Improvement of gamete quality and its short-term storage: an approach for biotechnology in laboratory fish

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Managing Large Data Sets Using Support Vector Machines

Hundreds of Terabytes of CMS (Compact Muon Solenoid) data are being accumulated for storage day by day at the University of Nebraska-Lincoln, which is one of the eight US CMS Tier-2 sites. Managing this data includes retaining useful CMS data sets and clearing storage space for newly arriving data by deleting less useful data sets. This is an important task that is currently being done manually and it requires a large amount of time. The overall objective of this study was to develop a methodology to help identify the data sets to be deleted when there is a requirement for storage space. CMS data is stored using HDFS (Hadoop Distributed File System). HDFS logs give information regarding file access operations. Hadoop MapReduce was used to feed information in these logs to Support Vector Machines (SVMs), a machine learning algorithm applicable to classification and regression which is used in this Thesis to develop a classifier. Time elapsed in data set classification by this method is dependent on the size of the input HDFS log file since the algorithmic complexities of Hadoop MapReduce algorithms here are O(n). The SVM methodology produces a list of data sets for deletion along with their respective sizes. This methodology was also compared with a heuristic called Retention Cost which was calculated using size of the data set and the time since its last access to help decide how useful a data set is. Accuracies of both were compared by calculating the percentage of data sets predicted for deletion which were accessed at a later instance of time. Our methodology using SVMs proved to be more accurate than using the Retention Cost heuristic. This methodology could be used to solve similar problems involving other large data sets.

Effects of curing protocol and storage time on the micro-hardness of resin cements used to lute fiber-reinforced resin posts

Objectives: To determine the micro-hardness profile of two dual cure resin cements (RelyX - U100 (R), 3M-ESPE and Panavia F 2.0 (R), Kuraray) used for cementing fiber-reinforced resin posts (Fibrekor (R) - Jeneric Pentron) under three different curing protocols and two water storage times. Material and methods: Sixty 16mm long bovine incisor roots were endodontically treated and prepared for cementation of the Fibrekor posts. The cements were mixed as instructed, dispensed in the canal, the posts were seated and the curing performed as follows: a) no light activation; b) light-activation immediately after seating the post, and; c) light-activation delayed 5 minutes after seating the post. The teeth were stored in water and retrieved for analysis after 7 days and 3 months. The roots were longitudinally sectioned and the microhardness was determined at the cervical, middle and apical regions along the cement line. The data was analyzed by the three-way ANOVA test (curing mode, storage time and thirds) for each cement. The Tukey test was used for the post-hoc analysis. Results: Light-activation resulted in a significant increase in the microhardness. This was more evident for the cervical region and for the Panavia cement. Storage in water for 3 months caused a reduction of the micro-hardness for both cements. The U100 cement showed less variation in the micro-hardness regardless of the curing protocol and storage time. Conclusions: The micro-hardness of the cements was affected by the curing and storage variables and were material-dependent.

The SB-index and the HSB-index: efficient indices for spatial data warehouses

Spatial data warehouses (SDWs) allow for spatial analysis together with analytical multidimensional queries over huge volumes of data. The challenge is to retrieve data related to ad hoc spatial query windows according to spatial predicates, avoiding the high cost of joining large tables. Therefore, mechanisms to provide efficient query processing over SDWs are essential. In this paper, we propose two efficient indices for SDW: the SB-index and the HSB-index. The proposed indices share the following characteristics. They enable multidimensional queries with spatial predicate for SDW and also support predefined spatial hierarchies. Furthermore, they compute the spatial predicate and transform it into a conventional one, which can be evaluated together with other conventional predicates by accessing a star-join Bitmap index. While the SB-index has a sequential data structure, the HSB-index uses a hierarchical data structure to enable spatial objects clustering and a specialized buffer-pool to decrease the number of disk accesses. The advantages of the SB-index and the HSB-index over the DBMS resources for SDW indexing (i.e. star-join computation and materialized views) were investigated through performance tests, which issued roll-up operations extended with containment and intersection range queries. The performance results showed that improvements ranged from 68% up to 99% over both the star-join computation and the materialized view. Furthermore, the proposed indices proved to be very compact, adding only less than 1% to the storage requirements. Therefore, both the SB-index and the HSB-index are excellent choices for SDW indexing. Choosing between the SB-index and the HSB-index mainly depends on the query selectivity of spatial predicates. While low query selectivity benefits the HSB-index, the SB-index provides better performance for higher query selectivity.

