"Evaluación de la compatibilidad de tinciones no fluorescentes de Diffquik, Giemsa, Fastblast y de Feulgen con el Bioensayo Cometa en el ADN espermático humano."

La fertilidad masculina puede ser medida mediante un espermatograma convencional, sin embargo este examen no incluye la valoración de la integridad del ADN espermático. Esta variable ha sido correlacionada con las tasas de fertilización, viabilidad y desarrollo del embrión, convirtiéndose en una herramienta de importancia clínica tanto para los programas de reproducción animal como los tratamientos de fertilidad asistida. El bioensayo Cometa es capaz de determinar de una manera exacta el valor de la integridad del ADN espermático, lamentablemente este examen no es de uso rutinario por su elevado costo de implementación ya que utiliza microscopia especializada y tinciones fluorescentes para evidenciar la migración del ADN. El objetivo de esta investigación fue evaluar la compatibilidad de las tinciones no fluorescentes Diffquik, Giemsa, de Feulgen y FastBlast en el bioensayo Cometa usando un método visual y automatizado. Se utilizaron 15 eyaculados previamente seleccionados de acuerdo al manual OMS 2010, para luego ser capacitados en búsqueda de homogeneidad adecuada para la experimentación. Cada muestra fue expuesta a una gradiente de Peróxido de hidrogeno (0, 10, 30,60 y 100 mM) por 1 hora a 4°C para luego evaluar el coeficiente de daño mediante el método visual y porcentaje de ADN en la cola mediante el método automatizado. Las pendientes de la regresión lineal en el método visual indican que los valores obtenidos por la tinción control SybrGreen (m=3,69) difieren con Giemsa (m=3,45) y Diffquik (m=2,57). En el método automatizado de igual manera SybrGreen (m=0.83), Giemsa (m=0,79) y Diffquik (m=0,77). Sin embargo SybrGreen es 1,06 veces más efectivo que Giemsa en el visual y 1,05 veces en el automatizado, sugiriendo una compatibilidad con el bioensayo cometa. De igual manera SybrGreen es 1,07 veces más efectivo que Diffquik en el visual y 1,44 veces en el automatizado, concluyendo una compatibilidad solo en el método visual.Male fertility can be measured by a conventional semen analysis, however, this examination does not include the assessment of sperm DNA integrity. This variable has been correlated with fertilization rates, embryo viability and development, becoming a tool of clinical importance for both animal breeding programs and assisted fertility treatments. Comet bioassay is able to determine an exact way the value of sperm DNA integrity, unfortunately this test is not routinely used because of its high cost of implementation because it uses specialized microscopy and fluorescent dyes to demonstrate DNA migration. The objective of this research was to evaluate the compatibility of non-fluorescent dyes Diffquik, Giemsa, Feulgen and Comet FastBlast in the bioassay using a visual and automated method. 15 ejaculates were used previously manually selected according to WHO 2010 and then be trained in finding adequate homogeneity for experimentation. Each sample was exposed to a hydrogen peroxide gradient (0, 10, 30,60 and 100 mM) for 1 hour at 4 ° C and then assess the damage coefficient by visual method and percentage of DNA in the tail by automated method. The slopes of the linear regressions on the visual method indicate that the values obtained by the SybrGreen Control staining (m = 3.69) differ with Giemsa (m = 3.45) and Diffquik (m = 2.57). In the same way automated method SybrGreen (m = 0.83), Giemsa (m = 0.79) and Diffquik (m = 0.77). However SybrGreen is 1.06 times more effective than Giemsa visual and 1.05 times in the automated, suggesting a comet support bioassay. Similarly SybrGreen is 1.07 times more effective than Diffquik visual and 1.44 times in the automated, concluding compatibility only in the visual method.Tesi

Migration of tools and methodologies for performance prediction and efficient HPC on cloud environments: results and conclusion

Progress in the parallel programming field has allowed scientific applications to be developed with more complexity and accuracy. However, such precision requires greater computational power in order to be executed. How- ever, updating the local systems could be considered an expensive decision. For this reason, cloud computing is emerging as a commercial infrastructure that allows us to eliminate maintaining the computing hardware. For this reason, cloud is promising to be a computing alternative to clusters, grids and supercomputing for executing these applications. In this sense, this work is focused on describing the manner of migrating our prediction tool PAS2P (parallel application signature for performance prediction), and how we have to analyze our method for executing SPMD ap- plications efficiently on these cloud environments. In both cases, cloud could be considered a huge challenge due to the environment virtualization and the communication heterogeneities, which can seriously affect the application performance. However, our experimental evaluations make it clear that our prediction tool can predict with an error rate lower than 6,46%, considering that the signature for prediction represents a small portion of the execution time. On the other hand, analyzing the application parameters over the cloud computing allows us to find through an analytical model, which is the ideal number of virtual cores needed to obtain the maximum speedup under a defined efficiency. In this case the error rate was lower that 9% for the application tested.Facultad de Informátic

