Genome-wide DNA polymorphism analyses using VariScan

BACKGROUND: DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis. RESULTS: We have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i) exhaustive population-genetic analyses including those based on the coalescent theory; ii) analysis adapted to the shallow data generated by the high-throughput genome projects; iii) use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv) identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v) visualization of the results integrated with current genome annotations in commonly available genome browsers. CONCLUSION: VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data.

Seismic detection and characterization of landslides and other mass movements

Seismic methods used in the study of snow avalanches may be employed to detect and characterize landslides and other mass movements, using standard spectrogram/sonogram analysis. For snow avalanches, the spectrogram for a station that is approached by a sliding mass exhibits a triangular time/frequency signature due to an increase over time in the higher-frequency constituents. Recognition of this characteristic footprint in a spectrogram suggests a useful metric for identifying other mass-movement events such as landslides. The 1 June 2005 slide at Laguna Beach, California is examined using data obtained from the Caltech/USGS Regional Seismic Network. This event exhibits the same general spectrogram features observed in studies of Alpine snow avalanches. We propose that these features are due to the systematic relative increase in high-frequency energy transmitted to a seismometer in the path of a mass slide owing to a reduction of distance from the source signal. This phenomenon is related to the path of the waves whose high frequencies are less attenuated as they traverse shorter source-receiver paths. Entrainment of material in the course of the slide may also contribute to the triangular time/frequency signature as a consequence of the increase in the energy involved in the process; in this case the contribution would be a source effect. By applying this commonly observed characteristic to routine monitoring algorithms, along with custom adjustments for local site effects, we seek to contribute to the improvement in automatic detection and monitoring methods of landslides and other mass movements.

A subcritical instability of wave-driven alongshore currents

The development of shear instabilities of a wave-driven alongshore current is investigated. In particular, we use weakly nonlinear theory to investigate the possibility that such instabilities, which have been observed at various sites on the U.S. coast and in the laboratory, can grow in linearly stable flows as a subcritical bifurcation by resonant triad interaction, as first suggested by Shrira eta/. [1997]. We examine a realistic longshore current profile and include the effects of eddy viscosity and bottom friction. We show that according to the weakly nonlinear theory, resonance is possible and that these linearly stable flows may exhibit explosive instabilities. We show that this phenomenon may occur also when there is only approximate resonance, which is more likely in nature. Furthermore, the size of the perturbation that is required to trigger the instability is shown in some circumstances to be consistent with the size of naturally occurring perturbations. Finally, we consider the differences between the present case examined and the more idealized case of Shrira et a/. [ 1997]. It is shown that there is a possibility of coupling between triads, due to the richer modal structure in more realistic flows, which may act to stabilize the flow and act against the development of subcritical bifurcations. Extensive numerical tests are called for.

Theory of Wetting-Induced Fluid Entrainment by Advancing Contact Lines on Dry Surfaces

We report on the onset of fluid entrainment when a contact line is forced to advance over a dry solid of arbitrary wettability. We show that entrainment occurs at a critical advancing speed beyond which the balance between capillary, viscous, and contact-line forces sustaining the shape of the interface is no longer satisfied. Wetting couples to the hydrodynamics by setting both the morphology of the interface at small scales and the viscous friction of the front. We find that the critical deformation that the interface can sustain is controlled by the friction at the contact line and the viscosity contrast between the displacing and displaced fluids, leading to a rich variety of wetting-entrainment regimes. We discuss the potential use of our theory to measure contact-line forces using atomic force microscopy and to study entrainment under microfluidic conditions exploiting colloid-polymer fluids of ultralow surface tension.

Hand detection in cluttered scene images using Fourier-Mellin invariant features

This paper proposes an automatic hand detection system that combines the Fourier-Mellin Transform along with other computer vision techniques to achieve hand detection in cluttered scene color images. The proposed system uses the Fourier-Mellin Transform as an invariant feature extractor to perform RST invariant hand detection. In a first stage of the system a simple non-adaptive skin color-based image segmentation and an interest point detector based on corners are used in order to identify regions of interest that contains possible matches. A sliding window algorithm is then used to scan the image at different scales performing the FMT calculations only in the previously detected regions of interest and comparing the extracted FM descriptor of the windows with a hand descriptors database obtained from a train image set. The results of the performed experiments suggest the use of Fourier-Mellin invariant features as a promising approach for automatic hand detection.

