Why so many polyploids? Accounting for environmental stochasticity in unreduced gamete formation lowers the perceived barriers to polyploid establishment.

While polyploids are common in nature, existing models suggest that polyploid establishment should be difficult and rare. We explore this apparent paradox by focussing on the role of unreduced gametes, as their union is the main route for the formation of neopolyploids. Production of such gametes is affected by genetic and environmental factors, resulting in variation in the formation rate of unreduced gametes (u). Once formed, neopolyploids face minority cytotype exclusion (MCE) due to a lack of viable mating opportunities. More than a dozen theoretical models have explored factors that could permit neopolyploids to overcome MCE and become established. Until now, however, none have explored variability in u and its consequences for the rate of polyploid establishment. Here, we determine the distribution that best fits the available empirical data on u. We perform a global sensitivity analysis exploring the consequences of using empirical distributions of u to investigate effects on polyploid establishment. We determined that in many cases, u is best fit by a log-normal distribution. We found environmental stochasticity in u dramatically impacts model predictions when compared to a static u. Our results help reconcile previous modelling results suggesting high barriers to the polyploid establishment with the observation that polyploids are common in nature.

Distinguishing viruses responsible for influenza-like illness.

The many respiratory viruses that cause influenza-like illness (ILI) are reported and tracked as one entity, defined by the CDC as a group of symptoms that include a fever of 100 degrees Fahrenheit, a cough, and/or a sore throat. In the United States alone, ILI impacts 9-49 million people every year. While tracking ILI as a single clinical syndrome is informative in many respects, the underlying viruses differ in parameters and outbreak properties. Most existing models treat either a single respiratory virus or ILI as a whole. However, there is a need for models capable of comparing several individual viruses that cause respiratory illness, including ILI. To address this need, here we present a flexible model and simulations of epidemics for influenza, RSV, rhinovirus, seasonal coronavirus, adenovirus, and SARS/MERS, parameterized by a systematic literature review and accompanied by a global sensitivity analysis. We find that for these biological causes of ILI, their parameter values, timing, prevalence, and proportional contributions differ substantially. These results demonstrate that distinguishing the viruses that cause ILI will be an important aspect of future work on diagnostics, mitigation, modeling, and preparation for future pandemics.

Optimizing homeostatic cell renewal in hierarchical tissues.

In order to maintain homeostasis, mature cells removed from the top compartment of hierarchical tissues have to be replenished by means of differentiation and self-renewal events happening in the more primitive compartments. As each cell division is associated with a risk of mutation, cell division patterns have to be optimized, in order to minimize or delay the risk of malignancy generation. Here we study this optimization problem, focusing on the role of division tree length, that is, the number of layers of cells activated in response to the loss of terminally differentiated cells, which is related to the balance between differentiation and self-renewal events in the compartments. Using both analytical methods and stochastic simulations in a metapopulation-style model, we find that shorter division trees are advantageous if the objective is to minimize the total number of one-hit mutants in the cell population. Longer division trees on the other hand minimize the accumulation of two-hit mutants, which is a more likely evolutionary goal given the key role played by tumor suppressor genes in cancer initiation. While division tree length is the most important property determining mutant accumulation, we also find that increasing the size of primitive compartments helps to delay two-hit mutant generation.

Evidence of cryptic incidence in childhood diseases.

Persistence and extinction are key processes in infectious disease dynamics that, owing to incomplete reporting, are seldom directly observable. For fully immunizing diseases, reporting probabilities can be readily estimated from demographic records and case reports. Yet reporting probabilities are not sufficient to unambiguously reconstruct disease incidence from case reports. Here, we focus on disease presence (i.e. marginal probability of non-zero incidence), which provides an upper bound on the marginal probability of disease extinction. We examine measles and pertussis in pre-vaccine era United States (US) cities, and describe a conserved scaling relationship between population size, reporting probability and observed presence (i.e. non-zero case reports). We use this relationship to estimate disease presence given perfect reporting, and define cryptic presence as the difference between estimated and observed presence. We estimate that, in early twentieth century US cities, pertussis presence was higher than measles presence across a range of population sizes, and that cryptic presence was common in small cities with imperfect reporting. While the methods employed here are specific to fully immunizing diseases, our results suggest that cryptic incidence deserves careful attention, particularly in diseases with low case counts, poor reporting and longer infectious periods.

