Genomic mining for complex disease traits with “random chemistry”

Our rapidly growing knowledge regarding genetic variation in the human genome offers great potential for understanding the genetic etiology of disease. This, in turn, could revolutionize detection, treatment, and in some cases prevention of disease. While genes for most of the rare monogenic diseases have already been discovered, most common diseases are complex traits, resulting from multiple gene–gene and gene-environment interactions. Detecting epistatic genetic interactions that predispose for disease is an important, but computationally daunting, task currently facing bioinformaticists. Here, we propose a new evolutionary approach that attempts to hill-climb from large sets of candidate epistatic genetic features to smaller sets, inspired by Kauffman’s “random chemistry” approach to detecting small auto-catalytic sets of molecules from within large sets. Although the algorithm is conceptually straightforward, its success hinges upon the creation of a fitness function able to discriminate large sets that contain subsets of interacting genetic features from those that don’t. Here, we employ an approximate and noisy fitness function based on the ReliefF data mining algorithm. We establish proof-of-concept using synthetic data sets, where individual features have no marginal effects. We show that the resulting algorithm can successfully detect epistatic pairs from up to 1,000 candidate single nucleotide polymorphisms in time that is linear in the size of the initial set, although success rate degrades as heritability declines. Research continues into seeking a more accurate fitness approximator for large sets and other algorithmic improvements that will enable us to extend the approach to larger data sets and to lower heritabilities.     

The who and the what of usage of two cancer online communities

The explosion of use of Internet-based communication for health requires attention to the ways survivors of specific diseases and those close to them participate in using resources. This research focuses on two cancer groups – breast and prostate – and how they use WebMD asynchronous bulletin boards. Four hundred and eighty two messages were coded for communicator (survivors, spouses, others) and content of messages. Most common communicators were survivors, but the two groups differed in percentages of communicator. Of four main categories of content – medical/treatment, intimacy/sexuality, emotional expression, and support – most common were support and medical/treatment. The groups differed significantly on those four categories, with breast cancer more support-dominated and prostate more medical/treatment-dominated and more intimacy/sexuality messages. There were no group differences in emotional-toned vs. social support seeking vs. providing support, or positive vs. negative emotions expressed. Generally, there was considerable commonality, and the differences found primarily supported gender-specific notions of communication and need.     

Further explorations of perceptual speed abilities in the context of assessment methods, cognitive abilities, and individual differences during skill acquisition.

Measures of perceptual speed ability have been shown to be an important part of assessment batteries for predicting performance on tasks and jobs that require a high level of speed and accuracy. However, traditional measures of perceptual speed ability sometimes have limited cost-effectiveness because of the requirements for administration and scoring of paper-and-pencil tests. There have also been concerns about the validity of previous computer approaches to administering perceptual speed tests (e.g., see Mead & Drasgow, 1993). The authors developed two sets of computerized perceptual speed tests, with touch-sensitive monitors, that were designed to parallel several paper-and-pencil tests. The reliability and validity of the tests were explored across three empirical studies (N = 167, 160, and 117, respectively). The final study included two criterion tasks with 4.67 and 10 hours of time-on-task practice, respectively. Results indicated that these new measures provide both high levels of reliability and substantial validity for performance on the two skill-learning tasks. Implications for research and application for computerized perceptual speed tests are discussed. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Researching haptics in higher education: The complexity of developing haptics virtual learning systems and evaluating its impact on students’ learning

hapTEL, an interdisciplinary project funded by two UK research councils from 2007 to 2011, involves a large interdisciplinary team (with undergraduate and post-graduate student participants) which has been developing and evaluating a virtual learning system within an HE healthcare education setting, working on three overlapping strands. Strand 1 involves the technical development and evaluation of the hapTEL workstation which simulates clinical conditions for dental training including haptics (sense of touch). Strand 2 involves examining the traditional undergraduate curriculum and how this could benefit from the use of haptics. Strand 3 is concerned with the educational evaluation of the impact of the work carried out within Strands 1 and 2. Two theoretical frameworks (Entwistle, (1987) and Webb and Cox (2004)) have been used to identify as many factors as possible which could affect the impact of Technology Enhanced Learning (TEL) on the quality of the learning achieved. These frameworks have formed a foundation for measuring the impact of TEL on curriculum change, teachers’ pedagogical practices, students’ learning and on institutional practices. A range of quantitative and qualitative methods were designed, piloted and evaluated in order to measure the impact of TEL on teaching and learning; and to have a rich and robust data set which also addresses the variables in the frameworks. The results from using these frameworks show that institutional and departmental factors should be considered when evaluating the impact of TEL in higher education and that these had a major influence on the design and curriculum integration of the hapTEL systems. We have also shown that by involving the end users from the beginning enabled not only an enhancement of the students’ learning experiences but also a modification to the traditional curriculum itself and the successful integration of TEL within a very traditional undergraduate higher education dental curriculum. The conclusions from this paper confirm earlier reviews of researching TEL that technology integration is extremely complex and the related research requires a comprehensive approach of both quantitative and qualitative methods if one is to take account of the range of variables identified by theoretical frameworks. Finally, repeating the range of empirical investigations for a second year enables researchers to validate the effectiveness of the methods used in the initial year and thereby maximise the reliability and generalisability of the research outcomes.     

