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The phenomenon of near death and dying experiences has been both of popular interest and of scientific speculation. However, the reality of mental perception at the point of death is currently a subjective experience and has not been formally evaluated. While postmortem gene expression, even in humans, has been evaluated, restoration of postmortem brain activity has heretofore only been attempted in animal models, at the molecular and cellular levels. Meanwhile, progress has been made to translate brain activity of living humans into speech and images. This paper proposes two inter-related thought experiments. First, assuming progress and refinement of the technology of translating human brain activity into interpretable speech and images, can an objective analysis of death experiences be obtained by utilizing these technologies on dying humans? Second, can human brain function be revived postmortem and, if so, can the relevant technologies be utilized for communication with (recently) deceased individuals? In this paper, these questions are considered and possible implications explored. [ABSTRACT FROM AUTHOR]

Until the mid-nineteenth century, "physiology" was a comprehensive theory of life, expounded and shaped by Johannes P. Müller (1801–1858). Biologists and medical doctors still refer to him today. In the summer term of 1851, Müller gave a lecture on the Comparative Anatomy of animals. This lecture was attended and recorded by Ernst Zeller (1830–1902), a future physician and zoologist, and has recently been published together with a German transcript. In this paper, we situate Johannes Müller within the intellectual history of his time. Through his "empirical idealism," we show how he opposed the speculative tendencies of the romantic understanding of nature, the emerging evolutionism, and the growing splits in the natural sciences. Müller focused on recognizing living nature as a whole and realizing ideal "phenomena" through his empirical research. He considered the notion of the soul of the world. Müller's lecture transcript serves as a poignant testament to German scientific culture in the mid-nineteenth century, a few years before the publication of Darwin's Origin of Species. It also provides valuable insights into the self-contained epistemological foundations of morphology. [ABSTRACT FROM AUTHOR]

Cervical cancer is one of the most severe threats to women worldwide and holds fourth rank in lethality. It is estimated that 604, 127 cervical cancer cases have been reported in 2020 globally. With advancements in high throughput technologies and bioinformatics, several cervical candidate genes have been proposed for better therapeutic strategies. In this paper, we intend to prioritize the candidate genes that are involved in cervical cancer progression through a fractal time series-based cross-correlations approach. we apply the chaos game representation theory combining a two-dimensional multifractal detrended cross-correlations approach among the known and candidate genes involved in cervical cancer progression to prioritize the candidate genes. We obtained 16 candidate genes that showed cross-correlation with known cancer genes. Functional enrichment analysis of the candidate genes shows that they involve GO terms: biological processes, cell–cell junction assembly, cell–cell junction organization, regulation of cell shape, cortical actin cytoskeleton organization, and actomyosin structure organization. KEGG pathway analysis revealed genes' role in Rap1 signaling pathway, ErbB signaling pathway, MAPK signaling pathway, PI3K-Akt signaling pathway, mTOR signaling pathway, Acute myeloid leukemia, chronic myeloid leukemia, Breast cancer, Thyroid cancer, Bladder cancer, and Gastric cancer. Further, we performed survival analysis and prioritized six genes CDH2, PAIP1, BRAF, EPB41L3, OSMR, and RUNX1 as potential candidate genes for cervical cancer that has a crucial role in tumor progression. We found that our study through this integrative approach an efficient tool and paved a new way to prioritize the candidate genes and these genes could be evaluated experimentally for potential validation. We suggest this may be useful in analyzing the nucleotide sequences and protein sequences for clustering, classification, class affiliation, etc. [ABSTRACT FROM AUTHOR]

The present study provides new insight into the key aspects of the early formative period of the ecosystem concept in aquatic ecology. Raymond Lindeman's trophodynamics is known to be a starting point for the development of the modern concept of ecosystem. The trophodynamic approach in ecology was proposed by Lindeman in his widely cited paper of 1942. Lindeman's views are analyzed in comparison with the contemporary production studies in aquatic ecology. It is shown that a similar theoretical system has been proposed in the USSR at the end of the 1930s by Georgiy G. Vinberg. He introduced the concept of biotic balance based on the wide appraisal of the dark and light bottles method. The study shows that both Lindeman's trophodynamics and Vinberg's concept of biotic balance relied on an energy-based approach in considering the wholeness of a water body. The two scientists, however, differed in several important aspects concerning the interpretation of the role of living organisms. The holistic interpretation of ecosystem by Lindeman and Vinberg can be seen as part of the dilemma between physicalism and organicism. At the same time, the main emphasis in the concepts of both Vinberg and Lindemann was on the primary production component, a feature that was common to the first holistic systems in production hydrobiology (e.g., E. Naumann's regional limnology). It is clear that modern problems of aquatic ecology should be addressed from the perspective of the organismocentric understanding of the ecosystem, but undoubtedly at the new level of development of this view. [ABSTRACT FROM AUTHOR]

In this paper, we investigate the asymptotic behavior of a modified chemostat model. We first demonstrate the existence of equilibria. Then, we present a mathematical analysis for the model, the invariance, the positivity, the persistence of the solutions, and the asymptotic global stability of the interior equilibrium. Some numerical simulations are carried out to illustrate the main results. [ABSTRACT FROM AUTHOR]

The multilevel model of behavioral selection (MLBS) by Borgstede and Eggert (Behav Process 186:104370. 10.1016/j.beproc.2021.104370, 2021) provides a formal framework that integrates reinforcement learning with natural selection using an extended Price equation. However, the MLBS is so far only formulated for homogeneous populations, thereby excluding all sources of variation between individuals. This limitation is of primary theoretical concern because any application of the MLBS to real data requires to account for variation between individuals. In this paper, I extend the MLBS to account for inter-individual variation by dividing the population into homogeneous sub-populations and including class-specific reproductive values as weighting factors for an individual's evolutionary fitness. The resulting formalism closes the gap between the theoretical underpinnings of behavioral selection and the application of the theory to empirical data, which naturally includes inter-individual variation. Furthermore, the extended MLBS is used to establish an explicit connection between the dynamics of learning and the maximization of individual fitness. These results expand the scope of the MLBS as a general theoretical framework for the quantitative analysis of learning and evolution. [ABSTRACT FROM AUTHOR]

