New integrative computational approaches unveil the Saccharomyces cerevisiae pheno-metabolomic fermentative profile and allow strain selection for winemaking

During must fermentation by Saccharomyces cerevisiae strains thousands of volatile aroma compounds are formed. The objective of the present work was to adapt computational approaches to analyze pheno-metabolomic diversity of a S. cerevisiae strain collection with different origins. Phenotypic and genetic characterization together with individual must fermentations were performed, and metabolites relevant to aromatic profiles were determined. Experimental results were projected onto a common coordinates system, revealing 17 statistical-relevant multi-dimensional modules, combining sets of most-correlated features of noteworthy biological importance. The present method allowed, as a breakthrough, to combine genetic, phenotypic and metabolomic data, which has not been possible so far due to difficulties in comparing different types of data. Therefore, the proposed computational approach revealed as successful to shed light into the holistic characterization of S. cerevisiae pheno-metabolome in must fermentative conditions. This will allow the identification of combined relevant features with application in selection of good winemaking strains.

El impacto de las aplicaciones intensivas de E/S en la planificación de trabajos en clusters no-dedicados

Con la mayor capacidad de los nodos de procesamiento en relación a la potencia de cómputo, cada vez más aplicaciones intensivas de datos como las aplicaciones de la bioinformática, se llevarán a ejecutar en clusters no dedicados. Los clusters no dedicados se caracterizan por su capacidad de combinar la ejecución de aplicaciones de usuarios locales con aplicaciones, científicas o comerciales, ejecutadas en paralelo. Saber qué efecto las aplicaciones con acceso intensivo a dados producen respecto a la mezcla de otro tipo (batch, interativa, SRT, etc) en los entornos no-dedicados permite el desarrollo de políticas de planificación más eficientes. Algunas de las aplicaciones intensivas de E/S se basan en el paradigma MapReduce donde los entornos que las utilizan, como Hadoop, se ocupan de la localidad de los datos, balanceo de carga de forma automática y trabajan con sistemas de archivos distribuidos. El rendimiento de Hadoop se puede mejorar sin aumentar los costos de hardware, al sintonizar varios parámetros de configuración claves para las especificaciones del cluster, para el tamaño de los datos de entrada y para el procesamiento complejo. La sincronización de estos parámetros de sincronización puede ser demasiado compleja para el usuario y/o administrador pero procura garantizar prestaciones más adecuadas. Este trabajo propone la evaluación del impacto de las aplicaciones intensivas de E/S en la planificación de trabajos en clusters no-dedicados bajo los paradigmas MPI y Mapreduce.

MR MAQ: algorisme de Read Mapping utilitzant la plataforma Hadoop

L’èxit del Projecte Genoma Humà (PGH) l’any 2000 va fer de la “medicina personalitzada” una realitat més propera. Els descobriments del PGH han simplificat les tècniques de seqüenciació de tal manera que actualment qualsevol persona pot aconseguir la seva seqüència d’ADN complerta. La tecnologia de Read Mapping destaca en aquest tipus de tècniques i es caracteritza per manegar una gran quantitat de dades. Hadoop, el framework d’Apache per aplicacions intensives de dades sota el paradigma Map Reduce, resulta un aliat perfecte per aquest tipus de tecnologia i ha sigut l’opció escollida per a realitzar aquest projecte. Durant tot el treball es realitza l’estudi, l’anàlisi i les experimentacions necessàries per aconseguir un Algorisme Genètic innovador que utilitzi tot el potencial de Hadoop.

Metodologies de Desenvolupament Dirigides per Models

En aquest treball, s'introduiran dos de les metodologies de desenvolupament dirigides per models més significatives: Model Driven Architecture (MDA) i Domain Specific Modeling (DSM). Així mateix, es presentarà un estudi comparatiu d'algunes de les diferents eines existents actualment al mercat que els hi donen suport.

Heel and toe clearance estimation for gait analysis using wireless inertial sensors.

Tripping is considered a major cause of fall in older people. Therefore, foot clearance (i.e., height of the foot above ground during swing phase) could be a key factor to better understand the complex relationship between gait and falls. This paper presents a new method to estimate clearance using a foot-worn and wireless inertial sensor system. The method relies on the computation of foot orientation and trajectory from sensors signal data fusion, combined with the temporal detection of toe-off and heel-strike events. Based on a kinematic model that automatically estimates sensor position relative to the foot, heel and toe trajectories are estimated. 2-D and 3-D models are presented with different solving approaches, and validated against an optical motion capture system on 12 healthy adults performing short walking trials at self-selected, slow, and fast speed. Parameters corresponding to local minimum and maximum of heel and toe clearance were extracted and showed accuracy ± precision of 4.1 ± 2.3 cm for maximal heel clearance and 1.3 ± 0.9 cm for minimal toe clearance compared to the reference. The system is lightweight, wireless, easy to wear and to use, and provide a new and useful tool for routine clinical assessment of gait outside a dedicated laboratory.

