Objective(s): The study was intended to investigate the combined influence of two neuroprotective agents pramipexole and n-acetylcysteine on global cerebral ischemic reperfusion injury (GCIRI) model in rats.Materials and Methods: GCIRI was induced by bilateral common carotid artery ligation (BCCA) in rats. Animals were divided into six groups. Groups I, II, and III received saline intraperitone...

Gene expression is intrinsically stochastic due to the small number of molecules involved in some of the underlying biochemical reactions. The resulting molecule-count random fluctuations are known as biochemical noise. The dynamic effects of intrinsic noise (that originated within the system) have been widely studied. However, the effects of the noise coming from other sources the system is in...

Purpose. The purpose of this study is to investigate whether the clinicopathological biopsy findings can predict the oncological outcome in patients who undergo radical prostatectomy. Materials and Methods. Between January 1997 and March 2006, 255 patients with clinically localized adenocarcinoma of the prostate (clinical T1-3N0M0) who had undergone retropubic radical prostatectomy were enrolle...

Sensitivity analysis is an indispensable tool for studying the robustness and fragility properties of biochemical reaction systems as well as for designing optimal approaches for selective perturbation and intervention. Deterministic sensitivity analysis techniques, using derivatives of the system response, have been extensively used in the literature. However, these techniques suffer from seve...

Switch like responses appear as common strategies in the regulation of cellular systems. Here we present a method to characterize bistable regimes in biochemical reaction networks that can be of use to both direct and reverse engineering of biological switches. In the design of a synthetic biological switch, it is important to study the capability for bistability of the underlying biochemical n...

OBJECTIVE High-risk clinically localized prostate cancer is seen in a highly heterogeneous population with a wide variation of clinical aggressiveness and a novel subclassification for the better prediction of clinical outcomes is needed. The aim of this study is to validate a modified D'Amico risk criteria for substratification of high-risk prostate cancer with regard to the prediction of bioc...

Biochemical reactions are fundamentally noisy at a molecular scale. This limits the precision of reaction networks, but also allows fluctuation measurements which may reveal the structure and dynamics of the underlying biochemical network. Here, we study non-equilibrium reaction cycles, such as the mechanochemical cycle of molecular motors, the phosphorylation cycle of circadian clock proteins,...

Systems biologists build models of bio-molecular processes from knowledge acquired both at the gene and protein levels, and at the phenotype level through experiments done in wild-life and mutated organisms. In this chapter, we present qualitative and quantitative logic learning tools, and illustrate how they can be useful to the modeler. We focus on biochemical reaction models written in the S...

Mathematical models of biochemical reaction networks are usually high dimensional, nonlinear, and have many unknown parameters, such as reaction rate constants, or unspecified types of chemical kinetics (such as mass-action, Michaelis-Menten, or Hill kinetics). On the other hand, important properties of these dynamical systems are often determined by the network structure, and do not depend on ...

Sensitivity analysis of biochemical reactions aims at quantifying the dependence of the reaction dynamics on the reaction rates. The computation of the parameter sensitivities poses many computational challenges when taking stochastic noise into account. This paper proposes a new efficient finite difference method for computing parameter sensitivities of biochemical reactions. We employ propens...