Dynamic visualization of coexpression in systems genetics data

Biologists hope to address grand scientific challenges by exploring the abundance of data made available through modern microarray technology and other high-throughput techniques. The impact of this data, however, is limited unless researchers can effectively assimilate such complex information and integrate it into their daily research; interactive visualization tools are called for to support the effort. Specifically, typical studies of gene co-expression require novel visualization tools that enable the dynamic formulation and fine-tuning of hypotheses to aid the process of evaluating sensitivity of key parameters. These tools should allow biologists to develop an intuitive understanding of the structure of biological networks and discover genes residing in critical positions in networks and pathways. By using a graph as a universal representation of correlation in gene expression, our system employs several techniques that when used in an integrated manner provide innovative analytical capabilities. Our tool for interacting with gene co-expression data integrates techniques such as: graph layout, qualitative subgraph extraction through a novel 2D user interface, quantitative subgraph extraction using graph-theoretic algorithms or by compound queries, dynamic level-of-detail abstraction, and template-based fuzzy classification. We demonstrate our system using a real-world workflow from a large-scale, systems genetics study of mammalian gene co-expression.     

Public Works and Public Space: Rethinking the Urban Park

Infrastructure has always played a significant role in shaping the city and giving rise to new landscape types. This paper examines the historical relationship between public works and public space and explores the potential for redefining the contemporary park as an extension of urban infrastructure. Recent examples of such hybrid working landscapes are discussed, including the Productive Park design study in New York and Garrison Creek Demonstration Project in Toronto. These issues are investigated further through the student work of two landscape architecture studios at the University of Virginia dealing with waterworks sites: McMillan Sand Filtration Plant in Washington, D.C., and Highbridge Park, New York.     

Validation of the Social Interaction Anxiety Scale and the Social Phobia Scale across the anxiety disorders.

The psychometric adequacy of the Social Interaction Anxiety Scale (SIAS; R. P. Mattick & J. C. Clark, 1989), a measure of social interaction anxiety, and the Social Phobia Scale (SPS; R. P. Mattick & J. C. Clark, 1989), a measure of anxiety while being observed by others, was evaluated in anxious patients and normal controls. Social phobia patients scored higher on both scales and were more likely to be identified as having social phobia than other anxious patients (except for agoraphobic patients on the SPS) or controls. Clinician-rated severity of social phobia was moderately related to SIAS and SPS scores. Additional diagnoses of mood or panic disorder did not affect SIAS or SPS scores among social phobia patients, but an additional diagnosis of generalized anxiety disorder was associated with SIAS scores. Number of reported feared social interaction situations was more highly correlated with scores on the SIAS, whereas number of reported feared performance situations was more highly correlated with scores on the SPS. These scales appear to be useful in screening, designing individualized treatments, and evaluating the outcomes of treatments for social phobia. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

The effects of message framing on mammography utilization.

This experiment compared the effectiveness of gain- versus loss-framed messages to persuade women to obtain mammography screening. One hundred and thirty-three women 40 years and older and not adhering to current guidelines for obtaining mammography screening were assigned randomly to view either gain-framed (emphasizing the benefits of obtaining mammography) or loss-framed (emphasizing the risks of not obtaining mammography) persuasive videos that were factually equivalent. Attitudes and beliefs were measured before and immediately following the intervention. Mammography utilization was assessed 6 and 12 months later. Consistent with predictions based on prospect theory, women who viewed the loss-framed message were more likely to have obtained a mammogram within 12 months of the intervention. These findings suggest that loss-framed messages may have an advantage in the promotion of detection behaviors such as mammography. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Inference of beliefs and emotions in patients with Alzheimer's disease.

