Review and Outlooks of the Means for Visualization of Syntax Semantics and Source Code. Procedural and Object Oriented Paradigm – Differences

In the article, we have reviewed the means for visualization of syntax, semantics and source code for programming languages which support procedural and/or object-oriented paradigm. It is examined how the structure of the source code of the structural and object-oriented programming styles has influenced different approaches for their teaching. We maintain a thesis valid for the object-oriented programming paradigm, which claims that the activities for design and programming of classes are done by the same specialist, and the training of this specialist should include design as well as programming skills and knowledge for modeling of abstract data structures. We put the question how a high level of abstraction in the object-oriented paradigm should be presented in simple model in the design stage, so the complexity in the programming stage stay low and be easily learnable. We give answer to this question, by building models using the UML notation, as we take a concrete example from the teaching practice including programming techniques for inheritance and polymorphism.

Modelo cognitivo informacional de suporte a decisão aplicado à gestão de bacias urbanas

A pesquisa foi realizada a partir da escolha da área correspondente à bacia do igarapé Tucunduba, na zona urbana de Belém, capital do Estado do Pará, e é voltada para o desenvolvimento de uma estrutura cognitiva causal computacional capaz de identificar e qualificar os potenciais processos indicadores de conflitos gerados pelos usos múltiplos da água nesta bacia hidrográfica urbana, e com isto viabilizar decisões no âmbito das medidas estruturais e não estruturais. A utilização de um modelo qualitativo, utilizando metodologias informacionais, como o software Decision Explorer, na área de recursos hídricos, visa entender não somente os aspectos hidrológicos, mas também os aspectos sociais, indispensáveis na tomada de decisão diante de um cenário de conflitualidade quanto ao uso desses recursos. Este software é uma ferramenta para o desenvolvimento do mapeamento cognitivo, através do qual serão agrupados os conceitos unindo causas e efeitos representativos por meio de visualização codificada dos mesmos. A identificação e qualificação dos conflitos decorrentes dos usos múltiplos da água foram realizadas a partir de entrevistas com especialistas na área de gestão e saneamento, sendo posteriormente gerados os mapas cognitivos possibilitando assim a descrição do sistema escolhido e a identificação das possíveis soluções mediadoras para os conflitos ali identificados. O resultado obtido a partir das entrevistas foi agregado em um único mapa com o intuito de comprovar a hipótese formulada na pesquisa, por meio das ferramentas de análise, ou seja, auxiliar na identificação dos conflitos pelo uso múltiplo da água, a partir das medidas estruturais e não estruturais existentes (ou propostas), a fim de proporcionar ao gestor a tomador de decisão de forma mais eficaz na solução desses conflitos. Neste caso, poderíamos dizer que este grupo de construtos ilustra as principais medidas a serem observadas pelo tomador de decisão, a fim de solucionar os conflitos pelo uso múltiplo na bacia do Tucunduba, evidenciados pelos facilitadores através das entrevistas e mapas cognitivos individuais. As conclusões e recomendações estão contidas no capítulo final são obtidas não somente através dos resultados extraídos do software empregado, mas principalmente por maio da intervenção e interpretação dos dados pelo pesquisador, que obtém a partir dessas análises o entendimento do funcionamento do sistema, a identificação dos conflitos potenciais, suas causas e efeitos, assim como as medidas mitigadoras a serem sugeridas ao tomador de decisão. Estão incluídas neste capítulo sugestões visando o aprimoramento do modelo criado.

Analysis of Forest Fires by means of Pseudo Phase Plane and Multidimensional Scaling Methods

Forest fires dynamics is often characterized by the absence of a characteristic length-scale, long range correlations in space and time, and long memory, which are features also associated with fractional order systems. In this paper a public domain forest fires catalogue, containing information of events for Portugal, covering the period from 1980 up to 2012, is tackled. The events are modelled as time series of Dirac impulses with amplitude proportional to the burnt area. The time series are viewed as the system output and are interpreted as a manifestation of the system dynamics. In the first phase we use the pseudo phase plane (PPP) technique to describe forest fires dynamics. In the second phase we use multidimensional scaling (MDS) visualization tools. The PPP allows the representation of forest fires dynamics in two-dimensional space, by taking time series representative of the phenomena. The MDS approach generates maps where objects that are perceived to be similar to each other are placed on the map forming clusters. The results are analysed in order to extract relationships among the data and to better understand forest fires behaviour.

