Faculty Bibliography

Although central leptin signaling appears to play a major role in the regulation of food intake and energy metabolism, the physiological role of peripheral leptin signaling and its relative contribution to whole-body energy metabolism remain unclear. To address this question, we created a mouse model (Cre-Tam mice) with an intact leptin receptor in the brain but a near-complete deletion of the signaling domain of leptin receptor in liver, adipose tissue, and small intestine using a tamoxifen (Tam)-inducible Cre-LoxP system. Cre-Tam mice developed marked hyperleptinemia (approximately 4-fold; P < 0.01) associated with 2.3-fold increase (P < 0.05) in posttranscriptional production of leptin. Whereas this is consistent with the disruption of a negative feedback regulation of leptin production in adipose tissue, there were no discernable changes in energy balance, thermoregulation, and insulin sensitivity. Hypothalamic levels of phosphorylated signal transducer and activator of transcription 3, neuropeptide expression, and food intake were not changed despite hyperleptinemia. The percentage of plasma-bound leptin was markedly increased (90.1-96 vs. 41.8-74.7%; P < 0.05), but plasma-free leptin concentrations remained unaltered in Cre-Tam mice. We conclude from these results that 1) the relative contribution to whole-body energy metabolism from peripheral leptin signaling is insignificant in vivo, 2) leptin signaling in adipocyte constitutes a distinct short-loop negative feedback regulation of leptin production that is independent of tissue metabolic status, and 3) perturbation of peripheral leptin signaling alone, although increasing leptin production, may not be sufficient to alter the effective plasma levels of leptin because of the counter-regulatory increase in the level of leptin binding protein(s).

Virology laboratories historically have used direct fluorescent-antibody assay (DFA) and culture to detect six or seven respiratory viruses. Following the discovery of five new human respiratory viruses since 2000, there is an increasing need for diagnostic tests to detect these emerging viruses. We have developed a new test that can detect 20 different respiratory virus types/subtypes in a single 5-h test. The assay employs multiplex PCR using 14 virus-specific primer pairs, followed by a multiplexed target-specific primer extension (TSPE) reaction using 21 primers for specific respiratory virus types and subtypes. TSPE products were sorted and identified by using a fluid microsphere-based array (Universal Array; TmBioscience Corporation, Toronto, Canada) and the Luminex x-MAP system. The assay detected influenza A and B viruses; influenza A virus subtypes H1, H3, and H5 (including subtype H5N1 of the Asian lineage); parainfluenza virus types 1, 2, 3, and 4; respiratory syncytial virus types A and B; adenovirus; metapneumovirus; rhinovirus; enterovirus; and coronaviruses OC43, 229E, severe acute respiratory syndrome coronavirus, NL63, and HKU1. In a prospective evaluation using 294 nasopharyngeal swab specimens, DFA/culture detected 119 positives and the respiratory virus panel (RVP) test detected 112 positives, for a sensitivity of 97%. The RVP test detected an additional 61 positive specimens that either were not detected by DFA/culture or were positive for viruses not tested for by DFA/culture. After resolution of discordant results by using a second unique PCR assay and by using a combined reference standard of positivity, the RVP test detected 180 of 183 true positives, for a sensitivity of 98.5%, whereas DFA and culture detected only 126 of 183 true positives, for a sensitivity of 68.8%. The RVP test should improve the capabilities of hospital and public health laboratories for diagnosing viral respiratory tract infections and should assist public health agencies in identifying etiologic agents in respiratory tract infection outbreaks.

