Stochastic Modeling of Expression Kinetics Identifies Messenger Half-Lives and Reveals Sequential Waves of Co-ordinated Transcription and Decay

The transcriptome in a cell is finely regulated by a large number of molecular mechanisms able to control the balance between mRNA production and degradation. Recent experimental findings have evidenced that fine and specific regulation of degradation is needed for proper orchestration of a global cell response to environmental conditions. We developed a computational technique based on stochastic modeling, to infer condition-specific individual mRNA half-lives directly from gene expression time-courses. Predictions from our method were validated by experimentally measured mRNA decay rates during the intraerythrocytic developmental cycle of Plasmodium falciparum. We then applied our methodology to publicly available data on the reproductive and metabolic cycle of budding yeast. Strikingly, our analysis revealed, in all cases, the presence of periodic changes in decay rates of sequentially induced genes and co-ordination strategies between transcription and degradation, thus suggesting a general principle for the proper coordination of transcription and degradation machinery in response to internal and/or external stimuli. Citation: Cacace F, Paci P, Cusimano V, Germani A, Farina L (2012) Stochastic Modeling of Expression Kinetics Identifies Messenger Half-Lives and Reveals Sequential Waves of Co-ordinated Transcription and Decay. PLoS Comput Biol 8(11): e1002772. doi:10.1371/journal.pcbi.100277

An exponential observer for discrete-time systems with bilinear drift and rational output functions

Abstract-This paper presents an observer with exponential error decay for systems described by bilinear input-state dynamics and output functions that are ratios of polynomials in the state. It is shown that such kind of systems can be immersed into systems of higher dimension, with time-varying linear state dynamics and linear output map. The observer here presented is derived exploiting the structure of the extended system. Conditions of global exponential convergence are given and discussed. Computer simulations demonstrate good behavior of the observer, even in the presence of disturbances on the state and output equations

Distributed kalman filtering over sensor networks with unknown random link failures

In this letter we consider the distributed consensus-based filtering problem for linear time-invariant systems over sensor networks subject to random link failures when the failure sequence is not known at the receiving side. We assume that the information exchanged, traveling along the channel, is corrupted by a noise and hence, it is no more possible to discriminate with certainty if a link failure has occurred. Therefore, in order to process the only significant information, we endow each sensor with detectors which decide on the presence of link failures. At each sensor the proposed approach consists of three steps: 1) failure detection; 2) local data aggregation; and 3) Kalman consensus filtering. Numerical examples show the effectiveness of this method

Polynomial Approach for Filtering and Identification of a Class of Uncertain Systems

Abstract this paper considers the filtering and identification problems for a class of discrete-time uncertain stochastic systems that admit a finite number of linear working modes. It is shown here that this class of uncertain systems can be modeled by using a suitably defined extended system, whose state evolves according to a bilinear model. A polynomial filtering algorithm is derived for such extended system, which readily provides the polynomial estimates of both the original state and the working mode. Simulations show the effectiveness of the proposed approach and the improvements with respect to standard linear filtering algorithms

DISTRIBUTED-DELAY MODELS OF THE GLUCOSE-INSULIN HOMEOSTASIS AND ASYMPTOTIC STATE OBSERVATION

Abstract In this paper the problem of the real-time reconstruction of plasma insulin concentration by using only blood glucose measurements is investigated. This is an interesting problem because the knowledge of the time course of the glucose and insulin concentrations in an individual provides precious informations concerning its health state, and may assume the role of a clinical instrument. For the purpose of the reconstruction of the insulinemia a dynamical model of the glucose-insuline homeostasis is required. The present work considers distributed delay models. Such models have been preferred in recent papers with respect to the standard Minimal Models, available in literature from 70's, because they allow to couple the glucose and insulin dynamics in a unique extended system, whose solutions have been proven to be positive, bounded, and globally asymptotically stable around the basal values of the equilibrium point. Data are acquired according to the Intra Venous Glucose Tolerance Test (IVGTT). Simulation results are reported in order to validate the developed theory

The role of the pion in the lineshape of the X(3872)X(3872)

We determine the contribution of long-range pion interactions to the $X(3872)$ dynamics, assuming it is a loosely bound $D^0 \bar{D}^{*0}$ molecule. Our result is based on the distorted wave Born approximation in non-relativistic quantum mechanics. Despite their long-range nature, we find that pion interactions cannot produce a large and negative effective range. Nonetheless, they introduce imaginary parts. In particular, they contribute to the total decay width of the $X(3872)$ with a term associated with, but not precisely corresponding to, the $D^*$ width. Our approach can also be applied to the recently discovered $T_{cc}^+$ states.Comment: 9 pages, 1 figur