This paper addresses the relationship between information and structure of the genetic code. The code has two puzzling anomalies: First, when viewed as 64 sub-cubes of a 4 × 4 × 4 cube, the codons for serine (S) are not contiguous, and there are amino acid codons with zero redundancy, which goes counter to the objective of error correction. To make sense of this, the paper shows that the genetic code must be viewed not only on stereochemical, co-evolution, and error-correction considerations, but also on two additional factors of significance to natural systems, that of an information-theoretic dimensionality of the code data, and the principle of maximum entropy. One implication of non-integer dimensionality associated with data dimensions is self-similarity to different scales, and it is shown that the genetic code does satisfy this property, and it is further shown that the maximum entropy principle operates through the scrambling of the elements in the sense of maximum algorithmic information complexity, generated by an appropriate exponentiation mapping. It is shown that the new considerations and the use of maximum entropy transformation create new constraints that are likely the reasons for the non-uniform codon groups and codons with no redundancy. [ABSTRACT FROM AUTHOR]

In our paper, we analyse the relationship of the evolutionary philosophy of Charles Sanders Peirce to Lamarckian natural philosophy and link it to concepts of teleology, focusing especially on Aristotelian and Peircean conceptions of the final cause. Peirce commented on evolution in many of his writings, especially in 1891–1893 in essays such as 'Evolutionary Love' (1893) or 'Man's Glassy Essence' (1892). After introducing the three types of evolution distinguished by Peirce, we compare Peirce's and Lamarck's views on evolution, habit, and teleology. From a synthesis of concepts formulated by Peirce, Aristotle, nineteenth-century neo-Lamarckians, and current knowledge regarding epigenetics, there should emerge our own concept of biological teleology unburdened by panpsychism, subjective intentions, or determinism. We believe it could be a concept acceptable to current biology. [ABSTRACT FROM AUTHOR]

In this paper, we develop a network-based methodology to investigate the problems related to matrix stability and bifurcations in nonlinear dynamical systems. By matching a matrix with a network, i.e., interaction graph, we propose a new network-based matrix analysis method by proving a theorem about matrix determinant under which matrix stability can be considered in terms of feedback loops. Especially, the approach can tell us how a node, a path, or a feedback loop in the interaction graph affects matrix stability. In addition, the roles played by a node, a path, or a feedback loop in determining bifurcations in nonlinear dynamical systems can also be revealed. Therefore, the approach can help us to screen optimal node or node combinations. By perturbing them, unstable matrices can be stabilized more efficiently or bifurcations can be induced more easily to realize desired state transitions. To illustrate feasibility and efficiency of the approach, some simple matrices are used to show how single or combinatorial perturbations affect matrix stability and induce bifurcations. In addition, the main idea is also illustrated through a biological problem related to T cell development with three nodes: TCF-1, GATA3, and PU.1, which can be considered to be a three-variable nonlinear dynamical system. The approach is especially helpful in understanding crucial roles of single or molecule combinations in biomolecular networks. The approach presented here can be expected to analyze other biological networks related to cell fate transitions and systematic perturbation strategy selection. [ABSTRACT FROM AUTHOR]

Mathematical models of cancer and bacterial evolution have generally stemmed from a gene-centric framework, assuming clonal evolution via acquisition of resistance-conferring mutations and selection of their corresponding subpopulations. More recently, the role of phenotypic plasticity has been recognized and models accounting for phenotypic switching between discrete cell states (e.g., epithelial and mesenchymal) have been developed. However, seldom do models incorporate both plasticity and mutationally driven resistance, particularly when the state space is continuous and resistance evolves in a continuous fashion. In this paper, we develop a framework to model plastic and mutational mechanisms of acquiring resistance in a continuous gradual fashion. We use this framework to examine ways in which cancer and bacterial populations can respond to stress and consider implications for therapeutic strategies. Although we primarily discuss our framework in the context of cancer and bacteria, it applies broadly to any system capable of evolving via plasticity and genetic evolution. [ABSTRACT FROM AUTHOR]

In this paper a Feynman-type path integral control approach is used for a recursive formulation of a health objective function subject to a fatigue dynamics, a forward-looking stochastic multi-risk susceptible–infective–recovered (SIR) model with risk-group's Bayesian opinion dynamics toward vaccination against COVID-19. My main interest lies in solving a minimization of a policy-maker's social cost which depends on some deterministic weight. I obtain an optimal lock-down intensity from a Wick-rotated Schrödinger-type equation which is analogous to a Hamiltonian–Jacobi–Bellman (HJB) equation. My formulation is based on path integral control and dynamic programming tools facilitates the analysis and permits the application of algorithm to obtain numerical solution for pandemic control model. [ABSTRACT FROM AUTHOR]

There is an old attempt to divide the sciences into sciences of laws and the historical sciences. More recently, John Beatty has drawn the distinction so that biology is a historical science and urged that there are no genuinely biological laws. This paper shows that there are indeed biological laws, specifically statistical ones, notably in evolutionary theory. Moreover, all or almost all other areas of biology involve laws as well. Even history involves laws. Finally, the paper shows that this pervasiveness of laws is compatible with the most basic commitments of those who, like Beatty, would claim that biology is only historical. [ABSTRACT FROM AUTHOR]

The bio-cell cycle is controlled by a complex biochemical network of signaling pathways. Modeling such challenging networks accurately is imperative for the understanding of their detailed dynamical behavior. In this paper, we construct, analyze, and verify a hybrid Petri net (HPN) model of a complex biochemical network that captures the role of an important protein (namely p53) in deciding the fate of the cell. We model the behavior of the cell nucleus and cytoplasm as two stochastic and continuous Petri nets, respectively, combined together into a single HPN. We use simulative model checking to verify three different properties that capture the dynamical behavior of p53 protein with respect to the intensity of the ionizing radiation (IR) to which the cell is exposed. For each IR dose, 1000 simulation runs are carried out to verify each property. Our verification results showed that the fluctuations in p53, which relies on IR intensity, are compatible with the findings of the preceding simulation studies that have previously examined the role of p53 in cell fate decision. [ABSTRACT FROM AUTHOR]

