Bovine Tuberculosis in Swedish Farmed Deer: Detection and Control of the Disease

Bovine tuberculosis (BTB) was introduced into Swedish farmed deer herds in 1987. Epidemiological investigations showed that 10 deer herds had become infected (July 1994) and a common source of infection, a consignment of 168 imported farmed fallow deer, was identified (I). As trace-back of all imported and in-contact deer was not possible, a control program, based on tuberculin testing, was implemented in July 1994. As Sweden has been free from BTB since 1958, few practicing veterinarians had experience in tuberculin testing. In this test, result relies on the skill, experience and conscientiousness of the testing veterinarian. Deficiencies in performing the test may adversely affect the test results and thereby compromise a control program. Quality indicators may identify possible deficiencies in testing procedures. For that purpose, reference values for measured skin fold thickness (prior to injection of the tuberculin) were established (II) suggested to be used mainly by less experienced veterinarians to identify unexpected measurements. Furthermore, the within-veterinarian variation of the measured skin fold thickness was estimated by fitting general linear models to data (skin fold measurements) (III). The mean square error was used as an estimator of the within-veterinarian variation. Using this method, four (6%) veterinarians were considered to have unexpectedly large variation in measurements. In certain large extensive deer farms, where mustering of all animals was difficult, meat inspection was suggested as an alternative to tuberculin testing. The efficiency of such a control was estimated in paper IV and V. A Reed Frost model was fitted to data from seven BTB-infected deer herds and the spread of infection was estimated (< 0.6 effective contacts per deer and year) (IV). These results were used to model the efficiency of meat inspection in an average extensive Swedish deer herd. Given a 20% annual slaughter and meat inspection, the model predicted that BTB would be either detected or eliminated in most herds (90%) 15 years after introduction of one infected deer. In 2003, an alternative control for BTB in extensive Swedish deer herds, based on the results of paper V, was implemented.

Analysis and Transformation of Pipe-like Web Mashups for End User Programmers

Mashups are becoming increasingly popular as end users are able to easily access, manipulate, and compose data from several web sources. To support end users, communities are forming around mashup development environments that facilitate sharing code and knowledge. We have observed, however, that end user mashups tend to suffer from several deficiencies, such as inoperable components or references to invalid data sources, and that those deficiencies are often propagated through the rampant reuse in these end user communities. In this work, we identify and specify ten code smells indicative of deficiencies we observed in a sample of 8,051 pipe-like web mashups developed by thousands of end users in the popular Yahoo! Pipes environment. We show through an empirical study that end users generally prefer pipes that lack those smells, and then present eleven specialized refactorings that we designed to target and remove the smells. Our refactorings reduce the complexity of pipes, increase their abstraction, update broken sources of data and dated components, and standardize pipes to fit the community development patterns. Our assessment on the sample of mashups shows that smells are present in 81% of the pipes, and that the proposed refactorings can reduce that number to 16%, illustrating the potential of refactoring to support thousands of end users developing pipe-like mashups.

JVM-based Techniques for Improving Java Observability

Observability measures the support of computer systems to accurately capture, analyze, and present (collectively observe) the internal information about the systems. Observability frameworks play important roles for program understanding, troubleshooting, performance diagnosis, and optimizations. However, traditional solutions are either expensive or coarse-grained, consequently compromising their utility in accommodating today’s increasingly complex software systems. New solutions are emerging for VM-based languages due to the full control language VMs have over program executions. Existing such solutions, nonetheless, still lack flexibility, have high overhead, or provide limited context information for developing powerful dynamic analyses. In this thesis, we present a VM-based infrastructure, called marker tracing framework (MTF), to address the deficiencies in the existing solutions for providing better observability for VM-based languages. MTF serves as a solid foundation for implementing fine-grained low-overhead program instrumentation. Specifically, MTF allows analysis clients to: 1) define custom events with rich semantics ; 2) specify precisely the program locations where the events should trigger; and 3) adaptively enable/disable the instrumentation at runtime. In addition, MTF-based analysis clients are more powerful by having access to all information available to the VM. To demonstrate the utility and effectiveness of MTF, we present two analysis clients: 1) dynamic typestate analysis with adaptive online program analysis (AOPA); and 2) selective probabilistic calling context analysis (SPCC). In addition, we evaluate the runtime performance of MTF and the typestate client with the DaCapo benchmarks. The results show that: 1) MTF has acceptable runtime overhead when tracing moderate numbers of marker events; and 2) AOPA is highly effective in reducing the event frequency for the dynamic typestate analysis; and 3) language VMs can be exploited to offer greater observability.