Dynamical Analysis and Visualization of Tornadoes Time Series

In this paper we analyze the behavior of tornado time-series in the U.S. from the perspective of dynamical systems. A tornado is a violently rotating column of air extending from a cumulonimbus cloud down to the ground. Such phenomena reveal features that are well described by power law functions and unveil characteristics found in systems with long range memory effects. Tornado time series are viewed as the output of a complex system and are interpreted as a manifestation of its dynamics. Tornadoes are modeled as sequences of Dirac impulses with amplitude proportional to the events size. First, a collection of time series involving 64 years is analyzed in the frequency domain by means of the Fourier transform. The amplitude spectra are approximated by power law functions and their parameters are read as an underlying signature of the system dynamics. Second, it is adopted the concept of circular time and the collective behavior of tornadoes analyzed. Clustering techniques are then adopted to identify and visualize the emerging patterns.

Inversion prepared coronary MR angiography: direct visualization of coronary blood flow.

PURPOSE: Visualization of coronary blood flow by means of a slice-selective inversion pre-pulse in concert with bright-blood coronary MRA. MATERIALS AND METHODS: Coronary magnetic resonance angiography (MRA) of the right coronary artery (RCA) was performed in eight healthy adult subjects on a 1.5 Tesla MR system (Gyroscan ACS-NT, Philips Medical Systems, Best, NL) using a free-breathing navigator-gated and cardiac-triggered 3D steady-state free-precession (SSFP) sequence with radial k-space sampling. Imaging was performed with and without a slice-selective inversion pre-pulse, which was positioned along the main axis of the coronary artery but perpendicular to the imaging volume. Objective image quality parameters such as SNR, CNR, maximal visible vessel length, and vessel border definition were analyzed. RESULTS: In contrast to conventional bright-blood 3D coronary MRA, the selective inversion pre-pulse provided a direct measure of coronary blood flow. In addition, CNR between the RCA and right ventricular blood pool was increased and the vessels had a tendency towards better delineation. Blood SNR and CNR between right coronary blood and epicardial fat were comparable in both sequences. CONCLUSION: The combination of a free-breathing navigator-gated and cardiac-triggered 3D SSFP sequence with a slice-selective inversion pre-pulse allows for direct and directional visualization of coronary blood flow with the additional benefit of improved contrast between coronary and right ventricular blood pool.

Magnetization transfer-based 3D visualization of foot peripheral nerves.

PURPOSE: To investigate magnetization transfer (MT) effects as a new source of contrast for imaging and tracking of peripheral foot nerves. MATERIALS AND METHODS: Two sets of 3D spoiled gradient-echo images acquired with and without a saturation pulse were used to generate MT ratio (MTR) maps of 260 μm in-plane resolution for eight volunteers at 3T. Scan parameters were adjusted to minimize signal loss due to T2 dephasing, and a dedicated coil was used to improve the inherently low signal-to-noise ratio of small voxels. Resulting MTR values in foot nerves were compared with those in surrounding muscle tissue. RESULTS: Average MTR values for muscle (45.5 ± 1.4%) and nerve (21.4 ± 3.1%) were significantly different (P < 0.0001). In general, the difference in MTR values was sufficiently large to allow for intensity-based segmentation and tracking of foot nerves in individual subjects. This procedure was termed MT-based 3D visualization. CONCLUSION: The MTR serves as a new source of contrast for imaging of peripheral foot nerves and provides a means for high spatial resolution tracking of these structures. The proposed methodology is directly applicable on standard clinical MR scanners and could be applied to systemic pathologies, such as diabetes.

EasyStrata: evaluation and visualization of stratified genome-wide association meta-analysis data.

