Latest in q-bio.pe

total 5863took 0.12s
Single-cell approaches to cell competition: high-throughput imaging, machine learning and simulationsMar 25 2019Cell competition is a quality control mechanism in tissues that results in the elimination of less fit cells. Over the past decade, the phenomenon of cell competition has been identified in many physiological and pathological contexts, driven either by ... More
Open Quasispecies Models: Stability, Optimization, and Distributed ExtensionMar 22 2019We suggest a natural approach that leads to a modification of classical quasispecies models and incorporates the possibility of population extinction in addition to growth. The resulting modified models are called open. Their essential properties, regarding ... More
Consensus and diversity in multi-state noisy voter modelsMar 21 2019We study a variant of the voter model with multiple opinions; individuals can imitate each other and also change their opinion randomly in mutation events. We focus on the case of a population with all-to-all interaction. A noise-driven transition between ... More
Notes on Markov embeddingMar 20 2019The representation problem of finite-dimensional Markov matrices in Markov semigroups is revisited, with emphasis on concrete criteria for matrix subclasses of theoretical or practical relevance, such as equal-input, circulant, symmetric or doubly stochastic ... More
Cellular reproduction number, generation time and growth rate differ between human- and avian-adapted influenza strainsMar 19 2019When analysing in vitro data, growth kinetics of influenza strains are often compared by computing their growth rates, which are sometimes used as proxies for fitness. However, analogous to mechanistic epidemic models, the growth rate can be defined as ... More
Reciprocal Best Match GraphsMar 19 2019Reciprocal best matches play an important role in numerous applications in computational biology, in particular as the basis of many widely used tools for orthology assessment. Nevertheless, very little is known about their mathematical structure. Here, ... More
Beyond Activity Space: Detecting Communities in Ecological NetworksMar 18 2019Emerging research suggests that the extent to which activity spaces -- the collection of an individual's routine activity locations -- overlap provides important information about the functioning of a city and its neighborhoods. To study patterns of overlapping ... More
Efficient vaccination strategies for epidemic control using network informationMar 18 2019Network-based interventions against epidemic spread are most powerful when the full network structure is known. However, in practice, resource constraints require decisions to be made based on partial network information. We investigated how the accuracy ... More
Vegetation pattern formation in a sinuous free-scale landscapeMar 18 2019The original Hardenberg's model of biomass patterns in arid and semi-arid regions is revisited to extend it to more general non flat regions. It is proposed a technique to study these more generalized (non-flat) regions using both a conservation criterion ... More
General selection models: Bernstein duality and minimal ancestral structuresMar 15 2019The $\Lambda$-Wright--Fisher process describes the type-frequency evolution of an infinite population. We model frequency-dependent selection pressure with a general polynomial drift vanishing at the boundary. An appropriate decomposition of the drift ... More
Resilience Analysis for Competing PopulationsMar 14 2019Ecological resilience refers to the ability of a system to retain its state when subject to state variables perturbations or parameter changes. While understanding and quantifying resilience is crucial to anticipate the possible regime shifts, characterizing ... More
What could re-infection tell us about R0? a modeling case-study of syphilis transmissionMar 14 2019Many infectious diseases can lead to re-infection. We examined the relationship between the prevalence of repeat infection and the basic reproductive number (R0). First we solved a generic, deterministic compartmental model of re-infection to derive an ... More
Designing wildlife crossing structures for ungulates in a desert landscape: A case study in ChinaMar 14 2019This paper reports on the design of wildlife crossing structures (WCSs) along a new expressway in China, which exemplifies the country's increasing efforts on wildlife protection in infrastructure projects. The expert knowledge and field surveys were ... More
Antibody-mediated cross-linking of gut bacteria hinders the spread of antibiotic resistanceMar 13 2019The body is home to a diverse microbiota, mainly in the gut. Resistant bacteria are selected for by antibiotic treatments, and once resistance becomes widespread in a population of hosts, antibiotics become useless. Here, we develop a multiscale model ... More
Spatial memory and taxis-driven pattern formation in model ecosystemsMar 13 2019Mathematical models of spatial population dynamics typically focus on the interplay between dispersal events and birth/death processes. However, for many animal communities, significant arrangement in space can occur on shorter timescales, where births ... More
Who and When to Screen: Multi-Round Active Screening for Recurrent Infectious Diseases Under UncertaintyMar 13 2019Controlling recurrent infectious diseases is a vital yet complicated problem. In this paper, we propose a novel active screening model (ACTS) and algorithms to facilitate active screening for recurrent diseases (no permanent immunity) under infection ... More
