Biosystems最新文献_第3页

Influence of oxidative stress on women’s fertility: A model with a generational age Caputo’s fractional derivative 氧化应激对女性生育能力的影响：一个具有代际年龄的卡普托分数导数模型

IF 1.9 4区生物学

Biosystems Pub Date : 2025-09-08 DOI: 10.1016/j.biosystems.2025.105577

A.M. Portillo , J.A. García-Velasco , E. Varela

{"title":"Influence of oxidative stress on women’s fertility: A model with a generational age Caputo’s fractional derivative","authors":"A.M. Portillo , J.A. García-Velasco , E. Varela","doi":"10.1016/j.biosystems.2025.105577","DOIUrl":"10.1016/j.biosystems.2025.105577","url":null,"abstract":"<div><div>Cellular aging associated with telomeric shortening plays an important role in female fertility. In addition to natural decline, due to the loss of telomeric repeats during cell division, other factors such oxidative stress (OS), accelerate telomere shortening by causing a dramatic loss of telomeric repeats. Thus, mathematical models to better understand the accelerated aging leading to infertility are lacking in the literature. An initial and boundary value problem (IBVP) with a diffusion-advection equation was considered to describe the evolution of a cell population undergoing a gradual decrease of the proliferation potential due to the end-replication problem (<span><span>Olovnikov, 1973</span></span>). In this paper we propose a continuum model that attempts to capture the random telomere shortening caused by OS, replacing the advection term with a Caputo’s fractional derivative of order <span><math><mi>β</mi></math></span>, <span><math><mrow><mn>0</mn><mo><</mo><mi>β</mi><mo><</mo><mn>1</mn></mrow></math></span>, with respect to the generational age. The distance between the order of the Caputo derivative and 1 was considered the oxidation parameter. The mathematical model was applied to the human follicular growth from preantral to pre-ovulatory follicle, in young and older women to study the influence of oxidation and low telomerase activity on the aging rate of the pre-ovulatory follicle. We observed that as OS increases, the generational age of granulosa cells (GCs) increases as well, suggesting that telomeres of these GCs will be aged. Although middle-aged women treated with antioxidants could reduce the negative effects of OS on telomeres, antioxidants in combination with good levels of telomerase activity yield the best results regarding the reduction of generational aging of GCs.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105577"},"PeriodicalIF":1.9,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145027121","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}

引用次数: 0

Viscous DNA and RNA: Quantum damped dynamical random systems 粘性DNA和RNA：量子阻尼的动态随机系统

IF 1.9 4区生物学

Biosystems Pub Date : 2025-09-08 DOI: 10.1016/j.biosystems.2025.105578

Hamze Mousavi, Samira Jalilvand

{"title":"Viscous DNA and RNA: Quantum damped dynamical random systems","authors":"Hamze Mousavi, Samira Jalilvand","doi":"10.1016/j.biosystems.2025.105578","DOIUrl":"10.1016/j.biosystems.2025.105578","url":null,"abstract":"<div><div>From a physics perspective, DNA and RNA molecules are characterized as dynamic biological structures that exhibit vibrations across a range of time scales. To conduct a more accurate investigation of their dynamic properties, it is essential to consider the environmental conditions surrounding these molecules. A harmonic Hamiltonian that incorporates damping, along with the Green’s function method, has been utilized to analyze the vibrational responses of viscous DNA and RNA strands. The DNA molecule is represented using a fishbone model alongside two distinct double-strand configurations, while a half-ladder model is applied to the RNA molecule. The interconnections between sub-sites are represented by linear springs, with the stiffness of the vertical springs and the damping coefficients of the dashpots varying randomly throughout the length of the systems. Furthermore, each model is examined under three distinct configurations: infinite, finite, and cyclic. The results reveal that the fluctuations in the density of states curves exhibit a gradual decline, leading to a broadening of the sharp peaks as the damping coefficient increases. Additionally, the vibrational modes become progressively less distinct with an increase in system damping, a finding that aligns well with the principles of wave mechanics and vibrational motion.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105578"},"PeriodicalIF":1.9,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145027122","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}

