A generic algorithm for layout of biological networks

BackgroundBiological networks are widely used to represent processes in biological systems and to capture interactions and dependencies between biological entities. Their size and complexity is steadily increasing due to the ongoing growth of knowledge in the life sciences. To aid understanding of biological networks several algorithms for laying out and graphically representing networks and network analysis results have been developed. However, current algorithms are specialized to particular layout styles and therefore different algorithms are required for each kind of network and/or style of layout. This increases implementation effort and means that new algorithms must be developed for new layout styles. Furthermore, additional effort is necessary to compose different layout conventions in the same diagram. Also the user cannot usually customize the placement of nodes to tailor the layout to their particular need or task and there is little support for interactive network exploration.ResultsWe present a novel algorithm to visualize different biological networks and network analysis results in meaningful ways depending on network types and analysis outcome. Our method is based on constrained graph layout and we demonstrate how it can handle the drawing conventions used in biological networks.ConclusionThe presented algorithm offers the ability to produce many of the fundamental popular drawing styles while allowing the exibility of constraints to further tailor these layouts.publishe

Planetary bearing defect detection in a commercial helicopter main gearbox with vibration and acoustic emission

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.Helicopter gearboxes significantly differ from other transmission types and exhibit unique behaviors that reduce the effectiveness of traditional fault diagnostics methods. In addition, due to lack of redundancy, helicopter transmission failure can lead to catastrophic accidents. Bearing faults in helicopter gearboxes are difficult to discriminate due to the low signal to noise ratio (SNR) in the presence of gear vibration. In addition, the vibration response from the planet gear bearings must be transmitted via a time-varying path through the ring gear to externally mounted accelerometers, which cause yet further bearing vibration signal suppression. This research programme has resulted in the successful proof of concept of a broadband wireless transmission sensor that incorporates power scavenging whilst operating within a helicopter gearbox. In addition, this paper investigates the application of signal separation techniques in detection of bearing faults within the epicyclic module of a large helicopter (CS-29) main gearbox using vibration and Acoustic Emissions (AE). It compares their effectiveness for various operating conditions. Three signal processing techniques including an adaptive filter, spectral kurtosis and envelope analysis, were combined for this investigation. In addition, this research discusses the feasibility of using AE for helicopter gearbox monitoring

Application of Approximate Pattern Matching in Two Dimensional Spaces to Grid Layout for Biochemical Network Maps

Background For visualizing large-scale biochemical network maps, it is important to calculate the coordinates of molecular nodes quickly and to enhance the understanding or traceability of them. The grid layout is effective in drawing compact, orderly, balanced network maps with node label spaces, but existing grid layout algorithms often require a high computational cost because they have to consider complicated positional constraints through the entire optimization process. Results We propose a hybrid grid layout algorithm that consists of a non-grid, fast layout (preprocessor) algorithm and an approximate pattern matching algorithm that distributes the resultant preprocessed nodes on square grid points. To demonstrate the feasibility of the hybrid layout algorithm, it is characterized in terms of the calculation time, numbers of edge-edge and node-edge crossings, relative edge lengths, and F-measures. The proposed algorithm achieves outstanding performances compared with other existing grid layouts. Conclusions Use of an approximate pattern matching algorithm quickly redistributes the laid-out nodes by fast, non-grid algorithms on the square grid points, while preserving the topological relationships among the nodes. The proposed algorithm is a novel use of the pattern matching, thereby providing a breakthrough for grid layout. This application program can be freely downloaded from http://www.cadlive.jp/hybridlayout/hybridlayout.html

Extensor tendon release in tennis elbow: results and prognostic factors in 80 elbows

