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Dynamics of neural fields with exponential temporal kernel Theory Biosci. (IF 1.1) Pub Date : 2024-03-09
Abstract We consider the standard neural field equation with an exponential temporal kernel. We analyze the time-independent (static) and time-dependent (dynamic) bifurcations of the equilibrium solution and the emerging spatiotemporal wave patterns. We show that an exponential temporal kernel does not allow static bifurcations such as saddle-node, pitchfork, and in particular, static Turing bifurcations
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Behavioral selection in structured populations Theory Biosci. (IF 1.1) Pub Date : 2024-03-05 Matthias Borgstede
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
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Optimal dispersal and diffusion-enhanced robustness in two-patch metapopulations: origin’s saddle-source nature matters Theory Biosci. (IF 1.1) Pub Date : 2024-02-21 Marc Jorba-Cuscó, Ruth I. Oliva-Zúniga, Josep Sardanyés, Daniel Pérez-Palau
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Modeling stress-induced responses: plasticity in continuous state space and gradual clonal evolution Theory Biosci. (IF 1.1) Pub Date : 2024-01-30 Anuraag Bukkuri
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Speciation, natural selection, and networks: three historians versus theoretical population geneticists Theory Biosci. (IF 1.1) Pub Date : 2024-01-29 Donald R. Forsdyke
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Thomas S. Kuhn: key to a better understanding of the extended evolutionary synthesis Theory Biosci. (IF 1.1) Pub Date : 2023-11-17 Koen B. Tanghe
In recent years, some scholars have explicitly questioned the desirability or utility of applying the classical and “old-fashioned” theories of scientific change by the likes of Karl Popper and Thomas S. Kuhn to the question of the precise nature and significance of the extended evolutionary synthesis (EES). Supposedly, these twentieth-century philosophers are completely irrelevant for a better understanding
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Normalizing need not be the norm: count-based math for analyzing single-cell data Theory Biosci. (IF 1.1) Pub Date : 2023-11-10 Samuel H. Church, Jasmine L. Mah, Günter Wagner, Casey W. Dunn
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On a population model with density dependence and Allee effect Theory Biosci. (IF 1.1) Pub Date : 2023-10-02 J. S. Cánovas, M. Muñoz-Guillermo
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Matrix stability and bifurcation analysis by a network-based approach Theory Biosci. (IF 1.1) Pub Date : 2023-09-27 Zhenzhen Zhao, Ruoyu Tang, Ruiqi Wang
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Myths of past biases and progress in biology Theory Biosci. (IF 1.1) Pub Date : 2023-09-23 Jani Raerinne
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Evolution by habit: Peirce, Lamarck, and teleology in biology Theory Biosci. (IF 1.1) Pub Date : 2023-09-25 Jana Švorcová, Ľudmila Lacková, Eliška Fulínová
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’
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A biosemiotic interpretation of certain genital morphological structures in the spiders Dysdera erythrina and Dysdera crocata (Araneae: Dysderidae) Theory Biosci. (IF 1.1) Pub Date : 2023-09-13 Joachim Schult, Onno Preik, Stefan Kirschner, Frank Friedrich
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MLACNN: an attention mechanism-based CNN architecture for predicting genome-wide DNA methylation Theory Biosci. (IF 1.1) Pub Date : 2023-08-30 JianGuo Bai, Hai Yang, ChangDe Wu
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Clustering systems of phylogenetic networks Theory Biosci. (IF 1.1) Pub Date : 2023-08-12 Marc Hellmuth, David Schaller, Peter F. Stadler
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The emergence of dynamic networks from many coupled polar oscillators: a paradigm for artificial life Theory Biosci. (IF 1.1) Pub Date : 2023-07-29 Alessandro Scirè, Valerio Annovazzi-Lodi
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Investigation of memory influences on bio-heat responses of skin tissue due to various thermal conditions Theory Biosci. (IF 1.1) Pub Date : 2023-07-20 Rakhi Tiwari, Abhinav Singhal, Rajneesh Kumar, Pappu Kumar, Suniti Ghangas
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An epidemic dynamics model with limited isolation capacity Theory Biosci. (IF 1.1) Pub Date : 2023-07-18 Ishfaq Ahmad, Hiromi Seno