The origins of innovation in science are typically understood using historical narratives that tend to be focused on small sets of influential authors, an approach that is rigorous but limited in scope. Here, we develop a framework for rigorously identifying innovation across an entire scientific field through automated analysis of a corpus of over 6000 documents that includes every paper published in the field of evolutionary medicine. This comprehensive approach allows us to explore statistical properties of innovation, asking where innovative ideas tend to originate within a field's pre-existing conceptual framework. First, we develop a measure of innovation based on novelty and persistence, quantifying the collective acceptance of novel language and ideas. Second, we study the field's conceptual landscape through a bibliographic coupling network. We find that innovations are disproportionately more likely in the periphery of the bibliographic coupling network, suggesting that the relative freedom allowed by remaining unconnected with well-established lines of research could be beneficial to creating novel and lasting change. In this way, the emergence of collective computation in scientific disciplines may have robustness–adaptability trade-offs that are similar to those found in other biosocial complex systems. [ABSTRACT FROM AUTHOR]

What role does nationality—or the image of a nation—play in how one thinks and receives scientific ideas? This paper investigates the commonly held ideas about "German science" and "French science" in early nineteenth-century France. During the politically turbulent time, the seemingly independent scientific community found itself in a difficult position: first, between the cosmopolitan ideals of scientific community and the invasive political reality, and second, between the popularized image of national differences and the actual comparisons of international scientific ideas. The tension between multiple sets of fictions and realities underscores the fragility of the concept of nationality as a scientific measure. A case study comparing morphological ideas, receptions in France, and the actual scientific texts of J. W. von Goethe and A. P. de Candolle further illustrates this fragility. Goethe and Candolle make an ideal comparative case because they were received in very different lights despite their similar concept of the plant type. Our sentence-classification and visualization methods are applied to their scientific texts, to compare the actual compositions and forms of the texts that purportedly represented German and French sciences. This paper concludes that there was a gap between what French readers assumed they read and what they really read, when it came to foreign scientific texts. The differences between Goethe's and Candolle's texts transcended the perceived national differences between German Romanticism and French Classicism. [ABSTRACT FROM AUTHOR]

What is the role of consciousness in volition and decision-making? Are our actions fully determined by brain activity preceding our decisions to act, or can consciousness instead affect the brain activity leading to action? This has been much debated in philosophy, but also in science since the famous experiments by Libet in the 1980s, where the current most common interpretation is that conscious free will is an illusion. It seems that the brain knows, up to several seconds in advance what "you" decide to do. These studies have, however, been criticized, and alternative interpretations of the experiments can be given, some of which are discussed in this paper. In an attempt to elucidate the processes involved in decision-making (DM), as an essential part of volition, we have developed a computational model of relevant brain structures and their neurodynamics. While DM is a complex process, we have particularly focused on the amygdala and orbitofrontal cortex (OFC) for its emotional, and the lateral prefrontal cortex (LPFC) for its cognitive aspects. In this paper, we present a stochastic population model representing the neural information processing of DM. Simulation results seem to confirm the notion that if decisions have to be made fast, emotional processes and aspects dominate, while rational processes are more time consuming and may result in a delayed decision. Finally, some limitations of current science and computational modeling will be discussed, hinting at a future development of science, where consciousness and free will may add to chance and necessity as explanation for what happens in the world. [ABSTRACT FROM AUTHOR]

To what extent do simultaneous innovations occur and are independently from each other? In this paper we use a novel persistent keyword framework to systematically identify innovations in a large corpus containing academic papers in evolutionary medicine between 2007 and 2011. We examine whether innovative papers occurring simultaneously are independent from each other by evaluating the citation and co-authorship information gathered from the corpus metadata. We find that 19 out of 22 simultaneous innovative papers do, in fact, occur independently from each other. In particular, co-authors of simultaneous innovative papers are no more geographically concentrated than the co-authors of similar non-innovative papers in the field. Our result suggests producing innovative work draws from a collective knowledge pool, rather than from knowledge circulating in distinct localized collaboration networks. Therefore, new ideas can appear at multiple locations and with geographically dispersed co-authorship networks. Our findings support the perspective that simultaneous innovations are the outcome of collective behavior. [ABSTRACT FROM AUTHOR]

In this paper, a new mathematical model that describes the dynamics of the within-host COVID-19 epidemic is formulated. We show the stochastic dynamics of Target-Latent-Infected-Virus free within the human body with discrete delay and noise. Positivity and uniqueness of the solutions are established. Our study shows the extinction and persistence of the disease inside the human body through the stability analysis of the disease-free equilibrium E 0 and the endemic equilibrium E ∗ , respectively. Moreover, we show the impact of delay tactics and noise on the extinction of the disease. The most interesting result is even if the deterministic system is inevitably pandemic at a specific point, extinction will become possible in the stochastic version of our model. [ABSTRACT FROM AUTHOR]

Breast cancer stem cells (BCSCs) with the ability to self-renew and differentiate have been identified in primary breast cancer tissues and cell lines. The BCSCs are often resistant to traditional radiation and/or chemotherapies. Previous studies have also shown that successful therapy must eradicate cancer stem cells. The purpose of this paper is to develop a mathematical model with self-feedback mechanism to illustrate the issues regarding the difficulties of absolutely eliminating a breast cancer. In addition, we introduce the mechanism of the epithelial-mesenchymal transition (EMT) to investigate the influence of EMT on the effects of breast cancer growth and treatment. Results indicate that the EMT mechanism facilitates the growth of breast cancer and makes breast cancer more difficult to be cured. Therefore, targeting the signals involved in EMT can halt tumor progression in breast cancer. Finally, we apply the experimental data to carry out numerical simulations and validate our theoretical conclusions. [ABSTRACT FROM AUTHOR]

