18 resultados para Gemstone Team PANACEA: Promoting A Novel Approach to Cellular (gene) Expression Alteration

em Universidad Politécnica de Madrid


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Transmission errors are the main cause of degradation of the quality of real broadcasted video services. Therefore, knowing their impact on the quality of experience of the end users is a crucial issue. For instance, it would help to improve the performance of the distribution systems, and to develop monitoring tools to automatically estimate the quality perceived by the end users. In this paper we validate a subjective evaluation approach specifically designed to obtain meaningful results of the effects of degradations caused by transmission errors. This methodology has been already used in our previous works with monoscopic and stereoscopic videos. The validation is done by comparing the subjective ratings obtained for typical transmission errors with the proposed methodology and with the standard method Absolute Category Rating. The results show that the proposed approach could provide more representative evaluations of the quality of experience perceived by end users of conventional and 3D broadcasted video services.

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La computación ubicua está extendiendo su aplicación desde entornos específicos hacia el uso cotidiano; el Internet de las cosas (IoT, en inglés) es el ejemplo más brillante de su aplicación y de la complejidad intrínseca que tiene, en comparación con el clásico desarrollo de aplicaciones. La principal característica que diferencia la computación ubicua de los otros tipos está en como se emplea la información de contexto. Las aplicaciones clásicas no usan en absoluto la información de contexto o usan sólo una pequeña parte de ella, integrándola de una forma ad hoc con una implementación específica para la aplicación. La motivación de este tratamiento particular se tiene que buscar en la dificultad de compartir el contexto con otras aplicaciones. En realidad lo que es información de contexto depende del tipo de aplicación: por poner un ejemplo, para un editor de imágenes, la imagen es la información y sus metadatos, tales como la hora de grabación o los ajustes de la cámara, son el contexto, mientras que para el sistema de ficheros la imagen junto con los ajustes de cámara son la información, y el contexto es representado por los metadatos externos al fichero como la fecha de modificación o la de último acceso. Esto significa que es difícil compartir la información de contexto, y la presencia de un middleware de comunicación que soporte el contexto de forma explícita simplifica el desarrollo de aplicaciones para computación ubicua. Al mismo tiempo el uso del contexto no tiene que ser obligatorio, porque si no se perdería la compatibilidad con las aplicaciones que no lo usan, convirtiendo así dicho middleware en un middleware de contexto. SilboPS, que es nuestra implementación de un sistema publicador/subscriptor basado en contenido e inspirado en SIENA [11, 9], resuelve dicho problema extendiendo el paradigma con dos elementos: el Contexto y la Función de Contexto. El contexto representa la información contextual propiamente dicha del mensaje por enviar o aquella requerida por el subscriptor para recibir notificaciones, mientras la función de contexto se evaa usando el contexto del publicador y del subscriptor. Esto permite desacoplar la lógica de gestión del contexto de aquella de la función de contexto, incrementando de esta forma la flexibilidad de la comunicación entre varias aplicaciones. De hecho, al utilizar por defecto un contexto vacío, las aplicaciones clásicas y las que manejan el contexto pueden usar el mismo SilboPS, resolviendo de esta forma la incompatibilidad entre las dos categorías. En cualquier caso la posible incompatibilidad semántica sigue existiendo ya que depende de la interpretación que cada aplicación hace de los datos y no puede ser solucionada por una tercera parte agnóstica. El entorno IoT conlleva retos no sólo de contexto, sino también de escalabilidad. La cantidad de sensores, el volumen de datos que producen y la cantidad de aplicaciones que podrían estar interesadas en manipular esos datos está en continuo aumento. Hoy en día la respuesta a esa necesidad es la computación en la nube, pero requiere que las aplicaciones sean no sólo capaces de escalar, sino de hacerlo de forma elástica [22]. Desgraciadamente no hay ninguna primitiva de sistema distribuido de slicing que soporte un particionamiento del estado interno [33] junto con un cambio en caliente, además de que los sistemas cloud actuales como OpenStack u OpenNebula no ofrecen directamente una monitorización elástica. Esto implica que hay un problema bilateral: cómo puede una aplicación escalar de forma elástica y cómo monitorizar esa aplicación para saber cuándo escalarla horizontalmente. E-SilboPS es la versión elástica de SilboPS y se adapta perfectamente como solución para el problema de monitorización, gracias al paradigma publicador/subscriptor basado en contenido y, a diferencia de otras soluciones [5], permite escalar eficientemente, para cumplir con la carga de trabajo sin sobre-provisionar o sub-provisionar recursos. Además está basado en un algoritmo recientemente diseñado que muestra como añadir elasticidad a una aplicación con distintas restricciones sobre el estado: sin estado, estado aislado con coordinación externa y estado compartido con coordinación general. Su evaluación enseña como se pueden conseguir notables speedups, siendo el nivel de red el principal factor limitante: de hecho la eficiencia calculada (ver Figura 5.8) demuestra cómo se comporta cada configuración en comparación con las adyacentes. Esto permite conocer la tendencia actual de todo el sistema, para saber si la siguiente configuración compensará el coste que tiene con la ganancia que lleva en el throughput de notificaciones. Se tiene que prestar especial atención en la evaluación de los despliegues