Information visualization for DNA microarray data analysis: A critical review

Graphical representation may provide effective means of making sense of the complexity and sheer volume of data produced by DNA microarray experiments that monitor the expression patterns of thousands of genes simultaneously. The ability to use ldquoabstractrdquo graphical representation to draw attention to areas of interest, and more in-depth visualizations to answer focused questions, would enable biologists to move from a large amount of data to particular records they are interested in, and therefore, gain deeper insights in understanding the microarray experiment results. This paper starts by providing some background knowledge of microarray experiments, and then, explains how graphical representation can be applied in general to this problem domain, followed by exploring the role of visualization in gene expression data analysis. Having set the problem scene, the paper then examines various multivariate data visualization techniques that have been applied to microarray data analysis. These techniques are critically reviewed so that the strengths and weaknesses of each technique can be tabulated. Finally, several key problem areas as well as possible solutions to them are discussed as being a source for future work

Sensory sensitivity as a link between concussive traumatic brain injury and PTSD.

Traumatic brain injury (TBI) is one of the most common injuries to military personnel, a population often exposed to stressful stimuli and emotional trauma. Changes in sensory processing after TBI might contribute to TBI-post traumatic stress disorder (PTSD) comorbidity. Combining an animal model of TBI with an animal model of emotional trauma, we reveal an interaction between auditory sensitivity after TBI and fear conditioning where 75 dB white noise alone evokes a phonophobia-like phenotype and when paired with footshocks, fear is robustly enhanced. TBI reduced neuronal activity in the hippocampus but increased activity in the ipsilateral lateral amygdala (LA) when exposed to white noise. The white noise effect in LA was driven by increased activity in neurons projecting from ipsilateral auditory thalamus (medial geniculate nucleus). These data suggest that altered sensory processing within subcortical sensory-emotional circuitry after TBI results in neutral stimuli adopting aversive properties with a corresponding impact on facilitating trauma memories and may contribute to TBI-PTSD comorbidity

On encouraging multiple views for visualization

Visualization enables 'seeing the unseen', and provides new insight into the underlying data. However users far too easily believe or rely on a single representation of the data; this view may be a favourite method, the simplest to perform, or a method that has always been used! But, a single representation may generate a misinterpretation of the information or provide a situation where the user is missing the 'richness' of the data content! By displaying the data in multiple ways a user may understand the information through different perspectives, overcome possible misinterpretations and perform interactive investigative visualization through correlating the information between views. Thus, the use of multiple views of the same information should be encouraged. We believe the visualization system itself should actively encourage the generation of multiple views by providing appropriate tools to aid in this operation. We present and categorise issues for encouraging multiple views and provide a framework for the generation, management and manipulation of such views

Visualizing and Interacting with Concept Hierarchies

Concept Hierarchies and Formal Concept Analysis are theoretically well grounded and largely experimented methods. They rely on line diagrams called Galois lattices for visualizing and analysing object-attribute sets. Galois lattices are visually seducing and conceptually rich for experts. However they present important drawbacks due to their concept oriented overall structure: analysing what they show is difficult for non experts, navigation is cumbersome, interaction is poor, and scalability is a deep bottleneck for visual interpretation even for experts. In this paper we introduce semantic probes as a means to overcome many of these problems and extend usability and application possibilities of traditional FCA visualization methods. Semantic probes are visual user centred objects which extract and organize reduced Galois sub-hierarchies. They are simpler, clearer, and they provide a better navigation support through a rich set of interaction possibilities. Since probe driven sub-hierarchies are limited to users focus, scalability is under control and interpretation is facilitated. After some successful experiments, several applications are being developed with the remaining problem of finding a compromise between simplicity and conceptual expressivity