Success of Alignment-Free Oligonucleotide (k-mer) Analysis Confirms Relative Importance of Genomes not Genes in Speciation and PhylogenyMar 12 2019The utility of DNA sequence substrings (k-mers) in alignment-free phylogenetic classification, including that of bacteria and viruses, is increasingly recognized. However, its biological basis eludes many twenty-first century practitioners. A path from ... More
First Record of Echinoparyphium recurvatum (Trematoda, Echinostomatidae) in Pakistan with New Avian Definitive Host, Vanellus leucurusMar 12 2019Parasitological examinations of White-tailed Lapwing Vanellus leucurus (Charadriiformes: Charadriidae) collected from Dadu district (Sindh Province, Southern Pakistan) were carried out at the Department of Zoology, University of Sindh, Jamshoro. A total ... More
Toxin-mediated competition in weakly motile bacteriaMar 11 2019Mar 13 2019Many bacterial species produce toxins that inhibit their competitors. We model this phenomenon by extending classic two-species Lotka-Volterra competition in one spatial dimension to incorporate toxin production by one species. Considering solutions comprising ... More
Toxin-mediated competition in weakly motile bacteriaMar 11 2019Many bacterial species produce toxins that inhibit their competitors. We model this phenomenon by extending classic two-species Lotka-Volterra competition in one spatial dimension to incorporate toxin production by one species. Considering solutions comprising ... More
Individual-Level SNP Diversity and Similarity ProfilesMar 11 2019Classic concepts of genetic (gene) diversity (heterozygosity) such as Nei (1973: PNAS) and Nei and Li (1979: PNAS) nucleotide diversity were defined within the context of populations. Although variations are often measured in population context, the basic ... More
Reactive learning strategies for iterated gamesMar 11 2019In an iterated game between two players, there is much interest in characterizing the set of feasible payoffs for both players when one player uses a fixed strategy and the other player is free to switch. Such characterizations have led to extortionists, ... More
Interactions between spatial and temporal scales in the evolution of dispersal rateMar 11 2019The evolution of dispersal rate is studied with a model of several local populations linked by dispersal. Three dispersal strategies are considered where all, half, or none of the offspring disperse. The spatial scale (number of patches) and the temporal ... More
On the convergence of the maximum likelihood estimator for the transition rate under a 2-state symmetric modelMar 10 2019Maximum likelihood estimators are used extensively to estimate unknown parameters of stochastic trait evolution models on phylogenetic trees. Although the MLE has been proven to converge to the true value in the independent-sample case, we cannot appeal ... More
Transition from endemic behavior to eradication of malaria due to combined drug therapies: an agent-model approachMar 08 2019We introduce an agent-based model describing a susceptible-infectious-susceptible (SIS) system of humans and mosquitoes to predict malaria epidemiological scenarios in realistic biological conditions. Emphasis is given to the transition from endemic behavior ... More
On the natural selection of macromolecular network and biological complexityMar 07 2019Modern biological tools have made it possible to unequivocally demonstrate the deep relationship among species in terms of genes and basic molecular mechanisms. In addition, results from genetic, physical and physiological approaches applied to individual ... More
Combining sale records of landings and fishers knowledge for predicting metiers in a small-scale, multi-gear, multispecies fisheryMar 07 2019Stock management should be guided by assessment models that, among others, need to be fed by reliable data of catch and effort. However, precise data are difficult to obtain in heterogeneous fisheries. Specifically, small scale, multi gear, multispecies ... More
Generosity, selfishness and exploitation as optimal greedy strategies for resource sharingMar 07 2019There is increasing evidence that fairness and generosity are not exclusive human traits. Indeed, several experiments on chimpanzees, monkeys and other mammals show an inequity-aversion behavior. Namely, if some valuable resource, e.g. food, is unevenly ... More
How can a knowledge of microbiota-pathogen interactions in cereal cropping systems help us to manage residue-borne fungal diseases?Mar 06 2019The epidemiological contribution of crop residues as a source of inoculum for fungal diseases on plants, especially in cereal cropping systems, is well established. However, microbial ecologists have long reported positive effects of crop residues on ... More
From cosmic explosions to terrestrial fires?Mar 04 2019Multiple lines of evidence point to one or more moderately nearby supernovae, with the strongest signal ~2.6 Ma. We build on previous work to argue for the likelihood of cosmic ray ionization of the atmosphere and electron cascades leading to more frequent ... More
Early Detection of Influenza outbreaks in the United StatesMar 04 2019Public health surveillance systems often fail to detect emerging infectious diseases, particularly in resource limited settings. By integrating relevant clinical and internet-source data, we can close critical gaps in coverage and accelerate outbreak ... More
Stability of a fractional HIV/AIDS modelMar 02 2019We propose a fractional order model for HIV/AIDS transmission. Local and uniform stability of the fractional order model is studied. The theoretical results are illustrated through numerical simulations.
