Broader comprehension of gene expression regulatory mechanisms can be gained from a global analysis of how transcription and degradation are coordinated to orchestrate complex cell responses. The role of messenger RNA (mRNA) turnover modulation in gene expression levels has become increasingly recognized. From such perspective, in this review we briefly illustrate how a simple but effective mathematical model of mRNA turnover and some experimental findings, may together shed light on the molecular mechanisms underpinning the major role of mRNA decay rates in shaping the kinetics of gene activation and repression

Background: Direct-acting antiviral drugs (DAA) regimen improve the SVR rate. However, adverse effects often lead to therapy interruption. This underlines the importance to find some predictive parameters of response in order to consider the possibility of a shorter time of antiviral treatment in the appearance of adverse effects without affecting the success of the therapy. Objectives: We aimed to examine the HCVAg kinetics in the early phase of treatment and its predictive value of SVR in patients undergoing TPV/Peg-IFN/RBV treatment. Study design: Twenty-three patients infected by HCV genotype 1 (1a n = 11; 1b n = 12) were included in this prospective study. Results: At baseline the median Log of HCVAg concentration in RVR and EVR patients were 3.15 fmol/L and 3.45 fmol/L, respectively with no significant differences. The baseline median HCV-RNA to HCVAg ratio was 233.77, this ratio was significantly lower when measured on day 1 (27.52) and on day 6 (24.84) (p < 0.001). The two-tailed Fisher's exact test indicated that the SVR response is statistically significantly different in patients with detected HCVAg at week1 compared to patients with no detectable HCVAg (p = 0.05). The sensitivity, specificity, and negative and positive predictive values (NPV, PPV) were 53.8, 87.5, 53.8 and 87.5%, respectively. The area under the ROC curve was 0.71 at day T6, the best cut-off of 3 fmol/L when evaluated with the HCVAg plasma concentration at dayT6. Conclusion: Undetectable HCVAg in the early phase of TPV/Peg-IFN/RBV treatment could represent an important parameter for predicting SVR.

Understanding the conditions ensuring the persistence of a population is an issue of primary importance in population biology. The first theoretical approach to the problem dates back to the 1950s with the Kierstead, Slobodkin, and Skellam (KiSS) model, namely a continuous reaction-diffusion equation for a population growing on a patch of finite size L surrounded by a deadly environment with infinite mortality, i.e., an oasis in a desert. The main outcome of the model is that only patches above a critical size allow for population persistence. Here we introduce an individual-based analog of the KiSS model to investigate the effects of discreteness and demographic stochasticity. In particular, we study the average time to extinction both above and below the critical patch size of the continuous model and investigate the quasistationary distribution of the number of individuals for patch sizes above the critical threshold.

We consider Volterra integral equations on time scales and present our study about the long time behavior of their solutions. We provide sufficient conditions for the stability and investigate the convergence properties when the kernel of the equations vanishes at infinity.

In the present work the simulation of water impacts is discussed. The investigation is mainly focused on the energy dissipation involved in liquid impacts in both the frameworks of the weakly compressible and incompressible models. A detailed analysis is performed using a weakly compressible Smoothed Particle Hydrodynamics (SPH) solver and the results are compared with the solutions computed by an incompressible mesh-based Level-Set Finite Volume Method (LS-FVM). Impacts are numerically studied using single-phase models through prototypical problems in 1D and 2D frameworks. These problems were selected for the conclusions to be of interest for, e.g., the numerical computation of the flow around plunging breaking waves. The conclusions drawn are useful not only to SPH or LS-FVM users but also for other numerical models, for which accurate results on benchmark test-cases are provided.

MIPAS measurements on ENVISAT represent a unique database for the study of atmospheric composition and of the time variation of atmospheric constituents. For trend studies it is important that instrumental drifts are reduced. Some of the MIPAS spectral bands are affected by time-dependent non-linearity which have been recently corrected. In addition to this non-linearity correction, the forthcoming new version of MIPAS products (Version 7) contains several other improvements: a new approach for handling continuum capable of making the retrieval more stable, a new selection of spectral intervals selected for the analysis of the full resolution measurements aimed to reduce the bias between full resolution and optimized resolution measurements, the regularization of the H2O profiles, the products of five new species (HCFC-22, CFC-14, HCN, COF2, CCl4), which makes equal to 15 the total number of retrieved species. The latest improvements implemented in the ESA processor and some of the results on trend will be presented and discussed.

