Biosystems最新文献_第4页

A hybrid DNN model using novel integrated interface features for predicting protein-protein complexes binding affinity 利用新型集成界面特征预测蛋白质复合物结合亲和力的混合DNN模型。

IF 1.9 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2025-12-30 DOI: 10.1016/j.biosystems.2025.105688

Lichao Zhang , Zhengyan Bian , Xue Wang , Liang Kong

Accurately predicting binding affinity of protein-protein complexes is significant for gaining deeper insights into complex biological mechanisms. Given that binding between proteins primarily occurs at the interface region, previous studies have demonstrated that the number of inter-residue contacts (ICs) and the buried surface area (BSA) are critical interface features. However, existing models generally used these two types of interface features separately, ignoring integrating them effectively to achieve high prediction accuracy. In this study, utilizing kernel density estimation-based mutual information and the Hadamard product, we proposed an effective approach that integrates BSA and ICs to construct the novel integrated interface features that embody dual structural information, and further derived our feature set. Subsequently, the proposed feature set was input Deep Neural Network (DNN), and a hybrid DNN model was further developed following our hybrid modeling strategy. To enhance its prediction performance, a combined activation function was customized for the output layers. Ultimately, using four-fold cross-validation, our hybrid DNN model achieved a Pearson correlation coefficient (R) of 0.88 and a root mean square error (RMSE) of 1.301 kcal/mol, and we verified its good generalization capability, achieving R = 0.82 and RMSE = 1.21 kcal/mol on the external test set derived from the SKEMPI 2.0 database. Compared with existing approaches, our method consistently exhibited superior predictive performance, validating the effectiveness of the proposed method for protein-protein binding affinity prediction. Moreover, the integration strategy for binding affinity representation and the hybrid modeling method may be helpful for related research.

准确预测蛋白质复合物的结合亲和力对于深入了解复杂的生物机制具有重要意义。鉴于蛋白质之间的结合主要发生在界面区域，先前的研究表明，残基间接触（ICs）的数量和埋藏表面积（BSA）是关键的界面特征。然而，现有的模型一般将这两类界面特征分别使用，忽略了将两者有效地整合以达到较高的预测精度。在本研究中，我们利用核密度估计的互信息和Hadamard积，提出了一种有效的方法，将BSA和ic集成在一起，构建新的包含双结构信息的集成接口特征，并进一步推导出我们的特征集。随后，将提出的特征集输入深度神经网络（DNN），并根据我们的混合建模策略进一步开发混合DNN模型。为了提高其预测性能，为输出层定制了组合激活函数。最终，通过四重交叉验证，混合DNN模型的Pearson相关系数(R)为0.88，均方根误差（RMSE）为1.301 kcal/mol，并验证了其良好的泛化能力，在SKEMPI 2.0数据库的外部测试集上实现了R = 0.82, RMSE = 1.21 kcal/mol。与现有方法相比，我们的方法始终表现出优越的预测性能，验证了所提出的方法用于蛋白质-蛋白质结合亲和力预测的有效性。此外，结合亲和表示的集成策略和混合建模方法可能有助于相关研究。

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引用次数: 0

Defining and finding lifelike entities with a lazy filter 使用惰性过滤器定义和查找逼真的实体。

IF 1.9 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2025-12-26 DOI: 10.1016/j.biosystems.2025.105672

Mario Martinez-Saito

Our binary intuitive understanding of life and lifelikeness is good enough for daily life, but not for research in the natural sciences. Here we propose an operational definition of the lifeness of an entity, or object defined by its structure, as a scalar, namely the product of its defining information (algorithmic complexity) integrated over its lifetime. We provide a hierarchical Gaussian, yet parameter-free, dynamical filtering algorithm that can efficiently and on-the-fly fit configurations of entities constituted by moving particles to a tree structure that can model a wide range of hierarchical system entities, while extracting and calculating the complexity, lifespan, and lifeness of the entity and all of its constituting subtrees or subentities. We simulated 41 interacting particle worlds and found preliminary evidence suggesting that the lifeness of entities is associated with the distance to criticality, as roughly measured by the range of the pairwise interaction forces of the elemental particles of the worlds they inhabit. This study is a proof of concept that defining, measuring, and quantifying lifeness is (1) feasible, useful for (2) simplifying theoretical discussions, for (3) hierarchically assessing biotic properties such as number of hierarchical levels and predicted longevity and for (4) classifying both artificial and biological entities, respectively via computer simulations and a combination of evolutionary and molecular biology approaches.