This paper is aimed at demonstrating that some geometrical and topological transformations and operations serve not only as promoters of many specific genetic and cellular events in multicellular living organisms, but also as initiators of the organization and regulation of their functions. Thus, changes in the form and structure of macromolecular and cellular systems must be directly associated to their functions. There are specific classes of enzymes that manipulate the geometry and topology of complex DNA–protein structures, and thereby they perform many important cellular processes, including segregation of daughter chromosomes, gene regulation, and DNA repair. We argue that form has an organizing power, hence a causal action, in the sense that it enables to induce functional events during different biological processes, at the supramolecular, cellular, and organismal levels of organization. Clearly, topological forms must be matched with specific kinetic and dynamical parameters to have a functional effectiveness in living systems. This effectiveness is remarkably apparent, to give an example, in the regulation of the genome functions and in cell activity. In more general terms, we try to show that the conformational plasticity of biological systems depends on different kinds of topological manipulations performed by specific families of enzymes. In doing so, they catalyze all those spatial and dynamical changes of biological structures that are suitable for the functions to be acted by the organism. [ABSTRACT FROM AUTHOR]

In this paper, we understand the emergence of life as a pure individuation process. Individuation already occurs in open thermodynamics systems near equilibrium. We understand such open systems, as already recursively characterized (R1) by the relation between their internal properties, and their boundary conditions. Second, global properties emerge in such physical systems. We interpret this change as the fact that their structure is the recursive result of their operations (R2). We propose a simulation of the emergence of life in Earth by a mapping (R) through which (R1R2) operators are applied to themselves, so that RN = (R1R2)N. We suggest that under specific thermodynamic (open systems out of equilibrium) and chemical conditions (autocatalysis, kinetic dynamic stability), this mapping can go up to a limit characterized by a fixed-point equation: R = ϕ 1 ϕ 2 R . In this equation, ( ϕ 1 ) symbolizes a regime of permanent resonance characterizing the biosphere, as open from inside, by the recursive differential relation between the biosphere and all its holobionts. As such the biosphere is closed on itself as a pure differential entity. ( ϕ 2 ) symbolizes the regime of permanent change characterizing the emergence of evolution in the biosphere. As such the biosphere is closed on itself, by the principle of descent with modifications, and by the fact that every holobiont evolves in a niche, while evolving with it. [ABSTRACT FROM AUTHOR]

Alfred Russel Wallace (1823-1913) and Charles Darwin (1809-1882) are honored as the founders of modern evolutionary biology. Accordingly, much attention has focused on their relationship, from their independent development of the principle of natural selection to the receipt by Darwin of Wallace's essay from Ternate in the spring of 1858, and the subsequent reading of the Wallace and Darwin papers at the Linnean Society on 1 July 1858. In the events of 1858 Wallace and Darwin are typically seen as central players, with Darwin's friends Charles Lyell (1797-1875) and Joseph Dalton Hooker (1817-1911) playing supporting roles. This narrative has resulted in an under-appreciation of a more central role for Charles Lyell as both Wallace's inspiration and foil. The extensive anti-transmutation arguments in Lyell's landmark Principles of Geology were taken as the definitive statement on the subject. Wallace, in his quest to solve the mystery of species origins, engaged with Lyell's arguments in his private field notebooks in a way that is concordant with his engagement with Lyell in the 1855 and 1858 papers. I show that Lyell was the object of Wallace's Sarawak Law and Ternate papers through a consideration of the circumstances that led Wallace to send his Ternate paper to Darwin, together with an analysis of the material that Wallace drew upon from the Principles. In this view Darwin was, ironically, intended for a supporting role in mediating Wallace's attempted dialog with Lyell. [ABSTRACT FROM AUTHOR]

A mathematical model for the quantitative analysis of the interaction between cancer cells and cell-mediated immune system with two discrete-time delays, considering the role of antibodies, is studied in this paper. The model is analyzed both analytically and numerically to understand the dynamics of interaction delay and proliferation enhancement effect delay in the eradication of cancer. Hopf bifurcation occurs when one-time delay crosses the critical value in the absence of the other. It is also observed that as we increase any of the delays, it will increase the cancer burden. The analysis shows that a cancer-free state cannot be obtained solely by the killing rate of cytotoxic T-lymphocytes, but humoral response in combination with cell-mediated immune responses plays an important role to eradicate cancer. [ABSTRACT FROM AUTHOR]

Fungi show a high degree of morphological convergence. Regarded for a long time as an obstacle for phylogenetic studies, homoplasy has also been proposed as a source of information about underlying morphogenetic patterning mechanisms. The "local-activation and long-range inhibition principle" (LALIP), underlying the famous reaction–diffusion model proposed by Alan Turing in 1952, appears to be one of the universal phenomena that can explain the ontogenetic origin of seriate patterns in living organisms. Reproductive structures of fungi in the class Agaricomycetes show a highly periodic structure resulting in, for example, poroid, odontoid, lamellate or labyrinthic hymenophores. In this paper, we claim that self-organized patterns might underlie the basic ontogenetic processes of these structures. Simulations based on LALIP-driven models and covering a wide range of parameters show an absolute mutual correspondence with the morphospace explored by extant agaricomycetes. This could not only explain geometric particularities but could also account for the limited possibilities displayed by hymenial configurations, thus making homoplasy a direct consequence of the limited morphospace resulting from the proposed patterning dynamics. [ABSTRACT FROM AUTHOR]

We study the dynamics of a discrete model with two different stages of the population, the pre-adult stage governed by a Beverton–Holt-type map and the adult stage by a γ -Ricker map. The composition of both maps gives the dynamics. The existence of the Allee effect is easily observed. We check that the model can evolve from a sure extinction to complicated dynamics. The presence of an almost sure extinction is proved to exist when the dynamical complexity is the highest possible. [ABSTRACT FROM AUTHOR]

Methylation is an important epigenetic regulation of methylation genes that plays a crucial role in regulating biological processes. While traditional methods for detecting methylation in biological experiments are constantly improving, the development of artificial intelligence has led to the emergence of deep learning and machine learning methods as a new trend. However, traditional machine learning-based methods rely heavily on manual feature extraction, and most deep learning methods for studying methylation extract fewer features due to their simple network structures. To address this, we propose a bottomneck network based on an attention mechanism and use new methods to ensure that the deep network can learn more effective features while minimizing overfitting. This approach enables the model to learn more features from nucleotide sequences and make better predictions of methylation. The model uses three coding methods to encode the original DNA sequence and then applies feature fusion based on attention mechanisms to obtain the best fusion method. Our results demonstrate that MLACNN outperforms previous methods and achieves more satisfactory performance. [ABSTRACT FROM AUTHOR]

