Beyond position weight matrices: nucleotide correlations in transcription factor binding sites and their description

The identification of transcription factor binding sites (TFBSs) on genomic DNA is of crucial importance for understanding and predicting regulatory elements in gene networks. TFBS motifs are commonly described by Position Weight Matrices (PWMs), in which each DNA base pair independently contributes to the transcription factor (TF) binding, despite mounting evidence of interdependence between base pairs positions. The recent availability of genome-wide data on TF-bound DNA regions offers the possibility to revisit this question in detail for TF binding {\em in vivo}. Here, we use available fly and mouse ChIPseq data, and show that the independent model generally does not reproduce the observed statistics of TFBS, generalizing previous observations. We further show that TFBS description and predictability can be systematically improved by taking into account pairwise correlations in the TFBS via the principle of maximum entropy. The resulting pairwise interaction model is formally equivalent to the disordered Potts models of statistical mechanics and it generalizes previous approaches to interdependent positions. Its structure allows for co-variation of two or more base pairs, as well as secondary motifs. Although models consisting of mixtures of PWMs also have this last feature, we show that pairwise interaction models outperform them. The significant pairwise interactions are found to be sparse and found dominantly between consecutive base pairs. Finally, the use of a pairwise interaction model for the identification of TFBSs is shown to give significantly different predictions than a model based on independent positions

A Differential Approach for Gaze Estimation

Non-invasive gaze estimation methods usually regress gaze directions directly from a single face or eye image. However, due to important variabilities in eye shapes and inner eye structures amongst individuals, universal models obtain limited accuracies and their output usually exhibit high variance as well as biases which are subject dependent. Therefore, increasing accuracy is usually done through calibration, allowing gaze predictions for a subject to be mapped to his/her actual gaze. In this paper, we introduce a novel image differential method for gaze estimation. We propose to directly train a differential convolutional neural network to predict the gaze differences between two eye input images of the same subject. Then, given a set of subject specific calibration images, we can use the inferred differences to predict the gaze direction of a novel eye sample. The assumption is that by allowing the comparison between two eye images, annoyance factors (alignment, eyelid closing, illumination perturbations) which usually plague single image prediction methods can be much reduced, allowing better prediction altogether. Experiments on 3 public datasets validate our approach which constantly outperforms state-of-the-art methods even when using only one calibration sample or when the latter methods are followed by subject specific gaze adaptation.Comment: Extension to our paper A differential approach for gaze estimation with calibration (BMVC 2018) Submitted to PAMI on Aug. 7th, 2018 Accepted by PAMI short on Dec. 2019, in IEEE Transactions on Pattern Analysis and Machine Intelligenc

La inmersión en apnea. Análisis i secuenciación de las actividades físicas en la naturaleza para secundaria.

Las actividades físicas en la naturaleza han sido el caballo de batalla en una gran parte del profesorado de educación física durante mucho tiempo al entender que la riqueza de contenidos que nos puede ofrecer su práctica es muy superior a los planteamientos expresados en una sala polideportiva, si bien parece ser que en los grandes núcleos de población se hace difícil trabajar de forma continuada en esta línea. El presente artículo intenta hacer una reflexión sobre como podemos integrar estas actividades de una manera real y práctica dentro del marco escolar, esta vez mediante la propuesta de la Inmersión en Apnea

La immersió en apnea. Anàlisi i seqüenciament de les activitats físiques a la naturalesa per a secundària.

Les activitats físiques a la naturalesa han esta el cavall de batalla d'una gran part del professora d'educació física durant molt de temps, ja que entenien que la riquesa de continguts que ens pot oferir la seva pràctica és molt superior als plantejaments expressats en una sala poliesportiva, si bé, semblar ser que en els grans nuclis de població es fa difícil treballar de forma continuada en aquesta línia. El present article intenta fer una reflexió sobre com podem integrar aquestes activitats d'una manera real i pràctica dins el marc escolar, aquesta vegada mitjançant la proposta de la immersió en Apnea

Interaction of Guided Waves with Cracks in an Embedded Multilayered Anisotropic Plate by Using a Boundary Element Approach

