Immobilization of antibodies and enzymes on 3-aminopropyltriethoxysilane-functionalized bioanalytical platforms for biosensors and diagnostics - Vashist, Sandeep Kumar; Lam, Edmond; Hrapovic, Sabahudin; Male, Keith B.; Luong, John H. T. (Chemical Reviews, 2014)
Biosensing and diagnostic platforms with high sensitivity, specificity, and fast response time are based on immobilized biomolecules such as antibodies (Abs), aptamers, enzymes, nucleic acids, receptors, and whole cells for the detection of target analytes. Such sensing biomolecules should be bound to the surface of a signal transducer with a required specific chemical, electrical, or optical property. The biological recognition event generates a quantifiable signal, which is equated to the amount or concentration of the analyte. APTES can be deposited on solid materials, electrode materials, nanomaterials, and nanocomposites under variable conditions of concentration, solvent, temperature, and time. In addition, curing conditions such as air/heat drying might be necessary depending upon the intended application. Pertinent information on the thickness, morphology, and conformation of the APTES layer reported in the literature is often different and conflicting.
Keywords: Antibodies; Biomolecules; Chemical detection; Curing; Nucleic acids; Opitical properties; Bioanalytical platforms; Biological recognition; Curing condition; Electrode material; Fast response time; High sensitivity; Signal transducers; Variable conditions; Enzyme immobilization

Development of the McGill simulator for endoscopic sinus surgery : a new high-fidelity virtual reality simulator for endoscopic sinus surgery - Varshney, Rickul; Frenkiel, Saul; Nguyen, Lily H. P.; Young, Meredith; Del Maestro, Rolando; Zeitouni, Anthony; Tewfik, Marc A.; National Research Council of Canada (American Journal of Rhinology and Allergy, 2014)
Background: The technical challenges of endoscopic sinus surgery (ESS) and the high risk of complications support the development of alternative modalities to train residents in these procedures. Virtual reality simulation is becoming a useful tool for training the skills necessary for minimally invasive surgery; however, there are currently no ESS virtual reality simulators available with valid evidence supporting their use in resident education. Our aim was to develop a new rhinology simulator, as well as to define potential performance metrics for trainee assessment. Methods: The McGill simulator for endoscopic sinus surgery (MSESS), a new sinus surgery virtual reality simulator with haptic feedback, was developed (a collaboration between the McGill University Department of Otolaryngology-Head and Neck Surgery, the Montreal Neurologic Institute Simulation Lab, and the National Research Council of Canada). A panel of experts in education, performance assessment, rhinology, and skull base surgery convened to identify core technical abilities that would need to be taught by the simulator, as well as performance metrics to be developed and captured. Results: The MSESS allows the user to perform basic sinus surgery skills, such as an ethmoidectomy and sphenoidotomy, through the use of endoscopic tools in a virtual nasal model. The performance metrics were developed by an expert panel and include measurements of safety, quality, and efficiency of the procedure. Conclusion: The MSESS incorporates novel technological advancements to create a realistic platform for trainees. To our knowledge, this is the first simulator to combine novel tools such as the endonasal wash and elaborate anatomic deformity with advanced performance metrics for ESS.
Keywords: Education; endoscopic sinus surgery; haptic; minimally invasive surgery; nasal model; performance metrics; resident; rhinology; simulation; technical abilities; training; virtual reality

Thermally stable gold/alumina aerogel catalysts prepared by a simultaneous synthesis process for solvent-free aerobic benzyl alcohol oxidation - Li, Z.; Ji, Y.; Cadigan, C.; Richards, R. M. (Catalysis Science and Technology, 2014)
Gold nanoparticles supported on an alumina aerogel have been prepared through a simultaneous synthesis process in which the formation of the gold nanoclusters capped with (3-aminopropyl)triethoxysilane (APTES) and the hydrolyzation/co-condensation of the APTES and aluminum alkoxide occur concurrently. The obtained gold nanoparticles are trapped in and physically protected by the framework of the alumina aerogel providing excellent thermal stability with no observable sintering at 650 °C. In the catalysis test for the solvent-free aerobic benzyl alcohol oxidation, this catalyst exhibits significantly better activity than reference gold/alumina aerogel catalysts prepared through a deposition precipitation and conventional wet impregnation methods, especially at high temperature.

Survival life analysis of the cutting tools during turning titanium metal matrix composites (Ti-MMCs) - Aramesh, M.; Shaban, Y.; Balazinski, M.; Attia, H.; Kishawy, H. A.; Yacout, S. (Procedia CIRP, 2014)
Metal matrix composites (MMCs), as a new generation of materials; have proven to be viable materials in various industrial fields such as biomedical and aerospace. In order to achieve a valuable modification in various properties of materials, metallic matrices are reinforced with additional phases based on the chemical and/or physical properties required in the in-service operating conditions. The presence of the reinforcements in MMCs improves the physical, mechanical and thermal properties of the composite; however it induces significant issues in the domain of machining, such as high tool wear and inferior surface finish. The interaction between the tool and abrasive hard reinforcing particles induces complex deformation behaviour in the MMC structure. Sever tool wear is technically the most important drawback of machining MMCs. In this study a statistical model is developed to estimate the mean residual life (MRL) of the cutting tool during machining Ti-MMCs. Initial wear, steady wear and rapid wear regions in the tool wear curve are regarded as the different states in the statistical model. Hence, the valuable information regarding the estimated total time spent in each state, called the sojourn time, and the transition times between the states are obtained from the model. In this paper the standard cutting conditions, based on the recommendation of the tool supplier, are adopted. Based on a Weibull model, the reliability and hazard functions are obtained and are utilized in order to calculate the MRL and the sojourn times. © 2014 Published by Elsevier B.V.
Keywords: Metal matrix composites; survival analysis; reliability function

Phase measurement error in summation of electron holography series - McLeod, Robert A.; Bergen, Michael; Malac, Marek (Ultramicroscopy, 2014)
Off-axis electron holography is a method for the transmission electron microscope (TEM) that measures the electric and magnetic properties of a specimen. The electrostatic and magnetic potentials modulate the electron wavefront phase. The error in measurement of the phase therefore determines the smallest observable changes in electric and magnetic properties. Here we explore the summation of a hologram series to reduce the phase error and thereby improve the sensitivity of electron holography. Summation of hologram series requires independent registration and correction of image drift and phase wavefront drift, the consequences of which are discussed. Optimization of the electro-optical configuration of the TEM for the double biprism configuration is examined. An analytical model of image and phase drift, composed of a combination of linear drift and Brownian random-walk, is derived and experimentally verified. The accuracy of image registration via cross-correlation and phase registration is characterized by simulated hologram series. The model of series summation errors allows the optimization of phase error as a function of exposure time and fringe carrier frequency for a target spatial resolution. An experimental example of hologram series summation is provided on WS2 fullerenes. A metric is provided to measure the object phase error from experimental results and compared to analytical predictions. The ultimate experimental object root-mean-square phase error is 0.006rad (2π/1050) at a spatial resolution less than 0.615nm and a total exposure time of 900s. The ultimate phase error in vacuum adjacent to the specimen is 0.0037rad (2π/1700). The analytical prediction of phase error differs with the experimental metrics by +7% inside the object and -5% in the vacuum, indicating that the model can provide reliable quantitative predictions.
Keywords: Off-axis electron holography; Transmission electron microscope; Complex circular random variables; Phase error; Phase resolution; Random-walk; Quantitative electron microscopy; TEM optimization; Specimen drift; Microscope instabilities

The outer halo globular cluster system of M31 - I. The final PAndAS catalogue - Huxor, A. P.; Mackey, A. D.; Ferguson, A. M. N.; Irwin, M. J.; Martin, N. F.; Tanvir, N. R.; Veljanoski, J.; McConnachie, A.; Fishlock, C. K.; Ibata, R.; Lewis, G. F. (Monthly Notices of the Royal Astronomical Society, 2014)
We report the discovery of 59 globular clusters (GCs) and two candidate GCs in a search of the halo of M31, primarily via visual inspection of Canada-France-Hawaii Telescope/MegaCam imagery from the Pan-Andromeda Archaeological Survey (PAndAS). The superior quality of these data also allows us to check the classification of remote objects in the Revised Bologna Catalogue (RBC), plus a subset of GC candidates drawn from Sloan Digital Sky Survey (SDSS) imaging. We identify three additional new GCs from the RBC, and confirm the GC nature of 11 SDSS objects (8 of which appear independently in our remote halo catalogue); the remaining 188 candidates across both lists are either foreground stars or background galaxies. Our new catalogue represents the first uniform census of GCs across the M31 halo - we find clusters to the limit of the PAndAS survey area at projected radii of up to Rproj ~ 150 kpc. Tests using artificial clusters reveal that detection incompleteness cuts in at luminosities below MV = -6.0; our 50 per cent completeness limit is MV ≈ -4.1. We construct a uniform set of PAndAS photometric measurements for all known GCs outside Rproj = 25 kpc, and any new GCs within this radius. With these data, we update results from Huxor et al., investigating the luminosity function (LF), colours and effective radii of M31 GCs with a particular focus on the remote halo.We find that the GCLF is clearly bimodal in the outer halo (Rproj > 30 kpc), with the secondary peak at MV ~ -5.5. We argue that the GCs in this peak have most likely been accreted along with their host dwarf galaxies. Notwithstanding, we also find, as in previous surveys, a substantial number of GCs with above-average luminosity in the outer M31 halo - a population with no clear counterpart in the Milky Way.
Keywords: galaxies: evolution; galaxies: haloes; galaxies: individual: M31; galaxies: star clusters: general

The outer halo globular cluster system of M31 - II. Kinematics - Veljanoski, J.; Mackey, A. D.; Ferguson, A. M. N.; Huxor, A. P.; Côté, P.; Irwin, M. J.; Tanvir, N. R.; Peñarrubia, J.; Bernard, E. J.; Fardal, M.; Martin, N. F.; McConnachie, A.; et al. (Monthly Notices of the Royal Astronomical Society, 2014)
We present a detailed kinematic analysis of the outer halo globular cluster system of the Andromeda galaxy (M31). Our basis for this is a set of new spectroscopic observations for 78 clusters lying at projected distances between Rproj ~ 20-140 kpc from the M31 centre. These are largely drawn from the recent Pan-Andromeda Archaeological Survey globular cluster catalogue; 63 of our targets have no previous velocity data. Via a Bayesian maximum likelihood analysis, we find that globular clusters with Rproj > 30 kpc exhibit coherent rotation around the minor optical axis ofM31, in the same direction as more centrally located globular clusters, but with a smaller amplitude of 86±17 km s-1. There is also evidence that the velocity dispersion of the outer halo globular cluster system decreases as a function of projected distance from the M31 centre, and that this relation can be well described by a power law of index ≈-0.5. The velocity dispersion profile of the outer halo globular clusters is quite similar to that of the halo stars, at least out to the radius up to which there is available information on the stellar kinematics. We detect and discuss various velocity correlations amongst subgroups of globular clusters that lie on stellar debris streams in the M31 halo. Many of these subgroups are dynamically cold, exhibiting internal velocity dispersions consistent with zero. Simple Monte Carlo experiments imply that such configurations are unlikely to form by chance, adding weight to the notion that a significant fraction of the outer halo globular clusters in M31 have been accreted alongside their parent dwarf galaxies. We also estimate the M31 mass within 200 kpc via the Tracer Mass Estimator (TME), finding (1.2-1.6) ± 0.2 × 1012M⊙. This quantity is subject to additional systematic effects due to various limitations of the data, and assumptions built in into the TME. Finally, we discuss our results in the context of formation scenarios for the M31 halo.
Keywords: globular clusters: general; galaxies: haloes; galaxies: individual: M31; galaxies: kinematics and dynamic; Local Group

A reference system for on-site calibration of high-voltage revenue metering systems - Rietveld, Gert; Fransen, Martin; Blanc, Nicolas; Houtzager, Ernest; So, Eddy (CPEM Digest (Conference on Precision Electromagnetic Measurements), 2014)
A reference system for on-site calibration and validation of revenue metering systems is realized. The system consists of a three-phase power meter and high-accuracy current and voltage transformers (CTs and VTs). Measurements can be made up to 150 kV (system voltage) and line currents up to 5000 A. The power meter, the CTs, and the VTs were all calibrated. Based on the excellent results of the calibration of these components it is possible to predict the full system performance with an uncertainty of less than 100 μW/VA. This estimation was verified with a full system validation, showing that the system is much more accurate than required and that detrimental effects to the accuracy are well understood.
Keywords: billing; High currents; High voltage; power; Power meters; Precision measurement; substation; traceability; Voltage transformer; Electric instrument transformers; revenue metering

Mechanism of DNA trapping in nanoporous structures during asymmetric pulsed-field electrophoresis - Zhou, Ya; Sheng, Huiying; Harrison, D. Jed (Analyst, 2014)
We investigate the trapping mechanism of individual DNA molecules in ordered nanoporous structures generated by crystalline particle arrays. Two requisites for trapping are revealed by the dynamics of single trapped DNA, fully-stretched U/J shapes and hernia formation. The experimental results show there is a stronger possibility for hernias to lead the reorientation upon switching directions of the voltage at high field strengths, where trapping occurs. Fully stretched DNA has longer unhooking times than expected by a classic rope-on-pulley model. We propose a dielectrophoretic (DEP) force reduces the mobility of segments at the apex of the U or J, where field gradients are highest, based on simulations and observations of the trapping force dependence on field strength. A modified model for unhooking time is obtained after the DEP force is introduced. The new model explains the unhooking time data by predicting an infinite trapping time when the ratio of arm length differences (of the U or J) to molecule length Δx/L < β, where β is a DEP parameter that is found to strongly increase with electric field. The DNA polarizability calculated with the DEP model and experimental value of β is of the same magnitude of reported value. The results indicate the tension at the apex of U/J shape DNA is the primary reason for DNA trapping during pulsed field separation, instead of hernias.

Structure and performance of tin-cobalt-carbon alloys prepared by attriting, roller milling and sputtering - Ferguson, P. P.; Todd, A. D. W.; Martine, M. L.; Dahnd, J. R. (Journal of the Electrochemical Society, 2014)
Samples of (Sn5oCo5o)1-yC100y for 0 ≤ y ≤ 0.8 have been prepared in increments of y = 0.1 using a vertical-axis attritor and a horizontal roller mill. The effect of the carbon content on the structure and performance as a negative electrode material of the Sn-Co-C composites was examined by X-ray diffraction (XRD), small angle neutron scattering (SANS) and electrochemical methods. These results were compared to similar alloys prepared by magnetron sputtering. XRD experiments of all of the prepared samples show diffraction patterns characteristic of nanostructured materials except for the samples made without carbon which show broad Bragg peaks of Co3Sn2. The nanostructured samples were best described as Co-Sn grains surrounded by a carbon matrix. SANS results showed that samples prepared by roller milling and by attriting had Co-Sn grains of about 45 Å and 75 Å, respectively, while those prepared by sputtering were either amorphous or had Co-Sn grains of about 10 Å. Excellent charge-discharge capacity retention was observed for samples with y > 0.3. It is believed that this concentration marks the point at which the Co-Sn grains become isolated in the matrix of carbon.

The absolute magnitude distribution of Kuiper Belt objects - Fraser, Wesley C.; Brown, Michael E.; Morbidelli, Alessandro; Parker, Alex; Batygin, Konstantin (The Astrophysical Journal, 2014)
Here we measure the absolute magnitude distributions (H-distribution) of the dynamically excited and quiescent (hot and cold) Kuiper Belt objects (KBOs), and test if they share the same H-distribution as the Jupiter Trojans. From a compilation of all useable ecliptic surveys, we find that the KBO H-distributions are well described by broken power laws. The cold population has a bright-end slope and break magnitude (r′-band). The hot population has a shallower bright-end slope of and break magnitude. Both populations share similar faint-end slopes of α2 0.2. We estimate the masses of the hot and cold populations are 0.01 and 3 × 10-4 M ⊕. The broken power-law fit to the Trojan H-distribution has α1 = 1.0 ± 0.2, α2 = 0.36 ± 0.01, and H B = 8.3. The Kolmogorov-Smirnov test reveals that the probability that the Trojans and cold KBOs share the same parent H-distribution is less than 1 in 1000. When the bimodal albedo distribution of the hot objects is accounted for, there is no evidence that the H-distributions of the Trojans and hot KBOs differ. Our findings are in agreement with the predictions of the Nice model in terms of both mass and H-distribution of the hot and Trojan populations. Wide-field survey data suggest that the brightest few hot objects, with , do not fall on the steep power-law slope of fainter hot objects. Under the standard hierarchical model of planetesimal formation, it is difficult to account for the similar break diameters of the hot and cold populations given the low mass of the cold belt.
Keywords: Kuiper belt: general; minor planets, asteroids: general

The masses of local group dwarf spheroidal galaxies : the death of the universal mass profile - Collins, Michelle L. M.; Chapman, Scott C.; Rich, R. M.; Ibata, Rodrigo A.; Martin, Nicolas F.; Irwin, Michael J.; Bate, Nicholas F.; Lewis, Geraint F.; Peñarrubia, Jorge; Arimoto, Nobuo; Casey, Caitlin M.; Ferguson, Annette M. N.; et al. (The Astrophysical Journal, 2014)
We investigate the claim that all dwarf spheroidal galaxies (dSphs) reside within halos that share a common, universal mass profile as has been derived for dSphs of the galaxy. By folding in kinematic information for 25 Andromeda dSphs, more than doubling the previous sample size, we find that a singular mass profile cannot be found to fit all of the observations well. Further, the best-fit dark matter density profile measured solely for the Milky Way dSphs is marginally discrepant with that of the Andromeda dSphs (at just beyond the 1σ level), where a profile with lower maximum circular velocity, and hence mass, is preferred. The agreement is significantly better when three extreme Andromeda outliers, And XIX, XXI, and XXV, all of which have large half-light radii (≳ 600 pc) and low-velocity dispersions (σ v <5 km s-1), are omitted from the sample. We argue that the unusual properties of these outliers are likely caused by tidal interactions with the host galaxy.
Keywords: dark matter; galaxies: dwarf; galaxies: fundamental parameter; galaxies: kinematics and dynamics; Local Group

Simultaneous epicardial and noncontact endocardial mapping of the canine right atrium : simulation and experiment - Sabouri, Sepideh; Matene, Elhacene; Vinet, Alain; Richer, Louis-Philippe; Cardinal, René; Armour, J. Andrew; Pagé, Pierre; Kus, Teresa; Jacquemet, Vincent (PLoS ONE, 2014)
Epicardial high-density electrical mapping is a well-established experimental instrument to monitor in vivo the activity of the atria in response to modulations of the autonomic nervous system in sinus rhythm. In regions that are not accessible by epicardial mapping, noncontact endocardial mapping performed through a balloon catheter may provide a more comprehensive description of atrial activity. We developed a computer model of the canine right atrium to compare epicardial and noncontact endocardial mapping. The model was derived from an experiment in which electroanatomical reconstruction, epicardial mapping (103 electrodes), noncontact endocardial mapping (2048 virtual electrodes computed from a 64-channel balloon catheter), and direct-contact endocardial catheter recordings were simultaneously performed in a dog. The recording system was simulated in the computer model. For simulations and experiments (after atrio-ventricular node suppression), activation maps were computed during sinus rhythm. Repolarization was assessed by measuring the area under the atrial T wave (ATa), a marker of repolarization gradients. Results showed an epicardial-endocardial correlation coefficients of 0.80 and 0.63 (two dog experiments) and 0.96 (simulation) between activation times, and a correlation coefficients of 0.57 and 0.46 (two dog experiments) and 0.92 (simulation) between ATa values. Despite distance (balloon-atrial wall) and dimension reduction (64 electrodes), some information about atrial repolarization remained present in noncontact signals.

Widespread nanoparticle-assay interference : implications for nanotoxicity testing - Ong, Kimberly J.; MacCormack, Tyson J.; Clark, Rhett J.; Ede, James D.; Ortega, Van A.; Felix, Lindsey C.; Dang, Michael K. M.; Ma, Guibin; Fenniri, Hicham; Veinot, Jonathan G. C.; Goss, Gregg G. (PLoS ONE, 2014)
The evaluation of engineered nanomaterial safety has been hindered by conflicting reports demonstrating differential degrees of toxicity with the same nanoparticles. The unique properties of these materials increase the likelihood that they will interfere with analytical techniques, which may contribute to this phenomenon. We tested the potential for: 1) nanoparticle intrinsic fluorescence/absorbance, 2) interactions between nanoparticles and assay components, and 3) the effects of adding both nanoparticles and analytes to an assay, to interfere with the accurate assessment of toxicity. Silicon, cadmium selenide, titanium dioxide, and helical rosette nanotubes each affected at least one of the six assays tested, resulting in either substantial over- or under-estimations of toxicity. Simulation of realistic assay conditions revealed that interference could not be predicted solely by interactions between nanoparticles and assay components. Moreover, the nature and degree of interference cannot be predicted solely based on our current understanding of nanomaterial behaviour. A literature survey indicated that ca. 95% of papers from 2010 using biochemical techniques to assess nanotoxicity did not account for potential interference of nanoparticles, and this number had not substantially improved in 2012. We provide guidance on avoiding and/or controlling for such interference to improve the accuracy of nanotoxicity assessments.

