Identifying common and specific microRNAs expressed in peripheral blood mononuclear cell of type 1, type 2, and gestational diabetes mellitus patients

Abstract Background Regardless the regulatory function of microRNAs (miRNA), their differential expression pattern has been used to define miRNA signatures and to disclose disease biomarkers. To address the question of whether patients presenting the different types of diabetes mellitus could be distinguished on the basis of their miRNA and mRNA expression profiling, we obtained peripheral blood mononuclear cell (PBMC) RNAs from 7 type 1 (T1D), 7 type 2 (T2D), and 6 gestational diabetes (GDM) patients, which were hybridized to Agilent miRNA and mRNA microarrays. Data quantification and quality control were obtained using the Feature Extraction software, and data distribution was normalized using quantile function implemented in the Aroma light package. Differentially expressed miRNAs/mRNAs were identified using Rank products, comparing T1DxGDM, T2DxGDM and T1DxT2D. Hierarchical clustering was performed using the average linkage criterion with Pearson uncentered distance as metrics. Results The use of the same microarrays platform permitted the identification of sets of shared or specific miRNAs/mRNA interaction for each type of diabetes. Nine miRNAs (hsa-miR-126, hsa-miR-1307, hsa-miR-142-3p, hsa-miR-142-5p, hsa-miR-144, hsa-miR-199a-5p, hsa-miR-27a, hsa-miR-29b, and hsa-miR-342-3p) were shared among T1D, T2D and GDM, and additional specific miRNAs were identified for T1D (20 miRNAs), T2D (14) and GDM (19) patients. ROC curves allowed the identification of specific and relevant (greater AUC values) miRNAs for each type of diabetes, including: i) hsa-miR-1274a, hsa-miR-1274b and hsa-let-7f for T1D; ii) hsa-miR-222, hsa-miR-30e and hsa-miR-140-3p for T2D, and iii) hsa-miR-181a and hsa-miR-1268 for GDM. Many of these miRNAs targeted mRNAs associated with diabetes pathogenesis. Conclusions These results indicate that PBMC can be used as reporter cells to characterize the miRNA expression profiling disclosed by the different diabetes mellitus manifestations. Shared miRNAs may characterize diabetes as a metabolic and inflammatory disorder, whereas specific miRNAs may represent biological markers for each type of diabetes, deserving further attention.

Development of oil spill detection techniques for satellite optical sensors and their application to monitor oil spill discharge in Mediterranean sea

Satellite remote sensing has proved to be an effective support in timely detection and monitoring of marine oil pollution, mainly due to illegal ship discharges. In this context, we have developed a new methodology and technique for optical oil spill detection, which make use of MODIS L2 and MERIS L1B satellite top of atmosphere (TOA) reflectance imagery, for the first time in a highly automated way. The main idea was combining wide swaths and short revisit times of optical sensors with SAR observations, generally used in oil spill monitoring. This arises from the necessity to overcome the SAR reduced coverage and long revisit time of the monitoring area. This can be done now, given the MODIS and MERIS higher spatial resolution with respect to older sensors (250-300 m vs. 1 km), which consents the identification of smaller spills deriving from illicit discharge at sea. The procedure to obtain identifiable spills in optical reflectance images involves removal of oceanic and atmospheric natural variability, in order to enhance oil-water contrast; image clustering, which purpose is to segment the oil spill eventually presents in the image; finally, the application of a set of criteria for the elimination of those features which look like spills (look-alikes). The final result is a classification of oil spill candidate regions by means of a score based on the above criteria.

