A Knowledge-based System for Intelligent Support in Pharmacogenomics Evidence Assessment: Ontology-driven Evidence Representation, Retrieval, Classification and Interpretation

Thesis (Ph.D.)--University of Washington, 2016-06

Masculinity-femininity as a national characteristic and its relationship with national agoraphobic fear levels: Fodor's sex role hypothesis revitalized

Hofstede's dimension of national culture termed Masculinity-Femininity [Hofstede (1991). Cultures and organizations: software of the mind. London: McGraw-Hill] is proposed to be of relevance for understanding national-level differences in self-assessed agoraphobic fears. This prediction is based on the classical work of Fodor [Fodor (1974). In: V. Franks & V. Burtle (Eds.), Women in therapy: new psychotherapies for a changing society. New York: Brunner/Mazel]. A unique data set comprising 11 countries (total N = 5491 students) provided the opportunity of scrutinizing this issue. It was hypothesized and found that national Masculinity (the degree to which cultures delineate sex roles, with masculine or tough societies making clearer differentiations between the sexes than feminine or modest societies do) would correlate positively with national agoraphobic fear levels (as assessed with the Fear Survey Schedule-III). Following the correction for sex and age differences across national samples, a significant and large effect-sized national-level (ecological) r = +0.67 (P = 0.01) was found. A highly feminine society such as Sweden had the lowest, whereas the champion among the masculine societies, Japan, had the highest national Agoraphobic fear score. (C) 2003 Elsevier Science Ltd. All rights reserved.

Recommendations for animal DNA forensic and identity testing

Genetic analysis in animals has been used for many applications, such as kinship analysis, for determining the sire of an offspring when a female has been exposed to multiple males, determining parentage when an animal switches offspring with another dam, extended lineage reconstruction, estimating inbreeding, identification in breed registries, and speciation. It now also is being used increasingly to characterize animal materials in forensic cases. As such, it is important to operate under a set of minimum guidelines that assures that all service providers have a template to follow for quality practices. None have been delineated for animal genetic identity testing. Based on the model for human DNA forensic analyses, a basic discussion of the issues and guidelines is provided for animal testing to include analytical practices, data evaluation, nomenclature, allele designation, statistics, validation, proficiency testing, lineage markers, casework files, and reporting. These should provide a basis for professional societies and/or working groups to establish more formalized recommendations.

User dyads in software testing: bypassing the need for expert observers

This paper arises out of a research study into the online help facilities provided in popular software applications such as word processors. Its particular focus is on experimental methods of evaluating the effectiveness and usability of those facilities. Focus groups, questionnaires, and online surveys had already been used in other phases of the study, but it was judged that these approaches would be unsuitable for measuring effectiveness and usability because they are susceptible to respondents' subjectivity. Direct observation of people working on set word-processing tasks was ruled out initially because of a lack of trained observers; it would have taken too long for the investigator to observe a large enough sample by himself. Automatic recording of users' actions was also rejected, as it would have demanded equipment and/or software that was not available and seemed too expensive to acquire. The approach and techniques described here were an attempt to overcome these difficulties by using observers drawn from the same population of students that provided the test subjects; as a by-product, this may also have enhanced the acceptability (and hence possibly the validity) of the experiments by reducing the exam pressure perceived by participants.

Formal change impact analyses for emulated control software

Processor emulators are a software tool for allowing legacy computer programs to be executed on a modern processor. In the past emulators have been used in trivial applications such as maintenance of video games. Now, however, processor emulation is being applied to safety-critical control systems, including military avionics. These applications demand utmost guarantees of correctness, but no verification techniques exist for proving that an emulated system preserves the original system’s functional and timing properties. Here we show how this can be done by combining concepts previously used for reasoning about real-time program compilation, coupled with an understanding of the new and old software architectures. In particular, we show how both the old and new systems can be given a common semantics, thus allowing their behaviours to be compared directly.

