Robustness analysis of a nucleic acid controller for a dynamic biomolecular process using the structured singular value

In the field of synthetic biology, theoretical frameworks and software tools are now available that allow control systems represented as chemical reaction networks to be translated directly into nucleic acid-based chemistry, and hence implement embedded control circuitry for biomolecular processes. However, the development of tools for analysing the robustness of such controllers is still in its infancy. An interesting feature of such control circuits is that, although the transfer function of a linear system can be easily implemented via a chemical network of catalysis, degradation and annihilation reactions, this introduces additional nonlinear dynamics, due to the annihilation kinetics. We exemplify this problem for a dynamical biomolecular feedback system, and demonstrate how the structured singular value (μ) analysis framework can be extended to rigorously analyse the robustness of this class of system. We show that parametric uncertainty in the system affects the location of its equilibrium, and that this must be taken into account in the analysis. We also show that the parameterisation of the system can be scaled for experimental feasibility without affecting its robustness properties, and that a statistical analysis via Monte Carlo simulation fails to uncover the worst-case uncertainty combination found by μ-analysis.</p

On the Feasibility of Indoor Light Energy Harvesting for Wireless Sensor Networks

AbstractThis paper presents the important issues about the design of a low cost, micro power, indoor light energy harvesting system to supply a node of a wireless sensor network (WSN). Possible technology options, available for the photovoltaic (PV) cells, are discussed. Light power and irradiance measurements, in a real indoor environment, are performed and results are presented. From these results, a possible solution for cell sizing is described

Generation of reconfigurable circuits from machine code

Tese de mestrado integrado. Engenharia Electrotécnica e de Computadores. Telecomunicações. Universidade do Porto. Faculdade de Engenharia. 201

The role of human paraoxonase 1 (PON-1) in viral infections

Dissertação para obtenção do grau de Mestre no Instituto Superior de Ciências da Saúde Egas MonizAccording to the World Health Organization, Human Immunodeficiency Virus, Hepatitis B virus and Hepatitis C virus are one of the most common causes of chronic viral related disease. The Paraoxonase-1enzyme is a calcium-dependent enzyme associated to high density lipoprotein, with various activities, including paraxaonase, arylesterase and lactonase. This ability to hydrolase various subtracts seems to give the enzyme antioxidant properties and sensibility to oxidative stress. This review cross references the information of most of the recent and available studies done in the area and tries to demonstrate the connections and the importance of the Paraoxonase-1 enzyme that could provide invaluable clinical information. Several studies conclude that significant alterations occur on the enzymatic activity of Paraoxonase-1 in Human Immunodeficiency Virus, Hepatitis B virus and Hepatitis C virus infected patients. This modifications seem to occur due to the increased levels caused by the infections on the organism, leading to multiple disruption on antioxidant and anti-inflammatory pathways that were demonstrated to involve Paraoxonase-1. Although Paraoxonase-1 activity alterations seem to be caused by malignant causes, positive and useful clinical information might be extracted by measuring such alterations. Paraoxonase-1 possibly will be used with more research in future as a biomarker for some viral infections.De acordo com a Organização Mundial da Saúde, o Vírus da Imunodeficiência Humana, o vírus da Hepatite B e o vírus da Hepatite C são uma das causas mais comuns de doença crónica com origem viral em todo o mundo. A enzima Paraoxonase-1 é uma enzima dependente do cálcio associada às lipoproteínas de alta densidade, com várias atividades, incluindo paraxaonase, arilesterase e lactonase. A capacidade de hidrolisar vários substratos parece dar à enzima propriedades antioxidantes e sensibilidade ao estresse oxidativo. Este trabalho faz uma revisão dos estudos mais recentes e relevantes na área e tenta demonstrar as interligações e importância da enzima Paraoxonase-1, que pode fornecer informações clínicas significativas. Vários estudos apontam para alterações significativas que ocorrem na atividade enzimática da Paraxonase-1 em pacientes infetados com vírus da Imunodeficiência Humana, vírus da Hepatite B e vírus da Hepatite C. Estas modificações parecem ocorrer devido as alterações das atividades da enzima causados pelas infeções no organismo, conduzindo a várias perturbações nas vias anti-oxidantes e anti-inflamatórias, que parecem envolver a Paraoxonase-1. Sendo as alterações na atividade da Paraoxonase-1 aparentemente motivadas por causas malignas, podem ser retiradas informações clínicas úteis através da avaliação de tais alterações. A enzima Paraoxonase-1 possivelmente poderá ser usada, com mais pesquisas no futuro, como biomarcador para as infeções virais

