Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip

Background: Recent studies in pigs have detected copy number variants (CNVs) using the Comparative Genomic Hybridization technique in arrays designed to cover specific porcine chromosomes. The goal of this study was to identify CNV regions (CNVRs) in swine species based on whole genome SNP genotyping chips. Results: We used predictions from three different programs (cnvPartition, PennCNV and GADA) to analyze data from the Porcine SNP60 BeadChip. A total of 49 CNVRs were identified in 55 animals from an Iberian x Landrace cross (IBMAP) according to three criteria: detected in at least two animals, contained three or more consecutive SNPs and recalled by at least two programs. Mendelian inheritance of CNVRs was confirmed in animals belonging to several generations of the IBMAP cross. Subsequently, a segregation analysis of these CNVRs was performed in 372 additional animals from the IBMAP cross and its distribution was studied in 133 unrelated pig samples from different geographical origins. Five out of seven analyzed CNVRs were validated by real time quantitative PCR, some of which coincide with well known examples of CNVs conserved across mammalian species. Conclusions: Our results illustrate the usefulness of Porcine SNP60 BeadChip to detect CNVRs and show that structural variants can not be neglected when studying the genetic variability in this species.

Avoiding sensor blindness in Geiger mode avalanche photodiode arrays fabricated in a conventional CMOS process

The need to move forward in the knowledge of the subatomic world has stimulated the development of new particle colliders. However, the objectives of the next generation of colliders sets unprecedented challenges to the detector performance. The purpose of this contribution is to present a bidimensional array based on avalanche photodiodes operated in the Geiger mode to track high energy particles in future linear colliders. The bidimensional array can function in a gated mode to reduce the probability to detect noise counts interfering with real events. Low reverse overvoltages are used to lessen the dark count rate. Experimental results demonstrate that the prototype fabricated with a standard HV-CMOS process presents an increased efficiency and avoids sensor blindness by applying the proposed techniques.

On-line event detection by recursive dynamic principal component analysis and gas sensor arrays under drift conditions

Leakage detection is an important issue in many chemical sensing applications. Leakage detection hy thresholds suffers from important drawbacks when sensors have serious drifts or they are affected by cross-sensitivities. Here we present an adaptive method based in a Dynamic Principal Component Analysis that models the relationships between the sensors in the may. In normal conditions a certain variance distribution characterizes sensor signals. However, in the presence of a new source of variance the PCA decomposition changes drastically. In order to prevent the influence of sensor drifts the model is adaptive and it is calculated in a recursive manner with minimum computational effort. The behavior of this technique is studied with synthetic signals and with real signals arising by oil vapor leakages in an air compressor. Results clearly demonstrate the efficiency of the proposed method.

Nonlinear inverse dynamic models of gas sensing systems based on chemical sensor arrays for quantitative measurements

Gas sensing systems based on low-cost chemical sensor arrays are gaining interest for the analysis of multicomponent gas mixtures. These sensors show different problems, e.g., nonlinearities and slow time-response, which can be partially solved by digital signal processing. Our approach is based on building a nonlinear inverse dynamic system. Results for different identification techniques, including artificial neural networks and Wiener series, are compared in terms of measurement accuracy.

Competitive evaporation in arrays of droplets

We consider the evaporation of periodic arrays of initially equal droplets in two-dimensional systems with open (absorbing) boundaries. Our study is based on the numerical solution of the Cahn-Hilliard equation. We show that due to cooperative effects the droplets which are further from the boundary may evaporate earlier than those in the boundary¿s vicinity. The time evolution of the overall amount of matter in the system is also studied.

Pulse propagation sustained by noise in arrays of bistable electronic circuits

One-dimensional arrays of nonlinear electronic circuits are shown to support propagation of pulses when operating in a locally bistable regime, provided the circuits are under the influence of a global noise. These external random fluctuations are applied to the parameter that controls the transition between bistable and monostable dynamics in the individual circuits. As a result, propagating fronts become destabilized in the presence of noise, and the system self-organizes to allow the transmission of pulses. The phenomenon is also observed in weakly coupled arrays, when propagation failure arises in the absence of noise.