An online data access prediction and optimization approach for distributed systems

Current scientific applications have been producing large amounts of data. The processing, handling and analysis of such data require large-scale computing infrastructures such as clusters and grids. In this area, studies aim at improving the performance of data-intensive applications by optimizing data accesses. In order to achieve this goal, distributed storage systems have been considering techniques of data replication, migration, distribution, and access parallelism. However, the main drawback of those studies is that they do not take into account application behavior to perform data access optimization. This limitation motivated this paper which applies strategies to support the online prediction of application behavior in order to optimize data access operations on distributed systems, without requiring any information on past executions. In order to accomplish such a goal, this approach organizes application behaviors as time series and, then, analyzes and classifies those series according to their properties. By knowing properties, the approach selects modeling techniques to represent series and perform predictions, which are, later on, used to optimize data access operations. This new approach was implemented and evaluated using the OptorSim simulator, sponsored by the LHC-CERN project and widely employed by the scientific community. Experiments confirm this new approach reduces application execution time in about 50 percent, specially when handling large amounts of data.

Memory hierarchy and data communication in heterogeneous reconfigurable SoCs

The miniaturization race in the hardware industry aiming at continuous increasing of transistor density on a die does not bring respective application performance improvements any more. One of the most promising alternatives is to exploit a heterogeneous nature of common applications in hardware. Supported by reconfigurable computation, which has already proved its efficiency in accelerating data intensive applications, this concept promises a breakthrough in contemporary technology development. Memory organization in such heterogeneous reconfigurable architectures becomes very critical. Two primary aspects introduce a sophisticated trade-off. On the one hand, a memory subsystem should provide well organized distributed data structure and guarantee the required data bandwidth. On the other hand, it should hide the heterogeneous hardware structure from the end-user, in order to support feasible high-level programmability of the system. This thesis work explores the heterogeneous reconfigurable hardware architectures and presents possible solutions to cope the problem of memory organization and data structure. By the example of the MORPHEUS heterogeneous platform, the discussion follows the complete design cycle, starting from decision making and justification, until hardware realization. Particular emphasis is made on the methods to support high system performance, meet application requirements, and provide a user-friendly programmer interface. As a result, the research introduces a complete heterogeneous platform enhanced with a hierarchical memory organization, which copes with its task by means of separating computation from communication, providing reconfigurable engines with computation and configuration data, and unification of heterogeneous computational devices using local storage buffers. It is distinguished from the related solutions by distributed data-flow organization, specifically engineered mechanisms to operate with data on local domains, particular communication infrastructure based on Network-on-Chip, and thorough methods to prevent computation and communication stalls. In addition, a novel advanced technique to accelerate memory access was developed and implemented.

