Gremlin: an interactive visualization model for analyzing genomic rearrangements

In this work we present, apply, and evaluate a novel, interactive visualization model for comparative analysis of structural variants and rearrangements in human and cancer genomes, with emphasis on data integration and uncertainty visualization. To support both global trend analysis and local feature detection, this model enables explorations continuously scaled from the high-level, complete genome perspective, down to the low-level, structural rearrangement view, while preserving global context at all times. We have implemented these techniques in Gremlin, a genomic rearrangement explorer with multi-scale, linked interactions, which we apply to four human cancer genome data sets for evaluation. Using an insight-based evaluation methodology, we compare Gremlin to Circos, the state-of-the-art in genomic rearrangement visualization, through a small user study with computational biologists working in rearrangement analysis. Results from user study evaluations demonstrate that this visualization model enables more total insights, more insights per minute, and more complex insights than the current state-of-the-art for visual analysis and exploration of genome rearrangements.     

Fuzzy induced generalized aggregation operators and its application in multi-person decision making

We present a wide range of fuzzy induced generalized aggregation operators such as the fuzzy induced generalized ordered weighted averaging (FIGOWA) and the fuzzy induced quasi-arithmetic OWA (Quasi-FIOWA) operator. They are aggregation operators that use the main characteristics of the fuzzy OWA (FOWA) operator, the induced OWA (IOWA) operator and the generalized (or quasi-arithmetic) OWA operator. Therefore, they use uncertain information represented in the form of fuzzy numbers, generalized (or quasi-arithmetic) means and order inducing variables. The main advantage of these operators is that they include a wide range of mean operators such as the FOWA, the IOWA, the induced Quasi-OWA, the fuzzy IOWA, the fuzzy generalized mean and the fuzzy weighted quasi-arithmetic average (Quasi-FWA). We further generalize this approach by using Choquet integrals, obtaining the fuzzy induced quasi-arithmetic Choquet integral aggregation (Quasi-FICIA) operator. We also develop an application of the new approach in a strategic multi-person decision making problem.     

Strategies for collaborative writing and phases of knowledge construction in CSCL environments

Within the framework of research that describes the processes of collaborative knowledge construction in computer-supported collaborative learning (CSCL) environments, the present work has three objectives: (i) the identification of the strategies of six small groups of university students for the elaboration of written products in a CSCL environment; (ii) seek relations between the identified writing strategies and the processes and phases of collaborative knowledge construction in the groups; and (iii) relate these strategies and phases with the learning results obtained by the groups. We carried out a multiple-case study, with the analysis of four different didactic sequences, in two different virtual learning and teaching settings. In each setting, three student groups were studied, where each had to collaboratively develop between four and eight written products. For all the studied groups, the analysis enabled the identification of five types of strategies in the preparation of the elaboration of written products, and four types of phases of collaborative knowledge construction, which are interrelated and also connected with the grades that the groups obtained in each case.     

On the convective nature of the instability of a front undergoing a supercritical Turing bifurcation

Fronts are traveling waves in spatially extended systems that connect two different spatially homogeneous rest states. If the rest state behind the front undergoes a supercritical Turing instability, then the front will also destabilize. On the linear level, however, the front will be only convectively unstable since perturbations will be pushed away from the front as it propagates. In other words, perturbations may grow but they can do so only behind the front. It is of interest to show that this behavior carries over to the full nonlinear system. It has been successfully done in a case study by Ghazaryan and Sandstede [A. Ghazaryan, B. Sandstede, Nonlinear convective instability of Turing-unstable fronts near onset: a case study, SIAM J. Appl. Dyn. Syst. 6 (2007) 319–347]. In the present paper, analogous results are obtained for the same system as in Ghazaryan and Sandstede (2007), but for a different parameter regime.     

Interaction of Langmuir–Blodgett and spin-coated films of μ-carbido-bridged ironphthalocyanine with NO2: Optical and conductimetric behaviour

The present study investigates the interaction of NO₂ gas and μ-carbido-bridged iron phthalocyanine (PcFeCFePc) films obtained by Langmuir–Blodgett (LB) and spin-coating (SC) techniques. The phthalocyanine bridged dimer under study belongs to the polynuclear unsubstituted phthalocyanines class and presents poor solubility: in contrast the corresponding N-base bis-adducts are soluble enough in organic solvents to be deposited by Langmuir–Blodgett and spin-coating techniques. The reaction with NO₂ is monitored by visible spectra variation that shows identical behaviour for both kinds of films, indicating that the chemical reaction between the gas and the films is independent of the deposition method. The electrical conductivity change as a function of time with NO₂ is instead dissimilar: for spin-coated films it shows a behaviour already observed for sandwich-type phthalocyanine whereas for LB films it resembles that of monomeric phthalocyanine. Such a response implies that the charges (holes) generated in the oxidation/reduction process are carried differently through the material, and we attempt to explain this behaviour taking into account the two different structural and morphological features induced by the two techniques.     