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Stability of a diffusive-delayed HCV infection model with general cell-to-cell incidence function incorporating immune response and cell proliferation Theory Biosci. (IF 1.1) Pub Date : 2023-07-12 Alexis Nangue, Yanick Junior Tchuimeni
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
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Growth modeling approach with the Verhulst coexistence dynamic properties for regulation purposes Theory Biosci. (IF 1.1) Pub Date : 2023-07-08 A. J. Morales-Erosa, J. Reyes-Reyes, C. M. Astorga-Zaragoza, G. L. Osorio-Gordillo, C. D. García-Beltrán, G. Madrigal-Espinosa
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Symmetrical distributions of aminoacyl-tRNA synthetases during the evolution of the genetic code Theory Biosci. (IF 1.1) Pub Date : 2023-07-05 Marco V. José, Juan R. Bobadilla, Gabriel S. Zamudio, Sávio Torres de Farías
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Self-similarity and the maximum entropy principle in the genetic code Theory Biosci. (IF 1.1) Pub Date : 2023-07-04 Subhash Kak
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Kin term mimicry hypothesis Theory Biosci. (IF 1.1) Pub Date : 2023-06-05 Bogusław Pawłowski, Anna Chmielińska
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
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Stationary distribution and density function analysis of SVIS epidemic model with saturated incidence and vaccination under stochastic environments Theory Biosci. (IF 1.1) Pub Date : 2023-05-16 Prasenjit Mahato, Sanat Kumar Mahato, Subhashis Das, Partha Karmakar
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A biological and a mathematical model of SLE treated by mesenchymal stem cells covering all the stages of the disease Theory Biosci. (IF 1.1) Pub Date : 2023-04-18 Ali Yazdani, Fariba Bahrami, Arash Pourgholaminejad, Reza Moghadasali
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A computational investigation of cis-gene regulation in evolution Theory Biosci. (IF 1.1) Pub Date : 2023-04-11 Mohammed Mahmud, Mulugeta Bekele, Narayan Behera
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Hypothesis: functional age and onset of autosomal dominant genetic prion disease Theory Biosci. (IF 1.1) Pub Date : 2023-04-05 Michael Bordonaro
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Path integral control of a stochastic multi-risk SIR pandemic model Theory Biosci. (IF 1.1) Pub Date : 2023-03-11 Paramahansa Pramanik
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Evolutionary honing in and mutational replacement: how long-term directed mutational responses to specific environmental pressures are possible Theory Biosci. (IF 1.1) Pub Date : 2023-03-11 Adi Livnat, Daniel Melamed
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Wartime forced sex as a male mating strategy Theory Biosci. (IF 1.1) Pub Date : 2023-01-30 Christopher Mogielnicki
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Biology as involving laws and inconceivable without them Theory Biosci. (IF 1.1) Pub Date : 2023-01-22 Richard Creath
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
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Descriptive versus causal morphology: gynandromorphism and intersexuality Theory Biosci. (IF 1.1) Pub Date : 2023-01-12 Giuseppe Fusco, Alessandro Minelli
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Molecular characterization of chilli leaf curl Ahmedabad virus: homology modelling and evaluation of viral proteins interacting with host protein SnRK1 and docking against flavonoids—an in silico approach Theory Biosci. (IF 1.1) Pub Date : 2023-01-06 G. Sravya, Gnanaprakash Jeyaraj, Aanand Vadivelu, Habeeb Shaik Mohideen, A. Swapna Geetanjali
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Formal verification confirms the role of p53 protein in cell fate decision mechanism Theory Biosci. (IF 1.1) Pub Date : 2022-12-12 Eman Abdelaziz Mahmoud, Mostafa Herajy, Ibrahim E. Ziedan, Hazem I. Shehata
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Radioresistance and radiosensitivity: a biophysical approach on bacterial cells robustness Theory Biosci. (IF 1.1) Pub Date : 2022-12-03 João Dias de Toledo Arruda-Neto, Henriette Righi, José Gregório Cabrera Gomez, Luiziana Ferreira da Silva, Evandro Drigo, Aline Carolina da Costa Lemos
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An almost periodic model to describe phenology mismatches in mutualistic interactions Theory Biosci. (IF 1.1) Pub Date : 2022-10-12 Díaz-Marín Homero, Osuna Osvaldo, Villavicencio-Pulido Geiser
