Análise de repetições em dados biológicos

The decoding of the genomes has created new challenges on the scientific community linked to the area of computation and information technologies. Daily, new data is added to numerous databases with billions of records, coming from more advanced equipment, helping in decoding the genomes. Determine how important and relevant are these data in order to find value-added information and obviously turn them into knowledge,is the main challenge for the bioinformatics research community. The analysis of genomes and proteomes of several organisms allow us to observe the behaviour at the evolution of species. In this study, our focus goes to a particular aspect of this analysis: the repetition of some codons and their amino acids inside several orthologous genes in eukaryotic organisms. Belonging to different stages of evolution, the main objective focuses on achieving results on the evolution of these repetitions over millions of years. We now know that these repetitions in humans are the source of several neurodegenerative diseases among others. This analysis will verify the conservation or repression, of these repetitions throughout the process of speciation as well at the level of relationship that may exist between these repetitions and those diseases. For this study we have developed an algorithm for A descodificação dos genomas veio criar novos desafios na comunidade científica ligada à área da computação e da informática. Diariamente são alimentadas inúmeras bases de dados com biliões de registos provenientes de equipamentos cada vez mais evoluídos, que auxiliam na descodificação dos genomas. Determinar o quão importante e relevante são esses dados, de forma a retirar valor acrescentado – informação, e obviamente transformá-los em conhecimento, é o grande desafio actual para a comunidade de investigadores de bioinformática. A análise de genomas, bem como dos proteomas dos vários organismos permitem-nos observar o comportamento ao nível da evolução das espécies. Neste estudo focamos a atenção num aspecto particular dessa análise: as repetições de determinados codões e dos respectivos aminoácidos nos vários organismos eucariotas, especificamente em genes ortólogos. Pertencente a várias fases da evolução das espécies, o objectivo principal centra-se na obtenção de resultados quanto à evolução dessas repetições ao longo de milhões de anos. Sabemos hoje que essas repetições no ser humano são a causa de diversas doenças neuro-degenerativas, entre outras, pelo que esta análise permitirá verificar o estado de conservação ou repressão, dessas repetições ao longo do processo de especiação, bem como ao nível do relacionamento que poderá existir entre essas repetições e as doenças nos seres superiormente evoluídos. Para este estudo foi desenvolvido um algoritmo de detecção de padrões de repetição, que possibilita uma análise detalhada da localização de uma determinada sequência, bem como das sequências que melhor se ajustam ao padrão de repetição inicial.Centro de Estudos em Educação, Tecnologias e Saúd

Análise de repetições em dados biológicos

The decoding of the genomes has created new challenges on the scientific community linked to the area of computation and information technologies. Daily, new data is added to numerous databases with billions of records, coming from more advanced equipment, helping in decoding the genomes. Determine how important and relevant are these data in order to find value-added information and obviously turn them into knowledge,is the main challenge for the bioinformatics research community. The analysis of genomes and proteomes of several organisms allow us to observe the behaviour at the evolution of species. In this study, our focus goes to a particular aspect of this analysis: the repetition of some codons and their amino acids inside several orthologous genes in eukaryotic organisms. Belonging to different stages of evolution, the main objective focuses on achieving results on the evolution of these repetitions over millions of years. We now know that these repetitions in humans are the source of several neurodegenerative diseases among others. This analysis will verify the conservation or repression, of these repetitions throughout the process of speciation as well at the level of relationship that may exist between these repetitions and those diseases. For this study we have developed an algorithm for A descodificação dos genomas veio criar novos desafios na comunidade científica ligada à área da computação e da informática. Diariamente são alimentadas inúmeras bases de dados com biliões de registos provenientes de equipamentos cada vez mais evoluídos, que auxiliam na descodificação dos genomas. Determinar o quão importante e relevante são esses dados, de forma a retirar valor acrescentado – informação, e obviamente transformá-los em conhecimento, é o grande desafio actual para a comunidade de investigadores de bioinformática. A análise de genomas, bem como dos proteomas dos vários organismos permitem-nos observar o comportamento ao nível da evolução das espécies. Neste estudo focamos a atenção num aspecto particular dessa análise: as repetições de determinados codões e dos respectivos aminoácidos nos vários organismos eucariotas, especificamente em genes ortólogos. Pertencente a várias fases da evolução das espécies, o objectivo principal centra-se na obtenção de resultados quanto à evolução dessas repetições ao longo de milhões de anos. Sabemos hoje que essas repetições no ser humano são a causa de diversas doenças neuro-degenerativas, entre outras, pelo que esta análise permitirá verificar o estado de conservação ou repressão, dessas repetições ao longo do processo de especiação, bem como ao nível do relacionamento que poderá existir entre essas repetições e as doenças nos seres superiormente evoluídos. Para este estudo foi desenvolvido um algoritmo de detecção de padrões de repetição, que possibilita uma análise detalhada da localização de uma determinada sequência, bem como das sequências que melhor se ajustam ao padrão de repetição inicial.Centro de Estudos em Educação, Tecnologias e Saúd