The R package EasyStrata facilitates the evaluation and visualization of stratified genome-wide association meta-analyses (GWAMAs) results. It provides (i) statistical methods to test and account for between-strata difference as a means to tackle gene-strata interaction effects and (ii) extended graphical features tailored for stratified GWAMA results. The software provides further features also suitable for general GWAMAs including functions to annotate, exclude or highlight specific loci in plots or to extract independent subsets of loci from genome-wide datasets. It is freely available and includes a user-friendly scripting interface that simplifies data handling and allows for combining statistical and graphical functions in a flexible fashion. AVAILABILITY: EasyStrata is available for free (under the GNU General Public License v3) from our Web site www.genepi-regensburg.de/easystrata and from the CRAN R package repository cran.r-project.org/web/packages/EasyStrata/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A Web Map Service implementation for the visualization of multidimensional gridded environmental data

We describe ncWMS, an implementation of the Open Geospatial Consortium’s Web Map Service (WMS) specification for multidimensional gridded environmental data. ncWMS can read data in a large number of common scientific data formats – notably the NetCDF format with the Climate and Forecast conventions – then efficiently generate map imagery in thousands of different coordinate reference systems. It is designed to require minimal configuration from the system administrator and, when used in conjunction with a suitable client tool, provides end users with an interactive means for visualizing data without the need to download large files or interpret complex metadata. It is also used as a “bridging” tool providing interoperability between the environmental science community and users of geographic information systems. ncWMS implements a number of extensions to the WMS standard in order to fulfil some common scientific requirements, including the ability to generate plots representing timeseries and vertical sections. We discuss these extensions and their impact upon present and future interoperability. We discuss the conceptual mapping between the WMS data model and the data models used by gridded data formats, highlighting areas in which the mapping is incomplete or ambiguous. We discuss the architecture of the system and particular technical innovations of note, including the algorithms used for fast data reading and image generation. ncWMS has been widely adopted within the environmental data community and we discuss some of the ways in which the software is integrated within data infrastructures and portals.

Radiolabeling of defined polymer architectures with fluorine-18 and iodine-131 for ex vivo and in vivo evaluation : visualization of structure-property relationships

Nuclear medicine imaging techniques such as PET are of increasing relevance in pharmaceutical research being valuable (pre)clinical tools to non-invasively assess drug performance in vivo. Therapeutic drugs, e.g. chemotherapeutics, often suffer from a poor balance between their efficacy and toxicity. Here, polymer based drug delivery systems can modulate the pharmacokinetics of low Mw therapeutics (prolonging blood circulation time, reducing toxic side effects, increasing target site accumulation) and therefore leading to a more efficient therapy. In this regard, poly-N-(2-hydroxypropyl)-methacrylamide (HPMA) constitutes a promising biocompatible polymer. Towards the further development of these structures, non-invasive PET imaging allows insight into structure-property relationships in vivo. This performant tool can guide design optimization towards more effective drug delivery. Hence, versatile radiolabeling strategies need to be developed and establishing 18F- as well as 131I-labeling of diverse HPMA architectures forms the basis for short- as well as long-term in vivo evaluations. By means of the prosthetic group [18F]FETos, 18F-labeling of distinct HPMA polymer architectures (homopolymers, amphiphilic copolymers as well as block copolymers) was successfully accomplished enabling their systematic evaluation in tumor bearing rats. These investigations revealed pronounced differences depending on individual polymer characteristics (molecular weight, amphiphilicity due to incorporated hydrophobic laurylmethacrylate (LMA) segments, architecture) as well as on the studied tumor model. Polymers showed higher uptake for up to 4 h p.i. into Walker 256 tumors vs. AT1 tumors (correlating to a higher cellular uptake in vitro). Highest tumor concentrations were found for amphiphilic HPMA-ran-LMA copolymers in comparison to homopolymers and block copolymers. Notably, the random LMA copolymer P4* (Mw=55 kDa, 25% LMA) exhibited most promising in vivo behavior such as highest blood retention as well as tumor uptake. Further studies concentrated on the influence of PEGylation (‘stealth effect’) in terms of improving drug delivery properties of defined polymeric micelles. Here, [18F]fluoroethylation of distinct PEGylated block copolymers (0%, 1%, 5%, 7%, 11% of incorporated PEG2kDa) enabled to systematically study the impact of PEG incorporation ratio and respective architecture on the in vivo performance. Most strikingly, higher PEG content caused prolonged blood circulation as well as a linear increase in tumor uptake (Walker 256 carcinoma). Due to the structural diversity of potential polymeric carrier systems, further versatile 18F-labeling strategies are needed. Therefore, a prosthetic 18F-labeling approach based on the Cu(I)-catalyzed click reaction was established for HPMA-based polymers, providing incorporation of fluorine-18 under mild conditions and in high yields. On this basis, a preliminary µPET study of a HPMA-based polymer – radiolabeled via the prosthetic group [18F]F-PEG3-N3 – was successfully accomplished. By revealing early pharmacokinetics, 18F-labeling enables to time-efficiently assess the potential of HPMA polymers for efficient drug delivery. Yet, investigating the long-term fate is essential, especially regarding prolonged circulation properties and passive tumor accumulation (EPR effect). Therefore, radiolabeling of diverse HPMA copolymers with the longer-lived isotope iodine-131 was accomplished enabling in vivo evaluation of copolymer P4* over several days. In this study, tumor retention of 131I-P4* could be demonstrated at least over 48h with concurrent blood clearance thereby confirming promising tumor targeting properties of amphiphilic HPMA copolymer systems based on the EPR effect.