我们对生命和逼真的二元直觉理解对于日常生活来说足够好，但对于自然科学的研究来说就不够了。在这里，我们提出了一个实体或由其结构定义的对象的生命度的操作定义，作为一个标量，即其定义信息（算法复杂性）在其生命周期内集成的乘积。我们提供了一种分层高斯、无参数的动态滤波算法，该算法可以有效地、实时地拟合由移动粒子构成的实体的配置，该结构可以模拟广泛的分层系统实体，同时提取和计算实体及其所有构成子树或子实体的复杂性、寿命和寿命。我们模拟了41个相互作用的粒子世界，发现了初步的证据，表明实体的生命与临界距离有关，粗略地用它们所居住的世界中元素粒子的成对相互作用力的范围来衡量。这项研究证明了定义、测量和量化生命是(1)可行的，有助于(2)简化理论讨论，(3)分层评估生物特性，如分层水平的数量和预测寿命，以及(4)通过计算机模拟和进化与分子生物学方法的结合，分别对人工实体和生物实体进行分类。

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引用次数: 0

Bayesian consolidation of retinal micro(nano)plastic hypothesis: From existential confirmation to spatial–phenotypic inference 视网膜微（纳米）塑性假说的贝叶斯巩固：从存在确认到空间表型推断。

IF 1.9 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2025-12-23 DOI: 10.1016/j.biosystems.2025.105685

Tan Aik Kah

Recent empirical confirmation of polymeric micro- and nanoplastics (MNPs) in human retinal tissue marks a decisive epistemic shift—from theoretical plausibility to verified biological occurrence. Five months before this discovery, a Bayesian hypothesis framework published in BioSystems proposed that MNPs may exist in the human retina and could plausibly explain certain imaging anomalies, despite the absence of direct evidence. The present work extends that framework by formalizing how definitive empirical detection collapses existential uncertainty and advances the Bayesian model toward its next inferential stage.

Using the posterior probability (P = 0.023) derived in the original model as a new prior, strong empirical evidence (P (E | H) = 0.99; P (E | ￢H) = 0.01 or 0.001) yields posteriors between 0.7 and 0.96—representing more than a thirty-fold increase in belief. Sensitivity analysis demonstrates that above a 90 % detection rate, posterior belief asymptotically approaches unity, signifying epistemic closure of the existential hypothesis (H₁: retinal MNPs exist). This quantitative update does not re-analyze laboratory data but illustrates the formal process by which definitive evidence transforms a probabilistic conjecture into an empirically anchored premise. The resulting posterior of H₁ becomes the prior for a second-stage hypothesis (H₂): retinal MNP distribution and polymer profile correlate with specific imaging or pathological phenotypes. Framed within an iterative Bayesian logic, this transition exemplifies how probabilistic reasoning can integrate theoretical prediction and empirical validation—converting a speculative biological proposition into a structured platform for future mechanistic exploration.