GeneBrowser 2: an application to explore and identify common biological traits in a set of genes

<p>Abstract</p> <p>Background</p> <p>The development of high-throughput laboratory techniques created a demand for computer-assisted result analysis tools. Many of these techniques return lists of genes whose interpretation requires finding relevant biological roles for the problem at hand. The required information is typically available in public databases, and usually, this information must be manually retrieved to complement the analysis. This process is a very time-consuming task that should be automated as much as possible.</p> <p>Results</p> <p>GeneBrowser is a web-based tool that, for a given list of genes, combines data from several public databases with visualisation and analysis methods to help identify the most relevant and common biological characteristics. The functionalities provided include the following: a central point with the most relevant biological information for each inserted gene; a list of the most related papers in PubMed and gene expression studies in ArrayExpress; and an extended approach to functional analysis applied to Gene Ontology, homologies, gene chromosomal localisation and pathways.</p> <p>Conclusions</p> <p>GeneBrowser provides a unique entry point to several visualisation and analysis methods, providing fast and easy analysis of a set of genes. GeneBrowser fills the gap between Web portals that analyse one gene at a time and functional analysis tools that are limited in scope and usually desktop-based.</p

Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays

<p>Abstract</p> <p>Background</p> <p>Current commercial high-density oligonucleotide microarrays can hold millions of probe spots on a single microscopic glass slide and are ideal for studying the transcriptome of microbial genomes using a tiling probe design. This paper describes a comprehensive computational pipeline implemented specifically for designing tiling probe sets to study microbial transcriptome profiles.</p> <p>Results</p> <p>The pipeline identifies every possible probe sequence from both forward and reverse-complement strands of all DNA sequences in the target genome including circular or linear chromosomes and plasmids. Final probe sequence lengths are adjusted based on the maximal oligonucleotide synthesis cycles and best isothermality allowed. Optimal probes are then selected in two stages - sequential and gap-filling. In the sequential stage, probes are selected from sequence windows tiled alongside the genome. In the gap-filling stage, additional probes are selected from the largest gaps between adjacent probes that have already been selected, until a predefined number of probes is reached. Selection of the highest quality probe within each window and gap is based on five criteria: sequence uniqueness, probe self-annealing, melting temperature, oligonucleotide length, and probe position.</p> <p>Conclusions</p> <p>The probe selection pipeline evaluates global and local probe sequence properties and selects a set of probes dynamically and evenly distributed along the target genome. Unique to other similar methods, an exact number of non-redundant probes can be designed to utilize all the available probe spots on any chosen microarray platform. The pipeline can be applied to microbial genomes when designing high-density tiling arrays for comparative genomics, ChIP chip, gene expression and comprehensive transcriptome studies.</p

Comparative study of classification algorithms using molecular descriptors in toxicological databases

The rational development of new drugs is a complex and expensive process, comprising several steps. Typically, it starts by screening databases of small organic molecules for chemical structures with potential of binding to a target receptor and prioritizing the most promising ones. Only a few of these will be selected for biological evaluation and further refinement through chemical synthesis. Despite the accumulated knowledge by pharmaceutical companies that continually improve the process of finding new drugs, a myriad of factors affect the activity of putative candidate molecules in vivo and the propensity for causing adverse and toxic effects is recognized as the major hurdle behind the current "target-rich, lead-poor" scenario. In this study we evaluate the use of several Machine Learning algorithms to find useful rules to the elucidation and prediction of toxicity using ID and 2D molecular descriptors. The results indicate that: i) Machine Learning algorithms can effectively use ID molecular descriptors to construct accurate and simple models; ii) extending the set of descriptors to include 2D descriptors improve the accuracy of the models