Hand detection in cluttered scene images using Fourier-Mellin invariant features

This paper proposes an automatic hand detection system that combines the Fourier-Mellin Transform along with other computer vision techniques to achieve hand detection in cluttered scene color images. The proposed system uses the Fourier-Mellin Transform as an invariant feature extractor to perform RST invariant hand detection. In a first stage of the system a simple non-adaptive skin color-based image segmentation and an interest point detector based on corners are used in order to identify regions of interest that contains possible matches. A sliding window algorithm is then used to scan the image at different scales performing the FMT calculations only in the previously detected regions of interest and comparing the extracted FM descriptor of the windows with a hand descriptors database obtained from a train image set. The results of the performed experiments suggest the use of Fourier-Mellin invariant features as a promising approach for automatic hand detection.

Genome-wide DNA polymorphism analyses using VariScan

BACKGROUND: DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis. RESULTS: We have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i) exhaustive population-genetic analyses including those based on the coalescent theory; ii) analysis adapted to the shallow data generated by the high-throughput genome projects; iii) use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv) identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v) visualization of the results integrated with current genome annotations in commonly available genome browsers. CONCLUSION: VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data.

DnaSP v5: A software for comprehensive analysis of DNA polymorphism data

DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large datasets. Among other features, the newly implemented methods allow for: (i) analyses on multiple data files; (ii) haplotype phasing; (iii) analyses on insertion/deletion polymorphism data; (iv) visualizing sliding window results integrated with available genome annotations in the UCSC browser.

Expresiones para la determinación del factor de fricción en ríos de fuerte pendiente

Con base en una selección de 145 datos pertenecientes a ríos de montaña de fuerte pendiente (³ 1%) se han desarrollado cinco expresiones para determinar el factor de fricción de Darcy-Weisbach. La primera expresión se fundamenta en la aplicación para flujo turbulento rugoso en lámina libre de la ley semilogarítmica de Prandtl-Kárman, que es función de la sumersión relativa (relación entre el calado medio y la rugosidad equivalente). La segunda y tercera corresponden a correciones de la primera para flujo macrorrugoso, propuestas por Thompson y Campbell (1979) y Aguirre-Pe y Fuentes (1990) respectivamente. La cuarta ecuación consiste una en potencia de la sumersión relativa, mientras que la quinta corrige la fórmula anterior incorporando una potencia de la pendiente, tal y como propugnan Meunier (1989) y Rickenmann (1990). Las expresiones derivadas presentan un ajuste significativo, si se tienen en cuenta las limitaciones hidrométricas existentes en ríos de material grueso y fuerte pendiente. Destaca el mayor ajuste conseguido con las ecuaciones con las ecuaciones del tipo potencial frente a las del tipo semilogarítmico. Se ha encontrado, asimismo, una capacidad de predicción ligeramente superior en aquellas expresiones que incluyen modificaciones respecto a la ecuación original, ecuaciones del tipo segundo, tercero y quinto anteriormente indicado.

Obtencion de recubrimientos autolubricados por proyeccion termica de plasma atmosferico (APS) como alternativa a los lubricantes liquidos

La obtención de recubrimientos con bajos coeficientes de fricción, es una innovadora respuesta a la creciente demanda industrial de alternativas para los tradicionales sistemas lubricados con aceites. Para este fin, la introducción de un sólido lubricante, en una matriz con buenas propiedades mecánicas, ha de conferir al conjunto un bajo coeficiente de fricción y mejorar la resistencia al desgaste del recubrimiento, favoreciendo además, la utilización a elevadas temperaturas, en las que los lubricantes líquidos convencionales presentan limitaciones. En el Centro de Proyección Térmica (CPT) de la Universidad de Barcelona se han obtenido mediante proyección de Plasma Atmosférico (APS) recubrimientos autolubricados de Ni-Grafito y Cr2O3-CaF2, estudiando con especial interés las propiedades y el efecto que produce el grafito y el CaF2 en las matrices metálica y cerámica respectivamente. Se ha determinado en los dos casos que el desgaste originado en los recubrimientos es bajo, si bien los coeficientes de fricción varían ostensiblemente en función del sistema indicado. Los resultados obtenidos indican que el recubrimiento de Ni-Grafito posee un comportamiento idóneo capaz de competir con los tradicionales lubricantes líquidos.