最近对人类视网膜组织中聚合物微塑料和纳米塑料（MNPs）的实证证实标志着一个决定性的认知转变——从理论上的合理性到经过验证的生物学发生。在这一发现的5个月前，发表在《生物系统》杂志上的贝叶斯假设框架提出，尽管缺乏直接证据，MNPs可能存在于人类视网膜中，并且可以合理地解释某些成像异常。目前的工作通过形式化确定经验检测如何瓦解存在的不确定性并将贝叶斯模型推向下一个推理阶段来扩展该框架。利用原模型中导出的后验概率（P = 0.023）作为新的先验，得到强有力的经验证据(P(E b| H) = 0.99；P(E b| H) = 0.01或0.001)的后验值介于0.7和0.96之间，这意味着人们的信心增加了30多倍。灵敏度分析表明，在90%的检出率以上，后验信念渐近统一，表明存在假设的认知闭合（H1：视网膜MNPs存在）。这一定量更新并没有重新分析实验室数据，而是说明了确定的证据将概率猜想转化为经验锚定前提的正式过程。由此产生的H1后缘成为第二阶段假设（H2）的先验：视网膜MNP分布和聚合物剖面与特定的成像或病理表型相关。在迭代贝叶斯逻辑的框架内，这种转变体现了概率推理如何将理论预测和经验验证结合起来，将推测性的生物学命题转化为未来机械探索的结构化平台。

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引用次数: 0

Variability in resource productivity drives community dynamics in intraguild predation systems 资源生产力的变化驱动着群落内部捕食系统的动态。

IF 1.9 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2025-12-22 DOI: 10.1016/j.biosystems.2025.105684

Liyun Hou

Energy transfer across trophic levels underpins community structure and stability, yet fluctuations in primary productivity challenge the persistence of species at higher trophic levels. We use an intraguild predation model—with resource, consumer, and a stage-structured predator—to show that variability in resource productivity profoundly reshapes trophic interactions and biomass distribution. We find that the amplitude of resource productivity fluctuations (ψ), rather than its period (Y), is the primary driver of dynamics. As ψ increases, the predator biomass shifts from juvenile to adult dominance and undergoes recurrent starvation-recovery cycles, which in turn regulate consumer biomass. Trophic responses to ψ are highly asymmetric: resources biomass remain largely stable, consumers biomass gain modestly, but total predator biomass declines consistently with ψ and collapses once ψ > 0.5. Both deterministic and stochastic resource variability yielded consistent results on population biomass and fluctuation amplitude. Furthermore, the system's equilibrium state—whether resource-only, consumer-resource, full coexistence, or predator-resource—was determined by the interaction between maximum resource density (R_max) and the predator's ontogenetic diet shift (θ). Critically, the amplitude ψ modulates this R_max – θ interaction, expanding or contracting the parameter regions supporting these distinct states.

跨营养级的能量转移是群落结构和稳定的基础，但初级生产力的波动挑战了物种在更高营养级的持久性。我们使用了一个包含资源、消费者和阶段结构捕食者的野生动物捕食模型，以表明资源生产力的变化深刻地重塑了营养相互作用和生物量分布。我们发现，资源生产率波动的幅度（ψ），而不是其周期(Y)，是动态的主要驱动因素。当ψ值增加时，捕食者的生物量从幼虫转变为成虫，并经历反复的饥饿-恢复周期，这反过来又调节了消耗者的生物量。对ψ的营养响应是高度不对称的：资源生物量基本保持稳定，消费者生物量适度增加，但总捕食者生物量随着ψ持续下降，并在ψ >.5时崩溃。确定性和随机资源变异在种群生物量和波动幅度上的结果一致。此外，系统的均衡状态——资源纯态、消费-资源态、完全共存态和捕食者-资源态——由最大资源密度（Rmax）和捕食者的个体发生饮食转移（θ）之间的相互作用决定。关键的是，振幅ψ调制这个Rmax - θ相互作用，扩展或收缩支持这些不同状态的参数区域。

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引用次数: 0

Reframing neural decussation: A vision-based theory for contralateral control 重构神经对话：一个基于视觉的对侧控制理论。

IF 1.9 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2025-12-20 DOI: 10.1016/j.biosystems.2025.105683

