Iteratively predict protein functions from protein-protein interactions

Current similarity-based approaches of predicting protein functions from protein-protein interaction (PPI) data usually make use of available information in the PPI network to predict functions of un-annotated proteins, and the prediction is a one-off procedure. However the interactions between proteins are more likely to be mutual rather than static and mono-directed. In other words, the un-annotated proteins, once their functions are predicted, will in turn affect the similarities between proteins. In this paper, we propose an innovative iteration algorithm that incorporates this dynamic feature of protein interaction into the protein function prediction, aiming to achieve higher prediction accuracies and get more reasonable results. With our algorithm, instead of one-off function predictions, functions are assigned to an unannotated protein iteratively until the functional similarities between proteins achieve a stable state. The experimental results show that our iterative method can provide better prediction results than one-off prediction methods with higher prediction accuracies, and is stable for large protein datasets.

Dynamically predicting protein functions from semantic associations of proteins

Predicting functions of un-annotated proteins is a significant challenge in the post-genomics era. Among existing computational approaches, exploiting interactions between proteins to predict functions of un-annotated proteins is widely used. However, it remains difficult to extract semantic associations between proteins (i.e. protein associations in terms of protein functionality) from protein interactions and incorporate extracted semantic associations to more effectively predict protein functions. Furthermore, existing approaches and algorithms regard the function prediction as a one-off procedure, ignoring dynamic and mutual associations between proteins. Therefore, deriving and exploiting semantic associations between proteins to dynamically predict functions are a promising and challenging approach for achieving better prediction results. In this paper, we propose an innovative algorithm to incorporate semantic associations between proteins into a dynamic procedure of protein function prediction. The semantic association between two proteins is measured by the semantic similarity of two proteins which is defined by the similarities of functions two proteins possess. To achieve better prediction results, function similarities are also incorporated into the prediction procedure. The algorithm dynamically predicts functions by iteratively selecting functions for the un-annotated protein and updating the similarities between the un-annotated protein and its neighbour annotated proteins until such suitable functions are selected that the similarities no longer change. The experimental results on real protein interaction datasets demonstrated that our method outperformed the similar and non-dynamic function prediction methods. Incorporating semantic associations between proteins into a dynamic procedure of function prediction reflects intrinsic relationships among proteins as well as dynamic features of protein interactions, and therefore, can significantly improve prediction results.

On the use of restricted dissimilarity and dissimilarity-like functions for defining penalty functions

In this work we study the relation between restricted dissimilarity functions-and, more generally, dissimilarity-like functions- and penalty functions and the possibility of building the latter using the former. Several results on convexity and quasiconvexity are also considered.

Multitasking: multiple, domain-specific cognitive functions in a virtual environment

Multitasking among three or more different tasks is a ubiquitous requirement of everyday cognition, yet rarely is it addressed in research on healthy adults who have had no specific training in multitasking skills. Participants completed a set of diverse subtasks within a simulated shopping mall and office environment, the Edinburgh Virtual Errands Test (EVET). The aim was to investigate how different cognitive functions, such as planning, retrospective and prospective memory, and visuospatial and verbal working memory, contribute to everyday multitasking. Subtasks were chosen to be diverse, and predictions were derived from a statistical model of everyday multitasking impairments associated with frontal-lobe lesions (Burgess, Veitch, de Lacy Costello, & Shallice, 2000b). Multiple regression indicated significant independent contributions from measures of retrospective memory, visuospatial working memory, and online planning, but not from independent measures of prospective memory or verbal working memory. Structural equation modelling showed that the best fit to the data arose from three underlying constructs, with Memory and Planning having a weak link, but with both having a strong directional pathway to an Intent construct that reflected implementation of intentions. Participants who followed their preprepared plan achieved higher scores than those who altered their plan during multitask performance. This was true regardless of whether the plan was efficient or poor. These results substantially develop and extend the Burgess et al. (2000b) model to healthy adults and yield new insight into the poorly understood area of everyday multitasking. The findings also point to the utility of using virtual environments for investigating this form of complex human cognition.

Effectiveness and feasibility of virtual reality and gaming system use at home by older adults for enabling physical activity to improve health-related domains: a systematic review

Background
use of virtual reality and commercial gaming systems (VR/gaming) at home by older adults is receiving attention as a means of enabling physical activity.

Objective
to summarise evidence for the effectiveness and feasibility of VR/gaming system utilisation by older adults at home for enabling physical activity to improve impairments, activity limitations or participation.

Methods
a systematic review searching 12 electronic databases from 1 January 2000–10 July 2012 using key search terms. Two independent reviewers screened yield articles using pre-determined selection criteria, extracted data using customised forms and applied the Cochrane Collaboration Risk of Bias Tool and the Downs and Black Checklist to rate study quality.

Results
fourteen studies investigating the effects of VR/gaming system use by healthy older adults and people with neurological conditions on activity limitations, body functions and physical impairments and cognitive and emotional well-being met the selection criteria. Study quality ratings were low and, therefore, evidence was not strong enough to conclude that interventions were effective. Feasibility was inconsistently reported in studies. Where feasibility was discussed, strong retention (≥70%) and adherence (≥64%) was reported. Initial assistance to use the technologies, and the need for monitoring exertion, aggravation of musculoskeletal symptoms and falls risk were reported.

Conclusions
existing evidence to support the feasibility and effectiveness VR/gaming systems use by older adults at home to enable physical activity to address impairments, activity limitations and participation is weak with a high risk of bias. The findings of this review may inform future, more rigorous research.

Image reduction operators based on non-monotonic averaging functions

Image reduction is a crucial task in image processing, underpinning many practical applications. This work proposes novel image reduction operators based on non-monotonic averaging aggregation functions. The technique of penalty function minimisation is used to derive a novel mode-like estimator capable of identifying the most appropriate pixel value for representing a subset of the original image. Performance of this aggregation function and several traditional robust estimators of location are objectively assessed by applying image reduction within a facial recognition task. The FERET evaluation protocol is applied to confirm that these non-monotonic functions are able to sustain task performance compared to recognition using nonreduced images, as well as significantly improve performance on query images corrupted by noise. These results extend the state of the art in image reduction based on aggregation functions and provide a basis for efficiency and accuracy improvements in practical computer vision applications.