PubDNA Finder in a Nutshell. Searching the Life Sciences Literature with Sequences of Nucleic Acids

Biomedical researchers and clinicians working with molecular technologies in routine clinical practice often need to review the available literature to gather information regarding specific sequences of nucleic acids. This includes, for instance, finding articles related to a concrete DNA sequence, or identifying empirically-validated primer/probe sequences to evaluate the presence of different micro-organisms. Unfortunately, these hard and time-consuming tasks often need to be manually performed by researchers themselves since no publicly available biomedical literature search engine, e.g. PubMed, PubMed Central (PMC), etc., provides the required search functionalities. In this article, we describe PubDNA Finder, a web service that enables users to perform advanced searches on PubMed Central-indexed full text articles with sequences of nucleic acids

Mapping wide row crops with video sequences acquired from a tractor moving at treatment speed

This paper presents a mapping method for wide row crop fields. The resulting map shows the crop rows and weeds present in the inter-row spacing. Because field videos are acquired with a camera mounted on top of an agricultural vehicle, a method for image sequence stabilization was needed and consequently designed and developed. The proposed stabilization method uses the centers of some crop rows in the image sequence as features to be tracked, which compensates for the lateral movement (sway) of the camera and leaves the pitch unchanged. A region of interest is selected using the tracked features, and an inverse perspective technique transforms the selected region into a bird’s-eye view that is centered on the image and that enables map generation. The algorithm developed has been tested on several video sequences of different fields recorded at different times and under different lighting conditions, with good initial results. Indeed, lateral displacements of up to 66% of the inter-row spacing were suppressed through the stabilization process, and crop rows in the resulting maps appear straight

MRI and Bidimensional relaxometry sequences for macro and microstructure assessment in food models.

Physico-chemical and organoleptic characteristics of food depend largely on the microscopic level distribution of gases and water, and connectivity and mobility through the pores. Microstructural characterization of food can be accomplished by Magnetic Resonance Imaging (MRI) and Nuclear Magnetic Spectroscopy (NMR) combined with the application of methods of dissemination and multidimensional relaxometry. In this work, funded by the EC Project InsideFood, several artificial food models, based on foams and gels were studied using MRI and 2D relaxometry. Two different kinds of foams were used: a sugarless and a sugar foam. Then, a half of a syringe was filled with the sugarless foam and the other half with the sugar foam. Then, MRI and NMR experiments were performed and the sample evolution was observed along 3 days in order to quantify macrostructural changes through proton density images and microstructural ones using T1T2 maps, using an inversion CPMG sequence. On the proton density images it may be seen that after 16 hours it was possible to differentiate the macrostructural changes, as the apparition of free water due to a syneresis phenomenon. On the interface it can be seen a brighter area after 16 hours, due to the occurrence of free water. Moreover, thanks to the bidimensional relaxometry (T1-T2) it was possible to differentiate among microscopic changes. Differences between the pores size can be observed as well as the microstructure evolution after 30.5 hours, as a consequence differences are shown on free water redistribution through larger pores and capillarity phenomena between both foams.

Procesos configurativos: de la trama a la noción de campo en los "mat buildings"