Shocks and star formation in Stephan's Quintet. I. Gemini spectroscopy of Hα-bright knots - Konstantopoulos, I. S.; Appleton, P. N.; Guillard, P.; Trancho, G.; Cluver, M. E.; Bastian, N.; Charlton, J. C.; Fedotov, K.; Gallagher, S. C.; Smith, L. J.; Struck, C. J. (The Astrophysical Journal, 2014)
We present a Gemini-GMOS spectroscopic study of Hubble Space Telescope (HST)-selected Hα-emitting regions in Stephan's Quintet (HCG 92), a nearby compact galaxy group, with the aim of disentangling the processes of shock-induced heating and star formation in its intra-group medium. The ≈40 sources are distributed across the system, but most densely concentrated in the ∼kiloparsec-long shock region. Their spectra neatly divide them into narrow- and broad-line emitters, and we decompose the latter into three or more emission peaks corresponding to spatial elements discernible in HST imaging. The emission-line ratios of the two populations of Hα-emitters confirm their nature as H II regions (90% of the sample) or molecular gas heated by a shock front propagating at ≲300 km s-1. Their redshift distribution reveals interesting three-dimensional structure with respect to gas-phase baryons, with no H II regions associated with shocked gas, no shocked regions in the intruder galaxy NGC 7318B, and a sharp boundary between shocks and star formation. We conclude that star formation is inhibited substantially, if not entirely, in the shock region. Attributing those H II regions projected against the shock to the intruder, we find a lopsided distribution of star formation in this galaxy, reminiscent of pileup regions in models of interacting galaxies. The Hα luminosities imply mass outputs, star formation rates, and efficiencies similar to nearby star-forming regions. Two large knots are an exception to this, being comparable in stellar output to the prolific 30 Doradus region. We also examine Stephan's Quintet in the context of compact galaxy group evolution, as a paradigm for intermittent star formation histories in the presence of a rich, X-ray-emitting intra-group medium. All spectra are provided as supplemental materials.
Keywords: galaxies: groups: individual (HCG 92); galaxies: individual (NGC 7317, NGC 7318A, NGC 7318B, NGC 7319); galaxies: interactions; galaxies: star formation; intergalactic medium; shock waves

Cavity optomechanics in gallium phosphide microdisks - Mitchell, Matthew; Hryciw, Aaron C.; Barclay, Paul E. (Applied Physics Letters, 2014)
We demonstrate gallium phosphide (GaP) microdisk optical cavities with intrinsic quality factors < 2.8 × 10⁵ and mode volumes <10(λ/n)³, and study their nonlinear and optomechanical properties. For optical intensities up to 8.0 × 10⁴intracavity photons, we observe optical loss in the microcavity to decrease with increasing intensity, indicating that saturable absorption sites are present in the GaP material, and that two-photon absorption is not significant. We observe optomechanical coupling between optical modes of the microdisk around 1.5 μm and several mechanical resonances, and measure an optical spring effect consistent with a theoretically predicted optomechanical coupling rate g₀/2π∼30 kHz for the fundamental mechanical radial breathing mode at 488 MHz.

The DiskMass Survey. VIII. On the relationship between disk stability and star formation - Westfall, Kyle B.; Andersen, David R.; Bershady, Matthew A.; Martinsson, Thomas P. K.; Swaters, Robert A.; Verheijen, Mark A. W. (The Astrophysical Journal, 2014)
We study the relationship between the stability level of late-type galaxy disks and their star-formation activity using integral-field gaseous and stellar kinematic data. Specifically, we compare the two-component (gas+stars) stability parameter from Romeo & Wiegert (Q RW), incorporating stellar kinematic data for the first time, and the star-formation rate estimated from 21 cm continuum emission. We determine the stability level of each disk probabilistically using a Bayesian analysis of our data and a simple dynamical model. Our method incorporates the shape of the stellar velocity ellipsoid (SVE) and yields robust SVE measurements for over 90% of our sample. Averaging over this subsample, we find a meridional shape of for the SVE and, at 1.5 disk scale lengths, a stability parameter of Q RW = 2.0 ± 0.9. We also find that the disk-averaged star-formation-rate surface density () is correlated with the disk-averaged gas and stellar mass surface densities (Σ e, g and Σ e, *) and anti-correlated with Q RW. We show that an anti-correlation between and Q RW can be predicted using empirical scaling relations, such that this outcome is consistent with well-established statistical properties of star-forming galaxies. Interestingly, is not correlated with the gas-only or star-only Toomre parameters, demonstrating the merit of calculating a multi-component stability parameter when comparing to star-formation activity. Finally, our results are consistent with the Ostriker et al. model of self-regulated star-formation, which predicts . Based on this and other theoretical expectations, we discuss the possibility of a physical link between disk stability level and star-formation rate in light of our empirical results.
Keywords: galaxies: evolution; galaxies: kinematics and dynamics; galaxies: spiral; galaxies: star formation

Real-time resistance, transmission and figure-of-merit analysis for transparent conductors under stretching-mode strain - Hauger, T. C.; Zeberoff, A.; Worfolk, B. J.; Elias, A. L.; Harris, K. D. (Solar Energy Materials and Solar Cells, 2014)
In this paper, we describe an apparatus capable of measuring electrical resistance and light transmission through a flexible transparent conductor (TC) as it is actively deformed. The measurements are performed in situ with time resolution on the order of ~100 ms, and the resistance/transmission data is further used to calculate TC figures-of-merit in real-time. With this instrument, we are able to track and compare the evolution of figures-of-merit for different TCs as they are actively deformed. To demonstrate the tool, we evaluate several common TCs including indium tin oxide, poly(3,4- ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS), and silver nanowires, as well as a more unconventional nanowire/PEDOT:PSS hybrid. As expected, indium tin oxide degrades rapidly with strain, while the more flexible PEDOT:PSS is far more strain tolerant. The nanowire/PEDOT:PSS composite is found to produce an advantageous effect, as the silver nanowires generate large figures-of-merit at low strain, and the addition of a PEDOT:PSS component vastly improves strain tolerance.
Keywords: Flexible electronics; Stretchable electronics; Transparent conductors; Printable electronics; Mechanical testing; Strain tolerance

Hubble Space Telescope and ground-based observations of the Type Iax Supernovae SN 2005HK and SN 2008A - McCully, Curtis; Jha, Saubabh W.; Foley, Ryan J.; Chornock, Ryan; Holtzman, Jon A.; Balam, David D.; Branch, David; Filippenko, Alexi V.; Frieman, Joshua; Fynbo, Johan; Galbany, Lluis; Ganeshalingam, Mohan; et al. (The Astrophysical Journal, 2014)
We present Hubble Space Telescope (HST) and ground-based optical and near-infrared observations of SN 2005hk and SN 2008A, typical members of the Type Iax class of supernovae (SNe). Here we focus on late-time observations, where these objects deviate most dramatically from all other SN types. Instead of the dominant nebular emission lines that are observed in other SNe at late phases, spectra of SNe 2005hk and 2008A show lines of Fe II, Ca II, and FeI more than a year past maximum light, along with narrow [FeII] and [CaII] emission. We use spectral features to constrain the temperature and density of the ejecta, and find high densities at late times, with ne ≳ 109 cm-3. Such high densities should yield enhanced cooling of the ejecta, making these objects good candidates to observe the expected "infrared catastrophe," a generic feature of SN Ia models. However, our HSTphotometry of SN 2008A does not match the predictions of an infrared catastrophe. Moreover, our HST observations rule out a "complete deflagration" that fully disrupts the white dwarf for these peculiar SNe, showing no evidence for unburned material at late times. Deflagration explosion models that leave behind a bound remnant can match some of the observed properties of SNe Iax, but no published model is consistent with all of our observations of SNe 2005hk and 2008A.
Keywords: supernovae: general; supernovae: individual (SN 2002cx, SN 2005hk, SN 2008A)

Nanostructured Sn₃₀Co₃₀C₄₀ alloys for lithium-ion battery negative electrodes prepared by horizontal roller milling - Ferguson, P. P.; Le, Dinh-Ba; Todd, A. D. W.; Martine, M. L.; Trussler, S.; Obrovac, M. N.; Dahn, J. R. (Journal of Alloys and Compounds, 2014)
Horizontal roller milling was used to prepare Sn₃₀Co₃₀C₄₀ electrode materials. By varying the milling conditions, it was possible to obtain nanostructured materials whose X-ray diffraction patterns mimicked the diffraction pattern of the same material obtained by vertical-axis attritor milling or by co-sputtering. Electrochemical testing showed that composite electrodes made from each of the prepared materials showed stable charge-discharge capacity for at least 100 charge discharge cycles and displayed stable differential capacity versus potential profiles. Small angle neutron scattering results showed that samples prepared by roller milling and by attriting showed similar nanostructure with Co-Sn grains of about 60 Å in a carbon matrix.
Keywords: Alloy negative electrodes; Roller milling; Nanostructured materials; Lithium-ion batteries

The PAndAS field of streams : stellar structures in the Milky Way halo toward Andromeda and Triangulum - Martin, Nicholas F.; Ibata, Rodrigo A.; Rich, R. Michael; Collins, Michelle L. M.; Fardal, Mark A.; Irwin, Michael J.; Lewis, Geraint F.; McConnachie, Alan W.; Babul, Arif; Bate, Nicholas F.; Chapman, Scott C.; Conn, Anthony R.; et al. (The Astrophysical Journal, 2014)
We reveal the highly structured nature of the Milky Way (MW) stellar halo within the footprint of the Pan-Andromeda Archaeological Survey (PAndAS) photometric survey from blue main sequence (MS) and MS turn-off stars. We map no fewer than five stellar structures within a heliocentric range of 5-30 kpc. Some of these are known (the Monoceros Ring, the Pisces/Triangulum globular cluster stream), but we also uncover three well-defined stellar structures that could be, at least partly, responsible for the so-called Triangulum/Andromeda and Triangulum/Andromeda 2 features. In particular, we trace a new faint stellar stream located at a heliocentric distance of 17 kpc. With a surface brightness of Σ V 32-32.5 mag arcsec-2, it follows an orbit that is almost parallel to the Galactic plane north of M31 and has so far eluded surveys of the MW halo as these tend to steer away from regions dominated by the Galactic disk. Investigating our follow-up spectroscopic observations of PAndAS, we serendipitously uncover a radial velocity signature from stars that have colors and magnitudes compatible with the stream. From the velocity of eight likely member stars, we show that this stellar structure is dynamically cold, with an unresolved velocity dispersion that is lower than 7.1 km s-1 at the 90% confidence level. Along with the width of the stream (300-650 pc), its dynamics point to a dwarf-galaxy-accretion origin. The numerous stellar structures we can map in the MW stellar halo between 5 and 30 kpc and their varying morphology is a testament to the complex nature of the stellar halo at these intermediate distances.
Keywords: Galaxy: halo; Galaxy: structure; Local Group

Fabrication of nanoelectromechanical systems via the integration of high surface area glancing angle deposition thin films - Westwood, J. N.; Sauer, V. T. K.; Kwan, J. K.; Hiebert, W. K.; Sit, J. C. (Journal of Micromechanics and Microengineering, 2014)
Nanoelectromechanical systems (NEMS) coated with a high surface area thin film are fabricated. Glancing angle deposition (GLAD) is used to uniformly deposit high surface area, nanostructured SiO2 films on top of released NEMS. The resonance frequencies and quality factors are measured to assess the potential of the high surface area NEMS for sensing experiments. Resonance frequencies of coated cantilevers, although reduced by mass loading, can be predicted accurately using our derived model. Compressive stress makes the resonance frequencies of coated doubly-clamped beams difficult to predict. The quality factors of the coated NEMS are reduced by one order of magnitude by a quasi-continuous layer at the base of the GLAD film, which also introduces an estimated compressive stress of 5.3-9.3 MPa. The limit of detection is demonstrated to be ∼2 pg cm-2. With this successful proof-of-concept demonstration, we anticipate the future use of these devices as high surface area gravimetric mass sensors for applications such as gas chromatography.
Keywords: glancing angle deposition; nanoelectromechanical systems; thin films; nanofabrication

Bimodal dwell-fatigue Weibull distribution of forged titanium IMI 834 - Toubal, Lofti; Bocher, Philippe; Moreau, André (International Journal of Damage Mechanics, 2014)
This study addresses cumulative damage and its evolution during the cold dwell fatigue of a near-α titanium alloy. An experimental study was undertaken to examine the evolution of life, strain, strength and damage of 13 titanium IMI 834 samples cut from a single disk forging. The samples were tested in the same dwell-fatigue loading conditions. In the dwell phase, the load is maintained at 80% of ultimate tensile strength (824 MPa, 90% of yield strength) for 30 s. The secant Young’s modulus and inelastic strain at minimum load were measured in order to document the evolution of the irreversible damage against the number of cycles for all specimens. Experimental observations show significant differences in dwell-fatigue life and damage behavior. This mechanical analysis and an analysis of the cumulative Weibull reliability distribution suggest a bimodal dwell-fatigue failure process. Some features of the mechanical behavior can be used to sort the samples according to each of the two failure modes and improve the reliability of the fatigue test campaign.
Keywords: Titanium alloy; dwell fatigue; bimodal Weibull distribution; damage; strain

Shaking alone induces de novo conversion of recombinant prion proteins to β-sheet rich oligomers and fibrils - Ladner, Carol L.; Griffith, Bethany J.; Wishart, David S. (PLoS ONE, 2014)
The formation of β-sheet rich prion oligomers and fibrils from native prion protein (PrP) is thought to be a key step in the development of prion diseases. Many methods are available to convert recombinant prion protein into β-sheet rich fibrils using various chemical denaturants (urea, SDS, GdnHCl), high temperature, phospholipids, or mildly acidic conditions (pH 4). Many of these methods also require shaking or another form of agitation to complete the conversion process. We have identified that shaking alone causes the conversion of recombinant PrP to β-sheet rich oligomers and fibrils at near physiological pH (pH 5.5 to pH 6.2) and temperature. This conversion does not require any denaturant, detergent, or any other chemical cofactor. Interestingly, this conversion does not occur when the water-air interface is eliminated in the shaken sample. We have analyzed shaking-induced conversion using circular dichroism, resolution enhanced native acidic gel electrophoresis (RENAGE), electron microscopy, Fourier transform infrared spectroscopy, thioflavin T fluorescence and proteinase K resistance. Our results show that shaking causes the formation of β-sheet rich oligomers with a population distribution ranging from octamers to dodecamers and that further shaking causes a transition to β-sheet fibrils. In addition, we show that shaking-induced conversion occurs for a wide range of full-length and truncated constructs of mouse, hamster and cervid prion proteins. We propose that this method of conversion provides a robust, reproducible and easily accessible model for scrapie-like amyloid formation, allowing the generation of milligram quantities of physiologically stable β-sheet rich oligomers and fibrils. These results may also have interesting implications regarding our understanding of prion conversion and propagation both within the brain and via techniques such as protein misfolding cyclic amplification (PMCA) and quaking induced conversion (QuIC).

Searching for dust around hyper metal poor stars - Venn, Kim A.; Puzia, Thomas H.; Divell, Mike; Côté, Stephanie; Lambert, David L.; Starkenburg, Else (The Astrophysical Journal, 2014)
We examine the mid-infrared fluxes and spectral energy distributions for stars with iron abundances [Fe/H] <-5, and other metal-poor stars, to eliminate the possibility that their low metallicities are related to the depletion of elements onto dust grains in the formation of a debris disk. Six out of seven stars examined here show no mid-IR excesses. These non-detections rule out many types of circumstellar disks, e.g., a warm debris disk (T ≤ 290 K), or debris disks with inner radii ≤1 AU, such as those associated with the chemically peculiar post-asymptotic giant branch spectroscopic binaries and RV Tau variables. However, we cannot rule out cooler debris disks, nor those with lower flux ratios to their host stars due to, e.g., a smaller disk mass, a larger inner disk radius, an absence of small grains, or even a multicomponent structure, as often found with the chemically peculiar Lambda Bootis stars. The only exception is HE0107-5240, for which a small mid-IR excess near 10 μm is detected at the 2σ level; if the excess is real and associated with this star, it may indicate the presence of (recent) dust-gas winnowing or a binary system.
Keywords: dust, extinction; stars: abundances; stars: chemically peculiar; stars: individual; (HE0107-5240)

Chiromers : conformation-driven mirror-image supramolecular chirality isomerism identified in a new class of helical rosette nanotubes - Hemraz, Usha D.; El-Bakkari, Mounir; Yamazaki, Takeshi; Cho, Jae-Young; Beingessner, Rachel L.; Fenniri, Hicham (Nanoscale, 2014)
Rosette nanotubes are biologically inspired nanostructures, formed through the hierarchical organization of a hybrid DNA base analogue (G∧C), which features hydrogen-bonding arrays of guanine and cytosine. Several twin-G∧C motifs functionalized with chiral moieties, which undergo a self-assembly process under methanolic and aqueous conditions to produce helical rosette nanotubes (RNTs), were synthesized and characterized. The built-in molecular chirality in the twin-G∧C building blocks led to the supramolecular chirality exhibited by the RNTs, as evidenced by the CD activity. Depending on the motifs and environmental conditions, mirror-image supramolecular chirality due to absolute molecular chirality, solvent-induced and structure-dependent supramolecular chirality inversion, and pH-controlled chiroptical switching were observed.

Fundamental limitations of high contrast imaging set by small sample statistics - Mawet, D.; Milli, J.; Wahhaj, Z.; Pelat, D.; Absil, O.; Delacroix, C.; Boccaletti, A.; Kasper, M.; Kenworthy, M.; Marois, C.; Mennesson, B.; Pueyo, L. (The Astrophysical Journal, 2014)
In this paper, we review the impact of small sample statistics on detection thresholds and corresponding confidence levels (CLs) in high-contrast imaging at small angles. When looking close to the star, the number of resolution elements decreases rapidly toward small angles. This reduction of the number of degrees of freedom dramatically affects CLs and false alarm probabilities. Naively using the same ideal hypothesis and methods as for larger separations, which are well understood and commonly assume Gaussian noise, can yield up to one order of magnitude error in contrast estimations at fixed CL. The statistical penalty exponentially increases toward very small inner working angles. Even at 5-10 resolution elements from the star, false alarm probabilities can be significantly higher than expected. Here we present a rigorous statistical analysis that ensures robustness of the CL, but also imposes a substantial limitation on corresponding achievable detection limits (thus contrast) at small angles. This unavoidable fundamental statistical effect has a significant impact on current coronagraphic and future high-contrast imagers. Finally, the paper concludes with practical recommendations to account for small number statistics when computing the sensitivity to companions at small angles and when exploiting the results of direct imaging planet surveys.
Keywords: methods: statistical; techniques: high angular resolution

The massive survey. I. A volume-limited integral-field spectroscopic study of the most massive early-type galaxies within 108 Mpc - Ma, Chung-Pei; Greene, Jenny E.; McConnell, Nicholas; Janish, Ryan; Blakeslee, John P.; Thomas, Jens; Murphy, Jeremy D. (The Astrophysical Journal, 2014)
Massive early-type galaxies represent the modern day remnants of the earliest major star formation episodes in the history of the universe. These galaxies are central to our understanding of the evolution of cosmic structure, stellar populations, and supermassive black holes, but the details of their complex formation histories remain uncertain. To address this situation, we have initiated the MASSIVE Survey, a volume-limited, multi-wavelength, integral-field spectroscopic (IFS) and photometric survey of the structure and dynamics of the ∼100 most massive early-type galaxies within a distance of 108 Mpc. This survey probes a stellar mass range M∗ ≳ 1011.5 M⊙ and diverse galaxy environments that have not been systematically studied to date. Our wide-field IFS data cover about two effective radii of individual galaxies, and for a subset of them, we are acquiring additional IFS observations on sub-arcsecond scales with adaptive optics. We are also acquiring deep K-band imaging to trace the extended halos of the galaxies and measure accurate total magnitudes. Dynamical orbit modeling of the combined data will allow us to simultaneously determine the stellar, black hole, and dark matter halo masses. The primary goals of the project are to constrain the black hole scaling relations at high masses, investigate systematically the stellar initial mass function and dark matter distribution in massive galaxies, and probe the late-time assembly of ellipticals through stellar population and kinematical gradients. In this paper, we describe the MASSIVE sample selection, discuss the distinct demographics and structural and environmental properties of the selected galaxies, and provide an overview of our basic observational program, science goals and early survey results.
Keywords: dark matter; galaxies: elliptical and lenticular, cD; galaxies: evolution; galaxies: kinematics and dynamics; galaxies: stellar content; galaxies: structure

