Journal of The Royal Society Interface最新文献_第7页

Random walk models in the life sciences: including births, deaths and local interactions. 生命科学中的随机漫步模型：包括出生、死亡和局部相互作用。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-01-01 Epub Date: 2025-01-15 DOI: 10.1098/rsif.2024.0422

Michael J Plank, Matthew J Simpson, Ruth E Baker

{"title":"Random walk models in the life sciences: including births, deaths and local interactions.","authors":"Michael J Plank, Matthew J Simpson, Ruth E Baker","doi":"10.1098/rsif.2024.0422","DOIUrl":"10.1098/rsif.2024.0422","url":null,"abstract":"Random walks and related spatial stochastic models have been used in a range of application areas, including animal and plant ecology, infectious disease epidemiology, developmental biology, wound healing and oncology. Classical random walk models assume that all individuals in a population behave independently, ignoring local physical and biological interactions. This assumption simplifies the mathematical description of the population considerably, enabling continuum-limit descriptions to be derived and used in model analysis and fitting. However, interactions between individuals can have a crucial impact on population-level behaviour. In recent decades, research has increasingly been directed towards models that include interactions, including physical crowding effects and local biological processes such as adhesion, competition, dispersal, predation and adaptive directional bias. In this article, we review the progress that has been made with models of interacting individuals. We aim to provide an overview that is accessible to researchers in application areas, as well as to specialist modellers. We focus particularly on derivation of asymptotically exact or approximate continuum-limit descriptions and simplified deterministic models of mean-field behaviour and resulting spatial patterns. We provide worked examples and illustrative results of selected models. We conclude with a discussion of current areas of focus and future challenges.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 222","pages":"20240422"},"PeriodicalIF":3.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11732428/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142983554","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

Autonomous learning of generative models with chemical reaction network ensembles. 化学反应网络集成生成模型的自主学习。

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.2024.0373

William Poole, Thomas E Ouldridge, Manoj Gopalkrishnan

引用次数: 0

Optimizing contact tracing for avian influenza in poultry flocks. 优化禽群禽流感接触者追踪工作。

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.2024.0523

Sébastien Lambert, Lisa Fourtune, Peter H F Hobbelen, Julie Baca, José L Gonzales, Armin R W Elbers, Timothée Vergne

{"title":"Optimizing contact tracing for avian influenza in poultry flocks.","authors":"Sébastien Lambert, Lisa Fourtune, Peter H F Hobbelen, Julie Baca, José L Gonzales, Armin R W Elbers, Timothée Vergne","doi":"10.1098/rsif.2024.0523","DOIUrl":"https://doi.org/10.1098/rsif.2024.0523","url":null,"abstract":"Contact tracing is commonly used to manage infectious diseases of both humans and animals. It aims to detect early and control potentially infected individuals or farms that had contact with infectious cases. Because it is very resource-intensive, contact tracing is usually performed on a pre-defined time window, based on previous knowledge of the duration of the incubation period. However, pre-defined time windows may not be always relevant, reducing the efficiency of contact tracing. In this study, we estimated the day when farms were first infected with highly pathogenic avian influenza viruses, a devastating pathogen causing severe socio-economic damage in domestic poultry. The estimation was performed by fitting a stochastic mechanistic model to observed daily mortality data from 63 infected poultry farms in France and The Netherlands, using approximate Bayesian computation. Independent of the poultry species or country, the estimates of the time of first infection ranged between 3.4 (95% credible interval-CrI: 2.6, 4.6) and 19.9 (95% CrI: 11.9, 31.3) days prior to the last observation. We developed an online application to provide real-time support to policymakers by estimating realistic ranges of dates of first infection to inform contact tracing and improve its efficiency.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 222","pages":"20240523"},"PeriodicalIF":3.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11706645/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142950744","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

Mechanistic models of humoral kinetics following COVID-19 vaccination.

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.2024.0445

Daniel Stocks, Amy Thomas, Adam Finn, Leon Danon, Ellen Brooks-Pollock

{"title":"Mechanistic models of humoral kinetics following COVID-19 vaccination.","authors":"Daniel Stocks, Amy Thomas, Adam Finn, Leon Danon, Ellen Brooks-Pollock","doi":"10.1098/rsif.2024.0445","DOIUrl":"10.1098/rsif.2024.0445","url":null,"abstract":"COVID-19 vaccine programmes must account for variable immune responses and waning protection. Existing descriptions of antibody responses to COVID-19 vaccination convey limited information about the mechanisms of antibody production and maintenance. We describe antibody dynamics after COVID-19 vaccination with two biologically motivated mathematical models. We fit the models using Markov chain Monte Carlo to seroprevalence data from 14 602 uninfected individuals in England between May 2020 and September 2022. We analyse the effect of age, vaccine type, number of doses and the interval between doses on antibody production and longevity. We find evidence that individuals over 35 years old twice vaccinated with ChAdOx1-S generate a persistent antibody response suggestive of long-lived plasma cell induction. We also find that plasmablast productive capacity is greater in: younger people than older people (≤4.5-fold change in point estimates); people vaccinated with two doses than one dose (≤12-fold change); and people vaccinated with BNT162b2 than ChAdOx1-S (≤440-fold change). We find the half-life of an antibody to be 23-106 days. Routinely collected seroprevalence data are invaluable for characterizing within-host mechanisms of antibody production and persistence. Extended sampling and linking seroprevalence data to outcomes would enable conclusions about how humoral kinetics protect against disease.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 222","pages":"20240445"},"PeriodicalIF":3.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11775660/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143059380","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

Energy-based modelling of single actin filament polymerization using bond graphs.

