Assessing the gain of biological data integration in gene networks inference

Background: A current challenge in gene annotation is to define the gene function in the context of the network of relationships instead of using single genes. The inference of gene networks (GNs) has emerged as an approach to better understand the biology of the system and to study how several components of this network interact with each other and keep their functions stable. However, in general there is no sufficient data to accurately recover the GNs from their expression levels leading to the curse of dimensionality, in which the number of variables is higher than samples. One way to mitigate this problem is to integrate biological data instead of using only the expression profiles in the inference process. Nowadays, the use of several biological information in inference methods had a significant increase in order to better recover the connections between genes and reduce the false positives. What makes this strategy so interesting is the possibility of confirming the known connections through the included biological data, and the possibility of discovering new relationships between genes when observed the expression data. Although several works in data integration have increased the performance of the network inference methods, the real contribution of adding each type of biological information in the obtained improvement is not clear. Methods: We propose a methodology to include biological information into an inference algorithm in order to assess its prediction gain by using biological information and expression profile together. We also evaluated and compared the gain of adding four types of biological information: (a) protein-protein interaction, (b) Rosetta stone fusion proteins, (c) KEGG and (d) KEGG+GO. Results and conclusions: This work presents a first comparison of the gain in the use of prior biological information in the inference of GNs by considering the eukaryote (P. falciparum) organism. Our results indicates that information based on direct interaction can produce a higher improvement in the gain than data about a less specific relationship as GO or KEGG. Also, as expected, the results show that the use of biological information is a very important approach for the improvement of the inference. We also compared the gain in the inference of the global network and only the hubs. The results indicates that the use of biological information can improve the identification of the most connected proteins.

Nonlocal dissipative tunneling for high-fidelity quantum-state transfer between distant parties

In this work, we propose the nonlocal tunneling mechanism for high-fidelity state transfer between distant parties. The nonlocal tunneling follows from the overlap between the distant sending and receiving wave functions, which is indirectlymediated by the off-resonant normal modes of a quantum channel. This channel is made up of a network of dissipative quantum systems exhibiting the same bosonic or fermionic statistical nature as the sender and receiver. We demonstrate that the incoherence arising from quantum channel nonidealities is almost completely circumvented by the tunneling mechanism, which thus affords a high-fidelity transfer process.

Study of cerebral gene expression densities using Voronoi analysis

As the available public cerebral gene expression image data increasingly grows, the demand for automated methods to analyze such large amount of data also increases. An important study that can be carried out on these data is related to the spatial relationship between gene expressions. Similar spatial density distribution of expression between genes may indicate they are functionally correlated, thus the identification of these similarities is useful in suggesting directions of investigation to discover gene interactions and their correlated functions. In this paper, we describe the use of a high-throughput methodology based on Voronoi diagrams to automatically analyze and search for possible local spatial density relationships between gene expression images. We tested this method using mouse brain section images from the Allen Mouse Brain Atlas public database. This methodology provided measurements able to characterize the similarity of the density distribution between gene expressions and allowed the visualization of the results through networks and Principal Component Analysis (PCA). These visualizations are useful to analyze the similarity level between gene expression patterns, as well as to compare connection patterns between region networks. Some genes were found to have the same type of function and to be near each other in the PCA visualizations. These results suggest cerebral density correlations between gene expressions that could be further explored. (C) 2011 Elsevier B.V. All rights reserved.

