Effect of cholesterol on the lateral nanoscale dynamics of fluid membranes - Armstrong, Clare L.; Barrett, Matthew A.; Hiess, Arno; Salditt, Tim; Katsaras, John; Shi, An-chang; Rheinstädter, Maikel C. (European Biophysics Journal, 2012)
Inelastic neutron scattering was used to study the effect of 5 and 40 mol% cholesterol on the lateral nanoscale dynamics of phospholipid membranes. By measuring the excitation spectrum at several lateral q || values (up to q || = 3 Å−1), complete dispersion curves were determined of gel, fluid and liquid-ordered phase bilayers. The inclusion of cholesterol had a distinct effect on the collective dynamics of the bilayer’s hydrocarbon chains; specifically, we observed a pronounced stiffening of the membranes on the nanometer length scale in both gel and fluid bilayers, even though they were experiencing a higher degree of molecular disorder. Also, for the first time we determined the nanoscale dynamics in the high-cholesterol liquid-ordered phase of bilayers containing cholesterol. Namely, this phase appears to be “softer” than fluid bilayers, but better ordered than bilayers in the gel phase.
Keywords: Lipid membrane; Cholesterol; Lateral membrane dynamics; Nanoscale dynamics; Liquid-ordered phase; Inelastic neutron scattering; Dispersion relation

PVT characterization of polymeric nanocomposites - Utracki, Leszek A. (Characterization Techniques for Polymer Nanocomposites, 2012)

Systems biology methods help develop a better understanding of hepatitis C virus-induced liver injury - Singaravelu, Ragunath; Nasheri, Neda; Sherratt, Allison; Pezacki, John Paul (Hepatology, 2012)

Spatial MEG Laterality maps for language : clinical applications in epilepsy - D'arcy, Ryan C. N.; Bardouille, Timothy; Newman, Aaron J.; Mcwhinney, Sean R.; Debay, Drew; Sadler, R. Mark; Clarke, David B.; Esser, Michael J. (Human Brain Mapping, 2012)
Functional imaging is increasingly being used to provide a noninvasive alternative to intracarotid sodium amobarbitol testing (i.e., the Wada test). Although magnetoencephalography (MEG) has shown significant potential in this regard, the resultant output is often reduced to a simplified estimate of laterality. Such estimates belie the richness of functional imaging data and consequently limit the potential value. We present a novel approach that utilizes MEG data to compute “complex laterality vectors” and consequently “laterality maps” for a given function. Language function was examined in healthy controls and in people with epilepsy. When compared with traditional laterality index (LI) approaches, the resultant maps provided critical information about the magnitude and spatial characteristics of lateralized function. Specifically, it was possible to more clearly define low LI scores resulting from strong bilateral activation, high LI scores resulting from weak unilateral activation, and most importantly, the spatial distribution of lateralized activation. We argue that the laterality concept is better presented with the inherent spatial sensitivity of activation maps, rather than being collapsed into a one-dimensional index.
Keywords: magnetoencephalography; Wada test; presurgical functional mapping; neurological planning; language; memory; cognition

A photonic-microfluidic integrated device for reliable fluorescence detection and counting - Watts, Benjamin R.; Zhang, Zhiyi; Xu, Chang Qing; Cao, Xudong; Lin, Min (Electrophoresis, 2012)
A photonic-microfluidic integrated device is demonstrated with excellent and reliable fluorescence detection performance. CV values of 8% for 2.5-μm beads and 14% for 6-μm beads were achieved through the correct deployment of carefully formed excitation beam shapes via integrated on-chip optics even without the use of 3D hydrodynamic focusing or a high-quality laser source and single mode beam propagation. The devices are fabricated in a monolithic planar fashion using a system of microlenses and waveguides integrated with microfluidic channels on-chip and packaged using a high-quality and low-cost channel sealing and high-performance interconnecting technology developed from our earlier works. Beam geometry in the excitation region is shown to affect the variation of fluorescence intensity from specimens, hence configurations of beam geometry targeted for a specific bead sizes are examined to ensure proper deployment of the lens designs. The formed high-quality optical excitation regions ensure reliable detection even with relaxed hydrodynamic focusing to ensure applicability with multiple specimen sizes. Device performance with each bead size was found to be acceptable for a range of beam geometries with a different ideal configuration for each bead size. These device designs help to form a device that will supplement conventional flow cytometry in point-of-care and remote detection applications by performing specific detections with an inexpensive and replaceable device.
Keywords: Fluorescence detection; Integrated optics; Microbeads; Microfluidic devices

Integrated electrokinetic sample fractionation and solid-phase extraction in microfluidic devices - Wang, Zhen; Jemere, Abebaw B.; Harrison, D. Jed (Electrophoresis, 2012)
A microfluidic device that performs “in space” sample fractionation, collection, and preconcentration for proteomics is described. Effluents from a 2.75 mm long fractionation channel, focused via sheath flow, were sequentially delivered into an array of 36-collection channels containing monolithic polymer beds for SPE. Optimum conditions for the device design, and simultaneous photolytic fabrication of 36 monolithic columns in the 36 channels, as well as for their proper performance in electrokinetic sample fractionation and collection are described. A hydrophobic butyl methacrylate-based monolithic porous polymer was copolymerized with an ionizable monomer, acryloamido-methyl-propane sulfonate, to form a polymer monolith for SPE that also sustains cathodic electroosmotic flow. The SPE bed was made deep enough to greatly reduce the linear flow rate within the bed, in order to compensate for the lower electroosmotic mobility of the cationically charged SPE bed relative to the glass walled device. Under these conditions, electrokinetic fractionation of a protein sample resulted in tightly focused sample zones delivered into each of the 36-channel polymer beds with no observed crosscontamination. Monolithic columns showed reproducible performance with preconcentration factor of 30 for 2 min loading time. The ability to fractionate, collect, and preconcentrate samples on a microfluidic platform will be especially useful for automated or continuous operation of these devices in proteomics research.
Keywords: Capillary electrophoresis; Electrokinetic; Fractionation; Microfluidics; Solid-phase extraction

Thiogalactopyranosides are resistant to hydrolysis by α-galactosidases - Adlercreutz, Dietlind; Yoshimura, Yayoi; Mannerstedt, Karin; Wakarchuk, Warren W.; Bennett, Eric P.; Dovichi, Norman J.; Hindsgaul, Ole; Palcic, Monica M. (ChemBioChem, 2012)
Fluorescently tagged glycosides containing terminal α(1→3) and α(1→4)-linked thiogalactopyranosides have been prepared and tested for resistance to hydrolysis by α-galactosidases. Eight fluorescent glycosides containing either galactose or 5-thiogalactose as the terminal sugar were enzymatically synthesized using galactosyltransferases, with lactosyl glycosides as acceptors and UDP-galactose or UDP-5′-thiogalactose, respectively, as donors. The glycosides were incubated with human α-galactosidase A (CAZy family GH27, a retaining glycosidase), Bacteroides fragilis α-1,3-galactosidase (GH110, an inverting glycosidase), or homogenates of MCF-7 human breast cancer cells or NG108-15 rat glioma cells. Substrate hydrolysis was monitored by capillary electrophoresis with fluorescence detection. All compounds containing terminal O-galactose were readily degraded. Their 5-thiogalactose counterparts were resistant to hydrolysis by human α-galactosidase A and the enzymes present in the cell extracts. B. fragilis α-1,3-galactosidase hydrolyzed both thio- and O-galactoside substrates; however, the thiogalactosides were hydrolyzed at only 1–3 % of the rate of O-galactosides. The hydrolytic resistance of 5-thiogalactose was also confirmed by an in vivo study using cells in culture. The results suggest that 5-thiogalactosides may be useful tools for the study of anabolic pathways in cell extracts or in single cells.
Keywords: fluorescent probes; glycosidases; hydrolytic stability; thiogalactosides

Enhance fire resistance of cellulosic fibers for green polymer composites - Ngo, T.-D.; Ton That, M.-T.; Hu, W. (SAMPE Tech 2012 Conference and Exhibition : North Charleston, South Carolina, October 22-25, 2012 : Navigating the global landscape for the new composites, 2012)

A laser position sensing system for the study of accelerometer rocking motion due to cable strain - Wu, Lixue (Proceedings of the 18th International Congress on Sound and Vibration 2011, 2012)

Composite spectra: XVIII HR 6497, a triple system containing a baffling double secondary - Griffin, R. E. M.; Griffin, R. F. (Astromische Nachrichten (Astronomical Notes), 2012)
We present a full description of, and parameters for, the component stars in the triple-lined composite-spectrum system HR 6497. Both the outer and the inner orbits have already been computed with fair accuracy, but the improved orbits resulting from this new analysis have precisions that are up to an order of magnitude tighter. By applying the proven technique of spectral subtraction to a large sample of new, high-quality spectra we separate the spectra of the inner pair cleanly for the first time, and show that it has characteristics which cannot be explained at all easily by conventional models. Since the inner pair are separated by only 4 times their own radii, we expect their rotations to be synchronized to their orbital revolution, or close to 28 km/s, but in fact they have almost no visible rotation at all. The Mg II line at λ 4481 Å, itself a close doublet with a separation of 0.2 Å, is clearly resolved in the spectra of both components of the inner system. Such resolution is extremely rare in our experience, and we are unable to suggest a satisfactory explanation for it
Keywords: binaries: spectroscopic; stars: individual: (HR 6497); stars: fundamental parameters

Fluorescent silver nanoclusters as effective probes for highly selective detection of mercury(II) at parts-per-billion levels - Wang, Chuanxi; Xu, Lin; Wang, Yu; Zhang, Dan; Shi, Xiaodong; Dong, Fengxia; Yu, Kui; Lin, Quan; Yang, Bai (Chemistry - An Asian Journal, 2012)
Facile preparation of water-soluble and fluorescent Ag nanoclusters (NCs) stabilized by glutathione at room temperature is described. Although the glutathione layer was introduced to prevent the silver nanoparticles from decomposition and increase their water solubility, this simple surface optimization resulted in surprisingly high efficiency of selective Hg2+ sensing, where the limit of detection (LOD) was as low as 10−10 m (0.02 ppb, 0.1 nm). This result revealed a simple and practical strategy for Hg2+ detection using fluorescent Ag NCs as sensor probe, with the lowest detecting limits reported to date.
Keywords: nanoclusters; fluorescent probes; mercury; selective detection; silver

Durability design of high-performance concrete bridge decks using fine lightweight aggregate and shrinkage-reducing admixture - Cusson, Daniel; Margeson, Jim (The Economics, Performance and Sustainability of Internally Cured Concrete (ACI Fall Session), 2012)
Highway bridges and parking structures, subject to coupled effects of mechanical loads and corrosion, often show early signs of distress such as concrete cracking and rebar corrosion leading to reduced structural performance and shortened service life. One solution to this problem is to use low-shrinkage low-permeability high-performance concrete (HPC) for bridge decks exposed to de-icing salts and severe loading conditions. A new HPC was formulated to achieve low shrinkage and low permeability, high early-strength, and 28-day compressive strength over 60 MPa (8,700 psi). Its mechanical performance and durability were tested both in the lab and field under severe test conditions, including restrained shrinkage, cycling loading, freezing and thawing cycles, and application of de-icing salts. Prediction models were developed and calibrated to predict structural performance and service life of concrete bridge decks under severe exposure conditions. Prediction models indicate that bridge decks designed with low-shrinkage HPC can achieve a service life up to 100 years. Compared to normal concrete decks, short-to-medium span bridge decks using low-shrinkage HPC could be built at a comparable initial construction cost, but at less than 35 percent of the life-cycle cost.
Keywords: bridge decks; high-performance concrete; internal curing; lightweight aggregate; shrinkage-reducing admixture; durability; service life prediction; life-cycle cost analysis

Distinct models of induced hyperactivity in zebrafish larvae - Ellis, Lee David; Seibert, Jake; Soanes, Kelly Howard (Brain Research, 2012)
The analysis of behavioural hyperactivity can provide insights into how perturbations in normal activity may be linked to the altered function of the nervous system and possibly the symptoms of disease. As a small vertebrate zebrafish have numerous experimental advantages that are making them a powerful model for these types of studies. While the majority of behavioural studies have focused on adult zebrafish, it has become apparent that larvae can also display complex stereotypical patterns of behaviour. Here we have used three compounds (pentylenetetrazole (PTZ), aconitine and 4-aminopyridine) that have different neuronal targets (GABA, sodium and potassium channels), to induce distinct patterns of hyperactivity in larvae. Our studies have revealed that each compound produces a number of distinct concentration-dependent activity patterns. This work has shown for the first time that at sub-convulsive concentrations, PTZ can reverse the normal behavioural response to alternating periods of light and dark in zebrafish larvae. It also appears that both PTZ and 4-aminopyridine produce distinct changes in the normal startle response patterns immediately following light/dark transitions that may be the result of an elevation in stress/anxiety. Aconitine produces a general elevation in activity that eliminates the normal response to light and dark. In addition to differences in the patterns of behaviour each compound also produces a unique pattern of c-fos (an immediate early gene) expression in the brain. While more work is required to make direct links between region specific neuronal activity and individual behaviours, these models provide a framework with which to study and compare mechanistically different types of inducible behaviours.
Keywords: Zebrafish; disease model; hyperactivity; pentylenetrazole; aconitine; 4-aminopyridine

The cell motility modulator Slit2 is a potent inhibitor of platelet function - Patel, Sajedabanu; Huang, Yi-Wei; Reheman, Adili; Pluthero, Fred G.; Chaturvedi, Swasti; Mukovozov, Ilya M.; Tole, Soumitra; Liu, Guang-Ying; Li, Ling; Durocher, Yves; Ni, Heyu; Kahr, Walter H. A.; et al. (Circulation, 2012)
Background—Vascular injury and atherothrombosis involve vessel infiltration by inflammatory leukocytes, migration of medial vascular smooth muscle cells to the intimal layer, and ultimately acute thrombosis. A strategy to simultaneously target these pathological processes has yet to be identified. The secreted protein, Slit2, and its transmembrane receptor, Robo-1, repel neuronal migration in the developing central nervous system. More recently, it has been appreciated that Slit2 impairs chemotaxis of leukocytes and vascular smooth muscle cells toward diverse inflammatory attractants. The effects of Slit2 on platelet function and thrombus formation have never been explored.
Keywords: blood cells; blood platelets; thrombosis

Microencapsulated mammalian cells for simultaneous production of VEGF165b and IFNα - Afkhami, Fatemeh; Durocher, Yves; Prakash, Satya (Artificial Cells, Nanomedicine, and Biotechnology, 2012)
Targeted and simultaneous delivery VEGF165b and IFN alpha in anti-angiogenic and other applications could offer several advantages. For this a system was design using artificial cell alginate-poly-L-lysine- alginate (APA) microcapsules. Result confirms the ability of this system for simultaneous production of these proteins for 28-days. The IFN alpha on a 3 days period increased from 8 ± 0.36 μg/ml at day 10 to 27 ± 2.4 μg/ml at day 16 and then dropped to 6.5 ± 0.5 μg/ml. The VEGF165b on a 3 days period increased from 2.7 ± 0.7 μg/ml at day 10 to 6.9 ± 1 μg/ml at day 16.
Keywords: artificial cell; microcapsule; co-encapsulation; angiogenesis; IFNα; VEGF165b; alginate; poly-L-lysine; cell therapy

Optical model for prismatic glazing (1415-RP) - Laouadi, Abdelaziz; Saber, Hamed H.; Galasiu, Anca D.; Arsenault, Chantal (HVAC and R Journal, 2012)
Prismatic glazing is found in many building applications, such as complex fenestration systems to control solar heat gains and glare and re-direct sunlight to building interior spaces and daylighting (and lighting) systems to enhance their optical and lighting performance. However, modeling and simulation of such prismatic glazing has been a very difficult task due to its versatile and complex geometrics. This article presents the development and validation of a simplified model to compute the optical characteristics and dominant directions of the transmitted and reflected beam rays of sawtooth-like prismatic glazing. The model was based on tracing the average ray and was extensively validated using third-party data derived from ray tracing computer simulations and measurement using integrating spheres and goniophotometers. The model's predictions for the transmittance and reflectance of single and double prismatic panes compared well overall within the accuracy of the third-party data over all incidence angles.

Performance of ductile iron pipes. II : sampling scheme and inferring the pipe condition - Kleiner, Yehuda; Rajani, Balvant (Journal of Infrastructure Systems, 2012)
Ductile iron (DI) pipes have been used in North America since the late 1950s. This paper describes how understanding gained on the geometry of external corrosion pits is used to devise a sampling scheme and to infer the condition of ductile iron buried water mains. The companion paper describes the exhumation of varying lengths of ductile iron pipes in four North American water utilities. The exhumed pipes were cut into sections, sandblasted, and tagged. Soil samples extracted along the exhumed pipe were also provided. Pipe sections were scanned for external corrosion using a laser scanner to produce corrosion pit data sets. Statistical analyses were performed on geometric properties of corrosion pits such as pit depth, pit area, and pit volume. These analyses were developed further to assess the impact of the different soil characteristics on these pit properties. This paper describes the investigation of appropriate sampling schemes to represent the statistical properties of ductile iron pipe corrosion. With known statistical properties, an approach is developed to infer the condition of the pipe.
Keywords: Ductile iron pipe; Corrosion pits; Pipe sampling scheme; Pipe condition assessment

Performance of ductile iron pipes. I : characterization of external corrosion patterns - Kleiner, Yehuda; Rajani, Balvant; Krys, Dennis (Journal of Infrastructure Systems, 2012)
Ductile iron pipes have been used in North America since the late 1950s. This paper describes research that endeavored to gain a thorough understanding of the geometry of external corrosion pits and the factors (e.g., soil properties, appurtenances, and service connections) that influence this geometry. This understanding is subsequently used in the companion paper to devise a sampling scheme and to infer the condition of ductile iron buried water mains. Soil corrosivity is not a directly measurable parameter, and pipe external corrosion is primarily a random phenomenon. The literature is replete with methods and systems that attempt to use soil properties (e.g., resistivity, pH, and redox potential) to quantify soil corrosivity and subsequently predict pipe corrosion. In this research, varying lengths of ductile iron pipes were exhumed by several North American water utilities. The exhumed pipes were cut into short sections, sandblasted, and tagged. Soil samples were also obtained at discrete locations along the exhumed pipe. Pipe sections were scanned for external corrosion using a specially developed laser scanner. Scanned corrosion data were processed using specially developed software to obtain information on pit depth, pit area, and pit volume. Statistical analyses were subsequently performed on these three geometrical attributes. Various soil characteristics were investigated to determine their impact on the geometric properties of the corrosion pits. Subsequently, a method is proposed to assess the condition of a ductile iron pipe, based on the geometry of corrosion pits of several samples extracted along the pipe. This paper describes the pipe exhumation, data preparation, and statistical analysis of corrosion pits. The companion paper describes a sampling scheme to infer pipe condition of ductile iron buried water mains.
Keywords: ductile iron pipes; corrosion pit; corrosion pit geometry; soil properties; probability distribution; sampling

Characterization of the alkaloids in goldenseal (Hydrastis canadensis) root by high resolution Orbitrap LC-MSn - Le, Phuong Mai; McCooeye, Margaret; Windust, Anthony (Analytical and Bioanalytical Chemistry, 2012)
Liquid chromatography coupled to multistage mass spectrometry (LC-MSn) is being used increasingly in pharmaceutical research and for quality control in herbal medicines because of its superior sensitivity and selectivity. In this study, a rapid, high-resolution liquid chromatography-mass spectrometry (LC-MSn) method was developed to separate and identify alkaloids in the root extract of goldenseal, which is one of the 20 most popular herbal supplements used worldwide. In total, 28 alkaloids were separated and characterized including one novel compound and 21 identified, or tentatively identified, for the first time in goldenseal. The current high-resolution LC-MSn method provides a rapid and definitive means of profiling the composition of goldenseal root and will provide a useful tool in understanding the bioactivity of this medicinal plant.
Keywords: Hydrastis canadensis; alkaloid; structural characterization; LC-ESI-MSn

High-throughput quantitative analysis with cell growth kinetic curves for low copy number mutant cells - Xing, James Z.; Gabos, Stephan; Huang, Biao; Pan, Tianhong; Huang, Min; Chen, Jie (Analytical and Bioanalytical Chemistry, 2012)
The mutation rate in cells induced by environmental genotoxic hazards is very low and difficult to detect using traditional cell counting assays. The established genetic toxicity tests currently recognized by regulatory authorities, such as conventional Ames and hypoxanthine guanine phosphoribosyl-transferase (HPRT) assays, are not well suited for higher-throughput screening as they require large amounts of test compounds and are very time consuming. In this study, we developed a novel cell-based assay for quantitative analysis of low numbers of cell copies with HPRT mutation induced by an environmental mutagen. The HPRT gene mutant cells induced by the mutagen were selected by 6-thioguanine (6-TG) and the cell’s kinetic growth curve monitored by a real-time cell electronic sensor (RT-CES) system. When a threshold is set at a certain cell index (CI) level, samples with different initial mutant cell copies take different amounts of time in order for their growth (or CI accumulation) to cross this threshold. The more cells that are initially seeded in the test well, the faster the cell accumulation and therefore the shorter the time required to cross this threshold. Therefore, the culture time period required to cross the threshold of each sample corresponds to the original number of cells in the sample. A mutant cell growth time threshold (MT) value of each sample can be calculated to predict the number of original mutant cells. For mutagenesis determination, the RT-CES assay displayed an equal sensitivity (p > 0.05) and coefficients of variation values with good correlation to conventional HPRT mutagenic assays. Most importantly, the RT-CES mutation assay has a higher throughput than conventional cellular assays.
Keywords: RT-CES mutagenicity test; cell growth kinetic curve; high-throughput assay; low copy number mutant cell; baseline and threshold analyses

Laboratory x-ray powder diffraction - Whitfield, Pamela (Uniting Electron Crystallography and Powder Diffraction, 2012)
Laboratory diffractometers form the introduction to powder diffraction for most researchers. On a basic level for phase ID, etc., one diffractometer is very much like another. However when configuring a system for more challenging and advanced experiments, a variety of options and choices confront the experimentalist. Rather than cover the basics of diffractometer operation and geometry we will discover how a good understanding of the concepts behind laboratory diffractometers and their components is vital to getting the best from a system and pushing the limits of what can be achieved with lab instrumentation. Laboratory instrumentation will never compete with the sheer power and resolution of a synchrotron beamline. However, by departing from the conventional setups, it can be surprising what may be achieved in-house without resorting to the delay and inconvenience of synchrotron beamtime proposals.

Quantitative analysis of azaspiracids in Azadinium spinosum cultures - Jauffrais, Thierry; Herrenknecht, Christine; Séchet, Véronique; Sibat, Manoella; Tillmann, Urban; Krock, Bernd; Kilcoyne, Jane; Miles, Christopher O.; McCarron, Pearse; Amzil, Zouher; Hess, Philipp (Analytical and Bioanalytical Chemistry, 2012)
Azaspiracids (AZAs) are secondary metabolites of Azadinium spinosum that can accumulate in shellfish and cause food poisoning when consumed. We describe here an analytical procedure for the determination of AZAs in cultures of A. spinosum with a focus on the formation of AZA methyl esters as artefacts during extraction and sample pre-treatment. A. spinosum cells were collected from bioreactor cultures using centrifugation or filtration. Different extraction procedures were evaluated for formation of methyl ester artefacts, yield, and matrix effects. Filtration of cultures using glass-fibre filters led to increased formation of methyl esters, and centrifugation is recommended for recovery of cells. The extraction solvent (methanol (MeOH), acetone, and acetonitrile (MeCN)) did not significantly affect the yield of AZAs as long as the organic content was 80% or higher. However, the use of MeOH as extraction solvent led to increased formation of methyl esters. AZA1 recovery over two successive extractions was 100% at the 95% confidence level for acetone and MeOH. In standard-addition experiments, no significant matrix effects were observed in extracts of A. spinosum or Azadinium obesum up to a sample size of 4.5 × 10^9 μm^3. Moreover, experiments carried out to clarify the formation and structure of methylated AZA analogues led to the description of two AZA methyl esters and to the correction of the chemical structures of AZAs29–32.
Keywords: extraction procedure; extraction artefact; matrix effects; LC-MS/MS; azaspiracid methyl ester; dinoflagellate; liquid chromatography–mass spectrometry

Calibration of isotope amount ratios by analysis of isotope mixtures - Meija, Juris (Analytical and Bioanalytical Chemistry, 2012)
The question as to what constitutes a fully calibrated isotope amount ratio measurement still remains a topic of active research. For years, the definitive calibration approach has been by means of synthetic mixtures of highly enriched isotopes with known chemical purity to give gravimetrically defined ratios. This article outlines the core concepts and assumptions of this method and illustrates the recent developments in the practical metrology of isotope amount ratio measurements.
Keywords: metrology; mass spectrometry; isotope amount ratios

Conduction modulation of π-stacked ethylbenzene wires on Si(100) with substituent groups - Smeu, Manuel; Wolkow, Robert A.; Guo, Hong (Theoretical Chemistry Accounts, 2012)
For the realization of molecular electronics, one essential goal is the ability to systematically fabricate molecular functional components in a well-controlled manner. Experimental techniques have been developed such that π-stacked ethylbenzene molecules can now be routinely induced to self-assemble on an H-terminated Si(100) surface at precise locations and along precise directions. Electron transport calculations predict that such molecular wires could indeed carry an electrical current, but the Si substrate may play a considerable role as a competing pathway for conducting electrons. In this work, we investigate the effect of placing substituent groups of varying electron donating or withdrawing strengths on the ethylbenzene molecules to determine how they would affect the transport properties of such molecular wires. The systems consist of a line of π-stacked ethylbenzene molecules covalently bonded to a Si substrate. The ethylbenzene line is bridging two Al electrodes to model current through the molecular stack. For our transport calculations, we employ a first-principles technique where density functional theory (DFT) is used within the non-equilibrium Green’s function formalism (NEGF). The calculated density of states suggest that substituent groups are an effective way to shift molecular states relative to the electronic states associated with the Si substrate. The electron transmission spectra obtained from the NEGF–DFT calculations reveal that the transport properties could also be extensively modulated by changing substituent groups. For certain molecules, it is possible to have a transmission peak at the Fermi level of the electrodes, corresponding to high conduction through the molecular wire with essentially no leakage into the Si substrate.
Keywords: molecular wire; NEGF–DFT; Substituent group; conductance modulation; electron transport; ethylbenzene wire

The solvated interaction energy method for scoring binding affinities - Sulea, Traian; Purisima, Enrico O. (Computational Drug Discovery and Design, 2012)
The solvated interaction energy (SIE) is an end-point, physics-based scoring function for predicting ligand-binding affinities. It supplements the force-field interaction energy with the desolvation cost of binding. Parameters such as the solute dielectric constant, Born radii, a cavity term and an overall scaling coefficient and additive constant have been previously calibrated against a training set of 99 protein–ligand complexes. We describe the application of the method to estimating binding free energies from molecular dynamics trajectories of protein–ligand binding complexes.
Keywords: binding free energy; scoring function; protein-ligand binding; molecular dynamics

Computational modeling of extended systems - Dilabio, Gino A. (Theoretical Chemistry Accounts, 2012)
Advancements in computing architecture and in theoretical techniques allow for the modeling of complex, extended systems. This section of the 50th anniversary issue of Theoretical Chemistry Accounts highlights modeling work performed on nanostructured systems and underscores the enormous potential for synergy between theory and experiment in modern nanoscience.
Keywords: advances in computer architecture; synergy between nanoscience theory and experiment; molecular lines on silicon; nanoparticle-polymer nanocomposites; protein crystal structure modeling by density-functional theory

Results of the first North American comparison of absolute gravimeters, NACAG-2010 - Schmerge, D.; Francis, O.; Henton, J.; Ingles, D.; Jones, D.; Kennedy, J.; Krauterbluth, K.; Liard, J.; Newell, D.; Sands, R.; Schiel, A.; Silliker, J.; et al. (Journal of Geodesy, 2012)
The first North American Comparison of absolute gravimeters (NACAG-2010) was hosted by the National Oceanic and Atmospheric Administration at its newly renovated Table Mountain Geophysical Observatory (TMGO) north of Boulder, Colorado, in October 2010. NACAG-2010 and the renovation of TMGO are part of NGS’s GRAV-D project (Gravity for the Redefinition of the American Vertical Datum). Nine absolute gravimeters from three countries participated in the comparison. Before the comparison, the gravimeter operators agreed to a protocol describing the strategy to measure, calculate, and present the results. Nine sites were used to measure the free-fall acceleration of g. Each gravimeter measured the value of g at a subset of three of the sites, for a total set of 27 g-values for the comparison. The absolute gravimeters agree with one another with a standard deviation of 1.6 μGal (1 Gal ≡ 1 cm s −2). The minimum and maximum offsets are −2.8 and 2.7 μGal. This is an excellent agreement and can be attributed to multiple factors, including gravimeters that were in good working order, good operators, a quiet observatory, and a short duration time for the experiment. These results can be used to standardize gravity surveys internationally.
Keywords: absolute gravimetry; gravimeter; GRAV-D; comparison; offset

Experimental study on the effect of varying focal offset distance on laser micropolished surfaces - Chow, Michael T. C.; Bordatchev, Evgueni V.; Knopf, George K. (The International Journal of Advanced Manufacturing Technology, 2012)
Laser micropolishing (LμP) is an innovative part-finishing process that reduces machining roughness by melting a thin layer of material on the micromilled surface using a focused laser beam. The quality of the final polished surface is dependent upon the part material, initial surface topography and roughness, and the energy density of the beam. The focal offset distance (FOD) is one critical parameter that controls the amount of energy delivered to the workpiece. The impact of varying the FOD on final laser-polished surface quality is investigated by performing a series of experiments on carefully prepared AISI H13 test samples with known initial surface roughness and waviness due to the milled track periodicity. Three well-defined polishing regimes were observed when adjusting the FOD for a Q-switched Nd/YAG LμP system between 1.3 and 2.9 mm. Given the same initial micromilled surface geometry, each LμP regime (i.e., short FOD, <1.8 mm; long FOD, >2.2 mm; and intermediate FOD) reduced the surface roughness and periodic waviness in a distinct manner. For a micromilled sample with a 33-μm periodicity, the LμP with FOD of >2.2 mm was determined to be the most effective regime by improving surface quality by 39.7 %. The affects of repetitive exposure to the beam and increasing the applied laser power on improving surface quality are also investigated for the 3 LμP regimes.
Keywords: laser micropolishing; focal offset distance; surface roughness; surface waviness