Migration of tools and methodologies for performance prediction and efficient HPC on cloud environments: results and conclusion

Progress in the parallel programming field has allowed scientific applications to be developed with more complexity and accuracy. However, such precision requires greater computational power in order to be executed. How- ever, updating the local systems could be considered an expensive decision. For this reason, cloud computing is emerging as a commercial infrastructure that allows us to eliminate maintaining the computing hardware. For this reason, cloud is promising to be a computing alternative to clusters, grids and supercomputing for executing these applications. In this sense, this work is focused on describing the manner of migrating our prediction tool PAS2P (parallel application signature for performance prediction), and how we have to analyze our method for executing SPMD ap- plications efficiently on these cloud environments. In both cases, cloud could be considered a huge challenge due to the environment virtualization and the communication heterogeneities, which can seriously affect the application performance. However, our experimental evaluations make it clear that our prediction tool can predict with an error rate lower than 6,46%, considering that the signature for prediction represents a small portion of the execution time. On the other hand, analyzing the application parameters over the cloud computing allows us to find through an analytical model, which is the ideal number of virtual cores needed to obtain the maximum speedup under a defined efficiency. In this case the error rate was lower that 9% for the application tested.Facultad de Informátic

Evaluation of the quality of the ”Montecarlo plus K-means” heuristics using benchmark functions

The evaluation in terms of quality of the results obtained from the use of a heuristic method is necessary to, first, verify the obtained results since heuristic methods do not guarantee to reach the optimum because all the possibilities are not fully explored. Secondly, it becomes interesting to validate such method, thus granting a high-quality index. Through our proposal, starting on the analysis of the literature survey on many optimization test functions, we are proposing the evaluation of a heuristic method based on Montecarlo approaches in conjunction with K-means clustering. Besides this, we aim to evaluate the results obtained through the use of some complex optimization test functions. Also, we seek to add a defined quality index to the original heuristic method relying on the consequent improvement in the results. As a side-work, we would aim to validate the heuristic mentioned aboveand optimize the algorithm in terms of scalability and quality.Instituto de Investigación en InformáticaInstituto de Investigación en Informátic

Predicting the communication pattern evolution for scalability analysis

The performance of the message-passing applications on a parallel system can vary and cause ine ciencies as the applications grow. With the aim of providing scalability behavior information of these applications on a speci c system, we propose a methodology that allows to analyze and predict the application behavior in a bounded time and using a limited number of resources. The proposed methodology is based on the fact that most scienti c applications have been developed using speci c communicational and computational patterns, which have certain behavior rules. As the number of application processes increases, these patterns change their behavior following speci c rules, being functionally constants. Our methodology is focused on characterizing these patterns to nd its general behavior rules, in order to build a logical application trace to predict its performance. The methodology uses the PAS2P tool to obtain the application behavior information, that allow us to analyze quickly a set of relevant phases covering approximately 95% of the total application. In this paper, we present the entire methodology while the experimental validation, that has been validated for the NAS benchmarks, is focused on characterizing the communication pattern for each phase and to model its general behavior rules to predict the pattern as the number of processes increases.WPDP- XIII Workshop procesamiento distribuido y paraleloRed de Universidades con Carreras en Informática (RedUNCI

Predicting the communication pattern evolution for scalability analysis

The performance of the message-passing applications on a parallel system can vary and cause ine ciencies as the applications grow. With the aim of providing scalability behavior information of these applications on a speci c system, we propose a methodology that allows to analyze and predict the application behavior in a bounded time and using a limited number of resources. The proposed methodology is based on the fact that most scienti c applications have been developed using speci c communicational and computational patterns, which have certain behavior rules. As the number of application processes increases, these patterns change their behavior following speci c rules, being functionally constants. Our methodology is focused on characterizing these patterns to nd its general behavior rules, in order to build a logical application trace to predict its performance. The methodology uses the PAS2P tool to obtain the application behavior information, that allow us to analyze quickly a set of relevant phases covering approximately 95% of the total application. In this paper, we present the entire methodology while the experimental validation, that has been validated for the NAS benchmarks, is focused on characterizing the communication pattern for each phase and to model its general behavior rules to predict the pattern as the number of processes increases.WPDP- XIII Workshop procesamiento distribuido y paraleloRed de Universidades con Carreras en Informática (RedUNCI

