{"title":"Incorporating spatial diffusion into models of bursty stochastic transcription.","authors":"Christopher E Miles","doi":"10.1098/rsif.2024.0739","DOIUrl":"https://doi.org/10.1098/rsif.2024.0739","url":null,"abstract":"<p><p>The dynamics of gene expression are stochastic and spatial at the molecular scale, with messenger RNA (mRNA) transcribed at specific nuclear locations and then transported to the nuclear boundary for export. Consequently, the spatial distributions of these molecules encode their underlying dynamics. While mechanistic models for molecular counts have revealed numerous insights into gene expression, they have largely neglected now-available subcellular spatial resolution down to individual molecules. Owing to the technical challenges inherent in spatial stochastic processes, tools for studying these subcellular spatial patterns are still limited. Here, we introduce a spatial stochastic model of nuclear mRNA with two-state (telegraph) transcriptional dynamics. Observations of the model can be concisely described as following a spatial Cox process driven by a stochastically switching partial differential equation. We derive analytical solutions for spatial and demographic moments and validate them with simulations. We show that the distribution of mRNA counts can be accurately approximated by a Poisson-beta distribution with tractable parameters, even with complex spatial dynamics. This observation allows for efficient parameter inference demonstrated on synthetic data. Altogether, our work adds progress towards a new frontier of subcellular spatial resolution in inferring the dynamics of gene expression from static snapshot data.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20240739"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811607","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}
Devi Stuart-Fox, Katrina Joanne Rankin, Madeleine Shah Scott, Lu-Yi Wang, Amanda M Franklin
{"title":"Infrared camouflage in leaf-sitting frogs: a cautionary tale on adaptive convergence.","authors":"Devi Stuart-Fox, Katrina Joanne Rankin, Madeleine Shah Scott, Lu-Yi Wang, Amanda M Franklin","doi":"10.1098/rsif.2024.0771","DOIUrl":"https://doi.org/10.1098/rsif.2024.0771","url":null,"abstract":"<p><p>Many cryptic green animals match leaves in invisible near-infrared (NIR) wavelengths. This observation is an enduring puzzle because animals do not see NIR light, so NIR background matching is unlikely to contribute to visual camouflage. Two alternative explanations have been proposed-infrared camouflage (i.e. matching the temperature of the background) and thermoregulation-but neither hypothesis has been experimentally tested. To test these hypotheses, we developed bilayer coatings that mimicked the reflectivity of green leaf-sitting frogs with high NIR (HNIR) or low NIR (LNIR) reflectance. Under a solar simulator in the laboratory, agar model frogs with LNIR reflectance heated up more quickly and reached higher temperatures than those with HNIR reflectance. However, when placed in a tropical rainforest (natural habitat of leaf-sitting frogs), HNIR and LNIR models did not significantly differ in the similarity of surface temperature to the adjacent leaves or in core temperature, thus failing to support the infrared camouflage and thermoregulation hypotheses, respectively. The lack of difference between treatments is probably due to the limited exposure of frogs to direct solar radiation in their natural habitats. We propose an explanation for NIR background matching based on specific mechanisms underlying green coloration and translucence in frogs and caution against assuming adaptive convergence.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20240771"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811608","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}
{"title":"Indirect reciprocity in the public goods game with collective reputations.","authors":"Ming Wei, Xin Wang, Longzhao Liu, Hongwei Zheng, Yishen Jiang, Yajing Hao, Zhiming Zheng, Feng Fu, Shaoting Tang","doi":"10.1098/rsif.2024.0827","DOIUrl":"https://doi.org/10.1098/rsif.2024.0827","url":null,"abstract":"<p><p>Indirect reciprocity unveils how social cooperation is founded upon moral systems. Within the frame of dyadic games based on individual reputations, the 'leading-eight' strategies distinguish themselves in promoting and sustaining cooperation. However, in real-world societies, there are widespread interactions at the group level, where individuals need to make a singular action choice when facing multiple individuals with different reputations. Here, through introducing the assessment of collective reputations, we develop a framework that embeds group-level reputation structure into public goods games to study the evolution of