Experimental study of the effect of tool orientation in five-axis micro-milling of brass using ball-end mills - Fard, M. Javad Barakchi; Bordatchev, Evgueni V. (The International Journal of Advanced Manufacturing Technology, 2012)
The effect of tool orientation on the final surface geometry and quality in five-axis micro-milling of brass using ball-end mills is investigated. Straight grooves with a semicircular cross section are cut with different tool inclination and tilt angles, and the resulting surfaces are characterized using an optical profilometer and microscope. Micro-milling cutting forces are recorded synchronously with spindle electric current and cutting motions in order to investigate the correlation between the tool orientation and the achieved surface quality. Results of various cutting experiments and analysis of the final surface geometry show that varying the tool orientation reduces rubbing of the material at the bottom of the grooves, which often occurs in ball-end milling of brass, and improves the final surface quality. The experimental analysis for surface roughness shows that applying a tool inclination angle of 15° can considerably improve the surface roughness at the bottom of the grooves. Analysis of static and averaged peak-to-valley (P-to-V) values of the cutting forces show that the static cutting force values are reduced by half when the tool inclination was increased from 0 to 15°. P-to-V cutting force values in along-the-feed direction were also decreased in the inclined machining.
Keywords: micro-milling; five-axis; tool orientation; surface quality; cutting forces

Estimating 3D human shapes from measurements - Wuhrer, Stefanie; Shu, Chang (Machine Vision and Applications, 2012)
Recent advances in 3D imaging technologies give rise to databases of human shapes, from which statistical shape models can be built. These statistical models represent prior knowledge of the human shape and enable us to solve shape reconstruction problems from partial information. Generating human shape from traditional anthropometric measurements is such a problem, since these 1D measurements encode 3D shape information. Combined with a statistical shape model, these easy-to-obtain measurements can be leveraged to create 3D human shapes. However, existing methods limit the creation of the shapes to the space spanned by the database and thus require a large amount of training data. In this paper, we introduce a technique that extrapolates the statistically inferred shape to fit the measurement data using non-linear optimization. This method ensures that the generated shape is both human-like and satisfies the measurement conditions. We demonstrate the effectiveness of the method and compare it to existing approaches through extensive experiments, using both synthetic data and real human measurements.
Keywords: human models; statistical prior; three-dimensional reconstruction

Simple sequence repeat marker development from bacterial artificial chromosome end sequences and expressed sequence tags of flax (Linum usitatissimum L.) - Cloutier, Sylvie; Miranda, Evelyn; Ward, Kerry; Radovanovic, Natasa; Reimer, Elsa; Walichnowski, Andrzej; Datla, Raju; Rowland, Gordon; Duguid, Scott; Ragupathy, Raja (Theoretical and Applied Genetics, 2012)
Flax is an important oilseed crop in North America and is mostly grown as a fibre crop in Europe. As a self-pollinated diploid with a small estimated genome size of ~370 Mb, flax is well suited for fast progress in genomics. In the last few years, important genetic resources have been developed for this crop. Here, we describe the assessment and comparative analyses of 1,506 putative simple sequence repeats (SSRs) of which, 1,164 were derived from BAC-end sequences (BESs) and 342 from expressed sequence tags (ESTs). The SSRs were assessed on a panel of 16 flax accessions with 673 (58 %) and 145 (42 %) primer pairs being polymorphic in the BESs and ESTs, respectively. With 818 novel polymorphic SSR primer pairs reported in this study, the repertoire of available SSRs in flax has more than doubled from the combined total of 508 of all previous reports. Among nucleotide motifs, trinucleotides were the most abundant irrespective of the class, but dinucleotides were the most polymorphic. SSR length was also positively correlated with polymorphism. Two dinucleotide (AT/TA and AG/GA) and two trinucleotide (AAT/ATA/TAA and GAA/AGA/AAG) motifs and their iterations, different from those reported in many other crops, accounted for more than half of all the SSRs and were also more polymorphic (63.4 %) than the rest of the markers (42.7 %). This improved resource promises to be useful in genetic, quantitative trait loci (QTL) and association mapping as well as for anchoring the physical/genetic map with the whole genome shotgun reference sequence of flax.
Keywords: Association mapping; bacterial artificial chromosomes; comparative analysis; Dinucleotides; expressed sequence tags; genetic resources; genome sizes; genomics; limun usitatissimum; oil seed crops; quantitative trait locus; simple sequence repeats; simple sequence-repeat markers; trinucleotides; whole-genome shotgun

Real-time monitoring of influenza virus production kinetics in HEK293 cell cultures - Petiot, Emma; Kamen, Amine (Biotechnology Progress, 2012)
There is an increased interest from the vaccine industry to use mammalian cell cultures for influenza vaccine manufacturing. Therefore, it became important to study the influenza infection mechanism, the viral–host interaction, and the replication kinetics from a bioprocessing stand point to maximize the influenza viral production yield in cell culture. In the present work, influenza replication kinetics was studied in HEK293 cells. Two infection conditions were evaluated, a low (0.01) and a high multiplicity of infection (1.0). Critical time points of the viral production cycle (infection, protein synthesis, viral assembly and budding, viral release, and host-cell death) were identified in small-scale cell cultures. Additionally, cell growth, viability, and viral titers were monitored in the viral production process. The infection state of the cultivated cell population was assessed by influenza immunolabeling throughout the culture period. Influenza virus production kinetics were also on-line monitored by dielectric spectroscopy and successfully correlated to real-time capacitance measures. Overall, this work provided insights into the mechanisms associated with the infection of human HEK293 cell line by the influenza virus and demonstrated, once again, the usefulness of multifrequency scanning permittivity for in-line monitoring and supervision of cell-based viral production processes.
Keywords: influenza; cell culture; in-process monitoring; kinetics; vaccines

A novel polyethyleneimine-coated adeno-associated virus-like particle formulation for efficient siRNA delivery in breast cancer therapy : preparation and in vitro analysis - Shao, Wei; Paul, Arghya; Abbasi, Sana; Chahal, Parminder S.; Mena, Jimmy A.; Montes, Johnny; Kamen, Amine; Prakash, Satya (International Journal of Nanomedicine, 2012)
BACKGROUND: Systemic delivery of small interfering RNA (siRNA) is limited by its poor stability and limited cell-penetrating properties. To overcome these limitations, we designed an efficient siRNA delivery system using polyethyleneimine-coated virus-like particles derived from adeno-associated virus type 2 (PEI-AAV2-VLPs). METHODS: AAV2-VLPs were produced in insect cells by infection with a baculovirus vector containing three AAV2 capsid genes. Using this method, we generated well dispersed AAV2-VLPs with an average diameter of 20 nm, similar to that of the wild-type AAV2 capsid. The nanoparticles were subsequently purified by chromatography and three viral capsid proteins were confirmed by Western blot. The negatively charged AAV2-VLPs were surface-coated with PEI to develop cationic nanoparticles, and the formulation was used for efficient siRNA delivery under optimized transfection conditions. RESULTS: PEI-AAV2-VLPs were able to condense siRNA and to protect it from degradation by nucleases, as confirmed by gel electrophoresis. siRNA delivery mediated by PEI-AAV2-VLPs resulted in a high transfection rate in MCF-7 breast cancer cells with no significant cytotoxicity. A cell death assay also confirmed the efficacy and functionality of this novel siRNA formulation towards MCF-7 cancer cells, in which more than 60% of cell death was induced within 72 hours of transfection. CONCLUSION: The present study explores the potential of virus-like particles as a new approach for gene delivery and confirms its potential for breast cancer therapy.

Efficacy and site-specificity of adenoviral vector integration mediated by the phage φC31 integrase - Robert, Marc-André; Zeng, Yue; Raymond, Benoît; Desfossé, Laurie; Mairey, Emilie; Tremblay, Jacques P.; Massie, Bernard; Gilbert, Rénald (Human Gene Therapy Methods, 2012)
Adenoviral vectors deleted of all their viral genes (helper-dependent [HD]) are efficient gene-transfer vehicles. Because transgene expression is rapidly lost in actively dividing cells, we investigated the feasibility of using phage C31 integrase (C31-Int) to integrate an HD carrying an attB site and the puromycin resistance gene into human cells (HeLa) and murine myoblasts (C2C12) by co-infection with a second HD-expressing C31-Int. Because the HD genome is linear, we also investigated whether its circularization, through expression of Cre using a third HD, affects integration. Efficacy and specificity were determined by scoring the number of puromycin-resistant colonies and by sequencing integration sites. Unexpectedly, circularization of HD was unnecessary and it even reduced the integration efficacy. The maximum integration efficacy achieved was 0.5% in HeLa cells and 0.1% in C2C12 myoblasts. Up to 76% of the integration events occurred at pseudo attP sites and previously characterized hotspots were found. A small (two- to three-fold) increase in the number of γ-H2AX positive foci, accompanied by no noticeable change in γ-H2AX expression, indicated the low genotoxicity of C31-Int. In conclusion, integration of HD mediated by C31-Int is an attractive alternative to engineer cells, because it permits site-specific integration of large DNA fragments with low genotoxicity.

A mass spectrometry-based plasma protein panel targeting the tumor microenvironment in patients with breast cancer - Cohen, Alejandro; Wang, Edwin; Chisholm, Kenneth A.; Kostyleva, Ripsik; O'Connor-McCourt, Maureen; Pinto, Devanand M. (Journal of Proteomics, 2012)
Proteins secreted or shed by cancerous cells are seen as a rich source of biomarkers and novel therapeutic targets. Recently, the importance of the tumor microenvironment, which comprises the surrounding non-tumor cells, has received increased attention for its role in tumor progression. We developed a targeted proteomics assay to monitor a panel of plasma proteins postulated to be present in the tumor microenvironment. The plasma of 76 breast cancer patients was depleted of abundant circulating proteins, enzymatically digested and labeled by reductive methylation. The labeled digests were analyzed by tandem mass spectrometry using a multiple reaction monitoring acquisition method. The protein targets were correlated with the tumor characteristics, the extent of the disease and the clinical staging of the patients. Linear discriminant analysis revealed that infiltrating ductal and invasive mammary breast carcinomas could be grouped based on distinctive peptide levels of fibronectin, clusterin, gelsolin and α-1-microglobulin/Inter-α-trypsin inhibitor light chain precursor (AMBP). These proteins have been previously associated with breast cancer at the tissue level, however, this is the first study to measure plasma levels of these proteins and correlate these levels with clinical features. Significant variability was seen between unique peptides belonging to the same protein. This article is part of a Special Issue entitled: From protein structures to clinical applications.
Keywords: breast cancer; tumor microenvironment; plasma proteomics; intraprotein variability

A versatile coiled-coil tethering system for the oriented display of ligands on nanocarriers for targeted gene delivery - Fortier, Charles; De Crescenzo, Gregory; Durocher, Yves (Biomaterials, 2012)
Surface modification of non-viral gene delivery nanocarriers may provide advanced features such as receptor targeting, endosomal escape and nuclear import. We here report the design of a versatile and tunable immobilization protocol to functionalize nanocarriers for improved transient gene expression. Our strategy is based on specific interactions occurring between a coil-tagged ligand and a complementary coil-functionalized nanocarrier. As a proof of concept, targeting of DNA/polyethylenimine polyplexes to the epidermal growth factor receptor of A431 cells was investigated. Coiled-coil-mediated oriented tethering of epidermal growth factor triggered a drastic increase of the internalization rate of the targeted polyplexes. To explore the tunability of our platform, surface density of targeting ligand was varied; our results indicated that the internalization rate varied with the ligand-to-polyplex ratio in a “switch mode” fashion. This work prefigures possible avenues for our coiled-coil platform in multiplex functionalization to address transient gene expression bottlenecks in recombinant protein production.
Keywords: transfection; polyethylenimine; non-viral vector; targeting; oriented tethering; epidermal growth factor (EGF)

Sulfonation of glycopeptide antibiotics by sulfotransferase StaL depends on conformational flexibility of aglycone scaffold - Shi, Rong; Munger, Christine; Kalan, Lindsay; Sulea, Traian; Wright, Gerard D.; Cygler, Miroslaw (PNAS (Proceedings of the National Academy of Sciences of the United States of America), 2012)
Although glycopeptide antibiotics (GPAs), including vancomycin and teicoplanin, represent the most important class of antiinfective agents in the treatment of serious Gram-positive bacterial infections, their usefulness is threatened by the emergence of resistant strains. GPAs are complex natural products consisting of a heptapeptide skeleton assembled via nonribosomal peptide synthesis and constrained through multiple crosslinks, with diversity resulting from enzymatic modifications by a variety of tailoring enzymes, which can be used to produce GPA analogues that could overcome antibiotic resistance. GPA-modifying sulfotransferases are promising tools for generating the unique derivatives. Despite significant sequence and structural similarities, these sulfotransferases modify distinct side chains on the GPA scaffold. To provide insight into the spatial diversity of modifications, we have determined the crystal structure of the ternary complex of bacterial sulfotransferase StaL with the cofactor product 3′-phosphoadenosine 5′-phosphate and desulfo-A47934 aglycone substrate. Desulfo-A47934 binds with the hydroxyl group on the 4-hydroxyphenylglycine in residue 1 directed toward the 3′-phosphoadenosine 5′-phosphate and hydrogen-bonded to the catalytic His67. Homodimeric StaL can accommodate GPA substrate in only one of the two active sites because of potential steric clashes. Importantly, the aglycone substrate demonstrates a flattened conformation, in contrast to the cup-shaped structures observed previously. Analysis of the conformations of this scaffold showed that despite the apparent rigidity due to crosslinking between the side chains, the aglycone scaffold displays substantial flexibility, important for enzymatic modifications by the GPA-tailoring enzymes. We also discuss the potential of using the current structural information in generating unique GPA derivatives.
Keywords: substrate binding; substrate flexibility; substrate recognition

Seeking antifungal drug synergies - Whiteway, Malcolm (Microbe Magazine, 2012)

Molecular targeting of CEACAM6 using antibody probes of different sizes - Niu, Gang; Murad, Yanal M.; Gao, Haokao; Hu, Shuo; Guo, Ning; Jacobson, Orit; Nguyen, Thanh-Dung; Zhang, Jianbing; Chen, Xiaoyuan (Journal of Controlled Release, 2012)
Carcinocinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6) is overexpressed in a number of human malignancies, especially in pancreatic cancer. It has been demonstrated that CEACAM6 is a potential target for monoclonal antibody (mAb) therapy with a safe therapeutic index. Here, we labeled three anti-CEACAM6 antibodies of different sizes, including a single-domain antibody 2A3 (16 kDa), a heavy chain antibody 2A3-mFc (80 kDa) and a full length antibody 9A6 (150 kDa), with 64Cu to image CEACAM6 expression in a xenografted pancreatic tumor model. For positron emission tomography (PET) imaging, the tumor mice were intravenously injected with 64Cu-DOTA-antibodies and static scans were obtained at 5 min, 0.5, 1, 2, 4, 8 and 24 h post-injection (p.i.). All three antibodies showed strong CEACAM6 binding. Ex vivo immunostaining on tumor sections at 24 h after Ab injection demonstrated specific tumor targeting of both 2A3-mFc and 9A6. 64Cu-DOTA-2A3 showed fast BxPC3 tumor uptake and rapid whole-body clearance. At 24 h p.i., the tumor uptakes were 98.2 ± 6.12%ID/g for 64Cu-DOTA-2A3-mFc and 57.8 ± 3.73%ID/g for 64Cu-DOTA-9A6, respectively. Compared with the full length antibody 9A6, the heavy chain antibody 2A3-mFc showed higher tumor uptake, lower liver uptake and shorter circulation half-life. All the data supported that the heavy chain antibody 2A3-mFc is superior to the single domain antibody and the full-length antibody with regard to tumor detection and pharmacokinetics, which has great potential to be developed for CEACAM6-targeted pancreatic cancer imaging and therapy.
Keywords: CEACAM6; pancreatic cancer; heavy chain antibody; 64Cu; positron emission tomography (PET)

Alloy solid solution strengthening of Mg alloys: valence effect - Chen, Kuiying; Boyle, Kevin P. (physica status solidi (b), 2012)
Ab initio density functional theory (DFT) calculations were carried out to investigate alloy solid solution strengthening of hexagonal close packed (HCP) Mg. The binary solid solution Mg–X base alloys (X = Gd, Nd, Ce, Bi, In, and Sn) were examined to identify a possible valence effect on the solution strengthening in terms of electronic density of states (DOS) and electron localized function (ELF). An addition of rare earth (RE) elements Gd, Nd, and Ce in Mg results in a hybridization between the localized f electrons of RE elements and the p electrons of Mg. The hybridization is primarily responsible for the formation of covalent bonds between RE elements and Mg. This electronic structure was then validated by the calculated ELF, illustrating a distribution of localized electrons between Mg and RE atoms. This peculiar chemical bonding characteristic successfully explains the experimentally observed solid solution strengthening induced by Gd, Nd, and Ce additions. An addition of sp-elements of Bi, In, and Sn in Mg, however, leads to the formation of typical ionic bonds, which are not capable of inducing solid solution strengthening in Mg alloys. A discussion was made on a possible relationship between the chemical bonds and solid solution strengthening in Mg alloys.
Keywords: density functional theory; Mg alloys; solid solutions

Targeted glycomics by selected reaction monitoring for highly sensitive glycan compositional analysis - Zhang, Hongquan; Wang, Zhaohui; Stupak, Jacek; Ghribi, Othman; Geiger, Jonathan D.; Liu, Qing Yan; Li, Jianjun (Proteomics, 2012)
The development of glycomics increasingly requires the detection and quantification of large numbers of glycans, which is only partially achieved by current glycomics approaches. Taking advantage of selected reaction monitoring to enhance both sensitivity and selectivity, we report here a strategy termed targeted glycomics that enables highly sensitive and consistent identification and quantification of diverse glycans across multiple samples at the same time. In this proof-of-principle study, we validated the method by analyzing global N-glycans expressed in different systems: single proteins, cancer cells, and serum samples. A dynamic range of three orders of magnitude was obtained for the detection of all five glycans released from ribonuclease B. The limit of detection of 80 attomole for Man9GlcNAc2 demonstrated the excellent sensitivity of the method. The capability of the strategy to identify diverse glycans was demonstrated by identification and detection of 162 different glycans and isomers from pancreatic cancer cells. The sensitivity of the method was illustrated further by the ability to detect eight glycans from 250 cancer cells and five glycans released from 100 cancer cells. In serum obtained from rabbits fed control diet or diet enriched with 2% cholesterol, differences to 42 glycans were accurately measured and this indicates that this strategy might find use in studies of biomarker discovery and validation.
The authors affiliated with NRC were with the NRC Institute for Biological Sciences prior to April 1, 2012.
Keywords: Carbohydrate; Glycoproteomics; Glycosylation; LC-SRM; N-Glycan; Quantitative glycomics

Protein–ligand binding free energies from exhaustive docking - Purisima, Enrico O.; Hogues, Hervé (The Journal of Physical Chemistry B, 2012)
We explore the use of exhaustive docking as an alternative to Monte Carlo and molecular dynamics sampling for the direct integration of the partition function for protein–ligand binding. We enumerate feasible poses for the ligand and calculate the Boltzmann factor contribution of each pose to the partition function. From the partition function, the free energy, enthalpy, and entropy can be derived. All our calculations are done with a continuum solvation model that includes solving the Poisson equation. In contrast to Monte Carlo and molecular dynamics simulations, exhaustive docking avoids (within the limitations of a discrete sampling) the question of “Have we run long enough?” due to its deterministic complete enumeration of states. We tested the method on the T4 lysozyme L99A mutant, which has a nonpolar cavity that can accommodate a number of small molecules. We tested two electrostatic models. Model 1 used a solute dielectric of 2.25 for the complex apoprotein and free ligand and 78.5 for the solvent. Model 2 used a solute dielectric of 2.25 for the complex and apoprotein but 1.0 for the free ligand. For our test set of eight molecules, we obtain a reasonable correlation with a Pearson r2 = 0.66 using model 1. The trend in binding affinity ranking is generally preserved with a Kendall τ = 0.64 and Spearman ρ = 0.83. With model 2, the correlation is improved with a Pearson r2 = 0.83, Kendall τ = 0.93, and Spearman ρ = 0.98. This suggests that the energy function and sampling method adequately captured most of the thermodynamics of binding of the nonpolar ligands to T4 lysozyme L99A.
Keywords: protein-ligand binding; Monte Carlo and colecular dynamics simulations; elctrostatic models

Structure and morphology of new bio-based thermoplastic polyurethanes obtained from dimeric fatty acids - Bueno-Ferrer, Carmen; Hablot, Elodie; Perrin-Sarazin, Florence; Garrigós, M. Carmen; Jiménez, Alfonso; Averous, Luc (Macromolecular Materials and Engineering, 2012)
Bio-based TPUs from dimer acid-based polyols are synthesised by using a two-step prepolymer process including reactive processing. The effect of the polyol on the final chemical structures, morphologies and properties of bio-based TPUs is evaluated by different analytical techniques. It is observed that the percentage of hard segment (HS) distributed in organised and unorganised phases is a key factor to control the materials properties. DSC reveals that the percentages of HS dispersed in the soft domains are high at low experimental HS contents. Multiscale microscopies show better defined organised structures with increasing HS content in TPUs, highlighting the importance of the distribution between hard and soft segments in the material structure.
Keywords: atomic force microscopy; bio-based polyols; dimeric fatty acids; polyurethanes; structure-property relationships

Involvement of NOS3 in RA-induced neural differentiation of human NT2/D1 cells - Jezierski, Anna; Deb-Rinker, Paromita; Sodja, Caroline; Walker, P. Roy; Ly, Dao; Haukenfrers, Julie; Sandhu, Jagdeep K.; Bani-Yaghoub, Mahmud; Sikorska, Marianna (Journal of Neuroscience Research, 2012)
Nitric oxide (NO) plays a key role in neurogenesis as a regulator of cell proliferation and differentiation. NO is synthesized from the amino acid L-arginine by nitric oxide synthases (NOS1, NOS2, and NOS3), which are encoded by separate genes and display different tissue distributions. We used an in vitro model of RA-induced neural differentiation of NT2 cells to examine which of the three NO-synthesizing enzymes is involved in this process. The results revealed a transient induction of NOS3 (known as the constitutively expressed endothelial nitric oxide synthase; eNOS) during the time course of the RA treatment. The peak of gene expression and the nuclear presence of NOS3 protein coincided with cell cycle exit of NT2-derived neuronal precursors. The subsequent analysis of cytosine methylation and histone H3 acetylation of the human NOS3 5′ regulatory sequences indicated that epigenetic modifications, especially upstream of the proximal promoter (−734 to −989, relative to exon 2 TSS at +1), were also taking place. NOS1 was expressed only in the differentiated neurons (NT2-N), whereas NOS2 was not expressed at all in this cellular model. Thus, a burst of NO production, possibly required to inhibit neural cell proliferation, was generated by the transient expression of NOS3. This pattern of gene expression, in turn, required epigenetic remodeling of its regulatory region.
Keywords: endothelial nitric oxide synthase; nuclear localization; cell cycle exit; neurogenesis; chromatin remodeling; epigenetic regulation

Strength and muscle specificity of a compact promoter derived from the slow troponin I gene in the context of episomal (gutless adenovirus) and integrating (lentiviral) vectors - Robert, Marc-André; Lin, Yuanbang; Bendjelloul, Mehdi; Zeng, Yue; Dessolin, Sofien; Broussau, Sophie; Larochelle, Nancy; Nalbantoglu, Josephine; Massie, Bernard; Gilbert, Rénald (The Journal of Gene Medicine, 2012)
Background:Gutless adenovirus (helper-dependent adenoviral vector; HDAd) and lentiviral vectors (LV) are attractive vectors for the gene therapy of muscle diseases. Because the organization of their DNA (episomal versus integrated) differs, we investigated whether the strength and specificity of ΔUSEx3, a novel muscle-specific promoter previously tested with plasmid, were maintained in the context of these vectors. Methods: Two HDAds expressing β-galactosidase regulated by ΔUSEx3 or CAG [cytomegalovirus (CMV) enhancer/β-actin promoter], and three LV expressing green fluorescent protein regulated by ΔUSEx3, CMV or a modified skeletal α-actin promoter (SPcΔ5-12), were constructed. Gene expression was compared in cell culture and after intravenous (HDAd only) and intramuscular injection of mice. Results: Irrespective of the vector used, ΔUSEx3 remained poorly active in nonmuscle cells and tissues. In myotubes, ΔUSEx3 was as strong as CMV and SPcΔ5-12, although it was ten-fold weaker than CAG, a proven powerful promoter in muscle. In cell culture, ΔUSEx3 activity in the context of LV was more stable than CMV, indicating it is less prone to silencing. In the context of HDAd, the behavior of ΔUSEx3 in skeletal muscle mirrored that of cell culture (10% of the CAG activity and half the number of transduced fibers). Surprisingly, in muscles treated with LV, ΔUSEx3 activity was five-fold lower than SPcΔ5-12. Conclusions: The data obtained in the present study confirm that ΔUSEx3 is a strong and robust muscle-specific promoter in the context of HDAd (cell culture and in vivo) and LV (cell culture). However, it was less efficient in vivo in the context of LV.
Keywords: gutless adenovirus; helper-dependent adenovirus; lentivirus; muscle; muscular dystrophy; promoter

Efficient treatment of solvation shells in 3D molecular theory of solvation - Gusarov, Sergey; Pujari, Bhalchandra S.; Kovalenko, Andriy (Journal of Computational Chemistry, 2012)
We developed a technique to decrease memory requirements when solving the integral equations of three-dimensional (3D) molecular theory of solvation, a.k.a. 3D reference interaction site model (3D-RISM), using the modified direct inversion in the iterative subspace (MDIIS) numerical method of generalized minimal residual type. The latter provides robust convergence, in particular, for charged systems and electrolyte solutions with strong associative effects for which damped iterations do not converge. The MDIIS solver (typically, with 2 × 10 iterative vectors of argument and residual for fast convergence) treats the solute excluded volume (core), while handling the solvation shells in the 3D box with two vectors coupled with MDIIS iteratively and incorporating the electrostatic asymptotics outside the box analytically. For solvated systems from small to large macromolecules and solid–liquid interfaces, this results in 6- to 16-fold memory reduction and corresponding CPU load decrease in MDIIS. We illustrated the new technique on solvated systems of chemical and biomolecular relevance with different dimensionality, both in ambient water and aqueous electrolyte solution, by solving the 3D-RISM equations with the Kovalenko–Hirata (KH) closure, and the hypernetted chain (HNC) closure where convergent. This core–shell-asymptotics technique coupling MDIIS for the excluded volume core with iteration of the solvation shells converges as efficiently as MDIIS for the whole 3D box and yields the solvation structure and thermodynamics without loss of accuracy. Although being of benefit for solutes of any size, this memory reduction becomes critical in 3D-RISM calculations for large solvated systems, such as macromolecules in solution with ions, ligands, and other cofactors.
Keywords: solvation structure and thermodynamics; 3D-RISM molecular theory of solvation; MDIIS method of solving integral equations; core–shell-asymptotics technique; memory reduction

In vitro biocompatibility assessment of functionalized magnetite nanoparticles: biological and cytotoxicological effects - Mbeh, D. A.; França, R.; Merhi, Y.; Zhang, X. F.; Veres, T.; Sacher, E.; Yahia, L. (Journal of Biomedical Materials Research Part A, 2012)
In the biomedical field, nanomaterials have the potential for use in the targeted delivery of drugs in the human body and in the diagnosis and therapy of certain diseases. In the category of targeted delivery, magnetite (Fe3O4) nanoparticles have received much attention. As with any similar new therapy, when such nanoparticles are functionalized with chemical groups designed to permit the specific attachment of drugs, cytotoxicological testing is necessary before moving to animal models. Here, we consider several variously functionalized magnetite nanoparticles, including those prepared with (1) a monolayer of oleic acid (Fe3O4@OA), which is subsequently converted to (2) a shell of amine-containing silane (Fe3O4@NH2), (3) a shell of silica (Fe3O4@SiO2), and (4) a shell of amine-containing silane over a shell of silica (Fe3O4@SiO2@NH2). These latter three functionalities were evaluated for biocompatibility, cellular morphology, mitochondrial function (MTT assay), lactate dehydrogenase membrane leakage (LDH assay), and proinflammatory potential through enzyme linked immunosorbent assay (ELISA) for interleukin 6 (IL-6). Controlled tests were performed over a period of 72 h, with results showing LDH leakage and abnormal Il-6 secretion at high concentrations (>50 μg/mL). The tests showed that, in addition to the surface characteristics of the nanoparticles, both the nutrient medium and the time of suspension before exposure to cells also contribute to nanoparticle cytotoxicity.
Keywords: biocompatibility; cell viability; cytotoxicological effects; functionalized magnetite nanoparticles

Real-time diagnosing polymer processing in injection molding using ultrasound - Zhao, Lijuan; Lai, Yu; Pei, Chen; Jen, Cheng-Kui; Wu, Kuo-Ding (Journal of Applied Polymer Science, 2012)
Ultrasonic diagnosing technique with a new high-temperature ultrasonic transducer is developed to real-time diagnose polymer processing and its morphology changes in injection molding processing. Compared with the previous researches, the new technique can provide more and accurate information. In this study, ultrasound diagnosis shows that longitudinal wave can real-time characterize the data of the injection process and polymer morphology changes, including melt flow arrival time, the part ejection time, filling and packing stages, polymer solidification process, and the morphology changes during polymer crystallization. Shear waves can real-time diagnose Young's and shear storage modulus, anisotropy property of polymer in injection molding. During our research, real-time ultrasonic diagnosis shows that the storage modulus along the vertical direction is larger than that of the parallel to the melt flow direction under our setup injection conditions. Scanning electron microscopy and dynamic mechanical analysis measurements present that it is because the crystalline lamellas of HDPE are parallel arrangement and grow in a vertical to melt flow direction owing to injection shear force under a certain injection conditions.
Keywords: ultrasound; real-time; injection molding; processing; polymer storage modulus

