Journal of The Royal Society Interface最新文献_第5页

Time-varying reproduction number estimation: fusing compartmental models with generalized additive models.

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-01-01 Epub Date: 2025-01-29 DOI: 10.1098/rsif.2024.0518

Xiaoxi Pang, Yang Han, Elise Tressier, Nurin Abdul Aziz, Lorenzo Pellis, Thomas House, Ian Hall

{"title":"Time-varying reproduction number estimation: fusing compartmental models with generalized additive models.","authors":"Xiaoxi Pang, Yang Han, Elise Tressier, Nurin Abdul Aziz, Lorenzo Pellis, Thomas House, Ian Hall","doi":"10.1098/rsif.2024.0518","DOIUrl":"10.1098/rsif.2024.0518","url":null,"abstract":"The reproduction number, the mean number of secondary cases infected by each primary case, gives an indication of the effort required to control the disease. Beyond the well-known basic reproduction number, there are two natural extensions, namely the control and effective reproduction numbers. As behaviour, population immunity and viral characteristics can change with time, these reproduction numbers can vary over time. Real-world data can be complex, so in this work we consider a generalized additive model to smooth surveillance data through the explicit incorporation of day-of-the-week effects, to provide a simple measure of the time-varying growth rate associated with the data. Converting the resulting spline into an estimator for both the control and effective reproduction numbers requires assumptions on a model structure, which we here assume to be a compartmental model. The reproduction numbers calculated are based on both simulated and real-world data, and are compared with estimates from an already existing tool. The derived method for estimating the time-varying reproduction number is effective, efficient and comparable with other methods. It provides a useful alternative approach, which can be included as part of a toolbox of models, that is particularly apt at smoothing out day-of-the-week effects in surveillance.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 222","pages":"20240518"},"PeriodicalIF":3.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11776018/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143059433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A minimal model of cognition based on oscillatory and current-based reinforcement processes. 基于振荡和电流强化过程的最小认知模型。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-01-01 Epub Date: 2025-01-22 DOI: 10.1098/rsif.2024.0402

Linnéa Gyllingberg, Yu Tian, David J T Sumpter

{"title":"A minimal model of cognition based on oscillatory and current-based reinforcement processes.","authors":"Linnéa Gyllingberg, Yu Tian, David J T Sumpter","doi":"10.1098/rsif.2024.0402","DOIUrl":"10.1098/rsif.2024.0402","url":null,"abstract":"Building mathematical models of brains is difficult because of the sheer complexity of the problem. One potential starting point is basal cognition, which gives an abstract representation of a range of organisms without central nervous systems, including fungi, slime moulds and bacteria. We propose one such model, demonstrating how a combination of oscillatory and current-based reinforcement processes can be used to couple resources in an efficient manner, mimicking the way these organisms function. A key ingredient in our model, not found in previous basal cognition models, is that we explicitly model oscillations in the number of particles (i.e. the nutrients, chemical signals or similar, which make up the biological system) and the flow of these particles within the modelled organisms. Using this approach, our model builds efficient solutions, provided the environmental oscillations are sufficiently out of phase. We further demonstrate that amplitude differences can promote efficient solutions and that the system is robust to frequency differences. In the context of these findings, we discuss connections between our model and basal cognition in biological systems and slime moulds, in particular, how oscillations might contribute to self-organized problem-solving by these organisms.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 222","pages":"rsif20240402"},"PeriodicalIF":3.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11750385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143007762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Tissue stresses caused by invasive tumour: a biomechanical model. 侵袭性肿瘤引起的组织应力：生物力学模型。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-01-01 Epub Date: 2025-01-22 DOI: 10.1098/rsif.2024.0797

Shi-Lei Xue

引用次数: 0

Capacity and limitations of microfluidic flow to increase solute transport in three-dimensional cell cultures.

