We present the results of our numerical simulations of the Rayleigh-Taylor turbulence, performed using a recently proposed (Sbragaglia et al 2009 J. Fluid Mech. 628 299, Scagliarini et al 2010 Phys. Fluids 22 055101) lattice Boltzmann method that can describe consistently a thermal compressible flow subjected to an external forcing. The method allowed us to study the system in both the nearly Boussinesq regime and the strongly compressible regime. Moreover, we show that when the stratification is important, the presence of the adiabatic gradient causes the arrest of the mixing process.

Two T helper (Th) cell subsets, namely Th1 and Th2 cells, play an important role in inflammatory diseases. The two subsets are thought to counter-regulate each other, and alterations in their balance result in different diseases. This paradigm has been challenged by recent clinical and experimental data. Because of the large number of genes involved in regulating Th1 and Th2 cells, assessment of this paradigm by modeling or experiments is difficult. Novel algorithms based on formal methods now permit the analysis of large gene regulatory networks. By combining these algorithms with in silico knockouts and gene expression microarray data from human T cells, we examined if the results were compatible with a counterregulatory role of Th1 and Th2 cells. We constructed a directed network model of genes regulating Th1 and Th2 cells through text mining and manual curation. We identified four attractors in the network, three of which included genes that corresponded to Th0, Th1 and Th2 cells. The fourth attractor contained a mixture of Th1 and Th2 genes. We found that neither in silico knockouts of the Th1 and Th2 attractor genes nor gene expression microarray data from patients with immunological disorders and healthy subjects supported a counter-regulatory role of Th1 and Th2 cells. By combining network modeling with transcriptomic data analysis and in silico knockouts, we have devised a practical way to help unravel complex regulatory network topology and to increase our understanding of how network actions may differ in health and disease.

We state some pointwise estimates for the rate of weighted approximation of a continuous function on the semiaxis by polynomials. Furthermore we derive matching converse results and estimates involving the derivatives of the approximating polynomials. Using special weighted moduli of continuity, we bridge the gap between an old result by V.M. Fedorov based on the ordinary modulus of smoothness, and the recent norm estimates implicating the Ditzian-Toytik modulus of continuity.

Background: Pathological angiogenesis represents a critical issue in the progression of many diseases. Down syndrome is postulated to be a systemic anti-angiogenesis disease model, possibly due to increased expression of anti-angiogenic regulators on chromosome 21. The aim of our study was to elucidate some features of circulating endothelial progenitor cells in the context of this syndrome. Methods: Circulating endothelial progenitors of Down syndrome affected individuals were isolated, in vitro cultured and analyzed by confocal and transmission electron microscopy. ELISA was performed to measure SDF-1 alpha plasma levels in Down syndrome and euploid individuals. Moreover, qRT-PCR was used to quantify expression levels of CXCL12 gene and of its receptor in progenitor cells. The functional impairment of Down progenitors was evaluated through their susceptibility to hydroperoxide-induced oxidative stress with BODIPY assay and the major vulnerability to the infection with human pathogens. The differential expression of crucial genes in Down progenitor cells was evaluated by microarray analysis. Results: We detected a marked decrease of progenitors' number in young Down individuals compared to euploid, cell size increase and some major detrimental morphological changes. Moreover, Down syndrome patients also exhibited decreased SDF-1 alpha plasma levels and their progenitors had a reduced expression of SDF-1 alpha encoding gene and of its membrane receptor. We further demonstrated that their progenitor cells are more susceptible to hydroperoxide-induced oxidative stress and infection with Bartonella henselae. Further, we observed that most of the differentially expressed genes belong to angiogenesis, immune response and inflammation pathways, and that infected progenitors with trisomy 21 have a more pronounced perturbation of immune response genes than infected euploid cells. Conclusions: Our data provide evidences for a reduced number and altered morphology of endothelial progenitor cells in Down syndrome, also showing the higher susceptibility to oxidative stress and to pathogen infection compared to euploid cells, thereby confirming the angiogenesis and immune response deficit observed in Down syndrome individuals.

In recent years, the introduction of massively parallel sequencing platforms for Next Generation Sequencing (NGS) protocols, able to simultaneously sequence hundred thousand DNA fragments, dramatically changed the landscape of the genetics studies. RNA-Seq for transcriptome studies, Chip-Seq for DNA-proteins interaction, CNV-Seq for large genome nucleotide variations are only some of the intriguing new applications supported by these innovative platforms. Among them RNA-Seq is perhaps the most complex NGS application. Expression levels of specific genes, differential splicing, allele-specific expression of transcripts can be accurately determined by RNA-Seq experiments to address many biological-related issues. All these attributes are not readily achievable from previously widespread hybridization-based or tag sequence-based approaches. However, the unprecedented level of sensitivity and the large amount of available data produced by NGS platforms provide clear advantages as well as new challenges and issues. This technology brings the great power to make several new biological observations and discoveries, it also requires a considerable effort in the development of new bioinformatics tools to deal with these massive data files. The paper aims to give a survey of the RNA-Seq methodology, particularly focusing on the challenges that this application presents both from a biological and a bioinformatics point of view.

