Journal of The Royal Society Interface最新文献_第9页

Dynamics and bifurcations in genetic circuits with fibration symmetries. 具有纤维对称性的遗传电路的动力学和分岔。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2024-08-01 Epub Date: 2024-08-14 DOI: 10.1098/rsif.2024.0386

Ian Stewart, Saulo D S Reis, Hernán A Makse

{"title":"Dynamics and bifurcations in genetic circuits with fibration symmetries.","authors":"Ian Stewart, Saulo D S Reis, Hernán A Makse","doi":"10.1098/rsif.2024.0386","DOIUrl":"10.1098/rsif.2024.0386","url":null,"abstract":"Circuit building blocks of gene regulatory networks (GRN) have been identified through the fibration symmetries of the underlying biological graph. Here, we analyse analytically six of these circuits that occur as functional and synchronous building blocks in these networks. Of these, the lock-on, toggle switch, Smolen oscillator, feed-forward fibre and Fibonacci fibre circuits occur in living organisms, notably Escherichia coli; the sixth, the repressilator, is a synthetic GRN. We consider synchronous steady states determined by a fibration symmetry (or balanced colouring) and determine analytic conditions for local bifurcation from such states, which can in principle be either steady-state or Hopf bifurcations. We identify conditions that characterize the first bifurcation, the only one that can be stable near the bifurcation point. We model the state of each gene in terms of two variables: mRNA and protein concentration. We consider all possible 'admissible' models-those compatible with the network structure-and then specialize these general results to simple models based on Hill functions and linear degradation. The results systematically classify using graph symmetries the complexity and dynamics of these circuits, which are relevant to understand the functionality of natural and synthetic cells.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"21 217","pages":"20240386"},"PeriodicalIF":3.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11322742/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141976027","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

The academic Great Gatsby Curve. 学术上的盖茨比曲线

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2024-08-01 Epub Date: 2024-08-14 DOI: 10.1098/rsif.2024.0173

Ye Sun, Fabio Caccioli, Xiancheng Li, Giacomo Livan

引用次数: 0

A biomimetic branching signal-passing tile assembly model with dynamic growth and disassembly. 具有动态生长和分解功能的仿生分支信号传递瓦片组装模型。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2024-08-01 Epub Date: 2024-08-21 DOI: 10.1098/rsif.2023.0755

Daniel Fu, John Reif

{"title":"A biomimetic branching signal-passing tile assembly model with dynamic growth and disassembly.","authors":"Daniel Fu, John Reif","doi":"10.1098/rsif.2023.0755","DOIUrl":"10.1098/rsif.2023.0755","url":null,"abstract":"Natural biological branching processes can form tree-like structures at all scales and, moreover, can perform various functions to achieve specific goals; these include receiving stimuli, performing two-way communication along their branches, and dynamically reforming (extending or retracting branches). They underlie many biological systems with considerable diversity, frequency, and geometric complexity; these include networks of neurons, organ tissue, mycorrhizal fungal networks, plant growth, foraging networks, etc. This paper presents a biomimetic DNA tile assembly model (Y-STAM) to implement dynamic branching processes. The Y-STAM is a relatively compact mathematical model providing a design space where complex, biomimetic branch-like growth and behaviour can emerge from the appropriate parametrization of the model. We also introduce a class of augmented models (Y-STAM+) that provide time- and space-dependent modulations of tile glue strengths, which enable further diverse behaviours that are not possible in the Y-STAM; these additional behaviours include refinement of network assemblies, obstacle avoidance, and programmable growth patterns. We perform and discuss extensive simulations of the Y-STAM and the Y-STAM+. We envision that these models could be applied at the mesoscale and the molecular scale to dynamically assemble branching DNA nanostructures and offer insights into complex biological self-assembly processes.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"21 217","pages":"20230755"},"PeriodicalIF":3.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11335017/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142004510","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

Searching for the earliest archaeological record: insights from chimpanzee material landscapes. 寻找最早的考古记录：黑猩猩物质景观的启示。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2024-08-01 Epub Date: 2024-08-21 DOI: 10.1098/rsif.2024.0101

