Weak-form inference for hybrid dynamical systems in ecology.

Species subject to predation and environmental threats commonly exhibit variable periods of population boom and bust over long timescales. Understanding and predicting such behaviour, especially given the inherent heterogeneity and stochasticity of exogenous driving factors over short timescales, is an ongoing challenge. A modelling paradigm gaining popularity in the ecological sciences for such multi-scale effects is to couple short-term continuous dynamics to long-term discrete updates.

Direct Estimation of Parameters in ODE Models Using WENDy: Weak-Form Estimation of Nonlinear Dynamics.

We introduce the Weak-form Estimation of Nonlinear Dynamics (WENDy) method for estimating model parameters for non-linear systems of ODEs. Without relying on any numerical differential equation solvers, WENDy computes accurate estimates and is robust to large (biologically relevant) levels of measurement noise. For low dimensional systems with modest amounts of data, WENDy is competitive with conventional forward solver-based nonlinear least squares methods in terms of speed and accuracy.

Direct Estimation of Parameters in ODE Models Using WENDy: Weak-form Estimation of Nonlinear Dynamics.

We introduce the Weak-form Estimation of Nonlinear Dynamics (WENDy) method for estimating model parameters for non-linear systems of ODEs. Without relying on any numerical differential equation solvers, WENDy computes accurate estimates and is robust to large (biologically relevant) levels of measurement noise. For low dimensional systems with modest amounts of data, WENDy is competitive with conventional forward solver-based nonlinear least squares methods in terms of speed and accuracy.

Viral transmission and infection prevalence in a cannibalistic host-pathogen system.

Cannibalism, while prevalent in the natural world, is often viewed as detrimental to a cannibal's health, especially when they consume pathogen-infected conspecifics. The argument stems from the idea that cannibalizing infected individuals increases the chance of coming into contact with a pathogen and subsequently becoming infected. Using an insect pest, the fall armyworm (Spodoptera frugiperda), that readily cannibalizes at the larval stage and its lethal pathogen, we experimentally examined how cannibalism affects viral transmission at both an individual and population level.

Can Eco-Evo Theory Explain Population Cycles in the Field?

AbstractEfforts to explain animal population cycles often invoke consumer-resource theory, which has shown that consumer-resource interactions alone can drive population cycles. Eco-evo theory instead argues that population cycles are partly driven by fluctuating selection for resistance in the resource, but support for eco-evo theory has come almost entirely from laboratory microcosms. Here we ask, Can eco-evo theory explain population cycles in the field? We compared the ability of eco-evo models and classical "eco-only" models to explain data on cycles in the insect , in which outbreaks of the insect are terminated by a fatal baculovirus.

A note on species richness and the variance of epidemic severity.

The commonly observed negative correlation between the number of species in an ecological community and disease risk, typically referred to as "the dilution effect", has received a substantial amount of attention over the past decade. Attempts to test this relationship experimentally have revealed that, in addition to the mean disease risk decreasing with species number, so too does the variance of disease risk. This is referred to as the "variance reduction effect", and has received relatively little attention in the disease-diversity literature.

An Empirical Test of the Role of Small-Scale Transmission in Large-Scale Disease Dynamics.

A key assumption of epidemiological models is that population-scale disease spread is driven by close contact between hosts and pathogens. At larger scales, however, mechanisms such as spatial structure in host and pathogen populations and environmental heterogeneity could alter disease spread. The assumption that small-scale transmission mechanisms are sufficient to explain large-scale infection rates, however, is rarely tested.

Stochasticity and Infectious Disease Dynamics: Density and Weather Effects on a Fungal Insect Pathogen.

In deterministic models of epidemics, there is a host abundance threshold above which the introduction of a few infected individuals leads to a severe epidemic. Studies of weather-driven animal pathogens often assume that abundance thresholds will be overwhelmed by weather-driven stochasticity, but tests of this assumption are lacking. We collected observational and experimental data for a fungal pathogen, , that infects the gypsy moth, .

Tracking U.S. Pertussis Incidence: Correlation of Public Health Surveillance and Google Search Data Varies by State.

