SIFA: A tool for evaluation of high-grade security devices

We describe a tool for analysing information flow in security hardware. It identifies both sub-circuits critical to the preservation of security as well as the potential for information flow due to hardware failure. The tool allows for the composition of both logical and physical views of circuit designs. An example based on a cryptographic device is provided.

Development and evaluation of an automated annotation pipeline and cDNA annotation system

Manual curation has long been held to be the gold standard for functional annotation of DNA sequence. Our experience with the annotation of more than 20,000 full-length cDNA sequences revealed problems with this approach, including inaccurate and inconsistent assignment of gene names, as well as many good assignments that were difficult to reproduce using only computational methods. For the FANTOM2 annotation of more than 60,000 cDNA clones, we developed a number of methods and tools to circumvent some of these problems, including an automated annotation pipeline that provides high-quality preliminary annotation for each sequence by introducing an uninformative filter that eliminates uninformative annotations, controlled vocabularies to accurately reflect both the functional assignments and the evidence supporting them, and a highly refined, Web-based manual annotation tool that allows users to view a wide array of sequence analyses and to assign gene names and putative functions using a consistent nomenclature. The ultimate utility of our approach is reflected in the low rate of reassignment of automated assignments by manual curation. Based on these results, we propose a new standard for large-scale annotation, in which the initial automated annotations are manually investigated and then computational methods are iteratively modified and improved based on the results of manual curation.

Comparative evaluation of microscopic car-following behavior

Microscopic traffic-simulation tools are increasingly being applied to evaluate the impacts of a wide variety of intelligent transport, systems (ITS) applications and other dynamic problems that are difficult to solve using traditional analytical models. The accuracy of a traffic-simulation system depends highly on the quality of the traffic-flow model at its core, with the two main critical components being the car-following and lane-changing models. This paper presents findings from a comparative evaluation of car-following behavior in a number of traffic simulators [advanced interactive microscopic simulator for urban and nonurban networks (AIMSUN), parallel microscopic simulation (PARAMICS), and Verkehr in Statiten-simulation (VISSIM)]. The car-following algorithms used in these simulators have been developed from a variety of theoretical backgrounds and are reported to have been calibrated on a number of different data sets. Very few independent studies have attempted to evaluate the performance of the underlying algorithms based on the same data set. The results reported in this study are based on a car-following experiment that used instrumented vehicles to record the speed and relative distance between follower and leader vehicles on a one-lane road. The experiment was replicated in each tool and the simulated car-following behavior was compared to the field data using a number of error tests. The results showed lower error values for the Gipps-based models implemented in AIMSUN and similar error values for the psychophysical spacing models used in VISSIM and PARAMICS. A qualitative drift and goal-seeking behavior test, which essentially shows how the distance headway between leader and follower vehicles should oscillate around a stable distance, also confirmed the findings.

Screening for physical activity in family practice - Evaluation of two brief assessment tools

Background: Physical activity (PA) is relevant to the prevention and management of many health conditions in family practice. There is a need for an efficient, reliable, and valid assessment tool to identify patients in need of PA interventions. Methods: Twenty-eight family physicians in three Australian cities assessed the PA of their adult patients during 2004 using either a two- (2Q) or three-question (3Q) assessment. This was administered again approximately 3 days later to evaluate test-retest reliability. Concurrent validity was evaluated by measuring agreement with the Active Australia Questionnaire, and criterion validity by comparison with 7-day Computer Science Applications, Inc. (CSA) accelerometer counts. Results: A total of 509 patients participated, with 428 (84%) completing a repeat assessment, and 415 (82%) accelerometer monitoring. The brief assessments had moderate test-retest reliability (2Q k = 58.0%, 95% confidence interval [CI] = 47.2-68.8%; 3Q k = 55.6%, 95% CI = 43.8-67.4%); fair to moderate concurrent validity (2Q k = 46.7%, 95% CI = 35.657.9%; 3Q k = 38.7%, 95% CI = 26.4-51.1%); and poor to fair criterion validity (2Q k = 18.2%, 95% CI = 3.9-32.6%; 3Q k = 24.3%, 95% CI = 11.6-36.9%) for identifying patients as sufficiently active. A four-level scale of PA derived from the PA assessments was significantly correlated with accelerometer minutes (2Q rho = 0.39, 95% CI = 0.28-0.49; 3Q rho = 0.31, 95% CI = 0.18-0.43). Physicians reported that the assessments took I to 2 minutes to complete. Conclusions: Both PA assessments were feasible to use in family practice, and were suitable for identifying the least active patients. The 2Q assessment was preferred by clinicians and may be most appropriate for dissemination.