Biologically inspired visual landmark processing for simultaneous localization and mapping

This paper illustrates a method for finding useful visual landmarks for performing simultaneous localization and mapping (SLAM). The method is based loosely on biological principles, using layers of filtering and pooling to create learned templates that correspond to different views of the environment. Rather than using a set of landmarks and reporting range and bearing to the landmark, this system maps views to poses. The challenge is to produce a system that produces the same view for small changes in robot pose, but provides different views for larger changes in pose. The method has been developed to interface with the RatSLAM system, a biologically inspired method of SLAM. The paper describes the method of learning and recalling visual landmarks in detail, and shows the performance of the visual system in real robot tests.

Cluster scheduling and load balancing via TCP options

This paper describes an experiment in designing, implementing and testing a Transport layer cluster scheduling and dispatching architecture. The motivation for the experiment was the hypothesis that a Transport layer clustering solution may offer advantantages over the existing industry-standard Network layer and Data Link Layer approaches. The critical success factors initially established to guide and evaluate the experiment were reduced dispatcher work load, reduced dispatcher internal state memory requirements, distributed denial of service resilience, and cluster software design simplicity. The functional design stage of the experiment produced a Transport layer strategy for scheduling and load balancing based on the specification of two new TCP options. Implementation required the introduction of the newly specified TCP options into the Linux (2.4) kernel. The implementation produced an extended Linux Socket API to facilitate user-process access to the additional TCP capability. The testing stage of the experiment confirmed the operational efficiency of the solution.

A reference architecture for instructional educational software

Our extensive research has indicated that high-school teachers are reluctant to make use of existing instructional educational software (Pollard, 2005). Even software developed in a partnership between a teacher and a software engineer is unlikely to be adopted by teachers outside the partnership (Pollard, 2005). In this paper we address these issues directly by adopting a reusable architectural design for instructional educational software which allows easy customisation of software to meet the specific needs of individual teachers. By doing this we will facilitate more teachers regularly using instructional technology within their classrooms. Our domain-specific software architecture, Interface-Activities-Model, was designed specifically to facilitate individual customisation by redefining and restructuring what constitutes an object so that they can be readily reused or extended as required. The key to this architecture is the way in which the software is broken into small generic encapsulated components with minimal domain specific behaviour. The domain specific behaviour is decoupled from the interface and encapsulated in objects which relate to the instructional material through tasks and activities. The domain model is also broken into two distinct models - Application State Model and Domainspecific Data Model. This decoupling and distribution of control gives the software designer enormous flexibility in modifying components without affecting other sections of the design. This paper sets the context of this architecture, describes it in detail, and applies it to an actual application developed to teach high-school mathematical concepts.

Mapping genes for resistance to net form of net blotch and strip rust in barley (Hordeum vulgare L.)

A dihaploid mapping population comprising 65 lines was developed between barley parent varieties Tallon and Kaputar and used to construct a genetic linkage map. This map, comprising 195 amplified fragment length polymorphism and 38 simple sequence repeat markers, was used to identify markers linked to the net form of net blotch (Pyrenophora teres f.sp. teres) and to stripe rust (Puccinia striiformis f.sp. hordei) in barley. The population was screened with five pathotypes of net blotch at the seedling stage in the glasshouse and subjected to a natural inoculation in Hermitage, Queensland. Stripe rust screening was conducted at the adult plant stage in Toluca, Mexico. Analyses of the markers were performed using Mapmanager and Qgene software. One region on chromosome 6H was highly significantly associated with resistance to the net blotch (R2 = 79%). This association was consistent for all pathotypes studied. One region on chromosome 5H was found to be highly significantly associated with resistance to stripe rust (R2= 65%). There are a number of very closely linked markers showing strong associations in these regions, and these markers present an opportunity for marker assisted selection of these traits in barley breeding programs.

Verification and validation of autonomous systems

NASA is working on complex future missions that require cooperation between multiple satellites or rovers. To implement these systems, developers are proposing and using intelligent and autonomous systems. These autonomous missions are new to NASA, and the software development community is just learning to develop such systems. With these new systems, new verification and validation techniques must be used. Current techniques have been developed based on large monolithic systems. These techniques have worked well and reliably, but do not translate to the new autonomous systems that are highly parallel and nondeterministic.

