Dynamic simulation of regulatory networks using SQUAD.

BACKGROUND: The ambition of most molecular biologists is the understanding of the intricate network of molecular interactions that control biological systems. As scientists uncover the components and the connectivity of these networks, it becomes possible to study their dynamical behavior as a whole and discover what is the specific role of each of their components. Since the behavior of a network is by no means intuitive, it becomes necessary to use computational models to understand its behavior and to be able to make predictions about it. Unfortunately, most current computational models describe small networks due to the scarcity of kinetic data available. To overcome this problem, we previously published a methodology to convert a signaling network into a dynamical system, even in the total absence of kinetic information. In this paper we present a software implementation of such methodology. RESULTS: We developed SQUAD, a software for the dynamic simulation of signaling networks using the standardized qualitative dynamical systems approach. SQUAD converts the network into a discrete dynamical system, and it uses a binary decision diagram algorithm to identify all the steady states of the system. Then, the software creates a continuous dynamical system and localizes its steady states which are located near the steady states of the discrete system. The software permits to make simulations on the continuous system, allowing for the modification of several parameters. Importantly, SQUAD includes a framework for perturbing networks in a manner similar to what is performed in experimental laboratory protocols, for example by activating receptors or knocking out molecular components. Using this software we have been able to successfully reproduce the behavior of the regulatory network implicated in T-helper cell differentiation. CONCLUSION: The simulation of regulatory networks aims at predicting the behavior of a whole system when subject to stimuli, such as drugs, or determine the role of specific components within the network. The predictions can then be used to interpret and/or drive laboratory experiments. SQUAD provides a user-friendly graphical interface, accessible to both computational and experimental biologists for the fast qualitative simulation of large regulatory networks for which kinetic data is not necessarily available.

Innovation or Imitation? The effect of spillovers and competitive pressure on firms' R&D strategy choice

This article provides a theoretical and empirical analysis of a firm's optimal R&D strategy choice. In this paper a firm's R&D strategy is assumed to be endogenous and allowed to depend on both internal firms. characteristics and external factors. Firms choose between two strategies, either they engage in R&D or abstain from own R&D and imitate the outcomes of innovators. In the theoretical model this yields three types of equilibria in which either all firms innovate, some firms innovate and others imitate, or no firm innovates. Firms'equilibrium strategies crucially depend on external factors. We find that the efficiency of intellectual property rights protection positively affects firms'incentives to engage in R&D, while competitive pressure has a negative effect. In addition, smaller firms are found to be more likely to become imitators when the product is homogeneous and the level of spillovers is high. These results are supported by empirical evidence for German .rms from manufacturing and services sectors. Regarding social welfare our results indicate that strengthening intellectual property protection can have an ambiguous effect. In markets characterized by a high rate of innovation a reduction of intellectual property rights protection can discourage innovative performance substantially. However, a reduction of patent protection can also increase social welfare because it may induce imitation. This indicates that policy issues such as the optimal length and breadth of patent protection cannot be resolved without taking into account specific market and firm characteristics. Journal of Economic Literature Classification Numbers: C35, D43, L13, L22, O31. Keywords: Innovation; imitation; spillovers; product differentiation; market competition; intellectual property rights protection.

Anesthesia of Biomphalaria spp. (Mollusca, Gastropoda): sodium pentobarbital is the drug of choice

The anesthetic effect of some water-soluble anesthesic or narcotic drugs currently used in mice was tested in molluscs of the Biomphalaria genus. Sodium thiopental was very toxic to the snails resulting in high rates of mortality in all the treatment schedules tested. Cetamine base, at concentration of 0.25 mg/ml of water, resulted in partial snail anesthesia (40% of snails were anesthetized) only after 20 h of exposition. The association of Cetamine base with Tiazine chloridrate did not improve the anesthesic effect, and higher concentrations of these drugs were toxic to the snails. Sodium pentobarbital at 0.4 mg/ml in water for 8 h was the best treatment schedule to anesthetize Biomphalaria snails. In this schedule, the snails were anesthetized without any toxic effect. The procedure provides a powerful tool for in vivo studies that demande a complete state of snail anesthesia.

Discrete time Non-homogeneous Semi-Markov Processes applied to Models for Disability Insurance

In this paper, we present a stochastic model for disability insurance contracts. The model is based on a discrete time non-homogeneous semi-Markov process (DTNHSMP) to which the backward recurrence time process is introduced. This permits a more exhaustive study of disability evolution and a more efficient approach to the duration problem. The use of semi-Markov reward processes facilitates the possibility of deriving equations of the prospective and retrospective mathematical reserves. The model is applied to a sample of contracts drawn at random from a mutual insurance company.

