Journal of The Royal Society Interface最新文献_第10页

Optimal control for anti-abeta treatment in Alzheimer's disease using a reaction-diffusion model. 反应-扩散模型用于阿尔茨海默病抗-治疗的最优控制。

IF 3.4 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2026-07-08 DOI: 10.1098/rsif.2025.1158

Sun Lee, Chiu-Yen Kao, Zhiyuan Li, Tingting Dan, Guorong Wu, Wenrui Hao

{"title":"Optimal control for anti-abeta treatment in Alzheimer's disease using a reaction-diffusion model.","authors":"Sun Lee, Chiu-Yen Kao, Zhiyuan Li, Tingting Dan, Guorong Wu, Wenrui Hao","doi":"10.1098/rsif.2025.1158","DOIUrl":"10.1098/rsif.2025.1158","url":null,"abstract":"Alzheimer's disease (AD) is a progressive neurodegenerative disorder that severely impairs survival and quality of life. While anti-amyloid beta (Aβ) therapies can slow disease progression, their efficacy depends on personalized dosing that maximizes benefits and minimizes risks, such as amyloid-related imaging abnormalities (ARIA). Mathematical modelling offers a powerful tool for understanding AD dynamics and optimizing treatment, yet most models focus solely on temporal behaviour, overlooking spatial heterogeneity within the brain. In this study, we propose a spatially explicit reaction-diffusion model to describe Aβ plaque dynamics. We formulate an optimal control problem to minimize plaque concentration while balancing therapeutic efficacy and treatment risk. Under reasonable assumptions, we establish well-posedness and uniqueness of the optimal solution. A finite element method (FEM)-based numerical framework is developed to compute personalized treatment strategies. Our model is calibrated using longitudinal Aβ positron emission tomography (PET) data from the Alzheimer's Disease Neuroimaging Initiative (ADNI), enabling estimation of patient-specific parameters, such as growth rate and effective diffusivity. Results show that optimized treatment strategies consistently outperform constant dosing regimens across patient groups, achieving substantial reductions in cumulative amyloid burden while minimizing side effects. This integrated, data-driven framework advances personalized, spatially informed therapeutic optimization for AD.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"23 240","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148405211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Methods for reproducible comparison of strategies in stochastic modelling. 随机建模中可重复比较策略的方法。

IF 3.4 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2026-07-08 DOI: 10.1098/rsif.2025.1081

Rob Sunnucks, Emma L Davis, Kat S Rock

{"title":"Methods for reproducible comparison of strategies in stochastic modelling.","authors":"Rob Sunnucks, Emma L Davis, Kat S Rock","doi":"10.1098/rsif.2025.1081","DOIUrl":"10.1098/rsif.2025.1081","url":null,"abstract":"Stochastic simulations are often used to model real-world phenomena such as infectious disease dynamics. In this modelling, differing strategies are often compared to one another by comparing the model outputs of each strategy. Hash-based matching, pseudo-random number generation is an approach for stochastic simulations that was implemented by Pearson and Abbott in the hashprng package to overcome challenges with comparing model simulations in a way that considers the dependency between model outputs. We demonstrate how methods based on this approach grant considerable benefit when comparing different strategies, and show when each of our three proposed methods ought to be used. We illustrate our methods with two epidemiological models: one simple model of a vaccine-preventable infection and one complex model of African sleeping sickness, which can be controlled through multiple interventions. We show how our Bernoulli hashing method works very well for simple models, and a variation of it can be used for more complex models in certain cases. Additionally, we discuss the properties of our methods for considering counterfactual scenarios and note that, compared to other attempts to obtain perfect counterfactuals, they demonstrate advantages in computational efficiency and their application to a wider variety of models.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"23 240","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148405084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Determining social mechanisms for sequential decision-making in a virtual pedestrian route choice experiment. 在虚拟行人路径选择实验中确定顺序决策的社会机制。

IF 3.4 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2026-07-08 DOI: 10.1098/rsif.2025.1214

