An amendment to this paper has been published and can be accessed via the original article.

In this rapid commentary, a mini-review is given of the present state-of-knowledge regarding the etiology and epidemiology of the new coronavirus 2019-nCoV and the risks for developing Acute respiratory distress syndrome (ARDS). The available knowledge on the viral genomics, molecular biology and pathogenicity of viruses of the Coronaviridae family and other Nidovirales, forms a helpful template for

This review essay reflects on recent discussions in evolutionary biology and philosophy of science on the central causes of evolution and the structure of causal explanations in evolutionary theory. In this debate, it has been argued that our view of evolutionary causation should be rethought by including more seriously developmental causes and causes of the individual acting organism. I use Tobias

Evolutionary theorists often talk as if natural selection were choosing the most adapted traits, or if organisms were deciding to do the most adaptive strategy. Moreover, the payoff of those decisions often depend on what others are doing, and since Hamilton (1964), biologists possess conceptual tools such as kin selection and inclusive fitness to make sense of outcomes of evolution in these contexts

In the 1960’s Brian Goodwin published a couple of mathematical models showing how feedback inhibition can lead to oscillations and discussed possible implications of this behaviour for the physiology of the cell. He also presented key ideas about the rich dynamics that may result from the coupling between such biochemical oscillators. Goodwin’s work motivated a series of theoretical investigations

The authors have retracted this article [1] because they found a fundamental mistake in the methodology that is not correctable at this time. This mistake is found in the methodology and the derivation of the model with Tukey and Huber's losses. Because of the error, the findings in the article are not reliable. All authors agree to this retraction.

In this review of Milan Ćirković's The Great Silence: Science and Philosophy of Fermi's Paradox, we attempt to reconstruct the logic of Fermi's paradox as understood by the author, and we critically examine the reasoning that leads to the paradox. We show that there is no plausible solution to Fermi's paradox that can satisfy all of Ćirković's proposed desiderata, which in turn suggests that the author's

An additional compartment of vaccinated individuals is considered in a SIS stochastic epidemic model with infection reintroduction. The quantification of the spread of the disease is modeled by a continuous time Markov chain. A well-known measure of the initial transmission potential is the basic reproduction number [Formula: see text], which determines the herd immunity threshold or the critical proportion

Correct interpretation of the data from integral laboratory tests, including Thrombin Generation Test (TGT), requires biochemistry-based mathematical models of blood coagulation. The purpose of this study is to describe the experimental TGT data from healthy donors and hemophilia A (HA) and B (HB) patients. We derive a simplified ODE model and apply it to analyze the TGT data from healthy donors and

Over the last few years, oncolytic virus therapy has been recognised as a promising approach in cancer treatment, due to the potential of these viruses to induce systemic anti-tumour immunity and selectively killing tumour cells. However, the effectiveness of these viruses depends significantly on their interactions with the host immune responses, both innate (e.g., macrophages, which accumulate in

Theoretical minimal RNA rings attempt to mimick life's primitive RNAs. At most 25 22-nucleotide-long RNA rings code once for each biotic amino acid, a start and a stop codon and form a stem-loop hairpin, resembling consensus tRNAs. We calculated, for each RNA ring's 22 potential splicing positions, similarities of predicted secondary structures with tRNA vs. rRNA secondary structures. Assuming rRNAs

Models of gene regulatory networks (GRN) have proven useful for understanding many aspects of the highly complex behavior of biological control networks. Randomly generated non-Boolean networks were used in experimental simulations to generate data on dynamic phenotypes as a function of several genotypic parameters. We found that predictive relationships between some phenotypes and quantitative genotypic

When relating genomic data to survival outcomes, there are three main challenges that are the censored survival outcomes, the high-dimensionality of the genomic data, and the non-normality of data. We propose a method to tackle these challenges simultaneously and obtain a robust estimation of detecting significant genes related to survival outcomes based on Accelerated Failure Time (AFT) model. Specifically

