In this paper we present mathematical tools inspired by the kinetic theory, which can be used to model the social behaviors of large communities of individuals. The focus is especially on human societies, such as the population of a certain country, and on the interplays between concurrent social dynamics, for instance economic issues linked to the formation of political opinions, which sometimes can even degenerate into dramatic extreme events with massive impact (Black Swans). Starting from Boltzmann-type models, we present an evolution of the classical approach of statistical mechanics, whose hallmark is the use of stochastic game theory for the description of social interactions. By this we mean that the latter are modeled as games whose payoffs, however, are known only in probability. This is consistent with the basic unpredictability of human reactions, which ultimately cannot be compared to deterministic mechanical-like "collisions".

In this paper we study a model for traffic flow on networks based on a hyperbolic system of conservation laws with discontinuous flux. Each equation describes the density evolution of vehicles having a common path along the network. In this formulation the junctions disappear since each path is considered as a single uninterrupted road. We consider a Godunov-based approximation scheme for the system which is very easy to implement. Besides basic properties like the conservation of cars and positive bounded solutions, the scheme exhibits other nice properties, being able to select automatically a solution at network's nodes without requiring external procedures (e.g., maximization of the flux via a linear programming method). Moreover, the scheme can be interpreted as a discretization of the traffic models with buffer, although no buffer is introduced here. Finally, we show how the scheme can be recast in the framework of the classical theory of traffic flow on networks, where a conservation law has to be solved on each arc of the network. This is achieved by solving the Riemann problem for a modified equation, and showing that its solution corresponds to the one computed by the numerical scheme.

The problem of diurnal variation in surface emissivity over the Sahara Desert during non-raining days is studied and assessed with observations from the Infrared Atmospheric Sounding Interferometer (IASI). The analysis has been performed over a Sahara Desert dune target area during July 2010. Spinning Enhanced Visible and Infrared Imager observations from the European geostationary platform Meteosat-9 (Meteorological Satellite 9) have been also used to characterize the target area. Although the amplitude of this daily cycle has been shown to be very small, we argue that suitable nighttime meteorological conditions and the strong contrast of the reststrahlen absorption bands of quartz (8-14 ?m) can amplify its effect over the surface spectral emissivity. The retrieval of atmospheric parameters show that, at nighttime, an atmospheric temperature inversion occurs close to the surface yielding a thin boundary layer which acts like a lid, keeping normal convective overturning of the atmosphere from penetrating through the inversion. This mechanism traps water vapor close to the land and drives the direct adsorption of water vapor at the surface during the night. The diurnal variation in emissivity at 8.7 ?m has been found to be as large as 0.03 with high values at night and low values during the day. At 10.8 ?m and 12 ?m, the variation has the same sign as that at 8.7 ?m, but with a smaller amplitude, 0.019 and 0.014, respectively. The impact of these diurnal variations on the retrieval of surface temperature and atmospheric parameters has been analyzed. Key Points Diurnal variation in desert emissivity during the dry season assessed with IASI Assessment of the meteorological conditions which favors the phenomenon Impact of emissivity variation on atmospheric parameters retrieval ©2013. American Geophysical Union. All Rights Reserved.

Results: We carried out a simulation study to assess the performance of 5 widely used tools, such as: CEM, Cufflinks, iReckon, RSEM, and SLIDE. All of them have been used with default parameters. In particular, we considered the effect of the following three different scenarios: the availability of complete annotation, incomplete annotation, and no annotation at all. Moreover, comparisons were carried out using the methods in three different modes of action. In the first mode, the methods were forced to only deal with those isoforms that are present in the annotation; in the second mode, they were allowed to detect novel isoforms using the annotation as guide; in the third mode, they were operating in fully data driven way (although with the support of the alignment on the reference genome). In the latter modality, precision and recall are quite poor. On the contrary, results are better with the support of the annotation, even though it is not complete. Finally, abundance estimation error often shows a very skewed distribution. The performance strongly depends on the true real abundance of the isoforms. Lowly (and sometimes also moderately) expressed isoforms are poorly detected and estimated. In particular, lowly expressed isoforms are identified mainly if they are provided in the original annotation as potential isoforms. Background: The main goal of the whole transcriptome analysis is to correctly identify all expressed transcripts within a specific cell/tissue- at a particular stage and condition - to determine their structures and to measure their abundances. RNA-seq data promise to allow identification and quantification of transcriptome at unprecedented level of resolution, accuracy and low cost. Several computational methods have been proposed to achieve such purposes. However, it is still not clear which promises are already met and which challenges are still open and require further methodological developments.