Water-soluble photoluminescent d-mannose and l-alanine functionalized silicon nanocrystals and their application to cancer cell imaging - Zhai, Yi; Dasog, Mita; Snitynsky, Ryan B.; Purkait, Tapas K.; Aghajamali, Maryam; Hahn, Allison H.; Sturdy, Christopher B.; Lowary, Todd L.; Veinot, Jonathan G. C. (Journal of Materials Chemistry B, 2014)
Herein, we report the straightforward synthesis, photoluminescent properties, and cell imaging studies of d-mannose and l-alanine functionalized silicon nanocrystals (SiNCs). Tailoring nanocrystal surface functionalization is essential to interfacing SiNCs with their environment and rendering them stable-surface modification also offers the opportunity to target specific cell types for imaging. A simple and versatile surface modification procedure was developed to tether biomolecules onto the SiNC surfaces and render them water-soluble. The presented approach is precious metal-catalyst free, straightforward, and provides carbohydrate and amino acid functionalized SiNCs. The functionalized SiNCs have been investigated by fluorescence microscopy and our results indicate that they can be internalized by MCF-7 human breast cancer cells as shown in the cell imaging studies. The obtained SiNCs were characterized using FTIR, XPS, PL, and TEM. This journal is
Keywords: Cancer cells; Functionalized; L-alanine; Silicon nanocrystals

A wideband MMIC low noise amplifier with series and shunt feedback - Rossi, Filippo; Chiong, Chau-Ching; Wang, Huei; Chen, Ming-Tang; Jiang, Frank; So, Poman; Claude, Stéphane; Bornemann, Jens (Proceedings - ANTEM 2014: 2014 16th International Symposium on Antenna Technology and Applied Electromagnetics, 2014)
A two-stage MMIC low noise amplifier design is presented using series and shunt feedbacks to achieve simultaneously low noise, input matching and gain flatness performances across the frequency range of 4 to 12 GHz. The amplifier fits into a small die of 2×1 mm2, and achieves a flat gain of 20 dB and a minimum noise figure of 1.5 dB.
Keywords: Amplifiers (electronic); Broadband amplifiers; Feedback; Feedback amplifiers; Monolithic microwave integrated circuits; Noise figure; Frequency ranges; Gain flatness; Input matching; LNA; Minimum noise figure; Mmic low noise amplifiers; Shunt feedback; Wide-band; Low noise amplifiers

Assessment and characterization of volcanic ash threat to gas turbine engine performance - Davison, Craig R.; Rutke, Timothy A. (Journal of Engineering for Gas Turbines and Power, 2014)
Multiple volcanoes erupt yearly propelling volcanic ash into the atmosphere and creating an aviation hazard. The plinian eruption type is most likely to create a significant aviation hazard. Plinian eruptions can eject large quantities of fine ash up to an altitude of 50,000 m (164,000 ft). While large airborne particles rapidly fall, smaller particles at reduced concentrations drift for days to weeks as they gradually descend and deposit on the ground. Very small particles, less than 1 μm, can remain aloft for years. An average of three aircraft encounters with volcanic ash was reported every year between 1973 and 2003. Of these, eight resulted in some loss of engine power, including a complete shutdown of all four engines on a Boeing 747. However, no crashes have been attributed to volcanic ash. The major forms of engine damage caused by volcanic ash are: (1) deposition of ash on turbine nozzles and blades due to glassification (2) erosion of compressor and turbine blades (3) carbon deposits on fuel nozzles. The combination of these effects can push the engine to surge and flame out. If a flame out occurs, engine restart may be possible. Less serious engine damage can also occur. In most cases the major damage will require an engine overhaul long before the minor damage becomes an operational issue, but under some conditions no sign of volcanic ash is evident and the turbine cooling system blockage could go unnoticed until an engine inspection is performed. Several organizations provide aircrew procedures to respond to encounters with a volcanic ash cloud. If a volcanic ash encounter is suspected, then an engine inspection, including borescope, should be performed with particular attention given to the turbine cooling system.
Keywords: Aircraft accidents; Aviation; Cooling systems; Deposits; Hazards; Nozzles; Thermoelectric equipment; Turbomachine blades; Volcanoes; Airborne particle; Aircraft encounters; Carbon deposites; Engine inspection; Operational issues; Plinian eruption; Turbine cooling systems; Volcanic ash clouds; Engines

A comparison of the effect of riveting and cold expansion on the strain distribution and fatigue performance of fiber metal laminates - Backman, David; Patterson, Eann A. (Journal of Strain Analysis for Engineering Design, 2014)
Fatigue tests carried out on three configurations (unexpanded, cold expanded and riveted) of fiber metal laminate material clearly demonstrated the beneficial effect of riveting compared to cold expansion in zero load transfer joints, for an approximately equivalent level of interference. Digital image correlation was used to measure the in-plane surface strain on cold expanded and riveted coupons during fatigue loading, and for the first time, digital image correlation was combined with pressure sensitive films to measure the strains resulting from the application of the rivet, including those under the rivet head. A comparison of the resultant strain field showed that the application of a rivet significantly reduces the stress concentration at the central hole and is effective in extending fatigue life. Some rivet heads were removed by milling, and the results from subsequent fatigue tests were used together with closed-form calculations to explain the findings of this study. It was concluded that the beneficial effect of riveting was less as a result of interference hole filling on the part of the rivet shank, but more a combination of the effect of interference and compression through the joint thickness.
Keywords: Composite materials; Fatigue of materials; Fatigue testing; Image analysis; Laminates; Riveting; Strain measurement; Stress concentration; Beneficial effects; Digital image correlations; fastening; Fatigue performance; Fiber metal laminates; Pressure films; Pressure sensitive films; Strain distributions

Graded piezoelectric cylinders subjected to high electric fields and comparison of their frequency response with piezoelectric plates - Babaei, M. H.; Akhras, G. (Meccanica, 2014)
In this paper we investigated a radially polarized piezoceramic cylinder with graded piezoelectric properties, and used a nonlinear model for piezoceramics subjected to high electric fields. We investigated the nonlinear behavior of this material by examining changes in its electric-field-dependent dielectric and piezoelectric coefficients caused by domain wall motion. The Galerkin finite-element method was used to solve the governing equations of the axisymmetrically loaded heterogeneous piezoceramic medium subjected to harmonic electrical loading. Stress, displacement, resonance, and frequency responses were compared for homogeneous and graded cylinders; additionally, we compared the results of linear and nonlinear studies. We showed that the effective stress was higher within the graded cylinder than within the homogeneous cylinder, and that the nonlinearity caused by domain wall motion was less pronounced for the graded cylinder than for the homogeneous cylinder. The frequency responses of homogeneous and heterogeneous piezocylinders were also compared with those of piezoelectric plates. We concluded that-unlike for graded plates, which have a more desirable frequency response than homogeneous plates-graded cylinders are not superior to homogeneous cylinders. The finite-element solution in this paper is verified by simulations using COMSOL Multiphysics software.
Keywords: Cylinders (shapes); Electric fields; Finite element method; Galerkin methods; Piezoelectric ceramics; Piezoelectric devices; Piezoelectricity; Domain wall motion; Functionally graded; High electric fields; Nonlinear behaviours; Piezoceramic cylinder; Piezoelectric coefficient; Piezoelectric cylinder; Piezoelectric property; Frequency response

Traceability of loss measurements of extra high voltage (EHV) three-phase shunt reactors - So, Eddy; Verhoeven, Rob (2014 Conference on Precision Electromagnetic Measurements (CPEM 2014), 2014)
An overview of traceability issues of loss measurements of EHV 3-phase shunt reactors is presented. Loss measurements of a 345 kV - 55 MVAr three-phase shunt reactor at SMIT Transformers, including their uncertainties, are presented and discussed. The measurement results are confirmed with those obtained using a special HV inductance bridge.
Keywords: Extra high voltage; Measurement uncertainty; Shunt reactors; Three phase; traceability

Aeromonas hydrophila flagella glycosylation: Involvement of a lipid carrier - Merino, Susana; Fulton, Kelly M.; Twine, Susan M.; Wilhelms, Markus; Molero, Raquel; Tomás, Juan M. (PLoS ONE, 2014)
Polar flagellin proteins from Aeromonas hydrophila strain AH-3 (serotype O34) were found to be O-glycosylated with a heterogeneous glycan. Mutants unable to produce WecP or Gne enzymes showed altered motility, and the study of their polar flagellin glycosylation showed that the patterns of glycosylation differed from that observed with wild type polar flagellin. This suggested the involvement of a lipid carrier in glycosylation. A gene coding for an enzyme linking sugar to a lipid carrier was identified in strain AH-3 (WecX) and subsequent mutation abolished completely motility, flagella production by EM, and flagellin glycosylation. This is the first report of a lipid carrier involved in flagella O-glycosylation. A molecular model has been proposed. The results obtained suggested that the N -acetylhexosamines are N-acetylgalactosamines and that the heptasaccharide is completely independent of the O34-antigen lipopolysaccharide. Furthermore, by comparing the mutants with differing degrees of polar flagellin glycosylation, we established their importance in A. hydrophila flagella formation and motility.
Keywords: ferredoxin nitrite reductase; flagellin; lipopolysaccharide; Aeromonas hydrophila; bacterial strain; bacterium isolation; biosynthesis; cell motility; controlled study; DNA fragmentation; enzyme specificity; epimerization; glycosylation; microscopy; molecular model; molecular weight; nucleotide sequence; plasmid; polymerase chain reaction; protein analysis; protein modification; protein purification; sequence alignment; tandem mass spectrometry; ubiquitination; Acetylgalactosamine; Amino Acid Sequence; Carbohydrate Conformation; Carbohydrate Sequence; Carrier Proteins; Gene Expression; Lipid Metabolism; Molecular Sequence Data; Protein Processing, Post-Translational

Complete photoionization experiments via ultrafast coherent control with polarization multiplexing - Hockett, P.; Wollenhaupt, M.; Lux, C.; Baumert, T. (Physical Review Letters, 2014)
Photoelectron angular distributions (PADs) obtained from ionization of potassium atoms using moderately intense femtosecond IR fields (∼1012  W cm−2) of various polarization states are shown to provide a route to “complete” photoionization experiments. Ionization occurs by a net three-photon absorption process, driven via the 4s→4p resonance at the one-photon level. A theoretical treatment incorporating the intrapulse electronic dynamics allows for a full set of ionization matrix elements to be extracted from 2D imaging data. 3D PADs generated from the extracted matrix elements are also compared to experimental, tomographically reconstructed, 3D photoelectron distributions, providing a sensitive test of their validity. Finally, application of the determined matrix elements to ionization via more complex, polarization-shaped, pulses is demonstrated, illustrating the utility of this methodology towards detailed understanding of complex ionization control schemes and suggesting the utility of such “multiplexed” intrapulse processes as powerful tools for measurement.
Keywords: Experiments; Photons; Polarization; Coherent control; Electronic dynamics; Ionization matrices; Photoelectron angular distributions; Polarization multiplexing; Polarization state; Theoretical treatments; Three photon absorption; Photoionization

Feature selection for high-dimensional class-imbalanced data sets using Support Vector Machines - Maldonado, Sebastián; Weber, Richard; Famili, Fazel (Information Sciences, 2014)
Feature selection and classification of imbalanced data sets are two of the most interesting machine learning challenges, attracting a growing attention from both, industry and academia. Feature selection addresses the dimensionality reduction problem by determining a subset of available features to build a good model for classification or prediction, while the class-imbalance problem arises when the class distribution is too skewed. Both issues have been independently studied in the literature, and a plethora of methods to address high dimensionality as well as class-imbalance has been proposed. The aim of this work is to simultaneously explore both issues, proposing a family of methods that select those attributes that are relevant for the identification of the target class in binary classification. We propose a backward elimination approach based on successive holdout steps, whose contribution measure is based on a balanced loss function obtained on an independent subset. Our experiments are based on six highly imbalanced microarray data sets, comparing our methods with well-known feature selection techniques, and obtaining a better prediction with consistently fewer relevant features.
Keywords: Feature selection; Imbalanced data set; Dimensionality reduction; Support vector machine; Data mining

The signature of dissipation in the mass-size relation: Are bulges simply spheroids wrapped in a disc? - Berg, Trystyn A. M.; Simard, Luc; Mendel, J. Trevor; Ellison, Sara L. (Monthly Notices of the Royal Astronomical Society: Letters, 2014)
The relation between the stellar mass and size of a galaxy's structural subcomponents, such as discs and spheroids, is a powerful way to understand the processes involved in their formation. Using very large catalogues of photometric bulge+disc structural decompositions and stellar masses from the Sloan Digital Sky Survey Data Release Seven, we carefully define two large subsamples of spheroids in a quantitative manner such that both samples share similar characteristics with one important exception: the 'bulges' are embedded in a disc and the 'pure spheroids' are galaxies with a single structural component. Our bulge and pure spheroid subsample sizes are 76 012 and 171 243, respectively. Above a stellar mass of ̃1010M⊙, the mass-size relations of both subsamples are parallel to one another and are close to lines of constant surface mass density. However, the relations are offset by a factor of 1.4, which may be explained by the dominance of dissipation in their formation processes. Whereas the size-mass relation of bulges in discs is consistent with gas-rich mergers, pure spheroids appear to have been formed via a combination of 'dry' and 'wet' mergers.
Keywords: galaxies: bulges; galaxies: elliptical and lenticular; galaxies: evolution; NOx

Advances in high-field magnetic resonance spectroscopy in Alzheimer's disease - Zhang, Ningnannan; Song, Xiaowei; Bartha, Robert; Beyea, Steven; D'Arcy, Ryan; Zhang, Yunting; Rockwood, Kenneth (Current Alzheimer Research, 2014)
Alzheimer's disease (AD) affects several important molecules in brain metabolism. The resulting neurochemical changes can be quantified non-invasively in localized brain regions using in vivo single-voxel proton magnetic resonance spectroscopy (SV 1H MRS). Although the often heralded diagnostic potential of MRS in AD largely remains unfulfilled, more recent use of high magnetic fields has led to significantly improved signal-to-noise ratios and spectral resolutions, thereby allowing clinical applications with increased measurement reliability. The present article provides a comprehensive review of SV 1H MRS studies on AD at high magnetic fields (3.0 Tesla and above). This review suggests that patterned regional differences and longitudinal alterations in several neurometabolites are associated with clinically established AD. Changes in multiple metabolites are identifiable even at early stages of AD development. By combining information of neurochemicals in different brain regions revealing either pathological or compensatory changes, high field MRS can be evaluated in AD diagnosis and in the detection of treatment effects. To achieve this, standardization of data acquisition and analytical approaches is needed.
Keywords: 4 aminobutyric acid; glucose; glutamic acid; glutamine; glutathione; inositol; lactic acid; n acetylaspartylglutamic acid; taurine; aging; Alzheimer disease; disease course; information processing; magnetic field; Medline; metabolite; nuclear magnetic resonance spectroscopy; single voxel proton magnetic resonance spectroscopy

The impact of cellulose nanocrystals on the aggregation and initial adhesion of Pseudomonas fluorescens bacteria - Sun, Xiaohui; Lu, Qingye; Boluk, Yaman; Liu, Yang (Soft Matter, 2014)
Deposition on silica surfaces of two Pseudomonas fluorescens strains (CHA0 and CHA19-WS) having different extracellular polymeric substance (EPS) producing capacities was studied in the absence and presence of cellulose nanocrystals (CNCs). Batch (batch soaking) and continuous flow (quartz crystal microbalance with dissipation) methods were used to evaluate the impact of CNCs on bacterial initial adhesion. This study demonstrated that bacterial initial adhesion to solid surfaces can be significantly hindered by CNCs using both methods. In the presence of CNCs, it was observed that bacteria with more EPS aggregated more significantly compared to bacteria with less EPS, and that bacterial deposition under this condition decreased to a greater extent. The classic DLVO theory failed to predict bacterial adhesion behavior in this study. A detailed discussion is provided regarding potential antibacterial adhesion mechanisms of CNCs.
Keywords: Cellulose nano-crystals; Initial adhesions; Pseudomonas fluorescens bacteria

FRIENDLY regulates mitochondrial distribution, fusion, and quality control in Arabidopsis - El Zawily, Amr M.; Schwarzländer, Markus; Finkemeier, Iris; Johnston, Iain G.; Benamar, Abdelilah; Cao, Yongguo; Gissot, Clémence; Meyer, Andreas J.; Wilson, Ken; Datla, Raju; Macherel, David; Jones, Nick S.; et al. (Plant Physiology, 2014)
Mitochondria are defining components of most eukaryotes. However, higher plant mitochondria differ biochemically, morphologically, and dynamically from those in other eukaryotes. FRIENDLY, a member of the CLUSTERED MITOCHONDRIA superfamily, is conserved among eukaryotes and is required for correct distribution of mitochondria within the cell. We sought to understand how disruption of FRIENDLY function in Arabidopsis (Arabidopsis thaliana) leads to mitochondrial clustering and the effects of this aberrant chondriome on cell and whole-plant physiology. We present evidence for a role of FRIENDLY in mediating intermitochondrial association, which is a necessary prelude to mitochondrial fusion. We demonstrate that disruption of mitochondrial association, motility, and chondriome structure in friendly affects mitochondrial quality control and leads to mitochondrial stress, cell death, and strong growth phenotypes.

Tensile properties of Al-Cu 206 cast alloys with various iron contents - Liu, K.; Cao, X.; Chen, X.-G. (Metallurgical and Materials Transactions A: Physical Metallurgy and Materials Science, 2014)
The Al-Cu 206 cast alloys with varying alloy compositions (i.e., different levels of Fe, Mn, and Si) were investigated to evaluate the effect of the iron-rich intermetallics on the tensile properties. It is found that the tensile strength decreases with increasing iron content, but its overall loss is less than 10 pct over the range of 0.15 to 0.5 pct Fe at 0.3 pct Mn and 0.3 pct Si. At similar iron contents, the tensile properties of the alloys with dominant Chinese script iron-rich intermetallics are generally higher than those with the dominant platelet phase. In the solution and artificial overaging condition (T7), the tensile strength of the 206 cast alloys with more than 0.15 pct Fe is satisfactory, but the elongation does not sufficiently meet the minimum requirement of ductility (>7 pct) for critical automotive applications. However, it was found that both the required ductility and tensile strength can be reached at high Fe levels of 0.3 to 0.5 pct for the alloys with well-controlled alloy chemistry and microstructure in the solution and natural aging condition (T4), reinforcing the motivation for developing recyclable high-iron Al-Cu 206 cast alloys.
Keywords: Aluminum; Cast iron; Copper alloys; Ductility; Intermetallics; Iron; Manganese; Silicon; Tensile strength; Alloy chemistry; Alloy compositions; Automotive applications; Cast alloys; Chinese script; Iron content; Minimum requirements; Natural aging; Iron alloys

Calibrations for resistance welding at high pulsed currents - Djokic, Branislav (2014 Conference on Precision Electromagnetic Measurements (CPEM 2014), 2014)
Rogowski coils are widely used as high pulsed current sensors in resistance welding. Their operating conditions reflect on requirements for their calibration. A new calibration system has been developed at NRC Canada for calibrating current sensing coils and weld current monitors for AC resistance welding. The calibration system, which includes a high current source and a coaxial copper cage, has been evaluated at peak pulsed currents of up to 80 kA, at 60 Hz. The best expanded measurement uncertainties (k=2) have been estimated to be within 250 Î¼A/A for magnitude and 175 Î¼rad for phase.
Keywords: AC current measurement; Digital sampling; Measurement uncertainty; Pulsed currents; Rogowski Coil; Weld current; Calibration