Preparation and properties of extruded thermoplastic starch/polymer blends - Huneault, Michel A.; Li, Hongbo (Journal of Applied Polymer Science, 2012)
This article examines the starch gelatinization and the blend morphology development in blends of thermoplastic starch (TPS) with high-density polyethylene, polypropylene, polystyrene, poly(lactic acid), and polycaprolactone. The TPS gelatinization and mixing with the second polymer was carried out on a twin-screw extrusion process, where the starch was sequentially gelatinized, devolatilized, and then mixed in the molten state with a synthetic polymer. The role of excess water and process temperature on starch gelatinization was assessed by measuring the X-ray scattering. All prepared blends included 25 % TPS that was dispersed in the synthetic polymer matrix. Compatibilized versions of these same blends were obtained by partially substituting the polymer matrices with maleated analogs. The blend morphology was probed by scanning electron microscopy. Complete starch gelatinization was obtained when the gelatinization process was carried out over 100°C regardless of amount of water used as co-plasticizer. The blend morphologies were greatly improved when a maleated compatibilizer was added. Only TPS/PCL blends exhibited a finely dispersed TPS phase without the use of a compatibilizer. In general, the addition of the TPS reduced slightly the tensile modulus and strength of the different polymers and more importantly the elongation at break.
Keywords: thermoplastic starch; polymer blends; polysaccharides; renewable resources; plastics

Recognition of sialylated poly-N-acetyllactosamine chains on N- and O-linked glycans by human and avian influenza A virus hemagglutinins - Nycholat, Corwin M.; Mcbride, Ryan; Ekiert, Damian C.; Xu, Rui; Rangarajan, Janani; Peng, Wenjie; Razi, Nahid; Gilbert, Michel; Wakarchuk, Warren; Wilson, Ian A.; Paulson, James C. (Angewandte Chemie International Edition, 2012)
Human influenza viruses are proposed to recognize sialic acids (pink diamonds) on glycans extended with poly-LacNAc chains (LacNAc=(yellow circle+blue square)). N- and O-linked glycans were extended with different poly-LacNAc chains with α2-3- and α2-6-linked sialic acids recognized by human and avian influenza viruses, respectively. The specificity of recombinant hemagglutinins (receptors in green) was investigated by using glycan microarray technology.
Keywords: glycans; hemagglutinins; influenza viruses; microarrays; sialic acids

Exploring the essential collective dynamics of interacting proteins: application to prion protein dimers - Issack, Bilkiss B.; Berjanskii, Mark; Wishart, David S.; Stepanova, Maria (Proteins: Structure, Function, and Bioinformatics, 2012)
Essential collective dynamics is a promising and robust approach for analysing the slow motions of macromolecules from short molecular dynamics trajectories. In this study, an extension of the method to treat a collection of interacting protein molecules is presented. The extension is applied to investigate the effects of dimerization on the collective dynamics of ovine prion protein molecules in two different arrangements. Examination of the structural plasticity shows that aggregation has a restricting effect on the local mobility of the prion protein molecules in the interfacial regions. Domain motions of the two dimeric ovine prion protein conformations are distinctly different and can be related to interatomic correlations at the interface. Correlated motions are among the slow collective modes extensively analysed by considering both main-chain and side-chain atoms. Correlation maps reveal the existence of a vast network of dynamically correlated side groups, which extends beyond individual subunits via interfacial interconnections. The network is formed by a core of hydrophobic side chains surrounded by hydrophilic groups at the periphery. The relevance of these findings are discussed in the context of mutations associated with prion diseases. The binding free energy of the dimeric conformations is evaluated to probe their thermodynamic stability. The descriptions afforded by the analysis of the essential collective dynamics of the prion dimers are consistent with their binding free energies. The agreement validates the extension of the methodology and provides a means of interpreting the collective dynamics in terms of the thermodynamic stability of ovine prion proteins.
Erratum published in Volume 80, Issue 9, page 2330, August 2012. Erratum DOI: 10.1002/prot.24139
Keywords: protein–protein interactions; flexibility; dynamic domains; correlated motions; binding free energy; molecular dynamics simulation; prion aggregation

Mach, the universe, and foundations of mechanics - Mashhoon, B.; Wesson, P. S. (Annalen der Physik, 2012)

Work function control of interfacial buffer layers for efficient and air-stable inverted low-bandgap organic photovoltaics - Worfolk, Brian J.; Hauger, Tate C.; Harris, Kenneth D.; Rider, David A.; Fordyce, Jordan A. M.; Beaupré, Serge; Leclerc, Mario; Buriak, Jillian M. (Advanced Energy Materials, 2012)
A water-soluble cationic polythiophene derivative, poly[3-(6-{4-tert-butylpyridiniumyl}-hexyl)thiophene-2,5-diyl] [P3(TBP)HT], is combined with anionic poly(3,4-ethylenedioxythiophene):poly(p-styrenesulfonate) (PEDOT:PSS) on indium tin oxide (ITO) substrates via electrostatic layer-by-layer (eLbL) assembly. By varying the number of eLbL layers, the electrode's work function is precisely controlled from 4.6 to 3.8 eV. These polymeric coatings are used as cathodic interfacial modifiers for inverted-mode organic photovoltaics that incorporate a photoactive layer composed of either poly[(3-hexylthiophene)-2,5-diyl] (P3HT) and the fullerene acceptor [6,6-phenyl-C61-butyric acid methyl ester (PC61BM) or the low bandgap polymer [poly({4,8-di(2-ethylhexyloxyl)benzo[1,2-b:4,5-b′]dithiophene}-2,6-diyl)-alt-({5-octylthieno[3,4-c]pyrrole-4,6-dione}-1,3-diyl) (PBDTTPD)] and the electron acceptor [6,6-phenyl-C71-butyric acid methyl ester (PC71BM)]. The power conversion efficiency (PCE) of the resulting photovoltaic device is dependent on the composition of the eLbL-assembled interface and permits the fabrication of devices with efficiencies of 3.8% and 5.6% for P3HT and PBDTTPD donor polymers, respectively. Notably, these devices demonstrate significant stability with a P3HT:PC61BM system maintaining 83% of its original PCE after 1 year of storage and a PBDTTPD:PC71BM system maintaining 97% of its original PCE after over 1000 h of storage in air, according to the ISOS-D-1 shelf protocol.
Keywords: air stable; cathodic interfacial buffer layers; low bandgap polymers; organic photovoltaics; work functions

Carbonized chicken eggshell membranes with 3D architectures as high-performance electrode materials for supercapacitors - Li, Zhi; Zhang, Li; Shalchi Amirkhiz, Babak; Tan, Xuehai; Xu, Zhanwei; Wang, Huanlei; Olsen, Brian C.; Holt, Chris M. B.; Mitlin, David (Advanced Energy Materials, 2012)
Supercapacitor electrode materials are synthesized by carbonizing a common livestock biowaste in the form of chicken eggshell membranes. The carbonized eggshell membrane (CESM) is a three-dimensional macroporous carbon film composed of interwoven connected carbon fibers containing around 10 wt% oxygen and 8 wt% nitrogen. Despite a relatively low surface area of 221 m2 g−1, exceptional specific capacitances of 297 F g−1 and 284 F g−1 are achieved in basic and acidic electrolytes, respectively, in a 3-electrode system. Furthermore, the electrodes demonstrate excellent cycling stability: only 3% capacitance fading is observed after 10 000 cycles at a current density of 4 A g−1. These very attractive electrochemical properties are discussed in the context of the unique structure and chemistry of the material.
Keywords: nitrogen-rich carbon; supercapacitors; eggshells; biomass waste; energy storage

CdSe magic-sized nuclei, magic-sized nanoclusters and regular nanocrystals : monomer effects on nucleation and growth - Yu, Kui (Advanced Materials, 2012)
Colloidal semiconductor quantum dots (QDs) have been well appreciated for their potential in nanophotonics with an unprecedented impact in various areas, including light emitting diodes (LEDs) and solar cells. There is an outstanding demand on the control of size and size distribution for the various applications, with rational design supported by fundamental understanding of nucleation and growth. This Research News introduces recent advances in the synthesis of colloidal CdSe magic-sized nuclei (MSN) exhibiting sharp bandgap emission, with a model proposed to illustrate the nature of monomers and their degree of supersaturation (DS) affecting the formation of various CdSe MSN, magic-sized nanoclusters (MSCs), and regular nanocrystals (RNCs). Also, this model addresses tuning the CdSe RNCs into the CdSe MSN with the presence of cadmium acetate (Cd(OAc)2) affecting the nature of the monomers.

Effects of the molecular weight and the side-chain length on the photovoltaic performance of dithienosilole/thienopyrrolodione copolymers - Chu, Ta-Ya; Lu, Jianping; Beaupré, Serge; Zhang, Yanguang; Pouliot, Jean-Rémi; Zhou, Jiayun; Najari, Ahmed; Leclerc, Mario; Tao, Ye (Advanced Functional Materials, 2012)
A series of low-bandgap alternating copolymers of dithienosilole and thienopyrrolodione (PDTSTPDs) are prepared to investigate the effects of the polymer molecular weight and the alkyl chain length of the thienopyrrole-4,6-dione (TPD) unit on the photovoltaic performance. High-molecular-weight PDTSTPD leads to a higher hole mobility, lower device series resistance, a larger fill factor, and a higher photocurrent in PDTSTPD:[6,6]-phenyl C71 butyric acid methyl ester (PC71BM) bulk-heterojunction solar cells. Different side-chain lengths show a significant impact on the interchain packing between polymers and affect the blend film morphology due to different solubilities. A high power conversion efficiency of 7.5% is achieved for a solar cell with a 1.0 cm2 active area, along with a maximum external quantum efficiency (EQE) of 63% in the red region.
Keywords: photovoltaic devices; solar cells; fullerenes; polymeric materials

Process planning for Floor machining of 2½D pockets based on a morphed spiral tool path pattern - Banerjee, Avisekh; Feng, Hsi-Yung; Bordatchev, Evgueni V. (Computers & Industrial Engineering, 2012)
This work proposes a process planning for machining of a Floor which is the most prominent elemental machining feature in a 2½D pocket. Traditionally, the process planning of 2½D pocket machining is posed as stand-alone problem involving either tool selection, tool path generation or machining parameter selection, resulting in sub-optimal plans. For this reason, the tool path generation and feed selection is proposed to be integrated with an objective of minimizing machining time under realistic cutting force constraints for given pocket geometry and cutting tool. A morphed spiral tool path consisting of G1 continuous biarc and arc spline is proposed as a possible tool path generation strategy with the capability of handling islands in pocket geometry. Proposed tool path enables a constant feed rate and consistent cutting force during machining in typical commercial CNC machine tool. The constant feed selection is based on the tool path and cutting tool geometries as well as dynamic characteristics of mechanical structure of the machine tool to ensure optimal machining performance. The proposed tool path strategy is compared with those generated by commercial CAM software. The calculated tool path length and measured dry machining time show considerable advantage of the proposed tool path. For optimal machining parameter selection, the feed per tooth is iteratively optimized with a pre-calibrated cutting force model, under a cutting force constraint to avoid tool rupture. The optimization result shows around 32% and 40% potential improvement in productivity with one and two feed rate strategies respectively.

Synthetic diversiﬁcation of natural products : semi-synthesis and evaluation of triazole jadomycins - Dupuis, Stephanie N.; Robertson, Andrew W.; Veinot, Thomas; Monro, Susan M. A.; Douglas, Susan E.; Syvitski, Ray T.; Goralski, Kerry B.; McFarland, Sherri A.; Jakeman, David L. (Chemical Science, 2012)
Growth of Streptomyces venezuelae ISP5230 with O-propargyl-L-serine led to the efﬁcient production of an alkyne-containing jadomycin. The installed alkyne functionality provided a uniquely reactive handle within the natural product and was subsequently reacted with a series of azides to afford an eight-member library of jadomycin triazoles. The compounds were evaluated for their DNA cleavage, antibacterial and cytotoxic properties.

Convenient contrast enhancement by a hole-free phase plate - Malac, Marek; Beleggia, Marco; Kawasaki, Masahiro; Li, Peng; Egerton, Ray F. (Ultramicroscopy, 2012)
Decrease of the irradiation dose needed to obtain a desired signal-to-noise ratio can be achieved by Zernike phase-plate imaging. Here we present results on a hole-free phase plate (HFPP) design that uses the incident electron beam to define the center of the plate, thereby eliminating the need for high precision alignment and with advantages in terms of ease of fabrication. The Zernike-like phase shift is provided by a charge distribution induced by the primary beam, rather than by a hole in the film. Compared to bright-field Fresnel-mode imaging, the hole-free phase plate (HFPP) results in two- to four-fold increase in contrast, leading to a corresponding decrease in the irradiation dose required to obtain a desired signal-to-noise ratio. A local potential distribution, developed due to electron beam-induced secondary-electron emission, is the most likely mechanism responsible for the contrast-transfer properties of the HFPP.
Keywords: phase plate; transmission electron microscope; contrast transfer function; charging; low dose TEM; radiation damage; contrast improvement; electron beam induced charging; Zernike phase plate; electron beam induced contamination; cryo TEM

Preferential face deposition of gold nanoparticles on silicon nanowires by galvanic displacement - Sayed, Sayed Youssef; Wang, Feng; Malac, Marek; Li, Peng; Wang, Dong; Buriak, Jillian (CrystEngComm, 2012)
We report the preferential growth of gold nanoparticles on certain crystallographic facets of Si nanowires (NWs). Our synthetic approach uses galvanic displacement, an electroless deposition method; Si NWs act as the source of electrons required for the reduction of gold ions to metallic gold nanoparticles. Si NWs grown along the <112> growth direction have a characteristic rectangular cross-section with two each of (111) and (110) facets. Through detailed transmission electron microscopy (TEM) and TEM tomography, we were able to show the selective growth of gold nanoparticles on the Si(110) facets of the Si NWs with <112> growth directions; gold deposition was not observed on the Si(111) facets. These results may be related to the high reactivity of Si(110) facets towards gold deposition via galvanic displacement as compared to the reactivity of Si(111) facets.

Grafting of lignin onto nanostructured silica SBA-15 : preparation and characterization - Saad, Rabih; Hawari, Jalal (Journal of Porous Materials, 2012)
The slow decline in oil reserves with mounting oil prices is pushing industry to find more sustainable sources for industrial manufacturing. Lignin is the second most abundant natural renewable biopolymer that is underutilized and has many functional groups (–OH, phenolics) that make the biopolymer a convenient substrate for materials manufacturing by the industry. The present study thus describes grafting of lignin onto nanostructured silica SBA-15 (Santa Barbara amorphous 15) by first silylating lignin with triethoxychlorosilane followed by treatment of silylated lignin with SBA-15. The resulting nanocomposite denoted as LIG–SBA-15-G was then characterized by powder X-ray diffraction, infra-red (FTIR), ³¹P nuclear magnetic resonance (³¹P NMR), N₂ adsorption (BET), scanning and transmission electron micrographs (SEM and TEM) and thermogravimetric analysis (TGA). X-ray data showed that LIG–SBA-15-G exhibited hexagonal structure closely similar to that observed for the SBA-15 host. FTIR of LIG–SBA-15-G showed characteristic absorption bands from lignin and attenuated Si–OH band due to its conversion to Si–O–Si ether bonds. Whereas, ³¹P NMR revealed that the majority of hydroxyl groups in lignin were replaced by Si–O–LIG ether bonds in LIG–SBA-15-G. SEM images of LIG–SBA-15-G displayed little changes in the macroscopic structure as compared to SBA-15. TEM images showed some disordered area in LIG–SBA-15-G and the grafted lignin appeared as black film on the silica surface. Using BET analysis the surface area of LIG–SBA-15-G was found to be 560 m² g⁻¹. Finally, TGA showed that LIG–SBA-15-G was more thermally stable than lignin and contained 13 % w/w lignin. Understanding the physicochemical and structural properties of the resulting lignin-nanosilica hybrid material should help engineer a robust and sustainable biomaterial suitable for various application, e.g. removal of contaminants from contaminated water.
Keywords: Lignin; nanostructured silica SBA-15; grafting; characterization

Monitoring the switch : the Warburg effect and targeted proteomic analysis of cancer metabolism - Murphy, J. Patrick; Côté, Patrice D.; Pinto, Devanand M. (Current Proteomics, 2012)
Cancer cells dramatically alter their metabolism in order to increase the production rate of intermediates required for nucleic and fatty acid biosynthesis in rapidly proliferating cells. While not well understood, dysregulation of oncogenes and tumour suppressors appears to result in the altered expression of specific isoforms of glycolysis proteins. A full understanding of glycolytic alterations in cancer through a systems biology approach requires tools to observe changes in the set of proteins that make up the glycolytic proteome. We propose that a targeted proteomics approach employing multiple reaction monitoring (MRM) is an excellent startegy to quatitatively monitor sets of proteins, such as those making up the glycolytic proteome. MRM is particularly well suited to proteins of glycolysis as they are of moderate to high abundance. Such systems-based efforts provide a means to understand the mechanisms for an altered glycolytic proteome in cancer, perhaps leading to novel drup targets and metabolic signatures for use in cancer prognosis.
Keywords: Cancer; glycolysis; MRM; targeted proteomics; warburg effect

Laboratory desalination experiments with some algal toxins - Laycock, Maurice V.; Anderson, Donald M.; Naar, Jerome; Goodman, Allan; Easy, Dorothy J.; Donovan, Mary Anne; Li, Aifeng; Quilliam, Michael A.; Al Jamali, Ebrahim; Alshihi, Rashid (Desalination, 2012)
Over the last several decades, countries throughout the world have experienced an escalating and worrisome trend in the incidence of harmful algal blooms (HABs). A concern is that highly potent algal toxins might be retained in the treated water, posing a threat to human health. Seawater contaminated with saxitoxins, domoic acid, okadaic acid, and brevetoxins was desalinated using small (b100 mL capacity) reverse osmosis and distillation equipment. Analyses of desalinated water samples indicated efﬁcient removal of the four toxins to greater than 99%, except brevetoxins for which some carry-over was observed during distillation. Hypochlorite concentrations of 4 ppm or higher were sufﬁcient to react with all of the saxitoxins, domoic acid and okadaic acid in the samples that contained initial toxin concentrations up to 1250 ng mL⁻¹ Brevetoxins appeared to be unaffected in experiments in which the toxins were exposed to up to 30 ppm hypochlorite in seawater at 35 °C for 60 min. These results and their implications in terms of desalination plant design and operation are discussed.
Keywords: HAB toxins; red tide; detoxification; saxitonxin; domoic acid; okadaic acid; brevetoxins

Ligand and pathogen speciﬁcity of the Atlantic salmon serum C-type lectin - Uribe, Elke; Steele, Thomas J.; Richards, Robert C.; Ewart, K. Vanya (Biochimica et Biophysica Acta (BBA) - General Subjects, 2012)
Background: An Atlantic salmon (Salmo salar) C-type lectin (SSL) binds to mannose and related sugars as well as to the surface of Aeromonas salmonicida. To characterize this lectin as a pathogen recognition receptor in salmon, aspects of its interaction with molecules and with intact pathogens were investigated. Methods: SSL was isolated using whole-yeast-afﬁnity and mannan-afﬁnity chromatography. The binding of SSL to the two major surface molecules of A. salmonicida, lipopolysaccharide (LPS) and A-layer protein was investigated by western blotting and enzyme-linked immunosorbent assays. Microbial binding speciﬁcity of SSL was examined by whole cell binding assays using a range of species. Carbohydrate ligand speciﬁcity of SSL was examined using glycan array analysis and frontal afﬁnity chromatography. Results: SSL showed binding to bacteria and yeast including, Pseudomonas ﬂuorescens, A. salmonicida, A. hydrophila, Pichia pastoris, and Saccharomyces cerevisiae, but there was no detectable binding to Yersinia ruckeri. In antimicrobial assays, SSL showed no activity against Escherichia coli, Bacillus subtilis, S. cerevisiae, or A. salmonicida, but it was found to agglutinate E. coli. The major surface molecule of A. salmonicida recognized by SSL was shown to be LPS and not the A-layer protein. LPS binding was mannose-inhibitable. Glycans containing N-acetylglucosamine were shown to be predominant ligands. Conclusion: SSL has a distinct ligand preference while allowing recognition of a wide variety of related carbohydrate structures.
Keywords: Atlantic salmon; Salmo salar; C-type lectin; Glycan array; Lipopolysaccharide; Pathogen recognition

A convenient method for electron tomography sample preparation using a focused ion beam - Wang, Xiongyao; Lockwood, Ross; Vick, Doug; Li, Peng; Meldrum, Al; Malac, Marek (Microscopy Research and Technique, 2012)
Here we report a new sample preparation method for three-dimensional electron tomography. The method uses the standard film deposition and focused ion beam (FIB) methods to significantly reduce the problems arising from the projected sample thickness at high tilt angles. The method can be used to prepare tomography samples that can be imaged up to a ±75° tilt range which is sufficient for many practical applications. The method can minimize the problem of Ga+ contamination, as compared to the case of FIB preparation of rod-shaped samples, and provides extended thin regions for standard 2D projection analyses.
Keywords: electron tomography; sample preparation; FIB; high tilt range; thin film deposition

Preparation and evaluation of hydrotreating catalysts based on activated carbon derived from oil sand petroleum coke - Shi, Yu; Chen, Jinwen; Chen, Jian; Macleod, Robb A.; Malac, Marek (Applied Catalysis A: General, 2012)
Novel Ni–Mo/activated carbon (AC) hydrotreating catalysts were prepared and evaluated for upgrading heavy vacuum gas oil (HVGO). The AC supports were derived from Alberta oil sand petroleum coke, i.e. fluid coke and/or delayed coke, hereafter referred to as OSP coke, through a chemical process. The BET surface area was as high as 2194 m2/g for the fluid coke derived AC and 2357 m2/g for the delayed coke derived AC. Both ACs contained a large number of micropores with pore volume as high as 1.2 cm3/g. Ni and Mo based active component precursors could be easily loaded on the activated carbon supports by chemical impregnation of nickel nitrate and ammonium molybdate followed by calcination in nitrogen at 773 K without further modification or oxidation treatment to the activated carbons. Scanning electron microscopy (SEM) observation showed highly porous surface structure of the bare activated carbon supports and well dispersed metal (oxide) precursor nanoparticles of 30–50 nm loaded on the AC supports. For comparison, two reference catalysts were also prepared by the same procedure but using commercial activated carbon and porous alumina as supports. After catalyst activation by sulfiding, the hydrotreating performance of the prepared catalysts was evaluated in a magnetically stirred autoclave with a HVGO feedstock to examine their hydrodesulfurization (HDS) and hydrodenitrogenation (HDN) activities. Two commercial hydrotreating catalysts were also tested and compared under similar conditions with the same feed. The results showed that the catalysts based on the activated carbon supports prepared from OSP coke had better hydrotreating performance than the other catalysts. Scanning transmission electron microscopy (STEM) characterization of the catalysts after activation showed that small particles of nanostructure (2–5 nm in size) were evenly embedded in the carbon matrix except for some bigger particles that were located on the catalyst surface. Energy dispersive X-ray (EDX) spectroscopy revealed that these particles were composed of Ni, Mo and S elements. The dispersed nanoparticles formed the active sites and were responsible for the observed high HDS and HDN activity. Elemental analysis and surface characterization of the spent catalysts showed that the formation of coke precursors was favored on the alumina supported catalyst, which resulted in catalyst deactivation.
Keywords: oil sand petroleum (OSP) coke; activated carbon (AC); hydrotreating; heavy vacuum gas oil (HVGO)

Tissue-specific differential induction of duplicated fatty acid-binding protein genes by the peroxisome proliferator, clofibrate, in zebrafish (Danio rerio) - Venkatachalam, Ananda B.; Lall, Santosh P.; Denovan-Wright, Eileen M.; Wright, Jonathan M. (BMC Evolutionary Biology, 2012)
Background: Force, Lynch and Conery proposed the duplication-degeneration-complementation (DDC) model in which partitioning of ancestral functions (subfunctionalization) and acquisition of novel functions (neofunctionalization) were the two primary mechanisms for the retention of duplicated genes. The DDC model was tested by analyzing the transcriptional induction of the duplicated fatty acid-binding protein (fabp) genes by clofibrate in zebrafish. Clofibrate is a specific ligand of the peroxisome proliferator-activated receptor (PPAR); it activates PPAR which then binds to a peroxisome proliferator response element (PPRE) to induce the transcriptional initiation of genes primarily involved in lipid homeostasis. Zebrafish was chosen as our model organism as it has many duplicated genes owing to a whole genome duplication (WGD) event that occurred ~230-400 million years ago in the teleost fish lineage. We assayed the steady-state levels of fabp mRNA and heterogeneous nuclear RNA(hnRNA) transcripts in liver, intestine, muscle, brain and heart for four sets of duplicated fabp genes, fabp1a/ fabp1b.1/fabp1b.2, fabp7a/fabp7b, fabp10a/fabp10b and fabp11a/fabp11b in zebrafish fed different concentrations of clofibrate. Result: Electron microscopy showed an increase in the number of peroxisomes and mitochondria in liver and heart, respectively, in zebrafish fed clofibrate. Clofibrate also increased the steady-state level of acox1 mRNA and hnRNA transcripts in different tissues, a gene with a functional PPRE. These results demonstrate that zebrafish is responsive to clofibrate, unlike some other fishes. The levels of fabp mRNA and hnRNA transcripts for the four sets of duplicated fabp genes was determined by reverse transcription, quantitative polymerase chain reaction (RT-qPCR). The level of hnRNA coded by a gene is an indirect estimate of the rate of transcriptional initiation of that gene. Clofibrate increased the steady-state level of fabp mRNAs and hnRNAs for both the duplicated copies of fabp1a/ fabp1b.1, and fabp7a/fabp7b, but in different tissues. Clofibrate also increased the steady-state level of fabp10a and fabp11a mRNAs and hnRNAs in liver, but not for fabp10b and fabp11b. Conclusion: Some duplicated fabp genes have, most likely, retained PPREs, but induction by clofibrate is over-ridden by an, as yet, unknown tissue-specific mechanism(s). Regardless of the tissue-specific mechanism(s), transcriptional control of duplicated zebrafish fabp genes by clofibrate has markedly diverged since the WGD event.