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-01-01 Epub Date: 2025-01-29 DOI: 10.1098/rsif.2024.0463

Willy V Bonneuil, Neeraj Katiyar, Maria Tenje, Shervin Bagheri

{"title":"Capacity and limitations of microfluidic flow to increase solute transport in three-dimensional cell cultures.","authors":"Willy V Bonneuil, Neeraj Katiyar, Maria Tenje, Shervin Bagheri","doi":"10.1098/rsif.2024.0463","DOIUrl":"10.1098/rsif.2024.0463","url":null,"abstract":"Culturing living cells in three-dimensional environments increases the biological relevance of laboratory experiments, but requires solutes to overcome a diffusion barrier to reach the centre of cellular constructs. We present a theoretical and numerical investigation that brings a mechanistic understanding of how microfluidic culture conditions, including chamber size, inlet fluid velocity and spatial confinement, affect solute distribution within three-dimensional cellular constructs. Contact with the chamber substrate reduces the maximally achievable construct radius by 15%. In practice, finite diffusion and convection kinetics in the microfluidic chamber further lower that limit. The benefits of external convection are greater if transport rates across diffusion-dominated areas are high. Those are omnipresent and include the diffusive boundary layer growing from the fluid-construct interface and regions near corners where fluid is recirculating. Such regions multiply the required convection to achieve a given solute penetration by up to 100, so chip designs ought to minimize them. Our results define conditions where complete solute transport into an avascular three-dimensional cell construct is achievable and applies to real chambers without needing to simulate their exact geometries.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 222","pages":"20240463"},"PeriodicalIF":3.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774591/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143059242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Feed-forward loop improves the transient dynamics of an antithetic biological controller. 前馈回路改善了仿生生物控制器的瞬态动力学特性。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-01-01 Epub Date: 2025-01-22 DOI: 10.1098/rsif.2024.0467

Thales R Spartalis, Mathias Foo, Xun Tang

{"title":"Feed-forward loop improves the transient dynamics of an antithetic biological controller.","authors":"Thales R Spartalis, Mathias Foo, Xun Tang","doi":"10.1098/rsif.2024.0467","DOIUrl":"10.1098/rsif.2024.0467","url":null,"abstract":"Integral controller is widely used in industry for its capability of endowing perfect adaptation to disturbances. To harness such capability for precise gene expression regulation, synthetic biologists have endeavoured in building biomolecular (quasi-)integral controllers, such as the antithetic integral controller. Despite demonstrated successes, challenges remain with designing the controller for improved transient dynamics and adaptation. Here, we explore and investigate the design principles of alternative RNA-based biological controllers, by modifying an antithetic integral controller with prevalently found natural feed-forward loops (FFL), to improve its transient dynamics and adaptation performance. With model-based analysis, we demonstrate that while the base antithetic controller shows excellent responsiveness and adaptation to system disturbances, incorporating the type-1 incoherent FFL into the base antithetic controller could attenuate the transient dynamics caused by changes in the stimuli, especially in mitigating the undesired overshoot in the output gene expression. Further analysis on the kinetic parameters reveals similar findings to previous studies that the degradation and transcription rates of the circuit RNA species would dominate in shaping the performance of the controllers.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 222","pages":"20240467"},"PeriodicalIF":3.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11750367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143007765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Skin adaptation in lower limb amputees assessed through Raman spectroscopy and mechanical characterization. 通过拉曼光谱和力学表征评估下肢截肢者的皮肤适应性。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-01-01 Epub Date: 2025-01-08 DOI: 10.1098/rsif.2024.0475

Jack Hayes, Jennifer Andrews, Omar Abdelwahab, Tomas Andriuskevicius, Tom Briggs, Ralph Gordon, Peter Worsley, Claire A Higgins, Marc Masen