Eugenio Elia Levi è stato uno dei più grandi matematici italiani del '900 (come del resto il fratello Beppo). Morì nell'ottobre del 1917, ucciso da un cecchino, nelle fasi iniziali della disfatta di Caporetto. Attivo interventista, allo scoppio della prima guerra mondiale si era arruolato volontariamente nel Genio Zappatori e fu poi promosso capitano per meriti di guerra. Eugenio Elia Levi si era laureato in Matematica nel 1904, studiando alla "Normale" di Pisa dove ebbe come maestri Luigi Bianchi e Ulisse Dini. Nel 1909 ottenne la cattedra di Analisi infinitesimale presso l'Università di Genova. La sua produzione scientifica fu tanto profonda quanto differenziata - ha riguardato i gruppi di Lie, le equazioni alle derivate parziali e la teoria delle funzioni di più variabili complesse - e venne immediatamente apprezzata negli ambienti matematici internazionali. Benché fosse di soli due anni più anziano di Mauro Picone (fondatore dell'IAC), quest'ultimo lo considerò sempre come un suo grande maestro, alla pari di Luigi Bianchi e Ulisse Dini.

MIPAS measurements on ENVISAT represent a unique database for the study of atmospheric composition and of the time variation of atmospheric constituents.For trend studies it is important that instrumental drifts are reduced. Some of the MIPAS spectral bands are affected by time-dependent non-linearity that have been recently corrected.In addition to this non-linearity correction, the forthcoming new version of MIPAS products (Version 7) contains several other improvements: a new approach for handling continuum leading to a more stable retrieval, a new selection of spectral intervals for the analysis of the full resolution measurements aiming to reduce the bias between full resolution and optimized resolution measurements, the regularization of the H2O profiles. Furthermore, the implementation of the retrieval of five new species (HCFC-22, CFC-14, HCN, COF2, CCl4) leads to a total of 15 species in ESA products.The latest improvements implemented in the ESA processor, the results of the validation of the products and some preliminary results on the trend of some ozone depleting substances will be presented and discussed.

A sharp integrability condition on the right-hand side of the p-Laplace system for all its solutions to be continuous is exhibited. Their uniform continuity is also analyzed and estimates for their modulus of continuity are provided. The relevant estimates are shown to be optimal as the right-hand side ranges in classes of rearrangement-invariant spaces, such as Lebesgue, Lorentz, Lorentz-Zygmund, and Marcinkiewicz spaces, as well as some customary Orlicz spaces.

We obtain a comparison result for solutions to nonlinear fully anisotropic elliptic problems by means of anisotropic symmetrization. As consequence we deduce a priori estimates for norms of the relevant solutions.

The hybrid use of exact and heuristic derivative-free methods for global unconstrained optimization problems is presented. Many real-world problems are modeled by computationally expensive functions, such as problems in simulationbased design of complex engineering systems. Objective-function values are often provided by systems of partial differential equations, solved by computationally expensive black-box tools. The objective-function is likely noisy and its derivatives are often not available. On the one hand, the use of exact optimization methods might be computationally too expensive, especially if asymptotic convergence properties are sought. On the other hand, heuristic methods do not guarantee the stationarity of their final solutions. Nevertheless, heuristic methods are usually able to provide an approximate solution at a reasonable computational cost, and have been widely applied to real-world simulation-based design optimization problems. Herein, an overall hybrid algorithm combining the appealing properties of both exact and heuristic methods is discussed, with focus on Particle Swarm Optimization (PSO) and line search-based derivative-free algorithms. The theoretical properties of the hybrid algorithm are detailed, in terms of limit points stationarity. Numerical results are presented for a specific test function and for two real-world optimization problems in ship hydrodynamics.

The book describes a computational model of the immune system reaction, C-ImmSim, built along the lines of the computer model known as the Celada-Seiden model (CS-model). The computational counterpart of the CS-model is called IMMSIM which stands for IMMune system SIMulator. IMMSIM was written in 1992 by the physicist Phil E. Seiden and the immunologist Franco Celada. This model was built around the idea of developing a computerized system to perform experiments similar in vivo experiments; a tool developed to help biologists testing theories and hypothesis about how the immune system works. C-ImmSim is best viewed as a collection of models in a single program. It incorporates the principal core facts of today's immunological knowledge, such as the diversity of specific elements, MHC restriction, clonal selection, thymic education of T cells, antigen processing and presentation (both the cytosolic and endocytic pathways are implemented), cell-cell cooperation, homeostasis of cells created by the bone marrow, hyper mutation of antibodies, maturation of the cellular and humoral response, and memory. Besides, an antigen can represent a bacterium, a virus, or an allergen or a tumor cell. C-ImmSim has been recently customized to simulate the HIV-1 infection. Moreover, it can simulate the immunotherapy for cancer. These features are all present in the code and people can choose to turn them on and off at compiling time. The book presents the basic model as well as the various customizations to implement the description of different diseases and the way they have been used in practice to produce new knowledge either from hypothesis or from lab-experiment data. In this respect, the book can be used as a practical guide to implement a computational model with which to study a specific disease and to try to address realistic clinical questions.

