Histogram-based DNA analysis for the visualization of chromosome, genome and species information

We describe a novel approach to explore DNA nucleotide sequence data, aiming to produce high-level categorical and structural information about the underlying chromosomes, genomes and species. The article starts by analyzing chromosomal data through histograms using fixed length DNA sequences. After creating the DNA-related histograms, a correlation between pairs of histograms is computed, producing a global correlation matrix. These data are then used as input to several data processing methods for information extraction and tabular/graphical output generation. A set of 18 species is processed and the extensive results reveal that the proposed method is able to generate significant and diversified outputs, in good accordance with current scientific knowledge in domains such as genomics and phylogenetics.

Sugar content in liquid oral medicines for children

The most sold and/or prescribed liquid oral medicines for children in Tubarão, Southern Brazil, were assessed. Their sugar concentration was tested and compared to those in their directions for use. All pharmacies and pediatricians working in the city were visited by a previously trained interviewer. Pre-tested questionnaires were applied in order to assess the most sold pediatric as well as the most prescribed pediatric liquid oral medicines. Three samples of each medicine were analyzed by Lane-Eynon general volumetric method. Among the 14 most sold/prescribed medicines only four did not have sugar contents (analgesic, cortisone, and syrups). Sugar concentration ranged from 8.59 g/100 g of drug (SD=0.29 g/100 g) to 67.0 g/100 g of drug (SD=6.07 g/100 g). Only 50.0% of the total medicines that presented sugar in their ingredients showed this information in their directions.

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.

Salt content in bread and dough from northern Portugal: method development and comparison

In the initial stage of this work, two potentiometric methods were used to determine the salt (sodium chloride) content in bread and dough samples from several cities in the north of Portugal. A reference method (potentiometric precipitation titration) and a newly developed ion-selective chloride electrode (ISE) were applied. Both methods determine the sodium chloride content through the quantification of chloride. To evaluate the accuracy of the ISE, bread and respective dough samples were analyzed by both methods. Statistical analysis (0.05 significance level) indicated that the results of these methods did not differ significantly. Therefore the ISE is an adequate alternative for the determination of chloride in the analyzed samples. To compare the results of these chloride-based methods with a sodium-based method, sodium was quantified in the same samples by a reference method (atomic absorption spectrometry). Significant differences between the results were verified. In several cases the sodium chloride content exceeded the legal limit when the chloride-based methods were used, but when the sodium-based method was applied this was not the case. This could lead to the erroneous application of fines and therefore the authorities should supply additional information regarding the analytical procedure for this particular control.

Comparing the content of instruments assessing environmental factors using the International Classification of Functioning, Disability and Health

Purpose: To describe and compare the content of instruments that assess environmental factors using the International Classification of Functioning, Disability and Health (ICF). Methods: A systematic search of PubMed, CINAHL and PEDro databases was conducted using a pre-determined search strategy. The identified instruments were screened independently by two investigators, and meaningful concepts were linked to the most precise ICF category according to published linking rules. Results: Six instruments were included, containing 526 meaningful concepts. Instruments had between 20% and 98% of items linked to categories in Chapter 1. The highest percentage of items from one instrument linked to categories in Chapters 2–5 varied between 9% and 50%. The presence or absence of environmental factors in a specific context is assessed in 3 instruments, while the other 3 assess the intensity of the impact of environmental factors. Discussion: Instruments differ in their content, type of assessment, and have several items linked to the same ICF category. Most instruments primarily assess products and technology (Chapter 1), highlighting the need to deepen the discussion on the theory that supports the measurement of environmental factors. This discussion should be thorough and lead to the development of methodologies and new tools that capture the underlying concepts of the ICF.

