Parallel approach to sliding window sums

Sliding window sums are widely used in bioinformatics applications, including sequence assembly, k-mer generation, hashing and compression. New vector algorithms which utilize the advanced vector extension (AVX) instructions available on modern processors, or the parallel compute units on GPUs and FPGAs, would provide a significant performance boost for the bioinformatics applications. We develop a generic vectorized sliding sum algorithm with speedup for window size w and number of processors P is O(P/w) for a generic sliding sum. For a sum with commutative operator the speedup is improved to O(P/log(w)). When applied to the genomic application of minimizer based k-mer table generation using AVX instructions, we obtain a speedup of over 5X.Comment: 10 pages, 5 figure

On the bi-stable nature of turbulent premixed bluff-body stabilized flames at elevated pressure and near lean blow-off

This study considers turbulent premixed bluff-body stabilized flames at elevated pressures. Specifically, the lean blow-off (LBO) limit of such flames is determined for a range of bulk velocities (5 U 50m/s) and operating pressures up to 3 bar. Two key observations emerge from this stability assessment. The first is that considering elevated pressure leads to two stability regimes: one at atmospheric conditions and those with elevated pressure and U & 20m/s (regime-a), and another at elevated pressures with U . 20m/s (regime-b). The second observation is that within these regimes, LBO limits are insensitive to pressure. Flames in regime-a (S-flames) are found to be more stable than those in regime-b (U-flames). Advanced image-based diagnostics were employed to understand reasons for this difference in stability. Flow field measurements indicate that U-flames are associated with an outer recirculation zone (ORZ) that formed as pressure increased but receded from the burner as U surpassed 20m/s. PLIF images of CH2O and OH demonstrated that the ORZ interacts with U-flames such that their downstream regions are prevented from collapsing to the inner recirculation zone (IRZ). Furthermore, analysis of the OH-PLIF images indicate that U-flames possess larger turbulent consumption rates, helping them form large IRZs and rendering them more susceptible to influence from the ORZ. Results of highspeed OH∗ imaging demonstrate that LBO events differ between U- and Sflames. Namely, while S-flames collapse to their IRZs during LBO, U-flames lift off from the burner, depleting their anchoring regions of reactions and hot products. Losing back-support in this region is what ultimately reduces the stability of U-flames. Finally, the reason U-flames lift off from the burner during LBO is elucidated by joint flow-flame measurements. Specifically, the anchoring regions of U-flames reside in regions of large axial velocity, which likely stems from their enhanced burning rates.No fundin

Temperature and water measurements in flames using 1064 nm Laser-Induced Grating Spectroscopy (LIGS)

Laser-Induced Grating Spectroscopy (LIGS) is applied to premixed CH4/ air laminar flat flames under operating pressures of 1 to 6 bar. For the first time, temperature and water concentration have been acquired simultaneously in a reacting flow environment using LIGS. A 1064 nm pulsed laser is used as pump to generate a temporary stationary intensity grating in the probe volume. Water molecules in the flame products absorb the laser energy and generate a thermal grating if sufficiently high energies are delivered by the laser pulses, here more than 100 mJ per pulse. Such energies allow the electric field to polarize the dielectric medium, resulting in a detectable electrostrictive grating as well. This creates LIGS signals containing both the electrostrictive and the thermal contributions. The local speed of sound is derived from the oscillation frequency of LIGS signals, which can be accurately measured from the single shot power spectrum. Data show that the ratio between the electrostrictive and the thermal peak intensities is an indicator of the local water concentration. The measured values of speed of sound, temperature, and water concentration in the flames examined compare favorably with flame simulations with Chemkin, showing an estimated accuracy of 0.5 to 2.5% and a precision of 1.4-2%. These results confirm the potential for 1064-nm LIGS-based thermometry for high-precision temperature measurements of combustion processes.Qualcomm, EPSRC, KAUS

A randomised controlled trial of laser scanning and casting for the construction of ankle foot orthoses

Study Design: Randomised controlled trial with blinding of orthotists and patients to the construction technique used. Background: Three-dimensional laser scanning has been used for patient measurement for cranial helmets and spinal braces. Ankle foot orthoses are commonly prescribed for children with orthopaedic conditions. This trial sought to compare ankle foot orthoses produced by laser scanning or traditional plaster casting. Objectives: Assessment of the effectiveness and efficiency of using laser scanning to produce AFOs. Methods: A randomised double blind trial comparing fabrication of AFOs from casts or laser scans. Results: The time spent in the rectification and moulding of scanned AFOs was around 50% less than for cast AFOs. A non-significant increase of 9 days was seen in the time to delivery to the patient for LSCAD/CAM. There was a higher incidence of problems with the scan-based AFOs at delivery of the device, but no difference in how long the AFOs lasted. Costs associated with laser scanning were not significantly different from traditional methods of AFO manufacture. Conclusions: Compared with conventional casting techniques laser scan based AFO manufacture neither significantly improved the quality of the final product nor delivered a useful saving in time

Introduction: looking beyond the walls

In its consideration of the remarkable extent and variety of non-university researchers, this book takes a broader view of ‘knowledge’ and ‘research’ than in the many hot debates about today’s knowledge society, ‘learning age’, or organisation of research. It goes beyond the commonly held image of ‘knowledge’ as something produced and owned by the full-time experts to take a look at those engaged in active knowledge building outside the university walls

Surfactant status and respiratory outcome in premature infants receiving late surfactant treatment.

BACKGROUND:Many premature infants with respiratory failure are deficient in surfactant, but the relationship to occurrence of bronchopulmonary dysplasia (BPD) is uncertain. METHODS:Tracheal aspirates were collected from 209 treated and control infants enrolled at 7-14 days in the Trial of Late Surfactant. The content of phospholipid, surfactant protein B, and total protein were determined in large aggregate (active) surfactant. RESULTS:At 24 h, surfactant treatment transiently increased surfactant protein B content (70%, p < 0.01), but did not affect recovered airway surfactant or total protein/phospholipid. The level of recovered surfactant during dosing was directly associated with content of surfactant protein B (r = 0.50, p < 0.00001) and inversely related to total protein (r = 0.39, p < 0.0001). For all infants, occurrence of BPD was associated with lower levels of recovered large aggregate surfactant, higher protein content, and lower SP-B levels. Tracheal aspirates with lower amounts of recovered surfactant had an increased proportion of small vesicle (inactive) surfactant. CONCLUSIONS:We conclude that many intubated premature infants are deficient in active surfactant, in part due to increased intra-alveolar metabolism, low SP-B content, and protein inhibition, and that the severity of this deficit is predictive of BPD. Late surfactant treatment at the frequency used did not provide a sustained increase in airway surfactant

The Cyprinodon variegatus genome reveals gene expression changes underlying differences in skull morphology among closely related species

Genes in durophage intersection set at 15 dpf. This is a comma separated table of the genes in the 15 dpf durophage intersection set. Given are edgeR results for each pairwise comparison. Columns indicating whether a gene is included in the intersection set at a threshold of 1.5 or 2 fold are provided. (CSV 13 kb