Predictors of anxiety after stroke: a systematic review of observational studies

Background: Anxiety disorders or symptoms are relatively common following stroke. A better understanding of the predictors of anxiety in stroke patients may improve the management of these disorders. The current review was conducted to determine the predictors of anxiety following stroke. Methods: Relevant articles concerning population, hospital or rehabilitation-based studies were identified by searching 10 electronic databases up to May 2014. Methodological quality appraisal, including the validity of prognostic models and data extraction were conducted by three reviewers. Results: A total of 18 studies were identified. Data from three population-based studies including 8130 patients, 8 hospital-based studies including 1199 patients, and 7 rehabilitation-based studies including 1103 patients was evaluated. Pre-stroke depression, stroke severity, early anxiety and dementia or cognitive impairment following stroke were the main predictors of post stroke anxiety. Older age, physical disability or impairment, and use of antidepressant drugs were not associated with presence of anxiety. Limitations of studies included wide variation in screening tools and cut-off scores, variability in the time frame of screening for anxiety, use of extensive exclusion criteria and questionable statistical internal and external validity of the models. Conclusions: Lack of methodological and statistical rigour affects the validity of proposed models to predict anxiety after stroke. Future research should focus on testing proposed models on both internal and external samples to ultimately inform future clinical practice

Waltz - An exploratory visualization tool for volume data, using multiform abstract displays

Although, visualization is now widely used, misinterpretations still occur. There are three primary solutions intended to aid a user interpret data correctly. These are: displaying the data in different forms (Multiform visualization); simplifying (or abstracting) the structure of the viewed information; and linking objects and views together (allowing corresponding objects to be jointly manipulated and interrogated). These well-known visualization techniques, provide an emphasis towards the visualization display. We believe however that current visualization systems do not effectively utilise the display, for example, often placing it at the end of a long visualization process. Our visualization system, based on an adapted visualization model, allows a display method to be used throughout the visualization process, in which the user operates a 'Display (correlate) and Refine' visualization cycle. This display integration provides a useful exploration environment, where objects and Views may be directly manipulated; a set of 'portions of interest' can be selected to generate a specialized dataset. This may subsequently be further displayed, manipulated and filtered

PICES Press, Vol. 15, No. 2, July 2007

Contents [Individual sections are downloadable from the official URL link listed below]: PICES Science in 2007 (pdf, 0.1 Mb) 2007 Wooster Award (pdf, 0.1 Mb) FUTURE - A milestone reached but our task is not done (pdf, < 0.1 Mb) International symposium on "Reproductive and Recruitment Processes of Exploited Marine Fish Stocks" (pdf, 0.1 Mb) Recent results of the micronekton sampling inter-calibration experiment (pdf, 0.1 Mb) 2007 PICES workshop on "Measuring and monitoring primary productivity in the North Pacific" (pdf, 0.1 Mb) 2007 Harmful Algal Bloom Section annual workshop events (pdf, 0.1 Mb) A global approach for recovery and sustainability of marine resources in Large Marine Ecosystems (pdf, 0.3 Mb) Highlights of the PICES Sixteenth Annual Meeting (pdf, 0.4 Mb) Ocean acidification of the North Pacific Ocean (pdf, 0.3 Mb) Workshop on NE Pacific Coastal Ecosystems (2008 Call for Salmon Survival Forecasts) (pdf, 0.1 Mb) The state of the western North Pacific in the first half of 2007 (pdf, 0.4 Mb) PICES Calendar (pdf, 0.4 Mb) The Bering Sea: Current status and recent events (pdf, 0.3 Mb) PICES Interns (pdf, 0.3 Mb) Recent trends in waters of the subarctic NE Pacific (pdf, 0.3 Mb) Election results at PICES (pdf, 0.2 Mb) A new PICES award for monitoring and data management activities (pdf, < 0.1 Mb

The Secret to Successful User Communities: An Analysis of Computer Associates’ User Groups

This paper provides the first large scale study that examines the impact of both individual- and group-specific factors on the benefits users obtain from their user communities. By empirically analysing 924 survey responses from individuals in 161 Computer Associates' user groups, this paper aims to identify the determinants of successful user communities. To measure success, the amount of time individual members save through having access to their user networks is used. As firms can significantly profit from successful user communities, this study proposes four key implications of the empirical results for the management of user communities