con igual coste, para ver cuál es la mejor solución en relación a una carga de trabajo dada. Como último análisis se ha estimado el overhead introducido por las distintas configuraciones a fin de identificar el principal factor limitante del throughput. Esto ayuda a determinar la parte secuencial y el overhead de base [26] en un despliegue óptimo en comparación con uno subóptimo. Efectivamente, según el tipo de carga de trabajo, la estimación puede ser tan baja como el 10 % para un óptimo local o tan alta como el 60 %: esto ocurre cuando se despliega una configuración sobredimensionada para la carga de trabajo. Esta estimación de la métrica de Karp-Flatt es importante para el sistema de gestión porque le permite conocer en que dirección (ampliar o reducir) es necesario cambiar el despliegue para mejorar sus prestaciones, en lugar que usar simplemente una política de ampliación. ABSTRACT The application of pervasive computing is extending from field-specific to everyday use. The Internet of Things (IoT) is the shiniest example of its application and of its intrinsic complexity compared with classical application development. The main characteristic that differentiates pervasive from other forms of computing lies in the use of contextual information. Some classical applications do not use any contextual information whatsoever. Others, on the other hand, use only part of the contextual information, which is integrated in an ad hoc fashion using an application-specific implementation. This information is handled in a one-off manner because of the difficulty of sharing context across applications. As a matter of fact, the application type determines what the contextual information is. For instance, for an imaging editor, the image is the information and its meta-data, like the time of the shot or camera settings, are the context, whereas, for a file-system application, the image, including its camera settings, is the information and the meta-data external to the file, like the modification date or the last accessed timestamps, constitute the context. This means that contextual information is hard to share. A communication middleware that supports context decidedly eases application development in pervasive computing. However, the use of context should not be mandatory; otherwise, the communication middleware would be reduced to a context middleware and no longer be compatible with non-context-aware applications. SilboPS, our implementation of content-based publish/subscribe inspired by SIENA [11, 9], solves this problem by adding two new elements to the paradigm: the context and the context function. Context represents the actual contextual information specific to the message to be sent or that needs to be notified to the subscriber, whereas the context function is evaluated using the publisher’s context and the subscriber’s context to decide whether the current message and context are useful for the subscriber. In this manner, context logic management is decoupled from context management, increasing the flexibility of communication and usage across different applications. Since the default context is empty, context-aware and classical applications can use the same SilboPS, resolving the syntactic mismatch that there is between the two categories. In any case, the possible semantic mismatch is still present because it depends on how each application interprets the data, and it cannot be resolved by an agnostic third party. The IoT environment introduces not only context but scaling challenges too. The number of sensors, the volume of the data that they produce and the number of applications that could be interested in harvesting such data are growing all the time. Today’s response to the above need is cloud computing. However, cloud computing applications need to be able to scale elastically [22]. Unfortunately there is no slicing, as distributed system primitives that support internal state partitioning [33] and hot swapping and current cloud systems like OpenStack or OpenNebula do not provide elastic monitoring out of the box. This means there is a two-sided problem: 1) how to scale an application elastically and 2) how to monitor the application and know when it should scale in or out. E-SilboPS is the elastic version of SilboPS. I t is the solution for the monitoring problem thanks to its content-based publish/subscribe nature and, unlike other solutions [5], it scales efficiently so as to meet workload demand without overprovisioning or underprovisioning. Additionally, it is based on a newly designed algorithm that shows how to add elasticity in an application with different state constraints: stateless, isolated stateful with external coordination and shared stateful with general coordination. Its evaluation shows that it is able to achieve remarkable speedups where the network layer is the main limiting factor: the calculated efficiency (see Figure 5.8) shows how each configuration performs with respect to adjacent configurations. This provides insight into the actual trending of the whole system in order to predict if the next configuration would offset its cost against the resulting gain in notification throughput. Particular attention has been paid to the evaluation of same-cost deployments in order to find out which one is the best for the given workload demand. Finally, the overhead introduced by the different configurations has been estimated to identify the primary limiting factor for throughput. This helps to determine the intrinsic sequential part and base overhead [26] of an optimal versus a suboptimal deployment. Depending on the type of workload, this can be as low as 10% in a local optimum or as high as 60% when an overprovisioned configuration is deployed for a given workload demand. This Karp-Flatt metric estimation is important for system management because it indicates the direction (scale in or out) in which the deployment has to be changed in order to improve its performance instead of simply using a scale-out policy.

