Bénéteau et al. investigate the estimations by several models of the dates of the beginning and the end of the SARS-CoV-2 epidemic in France. This is a difficult problem as the number of infected people on both tails of the epidemic is low, meaning that assumptions at the heart of commonly-used SIR-based deterministic models become inappropriate. They propose a new stochastic model, a version of which includes superspreaders, and compare the estimates of this model to a deterministic SIR-like model and to another published deterministic model that includes age stratification. They find that estimates of the end of the epidemic following lockdowns are more sensitive to the assumptions of the models used than estimates of its beginning.
{"title":"The importance of model assumptions in estimating the dynamics of the COVID-19 epidemic","authors":"Valery Forbes","doi":"10.24072/pci.mcb.100004","DOIUrl":"https://doi.org/10.24072/pci.mcb.100004","url":null,"abstract":"Bénéteau et al. investigate the estimations by several models of the dates of the beginning and the end of the SARS-CoV-2 epidemic in France. This is a difficult problem as the number of infected people on both tails of the epidemic is low, meaning that assumptions at the heart of commonly-used SIR-based deterministic models become inappropriate. They propose a new stochastic model, a version of which includes superspreaders, and compare the estimates of this model to a deterministic SIR-like model and to another published deterministic model that includes age stratification. They find that estimates of the end of the epidemic following lockdowns are more sensitive to the assumptions of the models used than estimates of its beginning.","PeriodicalId":326568,"journal":{"name":"Peer Community In Mathematical and Computational Biology","volume":"130 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115170403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A recommendation of: Alan R. Rogers An efficient algorithm for estimating population history from genetic data 10.1101/2021.01.23.427922
一种从遗传数据估计种群历史的有效算法10.1101/2021.01.23.427922
{"title":"An efficient implementation of legofit software to infer demographic histories from population genetic data","authors":"Matteo Fumagalli","doi":"10.24072/PCI.MCB.100003","DOIUrl":"https://doi.org/10.24072/PCI.MCB.100003","url":null,"abstract":"A recommendation of: Alan R. Rogers An efficient algorithm for estimating population history from genetic data 10.1101/2021.01.23.427922","PeriodicalId":326568,"journal":{"name":"Peer Community In Mathematical and Computational Biology","volume":"114 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125030557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Unlike a species tree, a gene tree results not only from speciation events, but also from events acting at the gene level, such as duplications and losses of gene copies, and gene transfer events [1]. The reconciliation of phylogenetic trees consists in embedding a given gene tree into a known species tree and, doing so, determining the location of these gene-level events on the gene tree [2]. Reconciled gene trees can be seen as phylogenetic trees where internal node labels are used to discriminate between different gene-level events. Comparing them is of foremost importance in order to assess the performance of various reconciliation methods (e.g. [3]).
{"title":"Comparing reconciled gene trees in linear time","authors":"Céline Scornavacca","doi":"10.24072/pci.mcb.100002","DOIUrl":"https://doi.org/10.24072/pci.mcb.100002","url":null,"abstract":"Unlike a species tree, a gene tree results not only from speciation events, but also from events acting at the gene level, such as duplications and losses of gene copies, and gene transfer events [1]. The reconciliation of phylogenetic trees consists in embedding a given gene tree into a known species tree and, doing so, determining the location of these gene-level events on the gene tree [2]. Reconciled gene trees can be seen as phylogenetic trees where internal node labels are used to discriminate between different gene-level events. Comparing them is of foremost importance in order to assess the performance of various reconciliation methods (e.g. [3]).","PeriodicalId":326568,"journal":{"name":"Peer Community In Mathematical and Computational Biology","volume":"21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127410426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
This study [1] used Bayesian models of the number of deaths through time across different regions of France to explore the effects of lockdown and other events (i.e., holding elections) on the dynamics of the SARS-CoV-2 epidemic. The models accurately predicted the number of deaths 2 to 3 weeks in advance, and results were similar to other recent models using different structure and input data. Viral reproduction numbers were not found to be different between weekends and week days, and there was no evidence that holding elections affected the number of deaths directly. However, exploring different scenarios of the timing of the lockdown showed that this had a substantial impact on the number of deaths. This is an interesting and important paper that can inform adaptive management strategies for controlling the spread of this virus, not just in France, but in other geographic areas. For example, the results found that there was a lag period between a change in management strategies (lockdown, social distancing, and the relaxing of controls) and the observed change in mortality. Also, there was a large variation in the impact of mitigation measures on the viral reproduction number depending on region, with lockdown