Synthesis, structural order and magnetic behavior of self-assembled epsilon-Co nanocrystal arrays

The synthesis of magnetic nanoparticles with monodispere size distributions, their self assembly into ordered arrays and their magnetic behavior as a function of structural order (ferrofluids and 2D assemblies) are presented. Magnetic colloids of monodispersed, passivated, cobalt nanocrystals were produced by the rapid pyrolysis of cobalt carbonyl in solution. The size, size distribution (std. dev.< 5%) and the shape of the nanocrystals were controlled by varying the surfactant, its concentration, the reaction rate and the reaction temperature. The Co particles are defect-free single crystals with a complex cubic structure related to the beta phase of manganese (epsilon-Co). In the 2D assembly, a collective behavior was observed in the low-field susceptibility measurements where the magnetization of the zero field cooled process increases steadily and the magnetization of the field cooling process is independent the temperature. This was different from the observed behavior in a sample comprised of disordered interacting particles. A strong paramagnetic contribution appears at very low temperatures where the magnetization increases drastically after field cooling the sample. This has been attributed to the Co surfactant-particle interface since no magnetic atomic impurities are present in these samples.

Competitive evaporation in arrays of droplets

We consider the evaporation of periodic arrays of initially equal droplets in two-dimensional systems with open (absorbing) boundaries. Our study is based on the numerical solution of the Cahn-Hilliard equation. We show that due to cooperative effects the droplets which are further from the boundary may evaporate earlier than those in the boundary¿s vicinity. The time evolution of the overall amount of matter in the system is also studied.

Enhanced pulse propagation in non-linear arrays of oscillators

The propagation of a pulse in a nonlinear array of oscillators is influenced by the nature of the array and by its coupling to a thermal environment. For example, in some arrays a pulse can be speeded up while in others a pulse can be slowed down by raising the temperature. We begin by showing that an energy pulse (one dimension) or energy front (two dimensions) travels more rapidly and remains more localized over greater distances in an isolated array (microcanonical) of hard springs than in a harmonic array or in a soft-springed array. Increasing the pulse amplitude causes it to speed up in a hard chain, leaves the pulse speed unchanged in a harmonic system, and slows down the pulse in a soft chain. Connection of each site to a thermal environment (canonical) affects these results very differently in each type of array. In a hard chain the dissipative forces slow down the pulse while raising the temperature speeds it up. In a soft chain the opposite occurs: the dissipative forces actually speed up the pulse, while raising the temperature slows it down. In a harmonic chain neither dissipation nor temperature changes affect the pulse speed. These and other results are explained on the basis of the frequency vs energy relations in the various arrays

Breathers and thermal relaxation in Fermi-Pasta-Ulam arrays

Breather stability and longevity in thermally relaxing nonlinear arrays depend sensitively on their interactions with other excitations. We review numerical results for the relaxation of breathers in Fermi¿Pasta¿Ulam arrays, with a specific focus on the different relaxation channels and their dependence on the interparticle interactions, dimensionality, initial condition, and system parameters

Application of Multi-SNP Approaches Bayesian LASSO and AUC-RF to Detect Main Effects of Inflammatory-Gene Variants Associated with Bladder Cancer Risk

The relationship between inflammation and cancer is well established in several tumor types, including bladder cancer. We performed an association study between 886 inflammatory-gene variants and bladder cancer risk in 1,047 cases and 988 controls from the Spanish Bladder Cancer (SBC)/EPICURO Study. A preliminary exploration with the widely used univariate logistic regression approach did not identify any significant SNP after correcting for multiple testing. We further applied two more comprehensive methods to capture the complexity of bladder cancer genetic susceptibility: Bayesian Threshold LASSO (BTL), a regularized regression method, and AUC-Random Forest, a machine-learning algorithm. Both approaches explore the joint effect of markers. BTL analysis identified a signature of 37 SNPs in 34 genes showing an association with bladder cancer. AUC-RF detected an optimal predictive subset of 56 SNPs. 13 SNPs were identified by both methods in the total population. Using resources from the Texas Bladder Cancer study we were able to replicate 30% of the SNPs assessed. The associations between inflammatory SNPs and bladder cancer were reexamined among non-smokers to eliminate the effect of tobacco, one of the strongest and most prevalent environmental risk factor for this tumor. A 9 SNP-signature was detected by BTL. Here we report, for the first time, a set of SNP in inflammatory genes jointly associated with bladder cancer risk. These results highlight the importance of the complex structure of genetic susceptibility associated with cancer risk.

