Theory in Biosciences最新文献

{"title":"The haunted Umwelt: a biosemiotic and hauntological account of immune semiotic corruption in field cancerization.","authors":"Anuraag Bukkuri","doi":"10.1007/s12064-026-00496-5","DOIUrl":"10.1007/s12064-026-00496-5","url":null,"abstract":"<p><p>Field cancerization, the process wherein prior insults corrupt the semiotic landscape through which immune cells detect and respond to \"the other\", persists even after the precipitating conditions resolve and the tissue histologically appears normal. This exemplifies a broader explanatory problem: How can we account for biomedical phenomena whose pathology is constituted by a history that standard mechanistic accounts cannot recover? I argue that a comprehensive understanding of field cancerization requires us to supplement molecular mechanistic explanations with lineage-level accounts, developed through a dialogue among Derrida's hauntology, ghost criminology, and von Uexküll's Umwelt as formalized through Peirce's triadic model of signs. This framework generates a three-ghost taxonomy of immune semiotic corruption, explains why treating the present condition without addressing historically constituted corruption fails, and suggests concrete therapeutic implications based on this framework.Keywords: field cancerization, immunology, biosemiotics, hauntology, ghost criminology, Umwelt, Derrida, Peirce.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"145 4","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13675323/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149208344","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Beyond formal equivalence: research questions and explanatory function in group and multilevel selection theory.","authors":"Pedro Henrique Martins, Fausto Nomura","doi":"10.1007/s12064-026-00495-6","DOIUrl":"10.1007/s12064-026-00495-6","url":null,"abstract":"<p><p>The debate over group and multilevel selection remains central to evolutionary biology, particularly in explanations of cooperation and social evolution. A persistent issue is whether group- and multilevel-selection models and kin-selection formulations are formally equivalent, that is, whether they can represent the same evolutionary change under specified assumptions, and what follows from such equivalence for explanation. We conducted a systematic review and thematic synthesis of 94 model-centered studies, characterized by explanatory orientation, Research Question, multilevel selection I/II classification, formal tool, decomposition role, causal interpretation, and equivalence claims. Explanatory orientations were heterogeneous, and formal-tool use overlapped substantially across them. Associations involving decomposition role weakened in sensitivity analyses, while predominant Research Question showed no detectable association with multilevel selection I/II classification. Among the 68 studies that substantively discussed equivalence, qualified positions predominated and categorical rejection was rare; most addressed multiple objects of equivalence. These results indicate that explanatory orientation, Research Questions, formal representations, causal interpretation, and equivalence claims are related but non-interchangeable dimensions of the debate. Formal equivalence can establish genuine relations between representations without determining that they identify the same causal structure, serve the same explanatory function, or support the same attribution of adaptation. Persistent disagreement is therefore better understood as concerning what formal translations preserve, which biological questions they answer, and what explanatory conclusions follow from them.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"145 4","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13645915/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149129310","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quaternionic response geometry for proteins: toward a noncommutative theory of ordered deformations.","authors":"Xiaoting Chen, Chon-Fai Kam, Yu Li, David Medina-Ortiz, Cedric Damour, Jean Pierre Chabriat, Alain Miranville, Miloud Bessafi, Frederic Cadet","doi":"10.1007/s12064-026-00494-7","DOIUrl":"10.1007/s12064-026-00494-7","url":null,"abstract":"<p><p>Protein function may depend not only on endpoint conformations but also on the ordered deformation histories through which they are reached. This distinction is relevant to allostery, conformational switching, mutation-induced rearrangements, and epistatic effects, where different perturbation sequences may produce similar visible structures while retaining distinct internal transport histories. Current state-centered or endpoint-centered representations do not always preserve this order-sensitive information. The practical motivation is therefore to provide a foundation for future descriptors of protein deformation trajectories that can distinguish ordered histories even when endpoint conformations are similar. Such descriptors could support analyses of allosteric switching, mutation-order effects, conformational memory, and path-dependent response in molecular-dynamics trajectories, NMR ensembles, structural families, and outputs of geometric generative models. We propose a deformation-first geometric framework based on quaternionic frame transport along the protein backbone. Local backbone frames are lifted to quaternionic variables, with infinitesimal rotation encoded by [Formula: see text]. Ordered concatenation of admissible deformation paths generates a noncommutative transport algebra, recording that deformation [Formula: see text] followed by [Formula: see text] need not be equivalent to [Formula: see text] followed by [Formula: see text]. From this ordered transport layer, we construct a spectral-response layer comprising a global Dirac-type operator, local spectral germs, a renormalized spectral density, and a mixed response form. A minimal realization on an idealized α-helix shows how localized pitch and bending perturbations can yield similar endpoint descriptors while producing a nonzero endpoint-derived ordered-transport discrepancy. At the formal level, the framework separates an order-sensitive transport-memory sector, lost under a commutative shadow, from a spectral-response sector that remains visible.