Kernel Methods for Tree Structured Data

Machine learning comprises a series of techniques for automatic extraction of meaningful information from large collections of noisy data. In many real world applications, data is naturally represented in structured form. Since traditional methods in machine learning deal with vectorial information, they require an a priori form of preprocessing. Among all the learning techniques for dealing with structured data, kernel methods are recognized to have a strong theoretical background and to be effective approaches. They do not require an explicit vectorial representation of the data in terms of features, but rely on a measure of similarity between any pair of objects of a domain, the kernel function. Designing fast and good kernel functions is a challenging problem. In the case of tree structured data two issues become relevant: kernel for trees should not be sparse and should be fast to compute. The sparsity problem arises when, given a dataset and a kernel function, most structures of the dataset are completely dissimilar to one another. In those cases the classifier has too few information for making correct predictions on unseen data. In fact, it tends to produce a discriminating function behaving as the nearest neighbour rule. Sparsity is likely to arise for some standard tree kernel functions, such as the subtree and subset tree kernel, when they are applied to datasets with node labels belonging to a large domain. A second drawback of using tree kernels is the time complexity required both in learning and classification phases. Such a complexity can sometimes prevents the kernel application in scenarios involving large amount of data. This thesis proposes three contributions for resolving the above issues of kernel for trees. A first contribution aims at creating kernel functions which adapt to the statistical properties of the dataset, thus reducing its sparsity with respect to traditional tree kernel functions. Specifically, we propose to encode the input trees by an algorithm able to project the data onto a lower dimensional space with the property that similar structures are mapped similarly. By building kernel functions on the lower dimensional representation, we are able to perform inexact matchings between different inputs in the original space. A second contribution is the proposal of a novel kernel function based on the convolution kernel framework. Convolution kernel measures the similarity of two objects in terms of the similarities of their subparts. Most convolution kernels are based on counting the number of shared substructures, partially discarding information about their position in the original structure. The kernel function we propose is, instead, especially focused on this aspect. A third contribution is devoted at reducing the computational burden related to the calculation of a kernel function between a tree and a forest of trees, which is a typical operation in the classification phase and, for some algorithms, also in the learning phase. We propose a general methodology applicable to convolution kernels. Moreover, we show an instantiation of our technique when kernels such as the subtree and subset tree kernels are employed. In those cases, Direct Acyclic Graphs can be used to compactly represent shared substructures in different trees, thus reducing the computational burden and storage requirements.

Design of alternative energy storage systems for hybrid vehicles based on statistical processing of driving cycles information

Hybrid vehicles represent the future for automakers, since they allow to improve the fuel economy and to reduce the pollutant emissions. A key component of the hybrid powertrain is the Energy Storage System, that determines the ability of the vehicle to store and reuse energy. Though electrified Energy Storage Systems (ESS), based on batteries and ultracapacitors, are a proven technology, Alternative Energy Storage Systems (AESS), based on mechanical, hydraulic and pneumatic devices, are gaining interest because they give the possibility of realizing low-cost mild-hybrid vehicles. Currently, most literature of design methodologies focuses on electric ESS, which are not suitable for AESS design. In this contest, The Ohio State University has developed an Alternative Energy Storage System design methodology. This work focuses on the development of driving cycle analysis methodology that is a key component of Alternative Energy Storage System design procedure. The proposed methodology is based on a statistical approach to analyzing driving schedules that represent the vehicle typical use. Driving data are broken up into power events sequence, namely traction and braking events, and for each of them, energy-related and dynamic metrics are calculated. By means of a clustering process and statistical synthesis methods, statistically-relevant metrics are determined. These metrics define cycle representative braking events. By using these events as inputs for the Alternative Energy Storage System design methodology, different system designs are obtained. Each of them is characterized by attributes, namely system volume and weight. In the last part the work, the designs are evaluated in simulation by introducing and calculating a metric related to the energy conversion efficiency. Finally, the designs are compared accounting for attributes and efficiency values. In order to automate the driving data extraction and synthesis process, a specific script Matlab based has been developed. Results show that the driving cycle analysis methodology, based on the statistical approach, allows to extract and synthesize cycle representative data. The designs based on cycle statistically-relevant metrics are properly sized and have satisfying efficiency values with respect to the expectations. An exception is the design based on the cycle worst-case scenario, corresponding to same approach adopted by the conventional electric ESS design methodologies. In this case, a heavy system with poor efficiency is produced. The proposed new methodology seems to be a valid and consistent support for Alternative Energy Storage System design.

Development of a microgrid with renewable energy sources and electrochemical storage system integration