Correcting for the influence of frozen lakes in satellite microwave radiometer observations through application of a microwave emission model

The spatial resolution of passive microwave observations from space is of the order of tens of kilometers with currently available instruments, such as the Special Sensor Microwave/Imager (SSM/I) and Advanced Microwave Scanning Radiometer (AMSR-E). The large field of view of these instruments dictates that the observed brightness temperature can originate from heterogeneous land cover, with different vegetation and surface properties.In this study, we assess the influence of freshwater lakes on the observed brightness temperature of AMSR-E in winter conditions. The study focuses on the geographic region of Finland, where lakes account for 10% of the total terrestrial area. We present a method to mitigate for the influence of lakes through forward modeling of snow covered lakes, as a part of a microwave emission simulation scheme of space-borne observations. We apply a forward model to predict brightness temperatures of snow covered sceneries over several winter seasons, using available data on snow cover, vegetation and lake ice cover to set the forward model input parameters. Comparison of model estimates with space-borne observations shows that the modeling accuracy improves in the majority of examined cases when lakes are accounted for, with respect to the case where lakes are not included in the simulation. Moreover, we present a method for applying the correction to the retrieval of Snow Water Equivalent (SWE) in lake-rich areas, using a numerical inversion method of the forward model. In a comparison to available independent validation data on SWE, also the retrieval accuracy is seen to improve when applying the influence of snow covered lakes in the emission model.     

Object query optimization through detecting independent subqueries

The problem of query optimization in object-oriented databases is addressed. We follow the Stack-Based Approach to query languages, which employs the naming-scoping-binding paradigm of programming languages rather than traditional database concepts such as relational/object algebras or calculi. The classical environment stack is a semantic basis for definitions of object query operators, such as selection, projection/navigation, dependent join, and quantifiers. We describe a general object data model and define a formalized OQL-like query language SBQL. Optimization by rewriting concerns queries containing so-called independent subqueries. It consists in detecting them and then factoring outside loops implied by query operators. The idea is based on the formal static analysis of scoping rules and binding names occurring in a query. It is more general than the classical pushing selections/projections before joins.     

Visualization of myocardial perfusion derived from coronary anatomy

Visually assessing the effect of the coronary artery anatomy on the perfusion of the heart muscle in patients with coronary artery disease remains a challenging task. We explore the feasibility of visualizing this effect on perfusion using a numerical approach. We perform a computational simulation of the way blood is perfused throughout the myocardium purely based on information from a three-dimensional anatomical tomographic scan. The results are subsequently visualized using both three-dimensional visualizations and bull's eye plots, partially inspired by approaches currently common in medical practice. Our approach results in a comprehensive visualization of the coronary anatomy that compares well to visualizations commonly used for other scanning technologies. We demonstrate techniques giving detailed insight in blood supply, coronary territories and feeding coronary arteries of a selected region. We demonstrate the advantages of our approach through visualizations that show information which commonly cannot be directly observed in scanning data, such as a separate visualization of the supply from each coronary artery. We thus show that the results of a computational simulation can be effectively visualized and facilitate visually correlating these results to for example perfusion data.     

Human pathogenic streptococcal proteomics and vaccine development

Gram-positive streptococci are non-motile, chain-forming bacteria commonly found in the normal oral and bowel flora of warm-blooded animals. Over the past decade, a proteomic approach combining 2-DE and MS has been used to systematically map the cellular, surface-associated and secreted proteins of human pathogenic streptococcal species. The public availability of complete streptococcal genomic sequences and the amalgamation of proteomic, genomic and bioinformatic technologies have recently facilitated the identification of novel streptococcal vaccine candidate antigens and therapeutic agents. The objective of this review is to examine the constituents of the streptococcal cell wall and secreted proteome, the mechanisms of transport of surface and secreted proteins, and describe the current methodologies employed for the identification of novel surface-displayed proteins and potential vaccine antigens.