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Modeling the stochastic within-host dynamics SARS-CoV-2 infection with discrete delay Theory Biosci. (IF 1.1) Pub Date : 2022-10-03 I. M. Elbaz, M. A. Sohaly, H. El-Metwally
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The shadow of “the Eclipse of Darwinism”: the problem of evolutionary mechanisms in Republican China, 1910s–1930s Theory Biosci. (IF 1.1) Pub Date : 2022-09-01 Zhixiang Cheng
How did Chinese scientific intellectuals react to the dispute over evolutionary mechanisms during the period of the “eclipse of Darwinism”? This is my focal question. To answer it, I survey the attitudes of three groups of people toward the debate in the early decades of the twentieth century: Chinese paleontologists and their general embrace of the anti-Darwinian position, a group of non-specialists
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Prebiotic chemical refugia: multifaceted scenario for the formation of biomolecules in primitive Earth Theory Biosci. (IF 1.1) Pub Date : 2022-08-30 Francisco Prosdocimi, Sávio Torres de Farias, Marco V. José
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Phenotypic plasticity in plasmodial slime molds and molecular phylogeny of terrestrial vs. aquatic species Theory Biosci. (IF 1.1) Pub Date : 2022-08-27 T. Hoppe, U. Kutschera
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Goethe and Candolle: National forms of scientific writing? Theory Biosci. (IF 1.1) Pub Date : 2022-08-11 Agatha Seo-Hyun Kim, Andrew McNutt
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Growth dynamics of breast cancer stem cells: effects of self-feedback and EMT mechanisms Theory Biosci. (IF 1.1) Pub Date : 2022-08-03 Liuyong Pang, Sanhong Liu, Zhong Zhao, Tianhai Tian, Xinan Zhang, Qiuying Li
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First principles of terrestrial life: exemplars for potential extra-terrestrial biology Theory Biosci. (IF 1.1) Pub Date : 2022-07-30 Ian von Hegner
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Thermodynamic principles for system biology and the patterns of flower pigmentation Theory Biosci. (IF 1.1) Pub Date : 2022-07-20 Qinyi Zhao
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Mathematical modeling for mutator phenotype and clonal selection advantage in the risk analysis of lung cancer Theory Biosci. (IF 1.1) Pub Date : 2022-06-04 Lingling Li, Ting Zhao, Xingshi He, Xinshe Yang, Tianhai Tian, Xinan Zhang
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The historical nature of biological complexity and the ineffectiveness of the mathematical approach to it Theory Biosci. (IF 1.1) Pub Date : 2022-05-18 Saverio Forestiero
Contemporary scientific knowledge is built on both methodological and epistemological reductionism. The discovery of the limitations of the reductionist paradigm in the mathematical treatment of certain physical phenomena originated the notion of complexity, both as a pattern and process. After clarifying some very general terms and ideas on biological evolution and biological complexity, the article
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Mathematics of life spaces: continuation of the 2018 large dimensions course Theory Biosci. (IF 1.1) Pub Date : 2022-05-10 Misha Gromov
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Network representation and analysis of energy coupling mechanisms in cellular metabolism by a graph-theoretical approach Theory Biosci. (IF 1.1) Pub Date : 2022-05-02 Sunil Nath
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A reappraisal of the form: function problem—theory and phenomenology Theory Biosci. (IF 1.1) Pub Date : 2022-04-26 Luciano Boi
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How much biology is in the product? Role and relevance of biological evolution and function for bio-inspired design Theory Biosci. (IF 1.1) Pub Date : 2022-03-28 Anita Roth-Nebelsick
Bio-inspired design (BID) means the concept of transferring functional principles from biology to technology. The core idea driving BID-related work is that evolution has shaped functional attributes, which are termed “adaptations” in biology, to a high functional performance by relentless selective pressure. For current methods and tools, such as data bases, it is implicitly supposed that the considered
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Geometry and phenomenology of the living: Limits and possibilities of mathematization, complexity and individuation in biological sciences Theory Biosci. (IF 1.1) Pub Date : 2022-03-04 Luciano Boi, Carlos Lobo