The design process and the ‘crisis’ in the UK information technology industry

The competitive position of UK information technology (IT) manufacturers in the expanding markets for IT equipment is declining. A recent report published by the National Economic Development Council (NEDC)¹ describes the situation facing the UK IT industry as one of ‘crisis’.This paper reports some of the findings of an investigation, conducted by the Design Innovation Group at the Open University, into the role of design in the competitiveness of manufacturers of IT equipment. The approach to design and development of four UK companies is examined in detail. It is argued that the supplier's lack of attention to design for user needs contributes to the ‘crisis’ situation expressed by the NEDC.     

Longitudinal predictors of reading and math trajectories through middle school for African American versus Caucasian students across two samples.

This study's primary purpose was to examine the relative contribution of social-behavioral predictors to reading and math skills. The study expands on Duncan et al.'s (2007) work by using longitudinal methodology from the National Institute of Child Health and Human Development's Study of Child Care and Youth Development (SECCYD) and the Early Childhood Longitudinal Study, Kindergarten Class of 1998–1999 (ECLS-K) databases, and by focusing on potential differences in patterns of early predictors of later reading and math trajectories for African American versus Caucasian students. Predictor measures were selected at kindergarten, and the outcomes included standardized reading and math scores obtained from Grades 1, 3, 5, and 9 for the SECCYD sample, and Grades 3, 5, and 8 for the ECLS-K sample. Consistent with Duncan et al.'s findings, results reflect the relative contributions of early reading and math skills to later functioning in these respective academic domains for both samples, and there are indications for the importance of early expressive language skills to both reading and math in the SECCYD sample. Findings related to the power of social-behavioral predictors, however, are not consistent across samples. Although the SECCYD sample evidenced no such predictors, several interactions in the ECLS-K sample suggested the moderating effects of early ratings of aggressive behaviors and internalizing behaviors on later reading and math for African American students. The moderating effects of early teacher ratings of attention and internalizing behaviors for African American students as compared with Caucasian students in later math growth also were noted. The importance of early social-behavioral functions as related to later academic skills remains an important area of inquiry. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Prospective predictors of posttraumatic stress disorder symptoms: Direct and mediated relations.

This study assessed the relations between pretrauma risk (neuroticism, negative affect, prior distress) and protective (self-esteem, optimism) factors and posttraumatic stress disorder (PTSD) symptoms and potential mediators (subjective event-related distress, unsupportive social interactions, perceived control) of those relations. Students (N = 1,528) at four U.S. universities completed online surveys assessing pretrauma risk and protective factors at Time 1 (T1); 84% (N = 1,281) completed a survey 2 months later (T2). PTSD symptoms and the three potential mediators were assessed among those who experienced potentially traumatic events between T1 and T2 (n = 264). PTSD symptoms related to prior traumas were controlled in all analyses. In structural equation modeling (SEM) analyses, the relation between risk factors and PTSD symptoms was mediated by unsupportive social interactions. Protective factors did not independently predict PTSD symptoms when risk factors also were included in the SEM models. Implications for research and practice are discussed. (PsycINFO Database Record (c) 2011 APA, all rights reserved)     

Right hemisphere dysfunction in nonverbal learning disabilities: Social, academic, and adaptive functioning in adults and children.

Addresses recent research on social and nonverbal learning disabilities. Involvement of right hemispheric dysfunction in these disabilities has been hypothesized, as studies with adults have suggested that documented right hemisphere damage may lead to deficits in social skills, prosody, spatial orientation, problem solving, and recognition of nonverbal cues. Studies of children purported to evidence nonverbal learning disabilities are reviewed and compared with the results from studies of adults with right hemisphere damage. Specific subtypes of nonverbal learning disabilities are reviewed, including the nonverbal perceptual-organization-output subtype, Asperger's syndrome, Developmental Gerstmann syndrome, left hemisyndrome, right hemisphere syndrome, and right parietal lobe syndrome. Finally, implications and future research needs are addressed. The need for a diagnostic nosology and improved and validated intervention techniques is stressed as is early identification of these types of specific nonverbal learning disabilities. (PsycINFO Database Record (c) 2010 APA, all rights reserved)