{"title":"Modeling the effect of lockdown and other events on the dynamics of SARS-CoV-2 in France","authors":"V. Forbes","doi":"10.24072/pci.mcb.100001","DOIUrl":"https://doi.org/10.24072/pci.mcb.100001","url":null,"abstract":"This study [1] used Bayesian models of the number of deaths through time across different regions of France to explore the effects of lockdown and other events (i.e., holding elections) on the dynamics of the SARS-CoV-2 epidemic. The models accurately predicted the number of deaths 2 to 3 weeks in advance, and results were similar to other recent models using different structure and input data. Viral reproduction numbers were not found to be different between weekends and week days, and there was no evidence that holding elections affected the number of deaths directly. However, exploring different scenarios of the timing of the lockdown showed that this had a substantial impact on the number of deaths. This is an interesting and important paper that can inform adaptive management strategies for controlling the spread of this virus, not just in France, but in other geographic areas. For example, the results found that there was a lag period between a change in management strategies (lockdown, social distancing, and the relaxing of controls) and the observed change in mortality. Also, there was a large variation in the impact of mitigation measures on the viral reproduction number depending on region, with lockdown","PeriodicalId":326568,"journal":{"name":"Peer Community In Mathematical and Computational Biology","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116861233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A model of optimal control of ventilation recently developed for humans has suggested that the localization of the transition between a convective and a diffusive transport of the respiratory gas determines how ventilation should be controlled to minimize its energetic cost at any metabolic regime. We generalized this model to any mammal, based on the core morphometric characteristics shared by all mammals' lungs and on their allometric scaling from the literature.Since the main energetic costs of ventilation are related to the convective transport, we prove that, for all mammals, the localization of the shift from an convective transport into a diffusive transport plays a critical role on keeping that cost low while fulfilling the lung's function. Our model predicts for the first time where this transition zone should occur in order to minimize the energetic cost of ventilation, depending on the mammals' mass and on the metabolic regime. From that optimal localization, we are able to derive predicted allometric scaling laws for both tidal volumes and breathing rates, at any metabolic regime. We ran our model for the three common metabolic rates -basal, field and maximal- and showed that our predictions accurately reproduce the experimental data available in the literature. Our analysis supports the hypothesis that the mammals' allometric scaling laws of tidal volumes and breathing rates are driven by a few core geometrical characteristics shared by the mammals' lungs, the physical processes of respiratory gas transport and the metabolic needs.
{"title":"How mammals adapt their breath to body activity – and how this depends on body size","authors":"F. Noel, C. Karamaoun, J. Dempsey, B. Mauroy","doi":"10.24072/pci.mcb.100005","DOIUrl":"https://doi.org/10.24072/pci.mcb.100005","url":null,"abstract":"A model of optimal control of ventilation recently developed for humans has suggested that the localization of the transition between a convective and a diffusive transport of the respiratory gas determines how ventilation should be controlled to minimize its energetic cost at any metabolic regime. We generalized this model to any mammal, based on the core morphometric characteristics shared by all mammals' lungs and on their allometric scaling from the literature.Since the main energetic costs of ventilation are related to the convective transport, we prove that, for all mammals, the localization of the shift from an convective transport into a diffusive transport plays a critical role on keeping that cost low while fulfilling the lung's function. Our model predicts for the first time where this transition zone should occur in order to minimize the energetic cost of ventilation, depending on the mammals' mass and on the metabolic regime. From that optimal localization, we are able to derive predicted allometric scaling laws for both tidal volumes and breathing rates, at any metabolic regime. We ran our model for the three common metabolic rates -basal, field and maximal- and showed that our predictions accurately reproduce the experimental data available in the literature. Our analysis supports the hypothesis that the mammals' allometric scaling laws of tidal volumes and breathing rates are driven by a few core geometrical characteristics shared by the mammals' lungs, the physical processes of respiratory gas transport and the metabolic needs.","PeriodicalId":326568,"journal":{"name":"Peer Community In Mathematical and Computational Biology","volume":"20 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116014737","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：