A mathematical model of the galvanic iron corrosion is, here, presented. The iron(III)-hydroxide formation is considered together with the redox reaction. The PDE system, assembled on the basis of the fundamental holding electro-chemistry laws, is numerically solved by a locally refined FD method. For verification purpose we have assembled an experimental galvanic cell; in the present work, we report two tests cases, with acidic and neutral electrolitical solution, where the computed electric potential compares well with the measured experimental one

Here we give mathematical support to the choice of the Helmholtz versus the Laplace equation for the formulation of an inverse problem in infrared thermography. Such a choice accounts for the values of physical parameters like the thermal conductivity and the Biot number. We check the effectiveness of the corresponding boundary value problems and compare the condition numbers. The Helmholtz choice is confirmed to be usually better, but there are cases in which Laplace (less expensive) works well.

A thin conducting plate has an inaccessible side in contact with aggressive external agents. On the other side, we are able to heat the plate and take temperature maps in laboratory conditions. Detecting and evaluating damages on the inaccessible side from thermal data requires the solution of a nonlinear inverse problem for the heat equation in presence of suitable boundary conditions for heat equation. We carry on this task using domain derivative and integral formulation of the corresponding boundary value problem. Under non restrictive hypothesis, we find explicit regularized schemes for Fourier reconstruction of damages.

A unified view to Semantic Web/Grid Information and Services Discovery and Management is being investigated at CNR both at the theoretical level and at the experimental level. The mathematical foundations are being developed with algebraic methods. An experimental prototype is being realized in the area of Cultural Heritage. The paper presents achievements and future directions

We present a multi-year database of atmospheric fields of the upper troposphere, stratosphere and lower mesosphere retrieved from satellite measurements adopting a 2-dimensional tomographic approach. The full mission of the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) instrument, on board the European Space Agency ENVISAT satellite, is analyzed with the Geofit Multi-Target Retrieval (GMTR) system to obtain the MIPAS2D database with atmospheric fields of pressure, temperature and volume mixing ratio of MIPAS main targets H2O, O3, HNO3, CH4, N2O, and NO2. The database covers both the MIPAS nominal observation mode measured at Full Resolution (FR) from July 2002 to March 2004 and the nominal observation mode of the new configuration, measured at Optimized Resolution (OR) and introduced in 2005. Further to the main targets, minor species N2O5, ClONO2, COF2, CFC-11, and CFC-12 for the FR mission only have been included in MIPAS2D to enhance its applicability in studies of stratospheric chemistry. The database is continuously updated with the analysis of the ongoing measurements that are planned to last until the end of 2013 and extended to other targets. The GMTR algorithm is operated on a fixed vertical grid coincident with the tangent altitudes of the FR nominal mode, spanning the altitude range from 6 to 68 km. In the horizontal domain, FR measurements are retrieved on both the observational grid and an equispaced 5 latitudinal-degrees grid which is made possible by the 2-dimensional retrieval algorithm. The analysis of MIPAS OR observations is operated on the same altitude-latitude fixed retrieval grid used for the FR measurements. This choice provides a database with a homogeneous altitude and latitude grid, over the whole globe, covering to date about seven years of measurements. The equispaced latitude grid provides a new and convenient layout for the much needed synergetic studies of data from various instrumental and modeling sources. MIPAS2D is available to the scientific community through the two web sites http://www.mbf.fci.unibo.it/mipas2d.html, and http://www.isac.cnr.it/~rss/mipas2d.htm

The statistics of velocity differences between pairs of heavy inertial point particles suspended in an incompressible turbulent flow is studied and found to be extremely intermittent. The problem is particularly relevant to the estimation of the efficiency of collisions among heavy particles in turbulence. We found that when particles are separated by distances within the dissipative subrange, the competition between regions with quiet regular velocity distributions and regions where very close particles have very different velocities (caustics) leads to a quasi bi-fractal behaviour of the particle velocity structure functions. Contrastingly, we show that for particles separated by inertial-range distances, the velocity-difference statistics can be characterized in terms of a local roughness exponent, which is a function of the scale-dependent particle Stokes number only. Results are obtained from high-resolution direct numerical simulations up to 2048 3 collocation points and with millions of particles for each Stokes number.

Bayesian Modeling in Bioinformatics discusses the development and application of Bayesian statistical methods for the analysis of high-throughput bioinformatics data arising from problems in molecular and structural biology and disease-related medical research, such as cancer. It presents a broad overview of statistical inference, clustering, and classification problems in two main high-throughput platforms: microarray gene expression and phylogenic analysis. Bayesian Modeling in Bioinformatics discusses the development and application of Bayesian statistical methods for the analysis of high-throughput bioinformatics data arising from problems in molecular and structural biology and disease-related medical research, such as cancer. It presents a broad overview of statistical inference, clustering, and classification problems in two main high-throughput platforms: microarray gene expression and phylogenic analysis.

10th Edition of the International IMACS/ISGG Workshop MASCOT Series, cosponsored by IAC-CNR and SIMAI, October 20-22, 2010, ULPGC - Edificio de Humanidades, Las Palmas de Gran Canaria, Spain

Minisimposio MSP 39 organizzato nell'ambito del Congresso SIMAI2010 (Cagliari, Giugno 21-25, 2010), Book of Abstracts, SIMAI, Cagliari, 2010, pp 315-322