Beside the traditional paradigm of "centralized" power generation, a new concept of "distributed" generation is emerging, in which the same user becomes pro-sumer. During this transition, the Energy Storage Systems (ESS) can provide multiple services and features, which are necessary for a higher quality of the electrical system and for the optimization of non-programmable Renewable Energy Source (RES) power plants. A ESS prototype was designed, developed and integrated into a renewable energy production system in order to create a smart microgrid and consequently manage in an efficient and intelligent way the energy flow as a function of the power demand. The produced energy can be introduced into the grid, supplied to the load directly or stored in batteries. The microgrid is composed by a 7 kW wind turbine (WT) and a 17 kW photovoltaic (PV) plant are part of. The load is given by electrical utilities of a cheese factory. The ESS is composed by the following two subsystems, a Battery Energy Storage System (BESS) and a Power Control System (PCS). With the aim of sizing the ESS, a Remote Grid Analyzer (RGA) was designed, realized and connected to the wind turbine, photovoltaic plant and the switchboard. Afterwards, different electrochemical storage technologies were studied, and taking into account the load requirements present in the cheese factory, the most suitable solution was identified in the high temperatures salt Na-NiCl2 battery technology. The data acquisition from all electrical utilities provided a detailed load analysis, indicating the optimal storage size equal to a 30 kW battery system. Moreover a container was designed and realized to locate the BESS and PCS, meeting all the requirements and safety conditions. Furthermore, a smart control system was implemented in order to handle the different applications of the ESS, such as peak shaving or load levelling.

Effect of antioxidant supplementation on pig and horse gamete storage

According to recent studies, antioxidant supplementation on gamete processing and/or storage solutions improvesgamete quality parameters, after cooling or storage at sub zero temperature. The aim of the present study was to investigate the effects of antioxidant supplementation on pig and horse gamete storage. The first study aimed to determine the effects of resveratrol (RESV) on the apoptotic status of porcine oocytes vitrified by Cryotop method, evaluating phosphatidylserine (PS) exteriorization and caspases activation. RESV(2µM) was added during: IVM (A); 2 h post-warming incubation (B); vitrification/warming and 2 h post-warming incubation (C); all previous phases (D). The obtained data demonstrate that RESV supplementation in the various steps of IVM and vitrification/warming procedure can modulate the apoptotic process, improving the resistance of porcine oocytes to cryopreservation-induced damage. In the second work different concentrations of RESV (10, 20, 40, and 80µM) were added during liquid storage of stallion sperm for 24 hours at either 10°C or 4°C, under anaerobic conditions. Our findings demonstrate that RESV supplementation does not enhance sperm quality of stallion semen after 24 hours of storage. Moreover, the highest RESV concentrations tested (40 and 80µM) could damage sperm functional status, probably acting as pro-oxidant. Finally, in the third work other two antioxidants, ascorbic acid (AA) (100 µM) and glutathione (GSH) (5mM) were added on boar freezing and/or thawing solutions. In our study different sperm parameters were evaluated before freezing and at 30 and 240 minutes after thawing. Our results showed that GSH and AA significantly improved boar sperm cryotolerance, especially when supplemented together to both freezing and thawing media. This improvement was observed in sperm viability and acrosome integrity, sperm motility, and nucleoprotein structure. Although ROS levels were not much increased by freeze-thawing procedures, the addition of GSH and AA to both freezing and thawing extenders significantly decreased intracellular peroxide levels.

Advanced data deduplication techniques and their application

Data deduplication describes a class of approaches that reduce the storage capacity needed to store data or the amount of data that has to be transferred over a network. These approaches detect coarse-grained redundancies within a data set, e.g. a file system, and remove them.rnrnOne of the most important applications of data deduplication are backup storage systems where these approaches are able to reduce the storage requirements to a small fraction of the logical backup data size.rnThis thesis introduces multiple new extensions of so-called fingerprinting-based data deduplication. It starts with the presentation of a novel system design, which allows using a cluster of servers to perform exact data deduplication with small chunks in a scalable way.rnrnAfterwards, a combination of compression approaches for an important, but often over- looked, data structure in data deduplication systems, so called block and file recipes, is introduced. Using these compression approaches that exploit unique properties of data deduplication systems, the size of these recipes can be reduced by more than 92% in all investigated data sets. As file recipes can occupy a significant fraction of the overall storage capacity of data deduplication systems, the compression enables significant savings.rnrnA technique to increase the write throughput of data deduplication systems, based on the aforementioned block and file recipes, is introduced next. The novel Block Locality Caching (BLC) uses properties of block and file recipes to overcome the chunk lookup disk bottleneck of data deduplication systems. This chunk lookup disk bottleneck either limits the scalability or the throughput of data deduplication systems. The presented BLC overcomes the disk bottleneck more efficiently than existing approaches. Furthermore, it is shown that it is less prone to aging effects.rnrnFinally, it is investigated if large HPC storage systems inhibit redundancies that can be found by fingerprinting-based data deduplication. Over 3 PB of HPC storage data from different data sets have been analyzed. In most data sets, between 20 and 30% of the data can be classified as redundant. According to these results, future work in HPC storage systems should further investigate how data deduplication can be integrated into future HPC storage systems.rnrnThis thesis presents important novel work in different area of data deduplication re- search.

