Hypothesis exploration with visualization of variance.

BackgroundThe Consortium for Neuropsychiatric Phenomics (CNP) at UCLA was an investigation into the biological bases of traits such as memory and response inhibition phenotypes-to explore whether they are linked to syndromes including ADHD, Bipolar disorder, and Schizophrenia. An aim of the consortium was in moving from traditional categorical approaches for psychiatric syndromes towards more quantitative approaches based on large-scale analysis of the space of human variation. It represented an application of phenomics-wide-scale, systematic study of phenotypes-to neuropsychiatry research.ResultsThis paper reports on a system for exploration of hypotheses in data obtained from the LA2K, LA3C, and LA5C studies in CNP. ViVA is a system for exploratory data analysis using novel mathematical models and methods for visualization of variance. An example of these methods is called VISOVA, a combination of visualization and analysis of variance, with the flavor of exploration associated with ANOVA in biomedical hypothesis generation. It permits visual identification of phenotype profiles-patterns of values across phenotypes-that characterize groups. Visualization enables screening and refinement of hypotheses about variance structure of sets of phenotypes.ConclusionsThe ViVA system was designed for exploration of neuropsychiatric hypotheses by interdisciplinary teams. Automated visualization in ViVA supports 'natural selection' on a pool of hypotheses, and permits deeper understanding of the statistical architecture of the data. Large-scale perspective of this kind could lead to better neuropsychiatric diagnostics

IDENTIFICATION AND ASSESSMENT OF PROBLEMATIC EXPANSIVE SOILS

Published ThesisIn the last few decades the construction of small dwellings, particularly government subsidy houses, has increased markedly in South Africa. Large numbers of these light structures have suffered severe damage and many have been demolished after being occupied for only a small fraction of their expected life-span. The research detailed in this thesis deals with a search for reasons for these widespread failures and investigations into economically feasible solutions. The investigation began with an assessment of the current methods of identification and assessment of potentially problematic expansive soils. This revealed serious shortcomings in a number of the standard testing procedures. These shortcomings may have consequences for a wider range of engineering projects than just housing development. Progress towards more reliable testing methods has led to an appreciation of the importance of variability of soil properties and the necessity of taking this into account in engineering design. Investigation of clay fraction determination by the hydrometer has led to the realization that the unreliability of this procedure has been a cause of failure in subsidy housing projects as well as other light structure developments. Assessment of expansive potential cannot safely rely on hydrometer determination of clay fraction, which is a principal parameter for a number of popular design procedures. It was also established that attractive alternatives in the form of automatic particle sizing equipment (designed for the analysis of industrial powders) are not suitable for natural soils containing the clays commonly found in South African soils. Alternative procedures, particularly small-scale suction testing, have been found to provide more reliable insights into design for expansive clays. The investigations suggest that some form of Reliability Based Design, which takes account of specific variability in soil properties, may be the only way to achieve rational design for foundations on expansive clay

Modeling the Risk of Fire/Explosion Due to Oxidizer/Fuel Leaks in the Ares I Interstage

A significant flight hazard associated with liquid propellants, such as those used in the upper stage of NASA's new Ares I launch vehicle, is the possibility of leakage of hazardous fluids resulting in a catastrophic fire/explosion. The enclosed and vented interstage of the Ares I contains numerous oxidizer and fuel supply lines as well as ignition sources. The potential for fire/explosion due to leaks during ascent depends on the relative concentrations of hazardous and inert fluids within the interstage along with other variables such as pressure, temperature, leak rates, and fluid outgasing rates. This analysis improves on previous NASA Probabilistic Risk Assessment (PRA) estimates of the probability of deflagration, in which many of the variables pertinent to the problem were not explicitly modeled as a function of time. This paper presents the modeling methodology developed to analyze these risks

Distinct Molecular Mechanisms of Host Immune Response Modulation by Arenavirus NP and Z Proteins

Endemic to West Africa and South America, mammalian arenaviruses can cross the species barrier from their natural rodent hosts to humans, resulting in illnesses ranging from mild flu-like syndromes to severe and fatal haemorrhagic zoonoses. The increased frequency of outbreaks and associated high fatality rates of the most prevalent arenavirus, Lassa, in West African countries, highlights the significant risk to public health and to the socio-economic development of affected countries. The devastating impact of these viruses is further exacerbated by the lack of approved vaccines and effective treatments. Differential immune responses to arenavirus infections that can lead to either clearance or rapid, widespread and uncontrolled viral dissemination are modulated by the arenavirus multifunctional proteins, NP and Z. These two proteins control the antiviral response to infection by targeting multiple cellular pathways; and thus, represent attractive targets for antiviral development to counteract infection. The interplay between the host immune responses and viral replication is a key determinant of virus pathogenicity and disease outcome. In this review, we examine the current understanding of host immune defenses against arenavirus infections and summarise the host protein interactions of NP and Z and the mechanisms that govern immune evasion strategies