Developing relational navigation to effectively understand software

Effective comprehension of complex software systems requires understanding of both the individual documents that represent software and the complex relationships that exist within and between documents. Relationships of all kinds play a vital role in a software engineer's comprehension of, and navigation within and between, software documents. User-determined relationships have the additional role of enabling the engineer to create and maintain relational documentation that cannot be generated by tools or derived from other relationships. We argue that for a software development environment to effectively support the understanding of complex software systems, relational navigation must be supported at both the document-focused (intra-document) and relation-focused (inter-document) levels. The need for a relation-focused approach is highlighted by an evaluation of an existing document-focused relational interface. We conclude with the requirements for a relation-focused approach to relational navigation. These requirements focus on the user's perspective when interacting with a collection of related documents. We define the requirements for a software development environment that effectively supports the understanding of the software documents and relationships that define a complex software system.

Proceedings Ninth Asia-Pacific Software Engineering Conference. ASPEC 2002

The following topics are dealt with: Requirements engineering; components; design; formal specification analysis; education; model checking; human computer interaction; software design and architecture; formal methods and components; software maintenance; software process; formal methods and design; server-based applications; review and testing; measurement; documentation; management and knowledge-based approaches.

The Internet and other IT resources:tools for translators within a translation programme

Information technology has increased both the speed and medium of communication between nations. It has brought the world closer, but it has also created new challenges for translation — how we think about it, how we carry it out and how we teach it. Translation and Information Technology has brought together experts in computational linguistics, machine translation, translation education, and translation studies to discuss how these new technologies work, the effect of electronic tools, such as the internet, bilingual corpora, and computer software, on translator education and the practice of translation, as well as the conceptual gaps raised by the interface of human and machine.

Linking the witness simulation software to an expert system to represent a decision-making process

Expert systems, and artificial intelligence more generally, can provide a useful means for representing decision-making processes. By linking expert systems software to simulation software an effective means of including these decision-making processes in a simulation model can be achieved. This paper demonstrates how a commercial-off-the-shelf simulation package (Witness) can be linked to an expert systems package (XpertRule) through a Visual Basic interface. The methodology adopted could be used for models, and possibly software, other than those presented here.

Mathematical modelling and optimal multivariable control of chemical processes

This work reports the developnent of a mathenatical model and distributed, multi variable computer-control for a pilot plant double-effect climbing-film evaporator. A distributed-parameter model of the plant has been developed and the time-domain model transformed into the Laplace domain. The model has been further transformed into an integral domain conforming to an algebraic ring of polynomials, to eliminate the transcendental terms which arise in the Laplace domain due to the distributed nature of the plant model. This has made possible the application of linear control theories to a set of linear-partial differential equations. The models obtained have well tracked the experimental results of the plant. A distributed-computer network has been interfaced with the plant to implement digital controllers in a hierarchical structure. A modern rnultivariable Wiener-Hopf controller has been applled to the plant model. The application has revealed a limitation condition that the plant matrix should be positive-definite along the infinite frequency axis. A new multi variable control theory has emerged fram this study, which avoids the above limitation. The controller has the structure of the modern Wiener-Hopf controller, but with a unique feature enabling a designer to specify the closed-loop poles in advance and to shape the sensitivity matrix as required. In this way, the method treats directly the interaction problems found in the chemical processes with good tracking and regulation performances. Though the ability of the analytical design methods to determine once and for all whether a given set of specifications can be met is one of its chief advantages over the conventional trial-and-error design procedures. However, one disadvantage that offsets to some degree the enormous advantages is the relatively complicated algebra that must be employed in working out all but the simplest problem. Mathematical algorithms and computer software have been developed to treat some of the mathematical operations defined over the integral domain, such as matrix fraction description, spectral factorization, the Bezout identity, and the general manipulation of polynomial matrices. Hence, the design problems of Wiener-Hopf type of controllers and other similar algebraic design methods can be easily solved.