{"title":"Skin adaptation in lower limb amputees assessed through Raman spectroscopy and mechanical characterization.","authors":"Jack Hayes, Jennifer Andrews, Omar Abdelwahab, Tomas Andriuskevicius, Tom Briggs, Ralph Gordon, Peter Worsley, Claire A Higgins, Marc Masen","doi":"10.1098/rsif.2024.0475","DOIUrl":"https://doi.org/10.1098/rsif.2024.0475","url":null,"abstract":"Following lower limb amputation residuum skin from the lower leg is used to reconstruct the residual limb. Unlike skin on the sole of the foot (plantar skin), leg skin is not inherently load bearing. Despite this, leg skin is required to be load bearing in the prosthetic socket. Current hypotheses propose that lower limb amputee skin can adapt to become load bearing with repeated prosthesis use. Here, we show using confocal Raman spectroscopy, mechanical characterization and cytokine analysis that adaptations occur which actually result in impaired barrier function, higher baseline inflammation, increased coefficient of friction and reduced stiffness. Our results demonstrate that repeated frictional trauma does not confer beneficial adaptations in amputee skin. We hypothesize that non-plantar skin lacks the biological capabilities to respond positively to repeated mechanical trauma in the same manner observed in plantar skin. This finding highlights the need for improved therapies as opposed to current mechanical conditioning or product solutions that directly relate to improving load-bearing capacity on the skin of lower limb amputees. This study also highlights the importance of measuring multiple parameters of application-specific skin at different scales for skin tribology applications.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 222","pages":"20240475"},"PeriodicalIF":3.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11706637/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142950745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

State-space modelling using wastewater virus and epidemiological data to estimate reported COVID-19 cases and the potential infection numbers. 利用废水病毒和流行病学数据进行状态空间建模，以估计报告的COVID-19病例和潜在感染人数。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-01-01 Epub Date: 2025-01-08 DOI: 10.1098/rsif.2024.0456

Syun-Suke Kadoya, Yubing Li, Yilei Wang, Hiroyuki Katayama, Daisuke Sano

{"title":"State-space modelling using wastewater virus and epidemiological data to estimate reported COVID-19 cases and the potential infection numbers.","authors":"Syun-Suke Kadoya, Yubing Li, Yilei Wang, Hiroyuki Katayama, Daisuke Sano","doi":"10.1098/rsif.2024.0456","DOIUrl":"https://doi.org/10.1098/rsif.2024.0456","url":null,"abstract":"The current situation of COVID-19 measures makes it difficult to accurately assess the prevalence of SARS-CoV-2 due to a decrease in reporting rates, leading to missed initial transmission events and subsequent outbreaks. There is growing recognition that wastewater virus data assist in estimating potential infections, including asymptomatic and unreported infections. Understanding the COVID-19 situation hidden behind the reported cases is critical for decision-making when choosing appropriate social intervention measures. However, current models implicitly assume homogeneity in human behaviour, such as virus shedding patterns within the population, making it challenging to predict the emergence of new variants due to variant-specific transmission or shedding parameters. This can result in predictions with considerable uncertainty. In this study, we established a state-space model based on wastewater viral load to predict both reported cases and potential infection numbers. Our model using wastewater virus data showed high goodness-of-fit to COVID-19 case numbers despite the dataset including waves of two distinct variants. Furthermore, the model successfully provided estimates of potential infection, reflecting the superspreading nature of SARS-CoV-2 transmission. This study supports the notion that wastewater surveillance and state-space modelling have the potential to effectively predict both reported cases and potential infections.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 222","pages":"20240456"},"PeriodicalIF":3.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11706650/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142950746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Can spatial self-organization inhibit evolutionary adaptation?

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-01-01 Epub Date: 2025-01-29 DOI: 10.1098/rsif.2024.0454

