The Java system dependence graph

The Program Dependence Graph was introduced by Ottenstein and Ottenstein in 1984 [14]. It was suggested to be a suitable internal program representation for monolithic programs, for the purpose of carrying out certain software engineering operations such as slicing and the computation of program metrics. Since then, Horwitz et al. have introduced the multi-procedural equivalent System Dependence Graph [9]. Many authors have proposed object-oriented dependence graph construction approaches [11, 10, 20, 12]. Every approach provides its own benefits, some of which are language specific. This paper is based on Java and combines the most important benefits from a range of approaches. The result is a Java System Dependence Graph, which summarises the key benefits offered by different approaches and adapts them (if necessary) to the Java language

Understanding object-oriented source code from the behavioural perspective

Comprehension is a key activity that underpins a variety of software maintenance and engineering tasks. The task of understanding object-oriented systems is hampered by the fact that the code segments that are related to a user-level function tend to be distributed across the system. We introduce a tool-supported code extraction technique that addresses this issue. Given a minimal amount of information about a behavioural element of the system that is of interest (such as a use-case), it extracts a trail of the methods (and method invocations) through the system that are needed in order to achieve an understanding of the implementation of the element of interest. We demonstrate the feasibility of our approach by implementing it as part of a code extraction tool, presenting a case study and evaluating the approach and tool against a set of established criteria for program comprehension tools

Accessibility of 3D Game Environments for People with Aphasia: An Exploratory Study

People with aphasia experience difficulties with all aspects of language and this can mean that their access to technology is substantially reduced. We report a study undertaken to investigate the issues that confront people with aphasia when interacting with technology, specifically 3D game environments. Five people with aphasia were observed and interviewed in twelve workshop sessions. We report the key themes that emerged from the study, such as the importance of direct mappings between users’ interactions and actions in a virtual environment. The results of the study provide some insight into the challenges, but also the opportunities, these mainstream technologies offer to people with aphasia. We discuss how these technologies could be more supportive and inclusive for people with language and communication difficulties

Nod1 signaling overcomes resistance of S. pneumoniae to opsonophagocytic killing

Airway infection by the Gram-positive pathogen Streptococcus pneumoniae (Sp) leads to recruitment of neutrophils but limited bacterial killing by these cells. Co-colonization by Sp and a Gram-negative species, Haemophilus influenzae (Hi), provides sufficient stimulus to induce neutrophil and complement-mediated clearance of Sp from the mucosal surface in a murine model. Products from Hi, but not Sp, also promote killing of Sp by ex vivo neutrophil-enriched peritoneal exudate cells. Here we identify the stimulus from Hi as its peptidoglycan. Enhancement of opsonophagocytic killing was facilitated by signaling through nucleotide-binding oligomerization domain-1 (Nod1), which is involved in recognition of γ-D-glutamyl-meso-diaminopimelic acid (meso-DAP) contained in cell walls of Hi but not Sp. Neutrophils from mice treated with Hi or compounds containing meso-DAP, including synthetic peptidoglycan fragments, showed increased Sp killing in a Nod1-dependent manner. Moreover, Nod1-/- mice showed reduced Hi-induced clearance of Sp during co-colonization. These observations offer insight into mechanisms of microbial competition and demonstrate the importance of Nod1 in neutrophil-mediated clearance of bacteria in vivo

TREATMENT OF CRANIOFACIAL DEFICITS ASSOCIATED WITH DOWN SYN-DROME IN A MOUSE MODEL

poster abstractTrisomy 21 is the genetic source of the group of phenotypes commonly known as Down syndrome (DS). These phenotypes include cognitive im-pairment, heart defects and craniofacial abnormalities, including a small mandible. The Ts65Dn mouse model contains three copies of approximately half the genes found on human chromosome 21 and exhibits similar pheno-types to individuals with DS including a small, dysmorphic mandible. Our lab has traced this deficit to a smaller first branchial arch (BA1) consisting of fewer neural crest cells (NCCs) at embryonic day 9.5 (E9.5). At E9.5, Dyrk1a, a gene known to affect craniofacial development, is upregulated in the BA1, likely contributing to its cell deficit. Using epigallocatechin gallate (EGCG), an extract from green tea and a known inhibitor of Dyrk1a, we are attempting to rescue this deficit. We hypothesize the consumption of EGCG by pregnant mothers at E7 and E8 will rescue the mandibular deficit in de-veloping embryos by reducing the expression or activity of Dyrk1a. From our data we conclude the treatment of pregnant mothers with EGCG results in increased embryo size of trisomic embryos. Further analysis will be done to determine embryo volume, the volume of the BA1, and number of NCCs within the BA1 to determine the effects of EGCG in vivo. This research will better our understanding of craniofacial development and could lead to po-tential genetic-based therapies in the future

Quantifying Temporal Variability in Stream Habitat Data: Implications for Restoration and Monitoring

Quantifying natural and anthropogenic-induced levels of temporal variability is essential for robust trend analyses and for evaluating the effectiveness of restoration activities or changed management actions. Here, we used data collected as part of the Pacfish/Infish Biological Effectiveness Monitoring Project to evaluate the extent of temporal variability in instream habitat collected at the reach scale. We integrated habitat data collected yearly (2001-2009) at 50 sites experiencing a range of management activities into our analyses to better understand the consistency of temporal variability in watersheds with inherently different landscape characteristics and disturbance regimes. We initially decomposed variance estimates to remove site-to-site variability, sampling error, and year effects and use the remaining variance as a measure of site-specific temporal variability. We then relate this temporal variability to landscape, management, and climate attributes at multiple scales to better understand which characteristics result in more or less variability in habitat attributes at specific sites. Our results suggest temporal variability differs significantly across individual sites and attributes within sites, indicating our ability to detect significant changes as a result of management changes and/or restoration efforts are context dependent. The spatial scale of landscape attributes, e.g., stream buffer vs. catchment, related to temporal variability also varied across individual attributes. Our efforts highlight the importance of considering site specific measures of temporal variability as they relate to specific restoration and management goals

Silicon photomultiplier arrays - a novel photon detector for a high resolution tracker produced at FBK-irst, Italy

A silicon photomultiplier (SiPM) array has been developed at FBK-irst having 32 channels and a dimension of 8.0 x 1.1 mm^2. Each 250 um wide channel is subdivided into 5 x 22 rectangularly arranged pixels. These sensors are developed to read out a modular high resolution scintillating fiber tracker. Key properties like breakdown voltage, gain and photon detection efficiency (PDE) are found to be homogeneous over all 32 channels of an SiPM array. This could make scintillating fiber trackers with SiPM array readout a promising alternative to available tracker technologies, if noise properties and the PDE are improved

Problem and treatment of DC offsets in FDTD simulations

Journal ArticleThis paper discusses the causes of and some solutions to the commonly observed problem of dc field offsets in finite-difference time-domain (FDTD) simulations. DC electric and magnetic field offsets are shown to be valid calculated responses of the modeled systems, resulting from interaction between the turn-on characteristics of the source and the properties of the models. The dc offsets may be avoided in the time domain by tailoring the source waveforms or in the frequency domain by post-processing the FDTD output