Comparison of five major trichome regulatory genes in Brassica villosa with orthologues within the Brassicaceae - Nayidu, Naghabushana K.; Kagale, Sateesh; Taheri, Ali; Withana-Gamage, Thushan S.; Parkin, Isobel A. P.; Sharpe, Andrew G.; Gruber, Margaret Y. (PLoS ONE, 2014)
Coding sequences for major trichome regulatory genes, including the positive regulators GLABRA 1(GL1), GLABRA 2 (GL2), ENHANCER OF GLABRA 3 (EGL3), and TRANSPARENT TESTA GLABRA 1 (TTG1) and the negative regulator TRIPTYCHON (TRY), were cloned from wild Brassica villosa, which is characterized by dense trichome coverage over most of the plant. Transcript (FPKM) levels from RNA sequencing indicated much higher expression of the GL2 and TTG1 regulatory genes in B. villosa leaves compared with expression levels of GL1 and EGL3 genes in either B. villosa or the reference genome species, glabrous B. oleracea; however, cotyledon TTG1 expression was high in both species. RNA sequencing and Q-PCR also revealed an unusual expression pattern for the negative regulators TRY and CPC, which were much more highly expressed in trichomerich B. villosa leaves than in glabrous B. oleracea leaves and in glabrous cotyledons from both species. The B. villosa TRY expression pattern also contrasted with TRY expression patterns in two diploid Brassica species, and with the Arabidopsis model for expression of negative regulators of trichome development. Further unique sequence polymorphisms, protein characteristics, and gene evolution studies highlighted specific amino acids in GL1 and GL2 coding sequences that distinguished glabrous species from hairy species and several variants that were specific for each B. villosa gene. Positive selection was observed for GL1 between hairy and non-hairy plants, and as expected the origin of the four expressed positive trichome regulatory genes in B. villosa was predicted to be from B. oleracea. In particular the unpredicted expression patterns for TRY and CPC in B. villosa suggest additional characterization is needed to determine the function of the expanded families of trichome regulatory genes in more complex polyploid species within the Brassicaceae. © 2014 Nayidu et al.
Keywords: amino acid; plant RNA; vegetable protein; Arabidopsis; article; Brassica oleracea; Brassica villosa; Brassicaceae; controlled study; cotyledon; diploidy; DNA polymorphism; ENHANCER OF GLABRA gene; gene expression profiling; genetic variability; GLABRA 1 gene; GLABRA 2 gene; molecular cloning; molecular evolution; nonhuman; nucleotide sequence; orthology; plant development; plant gene; plant genome; plant leaf; prediction; regulator gene; RNA sequence; RNA transcription; TRANSPARENT TESTA GLABRA 1 gene; trichome; TRIPTYCHON gene

Uracil excision by endogenous SMUG1 glycosylase promotes efficient Ig class switching and impacts on A:T substitutions during somatic mutation - Dingler, Felix A.; Kemmerich, Kristin; Neuberger, Michael S.; Rada, Cristina (European Journal of Immunology, 2014)
Excision of uracil introduced into the immunoglobulin loci by AID is central to antibody diversification. While predominantly carried out by the UNG uracil-DNA glycosylase as reflected by deficiency in immunoglobulin class switching in Ung-/- mice, the deficiency is incomplete, as evidenced by the emergence of switched IgG in the serum of Ung-/- mice. Lack of switching in mice deficient in both UNG and MSH2 suggested that mismatch repair initiated a backup pathway. We now show that most of the residual class switching in Ung-/- mice depends upon the endogenous SMUG1 uracil-DNA glycosylase, with in vitro switching to IgG1 as well as serum IgG3, IgG2b, and IgA greatly diminished in Ung-/-Smug1-/- mice, and that Smug1 partially compensates for Ung deficiency over time. Nonetheless, using a highly MSH2-dependent mechanism, Ung-/-Smug1-/- mice can still produce detectable levels of switched isotypes, especially IgG1. While not affecting the pattern of base substitutions, SMUG1 deficiency in an Ung-/- background further reduces somatic hypermutation at A:T base pairs. Our data reveal an essential requirement for uracil excision in class switching and in facilitating noncanonical mismatch repair for the A:T phase of hypermutation presumably by creating nicks near the U:G lesion recognized by MSH2.
Keywords: Class switching; DNA deamination; Somatic hypermutation; Uracil; Immunoglobulin A; Immunoglobulin Class Switching; Immunoglobulin G; Mice; Mutation; MutS Homolog 2 Protein; Uracil; Uracil-DNA Glycosidase

Candidate detector assessment for the CASTOR mission - Scott, Alan D.; Cote, Patrick; Rowlands, Neil; Daigle, Olivier (SPIE - International Society for Optical Engineering. Proceedings, 2014)
The Cosmological Advanced Survey Telescope for Optical and UV Research (CASTOR) is a proposed Canadian Space Agency (CSA) mission that would provide panoramic, high-resolution imaging of 1/8th of the sky in the UV/optical (150-550 nm) spectral region. This small-satellite class mission would provide high angular resolution ultra-deep imaging in three broad filters to supplement data from planned international dark energy missions (Euclid, WFIRST) as well as from the Large Synoptic Survey Telescope (LSST). One of the leading technical risks on this mission is the UV sensitivity required to approach 26th magnitude in the near UV band. We are planning to characterize a selected candidate technology down to 150 nm. We will review the main scientific and technical drivers for the mission and show how they constrain the available detector options. We will compare the sensitivity and general applicability of CCD, EMCCD, hybridized and monolithic CMOS FPA options.
Keywords: Detectors; Focal plane arrays; Image reconstruction; Infrared detectors; Silicon; Silicon detectors; Space telescopes; Surveys; Canadian Space Agency; High angular resolutions; High-resolution imaging; Large synoptic survey telescopes; NUV; Spectral region; Technical drivers; Technical risks; Astronomy

Water quality - Water main renewal planner (Q-WARP): Development and application - Sadiq, Rehan; Kleiner, Yehuda; Rajani, Balvant; Tesfamariam, Solomon; Haider, Husnain (Journal of Water Supply: Research and Technology - AQUA, 2014)
The impact of deteriorating pipes on water quality (WQ) in the distribution network has not been consistently taken into account in decision making related to pipe renewals. In this paper, a detailed modeling approach based on fuzzy cognitive maps is developed using fuzzy rule-based models and fuzzy measures theory to investigate potential of WQ (physical, chemical, and biological) failure in distribution networks. Based on information and data obtained from preliminary analysis, literature, and expert opinion, a decision support tool named Q-WARP (water quality - water main renewal planner) is developed to consider uncertain, subjective/linguistic and/or incomplete data. Q-WARP provides a plausible way to represent and comprehend ill-defined and complex relationships such as those that govern WQ in the distribution network. The proposed model has the capacity to perform the 'baseline analysis' that performs risk assessment and risk evaluation; and the 'decision analysis' that performs risk management and guides decision making. The developed model has also been applied to a case study in Stanley Street (Philadelphia) to evaluate the model's capability. The results manifested that the model can efficiently assess the 'potential' for WQ failures and can also be used in decision making for WQ improvements by making infrastructure changes in distribution systems.
Keywords: Electric power distribution; Sensitivity analysis; Water distribution systems; Baseline analysis; Development and applications; Water mains; Decision theory; baseline survey; decision making; distribution system; infrastructural development; model test; pipeline; renewal policy; risk assessment; sensitivity analysis; spatial cognition; water quality; Pennsylvania; Philadelphia

Dissipative particle dynamics with an effective pair potential from integral equation theory of molecular liquids - Kobryn, Alexander E.; Nikolić, Dragan; Lyubimova, Olga; Gusarov, Sergey; Kovalenko, Andriy (The Journal of Physical Chemistry B, 2014)
We present a method of DPD simulation based on a coarse-grained effective pair potential obtained from the DRISM-KH molecular theory of solvation. The theory is first used to calculate the radial distribution functions of all-atom solute monomers in all-atom solvent and then to invert them into an effective pair potential between coarse-grained beads such that their fluid without solvent accounts for molecular specificities and solvation effects in the all-atom system. Bonded interactions are sampled in relatively short MD of the all-atom system and modeled with best multi-Gaussian fit. Replacing the heuristically defined conservative force potential in DPD, the coarse-grained effective pair potential is free from the artificial restrictions on potential range and shape and on equal volume of solute and solvent blobs inherent in standard DPD. The procedure is flexible in specifying coarse-grained mapping and enormously increases computational efficiency by eliminating solvent. The method is validated on polystyrene chains of various length in toluene at finite concentrations for room and polystyrene glass transition temperature. It yields the chain elastic properties and diffusion coefficient in good agreement with experiment and all-atom MD simulations. DPD with coarse-grained effective pair potential is capable of predicting both structural and dynamic properties of polymer solutions and soft matter with high accuracy and computational efficiency.
Keywords: Dissipative particle dynamics; Effective pair potentials; Integral-equation theory; Molecular liquids

Photosynthetic capacity of the inflorescence is a major contributor to daily-C-gain and the responsiveness of growth to elevated CO2 in Arabidopsis thaliana with repressed expression of mitochondrial-pyruvate-dehydrogenase-kinase - Leonardos, Evangelos D.; Rauf, Shezad A.; Weraduwage, Sarathi M.; Marillia, Elizabeth-France; Taylor, David C.; Micallef, Barry J.; Grodzinski, Bernard (Environmental and Experimental Botany, 2014)
The balance between whole-plant net-photosynthesis (Pn) and dark-respiration (Rd) determines daily-C-gain (dC) and thus growth. However, in Arabidopsis thaliana, a well-studied organism, the contribution of the inflorescence as a respiring sink and a photosynthetic source has never been quantified together in either ambient CO2 (AC) or elevated CO2 (EC) conditions. When sink-strength is altered by modifying mitochondrial pyruvate metabolism increases in productivity can occur in both AC and EC. Rd and Pn during canopy transition from its rosette-leaf form to the highly branched inflorescence stages were quantified. Diel patterns of leaf and whole-plant gas exchange were measured at four critical developmental stages for controls (wild-type (WT) and plasmid (pBI121)) and two transgenics (3'1 and 10'4) Arabidopsis lines having partial constitutive repression of mitochondrial pyruvate dehydrogenase kinase (mtPDHK) grown at AC and EC. In all lines the mature inflorescence structures, although having higher Rd than the rosette leaves, contributed over 90% of Pn and dC at both AC and EC. Expressed on a plant basis, Pn, Rd and dC were 700-900% higher and water-use-efficiency (WUE) was double when the inflorescence was mature as when the rosette-leaves alone sustained growth. On a dry-matter basis Pn, Rd and dC were 50-75% lower, but on a surface-area basis these traits were remarkably constant during development, reflecting the high photosynthetic strength and carbon-use-efficiency (CUE) of the inflorescence. All lines demonstrated greater Pn, Rd, dC and WUE under EC, however, at the rosette stage the controls responded more to EC, whereas, during the inflorescence 3rd-stage it was the transgenics that responded more to EC.These results underscore the need for measuring key phenotype traits such as whole-plant Pn, Rd and dC to assess how source and sink strengths change during the life-cycle, especially following genetic modification of a primary metabolic process.
Keywords: carbon dioxide; dicotyledon; dry matter; enzyme activity; gene expression; growth rate; life cycle; nutrient use efficiency; photosynthesis; respiration; source-sink dynamics; transgenic plant

Fiber-chip grating coupler based on interleaved trenches with directionality exceeding 95% - Alonso-Ramos, C.; Cheben, P.; Ortega-Moñux, A.; Schmid, J. H.; Xu, D. -X.; Molina-Fernández, I. (Optics Letters, 2014)
We propose a fiber-chip grating coupler that interleaves the standard full and shallow etch trenches in a 220 nm thick silicon layer to provide a directionality upward exceeding 95%. By adjusting the separation between the two sets of trenches, constructive interference is achieved in the upward direction independent of the bottom oxide thickness and without any bottom reflectors, overlays, or customized etch depths. We implement a transverse subwavelength structure in the first two grating periods to minimize back-reflections. The grating coupler has a calculated coupling efficiency of CE ~ -1.05 dB with a 1 dB bandwidth of 30 nm and minimum feature size of 100 nm, compatible with deep-UV lithography.
Keywords: Grating couplers

Thermocapillary migration of a deformable droplet - Samareh, Babak; Mostaghimi, Javad; Moreau, Christian (International Journal of Heat and Mass Transfer, 2014)
In the present study a parallel three dimensional Volume of Fluid (VOF) method is developed to simulate Marangoni convection in immiscible fluids with variable surface tension. Conservation equations are solved based on cell-averaged one-field volume tracking scheme. Evaluating the convective term in the energy equation along the boundary between the fluids highly depends on the position and orientation of the interface; hence, using average cell values simply ignores the interface shape and leads to computational uncertainty. As a remedy to this issue, the original idea behind the volume tracking method is used not only to advect mass and momentum but also energy across cells. To verify the proposed algorithm, results are compared against theoretically predicted thermocapillary migration velocity of a droplet at the limit of zero Marangoni number. However, at relatively high Marangoni numbers, thermal boundary layers are very thin and challenging to resolve. To demonstrate the capabilities of the heat transfer module, simulation of a Fluorinert droplet moving in silicon oil under applied temperature gradient is compared against the available experimental results and the migration velocity of the droplet in microgravity is reported.
Keywords: Capillary flow; Heat convection; Surface tension; Computational uncertainties; Interfacial heat transfer; Marangoni convection; Position and orientations; Thermal boundary layer; Thermocapillary migration; Three-dimensional volume; Variable surface tension; Drops

Chronic kidney disease of unknown aetiology and ground-water ionicity : study based on Sri Lanka - Dharma-Wardana, M. W. C.; Amarasiri, S. L.; Dharmawardene, N.; Panabokke, C. R. (Environmental Geochemistry and Health, 2014)
High incidence of chronic kidney disease of unknown aetiology (CKDU) in Sri Lanka is shown to correlate with the presence of irrigation works and rivers that bring-in 'nonpoint source' fertilizer runoff from intensely agricultural regions. We review previous attempts to link CKDU with As, Cd and other standard toxins. Those studies (e.g. the WHO-sponsored study), while providing a wealth of data, are inconclusive in regard to aetiology. Here, we present new proposals based on increased ionicity of drinking water due to fertilizer runoff into the river system, redox processes in the soil and features of 'tank'-cascades and aquifers. The consequent chronic exposure to high ionicity in drinking water is proposed to debilitate the kidney via a Hofmeister-type (i.e. protein-denaturing) mechanism.

Application of direct analysis in real time to a multiphase chemical system : identification of polymeric arsanes generated by reduction of monomethylarsenate with sodium tetrahydroborate - Pagliano, Enea; Onor, Massimo; McCooeye, Margaret; D'Ulivo, Alessandro; Sturgeon, Ralph E.; Mester, Zoltan (International Journal of Mass Spectrometry, 2014)
Direct analysis in real time (DART) has been applied in conjunction with high-resolution Orbitrap mass spectrometry to characterize the aqueous reduction of monomethylarsenate by tetrahydroborate (B/As molar ratio ≈ 4 mol/mol). Under these conditions, the reaction gives rise to a complex mixture of arsenic compounds which result in the formation of a reddish precipitate. The use of the DART revealed the presence of a number of polymeric arsanes - up to eight arsenic atoms - associated with the liquid/solid phase of this reaction system. From a reactivity point-of-view, these polymers exhibit an uncommon ionization pathway. In fact, similar to the alkanes, the action of the DART results in the generation of [M - H]+ ions. Furthermore, for each oligomer MeHAs-(AsMe)n-AsHMe (n = 0-8), a series of oxidation products [(M + nO) - H]+ were also identified and their formation has been discussed.

A new calibration system for small AC voltages at power frequencies - Djokic, Branislav (2014 Conference on Precision Electromagnetic Measurements (CPEM 2014), 2014)
A new current-comparator-based dual-channel calibration system for AC voltages in the millivolt range for operation at power frequencies has been developed. The range of generated voltages is 1 mV - 100 mV. The calibration system in-phase and quadrature expanded measurement uncertainties (k=2) are estimated to be within 25Â·106. The traceability to SI units is established through the calibration of standard resistor, capacitor, and current comparator ratios.
Keywords: Ac voltage; Current comparators; Digital sampling; Measurement uncertainty; New calibration system; Power frequency; Calibration

Effect of water and dimethyl sulfoxide on oxygen reduction reaction in bis(trifluoromethanesulfonyl)imide-based ionic liquids - Yuan, Xiao-Zi; Alzate, Vanesa; Xie, Zhong; Ivey, Douglas G.; Dy, Eben; Qua, Wei (Journal of the Electrochemical Society, 2014)
In this work, we have investigated the conductivity, electrochemical window (ECW) and oxygen reduction reaction (ORR) in various bis(trifluoromethanesulfonyl)imide (TFSI)-based room temperature ionic liquids (RTILs). In an attempt to improve ORR activity in RTILs, water and/or dimethyl sulfoxide (DMSO) are added to one TFSI-based RTIL, 1-butyl-1-methylpyrrolidinium bis(trifluoromethanesulfonyl)imide (BMP-TFSI), and the effect of additives on its conductivity, ECW and ORR is explored. The results show that as-received TFSI-based ionic liquids (ILs) have a low conductivity due to their large constituent ions. The addition of water and/or DMSO has considerable effect on the conductivity of the IL mixture. The studied TFSI-based RTILs have wide ECWs and the presence of water and/or DMSO causes an apparent narrowing of the observed potential window. For all TFSI-based ILs, the oxygen redox peaks can be assigned to an O2/O2-* one-electron transfer process. By adding water, the O2/O2-* redox potential shifts in a more positive direction in BMP-TFSI; e.g., about 0.27 V more positive in BMP-TFSI with 1 wt% water addition, due to its high acceptor number (AN) and the proton effect. The addition of DMSO also contributes to the improvement in ORR activity in BMP-TFSI through enhanced conductivity and redox reversibility.
Keywords: Bis(trifluoromethane sulfonyl)imide; Dimethyl sulfoxide (DMSO); Electrochemical window; Enhanced conductivity; One-electron transfer; Oxygen reduction reaction; Room temperature ionic liquids; Electrolytic reduction; Ionic liquids; Redox reactions; Organic solvents

Power spectrum analysis of polarized emission from the Canadian Galactic Plane Survey - Stutz, R. A.; Rosolowsky, E. W.; Kothes, R.; Landecker, T. L. (The Astrophysical Journal, 2014)
Angular power spectra are calculated and presented for the entirety of the Canadian Galactic Plane Survey polarization data set at 1.4 GHz covering an area of 1060 deg2. The data analyzed are a combination of data from the 100 m Effelsberg Telescope, the 26 m Telescope at the Dominion Radio Astrophysical Observatory, and the Synthesis Telescope at the Dominion Radio Astrophysical Observatory, allowing all scales to be sampled down to arcminute resolution. The resulting power spectra cover multipoles from ℓ 60 to ℓ 104 and display both a power-law component at low multipoles and a flattening at high multipoles from point sources. We fit the power spectrum with a model that accounts for these components and instrumental effects. The resulting power-law indices are found to have a mode of 2.3, similar to previous results. However, there are significant regional variations in the index, defying attempts to characterize the emission with a single value. The power-law index is found to increase away from the Galactic plane. A transition from small-scale to large-scale structure is evident at b = 9°, associated with the disk-halo transition in a 15° region around l = 108°. Localized variations in the index are found toward H II regions and supernova remnants, but the interpretation of these variations is inconclusive. The power in the polarized emission is anticorrelated with bright thermal emission (traced by Hα emission) indicating that the thermal emission depolarizes background synchrotron emission.