Beltanelliformis brunsae Menner in Keller et al., 1974: an undoubted Ediacaran fossil from Neoproterozoic of Dobrogea (Romania)Feb 28 2019Ediacaran fossils are now largely known in different parts of the world. However, some countries are poorly documented on these remains of a still enigmatic life. Thus, rare fossils from the Neoproterozoic Histria Formation of central Dobrogea (Romania) ... More
Trade-offs between carbon stocks and biodiversity in European temperate forestsFeb 28 2019Policies to mitigate climate change and biodiversity loss often assume that protecting carbon-rich forests provides co-benefits in terms of biodiversity, due to the spatial congruence of carbon stocks and biodiversity at biogeographic scales. However, ... More
Current knowledge and future research opportunities for modeling annual crop mixtures. A reviewFeb 27 2019Growing mixtures of annual arable crop species or genotypes is a promising way to improve crop production without increasing agricultural inputs. To design optimal crop mixtures, choices of species, genotypes, sowing proportion, plant arrangement, and ... More
New insights into the population genetics of partially clonal organisms: when seagrass data meet theoretical expectationsFeb 26 2019Seagrass meadows are among the most important coastal ecosystems in terms of both spatial extent and ecosystem services but are declining worldwide. Understanding the drivers of seagrass meadow dynamics is essential for designing sound management, conservation ... More
Brownian motion tree models are toricFeb 26 2019Felsenstein's classical model for Gaussian distributions on a phylogenetic tree is shown to be a toric variety in the space of concentration matrices. We present an exact semialgebraic characterization of this model, and we demonstrate how the toric structure ... More
The discernible and hidden effects of clonality on the genotypic and genetic states of populations: improving our estimation of clonal ratesFeb 25 2019Mar 11 2019Partial clonality is widespread across the tree of life, but most population genetics models are conceived for exclusively clonal or sexual organisms. This gap hampers our understanding of the influence of clonality on evolutionary trajectories and the ... More
The discernible and hidden effects of clonality on the genotypic and genetic states of populations: improving our estimation of clonal ratesFeb 25 2019Partial clonality is widespread across the tree of life, but most population genetics models are conceived for exclusively clonal or sexual organisms. This gap hampers our understanding of the influence of clonality on evolutionary trajectories and the ... More
A comprehensive phase diagram for logistic populations in fluctuating environmentFeb 25 2019Population dynamics reflects an underlying birth-death process, where the rates associated with different events may depend on external environmental conditions and on the population density. A whole family of simple and popular deterministic models (like ... More
Diversity and its decomposition into variety, balance and disparityFeb 25 2019Feb 26 2019Diversity is a central concept in many fields. Despite its importance, there is no unified methodological framework to measure diversity and its three components of variety, balance and disparity. Current approaches take into account disparity of the ... More
Futuristic methods in virus genome evolution using the Third-Generation DNA sequencing and artificial neural networksFeb 25 2019The Third-Generation in DNA sequencing has emerged in the last few years using new technologies that allow the production of long-read sequences. Applications of the Third-Generation sequencing enable real-time and on-site data production, changing the ... More
Nutrient levels and trade-offs control diversity in a model seasonal ecosystemFeb 24 2019Microbial communities feature an immense diversity of species. Moreover, the extent of diversity correlates with outcomes ranging from ecosystem stability to favorable medical prognoses. Yet the mechanisms underlying microbial diversity are not well understood. ... More
Generation of Tree-Child phylogenetic networksFeb 24 2019Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary tree-child networks ... More
Time Distribution for Persistent Viral InfectionFeb 24 2019We study the early stages of viral infection, and the distribution of times to obtain a persistent infection. The virus population proliferates by entering and reproducing inside a target cell until a sufficient number of new virus particles are released ... More
Fitting stochastic epidemic models to gene genealogies using linear noise approximationFeb 24 2019Phylodynamics is a set of population genetics tools that aim at reconstructing demographic history of a population based on molecular sequences of individuals sampled from the population of interest. One important task in phylodynamics is to estimate ... More
