Pub Date : 2015-09-17DOI: 10.1007/978-81-322-2141-8_26
Reena Yadav, M. Ghatge, K. Hiremath, Ganesh Bagler
{"title":"Numerical Study of Variable Lung Ventilation Strategies","authors":"Reena Yadav, M. Ghatge, K. Hiremath, Ganesh Bagler","doi":"10.1007/978-81-322-2141-8_26","DOIUrl":"https://doi.org/10.1007/978-81-322-2141-8_26","url":null,"abstract":"","PeriodicalId":119149,"journal":{"name":"arXiv: Quantitative Methods","volume":"31 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122999752","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}
Possibilities for using geometry and topology to analyze statistical problems in biology raise a host of novel questions in geometry, probability, algebra, and combinatorics that demonstrate the power of biology to influence the future of pure mathematics. This expository article is a tour through some biological explorations and their mathematical ramifications. The article starts with evolution of novel topological features in wing veins of fruit flies, which are quantified using the algebraic structure of multiparameter persistent homology. The statistical issues involved highlight mathematical implications of sampling from moduli spaces. These lead to geometric probability on stratified spaces, including the sticky phenomenon for Frechet means and the origin of this mathematical area in the reconstruction of phylogenetic trees.
{"title":"Fruit flies and moduli: interactions between biology and mathematics","authors":"Ezra Miller","doi":"10.1090/noti1290","DOIUrl":"https://doi.org/10.1090/noti1290","url":null,"abstract":"Possibilities for using geometry and topology to analyze statistical problems in biology raise a host of novel questions in geometry, probability, algebra, and combinatorics that demonstrate the power of biology to influence the future of pure mathematics. This expository article is a tour through some biological explorations and their mathematical ramifications. The article starts with evolution of novel topological features in wing veins of fruit flies, which are quantified using the algebraic structure of multiparameter persistent homology. The statistical issues involved highlight mathematical implications of sampling from moduli spaces. These lead to geometric probability on stratified spaces, including the sticky phenomenon for Frechet means and the origin of this mathematical area in the reconstruction of phylogenetic trees.","PeriodicalId":119149,"journal":{"name":"arXiv: Quantitative Methods","volume":"139 2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128867116","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}
Pub Date : 2015-07-03DOI: 10.1140/epjnbp/s40366-015-0026-0
D. Sornette, Maroussia Favre
{"title":"Cancer risk is not (just) bad luck","authors":"D. Sornette, Maroussia Favre","doi":"10.1140/epjnbp/s40366-015-0026-0","DOIUrl":"https://doi.org/10.1140/epjnbp/s40366-015-0026-0","url":null,"abstract":"","PeriodicalId":119149,"journal":{"name":"arXiv: Quantitative Methods","volume":"82 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115575650","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}
Pub Date : 2015-02-25DOI: 10.7287/peerj.preprints.1396v1
J. D. F. Santos, F. Coelho, P. Bliman
Colony Collapse Disorder has become a global problem for beekeepers and for the crops which depend on bee polination. Multiple factors are known to increase the risk of colony colapse, and the ectoparasitic mite Varroa destructor that parasitizes honey bees is among the main threats to colony health. Although this mite is unlikely to, by itself, cause the collapse of hives, it plays an important role as it is a vector for many viral diseases. Such diseases are among the likely causes for Colony Collapse Disorder. The effects of V. destructor infestation are disparate in different parts of the world. Greater morbidity - in the form of colony losses - has been reported in colonies of European honey bees (EHB) in Europe, Asia and North America. However, this mite has been present in Brasil for many years and yet there are no reports of Africanized honey bee (AHB) colonies losses. Studies carried out in Mexico showed that some resistance behaviors to the mite - especially grooming and hygienic behavior - appear to be different in each subspecies. Could those difference in behaviors explain why the AHB are less susceptible to Colony Collapse Disorder? In order to answer this question, we propose a mathematical model of the coexistence dynamics of these two species, the bee and the mite, to analyze the role of resistance behaviors in the overall health of the colony, and, as a consequence, its ability to face epidemiological challenges.