La presente tesis aborda el estudio sobre los llamados mat buildings, que surgen entre los años cincuenta y sesenta del pasado siglo. Los mat buildings, también llamados “edificios esteras” o “edificios alfombras”, nacen en gran parte como consecuencia de los desacuerdos e insatisfacciones de los CIAM con el reduccionismo funcionalista y los principios de compartimentación funcional. Estos nuevos modelos remplazan el modelo de ciudad entendido como una colección de edificios individuales por una concepción de un patrón urbano. No es la suma de la longitud, la altura y el ancho sino más bien una densa alfombra bi-dimensional, con una configuración de formas que ofrece al mismo tiempo un orden repetitivo y una infinita diversidad de secuencias con infinitas posibilidades de adaptación donde el hombre vive y se desplaza. Estas características que irán apareciendo en la obras de muchos de los arquitectos que forman parte del grupo Team X son los que Alison Smithson empieza a revelar en su artículo, con la ambición de manifestar una nueva sensibilidad y una nueva forma de entender y ver la arquitectura. Los mat buildings y los cluster serán los códigos utilizados por diferentes miembros del Team X para pensar una arquitectura y un urbanismo alternativo al propuesto por los CIAM. Mediante ellos encuentran el camino para una nueva estética de la conexión con un desplazamiento desde una concepción determinista de la forma arquitectónica (una forma cerrada y en general definida a priori) hacia una actitud más libre, más abierta, fundamentada no tanto en la entereza de la forma global sino en cuanto a la intensidad de sus redes internas y de sus diferentes niveles de asociación. La tesis tiene como propósito final cuestionar si esta tipología de edificios, cuyo principio de base es siempre una matriz geométrica abierta (trama, retícula, malla), con crecimiento ilimitado, puede redefinir la frontera entre ciudad y edificio y, por tanto, entre público y privado, individual y colectivo, estructural e infraestructural, permanente y variable. Por ello, se presenta un estudio histórico y crítico en profundidad sobre los mat buildings, analizando detenidamente y por orden cronológico cinco de sus obras más paradigmáticas: el Orfanato en Ámsterdam de Aldo Van Eyck, la Universidad Libre en Berlín de Candilis, Josic y Woods, el Hospital de Venecia de Le Corbusier y Guillermo Jullián de la Fuente, el edificio administrativo de la Centraal Beheer en Apeldoorn de Herman Hertzberger, y por último el MUSAC en León, realizado por Mansilla y Tuñon. Las cuatro primeras obras pertenecen al periodo Team X y son precursoras de muchos otros proyectos que aparecerán a posteriori. La última obra analizada, el MUSAC, es estudiada conjuntamente con algunas obras del arquitecto japonés Sou Fujimoto y otros casos contemporáneos con la intención de manifestar cómo arquitectos de horizontes muy diferentes vuelven a recurrir a estos modelos de crecimientos ilimitados. Mediante el estudio de varios ejemplos contemporáneos se examinan las repercusiones, transformaciones y evoluciones que estos modelos han tenido. La exploración contrastada permite apreciar adecuadamente la pertinencia de estos modelos y los cambios de modalidades y de procesos que advienen con la aparición en el panorama contemporáneo de la noción de campo y los cambios de paradigma que conlleva. Estos nuevos modelos abren nuevos procesos y forma de abordar la arquitectura basada en las relaciones, flujos, movimientos y asociaciones que son caracterizados por diferentes patrones que vienen a alimentar todo el proceso del proyecto arquitectónico. El estudio de estos nuevos modelos nos indica las cualidades que puede ofrecer la revisión de estos métodos para empezar a tratar nuevas cuestiones que hoy en día parecen ser, permanentemente, parte de la condición urbana. XII ABSTRACT This thesis deals with the study of the so-called mat buildings which emerged between the fifties and sixties of the last century. Mat, or carpet, buildings appeared largely as a result of the CIAM’s disagreement and dissatisfaction with functionalist reductionism and the principles of functional compartmentalisation. These new models replaced the model of the city, seen as a collection of individual buildings, with the concept of an urban pattern. It is not the sum of the length, height and width but rather a dense, two- dimensional mat with a configuration of forms offering both a repetitive order and an infinite diversity of sequences with endless possibilities for adaptation, where man lives and circulates. These characteristics, which appeared in the works of many of the architects who formed part of Team X, are those that Alison Smithson started to reveal in her article with the aim of manifesting a new sensibility and a new way of understanding and seeing architecture. Mat buildings and clusters were the codes used by different members of Team X to plan an alternative architecture and urbanism to that proposed by the CIAM. With them, they found the path for a new aesthetic of connection, with a shift from a deterministic concept of the architectural form (closed and generally defined a priori) towards a more free, more open attitude based not so much on the integrity of the overall form but on the intensity of its internal networks and different levels of association. The end purpose of this thesis is to question whether this type of building, the basic principle of which is always an open geometric matrix (grid, recticle, network) with unlimited growth, can redefine the boundary between city and building and, thus, between public and private, individual and collective, structural and infrastructural, and permanent and variable. To this end, an in-depth historical and critical study of mat buildings is presented, analysing carefully and in chronological order five of the most paradigmatic works of this style: the Orphanage in Amsterdam, by Aldo Van Eyck; the Free University of Berlin, by Candilis, Josic and Woods; Venice Hospital, by Le Corbusier and Guillermo Jullián de la Fuente; the Centraal Beheer administration building in Apeldoorn, by Herman Hertzberger; and lastly, the MUSAC (Contemporary Art Museum) in León, designed by Mansilla and Tuñon. The first four works are from the Team X period and were the precursors to many other projects that would appear later. The last work analysed, the MUSAC, is studied together with some works by Japanese architect Sou Fujimoto and other contemporary cases to show how architects with very different perspectives revert to these models of limitless growth. Through the study of several contemporary examples we examine the repercussions, transformations and evolutions these models have had. The contrasted research XIII allows us to properly appreciate the importance of these models and the changes in forms and processes that came with the emergence of the idea of field in the contemporary arena and the paradigm shifts it entailed. These new models opened up new processes and a way of approaching architecture based on relationships, flows, movements and associations characterised by different patterns that feed the entire process of the architectural project. The study of these new models shows us the benefits that a review of these methods can contribute to addressing new issues that today appear to be a permanent part of the urban condition.