Bridging the Gap Between Experimental Data and Model Parameterization for Chikungunya Virus Transmission Predictions.

Chikungunya virus (CHIKV) has experienced 2 major expansion events in the last decade. The most recently emerged sublineage (ECSA-V) was shown to have increased efficiency in a historically secondary vector, Aedes albopictus, leading to speculation that this was a major factor in expansion. Subsequently, a number of experimental studies focused on the vector competence of CHIKV, as well as transmission modeling efforts. Mathematical models have used these data to inform their own investigations, but some have incorrectly parameterized the extrinsic incubation period (EIP) of the mosquitoes, using vector competence data. Vector competence and EIP are part of the same process but are not often correctly reported together. Thus, the way these metrics are used for model parameterization can be problematic. We offer suggestions for bridging this gap for the purpose of standardization of reporting and to promote appropriate use of experimental data in modeling efforts.

Dengue and chikungunya: modelling the expansion of mosquito-borne viruses into naïve populations.

With the recent global spread of a number of mosquito-borne viruses, there is an urgent need to understand the factors that contribute to the ability of viruses to expand into naïve populations. Using dengue and chikungunya viruses as case studies, we detail the necessary components of the expansion process: presence of the mosquito vector; introduction of the virus; and suitable conditions for local transmission. For each component we review the existing modelling approaches that have been used to understand recent emergence events or to assess the risk of future expansions. We identify gaps in our knowledge that are related to each of the distinct aspects of the human-mosquito transmission cycle: mosquito ecology; human-mosquito contact; mosquito-virus interactions; and human-virus interactions. Bridging these gaps poses challenges to both modellers and empiricists, but only through further integration of models and data will we improve our ability to better understand, and ultimately control, several infectious diseases that exert a significant burden on human health.

Conserved patterns of incomplete reporting in pre-vaccine era childhood diseases.

Incomplete observation is an important yet often neglected feature of observational ecological timeseries. In particular, observational case report timeseries of childhood diseases have played an important role in the formulation of mechanistic dynamical models of populations and metapopulations. Yet to our knowledge, no comprehensive study of childhood disease reporting probabilities (commonly referred to as reporting rates) has been conducted to date. Here, we provide a detailed analysis of measles and whooping cough reporting probabilities in pre-vaccine United States cities and states, as well as measles in cities of England and Wales. Overall, we find the variability between locations and diseases greatly exceeds that between methods or time periods. We demonstrate a strong relationship within location between diseases and within disease between geographical areas. In addition, we find that demographic covariates such as ethnic composition and school attendance explain a non-trivial proportion of reporting probability variation. Overall, our findings show that disease reporting is both variable and non-random and that completeness of reporting is influenced by disease identity, geography and socioeconomic factors. We suggest that variations in incomplete observation can be accounted for and that doing so can reveal ecologically important features that are otherwise obscured.

Comparing dengue and chikungunya emergence and endemic transmission in A. aegypti and A. albopictus.

Chikungunya and dengue are re-emerging mosquito-borne infectious diseases that are of increasing concern as human travel and expanding mosquito ranges increase the risk of spread. We seek to understand the differences in transient and endemic behavior of chikungunya and dengue; risk of emergence for different virus-vector assemblages; and the role that virus evolution plays in disease dynamics and risk. To address these questions, we adapt a mathematical mosquito-borne disease model to chikungunya and dengue in Aedes aegypti and Aedes albopictus mosquitoes. We derive analytical threshold conditions and important dimensionless parameters for virus transmission; perform sensitivity analysis on quantities of interest such as the basic reproduction number, endemic equilibrium, and first epidemic peak; and compute distributions for the quantities of interest across parameter ranges. We found that chikungunya and dengue exhibit different transient dynamics and long-term endemic levels. While the order of most sensitive parameters is preserved across vector-virus combinations, the magnitude of sensitivity is different across scenarios, indicating that risk of invasion or an outbreak can change with vector-virus assemblages. We found that the dengue - A. aegypti and new Rèunion strain of chikungunya - A. albopictus systems represent the highest risk across the range of parameters considered. These results inform future experimental and field research efforts and point toward effective mitigation strategies adapted to each disease.