Anna Sigalou, Yunhe Tong, Charlie Pilgrim, Richard P Mann, Nikolai W F Bode

{"title":"Determining social mechanisms for sequential decision-making in a virtual pedestrian route choice experiment.","authors":"Anna Sigalou, Yunhe Tong, Charlie Pilgrim, Richard P Mann, Nikolai W F Bode","doi":"10.1098/rsif.2025.1214","DOIUrl":"10.1098/rsif.2025.1214","url":null,"abstract":"Moving groups are routinely faced with a choice of different routes as part of their daily lives, such as choosing between exits from a building. Differences in moving speeds and environmental constraints often lead to individuals being able to observe the choices of others ahead. This social information can inform their decision-making, but exactly how this is being used remains an open question. Previous theoretical studies on animal groups have demonstrated that simple heuristics are plausible and accurate mechanisms, and some have further predicted that more recent decisions are more heavily weighted. Experiments with fish corroborate the importance of more recent decisions; however, experimental work is limited. Here, we conduct an online survey with human participants to identify which social decision-making mechanism individuals follow. Contrary to previous experimental work, we find little indication that recent decisions are weighted more heavily; instead, our results suggest that following the majority of previous decisions is the dominant behaviour. Furthermore, self-reported decision-making mechanisms correlate with our experimental findings despite their variability, suggesting that, on average, individuals can recognize their behavioural tendencies. Our findings provide insight into social sequential decision-making and an empirical foundation for integrating realistic social decision mechanisms into pedestrian movement models.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"23 240","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148405117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Agentic AI integrated with scientific knowledge: laboratory validation in systems biology. 集成科学知识的人工智能：系统生物学的实验室验证。

IF 3.4 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2026-07-08 DOI: 10.1098/rsif.2026.0043

Daniel Brunnsåker, Alexander Howard Gower, Prajakta Naval, Erik Yuusuke Bjurström, Filip Kronström, Ievgeniia Tiukova, Ross King

{"title":"Agentic AI integrated with scientific knowledge: laboratory validation in systems biology.","authors":"Daniel Brunnsåker, Alexander Howard Gower, Prajakta Naval, Erik Yuusuke Bjurström, Filip Kronström, Ievgeniia Tiukova, Ross King","doi":"10.1098/rsif.2026.0043","DOIUrl":"10.1098/rsif.2026.0043","url":null,"abstract":"Automation is transforming scientific discovery by enabling systematic exploration of complex hypotheses. Large language models (LLMs) perform well across diverse tasks and promise to accelerate research, but often struggle with logical structures. Here, we present a framework for biological discovery integrating LLM-based agents with laboratory automation, guided by logical scaffolds incorporating symbolic relational learning, structured vocabularies and experimental constraints. This integration improves coherence and reliability in automated workflows. We couple this AI-driven approach to automated cell-culture and metabolomics platforms, enabling integrated hypothesis validation and refinement, yielding a flexible discovery system. The system identified novel interactions in Saccharomyces cerevisiae, including glutamate-induced growth inhibition in spermine-treated cells and aminoadipate's partial rescue of formic-acid stress. All hypotheses, experiments and data are captured in a graph database employing controlled vocabularies. Existing ontologies are extended, and a novel representation of scientific hypotheses is presented using description logics. This work demonstrates the potential for a reliable machine-driven discovery process in systems biology.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"23 240","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148405177","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Collective ant transport outperforms gravity-based solvers on complex puzzles. 在复杂的谜题中，蚂蚁集体运输的表现优于基于重力的解决方案。

IF 3.4 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2026-07-08 DOI: 10.1098/rsif.2025.0989