Optimal Investment to Enable Evolutionary RescueFeb 23 2019'Evolutionary rescue' is the potential for evolution to enable population persistence in a changing environment. Even with eventual rescue, evolutionary time lags can cause the population size to temporarily fall below a threshold susceptible to extinction. ... More
Embeddability and rate identifiability of Kimura 2-parameter matricesFeb 22 2019Deciding whether a Markov matrix is embeddable (i.e. can be written as the exponential of a rate matrix) is an open problem even for $4\times 4$ matrices. We study the embedding problem and rate identifiability for the K80 model of nucleotide substitution. ... More
Modelling honey bee colonies in winter using a Keller-Segel model with a sign-changing chemotactic coefficientFeb 22 2019Thermoregulation in honey bee colonies during winter is thought to be self-organised. We added mortality of individual honey bees to an existing model of thermoregulation to account for elevated losses of bees that are reported worldwide. The aim of analysis ... More
First assessment of the plant phenology index (PPI) for estimating gross primary productivity in African semi-arid ecosystemsFeb 21 2019The importance of semi-arid ecosystems in the global carbon cycle as sinks for CO2 emissions has recently been highlighted. Africa is a carbon sink and nearly half its area comprises arid and semi-arid ecosystems. However, there are uncertainties regarding ... More
Cell pelotons: a model of early evolutionary cell sorting, with application to slime mold D. discoideumFeb 20 2019A theoretical model is presented for early evolutionary cell sorting within cellular aggregates. The model involves an energy-saving mechanism and principles of collective self-organization analogous to those observed in bicycle pelotons (groups of cyclists). ... More
Recombination and mutational robustness in neutral fitness landscapesFeb 19 2019Mutational robustness quantifies the effect of random mutations on fitness. When mutational robustness is high, most mutations do not change fitness or have only a minor effect on it. From the point of view of fitness landscapes, robust genotypes form ... More
A stochastic individual based model for the growth of a stand of Japanese knotweed including mowing as a management techniqueFeb 19 2019Invasive alien species are a growing threat for environment and health. They also have a major economic impact, as they can damage many infrastructures. The Japanese knotweed (Fallopia japonica), present in North America, Northern and Central Europe as ... More
Mean and variance of first passage time in Markov chains with unknown parametersFeb 18 2019Mar 01 2019There are known expressions to calculate the moments of the first passage time in Markov chains. Nevertheless, it is commonly forgotten that in most applications the parameters of the Markov chain are constructed using estimates based upon empirical data ... More
Mean and variance of first passage time in Markov chains with unknown parametersFeb 18 2019There are known expressions to calculate the moments of the first passage time in Markov chains. Nevertheless, it is commonly forgotten that in most applications the parameters of the Markov chain are constructed using estimates based upon empirical data ... More
Evolutionary dynamics determines adaptation to inactivation of an essential geneFeb 18 2019Genetic inactivation of essential genes creates an evolutionary scenario distinct from escape from drug inhibition, but the mechanisms of microbe adaptations in such cases remain unknown. Here we inactivate E. coli dihydrofolate reductase (DHFR) by introducing ... More
Methods for approximating stochastic evolutionary dynamics on graphsFeb 18 2019Population structure can have a significant effect on evolution. For some systems with sufficient symmetry, analytic results can be derived within the mathematical framework of evolutionary graph theory which relate to the outcome of the evolutionary ... More
Molecular Phylogeny of Chinese Thuidiaceae with emphasis on Thuidium and PelekiumFeb 16 2019We present molecular phylogenetic investigation of Thuidiaceae, especially on Thudium and Pelekium. Three chloroplast sequences (trnL-F, rps4, and atpB-rbcL) and one nuclear sequence (ITS) were analyzed. Data partitions were analyzed separately and in ... More
Competition-driven evolution of organismal complexityFeb 15 2019Non-uniform rates of morphological evolution and evolutionary increases in organismal complexity, captured in metaphors like "adaptive zones", "punctuated equilibrium" and "blunderbuss patterns", require more elaborate explanations than a simple gradual ... More
