FastEpistasis: a high performance computing solution for quantitative trait epistasis.

Motivation: Genome-wide association studies have become widely used tools to study effects of genetic variants on complex diseases. While it is of great interest to extend existing analysis methods by considering interaction effects between pairs of loci, the large number of possible tests presents a significant computational challenge. The number of computations is further multiplied in the study of gene expression quantitative trait mapping, in which tests are performed for thousands of gene phenotypes simultaneously. Results: We present FastEpistasis, an efficient parallel solution extending the PLINK epistasis module, designed to test for epistasis effects when analyzing continuous phenotypes. Our results show that the algorithm scales with the number of processors and offers a reduction in computation time when several phenotypes are analyzed simultaneously. FastEpistasis is capable of testing the association of a continuous trait with all single nucleotide polymorphism ( SNP) pairs from 500 000 SNPs, totaling 125 billion tests, in a population of 5000 individuals in 29, 4 or 0.5 days using 8, 64 or 512 processors.

The Glass Floor.

A photographic and video record of the project to recreate and reconstruct the glass floor for the opening between the ground and first floors in the rotunda of the Iowa State Capitol. The original glass floor was removed in the early 20th century, but the decision was made to put a new one in to help improve the acoustics and air flow in the building.

Smart suction device for less blood trauma: a comparison with Cell Saver.

OBJECTIVE: The major source of hemolysis during cardiopulmonary bypass remains the cardiotomy suction and is primarily due to the interaction between air and blood. The Smart suction system involves an automatically controlled aspiration designed to avoid the mixture of blood with air. This study was set-up to compare this recently designed suction system to a Cell Saver system in order to investigate their effects on blood elements during prolonged intrathoracic aspiration. METHODS: In a calf model (n=10; mean weight, 69.3+/-4.5 kg), a standardized hole was created in the right atrium allowing a blood loss of 100 ml/min, with a suction cannula placed into the chest cavity into a fixed position during 6 h. The blood was continuously aspirated either with the Smart suction system (five animals) or the Cell Saver system (five animals). Blood samples were taken hourly for blood cell counts and biochemistry. RESULTS: In the Smart suction group, red cell count, plasma protein and free hemoglobin levels remained stable, while platelet count exhibited a significant drop from the fifth hour onwards (prebypass: 683+/-201*10(9)/l, 5 h: 280+/-142*10(9)/l, P=0.046). In the Cell Saver group, there was a significant drop of the red cell count from the third hour onwards (prebypass: 8.6+/-0.9*10(12)/l, 6 h: 6.3+/-0.4*10(12)/l, P=0.02), of the platelet count from the first hour onwards (prebypass: 630+/-97*10(9)/l, 1 h: 224+/-75*10(9)/l, P<0.01), and of the plasma protein level from the first hour onwards (prebypass: 61.7+/-0.6 g/l, 1 h: 29.3+/-9.1 g/l, P<0.01). CONCLUSIONS: In this experimental set-up, the Smart suction system avoids damage to red cells and affects platelet count less than the Cell Saver system which induces important blood cell destruction, as any suction device mixing air and blood, as well as severe hypoproteinemia with its metabolic, clotting and hemodynamic consequences.

Comment on ‘‘Relaxation Kinetics of Nanoscale Indents in a Polymer Glass’’

A Comment on the Letter by A. Knoll, D. Wiesmann, B. Gotsmann, and U. Duerig, published in Physical Review Letter, 2009, vol. 102, p.117801

Nutrition préopératoire en chirurgie viscérale: recommandations et réalité [Preoperative nutrition in abdominal surgery: recommendations and reality].

Malnutrition concerns up to 50% at in-hospital admission. Its diagnosis and treatment are fundamental parts of the surgical approach because nutritional status directly influences the clinical outcome. The Nutritional Risk Score (NRS-2002) represents the recommended screening tool by the European Society of Parenteral and Enteral Nutrition (ESPEN). Patients with a score > or = 3 and aged > 70 years old, should receive a nutritional support during 7-14 day before surgery. Depending on patient's clinical conditions, the enteral route of administration should be preferred. Despite strong evidence in favor of nutritional supplementation, much effort must be done to implement these supportive strategies in the everyday clinical practice.

Apprendre ensemble pourtravailler ensemble: l'education interprofessionnelle, un mythe ou une réalité [Learning together to work together: interprofessional education, a myth or reality?].

This article offers a review of the literature on interprofessional education (EIP), a form of education which brings together members of two or more professions in a joint training. In this course, participants gain knowledge through other professionals and about them. The goal of EIP is to improve collaboration between health professionals and the quality of patient care. The EIP is booming worldwide and seems for from a mere fad. This expansion can be explained by several factors: the increasing importance attributed to the quality of care and patient safety, care changes (aging population and increasing chronic diseases) and the shortage of health professionals. The expectations of the EIP are large, while the evidence supporting its effectiveness is being built.

A novel approach to reducing number of sensing units for wearable gait analysis systems.