How new online communication tools and the availability of content influence the audiences and the creative process

We live in a changing world. At an impressive speed, every day new technological resources appear. We increasingly use the Internet to obtain and share information, and new online communication tools are emerging. Each of them encompasses new potential and creates new audiences. In recent years, we witnessed the emergence of Facebook, Twitter, YouTube and other media platforms. They have provided us with an even greater interactivity between sender and receiver, as well as generated a new sense of community. At the same time we also see the availability of content like it never happened before. We are increasingly sharing texts, videos, photos, etc. This poster intends to explore the potential of using these new online communication tools in the cultural sphere to create new audiences, to develop of a new kind of community, to provide information as well as different ways of building organizations’ memory. The transience of performing arts is accompanied by the need to counter that transience by means of documentation. This desire to ‘save’ events reaches its expression with the information archive of the different production moments as well as the opportunity to record the event and present it through, for instance, digital platforms. In this poster we intend to answer the following questions: which online communication tools are being used to engage audiences in the cultural sphere (specifically between theater companies in Lisbon)? Is there a new relationship with the public? Are online communication tools creating a new kind of community? What changes are these tools introducing in the creative process? In what way the availability of content and its archive contribute to the organization memory? Among several references, we will approach the two-way communication model that James E. Grunig & Todd T. Hunt (1984) already presented and the concept of mass self-communication of Manuel Castells (2010). Castells also tells us that we have moved from traditional media to a system of communication networks. For Scott Kirsner (2010), we have entered an era of digital creativity, where artists have the tools to do what they imagined and the public no longer wants to just consume cultural goods, but instead to have a voice and participate. The creativity process is now depending on the public choice as they wander through the screen. It is the receiver who owns an object which can be exchanged. Virtual reality has encouraged the receiver to abandon its position of passive observer and to become a participant agent, which implies a challenge to organizations: inventing new forms of interfaces. Therefore, we intend to find new and effective online tools that can be used by cultural organizations; the best way to manage them; to show how organizations can create a community with the public and how the availability of online content and its archive can contribute to the organizations’ memory.

Extensible metadata repository for information systems

Thesis submitted to Faculdade de Ciências e Tecnologia of the Universidade Nova de Lisboa, in partial fulfillment of the requirements for the degree of Master in Computer Science

Bertrand model under incomplete information

We consider a Bertrand duopoly model with unknown costs. The firms' aim is to choose the price of its product according to the well-known concept of Bayesian Nash equilibrium. The chooses are made simultaneously by both firms. In this paper, we suppose that each firm has two different technologies, and uses one of them according to a certain probability distribution. The use of either one or the other technology affects the unitary production cost. We show that this game has exactly one Bayesian Nash equilibrium. We analyse the advantages, for firms and for consumers, of using the technology with highest production cost versus the one with cheapest production cost. We prove that the expected profit of each firm increases with the variance of its production costs. We also show that the expected price of each good increases with both expected production costs, being the effect of the expected production costs of the rival dominated by the effect of the own expected production costs.

A survey on e-learning content standardization

eLearning has been evolved in a gradual and consistent way. Along with this evolution several specialized and disparate systems appeared to fulfill the needs of teachers and students such as repositories of learning objects, intelligent tutors, or automatic evaluators. This heterogeneity poses issues that are necessary to address in order to promote interoperability among systems. Based on this fact, the standardization of content takes a leading role in the eLearning realm. This article presents a survey on current eLearning content standards. It gathers information on the most emergent standards and categorizes them according three distinct facets: metadata, content packaging and educational design.