{"title":"Behavioral modulation of the coexistence between Apis melifera and Varroa destructor: A defense against colony colapse disorder?","authors":"J. D. F. Santos, F. Coelho, P. Bliman","doi":"10.7287/peerj.preprints.1396v1","DOIUrl":"https://doi.org/10.7287/peerj.preprints.1396v1","url":null,"abstract":"Colony Collapse Disorder has become a global problem for beekeepers and for the crops which depend on bee polination. Multiple factors are known to increase the risk of colony colapse, and the ectoparasitic mite Varroa destructor that parasitizes honey bees is among the main threats to colony health. Although this mite is unlikely to, by itself, cause the collapse of hives, it plays an important role as it is a vector for many viral diseases. Such diseases are among the likely causes for Colony Collapse Disorder. \u0000The effects of V. destructor infestation are disparate in different parts of the world. Greater morbidity - in the form of colony losses - has been reported in colonies of European honey bees (EHB) in Europe, Asia and North America. However, this mite has been present in Brasil for many years and yet there are no reports of Africanized honey bee (AHB) colonies losses. \u0000Studies carried out in Mexico showed that some resistance behaviors to the mite - especially grooming and hygienic behavior - appear to be different in each subspecies. Could those difference in behaviors explain why the AHB are less susceptible to Colony Collapse Disorder? \u0000In order to answer this question, we propose a mathematical model of the coexistence dynamics of these two species, the bee and the mite, to analyze the role of resistance behaviors in the overall health of the colony, and, as a consequence, its ability to face epidemiological challenges.","PeriodicalId":119149,"journal":{"name":"arXiv: Quantitative Methods","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116438640","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}
Pub Date : 2014-12-30DOI: 10.1146/ANNUREV-CONMATPHYS-031214-014803
Gavsper Tkavcik, W. Bialek
Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been possible to measure, directly, the flow of information in biological networks, or more generally where information theoretic ideas have been used to guide the analysis of experiments. Systems of interest range from single molecules (the sequence diversity in families of proteins) to groups of organisms (the distribution of velocities in flocks of birds), and all scales in between. Many of these analyses are motivated by the idea that biological systems may have evolved to optimize the gathering and representation of information, and we review the experimental evidence for this optimization, again across a wide range of scales.
{"title":"Information processing in living systems","authors":"Gavsper Tkavcik, W. Bialek","doi":"10.1146/ANNUREV-CONMATPHYS-031214-014803","DOIUrl":"https://doi.org/10.1146/ANNUREV-CONMATPHYS-031214-014803","url":null,"abstract":"Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been possible to measure, directly, the flow of information in biological networks, or more generally where information theoretic ideas have been used to guide the analysis of experiments. Systems of interest range from single molecules (the sequence diversity in families of proteins) to groups of organisms (the distribution of velocities in flocks of birds), and all scales in between. Many of these analyses are motivated by the idea that biological systems may have evolved to optimize the gathering and representation of information, and we review the experimental evidence for this optimization, again across a wide range of scales.","PeriodicalId":119149,"journal":{"name":"arXiv: Quantitative Methods","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129251165","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}
Pub Date : 2014-12-10DOI: 10.6084/M9.FIGSHARE.858921.V2
H. Helene, P. Joel
Scientific fraud is an increasingly vexing problem. Many current programs for fraud detection focus on image manipulation, while techniques for detection based on anomalous patterns that may be discoverable in the underlying numerical data get much less attention, even though these techniques are often easy to apply. We employed three such techniques in a case study in which we considered data sets from several hundred experiments. We compared patterns in the data sets from one research teaching specialist (RTS), to those of 9 other members of the same laboratory and from 3 outside laboratories. Application of two conventional statistical tests and a newly developed test for anomalous patterns in the triplicate data commonly produced in such research to various data sets reported by the RTS resulted in repeated rejection of the hypotheses (often at p-levels well below 0.001) that anomalous patterns in his data may have occurred by chance. This analysis emphasizes the importance of access to raw data that form the bases of publications, reports and grant applications in order to evaluate the correctness of the conclusions, as well as the utility of methods for detecting anomalous, especially fabricated, numerical results.