Robust Detection of Incumbents in Cognitive Radio Networks Using Groups

Cognitive radio is a wireless technology aimed at improvingthe efficiency use of the radio-electric spectrum, thus facilitating a reductionin the load on the free frequency bands. Cognitive radio networkscan scan the spectrum and adapt their parameters to operate in the unoccupiedbands. To avoid interfering with licensed users operating on a givenchannel, the networks need to be highly sensitive, which is achieved byusing cooperative sensing methods. Current cooperative sensing methodsare not robust enough against occasional or continuous attacks. This articleoutlines a Group Fusion method that takes into account the behavior ofusers over the short and long term. On fusing the data, the method is basedon giving more weight to user groups that are more unanimous in their decisions.Simulations have been performed in a dynamic environment withinterferences. Results prove that when attackers are present (both reiterativeor sporadic), the proposed Group Fusion method has superior sensingcapability than other methods.

Social network extraction and analysis based on multimodal dyadic interaction

Social interactions are a very important component in people"s lives. Social network analysis has become a common technique used to model and quantify the properties of social interactions. In this paper, we propose an integrated framework to explore the characteristics of a social network extracted from multimodal dyadic interactions. For our study, we used a set of videos belonging to New York Times" Blogging Heads opinion blog. The Social Network is represented as an oriented graph, whose directed links are determined by the Influence Model. The links" weights are a measure of the"influence" a person has over the other. The states of the Influence Model encode automatically extracted audio/visual features from our videos using state-of-the art algorithms. Our results are reported in terms of accuracy of audio/visual data fusion for speaker segmentation and centrality measures used to characterize the extracted social network.

Security in multicast communication

Multicast is one method to transfer information in IPv4 based communication. Other methods are unicast and broadcast. Multicast is based on the group concept where data is sent from one point to a group of receivers and this remarkably saves bandwidth. Group members express an interest to receive data by using Internet Group Management Protocol and traffic is received by only those receivers who want it. The most common multicast applications are media streaming applications, surveillance applications and data collection applications. There are many data security methods to protect unicast communication that is the most common transfer method in Internet. Popular data security methods are encryption, authentication, access control and firewalls. The characteristics of multicast such as dynamic membership cause that all these data security mechanisms can not be used to protect multicast traffic. Nowadays the protection of multicast traffic is possible via traffic restrictions where traffic is allowed to propagate only to certain areas. One way to implement this is packet filters. Methods tested in this thesis are MVR, IGMP Filtering and access control lists which worked as supposed. These methods restrict the propagation of multicast but are laborious to configure in a large scale. There are also a few manufacturerspecific products that make possible to encrypt multicast traffic. These separate products are expensive and mainly intended to protect video transmissions via satellite. Investigation of multicast security has taken place for several years and the security methods that will be the results of the investigation are getting ready. An IETF working group called MSEC is standardizing these security methods. The target of this working group is to standardize data security protocols for multicast during 2004.

Modelling the disability severity score in motor insurance claims: an application to the Spanish case

Bodily injury claims have the greatest impact on the claim costs of motor insurance companies. The disability severity of motor claims is assessed in numerous European countries by means of score systems. In this paper a zero inflated generalized Poisson regression model is implemented to estimate the disability severity score of victims in-volved in motor accidents on Spanish roads. We show that the injury severity estimates may be automatically converted into financial terms by insurers at any point of the claim handling process. As such, the methodology described may be used by motor insurers operating in the Spanish market to monitor the size of bodily injury claims. By using insurance data, various applications are presented in which the score estimate of disability severity is of value to insurers, either for computing the claim compensation or for claim reserve purposes.

Review of Robust Cooperative Spectrum Sensing Techniques for Cognitive Radio Networks

Cognitive radio networks sense spectrum occupancy and manage themselvesto operate in unused bands without disturbing licensed users. The detection capability of aradio system can be enhanced if the sensing process is performed jointly by a group of nodesso that the effects of wireless fading and shadowing can be minimized. However, taking acollaborative approach poses new security threats to the system as nodes can report falsesensing data to reach a wrong decision. This paper makes a review of secure cooperativespectrum sensing in cognitive radio networks. The main objective of these protocols is toprovide an accurate resolution about the availability of some spectrum channels, ensuring thecontribution from incapable users as well as malicious ones is discarded. Issues, advantagesand disadvantages of such protocols are investigated and summarized.

