Constraint-based analysis of gene interactions using restricted boolean networks and time-series data

Abstract Background A popular model for gene regulatory networks is the Boolean network model. In this paper, we propose an algorithm to perform an analysis of gene regulatory interactions using the Boolean network model and time-series data. Actually, the Boolean network is restricted in the sense that only a subset of all possible Boolean functions are considered. We explore some mathematical properties of the restricted Boolean networks in order to avoid the full search approach. The problem is modeled as a Constraint Satisfaction Problem (CSP) and CSP techniques are used to solve it. Results We applied the proposed algorithm in two data sets. First, we used an artificial dataset obtained from a model for the budding yeast cell cycle. The second data set is derived from experiments performed using HeLa cells. The results show that some interactions can be fully or, at least, partially determined under the Boolean model considered. Conclusions The algorithm proposed can be used as a first step for detection of gene/protein interactions. It is able to infer gene relationships from time-series data of gene expression, and this inference process can be aided by a priori knowledge available.

Lean diesel technology and human health: a case study in six Brazilian metropolitan regions

OBJECTIVE: Due to their toxicity, diesel emissions have been submitted to progressively more restrictive regulations in developed countries. However, in Brazil, the implementation of the Cleaner Diesel Technologies policy (Euro IV standards for vehicles produced in 2009 and low-sulfur diesel with 50 ppm of sulfur) was postponed until 2012 without a comprehensive analysis of the effect of this delay on public health parameters. We aimed to evaluate the impact of the delay in implementing the Cleaner Diesel Technologies policy on health indicators and monetary health costs in Brazil. METHODS: The primary estimator of exposure to air pollution was the concentration of ambient fine particulate matter (particles with aerodynamic diameters, <2.5 mu m, [PM2.5]). This parameter was measured daily in six Brazilian metropolitan areas during 2007-2008. We calculated 1) the projected reduction in the PM2.5 that would have been achieved if the Euro IV standards had been implemented in 2009 and 2) the expected reduction after implementation in 2012. The difference between these two time curves was transformed into health outcomes using previous dose-response curves. The economic valuation was performed based on the DALY (disability-adjusted life years) method. RESULTS: The delay in implementing the Cleaner Diesel Technologies policy will result in an estimated excess of 13,984 deaths up to 2040. Health expenditures are projected to be increased by nearly US$ 11.5 billion for the same period. CONCLUSIONS: The present results indicate that a significant health burden will occur because of the postponement in implementing the Cleaner Diesel Technologies policy. These results also reinforce the concept that health effects must be considered when revising fuel and emission policies.

A relaxed constant positive linear dependence constraint qualification and applications

In this work we introduce a relaxed version of the constant positive linear dependence constraint qualification (CPLD) that we call RCPLD. This development is inspired by a recent generalization of the constant rank constraint qualification by Minchenko and Stakhovski that was called RCRCQ. We show that RCPLD is enough to ensure the convergence of an augmented Lagrangian algorithm and that it asserts the validity of an error bound. We also provide proofs and counter-examples that show the relations of RCRCQ and RCPLD with other known constraint qualifications. In particular, RCPLD is strictly weaker than CPLD and RCRCQ, while still stronger than Abadie's constraint qualification. We also verify that the second order necessary optimality condition holds under RCRCQ.

The McDonald extended distribution: properties and applications

We study a five-parameter lifetime distribution called the McDonald extended exponential model to generalize the exponential, generalized exponential, Kumaraswamy exponential and beta exponential distributions, among others. We obtain explicit expressions for the moments and incomplete moments, quantile and generating functions, mean deviations, Bonferroni and Lorenz curves and Gini concentration index. The method of maximum likelihood and a Bayesian procedure are adopted for estimating the model parameters. The applicability of the new model is illustrated by means of a real data set.