Brandon claims that to explain adaptation one must specify fitnesses in each selective environment and specify the distribution of individuals across selective environments. Glymour claims, using an example of the adaptive evolution of costly plasticity in a symmetric environment, that there are some predictive or explanatory tasks for which Brandon's claim is limited. In this paper, I provide necessary

The aim of this study is to provide a feedback control, called the Chemotherapy Protocol Law, with the purpose to keep the density of tumor cells that are treated by chemotherapy below a "tolerance level" [Formula: see text], while retaining the density of normal cells above a "healthy level" [Formula: see text]. The mathematical model is a controlled dynamical system involving three nonlinear differential

The aim of this article is to show how a tumor can modify energy substrates fluxes in the brain to support its own growth. To address this question we use a modeling approach to explain brain nutrient kinetics. In particular we set up a system of 17 equations for oxygen, lactate, glucose concentrations and cells number in the brain. We prove the existence and uniqueness of nonnegative solutions and

This paper aims to provide a philosophical and theoretical account of biological communication grounded in the notion of organisation. The organisational approach characterises living systems as organised in such a way that they are capable to self-produce and self-maintain while in constant interaction with the environment. To apply this theoretical framework to the study of biological communication

Evolutionary theory coheres with its neighboring theories, such as the theory of plate tectonics, molecular biology, electromagnetic theory, and the germ theory of disease. These neighboring theories were previously unconceived, but they were later conceived, and then they cohered with evolutionary theory. Since evolutionary theory has been strengthened by its several neighboring theories that were

A mathematical model of the dynamics of the immune system is considered to illustrate the effect of its response to HIV infection, i.e. on viral growth and on T-cell dynamics. The specific immune response is measured by the levels of cytotoxic lymphocytes in a human body. The existence and stability analyses are performed for infected steady state and uninfected steady state. In order to keep infection

Biologists and philosophers often use the language of determination in order to describe the nature of developmental phenomena. Accounts in terms of determination have often been reductionist. One common idea is that DNA is supposed to play a special explanatory role in developmental explanations, namely, that DNA is a developmental determinant. In this article we try to make sense of determination

Synthetic biology is described as a new field of biotechnology that models itself on engineering sciences. However, this view of synthetic biology as an engineering field has received criticism, and both biologists and philosophers have argued for a more nuanced and heterogeneous understanding of the field. This paper elaborates the heterogeneity of synthetic biology by clarifying the role of design

A new multi-stage deterministic model for the transmission dynamics of syphilis, which incorporates disease transmission by individuals in the early latent stage of syphilis infection and the reversions of early latent syphilis to the primary and secondary stages, is formulated and rigorously analysed. The model is used to assess the population-level impact of preventive (condom use) and therapeutic

Busseola fusca is a maize and sorghum pest that can cause significant damage to both crops. Given that maize is one of the main cereals grown in the worldwide, this pest is a major challenge for maize production and therefore for the economies of several countries . In this paper , based on the life cycle of B. fusca, we propose a mathematical model to study the population dynamics of this insect pest

In the original publication of the article, the y axis labels present in Figs. 1a and 2a are incorrect. The correct Figs. 1a and 2a are provided here.

The Canadian lynx and snowshoe hare pelt data by the Hudson Bay Company did not fit the classical predator-prey theory. Rather than following the peak density of the hare, that of the lynx leads it, creating the hares-eat-lynx (HEL) paradox. Although trappers were suspected to play a role, no mathematical model has ever demonstrated the HEL effect. Here we show that the long-held assumption that the

The main concern of this paper is to study the dynamic of a predator-prey system with diffusion. It incorporates the Holling-type-II and a modified Leslie-Gower functional responses under Robin boundary conditions. More concretely, we study the dissipativeness of the system by using the comparison principle, and we derive a criteria for permanence and for predator extinction.