Ghassan Ahmed Mubasher Mohamedsalih

Neural decussation, the systematic crossing of sensory and motor pathways at the midline, is one of the most prominent features of the vertebrate nervous system, yet its functional rationale has remained unresolved. This work proposes the Visual-Origin Theory of Neuronal Decussation, which argues that contralateral organization arises as a direct consequence of visual field optical geometry. Light rays from the right visual hemifield physically cross the midsagittal plane before reaching the temporal retina, and so do rays from the left hemifield in the opposite direction. The decussation of nasal retinal fibers in the optic chiasm does not create this crossing; it preserves a pre-existing physical pattern, thereby aligning each cerebral hemisphere with the contralateral half of external space, the only configuration that places a processing center directly “behind” the region of the world it must monitor and act upon. Once hemispheric ownership of visual space is established, motor pathways must follow the same spatial logic. The sensorimotor decussations are therefore the downstream continuation of the same spatial imperative: the shortest, fastest, and most coherent route from a field-specific sensory representation to the effectors acting in that same field is a single midline crossing in the brainstem. A proof-by-exclusion analysis shows that alternative wiring schemes, including fully ipsilateral or reversed crossing patterns, disrupt binocular vision, slow rapid left–right motor responses, and generate visuomotor instabilities observed in clinical disorders of wiring. Comparative evidence across vertebrates, and contrasts with arthropods support the conclusion that neural decussation is an inevitable consequence of vision.

神经讨论，即感觉和运动通路在中线的系统交叉，是脊椎动物神经系统最显著的特征之一，但其功能原理仍未得到解决。这项工作提出了神经元讨论的视觉起源理论，该理论认为对侧组织的产生是视野光学几何的直接结果。来自右半视野的光线在到达颞视网膜之前穿过正中矢状面，而来自左半视野的光线也是相反方向。鼻视网膜纤维在视交叉中的讨论并没有产生这个交叉；它保留了预先存在的物理模式，从而使每个大脑半球与对侧的外部空间对齐，唯一的配置是将处理中心直接放置在它必须监控和行动的世界区域的“后面”。一旦大脑半球对视觉空间的所有权建立，运动通路必须遵循相同的空间逻辑。因此，感觉运动讨论是同一空间命令的下游延续：从特定领域的感觉表征到在同一领域中起作用的效应器的最短、最快和最连贯的路线是脑干中的一条中线交叉。一项排除性证明分析表明，包括完全同侧或反向交叉模式在内的其他连线方案会破坏双眼视觉，减缓快速的左右运动反应，并产生视觉运动不稳定，这在临床连线障碍中观察到。脊椎动物之间的比较证据，以及与节肢动物的对比，支持神经对话是视觉不可避免的结果的结论。

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引用次数: 0

Evolutionary computation for reconstructing threshold networks of the tryptophan operon in Escherichia coli 大肠杆菌色氨酸操纵子阈值网络重构的进化计算。

IF 1.9 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2025-12-18 DOI: 10.1016/j.biosystems.2025.105682

Gonzalo A. Ruz , Thomas Ledger , Matthew Macauley

A recent Boolean model of the tryptophan operon in Escherichia coli has been developed, aiming to capture the operon’s on/off states through a set of fixed points. However, when updated synchronously, the model also reveals the presence of unwanted spurious limit cycles, that have a larger basin of attraction. This study introduces an evolutionary computation framework to search for threshold network models that accurately portray the desired fixed points while eliminating occurrences of limit cycles. Employing both differential evolution and particle swarm optimization within the proposed framework, the latter emerges as the most efficient and effective method based on simulation results. Notably, networks were successfully identified for both continuous weight matrix values within the real interval

[- 1, 1]

and discrete values limited to

{- 1, 0, 1}

. The results confirm that the proposed evolutionary computation framework is capable of identifying threshold networks that accurately model the asymptotic behavior of the tryptophan operon in Escherichia coli.