Plan de negocio para la implementaci?n de un directorio electr?nico de servicios profesionales a domicilio

El presente plan de negocios describe la implementaci?n y puesta en marcha exitosa de un directorio electr?nico de servicios profesionales a domicilio, considerando el amplio universo de servicios profesionales que existen en el mercado, el alcance del estudio de tesis abarcar? la implementaci?n de un directorio virtual para la publicaci?n de clases particulares a domicilio mediante una aplicaci?n m?vil cuyo nombre ser? Genius Class. El modelo de negocio se basa en el cobro de una comisi?n a quienes deseen publicar servicios de dictado de clases particulares a domicilio a trav?s de la aplicaci?n que les permitir? acceder a los demandantes de dictado de clases particulares a domicilio

Ambient vibration re-testing and operational modal analysis of the Humber Bridge

An ambient vibration survey of the Humber Bridge was carried out in July 2008 by a combined team from the UK, Portugal and Hong Kong. The exercise had several purposes that included the evaluation of the current technology for instrumentation and system identification and the generation of an experimental dataset of modal properties to be used for validation and updating of finite element models for scenario simulation and structural health monitoring. The exercise was conducted as part of a project aimed at developing online diagnosis capabilities for three landmark European suspension bridges. Ten stand-alone tri-axial acceleration recorders were deployed at locations along all three spans and in all four pylons during five days of consecutive one-hour recordings. Time series segments from the recorders were merged, and several operational modal analysis techniques were used to analyse these data and assemble modal models representing the global behaviour of the bridge in all three dimensions for all components of the structure. The paper describes the equipment and procedures used for the exercise, compares the operational modal analysis (OMA) technology used for system identification and presents modal parameters for key vibration modes of the complete structure. The results obtained using three techniques, natural excitation technique/eigensystem realisation algorithm, stochastic subspace identification and poly-Least Squares Frequency Domain method, are compared among themselves and with those obtained from a 1985 test of the bridge, showing few significant modal parameter changes over 23 years in cases where direct comparison is possible. The measurement system and the much more sophisticated OMA technology used in the present test show clear advantages necessary due to the compressed timescales compared to the earlier exercise. Even so, the parameter estimates exhibit significant variability between different methods and variations of the same method, while also varying in time and having inherent variability. (C) 2010 Elsevier Ltd. All rights reserved

Evaluation of a heuristic search algorithm based on sampling and clustering

Systems have evolved in such a way that today’s parallel systems are capable of offering high capacity and better performance. The design of approaches seeking for the best set of parameters in the context of a high-performance execution is fundamental. Although complex, heuristic methods are strategies that deal with high-dimensional optimization problems. We are proposing to enhance the evaluation method of a baseline heuristic that uses sampling and clustering techniques to optimize a complex, large and dynamic system. To carry out our proposal we selected the benchmark test functions and perform a density-based analysis along with k-means to cluster into feasible regions, discarding the non-relevant areas. With this, we aim to avoid getting trapped in local minima. Ultimately, the recursive execution of our methodology will guarantee to obtain the best value, thus, getting closer to method validation without forgetting the future lines, e.g. its distributed parallel implementation. Preliminary results turned out to be satisfactory, having obtained a solution quality above 99%.Facultad de Informátic

Benchmark based on application signature to analyze and predict their behavior

Currently, there are benchmark sets that measure the performance of HPC systems under specific computing and communication properties. These benchmarks represent the kernels of applications that measure specific hardware components. If the user’s application is not represented by any benchmark, it is not possible to obtain an equivalent performance metric. In this work, we propose a benchmark based on the signature of an MPI application obtained by the PAS2P method. PAS2P creates the application signature in order to predict the execution time, which we believe will be very adjusted in relation to the execution time of the full application. The signature has two performance qualities: the bounded time to execute it (a benchmark property) and the quality of prediction. Therefore, we propose to extend the signature by giving the benchmark capacities such as the efficiency of the application over the HPC system. The performance metrics will be performed by the benchmark proposed. The experimentation validates our proposal with an average error of prediction close to 7%.Instituto de Investigación en Informátic