Experimental evaluation of four feature detection methods for close range and distant airborne targets for Unmanned Aircraft Systems applications - Tulpan, Dan; Belacel, Nabil; Famili, Fazel; Ellis, Kristopher (2014 International Conference on Unmanned Aircraft Systems, ICUAS 2014 - Conference Proceedings, 2014)
Feature detection for Unmanned Aircraft Systems (UAS) sense and avoid scenarios is a crucial preliminary step for target detection. Its importance culminates when distant (pixel size) targets representing incoming aircraft are considered. This paper presents an experimental evaluation of four popular feature detection methods using flight test data and based on evaluation criteria such as first detection distance and percentage of frames with detected target features. Our results show that for close range targets all four methods have similar performance, while for distant (pixel-size) targets, the Shi and Tomasi method outperforms the other three methods (Harris-Stephens-Plessey, SUSAN and FAST).
Keywords: Aircraft; Pixels; Unmanned aerial vehicles (UAV); Airborne target; Evaluation criteria; Experimental evaluation; Feature detection; Flight test data; Sense and avoid; Target feature; Unmanned aircraft system; Aircraft detection

Spatial heterodyne Fourier-transform waveguide spectrometers - Velasco, Aitor V.; Cheben, Pavel; Florjańczyk, Mirosław; Calvo, Maria L. (Progress in Optics, 2014)
Overcoming current resolution limits of optical spectroscopy could revolutionize research in diverse fields such as atomic and molecular spectroscopy, bio-chemistry, and astronomy. In this chapter, we explore the opportunities opened by spatial heterodyne Fourier-transform spectroscopy, presenting both its early bulk-optics implementations and its latest applications in waveguide optics and silicon photonics. Spatial heterodyne Fourier-transform spectrometers provide a plurality of simultaneous interferometric measurements, from which the source spectrum is retrieved in a single capture. Independent access to each interferometric measurement enables spectral retrieval algorithms to correct fabrication and experimental deviations from ideal behavior without any hardware modifications. Furthermore, the straightforward scalability of these devices represents a significant milestone toward pushing current resolution boundaries of stationary spectroscopy.
Keywords: Spectroscopy; Fourier transform; Integrated optics; Silicon on insulator; Spectral retrieval

Process control based on pattern recognition for routing carbon fiber reinforced polymer - Shaban, Yasser; Meshreki, Mouhab; Yacout, Soumaya; Balazinski, Marek; Attia, Helmi (Journal of Intelligent Manufacturing, 2014)
Carbon fiber reinforced polymer (CFRP) is an important composite material. It has many applications in aerospace and automotive fields. The little information available about the machining process of this material, specifically when routing process is considered, makes the process control quite difficult. In this paper, we propose a new process control technique and we apply it to the routing process for that important material. The measured machining conditions are used to evaluate the quality and the geometric profile of the machined part. The machining conditions, whether controllable or uncontrollable are used to control part accuracy and its quality. We present a pattern-based machine learning approach in order to detect the characteristic patterns, and use them to control the quality of a machined part at specific range. The approach is called logical analysis of data (LAD). LAD finds the characteristic patterns which lead to conforming products and those that lead to nonconforming products. As an example, LAD is used for online control of a simulated routing process of CFRP. We introduce the LAD technique, we apply it to the high speed routing of woven carbon fiber reinforced epoxy, and we compare the accuracy of LAD to that of an artificial neural network, since the latter is the most known machine learning technique. By using experimental results, we show how LAD is used to control the routing process by tuning autonomously the routing conditions. We conclude with a discussion of the potential use of LAD in manufacturing.
Keywords: Machining; Pattern recognition; Process control; Carbon fiber reinforced polymer; Knowledge extraction; Logical analysis of data; Carbon fiber reinforced plastics

Carrier recombination in tailored multilayer Si/Si1-xGex nanostructures - Mala, S. A.; Tsybeskov, L.; Lockwood, D. J.; Wu, X.; Baribeau, J. -M. (Physica B: Condensed Matter, 2014)
Photoluminescence (PL) measurements were performed in Si/Si1-xGex nanostructures with a single Si0.92Ge0.08 nanometer-thick layer incorporated into Si/Si0.6Ge0.4 cluster multilayers. Under pulsed laser excitation, the PL decay associated with the Si0.92Ge0.08 nano-layer is found to be nearly a 1000 times faster compared to that in Si/Si0.6Ge0.4 cluster multilayers. A model considering Si/SiGe hetero-interface composition and explaining the fast and slow time-dependent recombination rates is proposed.
Keywords: Carrier recombination; Si/SiGe; Photoluminescence

Phase transformation in plasma electrolytic oxidation coatings on 6061 aluminum alloy - Dehnavi, Vahid; Liu, Xing Yang; Luan, Ben Li; Shoesmith, David W.; Rohani, Sohrab (Surface and Coatings Technology, 2014)
Oxide coatings were produced on a 6061 aluminum alloy using a pulsed unipolar plasma electrolytic oxidation (PEO) process. The effect of electrical parameters including pulse frequency, duty cycle and current density on phase formation in the coatings was revealed using conventional and glancing angle X-ray diffraction. The results show that PEO coatings are mainly composed of γ-Al2O3. Depending on the electrical parameters employed, the coatings can also contain α-Al2O3 and mullite with varying concentrations. Higher current densities and higher duty cycle were found to favor the formation of mullite. Under the experimental conditions used, the ratio of the integrated XRD peaks for α- and γ-Al2O3 varied from 0 to about 0.6, indicating that the relative content of α-Al2O3 in the PEO coatings varied over a wide range. Longer pulse on-times and higher current densities promoted the gamma to alpha-alumina phase transformation. Depth profiling of PEO ceramic coatings using glancing angle XRD with different incident beam angles revealed that mullite was more concentrated in the top surface of the coatings. No significant variation in α-Al2O3 concentration across the coatings could be concluded in this study, unlike the results of some other studies.
Keywords: Plasma electrolytic oxidation; Phase transformation; Alpha alumina; Gamma alumina; Electrical parameters

Polarimetric analysis of the Thirty Meter Telescope (TMT) for modeling instrumental polarization characteristics - Atwood, Jenny; Skidmore, Warren; Anupama, G. C.; Anche, Ramya M.; Reddy, Krishna; Sen, Asoke (SPIE - International Society for Optical Engineering. Proceedings, 2014)
The Thirty Meter Telescope (TMT) will be called upon to support a polarimetric observing capability. Many different observing programs covering a range of different science areas are being considered for the TMT and a model of the overall polarization characteristics is being developed. The instrument development program will provide a means for polarimetric instruments to be developed, however the telescope itself and the AO system must be able to support polarimetric instruments. As a first step to defining the necessary polarimetric technical requirements we have created an international working group to carry out a study in which technical and cost implications will be balanced with scientific impact; new requirements will be generated with supporting science cases. We present here initial results of the instrumental polarization sensitivity of TMT with NFIRAOS, the first-light adaptive optics system.
Keywords: Analytic equipment; Optical telescopes; Polarimeters; Polarization; Project management; Systems engineering; Telescopes; First-light adaptive optics system; Instrument development; Instrumental polarization; NFIRAOS; Polarization characteristics; Technical requirement; Thirty Meter Telescope; TMT; Astronomy

Security versus reliability analysis of opportunistic relaying - Zou, Yulong; Wang, Xianbin; Shen, Weiming; Hanzo, Lajos (IEEE Transactions on Vehicular Technology, 2014)
Physical-layer security is emerging as a promising paradigm of securing wireless communications against eavesdropping between legitimate users, when the main link spanning from a source to a destination has better propagation conditions than the wiretap link from a source to an eavesdropper. In this paper, we identify and analyze the tradeoffs between the security and reliability of wireless communications in the presence of eavesdropping attacks. Typically, the reliability of the main link can be improved by increasing the source's transmit power (or decreasing its date rate) to reduce the outage probability (OP), which unfortunately increases the risk that an eavesdropper succeeds in intercepting the source message through the wiretap link, since the OP of the wiretap link also decreases when a higher transmit power (or lower date rate) is used. We characterize the security-reliability tradeoffs (SRT) of conventional direct transmission from the source to the destination in the presence of an eavesdropper, where the security and reliability are quantified in terms of the intercept probability (IP) by an eavesdropper and the OP experienced at the destination, respectively. To improve the SRT, we then propose opportunistic relay selection (ORS) and quantify the attainable SRT improvement upon increasing the number of relays. It is shown that given the maximum tolerable IP, the OP of our ORS scheme approaches zero for N → ∞, where N is the number of relays. Conversely, given the maximum tolerable OP, the IP of our ORS scheme tends to zero for N → ∞.
Keywords: Cooperative communication; Outages; Reliability; Security systems; Wireless telecommunication systems; Eavesdropping attacks; Opportunistic relay selections; Opportunistic relaying; Outage probability; Physical-layer securities; Security and reliabilities; Security-reliability tradeoff; Wireless communications; Network security

Chemical basis of the tribological properties of AgTaO3 crystal surfaces - Gao, Hongyu; Otero-de-la-Roza, Alberto; Aouadi, Samir M.; Martini, Ashlie; Johnson, Erin R. (The Journal of Physical Chemistry C, 2014)
The chemical properties of a surface determine the friction and wear behavior of a material during sliding. In this article, we study the mechanisms underlying the sliding behavior of the AgTaO3 perovskite material, a promising high-temperature solid lubricant that presents excellent friction properties and is chemically inert. In particular, by employing a combination of molecular dynamics simulations and density-functional theory calculations, we show that the low friction of AgTaO3 at high temperature is explained by silver aggregation on the surface, which is enabled by the low energy barriers associated with silver migration. Two different surface terminations (AgO and TaO2) are studied, and we show that the migration barrier on the AgO surface is smaller, favoring silver aggregation, which affects both friction and wear. Regardless of the termination, the formation of soft silver clusters dominates the sliding behavior when enough energy (mechanical or thermal) is imparted to the surface.
Keywords: Friction; Molecular dynamics; Silver oxides; Solid lubricants; Wear of materials; Density-functional theory calculations; Friction and wear; Friction and wear behaviors; Friction properties; Migration barriers; Molecular dynamics simulations; Surface termination; Tribological properties; Agglomeration

Internal conversion versus intersystem crossing: What drives the gas phase dynamics of cyclic α,β-enones? - Schalk, Oliver; Schuurman, Michael S.; Wu, Guorong; Lang, Peter; Mucke, Melanie; Feifel, Raimund; Stolow, Albert (The Journal of Physical Chemistry A, 2014)
We investigate the competition between intersystem crossing (ISC) and internal conversion (IC) as nonradiative relaxation pathways in cyclic α,β-unsaturated enones following excitation to their lowest lying 1ππ* state, by means of time-resolved photoelectron spectroscopy and ab initio computation. Upon excitation, the 1ππ* state of 2-cyclopentenone decays to the lowest lying 1nπ* state within 120 ± 20 fs. Within 1.2 ± 0.2 ps, the molecule subsequently decays to the triplet manifold and the singlet ground state, with quantum yields of 0.35 and 0.65, respectively. The corresponding dynamics in modified derivatives, obtained by selective methylation, show a decrease in both IC and ISC rates, with the quantum yields of ISC varying between 0.35 and 0.08. The rapid rates of ISC are explained by a large spin orbit coupling of 45-60 cm-1 over an extended region of near degeneracy between the singlet and triplet state. Furthermore, the rate of IC is depressed by the existence of a well-defined minimum on the 1nπ* potential energy surface. The nonadiabatic pathways evinced by the present results highlight the fact that these molecular systems conceptually represent "intermediate cases" between ultrafast dynamics mediated by vibrational motions at conical intersections versus those by statistical decay mechanisms.
Keywords: Alkylation; Photoelectron spectroscopy; Quantum chemistry; Quantum yield; Ab initio computations; Conical intersection; Inter-system crossings; Internal conversions; Non-radiative relaxation; Singlet and triplet state; Singlet ground state; Time-resolved photoelectron spectroscopy; Quantum theory

Chemical composition and nutritional properties of freshwater and marine microalgal biomass cultured in photobioreactors - Tibbetts, Sean M.; Milley, Joyce E.; Lall, Santosh P. (Journal of Applied Phycology, 2014)
Proximate, amino acid and elemental composition, total phenolic content (TPC), and in vitro protein digestibility (IVPD) of microalgal biomass were determined. Microalgae contained low to moderate ash (5–17 %), moderate to high carbohydrate (18–46 %), crude protein (18–46 %), high crude lipid (12–48 %), and energy (19–27 MJ kg−1). Characteristic of microalgae, non-essential amino acids (AAs), aspartic and glutamic acids, were predominant (20–30 % of protein; 8–12 % of dry weight). Microalgae had favorable essential AA profiles with high essential amino acid (EAA) indices (0.9–1.2). Expressed as g EAA 100 g protein−1, Porphyridium aerugineum was rich in leucine (11.9), lysine (8.0), arginine (8.6), and tryptophan (3.3); Nannochloropsis granulata (A) in leucine (11.0), lysine (8.5), and tryptophan (2.8); Tetraselmis chuii and Botryococcus braunii in arginine (9.4 and 20.5, respectively); and Phaeodactylum tricornutum in lysine (6.4) and tryptophan (2.6). Mineral compositions (%) were calcium (0.1–3.0), magnesium (0.3–0.7), phosphorous (0.7–1.5), potassium (0.7–2.4), sodium (0.8–2.7), and sulfur (0.4–1.4), and trace element compositions (mg kg−1) were copper (18–102), iron (1,395–11,101), manganese (45–454), selenium (0–0.5), and zinc (28–64). Microalgae contained low TPC (6–13 mg gallic acid equivalents (GAE) g−1 DW), except T. chuii (20 mg GAE g−1 DW). IVPD was high (>90 %) for B. braunii (A), P. aerugineum, and lipid-extracted N. granulata (B); mid-range (80–89 %) for P. tricornutum, N. granulata (A), B. braunii (B), Neochloris oleoabundans, T. chuii, and whole N. granulata (B); and lower (<80 %) for Acutodesmus dimorphus. Microalgal species P. tricornutum, B. braunii, N. granulata, and T. chuii had high protein (40–52 %), IVPD (82–97 %), and digestible protein (35–50 %), comparable to plant proteins used in animal feeds and aquaculture.
Keywords: Microalgae; Composition; Amino acids; In vitro protein digestibility; Total phenolic content

High-density sodium and lithium ion battery anodes from banana peels - Memarzadeh Lotfabad, Elmira; Ding, Jia; Cui, Kai; Kohandehghan, Alireza; Kalisvaart, W. Peter; Hazelton, Michael; Mitlin, David (ACS Nano, 2014)
Banana peel pseudographite (BPPG) offers superb dual functionality for sodium ion battery (NIB) and lithium ion battery (LIB) anodes. The materials possess low surface areas (19-217 m2 g-1) and a relatively high electrode packing density (0.75 g cm-3 vs ∼1 g cm -3 for graphite). Tested against Na, BPPG delivers a gravimetric (and volumetric) capacity of 355 mAh g-1 (by active material ∼700 mAh cm-3, by electrode volume ∼270 mAh cm-3) after 10 cycles at 50 mA g-1. A nearly flat ∼200 mAh g-1 plateau that is below 0.1 V and a minimal charge/discharge voltage hysteresis make BPPG a direct electrochemical analogue to graphite but with Na. A charge capacity of 221 mAh g-1 at 500 mA g-1 is degraded by 7% after 600 cycles, while a capacity of 336 mAh g-1 at 100 mAg -1 is degraded by 11% after 300 cycles, in both cases with ∼100% cycling Coulombic efficiency. For LIB applications BPPG offers a gravimetric (volumetric) capacity of 1090 mAh g-1 (by material ∼2200 mAh cm-3, by electrode ∼900 mAh cm-3) at 50 mA g -1. The reason that BPPG works so well for both NIBs and LIBs is that it uniquely contains three essential features: (a) dilated intergraphene spacing for Na intercalation at low voltages; (b) highly accessible near-surface nanopores for Li metal filling at low voltages; and (c) substantial defect content in the graphene planes for Li adsorption at higher voltages. The <0.1 V charge storage mechanism is fundamentally different for Na versus for Li. A combination of XRD and XPS demonstrates highly reversible Na intercalation rather than metal underpotential deposition. By contrast, the same analysis proves the presence of metallic Li in the pores, with intercalation being much less pronounced.
Keywords: Carbon; graphite; graphene; battery; capacitor; SIB; NIB; NAB

Anodic Cu2S and CuS nanorod and nanowall arrays: Preparation, properties and application in CO2 photoreduction - Kar, Piyush; Farsinezhad, Samira; Zhang, Xiaojiang; Shankar, Karthik (Nanoscale, 2014)
Copper sulfide semiconductors made from earth-abundant elements have an optical absorption edge at ca. 1.2 eV, nearly ideal for solar energy harvesting. We report the growth and formation mechanism of vertically oriented arrays of copper sulfide nanostructures formed by electrochemical anodization. Key parameters that affect the morphology and phase of the nanostructures are type and strength of electrolyte, anodization voltage and duration. Cu2S and CuS nanostructures were obtained on both copper foil and copper-coated flexible Kapton substrates, and depending on the anodization parameters, consisted of vertically oriented arrays of nanowalls, nanoleafs or rods with branched nanodendrites. The anodization parameters also controlled the phase and stoichiometry of the nanostructures. p-type conduction for Cu2S nanostructures and n-type conduction for CuS nanostructures were revealed by admittance spectroscopy and Mott Schottky analysis. We also observed a weak, but nevertheless promising and previously unnoticed, photocatalytic action in copper sulfide nanorod and platelet arrays for the sunlight-driven conversion of CO2 into CH4. Under irradiation by AM 1.5G simulated sunlight at room temperature, a CH4 production rate as high as 38 μmol m-2 h-1 was obtained using the copper sulfide nanostructure arrays as stand-alone photocatalysts for CO2 photoreduction.
Keywords: Nanowalls; Photo-reduction

Comprehensive transcriptome assembly of chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: development and applications - Kudapa, Himabindu; Azam, Sarwar; Sharpe, Andrew G.; Taran, Bunyamin; Li, Rong; Deonovic, Benjamin; Cameron, Connor; Farmer, Andrew D.; Cannon, Steven B.; Varshney, Rajeev K. (PLoS ONE, 2014)
A comprehensive transcriptome assembly of chickpea has been developed using 134.95 million Illumina single-end reads, 7.12 million single-end FLX/454 reads and 139,214 Sanger expressed sequence tags (ESTs) from >17 genotypes. This hybrid transcriptome assembly, referred to as Cicer arietinum Transcriptome Assembly version 2 (CaTA v2, available at http://data.comparative-legumes.org/ transcriptomes/cicar/lista-cicar-201201), comprising 46,369 transcript assembly contigs (TACs) has an N50 length of 1,726 bp and a maximum contig size of 15,644 bp. Putative functions were determined for 32,869 (70.8%) of the TACs and gene ontology assignments were determined for 21,471 (46.3%). The new transcriptome assembly was compared with the previously available chickpea transcriptome assemblies as well as to the chickpea genome. Comparative analysis of CaTA v2 against transcriptomes of three legumes - Medicago, soybean and common bean, resulted in 27,771 TACs common to all three legumes indicating strong conservation of genes across legumes. CaTA v2 was also used for identification of simple sequence repeats (SSRs) and intron spanning regions (ISRs) for developing molecular markers. ISRs were identified by aligning TACs to the Medicago genome, and their putative mapping positions at chromosomal level were identified using transcript map of chickpea. Primer pairs were designed for 4,990 ISRs, each representing a single contig for which predicted positions are inferred and distributed across eight linkage groups. A subset of randomly selected ISRs representing all eight chickpea linkage groups were validated on five chickpea genotypes and showed 20% polymorphism with average polymorphic information content (PIC) of 0.27. In summary, the hybrid transcriptome assembly developed and novel markers identified can be used for a variety of applications such as gene discovery, marker-trait association, diversity analysis etc., to advance genetics research and breeding applications in chickpea and other related legumes.
Keywords: contig; chickpea; expressed sequence tag; gene sequence; genetic conservation; genetic polymorphism; genetic transcription; genotype; intron; Medicago; next generation sequencing; Phaseolus vulgaris; plant chromosome; plant genome; Sanger sequencing; simple sequence repeat; soybean; species comparison; Cicer; Gene Expression Profiling; Genes, Plant; Genetic Linkage; Genetic Markers; High-Throughput Nucleotide Sequencing; Microsatellite Repeats; Molecular Sequence Annotation; Plant Proteins; Sequence Analysis, DNA; Synteny; transcriptome

Broadband transmission filters from the 2013 Optical Interference Coatings manufacturing problem contest [Invited] - Li, Li; Dobrowolski, J. A.; Jacobson, Michael; Cooksey, Catherine (Applied Optics, 2014)
A broadband transmission filter from 400 to 1100 nm was selected for the manufacturing problem contest. The purpose of the contest is to test the state of the art of current optical thin film manufacturing capabilities. A total of 37 people from 15 teams participated in the contest and submitted 17 samples. Diverse approaches were taken by participants to tackle the problem. A range of different solutions was obtained where the number of layers varied from 22 to 608, and the total layer thickness ranged from 1.859 to 23.099 μm. Two independent laboratories performed sample evaluation measurements. Three teams shared the best result with the lowest average measured merit function.
Keywords: Broadband transmission; Optical interference coatings

Studying the chemistry of cationized triacylglycerols using electrospray ionization mass spectrometry and density functional theory computations - Grossert, J. Stuart; Herrera, Lisandra Cubero; Ramaley, Louis; Melanson, Jeremy E. (Journal of the American Society for Mass Spectrometry, 2014)
Analysis of triacylglycerols (TAGs), found as complex mixtures in living organisms, is typically accomplished using liquid chromatography, often coupled to mass spectrometry. TAGs, weak bases not protonated using electrospray ionization, are usually ionized by adduct formation with a cation, including those present in the solvent (e.g., Na+). There are relatively few reports on the binding of TAGs with cations or on the mechanisms by which cationized TAGs fragment. This work examines binding efficiencies, determined by mass spectrometry and computations, for the complexation of TAGs to a range of cations (Na+, Li+, K+, Ag+, NH 4 +). While most cations bind to oxygen, Ag+ binding to unsaturation in the acid side chains is significant. The importance of dimer formation, [2TAG + M]+ was demonstrated using several different types of mass spectrometers. From breakdown curves, it became apparent that two or three acid side chains must be attached to glycerol for strong cationization. Possible mechanisms for fragmentation of lithiated TAGs were modeled by computations on tripropionylglycerol. Viable pathways were found for losses of neutral acids and lithium salts of acids from different positions on the glycerol moiety. Novel lactone structures were proposed for the loss of a neutral acid from one position of the glycerol moiety. These were studied further using triple-stage mass spectrometry (MS3). These lactones can account for all the major product ions in the MS3 spectra in both this work and the literature, which should allow for new insights into the challenging analytical methods needed for naturally occurring TAGs.
Keywords: Binding efficiencies of cations to triacylglycerols; Breakdown curves; Lithiated triglycerides; MS/MS/MS product ions; Solvent-cation interactions in ESI