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Next Generation Networks (NGN) provide Telecommunications operators with the possibility to share their resources and infrastructure, facilitate the interoperability with other networks, and simplify and unify the management, operation and maintenance of service offerings, thus enabling the fast and cost-effective creation of new personal, broadband ubiquitous services. Unfortunately, service creation over NGN is far from the success of service creation in the Web, especially when it comes to Web 2.0. This paper presents a novel approach to service creation and delivery, with a platform that opens to non-technically skilled users the possibility to create, manage and share their own convergent (NGN-based and Web-based) services. To this end, the business approach to user-generated services is analyzed and the technological bases supporting the proposal are explained.

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In the field of detection and monitoring of dynamic objects in quasi-static scenes, background subtraction techniques where background is modeled at pixel-level, although showing very significant limitations, are extensively used. In this work we propose a novel approach to background modeling that operates at region-level in a wavelet based multi-resolution framework. Based on a segmentation of the background, characterization is made for each region independently as a mixture of K Gaussian modes, considering the model of the approximation and detail coefficients at the different wavelet decomposition levels. Background region characterization is updated along time, and the detection of elements of interest is carried out computing the distance between background region models and those of each incoming image in the sequence. The inclusion of the context in the modeling scheme through each region characterization makes the model robust, being able to support not only gradual illumination and long-term changes, but also sudden illumination changes and the presence of strong shadows in the scene

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Recent approaches to mobile code safety, like proof- arrying code, involve associating safety information to programs. The code supplier provides a program and also includes with it a certifícate (or proof) whose validity entails compliance with a predefined safety policy. The intended benefit is that the program consumer can locally validate the certifícate w.r.t. the "untrusted" program by means of a certifícate checker—a process which should be much simpler, eflicient, and automatic than generating the original proof. We herein introduce a novel approach to mobile code safety which follows a similar scheme, but which is based throughout on the use of abstract interpretation techniques. In our framework the safety policy is specified by using an expressive assertion language defined over abstract domains. We identify a particular slice of the abstract interpretation-based static analysis results which is especially useful as a certifícate. We propose an algorithm for checking the validity of the certifícate on the consumer side which is itself in fact a very simplified and eflicient specialized abstract-interpreter. Our ideas are illustrated through an example implemented in the CiaoPP system. Though further experimentation is still required, we believe the proposed approach is of interest for bringing the automation and expressiveness which is inherent in the abstract interpretation techniques to the área of mobile code safety.

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A gene expression atlas is an essential resource to quantify and understand the multiscale processes of embryogenesis in time and space. The automated reconstruction of a prototypic 4D atlas for vertebrate early embryos, using multicolor fluorescence in situ hybridization with nuclear counterstain, requires dedicated computational strategies. To this goal, we designed an original methodological framework implemented in a software tool called Match-IT. With only minimal human supervision, our system is able to gather gene expression patterns observed in different analyzed embryos with phenotypic variability and map them onto a series of common 3D templates over time, creating a 4D atlas. This framework was used to construct an atlas composed of 6 gene expression templates from a cohort of zebrafish early embryos spanning 6 developmental stages from 4 to 6.3 hpf (hours post fertilization). They included 53 specimens, 181,415 detected cell nuclei and the segmentation of 98 gene expression patterns observed in 3D for 9 different genes. In addition, an interactive visualization software, Atlas-IT, was developed to inspect, supervise and analyze the atlas. Match-IT and Atlas-IT, including user manuals, representative datasets and video tutorials, are publicly and freely available online. We also propose computational methods and tools for the quantitative assessment of the gene expression templates at the cellular scale, with the identification, visualization and analysis of coexpression patterns, synexpression groups and their dynamics through developmental stages.