Tabea Dreyer, Ehud Fonio, Ofer Feinerman

{"title":"Collective ant transport outperforms gravity-based solvers on complex puzzles.","authors":"Tabea Dreyer, Ehud Fonio, Ofer Feinerman","doi":"10.1098/rsif.2025.0989","DOIUrl":"10.1098/rsif.2025.0989","url":null,"abstract":"Collective cognition, in which groups display enhanced problem-solving abilities compared with individuals, is a hallmark of ant behaviour. For instance, in navigation tasks, such as the piano movers' problem, a short-term memory-like directional persistence emerges in large enough ant groups and aids them in implementing an effective wall-following heuristic. Here, we investigate the collective problem-solving abilities of Paratrechina longicornis by presenting groups of varying sizes with an array of piano movers' puzzles. We find that increasingly complex puzzles reveal performance differences between small and large groups. To benchmark these results, we compare the performance of the ants to a simulated physics-based null model incorporating gravity and noise. Although the null model performs comparably with ants in simple puzzles, it fails in more challenging ones. Introducing ant-inspired mechanisms, including attachment along edges or transient leadership, enables the simulated solver to match ant performance across group sizes and tasks. Beyond these features, we show that ants solve a broad spectrum of puzzles without prior knowledge of geometry, whereas the simulated solver requires parameter adjustments tailored to each puzzle. Our findings highlight the flexibility and robustness of collective cognition in ant groups and provide a framework for integrating biological strategies into artificial problem-solving systems.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"23 240","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148405159","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Distinct geometrical landscapes distinguish between modes of tristability in gene regulatory networks. 不同的几何景观区分了基因调控网络的三稳定性模式。

IF 3.4 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2026-07-01 DOI: 10.1098/rsif.2025.1065

Atchuta Srinivas Duddu, Pradyumna Harlapur, Mohit Kumar Jolly, Archishman Raju

{"title":"Distinct geometrical landscapes distinguish between modes of tristability in gene regulatory networks.","authors":"Atchuta Srinivas Duddu, Pradyumna Harlapur, Mohit Kumar Jolly, Archishman Raju","doi":"10.1098/rsif.2025.1065","DOIUrl":"10.1098/rsif.2025.1065","url":null,"abstract":"Geometrical models have recently been used to construct landscapes for cell-fate decisions inferred directly from experimental data. However, such quantitative cell-fate data are available for only a few systems; instead, gene regulatory network dynamics have been studied across a broader set of biological decision-making scenarios. Thus, connecting the geometry of cell-fate decisions to their underlying regulatory networks remains an open question. Recently, two regulatory networks have been shown to exhibit tristability-a toggle switch with self-activation and a toggle triad. Here, we show that these two motifs are distinct from a geometrical point of view, and identify two bifurcations in their behaviour: the standard cusp and the elliptic umbilic. We study experimentally accessible signatures of the differences in tristability between the two motifs. We also show how the standard cusp can be used to quantitatively model cell-fate transition data for the epithelial to mesenchymal transition on TGF-β induction in the context of cancer cells. Our work uncovers geometrical signatures of gene regulatory motifs and demonstrates how different gene regulatory networks can encode tristability in dynamically distinct ways.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"23 240","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148361396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Slow modulation of the contraction patterns in Physarum polycephalum. 多头绒泡菌收缩模式的缓慢调节。

IF 3.4 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2026-07-01 DOI: 10.1098/rsif.2025.0971

Raphael Saiseau, Valentin Busson, Marc Durand

{"title":"Slow modulation of the contraction patterns in Physarum polycephalum.","authors":"Raphael Saiseau, Valentin Busson, Marc Durand","doi":"10.1098/rsif.2025.0971","DOIUrl":"10.1098/rsif.2025.0971","url":null,"abstract":"The slime mould Physarum polycephalum has emerged as a model system for self-organization and coordination of contractile activity at large spatial scales. This organization results from cytoplasmic flows generated by propagating contractile waves of the actomyosin cortex. In addition to these relatively fast travelling waves, slower modulations of contractile activity occur on timescales much longer than the primary oscillation period, yet remain poorly characterized. Here, we investigate these slow modulations by confining organisms inside annular geometries, and quantifying contractile activity across the organism over long recordings. We reveal correlations between contractile wave direction, amplitude modulation and slow variations of the mean vein diameter. Using an automatic Fourier-based classification, we identify three families of slow modulation modes: fundamental rotating modes, higher order modes and standing modes. Fundamental rotating modes dominate and exhibit periods compatible with linear scaling with system size. Remarkably, measured periods cluster near integer multiples of an intrinsic modulation timescale obtained independently from statistical analysis. These observations are consistent with a transport-mediated scenario in which a slowly advected regulator biases local excitability and mechanical properties, coordinating activity across the organism on long timescales.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"23 240","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148361503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Individual detachment-reintegration events in homing pigeon flocks and the dominance of directional adjustment in their kinematic features. 信鸽群中的个体分离-重新融合事件及其运动学特征中方向调整的优势。