Evaluation of a cloud infrastructure for the CMS distributed data analysis in the top quark sector at the LHC

Nella fisica delle particelle, onde poter effettuare analisi dati, è necessario disporre di una grande capacità di calcolo e di storage. LHC Computing Grid è una infrastruttura di calcolo su scala globale e al tempo stesso un insieme di servizi, sviluppati da una grande comunità di fisici e informatici, distribuita in centri di calcolo sparsi in tutto il mondo. Questa infrastruttura ha dimostrato il suo valore per quanto riguarda l'analisi dei dati raccolti durante il Run-1 di LHC, svolgendo un ruolo fondamentale nella scoperta del bosone di Higgs. Oggi il Cloud computing sta emergendo come un nuovo paradigma di calcolo per accedere a grandi quantità di risorse condivise da numerose comunità scientifiche. Date le specifiche tecniche necessarie per il Run-2 (e successivi) di LHC, la comunità scientifica è interessata a contribuire allo sviluppo di tecnologie Cloud e verificare se queste possano fornire un approccio complementare, oppure anche costituire una valida alternativa, alle soluzioni tecnologiche esistenti. Lo scopo di questa tesi è di testare un'infrastruttura Cloud e confrontare le sue prestazioni alla LHC Computing Grid. Il Capitolo 1 contiene un resoconto generale del Modello Standard. Nel Capitolo 2 si descrive l'acceleratore LHC e gli esperimenti che operano a tale acceleratore, con particolare attenzione all’esperimento CMS. Nel Capitolo 3 viene trattato il Computing nella fisica delle alte energie e vengono esaminati i paradigmi Grid e Cloud. Il Capitolo 4, ultimo del presente elaborato, riporta i risultati del mio lavoro inerente l'analisi comparata delle prestazioni di Grid e Cloud.

LoneStar : Design and evaluation of an energy-efficient, disk-based archival storage system

Bandlaufwerke waren bisher die vorherrschende Technologie, um die anfallenden Datenmengen in Archivsystemen zu speichern. Mit Zugriffsmustern, die immer aktiver werden, und Speichermedien wie Festplatten die kostenmäßig aufholen, muss die Architektur vor Speichersystemen zur Archivierung neu überdacht werden. Zuverlässigkeit, Integrität und Haltbarkeit sind die Haupteigenschaften der digitalen Archivierung. Allerdings nimmt auch die Zugriffsgeschwindigkeit einen erhöhten Stellenwert ein, wenn aktive Archive ihre gesamten Inhalte für den direkten Zugriff bereitstellen. Ein band-basiertes System kann die hierfür benötigte Parallelität, Latenz und Durchsatz nicht liefern, was in der Regel durch festplattenbasierte Systeme als Zwischenspeicher kompensiert wird.rnIn dieser Arbeit untersuchen wir die Herausforderungen und Möglichkeiten ein festplattenbasiertes Speichersystem zu entwickeln, das auf eine hohe Zuverlässigkeit und Energieeffizienz zielt und das sich sowohl für aktive als auch für kalte Archivumgebungen eignet. Zuerst analysieren wir die Speichersysteme und Zugriffsmuster eines großen digitalen Archivs und präsentieren damit ein mögliches Einsatzgebiet für unsere Architektur. Daraufhin stellen wir Mechanismen vor um die Zuverlässigkeit einer einzelnen Festplatte zu verbessern und präsentieren sowie evaluieren einen neuen, energieeffizienten, zwei- dimensionalen RAID Ansatz der für „Schreibe ein Mal, lese mehrfach“ Zugriffe optimiert ist. Letztlich stellen wir Protokollierungs- und Zwischenspeichermechanismen vor, die die zugrundeliegenden Ziele unterstützen und evaluieren das RAID System in einer Dateisystemumgebung.

