Analysis and visualization of chromosome information

This paper analyzes the DNA code of several species in the perspective of information content. For that purpose several concepts and mathematical tools are selected towards establishing a quantitative method without a priori distorting the alphabet represented by the sequence of DNA bases. The synergies of associating Gray code, histogram characterization and multidimensional scaling visualization lead to a collection of plots with a categorical representation of species and chromosomes.

Can power laws help us understand gene and proteome information?

Proteins are biochemical entities consisting of one or more blocks typically folded in a 3D pattern. Each block (a polypeptide) is a single linear sequence of amino acids that are biochemically bonded together. The amino acid sequence in a protein is defined by the sequence of a gene or several genes encoded in the DNA-based genetic code. This genetic code typically uses twenty amino acids, but in certain organisms the genetic code can also include two other amino acids. After linking the amino acids during protein synthesis, each amino acid becomes a residue in a protein, which is then chemically modified, ultimately changing and defining the protein function. In this study, the authors analyze the amino acid sequence using alignment-free methods, aiming to identify structural patterns in sets of proteins and in the proteome, without any other previous assumptions. The paper starts by analyzing amino acid sequence data by means of histograms using fixed length amino acid words (tuples). After creating the initial relative frequency histograms, they are transformed and processed in order to generate quantitative results for information extraction and graphical visualization. Selected samples from two reference datasets are used, and results reveal that the proposed method is able to generate relevant outputs in accordance with current scientific knowledge in domains like protein sequence/proteome analysis.

European information users: topics from a comparative analysis within the European Union

Purpose – The aim of this article is to present some results from research undertaken into the information behaviour of European Documentation Centre (EDC) users. It will reflect on the practices of a group of 234 users of 55 EDCs covering 21 Member States of the European Union (EU), used to access European information. Design/methodology/approach – In order to collect the data presented here, five questionnaires were sent to users in all the EDCs in Finland, Ireland, Hungary and Portugal. In the remaining EU countries, five questionnaires were sent to two EDCs chosen at random. The questionnaires were sent by post, following telephone contact with the EDC managers. Findings – Factors determining access to information on the European Union and the frequency of this access are identified. The information providers most commonly used to access European information and the information sources considered the most reliable by respondents will also be analysed. Another area of analysis concerns the factors cited by respondents as facilitating access to information on Europe or, conversely, making it more difficult to access. Parallel to this, the aspects of accessing information on EU that are valued most by users will also be assessed. Research limitations/implications – Questionnaires had to be used, as the intention was to cover a very extensive geographical area. However, in opting for closed questions, it is acknowledged that standard responses have been obtained with no scope for capturing the individual circumstances of each respondent, thus making a qualitative approach difficult. Practical implications – The results provide an overall picture of certain aspects of the information behaviour of EDC users. They may serve as a starting point for planning training sessions designed to develop the skills required to search, access, evaluate and apply European information within an academic context. From a broader perspective, they also constitute factors which the European Commission should take into consideration when formulating its information and communication policy. Originality/value – This is the first piece of academic research into the EDCs and their users, which aimed to cover all Members State of the EU.

Group decision making and Quality-of-information in e-Health systems

Knowledge is central to the modern economy and society. Indeed, the knowledge society has transformed the concept of knowledge and is more and more aware of the need to overcome the lack of knowledge when has to make options or address its problems and dilemmas. One’s knowledge is less based on exact facts and more on hypotheses, perceptions or indications. Even when we use new computational artefacts and novel methodologies for problem solving, like the use of Group Decision Support Systems (GDSSs), the question of incomplete information is in most of the situations marginalized. On the other hand, common sense tells us that when a decision is made it is impossible to have a perception of all the information involved and the nature of its intrinsic quality. Therefore, something has to be made in terms of the information available and the process of its evaluation. It is under this framework that a Multi-valued Extended Logic Programming language will be used for knowledge representation and reasoning, leading to a model that embodies the Quality-of-Information (QoI) and its quantification, along the several stages of the decision-making process. In this way, it is possible to provide a measure of the value of the QoI that supports the decision itself. This model will be here presented in the context of a GDSS for VirtualECare, a system aimed at sustaining online healthcare services.