Microstructure and properties of poly(ethylene terephthalate)/organoclay nanocomposites prepared by water-assisted extrusion: Effect of organoclay concentration - Dini, Maryam; Mousavand, Tahereh; Carreau, Pierre J.; Kamal, Musa R.; Ton-That, Minh-Tan (Polymer Engineering and Science, 2014)
Poly(ethylene terephthalate) (PET)/Cloisite 30B (C30B) nanocomposites containing different concentrations of the organoclay were prepared using two different twin-screw extrusion processes: conventional melt mixing and water-assisted melt mixing. The reduction of the molecular weight of the PET matrix, caused by hydrolysis during the water-assisted extrusion, was compensated by subsequent solid-state polymerization (SSP). X-ray diffraction, scanning electron microscopy, and transmission electron microscopy analyses showed intercalated/exfoliated morphology in all PET/C30B nanocomposites, with a higher degree of intercalation and delamination for the water-assisted process. Rheological, thermal, mechanical, and gas barrier properties of the PET nanocomposites were also studied. Enhanced mechanical and barrier properties were obtained in PET-C30B nanocomposites compared to the neat PET. The nanocomposites exhibited higher tensile modulus and lower oxygen permeability after SSP. The elongation at break was significantly higher for SSP nanocomposites than for nanocomposites processed by conventional melt mixing.
Keywords: Extrusion; Mixing; Organoclay; Polyethylene terephthalates; Scanning electron microscopy; Transmission electron microscopy; X ray diffraction; Elongation at break; Gas barrier properties; Mechanical and barriers; Microstructure and properties; Poly(ethylene terephthalate) (PET); Solid state polymerization; Transmission electron; Twin screw extrusion; Nanocomposites

Evolution of flow stress and microstructure during isothermal compression of Waspaloy - Chamanfar, A.; Jahazi, M.; Gholipour, J.; Wanjara, P.; Yue, S. (Materials Science and Engineering A, 2014)
The evolution of the flow stress and microstructure for Waspaloy was studied in the 950-1140°C temperature range under constant true strain rate conditions of 0.001-1s-1 up to a true strain of 0.83 using isothermal hot compression testing. The impact of friction at the sample/anvil interface and adiabatic heating during deformation on the flow stress evolution was also examined. Mathematical models relating the flow stress to the deformation temperature and strain rate were derived using a power-law relationship. The strain rate sensitivity and the activation energy for hot deformation of Waspaloy were found to be considerably different for deformation in the subsolvus and supersolvus temperature ranges. According to the microstructural investigations, at 950°C dynamic recovery (DRV) was the main softening mechanism. By contrast, dynamic recrystallization (DRX), partial or complete, occurred at temperatures above 950°C and resulted in flow softening.
Keywords: Waspaloy; Isothermal hot compressions; Friction; Adiabatic heating; Flow stress; Microstructure

Dynamic mechanical thermoanalysis of layered calcium silicate hydrates - Pourbeik, P.; Beaudoin, J. J.; Alizadeh, R.; Raki, L. (Journal of Thermal Analysis and Calorimetry, 2014)
Dynamic mechanical thermoanalysis (DMTA) was conducted on compacted specimens of calcium silicate hydrates (C-S-H), 1.4 nm tobermorite, jennite, and compacted hydrated Portland cement paste powders, as well as hardened cement paste. The synthetic silicates are key elements for compositional models of the hydrated calcium silicates present in cement paste. The study focuses on the nanostructural effects due to the removal of water from the 11 % RH condition. The DMTA results (E and tan versus temperature curves) in the 25-110 °C range mimicked those of DMA (E and tan versus mass loss curves) conducted at room temperature for C-S-H and cement paste. In addition, the DMTA curves for 1.4 nm tobermorite and jennite in the temperature range 110-300 °C were sensitive to phase changes including the transition of 1.4 nm tobermorite to 1.1 nm tobermorite and other forms, as well as the transition of jennite to metajennite. The DMTA curves of a 50/50 mixture of 1.4 nm tobermorite and jennite exhibit similarities and differences to that of hydrated cement paste that are influenced by porosity and the amorphous nature of C-S-H in the cement paste. The study provides useful data for evaluating Taylor's concept of a possible tobermorite-jennite model for the C-S-H present in hydrated cement paste.
Keywords: C-S-H; Cement paste; Dynamic mechanical; Jennite; Tobermorite

Highly active Pt-on-Au catalysts for methanol oxidation in alkaline media involving a synergistic interaction between Pt and Au - Wang, Jianshe; Shi, Ranran; Guo, Xun; Xi, Jingyu; Zhao, Jianhong; Song, Chengying; Wang, Liucheng; Zhang, Jiujun (Electrochimica Acta, 2014)
Several Pt-on-Au/SnO2-CNTs catalysts with different Pt loadings are synthesized through site-selective electrodeposition for catalytic methanol oxidation reaction (MOR) in alkaline media. The catalysts are tested to exhibit extremely high Pt mass activity towards MOR, and the catalytic mechanism is proposed based on the synergetic effect between Pt and Au, in which the Pt entities provide Pt-OH for oxidation of alkoxide (CH3O-) while the Au surfaces provide adsorption sites for alkoxide. It is expected that this mechanism could be extended to developing high performance non-Pt catalysts for MOR in alkaline media.
Keywords: Adsorption site; Catalytic mechanisms; Methanol Oxidation; Methanol oxidation reactions; Site selective; Synergetic effect; Synergism; Synergistic interaction; Catalysts; Electrodeposition; Excitons; Methanol; Platinum

Occurrence and biological activities of eremophilane-type sesquiterpenes - Hou, Chenjie; Kulka, Marianna; Zhang, Junzeng; Li, Yiming; Guo, Fujiang (Mini-Reviews in Medicinal Chemistry, 2014)
As important members of the terpenes family, sesquiterpenes represent a group of natural compounds with diverse skeletal types. Among them, the eremophilane-type sesquiterpenes, widely present in several genera (such as Ligularia, Senecio, Cacalia) of Asteraceae, account for a small number of natural compounds and form differently from other sesquiterpenes because they challenged the isoprene rule of biosynthesis. Due to the unique structural features and various functional groups, these compounds possess a number of biological activities such as anti-tumor, anti-bacterial and anti-inflammatory, having received increasing interest in the recent years. This review summarizes the occurrence of eremophilane-type sesquiterpenes and research progresses on their biological activities since the 1990s.
Keywords: anti-tumor; anti-microbial; anti-inflammatory; anti-allergy; eremophilane-type sesquiterpenes

Liuwei Dihuang, a traditional Chinese herbal formula, suppresses chronic inflammation and oxidative stress in obese rats - Perry, Benjamin; Zhang, Junzeng; Saleh, Tarek; Wang, Yanwen (Journal of Integrative Medicine, 2014)
Objective To investigate the anti-inflammatory, anti-oxidative stress, and adipokine-ameliorating effects of Liuwei Dihuang (LWDH), a traditional Chinese herbal formula, in obese rats. Methods After 2 weeks of acclimation with free access to regular rodent chow and water, obese-prone-caesarean-derived (OP-CD) rats were fed a modified AIN-93G diet containing 60% energy from fat. Treatment was performed twice daily by gavage feeding with 500, 1 500, or 3 500 mg/kg body weight LWDH suspended in water (n=12 rats per group). Twelve obese-resistant-CD (OR-CD) rats were fed the atherogenic diet and gavaged with water, and served as the normal control. Blood biomarkers of inflammation, oxidative stress and adiponectin were measured post-sacrifice and used to determine the treatment effect of LWDH and assess the suitability of OR/OP-CD rats for studying these parameters. Results After 9 weeks of treatment, LWDH lowered serum C-reactive protein (CRP) and tumour necrosis factor-α (TNF-α) levels. Serum interleukin-6 (IL-6) levels showed a tendency towards reduction, but were not significantly different from the OP-CD control. Liver superoxide dismutase (SOD) activity was increased in response to all three doses of LWDH, while the levels of reduced (GSH) and oxidized glutathione (GSSG) and thiobarbituric acid reactive substances (TBARS) were unchanged. Serum adiponectin levels were increased in response to oral administration of LWDH at the dose of either 500 or 1 500 mg/kg body weight. In addition, comparisons between OR-CD and OP-CD rats revealed differential, and for some biomarkers, conflicting characteristics of high-fat diet-fed OP-CD rats in reference to obese human subjects in terms of inflammatory and oxidative stress biomarkers and circulating adiponectin levels. Conclusion The results show, for the first time, the anti-inflammatory, anti-oxidative stress and adiponectin-ameliorating effects of LWDH in obese rats. The suitability of the OR/OP-CD rat model as a research tool to study inflammation, oxidative stress, and adipokine production requires further investigation.
Keywords: adiponectin; durgs, Chinese herbal; inflammation; Liuwei Dihuang; obesity; oxidative stress; rats

Time-resolved photoelectron spectra of CS2: Dynamics at conical intersections - Wang, Kwanghsi; McKoy, Vincent; Hockett, Paul; Schuurman, Michael S. (Physical Review Letters, 2014)
We report results of the application of a fully ab initio approach for simulating time-resolved molecular-frame photoelectron angular distributions around conical intersections in CS2. The technique employs wave packet densities obtained with the multiple spawning method in conjunction with geometry- and energy-dependent photoionization matrix elements. The robust agreement of these results with measured molecular-frame photoelectron angular distributions for CS2 demonstrates that this technique can successfully elucidate, and disentangle, the underlying nuclear and photoionization dynamics around conical intersections in polyatomic molecules.
Keywords: Photoionization; Ab initio approach; Conical intersection; Energy dependent; Matrix elements; Photoelectron angular distributions; Photoelectron spectrum; Photoionization dynamics; Polyatomic molecules; Photoelectrons

Carbon nanotube conductive networks through the double percolation concept in polymer systems - Abbasi, S.; Derdouri, A.; Carreau, P. J. (International Polymer Processing, 2014)
We investigated the electrical conductivity and percolation behavior of binary and ternary nanocomposites based on multiwalled carbon nanotubes (MWCNs) using polypropylene (PP) and a blend of PP with cyclic butylene terephthalate (CBT). The nanocomposites were prepared by diluting a commercial 20 %wtMWCNT PP masterbatch using optimized melt-mixing conditions. The concentration of carbon nanotubes in the diluted PP samples was as low as 0.5% and as high as 15 % in weight. For the PP/CBT blend CBT concentration was varied up to 40 %wt while the loading of CNT was from 0 to 5 %wt. SEM and TEM techniques were used to examine the quality of the dispersion and the formation of nanotube networks within the polymer matrix. TEM and Raman spectroscopy results showed that for the diluted PP/MWCNT composites the nanotubes are well aligned in samples obtained the microinjection molding process, although the level of alignment is less with crystalline PP than in an amorphous matrix such as polycarbonate (PC). FTIR and XRD results revealed that the orientation of both polymer chains and crystals decreased with the incorporation of nanotubes into PP. The electrical conductivity was also significantly altered by the nanotube alignment in a PP matrix, as was previously observed for PC/MWCNT composites; the conductivity decreased and the percolation threshold rose in highly sheared samples; however, the presence of a crystalline phase improved the conductivity even for high shear conditions through the phenomenon of double percolation threshold. This last concept refers to the requirement that the filler-rich phase be continuous and conductive and not to the existence of two percolation thresholds at two different CNT concentrations. The electrical conductivity of PP/CBT blends was also improved through a double percolation that is the basic requirement for the conductivity of the ternary nanocomposites.
Keywords: Amorphous matrices; Conductive networks; Cyclic butylene terephthalates; Electrical conductivity; Micro-injection molding; Percolation behavior; Percolation thresholds; Ternary nanocomposites; Crystal orientation; Crystalline materials; Electric conductivity of solids; Multiwalled carbon nanotubes (MWCN); Nanocomposites; Percolation (computer storage); Percolation (fluids); Polypropylenes

Results of the SIM.EM-K5 key comparison of 50/60 Hz power - Carranza, R.; Campos, S.; Castruita, A.; Nelson, T.; Ribeiro, A.; So, E.; Di Lillo, L.; Spaggiari, A.; Slomovitz, D.; Izquierdo, Daniel; Faverio, Carlos; Postigo, H.; et al. (2014 Conference on Precision Electromagnetic Measurements (CPEM 2014), 2014)
From years 2010 to 2012, a key comparison of power standards at 50/60 Hz was conducted in the SIM region. The comparison included measurements of active and reactive power at three frequencies, aiming at providing support to high accuracy measurement needs of reactive power. This paper presents the results of the SIM.EM-K5 comparison and the assessment of the link between this comparison and the CCEM-K5 key comparison on 50/60 Hz power completed in 2001.
Keywords: Key comparison; Measurement standards; Regression fitting; Reproducibilities; Uncertainty

Determining the mechanism of in-service cylinder distortion in aluminum engine blocks with cast-in gray iron liners - Lombardi, Anthony; Ravindran, Comondore; Sediako, Dmitry; Mackay, Robert (Metallurgical and Materials Transactions A: Physical Metallurgy and Materials Science, 2014)
In recent years, stringent government legislation on vehicle fuel efficiency has pushed the automotive industry to replace steel and cast iron power train components with light weight Al alloys. However, unlike their ferrous-based equivalents, Al-Si alloy engine blocks are prone to permanent dimensional distortion in critical locations such as the cylinder bore regions. Understanding the mechanisms that cause distortion will promote the use of Al alloys over ferrous alloys for power train applications and enable automotive manufacturers to meet emission standards and reduce fuel consumption. In this study, neutron diffraction was used to evaluate residual stress along the Al cylinder bridge and the gray cast iron liners of distorted and undistorted engine blocks. Microstructural analysis was carried out using OM, SEM, and TEM, while mechanical testing was accomplished via ambient and elevated temperature [~453 K (180 °C)] tensile testing. The results suggest that the distorted engine block had high tensile residual stress in the Al cylinder bridge, reaching a maximum of 170 MPa in the hoop direction, which triggered permanent dimensional distortion in the cylinders when exposed to service conditions. In addition, the middle of the cylinder had the highest magnitude of distortion since this region had a combination of high tensile residual stress (hoop stress of 150 MPa) and reduced strength compared with the bottom of the cylinder.
Keywords: Aluminum engines; Gray irons

Enhancement of photovoltaic cell performance using periodic triangular gratings - Bordatchev, Evgueni; Tauhiduzzaman, Mohammed; Dey, Rajat (Journal of Photonics for Energy, 2014)
The solar energy industry strives to produce more efficient and yet cost effective solar panels each consisting of an array of photovoltaic (PV) cells. The goal of this study was to enhance the performance of PV cells through increasing the cells' optical efficiency defined as a percentage of surface incident light that reaches the PV material. This was achieved through the reduction of waveguide decoupling loss and Fresnel reflection losses by integrating specific nonimaging micro-optical structures on the top surface of existing PV cells. Due to this integration, optical efficiency and performance were increased through the enhancement of light trapping, light guiding, and in-coupling functionalities. Periodic triangular gratings (PTGs) were designed, nonsequentially modeled, optimized, and fabricated in polydimethylsiloxane as proposed micro-optical structures. Then the performance of PV cells with and without integrated PTGs was evaluated and compared. Initial optical simulation results show that an original PV cell (without PTG) exhibits an average optical efficiency of 32.7% over a range of incident light angles between 15 and 90 deg. Integration of the PTG allows the capture of incoming sunlight by total internal reflection (TIR), whence it is reflected back onto the PV cell for multiple consecutive chances for absorption and PV conversion. Geometry of the PTG was optimized with respect to an angle of light incidence of {15, 30, 45, 60, 75, 90} deg. Optical efficiency of the geometrically optimized PTGs was then analyzed under the same set of incident light angles and a maximum optical efficiency of 54.1% was observed for a PV cell with integrated PTG optimized at 90 deg. This is a 53.3% relative improvement in optical performance when compared to an original PV cell. Functional PTG prototypes were then fabricated with optical surface quality (below 10 nm Ra) and integrated with PV cells demonstrating an increase in maximum power by 1.08 mW/cm2 (7.6% improvement in PV performance) and in short circuit current by 2.39 mA/cm 2 (6.4% improvement).
Keywords: Cells; Cytology; Efficiency; Micromachining; Optimization; Periodic structures; Photoelectrochemical cells; Refractive index; Silicones; Solar energy; Micro-optical structure; Optical efficiency; Optical modeling; Photovoltaic cell performance; Photovoltaic performance; Solar energy industries; Total internal reflections; Triangular gratings; Photovoltaic cells

A review of graphene and graphene oxide sponge: Material synthesis and applications to energy and the environment - Chabot, Victor; Higgins, Drew; Yu, Aiping; Xiao, Xingcheng; Chen, Zhongwei; Zhang, Jiujun (Energy and Environmental Science, 2014)
This paper gives a comprehensive review about the most recent progress in synthesis, characterization, fundamental understanding, and the performance of graphene and graphene oxide sponges. Practical applications are considered including use in composite materials, as the electrode materials for electrochemical sensors, as absorbers for both gases and liquids, and as electrode materials for devices involved in electrochemical energy storage and conversion. Several advantages of both graphene and graphene oxide sponges such as three dimensional graphene networks, high surface area, high electro/thermo conductivities, high chemical/electrochemical stability, high flexibility and elasticity, and extremely high surface hydrophobicity are emphasized. To facilitate further research and development, the technical challenges are discussed, and several future research directions are also suggested in this paper.
Keywords: Elasticity; Electrochemical energy storage; Energy and the environment; Future research directions; Material synthesis; Research and development; Surface hydrophobicity; Technical challenges; Three-dimensional graphene; Graphene; carbon; composite; electrical power; electrode; hydrophobicity; oxide; sensor; storage structure; technological development

Synthesis, characterization and electrochemical performance of high-density aluminum substituted α-nickel hydroxide cathode material for nickel-based rechargeable batteries - Li, Jin; Shangguan, Enbo; Guo, Dan; Tian, Meng; Wang, Yanbin; Li, Quanmin; Chang, Zhaorong; Yuan, Xiao-Zi; Wang, Haijing (Journal of Power Sources, 2014)
Positive electrode active materials, Al-substituted α-Ni(OH) 2, with a high tap-density and high performance for alkaline nickel-based rechargeable batteries have successfully been synthesized using a polyacrylamide (PAM) assisted two-step drying method and subsequent hydrothermal treatment at 140 °C for 2 h. X-ray diffraction (XRD), infrared spectroscopy (IR), scanning electron microscopy (SEM), laser particle size analysis, tap-density measurement, cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), and charge-discharge test are used to characterize the physical and electrochemical properties of the synthesized material. The tap-density of the resulting powders reaches 1.84 g cm-3, which is significantly higher than that of α-Ni(OH)2 powders obtained by the conventional co-precipitation (CCP) and hydrothermal (HT) methods. Compared with commercial spherical β-Ni(OH)2, the resulting sample is electrochemically more active, providing discharge capacities of 315.0 and 255.2 mAh g-1, and volume capacities of 579.6 and 469.6 mAh cm -3 at rates of 0.2 C and 5 C, respectively. It is also found that although the hydrothermal treatment has a slight negative effect on the tap-density, it can improve the crystallinity of α-Ni(OH)2 and promote the anion exchange of NO3 - by OH-, resulting in a much better electrochemical performance.
Keywords: α-Nickel hydroxide; High tap-density; Nickel-based rechargeable batteries; Cathode materials

Small head-to-tail macrocyclic α-peptoids - Culf, Adrian S.; Čuperlović-Culf, Miroslava; Léger, Daniel A.; Decken, Andreas (Organic Letters, 2014)
A convenient and efficient methodology for the head-to-tail macrocyclization of small 3-mer, 4-mer, and 5-mer α-peptoid acids (9-, 12-, and 15-atom N-substituted glycine oligomers) is described. The cyclic trimer has a ccc amide sequence in the crystal structure, whereas the tetramer has ctct and the pentamer has ttccc stereochemistry. NMR analysis reveals rigid structures in solution. These synthetic macrocycles may prove useful in medicinal and materials applications.
Keywords: glycine; peptoid; article; chemical structure; chemistry; conformation; nuclear magnetic resonance; protein folding; protein secondary structure; stereoisomerism; synthesis; X ray crystallography; Crystallography, X-Ray; Glycine; Models, Molecular; Molecular Conformation; Molecular Structure; Nuclear Magnetic Resonance, Biomolecular; Peptoids; Protein Folding; Protein Structure, Secondary; Stereoisomerism