A larval zebraﬁsh model of bipolar disorder as a screening platform for neuro-therapeutics - Ellis, Lee David; Soanes, Kelly Howard (Behavioural Brain Research, 2012)
Modelling neurological diseases has proven extraordinarily difﬁcult due to the phenotypic complexity of each disorder. The zebraﬁsh has become a useful model system with which to study abnormal neurological and behavioural activity and holds promise as a model of human disease. While most of the disease modelling using zebraﬁsh has made use of adults, larvae hold tremendous promise for the highthroughput screening of potential therapeutics. The further development of larval disease models will strengthen their ability to contribute to the drug screening process. Here we have used zebraﬁsh larvae to model the symptoms of bipolar disorder by treating larvae with sub-convulsive concentrations of the GABA antagonist pentylenetetrazol (PTZ). A number of therapeutics that act on different targets, in addition to those that have been used to treat bipolar disorder, were tested against this model to assess its predictive value. Carbamazepine, valproic acid, baclofen and honokiol, were found to oppose various aspects of the PTZ-induced changes in activity. Lidocaine and haloperidol exacerbated the PTZ-induced activity changes and sulpiride had no effect. By comparing the degree of phenotypic rescue with the mechanism of action of each therapeutic we have shown that the low-concentration PTZ model can produce a number of intermediate phenotypes that model symptoms of bipolar disorder, may be useful in modelling other disease states, and will help predict the efﬁcacy of novel therapeutics.
Keywords: Zebrafish larvae; Disease model; Hyperactivity; Pentylenetrazole; Bipolar disorder

Mono- and digalactosyldiacylglycerols : potent nitric oxide inhibitors from the marine microalga Nannochloropsis granulata - Banskota, Arjun H.; Stefanova, Roumiana; Gallant, Pamela; McGinn, Patrick J. (Journal of Applied Phycology, 2012)
Chemical investigation of a marine microalga, Nannochloropsis granulata, led to the isolation of four digalactosyldiacylglycerols namely, (2S)-1-O-eicosapentaenoyl-2-O-palmitoyl-3-O-(β-D-galactopyranosyl-6-1α-D-galactopyranosyl)-glycerol (1), (2S)-1-O-eicosapentaenoyl-2-O-palmitoleoyl-3-O-(β-D-galactopyranosyl-6-1α-D-galactopyranosyl)- glycerol (2), (2S)-1-O-eicosapentaenoyl-2-O-myristoyl-3-O-(β-D-galactopyranosyl-6-1α-D-galactopyranosyl)-glycerol (3), and (2S)-1,2-bis-O-eicosapentaenoyl-3-O-(β-D-galactopyranosyl-6-1α-D-galactopyranosyl)-glycerol (4), together with their monogalactosyl analogs (5–8). Among the isolated galactolipids 2 and 3 were new natural products. Complete stereochemistry of 1, 4, 5, 7, and 8 was determined for the first time by both spectroscopic techniques and classical degradation methods. Both mono- and digalactosyldiacylglycerols isolated from N. granulata poss e s s ed s t rong n i t r i c oxide (NO) inhibi tory a c t ivi ty against lipopolysaccharide-induced NO production in RAW264.7 macrophage cells through downregulation of inducible nitric oxide synthase expression indicating the possible use as anti-inflammatory agents.
Keywords: Nannochloropsis granulata; Monogalactosyldiacylglycerol; Digalactosyldiacylglycerol; Nitric oxide; Inducible nitric oxide synthase

Study of possible combined toxic effects of azaspiracid-1 and okadaic acid in mice via the oral route - Aune, Tore; Espenes, Arild; Bunæs Aasen, John A.; Quilliam, Michael A.; Hess, Philipp; Larsen, Stig (Toxicon, 2012)
Toxins from the okadaic acid (OA) and azaspiracid (AZA) group cause considerable negative health effects in consumers when present in shellﬁsh above certain levels. The main symptoms, dominated by diarrhoea, are caused by damage to the gastrointestinal (GI) tract. Even though OA and AZAs exert toxicity via different mechanisms, it is important to ﬁnd out whether they may enhance the health effects if present together since they act on the same organs and are regulated individually. In this study, the main issue was the possibility of enhanced lethality in mice upon combined oral exposure to OA and AZA1. In addition, pathological effects in several organs and effects on absorption from the GI tract were studied. Although the number of mice was small due to low availability of AZA1, the results indicate no additive or synergistic effect on lethality when AZA1 and OA were given together. Similar lack of increased toxicity was observed concerning pathological effects that were restricted to the GI-tract. OA and AZA1 were absorbed from the GI-tract to a very low degree, and when given together, uptake was reduced. Taken together, these results indicate that the present practice of regulating toxins from the OA and AZA group individually does not present an unwanted increased risk for consumers of shellﬁsh.
Keywords: Azaspiracid; Okadaic acid; Toxicity

Toxins in mussels (Mytilus galloprovincialis) associated with diarrhetic shellﬁsh poisoning episodes in China - Li, Aifeng; Ma, Jinggang; Cao, Jijuan; McCarron, Pearse (Toxicon, 2012)
More than 200 people in China suffered illness with symptoms of diarrhetic shellﬁsh poisoning (DSP) following consumption of mussels (Mytilus galloprovincialis). The event occurred in the cities of Ningbo and Ningde near the East China Sea in May, 2011. LC–MS/ MS analysis showed that high concentrations of okadaic acid, dinophysistoxin-1, and their acyl esters were responsible for the incidents. The total concentration was more than 40 times the EU regulatory limit of 160 μg OA eq./kg. Pectentoxin-2 and its seco-acids were also present in the mussels. Additionally, yessotoxins were found to be responsible for positive mouse bioassay results on scallop (Patinopecten yessoensis) and oyster (Crassostrea talienwhanensis) samples collected from the North Yellow Sea in June, 2010. This work shows that high levels of lipophilic toxins can accumulate in shellﬁsh from the Chinese coast and it emphasises that adequate chemical analytical methodologies are needed for monitoring purposes. Further research is required to broaden the knowledge on the occurrence of lipophilic toxins in Chinese shellﬁsh.
Keywords: Diarrhetic shellfish poinsoning (DSP); Lipophilic toxins; Fatty acid esters; Mytilus galloprovincialis; LC-MS/MS

Identification of Pinnatoxins and discovery of their fatty acid Ester Metabolites in mussels (Mytilus edulis) from Eastern Canada - McCarron, Pearse; Rourke, Wade A.; Hardstaff, William; Pooley, Brandy; Quilliam, Michael A. (Journal of Agricultural and Food Chemistry, 2012)
Pinnatoxins are a group of fast-acting cyclic imine toxins previously identified in shellfish from Asia, the southern Pacific, and northern Europe. In this work pinnatoxins were detected in mussels from locations across the eastern coast of Canada. Pinnatoxin G (6) was the major structural variant present, sometimes at levels >80 μg/kg, whereas much lower levels of pinnatoxin A (1) were detected in some samples. Increased concentrations were observed following base hydrolysis of extracts, leading to the discovery by LC-MS of a range of fatty acid esters of 6. Information on the structures of these acylated derivatives was provided through a series of mass spectrometric experiments, supported by partial synthesis, and it is proposed that the compounds are 28-O-acyl esters of 6. Although acyl esters of a range of other phycotoxins are known to form as metabolites in shellfish, this is the first report of their existence for this particular toxin class. The occurrence of pinnatoxins in North American shellfish further highlights the international distribution of these toxins.
Keywords: Pinnatoxins; shellfish; Canada; fatty acids; esters; metabolites; LC-MS

Assessment of the bioenergy and bioremediation potentials of the microalga Scenedesmus sp. AMDD cultivated in municipal wastewater efﬂuent in batch and continuous mode - McGinn, Patrick J.; Dickinson, Kathryn E.; Park, Kyoung C.; Whitney, Crystal G.; MacQuarrie, Scott P.; Black, Frank J.; Frigon, Jean-Claude; Guiot, Serge R.; O'Leary, Stephen J. B. (Algal Research, 2012)
Municipal wastewater is a major source of nutrients and pollutants to freshwater and marine ecosystems and current treatment technologies are either expensive or only partially effective at removing them. We cultivated the alga Scenedesmus sp. AMDD at different pH in chemostats and batch photobioreactors in wastewater obtained from a local treatment plant. In batch mode, biomass productivities averaged 130 mg dry weight L⁻¹d⁻¹, with no signiﬁcant effect of growth pH detected. Maximum nitrogen and phosphorus removal rates were equivalent to 7% and 0.7% of the biomass productivity rates. Average hydraulic retention times for 90% N and P removal ranged from 6.55 to 6.65 days and 6.50–6.56 days, respectively. Recovered biomass yields ranged from 0.23 to 0.65 kg m⁻³ wastewater, equivalent to approximately 5–15 MJ bioenergy m⁻³ wastewater based on an average caloriﬁc value of 23 MJ kg⁻¹ d.w. algal biomass. Approximately 65% of energy equivalent could potentially be recovered from the biomass through anaerobic digestion to methane. Cellular N and P content varied, with cells held longer in stationary phase showing higher C:N and C:P ratios indicative of N- and Plimitation, respectively. Analysis of trace metals in the algal biomass indicated near total depletion of Fe, Zn and Cd from the wastewater, and lower, but substantial, uptake and/or adsorption of seven other elements. Cultivation in 2 L continuous chemostats containing wastewater was also conducted. Biomass productivities in chemostats were almost 2-fold greater than the maximum rates in batch cultures. Dissolved N and P in chemostats were both either undetectable or >99% reduced compared to the wastewater. Production of bioenergy from the chemostats was estimated to be roughly 5.3–6.1 MJ m⁻³d⁻¹, signiﬁcantly higher than in batch culture
Keywords: Microalgae; Bioenergy; Anaerobic digestion; Photosynthesis; Wastewater; Methane

Dereplication, residual complexity, and rational naming : the case of the Actaea Triterpenes - Qiu, Feng; Imai, Ayano; McAlpine, James B.; Lankin, David C.; Burton, Ian; Karakach, Tobias; Farnsworth, Norman R.; Chen, Shao-Nong; Pauli, Guido F. (Journal of Natural Products, 2012)
The genus Actaea (including Cimicifuga) has been the source of ~200 cycloartane triterpenes. While they are major bioactive constituents of complementary and alternative medicines, their structural similarity is a major dereplication problem. Moreover, their trivial names seldom indicate the actual structure. This project develops two new tools for Actaea triterpenes that enable rapid dereplication of more than 170 known triterpenes and facilitates elucidation of new compounds. A predictive computational model based on classification binary trees (CBTs) allows in silico determination of the aglycone type. This tool utilizes the Me ¹H NMR chemical shifts and has potential to be applicable to other natural products. Actaea triterpene dereplication is supported by a new systematic naming scheme. A combination of CBTs, ¹H NMR deconvolution, characteristic ¹H NMR signals, and quantitative ¹H NMR (qHNMR) led to the unambiguous identification of minor constituents in residually complex triterpene samples. Utilizing a 1.7 mm cryo-microprobe at 700 MHz, qHNMR enabled characterization of residual complexity at the 10–20 μg level in a 1–5 mg sample. The identification of five co-occurring minor constituents, belonging to four different triterpene skeleton types, in a repeatedly purified natural product emphasizes the critical need for the evaluation of residual complexity of reference materials, especially when used for biological assessment.

Profiling phlorotannins in brown Macroalgae by liquid chromatography-high resolution mass spectronmetry - Steevensz, Aaron J.; MacKinnon, Shawna L.; Hankinson, Rachael; Craft, Cheryl; Connan, Solène; Stengel, Dagmar B.; Melanson, Jeremy E. (Phytochemical Analysis, 2012)
Introduction – Phlorotannins, phenolic compounds produced exclusively by Phaeophyceae (brown algae), have recently been associated with a wide variety of beneﬁcial bioactivities. Several studies have measured the total phenolic content in extracts from various species, but little characterisation of individual phlorotannin components has been demonstrated. Objective – The purpose of this study was to develop a liquid chromatography–mass spectrometry (LC-MS) based method for rapid proﬁling of phlorotannins in brown algae. Methodology – Phlorotannin-enriched extracts from ﬁve phaeophyceaen species were analysed by ultrahigh-pressure liquid chromatography (UHPLC) operating in hydrophilic interaction liquid chromatography (HILIC) mode combined with high resolution mass spectrometry (HRMS). The method was optimised using an extract of Fucus vesiculosus; separation was achieved in less than 15 min. The basic mobile phase enhanced negative-ion electrospray ionisation (ESI), and generated multiply charged ions that allowed detection of high molecular weight phlorotannins. Results – The phlorotannin proﬁles of Pelvetia canaliculata, Fucus spiralis, F. vesiculosus, Ascophyllum nodosum and Saccharina longicruris differed signiﬁcantly. Fucus vesiculosus yielded a high abundance of low molecular weight (< 1200 Da) phlorotannins, while P. canaliculata exhibited a more evenly distributed proﬁle, with moderate degrees of polymerisation ranging from 3 to 49. HRMS enabled the identiﬁcation of phlorotannins with masses up to 6000 Da using a combination of accurate mass and ¹³C isotopic patterns. Conclusion – The UHPLC-HRMS method described was successful in rapidly proﬁling phlorotannins in brown seaweeds based on their degree of polymerisation. HILIC was demonstrated to be an effective separation mode, particularly for low molecular weight phlorotannins.
Keywords: High resolution mass spectrometry; hydrophilic interaction chromatography; brown seaweed; phlorotannins; polyphenols

Analysis of paralytic shellfish toxins and their metabolites in shellfish from the North Yellow Sea of China - Li, A.; Ma, J.; Cao, J.; Wang, Q.; Yu, R.; Thomas, K.; Quilliam, M. A. (Food Additives & Contaminants : Part A, 2012)
Samples of toxic scallop (Patinopecten yessoensis) and clam (Saxidomus purpuratus) collected on the northern coast of China from 2008 to 2009 were analysed. High-performance liquid chromatography with post-column oxidation and fluorescence detection was used to determine the profile of the main paralytic shellfish poisoning (PSP) toxins in these samples and their total toxicity. Hydrophilic interaction liquid ion chromatography with mass spectrometric detection confirmed the toxin profile and detected several metabolites in the shellfish. Results show that C1/2 toxins were the most dominant toxins in the scallop and clam samples. However, GTX1/4 and GTX2/3 were also present. M1 was the predominant metabolite in all the samples, but M3 and M5 were also identified, along with three previously unreported presumed metabolites, M6, M8 and M10. The results indicate that the biotransformation of toxins was species specific. It was concluded that the reductive enzyme in clams is more active than in scallops and that an enzyme in scallops is more apt to catalyse hydrolysis of both the sulfonate moiety at the N-sulfocabamoyl of C toxins and the 11-hydroxysulfate of C and GTX toxins to produce metabolites. This is the first report of new metabolites of PSP toxins in scallops and clams collected in China.
Keywords: paralytic shellfish toxins (PST); metabolite; LC-MS/MS; Patinopecten yessoensis; Saxidomus purpuratus

Limitations on accurate shape determination using amplitude modulation atomic force microscopy - Eves, B. J.; Green, R. G. (Ultramicroscopy, 2012)
The limitations of amplitude modulation atomic force microscopy to accurately measure the shape or form of features are investigated. The control feedback loop and the dynamics of the cantilever limit the response time of the atomic force microscope. Simply subtracting appropriately scaled amplitude (error) signal from the topography data significantly improves the accuracy of the data and can correct for the slow response time of the feedback loop. Two mechanisms were found to induce topographic errors independent of scan speed. The first is the change in tip/surface interaction at a step edge observed by comparison with results from a ‘virtual’ sample. The second is due to friction between the probe and sample but only for a specifically oriented step edge determined by the direction of oscillation of the cantilever.
Keywords: atomic forcemicroscopy(AFM); measurement ofshape/form; errors andlimitations

State-of-the art comparability of corrected emission spectra. 2. Field laboratory assessment of calibration performance using spectral fluorescence standards - Resch-Genger, Ute; Bremser, Wolfram; Pfeifer, Dietmar; Spieles, Monika; Hoffmann, Angelika; DeRose, Paul C.; Zwinkels, Joanne C.; Gauthier, François; Ebert, Bernd; Taubert, R. Dieter; Voigt, Jan; Hollandt, Jörg; et al. (Analytical Chemistry, 2012)
In the second part of this two-part series on the state-of-the-art comparability of corrected emission spectra, we have extended this assessment to the broader community of fluorescence spectroscopists by involving 12 field laboratories that were randomly selected on the basis of their fluorescence measuring equipment. These laboratories performed a reference material (RM)- based fluorometer calibration with commercially available spectral fluorescence standards following a standard operating procedure that involved routine measurement conditions and the data evaluation software LINKCORR developed and provided by the Federal Institute for Materials Research and Testing (BAM). This instrument-specific emission correction curve was subsequently used for the determination of the corrected emission spectra of three test dyes, X, QS, and Y, revealing an average accuracy of 6.8% for the corrected emission spectra. This compares well with the relative standard uncertainties of 4.2% for physical standard-based spectral corrections demonstrated in the first part of this study (previous paper in this issue) involving an international group of four expert laboratories. The excellent comparability of the measurements of the field laboratories also demonstrates the effectiveness of RM-based correction procedures.

State-of-the art comparability of corrected emission spectra.1. Spectral correction with physical transfer standards and spectral fluorescence standards by expert laboratories - Resch-Genger, Ute; Bremser, Wolfram; Pfeifer, Dietmar; Spieles, Monika; Hoffmann, Angelika; DeRose, Paul C.; Zwinkels, Joanne C.; Gauthier, François; Ebert, Bernd; Taubert, R. Dieter; Monte, Christian; Voigt, Jan; et al. (Analytical Chemistry, 2012)
The development of fluorescence applications in the life and material sciences has proceeded largely without sufficient concern for the measurement uncertainties related to the characterization of fluorescence instruments. In this first part of a two-part series on the state-of-the-art comparability of corrected emission spectra, four National Metrology Institutes active in high-precision steady-state fluorometry performed a first comparison of fluorescence measurement capabilities by evaluating physical transfer standard (PTS)-based and reference material (RM)-based calibration methods. To identify achievable comparability and sources of error in instrument calibration, the emission spectra of three test dyes in the wavelength region from 300 to 770 nm were corrected and compared using both calibration methods. The results, obtained for typical spectrofluorometric (0°/90° transmitting) and colorimetric (45°/0° front-face) measurement geometries, demonstrated a comparability of corrected emission spectra within a relative standard uncertainty of 4.2% for PTS- and 2.4% for RM-based spectral correction when measurements and calibrations were performed under identical conditions. Moreover, the emission spectra of RMs F001 to F005, certified by BAM, Federal Institute for Materials Research and Testing, were confirmed. These RMs were subsequently used for the assessment of the comparability of RM-based corrected emission spectra of field laboratories using common commercial spectrofluorometers and routine measurement conditions in part 2 of this series (subsequent paper in this issue).

Strategic identiﬁcation of in vitro metabolites of 13-desmethyl spirolide C using liquid chromatography/high-resolution mass spectrometry - Hui, Joseph P. M.; Grossert, J. Stuart; Cutler, Murray J.; Melanson, Jeremy E. (Rapid Communications in Mass Spectrometry, 2012)
A strategy to identify metabolites of a marine biotoxin, 13-desmethyl spirolide C, has been developed using liquid chromatography coupled to high-resolution mass spectrometry (LC/HRMS). Metabolites were generated in vitro through incubation with human liver microsomes. A list of metabolites was established by selecting precursor ions of a common fragment ion characteristic of the spirolide toxin which was known to contain a cyclic imine ring. Accurate mass measurements were subsequently used to conﬁrm the molecular formula of each biotransformation product. Using this approach, a total of nine phase I metabolites was successfully identiﬁed with deviations of mass accuracy less than 2 ppm. The biotransformations observed included hydroxylation, dihydroxylation, oxidation of a quaternary methyl group to hydroxymethyl or carboxylic acid groups, dehydrogenation and hydroxylation, as well as demethylation and dihydroxylation reactions. In a second step, tandem mass spectrometry (MS/MS) was performed to elucidate structures of the metabolites. Using the unique fragment ions in the spectra, the structures of the three major metabolites, 13,19-didesmethyl-19-carboxy spirolide C, 13,19-didesmethyl-19-hydroxymethyl spirolide C and 13-desmethyl-17-hydroxy spirolide C, were assigned. Levels of 13-desmethyl spirolide C and its metabolites were monitored at selected time points over a 32-h incubation period with human liver microsomes. It was determined that 13,19-didesmethyl-19-carboxy spirolide C became the predominant metabolite after 2 h of incubation. The stability plot of 13-desmethyl spirolide C showed ﬁrst-order kinetics for its metabolism and the intrinsic clearance was calculated to be 41 mL/min/mg, suggesting ﬁrst-pass metabolism may contribute to limiting oral toxicity of 13-desmethyl spirolide C.

Gas-substrate heat exchange during cold-gas dynamic spraying - McDonald, A. G.; Ryabinin, A. N.; Irissou, É.; Legoux, J.-G. (Journal of Thermal Spray Technology, 2012)
In this study, the temperature distribution of the surfaces of several substrates under an impinging gas jet from a cold spray nozzle was determined. A low-pressure cold-gas dynamic spraying unit was used to generate a jet of hot compressed nitrogen that impinged upon ﬂat substrates. Computer codes based on a ﬁnite differences method were used to solve a simpliﬁed 2D temperature distribution equation for the substrate to produce nondimensional relationships between the surface temperature and the radius of the impinging ﬂuid jet, the axial velocity of the cold spray nozzle, the substrate thickness, and the heating time. It was found that a single proﬁle of the transient nondimensional maximum surface temperature could be used to estimate the dimensional maximum surface temperature, regardless of the value of the compressed gas temperature. It was found further that, as the thermal conductance of the substrate increased, the maximum surface temperature of the substrate beneath the gas jet decreased. Heat exchange between the substrate and the compressed gas jet during motion of the nozzle to produce heat conduction within the substrate was characterized by the nondimensional Pecle´t number. It was found that lower Pecle´t numbers produced higher temperatures within the substrate. The close agreement of the numerical results with the experimental results suggests that the nondimensionalized results may be applied to a wide range of conditions and materials.
Keywords: Cold spraying; heat transfer; jet impingement; Peclét number; temperature distribution

Study of optical and electrical properties of ZnO/Cu/ZnO multilayers deposited on ﬂexible substrate - Ionescu, Mihnea Ioan; Bensebaa, Farid; Luan, Ben Li (Thin Solid Films, 2012)
Transparent conducting oxide thin ﬁlms have been extensively studied because they are essential elements in optoelectronic applications. In this communication, we report transparent conductive ZnO/Cu/ZnO multilayer ﬁlms prepared by RF sputtering of ZnO and DC sputtering of Cu on ﬂexible polyethylene naphthalate substrates. The optical and electrical properties of the multilayers were studied for different thicknesses of Cu and ZnO layers. Controlling the thickness of the ZnO layer for a speciﬁc Cu thickness affects the transmittance of the multilayer. Electrical properties are inﬂuenced by the thickness of ZnO and Cu layers. Sheet resistance of the stack rises with the decrease of Cu thickness and the increase of ZnO thickness. Repeated bending of the stack, after an initial 20% increase of sheet resistance, has no signiﬁcant effect on the electrical performance of the multilayers.
Keywords: Transparent conducting oxide; multilayer; zinc oxide; copper; flexible substrate; sputtering

Modular ultrasonic Lysis system for rapid nucleic acid extraction and sample transfer of Bacillus spores - Geissler, Matthias; Isabel, Sandra; Voisin, Benoît; Fauvel, Chantal; Boissinot, Maurice; Bergeron, Michel G.; Veres, Teodor (Journal of Bioterrorism & Biodefense, 2012)
This paper describes the design, functioning and use of an ultrasonic modular system intended for rapid extraction and fragmentation of DNA from microbial organisms following sample collection in the field. PCR assessment of the DNA extracts revealed that the system can disrupt Bacillus atrophaeus spores, a simulant for Bacillus anthracis, in less than 1 min, providing a DNA yield equivalent to that of a commercial nucleic acid extraction method. Simulation of the transfer from a contaminated to a secure area confirmed that the sample remained confined within the module while the exterior surface can be decontaminated through immersion in a disinfectant solution.
Keywords: Bacillus spores; sonication; spore lysis; PCR; Sample transfer

Review of tissue simulating phantoms with controllable optical, mechanical and structural properties for use in optical coherence tomography - Lamouche, Guy; Kennedy, Brendan F.; Kennedy, Kelsey M.; Bisaillon, Charles-Etienne; Curatolo, Andrea; Campbell, Gord; Pazos, Valérie; Sampson, David D. (Biomedical Optics Express, 2012)
We review the development of phantoms for optical coherence tomography (OCT) designed to replicate the optical, mechanical and structural properties of a range of tissues. Such phantoms are a key requirement for the continued development of OCT techniques and applications. We focus on phantoms based on silicone, fibrin and poly(vinyl alcohol) cryogels (PVA-C), as we believe these materials hold the most promise for durable and accurate replication of tissue properties.

Mullite–YSZ multilayered environmental barrier coatings tested in cycling conditions under water vapor atmosphere - Mesquita-Guimarães, J.; Garcia, E.; Miranzo, P.; Osendi, M. I.; Cojocaru, C. V.; Lima, R. S. (Surface and Coatings Technology, 2012)
Plasma sprayed mullite/YSZ graded coatings on SiC substrates were examined as environmental barrier coatings (EBCs). Several coating systems with various layer arrangements were subjected to thermal aging at 1300°C in cycling (50 and 100 cycles, i.e. 100 and 200 h) conditions under rich water vapor atmosphere. The level of porosity and the crack population were quantiﬁed using cross section SEM images of these coatings. The thickness of the thermally grown silica (TGS) layer developed was estimated and the presence of cristobalite in its structure was evidenced by micro-Raman spectroscopy. Hardness and elastic modulus were also determined by the use of instrumented indentation for each layer in the different coatings. The evolution of all these parameters conﬁrmed that EBC architectures formed by compliant porous layers resulted more effective in reducing cracks and the effects of aging than EBCs with dense graded compositions.
Keywords: Plasma spraying; Environmental barrier coatings (EBCs); Water vapor corrosion; Mullite; ZrO₂

Properties of titanium foams for biomedical application - Lefebvre, Louis-Philippe; Baril, Éric (Advanced Engineering Materials Special Issue : Porous Metals and Metal Foams, 2012)
Titanium foams are presently used in various load bearing orthopedic applications. Such foams are characterized by an open network of porosity with high surface area. This paper presents the structure, microstructure, and properties of titanium foams produced with a powder metallurgy process. Fully porous CpTi and Ti6Al4V cylinders and CpTi foam coating on CpTi and Ti6Al4V substrates were produced and characterized. The microstructure of the foam cell walls is representative of annealed CpTi and Ti6Al4V. Alloying elements and oxygen in solution increase the mechanical strength of the foams but lower their ductility. Ductility affects the fatigue life of the material. When CpTi foam is bonded to Ti6Al4V substrates, migration of alloying elements in the foam cell walls is observed. Good metallurgical bonding is created between the coatings and the dense substrate and shear strength above the requirements of the FDA guidelines are obtained.
Keywords: Titanium; foam; orthopedic implant; microstructure; mechanical properties

Dry rolling-sliding wear resistance of high density PM steel parts - Bernier, Fabrice; Gauthier, Maxime; Baril, Éric; Jiang, Jiaren; Xue, Lijue (Advances in Powder Metallurgy & Particulate Materials—2012 : Proceedings of the 2012 International Conference on Powder Metallurgy & Particulate Materials, June 10–13, Nashville, Tennessee, 2012)
As PM steel reach ever higher static and dynamic properties, their use in high performance applications is increasingly acknowledged by end-users. PM steels are now being pushed in applications where high wear resistance is required while maintaining good overall properties. Indeed, gears and cams can be subject to both rolling and sliding wear, leading to premature failure. This paper explores the effect of different alloys and process conditions on material loss in dry wear conditions. The impact of the rolling/sliding ratio is also studied. The PM component results are then compared those obtained for a wrought steel generally used in gear applications. The comparison shows that similar or even higher wear resistance can be reached by high density, high hardness PM steels.

Novel high-performance lubricants for conventional and high-density compaction - Paris, Vincent; St-Laurent, Sylvain; Thomas, Yannig (Advances in Powder Metallurgy & Particulate Materials—2012 : Proceedings of the 2012 International Conference on Powder Metallurgy & Particulate Materials, 10-13 June, Nashville, Tennessee, 2012)
With an ever increasing variety and complexity of PM parts being produced, many parts producers are looking for a powder feedstock that can allow for high green and sintered densities, improved filling performance, excellent lubricating properties and clean burn-off. Lubricants and other organics used as binders play a key role in responding to all these requirements. Consequently, many efforts have recently been put in the design of proper organic systems to improve the compaction and lubrication behaviour of powder mixes. This paper presents the characteristics of innovative lubricant systems under development with improved lubrication properties compared to the conventional lubricants used in PM. The focus is shared between two development axes: obtaining high green densities and lowering ejection forces. The lubricants were tested at high shear stresses on an industrial press at different compacting pressure and temperatures, which adequately mimics the conditions most parts manufacturers will encounter.

Design and manufacturing of a representative thermoplastic composite primary aerospace structure - Khoun, L.; Wedeking, M.; Demaria, C.; Baier, H.; Trudel-Boucher, D.; Hubert, P. (SAMPE International Symposium and Exhibition - Emerging Opportunities : Materials and Process Solutions, 2012)
The use of high performance thermoplastic composite structures in aerospace has seen a great increase in the past decade. Thermoplastic composites present many advantages over thermoset composites in terms of processing and performance, such as high toughness, high temperature performance, chemical resistance and low flammability. However, compared to thermoset matrices, the lack of material database and the limited knowledge available in the open literature regarding the manufacturing techniques have restrained their use to a relatively small number of composite structural applications. In this study, the design and the autoclave manufacturing of a PEEK/carbon hat-stiffened panel representative of an aerospace primary structure were investigated. Design and mechanical performances, including strength and stability issues, were first evaluated with finite element analysis and analytical methods. Process simulations were also performed to define the tooling material and geometry to be used, based on the evolution of the thermo-mechanical material properties during the autoclave process.
Keywords: Aerospace structure; Analytical method; Autoclave process; Hat-stiffened panels; High temperature performance; High toughness; Manufacturing techniques; Mechanical performance; Panel design; Panel skin; Primary structures; Process simulations; Stability issues; Structural applications; Thermo-mechanical; Thermoplastic composite; Thermoset composites; Tooling materials; Chemical resistance; Composite materials; Composite structures; Computer simulation; Finite element method; Mechanical properties; Pressure vessels; Structure (composition); Thermoplastics; Thermosets

Influence of cooling rates on microstructure and mechanical performance of continuous fiber reinforced PPS composites - Trudel-Boucher, David; Esquirol, A.-L.; Bureau, Martin N. (SAMPE International Symposium and Exhibition - Emerging Opportunities : Materials and Process Solutions, 2012)
In this study, the influence of the cooling rate on the crystallization temperature, level of crystallinity, spherulite size and mechanical properties was investigated for two continuous fibers reinforced polyphenylene sulfide (PPS) composites. Crystallization temperature and level of crystallinity were first studied by differential scanning calorimetry (DSC) for cooling rates comprised between 5 and 70°C/min. Results obtained showed that level of crystallinity was not significantly influenced by the cooling rate, while crystallization temperature decreased with increasing cooling rate. Matrix microstructure and composite short beam shear strength were then characterized for cooling rates of 3, 15 and 20°C/min. These cooling rates were chosen because they are representative of cooling rates used in autoclave manufacturing and compression molding. To enhance the microstructure of the PPS matrix, an etching solution based on potassium permanganate and orthophosphoric acid was used.

Engineering HVOF-Sprayed Cr3C2-NiCr coatings : the effect of particle morphology and spraying parameters on the microstructure, properties and high temperature wear performance - Poirier, D.; Legoux, J.-G.; Lima, R. S. (Thermal Spray 2012: Proceedings of the International Thermal Spray Conference, 2012)
Chromium carbide-based thermally sprayed coatings are widely used for high temperature wear applications. In these extreme environments at those temperatures, several phenomena will degrade, oxidize and change the microstructure of the coatings, thereby affecting their wear behaviour. Although it can be easily conceived that the Cr3C2-NiCr coating microstructure evolution after high temperature exposure will depend on the as-sprayed microstructure and spraying parameters, very little has been done in this regard. This study intends to develop a better understanding of the effect of spraying parameters on the resulting chromium carbide coating microstructure after high temperature operation and high temperature sliding wear properties. The microstructures of different coatings produced from two morphologies of Cr3C2-NiCr powders and under a window of in-flight particle temperature and velocity values were characterized through X-ray diffraction (XRD) and scanning electron microscopy (SEM). Sliding wear at 800°C was performed and the wear behaviour correlated to the spraying parameters and coating microstructure. Vickers microhardness (300 gf) of the coatings before and after sliding wear was also measured.

Metabolism and metabonomics in cancer risk Assessment, diagnosis, prognosis and treatment - Cuperlovic-Culf, M. (Journal of Metabonomics & Metabolites, 2012)

Learning machine translation from in-domain and out-of-domain data - Turchi, Marco; Goutte, Cyril; Cristianini, Nello (Proceedings of the 16th Annual Conference of the European Association for Machine Translation, 2012)
The performance of Phrase-Based Statistical Machine Translation (PBSMT) systems mostly depends on training data. Many papers have investigated how to create new resources in order to increase the size of the training corpus in an attempt to improve PBSMT performance. In this work, we analyse and characterize the way in which the in-domain and outof- domain performance of PBSMT is impacted when the amount of training data increases. Two different PBSMT systems, Moses and Portage, two of the largest parallel corpora, Giga (French-English) and UN (Chinese-English) datasets and several in- and out-of-domain test sets were used to build high quality learning curves showing consistent logarithmic growth in performance. These results are stable across language pairs, PBSMT systems and domains. We also analyse the respective impact of additional training data for estimating the language and translation models. Our proposed model approximates learning curves very well and indicates the translation model contributes about 30% more to the performance gain than the language model.

