by TOFT.
PubDate: 2017-03-01
DOI: 10.1007/s10441-016-9286-z
Issue No: Vol. 65, No. 1 (2017)

• On Scott-Phillips’ General Account of Communication
• Authors: Ronald J. Planer
Abstract: The purpose of this paper is to critically engage with a recent attempt by Thom Scott-Phillips to offer a general account of communication. As a general account, it is intended to apply equally well to both non-human and human interactions which are prima facie communicative in character. However, so far, Scott-Phillips has provided little detail regarding how his account is supposed to apply to the latter set of cases. After presenting what I take to be the most plausible way of filling in those details, I argue that his account would appear to be too narrow: it (minimally) fails to capture a range of human interactions which strike us as instances of communication. To wit, these are cases in which some but not all of the information an act is designed to convey to a reactor actually reaches that reactor. An alternative account incorporating Scott-Phillips’ main insights is then sketched, and it is suggested that this account, or something like it, would accommodate the full range of non-human and human interactions that are intuitively communicative.
PubDate: 2017-08-08
DOI: 10.1007/s10441-017-9313-8

• Microscale Gaseous Slip Flow in the Insect Trachea and Tracheoles
• Authors: S. M. Simelane; S. Abelman; F. D. Duncan
Abstract: An analytical investigation into compressible gas flow with slight rarefactions through the insect trachea and tracheoles during the closed spiracle phase is undertaken, and a complete set of asymptotic analytical solutions is presented. We first obtain estimates of the Reynolds and Mach numbers at the channel terminal ends where the tracheoles directly deliver respiratory gases to the cells, by comparing the magnitude of the different forces in the compressible gas flow. The 2D Navier–Stokes equations with a slip boundary condition are used to investigate compressibility and rarefied effects in the trachea and tracheoles. Expressions for the velocity components, pressure gradients and net flow inside the trachea are then presented. Numerical simulations of the tracheal compressible flow are performed to validate the analytical results from this study. This work extends previous work of Arkilic et al. (J Microelectromech Syst 6(2):167–178, 1997) on compressible flows through a microchannel. Novel devices for microfluidic compressible flow transport may be invented from results obtained in this study.
PubDate: 2017-07-11
DOI: 10.1007/s10441-017-9312-9

• What do Biologists Make of the Species Problem?
• Authors: Bruno Pušić; Pavel Gregorić; Damjan Franjević
Abstract: The concept of species is one of the core concepts in biology and one of the cornerstones of evolutionary biology, yet it is rife with conceptual problems. Philosophers of biology have been discussing the concept of species for decades, and in doing so they sometimes appeal to the views of biologists. However, their statements as to what biologists think are seldom supported by empirical data. In order to investigate what biologists actually think about the key issues related to the problem of species, we have conducted a survey on the sample of 193 biologists from the population of biologists from over 150 biology departments at universities in the US and the EU. This article presents and discusses the results of the survey. Some results confirm and others falsify the reiterated statements of philosophers of biology as to what biologists think, but all results we obtained should be informative and relevant for future discussions of the problem of species.
PubDate: 2017-05-13
DOI: 10.1007/s10441-017-9311-x

• Establishing a Framework for a Natural Area Taxonomy
• Authors: Malte C. Ebach; Bernard Michaux
Abstract: The identification of areas of endemism is essential in building an area classification, but plays little role in how natural areas are discovered. Rather area monophyly, derived from cladistics, is essential in the discovery of natural area classifications or area taxonomy. We propose Area Taxonomy to be a new sub-discipline of historical biogeography, one that can be revised and debated, and which has its own area nomenclature. Separately to area taxonomy, we outline how natural areas may be discovered by transcribing the concepts of homology and monophyly from biological systematics to historical biogeography, in the form of area homologues, area homologies and area monophyly.
PubDate: 2017-05-10
DOI: 10.1007/s10441-017-9310-y