Side information creation for efficient Wyner-Ziv video coding: Classifying and reviewing

Video coding technologies have played a major role in the explosion of large market digital video applications and services. In this context, the very popular MPEG-x and H-26x video coding standards adopted a predictive coding paradigm, where complex encoders exploit the data redundancy and irrelevancy to 'control' much simpler decoders. This codec paradigm fits well applications and services such as digital television and video storage where the decoder complexity is critical, but does not match well the requirements of emerging applications such as visual sensor networks where the encoder complexity is more critical. The Slepian Wolf and Wyner-Ziv theorems brought the possibility to develop the so-called Wyner-Ziv video codecs, following a different coding paradigm where it is the task of the decoder, and not anymore of the encoder, to (fully or partly) exploit the video redundancy. Theoretically, Wyner-Ziv video coding does not incur in any compression performance penalty regarding the more traditional predictive coding paradigm (at least for certain conditions). In the context of Wyner-Ziv video codecs, the so-called side information, which is a decoder estimate of the original frame to code, plays a critical role in the overall compression performance. For this reason, much research effort has been invested in the past decade to develop increasingly more efficient side information creation methods. This paper has the main objective to review and evaluate the available side information methods after proposing a classification taxonomy to guide this review, allowing to achieve more solid conclusions and better identify the next relevant research challenges. After classifying the side information creation methods into four classes, notably guess, try, hint and learn, the review of the most important techniques in each class and the evaluation of some of them leads to the important conclusion that the side information creation methods provide better rate-distortion (RD) performance depending on the amount of temporal correlation in each video sequence. It became also clear that the best available Wyner-Ziv video coding solutions are almost systematically based on the learn approach. The best solutions are already able to systematically outperform the H.264/AVC Intra, and also the H.264/AVC zero-motion standard solutions for specific types of content. (C) 2013 Elsevier B.V. All rights reserved.

Optimization, high availability and redundancy in information communications and technology using networks and systems virtualization architectures

Mestrado em Engenharia Informática

A denoising approach for iterative side information creation in distributed video coding

In distributed video coding, motion estimation is typically performed at the decoder to generate the side information, increasing the decoder complexity while providing low complexity encoding in comparison with predictive video coding. Motion estimation can be performed once to create the side information or several times to refine the side information quality along the decoding process. In this paper, motion estimation is performed at the decoder side to generate multiple side information hypotheses which are adaptively and dynamically combined, whenever additional decoded information is available. The proposed iterative side information creation algorithm is inspired in video denoising filters and requires some statistics of the virtual channel between each side information hypothesis and the original data. With the proposed denoising algorithm for side information creation, a RD performance gain up to 1.2 dB is obtained for the same bitrate.

Analysis and visualization of seismic data using mutual information

Seismic data is difficult to analyze and classical mathematical tools reveal strong limitations in exposing hidden relationships between earthquakes. In this paper, we study earthquake phenomena in the perspective of complex systems. Global seismic data, covering the period from 1962 up to 2011 is analyzed. The events, characterized by their magnitude, geographic location and time of occurrence, are divided into groups, either according to the Flinn-Engdahl (F-E) seismic regions of Earth or using a rectangular grid based in latitude and longitude coordinates. Two methods of analysis are considered and compared in this study. In a first method, the distributions of magnitudes are approximated by Gutenberg-Richter (G-R) distributions and the parameters used to reveal the relationships among regions. In the second method, the mutual information is calculated and adopted as a measure of similarity between regions. In both cases, using clustering analysis, visualization maps are generated, providing an intuitive and useful representation of the complex relationships that are present among seismic data. Such relationships might not be perceived on classical geographic maps. Therefore, the generated charts are a valid alternative to other visualization tools, for understanding the global behavior of earthquakes.

Influence of network effects on the diffusion of information systems: the case of open source

Doutoramento em Gestão

Need for, demand for, and use of European Union information

The discussion and analysis of the diverse outreach activities in this article provide guidance and suggestions for academic librarians who are interested in outreach and community engagement of any scale and nature. Cases are draw from a wide spectrum and are particularly strong in the setting of large academic libraries, special collections and programming for multicultural populations. The aim of this study is to present the results of research carried out regarding the needs, demand and consumption of European Union information by users in European Documentation Centres (EDC). A quantitative methodology was chosen based on a questionnaire with 24 items. This questionnaire was distributed within the EDC of Salamanca, Spain, and the EDC of Porto, Portugal, during specific time intervals between 2010 and 2011. We examined the level of EU information that EDC users possess, and identified the factors that facilitate or hinder access to EU information, the topics most demanded, and the types of documents consulted. Analysis was made of the use that the consumer of European information makes of databases and their behaviour during the consultation. Although the sample used was not very significant owing to its small size, it is a faithful reflection of the scarce visits made to EDCs. This study can be of use to managers of EDCs, providing them with better knowledge of the information needs and demands of their users. Ultimately this should lead to improvements in the services offered. The study lies within a frame of research scarcely addressed in specialized scholarly literature: European Union information.