Jonathan S Reeves, Tomos Proffitt, Soiret Serge Pacome, Lydia V Luncz

{"title":"Searching for the earliest archaeological record: insights from chimpanzee material landscapes.","authors":"Jonathan S Reeves, Tomos Proffitt, Soiret Serge Pacome, Lydia V Luncz","doi":"10.1098/rsif.2024.0101","DOIUrl":"10.1098/rsif.2024.0101","url":null,"abstract":"The origin of tool use is a central question in human evolutionary studies. Plio-Pleistocene core and flake technologies represent the earliest evidence of tool use in the human lineage. Some suggest this form of tool use is probably pre-dated by a phase of percussive tool use. However, there is currently no evidence for such a record. The archaeological signature of solely percussive behaviours is not as well understood as that associated with cores and flakes. The durable nature of primate percussive stone tools and their by-products provide an opportunity to investigate what such a record looks like. Here, we present a landscape-scale study of the chimpanzee (Pan troglodytes verus) material culture from the Djouroutou Chimpanzee Project, Taï Forest, Cote d'Ivoire. This study explores the interplay between behavioural and environmental factors in shaping the stone record of nut cracking. Through a survey of nut-cracking sites, the available nut species, and raw materials, we show how resource availability influences the resulting material signature of nut cracking. These results also reveal the diversity of material signatures associated with a purely percussive material record. We gain insight into the range of signatures that may be associated with a pre-core and flake archaeological record, providing new expectations for an earlier record of tool use.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"21 217","pages":"20240101"},"PeriodicalIF":3.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11335018/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142004511","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

Reconstructing blood flow in data-poor regimes: a vasculature network kernel for Gaussian process regression. 在数据匮乏的情况下重建血流：用于高斯过程回归的血管网络核。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2024-08-01 Epub Date: 2024-08-22 DOI: 10.1098/rsif.2024.0194

Shaghayegh Z Ashtiani, Mohammad Sarabian, Kaveh Laksari, Hessam Babaee

{"title":"Reconstructing blood flow in data-poor regimes: a vasculature network kernel for Gaussian process regression.","authors":"Shaghayegh Z Ashtiani, Mohammad Sarabian, Kaveh Laksari, Hessam Babaee","doi":"10.1098/rsif.2024.0194","DOIUrl":"10.1098/rsif.2024.0194","url":null,"abstract":"Blood flow reconstruction in the vasculature is important for many clinical applications. However, in clinical settings, the available data are often quite limited. For instance, transcranial Doppler ultrasound is a non-invasive clinical tool that is commonly used in clinical settings to measure blood velocity waveforms at several locations. This amount of data is grossly insufficient for training machine learning surrogate models, such as deep neural networks or Gaussian process regression. In this work, we propose a Gaussian process regression approach based on empirical kernels constructed by data generated from physics-based simulations-enabling near-real-time reconstruction of blood flow in data-poor regimes. We introduce a novel methodology to reconstruct the kernel within the vascular network. The proposed kernel encodes both spatiotemporal and vessel-to-vessel correlations, thus enabling blood flow reconstruction in vessels that lack direct measurements. We demonstrate that any prediction made with the proposed kernel satisfies the conservation of mass principle. The kernel is constructed by running stochastic one-dimensional blood flow simulations, where the stochasticity captures the epistemic uncertainties, such as lack of knowledge about boundary conditions and uncertainties in vasculature geometries. We demonstrate the performance of the model on three test cases, namely, a simple Y-shaped bifurcation, abdominal aorta and the circle of Willis in the brain.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"21 217","pages":"20240194"},"PeriodicalIF":3.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11341099/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142036192","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

Near-field hydrodynamic interactions determine travelling wave directions of collectively beating cilia. 近场流体动力相互作用决定了集体跳动纤毛的行波方向。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2024-08-01 Epub Date: 2024-08-07 DOI: 10.1098/rsif.2024.0221

