Inferring Phylogenetic Trees Using Answer Set Programming

We describe the reconstruction of a phylogeny for a set of taxa, with a character-based cladistics approach, in a declarative knowledge representation formalism, and show how to use computational methods of answer set programming to generate conjectures about the evolution of the given taxa. We have applied this computational method in two domains: historical analysis of languages and historical analysis of parasite-host systems. In particular, using this method, we have computed some plausible phylogenies for Chinese dialects, for Indo-European language groups, and for Alcataenia species. Some of these plausible phylogenies are different from the ones computed by other software. Using this method, we can easily describe domain-specific information (e.g., temporal and geographical constraints), and thus prevent the reconstruction of some phylogenies that are not plausible. This paper is a revised and extended version of [3].     

A hybrid PET‐MRI: An integrated molecular‐genetic imaging system with HRRT‐PET and 7.0‐T MRI

A PET‐MRI fusion system is developed for molecular‐genetic imaging. The purpose of the system is to obtain images of the in‐vivo human brain using two high‐end imaging devices, an advanced PET and an ultrahigh‐field MRI. These are the HRRT‐PET, a high‐resolution research tomograph dedicated to brain imaging on the molecular level, and the 7.0‐T MRI, an ultrahigh field version used for morphological imaging. HRRT‐PET delivers high‐resolution molecular imaging with a resolution down to 2.5 mm FWHM, which is currently the highest spatial resolution available for the observation of the human brain's molecular activities, including enzymes and receptors, which are manipulated genetically, such as reporter genes and probes. The 7.0‐T MRI began to reveal submillimeter resolution images of the cortical as well as deep brain areas, down to 250 μm, which allows us to visualize the fine details of the cortical and brainstem areas, including the line of Gennari in the visual cortex and the corticospinal tracts in the pontine area. The current PET‐MRI fusion imaging system produces the highest quality images of molecular and genetic activities of the human brain in vivo. It is starting to provide many answers to the key questions about the neurological diseases. Some of these start providing answers to many cognitive neuroscience problems with clear molecular and genetic bases. There is great potential in the PET‐MRI for early diagnosis of cancers as well as other neurological diseases, which we were previously unable to diagnose, such as microscopic molecular changes that occur in Parkinson's and Alzheimer's diseases. © 2007 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 17, 252–265, 2007     

Effects of computer-based educational achievement test on test performance and test takers’ motivation

There has been an increasing interest in recent years in developing and using computer-based tests in educational assessment. To replace paper-based tests with computer-based ones, the standards for developing computerized-assessment (International Test Commission., 2004) requires equivalent test scores to be established for the new computer-based test and the conventional paper-based test. However, in most test mode comparability studies, the actual test items used have been identical, and yet significant differences have been found in test scores in paper-based and computer-based modes. This has been reported for several subjects, including science, languages and mathematics. The validity of using computer-based tests in educational assessment must therefore be questioned. This study involves a biology test and a biology motivation questionnaire using a Solomon four-group experimental design to examine the validity of the computer-based test and its effects on test performance and the motivation of test-takers. The findings provide supportive evidence for the validity of computer-based test in educational assessment.     

The metacognitive loop I: Enhancing reinforcement learning with metacognitive monitoring and control for improved perturbation tolerance

Maintaining adequate performance in dynamic and uncertain settings has been a perennial stumbling block for intelligent systems. Nevertheless, any system intended for real-world deployment must be able to accommodate unexpected change—that is, it must be perturbation tolerant. We have found that metacognitive monitoring and control—the ability of a system to self-monitor its own decision-making processes and ongoing performance, and to make targeted changes to its beliefs and action-determining components—can play an important role in helping intelligent systems cope with the perturbations that are the inevitable result of real-world deployment. In this article we present the results of several experiments demonstrating the efficacy of metacognition in improving the perturbation tolerance of reinforcement learners, and discuss a general theory of metacognitive monitoring and control, in a form we call the metacognitive loop.     

Estimating boreal forest species type with airborne polarimetric synthetic aperture radar

We have applied a non-parametric classifier (k nearest neighbour) to two calibrated orthogonal passes of airborne polarimetric synthetic aperture radar (POLSAR) image data over boreal forest for the purpose of discriminating canopy tree species of predefined stands. We found that a single classifier based on a single feature space (i.e. one set of POLSAR variables for all species) was less accurate than a hierarchical two-stage classifier that used different POLSAR variables for each species. We designed a two-stage classifier that first grouped stands into broad classes: pine, spruce and deciduous, and then classified each sample within the broad classes into individual species. We found that the most effective feature spaces had two or three dimensions. The two-stage classifier attained overall accuracies of between 60% and 75%.