The Morbidity and Mortality Weekly Reports of the U.S. Centers for Disease Control and Prevention document a raw proxy for counts of pertussis cases in the U.

Recurring infection with ecologically distinct HPV types can explain high prevalence and diversity.

The high prevalence of human papillomavirus (HPV), the most common sexually transmitted infection, arises from the coexistence of over 200 genetically distinct types. Accurately predicting the impact of vaccines that target multiple types requires understanding the factors that determine HPV diversity. The diversity of many pathogens is driven by type-specific or "homologous" immunity, which promotes the spread of variants to which hosts have little immunity.

Eco-Evolutionary Theory and Insect Outbreaks.

Eco-evolutionary theory argues that population cycles in consumer-resource interactions are partly driven by natural selection, such that changes in densities and changes in trait values are mutually reinforcing. Evidence that the theory explains cycles in nature, however, is almost nonexistent. Experimental tests of model assumptions are logistically impractical for most organisms, while for others, evidence that population cycles occur in nature is lacking.

Flexible modeling of the hazard rate and treatment effects in long-term survival studies.

The effects of predictors on time to failure may be difficult to assess in cancer studies with longer follow-up, as the commonly used assumption of proportionality of hazards holding over an extended period is often questionable. Motivated by a long-term prostate cancer clinical trial, we contrast and compare four powerful methods for estimation of the hazard rate. These four methods allow for varying degrees of smoothness as well as covariates with effects that vary over time.

Effects of host heterogeneity on pathogen diversity and evolution.

Phenotypic variation is common in most pathogens, yet the mechanisms that maintain this diversity are still poorly understood. We asked whether continuous host variation in susceptibility helps maintain phenotypic variation, using experiments conducted with a baculovirus that infects gypsy moth (Lymantria dispar) larvae. We found that an empirically observed tradeoff between mean transmission rate and variation in transmission, which results from host heterogeneity, promotes long-term coexistence of two pathogen types in simulations of a population model.

Research on Emissions, Air quality, Climate, and Cooking Technologies in Northern Ghana (REACCTING): study rationale and protocol.

Background: Cooking over open fires using solid fuels is both common practice throughout much of the world and widely recognized to contribute to human health, environmental, and social problems. The public health burden of household air pollution includes an estimated four million premature deaths each year. To be effective and generate useful insight into potential solutions, cookstove intervention studies must select cooking technologies that are appropriate for local socioeconomic conditions and cooking culture, and include interdisciplinary measurement strategies along a continuum of outcomes.

Survival Analysis with Electronic Health Record Data: Experiments with Chronic Kidney Disease.

This paper presents a detailed survival analysis for chronic kidney disease (CKD). The analysis is based on the EHR data comprising almost two decades of clinical observations collected at New York-Presbyterian, a large hospital in New York City with one of the oldest electronic health records in the United States. Our survival analysis approach centers around Bayesian multiresolution hazard modeling, with an objective to capture the changing hazard of CKD over time, adjusted for patient clinical covariates and kidney-related laboratory tests.

Pathogen growth in insect hosts: inferring the importance of different mechanisms using stochastic models and response-time data.

Pathogen population dynamics within individual hosts can alter disease epidemics and pathogen evolution, but our understanding of the mechanisms driving within-host dynamics is weak. Mathematical models have provided useful insights, but existing models have only rarely been subjected to rigorous tests, and their reliability is therefore open to question. Most models assume that initial pathogen population sizes are so large that stochastic effects due to small population sizes, so-called demographic stochasticity, are negligible, but whether this assumption is reasonable is unknown.

Modeling the transmission of community-associated methicillin-resistant Staphylococcus aureus: a dynamic agent-based simulation.

Background: Methicillin-resistant Staphylococcus aureus (MRSA) has been a deadly pathogen in healthcare settings since the 1960s, but MRSA epidemiology changed since 1990 with new genetically distinct strain types circulating among previously healthy people outside healthcare settings. Community-associated (CA) MRSA strains primarily cause skin and soft tissue infections, but may also cause life-threatening invasive infections. First seen in Australia and the U.

Nonconvulsive seizures in subarachnoid hemorrhage link inflammation and outcome.