Evaluation of brief dietary questions to estimate vegetable and fruit consumption - using serum carotenoids and red-cell folate

Objective: To evaluate responses to self-administered brief questions regarding consumption of vegetables and fruit by comparison with blood levels of serum carotenoids and red-cell folate. Design: A cross-sectional study in which participants reported their usual intake of fruit and vegetables in servings per day, and serum levels of five carotenoids (alpha-carotene, beta-carotene, beta-cryptoxanthin, lutein/zeaxanthin and lycopene) and red-cell folate were measured. Serum carotenoid levels were determined by high-performance liquid chromatography, and red-cell folate by an automated immunoassay system. Settings and subjects: Between October and December 2000, a sample of 1598 adults aged 25 years and over, from six randomly selected urban centres in Queensland, Australia, were examined as part of a national study conducted to determine the prevalence of diabetes and associated cardiovascular risk factors. Results: Statistically significant (P < 0.01) associations with vegetable and fruit intake ( categorised into groups: = 4 servings per day) were observed for alpha-carotene, beta-carotene, beta-cryptoxanthin, lutein/zeaxanthin and red-cell folate. The mean level of these carotenoids and of red-cell folate increased with increasing frequency of reported servings of vegetables and fruit, both before and after adjusting for potential confounding factors. A significant association with lycopene was observed only for vegetable intake before adjusting for confounders. Conclusions: These data indicate that brief questions may be a simple and valuable tool for monitoring vegetable and fruit intake in this population.

Functional capacity evaluation as a performance measure - Evidence for a new approach for clients with chronic back pain

Objectives: To report the research and development of a new approach to Functional Capacity Evaluation, the Gibson Approach to Functional Capacity Evaluation (GAPP FCE) for chronic back pain clients. Methods: Four Studies, including pilot and feasibility testing, expert review, and preliminary interrater reliability examination, are described here. Participants included 7 healthy young adults and 19 rehabilitation clients with back pain who underwent assessment using the GAPP FCE. Thirteen therapists were trained in the approach and were silently observed administering the Functional Capacity Evalutions by at least 1 other trained therapists or the first investigator Or both. An expert review using 5 expert occupational therapists was also conducted. Results: Study 1, the pilot with healthy individuals, indicated that the GAPP FCE was a feasible approach with good utility. Study 2, a pilot using 2 trained therapists assessing 5 back pain clients, supported the clinical feasibility of the approach. The expert review in Study 3 found support for GAPP FCE. Study 4, a trial of the approach with 14 rehabilitation clients, found support for the interrater reliability of recommendations for return to work based on performance in the GAPP FCE. Discussion: The evidence thus far available supports the GAPP FCE as ail approach that provides a Sound method for evaluating the performance of the physical demands of work with clients with chronic back pain. The tool has been shown to have good face and content validity, to meet acceptable test standards, and to have reasonable interrater reliability. Further research is occurring to look at a larger interrater reliability study, to further examine content validity, and to examine predictive validity.

Preliminary evaluation of the occurrence of herbicides and PAHs in the Wet Tropics region of the Great Barrier Reef, Australia, using passive samplers

The proximity of the Great Barrier Reef (GBR) Marine Park to areas of intensive agriculture and increasing urbanisation places the park under potential threat of contamination by land-based pollutants. Passive samplers were deployed at inshore reef and river mouth sites in the Wet Tropics region of the GBR during a dry and a wet season to measure levels of land-based organic pollutants in this environment. Two types of passive sampling devices were deployed: (i) a polar sampler, which can be used to monitor polar herbicides and (ii) semipermeable membrane devices (SPMDs) which sequester more hydrophobic compounds (e.g. PAHs, chlorpyrifos). Herbicides (diuron, simazine, atrazine, hexazinone and/or flumeturon) were detected at low concentrations (ng L-1) at all sites sampled and in both seasons. Chlorpyrifos was not detected while PAHs were present in SPMDs at levels below limits of detection. The results show that the GBR environment does contain low levels of organic pollutants and that passive sampling provides a sensitive monitoring tool for measuring waterborne organic pollutants. (c) 2005 Elsevier Ltd. All rights reserved.

The development of an observation tool for use with parents with psychiatric disability and their preschool children

Community-based treatment and care of people with psychiatric disabilities has meant that they are now more likely to engage in the parenting role. This has led to the development of programs designed to enhance the parenting skills of people with psychiatric disabilities. Evaluation of these programs has been hampered by a paucity of evaluation tools. This study's aim was to develop and trial a tool that examined the parent-child interaction within a group setting, was functional and easy to use, required minimum training and equipment, and had acceptable levels of reliability and validity. The revised tool yielded a single scale with acceptable reliability. It had discriminative validity and concurrent validity with non-independent global ratings of parenting. Sensitivity to change was not investigated. The findings suggest that this method of evaluating parenting is likely to have both clinical and research utility and further investigation of the psychometric properties of the tool is warranted.

Statistical racing techniques for improved empirical evaluation of evolutionary algorithms

In empirical studies of Evolutionary Algorithms, it is usually desirable to evaluate and compare algorithms using as many different parameter settings and test problems as possible, in border to have a clear and detailed picture of their performance. Unfortunately, the total number of experiments required may be very large, which often makes such research work computationally prohibitive. In this paper, the application of a statistical method called racing is proposed as a general-purpose tool to reduce the computational requirements of large-scale experimental studies in evolutionary algorithms. Experimental results are presented that show that racing typically requires only a small fraction of the cost of an exhaustive experimental study.