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Breve storia degli strumenti per il Calcolo scientifico seguendo un percorso tra i musei italiani che espongono materiali ad essi relativi.

In recent years, the development of high throughput devices for the massive parallel analyses of genomic data has lead to the generation of large amount of new biological evidences and has triggered the proliferation of data mining algorithms for the extraction of meaningful information. Microarrays for gene expression analyses are part of this revolution and provide important insight in molecular biology often in the form of coherent sets of genes representing previously uncharacterized processes. Large amount of data are continuously produced in this form, and computational approaches can significantly improve the efficient use of these results, since comparison among numbers of genes sets can give new meaningful information at no cost from the experimental biology point of view. To address this opportunity we designed and implemented FIT, a scalable, unsupervised algorithm that quantitatively compares different populations of gene sets using two distinct measures of similarity between any two gene sets. These measures are then used to obtain a summary statistic that describes the tightness of fit between sets belonging to two distinct populations of gene sets. We present the results of FIT on two data sets for the study of Lymphoma and Acute Lymphoblastic Leukemia. In both cases FIT was able to recapitulate the previous analyses on these datasets, to extend the results and to extract information likely to offer potential insights into the underlying biology.

The massive production of biological data by means of highly parallel devices like microarrays for gene expression has paved the way to new possible approaches in molecular genetics. Among them the possibility of inferring biological answers by querying large amounts of expression data. Based on this principle, we present here TOM, a web-based resource for the efficient extraction of candidate genes for hereditary diseases. The service requires the previous knowledge of at least another gene responsible for the disease and the linkage area, or else of two disease associated genetic intervals. The algorithm uses the information stored in public resources, including mapping, expression and functional databases. Given the queries, TOM will select and list one or more candidate genes. This approach allows the geneticist to bypass the costly and time consuming tracing of genetic markers through entire families and might improve the chance of identifying disease genes, particularly for rare diseases. We present here the tool and the results obtained on known benchmark and on hereditary predisposition to familial thyroid cancer. Our algorithm is available at http://www-micrel.deis.unibo.it/similar to tom/.

The importance of circuits and systems for high-throughput biological data acquisition in biomedical research are discussed. High-throughput biological data acquisition and processing technologies have shifted the focus of biological research from the the traditional experimental science to that of information science. Powerful computation and communication means can be applied to a very large amount of apparently incoherent data coming from biomedical research. The concept of Laboratory on Chip (LoC) is the natural evolution of System on Chip (SoC) by using an array of heterogeneous technologies. DNA sequencing is the process of finding the exact sequence of bases in a DNA sample and with sequencing it has been possible to determine the gene structure of homo sapiens and other species. In ISFET technology transistor arrays are fabricated and electrical readout circuits can provide a direct measure of the gene expression levels.

In bioventing, air is forced into the subsoil to exploit the biodegradation activity of bacteria. The problem of optimization consists of choosing the best positions and volumetric flow rates of injection or extraction wells within the polluted soil. A mathematical model for the unsaturated zone which also describes the bacteria population dynamics and the pollutant removal will be presented. It is possible to identify several kinds of optimization criteria and the related numerical issues will be examined. Numerical tests of the model and of the optimization procedures will be shown.

We discuss solvability properties of a nonlinear hypersingular integral equation of Prandtl's type using monotonicity arguments together with different collocation iteration schemes for the numerical solution of such equations.

Motivation: Immune cells coordinate their efforts for the correct and efficient functioning of the immune system (IS). Each cell type plays a distinct role and communicates with other cell types through mediators such as cytokines, chemokines and hormones, among others, that are crucial for the functioning of the IS and its fine tuning. Nevertheless, a quantitative analysis of the topological properties of an immunological network involving this complex interchange of mediators among immune cells is still lacking. Results: Here we present a method for quantifying the relevance of different mediators in the immune network, which exploits a definition of centrality based on the concept of efficient communication. The analysis, applied to the human IS, indicates that its mediators differ significantly in their network relevance. We found that cytokines involved in innate immunity and inflammation and some hormones rank highest in the network, revealing that the most prominent mediators of the IS are molecules involved in these ancestral types of defence mechanisms which are highly integrated with the adaptive immune response, and at the interplay among the nervous, the endocrine and the immune systems. © The Author 2004. Published by Oxford University Press. All rights reserved.

We study the kinetics of domain growth of fluid mixtures quenched from a disordered to a lamellar phase. At low viscosities, in two dimensions, when hydrodynamic modes become important, dynamical scaling is verified in the form C(k, t) ~ L ? f[(k - kM)L], where C is the structure factor with maximum at kM and L is a typical length with logarithmic growth at late times. The presence of extended defects can explain the behavior of L. Three-dimensional simulations confirm that diffuse grain boundaries inhibit complete ordering of lamellae. Applied shear flow alleviates frustration and gives power law growth at all times.