IF 3.4 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2026-07-01 DOI: 10.1098/rsif.2026.0296

Yinggang Huang, Mengmeng Li, Zhigang Shang, Lifang Yang

{"title":"Individual detachment-reintegration events in homing pigeon flocks and the dominance of directional adjustment in their kinematic features.","authors":"Yinggang Huang, Mengmeng Li, Zhigang Shang, Lifang Yang","doi":"10.1098/rsif.2026.0296","DOIUrl":"10.1098/rsif.2026.0296","url":null,"abstract":"Individual detachment-reintegration processes offer a useful window into brief non-steady reorganization in collective flight, but whether such events can be identified objectively across flight trials remains unclear. Using high-resolution three-dimensional trajectory data from homing pigeon flocks, we first tested whether nearest-neighbour distance distributions contained a separable second spatial scale. Only in trials that passed this test did we define a trial-specific event threshold and extract validated events using temporal continuity screening and reintegration-stability verification. Of four homing-flight trials, only two satisfied the separability criterion, yielding 17 validated events. Within these events, directional adjustment provided a more consistent kinematic signature than speed difference: median lateral steering ratios Rsteer were 0.674 and 0.715, and median acceleration-direction deviation angles ∠aout were 93.27∘ and 90.15∘, whereas speed difference Δv showed no consistent unidirectional change across trials. Comparisons with matched non-event baselines and robustness analyses further indicated that event specificity was expressed primarily as enhanced directional adjustment.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"23 240","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148361444","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The aerial combat strategy of dragonflies. 蜻蜓的空战策略。

IF 3.4 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2026-07-01 DOI: 10.1098/rsif.2026.0131

Samuel T Fabian, Alexandra M Yarger, Szu-Lung Chen, Huai-Ti Lin

引用次数: 0

RNA-ligand complexes and the attenuation of neutral confinement in the evolution of RNA secondary structures. RNA-配体复合物与中性约束在RNA二级结构演化中的衰减。

IF 3.4 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2026-07-01 DOI: 10.1098/rsif.2026.0102

Antonio Loreto, Edgardo Ugalde, Carlos Espinosa-Soto

{"title":"RNA-ligand complexes and the attenuation of neutral confinement in the evolution of RNA secondary structures.","authors":"Antonio Loreto, Edgardo Ugalde, Carlos Espinosa-Soto","doi":"10.1098/rsif.2026.0102","DOIUrl":"10.1098/rsif.2026.0102","url":null,"abstract":"RNA molecules with identical nucleotide sequences can adopt different structures. Mutations can alter their properties; for example, some mutations increase the stability of a functionally relevant structure at the expense of other structures' stability. Interestingly, the structural diversity a sequence produces is correlated with the number of structures it can access upon mutation. Thus, enhancing a structure's stability can lead to neutral confinement, an evolutionary dead-end in which mutational access to novel structures is increasingly difficult. If the structure is critical to biological function, how do RNA molecules escape neutral confinement? We have developed a model in which an RNA molecule's function depends on binding to a ligand, and we applied it to study sequences that fold according to RNA biophysics, also simulating their evolution. Our analyses and simulations have identified effects that decrease the selective advantage of augmenting a structure's stability. By disfavouring the evolution of highly stable structures and favouring the accumulation of genetic variation, these effects hinder neutral confinement. The most important effect stems from the sequestration of high-affinity structures in RNA-ligand complexes and their replenishment through thermal fluctuations. In this perspective, a common scenario may help to explain how RNA evolution avoids coming to a halt.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"23 240","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148361513","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0