B K Bera, O Tzuk, J J R Bennett, U Dieckmann, E Meron

{"title":"Can spatial self-organization inhibit evolutionary adaptation?","authors":"B K Bera, O Tzuk, J J R Bennett, U Dieckmann, E Meron","doi":"10.1098/rsif.2024.0454","DOIUrl":"10.1098/rsif.2024.0454","url":null,"abstract":"Plants often respond to drier climates by slow evolutionary adaptations from fast-growing to stress-tolerant species. These evolutionary adaptations increase the plants' resilience to droughts but involve productivity losses that bear on agriculture and food security. Plants also respond by spatial self-organization, through fast vegetation patterning involving differential plant mortality and increased water availability to the surviving plants. The manners in which these two response forms intermingle and affect productivity and resilience have not been studied. Here we ask: can spatial patterning inhibit undesired evolutionary adaptation without compromising ecosystem resilience? To address this question, we integrate adaptive dynamics and vegetation pattern-formation theories and show that vegetation patterning can inhibit evolutionary adaptations to less productive, more stress-tolerant species over a wide precipitation range while increasing their resilience to water stress. This evolutionary homeostasis results from the high spatial plasticity of vegetation patterns, associated with patch thinning and patch dilution, which maintains steady local water availability despite decreasing precipitation. Spatial heterogeneity expedites the onset of vegetation patterning and induces evolutionary homeostasis at an earlier stage of evolutionary adaptation, thereby mitigating the productivity loss that occurs while the vegetation remains spatially uniform. We conclude by discussing our results in a broader context of evolutionary retardation.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 222","pages":"20240454"},"PeriodicalIF":3.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774593/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143059223","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Quantifying the configurational complexity of biological systems in multivariate 'complexity space'.

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-01-01 Epub Date: 2025-01-29 DOI: 10.1098/rsif.2024.0558

Tim Rock, Matthew A Wills

{"title":"Quantifying the configurational complexity of biological systems in multivariate 'complexity space'.","authors":"Tim Rock, Matthew A Wills","doi":"10.1098/rsif.2024.0558","DOIUrl":"10.1098/rsif.2024.0558","url":null,"abstract":"An increasing number of evolutionary studies seek to quantify the morphological complexity of organisms, particularly those comprising serially homologous elements at different hierarchical levels of organization. Numerous operational frameworks have been proposed for doing this, but most focus on one or multiple conflated aspects of what is really a multidimensional concept. Here, we advocate the use of 'complexity spaces': multidimensional spaces defined by different vectors of complexity. We explore their application to biological systems composed of homologous parts and identify three axes on which those systems differ: part number, part differentiation and the regularity of that differentiation. Such complexity spaces can be constructed for systems at different hierarchical levels of biological organization. To illustrate this, we explore the complexity spaces for trilobite body plans (comprising body segments of varying number and form), and for ant colonies (comprising differentiated worker polymorphisms of varying number and form within a 'superorganism'). Many different complexity spaces are possible, but all seek to distinguish different aspects of complexity within an information-theoretic framework, and thereby to clarify patterns of complexity evolution.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 222","pages":"20240558"},"PeriodicalIF":3.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774595/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143059425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cooperative bots exhibit nuanced effects on cooperation across strategic frameworks.

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-01-01 Epub Date: 2025-01-29 DOI: 10.1098/rsif.2024.0427

Zehua Si, Zhixue He, Chen Shen, Jun Tanimoto

{"title":"Cooperative bots exhibit nuanced effects on cooperation across strategic frameworks.","authors":"Zehua Si, Zhixue He, Chen Shen, Jun Tanimoto","doi":"10.1098/rsif.2024.0427","DOIUrl":"10.1098/rsif.2024.0427","url":null,"abstract":"The positive impact of cooperative bots on cooperation within evolutionary game theory is well-documented. However, prior studies predominantly use discrete strategic frameworks with deterministic actions. This article explores continuous and mixed strategic approaches. Continuous strategies use intermediate probabilities for varying degrees of cooperation and focus on expected payoffs, while mixed strategies calculate immediate payoffs from actions taken within these probabilities. Using the prisoner's dilemma game, this study examines the effects of cooperative bots on human cooperation in both well-mixed and structured populations across these strategic approaches. Our findings reveal that cooperative bots significantly enhance cooperation in both population types under weak imitation scenarios, where players are less concerned with material gains. Conversely, under strong imitation scenarios, cooperative bots do not alter the defective equilibrium in well-mixed populations but have varied impacts in structured populations. Specifically, they disrupt cooperation under discrete and continuous strategies but facilitate it under mixed strategies. These results highlight the nuanced effects of cooperative bots within different strategic frameworks and underscore the need for careful deployment, as their effectiveness is highly sensitive to how humans update their actions and their chosen strategic approach.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 222","pages":"20240427"},"PeriodicalIF":3.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11775664/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143059244","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0