Ziqi Cheng, Andrej Vilfan, Yanting Wang, Ramin Golestanian, Fanlong Meng

{"title":"Near-field hydrodynamic interactions determine travelling wave directions of collectively beating cilia.","authors":"Ziqi Cheng, Andrej Vilfan, Yanting Wang, Ramin Golestanian, Fanlong Meng","doi":"10.1098/rsif.2024.0221","DOIUrl":"10.1098/rsif.2024.0221","url":null,"abstract":"Cilia can beat collectively in the form of a metachronal wave, and we investigate how near-field hydrodynamic interactions between cilia can influence the collective response of the beating cilia. Based on the theoretical framework developed in the work of Meng et al. (Meng et al. 2021 Proc. Natl Acad. Sci. USA 118, e2102828118), we find that the first harmonic mode in the driving force acting on each individual cilium can determine the direction of the metachronal wave after considering the finite size of the beating trajectories, which is confirmed by our agent-based numerical simulations. The stable wave patterns, e.g. the travelling direction, can be controlled by the driving forces acting on the cilia, based on which one can change the flow field generated by the cilia. This work can not only help to understand the role of the hydrodynamic interactions in the collective behaviours of cilia, but can also guide future designs of artificial cilia beating in the desired dynamic mode.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"21 217","pages":"20240221"},"PeriodicalIF":3.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11303030/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897734","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 two-dimensional vertex model for curvy cell-cell interfaces at the subcellular scale. 亚细胞尺度上弯曲细胞-细胞界面的二维顶点模型。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2024-08-01 Epub Date: 2024-08-28 DOI: 10.1098/rsif.2024.0193

Kyungeun Kim, J M Schwarz, Martine Ben Amar

{"title":"A two-dimensional vertex model for curvy cell-cell interfaces at the subcellular scale.","authors":"Kyungeun Kim, J M Schwarz, Martine Ben Amar","doi":"10.1098/rsif.2024.0193","DOIUrl":"10.1098/rsif.2024.0193","url":null,"abstract":"Cross-sections of cell shapes in a tissue monolayer typically resemble a tiling of convex polygons. Yet, examples exist where the polygons are not convex with curved cell-cell interfaces, as seen in the adaxial epidermis. To date, two-dimensional vertex models predicting the structure and mechanics of cell monolayers have been mostly limited to convex polygons. To overcome this limitation, we introduce a framework to study curvy cell-cell interfaces at the subcellular scale within vertex models by using a parametrized curve between vertices that is expanded in a Fourier series and whose coefficients represent additional degrees of freedom. This extension to non-convex polygons allows for cells with the same shape index, or dimensionless perimeter, to be, for example, either elongated or globular with lobes. In the presence of applied, anisotropic stresses, we find that local, subcellular curvature or buckling can be energetically more favourable than larger scale deformations involving groups of cells. Inspired by recent experiments, we also find that local, subcellular curvature at cell-cell interfaces emerges in a group of cells in response to the swelling of additional cells surrounding the group. Our framework, therefore, can account for a wider array of multicellular responses to constraints in the tissue environment.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"21 217","pages":"20240193"},"PeriodicalIF":3.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11407580/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080656","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

Symptom propagation in respiratory pathogens of public health concern: a review of the evidence. 引起公共卫生关注的呼吸道病原体的症状传播：证据综述。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2024-07-01 Epub Date: 2024-07-24 DOI: 10.1098/rsif.2024.0009

Phoebe Asplin, Rebecca Mancy, Thomas Finnie, Fergus Cumming, Matt J Keeling, Edward M Hill

{"title":"Symptom propagation in respiratory pathogens of public health concern: a review of the evidence.","authors":"Phoebe Asplin, Rebecca Mancy, Thomas Finnie, Fergus Cumming, Matt J Keeling, Edward M Hill","doi":"10.1098/rsif.2024.0009","DOIUrl":"10.1098/rsif.2024.0009","url":null,"abstract":"Symptom propagation occurs when the symptom set an individual experiences is correlated with the symptom set of the individual who infected them. Symptom propagation may dramatically affect epidemiological outcomes, potentially causing clusters of severe disease. Conversely, it could result in chains of mild infection, generating widespread immunity with minimal cost to public health. Despite accumulating evidence that symptom propagation occurs for many respiratory pathogens, the underlying mechanisms are not well understood. Here, we conducted a scoping literature review for 14 respiratory pathogens to ascertain the extent of evidence for symptom propagation by two mechanisms: dose-severity relationships and route-severity relationships. We identify considerable heterogeneity between pathogens in the relative importance of the two mechanisms, highlighting the importance of pathogen-specific investigations. For almost all pathogens, including influenza and SARS-CoV-2, we found support for at least one of the two mechanisms. For some pathogens, including influenza, we found convincing evidence that both mechanisms contribute to symptom propagation. Furthermore, infectious disease models traditionally do not include symptom propagation. We summarize the present state of modelling advancements to address the methodological gap. We then investigate a simplified disease outbreak scenario, finding that under strong symptom propagation, isolating mildly infected individuals can have negative epidemiological implications.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"21 216","pages":"20240009"},"PeriodicalIF":3.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11267474/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141751982","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