Real-time visualization of ultrasound-guided retrobulbar blockade: an imaging study

BACKGROUND: /st> Retrobulbar anaesthesia allows eye surgery in awake patients. Severe complications of the blind techniques are reported. Ultrasound-guided needle introduction and direct visualization of the spread of local anaesthetic may improve quality and safety of retrobulbar anaesthesia. Therefore, we developed a new ultrasound-guided technique using human cadavers. METHODS: /st> In total, 20 blocks on both sides in 10 embalmed human cadavers were performed. Using a small curved array transducer and a long-axis approach, a 22 G short bevel needle was introduced under ultrasound guidance lateral and caudal of the eyeball until the needle tip was seen 2 mm away from the optic nerve. At this point, 2 ml of contrast dye as a substitute for local anaesthetic was injected. Immediately after the injection, the spread of the contrast dye was documented by means of CT scans performed in each cadaver. RESULTS: /st> The CT scans showed the distribution of the contrast dye in the muscle cone and behind the posterior sclera in all but one case. No contrast dye was found inside the optic nerve or inside the eyeball. In one case, there could be an additional trace of contrast dye behind the orbita. CONCLUSIONS: /st> Our new ultrasound-guided technique has the potential to improve safety and efficacy of the procedure by direct visualization of the needle placement and the distribution of the injected fluid. Furthermore, the precise injection near the optic nerve could lead to a reduction of the amount of the local anaesthetic needed with fewer related complications.

Timely Reporting and Interactive Visualization of Animal Health and Slaughterhouse Surveillance Data in Switzerland

The reporting of outputs from health surveillance systems should be done in a near real-time and interactive manner in order to provide decision makers with powerful means to identify, assess, and manage health hazards as early and efficiently as possible. While this is currently rarely the case in veterinary public health surveillance, reporting tools do exist for the visual exploration and interactive interrogation of health data. In this work, we used tools freely available from the Google Maps and Charts library to develop a web application reporting health-related data derived from slaughterhouse surveillance and from a newly established web-based equine surveillance system in Switzerland. Both sets of tools allowed entry-level usage without or with minimal programing skills while being flexible enough to cater for more complex scenarios for users with greater programing skills. In particular, interfaces linking statistical softwares and Google tools provide additional analytical functionality (such as algorithms for the detection of unusually high case occurrences) for inclusion in the reporting process. We show that such powerful approaches could improve timely dissemination and communication of technical information to decision makers and other stakeholders and could foster the early-warning capacity of animal health surveillance systems.