A series of papers, all under the title of Algorithmic Algebraic Model Checking (AAMC), has sought to combine techniques from algorithmic algebra, model checking and dynamical systems to examine how a biochemical hybrid dynamical system can be made amenable to temporal analysis, even when the initial conditions and unknown parameters may only be treated as symbolic variables. This paper examines how to specialize this framework to metabolic control analysis (MCA) involving many reactions operating at many dissimilar time-scales. In the earlier AAMC papers, it has been shown that the dynamics of various biochemical semi-algebraic hybrid automata could be unraveled using powerful techniques from computational real algebraic geometry. More specifically, the resulting algebraic model checking techniques were found to be suitable for biochemical networks modeled using general mass action (GMA) based ODEs. This paper scrutinizes how the special properties of metabolic networks - a subclass of the biochemical networks previously handled - can be exploited to gain improvement in computational efficiency. The paper introduces a general framework for performing symbolic temporal reasoning over metabolic network hybrid automata that handles both GMA-based equilibrium estimation and flux balance analysis (FBA). While algebraic polynomial equations over ?[x 1,..., x n] can be symbolically solved using Gröbner bases or Wu-Ritt characteristic sets, the FBA-based estimation can be performed symbolically by rephrasing the algebraic optimization problem as a quantifier elimination problem. Effectively, an approximate hybrid automaton that simulates the metabolic network is derived, and is thus amenable to manipulation by the algebraic model checking techniques previously described in the AAMC papers.

PLAN C, an Agent-Based Model platform for urban disaster simulation and emergency planning, features a variety of reality-based agents interacting on a realistic city map and can simulate the complex dynamics of emergency responses in different urban catastrophe scenarios. Work reported here focuses on the incorporation of specific subpopulations of person agents, reflecting the existence of individuals with specific defining characteristics and needs, and their interactions with the available resources. Performance of these subpopulations are compared in both point-source attack and distributed disaster scenarios for disasters of different magnitudes. Specific ""recovery points"" can be derived both for total- and sub-populations, which estimate the duration of a response system's/city's vulnerability. The effect of varying topologies of available resources, i.e. different hospital maps, provides particular insight into the dynamics that can emerge in this complex system. PLAN C produces interesting emergent behavior which is often consistent with the literature on emergency medicine of previous events.

Fibrillins are the structural components of extracellular microfibrils that impart physical properties to tissues, alone or together with elastin as elastic fibers. Genetic studies in mice have revealed that fibrillin-rich microfibrils are also involved in regulating developmental programs and homeostatic processes through the modulation of TGF-beta/BMP signaling events. A new paradigm has thus emerged whereby the spatiotemporal organization of microfibrils dictates both the cellular activities and physical properties of connective tissues. These observations have paved the way to novel therapeutic approaches aimed at counteracting the life-threatening complications in human conditions caused by dysfunctions of fibrillin-rich microfibrils.

Current symbolic techniques for the automated reasoning over undecidable hybrid automata, force one to choose between the refinement of either an overapproximation or an underapproximation of the set of reachable states. When the analysis of branching time temporal properties is considered, the literature has developed a number of abstractions techniques based on the simulation preorder, that allow the preservation of only true universally quantified formulæ. This paper suggests a way to surmount these difficulties by defining a succession of abstractions of hybrid automata, which not only (1) allow the detection and the refinement of both over- and under-approximated reachable sets symmetrically, but also (2) preserves the full set of branching time temporal properties (when interpreted on a dense time domain). Moreover, our approach imposes on the corresponding set of abstractions a desirable monotonicity property with respect to the set of model-checked formulaæ.

This paper addresses questions regarding the decidability of hybrid automata that may be constructed hierarchically and in a modular way, as is the case in many exemplar systems, be it natural or engineered. Since an important step in such constructions is a product operation, which constructs a new product hybrid automaton by combining two simpler component hybrid automata, an essential property that would be desired is that the reachability property of the product hybrid automaton be decidable, provided that the component hybrid automata belong to a suitably restricted family of automata. Somewhat surprisingly, the product operation does not assure a closure of decidability for the reachability problem. Nonetheless, this paper establishes the decidability of the reachability condition over automata which are obtained by composing two semi-algebraic o-minimal systems. The class of semi-algebraic o-minimal automata is not even closed under composition, i.e., the product of two automata of this class is not necessarily a semi-algebraic o-minimal automaton. However, we can prove our decidability result combining the decidability of both semi-algebraic formulae over the reals and linear Diophantine equations. All the proofs of the results presented in this paper can be found in [1].