Detecting acronyms from capital letter sequences in Spanish

This paper presents an automatic strategy to decide how to pronounce a Capital Letter Sequence (CLS) in a Text to Speech system (TTS). If CLS is well known by the TTS, it can be expanded in several words. But when the CLS is unknown, the system has two alternatives: spelling it (abbreviation) or pronouncing it as a new word (acronym). In Spanish, there is a high relationship between letters and phonemes. Because of this, when a CLS is similar to other words in Spanish, there is a high tendency to pronounce it as a standard word. This paper proposes an automatic method for detecting acronyms. Additionaly, this paper analyses the discrimination capability of some features, and several strategies for combining them in order to obtain the best classifier. For the best classifier, the classification error is 8.45%. About the feature analysis, the best features have been the Letter Sequence Perplexity and the Average N-gram order.

Application of a dynamic event tree methodolgy to steam generator tube rupture sequences

The Integrated Safety Assessment (ISA) methodology, developed by the Spanish Nuclear Safety Council (CSN), has been applied to a thermo-hydraulical analysis of a Westinghouse 3-loop PWR plant by means of the dynamic event trees (DET) for Steam Generator Tube Rupture (SGTR) sequences. The ISA methodology allows obtaining the SGTR Dynamic Event Tree taking into account the operator actuation times. Simulations are performed with SCAIS (Simulation Code system for Integrated Safety Assessment), which includes a dynamic coupling with MAAP thermal hydraulic code. The results show the capability of the ISA methodology and SCAIS platform to obtain the DET of complex sequences.

Sequences of bifurcations and transition to chaos in an optical processing element

Digital chaotic behaviour in an Optical-Processing Element is reported. It is obtained as the result of processing two fixed trains of bits. Period doublings in a Feigenbaum-like scenario have been obtained. A new method to characterize digital chaos is reported

Direct and Inverse Results on Row Sequences of Hermite-Pad, Approximants

We give necessary and sufficient conditions for the convergence with geometric rate of the common denominators of simultaneous rational interpolants with a bounded number of poles. The conditions are expressed in terms of intrinsic properties of the system of functions used to build the approximants. Exact rates of convergence for these denominators and the simultaneous rational approximants are provided.

On-line MRI sequences for the evaluation of apple internal quality.

On-line dynamic MRI, which is oriented to industrial grading lines, requires high-speed sequences with motion correction artefacts. In this study two different types of motion correction sequences have been used and have been implemented in real-time (FLASH and UFLARE). They are based on T2* and T2 respectively and their selection depends on the expected contrast effect of the disorder: while watercore enhances bright areas due to higher fluid mobility, internal breakdown potentiates low signal due to texture degradation. For watercore study, five different apple cultivars were used (Normanda-18-, Fuji-35-, Helada-36-, Verde Doncella-54-, Esperiega-75-) along two seasons (2011 and 2012). In total 218 fruits were measured under both, static conditions (20 slices per fruit) and under dynamic conditions (3 repetitions without slice selection). For internal breakdown, Braeburn cultivar has been studied (in total 106 fruits) under both static (20 slices per fruit) and dynamic conditions (3 replicates with slice selection). Metrological aspects such as repeatability of dynamic images and subsequent histogram feature stability become of major interest for further industrial application. Segregation ability among varying degrees of disorder is also analyzed.