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"145 4","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13593740/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149018893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transition of neimark-sacker to flip bifurcation in a discrete prey-predator model with bazykin functional response and harvesting.","authors":"Siti Nur Nadhirah Yahaya, Tau Keong Ang, Yeou Jiann Lim","doi":"10.1007/s12064-026-00492-9","DOIUrl":"10.1007/s12064-026-00492-9","url":null,"abstract":"<p><p>This paper discusses on the dynamics and bifurcations of a two-dimensional discrete prey-predator model with Bazykin functional response and linear harvesting in predator. Compared to Bazykin prey-predator model which focuses on competition for other resources, Bazykin functional response include predator competition for prey and predator saturation. Limited studies on Bazykin functional response especially in discrete model highlight the novelty of this research. A semi-discretisation method is applied to derive the model from continuous to discrete. The stability at each fixed point is summarised by applying related lemma and definition. The occurrences of Neimark-Sacker and flip bifurcations are established through the Centre Manifold Theorem and supported by numerical simulations. The coexistence fixed point first loses stability through Neimark-Sacker bifurcation before becoming stable over an intermediate parameter range. Then, the fixed point undergoes flip bifurcation giving rise to periodic and chaotic dynamics. Simulations by MATLAB and MATCONTM are included by providing the bifurcation, phase portrait and time series diagrams. The discrete model displays interesting dynamical behaviours such as transition of Neimark-Sacker to flip bifurcation, quasiperiodic oscillations, periodic solutions and chaos brought on by harvesting. This paper highlights that intensive harvesting leads to chaotic behaviour of prey population and subsequently lead to predator extinction. The results signifies that intensive harvesting combined with predator competition can drastically alter the system dynamics, offering crucial ecological insights into sustainable harvesting strategies.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"145 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148898517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Macroquantum PID as an alternative core meaning for plant signaling: a comment on Ansari et al.","authors":"Salvatore Chirumbolo","doi":"10.1007/s12064-026-00493-8","DOIUrl":"10.1007/s12064-026-00493-8","url":null,"abstract":"","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"145 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148892825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mathematical modeling of silkworm-virus dynamics for sustainable sericulture using piezoelectric-based temperature control.","authors":"Nusrat Yesmin Kona, Md Haider Ali Biswas","doi":"10.1007/s12064-026-00491-w","DOIUrl":"10.1007/s12064-026-00491-w","url":null,"abstract":"<p><p>Sericulture is an important socioeconomic sector in many developing countries; however, environmental temperature changes and Nuclear Polyhedrosis Virus (NPV) epidemics significantly limit its output. A new nonlinear five compartmental mathematical model that integrates silkworm population dynamics, NPV transmission, environmental viral persistence, piezoelectric energy generation and temperature regulation is developed and analyzed in this work. Newtonian heat exchange controlled by piezoelectric-assisted thermal control, temperature-dependent viral transmission and mortality, Holling type II saturation in environmental virus accumulation and the logistic growth of healthy silkworms are all included in the model. Extensive analytical studies establish the existence and uniqueness of solutions, positivity and boundedness. Eigenvalue criteria and Jacobian analysis are used to determine local stability conditions and identify virus-free and endemic equilibrium points. The virus-free equilibrium is shown to be globally asymptotically stable under threshold conditions defined by fundamental reproduction number using a Lyapunov function. The main determinants of system behavior, according to sensitivity analysis, are infection rate, virus decay rate and temperature dependent mortality. According to numerical simulations, maintaining favorable thermal condition is associated with reduced NPV proliferation and improved silkworm survival, while suboptimal temperatures are associated with increased viral amplification and higher larval mortality. By using piezoelectric energy harvesting, rearing temperature may potentially be regulated, outbreak intensity may decrease and healthy silkworm persistence may improve under modeled conditions. In addition, three-dimensional phase trajectories illustrate the interdependent feedback between environmental regulatory mechanisms, viral load and host activity. The proposed framework connects epidemiological dynamics with temperature regulation based on renewable energy, may provide a theoretical basis for future studies on temperature-regulated and energy-assisted sericulture systems. This study presents a unified modeling approach that may support the development of more stable silk production systems in line with global sustainability goals by combining mathematical ecology, virology, and green energy technology.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"145 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148801109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bifurcation and chaos design of radial basis neural network for predictive modeling of fractional double-strain HIV co-infection model with intercellular delays and stochastic effects.","authors":"Muhammad Wajahat Anjum, Noreen Sher Akbar, M Bilal Habib, A Alzubaidi, S Saleem","doi":"10.1007/s12064-026-00468-9","DOIUrl":"10.1007/s12064-026-00468-9","url":null,"abstract":"<p><p>The aim of the present study is to obtain the numerical solutions of the fractional double-strain HIV co-infection model with intercellular delays and stochastic effects (FDS-HIV-IDS) by employing a novel radial basis neural network with Levenberg-Marquardt backpropagation (RBNN-LMB). The nonlinear model accounts for multiple interacting populations, and logistic growth is introduced to describe the interaction between wild-type and drug-resistant HIV strains. The