Studi di data popularity nell'analisi distribuita su Grid dell'esperimento CMS a LHC

L’esperimento CMS a LHC ha raccolto ingenti moli di dati durante Run-1, e sta sfruttando il periodo di shutdown (LS1) per evolvere il proprio sistema di calcolo. Tra i possibili miglioramenti al sistema, emergono ampi margini di ottimizzazione nell’uso dello storage ai centri di calcolo di livello Tier-2, che rappresentano - in Worldwide LHC Computing Grid (WLCG)- il fulcro delle risorse dedicate all’analisi distribuita su Grid. In questa tesi viene affrontato uno studio della popolarità dei dati di CMS nell’analisi distribuita su Grid ai Tier-2. Obiettivo del lavoro è dotare il sistema di calcolo di CMS di un sistema per valutare sistematicamente l’ammontare di spazio disco scritto ma non acceduto ai centri Tier-2, contribuendo alla costruzione di un sistema evoluto di data management dinamico che sappia adattarsi elasticamente alle diversi condizioni operative - rimuovendo repliche dei dati non necessarie o aggiungendo repliche dei dati più “popolari” - e dunque, in ultima analisi, che possa aumentare l’“analysis throughput” complessivo. Il Capitolo 1 fornisce una panoramica dell’esperimento CMS a LHC. Il Capitolo 2 descrive il CMS Computing Model nelle sue generalità, focalizzando la sua attenzione principalmente sul data management e sulle infrastrutture ad esso connesse. Il Capitolo 3 descrive il CMS Popularity Service, fornendo una visione d’insieme sui servizi di data popularity già presenti in CMS prima dell’inizio di questo lavoro. Il Capitolo 4 descrive l’architettura del toolkit sviluppato per questa tesi, ponendo le basi per il Capitolo successivo. Il Capitolo 5 presenta e discute gli studi di data popularity condotti sui dati raccolti attraverso l’infrastruttura precedentemente sviluppata. L’appendice A raccoglie due esempi di codice creato per gestire il toolkit attra- verso cui si raccolgono ed elaborano i dati.

Online Stream Processing di Big Data su Apache Storm per Applicazioni di Instant Coupon

Big data è il termine usato per descrivere una raccolta di dati così estesa in termini di volume,velocità e varietà da richiedere tecnologie e metodi analitici specifici per l'estrazione di valori significativi. Molti sistemi sono sempre più costituiti e caratterizzati da enormi moli di dati da gestire,originati da sorgenti altamente eterogenee e con formati altamente differenziati,oltre a qualità dei dati estremamente eterogenei. Un altro requisito in questi sistemi potrebbe essere il fattore temporale: sempre più sistemi hanno bisogno di ricevere dati significativi dai Big Data il prima possibile,e sempre più spesso l’input da gestire è rappresentato da uno stream di informazioni continuo. In questo campo si inseriscono delle soluzioni specifiche per questi casi chiamati Online Stream Processing. L’obiettivo di questa tesi è di proporre un prototipo funzionante che elabori dati di Instant Coupon provenienti da diverse fonti con diversi formati e protocolli di informazioni e trasmissione e che memorizzi i dati elaborati in maniera efficiente per avere delle risposte in tempo reale. Le fonti di informazione possono essere di due tipologie: XMPP e Eddystone. Il sistema una volta ricevute le informazioni in ingresso, estrapola ed elabora codeste fino ad avere dati significativi che possono essere utilizzati da terze parti. Lo storage di questi dati è fatto su Apache Cassandra. Il problema più grosso che si è dovuto risolvere riguarda il fatto che Apache Storm non prevede il ribilanciamento delle risorse in maniera automatica, in questo caso specifico però la distribuzione dei clienti durante la giornata è molto varia e ricca di picchi. Il sistema interno di ribilanciamento sfrutta tecnologie innovative come le metriche e sulla base del throughput e della latenza esecutiva decide se aumentare/diminuire il numero di risorse o semplicemente non fare niente se le statistiche sono all’interno dei valori di soglia voluti.