An intelligent robotic inspection system for airframe structures

Robot trajectory control is currently performed in an open loop fashion with the trajectory being specified as either a series of end point positions or as a series of joint angle values which are passed through in sequence. In order to perform any complex tasks in an unstructured or semi-structured environment an 'intelligent' robot is required which can sense its environment and alter its trajectory accordingly. This thesis describes the development of an 'intelligent' robotic inspection system which is capable of automatically deploying test probes for the inspection of the structures commonly found in modern airframes with no prior knowledge of the structure being inspected. It utilises a Puma 560 (articulated arm) industrial robot which is under supervisory control from an IBM ps2 personal computer and a wrist-mounted CCD camera with a low power industrial laser to acquire information about the robot's environment. In order to improve the positional accuracy of the Puma it has been calibrated using a computerised surveying system. Extensive use is made of image processing, pattern recognition and mathematical surface modelling to build up a model of the structure being examined and this is used to define the trajectory of the end point of the Puma

Ebolavirus is evolving but not changing: No evidence for functional change in EBOV from 1976 to the 2014 outbreak

The 2014 epidemic of Ebola virus disease (EVD) has had a devastating impact in West Africa. Sequencing of ebolavirus (EBOV) from infected individuals has revealed extensive genetic variation, leading to speculation that the virus may be adapting to humans, accounting for the scale of the 2014 outbreak. We computationally analyze the variation associated with all EVD outbreaks, and find none of the amino acid replacements lead to identifiable functional changes. These changes have minimal effect on protein structure, being neither stabilizing nor destabilizing, are not found in regions of the proteins associated with known functions and tend to cluster in poorly constrained regions of proteins, specifically intrinsically disordered regions. We find no evidence that the difference between the current and previous outbreaks is due to evolutionary changes associated with transmission to humans. Instead, epidemiological factors are likely to be responsible for the unprecedented spread of EVD

Artefacts and biases affecting the evaluation of scoring functions on decoy sets for protein structure prediction

Motivation: Decoy datasets, consisting of a solved protein structure and numerous alternative native-like structures, are in common use for the evaluation of scoring functions in protein structure prediction. Several pitfalls with the use of these datasets have been identified in the literature, as well as useful guidelines for generating more effective decoy datasets. We contribute to this ongoing discussion an empirical assessment of several decoy datasets commonly used in experimental studies

Secondary structure assignment that accurately reflects physical and evolutionary characteristics.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.BACKGROUND: Secondary structure is used in hierarchical classification of protein structures, identification of protein features, such as helix caps and loops, for fold recognition, and as a precursor to ab initio structure prediction. There are several methods available for assigning secondary structure if the three-dimensional structure of the protein is known. Unfortunately they differ in their definitions, particularly in the exact positions of the termini. Additionally, most existing methods rely on hydrogen bonding, which means that important secondary structural classes, such as isolated beta-strands and poly-proline helices cannot be identified as they do not have characteristic hydrogen-bonding patterns. For this reason we have developed a more accurate method for assigning secondary structure based on main chain geometry, which also allows a more comprehensive assignment of secondary structure. RESULTS: We define secondary structure based on a number of geometric parameters. Helices are defined based on whether they fit inside an imaginary cylinder: residues must be within the correct radius of a central axis. Different types of helices (alpha, 3(10) or pi) are assigned on the basis of the angle between successive peptide bonds. beta-strands are assigned based on backbone dihedrals and with alternating peptide bonds. Thus hydrogen bonding is not required and beta-strands can be within a parallel sheet, antiparallel sheet, or can be isolated. Poly-proline helices are defined similarly, although with three-fold symmetry. CONCLUSION: We find that our method better assigns secondary structure than existing methods. Specifically, we find that comparing our methods with those of others, amino-acid trends at helix caps are stronger, secondary structural elements less likely to be concatenated together and secondary structure guided sequence alignment is improved. We conclude, therefore, that secondary structure assignments using our method better reflects physical and evolutionary characteristics of proteins. The program is available from http://www.bioinf.man.ac.uk/~lovell/segno.shtml

Real-Time Quantitative Bronchoscopy

The determination of motion within a sequence of images remains one of the fundamental problems in computer vision after more than 30 years of research. Despite this work, there have been relatively few applications of these techniques to practical problems outside the fields of robotics and video encoding. In this paper, we present the continuing work to apply optical flow and egomotion recovery to the problem of measuring and navigating through the airway using a bronchoscope during a standard procedure, without the need for any additional data, localization systems or other external components. The current implementation uses a number of techniques to provide a range of numerical measurements and estimations to physicians in real time, using standard computer hardware

Sequencing and characterisation of rearrangements in three S. pastorianus strains reveals the presence of chimeric genes and gives evidence of breakpoint reuse

Gross chromosomal rearrangements have the potential to be evolutionarily advantageous to an adapting organism. The generation of a hybrid species increases opportunity for recombination by bringing together two homologous genomes. We sought to define the location of genomic rearrangements in three strains of Saccharomyces pastorianus, a natural lager-brewing yeast hybrid of Saccharomyces cerevisiae and Saccharomyces eubayanus, using whole genome shotgun sequencing. Each strain of S. pastorianus has lost species-specific portions of its genome and has undergone extensive recombination, producing chimeric chromosomes. We predicted 30 breakpoints that we confirmed at the single nucleotide level by designing species-specific primers that flank each breakpoint, and then sequencing the PCR product. These rearrangements are the result of recombination between areas of homology between the two subgenomes, rather than repetitive elements such as transposons or tRNAs. Interestingly, 28/30 S. cerevisiae- S. eubayanus recombination breakpoints are located within genic regions, generating chimeric genes. Furthermore we show evidence for the reuse of two breakpoints, located in HSP82 and KEM1, in strains of proposed independent origin

Scintillation in the Circinus Galaxy water megamasers

We present observations of the 22 GHz water vapor megamasers in the Circinus galaxy made with the Tidbinbilla 70m telescope. These observations confirm the rapid variability seen earlier by Greenhill et al (1997). We show that this rapid variability can be explained by interstellar scintillation, based on what is now known of the interstellar scintillation seen in a significant number of flat spectrum AGN. The observed variability cannot be fully described by a simple model of either weak or diffractive scintillation.Comment: 10 pages, 5 figures. AJ accepte