Probabilistic measures of persistence and extinction in measles (meta)populations.

Persistence and extinction are fundamental processes in ecological systems that are difficult to accurately measure due to stochasticity and incomplete observation. Moreover, these processes operate on multiple scales, from individual populations to metapopulations. Here, we examine an extensive new data set of measles case reports and associated demographics in pre-vaccine era US cities, alongside a classic England & Wales data set. We first infer the per-population quasi-continuous distribution of log incidence. We then use stochastic, spatially implicit metapopulation models to explore the frequency of rescue events and apparent extinctions. We show that, unlike critical community size, the inferred distributions account for observational processes, allowing direct comparisons between metapopulations. The inferred distributions scale with population size. We use these scalings to estimate extinction boundary probabilities. We compare these predictions with measurements in individual populations and random aggregates of populations, highlighting the importance of medium-sized populations in metapopulation persistence.

Identification of blood meal sources in Aedes vexans and Culex quinquefasciatus in Bernalillo County, New Mexico.

Culex quinquefasciatus Say (Diptera: Culicidae) and Aedes vexans Meigen are two of the most abundant mosquitoes in Bernalillo County, New Mexico, USA. In this study, a polymerase chain reaction based methodology was used to identify the sources of blood meals taken by these two species. Ae. vexans was found to take a large proportion of its meals from mammals. Although less specific in terms of its blood meal preferences, Cx. quinquefasciatus was found to feed more commonly on birds. The results for Ae. vexans are similar to those reported for this species in other parts of their geographic range. Cx. quinquefasciatus appears to be more variable in terms of its host feeding under different environmental or seasonal circumstances. The implications of these results for arbovirus transmission are discussed.

Streamlining physiologically-based pharmacokinetic model design for intravenous delivery of nanoparticle drugs.

Physiologically-based pharmacokinetic (PBPK) modeling for nanoparticles elucidates the nanoparticle drug's disposition in the body and serves a vital role in drug development and clinical studies. This paper offers a systematic and tutorial-like approach to developing a model structure and writing distribution ordinary differential equations based on asking binary questions involving the physicochemical nature of the drug in question. Further, by synthesizing existing knowledge, we summarize pertinent aspects in PBPK modeling and create a guide for building model structure and distribution equations, optimizing nanoparticle and non-nanoparticle specific parameters, and performing sensitivity analysis and model validation. The purpose of this paper is to facilitate a streamlined model development process for students and practitioners in the field.

How do i bite thee? let me count the ways: Exploring the implications of individual biting habits of Aedes aegypti for dengue transmission.

In models of mosquito-borne transmission, the mosquito biting rate is an influential parameter, and understanding the heterogeneity of the process of biting is important, as biting is usually assumed to be relatively homogeneous across individuals, with time-between-bites described by an exponentially distributed process. However, these assumptions have not been addressed through laboratory experimentation. We experimentally investigated the daily biting habits of Ae. aegypti at three temperatures (24°C, 28°C, and 32°C) and determined that there was individual heterogeneity in biting habits (number of bites, timing of bites, etc.). We further explored the consequences of biting heterogeneity using an individual-based model designed to examine whether a particular biting profile determines whether a mosquito is more or less likely to 1) become exposed given a single index case of dengue (DENV) and 2) transmit to a susceptible human individual. Our experimental results indicate that there is heterogeneity among individuals and among temperature treatments. We further show that this results in altered probabilities of transmission of DENV to and from individual mosquitoes based on biting profiles. While current model representation of biting may work under some conditions, it might not uniformly be the best fit for this process. Our data also confirm that biting is a non-monotonic process with temperatures around 28°C being optimum.

Estimating the duration of pertussis immunity using epidemiological signatures.

