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.

Dual source/dual energy-renal applications

Development of Dual Source Computed Tomography (Definition, Siemens Medical Solutions, Erlanger, Germany) allowed advances in temporal resolution, with the addition of a second X-ray source and an array of detectors to the TCM 64 slices. The ability to run exams on Dual Energy, allows greater differentiation of tissues, showing differences between closer attenuation coefficients. In terms of renal applications, the distinction of kidney stones and masses become one of the main advantages of the use of dual-energy technology. This article pretends to demonstrate operating principles of this equipment, as its main renal applications.

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.

Espresso coffee residues: a valuable source of unextracted compounds

Espresso spent coffee grounds were chemically characterized to predict their potential, as a source of bioactive compounds, by comparison with the ones from the soluble coffee industry. Sampling included a total of 50 samples from 14 trademarks, collected in several coffee shops and prepared with distinct coffee machines. A high compositional variability was verified, particularly with regard to such water-soluble components as caffeine, total chlorogenic acids (CGA), and minerals, supported by strong positive correlations with total soluble solids retained. This is a direct consequence of the reduced extraction efficiency during espresso coffee preparation, leaving a significant pool of bioactivity retained in the extracted grounds. Besides the lipid (12.5%) and nitrogen (2.3%) contents, similar to those of industrial coffee residues, the CGA content (478.9 mg/100 g), for its antioxidant capacity, and its caffeine content (452.6 mg/100 g), due to its extensive use in the food and pharmaceutical industries, justify the selective assembly of this residue for subsequent use.

Contributo para a construção de um code set da classificação internacional de funcionalidade, incapacidade e saúde, para terapeutas ocupacionais, em unidades de cuidados continuados integrados

A CIF é uma ferramenta universal desenvolvida pela OMS que permite a classificação de funcionalidade e incapacidade, através de uma visualização global do que condiciona o desempenho do indivíduo na concretização de atividades e na participação em ocupações. A ideologia da CIF e os seus componentes interrelacionam-se com a essência da TO, indo ao encontro dos modelos da profissão. As UCCI constituem uma atualidade em Portugal e o terapeuta ocupacional é um dos profissionais obrigatórios na equipa multidisciplinar destas unidades. Atendendo à relevância internacional da CIF, à sua ligação com a TO e à necessidade de tornar a CIF operacional na prática clínica diária dado que é uma ferramenta complexa e extensa, é objetivo deste estudo contribuir para a construção de um code set da CIF para terapeutas ocupacionais que exercem funções em UCCI, especificamente em UC, UMDR e ULDM. Para a concretização desta investigação, utilizou-se a técnica de Delphi, que envolveu duas rondas. Na primeira ronda foi possível contar com a participação de 37 terapeutas ocupacionais experientes na área, uma vez que exercem funções em UCCI, e na segunda ronda contou-se com a participação de 20 elementos. Obtiveram consenso na última ronda de Delphi um total de 96 categorias, constituindo esta listagem uma proposta de code set para UCCI. No que se refere às tipologias de unidades, 69 categorias obtiveram consenso em UC, 91 em UMDR e 41 em ULDM. Concluiu-se que a criação de code sets poderá constituir uma mais-valia em contexto de equipa multidisciplinar das UCCI, sendo uma forma de tornar a CIF operacional na prática clínica diária.

Mental imagery in interpreting – a neurocognitive perspective

The paper discusses mental imagery as an important part of information processing performed during interpreting. Mental imagery is examined to see if visual processing used to remember the source text or to facilitate its understanding helps to ‗off-load‘ other cognitive (mainly linguistic) resources in interpreting. The discussion is based on a neurocognitively-oriented depictivist model by Kosslyn (1994). The overview of mental imagery processes and systems is followed by the discussion of imagery used in interpreting. First, imagery development in student interpreters is described on the basis of a note-taking course for would-be consecutive interpreters organized by the author at AMU. The initial part of the course devoted to imagery involves visualizations of geographical, descriptive and narrative texts. The description abounds in authentic examples and presents conclusions for interpreting trainers. Later, imagery as employed by professional interpreters is discussed on the basis of a qualitative survey. General implications of the use of mental imagery for cognitive processing limitations in interpreting are presented in the concluding section.