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Topology control is an important technique to improve the connectivity and the reliability of Wireless Sensor Networks (WSNs) by means of adjusting the communication range of wireless sensor nodes. In this paper, a novel Fuzzy-logic Topology Control (FTC) is proposed to achieve any desired average node degree by adaptively changing communication range, thus improving the network connectivity, which is the main target of FTC. FTC is a fully localized control algorithm, and does not rely on location information of neighbors. Instead of designing membership functions and if-then rules for fuzzy-logic controller, FTC is constructed from the training data set to facilitate the design process. FTC is proved to be accurate, stable and has short settling time. In order to compare it with other representative localized algorithms (NONE, FLSS, k-Neighbor and LTRT), FTC is evaluated through extensive simulations. The simulation results show that: firstly, similar to k-Neighbor algorithm, FTC is the best to achieve the desired average node degree as node density varies; secondly, FTC is comparable to FLSS and k-Neighbor in terms of energy-efficiency, but is better than LTRT and NONE; thirdly, FTC has the lowest average maximum communication range than other algorithms, which indicates that the most energy-consuming node in the network consumes the lowest power.

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This paper presents a formal initiative for monitoring the competence acquisition by a team of students with different backgrounds facing the experience of being working by projects and in a project. These students are inexperienced in the project management field and they play this game on a time-shared manner along with other activities. The goal of this experience is to make some improvements in determining the competence levels acquired by means of how the work is being done. The use of this information, which is out of the scope of this particular work, could make possible to bring additional information to the students involved in terms of their individual competencies and the identification of new opportunities of personal improvement.

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The main goal of the bilingual and monolingual participation of the MIRACLE team in CLEF 2004 was to test the effect of combination approaches on information retrieval. The starting point was a set of basic components: stemming, transformation, filtering, generation of n-grams, weighting and relevance feedback. Some of these basic components were used in different combinations and order of application for document indexing and for query processing. A second order combination was also tested, mainly by averaging or selective combination of the documents retrieved by different approaches for a particular query.

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In this paper, a system that allows applying precision agriculture techniques is described. The application is based on the deployment of a team of unmanned aerial vehicles that are able to take georeferenced pictures in order to create a full map by applying mosaicking procedures for postprocessing. The main contribution of this work is practical experimentation with an integrated tool. Contributions in different fields are also reported. Among them is a new one-phase automatic task partitioning manager, which is based on negotiation among the aerial vehicles, considering their state and capabilities. Once the individual tasks are assigned, an optimal path planning algorithm is in charge of determining the best path for each vehicle to follow. Also, a robust flight control based on the use of a control law that improves the maneuverability of the quadrotors has been designed. A set of field tests was performed in order to analyze all the capabilities of the system, from task negotiations to final performance. These experiments also allowed testing control robustness under different weather conditions.

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A novel methodology based on instrumented indentation was developed to characterize the mechanical properties of amorphous materials. The approach is based on the concept of a universal postulate that assumes the existence of a characteristic indentation pressure proportional to the hardness. This hypothesis was numerically validated. This method overcomes the limitation of the conventional indentation models (pile-up effects and pressure sensitivity materials).

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This paper describes a novel deployment of an intelligent user-centered HVAC (Heating, Ventilating and Air Conditioner) control system. The main objective of this system is to optimize user comfort and to reduce energy consumption in office buildings. Existing commercial HVAC control systems work in a fixed and predetermined way. The novelty of the proposed system is that it adapts dynamically to the user and to the building environment. For this purpose the system architecture has been designed under the paradigm of Ambient Intelligence. A prototype of the system proposed has been tested in a real-world environment.