引用次数: 0

Shear-stress-induced swirling flow in biological systems 生物系统中剪切应力诱导的旋流。

IF 1.9 4区生物学

Biosystems Pub Date : 2025-09-06 DOI: 10.1016/j.biosystems.2025.105588

Ivana Pajic-Lijakovic , Milan Milivojevic , Peter V.E. McClintock

{"title":"Shear-stress-induced swirling flow in biological systems","authors":"Ivana Pajic-Lijakovic , Milan Milivojevic , Peter V.E. McClintock","doi":"10.1016/j.biosystems.2025.105588","DOIUrl":"10.1016/j.biosystems.2025.105588","url":null,"abstract":"<div><div>Swirling motion is an essential phenomenon that significantly influences numerous biological processes, such as the mixing of molecular components within living cells, nutrient transport, the structural changes of the cytoskeletons of contractile cells and the rearrangement of multicellular systems caused by collective cell migration. The dynamical relationship between subcellular and supracellular rearrangements enhances cell migration and contributes to tissue homeostasis. However, the basic mechanisms that drive swirling motion in biological contexts remain a matter of ongoing inquiry. Several complex biological systems, including synovial fluid, blood, mucus, cytoskeleton, and epithelial and mesenchymal multicellular systems, are examined in the context of possible swirling motion. Despite their diverse structures and fluid properties, they all exhibited swirling behaviour. Shared characteristics among these systems include: (i) a heterogeneous distribution of density and mechanical stress, (ii) viscoelastic properties, (iii) anisotropic behaviour, and (iv) non-uniform flow patterns. This multifaceted phenomenon is analysed through the integration of experimental findings from the existing literature with modelling considerations, aiming to identify the primary physical factors that contribute to the occurrence of swirling motion such as: lift force and normal stress differences that appear as a consequence of generated shear stress.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105588"},"PeriodicalIF":1.9,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145024678","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}

引用次数: 0

On some models of extended mechanism in code biology 密码生物学中扩展机制的几个模型。

IF 1.9 4区生物学

Biosystems Pub Date : 2025-09-05 DOI: 10.1016/j.biosystems.2025.105587

Lukáš Zámečník, Barbora Jurková

{"title":"On some models of extended mechanism in code biology","authors":"Lukáš Zámečník, Barbora Jurková","doi":"10.1016/j.biosystems.2025.105587","DOIUrl":"10.1016/j.biosystems.2025.105587","url":null,"abstract":"<div><div>Barbieri's semantic biology (originally Barbieri, 1985) provides an extension of the standard biological ontology, through a new theoretical entity: the code. A specific feature of Barbieri's semantic turn in biology is the use of mechanistic explanations of living systems. This approach allows to work with meaning as the ‘new observable’ of biology. The relationship between meaning and code is expressed by Barbieri as follows: “[ …] meaning is an entity which is related to another entity by a code.” (Barbieri, 2015, 26). Barbieri refers to the mechanistic model of meaning as an ‘extended mechanism’.</div><div>This work is a follow-up to a previously published paper in which we concluded that the von Neumann probe (and thus the Turing machine) can serve as a “minimal sufficient model of Barbieri's extended mechanism” (Jurková and Zámečník, 2023a). We now build on this by connecting the concept of self-reproduction as conceived by Norbert Wiener. Firstly, in order to further explore the ‘extended mechanism’, but also in an attempt to highlight the importance of self-reproduction as a model of biological processes. We want to highlight the extent to which von Neumann and Wiener collaborated, but also where their understanding and conception of self-reproduction diverge.</div><div>Wiener, unlike von Neumann, emphasizes that such a machine is “an agency for accomplishing certain definite purposes” (Wiener, 2019/1948, 245) and self-propagation “is the creation of a replica capable of the same functions” (Wiener, 2019/1948, 245). We suggest that when Wiener views the machine in terms of an ‘operative procedure’ that enables machine self-propagation, he is implicitly referring to the role of code as thematized in Barbieri's extended mechanism (Wiener, 2019/1948, 249). We want to focus not only on classical scientific publications, but also to analyse the personal correspondence between von Neumann and Wiener in which they discussed the issue and how it can change the way we perceive self-reproducing machine.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105587"},"PeriodicalIF":1.9,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145016531","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}