analysis of the model considers threshold criteria for both local and global stability of infection-free, dominant, and coexistence equilibria. The nonlinear model incorporates multiple interacting groups, and its numerical solutions are approximated through the stochastic RBNN-LMB framework. Consequently, double-strain dynamics transition from stability to instability (periodic oscillations to chaos) more frequently and at earlier stages. This also leads to a higher total viral load compared to single-strain scenarios, highlighting the greater risk of treatment failure when resistance emerges. A dataset is generated using the numerical predictor-corrector method, where the data are split into 75% for training and 10% for validation and 15% for testing, in order to minimize the mean square error (MSE). The solver architecture consists of fifteen hidden neurons, a single input structure, and a radial basis activation function to approximate the system dynamics effectively. The accuracy of the method is demonstrated through the overlapping of predicted and reference outputs, while the very small absolute error (AE) values confirm its precision. Furthermore, statistical evaluations using different operators support the reliability and robustness of the proposed approach.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"145 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148632607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimal strategies for fair vaccine allocation: integrating non-pharmaceutical interventions, regional quarantine, and social challenges in epidemic control.","authors":"Fatemeh Mirsaeedi, Mohammad Sheikhalishahi, Mehrdad Mohammadi","doi":"10.1007/s12064-026-00488-5","DOIUrl":"10.1007/s12064-026-00488-5","url":null,"abstract":"<p><p>It is essential to control epidemic diseases and adopt an optimal strategy when an epidemic occurs. In this research, a myopic model is presented. In this regard, an epidemic model is presented considering social challenges such as vaccine acceptance, quarantine of infected individuals, and regional quarantine. The vaccine allocation model was constructed to incorporate specific outputs from the epidemiological model, including (i) the weight of each cluster within each region, (ii) the vaccine demand of each cluster in each region, (iii) the relative infectiousness of region g, and (iv) the relative susceptibility of region g. By integrating these parameters, the allocation model determines equitable distribution strategies that aim to reduce the effective reproduction number. The model is run based on the data provided in similar articles, and its results are analyzed. By incorporating economic factors, like the costs of interventions, along with social factors such as individuals' willingness to get vaccinated, this model allows for an exploration of various aspects related to the fair allocation of vaccines. The rationality of the model's outcomes, supported by expert validation and reinforced through sensitivity analysis, underscores its accuracy and reliability.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"145 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148632674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The exact mathematical form of the Pareto principle.","authors":"Subhash Kak","doi":"10.1007/s12064-026-00490-x","DOIUrl":"10.1007/s12064-026-00490-x","url":null,"abstract":"<p><p>The exact mathematical form of the empirical Pareto Principle is derived using the optimum power law which is based on information theory. It is shown that the 80-20 Rule is approximately 70-20 for populations below 400, which means that 20% of the individuals have 70% of the resources. Around the population of 100,000 it is nearly 80% but as the population goes into billions, the top 20% get to have nearly 84% of the resources increasing the disparity. This implies that more dense populations have greater inequality than less dense ones which is an unexpected result.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"145 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148563599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analytical construction of lump, rogue, and multi-wave structures in a nonlinear neuron membrane model via bilinear neural network approach.","authors":"Mati Ur Rahman, Sonia Akram, Laila A Al-Essa, Khalid Aldawsari","doi":"10.1007/s12064-026-00474-x","DOIUrl":"10.1007/s12064-026-00474-x","url":null,"abstract":"<p><p>In this article, we study a nonlinear neuron membrane model describing the propagation of action potentials along nerve fibers, incorporating nonlinear elastic effects and higher-order dispersion. By applying the Hirota bilinear transformation, the given equation is converted into an equivalent bilinear form, which provides a suitable analytical framework for systematic construction of exact solutions. To enrich the functional solution space, we introduce a bilinear neural network method (BNNM), where neural network architectures are used as structured symbolic generators rather than numerical approximators. Both single-hidden-layer and double-hidden-layer configurations are constructed to generate exact analytical solutions. Through symbolic coefficient matching assisted by MAPLE, multiple admissible parameter sets are obtained. The presented framework yields a diverse family of exact wave structures, involving lump solutions, breather-type oscillatory waves, soliton-lump interaction states, double-period lump superpositions, three-wave interaction patterns, and hybrid lump-rogue wave excitations. The derived solutions are expressed in compact Hirota form and signified via three-dimensional, density, and contour visualizations, revealing strong spatial localization, temporal modulation, nonlinear energy redistribution, and coherent phase-locked propagation. The results represent that the neural-bilinear approach offers a powerful and systematic mechanism for constructing rich nonlinear wave families in neuron-type models. These analytical structures contribute to understanding localized pulse transmission, multi-wave interaction dynamics, and transient amplification phenomena in excitable biological media.</p>","PeriodicalId":54428,"journal":{"name":"Theory in Biosciences","volume":"145 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148498375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}