NAMA3DS1-COSPAD1: Subjective video quality assessment database on coding conditions introducing freely available high quality 3D stereoscopic sequences

Research in stereoscopic 3D coding, transmission and subjective assessment methodology depends largely on the availability of source content that can be used in cross-lab evaluations. While several studies have already been presented using proprietary content, comparisons between the studies are difficult since discrepant contents are used. Therefore in this paper, a freely available dataset of high quality Full-HD stereoscopic sequences shot with a semiprofessional 3D camera is introduced in detail. The content was designed to be suited for usage in a wide variety of applications, including high quality studies. A set of depth maps was calculated from the stereoscopic pair. As an application example, a subjective assessment has been performed using coding and spatial degradations. The Absolute Category Rating with Hidden Reference method was used. The observers were instructed to vote on video quality only. Results of this experiment are also freely available and will be presented in this paper as a first step towards objective video quality measurement for 3DTV.

Assessment of diastolic chamber properties of the right ventricle by global fitting of pressure-volume data and conformational analysis of 3D + T echocardiographic sequences

Assessment of diastolic chamber properties of the right ventricle by global fitting of pressure-volume data and conformational analysis of 3D + T echocardiographic sequences

Analysis of the damage domains of sbo sequences with rcp passive thermal shutdown

The integrated Safety Assessment (ISA) methodology, developed by the Spanish Nuclear Safety Council (CSN), has been applied to a thermal-hydraulic analysis of PWR Station Blackout (SBO) sequences in the context of the IDPSA (Integrated Deterministic-Probabilistic Safety Assessment) network objectives. The ISA methodology allows obtaining the damage domain (the region of the uncertain parameters space where the damage limit is exceeded) for each sequence of interest as a function of the operator actuations times. Given a particular safety limit or damage limit, several data of every sequence are necessary in order to obtain the exceedance frequency of that limit. In this application these data are obtained from the results of the simulations performed with MAAP code transients inside each damage domain and the time-density probability distributions of the manual actions. Damage limits that have been taken into account within this analysis are: local cladding damage (PCT>1477 K); local fuel melting (T>2499 K); fuel relocation in lower plenum and vessel failure. Therefore, to every one of these damage variables corresponds a different damage domain. The operation of the new passive thermal shutdown seals developed by several companies since Fukushima accident is considered in the paper. The results show the capability and necessity of the ISA methodology, or similar, in order to obtain accurate results that take into account time uncertainties.

Insertion of impairments in test video sequences for quality assessment based on psychovisual characteristics

Assessing video quality is a complex task. While most pixel-based metrics do not present enough correlation between objective and subjective results, algorithms need to correspond to human perception when analyzing quality in a video sequence. For analyzing the perceived quality derived from concrete video artifacts in determined region of interest we present a novel methodology for generating test sequences which allow the analysis of impact of each individual distortion. Through results obtained after subjective assessment it is possible to create psychovisual models based on weighting pixels belonging to different regions of interest distributed by color, position, motion or content. Interesting results are obtained in subjective assessment which demonstrates the necessity of new metrics adapted to human visual system.

Optical sensing of the fatigue damage state of CFRP under realistic aeronautical load sequences

We present an optical sensing methodology to estimate the fatigue damage state of structures made of carbon fiber reinforced polymer (CFRP), by measuring variations on the surface roughness. Variable amplitude loads (VAL), which represent realistic loads during aeronautical missions of fighter aircraft (FALSTAFF) have been applied to coupons until failure. Stiffness degradation and surface roughness variations have been measured during the life of the coupons obtaining a Pearson correlation of 0.75 between both variables. The data were compared with a previous study for Constant Amplitude Load (CAL) obtaining similar results. Conclusions suggest that the surface roughness measured in strategic zones is a useful technique for structural health monitoring of CFRP structures, and that it is independent of the type of load applied. Surface roughness can be measured in the field by optical techniques such as speckle, confocal perfilometers and interferometry, among others.