Deep learning for computer vision: a comparison between convolutional neural networks and hierarchical temporal memories on object recognition tasks

In recent years, Deep Learning techniques have shown to perform well on a large variety of problems both in Computer Vision and Natural Language Processing, reaching and often surpassing the state of the art on many tasks. The rise of deep learning is also revolutionizing the entire field of Machine Learning and Pattern Recognition pushing forward the concepts of automatic feature extraction and unsupervised learning in general. However, despite the strong success both in science and business, deep learning has its own limitations. It is often questioned if such techniques are only some kind of brute-force statistical approaches and if they can only work in the context of High Performance Computing with tons of data. Another important question is whether they are really biologically inspired, as claimed in certain cases, and if they can scale well in terms of "intelligence". The dissertation is focused on trying to answer these key questions in the context of Computer Vision and, in particular, Object Recognition, a task that has been heavily revolutionized by recent advances in the field. Practically speaking, these answers are based on an exhaustive comparison between two, very different, deep learning techniques on the aforementioned task: Convolutional Neural Network (CNN) and Hierarchical Temporal memory (HTM). They stand for two different approaches and points of view within the big hat of deep learning and are the best choices to understand and point out strengths and weaknesses of each of them. CNN is considered one of the most classic and powerful supervised methods used today in machine learning and pattern recognition, especially in object recognition. CNNs are well received and accepted by the scientific community and are already deployed in large corporation like Google and Facebook for solving face recognition and image auto-tagging problems. HTM, on the other hand, is known as a new emerging paradigm and a new meanly-unsupervised method, that is more biologically inspired. It tries to gain more insights from the computational neuroscience community in order to incorporate concepts like time, context and attention during the learning process which are typical of the human brain. In the end, the thesis is supposed to prove that in certain cases, with a lower quantity of data, HTM can outperform CNN.

Computer-aided diagnosis of carotid atherosclerosis based on ultrasound image statistics, laws' texture and neural networks

Quantitative characterisation of carotid atherosclerosis and classification into symptomatic or asymptomatic is crucial in planning optimal treatment of atheromatous plaque. The computer-aided diagnosis (CAD) system described in this paper can analyse ultrasound (US) images of carotid artery and classify them into symptomatic or asymptomatic based on their echogenicity characteristics. The CAD system consists of three modules: a) the feature extraction module, where first-order statistical (FOS) features and Laws' texture energy can be estimated, b) the dimensionality reduction module, where the number of features can be reduced using analysis of variance (ANOVA), and c) the classifier module consisting of a neural network (NN) trained by a novel hybrid method based on genetic algorithms (GAs) along with the back propagation algorithm. The hybrid method is able to select the most robust features, to adjust automatically the NN architecture and to optimise the classification performance. The performance is measured by the accuracy, sensitivity, specificity and the area under the receiver-operating characteristic (ROC) curve. The CAD design and development is based on images from 54 symptomatic and 54 asymptomatic plaques. This study demonstrates the ability of a CAD system based on US image analysis and a hybrid trained NN to identify atheromatous plaques at high risk of stroke.

A computer-aided diagnostic system to characterize CT focal liver lesions: design and optimization of a neural network classifier

In this paper, a computer-aided diagnostic (CAD) system for the classification of hepatic lesions from computed tomography (CT) images is presented. Regions of interest (ROIs) taken from nonenhanced CT images of normal liver, hepatic cysts, hemangiomas, and hepatocellular carcinomas have been used as input to the system. The proposed system consists of two modules: the feature extraction and the classification modules. The feature extraction module calculates the average gray level and 48 texture characteristics, which are derived from the spatial gray-level co-occurrence matrices, obtained from the ROIs. The classifier module consists of three sequentially placed feed-forward neural networks (NNs). The first NN classifies into normal or pathological liver regions. The pathological liver regions are characterized by the second NN as cyst or "other disease." The third NN classifies "other disease" into hemangioma or hepatocellular carcinoma. Three feature selection techniques have been applied to each individual NN: the sequential forward selection, the sequential floating forward selection, and a genetic algorithm for feature selection. The comparative study of the above dimensionality reduction methods shows that genetic algorithms result in lower dimension feature vectors and improved classification performance.