The impact of sentence alignment errors on phrase-based machine translation performance - Goutte, Cyril; Carpuat, Marine; Foster, George (Proceedings of the Tenth Conference of the Association for Machine Translation in the Americas, 2012)
When parallel or comparable corpora are harvested from the web, there is typically a tradeoff between the size and quality of the data. In order to improve quality, corpus collection efforts often attempt to fix or remove misaligned sentence pairs. But, at the same time, Statistical Machine Translation (SMT) systems are widely assumed to be relatively robust to sentence alignment errors. However, there is little empirical evidence to support and characterize this robustness. This contribution investigates the impact of sentence alignment errors on a typical phrase-based SMT system. We confirm that SMT systems are highly tolerant to noise, and that performance only degrades seriously at very high noise levels. Our findings suggest that when collecting larger, noisy parallel data for training phrase-based SMT, cleaning up by trying to detect and remove incorrect alignments can actually degrade performance. Although fixing errors, when applicable, is a preferable strategy to removal, its benefits only become apparent for fairly high misalignment rates. We provide several explanations to support these findings.

A poor man’s translation memory using machine translation evaluation metrics - Simard, Michel; Fujita, Atsushi (Proceedings of the Tenth Conference of the Association for Machine Translation in the Americas, 2012)
We propose straightforward implementations of translation memory (TM) functionality for research purposes, using machine translation evaluation metrics as similarity functions. Experiments under various conditions demonstrate the effectiveness of the approach, but also highlight problems in evaluating the results using an MT evaluation methodology.

Fast and efficient face recognition system using Random Forest and Histograms of Oriented Gradients - Salhi, Abdel Ilah; Kardouchi, Mustapha; Belacel, Nabil (Proceedings of the International Conference of the Biometrics Special Interest Group (BIOSIG), 2012)
The efficient face recognition systems are those which are able to achieve higher recognition rate with lower computational cost. To develop such systems both feature representation and classification method should be accurate and less time consuming.Aiming to satisfy these criteria we coupled the HOG descriptor (Histograms of Oriented Gradients) with the Random Forest classifier (RF). Although rarely used in face recognition, HOG have proven to be a power descriptor in this task with a lower computational time. As regards classification method, recent works have shown that apart from their accuracy when compared with its competitors, Random Forest exhibits a low computational time in both training and testing phase. Experimental results on ORL database have demonstrated the efficiency of this combination.

Learning to translate : a statistical and computational analysis - Turchi, Marco; De Bie, Tijl; Goutte, Cyril; Cristianini, Nello (Advances in Artificial Intelligence, 2012)
We present an extensive experimental study of Phrase-based Statistical Machine Translation, from the point of view of its learning capabilities. Very accurate Learning Curves are obtained, using high-performance computing, and extrapolations of the projected performance of the system under different conditions are provided. Our experiments confirm existing and mostly unpublished beliefs about the learning capabilities of statistical machine translation systems. We also provide insight into the way statistical machine translation learns from data, including the respective influence of translation and language models, the impact of phrase length on performance, and various unlearning and perturbation analyses. Our results support and illustrate the fact that performance improves by a constant amount for each doubling of the data, across different language pairs, and different systems. This fundamental limitation seems to be a direct consequence of Zipf law governing textual data. Although the rate of improvement may depend on both the data and the estimation method, it is unlikely that the general shape of the learning curve will change without major changes in the modeling and inference phases. Possible research directions that address this issue include the integration of linguistic rules or the development of active learning procedures.

Real-time blood circulation and bleeding model for surgical training - Boisvert, Jonathan; Poirier, Guillaume; Borgeat, Louis; Godin, Guy (IEEE Transactions on Biomedical Engineering, 2012)
Intraoperative management of bleeding is a critical skill all surgeons must possess. It is, however, very challenging to create a safe and realistic learning environment for its acquisition. In this paper, we propose a simple and efficient approach to integrate blood circulation to computerized surgical simulation systems and allow for real-time processing of punctures, ruptures, and cauterization of blood vessels. Blood pressures and flows are calculated using a system of ordinary differential equations, which can be simulated very efficiently. The equation system itself is constructed using a graph of the vessels’ connectivity extracted from magnetic resonance angiograms (MRA) and completed with virtual vessels deduced from the principle of minimum work. Realtime performances of the method are assessed and results are demonstrated on ten patients who underwent a MRA before removal of a brain tumor.
Keywords: fluid flow; hemostasis; medical simulation; personalized modelling; surgery; vascular model

Communication : the structures of small cationic gas-phase platinum clusters - Harding, Dan J.; Kerpal, Christian; Rayner, David M.; Fielicke, André (Journal of Chemical Physics, 2012)
The structures of small platinum clusters Pt 3−5+ are determined using far-infrared multiple photon dissociation spectroscopy of their argon complexes combined with density functional theory calculations. The clusters are found to have compact structures, and Pt 4+ and Pt 5+ already favor three-dimensional geometries, in contrast to a number of earlier predictions. Challenges in applying density functional theory to 3rd row transition metal clusters are addressed. Preliminary calculations suggest that the effects of spin-orbit coupling do not change the favoured lowest-energy isomers

Coulomb asymmetry and sub-cycle electron dynamics in multiphoton multiple ionization of H2 - Spanner, M.; Grafe, S.; Chelkowski, S.; Pavicic, D.; Meckel, M.; Zeidler, D.; Bardon, A. B.; Ulrich, B.; Bandrauk, A. D.; Villeneuve, D. M.; Dorner, R.; Corkum, P. B.; et al. (Journal of Physics B : Atomic, Molecular and Optical Physics, 2012)
We present a systematic study of the molecular-frame photo-electron angular distributions produced by multiphoton double ionization of H2 using circularly polarized 800 nm, femtosecond laser pulses. We compare experimental results to numerical results obtained from a reduced-dimensionality time-dependent Schr¨odinger equation (TDSE) model. In addition, we implement a TDSE-like version of the strong-field approximation to isolate the effect of the parent ion’s Coulomb potential on the continuum electron in our simulations. Thereby we identify the contributions of the parent ion potential, and light induced sub-optical cycle electron dynamics on the observable energy and angular distributions.

Observation of Cooper minimum in krypton using high harmonic spectroscopy - Shiner, A. D.; Schmidt, B. E.; Trallero-Herrero, C.; Corkum, P. B.; Kieffer, J-C.; Légaré, F.; Villeneuve, D. M. (Journal of Physics B : Atomic, Molecular and Optical Physics, 2012)
High harmonic spectroscopy utilizes the methods of attosecond science to study electronic properties of atoms and molecules. We use a 1.8 μm 11 fs laser source to generate high harmonic spectra beyond 150 eV. The Cooper minimum in krypton is clearly visible in these spectra, and would otherwise be difficult to observe with 800 nm laser sources. We relate the shape of the spectrum to the photoionization cross section of krypton.

High harmonic generation with long-wavelength few-cycle laser pulses - Schmidt, Bruno E.; Shiner, Andrew D.; Giguère, Mathieu; Lassonde, Philippe; Trallero-Herrero, Carlos A.; Kieffer, J-C.; Corkum, P. B.; Villeneuve, D. M.; Légaré, Francois (Journal of Physics B : Atomic, Molecular and Optical Physics, 2012)
We report the extension of hollow-core fibre pulse compression to longer wavelengths. High-energy multi-cycle infrared pulses are generated via optical parametric amplification and subsequently broadened in the fibre. 2.5-cycle pulses at the Signal wavelength (1.4 µm) and 1.6-cycle pulses at the Idler wavelength (1.8 µm) in the sub-millijoule regime have been generated. New compression schemes can be applied at 1.8 µm and beyond. In this manner, 1.6-cycle carrier envelope phase stable pulses were generated by linear propagation in the anomalous dispersion regime of bulk glass which surprisingly enables compression below its third-order dispersion limit. Furthermore, a dispersion-free way of controlling the carrier envelope phase is demonstrated. Moreover, we experimentally confirm the increase in high-harmonic cut-off energy with driving laser wavelength and demonstrate the beneficial effect of few-cycle pulses which enable higher saturation intensities on target compared to multi-cycle pulses. It will be an ideal tool for future synthesis of isolated attosecond pulses in the sub-keV regime. With this laser source, we revealed for the first time multi-electron effects in high harmonic generation in xenon.

All-optical measurement of high-harmonic amplitudes and phases in aligned molecules - Rupenyan, A.; Bertrand, J. B.; Villeneuve, D. M.; Worner, H. J. (Physical Review Letters, 2012)
We report a new all-optical approach to measuring the phase and amplitude of high-harmonic emission from aligned molecules. We combine the transient grating technique with a continuous rotation of the molecular alignment axis and develop an analytical model that enables the simultaneous determination of phases and amplitudes. Measurements in N2 molecules are shown to be in qualitative agreement with the results of ab initio quantum scattering calculations.

High-harmonic transient grating spectroscopy of NO2 electronic relaxation - Ruf, H.; Handschin, C.; Ferré, A.; Thiré, N.; Bertrand, J. B.; Bonnet, L.; Cireasa, R.; Constant, E.; Corkum, P. B.; Descamps, D.; Fabre, B.; Larregaray, P.; et al. (The Journal of Chemical Physics, 2012)
We study theoretically and experimentally the electronic relaxation of NO2 molecules excited by absorption of one ∼400 nm pump photon. Semiclassical simulations based on trajectory surface hopping calculations are performed. They predict fast oscillations of the electronic character around the intersection of the ground and first excited diabatic states. An experiment based on high-order harmonic transient grating spectroscopy reveals dynamics occurring on the same time scale. A systematic study of the detected transient is conducted to investigate the possible influence of the pump intensity, pump wavelength, and rotational temperature of the molecules. The quantitative agreement between measured and predicted dynamics shows that, in NO2, high harmonic transient grating spectroscopy encodes vibrational dynamics underlying the electronic relaxation.

Frequency-resolved optical gating for time-resolving knockout in double ionization with attosecond pulses - Price, H.; Staudte, A.; Corkum, P. B.; Emmanouilidou, A. (Physical Review A, 2012)
We develop the two-electron attosecond streak camera under realistic conditions using a quasiclassical model. We assume extreme ultraviolet (XUV) attosecond pulses with a full width at half maximum (FWHM) of 24 attoseconds, centered at 120 eV and a streaking infrared laser field of 1600 nm, and intensity of 1.8 × 1012 W/cm2. The proposed method is shown to be capable of time resolving two-electron collisions in double ionization.

High-pressure gas phase femtosecond laser ionization mass spectrometry - Peng, Jiahui; Puskas, Noah; Corkum, Paul B.; Rayner, David M.; Loboda, Alexandre V. (Analytical Chemistry, 2012)
We describe a novel ion source for analytical mass spectrometry based on femtosecond laser ionization at pressures at and above atmospheric and characterize its performance when coupled to a tandem quadrupole/time-of-flight mass spectrometer. We assess source saturation limits, ionization and sampling efficiencies, the effective ionization volume, and limits of detection. We demonstrate 100% efficient ionization for a set of organic compounds and show that the degree of ion fragmentation over a range of laser powers is favorable compared to electron impact ionization, especially in that a substantial parent ion signal is always observed. We show how collisional cooling plays a role in controlling fragmentation at high pressures and address how ion–molecule chemistry can be controlled or exploited. High-pressure femtosecond laser ionization will allow “universal” and efficient ionization, presenting a research direction that will broaden the options for gas phase analysis beyond the capabilities of electron impact ionization.

Time-resolved high-harmonic spectroscopy of nonadiabatic dynamics in NO2 - Kraus, P. M.; Arasaki, Y.; Bertrand, J. B.; Patchkovskii, S.; Corkum, P. B.; Villeneuve, D. M.; Takatsuka, K.; Worner, H. J. (Physical Review A, 2012)
Time-resolved high-harmonic spectroscopy is an emerging approach to measuring coupled electronic and nuclear dynamics in photochemical reactions. A general conceptual and theoretical model for the technique is derived from first principles and applied to study the sensitivity of the technique to nonadiabatic dynamics. By comparing the model with detailed experimental data on photoexcited NO2 molecules, we find that time-resolved high-harmonic spectroscopy is primarily sensitive to electronic population dynamics. The coordinate dependence of the vertical ionization potential and photorecombination matrix elements contribute also, but much less significantly, to the observed dynamics because of the rapid spreading of the wave packet in the excited state. We discuss the extension of the method to larger polyatomic molecules in light of this insight.

Intensity dependence of multiple orbital contributions and shape resonance in high-order harmonic generation of aligned N2 molecules - Jin, Cheng; Bertrand, Julien B.; Lucchese, R. R.; Worner, H. J.; Corkum, Paul B.; Villeneuve, D. M.; Le, Anh-Thu; Lin, C. D. (Physical Review A, 2012)
We report measurements and theoretical simulations of high-order harmonic generation (HHG) in aligned N2 molecules using a 1200-nm intense laser field when the generating pulse is perpendicular to the aligning one. With increasing laser intensity, the minimum in the HHG spectra first shifts its position and then disappears. Theoretical simulations including the macroscopic propagation effects in the medium reproduce these observations and the disappearance of the minimum is attributed to the additional contribution of HHG from inner orbitals. We also predict that the well-known shape resonance in the photoionization spectra of N2 should exist in the HHG spectra. It is most clearly seen when the generating laser is parallel to the aligning one and disappears gradually as the angle between the two lasers increases. No clear evidence of this shape resonance has been reported so far when using lasers with different wavelengths. Further experimentation is needed to draw conclusions.

Oriented rotational wave-packet dynamics studies via high harmonic generation - Frumker, E.; Hebeisen, C. T.; Kajumba, N.; Bertrand, J. B.; Worner, H. J.; Spanner, M.; Villeneuve, D. M.; Naumov, A.; Corkum, P. B. (Physical Review Letters, 2012)
We produce oriented rotational wave packets in CO and measure their characteristics via high harmonic generation. The wave packet is created using an intense, femtosecond laser pulse and its second harmonic. A delayed 800 nm pulse probes the wave packet, generating even-order high harmonics that arise from the broken symmetry induced by the orientation dynamics. The even-order harmonic radiation that we measure appears on a zero background, enabling us to accurately follow the temporal evolution of the wave packet. Our measurements reveal that, for the conditions optimum for harmonic generation, the orientation is produced by preferential ionization which depletes the sample of molecules of one orientation.

Order-dependent structure of high harmonic wavefronts - Frumker, E.; Paulus, G. G.; Niikura, H.; Naumov, A.; Villeneuve, D. M.; Corkum, P. B. (Optics Express, 2012)
The physics of high harmonics has led to the generation of attosecond pulses and to trains of attosecond pulses. Measurements that confirm the pulse duration are all performed in the far field. All pulse duration measurements tacitly assume that both the beam’s wavefront and intensity profile are independent of frequency. However, if one or both are frequency dependent, then the retrieved pulse duration depends on the location where the measurement is made. We measure that each harmonic is very close to a Gaussian, but we also find that both the intensity profile and the beam wavefront depend significantly on the harmonic order. Thus, our findings mean that the pulse duration will depend on where the pulse is observed. Measurement of spectrally resolved wavefronts along with temporal characterization at one single point in the beam would enable complete space-time reconstruction of attosecond pulses. Future attosecond science experiments need not be restricted to spatially averaged observables. Our approach paves the way to recovery of the single molecule response to the strong field.

Probing polar molecules with high harmonic spectroscopy - Frumker, E.; Kajumba, N.; Bertrand, J. B.; Worner, H. J.; Hebeisen, C. T.; Hockett, P.; Spanner, M.; Patchkowskii, S.; Paulus, G. G.; Villeneuve, D. M.; Naumov, A.; Corkum, P. B. (Physical Review Letters, 2012)
We bring the methodology of orienting polar molecules together with the phase sensitivity of high harmonic spectroscopy to experimentally compare the phase difference of attosecond bursts of radiation emitted upon electron recollision from different ends of a polar molecule. This phase difference has an impact on harmonics from aligned polar molecules, suppressing emission from the molecules parallel to the driving laser field while favoring the perpendicular ones. For oriented molecules, we measure the amplitude ratio of even to odd harmonics produced when intense light irradiates CO molecules and determine the degree of orientation and the phase difference of attosecond bursts using molecular frame ionization and recombination amplitudes. The sensitivity of the high harmonic spectrum to subtle phase differences in the emitted radiation makes it a detailed probe of polar molecules and will drive major advances in the theory of high harmonic generation.

Routes to formation of highly excited neutral atoms in the breakup of strongly driven H2 - Emmanouilidou, A.; Lazarou, C.; Staudte, A.; Eichmann, U. (Physical Review, 2012)
We present a theoretical quasiclassical treatment of the formation, during Coulomb explosion, of highly excited neutral H atoms (H∗) for strongly driven H2. This process, where after the laser field is turned off, one electron escapes to the continuum while the other occupies a Rydberg state, was recently reported in an experimental study [B. Manschwetus et al., Phys. Rev. Lett. 102, 113002 (2009)]. We find that two-electron effects are important in order to correctly account for all pathways leading to H∗ formation.We identify two pathways where the electron that escapes to the continuum does so either very quickly or after remaining bound for a few periods of the laser field. These two pathways of H∗ formation have distinct traces in the probability distribution of the escaping electron momentum components.

Revealing the cooper minimum of N2 by molecular frame high-harmonic spectroscopy - Bertrand, J. B.; Wörner, H. J.; Hockett, P.; Villeneuve, D. M.; Corkum, P. B. (Physical Review Letters, 2012)
Molecular frame high-harmonic spectra of aligned N2 molecules reveal a Cooper-like minimum. By deconvolving the laboratory frame alignment distribution, what was previously thought to be a maximum of emission along the molecular axis is found to be maxima at 35 degrees off axis, with a spectral minimum on axis. Both of these features are supported by photoionization calculations that underline the relationship between high-harmonic spectroscopy and photoionization measurements. The calculations reveal that the on axis spectral minimum is a Cooper-like minimum that arises from the destructive interference of the p and f partial wave contributions to high-harmonic photorecombination. Features such as Cooper minima and shape resonances are ubiquitous in molecular photoionization or recombination.

InAs quantum dots of engineered height for fabrication of broadband superluminescent diodes - Haffouz, S.; Barrios, P. J.; Al-Ahmadi, Ameenah (Fingerprints in the Optical and Transport Properties of Quantum Dots, 2012)

Tunable terahertz beat signal generation from an InAs/InP quantum-dot mode-locked laser combined with external-cavity - Jiao, Zhejing; Liu, Jiaren; Lu, Zhenguo; Zhang, Xiupu; Poole, Philip J.; Barrios, Pedro J.; Poitras, Daniel; Caballero, Juan (Photonics Technology Letters, IEEE, 2012)
Tunable terahertz beat signal generation is demonstrated by using a C-band InAs/InP quantum-dot (QD) mode-locked laser combined with external cavity of two fiber Bragg gratings (FBGs), where one of the FBGs is tunable in wavelength. Beat signals with ultra-high repetition rates quasi-continuously from 1 to 2.21 THz are observed between the two modes, which are phase-correlated due to intracavity four-wave mixing effect in the QD waveguide.
Keywords: Fiber Bragg gratings (FBGs); quantum-dot mode-locked lasers (QD MLLs); terahertz beat signal

High-resolution methane spectroscopy using InGaAsSb/AlInGaAsSb laterally-coupled index-grating distributed feedback laser diode at 3.23 μm - Gupta, J. A.; Bezinger, A.; Barrios, P. J.; Lapointe, J.; Poitras, D.; Waldron, P. (Electronics Letters, 2012)
A lateral etched-grating process was used to produce singlemode distributed feedback laser diodes at 3.23 μm. The devices are based on InGaAsSb/AlInGaAsSb type-I quantum well active regions grown on GaSb substrates by molecular beam epitaxy. The lasers were used in high-resolution spectroscopy of methane gas near the v3, R7 vibrational absorption transitions.

Linewidth enhancement factor of InAs/InP quantum dot lasers around 1.5 μm - Jiao, Z. J.; Lu, Z. G.; Liu, J. R.; Poole, P. J.; Barrios, P. J.; Poitras, D.; Pakulski, G.; Caballero, J.; Zhang, X. P. (Optics Communications, 2012)
Linewidth enhancement factor (LEF) of InAs/InP quantum dot (QD) multi-wavelength lasers (MWLs) emitting around 1.5 μm is investigated both above and below the threshold. Above the threshold, LEFs at three different wavelengths around the gain peak of 1.53 μm by the injection locking technique are obtained to be 1.63, 1.37 and 1.59. Then by Hakki–Paoli method LEF is found to decrease with increased current and shows a value of less than 1 below the threshold. These small LEF values have clearly indicated that our developed InAs/InP QDs are perfect and promising gain materials for QD MWLs, QD mode-locked lasers (QD MLLs) and QD distributed-feedback (QD DFB) lasers around 1.5 μm.
Keywords: InAs/InP quantum dot lasers; linewidth enhancement factor; injection locking technique; Hakki–Paoli method

Grain size, texture, and crystallinity in lanthanum monosulfide thin films grown by pulsed laser deposition - Fairchild, S.; Cahay, M.; Murray, P. T.; Grazulis, L.; Wu, X.; Poitras, D.; Lockwood, D. J. (Thin Solid Films, 2012)
We report a detailed investigation of the growth of lanthanum monosulfide (LaS) thin films by pulsed laser deposition on (001) magnesium oxide (MgO) substrates in a background of H2S for the purpose of optimizing their crystallinity, texture, and grain size. A variety of films were grown while varying the laser repetition rate, the temperature of the substrate, and the partial pressure of H2S. The thin films were characterized by X-ray diffraction (XRD), atomic force microscopy (AFM), Raman spectroscopy, and high resolution transmission electron microscopy. Films grown at 500 °C with a H2S background pressure of 3.4 × 10− 4 Pa and a laser repetition rate of 8 Hz produced the LaS film with the largest grains whose size averaged 293 nm. The XRD pattern of these films revealed that their orientation was predominantly (200). AFM images of the surface of these films showed large plate-like grains. This contrasts with the fine grain structure observed in LaS films grown at a lower substrate temperature and lower H2S pressure.
Keywords: pulsed laser deposition; X-ray diffraction; transmission electron microscopy; atomic force microscopy; Raman spectroscopy

Near-infrared ultrawide bandwidth LEDs using InAs quantum dots of equally tuned heights - Haffouz, Sofiane; Barrios, Pedro J.; Poitras, Daniel; Normandin, Richard (IEEE Photonics Technology Letters, 2012)
Ultrawide bandwidth light-emitting diodes (LEDs) using eight layers of InAs/GaAs quantum dots (QDs) of equally tuned heights are reported. Tilted and tapered waveguides of various dimensions are tested under continuous-wave operation conditions. An emission spectrum with 3-dB bandwidth up to 173 nm at a peak wavelength of 1064.5 nm is achieved. The measured emission spectra of the QDs–LEDs as a function of the injection current indicated that the obtained large bandwidth is related to the contribution of the excited states (p, d) from the ensemble of the dots to the recombination mechanism. Continuous-wave output power of 0.6 mW is measured in the corresponding device that is made of a 1-mm-long waveguide and with tilted and tapered angles of 6° and 2°, respectively.
Keywords: gallium arsenide; indium arsenide; light-emitting diodes (LEDs); molecular beam epitaxy; quantum dots (QDs)

Structural phase transitions induced by pressure in ammonium borohydride - Flacau, Roxana; Yao, Yansun; Klug, Dennis D.; Desgreniers, Serge; Ratcliffe, Christopher I. (Physical Chemistry Chemical Physics, 2012)
A combined experimental and theoretical study of hydrogen-rich ammonium borohydride (NH4BH4) subjected to pressures up to 10 GPa indicates two phase transitions, detected by synchrotron radiation powder X-ray diffraction, Raman spectroscopy and Car–Parrinello molecular dynamics calculations, at 1.5 and 3.4 GPa. The ambient pressure, face-centred cubic phase of NH4BH4 transforms into a highly disordered intermediate structure which then evolves upon increasing pressure into an orthorhombic, distorted CsCl structure. The structure of the latter phase was solved using ab initio computational techniques and from a Rietveld full pattern refinement of the powder X-ray diffraction data.

Overwintering of barges in the Beaufort - assessing ice issues and damage potential - Barker, Anne; Timco, Garry (Technical Report, 2012)
Overwintering of vessels and barges has been carried out in the Arctic for many years, in the Beaufort as well as in other regions of the Arctic and southern Canada. Draft guidelines from Transport Canada exist for this practice. However, there is uncertainty concerning the damage potential for structures that may be left to freeze-in within the landfast ice region of the Beaufort Sea, particularly those that contain petroleum products. This is a great concern for the Inuvialuit, among others. There is evidence that this freeze-in could be (and has been) done safely but it is not clear how often this has been done or the conditions required to ensure safe overwintering of vessels in the Beaufort Sea. No information exists on the likelihood of damage due to ice or its possible effects. A detailed study focused on the conditions of the Beaufort Sea would greatly aid many stakeholders on the magnitude of this problem and its possible impact. This study brought together different types of relevant data and information to resolve this important issue, with a focus on the ice loading considerations. As such, the objective of this project was to assess the damage potential for vessels or barges overwintering in land-fast ice. The project will inform the Inuvialuit and Regulators on the likelihood of damage and provide information on the best-available means of reducing the likelihood of damage to vessels overwintering in ice in the nearshore region of the Beaufort Sea. The report steps through illustrative scenarios, in order to provide examples of the types of ice loads that could occur in representative overwintering locations. These scenarios lead to the provision of a framework of methods used to evaluate ice loads on vessels. This framework can be applied to assess ice loads on a specific vessel with known structural integrity at a specific location, by a team of qualified operational, ice mechanic and naval architect experts. No design considerations are provided, as that assessment would be too case specific to be of use in an overview of this subject area. The authors conclude that a sheltered spot, with a limited fetch area, to limit pack ice driving forces is a key factor to minimizing the likelihood of damage due to ice. It is not sufficient to say that a vessel will be in landfast ice conditions throughout the winter. There are many locations where a vessel may be in landfast ice conditions for most of the winter, but the vessel may be in dynamic conditions come the spring break-up period. During this period, depending upon the location, ice crushing forces on a vessel and/or ice loads can be sufficient to break mooring lines and potentially damage a vessel. Thus, the overwintering location should have minimal dynamic ice movement in the spring, to avoid this scenario. Finally, in order to partially alleviate concerns about the practice of overwintering, and more specifically, overwintering of fuel barges, the authors recommend that the Inuvialuit Settlement Region implement their own record-keeping of fuel barges that are overwintering. This would take the form of a simple record of location, vessel and contact information. Having a record of overwintering, and a method of tracking it, may help to provide more data on the practice, guidance on best practices related to overwintering (such as notification for affected communities and those travelling in the vicinity of the vessel), and peace of mind in terms of sound site selection practices and monitoring.
Keywords: Overwinter; Barge; Landfast; Ice; Beafort

Deformation behavior of solid-solution-strengthened Mg-9 wt.% Al alloy subjected to uniaxial tension - Lee, S. Y.; Gharghouri, M. A.; Wang, H.; Nayyeri, G.; Wu, P. D.; Poole, W. J.; Wu, W.; An, K. (Proceedings of the 9th International Conference on Magnesium Alloys and their Applications (ICMAA12), 2012)
In-situ neutron diffraction has been used to measure lattice strains for different grain orientations as a function of applied stress in a solid-solution-strengthened extruded binary Mg-9wt.%Al alloy. An elastic-viscoplastic self-consistent (EVPSC) model of polycrystal plasticity was used to simulate the macroscopic stress-strain curve and the neutron diffraction data, yielding the relative contributions, critical resolved shear stresses and hardening behavior of the available slip and twinning modes. Non-linear behavior was observed during unloading after deforming the material into the fully plastic regime in tension. The model suggests that this non-linear behavior is mainly due to basal slip.
Keywords: magnesium; plastic deformation; neutron diffraction; self-consistent modeling

Deformation behaviour of AZ80 subject to multi-axial loading - Tomlinson, P. S.; Poole, W. J.; Sinclair, C. W.; Gharghouri, M. A. (Proceedings of the 9th International Conference on Magnesium Alloys and their Applications (ICMAA12), 2012)
A robust understanding of the deformation behaviour of magnesium alloys under complex loading paths is a prerequisite to the successful fabrication of parts and understanding of their in- service performance. To facilitate this, multi-axial testing has been conducted on thin walled cylindrical samples of cast AZ80 alloy possessing weak initial texture. Internal pressurization, controlled by closed-loop feedback system permits hoop stresses to be created within the sample wall. When generated in conjunction with axial loading this allows a range of biaxial tensile loadings to be induced within the tension-tension quadrant of stress space. In order to facilitate an understanding of the textural evolution of weakly textured AZ80 subjected to these loadings, texture measurements have been conducted on as tested samples via neutron diffraction. This work builds off of prior work which has characterized the behaviour of AZ80 in uniaxial tension and compression and integrates these results. These mechanical testing results have been compared to those predicted by crystal plasticity simulations in order to help understand the deformation behaviour well as texture evolution.
Keywords: magnesium; biaxial; deformation; texture; VPSC; model

Microstructure development in hypereutectic cast al-si alloys evaluated by metallurgical analysis and neutron diffraction - Kasprzak, W.; Sediako, D.; Aniolek, M.; Kurita, H. (ICAA13: 13th International Conference on Aluminum Alloys, 2012)
Keywords: hypereutectic Al-19%Si alloys; alloying with Cu; Mg; P; microstructure; in-situ neutron diffraction; thermal analysis; hardness; tensile strength

Neutron diffraction study on residual stress in aluminum engine blocks following machining and service testing - Lombardy, Anthony; Sediako, Dimitry; D'Elia, Francesco; Ravindran, C.; Mackay, Robert I. (SAE International Journal of Materials and Manufacturing, 2012)
Development of lightweight alloys suitable for automobile applications has been of great importance to the automotive industry in recent years. The use of 319 type aluminum alloy in the production of gasoline engine blocks is an example of this shift towards light alloys for large automobile components. However, excessive residual stress along the cylinder bores of these engine blocks may cause problems during engine operation. Therefore, in this study, neutron diffraction was used to evaluate residual stresses along the aluminum cylinder bridge and the gray cast iron liners. The strains were measured in the hoop, radial, and axial orientations, while stresses were subsequently calculated using generalized Hooke’s law. The results suggest that the residual stress magnitude for the aluminum cylinder bridge was tensile for all three measured components and gradually increased with cylinder depth towards the bottom of the cylinder. The residual stress in the gray cast iron liner was highly compressive with a relatively constant stress magnitude.