引用次数: 0

Dreams as a code language 梦是一种代码语言。

IF 1.9 4区生物学

Biosystems Pub Date : 2025-09-03 DOI: 10.1016/j.biosystems.2025.105586

João Ereiras Vedor

{"title":"Dreams as a code language","authors":"João Ereiras Vedor","doi":"10.1016/j.biosystems.2025.105586","DOIUrl":"10.1016/j.biosystems.2025.105586","url":null,"abstract":"<div><div>Since Freud, psychologists have sought to decipher the language of dreams, but no universal interpretive manual exists. Advances in dream neuroscience and the emergence of Code Biology have brought us closer to understanding the rules and functions underlying dream formation. Code Biology, which studies coding processes in living systems, offers a revolutionary framework for how neural and symbolic patterns generate dream narratives. Dreams are not epiphenomena; they serve crucial adaptive functions—emotional regulation, memory consolidation, and ego development. Despite energetic costs, their evolutionary conservation across species highlights their biological necessity. Cartwright's studies confirm dreams' essential regulatory role in survival.</div><div>This article argues that dreams are coded artifacts produced by multiple organic codes—biological, neuronal, symbolic, and cultural—mediated by archetypes. Drawing on Barbieri's, Major's and Goodwyn work, archetypes are reframed as artifacts of embodied organic codes regulating dream formation and symbolic imagery. Integrating affective neuroscience findings and Jung's theory, this perspective proposes emotional affects as archetypal neurodynamic patterns. A key methodological gap remains: the separation of neuroscience and clinical practice. Through clinical dream analysis, the article shows therapists act as “adaptors,” translating dream codes into meaningful narratives—a process termed psychic codepoiesis. Finally, it discusses how Large Language Models, trained on life-coding principles, may support but not replace embodied human adaptors, offering a new paradigm for understanding dreams as the foundational language of subjective life.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105586"},"PeriodicalIF":1.9,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145006713","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}

引用次数: 0

Learning and memory in soldier crabs: Evidence from escape task trials. 士兵蟹的学习和记忆：来自逃跑任务试验的证据。

IF 1.9 4区生物学

Biosystems Pub Date : 2025-09-01 Epub Date: 2025-07-23 DOI: 10.1016/j.biosystems.2025.105529

Takeshi Kawai, Yukio Pegio Gunji

引用次数: 0

From correlation to causation: Unraveling the impact of closure on open-ended evolution within the Kauffman model 从相关性到因果关系：在考夫曼模型中揭示封闭性对开放式进化的影响

IF 1.9 4区生物学

Biosystems Pub Date : 2025-08-31 DOI: 10.1016/j.biosystems.2025.105574

M. Faggian

{"title":"From correlation to causation: Unraveling the impact of closure on open-ended evolution within the Kauffman model","authors":"M. Faggian","doi":"10.1016/j.biosystems.2025.105574","DOIUrl":"10.1016/j.biosystems.2025.105574","url":null,"abstract":"<div><div>Evolution is a highly intricate process marked by the generation of novelty, which requires the historical and collective organization of individuals. In this paper, we investigate the relationship between biological organization and Open-Ended Evolution (OEE), with a particular focus on the causal connection between the two. To quantitatively investigate the causal relation within a chemical system, we utilize assembly theory to assess the influence of auto-catalytic sets on the complexity dynamics of Kauffman’s model. In the second part of the paper, we strengthen this conjecture by analyzing the effects of the simplest auto-catalytic set on the complexity dynamics in Kauffman’s model, specifically in the absence of parametric correlation. By interpreting auto-catalytic sets as organizational structures in chemical systems, our findings provide the first numerical support for investigating the causal relationship between biological organization and OEE. This work represents a promising area for the initial study of the dynamical relationship between OEE and biological organization, and may advance the understanding of their connection in theoretical biology.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105574"},"PeriodicalIF":1.9,"publicationDate":"2025-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144933781","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}

引用次数: 0

Constructing a bridge between functioning of oscillatory neuronal networks and quantum-like cognition along with quantum-inspired computation and AI 在振荡神经元网络的功能和量子认知以及量子启发的计算和人工智能之间建立一座桥梁

IF 1.9 4区生物学

Biosystems Pub Date : 2025-08-30 DOI: 10.1016/j.biosystems.2025.105573

Andrei Khrennikov , Atsushi Iriki , Irina Basieva

{"title":"Constructing a bridge between functioning of oscillatory neuronal networks and quantum-like cognition along with quantum-inspired computation and AI","authors":"Andrei Khrennikov , Atsushi Iriki , Irina Basieva","doi":"10.1016/j.biosystems.2025.105573","DOIUrl":"10.1016/j.biosystems.2025.105573","url":null,"abstract":"<div><div>Quantum-like (QL) modeling, one of the outcomes of the quantum information revolution, extends quantum theory methods beyond physics to decision theory and cognitive psychology. While effective in explaining paradoxes in decision making and effects in cognitive psychology, such as conjunction, disjunction, order, and response replicability, it lacks a direct link to neural information processing in the brain. This study bridges neurophysiology, neuropsychology, and cognitive psychology, exploring how oscillatory neuronal networks give rise to QL behaviors. Inspired by the computational power of neuronal oscillations and quantum-inspired computation (QIC), we propose a quantum-theoretical framework for coupling of cognition/decision making and neural oscillations - <em>QL oscillatory cognition</em>. This is a step, may be very small, toward clarification of the relation between mind and matter and the nature of perception and cognition. We formulate four conjectures within QL oscillatory cognition and in principle they can be checked experimentally. But such experimental tests need further theoretical and experimental elaboration. One of the conjectures (Conjecture 4) is on resolution of the binding problem by exploring QL states entanglement generated by the oscillations in a few neuronal networks. Our findings suggest that fundamental cognitive processes align with quantum principles, implying that humanoid AI should process information using quantum-theoretic laws. Quantum-Like AI (QLAI) can be efficiently realized via oscillatory networks performing QIC.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105573"},"PeriodicalIF":1.9,"publicationDate":"2025-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144933782","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}