In this work, the interaction of a transient guided elastic wave with a planar crack is studied by using a Boundary Finite Element approach on the crack. The originality of this work is to use the numerical Green functions of the multilayered plate. So, the key point of the method is to calculate rapidly and accurately these Green functions for such complex plane structures. For the space variables related to the plate surface, the fields are transformed in the 2D Fourier associated to the wave-vectors on this surface, and they are expressed in the partial-wave basis [1]. To ensure causality, the time dependence is dealt with in the Laplace domain. Surprisingly, this method, that involves 2D Fourier transform on the surface coupled with Laplace transform, has been rarely used in the ultrasonic community, while it is a useful tool which complements the much used technique based on generalized Lamb wave decomposition. By avoiding mode analysis, which can be problematic in some cases, exact numerical calculations of Green functions can be made in a relatively short time for immersed plates made of a stack of anisotropic viscoelastic layers. Even for 3D cases, numerical costs are relatively low. Numerical results show the effectiveness of this method. The examples presented emphasize the quality of the model and the robustness of the algorithm. Comparisons with Finite Element show excellent agreement. This approach is fast and low memory consuming for planar defects in arbitrary layered media, and can be extended to arbitrary shapes and boundary conditions for, of course, a higher computational cost. It is valid in 3D, however only the 2D case is considered in this work

The paradoxes of dairy farmers in Catalonia (Spain) : crisis and "double bind"

Altres ajuts: Acord transformatiu CRUE-CSICAltres ajuts: Institut de Recerca i Tecnologia Agroalimentàries (IRTA) (CF616633)We want to thank Marta Terra for her contribution to the research. To Miren Etxezarreta and Luis Enrique Alonso for the comments on the text. This work was supported by the Departament d'Agricultura Ramaderia i Pesca de la Generalitat de Catalunya within the framework of an agreement between the Institute of Agrifood Research and Technology (IRTA) and UAB: Project code CF616633The article analyses the crisis and 'double bind' situation to which Catalan dairy farmers find themselves subjected. Two contradictory commands are being imposed on them: 'act as if nature does not matter and increase production because, otherwise, the abandonment of livestock activity threatens you'; and 'reduce production and protect the environment to avoid an environmental catastrophe'. In the first part of the article, we study the socioeconomic crisis facing cattle farmers. In the second, we analyse farmers' discourse on the matter as a 'double bind'. Our conclusions indicate that in order to escape this paradoxical situation and gain some autonomy with respect to industry, farmers must establish a collective conscience and unite their interests: Although the path of producer cooperativism may be among the most realistic, it is not an easy one to follow

Geographic expansion and intensification of coffee-growing in Costa Rica during the green revolution (1950-1980): drivers and outcomes

This article presents fresh improved aggregated data on coffee-growing regional specialization in Costa Rica between the 1950s to the 1980s and discusses the determinants of the expansion of that coffee cropping frontier with a model that combines environmental and geo-economic drivers (...

Desenvolupament d'un sistema de mesura sense fil basat en sensors inercials per a l'optimització de l'entrenament de tècniques de Judo

Aquest projecte es basa en la fabricació d'un sistema cosit a la roba per poder monitorar les tècniques de judo i obtenir una millorar. Al mateix temps, està dotat d'un protocol HTTP per a l'enviament de dades mitjançant internet, perquè la visualització de dades no es realitzi connectant l'aparell a l'ordinador a través de cables que entorpirien l'entrenament de l'esportista. Per poder desenvolupar-lo s'ha utilitzat la placa de desenvolupament anomenada Arduino Nano 33 IOT, el qual aconsegueix les dades de 3 sensors inercials, 2 externs a la placa de desenvolupament i 1 integrat en el propi arduino, compostos per un acceleròmetre, un giroscopi i un magnetòmetre, que estaran situats en les articulacions dels braços o cames (canell, colze, turmell, genoll, espatlla i cintura). Per poder alimentar l'arduino sense cap cable usb es fan servir dos bateries en sèrie amb la capacitat suficient per tenir una vida de funcionament de 5 hores. Per a l'enviament de les dades, que s'han extret de cada un dels sensors, es connectarà la placa arduino a la mateixa xarxa wifi que l'ordinador, des d'on es visualitzaran les dades, i s'enviaran a partir d'un mètode anomenat GET del protocol HTTP, aquestes dades seran emmagatzemades a la base de dades que s’haurà creat prèviament. Un cop rebudes, es fa un emmagatzematge en una base de dades MYSQL i podrem extreure cada una d'aquestes dades creant una pàgina web, que es connecta amb la base de dades i representa, de la manera que més ens convingui, les acceleracions de cada un dels sensor