Purpose The objectives of this study were to evaluate the results in the outpatient treatment of recalcitrant lateral epicondylitis with release of the common extensor origin according to Hohmann and to determine any prognostic factors. Methods Eighty tennis elbows in 77 patients with a characteristic history of activity-related pain at the lateral epicondyle interfering with the activities of daily living refractory to conservative care for at least 6 months and a confirmatory physical examination were included. Clinical outcome was evaluated using the QuickDASH score system. Data were collected before the operation and at the medians of 18 months (range 6–36 months; short term) and 4 years (range 3–6 years; medium term) postoperatively. Results The mean QuickDASH was improved both at the short- and the medium-term follow-ups and did not change significantly between the follow-ups. At the final followup, the QuickDASH was improved in 78 out of 80 elbows and 81% was rated as excellent or good (QuickDASH\40 points). We found a weak correlation between residual symptoms (a high QuickDASH score) at the final follow-up and high level of baseline symptoms (r = 0.388), acute occurrence of symptoms (r = 0.362), long duration of symptoms (r = 0.276), female gender (r = 0.269) and young age (r = 0.203), whereas occurrence in dominant arm, a work-related cause or strenuous work did not correlate significantly with the outcome. Conclusion Open lateral extensor release performed as outpatient surgery results in improved clinical outcome at both short- and medium-term follow-ups with few complications. High baseline disability, sudden occurrence of symptoms, long duration of symptoms, female gender and young age were found to be weak predictors of poor outcome

Researchers' experience with project management in health and medical research: Results from a post-project review

<p>Abstract</p> <p>Background</p> <p>Project management is widely used to deliver projects on time, within budget and of defined quality. However, there is little published information describing its use in managing health and medical research projects. We used project management in the <it>Alcohol and Pregnancy Project </it>(2006-2008) <url>http://www.ichr.uwa.edu.au/alcoholandpregnancy</url> and in this paper report researchers' opinions on project management and whether it made a difference to the project.</p> <p>Methods</p> <p>A national interdisciplinary group of 20 researchers, one of whom was the project manager, formed the Steering Committee for the project. We used project management to ensure project outputs and outcomes were achieved and all aspects of the project were planned, implemented, monitored and controlled. Sixteen of the researchers were asked to complete a self administered questionnaire for a post-project review.</p> <p>Results</p> <p>The project was delivered according to the project protocol within the allocated budget and time frame. Fifteen researchers (93.8%) completed a questionnaire. They reported that project management increased the effectiveness of the project, communication, teamwork, and application of the interdisciplinary group of researchers' expertise. They would recommend this type of project management for future projects.</p> <p>Conclusions</p> <p>Our post-project review showed that researchers comprehensively endorsed project management in the <it>Alcohol and Pregnancy Project </it>and agreed that project management had contributed substantially to the research. In future, we will project manage new projects and conduct post-project reviews. The results will be used to encourage continuous learning and continuous improvement of project management, and provide greater transparency and accountability of health and medical research. The use of project management can benefit both management and scientific outcomes of health and medical research projects.</p

Evolutionary Repercussions of Avian Culling on Host Resistance and Influenza Virulence

Keeping pandemic influenza at bay is a global health priority. Of particular concern is the continued spread of the influenza subtype H5N1 in avian populations and the increasing frequency of transmission to humans. To decrease this threat, mass culling is the principal strategy for eradicating influenza in avian populations. Although culling has a crucial short-term epidemiological benefit, evolutionary repercussions on reservoir hosts and on the viral population have not been considered.To explore the epidemiological and evolutionary repercussions of mass avian culling, we combine population genetics and epidemiological influenza dynamics in a mathematical model parameterized by clinical, epidemiological, and poultry data. We model the virulence level of influenza and the selection on a dominant allele that confers resistance against influenza [1, 2] in a poultry population. Our findings indicate that culling impedes the evolution of avian host resistance against influenza. On the pathogen side of the coevolutionary race between pathogen and host, culling selects for heightened virulence and transmissibility of influenza.Mass culling achieves a short-term benefit at the expense of long-term detriments: a more genetically susceptible host population, ultimately greater mortality, and elevated influenza virulence