Code offloading on real-time multimedia systems: a framework for handling code mobility and code offloading in a QoS aware environment

Actualmente, os smartphones e outros dispositivos móveis têm vindo a ser dotados com cada vez maior poder computacional, sendo capazes de executar um vasto conjunto de aplicações desde simples programas de para tirar notas até sofisticados programas de navegação. Porém, mesmo com a evolução do seu hardware, os actuais dispositivos móveis ainda não possuem as mesmas capacidades que os computadores de mesa ou portáteis. Uma possível solução para este problema é distribuir a aplicação, executando partes dela no dispositivo local e o resto em outros dispositivos ligados à rede. Adicionalmente, alguns tipos de aplicações como aplicações multimédia, jogos electrónicos ou aplicações de ambiente imersivos possuem requisitos em termos de Qualidade de Serviço, particularmente de tempo real. Ao longo desta tese é proposto um sistema de execução de código remota para sistemas distribuídos com restrições de tempo-real. A arquitectura proposta adapta-se a sistemas que necessitem de executar periodicamente e em paralelo mesmo conjunto de funções com garantias de tempo real, mesmo desconhecendo os tempos de execução das referidas funções. A plataforma proposta foi desenvolvida para sistemas móveis capazes de executar o Sistema Operativo Android.

The invisible factors that can make the difference. Language management and knowledge transfer in multinational sites

The knowledge-based society we live in has stressed the importance of human capital and brought talent to the top of most wanted skills, especially to companies who want to succeed in turbulent environments worldwide. In fact, streams, sequences of decisions and resource commitments characterize the day-to-day of multinational companies (MNCs). Such decision-making activities encompass major strategic moves like internationalization and new market entries or diversification and acquisitions. In most companies, these strategic decisions are extensively discussed and debated and are generally framed, formulated, and articulated in specialized language often developed by the best minds in the company. Yet the language used in such deliberations, in detailing and enacting the implementation strategy is usually taken for granted and receives little if any explicit attention (Brannen & Doz, 2012) an can still be a “forgotten factor” (Marschan et al. 1997). Literature on language management and international business refers to lack of awareness of business managers of the impact that language can have not only in communication effectiveness but especially in knowledge transfer and knowledge management in business environments. In the context of MNCs, management is, for many different reasons, more complex and demanding than that of a national company, mainly because of diversity factors inherent to internationalization, namely geographical and cultural spaces, i.e, varied mindsets. Moreover, the way of functioning, and managing language, of the MNC depends on its vision, its values and its internationalization model, i.e on in the way the MNE adapts to and controls the new markets, which can vary essentially from a more ethnocentric to a more pluricentric focus. Regardless of the internationalization model followed by the MNC, communication between different business units is essential to achieve unity in diversity and business sustainability. For the business flow and prosperity, inter-subsidiary, intra-company and company-client (customers, suppliers, governments, municipalities, etc..) communication must work in various directions and levels of the organization. If not well managed, this diversity can be a barrier to global coordination and create turbulent environments, even if a good technological support is available (Feely et al., 2002: 4). According to Marchan-Piekkari (1999) the tongue can be both (i) a barrier, (ii) a facilitator and (iii) a source of power. Moreover, the lack of preparation for the barriers of linguistic diversity can lead to various costs, including negotiations’ failure and failure on internationalization.. On the other hand, communication and language fluency is not just a message transfer procedure, but above all a knowledge transfer process, which requires extra-linguistic skills (persuasion, assertiveness …) in order to promote credibility of both parties. For this reason, MNCs need a common code to communicate and trade information inside and outside the company, which will require one or more strategies, in order to overcome possible barriers and organization distortions.

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.