最近开发了大肠杆菌色氨酸操纵子的布尔模型，旨在通过一组固定点捕获操纵子的开/关状态。然而，当同步更新时，该模型还揭示了不需要的虚假极限环的存在，这些极限环具有更大的吸引力。本研究引入了一种进化计算框架来搜索阈值网络模型，该模型准确地描绘了期望的不动点，同时消除了极限环的出现。在提出的框架内同时采用差分进化和粒子群优化，仿真结果表明，后者是最有效和最有效的方法。值得注意的是，对于实数区间[-1,1]内的连续权矩阵值和限制在{-1,0,1}内的离散值，我们都成功地识别了网络。结果证实，提出的进化计算框架能够识别阈值网络，准确地模拟大肠杆菌中色氨酸操纵子的渐近行为。

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引用次数: 0

Natural born intelligence manifesto: Illustrating the dynamic perspective for consciousness 天生智慧宣言：阐释意识的动态视角。

IF 1.9 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2025-12-16 DOI: 10.1016/j.biosystems.2025.105677

Yukio-Pegio Gunji

This study proposes a new operational framework for distinguishing Artificial Intelligence (AI) from Natural Born Intelligence (NBI) based on a two-layer structure of representational schemas. AI constructs mappings within a fixed input and representational space, characterized by optimization and generalization inside this closed structure. In contrast, NBI employs (1) the Co-Applicability of multiple concept-schemas (Level 1) and (2) the meta-level attenuation of their applicability conditions (Level 2) to non-monotonically transform the representational space itself. This transformation enables the emergence of new interpretive domains outside the original categories, which are closely related to creativity and phenomenal consciousness. The proposed framework provides a formal foundation for differentiating AI from human creative intelligence.

本研究提出了一种基于表征模式的双层结构来区分人工智能（AI）和自然出生智能（NBI）的新操作框架。人工智能在一个固定的输入和表征空间内构建映射，在这个封闭的结构内以优化和泛化为特征。相比之下，NBI采用(1)多个概念模式的共同适用性（Level 1）和(2)其适用性条件的元水平衰减（Level 2）对表征空间本身进行非单调变换。这种转变使得在原有范畴之外出现了新的解释领域，这些解释领域与创造力和现象意识密切相关。提出的框架为区分人工智能和人类创造性智能提供了正式的基础。

引用次数: 0

Turing instability on multiplex simplicial epidemic networks with cross-diffusion and behavioral delay 具有交叉扩散和行为延迟的多重简单流行病网络的图灵不稳定性。

IF 1.9 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2025-12-16 DOI: 10.1016/j.biosystems.2025.105679

Yue Liu, Jianwei Shen

Modern epidemics are characterized by the emergence of spatial hotspots and periodic outbreaks. This paper reveals that such complex spatiotemporal patterns are driven by a combination of many-body transmission pathways and delayed behavioral responses. We propose a reaction–diffusion epidemic model defined on a multiplex simplicial complex and introduce the behavioral response delay. Through linear stability analysis, we derive the conditions for Turing instability and delay-induced Hopf bifurcation. The analysis reveals that higher-order topological structures and cross-diffusion expand the instability domain and promote the formation of spatial patterns. The higher-order aggregation of susceptible individuals is a key factor in triggering Turing instability, while the higher-order structure of the infected layer primarily modulates its extent. Furthermore, the behavioral response delay acts as a bifurcation parameter, inducing temporal oscillations when it exceeds a critical threshold. Numerical simulations corroborate our theoretical findings, reproducing clustered and periodic oscillation phenomena analogous to those observed during the COVID-19 pandemic. Our results provide the policy implication that dispersing higher-order susceptible clusters and reducing response delays can mitigate spatial heterogeneity and recurrent outbreaks. This work deepens the understanding of epidemic dynamics by elucidating how network topology and human behavior jointly shape complex contagion patterns.