A biosemiotic approach to the interpretation of morphological data is apt to highlight morphological traits that have hitherto gone unnoticed for their crucial roles in intraspecific sign interpretation and communication processes. Examples of such traits include specific genital structures found in the haplogyne spiders Dysdera erythrina (Walckenaer 1802) and Dysdera crocata (Koch 1838). In both D. erythrina and D. crocata, the distal sclerite of the male bulb and the anterior diverticulum of the female endogyne exhibit a striking, previously unreported correspondence in size and shape, allowing for a precise match between these structures during copulation. In D. erythrina, the sclerite at the tip of the bulb and the anterior diverticulum are semi-circular in shape, whereas in D. crocata they are rectangular. From the perspective of biosemiotics, which studies the production and interpretation of signs and codes in living systems, these structures are considered the morphological zones of an intraspecific sign interpretation process. This process constitutes one of the necessary prerequisites for sperm transfer and the achievement of fertilization. Therefore, these morphological elements deserve particular attention as they hold higher taxonomic value compared to morphological traits of the bulb for which a relevant role in mating and fertilization has not been proven. Thus, an approach to species delimitation based on biosemiotics, with its specific evaluation of morphological structures, provides new insights for the multidisciplinary endeavour of modern integrative taxonomy. [ABSTRACT FROM AUTHOR]

Rooted acyclic graphs appear naturally when the phylogenetic relationship of a set X of taxa involves not only speciations but also recombination, horizontal transfer, or hybridization that cannot be captured by trees. A variety of classes of such networks have been discussed in the literature, including phylogenetic, level-1, tree-child, tree-based, galled tree, regular, or normal networks as models of different types of evolutionary processes. Clusters arise in models of phylogeny as the sets C (v) of descendant taxa of a vertex v. The clustering system C N comprising the clusters of a network N conveys key information on N itself. In the special case of rooted phylogenetic trees, T is uniquely determined by its clustering system C T . Although this is no longer true for networks in general, it is of interest to relate properties of N and C N . Here, we systematically investigate the relationships of several well-studied classes of networks and their clustering systems. The main results are correspondences of classes of networks and clustering systems of the following form: If N is a network of type X , then C N satisfies Y , and conversely if C is a clustering system satisfying Y , then there is network N of type X such that C ⊆ C N .This, in turn, allows us to investigate the mutual dependencies between the distinct types of networks in much detail. [ABSTRACT FROM AUTHOR]

Advancement of new technologies such as laser, focused ultrasound, microwave and radio frequency for thermal therapy of skin tissue has increased numerous challenging situations in medical treatment. In this article, a new meticulous bio-heat transfer model based on memory-dependent derivative with dual-phase-lag has been developed under different thermal conditions such as thermal shock and harmonic-type heating. Laplace transform method is acquired to perceive the analytical consequences. Quantitative results are evaluated for displacement, strain and temperature along with stress distributions in time domain by adopting the technique of inverse Laplace transform. Impacts of the constituents of memory-dependent derivatives—kernel functions along with time-delay parameter are analysed on the studied fields (temperature, displacement, strain and stress) for both thermal conditions separately using computational results. It has been found that the insertion of the memory effect proves itself a unified model, and therefore, this model can better predict temperature field data for thermal treatment processes. [ABSTRACT FROM AUTHOR]

We consider a modified SIR model with a four-dimensional system of ordinary differential equations to consider the influence of a limited isolation capacity on the final epidemic size defined as the total number of individuals who experienced the disease at the end of an epidemic season. We derive the necessary and sufficient condition that the isolation reaches the capacity in a finite time on the way of the epidemic process, and show that the final epidemic size is monotonically decreasing in terms of the isolation capacity. We find further that the final epidemic size could have a discontinuous change at the critical value of isolation capacity below which the isolation reaches the capacity in a finite time. Our results imply that the breakdown of isolation with a limited capacity would cause a drastic increase of the epidemic size. Insufficient capacity of the isolation could lead to an unexpectedly severe epidemic situation, while such a severity would be avoidable with the sufficient isolation capacity. [ABSTRACT FROM AUTHOR]

This work concerns a many-body deterministic model that displays life-like properties such as emergence, complexity, self-organization, self-regulation, excitability and spontaneous compartmentalization. The model portraits the dynamics of an ensemble of locally coupled polar phase oscillators, moving in a two-dimensional space, that under certain conditions exhibit emergent superstructures. Those superstructures are self-organized dynamic networks, resulting from a synchronization process of many units, over length scales much greater than the interaction range. Such networks compartmentalize the two-dimensional space with no a priori constraints, due to the formation of porous transport walls, and represent a highly complex and novel non-linear behavior. The analysis is numerically carried out as a function of a control parameter showing distinct regimes: static pattern formation, dynamic excitable networks formation, intermittency and chaos. A statistical analysis is drawn to determine the control parameter ranges for the various behaviors to appear. The model and the results shown in this work are expected to contribute to the field of artificial life. [ABSTRACT FROM AUTHOR]

For this research, the properties of the logistic growth model for independent and coexisting species were used to set definitions for the possible regulation of one or two growth variables through their coupling parameters. The present analysis is done for the single-species Verhulst model without coupling, the single-species Verhulst model coupled with an exogenous signal, and the two-species Verhulst coexistence growth model which represents six different ecological regimes of interaction. The models' parameters, such as the intrinsic growth rate and the coupling, are defined. Finally, the control results are expressed as lemmas for regulation, and they are shown using a simulation example of a fish population growing independent of human interaction (no harvesting, no fishing) and the simulation of the regulation of said population when the coupling of fish and humans is involved (harvesting, fishing). [ABSTRACT FROM AUTHOR]