group-level indirect reciprocity. We show that changing the criteria of group assessment destabilizes the reputation dynamics of leading-eight strategies. In a particular range of social assessment criteria, all leading-eight strategies can break the social dilemma in public goods games and sustain cooperation. Specifically, there exists an optimal, moderately set assessment criterion that is most conducive to promoting cooperation. Moreover, in the evolution of assessment criteria, the preference of the leading-eight strategies for social strictness is inversely correlated with the payoff level. Our work reveals the impact of social strictness on prosocial behaviour, highlighting the importance of group-level interactions in the analysis of evolutionary games and complex social dynamics.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20240827"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764426","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}
Florian Diekert, Daniel Heyen, Frikk Nesje, Soheil Shayegh
{"title":"Do early warning signals of tipping points lead to better decisions?","authors":"Florian Diekert, Daniel Heyen, Frikk Nesje, Soheil Shayegh","doi":"10.1098/rsif.2024.0864","DOIUrl":"https://doi.org/10.1098/rsif.2024.0864","url":null,"abstract":"<p><p>Abrupt changes in some complex socio-ecological systems can be anticipated by observing their behaviour under increasing stress before they cross a tipping point. Despite notable progress in identifying statistical indicators that can provide early warning signals (EWS) of tipping points, they have yet to find direct application in management. Here, we develop a theoretical model of an early warning system (EWSys) that integrates EWS information into a simple decision-making process. This model consists of a tipping indicator, whose value increases as the system approaches the tipping point, and a trigger value, beyond which a binary EWS is sent. We demonstrate that although EWSys can help balance the risk of tipping by providing information to update the belief about the location of the tipping point, it may also result in more risky behaviour in the case that no EWS is received. This leads to a tension between better information about the location of the tipping point and increased risk of crossing it. Our framework complements the emergence of resilience indicators of complex human-natural systems by providing a better understanding of how, when and why they can be used to improve decision making.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20240864"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811605","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}
Bjarke Frost Nielsen, Chadi M Saad-Roy, C Jessica E Metcalf, Cécile Viboud, Bryan T Grenfell
{"title":"Eco-evolutionary dynamics of pathogen immune-escape: deriving a population-level phylodynamic curve.","authors":"Bjarke Frost Nielsen, Chadi M Saad-Roy, C Jessica E Metcalf, Cécile Viboud, Bryan T Grenfell","doi":"10.1098/rsif.2024.0675","DOIUrl":"10.1098/rsif.2024.0675","url":null,"abstract":"<p><p>The phylodynamic curve (Grenfell <i>et al</i>. 2004 <i>Science</i> <b>303</b>, 327-332 (doi:10.1126/science.1090727)) conceptualizes how immunity shapes the rate of viral adaptation in a non-monotonic fashion, through its opposing effects on viral abundance and the strength of selection. However, concrete and quantitative model realizations of this influential concept are rare. Here, we present an analytic, stochastic framework in which a population-scale phylodynamic curve emerges dynamically, allowing us to address questions regarding the risk and timing of the emergence of viral immune escape variants. We explore how pathogen- and population-specific parameters such as strength of immunity, transmissibility, seasonality and antigenic constraints affect the emergence risk. For pathogens exhibiting pronounced seasonality, we find that the timing of likely immune-escape variant emergence depends on the level of case importation between regions. Motivated by the COVID-19 pandemic, we probe the likely effects of non-pharmaceutical interventions (NPIs), and the lifting thereof, on the risk of viral escape variant emergence. Looking ahead, the framework has the potential to become a useful tool for probing how natural immunity, as well as choices in vaccine design and distribution and the implementation of NPIs, affect the evolution of common viral pathogens.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20240675"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11963905/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764422","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}
