Representation of probabilistic scientific knowledge

This article is available through the Brunel Open Access Publishing Fund. Copyright © 2013 Soldatova et al; licensee BioMed Central Ltd.The theory of probability is widely used in biomedical research for data analysis and modelling. In previous work the probabilities of the research hypotheses have been recorded as experimental metadata. The ontology HELO is designed to support probabilistic reasoning, and provides semantic descriptors for reporting on research that involves operations with probabilities. HELO explicitly links research statements such as hypotheses, models, laws, conclusions, etc. to the associated probabilities of these statements being true. HELO enables the explicit semantic representation and accurate recording of probabilities in hypotheses, as well as the inference methods used to generate and update those hypotheses. We demonstrate the utility of HELO on three worked examples: changes in the probability of the hypothesis that sirtuins regulate human life span; changes in the probability of hypotheses about gene functions in the S. cerevisiae aromatic amino acid pathway; and the use of active learning in drug design (quantitative structure activity relation learning), where a strategy for the selection of compounds with the highest probability of improving on the best known compound was used. HELO is open source and available at https://github.com/larisa-soldatova/HELO.This work was partially supported by grant BB/F008228/1 from the UK Biotechnology & Biological Sciences Research Council, from the European Commission under the FP7 Collaborative Programme, UNICELLSYS, KU Leuven GOA/08/008 and ERC Starting Grant 240186

On the mechanism of trailing vortex wandering

The mechanism of trailing vortex wandering has long been debated and is often attributed to either wind-tunnel effects or an instability. Using particle image velocimetry data obtained in the wake of a NACA0012 airfoil, we remove the effect of wandering from the measured velocity field and, through a triple decomposition, recover the coherent wandering motion. Based on this wandering motion, the most energetic structures are computed using the proper orthogonal decomposition (POD) and exhibit a helical mode with an azimuthal wavenumber of |m|=1 whose kinetic energy grows monotonically in the downstream direction. To investigate the nature of the vortex wandering, we perform a spatial stability analysis of a matched Batchelor vortex. The primary stability mode is found to be marginally stable and nearly identical in both size and structure to the leading POD mode. The strikingly similar structure, coupled with the measured energy growth, supports the proposition that the vortex wandering is the result of an instability. We conclude that the cause of the wandering is the non-zero radial velocity of the |m|=1 mode on the vortex centreline, which acts to transversely displace the trailing vortex, as observed in experiments. However, the marginal nature of the stability mode prevents a definitive conclusion regarding the specific type of instability

A Study of Restaurateurs\u27 Attitudes and Practices in Relation to Obesity

The dramatic increase in the rate of obesity in the United States is raising new public health concerns. Each year, obesity-related problems cause at least 300,000 deaths and cost around 100 billion dollars. Take a walk down the street, go to a shopping center or sport event, or pick up a newspaper or magazine and the severity of the obesity problem in the United States is becoming a critical problem to solve. About 65% of the U.S. adult population is overweight (35%) or obese (30%), which has doubled in only two decades. Obesity-related diseases such as type 2 diabetes, heart disease and stroke, arthritis, respiratory problems, cancer, and sleep apnea have become a major concern in our health care crisis. Poor diet and physical inactivity leading to excess body weight was identified as the second leading cause of death in the United States. While Americans are consuming more food outside the home, it may seem easy to assume a relationship between the increases in the success of the restaurant industry and national obesity rates. The growth in food away from home has created concern about its possible effect on dietary quality. Because so much food is eaten outside the home, restaurants do have a significant impact on the food consumption of the United States and play a considerable role in the shaping of American diets

Walking in Sync: Two is Company, Three's a Crowd.

Eventual gait synchronization between two individuals while walking and talking with each other has been shown to be an indicator of agreeableness and companionship. The inferred physical signal from this subconscious phenomenon can po-tentially be an indicator of cooperation or relation between two individuals. In this paper we investigate this effect, and whether having a third person actively engaging in the same act or conversation can reduce this synchronization level. Using high frequency accelerometer data from a ded-icated smartphone app, we perform a number of controlled experiments on a number of individuals in different group configuration. Our results bring an interesting insight: it is the non-verbal social signals such as the gaze, head orienta-tion and gestures that is the key factor in synchronization, not necessarily the number or configuration of the walkers. These early results can lead us on detecting relationships between individuals or detecting the group formation and numbers for crowd-sensing applications when only partial data is available. Categories and Subject Descriptors Human-centered computing [Ubiquitous and mobile com-puting]: Empirical studies in ubiquitous and mobile com-putin

A method for high-quality RNA extraction from tall fescue

The isolation of high-quality RNA was a precondition in molecular biology research of tall fescue. Two common approaches were adopted for the total RNA extraction by using leaves of tall fescue as the material in this experiment in order to seek the optimized total RNA extraction method of tall fescue, as well as the improvement of the extraction method used by the predecessors. The results showed that the Trizol method cost much and was not suitable for the large quantity of plant tissues extraction. The traditional isothiocyanate method resulted in protein contamination and RNA degradation. By employing the improved isothiocyanate method, we found that there were three bright bands in agarose gel electrophoresis (28S rRNA, 18S rRNA and 5S rRNA). The band of 28S rRNA was brighter than that of 18S rRNA, and the value of OD260/OD280 was 1.8 to 2.0. Clear bands and high polymorphisms were obtained by cDNA-AFLP analysis. These results indicated that the RNA isolated by the improved isothiocyanate method had a good integrity and high purity, which could be used for the later molecular researches.Key words: Tall fescue, RNA extraction, improved isothiocyanate method