In this work, we analyse the dynamics of a five-dimensional hepatitis C virus infection mathematical model including the spatial mobility of hepatitis C virus particles, the transmission of hepatitis C virus infection by mitosis process of infected hepatocytes with logistic growth, time delays, antibody response and cytotoxic T lymphocyte (CTL) immune response with general incidence functions for both modes of infection transmission, namely virus-to-cell as well as cell-to-cell. Firstly, we prove rigorously the existence, the uniqueness, the positivity and the boundedness of the solution of the initial value and boundary problem associated with the new constructed model. Secondly, we found that the basic reproductive number is the sum of the basic reproduction number determined by cell-free virus infection, determined by cell-to-cell infection and determined by proliferation of infected cells. It is proved the existence of five spatially homogeneous equilibria known as infection-free, immune-free, antibody response, CTL response and antibody and CTL responses. By using the linearization methods, the local stability of the latter is established under some rigorous conditions. Finally, we proved the existence of periodic solutions by highlighting the occurrence of a Hopf bifurcation for a certain threshold value of one delay. [ABSTRACT FROM AUTHOR]

Adaptive mimicry in animals is a well-known phenomenon. Here, we propose that a similarly adaptive strategy in humans is using kin terms for people who are not closely genetically related. Irrespective of the initiator attributing a kin term to a non-kin, we call this kin term mimicry (KTM). The emergence of human sociality and language allowed not only easy kin recognition, but also led to strong positive emotions related to such kin names as "mother," "father," "brother," "sister," "aunt" or "uncle." Although the phenomenon of using kin terms of genetically unrelated people is well known in the social sciences, here we discuss it in the light of evolution. We notice this is an evolutionary adaptive cooperation strategy, which allows us to predict in which ecological or social circumstances it will be more prevalent. We postulate specific testable factors that affect the prevalence of kin mimicry. We also discuss who is more likely to be an initiator of calling non-kin a fictive kin, and who benefits from such behavior. The KTM hypothesis postulates that an individual or social group initiating or bestowing kin terms usually receives more benefits (economic and/or psychological support) from such mimicry. [ABSTRACT FROM AUTHOR]

In the fight against the COVID-19 pandemic, many brilliant results have been achieved, but the thermodynamics of the novel SARS-CoV-2 coronavirus has been completely neglected. This is a serious systematic error, which can compromise the results of the entire pandemic virus SARS-CoV-2 research. In the present work, we therefore study the thermodynamics of SARS-CoV-2 in its environment, from air to endosome and endosome-independent cell entry pathways. In the study of the thermodynamics of the new coronavirus SARS-CoV-2 in air, the presence of pollen, bacteria, other viruses, spores, dust, but more particularly, that of nanoparticles of health interest at the same scale threshold as the spike proteins of the pandemic virus, such as particulate matter, cannot be neglected. This work therefore starts from a comparative study of the air environments in China and Italy, the first countries affected by the infection. Currently, a correlation between the spread of infection and pollution is still very controversial. But our paper is not concerned with this. We propose some methodological notes which lead us to the formulation of a general mathematical apparatus (an energy landscape theory), suitable to explain at the molecular level the energetic configurations of the quasi-species of the pandemic virus SARS-CoV-2 in its environment. We focus on complexes between the viral particle and other objects in its environment at the scale threshold of the spikes of the viral particle. Then, we wondered if such complexes can lead to the generation of more aggressive viral variants and how to predict their populations and energy configurations, in order to plan an adequate prophylaxis. [ABSTRACT FROM AUTHOR]

The central aim of this Special Issue, devoted to a multifocal study of the geometry and phenomenology of the living, is to show the need of working with models that integrate geometrical and topological objects and operations, dynamical variables and specific biological mechanisms and their relationships with one another. A multilevel and integrative approach has essentially to consider the fact that simply knowing the parts list of genes and proteins does not tell us much about how life's many biological processes works. The cellular organization is a complex dynamical system with hundreds of thousands of bio-molecules interacting with one another to execute organism's many related functions. It is argued that the production of complex living organisms owes much of its working to some topological mechanisms (i.e. four-dimensional transformations and deformations) which operate markedly on the three levels of the organization, regulation and evolution of biological systems. Thus, one can speak of a specific topology of the living acting very dynamically on the (non-fixed) substrate space of the physiological and metabolic activities of all complex living organisms. Philosophically, it is now clear that the genetic causality theory has several limitations, both intrinsic because of the multilevel complexity of biological processes, and extrinsic in that it disregards the influence of the phenotype on the genotype and in particular the possibility that certain acquired characteristics can be inherited. In a sense, we can say that the molecular biological conception of recent decades has limited or even misleadingly impacted our vision of the living world. New ideas are needed if we are to succeed in unravelling multifactorial genetic, epigenetic and environmental causation at higher levels of physiological function and so to explain fundamental living phenomena that genetics alone is unable to explain. Some of the most significant conclusions proposed in this issue are that (i) structural plasticity and biological functionality are deeply related, (ii) the biological information and signification is inherently spatial and temporal, it is not unidirectional, and it essentially evolve following a complex and changing network-like organization, (iii) finally, gene ontology is incomplete and it as to be supplied by integrating other fundamental levels of the organization and regulation of the living systems. [ABSTRACT FROM AUTHOR]

The classical theory of descent with modification by means of natural selection had no mother, but did have two English fathers, Charles Darwin (1809-1882) and Alfred Russel Wallace (1823-1913). In 1858, the Linnean Society of London published two contributions of these naturalists and acknowledged both authors as the proponents of a novel hypothesis on the driving force of organismic evolution. In the present report the most important sections of the Darwin-Wallace papers are summarized. This close reading of both publications reveals six striking differences in emphasis: Darwin and Wallace did not propose identical ideas. The species definitions of both authors are described and the further development of the concept of natural selection in wild populations is reviewed. It is shown that the contributions of A.R. Wallace, who died 90 years ago, are more significant than usually acknowledged. I conclude that natural selection's lesser known co-discoverer should be regarded as one of the most important pioneers of evolutionary biology, whose original contributions are underestimated by most contemporary scientists. [ABSTRACT FROM AUTHOR]