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
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Geometry and phenomenology of the living: Limits and possibilities of mathematization, complexity and individuation in biological sciences. Theory Biosci. (IF 1.1) Pub Date : 2022-03-04 Luciano Boi,Carlos Lobo
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
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Pattern formation features might explain homoplasy: fertile surfaces in higher fungi as an example Theory Biosci. (IF 1.1) Pub Date : 2022-02-16 Francisco Kuhar, Leticia Terzzoli, Eduardo Nouhra, Gerardo Robledo, Moritz Mercker
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
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Delay induced interaction of humoral- and cell-mediated immune responses with cancer Theory Biosci. (IF 1.1) Pub Date : 2022-02-14 Sumana Ghosh, Sandip Banerjee
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
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A mathematical model for viscoelastic properties of biological soft tissue Theory Biosci. (IF 1.1) Pub Date : 2022-02-03 Man Xi, Guohong Yun, B. Narsu
A quaternary viscoelastic structure model with two characteristic times is presented to describe the viscoelastic properties of parallel-fibered collagen tissue. The comparison results of model prediction and experimental data of rabbit medial collateral ligaments show that the model could accurately describe viscoelastic behavior such as stress-relaxation, strain-strengthening and creep of bio-soft-tissue
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A mathematical model for viscoelastic properties of biological soft tissue. Theory Biosci. (IF 1.1) Pub Date : 2022-02-03 Man Xi,Guohong Yun,B Narsu
A quaternary viscoelastic structure model with two characteristic times is presented to describe the viscoelastic properties of parallel-fibered collagen tissue. The comparison results of model prediction and experimental data of rabbit medial collateral ligaments show that the model could accurately describe viscoelastic behavior such as stress-relaxation, strain-strengthening and creep of bio-soft-tissue
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Is DNA repair controlled by a biological logic circuit? Theory Biosci. (IF 1.1) Pub Date : 2022-01-01 Philip G. Penketh
The possible utilization of biological logic circuit(s) in the integration and regulation of DNA repair is discussed. The author believes this mode of regulation likely applies to many other areas of cell biology; however, there are currently more experimental data to support its involvement in the control of DNA repair. Sequential logic processes always require a clock to orchestrate the orderly processing
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Is DNA repair controlled by a biological logic circuit? Theory Biosci. (IF 1.1) Pub Date : 2022-01-01 Philip G Penketh
The possible utilization of biological logic circuit(s) in the integration and regulation of DNA repair is discussed. The author believes this mode of regulation likely applies to many other areas of cell biology; however, there are currently more experimental data to support its involvement in the control of DNA repair. Sequential logic processes always require a clock to orchestrate the orderly processing
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Introduction to the special issue: quantifying collectivity. Theory Biosci. (IF 1.1) Pub Date : 2021-11-17 Bryan C Daniels,Manfred D Laubichler,Jessica C Flack
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Innovations are disproportionately likely in the periphery of a scientific network Theory Biosci. (IF 1.1) Pub Date : 2021-11-12 Painter, Deryc T., Daniels, Bryan C., Laubichler, Manfred D.
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
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Information transmission in a two-step cascade: interplay of activation and repression Theory Biosci. (IF 1.1) Pub Date : 2021-10-05 Roy, Tuhin Subhra, Nandi, Mintu, Biswas, Ayan, Chaudhury, Pinaki, Banik, Suman K.
We present an information-theoretic formalism to study signal transduction in four architectural variants of a model two-step cascade with increasing input population. Our results categorize these four types into two classes depending upon the effect of activation and repression on mutual information, net synergy, and signal-to-noise ratio. Using the Gaussian framework and linear noise approximation