{"title":"Statistical Detection of Potentially Fabricated Data","authors":"H. Helene, P. Joel","doi":"10.6084/M9.FIGSHARE.858921.V2","DOIUrl":"https://doi.org/10.6084/M9.FIGSHARE.858921.V2","url":null,"abstract":"Scientific fraud is an increasingly vexing problem. Many current programs for fraud detection focus on image manipulation, while techniques for detection based on anomalous patterns that may be discoverable in the underlying numerical data get much less attention, even though these techniques are often easy to apply. We employed three such techniques in a case study in which we considered data sets from several hundred experiments. We compared patterns in the data sets from one research teaching specialist (RTS), to those of 9 other members of the same laboratory and from 3 outside laboratories. Application of two conventional statistical tests and a newly developed test for anomalous patterns in the triplicate data commonly produced in such research to various data sets reported by the RTS resulted in repeated rejection of the hypotheses (often at p-levels well below 0.001) that anomalous patterns in his data may have occurred by chance. This analysis emphasizes the importance of access to raw data that form the bases of publications, reports and grant applications in order to evaluate the correctness of the conclusions, as well as the utility of methods for detecting anomalous, especially fabricated, numerical results.","PeriodicalId":119149,"journal":{"name":"arXiv: Quantitative Methods","volume":"15 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123924658","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}
Pub Date : 2014-10-28DOI: 10.1103/PHYSREVX.4.041015
A. Celani, E. Villermaux, M. Vergassola
The olfactory system of male moths is exquisitely sensitive to pheromones emitted by females and transported in the environment by atmospheric turbulence. Moths respond to minute amounts of pheromones and their behavior is sensitive to the fine-scale structure of turbulent plumes where pheromone concentration is detectible. The signal of pheromone whiffs is qualitatively known to be intermittent, yet quantitative characterization of its statistical properties is lacking. This challenging fluid dynamics problem is also relevant for entomology, neurobiology and the technological design of olfactory stimulators aimed at reproducing physiological odor signals in well-controlled laboratory conditions. Here, we develop a Lagrangian approach to the transport of pheromones by turbulent flows and exploit it to predict the statistics of odor detection during olfactory searches. The theory yields explicit probability distributions for the intensity and the duration of pheromone detections, as well as their spacing in time. Predictions are favorably tested by using numerical simulations, laboratory experiments and field data for the atmospheric surface layer. The resulting signal of odor detections lends to implementation with state-of-the-art technologies and quantifies the amount and the type of information that male moths can exploit during olfactory searches.
{"title":"Odor Landscapes in Turbulent Environments","authors":"A. Celani, E. Villermaux, M. Vergassola","doi":"10.1103/PHYSREVX.4.041015","DOIUrl":"https://doi.org/10.1103/PHYSREVX.4.041015","url":null,"abstract":"The olfactory system of male moths is exquisitely sensitive to pheromones emitted by females and transported in the environment by atmospheric turbulence. Moths respond to minute amounts of pheromones and their behavior is sensitive to the fine-scale structure of turbulent plumes where pheromone concentration is detectible. The signal of pheromone whiffs is qualitatively known to be intermittent, yet quantitative characterization of its statistical properties is lacking. This challenging fluid dynamics problem is also relevant for entomology, neurobiology and the technological design of olfactory stimulators aimed at reproducing physiological odor signals in well-controlled laboratory conditions. Here, we develop a Lagrangian approach to the transport of pheromones by turbulent flows and exploit it to predict the statistics of odor detection during olfactory searches. The theory yields explicit probability distributions for the intensity and the duration of pheromone detections, as well as their spacing in time. Predictions are favorably tested by using numerical simulations, laboratory experiments and field data for the atmospheric surface layer. The resulting signal of odor detections lends to implementation with state-of-the-art technologies and quantifies the amount and the type of information that male moths can exploit during olfactory searches.","PeriodicalId":119149,"journal":{"name":"arXiv: Quantitative Methods","volume":"41 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127921335","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}
Pub Date : 2014-10-15DOI: 10.1103/PHYSREVX.6.031009
C. Modes, M. Magnasco, E. Katifori
Natural and man-made transport webs are frequently dominated by dense sets of nested cycles. The architecture of these networks, as defined by the topology and edge weights, determines how efficiently the networks perform their function. Yet, the set of tools that can characterize such a weighted cycle-rich architecture in a physically relevant, mathematically compact way is sparse. In order to fill this void, we have developed a new algorithm that rests on an abstraction of the physical `tiling' in the case of a two dimensional network to an effective tiling of an abstract surface in space that the network may be thought to sit in. Generically these abstract surfaces are richer than the flat plane and as a result there are now two families of fundamental units that may aggregate upon cutting weakest links -- the plaquettes of the tiling and the longer `topological' cycles associated with the abstract surface itself. Upon sequential removal of the weakest links, as determined by the edge weight, neighboring plaquettes merge and a tree characterizing this merging process results. The properties of this characteristic tree can provide the physical and topological data required to describe the architecture of the network and to build physical models. The new algorithm can be used for automated phenotypic characterization of any weighted network whose structure is dominated by cycles, such as mammalian vasculature in the organs, the root networks of clonal colonies like quaking aspen, or the force networks in jammed granular matter.