An exploration of occupation in nursing home residents with dementia

Objectives: This study evaluated the sitting room environment of two nursing homes in Ireland, using interactive occupation and social engagement as outcome measures and defining these rooms as occupational spaces. Method: Snapshot observational recordings were made in the main sitting rooms during the periods of time when the rooms were in most active use. Narrative information was also recorded. Results: Residents were more likely to occupy their time in the main sitting room passively, rather than in interactive occupation and social engagement. The nursing home residents with dementia spent approximately 70% of their daily time in the main sitting room areas in states of occupational disengagement. Discussion: Additional insight is provided through pragmatic narrative descriptions of the functioning of the main sitting room environment in terms of interactive occupation and social engagement. Relevance: The research study demonstrates a methodology for evaluating the sitting room areas of a care environment, using interactive occupation and social engagement as outcome measures,which can be used for descriptive and comparative insights into the performance of care environments

Open ventral hernia repair with a composite ventral patch : final results of a multicenter prospective study

Background: This study assessed clinical outcomes, including safety and recurrence, from the two-year follow-up of patients who underwent open ventral primary hernia repair with the use of the Parietex (TM) Composite Ventral Patch (PCO-VP). Methods: A prospective single-arm, multicenter study of 126 patients undergoing open ventral hernia repair for umbilical and epigastric hernias with the PCO-VP was performed. Results: One hundred twenty-six subjects (110 with umbilical hernia and 16 with epigastric hernia) with a mean hernia diameter of 1.8cm (0.4-4.0) were treated with PCO-VP. One hundred subjects completed the two-year study. Cumulative hernia recurrence was 3.0% (3/101; 95%CI: 0.0-6.3%) within 24months. Median Numeric Rating Scale pain scores improved from 2 [0-10] at baseline to 0 [0-3] at 1 month (P<0.001) and remained low at 24months 0 [0-6] (P<0.001). 99% (102/103) of the patients were satisfied with their repair at 24months postoperative. Conclusions: The use of PCO-VP to repair primary umbilical and epigastric defects yielded a low recurrence rate, low postoperative and chronic pain, and high satisfaction ratings, confirming that PCO-VP is effective for small ventral hernia repair in the two-year term after implantation. Trial registration: The study was registered publically at clinicaltrials.gov (NCT01848184 registered May 7, 2013)

A new strategy for faster urinary biomarkers identification by Nano-LC-MALDI-TOF/TOF mass spectrometry

<p>Abstract</p> <p>Background</p> <p>LC-MALDI-TOF/TOF analysis is a potent tool in biomarkers discovery characterized by its high sensitivity and high throughput capacity. However, methods based on MALDI-TOF/TOF for biomarkers discovery still need optimization, in particular to reduce analysis time and to evaluate their reproducibility for peak intensities measurement. The aims of this methodological study were: (i) to optimize and critically evaluate each step of urine biomarker discovery method based on Nano-LC coupled off-line to MALDI-TOF/TOF, taking full advantage of the dual decoupling between Nano-LC, MS and MS/MS to reduce the overall analysis time; (ii) to evaluate the quantitative performance and reproducibility of nano-LC-MALDI analysis in biomarker discovery; and (iii) to evaluate the robustness of biomarkers selection.</p> <p>Results</p> <p>A pool of urine sample spiked at increasing concentrations with a mixture of standard peptides was used as a specimen for biological samples with or without biomarkers. Extraction and nano-LC-MS variabilities were estimated by analyzing in triplicates and hexaplicates, respectively. The stability of chromatographic fractions immobilised with MALDI matrix on MALDI plates was evaluated by successive MS acquisitions after different storage times at different temperatures.</p> <p>Low coefficient of variation (CV%: 10–22%) and high correlation (R²> 0.96) values were obtained for the quantification of the spiked peptides, allowing quantification of these peptides in the low fentomole range, correct group discrimination and selection of "specific" markers using principal component analysis. Excellent peptide integrity and stable signal intensity were found when MALDI plates were stored for periods of up to 2 months at +4°C. This allowed storage of MALDI plates between LC separation and MS acquisition (first decoupling), and between MS and MSMS acquisitions while the selection of inter-group discriminative ions is done (second decoupling). Finally the recording of MSMS spectra to obtain structural information was focused only on discriminative ions in order to minimize analysis time.</p> <p>Conclusion</p> <p>Contrary to other classical approaches with direct online coupling of chromatographic separation and on the flight MS and/or MSMS data acquisition for all detected analytes, our dual decoupling strategy allowed us to focus on the most discriminative analytes, giving us more time to acquire more replicates of the same urine samples thus increasing detection sensitivity and mass precision.</p