Interpreting the extended emission around three nearby debris disc host stars - Marshall, J. P.; Kirchschlager, F.; Ertel, S.; Augereau, J. -C.; Kennedy, G. M.; Booth, M.; Wolf, S.; Montesinos, B.; Eiroa, C.; Matthews, B. (Astronomy and Astrophysics, 2014)
Context. Cool debris discs are a relic of the planetesimal formation process around their host star, analogous to the solar system's Edgeworth-Kuiper belt. As such, they can be used as a proxy to probe the origin and formation of planetary systems like our own. Aims. The Herschel open time key programmes "DUst around NEarby Stars" (DUNES) and "Disc Emission via a Bias-free Reconnaissance in the Infrared/Submillimetre" (DEBRIS) observed many nearby, sun-like stars at far-infrared wavelengths seeking to detect and characterize the emission from their circumstellar dust. Excess emission attributable to the presence of dust was identified from around ~20% of stars. Herschel's high angular resolution (~7′′ FWHM at 100 μm) provided the capacity for resolving debris belts around nearby stars with radial extents comparable to the solar system (50-100 au). Methods. As part of the DUNES and DEBRIS surveys, we obtained observations of three debris disc stars, HIP 22263 (HD 30495), HIP 62207 (HD 110897), and HIP 72848 (HD 131511), at far-infrared wavelengths with the Herschel PACS instrument. Combining these new images and photometry with ancilliary data from the literature, we undertook simultaneous multi-wavelength modelling of the discs' radial profiles and spectral energy distributions using three different methodologies: single annulus, modified black body, and a radiative transfer code. Results. We present the first far-infrared spatially resolved images of these discs and new single-component debris disc models. We characterize the capacity of the models to reproduce the disc parameters based on marginally resolved emission through analysis of two sets of simulated systems (based on the HIP 22263 and HIP 62207 data) with the noise levels typical of the Herschel images. We find that the input parameter values are recovered well at noise levels attained in the observations presented here.
Keywords: Circumstellar matters; Debris discs; Host-stars; Infrared: star; Stars: individual

Engineering and pharmacology of blood-brain barrier-permeable bispecific antibodies - Stanimirovic, Danica; Kemmerich, Kristen; Haqqani, Arslan S.; Farrington, Graham K. (Pharmacology of the Blood Brain Barrier: Targeting CNS Disorders, 2014)
The development and approval of antibody-based therapeutics have progressed rapidly over the past decade. However, poor blood-brain barrier (BBB) permeability hinders the progress of antibody therapies for conditions in which the target is located in the central nervous system (CNS). Increased brain penetration of therapeutic antibodies can be achieved by engineering bispecific antibodies in which one antibody binding specificity recognizes a BBB receptor that undergoes receptor-mediated transcytosis (RMT) from the circulatory compartment into brain parenchyma, and the second binding specificity recognizes a therapeutic target within the CNS. These bispecific antibodies can be built using various antibody fragments as "building blocks," including monomeric single-domain antibodies, the smallest antigen-binding fragments of immunoglobulins. The development of BBB-crossing bispecific antibodies requires targeted antibody engineering to optimize multiple characteristics of "BBB carrier" and therapeutic arms, as well as other antibody properties impacting pharmacokinetics and effector function. Whereas several BBB-crossing bispecific antibodies have been developed using transferrin receptor antibodies as BBB carriers, the principal obstacle for capitalizing on the future promise of CNS-active antibodies remains the scarcity of known, characterized RMT receptors which could be exploited for the development of BBB carriers. This chapter reviews the recent advances and guiding principles for designing, engineering, and evaluating BBB-crossing bispecific antibodies and discusses approaches to identify and characterize novel BBB-crossing antibodies and RMT receptors.
Keywords: Bispecific antibodies; Single-domain antibodies; Receptor-mediated transcytosis; Blood–brain barrier

Selenomethionine and total methionine ratio is conserved in seed proteins of selenium-treated and nontreated soybean, flax, and potato - Fofana, B.; Main, D.; Ghose, K.; Grimmett, M.; Peters, R. D.; Martin, R. A.; Mester, Z.; Yang, L.; Locke, S.; Sweeney, M. (Crop Science, 2014)
Crop biofortification with Se is widely accepted. However, little is known about the efficiency of selenomethionine (Se-Met) incorporation into the seed and tuber protein fraction of crops. Here, we report on the efficiency of Se incorporation into the seed and tuber protein fraction of soybean, flax, and potato and the putative identity of some of the proteins that are likely targets for this random pretranslation modification. Soybean, flax, and potato plants received Se using different sodium selenate application methods and rates, and Se-Met was determined in seed, tuber, and their protein fractions. Selenium content in seed and tuber tissues and in protein fractions was increased by 2 to 86 times. The methionine (Met) pool was increased, as was the proportion of Se-Met in the Met pool, but the ratio of Se-Met:total Met was well conserved (1:1) between the treated and nontreated plants. After two-dimensional (2D) protein electrophoresis, five protein spots were identified as glycinin, trypsin inhibitor (soybean), patatin-3-Kuras-1, patain-B2, and phosphoenol carboxy kinase (potato), none of which showed S to Se substitution in their primary structure. Linking Se and three stress markers in fresh tuber extracts, glutathione (GSH) level, glutathione peroxidase (GPx), and glutathione reductase (GR) activities were increased by 20 to 35%. The data showed low protein modification in these non-Se-accumulator crops and indicated that rates of 5 to 10 g ha-1 Se, through foliar application, may ensure not only an adequate daily intake levels for humans but may also activate antioxidant enzyme systems within the tuber tissue.

Double-pulse LIBS combining short and long nanosecond pulses in the microjoule range - Elnasharty, Islam Y.; Doucet, François R.; Gravel, Jean-Francois Y.; Bouchard, Paul; Sabsabi, Mohamad (Journal of Analytical Atomic Spectrometry, 2014)
The present study investigates the collinear double-pulse LIBS (DP-LIBS) configuration using microjoule nanosecond pulses. It is shown that this approach can achieve typical double pulse improvement in the analytical performances for elemental analysis of aluminium alloys. In addition, the effect of the chronological sequence of the short and long nanosecond pulses in the collinear DP-LIBS experiment was also studied. The results show a significant increase of the intensity and repeatability of the emission signals in the double pulse configuration. Standard DP-LIBS signal improvement over the signal-to-noise ratio and the signal-to-background ratio for the analytical lines of different elements has been observed in comparison to single pulse LIBS of equal energy. Limits of detection in the low μg g-1 range have been obtained for the different elements studied. The improvement resulting from the use of DP-LIBS was about 2-4 fold when compared to SP-LIBS in all cases. These results are useful in the context of studies investigating how the μLIBS will assist in the development of portable LIBS systems and improve the utility of this spectroscopy technique for field applications. Finally, the plasma temperature is found to be approximately less than 15% higher with the double-pulse.
Keywords: Spectrometry; Analytical performance; Chronological sequences; Double-pulse LIBS; Field application; Limits of detection; Nanosecond pulse; Plasma temperature; Signal-to-background ratio; Measurements

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome - Sharpe, Andrew; Klassen, Darrin; International Wheat Genome Sequencing Consortium (Science, 2014)
An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.
Keywords: chromosome; gene expression; genetic marker; genome; polyploidy; wheat; diploidy; gene duplication; gene locus; gene loss; gene sequence; genetic conservation; plant chromosome; plant genome; polyploidy; sequence homology; tetraploidy; Triticum aestivum

Searching for a gas cloud surrounding the WASP-18 planetary system - Fossati, L.; Ayres, T. R.; Haswell, C. A.; Jenkins, J. S.; Bisikalo, D.; Bohlender, D.; Flöer, L.; Kochukhov, O. (Astrophysics and Space Science, 2014)
Near-UV (NUV) Hubble Space Telescope (HST) observations of the extreme hot-Jupiter WASP-12b revealed the presence of diffuse exospheric gas extending beyond the planet’s Roche lobe. Furthermore the NUV observations showed a complete lack of the normally bright core emission of the Mg ii h&k resonance lines, in agreement with the measured anomalously low stellar activity index (logR′HK). Comparisons with other distant and inactive stars, and the analysis of radio and optical measurements of the intervening interstellar medium (ISM), led us to the conclusion that the system is surrounded by a circumstellar gas cloud, likely formed of material lost by the planet. Similar anomalous logR′HK index deficiencies might therefore signal the presence of translucent circumstellar gas around other stars hosting evaporating planets; we identified five such systems and WASP-18 is one of them. Both radio and optical observations of the region surrounding WASP-18 point towards a negligible ISM absorption along the WASP-18 line of sight. Excluding the unlikely possibility of an intrinsic anomalously low stellar activity, we conclude that the system is probably surrounded by a circumstellar gas cloud, presumably formed of material lost by the planet. Nevertheless only a far-UV spectrum of the star would provide a definite answer. Theoretical modelling suggests WASP-18b undergoes negligible mass loss, in contrast to the probable presence of a circumstellar gas cloud formed of material lost by the planet. The solution might be the presence either of an extra energy source driving mass loss (e.g., the reconnection of the stellar and planetary magnetic fields inside the planet atmosphere) or of an evaporating third body (e.g., moon).

A comparison of flax shive and extracted flax shive reinforced PP composites - Hu, Wei; Zhang, Mingyao; Ton-That, Minh-Tan; Ngo, Tri-dung (Fibers and Polymers, 2014)
In this study, flax shive (FS) and extracted flax shive (EFS) were fully characterized. The results showed that EFS presented lower noncellulose content, smaller porous tunnels and better thermal stability than FS. The 5 % weight loss temperature of EFS was over 200 °C, which can meet the requirements of the processing conditions for the natural fiber reinforced polymer composites. Consequently, the flax shive and extracted flax shive reinforced PP composites were prepared and characterized. It was found that the thermal stability of EFS/PP composites was better than that of FS/PP composites, and both FS and EFS behaved as nucleation agents, which could accelerate the crystallization process of PP in the composites. Mechanical test showed that EFS could be used as a reinforcing material for PP composite when compatibilizer was applied. The flexural strength and modulus of the composites containing 30 % EFS were about 8 % and 100 % higher than that of pure polypropylene, respectively.

Validation of parameter estimation methods for determining optical properties of atherosclerotic tissues in intravascular OCT - Shalev, Ronny; Gargesha, Madhusudhana; Prabhu, David; Tanaka, Kentaro; Rollins, Andrew M.; Costa, Marco; Bezerra, Hiram G.; Lamouche, Guy; Wilson, David L. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE, 2014)
In this paper we present a new process for assessing optical properties of tissues from 3D pullbacks, the standard clinical acquisition method for iOCT data. Our method analyzes a volume of interest (VOI) consisting of about 100 A-lines spread across the angle of rotation (θ) and along the artery, z. The new 3D method uses catheter correction, baseline removal, speckle noise reduction, alignment of A-line sequences, and robust estimation. We compare results to those from a more standard, gold standard stationary acquisition where many image frames are averaged to reduce noise. To do these studies in a controlled fashion, we use a realistic optical artery phantom containing of multiple tissue types. Precision and accuracy for 3D pullback analysis are reported. Our results indicate that when implementing the process on a stationary acquisition dataset, the uncertainty improves at each stage while the uncertainty is reduced. When comparing stationary acquisition dataset to pullback dataset, the values were as follows: calcium: 3.8±1.09mm -1 in stationary and 3.9±1.2 mm-1 in a pullback; lipid: 11.025±0.417 mm-1 in stationary and 11.27±0.25 mm-1 in pullback; fibrous: 6.08±1.337 mm-1 in stationary and 5.58±2.0 mm-1. These results indicates that the process presented in this paper introduce minimal bias and only a small change in uncertainty when comparing a stationary and pullback dataset, thus paves the way to a highly accurate clinical plaque type discrimination, enabling automatic classification.
Keywords: Medical imaging; Noise abatement; Optical properties; Optical tomography; Tissue; Automatic classification; Intravascular imaging; IOCT; OCT; Optical parameter; Parameter estimation method; Speckle noise reduction; Volume of interest; Tissue engineering

Semi-supervised consensus clustering for gene expression data analysis - Wang, Yunli; Pan, Youlian (BioData Mining, 2014)
Background: Simple clustering methods such as hierarchical clustering and k-means are widely used for gene expression data analysis; but they are unable to deal with noise and high dimensionality associated with the microarray gene expression data. Consensus clustering appears to improve the robustness and quality of clustering results. Incorporating prior knowledge in clustering process (semi-supervised clustering) has been shown to improve the consistency between the data partitioning and domain knowledge. Methods. We proposed semi-supervised consensus clustering (SSCC) to integrate the consensus clustering with semi-supervised clustering for analyzing gene expression data. We investigated the roles of consensus clustering and prior knowledge in improving the quality of clustering. SSCC was compared with one semi-supervised clustering algorithm, one consensus clustering algorithm, and k-means. Experiments on eight gene expression datasets were performed using h-fold cross-validation. Results: Using prior knowledge improved the clustering quality by reducing the impact of noise and high dimensionality in microarray data. Integration of consensus clustering with semi-supervised clustering improved performance as compared to using consensus clustering or semi-supervised clustering separately. Our SSCC method outperformed the others tested in this paper.
Keywords: Semi-supervised clustering; Consensus clustering; Semi-supervised consensus clustering; Gene expression

Hanle measurements of electrodeposited Fe/GaAs spin tunnel contacts - Majumder, Sarmita; Hohertz, Donna; McNeil, James; Springthorpe, Anthony; Kavanagh, Karen L. (Journal of Applied Physics, 2014)
We report spin transport in electrodeposited Fe/n-GaAs tunnel diodes via three-terminal Hanle measurements. For temperatures between 20K and 150K, the spin resistance was up to 20 times higher than expected from theoretical calculations and 1000 times larger compared to a vacuum-deposited counterpart. This higher spin resistance was correlated with a higher contact resistance, and a higher concentration of oxygen impurities in the electrodeposited Fe film and interface, as detected via x-ray photoelectron and Auger spectroscopies, and inferred from Fe film nucleation rates. These results can be explained via a small effective tunnel-contact area of 5%, but extra spin filtering via interfacial states or magnetic oxide layers cannot be ruled out. The spin diffusion times (8.5 ± 0.4ns to 1.8 ± 0.4ns, for 20K to 150K) extracted from Lorentzian fits were in good agreement with values obtained from earlier 4-terminal Hanle measurements (7.8 ± 0.4ns to 3.2 ± 0.4ns, for 25K to 77K), both 10 times slower than reported vacuum-deposited contacts.
Keywords: Interfaces (materials); Iron; Metallic films; Vacuum; Auger spectroscopy; Interfacial state; Magnetic oxides; Nucleation rate; Theoretical calculations; Tunnel contacts; X-ray photoelectrons; Electrodeposition

Segmentation and classification of anthropometric data for the apparel industry - Paquet, E.; Viktor, H. L. (Anthropometry, Apparel Sizing and Design, 2014)
Acquisition systems based on laser triangulation or structured light are becoming commonplace in anthropometry. Such systems allow one to capture very detailed data to be used when addressing the sizing problem. This chapter introduces state-of-the-art approaches to describe, to segment and to cluster the data acquired by such systems. We describe methods used to address the deformable nature of human bodies. We introduce isometry-invariant descriptor creation algorithms that are suitable for indexing regions that contain soft tissues. Further, we describe how to cluster a specific population, found in a so-called human body space, into partitions of similar individuals.
Keywords: anthropometry; clustering; diffusion distance; geodesic distance; heat kernel; invariance; Isomap; Laplacian; multidimensional scaling (MDS); segmentation; spherical harmonics; Zernike

Magnetic field-assisted electroless anodization : TiO2 nanotube growth on discontinuous, patterned Ti films - Mohammadpour, Arash; Shankar, Karthik (Journal of Materials Chemistry A, 2014)
We present a magnetic field-assisted oxidation and etching process that transforms Ti thin films on arbitrary substrates into self-organized TiO 2 nanotube arrays without the direct application of an anodization voltage between the cathode and the Ti film/substrate. In effect, the Ti film/substrate electrode is at a floating potential determined by the ionic Hall voltage. The development of such a magnetic field-assisted electroless anodization process, frees the anodization technique of forming nanostructured semiconductors and metal oxides from the constraints of substrate conductivity and film continuity imposed by the traditional anodization process, and allows the creation of uniform anodic nanostructures on pre-existing high-aspect ratio patterns as well as on substrates containing both conductive and non-conductive areas. Using magnetic field assisted electroless anodization, we demonstrate the formation of microscale patterns of high quality TiO2 nanotubes from discontinuous Ti films deposited on thermal oxide-coated Si substrates and patterned by a lift-off process.
Keywords: Anodic oxidation; Aspect ratio; Electrodes; Magnetic fields; Nanotubes; Oxide films; Titanium; Anodization process; Anodization techniques; Anodization voltages; Floating potentials; High-aspect ratio; Microscale patterns; Nanostructured semiconductor; Substrate conductivity; Substrates

A modelling approach to evaluate the long-term effect of soil texture on spring wheat productivity under a rain-fed condition - He, Yong; Hou, Lingling; Wang, Hong; Hu, Kelin; McConkey, Brian (Scientific Reports, 2014)
Soil surface texture is an important environmental factor that influences crop productivity because of its direct effect on soil water and complex interactions with other environmental factors. Using 30-year data, an agricultural system model (DSSAT-CERES-Wheat) was calibrated and validated. After validation, the modelled yield and water use (WU) of spring wheat (Triticum aestivum L.) from two soil textures (silt loam and clay) under rain-fed condition were analyzed. Regression analysis showed that wheat grown in silt loam soil is more sensitive to WU than wheat grown in clay soil, indicating that the wheat grown in clay soil has higher drought tolerance than that grown in silt loam. Yield variation can be explained by WU other than by precipitation use (PU). These results demonstrated that the DSSAT-CERES-Wheat model can be used to evaluate the WU of different soil textures and assess the feasibility of wheat production under various conditions. These outcomes can improve our understanding of the long-term effect of soil texture on spring wheat productivity in rain-fed condition.

Nickel/iron oxide nanocrystals with a nonequilibrium phase: Controlling size, shape, and composition - Bau, Jeremy A.; Li, Peng; Marenco, Armando J.; Trudel, Simon; Olsen, Brian C.; Luber, Erik J.; Buriak, Jillian M. (Chemistry of Materials, 2014)
Mixed nickel iron oxide nanomaterials have great potential for use in fields as wide-ranging as optics, water oxidation catalysis, and biomedical applications; large-scale deployment for any of these applications is possible due to the abundance of iron and nickel in the earth's crust. Here, we describe single-crystal mixed nickel iron oxide nanoparticles with a rocksalt crystal structure and an iron content greater than >10 at%. The nanoparticles were synthesized via thermal decomposition of nickel and iron oleates, yielding monodisperse nanoparticles <12 nm in size. A range of compositions were accessible, ranging from iron-poor to iron-rich. Despite the predicted poor solubility of iron in the NiO lattice, as based upon the equilibrium phase diagram, and the general tendency of pure FexO to oxidize, the single-crystal nanoparticles are nonetheless kinetically persistent even at elevated temperatures (200 °C). Furthermore, by controlling the drying conditions and decomposition time of the oleate precursors as well as the initial ratio of nickel to iron in the precursor oleate mixture a variety of nanoparticle shapes-namely stars, cubes, and spheres-were formed. This control of shape and composition affords tunability of physical properties, exemplified by magnetic properties herein.
Keywords: Decomposition; Iron; Medical applications; Nanoparticles; Nickel; Single crystals; Structural geology; Biomedical applications; Elevated temperature; Equilibrium phase diagrams; Large-scale deployment; Monodisperse nanoparticles; Non-equilibrium phase; Oxide nanocrystals; Poor solubilities; Synthesis (chemical)

Accurate measurement of microwave power in the IEC: R-70 (WR-138) waveguide transmission line - Michaud, Alain (2014 Conference on Precision Electromagnetic Measurements (CPEM 2014), 2014)
We compare the accuracy of different techniques to measure guided RF power at 6.83 GHz. The transmission line is a standard rectangular metallic waveguide IEC: R-70 (WR-138). We used three calculable standards including a waveguide calorimeter, a coaxial calorimeter, and an atomic (quantum based) power meter based on laser cooled rubidium atoms.
Keywords: Accurate measurement; Microcalorimeter; Microwave power; Rabi oscillations; Radio frequency power; Waveguide transmission line; Laser cooling

Osteoblastic differentiation under controlled bioactive ion release by silica and titania doped sodium-free calcium phosphate-based glass - Mohammadi, Maziar Shah; Chicatun, Florencia; Stähli, Christoph; Muja, Naser; Bureau, Martin N.; Nazhat, Showan N. (Colloids and Surfaces B: Biointerfaces, 2014)
Sodium-free phosphate-based glasses (PGs) doped with both SiO2 and TiO2 (50P2O5-40CaO-xSiO2-(10-x)TiO2, where x=10, 7, 5, 3, and 0mol%) were developed and characterised for controlled ion release applications in bone tissue engineering. Substituting SiO2 with TiO2 directly increased PG density and glass transition temperature, indicating a cross-linking effect of Ti on the glass network which was reflected by significantly reduced degradation rates in an aqueous environment. X-ray diffraction confirmed the presence of Ti(P2O7) in crystallised TiO2-containing PGs, and nuclear magnetic resonance showed an increase in Q1 phosphate species with increasing TiO2 content. Substitution of SiO2 with TiO2 also reduced hydrophilicity and surface energy. In biological assays, MC3T3-E1 pre-osteoblasts effectively adhered to the surface of PG discs and the incorporation of TiO2, and hence higher stability of the PG network, significantly increased cell viability and metabolic activity indicating the biocompatibility of the PGs. Addition of SiO2 increased ionic release from the PG, which stimulated alkaline phosphatase (ALP) activity in MC3T3-E1 cells upon ion exposure. The incorporation of 3mol% TiO2 was required to stabilise the PG network against unfavourable rapid degradation in aqueous environments. However, ALP activity was greatest in PGs doped with 5-7mol% SiO2 due to up-regulation of ionic concentrations. Thus, the properties of PGs can be readily controlled by modifying the extent of Si and Ti doping in order to optimise ion release and osteoblastic differentiation for bone tissue engineering applications.
Keywords: Calcium phosphate-based glass; Silica; Osteoinduction; Alkaline phosphatase; Cell–material interaction; Bone repair; Ions