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2025-01-01 Epub Date: 2025-01-30 DOI: 10.1098/rsif.2024.0404

Peter J Gawthrop, Michael Pan, Vijay Rajagopal

{"title":"Energy-based modelling of single actin filament polymerization using bond graphs.","authors":"Peter J Gawthrop, Michael Pan, Vijay Rajagopal","doi":"10.1098/rsif.2024.0404","DOIUrl":"10.1098/rsif.2024.0404","url":null,"abstract":"Bond graphs provide an energy-based methodology for modelling complex systems hierarchically; at the moment, the method allows biological systems with both chemical and electrical subsystems to be modelled. Herein, the bond graph approach is extended to include chemomechanical transduction thus extending the range of biological systems to be modelled. Actin filament polymerization and force generation is used as an example of chemomechanical transduction, and it is shown that the TF (transformer) bond graph component provides a practical, and conceptually simple, alternative to the Brownian ratchet approach of Peskin, Odell, Oster and Mogilner. Furthermore, it is shown that the bond graph approach leads to the same equation as the Brownian ratchet approach in the simplest case. The approach is illustrated by showing that flexibility and non-normal incidence can be modelled by simply adding additional bond graph components and that compliance leads to non-convexity of the force-velocity curve. Energy flows are fundamental to life; for this reason, the energy-based approach is utilized to investigate the power transmission by the actin filament and its corresponding efficiency. The bond graph model is fitted to experimental data by adjusting the model physical parameters.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 222","pages":"20240404"},"PeriodicalIF":3.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11780404/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066637","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

I2Bot: an open-source tool for multi-modal and embodied simulation of insect navigation. I2Bot：一个开源工具，用于昆虫导航的多模式和具体化仿真。

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.2024.0586

Xuelong Sun, Michael Mangan, Jigen Peng, Shigang Yue

{"title":"I2Bot: an open-source tool for multi-modal and embodied simulation of insect navigation.","authors":"Xuelong Sun, Michael Mangan, Jigen Peng, Shigang Yue","doi":"10.1098/rsif.2024.0586","DOIUrl":"10.1098/rsif.2024.0586","url":null,"abstract":"Achieving a comprehensive understanding of animal intelligence demands an integrative approach that acknowledges the interplay between an organism's brain, body and environment. Insects, despite their limited computational resources, demonstrate remarkable abilities in navigation. Existing computational models often fall short in faithfully replicating the morphology of real insects and their interactions with the environment, hindering validation and practical application in robotics. To address these gaps, we present I2Bot, a novel simulation tool based on the morphological characteristics of real insects. This tool empowers robotic models with dynamic sensory capabilities, realistic modelling of insect morphology, physical dynamics and sensory capacity. By integrating gait controllers and computational models into I2Bot, we have implemented classical embodied navigation behaviours and revealed some fundamental navigation principles. By open-sourcing I2Bot, we aim to accelerate the understanding of insect intelligence and foster advances in the development of autonomous robotic systems.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 222","pages":"20240586"},"PeriodicalIF":3.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11750368/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143007766","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

Improving propulsive efficiency using bio-inspired intermittent locomotion. 利用仿生间歇运动提高推进效率。

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.2024.0624

Tristan Aurégan, Mathilde Lemoine, Benjamin Thiria, Sylvain Courrech du Pont

{"title":"Improving propulsive efficiency using bio-inspired intermittent locomotion.","authors":"Tristan Aurégan, Mathilde Lemoine, Benjamin Thiria, Sylvain Courrech du Pont","doi":"10.1098/rsif.2024.0624","DOIUrl":"10.1098/rsif.2024.0624","url":null,"abstract":"Many swimmers, especially small- to medium-sized animals, use intermittent locomotion that differs from continuous swimming of large species. This type of locomotion, called burst and coast, is often associated with an energetic advantage. In this work, we investigate the intermittent locomotion inspired by fish locomotion but applied to a propeller. The energy consumption of burst-and-coast cycles is measured and compared to the continuous rotation regime. We show that a substantial drag ratio between the active and passive phases of the motion, as observed in fish, is critical for energy savings. Such a contrast can be obtained using a folding propeller that passively opens and closes as the propeller starts and stops rotating. For this reconfigurable propeller, intermittent propulsion is found to be energetically advantageous, saving up to 24% of the energy required to cruise at a given speed. Using an analytical model, we show that intermittent motion is more efficient than continuous motion when the drag reduction in the coast phase exceeds 65%. For fish-like locomotion, this threshold seems to be closer to 30%. A formal analogy allows us to explain the difference between propeller propulsion and fish locomotion.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 222","pages":"20240624"},"PeriodicalIF":3.7,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11750389/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143007767","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