Simulation, modelling and development of the metris RCA

In partnership with Metris UK we discuss the utilisation of modelling and simulation methods in the development of a revolutionary 7-axis Robot CMM Arm (RCA). An offline virtual model is described, facilitating pre-emptive collision avoidance and assessment of optimal placement of the RCA relative to scan specimens. Workspace accessibility of the RCA is examined under a range of geometrical assumptions and we discuss the effects of arbitrary offsets resulting from manufacturing tolerances. Degeneracy is identified in the number of ways a given pose may be attained and it is demonstrated how a simplified model may be exploited to solve the inverse kinematics problem of finding the “correct” set of joint angles. We demonstrate how the seventh axis may be utilised to avoid obstacles or otherwise awkward poses, giving the unit greater dexterity than traditional CMMs. The results of finite element analysis and static force modelling on the RCA are presented which provide an estimate of the forces exerted on the internal measurement arm in a range of poses

Characteristics, accuracy and reverification of robotised articulated arm CMMs

VDI article 2617 specifies characteristics to describe the accuracy of articulated arm coordinate measuring machines (AACMMs) and outlines procedures for checking them. However the VDI prescription was written with a former generation of machines in mind: manual arms exploiting traditional touch probe technologies. Recent advances in metrology have given rise to noncontact laser scanning tools and robotic automation of articulated arms – technologies which are not adequately characterised using the VDI specification. In this paper we examine the “guidelines” presented in VDI 2617, finding many of them to be ambiguous and open to interpretation, with some tests appearing even to be optional. The engineer is left significant flexibility in the execution of the test procedures and the manufacturer is free to specify many of the test parameters. Such flexibility renders the VDI tests of limited value and the results can be misleading. We illustrate, with examples using the Nikon RCA, how a liberal interpretation of the VDI guidelines can significantly improve accuracy characterisation and suggest ways in which to mitigate this problem. We propose a series of stringent tests and revised definitions, in the same vein as VDI 2617 and similar US standards, to clarify the accuracy characterisation process. The revised methodology includes modified acceptance and reverification tests which aim to accommodate emerging technologies, laser scanning devices in particular, while maintaining the spirit of the existing and established standards. We seek to supply robust re-definitions for the accepted terms “zero point” and “useful arm length”, pre-supposing nothing about the geometry of the measuring device. We also identify a source of error unique to robotised AACMMs employing laser scanners – the forward-reverse pass error. We show how eliminating this error significantly improves the repeatability of a device and propose a novel approach to the testing of probing error based on statistical uncertainty

Risk Assessment Challenges in the Ares I Upper Stage

NASA Marshall Space Flight Center (MSFC) is currently at work developing hardware and systems for the Ares I rocket that will send future astronauts into orbit. Built on cutting-edge launch technologies, evolved powerful Apollo and Space Shuttle propulsion elements, and decades of NASA spaceflight experience, Ares I is the essential core of a safe, reliable, cost-effective space transportation system -- one that will carry crewed missions back to the moon, on to Mars and out into the solar system. Ares I is an in-line, two-stage rocket configuration topped by the Orion crew vehicle and its launch abort system. In addition to the vehicle's primary mission -carrying crews of four to six astronauts to Earth orbit --Ares I may also use its 25-ton payload capacity to deliver resources and supplies to the International Space Station, or to "park" payloads in orbit for retrieval by other spacecraft bound for the moon or other destinations. Crew transportation to the International Space Station is planned to begin no later than 2014. The first lunar excursion is scheduled for the 2020 timeframe. This paper presents the challenges in designing the Ares I upper stage for reliability and safety while minimizing weight and maximizing performance

The application of optical coherence tomography to image subsurface tissue structure of Antarctic krill Euphausia superba

Many small open ocean animals, such as Antarctic krill, are an important part of marine ecosystems. To discover what will happen to animals such as krill in a changing ocean, experiments are run in aquaria where conditions can be controlled to simulate water characteristics predicted to occur in the future. The response of individual animals to changing water conditions can be hard to observe, and with current observation techniques it is very difficult to follow the progress of an individual animal through its life. Optical coherence tomography (OCT) is an optical imaging technique that allows images at high resolution to be obtained from depths up to a few millimeters inside biological specimens. It is compatible with in vivo imaging and can be used repeatedly on the same specimens. In this work, we show how OCT may be applied to post mortem krill samples and how important physiological data such as shell thickness and estimates of organ volume can be obtained. Using OCT we find an average value for the thickness of krill exoskeleton to be (30±4) µm along a 1 cm length of the animal body. We also show that the technique may be used to provide detailed imagery of the internal structure of a pleopod joint and provide an estimate for the heart volume of (0.73±0.03) mm3