We provide a first use of an equivalency test applied to remote-sensing classification. We use Lloyd's test of equivalency to find equivalent classifiers and thus infer informative POLSAR variables. The POLSAR variables that were most informative varied between the two passes and between the various elements of the hierarchical classifier. For the initial three-class classifier the most informative POLSAR variables were the two circular polarization ratios, several of Touzi's Stokes vector variables, HHVV coherence, several texture measures such as the variance of several scattering coefficients and the order parameter of the K-distribution and characteristics of the polarization signature pedestal. These results demonstrate that C-band POLSAR has great potential for mapping boreal forest cover either on its own or in concert with other geospatial data.     

Minimum-time trajectory generation for constrained linear systems using flatness and B-splines

In this article, we discuss minimum-time trajectory generation for input-and-state constrained continuous-time LTI systems in the light of the notion of flatness and B-splines parametrisation. Flat systems have the useful property that the input and the state trajectories can be completely characterised by the (so-called) flat output. We propose a splines parametrisation for the flat output, and the corresponding parametrisations for the performance output, the states and the inputs. Using this parametrisation the problem of minimum-time constrained trajectory planning is cast into a feasibility-search problem in the splines control-point space, in which the constraint region is characterised by a polytope. A close approximation of the minimum-time trajectory is obtained by systematically searching the end-time that makes the constraint polytope to be minimally feasible.     

The Effect of Surface Roughness on Contact Fatigue Behavior Using Mesoscopic Approach

The effect of surface roughness on the contact fatigue was investigated in this study. To accomplish this goal, contact analysis based on the influence functions and the rectangular patch solutions was performed to obtain the subsurface stress. Mesoscopic multiaxial fatigue criterion is then applied to predict fatigue damage. Rainbow counting method and damage rule were used to evaluate the fatigue life under random loadings caused by the rough surface contact. As a result of the fatigue analysis, the relationship among the fatigue life, the crack initiation depth, and the surface roughness were revealed. It is observed that the fatigue life has hardly changed and a crack is initiated at subsurface for the surface with the surface roughness below a critical value. However, if the surface roughness exceeds the critical value, fatigue life is remarkably reduced and the site of crack initiation moves to the near surface.     

<Emphasis Type="Italic">In-Situ</Emphasis> Neutron Scattering Measurement of Stress-Strain Behavior of a Bulk Metallic Glass

Bulk metallic glasses (BMGs) are an emerging class of materials whose unique properties make them excellent choices for many applications. As with crystalline metals, the processing and forming techniques used to produce BMG components necessarily result in residual stresses. However, traditional diffraction stress analysis is difficult to apply to BMG components, because they lack the long-range order necessary to produce sharp diffraction patterns, and thus, the internal strains for BMG have not been examined until recently. In this work, in-situ neutron scattering was used to measure the local elastic internal strain distribution in a Zr₅₇Nb₅Cu_15.4Ni_12.6Al₁₀ BMG as a function of applied stress. Various techniques were used to evaluate the internal strain. The strain was determined in real space, by measuring changes in the atomic pair distribution function (PDF). These results can be used to help understand the elastic deformation of BMGs as well be to evaluate current models of BMG deformation. This article is based on a presentation given in the symposium entitled “Bulk Metallic Glasses IV,” which occurred February 25–March 1, 2007 during the TMS Annual Meeting in Orlando, Florida under the auspices of the TMS/ASM Mechanical Behavior of Materials Committee.     

Bush u-turn on renewables?

Despite early indications from the Bush Administration that renewable energy was neither a top priority nor to be funded at levels seen in the Clinton Administration, there appears to be a slow back peddling on this issue. President George W. Bush's proposed energy programme has been encountering mounting hostility on Capitol Hill in Washington as well as significantly growing opposition among many Americans. Don Smith, US correspondent for Refocus magazine reports.     

Improving the quality of operations in truckload trucking

In this paper, the authors discuss the quality of operations in the truckioad trucking industry. After introducing the concept of quality in the industry from the perspective of the customer, the carrier, and the driver, the authors introduce a new operational paradigm based on zone dispatching that leads to improved quality from all three perspectives. A review of the current literature indicates that the approach is unique. A comprehensive experimental design supports simulation experiments to examine operational design parameters and to determine solution robustness for zone dispatching alternatives. Results indicate that zone dispatching alternatives compare favorably with baseline point-to-point dispatching methods. Case studies supported by data provided by J.B. Hunt Transport, Inc. further demonstrate the efficacy of the approach as a means of improving the quality of operations in truckioad trucking. Additionally, a research framework is provided to guide future efforts in this area.