Computer vision profiling of neurite outgrowth dynamics reveals spatiotemporal modularity of Rho GTPase signaling

Rho guanosine triphosphatases (GTPases) control the cytoskeletal dynamics that power neurite outgrowth. This process consists of dynamic neurite initiation, elongation, retraction, and branching cycles that are likely to be regulated by specific spatiotemporal signaling networks, which cannot be resolved with static, steady-state assays. We present NeuriteTracker, a computer-vision approach to automatically segment and track neuronal morphodynamics in time-lapse datasets. Feature extraction then quantifies dynamic neurite outgrowth phenotypes. We identify a set of stereotypic neurite outgrowth morphodynamic behaviors in a cultured neuronal cell system. Systematic RNA interference perturbation of a Rho GTPase interactome consisting of 219 proteins reveals a limited set of morphodynamic phenotypes. As proof of concept, we show that loss of function of two distinct RhoA-specific GTPase-activating proteins (GAPs) leads to opposite neurite outgrowth phenotypes. Imaging of RhoA activation dynamics indicates that both GAPs regulate different spatiotemporal Rho GTPase pools, with distinct functions. Our results provide a starting point to dissect spatiotemporal Rho GTPase signaling networks that regulate neurite outgrowth.

A Noachian source region for the "Black Beauty" meteorite, and a source lithology for Mars surface hydrated dust?

The Martian surface is covered by a fine-layer of oxidized dust responsible for its red color in the visible spectral range (Bibring et al., 2006; Morris et al., 2006). In the near infrared, the strongest spectral feature is located between 2.6 and 3.6 mu m and is ubiquitously observed on the planet (Jouglet et al., 2007; Milliken et al., 2007). Although this absorption has been studied for many decades, its exact attribution and its geological and climatic implications remain debated. We present new lines of evidence from laboratory experiments, orbital and landed missions data, and characterization of the unique Martian meteorite NWA 7533, all converging toward the prominent role of hydroxylated ferric minerals. Martian breccias (so-called "Black Beauty" meteorite NWA7034 and its paired stones NWA7533 and NWA 7455) are unique pieces of the Martian surface that display abundant evidence of aqueous alteration that occurred on their parent planet (Agee et al., 2013). These dark stones are also unique in the fact that they arose from a near surface level in the Noachian southern hemisphere (Humayun et al., 2013). We used IR spectroscopy, Fe-XANES and petrography to identify the mineral hosts of hydrogen in NWA 7533 and compare them with observations of the Martian surface and results of laboratory experiments. The spectrum of NWA 7533 does not show mafic mineral absorptions, making its definite identification difficult through NIR remote sensing mapping. However, its spectra are virtually consistent with a large fraction of the Martian highlands. Abundant NWA 7034/7533 (and paired samples) lithologies might abound on Mars and might play a role in the dust production mechanism. (C) 2015 Elsevier B.V. All rights reserved.

Application of stellar photometry to the analysis of microarray images

Improvements in the analysis of microarray images are critical for accurately quantifying gene expression levels. The acquisition of accurate spot intensities directly influences the results and interpretation of statistical analyses. This dissertation discusses the implementation of a novel approach to the analysis of cDNA microarray images. We use a stellar photometric model, the Moffat function, to quantify microarray spots from nylon microarray images. The inherent flexibility of the Moffat shape model makes it ideal for quantifying microarray spots. We apply our novel approach to a Wilms' tumor microarray study and compare our results with a fixed-circle segmentation approach for spot quantification. Our results suggest that different spot feature extraction methods can have an impact on the ability of statistical methods to identify differentially expressed genes. We also used the Moffat function to simulate a series of microarray images under various experimental conditions. These simulations were used to validate the performance of various statistical methods for identifying differentially expressed genes. Our simulation results indicate that tests taking into account the dependency between mean spot intensity and variance estimation, such as the smoothened t-test, can better identify differentially expressed genes, especially when the number of replicates and mean fold change are low. The analysis of the simulations also showed that overall, a rank sum test (Mann-Whitney) performed well at identifying differentially expressed genes. Previous work has suggested the strengths of nonparametric approaches for identifying differentially expressed genes. We also show that multivariate approaches, such as hierarchical and k-means cluster analysis along with principal components analysis, are only effective at classifying samples when replicate numbers and mean fold change are high. Finally, we show how our stellar shape model approach can be extended to the analysis of 2D-gel images by adapting the Moffat function to take into account the elliptical nature of spots in such images. Our results indicate that stellar shape models offer a previously unexplored approach for the quantification of 2D-gel spots. ^

