Automated Fixing of Programs with Contracts

This paper describes AutoFix, an automatic debugging technique that can fix faults in general-purpose software. To provide high-quality fix suggestions and to enable automation of the whole debugging process, AutoFix relies on the presence of simple specification elements in the form of contracts (such as pre- and postconditions). Using contracts enhances the precision of dynamic analysis techniques for fault detection and localization, and for validating fixes. The only required user input to the AutoFix supporting tool is then a faulty program annotated with contracts; the tool produces a collection of validated fixes for the fault ranked according to an estimate of their suitability. In an extensive experimental evaluation, we applied AutoFix to over 200 faults in four code bases of different maturity and quality (of implementation and of contracts). AutoFix successfully fixed 42% of the faults, producing, in the majority of cases, corrections of quality comparable to those competent programmers would write; the used computational resources were modest, with an average time per fix below 20 minutes on commodity hardware. These figures compare favorably to the state of the art in automated program fixing, and demonstrate that the AutoFix approach is successfully applicable to reduce the debugging burden in real-world scenarios.Comment: Minor changes after proofreadin

Audit of Antenatal Testing of Sexually Transmissible Infections and Blood Borne Viruses at Western Australian Hospitals

In August 2007, the Western Australian Department of Health (DOH) released updated recommendations for testing of sexually transmissible infections (STI) and blood-borne viruses (BBV) in antenates. Prior to this, the Royal Australian & New Zealand College of Obstetricians & Gynaecologists (RANZCOG) antenatal testing recommendations had been accepted practice in most antenatal settings. The RANZCOG recommends that testing for HIV, syphilis, hepatitis B and C be offered at the first antenatal visit. The DOH recommends that in addition, chlamydia testing be offered. We conducted a baseline audit of antenatal STI/BBV testing in women who delivered at selected public hospitals before the DOH recommendations. We examined the medical records of 200 women who had delivered before 1st July 2007 from each of the sevenWAhospitals included in the audit. STI and BBV testing information and demographic data were collected. Of the 1,409 women included, 1,205 (86%) were non-Aboriginal and 200 (14%) were Aboriginal. High proportions of women had been tested for HIV (76%), syphilis (86%), hepatitis C (87%) and hepatitis B (88%). Overall, 72% of women had undergone STI/BBV testing in accordance with RANZCOG recommendations. However, chlamydia testing was evident in only 18% of records. STI/BBV prevalence ranged from 3.9% (CI 1.5– 6.3%) for chlamydia, to 1.7% (CI 1–2.4%) for hepatitis C, 0.7% (CI 0.3–1.2) for hepatitis B and 0.6% (CI 0.2–1) for syphilis. Prior to the DOH recommendations, nearly three-quarters of antenates had undergone STI/BBV testing in accordance with RANZCOG recommendations, but less than one fifth had been tested for chlamydia. The DOH recommendations will be further promoted with the assistance of hospitals and other stakeholders. A future audit will be conducted to determine the proportion of women tested according to the DOH recommendations. The hand book from this conference is available for download Published in 2008 by the Australasian Society for HIV Medicine Inc © Australasian Society for HIV Medicine Inc 2008 ISBN: 978-1-920773-59-

Focal Spot, Winter 2005/2006

https://digitalcommons.wustl.edu/focal_spot_archives/1101/thumbnail.jp

Finding Bugs in Web Applications Using Dynamic Test Generation and Explicit State Model Checking

Web script crashes and malformed dynamically-generated web pages are common errors, and they seriously impact the usability of web applications. Current tools for web-page validation cannot handle the dynamically generated pages that are ubiquitous on today's Internet. We present a dynamic test generation technique for the domain of dynamic web applications. The technique utilizes both combined concrete and symbolic execution and explicit-state model checking. The technique generates tests automatically, runs the tests capturing logical constraints on inputs, and minimizes the conditions on the inputs to failing tests, so that the resulting bug reports are small and useful in finding and fixing the underlying faults. Our tool Apollo implements the technique for the PHP programming language. Apollo generates test inputs for a web application, monitors the application for crashes, and validates that the output conforms to the HTML specification. This paper presents Apollo's algorithms and implementation, and an experimental evaluation that revealed 302 faults in 6 PHP web applications

Fall 2010, Biology @ SU

https://surface.syr.edu/bioalum_news/1001/thumbnail.jp

Kinetics of protein-based in vivo Imaging tracers for positron emission tomography

Within the framework of the “Sel-tag imaging project”, a novel method was used to rapidly label protein tracers and the in vivo targeting abilities of these tracers were studied in animal models of cancer using a preclinical positron emission tomography (PET) camera. To first evaluate and optimize preclinically the use of PET tracers can facilitate their translation to and implementation in human patient studies. The ultimate goal of the different projects within the Sel-tag imaging project was to find imaging biomarkers that could potentially be used for individualizing cancer treatment and thereby improve the therapeutic results. This thesis focuses on methods employed to describe the distribution of these protein-based tracers in human xenografts. Many of the techniques used had been developed for other imaging circumstances. Therefore verification for these imaging applications was an important aspect of these papers. Paper I examined the distribution in a tumour of a medium-sized AnnexinA5-based tracer that targeted phosphatidylserine externalised during cell death in tumours in two cases; first, with no pre-treatment (baseline) and, second, after pre-treatment with a chemotherapeutic agent. Small differences between tracer uptakes in the two cases required a macro parameter analysis method for quantifications. Evaluations of the influence of the enhanced permeability and retention effect by using a size-matched control were introduced. The AnnexinA5 results were compared to those of the metabolic tracer [18F]FDG and complemented with circulating serum markers to increase sensitivity. Paper II extended the analysis in paper I to incorporate more verifications that were also more thorough. The choice of input (blood or reference tissue) and the statistical significance of intergroup comparisons when using conventional uptake measurements and the more involved macro parameter analyses like in paper I were compared. We also proposed that distribution volume ratio was a more appropriate quantification parameter concept for these protein-based tracers with relatively large non-specific uptake. Paper III assessed the smaller Affibody™ tracer ZHER2:342 as an imaging biomarker for human epidermal growth factor 2 (HER2), whose overexpressions are associated with a poor prognosis for breast cancer patients. In order to demonstrate specific binding to HER2, pre-treatment of the tumour with unlabelled protein and uptake in xenografts with low HER2 expression was evaluated. Ex vivo immunohistochemistry of expression levels supported the imaging results. Paper IV examined a radiopharmaceutical that targeted the epidermal growth factor receptor (EGFR), whose overexposure in tumours is associated with a negative prognosis. Again an Affibody™ molecule, (ZEGFR:2377), was used and, as in in paper I, a size-matched control was also used to estimate the non-specific uptake. Uptakes, quantified by conventional uptake methods, varied in tumours with different EGFR expression levels. Ex vivo analyses of expression levels were also performed. Paper V addressed the non-uniform (heterogeneous) uptake of different tracers in a tumour tissue. An algorithm was written that aimed at incorporating all relevant aspects that will influence non-uniformity. Histograms were generated that visualized how the frequency and spread of deviations contributed to the heterogeneity. These aspects could not always be attended in a direct manner, but instead had to be handled in an indirect way. The effect of varying imaging parameters was examined as part of the validation procedure. The method developed is a robust, user-friendly tool for comparing heterogeneity in similar volume preclinical tumor tissues