{"title":"Unlocking the secrets of scenic beauty: a quantitative analysis of object variety and connections in scenic images.","authors":"Junjun Yin, Guangqing Chi, Bin Jiang","doi":"10.1098/rsif.2025.0045","DOIUrl":"10.1098/rsif.2025.0045","url":null,"abstract":"<p><p>The perception of beauty, though often subjective, is influenced by identifiable structural and spatial patterns that shape how individuals experience their surroundings. This study explores the roles of object variety and connections in scenic images in shaping perceptions of environmental aesthetics, using advanced computer vision techniques and regression analysis. Drawing on data from the Scenic-Or-Not project and leveraging the Segment Anything Model, we analysed landscape photographs to understand how object diversity and spatial arrangement affect aesthetic judgments. Our findings reveal a positive correlation between object diversity and perceived scenicness, emphasizing the importance of visual richness and complexity in enhancing scenic appeal. However, excessive object diversity can introduce visual clutter and diminish aesthetic value. Our analysis of object connections, measured through graph-based metrics like network density and clustering coefficient, reveals that denser and more interconnected arrangements enhance scenic appeal, while overly efficient local connections reduce visual interest. These results demonstrate the importance of balancing complexity, coherence and interconnectedness in scenic design. By situating these findings within established theoretical frameworks, this study provides insights for disciplines such as environmental science, urban planning and landscape management, offering guidance for creating environments that evoke positive aesthetic experiences while maintaining visual harmony and interest.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20250045"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11961261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764466","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}
{"title":"Mutual benefits of social learning and algorithmic mediation for cumulative culture.","authors":"Agnieszka Czaplicka, Fabian Baumann, Iyad Rahwan","doi":"10.1098/rsif.2024.0686","DOIUrl":"https://doi.org/10.1098/rsif.2024.0686","url":null,"abstract":"<p><p>The remarkable ecological success of humans is often attributed to our ability to develop complex cultural artefacts that enable us to cope with environmental challenges. The evolution of complex culture (cumulative cultural evolution) is usually modelled as a collective process in which individuals invent new artefacts (innovation) and copy information from others (social learning). This classic picture overlooks the growing role of intelligent algorithms in the digital age (e.g. search engines, recommender systems and large language models) in mediating information between humans, with potential consequences for cumulative cultural evolution. Building on a previous model, we investigate the combined effects of network-based social learning and a simplistic version of algorithmic mediation on cultural accumulation. We find that algorithmic mediation significantly impacts cultural accumulation and that this impact grows as social networks become less densely connected. Cultural accumulation is most effective when social learning and algorithmic mediation are combined, and the optimal ratio depends on the network's density. This work is an initial step towards formalizing the impact of intelligent algorithms on cumulative cultural evolution within an established framework. Models like ours provide insights into mechanisms of human-machine interaction in cultural contexts, guiding hypotheses for future experimental testing.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 225","pages":"20240686"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811620","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}
{"title":"A predictive surrogate model of blood haemodynamics for patient-specific carotid artery stenosis.","authors":"Mostafa Barzegar Gerdroodbary, Sajad Salavatidezfouli","doi":"10.1098/rsif.2024.0774","DOIUrl":"10.1098/rsif.2024.0774","url":null,"abstract":"<p><p>In this study, the haemodynamic factors inside the patient-specific carotid artery with stenosis are evaluated via a predictive surrogate model. The technique of proper orthogonal decomposition (POD) is used for reducing the order of the main model and consequently, the long short-term memory is employed for the prediction of main blood flow parameters, i.e. blood velocity and pressure along the patient-specific carotid artery with stenosis. The efficiency of the proposed machine learning technique has been evaluated in patient-specific carotid arteries with/without stenosis. Besides, the reconstruction error analysis is performed for different POD mode numbers. Our results demonstrate that the value of blood velocity at different stages of the cardiac cycle has a great impact on the efficiency of the proposed method for the estimation of blood haemodynamics. The presence of stenosis inside the patient-specific carotid artery intensifies the complexity of the blood flow, and consequently, the magnitude of the errors for the prediction is increased when the stenosis exists in the patient-specific carotid artery.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 224","pages":"20240774"},"PeriodicalIF":3.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879616/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143556861","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}