Case notifications of pertussis have shown an increase in a number of countries with high rates of routine pediatric immunization. This has led to significant public health concerns over a possible pertussis re-emergence. A leading proposed explanation for the observed increase in incidence is the loss of immunity to pertussis, which is known to occur after both natural infection and vaccination. Little is known, however, about the typical duration of immunity and its epidemiological implications. Here, we analyze a simple mathematical model, exploring specifically the inter-epidemic period and fade-out frequency. These predictions are then contrasted with detailed incidence data for England and Wales. We find model output to be most sensitive to assumptions concerning naturally acquired immunity, which allows us to estimate the average duration of immunity. Our results support a period of natural immunity that is, on average, long-lasting (at least 30 years) but inherently variable.

Modeling schistosomiasis transmission: the importance of snail population structure.

BACKGROUND: Schistosomiasis is a neglected tropical disease endemic in 54 countries. A major Schistosoma species, Schistosoma mansoni, is sustained via a life cycle that includes both human and snail hosts. Mathematical models of S. mansoni transmission, used to elucidate the complexities of the transmission cycle and estimate the impact of intervention efforts, often focus primarily on the human host. However, S. mansoni incurs physiological costs in snails that vary with the age of the snail when first infected. Snail demography and the age of snail infection could thus affect the force of infection experienced by humans, which is frequently used to predict the impact of various control strategies. METHODS: To address how these snail host and parasite interactions influence model predictions, we developed deterministic models of schistosomiasis transmission that include varying complexity in the snail population age structure. Specifically, we examined how model outputs, such as schistosome prevalence in human and snail populations, respond to the inclusion of snail age structure. RESULTS: Our models suggest that snail population age structure modifies the force of infection experienced by humans and the relationship between snail infection prevalence and corresponding human infection prevalence. There are significant differences in estimated snail infection, cercarial density and mean worm burden between models without snail population dynamics and those with snail populations, and between models with a homogeneous snail population and those with age stratification. The variation between finely age-stratified snail populations and those grouped into only juvenile and adult life stages is, however, minimal. CONCLUSIONS: These results indicate that including snails and snail age structure in a schistosomiasis transmission model alters the relationship between snail and human infection prevalence. This highlights the importance of accounting for a heterogeneous intermediate host population in models of schistosomiasis transmission where the impact of proposed control measures is being considered.

Age-structured vectorial capacity reveals timing, not magnitude of within-mosquito dynamics is critical for arbovirus fitness assessment.

BACKGROUND: Transmission dynamics of arboviruses like Zika virus are often evaluated by vector competence (the proportion of infectious vectors given exposure) and the extrinsic incubation period (EIP, the time it takes for a vector to become infectious), but vector age is another critical driver of transmission dynamics. Vectorial capacity (VC) is a measure of transmission potential of a vector-pathogen system, but how these three components, EIP, vector competence and vector age, affect VC in concert still needs study. METHODS: The interaction of vector competence, EIP, and mosquito age at the time of infection acquisition (Ageacquisition) was experimentally measured in an Aedes aegypti-ZIKV model system, as well as the age-dependence of probability of survival and the willingness to bite. An age-structured vectorial capacity framework (VCage) was then developed using both EIPMin and EIPMax, defined as the time to first observed minimum proportion of transmitting mosquitoes and the time to observed maximum proportion of transmitting mosquitoes. RESULTS: The within-mosquito dynamics of vector competence/EIP were not significant among treatments where mosquitoes were exposed at different ages. However, VCage revealed: (i) age-dependence in vector-virus interactions is important for transmission success; (ii) lower vector competence but at shorter EIPs was sufficient for transmission perpetuation; and (iii) R0 may be overestimated by using non-age-structured VC. CONCLUSIONS: The results indicate that ultimately the temporal component of the virus-vector dynamics is most critical, especially when exposure occurred at advanced mosquito age. While our study is limited to a single virus-vector system, and a multitude of other factors affect both vector competence and mosquito mortality, our methods can be extrapolated to these other scenarios. Results indicate that how 'highly' or 'negligibly' competent vectors are categorized may need adjustment.

Evolutionary consequences of feedbacks between within-host competition and disease control.

Lay Summary: Competition often occurs among diverse parasites within a single host, but control efforts could change its strength. We examined how the interplay between competition and control could shape the evolution of parasite traits like drug resistance and disease severity.

Temperature impacts on dengue emergence in the United States: Investigating the role of seasonality and climate change.