Destabilization of the Dystrophin-Glycoprotein Complex without Functional Deficits in α-Dystrobrevin Null Muscle

α-Dystrobrevin is a component of the dystrophin-glycoprotein complex (DGC) and is thought to have both structural and signaling roles in skeletal muscle. Mice deficient for α-dystrobrevin (adbn−/−) exhibit extensive myofiber degeneration and neuromuscular junction abnormalities. However, the biochemical stability of the DGC and the functional performance of adbn−/− muscle have not been characterized. Here we show that the biochemical association between dystrophin and β-dystroglycan is compromised in adbn−/− skeletal muscle, suggesting that α-dystrobrevin plays a structural role in stabilizing the DGC. However, despite muscle cell death and DGC destabilization, costamere organization and physiological performance is normal in adbn−/− skeletal muscle. Our results demonstrate that myofiber degeneration alone does not cause functional deficits and suggests that more complex pathological factors contribute to the development of muscle weakness in muscular dystrophy

Predicting Protein Phenotypes Based on Protein-Protein Interaction Network

BACKGROUND: Identifying associated phenotypes of proteins is a challenge of the modern genetics since the multifactorial trait often results from contributions of many proteins. Besides the high-through phenotype assays, the computational methods are alternative ways to identify the phenotypes of proteins. METHODOLOGY/PRINCIPAL FINDINGS: Here, we proposed a new method for predicting protein phenotypes in yeast based on protein-protein interaction network. Instead of only the most likely phenotype, a series of possible phenotypes for the query protein were generated and ranked according to the tethering potential score. As a result, the first order prediction accuracy of our method achieved 65.4% evaluated by Jackknife test of 1,267 proteins in budding yeast, much higher than the success rate (15.4%) of a random guess. And the likelihood of the first 3 predicted phenotypes including all the real phenotypes of the proteins was 70.6%. CONCLUSIONS/SIGNIFICANCE: The candidate phenotypes predicted by our method provided useful clues for the further validation. In addition, the method can be easily applied to the prediction of protein associated phenotypes in other organisms

Come for the looks, stay for the personality? A mixed methods investigation of reacquisition and owner recommendation of Bulldogs, French Bulldogs and Pugs

Brachycephalic breeds are proliferating internationally, with dramatic rises in popularity juxtaposed with common and severe breed-related health problems. Physical appearance is as a dominant factor attracting owners to brachycephalic breeds; however, whether these owners will choose their current breed for future ownership and develop 'breed-loyalty' in the face of health problems is not yet known. The aims of this study were (1) to quantify levels of, and explore factors associated with, brachycephalic dog owners' intentions to: (i) reacquire and/or (ii) recommend their current breed to potential first-time dog owners, and (2) to use qualitative methods to explore why brachycephalic dog owners would or would not recommend their current breed. This large mixed methods study reports on 2168 owners of brachycephalic breeds (Pugs: n = 789; French Bulldog: n = 741; Bulldogs: n = 638). Owners were highly likely to want to own their breed again in the future (93.0%) and recommend their breed to other owners (65.5%). Statistical modelling identified that first-time ownership and increased strength of the dog-owner relationship increased the likelihood of reacquisi-tion and/or recommendation. In contrast, an increased number of health problems, positive perception of their dog's health compared with the rest of their breed, and dog behaviour being worse than expected decreased the likelihood of reacquisition and/or recommendation. Thematic analyses constructed three themes describing why owners recommend their breed: positive behavioural attributes for a companion dog, breed suited to a sedentary lifestyle with limited space, and suitability for households with children. Five themes described why owners recommended against their breed: high prevalence of health problems, expense of ownership, ethical and welfare issues associated with breeding brachycephalic dogs, negative effects upon owner lifestyle and negative behavioural attributes. Understanding how breed-loyalty develops, and whether it can be attenuated, will be key to controlling the current population boom in brachycephalic breeds in the long-term