Criteria for software modularization

A central issue in programming practice involves determining the appropriate size and information content of a software module. This study attempted to determine the effectiveness of two widely used criteria for software modularization, strength and size, in reducing fault rate and development cost. Data from 453 FORTRAN modules developed by professional programmers were analyzed. The results indicated that module strength is a good criterion with respect to fault rate, whereas arbitrary module size limitations inhibit programmer productivity. This analysis is a first step toward defining empirically based standards for software modularization

Structural analysis of the GH43 enzyme Xsa43E from Butyrivibrio proteoclasticus

The rumen of dairy cattle can be thought of as a large, stable fermentation vat and as such it houses a large and diverse community of microorganisms. The bacterium Butyrivibrio proteoclasticus is a representative of a significant component of this microbial community. It is a xylan-degrading organism whose genome encodes a large number of open reading frames annotated as fibre-degrading enzymes. This suite of enzymes is essential for the organism to utilize the plant material within the rumen as a fuel source, facilitating its survival in this competitive environment. Xsa43E, a GH43 enzyme from B. proteoclasticus, has been structurally and functionally characterized. Here, the structure of selenomethionine-derived Xsa43E determined to 1.3 Å resolution using single-wavelength anomalous diffraction is reported. Xsa43E possesses the characteristic five-bladed β-propeller domain seen in all GH43 enzymes. GH43 enzymes can have a range of functions, and the functional characterization of Xsa43E shows it to be an arabinofuranosidase capable of cleaving arabinose side chains from short segments of xylan. Full functional and structural characterization of xylan-degrading enzymes will aid in creating an enzyme cocktail that can be used to completely degrade plant material into simple sugars. These molecules have a range of applications as starting materials for many industrial processes, including renewable alternatives to fossil fuels

Self-organized escape of oscillator chains in nonlinear potentials

We present the noise free escape of a chain of linearly interacting units from a metastable state over a cubic on-site potential barrier. The underlying dynamics is conservative and purely deterministic. The mutual interplay between nonlinearity and harmonic interactions causes an initially uniform lattice state to become unstable, leading to an energy redistribution with strong localization. As a result a spontaneously emerging localized mode grows into a critical nucleus. By surpassing this transition state, the nonlinear chain manages a self-organized, deterministic barrier crossing. Most strikingly, these noise-free, collective nonlinear escape events proceed generally by far faster than transitions assisted by thermal noise when the ratio between the average energy supplied per unit in the chain and the potential barrier energy assumes small values

Antimicrobial resistance characteristics and fitness of Gram-negative fecal bacteria from volunteers treated with minocycline or amoxicillin.

A yearlong study was performed to examine the effect of antibiotic administration on the bacterial gut flora. Gram-negative facultative anaerobic bacteria were recovered from the feces of healthy adult volunteers administered amoxicillin, minocycline or placebo, and changes determined in antimicrobial resistance (AMR) gene carriage. Seventy percent of the 1039 facultative anaerobic isolates recovered were identified by MALDI-TOF as Escherichia coli. A microarray used to determine virulence and resistance gene carriage demonstrated that AMR genes were widespread in all administration groups, with the most common resistance genes being bla TEM, dfr, strB, tet(A), and tet(B). Following amoxicillin administration, an increase in the proportion of amoxicillin resistant E. coli and a three-fold increase in the levels of bla TEM gene carriage was observed, an effect not observed in the other two treatment groups. Detection of virulence genes, including stx1A, indicated not all E. coli were innocuous commensals. Approximately 150 E. coli collected from 6 participants were selected for pulse field gel electrophoresis (PFGE), and a subset used for characterisation of plasmids and Phenotypic Microarrays (PM). PFGE indicated some E. coli clones had persisted in volunteers for up to 1 year, while others were transient. Although there were no unique characteristics associated with plasmids from persistent or transient isolates, PM assays showed transient isolates had greater adaptability to a range of antiseptic biocides and tetracycline; characteristics which were lost in some, but not all persistent isolates. This study indicates healthy individuals carry bacteria harboring resistance to a variety of antibiotics and biocides in their intestinal tract. Antibiotic administration can have a temporary effect of selecting bacteria, showing co-resistance to multiple antibiotics, some of which can persist within the gut for up to 1 year

Quantifying biological responses of catch-and-release angling in understudied fish species and practices