A combined oral contraceptive containing drospirenone changes neither endothelial function nor hemodynamic parameters in healthy young women: a prospective clinical trial

Background: Combined oral contraceptives (COCs) may lead to a rise in cardiovascular disease risk, possibly associated with changes in blood pressure and endothelial function. Study Design: The objective was to evaluate the impact of COC containing 20 mcg of ethinylestradiol (EE) and 3 mg of drospirenone (DRSP) on the arterial endothelial function, systolic and diastolic blood pressure (SBP and DBP, respectively), heart rate (HR), cardiac output (CO) and total peripheral resistance (TPR) of healthy young women. Of the 71 women in the study, 43 were evaluated before the introduction of COC and after 6 months of its use (case group) and 28, COC nonusers, were assessed for the same parameters at the same time interval (control group). Results: No significant changes in endothelium-dependent and endothelium-independent functions or in measures of SBP, DBP, HR, CO and TPR caused by COC use were observed in the case group (p>.05 for all variables) or in the control group. Conclusion: These data suggest COC with 20 mcg EE and 3 mg DRSP does not alter arterial endothelial function or hemodynamic parameters in healthy young women. (C) 2012 Elsevier Inc. All rights reserved.

Looking for meson molecules in B decays

We discuss the possibility of observing a loosely bound molecular state in a three-body hadronic B decay. In particular, we use the QCD sum rule approach to study eta' - pi molecular current. We consider an isovector-scalar I(G)J(PC) = 1(-)0(++) molecular current, and we use two- and three-point functions to study the mass and decay width of such a state. We consider the contributions of condensates up to dimension six, and we work at leading order in alpha(s). We obtain a mass around 1.1 GeV, consistent with a loosely bound state, and eta' - pi -> K+K- decay width around 10 MeV.

A theoretical contribution characterizing a potentially new molecular species: MgAs

A new molecular species, MgAs, is investigated theoretically for the first time at the CASSCF/MRCI level using quintuple-zeta quality basis sets. Potential energy curves for the lowest-lying electronic states are presented as well as the associated spectroscopic constants. Dipole and transition moment functions for selected states complement this characterization. Estimates of transition probabilities and radiative life-times for the most important transitions are also reported. The effect of spin-orbit interactions is clearly reflected on the potential energy curves. Comparisons with BeAs, BeN, and BeP are made where pertinent. (C) 2011 Elsevier B.V. All rights reserved.

The impact of asymptomatic vertebral fractures on quality of life in older community-dwelling women: the Sao Paulo Ageing & Health Study

OBJECTIVES: The aim of this study was to investigate the impact of asymptomatic vertebral fractures on the quality of life in older women as part of the Sao Paulo Ageing & Health Study. METHODS: This study was a cross-sectional study with a random sample of 180 women 65 years of age or older with or without vertebral fractures. The Quality of Life Questionnaire of the European Foundation for Osteoporosis was administered to all subjects. Anthropometric data were obtained by physical examination, and the body mass index was calculated. Lateral thoracic and lumbar spine X-ray scans were obtained to identify asymptomatic vertebral fractures using a semi-quantitative method. RESULTS: Women with asymptomatic vertebral fractures had lower total scores [61.4(15.3) vs. 67.1(14.2), p = 0.03] and worse physical function domain scores [69.5(20.1) vs. 77.3(17.1), p = 0.02] for the Quality of Life Questionnaire of the European Foundation for Osteoporosis compared with women without fractures. The total score of this questionnaire was also worse in women classified as obese than in women classified as overweight or normal. High physical activity was related to a better total score for this questionnaire (p = 0.01). Likewise, lower physical function scores were observed in women with higher body mass index values (p < 0.05) and lower physical activity levels (p < 0.05). Generalized linear models with gamma distributions and logarithmic link functions, adjusted for age, showed that lower total scores and physical function domain scores for the Quality of Life Questionnaire of the European Foundation for Osteoporosis were related to a high body mass index, lower physical activity, and the presence of vertebral fractures (p < 0.05). CONCLUSION: Vertebral fractures are associated with decreased quality of life mainly physical functioning in older community-dwelling women regardless of age, body mass index, and physical activity. Therefore, the results highlight the importance of preventing and controlling asymptomatic vertebral fractures to reduce their impact on quality of life among older women.