• Asymptotic Behavior of a Chemostat Model with Constant Recycle Sludge
Concentration
• Authors: Mohamed Amine Hamra; Karim Yadi
Abstract: In this work, we study a several species aerobic chemostat model with constant recycle sludge concentration in continuous culture. We reduce the number of parameters by considering a dimensionless model. First, the existence of a global positive uniform attractor for the model with different removal rates is proved using the theory of dissipative dynamical systems. Hence, we investigate the asymptotic behavior of the model under small perturbations using methods of singular perturbation theory and we prove that, in the case of two species in competition, the unique equilibrium which is positive is globally asymptotically stable. Finally, we establish the link between the open problem of the chemostat with different removal rates and monotone functional responses, and our model when two species compete on the same nutrient. We give some numerical simulations to illustrate the results.
PubDate: 2017-05-04
DOI: 10.1007/s10441-017-9309-4

• Skewed Exposure to Environmental Antigens Complements Hygiene Hypothesis
in Explaining the Rise of Allergy
• Authors: Wilfried Allaerts; Tse Wen Chang
Abstract: The Hygiene Hypothesis has been recognized as an important cornerstone to explain the sudden increase in the prevalence of asthma and allergic diseases in modernized culture. The recent epidemic of allergic diseases is in contrast with the gradual implementation of Homo sapiens sapiens to the present-day forms of civilization. This civilization forms a gradual process with cumulative effects on the human immune system, which co-developed with parasitic and commensal Helminths. The clinical manifestation of this epidemic, however, became only visible in the second half of the twentieth century. In order to explain these clinical effects in terms of the underlying IgE-mediated reactions to innocuous environmental antigens, the low biodiversity of antigens in the domestic environment plays a pivotal role. The skewing of antigen exposure as a cumulative effect of reducing biodiversity in the immediate human environment as well as in changing food habits, provides a sufficient and parsimonious explanation for the rise in allergic diseases in a highly developed and helminth-free modernized culture. Socio-economic tendencies that incline towards a further reduction of environmental biodiversity may provide serious concern for future health. This article explains that the “Hygiene Hypothesis”, the “Old Friends Hypothesis”, and the “Skewed Antigen Exposure Hypothesis” are required to more fully explain the rise of allergy in modern societies.
PubDate: 2017-03-24
DOI: 10.1007/s10441-017-9306-7

• Stability of a Stochastic Model of an SIR Epidemic with Vaccination
• Authors: P. J. Witbooi
Abstract: We prove almost sure exponential stability for the disease-free equilibrium of a stochastic differential equations model of an SIR epidemic with vaccination. The model allows for vertical transmission. The stochastic perturbation is associated with the force of infection and is such that the total population size remains constant in time. We prove almost sure positivity of solutions. The main result concerns especially the smaller values of the diffusion parameter, and describes the stability in terms of an analogue $$\mathcal{R}_\sigma$$ of the basic reproduction number $$\mathcal{R}_0$$ of the underlying deterministic model, with $$\mathcal{R}_\sigma \le \mathcal{R}_0$$ . We prove that the disease-free equilibrium is almost sure exponentially stable if $$\mathcal{R}_\sigma <1$$ .
PubDate: 2017-03-21
DOI: 10.1007/s10441-017-9308-5

• External Noise and External Signal Induced Transition of Gene Switch and
Coherence Resonance in the Genetic Regulatory System
• Authors: Jian-Cheng Shi; Min Luo; Tao Dong; Chu-Sheng Huang
Abstract: The transition of gene switch induced by external noises (multiplicative external noise and additive external noise) and external signals is investigated in the genetic regulatory system. Results show that the state-to-state transition of gene switch as well as resonant behaviors, such as the explicit coherence resonance (ECR), implicit coherence resonance (ICR) and control parameter coherence biresonance (CPCBR), can appear when noises are injected into the genetic regulatory system. The ECR is increased with the increase of the control parameter value when starting from the supercritical Hopf bifurcation parameter point, and there exists a critical control parameter value for the occurrence of ECR. However, the ICR is decreased as the control parameter value is increased when starting from the subcritical Hopf bifurcation point. In particular, the coherence of ECR is higher and more sensitive to noise than that of ICR. When an external signal is introduced into the system, the enhancement or suppression of the CPCBR and the number of peaks strongly depend on the frequency and amplitude of the external signal. Furthermore, the gene regulation system can selectively enhance or decrease the noise-induced oscillation signals at preferred frequency and amplitude of an external signal.
PubDate: 2017-03-17
DOI: 10.1007/s10441-017-9307-6