Exploring bioactive properties of marine cyanobacteria Isolated from the Portuguese coast: high potential as a source of anticancer compounds

The oceans remain a major source of natural compounds with potential in pharmacology. In particular, during the last few decades, marine cyanobacteria have been in focus as producers of interesting bioactive compounds, especially for the treatment of cancer. In this study, the anticancer potential of extracts from twenty eight marine cyanobacteria strains, belonging to the underexplored picoplanktonic genera, Cyanobium, Synechocystis and Synechococcus, and the filamentous genera, Nodosilinea, Leptolyngbya, Pseudanabaena and Romeria, were assessed in eight human tumor cell lines. First, a crude extract was obtained by dichloromethane:methanol extraction, and from it, three fractions were separated in a Si column chromatography. The crude extract and fractions were tested in eight human cancer cell lines for cell viability/toxicity, accessed with the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) and lactic dehydrogenase release (LDH) assays. Eight point nine percent of the strains revealed strong cytotoxicity; 17.8% showed moderate cytotoxicity, and 14.3% assays showed low toxicity. The results obtained revealed that the studied genera of marine cyanobacteria are a promising source of novel compounds with potential anticancer activity and highlight the interest in also exploring the smaller filamentous and picoplanktonic genera of cyanobacteria.

Fractional dynamics and MDS visualization of earthquake phenomena

This paper analyses earthquake data in the perspective of dynamical systems and fractional calculus (FC). This new standpoint uses Multidimensional Scaling (MDS) as a powerful clustering and visualization tool. FC extends the concepts of integrals and derivatives to non-integer and complex orders. MDS is a technique that produces spatial or geometric representations of complex objects, such that those objects that are perceived to be similar in some sense are placed on the MDS maps forming clusters. In this study, over three million seismic occurrences, covering the period from January 1, 1904 up to March 14, 2012 are analysed. The events are characterized by their magnitude and spatiotemporal distributions and are divided into fifty groups, according to the Flinn–Engdahl (F–E) seismic regions of Earth. Several correlation indices are proposed to quantify the similarities among regions. MDS maps are proven as an intuitive and useful visual representation of the complex relationships that are present among seismic events, which may not be perceived on traditional geographic maps. Therefore, MDS constitutes a valid alternative to classic visualization tools for understanding the global behaviour of earthquakes.

Nano-CF: a Coordination Framework for macro-programming in wireless sensor networks

Wireless Sensor Networks (WSN) are being used for a number of applications involving infrastructure monitoring, building energy monitoring and industrial sensing. The difficulty of programming individual sensor nodes and the associated overhead have encouraged researchers to design macro-programming systems which can help program the network as a whole or as a combination of subnets. Most of the current macro-programming schemes do not support multiple users seamlessly deploying diverse applications on the same shared sensor network. As WSNs are becoming more common, it is important to provide such support, since it enables higher-level optimizations such as code reuse, energy savings, and traffic reduction. In this paper, we propose a macro-programming framework called Nano-CF, which, in addition to supporting in-network programming, allows multiple applications written by different programmers to be executed simultaneously on a sensor networking infrastructure. This framework enables the use of a common sensing infrastructure for a number of applications without the users having to worrying about the applications already deployed on the network. The framework also supports timing constraints and resource reservations using the Nano-RK operating system. Nano- CF is efficient at improving WSN performance by (a) combining multiple user programs, (b) aggregating packets for data delivery, and (c) satisfying timing and energy specifications using Rate- Harmonized Scheduling. Using representative applications, we demonstrate that Nano-CF achieves 90% reduction in Source Lines-of-Code (SLoC) and 50% energy savings from aggregated data delivery.

Shannon information and power law analysis of the chromosome code

This paper studies the information content of the chromosomes of twenty-three species. Several statistics considering different number of bases for alphabet character encoding are derived. Based on the resulting histograms, word delimiters and character relative frequencies are identified. The knowledge of this data allows moving along each chromosome while evaluating the flow of characters and words. The resulting flux of information is captured by means of Shannon entropy. The results are explored in the perspective of power law relationships allowing a quantitative evaluation of the DNA of the species.

Shannon entropy analysis of the genome code

This paper studies the chromosome information of twenty five species, namely, mammals, fishes, birds, insects, nematodes, fungus, and one plant. A quantifying scheme inspired in the state space representation of dynamical systems is formulated. Based on this algorithm, the information of each chromosome is converted into a bidimensional distribution. The plots are then analyzed and characterized by means of Shannon entropy. The large volume of information is integrated by averaging the lengths and entropy quantities of each species. The results can be easily visualized revealing quantitative global genomic information.