Variegation of comet 67P/Churyumov-Gerasimenko in regions showing activity

Aims. We carried out an investigation of the surface variegation of comet 67P/Churyumov-Gerasimenko, the detection of regions showing activity, the determination of active and inactive surface regions of the comet with spectral methods, and the detection of fallback material. Methods. We analyzed multispectral data generated with Optical, Spectroscopic, and Infrared Remote Imaging System (OSIRIS) narrow angle camera (NAC) observations via spectral techniques, reflectance ratios, and spectral slopes in order to study active regions. We applied clustering analysis to the results of the reflectance ratios, and introduced the new technique of activity thresholds to detect areas potentially enriched in volatiles. Results. Local color inhomogeneities are detected over the investigated surface regions. Active regions, such as Hapi, the active pits of Seth and Ma'at, the clustered and isolated bright features in Imhotep, the alcoves in Seth and Ma'at, and the large alcove in Anuket, have bluer spectra than the overall surface. The spectra generated with OSIRIS NAC observations are dominated by cometary emissions of around 700 nm to 750 nm as a result of the coma between the comet's surface and the camera. One of the two isolated bright features in the Imhotep region displays an absorption band of around 700 nm, which probably indicates the existence of hydrated silicates. An absorption band with a center between 800-900 nm is tentatively observed in some regions of the nucleus surface. This absorption band can be explained by the crystal field absorption of Fe2+, which is a common spectral feature seen in silicates.

Vision-based vehicle detection and tracking with a mobile camera using a statistical framework