Yuyuan Liu, Lichen Wang, Ruqiang Guo, Shijia Hua, Linjie Liu, Liang Zhang, The Anh Han
{"title":"Evolution of trust in the <i>N</i>-player trust game with transformation incentive mechanism.","authors":"Yuyuan Liu, Lichen Wang, Ruqiang Guo, Shijia Hua, Linjie Liu, Liang Zhang, The Anh Han","doi":"10.1098/rsif.2024.0726","DOIUrl":"10.1098/rsif.2024.0726","url":null,"abstract":"<p><p>Trust game is commonly used to study the evolution of trust among unrelated individuals. It offers valuable insights into human interactions in a range of disciplines, including economics, sociology and psychology. Previous research has revealed that reward and punishment systems can effectively promote the evolution of trust. However, these investigations overlook the gaming environment, leaving unresolved the optimal conditions for employing distinct incentives to effectively facilitate trust level. To bridge this gap, we introduce a transformation incentive mechanism in an <i>N</i>-player trust game, where trustees are given different forms of incentives depending on the number of trustees in the group. Using the Markov decision process approach, our research shows that as incentives increase, the level of trust rises continuously, eventually reaching a high level of coexistence between investors and trustworthy trustees. Specifically, in the case of smaller incentives, rewarding trustworthy trustees is more effective. Conversely, in the case of larger incentives, punishing untrustworthy trustees is more effective. Additionally, we find that moderate incentives have a positive impact on increasing the average payoff within the group.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 224","pages":"20240726"},"PeriodicalIF":3.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11938300/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710406","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}
Tom White, Arístides López-Márquez, Carmen Badosa, Ceclila Jimenez-Mallebrera, Josep Samitier, Marina Inés Giannotti, Anna Lagunas
{"title":"Nanomechanics of cell-derived matrices as a functional read-out in collagen VI-related congenital muscular dystrophies.","authors":"Tom White, Arístides López-Márquez, Carmen Badosa, Ceclila Jimenez-Mallebrera, Josep Samitier, Marina Inés Giannotti, Anna Lagunas","doi":"10.1098/rsif.2024.0860","DOIUrl":"10.1098/rsif.2024.0860","url":null,"abstract":"<p><p>Changes in the mechanical properties of the extracellular matrix (ECM) are a hallmark of disease. Due to its relevance, several <i>in vitro</i> models have been developed for the ECM, including cell-derived matrices (CDMs). CDMs are decellularized natural ECMs assembled by cells that closely mimic the <i>in vivo</i> stromal fibre organization and molecular content. Here, we applied atomic force microscopy-force spectroscopy (AFM-FS) to evaluate the nanomechanical properties of CDMs obtained from patients diagnosed with collagen VI-related congenital muscular dystrophies (COL6-RDs). COL6-RDs are a set of neuromuscular conditions caused by pathogenic variants in any of the three major COL6 genes, which result in deficiency or dysfunction of the COL6 incorporated into the ECM of connective tissues. Current diagnosis includes the genetic confirmation of the disease and categorization of the phenotype based on maximum motor ability, as no direct correlation exists between genotype and phenotype of COL6-RDs. We describe differences in the elastic modulus (<i>E</i>) among CDMs from patients with different clinical phenotypes, as well as the restoration of <i>E</i> in CDMs obtained from genetically edited cells. Results anticipate the potential of the nanomechanical analysis of CDMs as a complementary clinical tool, providing phenotypic information about COL6-RDs and their response to gene therapies.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 224","pages":"20240860"},"PeriodicalIF":3.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897821/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143605275","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}