• Mapping Biological Transmission: An Empirical, Dynamical, and Evolutionary
Approach
• Authors: Francesca Merlin; Livio Riboli-Sasco
Abstract: The current debate over extending inheritance and its evolutionary impact has focused on adding new categories of non-genetic factors to the classical transmission of DNA, and on trying to redefine inheritance. Transmitted factors have been mainly characterized by their directions of transmission (vertical, horizontal, or both) and the way they store variations. In this paper, we leave aside the issue of defining inheritance. We rather try to build an evolutionary conceptual framework that allows for tracing most, if not all forms of transmission and makes sense of their different tempos and modes. We discuss three key distinctions that should in particular be the targets of theoretical and empirical investigation, and try to assess the interplay among them and evolutionary dynamics. We distinguish two channels of transmission (channel 1 and channel 2), two measurements of the temporal dynamics of transmission, respectively across and within generations (durability and residency), and two types of transmitted factors according to their evolutionary relevance (selectively relevant and neutral stable factors). By implementing these three distinctions we can then map different forms of transmission over a continuous space describing the combination of their varying dynamical features. While our aim is not to provide yet another model of inheritance, putting together these distinctions and crossing them, we manage to offer an inclusive conceptual framework of transmission, grounded in empirical observation, and coherent with evolutionary theory. This interestingly opens possibilities for qualitative and quantitative analyses, and is a necessary step, we argue, in order to question the interplay between the dynamics of evolution and the dynamics of multiple forms of transmission.
PubDate: 2017-02-14
DOI: 10.1007/s10441-017-9305-8

• Erratum to: Exploring Darwinian Worlds: From Darwin to the Extended
Synthesis
• Authors: Elena Casetta; Andrea Borghini
PubDate: 2017-02-06
DOI: 10.1007/s10441-017-9304-9

• On the Role of Imitation on Adolescence Methamphetamine Abuse Dynamics
• Authors: J. Mushanyu; F. Nyabadza; G. Muchatibaya; A. G. R. Stewart
Abstract: Adolescence methamphetamine use is an issue of considerable concern due to its correlation with later delinquency, divorce, unemployment and health problems. Understanding how adolescents initiate methamphetamine abuse is important in developing effective prevention programs. We formulate a mathematical model for the spread of methamphetamine abuse using nonlinear ordinary differential equations. It is assumed that susceptibles are recruited into methamphetamine use through imitation. An epidemic threshold value, $${\mathcal {R}}_a$$ , termed the abuse reproduction number, is proposed and defined herein in the drug-using context. The model is shown to exhibit the phenomenon of backward bifurcation. This means that methamphetamine problems may persist in the population even if $${\mathcal {R}}_a$$ is less than one. Sensitivity analysis of $${\mathcal {R}}_a$$ was performed to determine the relative importance of different parameters in methamphetamine abuse initiation. The model is then fitted to data on methamphetamine users less than 20 years old reporting methamphetamine as their primary substance of abuse in the treatment centres of Cape Town and parameter values that give the best fit are chosen. Results show that the proportion of methamphetamine users less than 20 years old reporting methamphetamine as their primary substance of abuse will continue to decrease in Cape Town of South Africa. The results suggest that intervention programs targeted at reducing adolescence methamphetamine abuse, are positively impacting methamphetamine abuse.
PubDate: 2016-12-18
DOI: 10.1007/s10441-016-9302-3

• Exploring Darwinian Worlds: From Darwin to the Extended Synthesis
• PubDate: 2016-10-03
DOI: 10.1007/s10441-016-9289-9

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