Geography of the Information Society

All every day activities take place in space. And it is upon this that all information and knowledge revolve. The latter are the key elements in the organisation of territories. Their creation, use and distribution should therefore occur in a balanced way throughout the whole territory in order to allow all individuals to participate in an egalitarian society, in which the flow of knowledge can take precedence over the flow of interests. The information society depends, to a large extent, on the technological capacity to disseminate information and, consequently, the knowledge throughout territory, thereby creating conditions which allow a more balanced development, from the both the social and economic points of view thus avoiding the existence of info-exclusion territories. Internet should therefore be considered more than a mere technology, given that its importance goes well beyond the frontiers of culture and society. It is already a part of daily life and of the new forms of thinking and transmitting information, thus making it a basic necessity essential, for a full socio-economic development. Its role as a platform of creation and distribution of content is regarded as an indispensable element for education in today’s society, since it makes information a much more easily acquired benefit.”…in the same way that the new technologies of generation and distribution of energy allowed factories and large companies to establish themselves as the organisational bases of industrial society, so the internet today constitutes the technological base of the organisational form that characterises the Information Era: the network” (CASTELLS, 2004:15). The changes taking place today in regional and urban structures are increasingly more evident due to a combination of factors such as faster means of transport, more efficient telecommunications and other cheaper and more advanced technologies of information and knowledge. Although their impact on society is obvious, society itself also has a strong influence on the evolution of these technologies. And although physical distance has lost much of the responsibility it had towards explaining particular phenomena of the economy and of society, other aspects such as telecommunications, new forms of mobility, the networks of innovation, the internet, cyberspace, etc., have become more important, and are the subject of study and profound analysis. The science of geographical information, allows, in a much more rigorous way, the analysis of problems thus integrating in a much more balanced way, the concepts of place, of space and of time. Among the traditional disciplines that have already found their place in this process of research and analysis, we can give special attention to a geography of new spaces, which, while not being a geography of ‘innovation’, nor of the ‘Internet’, nor even ‘virtual’, which can be defined as one of the ‘Information Society’, encompassing not only the technological aspects but also including a socio-economic approach. According to the last European statistical data, Portugal shows a deficit in terms of information and knowledge dissemination among its European partners. Some of the causes are very well identified - low levels of scholarship, weak investments on innovation and R&D (both private and public sector) - but others seem to be hidden behind socio-economical and technological factors. So, the justification of Portugal as the case study appeared naturally, on a difficult quest to find the major causes to territorial asymmetries. The substantial amount of data needed for this work was very difficult to obtain and for the islands of Madeira and Azores was insufficient, so only Continental Portugal was considered for this study. In an effort to understand the various aspects of the Geography of the Information Society and bearing in mind the increasing generalised use of information technologies together with the range of technologies available for the dissemination of information, it is important to: (i) Reflect on the geography of the new socio-technological spaces. (ii) Evaluate the potential for the dissemination of information and knowledge through the selection of variables that allow us to determine the dynamic of a given territory or region; (iii) Define a Geography of the Information Society in Continental Portugal.

Model morphisms (MoMo) to enable language independent information models and interoperable business networks

MSc. Dissertation presented at Faculdade de Ciências e Tecnologia of Universidade Nova de Lisboa to obtain the Master degree in Electrical and Computer Engineering

An Approach To Publish a Data Warehouse Content as Linked Data

Mestrado em Engenharia Informática - Área de Especialização em Tecnologias do Conhecimento e Decisão

Recommending media content based on machine learning methods

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

High-Content Analysis of Breast Cancer Using Single-Cell Deep Transfer Learning

High-content analysis has revolutionized cancer drug discovery by identifying substances that alter the phenotype of a cell, which prevents tumor growth and metastasis. The high-resolution biofluorescence images from assays allow precise quantitative measures enabling the distinction of small molecules of a host cell from a tumor. In this work, we are particularly interested in the application of deep neural networks (DNNs), a cutting-edge machine learning method, to the classification of compounds in chemical mechanisms of action (MOAs). Compound classification has been performed using image-based profiling methods sometimes combined with feature reduction methods such as principal component analysis or factor analysis. In this article, we map the input features of each cell to a particular MOA class without using any treatment-level profiles or feature reduction methods. To the best of our knowledge, this is the first application of DNN in this domain, leveraging single-cell information. Furthermore, we use deep transfer learning (DTL) to alleviate the intensive and computational demanding effort of searching the huge parameter's space of a DNN. Results show that using this approach, we obtain a 30% speedup and a 2% accuracy improvement.