Programming with heterogeneous structures: Manipulating XML data using bondi

Manipulating semistructured data, such as XML, does not fit well within conventional programming languages. A typical manipulation requires finding all occurrences of a structure matching a structured search pattern, whose context may be different in different places, and both aspects cause difficulty. If a special-purpose query language is used to manipulate XML, an interface to a more general programming environment is required, and this interface typically creates runtime overhead for type conversion. However, adding XML manipulation to a general-purpose programming language has proven difficult because of problems associated with expressiveness and typing. We show an alternative approach that handles many kinds of patterns within an existing strongly-typed general-purpose programming language called bondi. The key ideas are to express complex search patterns as structures of simple patterns, pass these complex patterns as parameters to generic data-processing functions and traverse heterogeneous data structures by a generalized form of pattern matching. These ideas are made possible by the language's support for pattern calculus, whose typing on structures and patterns enables path and pattern polymorphism. With this approach, adding a new kind of pattern is just a matter of programming, not language design. Copyright © 2006, Australian Computer Society, Inc

Nemo: a computational tool for analyzing nematode locomotion

The nematode Caenorhabditis elegans responds to an impressive range of chemical, mechanical and thermal stimuli and is extensively used to investigate the molecular mechanisms that mediate chemosensation, mechanotransduction and thermosensation. The main behavioral output of these responses is manifested as alterations in animal locomotion. Monitoring and examination of such alterations requires tools to capture and quantify features of nematode movement. In this paper, we introduce Nemo (nematode movement), a computationally efficient and robust two-dimensional object tracking algorithm for automated detection and analysis of C. elegans locomotion. This algorithm enables precise measurement and feature extraction of nematode movement components. In addition, we develop a Graphical User Interface designed to facilitate processing and interpretation of movement data. While, in this study, we focus on the simple sinusoidal locomotion of C. elegans, our approach can be readily adapted to handle complicated locomotory behaviour patterns by including additional movement characteristics and parameters subject to quantification. Our software tool offers the capacity to extract, analyze and measure nematode locomotion features by processing simple video files. By allowing precise and quantitative assessment of behavioral traits, this tool will assist the genetic dissection and elucidation of the molecular mechanisms underlying specific behavioral responses.Comment: 12 pages, 2 figures. accepted by BMC Neuroscience 2007, 8:8

The impact of delays to admission from the emergency department on inpatient outcomes

<p>Abstract</p> <p>Background</p> <p>We sought to determine the impact of delays to admission from the Emergency Department (ED) on inpatient length of stay (LOS), and IP cost.</p> <p>Methods</p> <p>We conducted a retrospective analysis of 13,460 adult (≥ 18 yrs) ED visits between April 1 2006 and March 30 2007 at a tertiary care teaching hospital with two ED sites in which the mode of disposition was admission to ICU, surgery or inpatient wards. We defined ED Admission Delay as ED time to decision to admit > 12 hours. The primary outcomes were IP LOS, and total IP cost.</p> <p>Results</p> <p>Approximately 11.6% (n = 1558) of admitted patients experienced admission delay. In multivariate analysis we found that admission delay was associated with 12.4% longer IP LOS (95% CI 6.6% - 18.5%) and 11.0% greater total IP cost (6.0% - 16.4%). We estimated the cumulative impact of delay on all delayed patients as an additional 2,183 inpatient days and an increase in IP cost of $2,109,173 at the study institution.</p> <p>Conclusions</p> <p>Delays to admission from the ED are associated with increased IP LOS and IP cost. Improving patient flow through the ED may reduce hospital costs and improve quality of care. There may be a business case for investments to reduce emergency department admission delays.</p

Skeletal muscle as a regulator of the longevity protein, Klotho

Klotho is a powerful longevity protein that has been linked to the prevention of muscle atrophy, osteopenia, and cardiovascular disease. Similar anti-aging effects have also been ascribed to exercise and physical activity. While an association between muscle function and Klotho expression has been previously suggested from longitudinal cohort studies, a direct relationship between circulating Klotho and skeletal muscle has not been investigated. In this paper, we present a review of the literature and preliminary evidence that, together, suggests Klotho expression may be modulated by skeletal muscle activity. Our pilot clinical findings performed in young and aged individuals suggest that circulating Klotho levels are upregulated in response to an acute exercise bout, but that the response may be dependent on fitness level. A similar upregulation of circulating Klotho is also observed in response to an acute exercise in young and old mice, suggesting that this may be a good model for mechanistically probing the role of physical activity on Klotho expression. Finally, we highlight overlapping signaling pathways that are modulated by both Klotho and skeletal muscle and propose potential mechanisms for cross-talk between the two. It is hoped that this review will stimulate further consideration of the relationship between skeletal muscle activity and Klotho expression, potentially leading to important insights into the well-documented systemic anti-aging effects of exercise. © 2014 Avin, Coen, Huang, Stolz, Sowa, Dubé, Goodpaster, O'Doherty and Ambrosio

Learning curves and long-term outcome of simulation-based thoracentesis training for medical students