Sequential importance sampling for multi-resolution Kingman-Tajima coalescent countingFeb 14 2019Statistical inference of evolutionary parameters from molecular sequence data relies on coalescent models to account for the shared genealogical ancestry of the samples. However, inferential algorithms do not scale to available data sets. A strategy to ... More
A Note on Estimating Optimal Dynamic Treatment Strategies Under Resource Constraints Using Dynamic Marginal Structural ModelsFeb 14 2019Existing strategies for determining the optimal treatment or monitoring strategy typically assume unlimited access to resources. However, when a health system has resource constraints, such as limited funds, access to medication, or monitoring capabilities, ... More
Cancer recurrence times from a branching process modelFeb 13 2019Cancer often spreads from a primary tumor and forms metastases, that are the main cause of cancer mortality. Here we investigate a conceptually simple model of metastasis formation where metastatic lesions are initiated at a rate which depends on the ... More
Selective Inference for Testing Trees and Edges in PhylogeneticsFeb 13 2019Selective inference is considered for testing trees and edges in phylogenetic tree selection from molecular sequences. This improves the previously proposed approximately unbiased test by adjusting the selection bias when testing many trees and edges ... More
Effects of empathy on the evolution of fairness in group-structured populationsFeb 12 2019The ultimatum game has been a prominent paradigm in studying the evolution of fairness. It predicts that responders should accept any nonzero offer and proposers should offer the smallest possible amount according to orthodox game theory. However, the ... More
MPA network design based on graph network theory and emergent properties of larval dispersalFeb 11 2019Mar 14 2019Understanding the connectivity patterns of marine populations is essential for their management and conservation. In the case of sedentary marine populations, connectivity stems not only from the stochastic nature of the physical environment that affects ... More
MPA network design based on graph network theory and emergent properties of larval dispersalFeb 11 2019Understanding the connectivity patterns of marine populations is essential for their management and conservation. In the case of sedentary marine populations, connectivity stems not only from the stochastic nature of the physical environment that affects ... More
MPA network design based on graph network theory and emergent properties of larval dispersalFeb 11 2019Mar 07 2019Understanding the connectivity patterns of marine populations is essential for their management and conservation. In the case of sedentary marine populations, connectivity stems not only from the stochastic nature of the physical environment that affects ... More
MPA network design based on graph network theory and emergent properties of larval dispersalFeb 11 2019Feb 27 2019Understanding the connectivity patterns of marine populations is essential for their management and conservation. In the case of sedentary marine populations, connectivity stems not only from the stochastic nature of the physical environment that affects ... More
Multi-Season Analysis Reveals the Spatial Structure of Disease SpreadFeb 11 2019Understanding the dynamics of infectious disease spread in a heterogeneous population is an important factor in designing control strategies. Here, we develop a novel tensor-driven multi-compartment version of the classic Susceptible-Infected-Recovered ... More
When do factors promoting balanced selection also promote population persistence? A demographic perspective on Gillespie's SAS-CFF modelFeb 09 2019Classical stochasticity demography predicts that environmental stochasticity reduces population growth rates and, thereby, can increase extinction risk. In contrast, the SAS-CFF model demonstrates that environmental stochasticity can promote genetic diversity. ... More
Exchangeable and Sampling Consistent Distributions on Rooted Binary TreesFeb 08 2019Mar 05 2019We introduce a notion of finite sampling consistency for phylogenetic trees and show that the set of finitely sampling consistent and exchangeable distributions on n leaf phylogenetic trees is a polytope. We use this polytope to show that the set of all ... More
Exchangeable and Sampling Consistent Distributions on Rooted Binary TreesFeb 08 2019We introduce a notion of finite sampling consistency for phylogenetic trees and show that the set of finitely sampling consistent and exchangeable distributions on n leaf phylogenetic trees is a polytope. We use this polytope to show that the set of all ... More