Study of ligand-based virtual screening tools in computer-aided drug design

Virtual screening is a central technique in drug discovery today. Millions of molecules can be tested in silico with the aim to only select the most promising and test them experimentally. The topic of this thesis is ligand-based virtual screening tools which take existing active molecules as starting point for finding new drug candidates. One goal of this thesis was to build a model that gives the probability that two molecules are biologically similar as function of one or more chemical similarity scores. Another important goal was to evaluate how well different ligand-based virtual screening tools are able to distinguish active molecules from inactives. One more criterion set for the virtual screening tools was their applicability in scaffold-hopping, i.e. finding new active chemotypes. In the first part of the work, a link was defined between the abstract chemical similarity score given by a screening tool and the probability that the two molecules are biologically similar. These results help to decide objectively which virtual screening hits to test experimentally. The work also resulted in a new type of data fusion method when using two or more tools. In the second part, five ligand-based virtual screening tools were evaluated and their performance was found to be generally poor. Three reasons for this were proposed: false negatives in the benchmark sets, active molecules that do not share the binding mode, and activity cliffs. In the third part of the study, a novel visualization and quantification method is presented for evaluation of the scaffold-hopping ability of virtual screening tools.

Design Space Exploration for MPSoC Architectures

Multiprocessor system-on-chip (MPSoC) designs utilize the available technology and communication architectures to meet the requirements of the upcoming applications. In MPSoC, the communication platform is both the key enabler, as well as the key differentiator for realizing efficient MPSoCs. It provides product differentiation to meet a diverse, multi-dimensional set of design constraints, including performance, power, energy, reconfigurability, scalability, cost, reliability and time-to-market. The communication resources of a single interconnection platform cannot be fully utilized by all kind of applications, such as the availability of higher communication bandwidth for computation but not data intensive applications is often unfeasible in the practical implementation. This thesis aims to perform the architecture-level design space exploration towards efficient and scalable resource utilization for MPSoC communication architecture. In order to meet the performance requirements within the design constraints, careful selection of MPSoC communication platform, resource aware partitioning and mapping of the application play important role. To enhance the utilization of communication resources, variety of techniques such as resource sharing, multicast to avoid re-transmission of identical data, and adaptive routing can be used. For implementation, these techniques should be customized according to the platform architecture. To address the resource utilization of MPSoC communication platforms, variety of architectures with different design parameters and performance levels, namely Segmented bus (SegBus), Network-on-Chip (NoC) and Three-Dimensional NoC (3D-NoC), are selected. Average packet latency and power consumption are the evaluation parameters for the proposed techniques. In conventional computing architectures, fault on a component makes the connected fault-free components inoperative. Resource sharing approach can utilize the fault-free components to retain the system performance by reducing the impact of faults. Design space exploration also guides to narrow down the selection of MPSoC architecture, which can meet the performance requirements with design constraints.

Silver-doped photopolymer media for holographic recording

Incorporation of silver ions into a dye-sensitized poly(vinyl alcohol)/acrylamide photopolymer is observed to give better performance compared to other metal-ion-doped photopolymer holographic recording media. Plane-wave transmission gratings were recorded in the photopolymer films using a He–Ne laser, and various holographic parameters were optimized so as to explore maximum potential of the material for various holographic applications. Silver-doped films showed good energy sensitivity, and gratings recorded in optimized film exhibited a diffraction efficiency of more than 75%. The potential of the material for holographic data storage applications is also studied using peristrophic multiplexing

Optimización del sistema de transporte en el colegio The English School

La optimización de sistemas y modelos se ha convertido en uno de los factores más importantes a la hora de buscar la mayor eficiencia de un proceso. Este concepto no es ajeno al transporte escolar, ambiente que cambia constantemente al ritmo de las necesidades de sus clientes, y que responde ante una fuerte responsabilidad frente a sus usuarios, los niños que hacen uso del servicio, en cuanto al cumplimiento de tiempos y seguridad, mientras busca constantemente la reducción de costos. Este proyecto expone las problemáticas presentadas en The English School en esta área y propone un modelo de optimización simple que permitirá notables mejoras en términos de tiempos y costos, de tal forma que genere beneficios para la institución en términos financieros y de satisfacción al cliente. Por medio de la implementación de este modelo será posible identificar errores comunes del proceso, se identificarán soluciones prácticas de fácil aplicación en el manejo del transporte y se presentarán los resultados obtenidos en la muestra utilizada para desarrollar el proyecto.

The accuracy of Doppler radar wind retrievals using insects as targets

Insect returns from the UK's Doppler weather radars were collected in the summers of 2007 and 2008, to ascertain their usefulness in providing information about boundary layer winds. Such observations could be assimilated into numerical weather prediction models to improve forecasts of convective showers before precipitation begins. Significant numbers of insect returns were observed during daylight hours on a number of days through this period, when they were detected at up to 30 km range from the radars, and up to 2 km above sea level. The range of detectable insect returns was found to vary with time of year and temperature. There was also a very weak correlation with wind speed and direction. Use of a dual-polarized radar revealed that the insects did not orient themselves at random, but showed distinct evidence of common orientation on several days, sometimes at an angle to their direction of travel. Observation minus model background residuals of wind profiles showed greater bias and standard deviation than that of other wind measurement types, which may be due to the insects' headings/airspeeds and to imperfect data extraction. The method used here, similar to the Met Office's procedure for extracting precipitation returns, requires further development as clutter contamination remained one of the largest error contributors. Wind observations derived from the insect returns would then be useful for data assimilation applications.