<p>Abstract</p> <p>Background</p> <p>Simulation-based medical education has been widely used in medical skills training; however, the effectiveness and long-term outcome of simulation-based training in thoracentesis requires further investigation. The purpose of this study was to assess the learning curve of simulation-based thoracentesis training, study skills retention and transfer of knowledge to a clinical setting following simulation-based education intervention in thoracentesis procedures.</p> <p>Methods</p> <p>Fifty-two medical students were enrolled in this study. Each participant performed five supervised trials on the simulator. Participant's performance was assessed by performance score (PS), procedure time (PT), and participant's confidence (PC). Learning curves for each variable were generated. Long-term outcome of the training was measured by the retesting and clinical performance evaluation 6 months and 1 year, respectively, after initial training on the simulator.</p> <p>Results</p> <p>Significant improvements in PS, PT, and PC were noted among the first 3 to 4 test trials (p < 0.05). A plateau for PS, PT, and PC in the learning curves occurred in trial 4. Retesting 6 months after training yielded similar scores to trial 5 (p > 0.05). Clinical competency in thoracentesis was improved in participants who received simulation training relative to that of first year medical residents without such experience (p < 0.05).</p> <p>Conclusions</p> <p>This study demonstrates that simulation-based thoracentesis training can significantly improve an individual's performance. The saturation of learning from the simulator can be achieved after four practice sessions. Simulation-based training can assist in long-term retention of skills and can be partially transferred to clinical practice.</p

Efficacy evaluation of iclaprim in a neutropenic rat lung infection model with methicillin-resistant Staphylococcus aureus entrapped in alginate microspheres

The objective of this study was to demonstrate the efficacy of iclaprim in a neutropenic rat lung infection model with methicillin-resistant Staphylococcus aureus (MRSA) entrapped in alginate beads. An inoculum of 5.25 × 10⁵ colony-forming units (CFU)/mL of S. aureus strain AH1252 was administered intratracheally to rats with prepared alginate bacteria suspensions. Beginning 2 h post-infection, rats received: (1) iclaprim 80 mg/kg (n = 16); (2) iclaprim 60 mg/kg (n = 16), or (3) vancomycin 50 mg/kg (n = 24), for 3 days via subcutaneous (SC) injection every 12 h. Twelve hours after the last treatment, rats were euthanized and lungs collected for CFU determination. Iclaprim administered at 80 mg/kg or 60 mg/kg or vancomycin 50 mg/kg SC twice a day for 3 days resulted in a 6.05 log10 CFU reduction (iclaprim 80 mg/kg compared with control, p < 0.0001), 5.11 log₁₀ CFU reduction (iclaprim 60 mg/kg compared with control, p < 0.0001), and 3.42 log₁₀ CFU reduction, respectively, from the controls (p < 0.0001). Iclaprim 80 mg/kg and 60 mg/kg resulted in 2.59 and 1.69 log₁₀ CFU reductions, respectively, from vancomycin-treated animals (80 mg/kg iclaprim vs. vancomycin, p = 0.0005; 60 mg/kg iclaprim vs. vancomycin, p = 0.07). Animals receiving iclaprim, vancomycin, and controls demonstrated 100%, 91.7%, and 48.3% survival, respectively. In this neutropenic rat S. aureus lung infection model, rats receiving iclaprim demonstrated a greater CFU reduction than the controls or those receiving vancomycin

Solutions of Several Coupled Discrete Models in terms of Lame Polynomials of Order One and Two

Coupled discrete models abound in several areas of physics. Here we provide an extensive set of exact quasiperiodic solutions of a number of coupled discrete models in terms of Lame polynomials of order one and two. Some of the models discussed are (i) coupled Salerno model, (ii) coupled Ablowitz-Ladik model, (iii) coupled saturated discrete nonlinear Schrodinger equation, (iv) coupled phi4 model, and (v) coupled phi6 model. Furthermore, we show that most of these coupled models in fact also possess an even broader class of exact solutions.Comment: 31 pages, to appear in Pramana (Journal of Physics) 201

Integrated multiple mediation analysis: A robustness–specificity trade-off in causal structure

Recent methodological developments in causal mediation analysis have addressed several issues regarding multiple mediators. However, these developed methods differ in their definitions of causal parameters, assumptions for identification, and interpretations of causal effects, making it unclear which method ought to be selected when investigating a given causal effect. Thus, in this study, we construct an integrated framework, which unifies all existing methodologies, as a standard for mediation analysis with multiple mediators. To clarify the relationship between existing methods, we propose four strategies for effect decomposition: two-way, partially forward, partially backward, and complete decompositions. This study reveals how the direct and indirect effects of each strategy are explicitly and correctly interpreted as path-specific effects under different causal mediation structures. In the integrated framework, we further verify the utility of the interventional analogues of direct and indirect effects, especially when natural direct and indirect effects cannot be identified or when cross-world exchangeability is invalid. Consequently, this study yields a robustness–specificity trade-off in the choice of strategies. Inverse probability weighting is considered for estimation. The four strategies are further applied to a simulation study for performance evaluation and for analyzing the Risk Evaluation of Viral Load Elevation and Associated Liver Disease/Cancer data set from Taiwan to investigate the causal effect of hepatitis C virus infection on mortality