Visualization of a student predictive model for 3D virtual environments driven to procedural training

This document presents theimplementation ofa Student Behavior Predictor Viewer(SBPV)for a student predictive model. The student predictive model is part of an intelligent tutoring system, and is built from logs of students’ behaviors in the “Virtual Laboratory of Agroforestry Biotechnology”implemented in a previous work.The SBPVis a tool for visualizing a 2D graphical representationof the extended automaton associated with any of the clusters ofthe student predictive model. Apart from visualizing the extended automaton, the SBPV supports the navigation across the automaton by means of desktop devices. More precisely, the SBPV allows user to move through the automaton, to zoom in/out the graphic or to locate a given state. In addition, the SBPV also allows user to modify the default layout of the automaton on the screen by changing the position of the states by means of the mouse. To developthe SBPV, a web applicationwas designedand implementedrelying on HTML5, JavaScript and C#.

Visualization of oligonucleotide probes and point mutations in interphase nuclei and DNA fibers using rolling circle DNA amplification

Rolling circle amplification (RCA) is a surface-anchored DNA replication reaction that can be exploited to visualize single molecular recognition events. Here we report the use of RCA to visualize target DNA sequences as small as 50 nts in peripheral blood lymphocytes or in stretched DNA fibers. Three unique target sequences within the cystic fibrosis transmembrane conductance regulator gene could be detected simultaneously in interphase nuclei, and could be ordered in a linear map in stretched DNA. Allele-discriminating oligonucleotide probes in conjunction with RCA also were used to discriminate wild-type and mutant alleles in the cystic fibrosis transmembrane conductance regulator, p53, BRCA-1, and Gorlin syndrome genes in the nuclei of cultured cells or in DNA fibers. These observations demonstrate that signal amplification by RCA can be coupled to nucleic acid hybridization and multicolor fluorescence imaging to detect single nucleotide changes in DNA within a cytological context or in single DNA molecules. This provides a means for direct physical haplotyping and the analysis of somatic mutations on a cell-by-cell basis.

Modeling of adsorption in finite cylindrical pores by means of density functional theory

Adsorption of argon at its boiling point infinite cylindrical pores is considered by means of the non-local density functional theory (NLDFT) with a reference to MCM-41 silica. The NLDFT was adjusted to amorphous solids, which allowed us to quantitatively describe argon adsorption isotherm on nonporous reference silica in the entire bulk pressure range. In contrast to the conventional NLDFT technique, application of the model to cylindrical pores does not show any layering before the phase transition in conformity with experimental data. The finite pore is modeled as a cylindrical cavity bounded from its mouth by an infinite flat surface perpendicular to the pore axis. The adsorption of argon in pores of 4 and 5 nm diameters is analyzed in canonical and grand canonical ensembles using a two-dimensional version of NLDFT, which accounts for the radial and longitudinal fluid density distributions. The simulation results did not show any unusual features associated with accounting for the outer surface and support the conclusions obtained from the classical analysis of capillary condensation and evaporation. That is, the spontaneous condensation occurs at the vapor-like spinodal point, which is the upper limit of mechanical stability of the liquid-like film wetting the pore wall, while the evaporation occurs via a mechanism of receding of the semispherical meniscus from the pore mouth and the complete evaporation of the core occurs at the equilibrium transition pressure. Visualization of the pore filling and empting in the form of contour lines is presented.

Interactive 3D Visualization of Bézier Curves using Java Open Graphics Library (JOGL)

We present a new program tool for interactive 3D visualization of some fundamental algorithms for representation and manipulation of Bézier curves. The program tool has an option for demonstration of one of their most important applications - in graphic design for creating letters by means of cubic Bézier curves. We use Java applet and JOGL as our main visualization techniques. This choice ensures the platform independency of the created applet and contributes to the realistic 3D visualization. The applet provides basic knowledge on the Bézier curves and is appropriate for illustrative and educational purposes. Experimental results are included.