现代流行病的特点是出现空间热点和周期性爆发。这种复杂的时空模式是由多体传递途径和延迟行为反应共同驱动的。我们提出了一个定义在多重简单复合体上的反应-扩散流行病模型，并引入了行为反应延迟。通过线性稳定性分析，导出了图灵不稳定性和时滞诱导Hopf分岔的条件。分析表明，高阶拓扑结构和交叉扩散扩大了不稳定域，促进了空间格局的形成。易感个体的高阶聚集是触发图灵不稳定的关键因素，而感染层的高阶结构主要调节其程度。此外，行为反应延迟作为一个分岔参数，当它超过一个临界阈值时，会引起时间振荡。数值模拟证实了我们的理论发现，再现了类似于COVID-19大流行期间观察到的聚集性和周期性振荡现象。我们的研究结果提供了政策启示，即分散高阶易感集群和减少响应延迟可以减轻空间异质性和复发性爆发。这项工作通过阐明网络拓扑和人类行为如何共同塑造复杂的传染模式，加深了对流行病动力学的理解。

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引用次数: 0

A Unified Holographic Framework for neural computation and consciousness: From lipid membranes to the Schumann resonance 神经计算和意识的统一全息框架：从脂质膜到舒曼共振。

IF 1.9 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2025-12-15 DOI: 10.1016/j.biosystems.2025.105669

Marco Cavaglià, Jack A. Tuszynski

Understanding conscious experience requires looking beyond neuronal circuits alone. We propose that lipid membranes, vicinal water, and cerebrospinal fluid (CSF) form a coherent substrate capable of holographic encoding and coupling to endogenous/exogenous electromagnetic fields (EMF). In what follows: (i) we formulate four postulates (membrane as holographic plate; water as coherence medium; holographic read–write; environmental coupling), (ii) we present a dual-layer model (membrane–water–CSF ↔ EMF) and a one-panel graphical overview, (iii) we integrate the framework with existing theories, and (iv) we outline falsifiable experimental strategies and metrics.

理解意识经验需要超越神经回路。我们提出脂质膜、附近的水和脑脊液（CSF）形成一个连贯的底物，能够全息编码和耦合内源性/外源性电磁场（EMF）。在以下内容中：(i)我们制定了四个假设（膜作为全息板；水作为相干介质；全息读写；环境耦合），（ii）我们提出了一个双层模型（膜-水- csf↔EMF）和一个单面板图形概述，（iii）我们将框架与现有理论相结合，（iv）我们概述了可证伪的实验策略和指标。

引用次数: 0

Morphospace engineering: Morphological computation in scaffold design 形态空间工程：支架设计中的形态计算。

IF 1.9 4区生物学 Q2 BIOLOGY

Biosystems

Pub Date : 2025-12-12 DOI: 10.1016/j.biosystems.2025.105676

C. Galli , M.T. Colangelo , M. Meleti , S. Guizzardi

Scaffold geometry does more than support tissue—it encodes the rules by which matter organizes into function. Morphology operates as a generative constraint, transforming physical configuration into causal instruction. From molecular folding to cellular migration, form computes what matter can become. This work formalizes that principle across scales: using cellular automata as minimal models of morphogenesis and extending the same logic to scaffold design for tissue regeneration. Each scaffold can be described as a point in a high-dimensional morphospace whose axes—curvature, porosity, stiffness, fiber orientation—act as local update rules guiding cell behavior. Within this space, a viability kernel delineates the geometries that sustain growth and differentiation. By treating geometry as computation, bioengineering shifts from designing materials that contain life to shaping forms that generate it—a shape-first paradigm where the causal arrow runs from form to function.

支架的几何结构不仅仅是支撑组织，它还编码了物质组织成功能的规则。形态学作为一种生成约束，将物理结构转化为因果指令。从分子折叠到细胞迁移，形态决定了物质可以变成什么。这项工作跨尺度形式化了这一原则：使用细胞自动机作为形态发生的最小模型，并将相同的逻辑扩展到组织再生的支架设计中。每个支架可以被描述为高维形态空间中的一个点，其轴-曲率，孔隙率，刚度，纤维方向-作为指导细胞行为的局部更新规则。在这个空间内，生存能力内核描绘了维持增长和分化的几何形状。通过将几何视为计算，生物工程从设计包含生命的材料转变为塑造产生生命的形式——形状优先的范式，其中因果箭头从形式到功能。

引用次数: 0