Spatial eco-evolutionary feedbacks mediate coexistence in prey-predator systemsFeb 08 2019Eco-evolutionary frameworks can explain certain features of communities in which ecological and evolutionary processes occur over comparable timescales. In the particular case of prey-predator systems, a combination of empirical and theoretical studies ... More
Synergistic Effects in Networked Epidemic Spreading DynamicsFeb 08 2019In this brief, we study epidemic spreading dynamics taking place in complex networks. We specifically investigate the effect of synergy, where multiple interactions between nodes result in a combined effect larger than the simple sum of their separate ... More
A Survey of the Individual-Based Model applied in Biomedical and EpidemiologyFeb 07 2019Individual-based model (IBM) has been used to simulate and to design control strategies for dynamic systems that are subject to stochasticity and heterogeneity, such as infectious diseases. In the IBM, an individual is represented by a set of specific ... More
Estimating resilience of annual crop production systems: theory and limitationsFeb 07 2019Agricultural production is affected by climate extremes, which are increasing because of global warming. This motivates the need of a proper evaluation of the agricultural production systems resilience to enhance food security, market stability, and the ... More
Combinatorial properties of phylogenetic diversity indices for rooted and unrooted treesFeb 07 2019Phylogenetic diversity indices provide a formal way to apportion 'evolutionary heritage' across species. Two natural diversity indices are Fair Proportion (FP) and Equal Splits (ES). FP is also called 'evolutionary distinctiveness' and, for rooted trees, ... More
Cannings models, populations size changes and multiple-merger coalescentsFeb 06 2019Multiple-merger coalescents, e.g. $\Lambda$-$n$-coalescents, have been proposed as models of the genealogy of $n$ sampled individuals for a range of populations whose genealogical structures are not captured well by Kingman's $n$-coalescent. $\Lambda$-$n$-coalescents ... More
Vaccination dilemma on an evolving social networkFeb 05 2019Vaccination is crucial for the control of epidemics. Yet it is a social dilemma since non-vaccinators can benefit from the herd immunity created by the vaccinators. Thus the optimum vaccination level is not reached via voluntary vaccination at times. ... More
Sex-ratio bias induced by mutationFeb 04 2019A question in evolutionary biology is why the number of males is approximately equal to that of females in many species, and Fisher's theory of equal investment answers that it is the evolutionarily stable state. The Fisherian mechanism can be given a ... More
Anderson-like localization transition of random walks with resettingFeb 02 2019We study several lattice random walk models with stochastic resetting and memory which exhibit a phase transition between an anomalous diffusive regime and a localization regime where diffusion is suppressed. The localized phase settles above a critical ... More
Waves of desertification in a competitive ecosystemJan 31 2019We study a mathematical model inspired by a common scenario in northern Patagonia consisting of humans and their livestock living together with native wildlife. The main production system in this area is sheep farming, which due to wrong historical management ... More
Numerical implementation of dynamical mean field theory for disordered systems: application to the Lotka-Volterra model of ecosystemsJan 28 2019Dynamical mean field theory (DMFT) is a tool that allows to analyze the stochastic dynamics of $N$ interacting degrees of freedom in terms of a self-consistent $1$-body problem. In this work, focusing on models of ecosystems, we present the derivation ... More
The Minimum Environmental Perturbation Principle: A New Perspective on Niche TheoryJan 28 2019Jan 29 2019Contemporary niche theory is a powerful conceptual framework for understanding how organisms interact with each other and with their shared environment. Here we show that a large segment of niche theory is equivalent to a Minimum Environmental Perturbation ... More
Fixation in Fluctuating PopulationsJan 24 2019We investigate the dynamics of the voter model in which the population itself changes endogenously via the birth-death process. There are two species of voters, labeled A and B, and the population of each species can grow or shrink by the birth-death ... More
Preventing exponential spread of infectious diseases with low $R_0$: insights from a spatial epidemic SIR modelJan 23 2019The spread of an epidemic is considered in the context of a SIR spatial stochastic model that includes a parameter $0\le p\le 1$ that assigns weights $p$ and $1-p$ to global and local infective contacts respectively. For diseases with low values of the ... More