引用次数: 0

Generalization power of threshold Boolean networks 阈值布尔网络的泛化能力。

IF 1.9 4区生物学

Biosystems Pub Date : 2025-08-28 DOI: 10.1016/j.biosystems.2025.105572

Gonzalo A. Ruz , Anthony D. Cho

{"title":"Generalization power of threshold Boolean networks","authors":"Gonzalo A. Ruz , Anthony D. Cho","doi":"10.1016/j.biosystems.2025.105572","DOIUrl":"10.1016/j.biosystems.2025.105572","url":null,"abstract":"<div><div>Threshold Boolean networks are widely used to model gene regulatory systems and social dynamics such as consensus formation. In these networks, each node takes a binary value (0 or 1), leading to an exponential growth in the number of possible configurations with the number of nodes (<span><math><msup><mrow><mn>2</mn></mrow><mrow><mi>n</mi></mrow></msup></math></span>). Inferring such networks involves learning a weight matrix and threshold vector from configuration data. However, in practice, the full state transition matrix is rarely available. This study investigates the generalization power of threshold Boolean networks, specifically, their ability to accurately infer the underlying network as the amount of available training data is reduced or degraded. We conducted experiments to empirically explore this generalization across networks with varying sizes and connectivities, using the perceptron learning algorithm for training. We also examined scenarios where data is degraded and evaluated the networks’ ability to preserve the original system’s fixed points. Our results reveal an inverse relationship between network size and the required portion of the state transition matrix: larger networks require less data to infer the original structure. For example, networks with five nodes required about 62.5% of the data, whereas networks with nine nodes needed only 46%. Conversely, we observed a positive correlation between node indegree and the amount of training data necessary for accurate inference. In terms of preserving fixed points, our findings indicate that using approximately 40% of the data is generally sufficient to retain the fixed points present in the complete dataset.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105572"},"PeriodicalIF":1.9,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144977393","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}

引用次数: 0

Balancing the cellular budget: Lessons in metabolism from microbes to cancer 平衡细胞预算：从微生物到癌症的新陈代谢课程

IF 1.9 4区生物学

Biosystems Pub Date : 2025-08-27 DOI: 10.1016/j.biosystems.2025.105571

B. Vibishan , Mohit Kumar Jolly , Akshit Goyal

{"title":"Balancing the cellular budget: Lessons in metabolism from microbes to cancer","authors":"B. Vibishan , Mohit Kumar Jolly , Akshit Goyal","doi":"10.1016/j.biosystems.2025.105571","DOIUrl":"10.1016/j.biosystems.2025.105571","url":null,"abstract":"<div><div>Cancer cells are often seen to prefer glycolytic metabolism over oxidative phosphorylation even in the presence of oxygen-a phenomenon termed the Warburg effect. Despite significant strides in the decades since its discovery, a clear basis is yet to be established for the Warburg effect and why cancer cells show such a preference for aerobic glycolysis. In this review, we draw on what is known about similar metabolic shifts both in normal mammalian physiology and overflow metabolism in microbes to shed new light on whether aerobic glycolysis in cancer represents some form of optimisation of cellular metabolism. From microbes to cancer, we find that metabolic shifts favouring glycolysis are sometimes driven by the need for faster growth, but the growth rate is by no means a universal goal of optimal metabolism. Instead, optimisation goals at the cellular level are often multi-faceted and any given metabolic state must be considered in the context of both its energetic costs and benefits over a range of environmental contexts. For this purpose, we identify the conceptual framework of resource allocation as a potential testbed for the investigation of the cost–benefit balance of cellular metabolic strategies. Such a framework is also readily integrated with dynamical systems modelling, making it a promising avenue for new answers to the age-old question of why cells, from cancers to microbes, choose the metabolic strategies they do.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"256 ","pages":"Article 105571"},"PeriodicalIF":1.9,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144913920","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}

引用次数: 0