Lipid bilayer – DNA interaction mediated by divalent metal cations : SANS and SAXD study - Uhríková, D.; Kučerka, N.; Lengyel, A.; Pullmannová, P.; Teixeira, J.; Murugova, T.; Funari, S. S.; Balgavý, P. (Journal of Physics : Conference Series, 2012)
The structure of aggregates formed due to DNA interaction with dipalmitoylphosphatidylcholine (DPPC) in presence of Ca2+ and Zn2+ is examined using small-angle synchrotron X-ray diffraction (SAXD) and small-angle neutron scattering (SANS). SAXD detected two structures: LC - condensed lamellar phase and LX - lamellar phase with DNA strands intercalated between the adjacent lipid bilayers, without regular packing at low cation concentration (~1 mM). The high concentration of Zn2+ induces a macroscopic phase separation in mixtures. The SANS curves of DPPC+ions2+ vesicles evaluated using the strip function model have shown different modes of cations binding to the DPPC bilayers.

Interaction of aspirin (Acetylsalicylic Acid) with lipid membranes - Barrett, Matthew A.; Zheng, Songbo; Roshankar, Golnaz; Alsop, Richard J.; Belanger, Randy K. R.; Huynh, Chris; Kučerka, Norbert; Rheinstädter, Maikel C. (PLoS ONE, 2012)
We studied the interaction of Aspirin (acetylsalicylic acid) with lipid membranes using x-ray diffraction for bilayers containing up to 50 mol% of aspirin. From 2D x-ray intensity maps that cover large areas of reciprocal space we determined the position of the ASA molecules in the phospholipid bilayers and the molecular arrangement of the molecules in the plane of the membranes. We present direct experimental evidence that ASA molecules participate in saturated lipid bilayers of DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine)and preferably reside in the head group region of the membrane. Up to 50 mol% ASA molecules can be dissolved in this type of bilayer before the lateral membrane organization is disturbed and the membranes are found to form an ordered, 2D crystal-like structure. Furthermore, ASA and cholesterol were found to co-exist in saturated lipid bilayers, with the ASA molecules residing in the head group region and the cholesterol molecules participating in the hydrophobic membrane core.

Molecular structures of fluid phase phosphatidylglycerol bilayers as determined by small angle neutron and X-ray scattering - Pan, Jianjun; Heberle, Frederick A.; Tristram-Nagle, Stephanie; Szymanski, Michelle; Koepfinger, Mary; Katsaras, John; Kučerka, Norbert (Biochimica et Biophysica Acta (BBA) - Biomembranes, 2012)
We have determined the molecular structures of commonly used phosphatidylglycerols (PGs) in the commonly accepted biologically relevant fluid phase. This was done by simultaneously analyzing small angle neutron and X-ray scattering data, with the constraint of measured lipid volumes. We report the temperature dependence of bilayer parameters obtained using the one-dimensional scattering density profile model – which was derived from molecular dynamics simulations – including the area per lipid, the overall bilayer thickness, as well as other intrabilayer parameters (e.g., hydrocarbon thickness). Lipid areas are found to be larger than their phosphatidylcholine (PC) counterparts, a result likely due to repulsive electrostatic interactions taking place between the charged PG headgroups even in the presence of sodium counterions. In general, PG and PC bilayers show a similar response to changes in temperature and chain length, but differ in their response to chain unsaturation. For example, compared to PC bilayers, the inclusion of a first double bond in PG lipids results in a smaller incremental change to the area per lipid and bilayer thickness. However, the extrapolated lipid area of saturated PG lipids to infinite chain length is found to be similar to that of PCs, an indication of the glycerol–carbonyl backbone's pivotal role in influencing the lipid–water interface.
Keywords: lipid bilayer; bilayer structure; area per lipid; bilayer thickness; molecular dynamics simulations; fluid phase

Model-based approaches for the determination of lipid bilayer structure from small-angle neutron and X-ray scattering data - Heberle, Frederick A.; Pan, Jianjun; Standaert, Robert F.; Drazba, Paul; Kučerka, Norbert; Katsaras, John (European Biophysics Journal, 2012)
Some of our recent work has resulted in the detailed structures of fully hydrated, fluid phase phosphatidylcholine (PC) and phosphatidylglycerol (PG) bilayers. These structures were obtained from the joint refinement of small-angle neutron and X-ray data using the scattering density profile (SDP) models developed by Kučerka et al. (Biophys J 95:2356–2367, 2008; J Phys Chem B 116:232–239, 2012). In this review, we first discuss models for the standalone analysis of neutron or X-ray scattering data from bilayers, and assess the strengths and weaknesses inherent to these models. In particular, it is recognized that standalone data do not contain enough information to fully resolve the structure of naturally disordered fluid bilayers, and therefore may not provide a robust determination of bilayer structure parameters, including the much-sought-after area per lipid. We then discuss the development of matter density-based models (including the SDP model) that allow for the joint refinement of different contrast neutron and X-ray data, as well as the implementation of local volume conservation within the unit cell (i.e., ideal packing). Such models provide natural definitions of bilayer thicknesses (most importantly the hydrophobic and Luzzati thicknesses) in terms of Gibbs dividing surfaces, and thus allow for the robust determination of lipid areas through equivalent slab relationships between bilayer thickness and lipid volume. In the final section of this review, we discuss some of the significant findings/features pertaining to structures of PC and PG bilayers as determined from SDP model analyses.
Keywords: lipid bilayer; bilayer structure; area per lipid; bilayer thickness; molecular dynamics simulations; fluid phase

Interactions between ether phospholipids and cholesterol as determined by scattering and molecular dynamics simulations - Pan, Jianjun; Cheng, Xiaolin; Heberle, Frederick A.; Mostofian, Barmak; Kučerka, Norbert; Drazba, Paul; Katsaras, John (The Journal of Physical Chemistry B, 2012)
Cholesterol and ether lipids are ubiquitous in mammalian cell membranes, and their interactions are crucial in ether lipid mediated cholesterol trafficking. We report on cholesterol’s molecular interactions with ether lipids as determined using a combination of small-angle neutron and X-ray scattering, and all-atom molecular dynamics (MD) simulations. A scattering density profile model for an ether lipid bilayer was developed using MD simulations, which was then used to simultaneously fit the different experimental scattering data. From analysis of the data the various bilayer structural parameters were obtained. Surface area constrained MD simulations were also performed to reproduce the experimental data. This iterative analysis approach resulted in good agreement between the experimental and simulated form factors. The molecular interactions taking place between cholesterol and ether lipids were then determined from the validated MD simulations. We found that in ether membranes cholesterol primarily hydrogen bonds with the lipid headgroup phosphate oxygen, while in their ester membrane counterparts cholesterol hydrogen bonds with the backbone ester carbonyls. This different mode of interaction between ether lipids and cholesterol induces cholesterol to reside closer to the bilayer surface, dehydrating the headgroup’s phosphate moiety. Moreover, the three-dimensional lipid chain spatial density distribution around cholesterol indicates anisotropic chain packing, causing cholesterol to tilt. These insights lend a better understanding of ether lipid-mediated cholesterol trafficking and the roles that the different lipid species have in determining the structural and dynamical properties of membrane associated biomolecules.

Growth kinetics of lipid-based nanodiscs to unilamellar vesicles—A time-resolved small angle neutron scattering (SANS) study - Mahabir, Suanne; Small, Darcy; Li, Ming; Wan, Wankei; Kučerka, Norbert; Littrell, Kenneth; Katsaras, John; Nieh, Mu-Ping (Biochimica et Biophysica Acta (BBA) - Biomembranes, 2012)
Mixtures of dimyristoyl-phosphatidylcholine (DMPC), dimyristoyl-phosphatidylglycerol (DMPG) and dihexanoylphosphatidylcholine (DHPC) in aqueous solutions spontaneously form monodisperse, bilayered nanodiscs (also known as “bicelles”) at or below the melting transition temperature of DMPC (TM ~23 °C). In dilute systems above the main transition temperature TM of DMPC, bicelles coalesce (increasing their diameter) and eventually self-fold into unilamellar vesicles (ULVs). Time-resolved small angle neutron scattering was used to study the growth kinetics of nanodiscs below and equal to TM over a period of hours as a function of temperature at two lipid concentrations in presence or absence of NaCl salt. Bicelles seem to undergo a sudden initial growth phase with increased temperature, which is then followed by a slower reaction-limited growth phase that depends on ionic strength, lipid concentration and temperature. The bicelle interaction energy was derived from the colloidal theory of Derjaguin and Landau, and Verwey and Overbeek (DLVO). While the calculated total energy between discs is attractive and proportional to their growth rate, a more detailed mechanism is proposed to describe the mechanism of disc coalescence. After annealing at low temperature (low-T), samples were heated to 50 °C in order to promote the formation of ULVs. Although the low-T annealing of samples has only a marginal effect on the mean size of end-state ULVs, it does affect their polydispersity, which increases with increased T, presumably driven by the entropy of the system.
Keywords: nanodisc; low temperature annealing; unilamellar vesicle; spontaneous formation; self-assemble; reaction limited coalescence

Measurement of the residual stress tensor in a compact tension weld specimen - Traore, Y.; Paddea, S.; Bouchard, P. J.; Gharghouri, M. A. (Experimental Mechanics, 2012)
Neutron diffraction measurements have been performed to determine the full residual stress tensor along the expected crack path in an austenitic stainless steel (Esshete 1250) compact tension weld specimen. A destructive slitting method was then implemented on the same specimen to measure the stress intensity factor profile associated with the residual stress field as a function of crack length. Finally deformations of the cut surfaces were measured to determine a contour map of the residual stresses in the specimen prior to the cut. The distributions of transverse residual stress measured by the three techniques are in close agreement. A peak tensile stress in excess of 600 MPa was found to be associated with an electron beam weld used to attach an extension piece to the test sample, which had been extracted from a pipe manual metal arc butt weld. The neutron diffraction measurements show that exceptionally high residual stress triaxiality is present at crack depths likely to be used for creep crack growth testing and where a peak stress intensity factor of 35 MPa√m was measured (crack depth of 21 mm). The neutron diffraction measurements identified maximum values of shear stress in the order of 50 MPa and showed that the principal stress directions were aligned to within ~20° of the specimen orthogonal axes. Furthermore it was confirmed that measurement of strains by neutron diffraction in just the three specimen orthogonal directions would have been sufficient to provide a reasonably accurate characterisation of the stress state in welded CT specimens.
Keywords: full stress tensor; neutron diffraction; slitting; contour method; finite element method

Orientation dependence of stress distributions in polycrystals deforming elastoplastically under biaxial loadings - Marin, T.; Dawson, P. R.; Gharghouri, M. A. (Journal of the Mechanics and Physics of Solids, 2012)
The influence of biaxiality of the loading on the crystallographic orientation dependence of crystal stress distributions is examined for polycrystalline solids deformed well into the elastoplastic regime. The examination is couched in terms of two decompositions of the stress. The first is a split of the tensor into its hydrostatic and deviatoric components; the second is a spectral decomposition of the deviatoric stress from which we express the relative values of the principal components as a function of the biaxiality of the stress. Using the framework provided by these decompositions, we investigate trends observed in the lattice strains in polycrystals subjected to biaxial loadings, comparing strains measured by neutron diffraction with finite element simulations. We conclude by showing how the orientation dependence of the stress distributions is influenced by the load biaxiality and by connecting features of the distributions to the elastic and plastic properties of the crystals. Implications of the results are discussed relative to the modeling of strain hardening and defect initiation.
Keywords: polycrystal plasticity; biaxial loading; neutron diffraction; finite element modeling; austenitic stainless steels

Neutron diffraction study on residual stress in aluminum engine blocks following machining and service testing - Lombardy, Anthony; Sediako, Dimitry; D'Elia, Francesco; Ravindran, C.; Mackay, Robert I. (SAE International Journal of Materials and Manufacturing, 2012)
Development of lightweight alloys suitable for automobile applications has been of great importance to the automotive industry in recent years. The use of 319 type aluminum alloy in the production of gasoline engine blocks is an example of this shift towards light alloys for large automobile components. However, excessive residual stress along the cylinder bores of these engine blocks may cause problems during engine operation. Therefore, in this study, neutron diffraction was used to evaluate residual stresses along the aluminum cylinder bridge and the gray cast iron liners. The strains were measured in the hoop, radial, and axial orientations, while stresses were subsequently calculated using generalized Hooke's law. The results suggest that the residual stress magnitude for the aluminum cylinder bridge was tensile for all three measured components and gradually increased with cylinder depth towards the bottom of the cylinder. The residual stress in the gray cast iron liner was highly compressive with a relatively constant stress magnitude.

Interplay between residual stresses, microstructure, process variables and engine block casting integrity - Lombardi, Anthony; D’Elia, Francesco; Ravindran, Comondore; Sediako, Dimitry; Murty, B. S.; MacKay, Robert (Metallurgical and Materials Transactions A, 2012)
The replacement of nodular cast iron with 319 type aluminum (Al) alloys in gasoline engine blocks is an example of the shift towards the use of lighter alloys in the automotive industry. However, excessive residual stress along the cylinder bore may lead to bore distortion, significantly reducing engine operating efficiency. In the current study, microstructure, mechanical properties and residual stress were characterized along the cylinder bridge of engine blocks following thermal sand reclamation (TSR), T7 heat treatment, and service testing of the casting. Neutron diffraction was effectively used to quantify the residual stress along both the Al cylinder bridge and the adjacent gray cast iron cylinder liners in the hoop, radial, and axial orientations with respect to the cylinder axis. The results suggest that an increase in cooling rate along the cylinder caused a significant refinement in microstructure at the bottom of the cylinder. In turn, this suggested an increase in alloy strength at the bottom of the cylinder relative to the top. This increased strength at the bottom of the cylinder likely reduced the susceptibility of the cylinder to rapid relief of residual stress at elevated temperature. In contrast, the coarse microstructure at the top of the cylinder likely triggered stress relief at an elevated temperature.

Patterson analysis for layer profile determination by neutron or X-ray reflectometry - Tun, Zin (Journal of Applied Crystallography, 2012)
The possibility of using Patterson analysis to interpret neutron or X-ray reflectometry data has been critically examined in terms of a hypothetical case study. The technique yields a highly accurate layer profile model provided the data are measured with a beam geometry that gives rise to unit reflectivity at Q = 0 only, i.e. Qc = 0. For those cases where a plateau of unit reflectivity extends out to finite Q, i.e. Qc > 0, a distorted model is obtained. A strategy to significantly improve this initial estimate of the model is proposed and demonstrated.
Keywords: neutron reflectometry; X-ray reflectometry; layer profile determination; Patterson analysis

Quantum oscillations of nitrogen atoms in uranium nitride - Aczel, A. A.; Granroth, G. E.; MacDougall, G. J.; Buyers, W. J. L.; Abernathy, D. L.; Samolyuk, G. D.; Stocks, G. M.; Nagler, S. E. (Nature Communications, 2012)
The vibrational excitations of crystalline solids corresponding to acoustic or optic one-phonon modes appear as sharp features in measurements such as neutron spectroscopy. In contrast, many-phonon excitations generally produce a complicated, weak and featureless response. Here we present time-of-flight neutron scattering measurements for the binary solid uranium nitride, showing well-defined, equally spaced, high-energy vibrational modes in addition to the usual phonons. The spectrum is that of a single atom, isotropic quantum harmonic oscillator and characterizes independent motions of light nitrogen atoms, each found in an octahedral cage of heavy uranium atoms. This is an unexpected and beautiful experimental realization of one of the fundamental, exactly solvable problems in quantum mechanics. There are also practical implications, as the oscillator modes must be accounted for in the design of generation IV nuclear reactors that plan to use uranium nitride as a fuel.

Evidence for anisotropic polar nanoregions in relaxor Pb(Mg1/3Nb2/3)O3 : a neutron study of the elastic constants and anomalous TA phonon damping in PMN - Stock, C.; Gehring, P. M.; Hiraka, H.; Swainson, I.; Xu, Guangyong; Ye, Z.-G.; Luo, H.; Li, J.-F.; Viehland, D. (Physical Review B, 2012)

Characterization of a liquid scintillator based on linear alkyl benzene for neutron detection - Bentoumi, G.; Dai, X.; Fritzsche, H.; Jonkmans, G.; Li, L.; Marleau, G.; Sur, B. (Nuclear Instruments and Methods in Physics Research A : Accelerators, Spectrometers, Detectors and Associated Equipment, 2012)
A liquid scintillator (LS) based on linear alkyl benzene (LAB) solvent has been characterized using multiple radiation sources. The results confirm that boron-loaded LAB is suitable for neutron detection in a gamma ray environment. To study indirectly the LAB pulse shape discrimination (PSD) capability between neutrons and gamma rays, a dissolved 212Pb source emitting alpha and beta particles was used to emulate the conditions in a mixed radiation field for detecting neutrons in the presence of a high gamma ray background. The quenching factor depends on the alpha energy and increases from 10 to 25 as the alpha energy decreases from 10 to 1 MeV. 10B loaded LAB-based LS has been tested in a neutron beam of energy which is equal to 14.56 meV. The observed peak at 60 keVee is attributed to the absorption of neutrons. Our results show that a boron-loaded LAB-based scintillator is a sensitive medium for neutron detection in a relatively large background of gamma rays. A neutron detector could be achieved with a figure of merit (FOM) of 1.75.
Keywords: scintillation; boron; linear alkyl benzene; neutron; pulse shape discrimination (PSD)

Magnetic order and fluctuations in the presence of quenched disorder in the kagome staircase system (Co1−xMgx)3V2O8 - Fritsch, K.; Yamani, Z.; Chang, S.; Qiu, Y.; Copley, J. R. D.; Ramazanoglu, M.; Dabkowska, H. A.; Gaulin, B. D. (Physical Review B, 2012)
Co3V2O8 is an orthorhombic magnet in which S=3/2 magnetic moments reside on two crystallographically inequivalent Co2+ sites, which decorate a stacked, buckled version of the two-dimensional kagome lattice, the stacked kagome staircase. The magnetic interactions between the Co2+ moments in this structure lead to a complex magnetic phase diagram at low temperature, wherein it exhibits a series of five transitions below 11 K that ultimately culminate in a ferromagnetic ground state below T∼6.2 K. Here we report magnetization measurements on single- and polycrystalline samples of (Co1−xMgx)3V2O8 for x<0.23, as well as elastic and inelastic neutron scattering measurements on single crystals of magnetically dilute (Co1−xMgx)3V2O8 for x=0.029 and x=0.194, in which nonmagnetic Mg2+ ions substitute for magnetic Co2+. We find that a dilution of 2.9% leads to a suppression of the ferromagnetic transition temperature by ∼15% while a dilution level of 19.4% is sufficient to destroy ferromagnetic long-range order in this material down to a temperature of at least 1.5 K. The magnetic excitation spectrum is characterized by two spin wave branches in the ordered phase for (Co1−xMgx)3V2O8 (x=0.029), similar to that of the pure x=0 material, and by broad diffuse scattering at temperatures below 10 K in (Co1−xMgx)3V2O8 (x=0.194). Such a strong dependence of the transition temperatures on long-range order in the presence of quenched nonmagnetic impurities is consistent with two-dimensional physics driving the transitions. We further provide a simple percolation model that semiquantitatively explains the inability of this system to establish long-range magnetic order at the unusually low dilution levels which we observe in our experiments.

Neutron scattering studies of spin excitations in superconducting Rb0.82Fe1.68Se2 - Wang, Miaoyin; Li, Chunhong; Abernathy, D. L.; Song, Yu; Carr, Scott V.; Lu, Xingye; Li, Shiliang; Yamani, Zahra; Hu, Jiangping; Xiang, Tao; Dai, Pengcheng (Physical Review B, 2012)
We use inelastic neutron scattering to show that superconducting (SC) rubidium iron selenide Rb0.82Fe1.68Se2 exhibits antiferromagnetic (AF) spin excitations near the in-plane wave vector Q = (π,0) identical to that for iron arsenide superconductors. Moreover, we find that these excitations change from incommensurate to commensurate with increasing energy and occur √ at the expense of spin waves associated with the coexisting 5 ×√5 block AF phase. Since these spin excitations cannot come from Fermi surface nesting based on angle resolved photoemission experiments, our results indicate the presence of local moments in SC Rb0.82Fe1.68Se2 that may have a similar origin as the hourglass-like spin excitations in copper oxide superconductors.

Electron doping evolution of the anisotropic spin excitations in BaFe2−xNixAs2 - Luo, Huiqian; Yamani, Zahra; Chen, Yanchao; Lu, Xingye; Wang, Meng; Li, Shiliang; Maier, Thomas A.; Danilkin, Sergey; Adroja, D. T.; Dai, Pengcheng (Physical Review B, 2012)

Spin ordering and electronic texture in the bilayer iridate Sr3Ir2O7 - Dhital, Chetan; Khadka, Sovit; Yamani, Z.; de la Cruz, Clarina; Hogan, T. C.; Disseler, S. M.; Pokharel, Mani; Lukas, K. C.; Tian, Wei; Opeil, C. P.; Wang, Ziqiang; Wilson, Stephen D. (Physical Review B, 2012)
Through a neutron scattering, charge transport, and magnetization study, the correlated ground state in the bilayer iridium oxide Sr3Ir2O7 is explored. Our combined results resolve scattering consistent with a high temperature magnetic phase that persists above 600 K, reorients at the previously defined TAF = 280 K, and coexists with an electronic ground state whose phase behavior suggests the formation of a fluctuating charge or orbital phase that freezes below T ∗ ≈ 70 K. Our study provides a window into the emergence of multiple electronic order parameters near the boundary of the metal to insulator phase transition of the 5d Jeff = 1/2Mott phase.

Neutron scattering study of URu2−xRexSi2 (x=0.10) : driving order towards quantum criticality - Williams, T. J.; Yamani, Z.; Butch, N. P.; Luke, G. M.; Maple, M. B.; Buyers, W. J. L. (Physical Review B, 2012)
We report inelastic neutron scattering measurements in the hidden order state of URu2−xRexSi2 with x = 0.10. We observe that towards the ferromagnetic quantum critical point induced by the negative chemical pressure of Re doping, the gapped incommensurate fluctuations are robust and comparable in intensity to the parent material. As the Re doping moves the system toward the quantum critical point, the commensurate spin fluctuations related to hidden order weaken, display a shortened lifetime, and slow down. Halfway to the quantum critical point, the hidden order phase survives, albeit weakened, in contrast to its destruction by hydrostatic pressure and by positive chemical pressure from Rh doping.

From once upon a time to happily ever after : tracking emotions in mail and books - Mohammad, Saif M. (Decision Support Systems, 2012)
In this paper, we show how sentiment analysis can be used in tandem with effective visualizations to quantify and track emotions in mail and books. We study a number of specific datasets and show, among other things, how collections of texts can be organized for affect-based search and how books portray different entities through co-occurring emotion words. Analysis of the Enron Email Corpus reveals that there are marked differences across genders in how they use emotion words in work-place email. Finally, we show that fairy tales have more extreme emotion densities than novels.
Keywords: emotion analysis; sentiment analysis; Lexicon; email; fairy tales; Enron Corpus; Google Books Corpus

Staying socially connected with online video communication : a case study - Molyneaux, Heather; O'Donnell, Susan; Milliken, Mary (Canadian Journal of Communication, 2012)
Video communication conducted online — online videos, video calls, and videoconferencing — is quickly becoming a fixture in the everyday lives of many Canadians. We conducted a case study of residents of a small Canadian city, exploring their use of video communication to maintain social relationships. Our study indicates high levels of acceptance for communicating using video with others at a geographical distance, especially where there is a cost savings, a close personal relationship between participants, and a need to “show” objects or expressions. Concern about privacy restrains more frequent use. The discussion considers these findings in the context of public sphere theory and the potential for online video communications to be a special kind of place for people to meet and socialize with others.
Keywords: electronic culture (internet based); video; visual communication

Data and knowledge visualization with virtual reality spaces, neural networks and rough sets : application to cancer and geophysical prospecting data - Valdés, Julio J.; Romero, Enrique; Barton, Alan J. (Expert Systems with Applications, 2012)
Visual data mining with virtual reality spaces is used for the representation of data and symbolic knowledge. High quality structure-preserving and maximally discriminative visual representations can be obtained using a combination of neural networks (SAMANN and NDA) and rough sets techniques, so that a proper subsequent analysis can be made. The approach is illustrated with two types of data: for gene expression cancer data, an improvement in classification performance with respect to the original spaces was obtained; for geophysical prospecting data for cave detection, a cavity was successfully predicted.
Keywords: data and knowledge visualization; visual data mining; virtual reality; data projection; neural networks; rough sets

PORT : a precision-order-recall MT evaluation metric for tuning - Chen, Boxing; Kuhn, Roland; Larkin, Samuel (Proceedings of the 50th Annual Meeting of the Association for Computational Linguistics (ACL 2012), 2012)
Many machine translation (MT) evaluation metrics have been shown to correlate better with human judgment than BLEU. In principle, tuning on these metrics should yield better systems than tuning on BLEU. However, due to issues such as speed, requirements for linguistic resources, and optimization difficulty, they have not been widely adopted for tuning. This paper presents PORT1 , a new MT evaluation metric which combines precision, recall and an ordering metric and which is primarily designed for tuning MT systems. PORT does not require external resources and is quick to compute. It has a better correlation with human judgment than BLEU. We compare PORT-tuned MT systems to BLEU-tuned baselines in five experimental conditions involving four language pairs. PORT tuning achieves consistently better performance than BLEU tuning, according to four automated metrics (including BLEU) and to human evaluation: in comparisons of outputs from 300 source sentences, human judges preferred the PORT-tuned output 45.3% of the time (vs. 32.7% BLEU tuning preferences and 22.0% ties).

Signal displacement in spiral-in acquisitions : simulations and implications for imaging in SFG regions - Brewer, Kimberly D.; Rioux, James A.; Klassen, Martyn; Bowen, Chris V.; Beyea, Steven D. (Magnetic Resonance Imaging, 2012)
Susceptibility field gradients (SFGs) cause problems for functional magnetic resonance imaging (fMRI) in regions like the orbital frontal lobes, leading to signal loss and image artifacts (signal displacement and “pile-up”). Pulse sequences with spiral-in k-space trajectories are often used when acquiring fMRI in SFG regions such as inferior/medial temporal cortex because it is believed that they have improved signal recovery and decreased signal displacement properties. Previously postulated theories explain differing reasons why spiral-in appears to perform better than spiral-out; however it is clear that multiple mechanisms are occurring in parallel. This study explores differences in spiral-in and spiral-out images using human and phantom empirical data, as well as simulations consistent with the phantom model. Using image simulations, the displacement of signal was characterized using point spread functions (PSFs) and target maps, the latter of which are conceptually inverse PSFs describing which spatial locations contribute signal to a particular voxel. The magnitude of both PSFs and target maps was found to be identical for spiral-out and spiral-in acquisitions, with signal in target maps being displaced from distant regions in both cases. However, differences in the phase of the signal displacement patterns that consequently lead to changes in the intervoxel phase coherence were found to be a significant mechanism explaining differences between the spiral sequences. The results demonstrate that spiral-in trajectories do preserve more total signal in SFG regions than spiral-out; however, spiral-in does not in fact exhibit decreased signal displacement. Given that this signal can be displaced by significant distances, its recovery may not be preferable for all fMRI applications.
Keywords: Functional MRI; Susceptibility; Artifacts; Spiral

Functional MRI of the thoracic spinal cord during vibration sensation - Kornelsen, Jennifer; Smith, Stephen D.; McIver, Theresa A.; Sboto-Frankenstein, Uta; Latta, Peter; Tomanek, Boguslaw (Journal of Magnetic Resonance Imaging, 2012)
Purpose: To demonstrate that it is possible to acquire accurate functional magnetic resonance images from thoracic spinal cord neurons. Materials and Methods: The lower thoracic spinal dermatomes (T7–T11) on the right side of the body were mechanically stimulated by vibration for 15 participants. Neuronal responses to vibration sensation were measured in the thoracic spinal cord using a HASTE sequence on a 3 Tesla MRI system. Results: Signal increases were observed in the corresponding lower thoracic spinal cord segments ipsilateral to the side of stimulation in the dorsal aspect of the spinal cord. Conclusion: This is the ﬁrst study to provide proof of principle that functional imaging of the entire thoracic spinal cord is possible, by detecting neuronal activity in the thoracic spinal cord during sensory stimulation using spinal fMRI.
Keywords: spinal cord; cord; functional magnetic resonance imaging; thoracic; vibration; sensory

ALEX: a mobile speech and language learning assistant - Munteanu, Cosmin; Molyneaux, Heather; McDonald, Daniel; Leung, Rock (2012)
For a very large number of adults in developed countries, tasks such as reading, understanding, and using everyday items are a challenge. Many community-based organizations offer resources and support for adults with limited literacy skills; unfortunately, current programs have difficulty reaching and retaining those that would benefit most. To address these challenges, we have developed a mobile application to support literacy programs and to assist low-literacy adults in today's information-centric society. ALEX© (Adult Literacy support application for EXperiential learning) is a mobile speech and language assistant that is designed to be used both in the classroom and in daily life in order to help low-literacy adults become increasingly literate and independent.
Keywords: mobile computing; interface design; mobile learning; assistive technology; speech and language support

Fast on-line learning for multilingual categorization - Kovesi, Michelle; Goutte, Cyril; Amini, Massih-Reza (SIGIR '12: Proceedings of the 35th international ACM SIGIR conference on Research and development in information retrieval, 2012)
Multiview learning has been shown to be a natural and efficient framework for supervised or semi-supervised learning of multilingual document categorizers. The state-of-the-art co-regularization approach relies on alternate minimizations of a combination of language-specific categorization errors and a disagreement between the outputs of the monolingual text categorizers. This is typically solved by repeatedly training categorizers on each language with the appropriate regularizer. We extend and improve this approach by introducing an on-line learning scheme, where language-specific updates are interleaved in order to iteratively optimize the global cost in one pass. Our experimental results show that this produces similar performance as the batch approach, at a fraction of the computational cost.
Keywords: multilingual text categorisation; on-line learning

Active 3D imaging systems - Drouin, Marc-Antoine; Beraldin, Jean-Angelo (3D Imaging, Analysis and Applications, 2012)
Active 3D imaging systems use artificial illumination in order to capture and record digital representations of objects. The use of artificial illumination allows the acquisition of dense and accurate range images of textureless objects that are difficult to acquire using passive vision systems. An active 3D imaging system can be based on different measurement principles that include time-of-flight, triangulation and interferometry. While time-of-flight and interferometry systems are briefly discussed, an in-depth description of triangulation-based systems is provided. The characterization of triangulation-based systems is discussed using both an error propagation framework and experimental protocols.