Gait analysis methods to estimate spatiotemporal measures, based on two, three or four gyroscopes attached on lower limbs have been discussed in the literature. The most common approach to reduce the number of sensing units is to simplify the underlying biomechanical gait model. In this study, we propose a novel method based on prediction of movements of thighs from movements of shanks. Datasets from three previous studies were used. Data from the first study (ten healthy subjects and ten with Parkinson's disease) were used to develop and calibrate a system with only two gyroscopes attached on shanks. Data from two other studies (36 subjects with hip replacement, seven subjects with coxarthrosis, and eight control subjects) were used for comparison with the other methods and for assessment of error compared to a motion capture system. Results show that the error of estimation of stride length compared to motion capture with the system with four gyroscopes and our new method based on two gyroscopes was close ( -0.8 ±6.6 versus 3.8 ±6.6 cm). An alternative with three sensing units did not show better results (error: -0.2 ±8.4 cm). Finally, a fourth that also used two units but with a simpler gait model had the highest bias compared to the reference (error: -25.6 ±7.6 cm). We concluded that it is feasible to estimate movements of thighs from movements of shanks to reduce number of needed sensing units from 4 to 2 in context of ambulatory gait analysis.

Augmented state Kalman filtering for AUV navigation

Addresses the problem of estimating the motion of an autonomous underwater vehicle (AUV), while it constructs a visual map ("mosaic" image) of the ocean floor. The vehicle is equipped with a down-looking camera which is used to compute its motion with respect to the seafloor. As the mosaic increases in size, a systematic bias is introduced in the alignment of the images which form the mosaic. Therefore, this accumulative error produces a drift in the estimation of the position of the vehicle. When the arbitrary trajectory of the AUV crosses over itself, it is possible to reduce this propagation of image alignment errors within the mosaic. A Kalman filter with augmented state is proposed to optimally estimate both the visual map and the vehicle position

Investigation of Glass Fiber Composite Dowel Bars for Highway Pavement Slabs, TR-408, 2001

Contractors, engineers, owners and manufacturers want to be certain that a new product or procedure will yield beneficial results when compared to the current method of construction. The following research was conducted in order to compare the performance of epoxy coated dowel bars to dowel bars of alternative shapes and materials such as stainless steel and glass fiber reinforced polymer (GFRP). Research was also done on the effect that dowel bar spacing has on the performance of concrete pavements. Four phases of this research are described in this report.

Small access (30F) clinical central venous smart cannulation: is it adequate?

OBJECTIVES: To assess the performance of 45F vs. 36F smartcanula in CPB with gravity drainage alone. METHODS: Twenty patients were randomly assigned to two groups receiving for venous drainage a smartcanula which is collapsed over a mandrel for trans-atrial insertion into the inferior vena cava and expanded in situ to either 45F or 36F. RESULTS: Valve replacement/repair was realized in 7/10 and/or CABG in 6/10 for 36F (69+/-13 years) vs. 5/10 and 5/10, respectively, for 45F (63+/-11 years: NS). Body weight and surface area (BSA) were 83+/-9 kg (1.9+/-0.2 m2, max 2.2 m2) for 36F vs. 79+/-6 kg: NS (1.9+/-0.1 m2 (NS), max 2.1 m2) for 45F. Insertion and access orifice diameter (area) was 6 mm and 10 mm (78.5 mm2) for the 36F vs. 6 mm and 13 mm (132 mm2) for the 45F (+69%). Calculated target pump flow (2.4 l/min/m2) was 4.7+/-0.4 l/min for 36F vs. 4.5+/-0.3 l/min for 45F. Achieved pump flow accounted for 5.0+/-0.3 l/min for 36F (8% above target) vs. 4.8+/-0.3 l/min for 45F (8% above target): NS. The water balance during the pump run (clear volume added minus hemofilter and urine output) was 2.2+/-0.3 l for 36F vs. 2.0 l for 45F: NS. CONCLUSION: Due to its 'open' wall (the vena cava provides the seal), its reduced wall thickness (range: 0.0-0.4 mm), and its self-expanding design, the 36F smartcanula requiring a 30F access orifice has sufficient drainage capacity by gravity alone for full CPB in adults with a BSA up to 2.2 mm2.

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.

The M-Coffee server is a web server that makes it possible to compute multiple sequence alignments (MSAs) by running several MSA methods and combining their output into one single model. This allows the user to simultaneously run all his methods of choice without having to arbitrarily choose one of them. The MSA is delivered along with a local estimation of its consistency with the individual MSAs it was derived from. The computation of the consensus multiple alignment is carried out using a special mode of the T-Coffee package [Notredame, Higgins and Heringa (T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000; 302: 205-217); Wallace, O'Sullivan, Higgins and Notredame (M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 2006; 34: 1692-1699)] Given a set of sequences (DNA or proteins) in FASTA format, M-Coffee delivers a multiple alignment in the most common formats. M-Coffee is a freeware open source package distributed under a GPL license and it is available either as a standalone package or as a web service from www.tcoffee.org.