TRANSLATION OF THE ORIGINAL DOCUMENT "NETWORK LITERACY" AVAILABLE AT https://sites.google.com/a/binghamton.edu/netscied/teaching-learning/network-concepts Mentre il nostro mondo diventa sempre più connesso attraverso l'uso di reti, o network, che rendono le comunicazioni e la diffusione di informazioni pressoché istantanee, il livello di comprensione di come queste reti funzionino avrà un ruolo importante nel determinare quanto la società trarrà beneficio da questa connettività accresciuta. In breve, una società connessa richiede un'alfabetizzazione sul concetto di rete, ossia una conoscenza di base di cosa siano le reti, come possano essere utilizzate come strumento per la scoperta e per i processi decisionali, nonché sulle problematiche e i potenziali vantaggi resi accessibili a tutti coloro che vivono nel mondo interconnesso di oggi.

In this paper we present a general model of drug release from a drug delivery device and the subsequent transport in biological tissue. The model incorporates drug diffusion, dissolution and solubility in the polymer coating, coupled with diffusion, convection and reaction in the biological tissue. Each layer contains bound and free drug phases so that the resulting model is a coupled two-phase two-layer system of partial differential equations. One of the novelties is the generality of the model in each layer. Within the drug coating, our model includes diffusion as well as three different models of dissolution. We show that the model may also be used in cases where dissolution is rapid or not relevant, and additionally when drug release is not limited by its solubility. Within the biological tissue, the model can account for nonlinear saturable reversible binding, with linear reversible binding and linear irreversible binding being recovered as special cases. The generality of our model will allow the simulation of the release from a wide range of drug delivery devices encompassing many different applications. To demonstrate the efficacy of our model we simulate results for the particular application of drug release from arterial stents.

Program summary We present the open-source computer program JETSPIN, specifically designed to simulate the electro-spinning process of nanofibers. Its capabilities are shown with proper reference to the underlying model, as well as a description of the relevant input variables and associated test-case simulations. The various interactions included in the electrospinning model implemented in JETSPIN are discussed in detail. The code is designed to exploit different computational architectures, from single to parallel processor workstations. This paper provides an overview of JETSPIN, focusing primarily on its structure, parallel implementations, functionality, performance, and availability.

We investigate the effects of dissipative air drag on the dynamics of electrified jets in the initial stage of the electrospinning process. The main idea is to use a Brownian noise to model air drag effects on the uniaxial elongation of the jets. The developed numerical model is used to probe the dynamics of electrified polymer jets at different conditions of air drag force, showing that the dynamics of the charged jet is strongly biased by the presence of air drag forces. This study provides prospective beneficial implications for improving forthcoming electrospinning experiments. (C) 2015 Elsevier Ltd. All rights reserved.

We present a nonlinear Langevin model to investigate the early-stage dynamics of electrified polymer jets in electrospinning experiments. In particular, we study the effects of air drag force on the uniaxial elongation of the charged jet, right after ejection from the nozzle. Numerical simulations show that the elongation of the jet filament close to the injection point is significantly affected by the nonlinear drag exerted by the surrounding air. These results provide useful insights for the optimal design of current and future electrospinning experiments.

In this paper we present a model of drug release from a drug eluting-stent and the subsequent drug transport in the arterial wall. In order to study the complete process, a two-phase mathematical model describing the transport of a drug between two coupled media of different properties and dimensions is presented. A system of partial differential equations describes both the solid-liquid transfer (dissolution) and diffusion processes in the polymeric substrate as well as diffusion, convection and reaction in the tissue layer. We adopt a semi-analytical approach in solving the four resulting equations. The model serves as a useful tool for providing insight into the influence of solid-liquid mass transfer in drug-eluting stent systems.