The state-of-art research in the field of life's organization confronts the need to investigate a number of interacting components, their properties and conditions of sustainable behaviour within a natural system. In biology, ecology and life sciences, the performance of such stable system is usually related to homeostasis, a property of the system to actively regulate its state within a certain allowable

This computational study generates a hypothesis for the coagulation protein whose initial concentration greatly influences the course of coagulation. Many clinical malignancies of blood coagulation arise due to abnormal initial concentrations of coagulation factors. Sensitivity analysis of mechanistic models of blood coagulation is a convenient method to assess the effect of such abnormalities. Accordingly

In this paper I critically evaluate Reisman and Forber's (Philos Sci 72(5):1113-1123, 2005) arguments that drift and natural selection are population-level causes of evolution based on what they call the manipulation condition. Although I agree that this condition is an important step for identifying causes for evolutionary change, it is insufficient. Following Woodward, I argue that the invariance

Systems biology is today such a widespread discipline that it becomes difficult to propose a clear definition of what it really is. For some, it remains restricted to the genomic field. For many, it designates the integrated approach or the corpus of computational methods employed to handle the vast amount of biological or medical data and investigate the complexity of the living. Although defining

A mathematical model for Vibrio Cholerae (V. Cholerae) in a closed environment is considered, with the aim of investigating the impact of climatic factors which exerts a direct influence on the bacterial metabolism and on the bacterial reservoir capacity. We first propose a V. Cholerae mathematical model in a closed environment. A sensitivity analysis using the eFast method was performed to show the

Darwin described biological species as groups of morphologically similar individuals. These groups of individuals can split into several subgroups due to natural selection, resulting in the emergence of new species. Some species can stay stable without the appearance of a new species, some others can disappear or evolve. Some of these evolutionary patterns were described in our previous works independently

Computational drug repositioning has been proven as a promising and efficient strategy for discovering new uses from existing drugs. To achieve this goal, a number of computational methods have been proposed, which are based on different data sources of drugs and diseases. These methods approach the problem using either machine learning- or network-based models with an assumption that similar drugs

The accurate annotation of an unknown protein sequence depends on extant data of template sequences. This could be empirical or sets of reference sequences, and provides an exhaustive pool of probable functions. Individual methods of predicting dominant function possess shortcomings such as varying degrees of inter-sequence redundancy, arbitrary domain inclusion thresholds, heterogeneous parameterization

This paper deals with designing a harvesting control strategy for a predator-prey dynamical system, with parametric uncertainties and exogenous disturbances. A feedback control law for the harvesting rate of the predator is formulated such that the population dynamics is asymptotically stabilized at a positive operating point, while maintaining a positive, steady state harvesting rate. The hierarchical

In this paper, we propose two four-base related 2D curves of DNA primary sequences (termed as F-B curves) and their corresponding single-base related 2D curves (termed as A-related, G-related, T-related and C-related curves). The constructions of these graphical curves are based on the assignments of individual base to four different sinusoidal (or tangent) functions; then by connecting all these points

Cognition in living entities-and their social groupings or institutional artifacts-is necessarily as complicated as their embedding environments, which, for humans, includes a particularly rich cultural milieu. The asymptotic limit theorems of information and control theories permit construction of a new class of empirical 'regression-like' statistical models for cognitive developmental processes,

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

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

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

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

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)

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

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 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

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

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

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

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

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

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

Ernst Mayr's concept of dual causality in biology with the two forms of causes (proximate and ultimate) continues to provide an essential foundation for the philosophy of biology. They are equivalent to functional (=proximate) and evolutionary (=ultimate) causes with both required for full biological explanations. The natural sciences can be classified into nomological, historical nomological and historical

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

Morphogenesis is a general concept in biology including all the processes which generate tissue shapes and cellular organizations in a living organism. Many hybrid formalizations (i.e., with both discrete and continuous parts) have been proposed for modelling morphogenesis in embryonic or adult animals, like gastrulation. We propose first to study the ventral furrow invagination as the initial step