Secondary succession impairment in restored mangroves

In this work it was hypothesized that secondary succession on sites that have been managed by single planting of mangrove species is compromised by residual stressors, which could reduce the ecosystem's structural development and lower its functions. Forest structure and environmental characteristics of three planted mangrove stands are compared with reference sites. Structural attributes showed significant differences in the comparison of planted and reference stands. Avicennia schaueriana was the dominant species within both natural regeneration and old-growth stands in terms of basal area (99.2 and 99.4 %, 69.6 and 84.5 %, and 59.0 and 87.1 % for Itacorubi, Saco Grande, and Ratones, respectively). Restoration stands were dominated by Laguncularia racemosa (80.6 and 94.2 % for Saco Grande and Ratones, respectively), except at one site (Itacorubi), where A. schaueriana prevailed (99.7 %). Even though restoration and regeneration stands at Itacorubi showed similar species composition and dominance, cohort sorting revealed an inferior regeneration potential in the restoration stand. Multiple correlation analysis indicated that variables related to elevation disruptions (p (w) = 0.521) were the environmental drivers responsible for the differences observed in forest structure. At restoration sites an impaired pattern of secondary succession was observed, indicating that single species plantings may be ineffective if characteristics of the site, as well as of the area surrounding it, are not considered. The inadequate management of restoration sites can therefore have implications for both immediate and long-term large-scale ecosystem services.

Reproducing kernel Hilbert spaces associated with kernels on topological spaces

We analyze reproducing kernel Hilbert spaces of positive definite kernels on a topological space X being either first countable or locally compact. The results include versions of Mercer's theorem and theorems on the embedding of these spaces into spaces of continuous and square integrable functions.

Implications of purinergic receptor-mediated intracellular calcium transients in neural differentiation

Purinergic receptors participate, in almost every cell type, in controlling metabolic activities and many physiological functions including signal transmission, proliferation and differentiation. While most of P2Y receptors induce transient elevations of intracellular calcium concentration by activation of intracellular calcium pools and forward these signals as waves which can also be transmitted into neighboring cells, P2X receptors produce calcium spikes which also include activation of voltage-operating calcium channels. P2Y and P2X receptors induce calcium transients that activate transcription factors responsible for the progress of differentiation through mediators including calmodulin and calcineurin. Expression of P2X2 as well as of P2X7 receptors increases in differentiating neurons and glial cells, respectively. Gene expression silencing assays indicate that these receptors are important for the progress of differentiation and neuronal or glial fate determination. Metabotropic receptors, mostly P2Y1 and P2Y2 subtypes, act on embryonic cells or cells at the neural progenitor stage by inducing proliferation as well as by regulation of neural differentiation through NFAT translocation. The scope of this review is to discuss the roles of purinergic receptor-induced calcium spike and wave activity and its codification in neurodevelopmental and neurodifferentiation processes.

The impact of asymptomatic vertebral fractures on quality of life in older community-dwelling women: the São Paulo Ageing & Health Study

OBJECTIVES: The aim of this study was to investigate the impact of asymptomatic vertebral fractures on the quality of life in older women as part of the Sao Paulo Ageing & Health Study. METHODS: This study was a cross-sectional study with a random sample of 180 women 65 years of age or older with or without vertebral fractures. The Quality of Life Questionnaire of the European Foundation for Osteoporosis was administered to all subjects. Anthropometric data were obtained by physical examination, and the body mass index was calculated. Lateral thoracic and lumbar spine X-ray scans were obtained to identify asymptomatic vertebral fractures using a semi-quantitative method. RESULTS: Women with asymptomatic vertebral fractures had lower total scores [61.4(15.3) vs. 67.1(14.2), p = 0.03] and worse physical function domain scores [69.5(20.1) vs. 77.3(17.1), p = 0.02] for the Quality of Life Questionnaire of the European Foundation for Osteoporosis compared with women without fractures. The total score of this questionnaire was also worse in women classified as obese than in women classified as overweight or normal. High physical activity was related to a better total score for this questionnaire (p = 0.01). Likewise, lower physical function scores were observed in women with higher body mass index values (p<0.05) and lower physical activity levels (p,0.05). Generalized linear models with gamma distributions and logarithmic link functions, adjusted for age, showed that lower total scores and physical function domain scores for the Quality of Life Questionnaire of the European Foundation for Osteoporosis were related to a high body mass index, lower physical activity, and the presence of vertebral fractures (p<0.05). CONCLUSION: Vertebral fractures are associated with decreased quality of life mainly physical functioning in older community-dwelling women regardless of age, body mass index, and physical activity. Therefore, the results highlight the importance of preventing and controlling asymptomatic vertebral fractures to reduce their impact on quality of life among older women.

