- Mathematical Biology Seminar
- Wednesday, April 15, 2020 - 11:00 for 1 hour (actually 50 minutes)
- Skiles 6
- Prof. Jun Xie – Department of Statistics, Purdue University – email@example.com
Zooplankton is an immensely numerous and diverse group of organisms occupying every corner of the oceans, seas and freshwater bodies on the planet. They form a crucial link between autotrophic phytoplankton and higher trophic levels such as crustaceans, molluscs, fish, and marine mammals. Changing environmental conditions such as rising water temperatures, salinities, and decreasing pH values currently create monumental challenges to their well-being.
A signi cant subgroup of zooplankton are crustaceans of sizes between 1 and 10 mm. Despite their small size, they have extremely acute senses that allow them to navigate their surroundings, escape predators, find food and mate. In a series of joint works with Rudi Strickler (Department of Biological Sciences, University of Wisconsin - Milwaukee) we have investigated various behaviors of crustacean zooplankton. These include the visualization of the feeding current of the copepod Leptodiaptomus sicilis, the introduction of the "ecological temperature" as a descriptor of the swimming behavior of the water flea Daphnia pulicaria and the communication by sex pheromones in the copepod Temora longicornis. The tools required for the studies stem from optics, ecology, dynamical systems, statistical physics, computational fluid dynamics, and computational neuroscience.
One of the most challenging aspects of designing human sensitive systems is in designing systems that assist decision makers in applying an effective intervention to a large group of individuals. This design challenge becomes especially difficult when the decision maker must operate under scarce resources and only partial knowledge of how each individual will react to the intervention.
In this talk, I will consider this problem from the perspective of a clinician that is designing a personalized weight loss program. Despite this focus, the precision analytics framework I propose for designing these interventions is quite general and can apply to many settings where a single coordinator must influence agents who make decisions by maximizing utility functions that depend on prior system states, inputs, and other parameters that are initially unknown. This precision analytics framework involves three steps: first, a predictive model that effectively captures the decision-making process of an agent; second, an optimization algorithm to estimate this model’s parameters for each agent and predict their future decisions; and third, an optimization model that uses these predictions to optimize a set of incentives that will be provided to each agent. A key advantage of this framework is that the calculated incentives are adapted as new information is collected. In the case of personalized weight loss interventions, this means that the framework can leverage patient level data from mobile and wearable sensors over the course of the intervention to personalize the recommended treatment for each individual.
I will present theoretical results that show that the incentives computed by this approach are asymptotically optimal with respect to a loss function that describes the coordinator's objective. I will also present an effective decomposition scheme to optimize the agent incentives, where each sub-problem solves the coordinator's problem for a single agent, and the master problem is a pure integer program. To validate this method I will present a numerical study that shows this proposed framework is more cost efficient and clinically effective than simple heuristics in a simulated environment. I will conclude by discussing the results of a randomized control trial (RCT) and pilot study where this precision analytics framework was applied for personalizing exercise goals for UC Berkeley staff and students. The results of these trials show that using personalized step goals calculated by the precision analytics algorithm result in a significant improvement over existing state of the art approaches in a real world setting.
The prediction of RNA secondary structures from sequence is a well developed task in computational RNA Biology. However, in a cellular environment RNA molecules are not isolated but rather interact with a multitude of proteins. RNA secondary structure affects those interactions with proteins and vice versa proteins binding the RNA affect its secondary structure. We have extended the dynamic programming approaches traditionally used to quantify the ensemble of RNA secondary structures in solution to incorporate protein-RNA interactions and thus quantify these effects of protein-RNA interactions and RNA secondary structure on each other. Using this approach we demonstrate that taking into account RNA secondary structure improves predictions of protein affinities from RNA sequence, that RNA secondary structures mediate cooperativity between different proteins binding the same RNA molecule, and that sequence variations (such as Single Nucleotide Polymorphisms) can affect protein affinity at a distance mediated by RNA secondary structures.
