Why do atherosclerotic plaques only occur at specific sites in the arteries? Does the surface geometry of the brain affect the way waves move through the cortex? These questions and many others in the physiological sphere contain implicitly a real difficulty for modellers. How do we contend with the multiple scale lengths. Plaques are quite large compared to cells making…
Circadian (~24-hour) rhythms offer one of the clearest examples of the interplay between different levels of nervous system organization, with dynamic changes in gene expression leading to daily rhythms in neural activity, physiology, and behavior. The main output signal of the master circadian clock in mammals has long been believed to be a simple day/night…
The pharmaceutical industry has increasingly embraced mathematical modeling as a method to predict drug-body interactions. In particular, issues of drug toxicity and drug-drug interactions impact the drug development and approval process. Initially begun as a private-public partnership, DILIsym Services is the leading software platform to help inform issues relating to drug-induced liver injury (DILI) by…
As the world’s rapidly growing population is driving ever increasing demand for food, feed and fuel, we are faced with the challenge to grow higher-yielding crops with less water and fewer inputs. Agriculture companies are focused on meeting these needs by delivering innovative products and technologies into the marketplace that improve crop performance. This requires…
In fibroblasts responding to gradients of platelet-derived growth factor (PDGF), an important chemoattractant in development and wound healing, signaling through the phospholipase C (PLC)/protein kinase C (PKC) pathway proved necessary for chemotaxis, whereas pathways that collaborate to activate the Arp2/3 complex were found to be dispensable. PKC is activated through its binding to the lipid…
Anticipating abrupt changes in ecosystem state is key for ecosystem management and preservation. Detailed knowledge of ecological mechanisms behind a critical transition is often difficult to attain, and the theory of resilience - assessment of the ability of a system to withstand disturbances - provides a pathway to circumvent this problem. Loss of system resilience…
Gene expression is a biochemical process driven by the chance collisions of molecules, which can result in strong stochastic signatures and cell-to-cell variability in gene network dynamics (e.g. oscillation). Biological oscillators co-exist in the same cell and can interact directly or indirectly through shared resources. Our lab uses modeling and experiments to understand how these…
The Valsalva maneuver (VM) is a quick, noninvasive, clinical procedure with a variety of uses. In particular, the VM can aid in the diagnosis of autonomic nervous system dysfunction. The VM induces changes in blood pressure, which reflexively induces a neural signaling cascade to adjust heart rate, heart contractility, peripheral vascular resistance, and venous compliance.…
This semester the Biomathematics GSA will be hosting student led tutorials on a variety of topics. The goal of these tutorials is to help graduate students develop computational tools. This week will cover data manipulation using R Studio. If you are interested in participating please bring a laptop with the necessary software (R and R…
This semester the Biomathematics GSA will be hosting student led tutorials on a variety of topics. The goal of these tutorials is to help graduate students develop computational tools. This week will cover data visualization using R Studio with the ggplot package. If you are interested in participating please bring a laptop with the necessary…
This semester the Biomathematics GSA will be hosting student led tutorials on a variety of topics. The goal of these tutorials is to help graduate students develop computational tools. This week will cover the development of interactive web applications using R Studio with the shiny package. If you are interested in participating please bring a…
Topology is dedicated to the study of shapes, and its starting point is an easy-sounding question: How can I tell if two objects are similar? While humans are very adept at distinguishing a large variety of shapes, it is not always easy to say precisely what makes this object similar to or distinct from that…
Intermittent androgen deprivation therapy (IADT) is an attractive treatment approach for biochemically recurrent prostate cancer (PCa), whereby cycling treatment on and off has been shown to limit toxicities and reduce cumulative dose. While IADT has been shown to delay the development of treatment resistance, underlying mechanisms and actionable biomarkers are required to accurately predict when…
The mitotic spindle is a complex, dynamic machine important for cell division. The spindle is composed of a network of microtubules and motor proteins that generate forces to form a bipolar spindle, with each pole organized around a single centrosome. Disruption in force generating activities through protein depletions or alterations to centrosome number, alter spindle…
Millions of Americans experience dry eye syndrome, a condition that decreases quality of vision and causes ocular discomfort. A phenomenon associated with dry eye syndrome is tear film breakup (TBU), or the formation of dry spots on the eye. The dynamics of the tear film can be studied using fluorescence imaging. Many parameters affecting tear…
In this talk I will present a Bayesian approach to quantify the uncertainty of model parameters and hemodynamic predictions in a one-dimensional fluid-dynamics model of the pulmonary system by integrating mouse imaging data and hemodynamic data. The long-term aim is to devise a calibrated patient-specific model. I emphasize an often neglected, though the important source…
Postural Orthostatic Tachycardia Syndrome (POTS) is characterized by an increase of heart rate of 30 beats per minute (40 bpm in patients aged 12-19 years) upon a postural change, combined with the presence of orthostatic symptoms. In addition to these criteria, recent studies have shown that POTS patients exhibit large low frequency ~0.1 Hz heart…
The emerging single-cell and spatial genomics techniques allow us to elucidate the governing rules of multicellular systems with unprecedented resolution and depth. These datasets are often high-dimensional, complex, and heterogeneous. Mathematical tools are needed to extract biological insights from such data. In this talk, we will discuss several mathematical and machine learning methods for exploring…
Dr. Timsina's Talk: Identifiability and optimal control analysis of HIV infection and opioid addiction model. Abstract: In a compartmental model of HIV infection and opioid addiction, dynamics such as equilibria, basic reproduction number, and invasion numbers are presented. Identifiability and estimation of the parameters of the model are highlighted. Moreover, the effect of four distinct controls such…
Gaussian processes (GPs) are widely employed as versatile modeling and predictive tools in spatial statistics, functional data analysis, computer modeling and diverse applications of machine learning. They have been widely studied over Euclidean spaces, where they are specified using covariance functions or covariograms for modelling complex dependencies. There is a growing literature on GPs over…