Knowing the past improves cooperation in the futureJan 22 2019Cooperation is the cornerstone of human evolutionary success. Like no other species, we champion the sacrifice of personal benefits for the common good, and we work together to achieve what we are unable to achieve alone. Knowledge and information from ... More
Collective learning from individual experiences and information transfer during group foragingJan 22 2019Living in groups brings benefits to many animals, such as a protection against predators and an improved capacity for sensing and making decisions while searching for resources in uncertain environments. A body of studies has shown how collective behaviors ... More
Consequences of delays and imperfect implementation of isolation in epidemic controlJan 21 2019For centuries isolation has been the main control strategy of unforeseen epidemic outbreaks. When implemented in full and without delay, isolation is very effective. However, flawless implementation is seldom feasible in practice. We present an epidemic ... More
Linking lineage and population observables in biological branching processesJan 21 2019Using a population dynamics inspired by an ensemble of growing cells, a set of fluctuation theorems linking observables measured at the lineage and population levels are derived. One of these relations implies inequalities comparing the population doubling ... More
Spatial interactions and oscillatory tragedies of the commonsJan 21 2019A tragedy of the commons (TOC) occurs when individuals acting in their own self-interest deplete commonly-held resources, leading to a worse outcome than had they cooperated. Over time, the depletion of resources can change incentives for subsequent actions. ... More
Integrability of Stochastic Birth-Death processes via Differential Galois TheoryJan 18 2019Stochastic birth-death processes are described as continuous-time Markov processes in models of population dynamics. A system of infinite, coupled ordinary differential equations (the so-called master equation) describes the time-dependence of the probability ... More
Hopf-bifurcation analysis of pneumococcal pneumonia with time delaysJan 15 2019In this paper, a mathematical model of pneumococcal pneumonia with time delays is proposed. The stability theory of delay differential equations is used to analyze the model. The results show that the disease-free equilibrium is asymptotically stable ... More
Transient Compartmentalization dynamics in the presence of mutations and noiseJan 15 2019We extend a recently introduced framework for transient compartmentalization of replicators with selection dynamics, by including the effect of mutations and noise in such systems. In the presence of mutations, functional replicators (ribozymes) are turned ... More
Roadblocked monotonic paths and the enumeration of coalescent histories for non-matching caterpillar gene trees and species treesJan 14 2019Given a gene tree topology and a species tree topology, a coalescent history represents a possible mapping of the list of gene tree coalescences to associated branches of a species tree on which those coalescences take place. Enumerative properties of ... More
A study of the persistence and extinction of malaria in a family of epidemic modelsJan 14 2019This paper investigates the deterministic extinction and permanence of a family of SEIRS malaria models with multiple random delays, and with a general nonlinear incidence rate. The conditions for the extinction and permanence of the disease are presented. ... More
The stochastic extinction and stability conditions for a class of malaria epidemic modelsJan 14 2019The stochastic extinction and stability in the mean of a family of SEIRS malaria models with a general nonlinear incidence rate is presented. The dynamics is driven by independent white noise processes from the disease transmission and natural death rates. ... More
Reducing measles risk in Turkey through social integration of Syrian refugeesJan 14 2019Turkey hosts almost 3.5M refugees and has to face a humanitarian emergency of unprecedented levels. We use mobile phone data to map the mobility patterns of both Turkish and Syrian refugees, and use these patterns to build data-driven computational models ... More
Game theoretic modelling of infectious disease dynamics and intervention methods: a mini-reviewJan 14 2019We review research papers which use game theory to model the decision making of individuals during an epidemic, attempting to classify the literature and identify the emerging trends in this field. We show that the literature can be classified based on ... More
A Combinatorial Model for Heterogeneous Microbial GrowthJan 13 2019Recent advances in quantifying phenotypic heterogeneity in bacteria have shown its broad prevalence in nature. However, evaluating the ultimate impact of single-organism heterogeneity at the population level remains an active area of research in microbiology. ... More