Indagine delle proprietà statistiche di serie temporali di posizione applicata al caso della stazione permanente GPS della base Mario Zucchelli in Terra Vittoria (Antartide)

Da ormai sette anni la stazione permanente GPS di Baia Terranova acquisisce dati giornalieri che opportunamente elaborati consentono di contribuire alla comprensione della dinamica antartica e a verificare se modelli globali di natura geofisica siano aderenti all’area di interesse della stazione GPS permanente. Da ricerche bibliografiche condotte si è dedotto che una serie GPS presenta molteplici possibili perturbazioni principalmente dovute a errori nella modellizzazione di alcuni dati ancillari necessari al processamento. Non solo, da alcune analisi svolte, è emerso come tali serie temporali ricavate da rilievi geodetici, siano afflitte da differenti tipologie di rumore che possono alterare, se non opportunamente considerate, i parametri di interesse per le interpretazioni geofisiche del dato. Il lavoro di tesi consiste nel comprendere in che misura tali errori, possano incidere sui parametri dinamici che caratterizzano il moto della stazione permanente, facendo particolare riferimento alla velocità del punto sul quale la stazione è installata e sugli eventuali segnali periodici che possono essere individuati.

Studio del comportamento meccanico di smalti porcellanati per substrati metallici

Composite porcelain enamels are inorganic coatings for metallic components based on a special ceramic-vitreous matrix in which specific additives are randomly dispersed. The ceramic-vitreous matrix is made by a mixture of various raw materials and elements and in particular it is based on boron-silicate glass added with metal oxides(1) of titanium, zinc, tin, zirconia, alumina, ecc. These additions are often used to improve and enhance some important performances such as corrosion(2) and wear resistance, mechanical strength, fracture toughness and also aesthetic functions. The coating process, called enamelling, depends on the nature of the surface, but also on the kind of the used porcelain enamel. For metal sheets coatings two industrial processes are actually used: one based on a wet porcelain enamel and another based on a dry-silicone porcelain enamel. During the firing process, that is performed at about 870°C in the case of a steel substrate, the enamel raw material melts and interacts with the metal substrate so enabling the formation of a continuous varying structure. The interface domain between the substrate and the external layer is made of a complex material system where the ceramic vitreous and the metal constituents are mixed. In particular four main regions can be identified, (i) the pure metal region, (ii) the region where the metal constituents are dominant compared with the ceramic vitreous components, (iii) the region where the ceramic vitreous constituents are dominant compared with the metal ones, and the fourth region (iv) composed by the pure ceramic vitreous material. It has also to be noticed the presence of metallic dendrites that hinder the substrate and the external layer passing through the interphase region. Each region of the final composite structure plays a specific role: the metal substrate has mainly the structural function, the interphase region and the embedded dendrites guarantee the adhesion of the external vitreous layer to the substrate and the external vitreous layer is characterized by an high tribological, corrosion and thermal shock resistance. Such material, due to its internal composition, functionalization and architecture can be considered as a functionally graded composite material. The knowledge of the mechanical, tribological and chemical behavior of such composites is not well established and the research is still in progress. In particular the mechanical performances data about the composite coating are not jet established. In the present work the Residual Stresses, the Young modulus and the First Crack Failure of the composite porcelain enamel coating are studied. Due to the differences of the porcelain composite enamel and steel thermal properties the enamelled steel sheets have residual stresses: compressive residual stress acts on the coating and tensile residual stress acts on the steel sheet. The residual stresses estimation has been performed by measuring the curvature of rectangular one-side coated specimens. The Young modulus and the First Crack Failure (FCF) of the coating have been estimated by four point bending tests (3-7) monitored by means of the Acoustic Emission (AE) technique(5,6). In particular the AE information has been used to identify, during the bending tests, the displacement domain over which no coating failure occurs (Free Failure Zone, FFZ). In the FFZ domain, the Young modulus has been estimated according to ASTM D6272-02. The FCF has been calculated as the ratio between the displacement at the first crack of the coating and the coating thickness on the cracked side. The mechanical performances of the tested coated specimens have also been related and discussed to respective microstructure and surface characteristics by double entry charts.