Objective: Nonconvulsive seizures (NCSz) are frequent following acute brain injury and have been implicated as a cause of secondary brain injury, but mechanisms that cause NCSz are controversial. Proinflammatory states are common after many brain injuries, and inflammation-mediated changes in blood-brain barrier permeability have been experimentally linked to seizures.

Methods: In this prospective observational study of aneurysmal subarachnoid hemorrhage (SAH) patients, we explored the link between the inflammatory response following SAH and in-hospital NCSz studying clinical (systemic inflammatory response syndrome [SIRS]) and laboratory (tumor necrosis factor receptor 1 [TNF-R1], high-sensitivity C-reactive protein [hsCRP]) markers of inflammation.

Population-level differences in disease transmission: a Bayesian analysis of multiple smallpox epidemics.

Estimates of a disease's basic reproductive rate R0 play a central role in understanding outbreaks and planning intervention strategies. In many calculations of R0, a simplifying assumption is that different host populations have effectively identical transmission rates. This assumption can lead to an underestimate of the overall uncertainty associated with R0, which, due to the non-linearity of epidemic processes, may result in a mis-estimate of epidemic intensity and miscalculated expenditures associated with public-health interventions.

Epidemics of community-associated methicillin-resistant Staphylococcus aureus in the United States: a meta-analysis.

Staphylococcus aureus is the most frequent cause of skin and soft tissue infections in humans. Methicillin-resistant strains of S. aureus (MRSA) that emerged in the 1960s presented a relatively limited public health threat until the 1990s, when novel community-associated (CA-) MRSA strains began circulating.

The Role of Weather in Meningitis Outbreaks in Navrongo, Ghana: A Generalized Additive Modeling Approach.

Bacterial (meningococcal) meningitis is a devastating infectious disease with outbreaks occurring annually during the dry season in locations within the 'Meningitis Belt', a region in sub-Saharan Africa stretching from Ethiopia to Senegal. Meningococcal meningitis occurs from December to May in the Sahel with large epidemics every 5-10 years and attack rates of up to 1000 infections per 100,000 people. High temperatures coupled with low humidity may favor the conversion of carriage to disease as the meningococcal bacteria in the nose and throat are better able to cross the mucosal membranes into the blood stream.

Who underreports smoking on birth records: a Monte Carlo predictive model with validation.

Background: Research has shown that self-reports of smoking during pregnancy may underestimate true prevalence. However, little is known about which populations have higher rates of underreporting. Availability of more accurate measures of smoking during pregnancy could greatly enhance the usefulness of existing studies on the effects of maternal smoking offspring, especially in those populations where underreporting may lead to underestimation of the impact of smoking during pregnancy.

Detecting graded exposure effects: a report on an East Boston pregnancy cohort.

Introduction: The effects of tobacco exposure are typically examined by comparing groups based on a cut-score of self-reported number of cigarettes or bioassays collected in cross-sectional studies. This study introduces a new fuzzy clustering method that facilitates detection of subtle exposure effects by objectively deriving subgroups from modeling multidimensional exposure measures. We test the new method on a known exposure effect (fetal growth) and report on the graded exposure effect detected in a pregnancy cohort.

Tracking Epidemics With Google Flu Trends Data and a State-Space SEIR Model.

In this article, we use Google Flu Trends data together with a sequential surveillance model based on state-space methodology to track the evolution of an epidemic process over time. We embed a classical mathematical epidemiology model [a susceptible-exposed-infected-recovered (SEIR) model] within the state-space framework, thereby extending the SEIR dynamics to allow changes through time. The implementation of this model is based on a particle filtering algorithm, which learns about the epidemic process sequentially through time and provides updated estimated odds of a pandemic with each new surveillance data point.

Surgical scientific publication and the 1991-1995 war in Croatia.

The aim of this study was to evaluate surgical scientific publication in relation to the 1991-1995 war in Croatia, based on the articles indexed in Medline database that were published in 1980-2005 period. The number of articles was extracted from PubMed and analysed with trend analysis, which is preferred analytic approach over calculation of crude publication rates. The results indicate sporadic pre-war output, which was almost completely reduced by the onset of war.