Many catch-and-release angling events involve air exposure and exhaustive exercise that elicit a physiological stress response, and depending on a variety of factors, delayed mortality is a possible outcome. There have been ample studies in this area, however, significant gaps exist in the literature for species that are targeted by more specialized anglers, such as freshwater drum (Aplodinotus grunniens). I quantified physiological and reflex responses in freshwater drum following angling, across seasons. Once a fish was on the line, the fight duration and time exposed to air were varied to account for differences in angler skill level (fight time range: 5 s to 2 min; air exposure range: 20 s to 3 min). Location and severity of injury were determined, blood biopsies were taken to quantify physiological stress, and reflex impairment was assessed. Thirtyone percent of fish captured were deeply hooked in the esophagus tissue. Freshwater drum experienced a disruption in homeostasis as blood glucose, plasma cortisol and plasma lactate increased significantly from baseline values following angling. Additionally, seasonal differences were observed for blood glucose and plasma cortisol as higher values were observed in the summer when compared to the spring. The ‘orientation’ reflex was the most frequently impaired (29 % of fish lacked this reflex), but impairment did not differ seasonally. Because freshwater drum have the largest latitudinal range of any North American freshwater fish and are being targeted more frequently by anglers as of late, it is important to fill this knowledge gap regarding their responses to angling events to develop best practices for anglers to promote conservation. The wide distribution of freshwater drum may also make them a candidate model species for addressing the convergence between assessing the impacts of catch-and-release angling and other environmental issues facing freshwater fishes, such as climate change.NSERC CGS-MMaster of Science in Bioscience, Technology, and Public Polic

Do colorectal cancer patients diagnosed as an emergency differ from non-emergency patients in their consultation patterns and symptoms? A longitudinal data-linkage study in England

Background: More than 20% of colorectal cancers are diagnosed following an emergency presentation. We aimed to examine pre-diagnostic primary-care consultations and related symptoms comparing patients diagnosed as emergencies with those diagnosed through non-emergency routes. Methods: Cohort study of colorectal cancers diagnosed in England 2005 and 2006 using cancer registration data individually linked to primary-care data (CPRD/GPRD), allowing a detailed analysis of clinical information referring to the 5-year pre-diagnostic period. Results: Emergency diagnosis occurred in 35% and 15% of the 1029 colon and 577 rectal cancers. ‘Background’ primary-care consultations (2–5 years before diagnosis) were similar for either group. In the year before diagnosis, >95% of emergency and non-emergency presenters had consulted their doctor, but emergency presenters had less frequently relevant symptoms (colon cancer: 48% vs 71% (P<0.001); rectal cancer: 49% vs 61% (P=0.043)). ‘Alarm’ symptoms were recorded less frequently in emergency presenters (e.g., rectal bleeding: 9 vs 24% (P=0.002)). However, about 1/5 of emergency presenters (18 and 23% for colon and rectal cancers) had ‘alarm’ symptoms the year before diagnosis. Conclusions: Emergency presenters have similar ‘background’ consultation history as non-emergency presenters. Their tumours seem associated with less typical symptoms, however opportunities for earlier diagnosis might be present in a fifth of them

Multi Visualization and Dynamic Query for Effective Exploration of Semantic Data

Semantic formalisms represent content in a uniform way according to ontologies. This enables manipulation and reasoning via automated means (e.g. Semantic Web services), but limits the user’s ability to explore the semantic data from a point of view that originates from knowledge representation motivations. We show how, for user consumption, a visualization of semantic data according to some easily graspable dimensions (e.g. space and time) provides effective sense-making of data. In this paper, we look holistically at the interaction between users and semantic data, and propose multiple visualization strategies and dynamic filters to support the exploration of semantic-rich data. We discuss a user evaluation and how interaction challenges could be overcome to create an effective user-centred framework for the visualization and manipulation of semantic data. The approach has been implemented and evaluated on a real company archive

Expert chess memory: Revisiting the chunking hypothesis

After reviewing the relevant theory on chess expertise, this paper re-examines experimentally the finding of Chase and Simon (1973a) that the differences in ability of chess players at different skill levels to copy and to recall positions are attributable to the experts' storage of thousands of chunks (patterned clusters of pieces) in long-term memory. Despite important differences in the experimental apparatus, the data of the present experiments regarding latencies and chess relations between successively placed pieces are highly correlated with those of Chase and Simon. We conclude that the 2-second inter-chunk interval used to define chunk boundaries is robust, and that chunks have psychological reality. We discuss the possible reasons why Masters in our new study used substantially larger chunks than the Master of the 1973 study, and extend the chunking theory to take account of the evidence for large retrieval structures (templates) in long-term memory

The Impact of Sectoral Minimum Wage Laws on Employment, Wages and Hours of Work in South Africa

This paper attempts to investigate the impact of sectoral wage laws in South Africa. Specifically, we examine the impact of minimum wage laws promulgated in the Retail, Domestic work, Forestry, Security, and Taxi sectors using 15 waves of biannual Labour Force Survey data for the 2000-2007 period

Wage returns to university disciplines in Greece: are Greek Higher Education degrees Trojan Horses?

This paper examines the wage returns to qualifications and academic disciplines in the Greek labour market. Exploring wage responsiveness across various degree subjects in Greece is interesting, as it is characterised by high levels of graduate unemployment, which vary considerably by field of study, and relatively low levels of wage flexibility. Using micro-data from recently available waves (2002-2003) of the Greek Labour Force Survey (LFS), the returns to academic disciplines are estimated by gender and public/private sector. Quantile regressions and cohort interactions are also used to capture the heterogeneity in wage returns across the various disciplines. The results show considerable variation in wage premiums across the fields of study, with lower returns for those that have a marginal role to play in an economy with a rising services/shrinking public sector. Educational reforms that pay closer attention to the future prospects of university disciplines are advocated