An improved resource allocation scheme for WiMAX using channel information

In recent years, tremendous progress has been made in wireless communication systems to provide wireless coverage to end users at different data rates. WiMAX technology provides wireless broadband access over an extended coverage area in both fixed and mobility environments. Most of the existing resource allocation schemes allocate resources based on respective service class of the incoming users’ requests. However, due to variation in channel conditions, user mobility and diverse resource requirements QoS based resource allocation either results in over or under utilization of allocated resources. Therefore, resource allocation is a challenging task in WiMAX. This research proposes an improved resource management mechanism that performs resource allocation by taking into consideration not only the user service class but also the respective channel status. Based on these two parameters, this research aims to achieve improved resource allocation in terms of resource utilization, fairness and network throughput. First, a Channel Based Resource Allocation scheme is introduced where priority in resource allocation is given to users’ requests with relatively higher service classes and better channel status. To maintain fairness in resource allocation process, a Fair Resource Allocation Based Service mechanism is developed where priority is given to users’ requests having less additional resources demand. Finally, to improve throughput of the network, a Channel Based Throughput Improvement approach is proposed which dynamically selects a threshold level of channel gain based on individual channel gain of users. During resource allocation process, users above the threshold level are selected for resource allocation such that priority is given to users with high channel gain. Different simulation scenario results reveal an overall improved resource utilization from 87% to 91% and the throughput improves up to 15% when compared to existing schemes. In conclusion the performance of resource utilization is improved if channel status is considered as an input parameter

Development of biomechatronic devices for measurement of wrenches occuring in animal and human prehension

Biomechatronics and in its context biosensors dedicate their ability to support new applications inspired from nature on automotive, exoskeleton systems, and intelligent robotics, with a combination of technical knowledge, biology, bionics and mechatronics. There is a market trend towards the use of intelligent sensors. The main reasons for this development are increased measurement accuracy, programmability, decreased inventory cost from the larger turndown available, and decreased maintenance costs by self­diagnostics. On the other hand, for climbing machines biomechatronics discovered important descriptive models of animal locomotion, in which each gross aspect of the animal’s movement is biologically clearly defined except grasping (cf. No. 10 of this book series). Adaptable and ergonomic grips used in cars need a deep and vast supportive knowledge about human grasping. This knowledge only can be won by experimentation in natural prehension. Hands and fingers have to be mapped through sensors to discover and understand the principles of manipulation. We propose a special design of sensor nodes to measure forces and torques in manipulation. Self-evidently, sensor technology should as well be oriented to the fulfillment of the requirements of new applications in industry. It is our deep desire that the sensor proposed finds a place in industrial and automotive applications.Biomechatronik und speziell Biosensoren unterstützen auf der Grundlage biologischer Inspiration das Entstehen neuer Anwendungen in der ganzen Spanne vom Fahrzeugbau bis zur Bio­Robotik. Dabei werden Mechatronik, technologisches Wissen, Bionik und Biologie miteinander kombiniert. “There is a market trend towards the use of intelligent sensors. In the past the main reasons for this have been increased measurement accuracy, programmability, decreased inventory cost from the larger turndown available, and a decreased maintenance cost for self­ diagnostics.” (Expertise,1997). Im speziellen Anwendungsfall der Kletterrobotik erlaubt der Einsatz von biokompatiblen Kraftgrößen­Sensoren die Etablierung dynamischer Modelle der Fortbewegung von Tieren als bionische Basis biologischer Inspiration. Ergonomische Gestaltung von Griffen bedarf fundierter Kenntnisse über die vektoriellen Greifkräfte. Im Rahmen dieser Arbeit wurden daher miniaturisierte 6 DOF­Kraftgrößensensoren entwickelt, die als aktive Knoten eines Sensor­Netzwerks firmieren können. Multisensorenanwendungen können die räumliche und zeitliche Auflösung eines Messaufbaus deutlich steigern. “Durch die Verknüpfung der Signale mehrerer Sensoren lassen sich die Zuverlässigkeit und der Anwendungsbereich vergrößern und die Signalqualität deutlich steigern. Neben einer Verbesserung der Signalqualität ergeben sich durch die Nutzung der in der Steuerung vorhanden Positions­ und Richtungsinformation neue Anwendungen“ (Adam, 2000). Dabei wird in der vorgelegten Arbeit Wert auf eine Detaillierung der Darstellung des Entwurfsprozesses gelegt, um in Zeiten fragmentierten Publizierens durch Dokumentation an einem Orte verallgemeinerbares Erfahrungswissen für die Entwicklung biokompatibler Kraftgrößensensoren zu sichern.Biomechatronics and biosensors dedicate their ability to support new applications inspired from nature on automotive, exoskeleton systems (Hwang & Moo, 2009), intelligent humanoid robots (Wu & Wu, 2010) and robotics (Qiakang Liang, 2010), with a combination of technical knowledge, biology, bionics and mechatronics. “There is a market trend towards the use of intelligent sensors. In the past the main reasons for this have been increased measurement accuracy, programmability, decreased inventory cost from the larger turndown available, and a decreased maintenance cost for self­ diagnostics.” (Expertise,1997). On the other hand, for climbing machines (Mämpel, Koch & Köhring, 2009) biomechatronics discovers important descriptive models of locomotion of monkeys, rats or chameleons in which each aspect of the animal’s movement is clearly defined (Witte, Lutherdt & Schilling, 2004). Adaptable and ergonomic grips used in cars, motorcycles and trains need a deep and vast supportive knowledge from human grasping. This knowledge cannot be won without the help of experimentation in animal and human prehension to produce enough evidence and valid data about the biological structures (Jeffrey, 2008). Hands and fingers will be mapped through sensors to discover and understand the principles of animal manipulation. This work explains a methodology for designing and construction of sensor nodes to measure forces and torques from animal or human manipulation in order to increase the spatial resolution and the precision of the measurement (Multisensorenanwendung). “Durch die Verknüpfung der Signale mehrerer Sensoren lassen sich die Zuverlässigkeit und der Anwendungsbereich vergrößern und die Signalqualität deutlich steigern. Neben einer Verbesserung der Signalqualität ergeben sich durch die Nutzung der in der Steuerung vorhanden Positions­ und Richtungsinformation neue Anwendungen“ (Adam, 2000). Sensor technology should be oriented to the fulfillment of the requirements of new applications in industry (Singh, 2004), and probably be based on a science oriented to market. It is our deep desire that this sensor finds a place in industrial and automotive applications (D'Ascoli, Tonarelli, & Melani, 2005)