Simulation results and applications of an advection bounded scheme to practical flows

This paper reports experiments on the use of a recently introduced advection bounded upwinding scheme, namely TOPUS (Computers & Fluids 57 (2012) 208-224), for flows of practical interest. The numerical results are compared against analytical, numerical and experimental data and show good agreement with them. It is concluded that the TOPUS scheme is a competent, powerful and generic scheme for complex flow phenomena.

On S-asymptotically omega-periodic functions and applications

Let (X, parallel to . parallel to) be a Banach space and omega is an element of R. A bounded function u is an element of C([0, infinity); X) is called S-asymptotically omega-periodic if lim(t ->infinity)[u(t + omega) - u(t)] = 0. In this paper, we establish conditions under which an S-asymptotically omega-periodic function is asymptotically omega-periodic and we discuss the existence of S-asymptotically omega-periodic and asymptotically omega-periodic solutions for an abstract integral equation. Some applications to partial differential equations and partial integro-differential equations are considered. (C) 2011 Elsevier Ltd. All rights reserved.

On a new class of abstract integral equations and applications

In this paper we introduce a new class of abstract integral equations which enables us to study in a unified manner several different types of differential equations. (C) 2012 Elsevier Inc. All rights reserved.

TWO NEW WEAK CONSTRAINT QUALIFICATIONS AND APPLICATIONS

We present two new constraint qualifications (CQs) that are weaker than the recently introduced relaxed constant positive linear dependence (RCPLD) CQ. RCPLD is based on the assumption that many subsets of the gradients of the active constraints preserve positive linear dependence locally. A major open question was to identify the exact set of gradients whose properties had to be preserved locally and that would still work as a CQ. This is done in the first new CQ, which we call the constant rank of the subspace component (CRSC) CQ. This new CQ also preserves many of the good properties of RCPLD, such as local stability and the validity of an error bound. We also introduce an even weaker CQ, called the constant positive generator (CPG), which can replace RCPLD in the analysis of the global convergence of algorithms. We close this work by extending convergence results of algorithms belonging to all the main classes of nonlinear optimization methods: sequential quadratic programming, augmented Lagrangians, interior point algorithms, and inexact restoration.

Recoupled separated-local-field experiments and applications to study intermediate-regime molecular motions

A specific separated-local-field NMR experiment, dubbed Dipolar-Chemical-Shift Correlation (DIPSHIFT) is frequently used to study molecular motions by probing reorientations through the changes in XH dipolar coupling and T-2. In systems where the coupling is weak or the reorientation angle is small, a recoupled variant of the DIPSHIFT experiment is applied, where the effective dipolar coupling is amplified by a REDOR-like pi-pulse train. However, a previously described constant-time variant of this experiment is not sensitive to the motion-induced T-2 effect, which precludes the observation of motions over a large range of rates ranging from hundreds of Hz to around a MHz. We present a DIPSHIFT implementation which amplifies the dipolar couplings and is still sensitive to T-2 effects. Spin dynamics simulations, analytical calculations and experiments demonstrate the sensitivity of the technique to molecular motions, and suggest the best experimental conditions to avoid imperfections. Furthermore, an in-depth theoretical analysis of the interplay of REDOR-like recoupling and proton decoupling based on Average-Hamiltonian Theory was performed, which allowed explaining the origin of many artifacts found in literature data. (C) 2012 Elsevier Inc. All rights reserved.

Lê–Greuel type formula for the Euler obstruction and applications

The Euler obstruction of a function f can be viewed as a generalization of the Milnor number for functions defined on singular spaces. In this work, using the Euler obstruction of a function, we establish several Lê–Greuel type formulas for germs f:(X,0)→(C,0) and g:(X,0)→(C,0). We give applications when g is a generic linear form and when f and g have isolated singularities.

Pullback exponential attractors for evolution processes in Banach spaces: properties and applications

This article is a continuation of our previous work [5], where we formulated general existence theorems for pullback exponential attractors for asymptotically compact evolution processes in Banach spaces and discussed its implications in the autonomous case. We now study properties of the attractors and use our theoretical results to prove the existence of pullback exponential attractors in two examples, where previous results do not apply.