The present study compared 20 patients with mild to moderate Alzheimer's disease with 20 older controls (ages 69-94 years) on their ability to make inferences about emotions and beliefs in others. Six tasks tested their ability to make 1st-order and 2nd-order inferences as well as to offer explanations and moral evaluations of human action by appeal to emotions and beliefs. Results showed that the ability to infer emotions and beliefs in 1st-order tasks remains largely intact in patients with mild to moderate Alzheimer's. Patients were able to use mental states in the prediction, explanation, and moral evaluation of behavior. Impairment on 2nd-order tasks involving inference of mental states was equivalent to impairment on control tasks, suggesting that patients' difficulty is secondary to their cognitive impairments. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Distant Melodies: Statistical Learning of Nonadjacent Dependencies in Tone Sequences.

Human listeners can keep track of statistical regularities among temporally adjacent elements in both speech and musical streams. However, for speech streams, when statistical regularities occur among nonadjacent elements, only certain types of patterns are acquired. Here, using musical tone sequences, the authors investigate nonadjacent learning. When the elements were all similar in pitch range and timbre, learners acquired moderate regularities among adjacent tones but did not acquire highly consistent regularities among nonadjacent tones. However, when elements differed in pitch range or timbre, learners acquired statistical regularities among the similar, but temporally nonadjacent, elements. Finally, with a moderate grouping cue, both adjacent and nonadjacent statistics were learned, indicating that statistical learning is governed not only by temporal adjacency but also by Gestalt principles of similarity. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

A semi-automated “blanket” method for renal segmentation from non-contrast T1-weighted MR images

Objective

To investigate the precision and accuracy of a new semi-automated method for kidney segmentation from single-breath-hold non-contrast MRI.

Materials and methods

The user draws approximate kidney contours on every tenth slice, focusing on separating adjacent organs from the kidney. The program then performs a sequence of fully automatic steps: contour filling, interpolation, non-uniformity correction, sampling of representative parenchyma signal, and 3D binary morphology. Three independent observers applied the method to images of 40 kidneys ranging in volume from 94.6 to 254.5 cm³. Manually constructed reference masks were used to assess accuracy.

Results

The volume errors for the three readers were: 4.4 % ± 3.0 %, 2.9 % ± 2.3 %, and 3.1 % ± 2.7 %. The relative discrepancy across readers was 2.5 % ± 2.1 %. The interactive processing time on average was 1.5 min per kidney.

Conclusions

Pending further validation, the semi-automated method could be applied for monitoring of renal status using non-contrast MRI.

     

‘Something from nothing’—constructing Israeli rurality

Abstract

This paper analyses the debates regarding native versus non-native plantings in the Israeli kibbutz and their role in the reinvention of the Israeli rural landscape. Based on the assumption that the representation of landscape is always tied to larger questions concerning culture and identity, the genesis of the landscape that has by now become fully naturalised as the new local rural landscape is examined through an analysis of the cultural and ideological roots of its planting design. The Israeli debates reflected the paradox at the heart of a culture that sought to be both ‘new’ and ‘native.’ The ethos of ‘something from nothing’—expressed as the creation of a new green landscape ex nihilo—as well as the advocates for the use of native plants, will be examined in relation to their respective constructions of a landscape narrative.     

Psychometric properties of the French and English versions of the Social Phobia Inventory.

The Social Phobia Inventory (SPIN; Connor et al., 2000) is a self-report measure assessing fear, avoidance, and physiological symptoms associated with social anxiety. To date, the psychometric properties of this English-language measure have been examined primarily in individuals with social phobia. This study examined the psychometric properties of the English SPIN and a newly developed French version of the SPIN in nonclinical groups of undergraduate students. The SPIN, along with several other questionnaires, was completed by 202 English-speaking and 222 French-speaking participants in their respective languages from three different universities. A subset of participants completed the questionnaire a second time approximately one month later to assess test-retest reliability. The SPIN total score exhibited excellent internal consistency and test-retest reliability, as well as strong convergent and divergent validity in both English and French. A revised confirmatory factor analysis suggested the three-factor model of the SPIN was a good fit in French and English; however, the psychometric properties of the fear, avoidance, and physiology subscales were not as strong as those of the total score of the SPIN. The excellent psychometric properties of the English and French SPIN total score support the use of this measure not only in clinical populations, but now also in a nonclinical student sample. (PsycINFO Database Record (c) 2010 APA, all rights reserved)