{"title":"Extracting Hidden Hierarchies in 3D Distribution Networks","authors":"C. Modes, M. Magnasco, E. Katifori","doi":"10.1103/PHYSREVX.6.031009","DOIUrl":"https://doi.org/10.1103/PHYSREVX.6.031009","url":null,"abstract":"Natural and man-made transport webs are frequently dominated by dense sets of nested cycles. The architecture of these networks, as defined by the topology and edge weights, determines how efficiently the networks perform their function. Yet, the set of tools that can characterize such a weighted cycle-rich architecture in a physically relevant, mathematically compact way is sparse. In order to fill this void, we have developed a new algorithm that rests on an abstraction of the physical `tiling' in the case of a two dimensional network to an effective tiling of an abstract surface in space that the network may be thought to sit in. Generically these abstract surfaces are richer than the flat plane and as a result there are now two families of fundamental units that may aggregate upon cutting weakest links -- the plaquettes of the tiling and the longer `topological' cycles associated with the abstract surface itself. Upon sequential removal of the weakest links, as determined by the edge weight, neighboring plaquettes merge and a tree characterizing this merging process results. The properties of this characteristic tree can provide the physical and topological data required to describe the architecture of the network and to build physical models. The new algorithm can be used for automated phenotypic characterization of any weighted network whose structure is dominated by cycles, such as mammalian vasculature in the organs, the root networks of clonal colonies like quaking aspen, or the force networks in jammed granular matter.","PeriodicalId":119149,"journal":{"name":"arXiv: Quantitative Methods","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125830657","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 new approach is developed to understand stability of a population and further understanding of population momentum.
提出了一种新的方法来理解种群的稳定性和进一步理解种群动量。
{"title":"Population Stability and Momentum","authors":"A. Rao","doi":"10.1090/NOTI1165","DOIUrl":"https://doi.org/10.1090/NOTI1165","url":null,"abstract":"A new approach is developed to understand stability of a population and further understanding of population momentum.","PeriodicalId":119149,"journal":{"name":"arXiv: Quantitative Methods","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130206652","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}
The phase response curve (PRC) is an important measure representing the interaction between oscillatory elements. To understand synchrony in biological systems, many research groups have sought to measure PRCs directly from biological cells including neurons. Ermentrout et al. and Ota et al. showed that PRCs can be identified through measurement of white-noise spike-triggered averages. The disadvantage of this method is that one has to collect more than ten-thousand spikes to ensure the accuracy of the estimate. In this paper, to achieve a more accurate estimation of PRCs with a limited sample size, we use colored noise, which has recently drawn attention because of its unique effect on dynamical systems. We numerically show that there is an optimal colored noise to estimate PRCs in the most rigorous fashion.
{"title":"Optimal Colored Noise for Estimating Phase Response Curves","authors":"Kazuhiko Morinaga, Ryota Miyata, T. Aonishi","doi":"10.7566/JPSJ.84.094801","DOIUrl":"https://doi.org/10.7566/JPSJ.84.094801","url":null,"abstract":"The phase response curve (PRC) is an important measure representing the interaction between oscillatory elements. To understand synchrony in biological systems, many research groups have sought to measure PRCs directly from biological cells including neurons. Ermentrout et al. and Ota et al. showed that PRCs can be identified through measurement of white-noise spike-triggered averages. The disadvantage of this method is that one has to collect more than ten-thousand spikes to ensure the accuracy of the estimate. In this paper, to achieve a more accurate estimation of PRCs with a limited sample size, we use colored noise, which has recently drawn attention because of its unique effect on dynamical systems. We numerically show that there is an optimal colored noise to estimate PRCs in the most rigorous fashion.","PeriodicalId":119149,"journal":{"name":"arXiv: Quantitative Methods","volume":"86 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2014-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128659764","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}
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