In this paper, the schooling behavior of prey fish population in a predator–prey interaction is investigated. By taking an economical interest which can be elaborated by the presence of nonselective harvesting into consideration, we studied the dynamical behavior. The existence, positivity and boundedness of solution have been established. The analysis of the equilibrium states is presented by studying the local and the global stability. The possible types of local bifurcation that the system can undergoes are discussed. The effect of fishing effort on the evolution of the species is examined. Further, by using Pontryagin's maximum principle a proper management strategy has been used for avoiding the extinction of the considered species and maximizing the benefits. For the validation of the theoretical result, several of graphical representations have been used. [ABSTRACT FROM AUTHOR]

The outbreak of coronavirus COVID-19 is spreading at an unprecedented rate to the human populations and taking several thousands of life all over the world. Scientists are trying to map the pattern of the transmission of coronavirus (SARS-CoV-2). Many countries are in the phase of lockdown in the globe. In this paper we predict about the effect of coronavirus COVID-19 and give a sneak peak when it will reduce the transmission rate in the world via mathematical modelling. In this research work our study is based on extensions of the well-known susceptible-exposed-infected-recovered (SEIR) family of compartmental models and later we observe the new model changes into (SEIR) without changing its physical meanings. The stability analysis of the coronavirus depends on changing of its basic reproductive ratio. The progress rate of the virus in the critically infected cases and the recovery rate have major roles to control this epidemic. The impact of social distancing, lockdown of the country, self-isolation, home quarantine and the wariness of global public health system have significant influence on the parameters of the model system that can alter the effect of recovery rates, mortality rates and active contaminated cases with the progression of time in the real world. The prognostic ability of mathematical model is circumscribed as of the accuracy of the available data and its application to the problem. [ABSTRACT FROM AUTHOR]

In biological processes involving gene networks, genes regulate other genes that determine the phenotypic traits. Gene regulation plays an important role in evolutionary dynamics. In a genetic algorithm, a trans-gene regulatory mechanism was shown to speed up adaptation and evolution. Here, we examine the effect of cis-gene regulation on an adaptive system. The model is haploid. A chromosome is partitioned into regulatory loci and structural loci. The regulatory genes regulate the expression and functioning of structural genes via the cis-elements in a probabilistic manner. In the simulation, the change in the allele frequency, the mean population fitness and the efficiency of phenotypic selection are monitored. Cis-gene regulation increases adaption and accelerates the evolutionary process in comparison with the case involving absence of gene regulation. Some special features of the simulation results are as follows. A low ratio of regulatory loci and structural loci gives higher adaptation for fixed total number of loci. Plasticity is advantageous beyond a threshold value. Adaptation is better for large number of total loci when the ratio of regulatory loci to structural loci is one. However, it reaches a saturation beyond which the increase in the total loci is not advantageous. Efficiency of the phenotypic selection is higher for larger value of the initial plasticity. [ABSTRACT FROM AUTHOR]

In this study, we proposed a biological model explaining the progress of autoimmune activation along different stages of systemic lupus erythematosus (SLE). For any upcoming stage of SLE, any new component is introduced, when it is added to the model. Particularly, the interaction of mesenchymal stem cells, with the components of the model, is specified in a way that both the inflammatory and anti-inflammatory functions of these cells would be covered. The biological model is then recapitulated to a model with less complexity that explains the main features of the problem. Later, a 7th-order mathematical model for SLE is proposed, based on this simplified model. Finally, the range of validity of the proposed mathematical model was assessed. For this purpose, we simulated the model and analyzed the simulation results in case of some known behaviors of the disease, such as tolerance breach, the appearance of systemic inflammation, development of clinical signs, and occurrence of flares and improvements. The model was able to reproduce these events, qualitatively. [ABSTRACT FROM AUTHOR]

Autosomal dominant diseases typically have an age-related onset. Here, I focus on genetic prion disease (gPrD), caused by various mutations in the PRNP gene. While gPrD typically occurs at or after middle age, there can be considerable variability in the specific age of onset. This variability can occur among patients with the same PRNP mutation; in some cases, these differences occur not only between families but even within the same family. It is not known why gPrD onset is typically delayed for decades when the causative mutation is present from birth. Mouse models of gPrD manifest disease; however, unlike human gPrD, which typically takes decades to manifest, mouse models exhibit disease within months. Therefore, the time to onset of prion disease is proportional to species lifespan; however, it is not known why this is the case. I hypothesize that the initiation of gPrD is strongly influenced by the process of aging; therefore, disease onset is related to proportional functional age (e.g., mice vs. humans). I propose approaches to test this hypothesis and discuss its significance with respect to delaying prion disease through suppression of aging. [ABSTRACT FROM AUTHOR]

Recent results have shown that the human malaria-resistant hemoglobin S mutation originates de novo more frequently in the gene and in the population where it is of adaptive significance, namely, in the hemoglobin subunit beta gene compared to the nonresistant but otherwise identical 20A → T mutation in the hemoglobin subunit delta gene, and in sub-Saharan Africans, who have been subject to intense malarial pressure for many generations, compared to northern Europeans, who have not. This finding raises a fundamental challenge to the traditional notion of accidental mutation. Here, we address this finding with the replacement hypothesis, according to which preexisting genetic interactions can lead directly and mechanistically to mutations that simplify and replace them. Thus, an evolutionary process under selection can gradually hone in on interactions of importance for the currently evolving adaptations, from which large-effect mutations follow that are relevant to these adaptations. We exemplify this hypothesis using multiple types of mutation, including gene fusion mutations, gene duplication mutations, A → G mutations in RNA-edited sites and transcription-associated mutations, and place it in the broader context of a system-level view of mutation origination called interaction-based evolution. Potential consequences include that similarity of mutation pressures may contribute to parallel evolution in genetically related species, that the evolution of genome organization may be driven by mutational mechanisms, that transposable element movements may also be explained by replacement, and that long-term directed mutational responses to specific environmental pressures are possible. Such mutational phenomena need to be further tested by future studies in natural and artificial settings. [ABSTRACT FROM AUTHOR]

The authors present their response to commentaries to their paper on gene and genon concepts. They note the need to emphasize their concepts of gene and genon based on eukaryotic cells inspired by progress in undertaking eukaryotic gene regulation. They mention the importance of their concept to reflect merely genetic inheritance and the transmission of genomes or parts of genomes. They emphasize their view of the cascade of regulation as an operative elementary system include in such network.