A Switched-Capacitor Band-Pass Biquad Filter Using a Simple Quasi-unity Gain Amplifier

Part 19: Electronics: AmplifiersInternational audienceThis paper presents a switched-capacitor (SC) band-pass biquad using a simple quasi-unity gain amplifier. In sub-nanometer CMOS technologies the intrinsic gain of the transistors is low; this increases the difficulty of designing high gain amplifiers. The proposed SC filter is based on the Sallen-Key biquad and it requires only a simple low gain amplifier. A differential filter circuit, including a suitable amplifier based on a fully-differential voltage-combiner is presented and analyzed. The correct functionality of this circuit is validated through electrical simulations of a second-order band-pass filter. These simulations show that, for a clock frequency of 100 MHz, the frequency response of the circuit is similar to the corresponding prototype filter

Sample size and power calculations for detecting changes in malaria transmission using antibody seroconversion rate.

BACKGROUND: Several studies have highlighted the use of serological data in detecting a reduction in malaria transmission intensity. These studies have typically used serology as an adjunct measure and no formal examination of sample size calculations for this approach has been conducted. METHODS: A sample size calculator is proposed for cross-sectional surveys using data simulation from a reverse catalytic model assuming a reduction in seroconversion rate (SCR) at a given change point before sampling. This calculator is based on logistic approximations for the underlying power curves to detect a reduction in SCR in relation to the hypothesis of a stable SCR for the same data. Sample sizes are illustrated for a hypothetical cross-sectional survey from an African population assuming a known or unknown change point. RESULTS: Overall, data simulation demonstrates that power is strongly affected by assuming a known or unknown change point. Small sample sizes are sufficient to detect strong reductions in SCR, but invariantly lead to poor precision of estimates for current SCR. In this situation, sample size is better determined by controlling the precision of SCR estimates. Conversely larger sample sizes are required for detecting more subtle reductions in malaria transmission but those invariantly increase precision whilst reducing putative estimation bias. CONCLUSIONS: The proposed sample size calculator, although based on data simulation, shows promise of being easily applicable to a range of populations and survey types. Since the change point is a major source of uncertainty, obtaining or assuming prior information about this parameter might reduce both the sample size and the chance of generating biased SCR estimates

Modelos de interacção genética de dois genes em fenótipos

Em trabalhos anteriores foram propostos diversos modelos estatísticos para a penetrância de forma a inferir a interacção de dois genes dial´elicos na construção de fenótipos binários complexos: modelos de acção independente, modelos de inibição e modelos de número mínimo de alelos. Estes modelos baseiam-se numa decomposição da penetrância através da abordagem por penetrâncias alélicas, que permitiu a inclusão dos conceitos mendelianos de dominância e recessividade alélica na sua modelação. Pretende-se aqui dar a conhecer os avanços mais recentes na parte da modelação da interacção genética, apresentando uma nova decomposição da penetrância e uma nova formulação matemática da dominância e da recessividade. Aplicam-se ainda ferramentas bayesianas para o ajustamento dos modelos de interacção genética a dados experimentais com recurso ao método de amostragem de Gibbs. Toda a metodologia é exemplificada num conjunto de dados de um estudo da susceptibilidade da malária cerebral em ratinhos

PID and state feedback controllers using DNA strand displacement reactions

Nucleic acid-based chemistry is a strong candidate framework for the construction of future synthetic biomolecular control circuits. Previous work has demonstrated the capacity of circuits based on DNA strand displacement (DSD) reactions to implement digital and analogue signal processing in vivo , including in mammalian cells. To date, however, feedback control system designs attempted within this framework have been restricted to extremely simple proportional or proportional-integral controller architectures. In this letter, we significantly extend the potential complexity of such controllers by showing how time-delays, numerical differentiation (to allow PID control), and state feedback may be implemented via chemical reaction network-based designs. Our controllers are implemented and tested using VisualDSD, a rapid-prototyping tool that allows precise analysis of computational devices implemented using nucleic acids, via both deterministic and stochastic simulations of the DSD reactions.11Nscopu