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Despite that Critical Infrastructures (CIs) security and surveillance are a growing concern for many countries and companies, Multi Robot Systems (MRSs) have not been yet broadly used in this type of facilities. This dissertation presents a novel study of the challenges arisen by the implementation of this type of systems and proposes solutions to specific problems. First, a comprehensive analysis of different types of CIs has been carried out, emphasizing the influence of the different characteristics of the facilities in the design of a security and surveillance MRS. One of the most important needs for the surveillance of a CI is the detection of intruders. From a technical point of view this problem can be abstracted as equivalent to the Detection and Tracking of Mobile Objects (DATMO). This dissertation proposes algorithms to solve this specific problem in a CI environment. Using 3D range images of the environment as input data, two detection algorithms for ground robots have been developed. These detection algorithms provide a list of moving objects in the robot detection area. Direct image differentiation and computer vision techniques are used when the robot is static. Alternatively, multi-layer ground reconstructions are compared to detect the dynamic objects when the robot is moving. Since CIs usually spread over large areas, it is very useful to incorporate aerial vehicles in the surveillance MRS. Therefore, a moving object detection algorithm for aerial vehicles has been also developed. This algorithm compares the real optical flow obtained from a down-face oriented camera with an artificial optical flow computed using a RANSAC based homography matrix. Two tracking algorithms have been developed to follow the moving objects trajectories. These algorithms can efficiently handle occlusions and crossings, as well as exchange information among robots. The multirobot tracking can be applied to any type of communication structure: centralized, decentralized or a combination of both. Even more, the developed tracking algorithms are independent of the detection algorithms and could be potentially used with other detection procedures or even with static sensors, such as cameras. In addition, using the 3D point clouds available to the robots, a relative localization algorithm has been developed to improve the position estimation of a given robot with observations from other robots. All the developed algorithms have been extensively tested in different simulated CIs using the Webots robotics simulator. Furthermore, the algorithms have also been validated with real robots operating in real scenarios. In conclusion, this dissertation presents a multirobot approach to Critical Infrastructure Surveillance, mainly focusing on Detecting and Tracking Dynamic Objects.

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There is general agreement within the scientific community in considering Biology as the science with more potential to develop in the XXI century. This is due to several reasons, but probably the most important one is the state of development of the rest of experimental and technological sciences. In this context, there are a very rich variety of mathematical tools, physical techniques and computer resources that permit to do biological experiments that were unbelievable only a few years ago. Biology is nowadays taking advantage of all these newly developed technologies, which are been applied to life sciences opening new research fields and helping to give new insights in many biological problems. Consequently, biologists have improved a lot their knowledge in many key areas as human function and human diseases. However there is one human organ that is still barely understood compared with the rest: The human brain. The understanding of the human brain is one of the main challenges of the XXI century. In this regard, it is considered a strategic research field for the European Union and the USA. Thus, there is a big interest in applying new experimental techniques for the study of brain function. Magnetoencephalography (MEG) is one of these novel techniques that are currently applied for mapping the brain activity1. This technique has important advantages compared to the metabolic-based brain imagining techniques like Functional Magneto Resonance Imaging2 (fMRI). The main advantage is that MEG has a higher time resolution than fMRI. Another benefit of MEG is that it is a patient friendly clinical technique. The measure is performed with a wireless set up and the patient is not exposed to any radiation. Although MEG is widely applied in clinical studies, there are still open issues regarding data analysis. The present work deals with the solution of the inverse problem in MEG, which is the most controversial and uncertain part of the analysis process3. This question is addressed using several variations of a new solving algorithm based in a heuristic method. The performance of those methods is analyzed by applying them to several test cases with known solutions and comparing those solutions with the ones provided by our methods.

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In this letter, we propose a novel method for unsupervised change detection (CD) in multitemporal Erreur Relative Globale Adimensionnelle de Synthese (ERGAS) satellite images by using the relative dimensionless global error in synthesis index locally. In order to obtain the change image, the index is calculated around a pixel neighborhood (3x3 window) processing simultaneously all the spectral bands available. With the objective of finding the binary change masks, six thresholding methods are selected. A comparison between the proposed method and the change vector analysis method is reported. The accuracy CD showed in the experimental results demonstrates the effectiveness of the proposed method.