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

Hybrid Photonic Crystal Fiber Sensing Of High Hydrostatic Pressure

The opto-mechanical response of Hybrid Photonic Crystal Fiber (HPCF) with Ge-doped inclusions is numerically modeled for high hydrostatic pressure sensing purpose. A typical photonic crystal fiber (PCF) consists of a silica solidcore and a cladding with a hexagonal lattice of air-holes. The HPCF is similar to the regular PCF, but a horizontal line of air-holes is substituted by solid high index rods of Ge-doped silica. The optical guidance in HPCFs is supported combining two physical effects: the modified total internal reflection and the photonic bandgap. In such fibers, the Gedoped inclusions induce residual birefringence. In our analysis, we evaluate the susceptibility of the phase modal birefringence and group birefringence to hydrostatic pressure. The analyses were performed at a photonic bandgap with central wavelength near to 1350 nm. The polarimetric pressure sensitivity is about 10 rad/MPa x m at λ = 1175 nm. © 2011 Copyright Society of Photo-Optical Instrumentation Engineers (SPIE).7753Oz Optics,Simbol Test Systems, Inc.,FISO Technologies, Inc.,CMC Microsystems Corporation,Innovative Economy: National Strategic Reference FrameworkCerqueira, A.S., Hybrid photonic crystal fiber (2006) Opt. Express, 14 (2), pp. 926-931Cerqueira, A.S., Recent progress and novel applications of photonic crystal fibers (2010) Rep. Prog. Phys., 73, p. 023301Cerqueira, A.S., Birefringence properties of hybrid photonic crystal fibers (2009) Proceedings of Microwave and Optoelectronics Conference (IMOC 2009), pp. 804-806. , Belem, Brazil, 03-06, NovemberFranco, M.A.R., Thermal tunability of photonic bandgaps in photonic crystal fibers selectively filled with nematic liquid crystal Proceedings of 2nd Workshop on Specialty Optical Fibers and Their Applications (WSOF-2), Oaxaca, Mexico, 13-15, October, (2010)Fleming, J.W., Dispersion in GeO2 -SiO2 glasses (1984) Appl. Opt., 23 (24), pp. 4486-4493Martynkien, T., Highly birefringent microstructured fibers with enhanced sensitivity to hydrostatic pressure (2010) Opt. Express, 18 (14), pp. 15113-15121Kühn, B., Schadrack, R., Thermal expansion of synthetic fused silica as a function of OH content and fictive temperature (2009) J. Non-Cryst. Solids, 355, pp. 323-326Gupta, D., Kumar, A., Thyagarajan, K., Polarization mode dispersion in single mode optical fibers due to core-ellipticity (2006) Opt. Commun., 263, pp. 36-41Koshiba, M., (1992) Optical Waveguide Theory by the Finite Element Method, pp. 133-160. , KTK Scientific Publishers and Kluwer Academic Publishers, TokyoUrbanczyk, W., Martynkien, T., Bock, W.J., Dispersion effects in elliptical-core highly birefringent fibers (2001) Appl. Opt., 40 (12), pp. 1911-1920Olszewski, J., Birefringence analysis in photonic crystal fibers with germanium-doped core (2009) J. Opt. A: Pure Appl. Opt., 11, pp. 1-10Martynkien, T., Urbanczyk, W., Modeling of spectral characteristics of Corning PMF-38 highly birefringent fiber (2002) Optik, 113 (1), pp. 25-30Hlubina, P., Broad spectral range measurements and modelling of birefringence dispersion in two-mode elliptical-core fibres (2010) J. Opt., 12, pp. 1-8Martynkien, T., Birefringence in microstructure fiber with elliptical GeO2 highly doped inclusion in the core (2008) Opt. Lett., 33 (23), pp. 2764-2766Verbandt, Y., Polarimetric Optical Fiber Sensors: Aspects of Sensitivity and Practical Implementation (1997) Opt. Rev., 4 (1 A), pp. 75-79Lagakos, N., Bucaro, J.A., Hughes, R., Acoustic sensitivity predictions of single-mode optical fibers using Brillouin scattering (1980) Appl. Opt., 19 (21), pp. 3668-3670Chiang, K.S., Sceats, Wong, D., Ultraviolet photolytic-induced changes in optical fibers: The thermal expansion coefficient (1993) Opt. Lett., 18 (12), pp. 965-96

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

Endovascular stenting of the ascending aorta for type A aortic dissections in patients at high risk for open surgery

Background: Open repair is the gold standard for type A aortic dissection (TAAD). Endovascular option has been proposed in very limited and selected TAAD patients. We report our experience with endovascular TAAD repair. Methods: Inclusion criteria were: (1) entry tear in the ascending aorta; (2) proximal landing zone of at least 2 cm; (3) distance between entry tear and brachio-cephalic trunk of at least 0.5 cm; (4) no signs of cardiac tamponade or severe aortic regurgitation and (5) no signs of aortic branches ischaemia. Patients with cardiac revascularisation from ascending aorta were excluded. Results: From April 2009 to June 2012, 37 patients with TAAD were admitted to our hospital. As many as 28 underwent surgical repair and 9 were considered at high surgical risk in a multidisciplinary meeting. Four met our inclusion criteria for an endovascular approach. Two of them had previous ascending aortic repair for TAAD and one had aortic valve replacement. Technical success was achieved in 100% of the patients. No mortality was registered during a median follow-up of 15 months (range 4-39 months), no migration of the graft and complete false lumen thrombosis of the ascending aorta in three patients. Conclusion: Endovascular treatment of TAAD is challenging but feasible in a selected subset of patients. Further research remains mandatory. © 2013 European Society for Vascular Surgery. Published by Elsevier Ltd. All rights reserved

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