Fabrication and optical properties of periodic long range order nanoholes on metallic films

Long range order periodic structures of subwavelength apertures on optically thick metallic films have been investigated for their anomalous optical properties. Light transmission through an array of nanoholes is surprisingly higher than the prediction of the classical diffraction theorem and there is a consensus that this would be attributed to the excitation of the surface plasmon modes, a collective oscillation of the electrons on the surface of the metal due to interaction with the incident electromagnetic field. Long-range-order nanoholes array systems, contrarily to the more commonly studied short range structures, would provide several distinct advantages but the challenging fabrication process for these systems would be a major obstacle to overcome for their realization. In this thesis, it has been shown that for the long range order nanostructures of nanoholes array the spectrum of the transmitted light through the holes still showed the signature of the maxima and minima found in the transmitted spectrum for short range order systems. Experimental analysis of the spectra of these structures is however greatly simplified due to the increased total light transmission. One of the important applications of these structures is biosensing. The theoretical calculations showed that the higher flux of energy through the long range order periodic structures potentially increases the sensitivity of the biosensors based on the extraordinary optical transmission phenomenon. Two lithographic techniques based respectively on Electron Beam Lithography (EBL) and Nanospheres Lithography (NSL) for the fabrication of long range nanohole structures have been introduced. Spectra analysis of the structures by numerical calculations based on the 3 Dimensional Finite Difference Time Domain (3-D FDTD) reveals that the primitive model of momentum matching is not sufficiently accurate to predict the transmission spectra features and hence should not be relied on as a design tool. Instead, the transmitted spectra are interpreted as resulting from a combination of scattering and resonance modes, namely localized surface plasmons resonance, Wood anomalies and Surface Plasmon Polaritons modes

Wireless remote patient monitoring on general hospital wards.

A novel approach which has potential to improve quality of patient care on general hospital wards is proposed. Patient care is a labour-intensive task that requires high input of human resources. A Remote Patient Monitoring (RPM) system is proposed which can go some way towards improving patient monitoring on general hospital wards. In this system vital signs are gathered from patients and sent to a control unit for centralized monitoring. The RPM system can complement the role of nurses in monitoring patients’ vital signs. They will be able to focus on holistic needs of patients thereby providing better personal care. Wireless network technologies, ZigBee and Wi-Fi, are utilized for transmission of vital signs in the proposed RPM system. They provide flexibility and mobility to patients. A prototype system for RPM is designed and simulated. The results illustrated the capability, suitability and limitation of the chosen technology