3D anthropometric data processing - Shu, Chang; Wuhrer, Stefanie; Xi, Pengcheng (International Journal of Human Factors Modelling and Simulation, 2012)
3D anthropometric data obtained from 3D imaging technology provide unprecedented information about the human shape. At the same time, 3D data present tremendous challenges. New software tools and analytical methods have to be designed to realise the full potential of the 3D data. One prominent character of the 3D data is that they are a collection of coordinates in 3-space and do not have a natural order. This poses problems for performing statistical analysis. In order to make sense about this type of data, 3D points have to be registered such that meaningful correspondences across all the models can be established. Other issues include data completion, compression, and visualisation. In this paper, we describe a framework and the techniques involved in processing the 3D anthropometric data for the purpose of making them usable for designing products that fit the human shapes.
Keywords: statistical shape analysis; 3D anthropometry; geometry processing; human shape models; digital human models; digital human modelling; DHM; anthropometric data processing; product design; data completion; data compression; visualisation

Targeting the latest hallmark of cancer : another attempt at 'magic bullet' drugs targeting cancers' metabolic phenotype - Cuperlovic-Culf, M.; Culf, A. S.; Touaibia, M.; Lefort, N. (Future Oncology, 2012)
The metabolism of tumors is remarkably different from the metabolism of corresponding normal cells and tissues. Metabolic alterations are initiated by oncogenes and are required for malignant transformation, allowing cancer cells to resist some cell death signals while producing energy and fulfilling their biosynthetic needs with limiting resources. The distinct metabolic phenotype of cancers provides an interesting avenue for treatment, potentially with minimal side effects. As many cancers show similar metabolic characteristics, drugs targeting the cancer metabolic phenotype are, perhaps optimistically, expected to be 'magic bullet' treatments. Over the last few years there have been a number of potential drugs developed to specifically target cancer metabolism. Several of these drugs are currently in clinical and preclinical trials. This review outlines examples of drugs developed for different targets of significance to cancer metabolism, with a focus on small molecule leads, chemical biology and clinical results for these drugs.

GD & T-based characterization of short-range non-contact 3D imaging systems - MacKinnon, David; Carrier, Benjamin; Beraldin, Jean-Angelo; Cournoyer, Luc (International Journal of Computer Vision, 2012)
We present a series of test metrics, artifacts, and procedures for characterizing and verifying the operating limits of a short-range non-contact three-dimensional imaging system. These metrics have been designed to correspond to dimensioning and tolerancing metrics that are widely used in industry (e.g. automotive, aerospace, etc.). We introduce operating limit metrics that correspond with the geometric dimensioning and tolerancing (GD&T) metrics of Form (Flatness and Circularity), Orientation (Angularity), Location (Sphere, Corner, and Hole Position Errors), and Size (Diameter, Sphere-spacing, Plane-spacing and Angle Errors). An example is presented to illustrate how these metrics, artifacts, and associated test procedures can be used in practice.
Keywords: characterization; GD & T; 3D imaging systems; quality analysis; spatial metrology; 3D metrology

Fast 3D spine reconstruction of postoperative patients using a multilevel statistical model - Lecron, Fabian; Boisvert, Jonathan; Mahmoudi, Saïd; Labelle, Hubert; Benjelloun, Mohammed (Medical Image Computing and Computer-Assisted Intervention – MICCAI 2012 : 15th International Conference, Nice, France, October 1-5, 2012, Proceedings, Part II, 2012)
Severe cases of spinal deformities such as scoliosis are usually treated by a surgery where instrumentation (hooks, screws and rods) is installed to the spine to correct deformities. Even if the purpose is to obtain a normal spine curve, the result is often straighter than normal. In this paper, we propose a fast statistical reconstruction algorithm based on a general model which can deal with such instrumented spines. To this end, we present the concept of multilevel statistical model where the data are decomposed into a within-group and a between-group component. The reconstruction procedure is formulated as a second-order cone program which can be solved very fast (few tenths of a second). Reconstruction errors were evaluated on real patient data and results showed that multilevel modeling allows better 3D reconstruction than classical models.
Keywords: 3D reconstruction; spine; statistical shape model; multilevel modeling

Crossing the barrier : a scalable simulator for course of fire training - Fournier, H.; Lapointe, J.-F.; Kondratova, I.; Emond, B.; Munteanu, C. (Proceedings of Interservice/Industry Training, Simulation, and Education Conference (I/ITSEC) 2012, 2012)
The growing training and operational needs of law enforcement and public safety personnel can no longer be met efficiently and effectively through existing infrastructure and resources. While the demands of day-to-day operations are constantly changing, the training of law enforcement personnel and certification process has largely stayed the same. While several technological solutions exist for enhancing training, widespread adoption of current approaches and solutions, such as virtual training, is hindered by significant cost barriers and by lack of scalability and reach. This creates challenges for smaller geographically disconnected units, which characterizes most rural police departments in North America. This paper presents MINT-PD, a technological solution for multimodal virtual Course of Fire (COF) training, along with field observations and validation of the technology. One specific application of MINT-PD is to help to increase the rate of success among the trainees who failed a first COF certification round. Success in this context represents significant cost savings by reducing active-duty officers' down-time due to the remedial training and reducing the need for the use of the live firing range. MINT-PD is based on the Multimodal Interactive Trainer (MINT) simulation platform developed by NRC, specifically adapted to address user needs in training and certification for a typical municipal police department. MINT-PD technology allows users to modify training scenarios, incorporate different types of laser guns and a flashlight, add avatars, and expand the training to include Use of Force scenarios. The conditions and parameters implemented in the virtual COF simulator have been derived from field observations and validated by COF trainers within a medium-size police department. This process of technology development and validation will be described in the paper.

Tracking complete deformable objects with finite elements - Wuhrer, Stefanie; Lang, Jochen; Shu, Chang (3DIMPVT 2012 Conference Proceedings, 2012)
We present an approach to robustly track the geometry of an object that deforms over time from a set of input point clouds captured from a single viewpoint. The deformations we consider are caused by applying forces to known locations on the object’s surface. Our method combines the use of prior information on the geometry of the object modeled by a smooth template and the use of a linear finite element method to predict the deformation. This allows the accurate reconstruction of both the observed and the unobserved sides of the object. We present tracking results for noisy low-quality point clouds acquired by a stereo camera and a Kinect sensor, and simulations with point clouds corrupted by different error terms. We show that our method is also applicable to large non-linear deformations.

Towards an ontology for autonomous robots - Paull, Liam; Severac, Gaetan; Raffo, Guilherme V.; Angel, Julian Mauricio; Boley, Harold; Durst, Phillip J.; Gray, Wendell; Habib, Maki; Nguyen, Bao; Ragavan, S. Veera; Saeedi G., Sajad; Sanz, Ricardo; et al. (2012 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS), 2012)
The IEEE RAS Ontologies for Robotics and Automation Working Group is dedicated to developing a methodology for knowledge representation and reasoning in robotics and automation. As part of this working group, the Autonomous Robots sub-group is tasked with developing ontology modules for autonomous robots. This paper describes the work in progress on the development of ontologies for autonomous systems. For autonomous systems, the focus is on the cooperation, coordination, and communication of multiple unmanned aerial vehicles (UAVs), unmanned ground vehicles (UGVs), and autonomous underwater vehicles (AUVs). The ontologies serve as a framework for working out concepts of employment with multiple vehicles for a variety of operational scenarios with emphasis on collaborative and cooperative missions.

Model fusion-based batch learning with application to oil spills detection - Yang, Chunsheng; Yang, Yubin; Liu, Jie (Advanced Research in Applied Artificial Intelligence, 2012)
Data split into batches is very common in real-world applications. In speech recognition and handwriting identification, the batches are different people. In areas like oil spill detection and train wheel failure prediction, the batches are the particular circumstances when the readings were recorded. The recent research has proved that it is important to respect the batch structure when learning models for batched data. We believe that such a batch structure is also an opportunity that can be exploited in the learning process. In this paper, we investigated the novel method for dealing with the batched data. We applied the developed batch learning techniques to detect oil spills using radar images collected from satellite stations. This paper reports some progress on the proposed batch learning method and the preliminary results obtained from oil spills detection.
Keywords: Batch Data; Batch Learning; Transfer Learning; Content-based Learning; Model Fusion; Oil Spill Detection

A phonon scattering assisted injection and extraction based terahertz quantum cascade laser - Dupont, E.; Fathololoumi, S.; Wasilewski, Z. R.; Aers, G.; Laframboise, S. R.; Lindskog, M.; Razavipour, S. G.; Wacker, A.; Ban, D.; Liu, H. C. (Journal of Applied Physics, 2012)
A lasing scheme for terahertz quantum cascade lasers, based on consecutive phonon-photon-phonon emissions per module, is proposed and experimentally demonstrated. The charge transport of the proposed structure is modeled using a rate equation formalism. An optimization code based on a genetic algorithm was developed to find a four-well design in the GaAs/Al0.25Ga0.75As material system that maximizes the product of population inversion and oscillator strength at 150 K. The fabricated devices using Au double-metal waveguides show lasing at 3.2 THz up to 138 K. The electrical characteristics display no sign of differential resistance drop at lasing threshold, which, in conjunction with the low optical power of the device, suggest—thanks to the rate equation model—a slow depopulation rate of the lower lasing state, a hypothesis confirmed by non-equilibrium Green’s function calculations.

Learning with aggregation and correlation in the presence of large fluctuations - Paquet, Eric; Viktor, Herna L.; Guo, Hongyu (Proceedings of New Frontiers in Mining Complex Patterns (NFMCP 2012), 2012)
Consider a scenario where one aims to learn models from dynamic and evolving data being characterized by very large fluctuations that are neither attributable to noise nor outliers. This may be the case, for instance, when predicting the potential future damages of earthquakes or oil spills, or when conducting financial data analysis. If follows that, in such a situation, the standard central limit theorem does not apply, since the associated Gaussian distribution exponentially suppresses large fluctuations. In this paper, we present an analysis of data aggregation and correlation in such scenarios. To this end, we introduce the Lévy, or stable, distribution which is a generalization of the Gaussian distribution. Our theoretical conclusions are illustrated with various simulations, as well as against a benchmarking financial database. We show which specific strategies should be adopted for aggregation, depending on the stability exponent of the Lévy distribution. Our results firstly show scenarios where it may be impossible to determine the mean and the standard deviation of an aggregate. Secondly, we discuss the case where an aggregate may have to be characterized with its largest fluctuations. Thirdly, we illustrate that the correlation in between two attributes may be underestimated if a Gaussian distribution is erroneously assumed.
Keywords: aggregation in relational learning; correlation-based analysis and covariance; lévy distribution; stable distribution

Conditional significance pruning : discarding more of huge phrase tables - Johnson, J. Howard (2012)
The technique of pruning phrase tables that are used for statistical machine translation (SMT) can achieve substantial reductions in bulk and improve translation quality, especially for very large corpora such at the Giga- FrEn. This can be further improved by conditioning each significance test on other phrase pair co-occurrence counts resulting in an additional reduction in size and increase in BLEU score. A series of experiments using Moses and the WMT11 corpora for French to English have been performed to quantify the improvement. By adhering strictly to the recommendations for the WMT11 baseline system, a strong reproducible research baseline was employed.

Thermal performance of wall assemblies with low emissivity - Saber, Hamed H. (Journal of Building Physics, 2012)
In wall systems, airspaces can increase thermal resistance if a reflective material such as foil with low emissivity is installed in a Furred-Airspace Assembly (FAA). In this paper, the present model, hygIRC-C, was used to investigate the steady-state thermal resistance of wall assemblies that incorporate foil adhered to expanded polystyrene (EPS) foam in a furred-assembly. To investigate the effect of the furring orientation, the furring was installed horizontally and vertically and compared to walls with no furring. For wall with vertical furring, the 3D version of the present model was used to capture the 3D effect of the thermal bridges. Because the foil emissivity can be affected by dust accumulation and/or water vapor condensation on the foil surface, consideration was given to investigate the effect of both varying foil emissivity and outdoor temperature on the thermal performance of the various wall specimens. Results showed that the thermal resistance (R-value) of the reference wall (no furring) is greater than the wall specimens with furring. Also, results showed that the contribution of the FAA to the R-value of wall specimen with vertical furring is higher than that for wall specimen with horizontal furring.
Keywords: Reflective insulation; furred-airspace assembly; low emissivity material; thermal modelling; thermal resistance test method; R-value; heat flow meter; ASTM C-518; ASTM C-1363; airflow; heat transfer by convection; conduction and radiation

Numerical modeling and experimental investigations of thermal performance of reflective insulations - Saber, Hamed H.; Maref, Wahid; Sherrer, Gordon; Swinton, Michael C. (Journal of Building Physics, 2012)
Reflective insulations are being used in attics, flat roof, and wall systems. Numerical modeling and experimental investigations were conducted to assess the thermal performance of assemblies with reflective insulations. In this article, the present model was used to verify the use of the ASTM C-518 test method for measuring the effective thermal resistances (R-values) of sample stacks comprising reflective insulations. Two tests were conducted on sample stacks using heat flow meter apparatus. The sample stack consists of two expanded polystyrene layers and a reflective insulation installed in between. The model predictions agreed with the measured heat fluxes within ±1%. The article also discusses the combined effect of heat transfer by convection and radiation in the airspace facing the reflective insulation, showing that the derived R-value from the test data resulted in underestimation of the effective R-value of the sample stack
Keywords: Reflective insulation; furred-airspace assembly; low emissivity material; thermal modelling; thermal resistance test method; R-value; heat flow meter; ASTM C-518; ASTM C-1363; airflow; heat transfer by convection; conduction and radiation

A new testing capability for seismic resistance assessment of structures damaged due to a fire - Mostafaei, Hossein (The 15th World Conference on Earthquake Engineering (WCEE) Proceedings, 2012)
This paper provides results of a hybrid structural test that simulates residual lateral load resistance of a structure after fire damage. The simulation was carried out at the National Research Council of Canada (NRC) using the NRC’s furnace facilities. The hybrid test included two substructures; a structural element/assembly specimen, here a column specimen, and a model component, here the remaining of the structure. Using this method, first, fire damage was imposed to a structure, a 6-storey reinforced concrete building, and six days later, after the entire structure had cooled down to the ambient temperature, the building was subjected to a lateral load, which was determined based on a design seismic load. The test results showed a reduction of both residual lateral stiffness and residual lateral load capacity of the structure after the fire damage. This paper will present the hybrid test, its application and the results for the 6-storey building.
Keywords: Fire damage; seismic resistance; reinforced concrete; column; hybrid test; fire resistance; performance-based evaluation

Effect of furring orientation on thermal response of wall systems with low emissivity material and furred-airspace - Saber, Hamed H.; Maref, Wahid (BEST 3 2012: The Building Enclosure Science and Technoloogy Conference Proceedings, 2012)
In wall systems, airspaces can contribute in obtaining a higher thermal resistance, if a reflective material such as foil with low emissivity is installed on one side or the other of a Furred-Airspace Assembly. In this paper, the present model, hygIRC-C, was used to investigate the steady-state thermal performance of wall specimens that incorporate foil bonded to expanded polystyrene (EPS) foam in a furred-assembly having airspace next to the foil. In order to investigate the effect of the furring orientation on the wall thermal performance, the furring was installed horizontally and/or vertically. Also, a reference wall similar to these walls but with no furring was considered. For the reference wall and wall with horizontal furring, the 2D version of the present model is suitable to model these wall assemblies. However, for wall with vertical furring, the 3D version of the present model was used in order to capture the 3D effect of the thermal bridges due to the vertical furring on the energy transport and momentum transport in the wall system. Consideration was given to investigate the effect the foil emissivity and outdoor temperature on the contribution of the FAA on the thermal performance of the wall systems. Results showed that the thermal resistance (R-value) of the reference wall (no furring) is greater than the wall systems with furring. Also, results showed that the contribution of the FAA to the R-value of wall system with vertical furring is higher than that for wall system with horizontal furring.
Keywords: Reflective insulation; Furred-Airspace Assembly (FAA); low emissivity material; thermal modelling; thermal resistance; R-value; airflow; heat transfer by convection; conduction and radiation

The effect of window-wall interface details on window condensation potential - Maref, W.; Van Den Bossche, N.; Armstrong, M.; Lacasse, M. A.; Elmahdy, H.; Glazer, R. (BEST 3 2012: Building Enclosure Science and Technology Conference Proceedings, 2012)
Considering all building components, windows typically have the lowest surface temperature, and will consequently be the primary location for interior surface condensation. Those surface temperatures can easily be calculated using thermal finite-element-models (FEM), and there is an ISO standard with guidelines for condensation risk assessment. However, both the FEM-simulations as the ISO standard generally omit the effect of air flows in and around window frames. When cold air is drawn into the construction, the airflow might cool down specific components of the window-wall interface depending on the location of the airflow path. Consequently, the current evaluation method for condensation risk assessment based on FEM-simulations might underestimate the actual risk. There is a need to determine if interface details become more susceptible for surface condensation due to pressure differences over the component. This paper reports on a laboratory evaluation of condensation risk assessment in a hotbox, with varying pressure differences and the introduction of deficiencies. It was concluded that the effect of the type of insulation in the window-wall interface was very low for isobaric boundary conditions, whereas it has a significant effect when pressure differences are applied. A full paper on this topic has been accepted for publication by the Journal of Building Physics.
Keywords: Laboratory test; condensation; window-wall interface; box-window

Reducing the size of databases for multirelational classification : a subgraph-based approach - Guo, Hongyu; Viktor, Herna L.; Paquet, Eric (Journal of Intelligent Information Systems, 2012)
Multirelational classification aims to discover patterns across multiple interlinked tables (relations) in a relational database. In many large organizations, such a database often spans numerous departments and/or subdivisions, which are involved in different aspects of the enterprise such as customer profiling, fraud detection, inventory management, financial management, and so on. When considering classification, different phases of the knowledge discovery process are affected by economic utility. For instance, in the data preprocessing process, one must consider the cost associated with acquiring, cleaning, and transforming large volumes of data. When training and testing the data mining models, one has to consider the impact of the data size on the running time of the learning algorithm. In order to address these utility-based issues, the paper presents an approach to create a pruned database for multirelational classification, while minimizing predictive performance loss on the final model. Our method identifies a set of strongly uncorrelated subgraphs from the original database schema, to use for training, and discards all others. The experiments performed show that our strategy is able to, without sacrificing predictive accuracy, significantly reduce the size of the databases, in terms of the number of relations, tuples, and attributes.The approach prunes the sizes of databases by as much as 94 %. Such reduction also results in decreasing computational cost of the learning process. The method improves the multirelational learning algorithms’ execution time by as much as 80 %. In particular, our results demonstrate that one may build an accurate model with only a small subset of the provided database.
Keywords: multi-relational classification; relational data mining

Fundamentals of Neurosurgery : virtual reality tasks for training and evaluation of technical skills - Choudhury, Nusrat; Gélinas-Phaneuf, Nicholas; Delorme, Sébastien; Del Maestro, Rolando (World Neurosurgery, 2012)
Background: Technical skills training in neurosurgery is mostly done in the operating room. New educational paradigms are encouraging the development of novel training methods for surgical skills. Simulation could answer some of these needs. This paper presents the development of a conceptual training framework for use on a virtual reality (VR) neurosurgical simulator. Methods: Appropriate tasks were identified by reviewing neurosurgical oncology curricula requirements and performing cognitive task analyses of basic techniques and representative surgeries. The tasks were then elaborated into training modules by including learning objectives, instructions, levels of difficulty and performance metrics. Surveys and interviews were iteratively conducted with subject matter experts (SMEs) to delimitate, review, discuss and approve each of the development stages. Results: Five tasks were selected as representative of basic and advanced neurosurgical skill. These tasks were: 1) ventriculostomy, 2) endoscopic nasal navigation, 3) tumour debulking, 4) hemostasis and 5) microdissection. The complete training modules were structured into easy, intermediate and advanced settings. Performance metrics were also integrated to provide feedback on outcome, efficiency and errors. The SMEs deemed the proposed modules as pertinent and useful for neurosurgical skills training. Conclusion: The conceptual framework presented here, the Fundamentals of Neurosurgery (FNS), represents a first attempt to develop standardized training modules for technical skills acquisition in neurosurgical oncology. The National Research Council Canada is currently developing NeuroTouch, a VR simulator for cranial microneurosurgery. The simulator presently includes the five FNS modules at varying stages of completion. A first pilot study has shown that neurosurgical residents obtained higher performance scores on the simulator than medical students. Further work will validate its components and use in a training curriculum.
Keywords: neurosurgery; clinical skills; computer simulation; training; virtual systems

Comparison of NRC goniometric and integrating sphere methods for realizing an absolute diffuse reflectance scale - Baribeau, Réjean; Zwinkels, Joanne (Reflection, Scattering, and Diffraction from Surfaces III, 2012)
At the National Research Council of Canada (NRC), the scale of diffuse spectral reflectance in the UV and visible range is realized using an integrating sphere method known as the Modified Sharp-Little method and has been wellcharacterized and validated. More recently, a gonioreflectometer has been designed to capture the bidirectional reflectance of reflecting objects. This system incorporates a diode-array spectroradiometer and is prone to non-linearity errors. In this paper the magnitude of this non-linearity error is evaluated using several diffusely reflecting materials by comparing the angular-integrated reflection indicatrix measured with the gonioreflectometer with results obtained using a transfer spectrophotometer that is traceable to the sphere-based NRC Absolute Reflectometer.
Keywords: diffuse reflectance; BRDF; goniometric method; sphere method; uncertainty

Apple peel flavonoid- and triterpene-enriched extracts differentially affect cholesterol homeostasis in hamsters - Thilakarathna, Surangi H.; Wang, Yanwen; Rupasinghe, H. P. Vasantha; Ghanam, Khadija (Journal of Functional Foods, 2012)
Flavonoids and triterpenes are two major groups of bioactive compounds in apple peels. This study determined whether flavonoid-rich (FAE) and triterpene-rich (TAE) apple peel extracts affect cholesterol metabolism in diet-induced hypercholesterolemic male Golden Syrian hamsters. Two groups of hamsters were supplemented with 50 mg bioactives/kg/d of FAE or TAE and the third group was the atherogenic control (AC). After 28 days, FAE reduced (p < 0.05) serum total cholesterol (TC) and non-high density lipoprotein cholesterol (non-HDL) compared to AC. In contrast, TAE increased (p < 0.05) serum TC. Extracts had no effect on serum triacylglycerol and HDL. Both FAE and TAE increased (p < 0.05) cholesterol absorption without any effect on cholesterol biosynthesis. Liver TC, free cholesterol, triacylglycerol, serum and liver oxidative stress biomarkers were not altered by any extract. FAE and TAE differentially affected cholesterol metabolism where FAE effectively lowered serum cholesterol, with the underlying mechanism awaiting further investigation.
Keywords: Apple peel extracts; Flavonoids; Triterpenes; Hamster; Cholesterol; Oxidative stress

Variable temperature 17O NMR studies allow quantitative evaluation of molecular dynamics and hydrogem bond energies in organic solids - Kong, Xianqi; O'Dell, Luke A.; Terskikh, Victor; Ye, Eric; Wang, Ruiyao; Wu, Gang (Journal of the American Chemical Society, 2012)
We report a comprehensive variable-temperature solid-state 17O NMR study of three 17O-labeled crystalline sulfonic acids: 2-aminoethane-1-sulfonic acid (taurine, T), 3- aminopropane-1-sulfonic acid (homotaurine, HT), and 4-aminobutane- 1-sulfonic acid (ABSA). In the solid state, all three compounds exist as zwitterionic structures, NH3+−R−SO3−, in which the SO3− group is involved in various degrees of O···H−N hydrogen bonding. High-quality 17O NMR spectra have been obtained for all three compounds under both static and magic angle spinning (MAS) conditions at 21.1 T, allowing the complete set of 17O NMR tensor parameters to be measured. Assignment of the observed 17O NMR parameters to the correct oxygen sites in the crystal lattice was achieved with the aid of DFT calculations. By modeling the temperature dependence of 17O NMR powder line shapes, we have not only confirmed that the SO3− groups in these compounds undergo a 3-fold rotational jump mechanism but also extracted the corresponding jump rates (102−105 s−1) and the associated activation energies (Ea) for this process (Ea = 48 ± 7, 42 ± 3, and 45 ± 1 kJ mol−1 for T, HT, and ABSA, respectively). This is the first time that SO3− rotational dynamics have been directly probed by solid-state 17O NMR. Using the experimental activation energies for SO3− rotation, we were able to evaluate quantitatively the total hydrogen bond energy that each SO3− group is involved in within the crystal lattice. The activation energies also correlate with calculated rotational energy barriers. This work provides a clear illustration of the utility of solid-state 17O NMR in quantifying dynamic processes occurring in organic solids. Similar studies applied to selectively 17O-labeled biomolecules would appear to be very feasible.

Dark state suppression and optimization of laser cooling and ﬂuorescence in a trapped alkaline-earth-metal single ion - Lindvall, T.; Merimaa, M.; Tittonen, I.; Madej, A. A. (Physical Review A, 2012)
We study the formation and destabilization of dark states in a single trapped ⁸⁸Sr⁺ ion caused by the cooling and repumping laser fields required for Doppler cooling and fluorescence detection of the ion. By numerically solving the time-dependent density matrix equations for the eight-level system consisting of the sublevels of the 5s 2 S1/2, 5p 2 P1/2, and 4d 2 D3/2 states, we analyze the different types of dark states and how to prevent them in order to maximize the scattering rate, which is crucial for both the cooling and the detection of the ion. The influence of the laser linewidths and ion motion on the scattering rate and the dark resonances is studied. The calculations are then compared with experimental results obtained with an endcap ion trap system located at the National Research Council of Canada and found to be in good agreement. The results are applicable also to other alkaline-earth-metal ions and isotopes without hyperfine structure.