Uncertainty in COVID-19 transmission could undermine our ability to predict long COVID. COVID-19传播的不确定性可能会削弱我们预测COVID-19长期传播的能力。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2024-12-01 Epub Date: 2024-12-11 DOI: 10.1098/rsif.2024.0438

Alexander B Beams, David J D Earn, Caroline Colijn

{"title":"Uncertainty in COVID-19 transmission could undermine our ability to predict long COVID.","authors":"Alexander B Beams, David J D Earn, Caroline Colijn","doi":"10.1098/rsif.2024.0438","DOIUrl":"10.1098/rsif.2024.0438","url":null,"abstract":"As SARS-CoV-2 has transitioned from a novel pandemic-causing pathogen into an established seasonal respiratory virus, focus has shifted to post-acute sequelae of COVID-19 (PASC, colloquially 'long COVID'). We use compartmental mathematical models simulating emergence of new variants to help identify key sources of uncertainty in PASC trajectories. Some parameters (such as the duration and equilibrium prevalence of infection, as well as the fraction of infections that develop PASC) matter more than others (such as the duration of immunity and secondary vaccine efficacy against PASC). Even if newer variants carry the same risk of PASC as older types, the dynamics of selection can give rise to greater PASC prevalence. However, identifying plausible PASC prevalence trajectories requires accurate knowledge of the transmission potential of COVID-19 variants in the endemic phase. Precise estimates for secondary vaccine efficacy and duration of immunity will not greatly improve forecasts for PASC prevalence. Researchers involved with Living Evidence Synthesis, or other similar initiatives focused on PASC, are well advised to ascertain primary efficacy against infection, duration of infection and prevalence of active infection in order to facilitate predictions.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"21 221","pages":"20240438"},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11631421/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807558","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

Nitric oxide modelling and its bioavailability influenced by red blood cells. 一氧化氮模型及其生物利用率受红细胞的影响。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2024-12-01 Epub Date: 2024-12-18 DOI: 10.1098/rsif.2024.0458

Ananta Kumar Nayak, Marco Canepari, Sovan Lal Das, Chaouqi Misbah

{"title":"Nitric oxide modelling and its bioavailability influenced by red blood cells.","authors":"Ananta Kumar Nayak, Marco Canepari, Sovan Lal Das, Chaouqi Misbah","doi":"10.1098/rsif.2024.0458","DOIUrl":"10.1098/rsif.2024.0458","url":null,"abstract":"Nitric oxide (NO) is an important vasodilator responsible for maintaining vascular tone in the human body. Its production in endothelial cells (ECs) is regulated by the rise of cytoplasmic Ca2+ concentration and shear stress perceived by blood flow. The increase in cytoplasmic Ca2+ concentration is mainly activated by adenosine triphosphate (ATP) released from red blood cells (RBCs) and ECs. However, RBCs, which act as NO scavengers, can affect the bioavailability of NO in blood vessels. In this study, we developed a model that incorporates ATP and shear stress-dependent NO production, integrating various biochemical pathways. The model results are qualitatively consistent with the experimental findings. Given that ATP concentration and shear stress vary spatially within blood circulation, influenced by factors such as vessel width, flow strength and RBC concentration, these variations can significantly affect NO bioavailability. Here, we study RBC flow, ATP release from RBCs and ECs, and [Formula: see text] and NO dynamics in a two-dimensional channel using the immersed boundary lattice Boltzmann method. The main findings from the study include: (i) an increase in RBC concentration leads to a rise in ATP and cytoplasmic Ca2+ concentrations for all variation in channel widths, while NO concentration exhibits a decrease; (ii) NO bioavailability is significantly influenced by RBC distribution, particularly in strongly confined channels; and (iii) two phases of NO bioavailability are observed in different regions of the blood vessels: one with a significant concentration change at low RBC concentration and another with a minimal concentration change at high RBC concentration, across all confinements. The outcomes of this study may provide valuable insights into the mechanisms of NO-dependent vasodilation and the transport of oxygen by RBCs within microvascular networks for future studies.","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"21 221","pages":"20240458"},"PeriodicalIF":3.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11653115/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142846805","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

Correction: 'The three-dimensional coarse-graining formulation of interacting elastohydrodynamic filaments and multi-body microhydrodynamics' (2023), by Fuchter and Bloomfield-Gadêlha. 更正：“相互作用弹性流体力学细丝和多体微流体力学的三维粗粒化公式”（2023），Fuchter和Bloomfield-Gadêlha。

IF 3.7 2区综合性期刊

Journal of The Royal Society Interface Pub Date : 2024-12-01 Epub Date: 2024-12-04 DOI: 10.1098/rsif.2024.0800

Paul Fuchter, Hermes Bloomfield-Gadêlha

引用次数: 0