The Employer of Choice

A strategy for managing and developing people in the Health and Personal Social Services

Interaction between the Intermediate Host of Schistosomiasis in Brazil Biomphalaria glabrata (Planorbidae) and a Possible Competitor Melanoides tuberculata (Thiaridae): I. Laboratory Experiments

The biological control of Biomphalaria glabrata, intermediate host of Schistosoma mansoni, is one the accepted options to fight schistosomiasis. One of the most promising candidates to control B. glabrata is the snail Melanoides tuberculata, a potential competitor. However, the mechanisms of interaction between the two species are not clear. Our objective is to determine if M. tuberculata indeed compete with B. glabrata, using two laboratory experiments. In Experiment 1, we tested the effect of the presence of M. tuberculata on the fecundity and mortality rates of B. glabrata. In Experiment 2, we tested if there was a direct or indirect interaction between the two species. In Experiment 1, M. tuberculata was eliminated after the peak in reproductive activity of B. glabrata. In Experiment 2, B. glabrata produced more egg masses when raised with M. tuberculata. The conditions leading to this unexpected positive effect of M. tuberculata on the fecundity of B. glabrata need further clarification, but emphasize that detailed studies of the interaction between these species in the conditions of the local environment should be considered.

A health promotion strategy: making the healthier choice the easier choice

The Primary Care Steering Group met on the 23rd and 24th September 2003 to discuss the ongoing implementation of the Primary Care Strategy in the context of the Health Service Reform Programme and to make recommendations in this regard to the Secretary General of the Department of Health & Children. At the outset the steering group acknowledges that the reform programme provides significant opportunity for the successful implementation of the primary care strategy. The implementation phase of ten project Primary Care Teams (PCTs) has to-date provided valuable information in relation to current barriers to successful implementation which may now be addressed within the overall reform process. Key themes arising from the discussions formed the basis for the recommendations which are considered by the steering group to be critical elements in achieving successful reform.

Variation of the Oviposition Preferences of Aedes aegypti in Function of Substratum and Humidity

Two Aedes aegypti (L.) populations were studied in the laboratory regarding the preference for three types of breeding sites, i.e., flasks containing only water, flasks with a plant and flasks with a stick. Each of these breeding units was placed in one cage and the choice of the oviposition sites was determined for individual females and three females per experimental unit at two humidity levels. Preference for ovipositing on the water surface was observed and varied according to experimental unit and humidity. Mean hatching of eggs in water surface was 46.6%. Experiments with three females showed a more marked difference than when only one female was used. Inter and intrapopulation variability regarding oviposition sites was observed. The discrimination between the different oviposition substrates, hatching in water surface and its implication for mosquito control are discussed.

An Adenovirus Vector Containing the Suicide Gene Thymidine Kinase for a Broad Application in Cancer Gene Therapy

Treatment of cancer using gene therapy is based on adding a property to the cell leading to its elimination. One possibility is the use of suicide genes that code for enzymes that transform a pro-drug into a cytotoxic product. The most extensively used is the herpes simplex virus thymidine kinase (TK) gene, followed by administration of the antiviral drug ganciclovir (GCV). The choice of the promoter to drive the transcription of a transgene is one of the determinants of a given transfer vector usefulness, as different promoters show different efficiencies depending on the target cell type. In the experiments presented here, we report the construction of a recombinant adenovirus carrying TK gene (Ad-TK) driven by three strong promoters (P CMV IE, SV40 and EN1) and its effectiveness in two cell types. Human HeLa and mouse CCR2 tumor cells were transduced with Ad-TK and efficiently killed after addition of GCV. We could detect two sizes of transcripts of TK gene, one derived from the close together P CMV IE/SV40 promoters and the other from the 1.5 Kb downstream EN1 promoter. The relative amounts of these transcripts were different in each cell type thus indicating a higher flexibility of this system.

Non-invasive detection of cocaine dissolved in wine bottles by (1) H magnetic resonance spectroscopy.

Recently, a number of cases of smuggling dissolved cocaine in wine bottles have been reported. The aim of the present study was to determine whether cocaine dissolved in wine can be detected by proton magnetic resonance spectroscopy ((1) H MRS) on a standard clinical MR scanner, in intact (i.e. unopened) wine bottles. (1) H MRS experiments were performed with a 3 Tesla clinical scanner on wine phantoms with or without cocaine contamination. The aromatic protons of cocaine displayed resonance peaks in the 7-8 ppm region of the spectrum, where no overlapping resonances of wine were present. Additional cocaine resonances were detected in the 2-3 ppm region of the spectrum, between the resonances of ethanol and other wine constituents. Detection of cocaine in wine (at 5 mM, i.e. ∼1.5 g/L) was feasible in a scan time of 1 min. We conclude that dissolved cocaine can be detected in intact wine bottles, on a standard clinical MR scanner. Thus, (1) H MRS is the technique of choice to examine this type of suspicious cargo, since it allows for a non-destructive and rapid content characterization. Copyright © 2010 John Wiley & Sons, Ltd.

Crossing experiments detect genetic incompatibility among populations of Triatoma brasiliensis Neiva, 1911 (Heteroptera, Reduviidae, Triatominae)

Triatoma brasiliensis is composed of at least four geographic populations (brasiliensis, melanica, macromelasoma, and juazeiro) that have distinct chromatic, morphologic, biologic and ecologic patterns, and genetic composition. Reciprocal crosses between all pairwise combinations were carried out in order to evaluate the genetic and reproductive compatibility of these four populations. The F1 individuals developed normally and the resulting adults were crossed again to test the F2 and F3 viability. Genetic incompatibility was found between melanica and brasiliensis populations.