Thermodynamic temperature measurements of the melting temperatures of Co-C, Pt-C, and Re-C fixed points at NRC - Todd, A. D. W.; Woods, D. J. (Metrologia, 2012)
This paper outlines measurements made at the National Research Council Canada (NRC) of the thermodynamic melting temperatures of Co–C, Pt–C and Re–C fixed points that have been part of the high-temperature fixed-point research plan of Working Group 5 of the Consultative Committee for Thermometry (CCT-WG5) to assign melting temperatures to those fixed points. This document will outline the equipment used, describe the scheme used to calibrate a pyrometer with traceability to a cryogenic electrical substitution radiometer, and detail the method of measuring the fixed points. It will then report the uncertainties in the measurements and the results. A brief description of the improvements that we plan to implement to the scheme to reduce the uncertainties for future measurements will be given. The thermodynamic temperatures determined for the three fixed points are: 1597.776 K with an expanded uncertainty of 0.36 K, 2011.390 K with an expanded uncertainty of 0.55 K, and 2748.056 K with an expanded uncertainty of 0.95 K, for the Co–C, Pt–C and Re–C fixed points, respectively (all expanded uncertainties assume a 95% confidence interval and a Gaussian distribution).
Keywords: instrumentation and measurement general; condensed matter: structural, mechanical & thermal

Effect of pH on neutral lipid and biomass accumulation in microalgal strains native to the Canadian prairies and the Athabasca oil sands - Skrupski, B.; Wison, K. E.; Goff, K. L.; Zou, J. (Journal of Applied Phycology, 2012)
Algal biodiesel has been a subject of growing importance in the realm of renewable energy due to carbon capture properties and its potential for photosynthetic efficiency with high lipid output. This study identified five isolates of freshwater green algae, belonging to the Chlorellaceae, and measured the lipid classes and fatty acid profiles of these species to determine suitability for biodiesel production. To induce the greater accumulation of lipids, especially in the form of triacylglycerols (TAGs) desired for biodiesel, we examined the lipid accumulation in cells stressed by nitrogen limitation, sulfur deficiency, or pH stress. Increases in biomass were monitored in order to determine if adjusting pH incrementally over the course of the experiment had any effect on growth and lipid accumulation of several isolates. TAG accumulation was visually screened by Nile Red fluorescence and further assessed by gas chromatography. Lipid amounts were comparably equal or better for pH stress treatments than for standard nutrient-deprivation treatments. Incrementally adjusted pH over the course of growth triggered lipid accumulation comparable to constant pH stress treatments, yet biomass accumulation was equivalent to unstressed growth. One isolate obtained from the Athabasca oil-sands region of Alberta, OS4-2, is a good candidate for biodiesel production, having accumulated over 45 % of its dry weight as lipid, with over 80 % of the lipid as triacylglycerols, and contains an abundance of 18:1 fatty acids. This class of fatty acids improves the cold flow and oxidative stability of biodiesel and is ideal for biofuel used in a Canadian climate.
Keywords: Biodiesel; Lipid; Oil Sands; pH Stress; Nile Red; Biomass; TAG

L-Tryptophan ethyl ester dilates small mesenteric arteries by inhibition of voltage-operated calcium channels in smooth muscle - Jadhav, Ashok; Liang, Wenbin; Balsevich, John; Bastin, Guillaume; Kroetsch, Jeff; Heximer, Scott; Backx, Peter H.; Gopalakrishnon, Venkat (British Journal of Pharmacology, 2012)
BACKGROUND AND PURPOSE: L-tryptophan (L-W) is a precursor of the vasoconstrictor, 5-HT. However, acute administration of L-W ethyl ester (L-Wee) lowered blood pressure. The mechanism of action is unknown. This study compares the vascular effects of L-W and L-Wee in intact animals, isolated aortic rings, small mesenteric arteries (MA) and explores possible mechanisms by studies in vascular smooth muscle cells (VSMC) of MA. EXPERIMENTAL APPROACH: Effects of L-W or L-Wee (5–50 mg kg⁻¹, i.v.) on mean arterial pressure (MAP) and heart rate (HR) were determined in male Sprague-Dawley rats. The effects of L-W and L-Wee on basal tone and of phenylephrine- or KCl-induced contractions of aortic and MA rings were assessed. Effects of L-Wee and L-W on voltage-operated calcium channels (VOCC) of VSMC of MA were also examined in patch-clamp studies. KEY RESULTS: Administration of L-Wee, but not L-W, evoked a rapid and transient dose-dependent decrease in MAP and HR. While both agents failed to affect basal tone, L-Wee decreased, concentration-dependently, (Imax > 98%) tension responses to phenylephrine and KCl in an endothelium-independent manner in aorta (IC₅₀ 2 mM) and MA (IC₅₀ 17 μM). L-Wee evoked concentration-dependent inhibition of VOCC currents (IC₅₀ 12 μM; Imax 90%) in VSMC of MA. CONCLUSIONS AND IMPLICATIONS: Esterified L-W (L-Wee), but not L-W, preferentially relaxed resistance vessels rather than conduit vessels. These effects were associated with blockade of VOCC by L-Wee. Our findings suggest that the falls in MAP and HR induced by L-Wee were due to blockade of VOCC by L-Wee.
Keywords: aorta; Ba²⁺ current; blood pressure; L-tryptophan; L-tryptophan ethyl ester; mesenteric artery; phenylephrine; potassium chloride; voltage-operated Ca²⁺ channel

Brassica carinata CIL1 mediates extracellular ROS production during Auxin- and ABA-regulated lateral root development - Gibson, Shawn W.; Conway, Alix J.; Zheng, Zhifu; Uchacz, Tina M.; Taylor, Janet L.; Todd, Christopher D. (Journal of Plant Biology, 2012)
ct In the plant cytoplasm signals from multiple sources interact to control development. Lateral root proliferation is controlled by the antagonistic action of the hormones auxin and abscisic acid (ABA). Auxin stimulates the separation of pericycle initials and cell expansion. ABA is required for lateral root initiation and elongation and acts as an antagonist through auxin-dependent pathways. These hormones also mediate reactive oxygen species (ROS) accumulation in growing roots and promote cell expansion. We describe the isolation and characterization of a copperand auxin-induced gene, COPPER INDUCED in LEAVES (CIL1), from Brassica carinata. Transgenic B. carinata seedlings expressing antisense CIL1 were used to determine the biological function of this gene. Lines with reduced CIL1 expression showed a decrease in lateral root development, as well as reduced sensitivity to auxin and ABA. Steady-state analysis of redox components showed a decrease in NADPH oxidase, superoxide dismutase, and catalase activity, accompanied by an increase in hydrogen peroxide concentration. GFP-tagged CIL1 accumulated at the plasma membrane and in the apoplast indicating CIL1 is likely extracellular. From these data we propose that CIL1 is an extracellular protein involved in ROS cycling mediating auxin and ABA signals.
Keywords: Abscisic acid; Auxin; Brassica carinata; Glucosylphosphatidylinositol-anchored protein; Lateral roots; Reactive oxygen species

Arabidopsis Clade I TGA transcription factors regulate plant defenses in an NPR1-independent fashion - Shearer, Heather L.; Cheng, Yu Ti; Wang, Lipu; Liu, Jinman; Boyle, Patrick; Després, Charles; Zhang, Yuelin; Li, Xin; Fobert, Pierre R. (Molecular Plant-Microbe Interactions, 2012)
Transcriptional reprogramming during induction of salicylic acid (SA)-mediated defenses is regulated primarily by NPR1 (NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1), likely through interactions with TGA bZIP transcription factors. To ascertain the contributions of clade I TGA factors (TGA1 and TGA4) to defense responses, a tga1-1 tga4-1 double mutant was constructed and challenged with Pseudomonas syringae and Hyaloperonospora arabidopsidis. Although the mutant displayed enhanced susceptibility to virulent P. syringae, it was not compromised in systemic acquired resistance against this pathogen or resistance against avirulent H. arabidopsidis. Microarray analysis of nonelicited and SA-treated plants indicated that clade I TGA factors regulate fewer genes than NPR1. Approximately half of TGA-dependent genes were regulated by NPR1 but, in all cases, the direction of change was opposite in the two mutants. In support of the microarray data, the NPR1-independent disease resistance observed in the autoimmune resistance (R) gene mutant snc1 is partly compromised by tga1-1 tga4-1 mutations, and a triple mutant of clade I TGA factors with npr1-1 is more susceptible than either parent. These results suggest that clade I TGA factors are required for resistance against virulent pathogens and avirulent pathogens mediated by at least some R gene specificities, acting substantially through NPR1-independent pathways.

Topological study of mechanistic diversity in conjugated fatty acid biosynthesis - Bhar, Palash; Reed, Darwin W.; Covello, Patrick S.; Buist, Peter H. (Angewandte Chemie International Edition, 2012)
Variations on an oxidative theme: The precision with which FAD2-type desaturases carry out C−H activation reactions on flexible lipidic substrates is astonishing. The conformational space available within the active site of these enzymes has been explored using deuterium-labeled substrates, and evidence for a novel quasi-eclipsed conformer has been uncovered. The scheme shows some prototypical substrate conformations.
Keywords: C−H activation; desaturases; enzyme mechanisms; kinetic isotope effects; conformation analysis

Laser-induced incandescence (LII) for the measurement of atmospheric black carbon - Smallwood, Gregory (2012)

Functional characterization of amyrin synthase involved in ursolic acid biosynthesis in Catharanthus roseus leaf epidermis - Yu, Fang; Thamm, Antje M. K.; Reed, Darwin; Villa-Ruano, Nemesio; Quesada, Alfonso Lara; Lozoya, Edmundo Gloria; Covello, Patrick; De Luca, Vincenzo (Phytochemistry, 2012)
Catharanthus roseus accumulates high levels of the pentacyclic triterpene, ursolic acid, as a component of its wax exudate on the leaf surface. Bioinformatic analyses of transcripts derived from the leaf epidermis provide evidence for the specialized role of this tissue in the biosynthesis of ursolic acid. Cloning and functional expression in yeast of a triterpene synthase derived from this tissue showed it to be predominantly an α-amyrin synthase (CrAS), since the α-amyrin to β-amyrin reaction products accumulated in a 5:1 ratio. Expression analysis of CrAS showed that triterpene biosynthesis occurs predominantly in the youngest leaf tissues and in the earliest stages of seedling development. Further studies using laser capture microdissection to harvest RNA from epidermis, mesophyll, idioblasts, laticifers and vasculature of leaves showed the leaf epidermis to be the preferred sites of CrAS expression and provide conclusive evidence for the involvement of this tissue in the biosynthesis of ursolic acid in C. roseus.
Keywords: Catharanthus amyrin synthase; Leaf epidermis expression; Ursolic acid; Secretion

Improved localization accuracy in magnetic source imaging using a 3-D laser scanner - Bardouille, Timothy; Krishnamurthy, Santosh V.; Ghosh Hajra, Sujoy; D'Arcy, Ryan C. N. (IEEE Transactions on Biomedical Engineering, 2012)
Brain source localization accuracy in magnetoencephalography (MEG) requires accuracy in both digitizing anatomical landmarks and coregistering to anatomical magnetic resonance images (MRI). We compared the source localization accuracy and MEG-MRI coregistration accuracy of two head digitization systems—a laser scanner and the current standard electromagnetic digitization system (Polhemus)—using a calibrated phantom and human data. When compared using the calibrated phantom, surface and source localization accuracy for data acquired with the laser scanner improved over the Polhemus by 141% and 132%, respectively. Laser scan digitization reduced MEG source localization error by 1.38 mm on average. In human participants, a laser scan of the face generated a 1000-fold more points per unit time than the Polhemus head digitization. An automated surfacematching algorithm improved the accuracy of MEG-MRI coregistration over the equivalent manual procedure. Simulations showed that the laser scan coverage could be reduced to an area around the eyes only while maintaining coregistration accuracy, suggesting that acquisition time can be substantially reduced. Our results show that the laser scanner can both reduce setup time and improve localization accuracy, in comparison to the Polhemus digitization system.
Keywords: Coregistration; laser scanner; localization accuracy; magnetic resonance imaging (MRI); magnetoencephalography (MEG)

Nonlinear optical microscopy in decoding arterial diseases - Ko, Alex C.-T.; Ridsdale, Andrew; Mostaço-Guidolin, Leila B.; Major, Arkady; Stolow, Albert; Sowa, Michael G. (Biophysical Reviews, 2012)
Pathological understanding of arterial diseases is mainly attributable to histological observations based on conventional tissue staining protocols. The emerging development of nonlinear optical microscopy (NLOM), particularly in second-harmonic generation, two-photon excited fluorescence and coherent Raman scattering, provides a new venue to visualize pathological changes in the extracellular matrix caused by atherosclerosis progression. These techniques in general require minimal tissue preparation and offer rapid three-dimensional imaging. The capability of label-free microscopic imaging enables disease impact to be studied directly on the bulk artery tissue, thus minimally perturbing the sample. In this review, we look at recent progress in applications related to arterial disease imaging using various forms of NLOM.
Keywords: Atherosclerosis; Nonlinear optical microscopy; Second-harmonic generation; Two-photon excited fluorescence; Coherent anti-Stokes Raman; Artery

A Lagrangian level set-like method for modelling and simulation in bioengineering - Mir, Hicham; Thibault, Francis (Computer Methods in Biomechanics and Biomedical Engineering, 2012)
The level set method has been used for 20 years in a wide range of physical applications to track moving interfaces instead of an explicit description of the geometry. This paper studies in detail the shape of the level set function, delimiting a sub-domain in solid mechanics, with an innovative update method based on the computation of a displacement field obtained with the values of the level set function. A criterion based on the values of the level set function is proposed in order to assign the material properties. With the help of this criterion, an optimal approach is proposed, which predicts an accurate evolution of the sub-domain boundary. To validate this method, it was first applied in two dimensions to a through-thickness hole plate case, and then to the cases of brain tumour expansion and grasping to demonstrate the applicability of the method.
Keywords: Lagrangian level set method; FEM; solid mechanics

Optimal signal processing of nonlinearity in swept-source and spectral-domain optical coherence tomography - Vergnole, Sébastien; Lévesque, Daniel; Bizheva, Kostadinka; Lamouche, Guy (Applied Optics, 2012)
We demonstrate the efficiency of the convolution using an optimized Kaiser–Bessel window to resample nonlinear data in wavenumber for Fourier-domain optical coherence tomography (OCT). We extend our previous experimental demonstration that was performed with a specific swept-source nonlinearity. The method is now applied to swept-source OCT data obtained for various simulated swept-source nonlinearities as well as spectral-domain OCT data obtained from both simulations and experiments. Results show that the new optimized method is the most efficient for handling all the different types of nonlinearities in the wavenumber domain that one can encounter in normal practice. The efficiency of the method is evaluated through comparison with common methods using resampling through interpolation prior to performing a fast-Fourier transform and with the accurate but time-consuming discrete Fourier transform for unequally spaced data, which involves Vandermonde matrices.

Non-destructive detection of lack of penetration defects in friction stir welds - Mandache, C.; Levesque, D.; Dubourg, L.; Gougeon, P. (Science and Technology of Welding & Joining, 2012)
This study focuses on the comparative investigation of different non-destructive inspection (NDI) techniques for detecting the lack of penetration discontinuities in butt joint friction stir (FS) welds. A variably sized lack of penetration has been introduced purposely by progressively changing the tool pin’s length. While inspecting the weld from the discontinuity side provides results of higher sensitivity, service inspection of the FS welded components requires evaluation of the welding tool’s side, opposite the defect containing one. Non-destructive techniques amenable for inspection from either the tool side or the far side of the weld are analysed, and results from inspection are presented for comparison. Subsequently, bending tests and metallographic examinations were employed to confirm the size of the lack of penetration defects and correlate these results with the NDI capabilities.
Keywords: Non-destructive evaluation; Friction stir welding; Lack of penetration; Eddy current; Ultrasonic waves; Inspection

Haptic collision handling for simulation of transnasal surgery - Neubauer, André; Brooks, Rupert; Brouwer, Iman; Debergue, Patricia; Laroche, Denis (Computer Animation and Virtual Worlds, 2012)
Simulation of endoscopic navigation in the narrow nasal cavity poses important challenges to the computation of adequate and near-realistic collision response and haptic feedback because extensive multidirectional contact and massive tissue deformations are inevitable. We present a virtual coupling algorithm that provides stable collision response as well as intuitive and smooth haptic interaction in all phases of the simulation. In each iteration, continuous collision detection between the point shell representing the surface of the virtual patient anatomy and the endoscope, represented by a cylinder, is performed. This allows for rolling back the instrument movement to the point in time the first collision occurred. Subsequently, a relaxation process locally optimizes the position and orientation of the instrument. A novel method of applying contact forces to colliding tissues and thus triggering appropriate deformations improves the fluency of navigation. This paper describes the algorithm and presents experimental results.
Keywords: surgical simulation; transnasal endoscopy; collision handling; haptics; virtual coupling

The inﬂuence of pore size on osteoblast phenotype expression in cultures grown on porous titanium - Teixeira, L. N.; Crippa, G. E.; Lefebvre, L.-P.; De Oliveira, P. T.; Rosa, A. L.; Beloti, M. M. (International Journal of Oral and Maxillofacial Surgery, 2012)
This study investigated the effect of pore size on osteoblastic phenotype development in cultures grown on porous titanium (Ti). Porous Ti discs with three different pore sizes, 312 μm (Ti 312), 130 μm (Ti 130) and 62 μm (Ti 62) were fabricated using a powder metallurgy process. Osteoblastic cells obtained from human alveolar bone were cultured on porous Ti samples for periods of up to 14 days. Cell proliferation was affected by pore size at day 3 (p = 0.0010), day 7 (p = 0.0005) and day 10 (p = 0.0090) in the following way: Ti 62 < Ti 130 < Ti 312. Gene expression of bone markers evaluated at 14 days was affected, RUNX2 (p = 0.0153), ALP (p = 0.0153), BSP (p = 0.0156), COL (p = 0.0156), and OPN (p = 0.0156) by pore size as follows: Ti 312 < Ti 130 < Ti 62. Based on these results, the authors suggest that porous Ti surfaces with pore sizes near 62 μm, compared with those of 312 μm and 130 μm, yield the highest expression of osteoblast phenotype as indicated by the lower cell proliferation rate and higher gene expression of bone markers.
Keywords: cell culture; osteoblast; dental implant; pore size; porous titanium

Melt-processing and properties of coaxial fibers incorporating carbon nanotubes - Laforgue, Alexis; Champagne, Michel F.; Dumas, Jean; Robitaille, Lucie (Journal of Engineered Fibers and Fabrics, 2012)
Polypropylene-multiwalled carbon nanotube (PPCNT) composites were spun into fibers using meltspinning methods. The CNT content was varied by diluting the commercial masterbatch with a low viscosity PP homopolymer grade. The conductivity, as well as the mechanical properties, of the fibers were systematically tested in order to find the optimal formulation. Post-stretching was used to improve the mechanical properties of the fibers as well as to decrease the fiber diameters. Fibers having a conductivity of 0.4 S/cm, a Young’s modulus of 5.4 GPa and a tensile strength of 250 MPa were obtained after a three-fold stretching. Trilayer coaxial fibers similar to data transfer coaxial cables (two conductive layers separated by an insulating layer) were then produced in a one-step melt-spinning method using a specially designed die, followed by solid state post-stretching.

Numerical simulation of ﬂuid–solid interaction using an immersed boundary ﬁnite element method - Ilinca, F.; Hétu, J.-F. (Computers & Fluids, 2012)
This paper presents applications of a recently proposed immersed boundary method to the solution of ﬂuid–solid interaction. Solid objects immersed into the ﬂuid are considered rigid and their movement is determined from the interaction forces with the ﬂuid. The use of body-conformal meshes to solve such problems may involve extensive mesh adaptation work that has to be repeated each time a change in the shape of the domain or in the position of immersed solids is needed. Mesh generation and solution interpolation between successive grids may be costly and introduce errors if the geometry changes signiﬁ- cantly during the course of the computation. These drawbacks are avoided when the solution algorithm can tackle grids that do not ﬁt the shape of immersed objects. We present here an extension of our recently developed immersed boundary (IB) ﬁnite element method to the computation of interaction forces between the ﬂuid and immersed solid bodies. A ﬁxed mesh is used covering both the ﬂuid and solid regions, and the boundary of immersed objects is deﬁned using a time dependent level-set function. Boundary conditions on the immersed solid surfaces are imposed accurately by using a Body Conformal Enrichment (BCE) method. In this approach, the ﬁnite element discretization of interface elements is enriched by including additional degrees of freedom which are latter eliminated at element level. The forces acting on the solid surfaces are computed from the enriched ﬁnite element solution and the solid movement is determined from the rigid solid momentum equations. Solutions are shown for various ﬂuid–solid interaction problems and the accuracy of the present approach is measured with respect to solutions on body-conformal meshes.
Keywords: Immersed boundary method; Fluid-solid interaction; Finite elements; Non-body-conformal mesh; Body conformal enrichment

The effect of deposition conditions on adhesion strength of Ti and Ti6Al4V cold spray splats - Goldbaum, Dina; Shockley, J. Michael; Chromik, Richard R.; Rezaeian, Ahmad; Yue, Stephen; Legoux, Jean-Gabriel; Irissou, Eric (Journal of Thermal Spray Technology, 2012)
Cold spray is a complex process where many parameters have to be considered in order to achieve optimized material deposition and properties. In the cold spray process, deposition velocity influences the degree of material deformation and material adhesion. While most materials can be easily deposited at relatively low deposition velocity (<700 m/s), this is not the case for high yield strength materials like Ti and its alloys. In the present study, we evaluate the effects of deposition velocity, powder size, particle position in the gas jet, gas temperature, and substrate temperature on the adhesion strength of cold spayed Ti and Ti6Al4V splats. A micromechanical test technique was used to shear individual splats of Ti or Ti6Al4V and measure their adhesion strength. The splats were deposited onto Ti or Ti6Al4V substrates over a range of deposition conditions with either nitrogen or helium as the propelling gas. The splat adhesion testing coupled with microstructural characterization was used to define the strength, the type and the continuity of the bonded interface between splat and substrate material. The results demonstrated that optimization of spray conditions makes it possible to obtain splats with continuous bonding along the splat/substrate interface and measured adhesion strengths approaching the shear strength of bulk material. The parameters shown to improve the splat adhesion included the increase of the splat deposition velocity well above the critical deposition velocity of the tested material, increase in the temperature of both powder and the substrate material, decrease in the powder size, and optimization of the flow dynamics for the cold spray gun nozzle. Through comparisons to the literature, the adhesion strength of Ti splats measured with the splat adhesion technique correlated well with the cohesion strength of Ti coatings deposited under similar conditions and measured with tubular coating tensile (TCT) test.
Keywords: adhesion; cold spray; splats; Ti; Ti6A14V

Thermal cycling of suspension plasma sprayed Alumina-YSZ coatings containing amorphous phases - Tarasi, Fariba; Medraj, Mamoun; Dolatabadi, Ali; Lima, Rogerio S.; Moreau, Christian (Journal of the American Ceramic Society, 2012)
Thermal cyclic test at 1080°C for various numbers of cycles was performed on suspension plasma-sprayed coatings of alumina-yttria-stabilized zirconia composites and yttria-stabilized zirconia (YSZ). The structural variations of composite coatings were studied to verify the possibility of production of nano-composite coatings with nano-dispersed oxides. The results showed that this composite exhibited a lower thermally grown oxide growth than that of the YSZ. New multi-constituent composites formed of alternative regions of nano-precipitates of alumina in zirconia matrix and nano-precipitates of zirconia in alumina matrix were developed via phase transformation through thermal cyclic process of amorphous-containing structure.
Keywords: thermal cyclic test; amorphous phase; composite ceramic; alumina-zirconia; thermal barrier coating

Non-contact biomedical photoacoustic and ultrasound imaging - Rousseau, Guy; Gauthier, Bruno; Blouin, Alain; Monchalin, Jean-Pierre (Journal of Biomedical Optics, 2012)
The detection of ultrasound in photoacoustic tomography (PAT) usually relies on ultrasonic transducers in contact with the biological tissue through a coupling medium. This is a major drawback for important potential applications such as surgery. Here we report the use of a remote optical method, derived from industrial laserultrasonics, to detect ultrasound in tissues. This approach enables non-contact PAT (NCPAT) without exceeding laser exposure safety limits. The sensitivity of the method is based on the use of suitably shaped detection laser pulses and a confocal Fabry-Perot interferometer in differential configuration. Reliable image reconstruction is obtained by measuring remotely the surface profile of the tissue with an optical coherence tomography system. The proposed method also allows non-contact ultrasound imaging (US) by applying a second reconstruction algorithm to the data acquired for NCPAT. Endogenous and exogenous inclusions exhibiting optical and acoustic contrasts were detected ex vivo in chicken breast and calf brain specimens. Inclusions down to 0.3 mm in size were detected at depths exceeding 1 cm. The method could expand the scope of photoacoustic and US to in-vivo biomedical applications where contact is impractical.
Keywords: photoacoustic tomography; tomography; photoacoustic imaging; ultrasound imaging; optical detection of ultrasound; optical coherence tomography; brain surgery; blood oxygenation

Performance of conventional and new lubricants used for single compaction of steel PM parts - Thomas, Yannig; St. Laurent, Sylvain; Paris, Vincent; Tinto, Rio (Advances in Powder Metallurgy & Particulate Materials—2012 : Proceedings of the 2012 International Conference on Powder Metallurgy & Particulate Materials, 10-13 June, Nashville, Tennessee, 2012)
The role of lubricant during compaction is crucial and is even more important those days with the increased number of PM parts with higher densities and/or challenging ejection conditions. It is for that reason that significant level of efforts were devoted during the last 20 years to the development of environmental friendly PM lubricants that improve both the compaction processing of steel pre-mixes such as the ejection, density, robustness, productivity, surface finish, etc., as well as the performances of the PM parts after sintering. The development of new lubricants for single compaction requires an excellent understanding of the lubrication mechanisms and the behaviour of these new compounds. In this presentation, the effect of different compacting processing parameters such as the pressure, temperature, compaction speed and part aspect ratio on the lubrication behaviour of iron-based powder mixes containing various types of lubricants are reviewed. A particular attention will also be given to the effect of the type and concentration of lubricants on the delubrication behaviour and mechanical properties obtained after sintering.

DLFT experiments with cyclic butylene terephtalate - Bravo, Victor L.; Mihalich, James; McLeod, Martin R.; Bureau, Martin N. (SPE Automotive and Composites Divisions - 12th Annual Automotive Composites Conference and Exhibition 2012, ACCE 2012: Unleashing the Power of Design, 2012)
Cyclic oligomers have low molecular weights and therefore exhibit very low viscosities (in the order of 20 mPa.s) in contrast to the resulting high viscosities related to high molecular weightsobtained after polymerization. This characteristic is very appealing for the production of polymer composites since by taking advantage of the low viscosity, fibres can be thoroughly wetted by the cyclic oligomer before starting the reactive process of polymerization. As a result, a homogeneous mixture with a uniform volumetric distribution of reinforcing fibres in the polymer matrix is expected with the use of appropriate processing equipment. Cyclic butylene terephthalate (CBT®) has been successfully polymerized into poly(butylene terephthalate) (PBT) using a variety of tin or titanate-based initiators. An exploratory project has been initiated by NRC at the Magna-NRC Composites Centre of Excellence (MNCCE) with the participation of Cyclics Corporation (Cyclics) as the supplier of CBT for trials using the D-LFT process. The goal is to assess a number of aspects involved in the simultaneous reactive extrusion/compounding process using CBT fibreglass reinforcement in a D-LFT process in order to determine the adequate processing conditions to produce parts. This paper presents a description of the experiments conducted up to date and the results obtained thereby. Parts were produced using a test specimen mould with a shot-pot device and a storage tub for automotive applications. Samples were characterized for tensile, flexural and impact tests. Density measurements were taken at different points of the tub to examine the uniformity of the composite material obtained. Plaques moulded with the test specimen mould showed good mechanical properties which exceed typical values for PP with 40% glass composites. The experiments proved the feasibility of the use of the open ring polymerization process in a D-LFT system. A set of operating conditions including temperature profile, screw speed and feed rate was established to achieve the adequate residence time and material temperature history for the effective processing of CBT in the D-LFT system.Mechanical properties measured from the moulded part (tub) showed significantly lower values than those for the test specimen mould. These were related to incomplete packing of the material in the cavity of the mould, the high residence time required and non-optimal shot size.High variability within the parts and between parts produced is thought to be a consequence of the processing difficulties for the tub mould.
Keywords: Automotive applications; Cyclic butylene terephthalates; High molecular weight; Homogeneous mixtures; Material temperature; Poly(butylene terephthalate); Polymerization process; Processing equipment; Automobile exhibitions; Butenes; Composite materials; Glass fibers; Mechanical properties; Molecular weight; Oligomers; Polymerization; Reinforcement; Residence time distribution; Viscosity; Molds

Effect of process variables on the performance of glass fibre reinforced composites made by high pressure resin transfer moulding - Khoun, Loleï; Maillard, Damien; Bureau, Martin N. (Proceedings of the 12th Annual Automotive Composites Conference & Exhibition (ACCE 2012), 2012)
The CAFE regulations will require average fuel consumption of cars and light duty trucks to be reduced from 27 mpg to 54.5 mpg by 2025. In order to reach this requirement, automakers have to improve both the vehicle powertrain efficiency and the vehicle weight. Polymer composite materials are a preferred alternative to achieve the needed weight reduction by combining a higher strength to weight ratio than steel and aluminum, superior fatigue and corrosion resistance than metal and very good crashworthiness characteristics. However, high throughput and cost effective composite manufacturing processes are essential for high performance fibre reinforced polymer composites to penetrate the automotive market to their full potential. High Pressure Resin Transfer Moulding (HP-RTM) process is a new process based on the Resin Transfer Moulding (RTM) technology that enables the processing of very reactive resins in very short cycle times (< 5-10 min i.e. >25,000 parts per year) with various types of reinforcement (glass, carbon, natural fibre). With HP-RTM’s unique self-cleaning impingement mixhead, resins that react in less than 1 minute (fast-curing epoxy or polyurethane systems) can still be processed. This process, combining the high mechanical performance of RTM parts with short cure cycle, thus presents a great interest for automotive applications. In this study, the effect of the process parameters, such as the injection flow rate, the vacuum assistance sequence and mould gap control, on the mechanical performance and quality of HP-RTM composite plates was determined and HP-RTM process mapping was established from the obtained mechanical results.

Atmospheric plasma sprayed forsterite (Mg2ASiO4) coatings : an investigation of the processing-microstructure-performance relationship - Cojocaru, C. V.; Lamarre, J.-M.; Legoux, J.-G.; Marple, B. R.; Lima, R. S.; Agarwal, A.; Hyland, M. M.; Lau, Y.-C.; Li, C.-J.; McDonald, A.; Toma, F.-L. (Thermal Spray 2012 : Proceedings from the International Spray Conference, 2012)
Evaluating and understanding the relationship between processing, microstructure and performance of a dielectric coating is essential for its practical usage and reliable application. In this study, the role of the powder feedstock on the properties of atmospheric plasma sprayed forsterite (Mg2SiO4) dielectric coatings was investigated by using different forsterite powder cuts. The microstructural and porosity characteristics of the coatings associated with the spray conditions employed were assessed via scanning electron microscopy (SEM) and image analysis. The phase composition of the coatings was studied via X-ray diffraction and their crystallinity index determined. The electrical insulating characteristics were investigated using the dielectric breakdown test. The obtained electrical properties were correlated with the microstructural characteristics. Ultimately, a performance comparison between forsterite and other dielectric coatings tested in similar conditions is presented.

A laser thermal cycling rig as a new method to characterize the evolution of coating adhesion under thermal cycle - Poirier, D.; Irissou, E.; Legoux, J. G.; Lima, R. S.; Agarwal, A.; Hyland, M. M.; Lau, Y.-C.; Li, C.-J.; McDonald, A.; Toma, F.-L. (Thermal Spray 2012 : Proceedings from the International Spray Conference, 2012)
Thermal sprayed coatings are often used for high temperature applications and, per se, are subjected to transient temperature gradients during operation. The recurrent temperature changes generate stresses that damage the coating with time, and can even lead to its delamination. The most common methods to evaluate coating behavior under thermal cycling are furnace testing or burner rigs. Both approaches cannot match the conditions reached in service for several applications, in term of the achievable heating rates for instance. As a consequence, a versatile and robust method to evaluate coating resistance to spalling under thermal cycles is still to be found. This paper presents the development of a thermal cycling rig where the heat input is provided by a laser. This rig allows easy testing of several samples jointly for heating rates as high as 55°C/s and for thousands of thermal cycles. Preliminary trials have allowed the development of different spalling criteria. Finally, it was found that SS430-based materials arc-sprayed on Al substrates exhibit higher delamination resistance (life) under rapid heating/cooling cycles than SS304 coatings on the same substrate. For such high heating rates, the thermal stresses generated in the coating would be more critical than the thermal mismatch at the interface coating/substrate.