Short communication. SNP analyses of the 5HT1R and STAT genes in Pacific white shrimp, Litopenaeus vannamei

La industria de la producción de camarón es una de las industrias acuícolas que se encuentra en más crecimiento en la actualidad. Los estudios para encontrar marcadores genéticos son muy efectivos para la mejora de sus propiedades y de gran interés para los productores de camarón. En este trabajo se utilizaron seis individuos de una población de Litopenaeus vannamei, donde se encontraron cuatro polimorfismos de nucleótido único (SNPs) en el gen 5HT1R (5-hidroxitriptamina receptor1) y un SNP en el gen STAT (transductor de señal y activador de la transcripción). Sin embargo, el polimorfismo en el gen STAT resultó ser homocigoto en una población diferente utilizada para análisis de asociación. Los presentes análisis revelaron que el alelo C, en dos polimorfismos SNP (C109T y C395G) del gen 5HT1R, tiende a estar asociado con el aumento del peso corporal. Consideramos que hay necesidad de hacer nuevos estudios utilizando una muestra más amplia y diversa de la población en cuestión.

A Write-Based Solver for SAT Modulo the Theory of Arrays

The extensional theory of arrays is one of the most important ones for applications of SAT Modulo Theories (SMT) to hardware and software verification. Here we present a new T-solver for arrays in the context of the DPLL(T) approach to SMT. The main characteristics of our solver are: (i) no translation of writes into reads is needed, (ii) there is no axiom instantiation, and (iii) the T-solver interacts with the Boolean engine by asking to split on equality literals between indices. As far as we know, this is the first accurate description of an array solver integrated in a state-of-the-art SMT solver and, unlike most state-of-the-art solvers, it is not based on a lazy instantiation of the array axioms. Moreover, it is very competitive in practice, specially on problems that require heavy reasoning on array literals

L'albedo lunar i els satèl·lits: Recerca sobre els efectes de l'albedo lunar en les plaques solars d'un satèl·lit artificial que orbita al voltant de la Lluna

Treball de recerca realitzat per una alumna d'ensenyament secundari i guardonat amb un Premi CIRIT per fomentar l'esperit científic del Jovent l'any 2009. L’albedo lunar i els satèl•lits és un treball que relaciona l’enginyeria aeroespacial amb l’astronomia. El seu objectiu principal investigar si l’albedo lunar, els rajos de sol reflectits a la superfície lunar, pot modificar significativament la temperatura de les plaques solars d’un satèl•lit artificial que orbiti la Lluna i, en conseqüència, afectar-ne el rendiment. El segon objectiu del treball és calcular si seria possible fer un mapa d’albedo lunar, a partir de la temperatura d’un satèl•lit en òrbita al voltant de la Lluna, que permetria conèixer amb més precisió la composició de la superfície lunar. Després d’adquirir els fonaments teòrics necessaris per a realitzar el treball, del procés per a trobar la manera de dur a terme els càlculs i d’efectuar els càlculs en si, les conclusions del treball són que l’albedo lunar causa un augment de temperatura en els satèl•lits prou significatiu per afectar-ne el rendiment; i que amb les temperatures enregistrades per un satèl•lit en òrbita al voltant de la Lluna es podria crear un mapa d’albedo. Aquesta recerca ha estat feta per suggeriment i sota la supervisió del CTAE (Centre de Tecnologia Aeroespacial) per analitzar si els resultats són aplicables al satèl•lit que s’enviarà a la Lluna, Lunar Mission BW1.