State observation for systems with linear state dynamics and polynomial output

This paper investigates the problem of asymptotic state reconstruction for a class of continuous-time systems characterized by linear input-state dynamics and polynomial state-output function. It is shown that the dynamics of systems in this class can be embedded into the dynamics of systems of higher dimension, with time-varying linear state dynamics and linear state-output map. An asymptotic state observer for the original system is presented, whose design is based on the equations of the extended system. The observer gain is computed on-line by solving a Riccati differential equation. The interest in this observer is in its capability of state reconstruction also in cases in which the original system is not drift-observable (observable for zero input) nor uniformly observable (observable for any input)

Design of observers for systems with rational output function

This note presents an approach for the design of asymptotic state observers for systems characterized by output functions that are ratios of polynomials in the state. The case of linear and bilinear input-state dynamics is considered, and conditions for exponential error decay are provided. The first step towards the construction of the observer is to show that the dynamics of a system in the considered class can be embedded into the dynamics of a system of higher dimension, with time-varying linear state dynamics and linear output map. The construction of the observer here proposed exploits the structure of the extended system. The solution of a Riccati differential equation provides the observer gain

Design of observers for systems with rational output function

Abstract-This note presents an approach for the design of asymptotic state observers for systems characterized by output functions that are ratios of polynomials in the state. The case of linear and bilinear input-state dynamics is considered, and conditions for exponential error decay are provided. The first step towards the construction of the observer is to show that the dynamics of a system in the considered class can be embedded into the dynamics of a system of higher dimension, with time-varying linear state dynamics and linear output map. The construction of the observer here proposed exploits the structure of the extended system. The solution of a Riccati differential equation provides the observer gain

O uso de tecnologias de informação e comunicação (TIC) em experiências de pós-graduação sobre promoção da saúde no Brasil e na Costa Rica

Global Conferences on Health Promotion underscore the need for reorientation of services as a field of action in the area. In particular the Bangkok Charter mentions the Information and Communication Technologies (ICT). In this sense, ICT-based teaching emerges as a way to strengthen learning how to learn, also in the area of health promotion, theme still latent into graduation´s health course. Objective: To describe the use of ICT in post-graduate focusing on health promotion. Method: This is a descriptive analysis of teaching approaches supported by ICT in three experiments. The first, in the form of update / specialization (sensu lato), is part of the activities of the department of internal medicine and has been incorporating ICT throughout its 10 years of existence. The second experiment deals with a post-graduate course in the strict sense of the public health program, under theresponsibility of the preventive medicine department. Finally, we present the discipline graduate also strict sense of Nursing, Faculty of Medicine at the University of Costa Rica. Results: We present summary tables on the use of different ICT as well as the desired educational objectives and the nature of the activity. Conclusion: The current use of ICT highlights the opportunity and incentive for space construction and re-construction of knowledge in Health Promotion. Recognize the potential and limits of the use of ICT contributes to interprofessional education of health promoters with emphasis in a transformative education. As Conferências Internacionais de promoção da saúde ressaltam a necessidade de reorientação dos serviços como campo de ação da área. Em especial a Carta de Bangkok menciona as Tecnologias de Informação e Comunicação (TIC). Nesta direção, o ensino baseado em TIC surge como forma de fortalecer o aprender a aprender, também na área de promoção da saúde, tema ainda latente nas graduações. Objetivo: Descrever o uso das TIC em cursos de pós-graduação com foco na promoção da saúde. Método: Trata-se de uma análise descritiva das abordagens de ensino apoiadas em TIC em três experiências. A primeira, na modalidade de atualização/especialização (lato senso), é parte das ações de extensão do Departamento de Clínica Médica e vem incorporando as TIC ao longo de seus 10 anos de existência. A segunda experiência aborda uma disciplina de pós-graduação stricto senso do Programa de Saúde Coletiva, sob responsabilidade do Departamento de Medicina Preventiva. Por fim, é apresentada a disciplina de pós-graduação também stricto senso de Enfermagem da Faculdade de Medicina na Universidade da Costa Rica. Resultados: Apresentam-se quadros sintéticos sobre o uso de diferentes TIC bem como os objetivos pedagógicos pretendidos e a natureza da atividade. Conclusão: O atual uso das TIC evidencia a oportunidade de espaço e estímulo para construção e re-construção do conhecimento em Educação e Promoção da Saúde. Reconhecer as potencialidades e os limites do uso de TIC contribui para a formação interprofissional de promotores da saúde com ênfase em uma educação transformadora