Discriminative pattern discovery for the characterization of different network populations

Motivation: An interesting problem is to study how gene co-expression varies in two different populations, associated with healthy and unhealthy individuals, respectively. To this aim, two important aspects should be taken into account: (i) in some cases, pairs/groups of genes show collaborative attitudes, emerging in the study of disorders and diseases; (ii) information coming from each single individual may be crucial to capture specific details, at the basis of complex cellular mechanisms; therefore, it is important avoiding to miss potentially powerful information, associated with the single samples. Results: Here, a novel approach is proposed, such that two different input populations are considered, and represented by two datasets of edge-labeled graphs. Each graph is associated to an individual, and the edge label is the co-expression value between the two genes associated to the nodes. Discriminative patterns among graphs belonging to different sample sets are searched for, based on a statistical notion of 'relevance' able to take into account important local similarities, and also collaborative effects, involving the co-expression among multiple genes. Four different gene expression datasets have been analyzed by the proposed approach, each associated to a different disease. An extensive set of experiments show that the extracted patterns significantly characterize important differences between healthy and unhealthy samples, both in the cooperation and in the biological functionality of the involved genes/proteins. Moreover, the provided analysis confirms some results already presented in the literature on genes with a central role for the considered diseases, still allowing to identify novel and useful insights on this aspect

Biferroic YCrO3

YCrO3 which has a monoclinic structure, shows weak ferromagnetism below 140 K (TN) and a ferroelectric transition at 473 K accompanied by hysteresis. We have determined the structure and energetics of YCrO3 with ferromagnetic and antiferromagnetic ordering by means of first-principles density functional theory calculations, based on pseudopotentials and a plane wave basis. The non-centrosymmetric monoclinic structure is found to be lower in energy than the orthorhombic structure, supporting the biferroic nature of YCrO3.Comment: 16 pages including figure

Dependence of simulated radiation damage on crystal structure and atomic misfit in metals

This study investigates radiation damage in three metals in the low temperature and high radiant flux regime using molecular dynamics and a Frenkel pair accumulation method to simulate up to $2.0$ displacements per atom. The metals considered include Fe, equiatomic CrCoNi, and a fictitious metal with identical bulk properties to the CrCoNi composed of a single atom type referred to as an A-atom. CrCoNi is found to sustain higher concentrations of dislocations than either the Fe or A-atom systems and more stacking faults than the A-atom system. The results suggest that the concentration of vacancies and interstitials are substantially higher for the CrCoNi than the A-atom system, perhaps reflecting that the recombination radius is smaller in CrCoNi due to the roughened potential energy landscape. A model that partitions the major contributions from defects to the stored energy is described, and serves to highlight a general need for higher fidelity approaches to point defect identification

Evolutionary and Ecological Trees and Networks

Evolutionary relationships between species are usually represented in phylogenies, i.e. evolutionary trees, which are a type of networks. The terminal nodes of these trees represent species, which are made of individuals and populations among which gene flow occurs. This flow can also be represented as a network. In this paper we briefly show some properties of these complex networks of evolutionary and ecological relationships. First, we characterize large scale evolutionary relationships in the Tree of Life by a degree distribution. Second, we represent genetic relationships between individuals of a Mediterranean marine plant, Posidonia oceanica, in terms of a Minimum Spanning Tree. Finally, relationships among plant shoots inside populations are represented as networks of genetic similarity.Comment: 6 pages, 5 figures. To appear in Proceedings of the Medyfinol06 Conferenc

Molecular mechanisms of retroviral integration site selection

Retroviral replication proceeds through an obligate integrated DNA provirus, making retroviral vectors attractive vehicles for human gene-therapy. Though most of the host cell genome is available for integration, the process of integration site selection is not random. Retroviruses differ in their choice of chromatin-associated features and also prefer particular nucleotide sequences at the point of insertion. Lentiviruses including HIV-1 preferentially integrate within the bodies of active genes, whereas the prototypical gammaretrovirus Moloney murine leukemia virus (MoMLV) favors strong enhancers and active gene promoter regions. Integration is catalyzed by the viral integrase protein, and recent research has demonstrated that HIV-1 and MoMLV targeting preferences are in large part guided by integrase-interacting host factors (LEDGF/p75 for HIV-1 and BET proteins for MoMLV) that tether viral intasomes to chromatin. In each case, the selectivity of epigenetic marks on histones recognized by the protein tether helps to determine the integration distribution. In contrast, nucleotide preferences at integration sites seem to be governed by the ability for the integrase protein to locally bend the DNA duplex for pairwise insertion of the viral DNA ends. We discuss approaches to alter integration site selection that could potentially improve the safety of retroviral vectors in the clinic

Exploring risk of falls and dynamic unbalance in cerebellar ataxia by inertial sensor assessment

Background. Patients suffering from cerebellar ataxia have extremely variable gait kinematic features. We investigated whether and how wearable inertial sensors can describe the gait kinematic features among ataxic patients. Methods. We enrolled 17 patients and 16 matched control subjects. We acquired data by means of an inertial sensor attached to an ergonomic belt around pelvis, which was connected to a portable computer via Bluetooth. Recordings of all the patients were obtained during overground walking. From the accelerometric data, we obtained the harmonic ratio (HR), i.e., a measure of the acceleration patterns, smoothness and rhythm, and the step length coefficient of variation (CV), which evaluates the variability of the gait cycle. Results. Compared to controls, patients had a lower HR, meaning a less harmonic and rhythmic acceleration pattern of the trunk, and a higher step length CV, indicating a more variable step length. Both HR and step length CV showed a high effect size in distinguishing patients and controls (p < 0.001 and p = 0.011, respectively). A positive correlation was found between the step length CV and both the number of falls (R = 0.672; p = 0.003) and the clinical severity (ICARS: R = 0.494; p = 0.044; SARA: R = 0.680; p = 0.003). Conclusion. These findings demonstrate that the use of inertial sensors is effective in evaluating gait and balance impairment among ataxic patients