In 1835, the meaning of the cleavage furrows in the division of frog eggs was the cause of a heated argument between the Italian naturalist Mauro Rusconi and Karl Ernst von Baer. These furrows were first described by Prévost and Dumas (Ann Sci Nat 2:100–121, 129–149, 1824b) who did not realize they cut the egg into separate masses. Rusconi (Développement de la grenouille comune depuis le moment de sa naissance jusque a son état parfait, Giusti, Milano, 1826) hypothesized a connection between the furrows and a peculiar crystallization of the content of the egg which eventually produced elementary molecules as the building blocks of the embryo. von Baer (Arch Anat Phys Wiss Med 6:481–509, 1834) was the first to establish a link between the furrows and an active process of dichotomous division he considered to be the basis for all further development and differentiation. The present paper analyses the theoretical reasons behind these divergent interpretations and focuses attention on their implications for the development of the cell theory and the conceptions of life. Prévost, Dumas and Rusconi interpreted cleavage and the whole embryonic development in the light of eighteenth-century scientific theories and the French materialism of the early nineteenth century, which explained life in terms of ordered molecular movement. Starting from other premises partly rooted in German philosophy von Baer (1834) gave a totally different picture which anticipated the cell theory and modern embryology. [ABSTRACT FROM AUTHOR]

In this paper we are concerned with how aggregated outcomes of individual behaviours, during interactions with other individuals (games) or with environmental factors, determine the vital rates constituting the growth rate of the population. This approach needs additional elements, namely the rates of event occurrence (interaction rates). Interaction rates describe the distribution of the interaction events in time, which seriously affects the population dynamics, as is shown in this paper. This leads to the model of a population of individuals playing different games, where focal game affected by the considered trait can be extracted from the general model, and the impact on the dynamics of other events (which is not neutral) can be described by an average background fertility and mortality. This leads to a distinction between two types of background fitness, strategically neutral elements of the focal games (correlated with the focal game events) and the aggregated outcomes of other interactions (independent of the focal game). The new approach is useful for clarification of the biological meaning of concepts such as weak selection. Results are illustrated by a Hawk-Dove example. [ABSTRACT FROM AUTHOR]

In this paper, we study the global properties of a computer virus propagation model. It is, interesting to note that the classical method of Lyapunov functions combined with the Volterra-Lyapunov matrix properties, can lead to the proof of the endemic global stability of the dynamical model characterizing the spread of computer viruses over the Internet. The analysis and results presented in this paper make building blocks towards a comprehensive study and deeper understanding of the fundamental mechanism in computer virus propagation model. A numerical study of the model is also carried out to investigate the analytical results. [ABSTRACT FROM AUTHOR]

Microbial symbioses based on nutrient exchange and interdependence are ubiquitous in nature and biotechnologically promising; however, an in-depth mathematical description of their exact underlying dynamics from first principles is still missing. Hence, in this paper a novel mechanistic mathematical model of such a relationship in a continuous chemostat culture is derived. In contrast to preceding works on the topic, only parameters which can be directly measured and understood from biological first principles are used, allowing for a higher degree of mechanistic understanding of the underlying processes compared to previous approaches. The predictive power of the model is validated by demonstrating that it accurately recapitulates both the temporal dynamics as well as the final state of a previously published cross-feeding experiment. The model is then used to examine the influence of the biological traits of the involved organisms on the position and stability of the equilibrium states of the system using bifurcation analyses. It is additionally demonstrated how manipulating the external metabolite concentrations of the system can shift the species interaction on a continuous spectrum ranging from mutualism over commensalism to parasitism. This further reinforces the idea of a continuous spectrum of symbiotic interactions as opposed to static and discrete categories. Finally, the practical implications of the results for the biotechnological application of such microbial consortia are discussed. [ABSTRACT FROM AUTHOR]

The aim of the paper is to identify psychosomatic evolutionary adaptations of hominids, which direct them at maximizing their reproductive success, and on the basis of which their various social structures are built. Selected features of the hominid last common ancestor were extracted; by reducing the influence of the social structure, they were defined as the hominid "sexual nature"; these considerations were supported by the analysis of sexual jealousy as a function of socio-environmental conditions. The "sexuality core" of a hominid female was defined as "selective polyandry"—the female selects the best males among those available; and of a hominid male as "tolerant promiscuity"—the male strives for multi-male and multi-female copulations with sexually attractive females. The extracted "sexuality cores" condemn hominids to a patriarchal social structure and thus to sexual coercion and jealousy. The source of male sexual jealousy is limited access to females. Hominid female jealousy of the male results mainly from the need for protection and support. Hominids' social structures are determined by females' sexual selectivity or opportunism and by their continuous or periodic proceptivity and estrus signaling. Evolutionary functions developed by women: out-estrus sexuality, copulation calls, multiple orgasms, allow them to obtain the best possible spermatozoid. The institution of marriage blocks the influence of sexual selection in the species Homo sapiens. [ABSTRACT FROM AUTHOR]

The idea that selection works in different ways during free population growth and at the equilibrium population size has been present in theoretical biology for a long time. It was first expressed as an r and K selection concept and later clarified in the debate on fitness measures in life history theory. The latest discussion related to this topic is focused on the nest site lottery mechanism and the resulting new population growth model. In this mechanistic biphasic model, the suppression of growth is induced by a shortage of free nest sites for newborns. Before it occurs, the population can grow exponentially. In this paper, the continuous version of the model and its selective properties are analysed. We show a continuous smooth transition between different fitness measures operating during the exponential growth and suppressed growth phase and at the equilibrium population size. Then, the model is extended to the case of a population of parasites, where a constant number of nest sites is replaced by the dynamics of a population of their hosts, in the role of the limiting supply. Parasite strategies are selected under exponential and suppressed growth phases of the population of hosts. Transitions between different fitness measures and conditions for extinction of hosts by parasites are analysed. An interesting result is the possibility of a continuum of fitness measures of parasites for the unsuppressed exponential growth of the host population. [ABSTRACT FROM AUTHOR]