Phytoplankton are the base of the marine food web. They are also responsible for much of the oxygen we breathe, and they remove carbon dioxide from the atmosphere. The mechanisms that govern the timing of seasonal phytoplankton blooms is one of the most debated topics in oceanography. Here, we present a macroscale plankton ecology model consisting of coupled, nonlinear reaction-diffusion equations with spatially and temporally changing coefficients to offer insight into the causes of phytoplankton blooms. This model simulates biological interactions between nutrients, phytoplankton and zooplankton. It also incorporates seasonally varying solar radiation, diffusion and depth of the ocean’s upper mixed layer because of their impact on phytoplankton growth. The model is analyzed using seasonal oceanic data with the goals of understanding the model’s dependence on its parameters and of understanding seasonal changes in plankton biomass. A study of varying parameter values and the resulting effects on the solutions, the stability of the steady-states, and the timing of phytoplankton blooms is carried out. The model’s simulated blooms result from a temporary attraction to one of the model’s steady-states.
The malaria parasite Plasmodium falciparum requires a vertebrate host, such as a human, and a vector host, the Anopheles mosquito, to complete a full life cycle. The portion of the life cycle in the mosquito harbors both the only time of sexual reproduction, expanding genetic complexity, and the most severe bottlenecks experienced, restricting genetic diversity, across the entire parasite life cycle. In previous work, we developed a two-stage stochastic model of parasite diversity within a mosquito, and demonstrated the importance of heterogeneity amongst parasite dynamics across a population of mosquitoes. Here, we focus on the parasite dynamics component to evaluate the first appearance of sporozoites, which is key for determining the time at which mosquitoes first become infectious. We use Bayesian inference techniques with simple models of within-mosquito parasite dynamics coupled with experimental data to estimate a posterior distribution of parameters. We determine that growth rate and the bursting function are key to the timing of first infectiousness, a key epidemiological parameter.
The relationship between biodiversity and ecological stability has long interested ecologists. The ongoing biodiversity loss has led to the increasing concern that it may impact ecosystem functioning, including ecosystem stability. Both early conceptual ideas and recent theory suggest a positive relationship between biodiversity and ecosystem stability. While quite a number of empirical studies, particularly experiments that directly manipulated species diversity, support this hypothesis, exceptions are not uncommon. This raises the question of whether there is a general positive diversity-stability relationship.
Literature survey shows that species diversity may not necessarily be an important determinant of ecosystem stability in natural communities. While experiments controlling for other environmental variables often report that ecosystem stability increases with species diversity, these other environmental variables are often more important than species diversity in influencing ecosystem stability. Studies that account for these environmental covariates tend to find a lack of relationship between species diversity and ecosystem stability. An important goal of future studies is to elucidate mechanisms driving the variation in the importance of species diversity in regulating ecosystem stability.
Pollen grain surface morphologies are famously diverse, and each species displays a unique, replicable pattern. The function of these microstructures, however, has not been elucidated. We show electron microscopy evidence that the templating of these patterns is formed by a phase separation of a polysaccharide mixture on the cell membrane surface. Here we present a Landau theory of phase transitions to ordered states describing all extant pollen morphologies. We show that 10% of all morphologies can be characterized as equilibrium states with a well-defined wavelength of the pattern. The rest of the patterns have a range of wavelengths on the surface that can be recapitulated by exploring the evolution of a conserved dynamics model. We then perform an evolutionary trait reconstruction. Surprisingly, we find that although the equilibrium states have evolved multiple times, evolution has not favored these ordered-polyhedral like shapes and perhaps their patterning is simply a natural consequence of a phase separation process without cross-linkers.
In both biological brains and artificial neural networks, the representational geometry - the shape and distribution of activity - at different layers in an artificial network or across different populations of neurons in the brain, can reveal important signatures of the underlying computations taking place. In this talk, I will describe how we are developing strategies for comparing and aligning neural representations, using a combination of tools from computational geometry and optimal transport.
I will discuss an ongoing project to reconstruct a gene network from time-series data from a mammalian signaling pathway. The data is generated from gene knockouts and the techniques involve computational algebra. Specifically, one creates an pseudomonomial "ideal of non-disposable sets" and applies a analogue of Stanley-Reisner theory and Alexander duality to it. Of course, things never work as well in practice, due to issue such as noise, discretization, and scalability, and so I will discuss some of these challenges and current progress.