En esta tesis se aborda la detección y el seguimiento automático de vehículos mediante técnicas de visión artificial con una cámara monocular embarcada. Este problema ha suscitado un gran interés por parte de la industria automovilística y de la comunidad científica ya que supone el primer paso en aras de la ayuda a la conducción, la prevención de accidentes y, en última instancia, la conducción automática. A pesar de que se le ha dedicado mucho esfuerzo en los últimos años, de momento no se ha encontrado ninguna solución completamente satisfactoria y por lo tanto continúa siendo un tema de investigación abierto. Los principales problemas que plantean la detección y seguimiento mediante visión artificial son la gran variabilidad entre vehículos, un fondo que cambia dinámicamente debido al movimiento de la cámara, y la necesidad de operar en tiempo real. En este contexto, esta tesis propone un marco unificado para la detección y seguimiento de vehículos que afronta los problemas descritos mediante un enfoque estadístico. El marco se compone de tres grandes bloques, i.e., generación de hipótesis, verificación de hipótesis, y seguimiento de vehículos, que se llevan a cabo de manera secuencial. No obstante, se potencia el intercambio de información entre los diferentes bloques con objeto de obtener el máximo grado posible de adaptación a cambios en el entorno y de reducir el coste computacional. Para abordar la primera tarea de generación de hipótesis, se proponen dos métodos complementarios basados respectivamente en el análisis de la apariencia y la geometría de la escena. Para ello resulta especialmente interesante el uso de un dominio transformado en el que se elimina la perspectiva de la imagen original, puesto que este dominio permite una búsqueda rápida dentro de la imagen y por tanto una generación eficiente de hipótesis de localización de los vehículos. Los candidatos finales se obtienen por medio de un marco colaborativo entre el dominio original y el dominio transformado. Para la verificación de hipótesis se adopta un método de aprendizaje supervisado. Así, se evalúan algunos de los métodos de extracción de características más populares y se proponen nuevos descriptores con arreglo al conocimiento de la apariencia de los vehículos. Para evaluar la efectividad en la tarea de clasificación de estos descriptores, y dado que no existen bases de datos públicas que se adapten al problema descrito, se ha generado una nueva base de datos sobre la que se han realizado pruebas masivas. Finalmente, se presenta una metodología para la fusión de los diferentes clasificadores y se plantea una discusión sobre las combinaciones que ofrecen los mejores resultados. El núcleo del marco propuesto está constituido por un método Bayesiano de seguimiento basado en filtros de partículas. Se plantean contribuciones en los tres elementos fundamentales de estos filtros: el algoritmo de inferencia, el modelo dinámico y el modelo de observación. En concreto, se propone el uso de un método de muestreo basado en MCMC que evita el elevado coste computacional de los filtros de partículas tradicionales y por consiguiente permite que el modelado conjunto de múltiples vehículos sea computacionalmente viable. Por otra parte, el dominio transformado mencionado anteriormente permite la definición de un modelo dinámico de velocidad constante ya que se preserva el movimiento suave de los vehículos en autopistas. Por último, se propone un modelo de observación que integra diferentes características. En particular, además de la apariencia de los vehículos, el modelo tiene en cuenta también toda la información recibida de los bloques de procesamiento previos. El método propuesto se ejecuta en tiempo real en un ordenador de propósito general y da unos resultados sobresalientes en comparación con los métodos tradicionales. ABSTRACT This thesis addresses on-road vehicle detection and tracking with a monocular vision system. This problem has attracted the attention of the automotive industry and the research community as it is the first step for driver assistance and collision avoidance systems and for eventual autonomous driving. Although many effort has been devoted to address it in recent years, no satisfactory solution has yet been devised and thus it is an active research issue. The main challenges for vision-based vehicle detection and tracking are the high variability among vehicles, the dynamically changing background due to camera motion and the real-time processing requirement. In this thesis, a unified approach using statistical methods is presented for vehicle detection and tracking that tackles these issues. The approach is divided into three primary tasks, i.e., vehicle hypothesis generation, hypothesis verification, and vehicle tracking, which are performed sequentially. Nevertheless, the exchange of information between processing blocks is fostered so that the maximum degree of adaptation to changes in the environment can be achieved and the computational cost is alleviated. Two complementary strategies are proposed to address the first task, i.e., hypothesis generation, based respectively on appearance and geometry analysis. To this end, the use of a rectified domain in which the perspective is removed from the original image is especially interesting, as it allows for fast image scanning and coarse hypothesis generation. The final vehicle candidates are produced using a collaborative framework between the original and the rectified domains. A supervised classification strategy is adopted for the verification of the hypothesized vehicle locations. In particular, state-of-the-art methods for feature extraction are evaluated and new descriptors are proposed by exploiting the knowledge on vehicle appearance. Due to the lack of appropriate public databases, a new database is generated and the classification performance of the descriptors is extensively tested on it. Finally, a methodology for the fusion of the different classifiers is presented and the best combinations are discussed. The core of the proposed approach is a Bayesian tracking framework using particle filters. Contributions are made on its three key elements: the inference algorithm, the dynamic model and the observation model. In particular, the use of a Markov chain Monte Carlo method is proposed for sampling, which circumvents the exponential complexity increase of traditional particle filters thus making joint multiple vehicle tracking affordable. On the other hand, the aforementioned rectified domain allows for the definition of a constant-velocity dynamic model since it preserves the smooth motion of vehicles in highways. Finally, a multiple-cue observation model is proposed that not only accounts for vehicle appearance but also integrates the available information from the analysis in the previous blocks. The proposed approach is proven to run near real-time in a general purpose PC and to deliver outstanding results compared to traditional methods.

Study of the effect of blurriness in image acquisition for Hand Biometrics in Mobile Devices

This paper presents a study on the effect of blurred images in hand biometrics. Blurred images simulates out-of-focus effects in hand image acquisition, a common consequence of unconstrained, contact-less and platform-free hand biometrics in mobile devices. The proposed biometric system presents a hand image segmentation based on multiscale aggregation, a segmentation method invariant to different changes like noise or blurriness, together with an innovative feature extraction and a template creation, oriented to obtain an invariant performance against blurring effects. The results highlight that the proposed system is invariant to some low degrees of blurriness, requiring an image quality control to detect and correct those images with a high degree of blurriness. The evaluation has considered a synthetic database created based on a publicly available database with 120 individuals. In addition, several biometric techniques could benefit from the approach proposed in this paper, since blurriness is a very common effect in biometric techniques involving image acquisition.