A simple strategy for defining polynomial spline spaces over hierarchical T-meses

[EN]We present a new strategy for constructing spline spaces over hierarchical T-meshes with quad- and octree subdivision scheme. The proposed technique includes some simple rules for inferring local knot vectors to define C 2 -continuous cubic tensor product spline blending functions. Our conjecture is that these rules allow to obtain, for a given T-mesh, a set of linearly independent spline functions with the property that spaces spanned by nested T-meshes are also nested, and therefore, the functions can reproduce cubic polynomials. In order to span spaces with these properties applying the proposed rules, the T-mesh should fulfill the only requirement of being a 0- balanced mesh...

Kernel Methods for Tree Structured Data

Machine learning comprises a series of techniques for automatic extraction of meaningful information from large collections of noisy data. In many real world applications, data is naturally represented in structured form. Since traditional methods in machine learning deal with vectorial information, they require an a priori form of preprocessing. Among all the learning techniques for dealing with structured data, kernel methods are recognized to have a strong theoretical background and to be effective approaches. They do not require an explicit vectorial representation of the data in terms of features, but rely on a measure of similarity between any pair of objects of a domain, the kernel function. Designing fast and good kernel functions is a challenging problem. In the case of tree structured data two issues become relevant: kernel for trees should not be sparse and should be fast to compute. The sparsity problem arises when, given a dataset and a kernel function, most structures of the dataset are completely dissimilar to one another. In those cases the classifier has too few information for making correct predictions on unseen data. In fact, it tends to produce a discriminating function behaving as the nearest neighbour rule. Sparsity is likely to arise for some standard tree kernel functions, such as the subtree and subset tree kernel, when they are applied to datasets with node labels belonging to a large domain. A second drawback of using tree kernels is the time complexity required both in learning and classification phases. Such a complexity can sometimes prevents the kernel application in scenarios involving large amount of data. This thesis proposes three contributions for resolving the above issues of kernel for trees. A first contribution aims at creating kernel functions which adapt to the statistical properties of the dataset, thus reducing its sparsity with respect to traditional tree kernel functions. Specifically, we propose to encode the input trees by an algorithm able to project the data onto a lower dimensional space with the property that similar structures are mapped similarly. By building kernel functions on the lower dimensional representation, we are able to perform inexact matchings between different inputs in the original space. A second contribution is the proposal of a novel kernel function based on the convolution kernel framework. Convolution kernel measures the similarity of two objects in terms of the similarities of their subparts. Most convolution kernels are based on counting the number of shared substructures, partially discarding information about their position in the original structure. The kernel function we propose is, instead, especially focused on this aspect. A third contribution is devoted at reducing the computational burden related to the calculation of a kernel function between a tree and a forest of trees, which is a typical operation in the classification phase and, for some algorithms, also in the learning phase. We propose a general methodology applicable to convolution kernels. Moreover, we show an instantiation of our technique when kernels such as the subtree and subset tree kernels are employed. In those cases, Direct Acyclic Graphs can be used to compactly represent shared substructures in different trees, thus reducing the computational burden and storage requirements.