Tropical mosquito-borne viruses have been expanding into more temperate regions in recent decades. This is partly due to the coupled effects of temperature on mosquito life history traits and viral infection dynamics and warming surface temperatures, resulting in more suitable conditions for vectors and virus transmission. In this study, we use a deterministic ordinary differential equations model to investigate how seasonal and diurnal temperature fluctuations affect the potential for dengue transmission in six U.S. cities. We specifically consider temperature-dependent mosquito larval development, adult mosquito mortality, and the extrinsic incubation period of the virus. We show that the ability of introductions to lead to outbreaks depends upon the relationship between a city's temperature profile and the time of year at which the initial case is introduced. We also investigate how the potential for outbreaks changes with predicted future increases in mean temperatures due to climate change. We find that climate change will likely lead to increases in suitability for dengue transmission and will increase the periods of the year in which introductions may lead to outbreaks, particularly in cities that typically have mild winters and warm summers, such as New Orleans, Louisiana, and El Paso, Texas. We discuss our results in the context of temperature heterogeneity within and across cities and how these differences may impact the potential for dengue emergence given present day and predicted future temperatures.

Antagonism between parasites within snail hosts impacts the transmission of human schistosomiasis.

Human disease agents exist within complex environments that have underappreciated effects on transmission, especially for parasites with multi-host life cycles. We examined the impact of multiple host and parasite species on transmission of the human parasite Schistosoma mansoni in Kenya. We show S. mansoni is impacted by cattle and wild vertebrates because of their role in supporting trematode parasites, the larvae of which have antagonistic interactions with S. mansoni in their shared Biomphalaria vector snails. We discovered the abundant cattle trematode, Calicophoron sukari, fails to develop in Biomphalaria pfeifferi unless S. mansoni larvae are present in the same snail. Further development of S. mansoni is subsequently prevented by C. sukari's presence. Modeling indicated that removal of C. sukari would increase S. mansoni-infected snails by two-fold. Predictable exploitation of aquatic habitats by humans and their cattle enable C. sukari to exploit S. mansoni, thereby limiting transmission of this human pathogen.

Metabolic asymmetry and the global diversity of marine predators.

Species richness of marine mammals and birds is highest in cold, temperate seas-a conspicuous exception to the general latitudinal gradient of decreasing diversity from the tropics to the poles. We compiled a comprehensive dataset for 998 species of sharks, fish, reptiles, mammals, and birds to identify and quantify inverse latitudinal gradients in diversity, and derived a theory to explain these patterns. We found that richness, phylogenetic diversity, and abundance of marine predators diverge systematically with thermoregulatory strategy and water temperature, reflecting metabolic differences between endotherms and ectotherms that drive trophic and competitive interactions. Spatial patterns of foraging support theoretical predictions, with total prey consumption by mammals increasing by a factor of 80 from the equator to the poles after controlling for productivity.

Modeling Mosquito-Borne Disease Spread in U.S. Urbanized Areas: The Case of Dengue in Miami.

Expansion of mosquito-borne pathogens into more temperate regions of the world necessitates tools such as mathematical models for understanding the factors that contribute to the introduction and emergence of a disease in populations naïve to the disease. Often, these models are not developed and analyzed until after a pathogen is detected in a population. In this study, we develop a spatially explicit stochastic model parameterized with publicly available U.S. Census data for studying the potential for disease spread in Urbanized Areas of the United States. To illustrate the utility of the model, we specifically study the potential for introductions of dengue to lead to autochthonous transmission and outbreaks in a population representative of the Miami Urbanized Area, where introductions of dengue have occurred frequently in recent years. We describe seasonal fluctuations in mosquito populations by fitting a population model to trap data provided by the Miami-Dade Mosquito Control Division. We show that the timing and location of introduced cases could play an important role in determining both the probability that local transmission occurs as well as the total number of cases throughout the entire region following introduction. We show that at low rates of clinical presentation, small outbreaks of dengue could go completely undetected during a season, which may confound mitigation efforts that rely upon detection. We discuss the sensitivity of the model to several critical parameter values that are currently poorly characterized and motivate the collection of additional data to strengthen the predictive power of this and similar models. Finally, we emphasize the utility of the general structure of this model in studying mosquito-borne diseases such as chikungunya and Zika virus in other regions.