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The study of a planing flat plate may be considered as a topic of wide interest for academic and industrial applications. From experimental and numerical studies, flow separation occurs near the stagnation point and a thin jet sprays forward along the plate, while a clear wave pattern develops downstream. In the present study, the effect on the jet-root position caused by a cushion pressure applied on the downstream free surface is considered and the consequent variation in lift and drag coefficients is studied. This canonical problem is important in the design of Surface Effects Ships (SES), the bow seal of which may be assumed as a planing deformable surface with a cushion pressure behind it. This study focuses on the hydrodynamic interaction between the plate and the cushion pressure; as such, the plate geometry is prescribed. A two-dimensional numerical study of this problem has been performed in the present work using a finite-volume Chimera-overlapping-grids approach to numerically solve the Navier-Stokes equations; the free surface is handled by means of two-phase level-set method. Validity of the results is assessed by the comparison with theoretical and numerical results available in the literature.

The analysis of a propeller operating in off-design conditions is one of the most attractive and challenging topics in naval hydrodynamics, because of its close connections with different aspects of ship design and performances. For these reasons, wake dynamics and propeller loads are analyzed in the present paper by means of a numerical code based on the solution of the Reynolds averaged Navier-Stokes equations, whose capability to capture propeller hydrodynamics in these extreme conditions are also investigated. The test case considered is the CNR-INSEAN E779A propeller model, for which a detailed experimental database exists for axial flow conditions; propeller geometry and computational domain are discretized by means of an overlapping grid approach.A wide range of incidence angles (10-50°) at two different loading conditions are considered, in order to analyze the propeller performance during severe off-design conditions, similar to those experienced during very complicated maneuvering scenarios. Details of average and instantaneous loads are reported, for both the complete propeller and for a single blade.The present paper is an extension of the analysis of propeller performance in oblique flow, recently proposed in [1]; here, the focus is on propeller performance at very high angle of incidence. The k - {small element of} and a DES turbulence models have been exploited also, in order to provide a reliable verification of the numerical results in the absence of experimental data in these extreme operating conditions. © 2013 Elsevier Ltd.

A Boundary Element Method (BEM) hydrodynamics combined with a flow-alignment technique to evaluate blades shed vorticity is presented and applied to a marine propeller in open water. Potentialities and drawbacks of this approach in capturing propeller performance, slipstream velocities, blade pressure distribution and pressure disturbance in the flow-field are highlighted by comparisons with available experiments and RANSE results. In particular, correlations between the shape of the convected vortex- sheet and the accuracy of BEM results are discussed throughout the paper. To this aim, the analysis of propeller thrust and torque is the starting point towards a detailed discussion on the capability of a 3-D free-wake BEM hydrodynamic approach to describe the local features of the flow-field behind the propeller disk, in view of applications to propulsive configurations where the shed wake plays a dominant role.

This chapter deals with models of living complex systems, chiefly human crowds, by methods of conservation laws and measure theory. We introduce a modeling framework which enables one to address both discrete and continuous dynamical systems in a unified manner using common phenomenological ideas and mathematical tools as well as to couple these two descriptions in a multiscale perspective. Furthermore, we present a basic theory of well-posedness and numerical approximation of initial-value problems and we discuss its implications on mathematical modeling.

The onset and the nature of dynamic instabilities experienced by the wake of a marine propeller set in oblique flow are investigated by means of detached eddy simulations. In particular, the destabilization process is inspected by a systematic comparison of the wake morphology of a propeller operating in pure axisymmetric flow and in drift with angle of 20 degrees, under different loading conditions. The wake behaviour in oblique flow shows a markedly different character with respect to the axisymmetric condition: in the latter, the destabilization is triggered by an increasing interaction of the main vorticity confined in the tip vortex; whereas, in the former, the role of the secondary vorticity (oriented in the streamwise direction) as well as the hub vortex seems to be crucial. The features of the wake have been investigated by the lambda(2) criterion (Jeong & Hussain, J. Fluid Mech., vol. 285, 1995, pp. 69-94) and typical flow variables (pressure, velocity and vorticity), for both the averaged and instantaneous flow fields. Moreover, in order to further inspect the evolution of the vortical structures, as well as their interaction and destabilization, the spectra of the kinetic energy have been considered. This investigation aims to broaden the knowledge from previous works on the subject of rotor wake instabilities, focusing on the differences between an ideal (axisymmetric) and actual operating conditions occurring in typical engineering applications.