Host behaviour driven by awareness of infection risk amplifies the chance of superspreading events. 受感染风险意识驱动的宿主行为扩大了超级传播事件的机会。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2024-07-01 Epub Date: 2024-07-24 DOI: 10.1098/rsif.2024.0325

Kris V Parag, Robin N Thompson

{"title":"Host behaviour driven by awareness of infection risk amplifies the chance of superspreading events.","authors":"Kris V Parag, Robin N Thompson","doi":"10.1098/rsif.2024.0325","DOIUrl":"10.1098/rsif.2024.0325","url":null,"abstract":"We demonstrate that heterogeneity in the perceived risks associated with infection within host populations amplifies chances of superspreading during the crucial early stages of epidemics. Under this behavioural model, individuals less concerned about dangers from infection are more likely to be infected and attend larger sized (riskier) events, where we assume event sizes remain unchanged. For directly transmitted diseases such as COVID-19, this leads to infections being introduced at rates above the population prevalence to those events most conducive to superspreading. We develop an interpretable, computational framework for evaluating within-event risks and derive a small-scale reproduction number measuring how the infections generated at an event depend on transmission heterogeneities and numbers of introductions. This generalizes previous frameworks and quantifies how event-scale patterns and population-level characteristics relate. As event duration and size grow, our reproduction number converges to the basic reproduction number. We illustrate that even moderate levels of heterogeneity in the perceived risks of infection substantially increase the likelihood of disproportionately large clusters of infections occurring at larger events, despite fixed overall disease prevalence. We show why collecting data linking host behaviour and event attendance is essential for accurately assessing the risks posed by invading pathogens in emerging stages of outbreaks.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"21 216","pages":"20240325"},"PeriodicalIF":3.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11268441/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141752038","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

Modelling Lassa virus dynamics in West African Mastomys natalensis and the impact of human activities. 拉沙病毒在西非蝠鲼中的动态模型及人类活动的影响。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2024-07-01 Epub Date: 2024-07-24 DOI: 10.1098/rsif.2024.0106

Reju Sam John, Hammed Olawale Fatoyinbo, David T S Hayman

{"title":"Modelling Lassa virus dynamics in West African Mastomys natalensis and the impact of human activities.","authors":"Reju Sam John, Hammed Olawale Fatoyinbo, David T S Hayman","doi":"10.1098/rsif.2024.0106","DOIUrl":"10.1098/rsif.2024.0106","url":null,"abstract":"Lassa fever is a West African rodent-borne viral haemorrhagic fever that kills thousands of people a year, with 100 000 to 300 000 people a year probably infected by Lassa virus (LASV). The main reservoir of LASV is the Natal multimammate mouse, Mastomys natalensis. There is reported asynchrony between peak infection in the rodent population and peak Lassa fever risk among people, probably owing to differing seasonal contact rates. Here, we developed a susceptible-infected-recovered ([Formula: see text])-based model of LASV dynamics in its rodent host, M. natalensis, with a persistently infected class and seasonal birthing to test the impact of changes to seasonal birthing in the future owing to climate and land use change. Our simulations suggest shifting rodent birthing timing and synchrony will alter the peak of viral prevalence, changing risk to people, with viral dynamics mainly stable in adults and varying in the young, but with more infected individuals. We calculate the time-average basic reproductive number, [Formula: see text], for this infectious disease system with periodic changes to population sizes owing to birthing using a time-average method and with a sensitivity analysis show four key parameters: carrying capacity, adult mortality, the transmission parameter among adults and additional disease-induced mortality impact the maintenance of LASV in M. natalensis most, with carrying capacity and adult mortality potentially changeable owing to human activities and interventions.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"21 216","pages":"20240106"},"PeriodicalIF":3.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11267396/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141752039","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