Towards hand biometrics in mobile devices

The increasing demand of security oriented to mobile applications has raised the attention to biometrics, as a proper and suitable solution for providing secure environment to mobile devices. With this aim, this document presents a biometric system based on hand geometry oriented to mobile devices, involving a high degree of freedom in terms of illumination, hand rotation and distance to camera. The user takes a picture of their own hand in the free space, without requiring any flat surface to locate the hand, and without removals of rings, bracelets or watches. The proposed biometric system relies on an accurate segmentation procedure, able to isolate hands from any background; a feature extraction, invariant to orientation, illumination, distance to camera and background; and a user classification, based on k-Nearest Neighbor approach, able to provide an accurate results on individual identification. The proposed method has been evaluated with two own databases collected with a HTC mobile. First database contains 120 individuals, with 20 acquisitions of both hands. Second database is a synthetic database, containing 408000 images of hand samples in different backgrounds: tiles, grass, water, sand, soil and the like. The system is able to identify individuals properly with False Reject Rate of 5.78% and False Acceptance Rate of 0.089%, using 60 features (15 features per finger)

A comparative study on unconstrained hand biometrics

Biometrics applied to mobile devices are of great interest for security applications. Daily scenarios can benefit of a combination of both the most secure systems and most simple and extended devices. This document presents a hand biometric system oriented to mobile devices, proposing a non-intrusive, contact-less acquisition process where final users should take a picture of their hand in free-space with a mobile device without removals of rings, bracelets or watches. The main contribution of this paper is threefold: firstly, a feature extraction method is proposed, providing invariant hand measurements to previous changes; second contribution consists of providing a template creation based on hand geometric distances, requiring information from only one individual, without considering data from the rest of individuals within the database; finally, a proposal for template matching is proposed, minimizing the intra-class similarity and maximizing the inter-class likeliness. The proposed method is evaluated using three publicly available contact-less, platform-free databases. In addition, the results obtained with these databases will be compared to the results provided by two competitive pattern recognition techniques, namely Support Vector Machines (SVM) and k-Nearest Neighbour, often employed within the literature. Therefore, this approach provides an appropriate solution to adapt hand biometrics to mobile devices, with an accurate results and a non-intrusive acquisition procedure which increases the overall acceptance from the final user.

Gaussian Multiscale Aggregation oriented to Hand Biometric Segmentation in Mobile Devices

New trends in biometrics are oriented to mobile devices in order to increase the overall security in daily actions like bank account access, e-commerce or even document protection within the mobile. However, applying biometrics to mobile devices imply challenging aspects in biometric data acquisition, feature extraction or private data storage. Concretely, this paper attempts to deal with the problem of hand segmentation given a picture of the hand in an unknown background, requiring an accurate result in terms of hand isolation. For the sake of user acceptability, no restrictions are done on background, and therefore, hand images can be taken without any constraint, resulting segmentation in an exigent task. Multiscale aggregation strategies are proposed in order to solve this problem due to their accurate results in unconstrained and complicated scenarios, together with their properties in time performance. This method is evaluated with a public synthetic database with 480000 images considering different backgrounds and illumination environments. The results obtained in terms of accuracy and time performance highlight their capability of being a suitable solution for the problem of hand segmentation in contact-less environments, outperforming competitive methods in literature like Lossy Data Compression image segmentation (LDC).

Unconstrained and Contactless Hand Geometry Biometrics

This paper presents a hand biometric system for contact-less, platform-free scenarios, proposing innovative methods in feature extraction, template creation and template matching. The evaluation of the proposed method considers both the use of three contact-less publicly available hand databases, and the comparison of the performance to two competitive pattern recognition techniques existing in literature: namely Support Vector Machines (SVM) and k-Nearest Neighbour (k-NN). Results highlight the fact that the proposed method outcomes existing approaches in literature in terms of computational cost, accuracy in human identification, number of extracted features and number of samples for template creation. The proposed method is a suitable solution for human identification in contact-less scenarios based on hand biometrics, providing a feasible solution to devices with limited hardware requirements like mobile devices