The conceptualization of immunological self is amongst the most important theories of modern biology, representing a sort of theoretical guideline for experimental immunologists, in order to understand how host constituents are ignored by the immune system (IS). A consistent advancement in this field has been represented by the danger/damage theory and its subsequent refinements, which at present represents the most comprehensive conceptualization of immunological self. Here, we present the new hypothesis of "liquid self," which integrates and extends the danger/damage theory. The main novelty of the liquid self hypothesis lies in the full integration of the immune response mechanisms into the host body's ecosystems, i.e., in adding the temporal, as well as the geographical/evolutionary and environmental, dimensions, which we suggested to call "immunological biography." Our hypothesis takes into account the important biological changes occurring with time (age) in the IS (including immunosenescence and inflammaging), as well as changes in the organismal context related to nutrition, lifestyle, and geography (populations). We argue that such temporal and geographical dimensions impinge upon, and continuously reshape, the antigenicity of physical entities (molecules, cells, bacteria, viruses), making them switching between "self" and "non-self" states in a dynamical, "liquid" fashion. Particular attention is devoted to oral tolerance and gut microbiota, as well as to a new potential source of unexpected self epitopes produced by proteasome splicing. Finally, our framework allows the set up of a variety of testable predictions, the most straightforward suggesting that the immune responses to defined molecules representing potentials antigens will be quantitatively and qualitatively quite different according to the immuno-biographical background of the host. © 2014 Grignolio, Mishto, Faria, Garagnani, Franceschi and Tieri.

A model of drug release from an eluting stent to the arterial wall is presented. The coating layer is described as a porous reservoir where the drug is initially loaded in a polymer-encapsulated solid phase, and is then released both to the coating and to the tissue of the arterial wall in a free phase. The wall is treated as a heterogeneous porous medium and the drug transfer through it is modeled by a non-homogeneous set of coupled partial differential equations that describe a convection-diffusion-reaction process. Change of phases due to drug dissolution in the coating and binding-unbinding reactions in the arterial wall are addressed. Numerical results show a strong coupling of the release kinetics in the polymer and the drug dynamics in the wall, and this coupling depends on the physico-chemical drug properties, the microstructure of the polymeric stent coating and the properties of the arterial wall.

We introduce a classification method (cumulative discriminant analysis) of the discriminant analysis type to discriminate between cloudy and clear-sky satellite observations in the thermal infrared. The tool is intended for the high-spectral-resolution infrared sounder (IRS) planned for the geostationary METEOSAT (Meteorological Satellite) Third Generation platform and uses IASI (Infrared Atmospheric Sounding Interferometer) data as a proxy. The cumulative discriminant analysis does not introduce biases intrinsic with the approximation of the probability density functions and is flexible enough to adapt to different strategies to optimize the cloud mask. The methodology is based on nine statistics computed from IASI spectral radiances, which exploit the high spectral resolution of the instrument and which effectively summarize information contained within the IASI spectrum. A principal component analysis prior step is also introduced, which makes the problem more consistent with the statistical assumptions of the methodology. An initial assessment of the scheme is performed based on global and regional IASI real data sets and cloud masks obtained from AVHRR (Advanced Very High Resolution Radiometer) and SEVIRI (Spinning Enhanced Visible and Infrared Imager) imagers. The agreement with these independent cloud masks is generally well above 80 %, except at high latitudes in the winter seasons.