Estudio Mediante Tecnicas Interferometricas de las Propiedades Tribologicas de la ZrO2 Obtenida por Proyeccion Termica

Las barreras térmicas poseen unas propiedades mecánicas y tribológicas limitadas. Los tratamientos térmicos de sintetizado pueden utilizarse como una posible solución para su mejora. En el presente trabajo se evalúa la evolución de diversas propiedades tribológicas y mecánicas, a diferentes tiempos de sinterización, a temperatura de 1.000 °C. Se observa que el sintetizado produce un aumento de la resistencia al desgaste, de la dureza y del módulo de Young. A partir de los ensayos ball-on-disk, realizados utilizando un par friccionante de ZrO2 y de acero, se han estudiado los mecanismos de desgaste dominantes para cada uno de los pares friccionantes. Se ha observado que la delaminación entre partículas y la fractura frágil durante el proceso de desgaste son los mecanismos principales que controlan el proceso. Los caminos de desgaste estudiados mediante microscopía electrónica de barrido (SEM) e interferometría de barrido de luz blanca (SWLI) han permitido cuantificar el desgaste en cada uno de los casos. A fin de poder estudiar los recubrimientos de ZrO2 mediante SEM y SWLI ha sido necesario realizar una metalización con oro para así aumentar la conductividad eléctrica y reflectividad de las muestras.

Newspaper attention and policy activities in Spain

Spain"s newspapers are characterised by strong partisan identities. We demonstrate that the two leading newspapers nonetheless show powerful similarities in the topics of their coverage over time. The media system is strongly related to the policy process and it shows similar levels of skew (attention focuses on just a few topics) and friction (attention lurches rapidly from topic to topic) as others have shown for policy processes more generally. Further, media attention is significantly related to parliamentary activities. Oral questions in parliament track closely with media attention over time. Our assessment is based on a comprehensive database of all front-page stories (over 95,000 stories) in El Paı´s and El Mundo, Spain"s largest daily newspapers, and all 7,446 oral questions from 1996 to 2009. The paper shows that explanations of friction and skew in governmental activities should incorporate media dynamics as well. Political leaders are clearly sensitive to media salience.

Anisotropic surface properties of micro/nanostructured a-C:H:F thin films with self-assembly applications

The singular properties of hydrogenated amorphous carbon (a-C:H) thin filmsdeposited by pulsed DC plasma enhanced chemical vapor deposition (PECVD), such as hardness and wear resistance, make it suitable as protective coating with low surface energy for self-assembly applications. In this paper, we designed fluorine-containing a-C:H (a-C:H:F) nanostructured surfaces and we characterized them for self-assembly applications. Sub-micron patterns were generated on silicon through laser lithography while contact angle measurements, nanotribometer, atomic force microscopy (AFM), and scanning electron microscopy (SEM) were used to characterize the surface. a-C:H:F properties on lithographied surfaces such as hydrophobicity and friction were improved with the proper relative quantity of CH4 and CHF3 during deposition, resulting in ultrahydrophobic samples and low friction coefficients. Furthermore, these properties were enhanced along the direction of the lithographypatterns (in-plane anisotropy). Finally, self-assembly properties were tested with silicananoparticles, which were successfully assembled in linear arrays following the generated patterns. Among the main applications, these surfaces could be suitable as particle filter selector and cell colony substrate.

SQualTrack: A Tool for Robust Fault Detection

One of the techniques used to detect faults in dynamic systems is analytical redundancy. An important difficulty in applying this technique to real systems is dealing with the uncertainties associated with the system itself and with the measurements. In this paper, this uncertainty is taken into account by the use of intervals for the parameters of the model and for the measurements. The method that is proposed in this paper checks the consistency between the system's behavior, obtained from the measurements, and the model's behavior; if they are inconsistent, then there is a fault. The problem of detecting faults is stated as a quantified real constraint satisfaction problem, which can be solved using the modal interval analysis (MIA). MIA is used because it provides powerful tools to extend the calculations over real functions to intervals. To improve the results of the detection of the faults, the simultaneous use of several sliding time windows is proposed. The result of implementing this method is semiqualitative tracking (SQualTrack), a fault-detection tool that is robust in the sense that it does not generate false alarms, i.e., if there are false alarms, they indicate either that the interval model does not represent the system adequately or that the interval measurements do not represent the true values of the variables adequately. SQualTrack is currently being used to detect faults in real processes. Some of these applications using real data have been developed within the European project advanced decision support system for chemical/petrochemical manufacturing processes and are also described in this paper