James W. Carey as critical theorist of the information age

This paper suggests that the thought of the North-American critical theorist James W. Carey provides a relevant perspective on communication and technology. Having as background American social pragmatism and progressive thinkers of the beginning of the 20th century (as Dewey, Mead, Cooley, and Park), Carey built a perspective that brought together the political economy of Harold A. Innis, the social criticism of David Riesman and Charles W. Mills and incorporated Marxist topics such as commodification and sociocultural domination. The main goal of this paper is to explore the connection established by Carey between modern technological communication and what he called the “transmissive model”, a model which not only reduces the symbolic process of communication to instrumentalization and to information delivery, but also politically converges with capitalism as well as power, control and expansionist goals. Conceiving communication as a process that creates symbolic and cultural systems, in which and through which social life takes place, Carey gives equal emphasis to the incorporation processes of communication.If symbolic forms and culture are ways of conditioning action, they are also influenced by technological and economic materializations of symbolic systems, and by other conditioning structures. In Carey’s view, communication is never a disembodied force; rather, it is a set of practices in which co-exist conceptions, techniques and social relations. These practices configure reality or, alternatively, can refute, transform and celebrate it. Exhibiting sensitiveness favourable to the historical understanding of communication, media and information technologies, one of the issues Carey explored most was the history of the telegraph as an harbinger of the Internet, of its problems and contradictions. For Carey, Internet was seen as the contemporary heir of the communications revolution triggered by the prototype of transmission technologies, namely the telegraph in the 19th century. In the telegraph Carey saw the prototype of many subsequent commercial empires based on science and technology, a pioneer model for complex business management; an example of conflict of interest for the control over patents; an inducer of changes both in language and in structures of knowledge; and a promoter of a futurist and utopian thought of information technologies. After a brief approach to Carey’s communication theory, this paper focuses on his seminal essay "Technology and ideology. The case of the telegraph", bearing in mind the prospect of the communication revolution introduced by Internet. We maintain that this essay has seminal relevance for critically studying the information society. Our reading of it highlights the reach, as well as the problems, of an approach which conceives the innovation of the telegraph as a metaphor for all innovations, announcing the modern stage of history and determining to this day the major lines of development in modern communication systems.

The cross crypto scheme cipher integration for securing SCADA component communication

Critical Infrastructures became more vulnerable to attacks from adversaries as SCADA systems become connected to the Internet. The open standards for SCADA Communications make it very easy for attackers to gain in-depth knowledge about the working and operations of SCADA networks. A number of Intenrnet SCADA security issues were raised that have compromised the authenticity, confidentiality, integrity and non-repudiation of information transfer between SCADA Components. This paper presents an integration of the Cross Crypto Scheme Cipher to secure communications for SCADA components. The proposed scheme integrates both the best features of symmetric and asymmetric encryptiontechniques. It also utilizes the MD5 hashing algorithm to ensure the integrity of information being transmitted.

Use of negative information in positioning and tracking algorithms

To avoid additional hardware deployment, indoor localization systems have to be designed in such a way that they rely on existing infrastructure only. Besides the processing of measurements between nodes, localization procedure can include the information of all available environment information. In order to enhance the performance of Wi-Fi based localization systems, the innovative solution presented in this paper considers also the negative information. An indoor tracking method inspired by Kalman filtering is also proposed.

Access and use of european information: a comparative analysis

This paper presents some results of a survey on access to European information among a group of 234 users of 55 European Documentation Centres (EDCs), from 21 European Union (EU) Member-States. The findings of the questionnaire made to 88 EDCs' managers, from 26 EU Member-States, will also be analyse. Two different points of view regarding issues related to reasons to access European information, the valued aspects during that access and the use of European databases will be compare.

The use of information and interactive processes in growth management

Tese de doutoramento em Engenharia do Ambiente, especialidade em Sistemas Sociais