In non-parametric regression analysis the advantage of frames with respect to classical orthonormal bases is that they can furnish an efficient representation of a more broad class of functions. For example, fast oscillating functions as audio, speech, sonar, radar, EEG and stock market are much more well represented by a frame, with similar oscillating characteristic, than by a classical orthonormal basis. In this respect, a new frame based shrinkage estimator is derived as the Empirical Regularized version of the optimal Shrinkage estimator generalized to the frame operator. An analytic expression of it is furnished leading to an efficient implementation. Results on standard and real test functions are shown. © 2014 Elsevier B.V. All rights reserved.

Gene therapy is a promising approach for treating a wide range of human pathologies such as genetic disorders as well as diseases acquired over time. Viral and non-viral vectors are used to convey sequences of genes that can be expressed for therapeutic purposes. Plasmid DNA is receiving considerable attention for intramuscular gene transfer due to its safety, simplicity and low cost of production. Nevertheless, strategies to improve DNA uptake into the nucleus of cells for its expression are required. Cytoskeleton plays an important role in the intracellular trafficking. The mechanism regulating this process must be elucidated. Here, we propose a new methodological approach based on the coupling of biology assays and predictive mathematical models, in order to clarify the mechanism of the DNA uptake and its expression into the cells. Once these processes are better clarified, we will be able to propose more efficient therapeutic gene transfer protocols for the treatment of human patients.

A new partial differential model for monitoring and detecting copper corrosion products (mainly brochantite and cuprite) is proposed to provide predictive tools suitable for describing the evolution of damage induced on bronze specimens by sulfur dioxide (SO2) pollution. This model is characterized by the movement of a double free boundary. Numerical simulations show a nice agreement with experimental result. (C) 2014 Elsevier Inc. All rights reserved.

Various molecular pharmacokinetic-pharmacodynamic (PK-PD) models have been proposed in the last decades to represent and predict drug effects in anticancer chemotherapies. Most of these models are cell population based since clearly measurable effects of drugs can be seen much more easily on populations of cells, healthy and tumour, than in individual cells. The actual targets of drugs are, however, cells themselves. The drugs in use either disrupt genome integrity by causing DNA strand breaks, and consequently initiate programmed cell death, or block cell proliferation mainly by inhibiting factors that enable cells to proceed from one cell cycle phase to the next through checkpoints in the cell division cycle. DNA damage caused by cytotoxic drugs (and also cytostatic drugs at high concentrations) activates, among others, the p53 protein-modulated signalling pathways that directly or indirectly force the cell to make a decision between survival and death. The paper aims to become the first-step in a larger scale enterprise that should bridge the gap between intracellular and population PK-PD models, providing oncologists with a rationale to predict and optimise the effects of anticancer drugs in the clinic. So far, it only sticks at describing p53 activation and regulation in single cells following their exposure to DNA damaging stress agents. We show that p53 oscillations that have been observed in individual cells can be reconstructed and predicted by compartmentalising cellular events occurring after DNA damage, either in the nucleus or in the cytoplasm, and by describing network interactions, using ordinary differential equations (ODEs), between the ATM, p53, Mdm2 and Wip1 proteins, in each compartment, nucleus or cytoplasm, and between the two compartments. This article is part of a Special Issue entitled: Computational Proteomics, Systems Biology 82 Clinical Implications. (C) 2013 Elsevier B.V. All rights reserved.

The intracellular signalling network of the p53 protein plays important roles in genome protection and the control of cell cycle phase transitions. Recently observed oscillatory behaviour in single cells under stress conditions has inspired several research groups to simulate and study the dynamics of the protein with the aim of gaining a proper understanding of the physiological meanings of the oscillations. We propose compartmental ODE and PDE models of p53 activation and regulation in single cells following DNA damage and we show that the p53 oscillations can be retrieved by plainly involving p53-Mdm2 and ATM-p53-Wip1 negative feedbacks, which are sufficient for oscillations experimentally, with no further need to introduce any delays into the protein responses and without considering additional positive feedback.

The complex differentiation process of the CD4+ T helper lymphocytes shapes the form and the range of the immune response to different antigenic challenges. Few mathematical and computational models have addressed this key phenomenon. We here present a multiscale approach in which two different levels of description, i.e. a gene regulatory network model and an agent-based simulator for cell population dynamics, are integrated into a single immune system model. We illustrate how such model integration allows bridging a gap between gene level information and cell level population, and how the model is able to describe a coherent immunological behaviour when challenged with different stimuli.