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.     

Object-based automatic terrain shadow removal from SNPP/VIIRS flood maps

Terrain shadow is a big challenge to land products such as flood extent and snow cover from moderate-resolution optical satellite data. Because terrain shadows share similar spectral features with floodwaters, they can be easily detected as floodwaters by flood detection algorithms based on spectral features in visible, near-infrared, and short-wave infrared channels, which decreases the accuracy of flood detection substantially. However, because terrain shadows appear in mountainous areas with large surface roughness while floodwaters accumulate in low-lying areas with small surface roughness, analysis on surface roughness between terrain shadows and floodwaters can be very effective to distinguish one from the other. Root-mean-square height, internal height difference, and external height difference are used as principal quantitative surface roughness parameters in this study and calculated upon water objects that are clustered from a group of adjacent water pixels. This object-based method is applied in terrain shadow removal from SNPP/VIIRS (Suomi National Polar Orbit Partnership/Visible Infrared Imager Radiometer Suite) near-real-time flood maps and shows promising results according to the tests with 10,000+ VIIRS granules across global areas. Quantitative evaluation in the northwest of the USA also indicates that more than 99% terrain shadow pixels could be removed from VIIRS flood maps by this method, which significantly improves the accuracy of near-real-time flood detection from SNPP/VIIRS imagery.     

Reduction and non-linear controllability of symmetric distributed systems

This paper considers the ‘reduction’ problem for distributed control systems. In particular, we consider controllability of systems containing multiple instances of diffeomorphic components where the overall system dynamics is invariant with respect to a discrete group action. A subclass of such systems are systems with a set of identical components where the overall system dynamics are invariant with respect to physically interchanging these components. The main result is a proposition which shows that for an equivalence class of symmetric systems of this type, controllability of the entire class of systems can be determined by analysing the member of the equivalence class with the smallest state space. The reduction methods developed are illustrated by considering the controllability of a team of mobile robots and a platoon of underwater vehicles.     

Star Diamond Introduces New 8″- 10″ Gem Making Arbor

After two years of total updating, the Grainger Hall of Gems opened to rave reviews in November 1985.     

Brainstorming Products for the Long-term Future

Research has recently been completed to determine how innovative organisations manage innovation over an extended period into the future. The purpose of the research was to determine what companies active in this area, were doing and, from the results, write the new standard BS 7000 part 1 ‘Guide to Innovation Management’. This paper considers one of the findings that organisations can extend the use of brainstorming as a means for: developing the organisational structure for planning the long-term, and envisaging the types of products and services that may be developed up to three generations ahead – typically ten years in many organisations.