Dispersion-correcting potentials can significantly improve the bond dissociation enthalpies and noncovalent binding energies predicted by density-functional theory - Dilabio, Gino A.; Koleini, Mohammad (Journal of Chemical Physics, 2014)
Dispersion-correcting potentials (DCPs) are atom-centered Gaussian functions that are applied in a manner that is similar to effective core potentials. Previous work on DCPs has focussed on their use as a simple means of improving the ability of conventional density-functional theory methods to predict the binding energies of noncovalently bonded molecular dimers. We show in this work that DCPs developed for use with the LC-ωPBE functional along with 6-31+G(2d,2p) basis sets are capable of simultaneously improving predicted noncovalent binding energies of van der Waals dimer complexes and covalent bond dissociation enthalpies in molecules. Specifically, the DCPs developed herein for the C, H, N, and O atoms provide binding energies for a set of 66 noncovalently bonded molecular dimers (the "S66" set) with a mean absolute error (MAE) of 0.21 kcal/mol, which represents an improvement of more than a factor of 10 over unadorned LC-ωPBE/6-31+G(2d,2p) and almost a factor of two improvement over LC-ωPBE/6-31+G(2d,2p) used in conjunction with the "D3" pairwise dispersion energy corrections. In addition, the DCPs reduce the MAE of calculated X-H and X-Y (X,Y = C, H, N, O) bond dissociation enthalpies for a set of 40 species from 3.2 kcal/mol obtained with unadorned LC-ωPBE/6-31+G(2d,2p) to 1.6 kcal/mol. Our findings demonstrate that broad improvements to the performance of DFT methods may be achievable through the use of DCPs.
Keywords: Chemical bonds; Density functional theory; Dimers; Dispersions; Van der Waals forces; Bond dissociation enthalpies; Dispersion energies; Effective core potential; Gaussian functions; Mean absolute error; Molecular dimers; Noncovalent binding; Van der Waals dimer; Binding energy

Homogeneous photometry VI: Variable stars in the Leo I Dwarf spheroidal galaxy - Stetson, Peter B.; Fiorentino, Giuliana; Bono, Giuseppe; Bernard, Edouard J.; Monelli, Matteo; Iannicola, Giacinto; Gallart, Carme; Ferraro, Ivan (Publications of the Astronomical Society of the Pacific, 2014)
From archival ground-based images of the Leo I dwarf spheroidal galaxy, we have identified and characterized the pulsation properties of 164 candidate RR Lyrae variables and 55 candidate anomalous and/or short-period Cepheids. We have also identified 19 candidate long-period variable stars and 13 other candidate variables whose physical nature is unclear, but due to the limitations of our observational material we are unable to estimate reliable periods for them. On the basis of its RR Lyrae star population, Leo I is confirmed to be an Oosterhoff-intermediate type galaxy, like several other dwarf spheroidals. From the RR Lyrae stars we have derived a range of possible distance moduli for Leo I: 22.06 ± 0.08 ≲ μ0 ≲ 22.25 ± 0.07 mag depending on the metallicity assumed for the old population ([Fe/H] from -1.43 to -2.15). This is in agreement with previous independent estimates. We show that in their pulsation properties, the RR Lyrae stars-representing the oldest stellar population in the galaxy-are not significantly different from those of five other nearby, isolated dwarf spheroidal galaxies. A similar result is obtained when comparing them to RR Lyrae stars in recently discovered ultra-faint dwarf galaxies. We are able to compare the period distributions and period-amplitude relations for a statistically significant sample of ab-type RR Lyrae stars in dwarf galaxies (~1300 stars) with those in the Galactic halo field (~14, 000 stars) and globular clusters (~1000 stars). Field RRLs show a significant change in their period distribution when moving from the inner (dG ≲ 14 kpc) to the outer (dG ≳ 14 kpc) halo regions. This suggests that the halo formed from (at least) two dissimilar progenitors or types of progenitor. Considered together, the RR Lyrae stars in classical dwarf spheroidal and ultra-faint dwarf galaxies-as observed today-do not appear to follow the well defined pulsation properties shown by those in either the inner or the outer Galactic halo, nor do they have the same properties as RR Lyraes in globular clusters. In particular, the samples of fundamental-mode RR Lyrae stars in dwarf galaxies seem to lack High Amplitudes and Short Periods ("HASP": AV≥1.0 mag and P ≲ 0.48 d) when compared with those observed in the Galactic halo field and globular clusters. The observed properties of RR Lyrae stars do not support the idea that currently existing classical dwarf spheroidal and ultra-faint dwarf galaxies are surviving representative examples of the original building blocks of the Galactic halo.

Mechanistic study of the role of primary amines in precursor conversions to semiconductor nanocrystals at low temperature - Yu, Kui; Liu, Xiangyang; Chen, Queena Y.; Yang, Huaqing; Yang, Mingli; Wang, Xinqin; Wang, Xin; Cao, Hong; Whitfield, Dennis M.; Hu, Changwei; Tao, Ye (Angewandte Chemie - International Edition, 2014)
Primary alkyl amines (RNH2) have been empirically used to engineer various colloidal semiconductor nanocrystals (NCs). Here, we present a general mechanism in which the amine acts as a hydrogen/proton donor in the precursor conversion to nanocrystals at low temperature, which was assisted by the presence of a secondary phosphine. Our findings introduce the strategy of using a secondary phosphine together with a primary amine as new routes to prepare high-quality NCs at low reaction temperatures but with high particle yields and reproducibility and thus, potentially, low production costs.
Keywords: Amines; Nanocrystals; Phosphorus compounds; Colloidal quantum dots; Colloidal semiconductor nanocrystals; phosphines; Precursor conversion; Reaction temperature; Secondary phosphines; Semiconductor nanocrystals; Semiconductor particles; Semiconductor quantum dots

Atomic structure and microstructures of supertetragonal multiferroic BiFeO 3 thin films - Pailloux, F.; Couillard, M.; Fusil, S.; Bruno, F.; Saidi, W.; Garcia, V.; Carrétéro, C.; Jacquet, E.; Bibes, M.; Barthélémy, A.; Botton, G. A.; Pacaud, J. (Physical Review B - Condensed Matter and Materials Physics, 2014)
We revisit the atomic structure and microstructure of the so-called supertetragonal phases of highly strained epitaxial BiFeO3 thin films. Quantitative atomic resolution scanning transmission electron microscopy is used to directly image the atomic positions. A crystallographic phase suggested by electron diffraction and predicted by ab initio calculations is evidenced. Microtwins are reported in thickest films. Electron energy loss spectroscopy is further employed to reveal subtle electronic structure features, which, interpreted in a framework of antiferrodistortive distortions coupling with the substrate, point towards a phase closer to the P4mm purely tetragonal phase.

Genetic control of susceptibility to candida albicans in SM/J mice - Radovanovic, Irena; Leung, Vicki; Iliescu, Alexandra; Bongfen, Silayuv E.; Mullick, Alaka; Langlais, David; Gros, Philippe (Journal of Immunology, 2014)
In the immunocompromised host, invasive infection with the fungal pathogen Candida albicans is associated with high morbidity and mortality. Sporadic cases in otherwise normal individuals are rare, and they are thought to be associated with genetic predisposition. Using a mouse model of systemic infection with C. albicans, we identified the SM/J mouse strain as unusually susceptible to infection. Genetic linkage studies in informative [C57BL/6JxSM/J]F2 mice identified a major locus on distal chromosome 15, given the appellation Carg5, that regulates C. albicans replication in SM/J mice. Cellular and molecular immunophenotyping experiments, as well as functional studies in purified cell populations from SM/J and C57BL/6J, and in [C57BL/ 6JxSM/J]F2 mice fixed for homozygous or heterozygous Carg5 alleles, indicate that Carg5-regulated susceptibility in SM/J is associated with a complex defect in the myeloid compartment of these mice. SM/J neutrophils express lower levels of Ly6G, and importantly, they show significantly reduced production of reactive oxygen species in response to stimulation with fMLF and PMA. Likewise, CD11b+Ly6G2Ly6Chi inflammatory monocytes were present at lower levels in the blood of infected SM/J, recruited less efficiently at the site of infection, and displayed blunted oxidative burst. Studies in F2 mice establish strong correlations between Carg5 alleles, Ly6G expression, production of serum CCL2 (MCP-1), and susceptibility to C. albicans. Genomic DNA sequencing of chromatin immunoprecipitated for myeloid proinflammatory transcription factors IRF1, IRF8, STAT1 and NF-kB, as well as RNA sequencing, were used to develop a "myeloid inflammatory score" and systematically analyze and prioritize potential candidate genes in the Carg5 interval.

Determination of PM mass emissions from an aircraft turbine engine using particle effective density - Durdina, L.; Brem, B. T.; Abegglen, M.; Lobo, P.; Rindlisbacher, T.; Thomson, K. A.; Smallwood, G. J.; Hagen, D.E.; Sierau, B.; Wang, J. (Atmospheric Environment, 2014)
Inventories of particulate matter (PM) emissions from civil aviation and air quality models need to be validated using up-to-date measurement data corrected for sampling artifacts. We compared the measured black carbon (BC) mass and the total PM mass determined from particle size distributions (PSD) and effective density for a commercial turbofan engine CFM56-7B26/3. The effective density was then used to calculate the PM mass losses in the sampling system. The effective density was determined using a differential mobility analyzer and a centrifugal particle mass analyzer, and increased from engine idle to take-off by up to 60%. The determined mass-mobility exponents ranged from 2.37 to 2.64. The mean effective density determined by weighting the effective density distributions by PM volume was within 10% of the unit density (1000kg/m3) that is widely assumed in aircraft PM studies. We found ratios close to unity between the PM mass determined by the integrated PSD method and the real-time BC mass measurements. The integrated PSD method achieved higher precision at ultra-low PM concentrations at which current mass instruments reach their detection limit. The line loss model predicted ~60% PM mass loss at engine idle, decreasing to ~27% at high thrust. Replacing the effective density distributions with unit density lead to comparable estimates that were within 20% and 5% at engine idle and high thrust, respectively. These results could be used for the development of a robust method for sampling loss correction of the future PM emissions database from commercial aircraft engines.
Keywords: Aviation; Aircraft; Emissions; Particulate matter; Effective density; Black carbon

Selective growth and ordering of SiGe nanowires for band gap engineering - Benkouider, A.; Ronda, A.; Gouyé, A.; Herrier, C.; Favre, L.; Lockwood, D. J.; Rowell, N. L.; Delobbe, A.; Sudraud, P.; Berbezier, I. (Nanotechnology, 2014)
Selective growth and self-organization of silicon-germanium (SiGe) nanowires (NWs) on focused ion beam (FIB) patterned Si(111) substrates is reported. In its first step, the process involves the selective synthesis of Au catalysts in SiO2-free areas; its second step involves the preferential nucleation and growth of SiGe NWs on the catalysts. The selective synthesis process is based on a simple, room-temperature reduction of gold salts (Au3+Cl?/4 ) in aqueous solution, which provides well-organized Au catalysts. By optimizing the reduction process, we are able to generate a bidimensional regular array of Au catalysts with self-limited sizes positioned in SiO2 -free windows opened in a SiO /Si2 (111) substrate by FIB patterning. Such Au catalysts subsequently serve as preferential nucleation and growth sites of well-organized NWs. Furthermore, these NWs with tunable position and size exhibit the relevant features and bright luminescence that would find several applications in optoelectronic nanodevices.
Keywords: nanowires (NWs); ordering; molecular beam epitaxy (MBE); selective growth; focused ion beam (FIB) patterning; photoluminescence

3D chemically cross-linked single-walled carbon nanotube buckypapers - Jakubinek, Michael B.; Ashrafi, Behnam; Guan, Jingwen; Johnson, Michel B.; White, Mary Anne; Simard, Benoit (RSC Advances, 2014)
Single-walled carbon nanotubes (SWCNTs) covalently modified with OH functional groups were assembled into buckypapers through solvent dispersion and vacuum filtration. These SWCNT-OH buckypaper sheets were subsequently crosslinked by wetting with bifunctional linkers followed by hot compression causing reaction between the functional groups of the reagent and OH functional groups on the side-walls of SWCNTs to create three-dimensional (3D) covalently cross-linked buckypapers. Cross-linking also was performed using SWCNTs encapsulated with a functionalized polymer wrapping in a core-shell structure, where OH or/and NH2 groups are available on the surface of the polymeric shell for reaction. The 3D cross-linked SWCNT buckypapers retain the porous character typical of buckypaper, and were characterized for their tensile properties and thermal and electrical conductivities. Several cross-linking approaches dramatically improved the mechanical properties. The strongest and stiffest papers (32 MPa, E = 3.1 GPa), which approach 10× stronger and stiffer than the pristine non-crosslinked buckypaper, were obtained at the expense of a loss of electrical conductivity. In other cases, such as cross-linking using a high-performance epoxy resin monomer, improvements in strength and stiffness of ∼5× were obtained while retaining electrical and thermal conductivity. Therefore, the optimal cross-linking approach would be determined by the desired, multifunctional properties. Additionally, the approach can be used in the preparation buckypaper composites and it is demonstrated that cross-linking using a multifunctional epoxy resin prior to impregnation with the same epoxy resin results in substantially better mechanical properties in comparison to just epoxy-impregnation of pristine buckypaper.
Keywords: Bucky paper

Impact of UV and peracetic acid disinfection on the prevalence of virulence and antimicrobial resistance genes in uropathogenic escherichia coli in wastewater effluents - Biswal, Basanta Kumar; Khairallah, Ramzi; Bibi, Kareem; Mazza, Alberto; Gehr, Ronald; Masson, Luke; Frigon, Dominic (Applied and Environmental Microbiology, 2014)
Wastewater discharges may increase the populations of pathogens, including Escherichia coli, and of antimicrobial-resistant strains in receiving waters. This study investigated the impact of UV and peracetic acid (PAA) disinfection on the prevalence of virulence and antimicrobial resistance genes in uropathogenic Escherichia coli (UPEC), the most abundant E. coli pathotype in municipal wastewaters. Laboratory disinfection experiments were conducted on wastewater treated by physicochemical, activated sludge, or biofiltration processes; 1,766 E. coli isolates were obtained for the evaluation. The target disinfection level was 200 CFU/100 ml, resulting in UV and PAA doses of 7 to 30 mJ/cm2 and 0.9 to 2.0 mg/liter, respectively. The proportions of UPECs were reduced in all samples after disinfection, with an average reduction by UV of 55% (range, 22% to 80%) and by PAA of 52% (range, 11% to 100%). Analysis of urovirulence genes revealed that the decline in the UPEC populations was not associated with any particular virulence factor. A positive association was found between the occurrence of urovirulence and antimicrobial resistance genes (ARGs). However, the changes in the prevalence of ARGs in potential UPECs were different following disinfection, i.e., UV appears to have had no effect, while PAA significantly reduced the ARG levels. Thus, this study showed that both UV and PAA disinfections reduced the proportion of UPECs and that PAA disinfection also reduced the proportion of antimicrobial resistance gene-carrying UPEC pathotypes in municipal wastewaters.
Keywords: Effluents; Escherichia coli; Genes; Microorganisms; Pathogens; Population statistics; Wastewater treatment; Activated sludge; Antimicrobial resistances; Biofiltration process; Municipal wastewaters; Uropathogenic Escherichia coli; Virulence factors; Wastewater discharge; Wastewater effluents; Disinfection

Class 0 protostars in the Perseus molecular cloud: A correlation between the youngest protostars and the dense gas distribution - Sadavoy, S. I.; Di Francesco, J.; André, PH.; Pezzuto, S.; Bernard, J.-P.; Maury, A.; Men'Shchikov, A.; Motte, F.; Nguỹên-Lu'O'Ng, Q.; Schneider, N.; Arzoumanian, D.; Benedettini, M.; et al. (The Astrophysical Journal Letters, 2014)
We use PACS and SPIRE continuum data at 160 μm, 250 μm, 350 μm, and 500 μm from the Herschel Gould Belt Survey to sample seven clumps in Perseus: B1, B1-E, B5, IC 348, L1448, L1455, and NGC 1333. Additionally, we identify and characterize the embedded Class 0 protostars using detections of compact Herschel sources at 70 μm as well as archival Spitzer catalogs and SCUBA 850 μm photometric data. We identify 28 candidate Class 0 protostars, four of which are newly discovered sources not identified with Spitzer. We find that the star formation efficiency of clumps, as traced by Class 0 protostars, correlates strongly with the flatness of their respective column density distributions at high values. This correlation suggests that the fraction of high column density material in a clump reflects only its youngest protostellar population rather than its entire source population. We propose that feedback from either the formation or evolution of protostars changes the local density structure of clumps.
Keywords: dust, extinction; ISM: individual objects (Perseus); stars: formation; stars: protostars

Modeling the transcriptional regulatory network that controls the early hypoxic response in Candida albicans - Sellam, Adnane; van het Hoog, Marco; Tebbji, Faiza; Beaurepaire, Cécile; Whiteway, Malcolm; Nantel, André (Eukaryotic Cell, 2014)
We determined the changes in transcriptional profiles that occur in the first hour following the transfer of Candida albicans to hypoxic growth conditions. The impressive speed of this response is not compatible with current models of fungal adaptation to hypoxia that depend on the depletion of sterol and heme. Functional analysis using Gene Set Enrichment Analysis (GSEA) identified the Sit4 phosphatase, Ccr4 mRNA deacetylase, and Sko1 transcription factor (TF) as potential regulators of the early hypoxic response. Cells mutated in these and other regulators exhibit a delay in their transcriptional responses to hypoxia. Promoter occupancy data for 29 TFs were combined with the transcriptional profiles of 3,111 in vivo target genes in a Network Component Analysis (NCA) to produce a model of the dynamic and highly interconnected TF network that controls this process. With data from the TF network obtained from a variety of sources, we generated an edge and node model that was capable of separating many of the hypoxia-upregulated and -downregulated genes. Upregulated genes are centered on Tye7, Upc2, and Mrr1, which are associated with many of the gene promoters that exhibit the strongest activations. The connectivity of the model illustrates the high redundancy of this response system and the challenges that lie in determining the individual contributions of specific TFs. Finally, treating cells with an inhibitor of the oxidative phosphorylation chain mimics most of the early hypoxic profile, which suggests that this response may be initiated by a drop in ATP production.

The Next Generation Virgo Cluster survey. V. Modeling the dynamics of M87 with the made-to-measure method - Zhu, L.; Long, R. J.; Mao, S.; Peng, E. W.; Liu, C.; Caldwell, N.; Li, B.; Blakeslee, J. P.; Côté, P.; Cuillandre, J.-C.; Durrell, P.; Emsellem, E.; et al. (The Astrophysical Journal, 2014)
We study the dynamics of the giant elliptical galaxy M87 from the central to the outermost regions with the made-to-measure (M2M) method. We use a new catalog of 922 globular cluster line-of-sight velocities extending to a projected radius of 180 kpc (equivalent to 25 M87 effective radii), and SAURON integral field unit data within the central 2.4 kpc. There are 263 globular clusters, mainly located beyond 40 kpc, newly observed by the Next Generation Virgo Survey. For the M2M modeling, the gravitational potential is taken as a combination of a luminous matter potential with a constant stellar mass-to-light ratio and a dark matter potential modeled as a logarithmic potential. Our best-fit dynamical model returns a stellar mass-to-light ratio in the I band of M/LI = 6.0 ± 0.3 with a dark matter potential scale velocity of 591 ± 50 km s-1 and scale radius of 42 ± 10 kpc. We determine the total mass of M87 within 180 kpc to be (1.5 ± 0.2) × 1013 M. The mass within 40 kpc is smaller than previous estimates determined using globular cluster kinematics that did not extend beyond ∼45 kpc. With our new globular cluster velocities at much larger radii, we see that globular clusters around 40 kpc show an anomalously large velocity dispersion which affected previous results. The mass we derive is in good agreement with that inferred from ROSAT X-ray observation out to 180 kpc. Within 30 kpc our mass is also consistent with that inferred from Chandra and XMM-Newton X-ray observations, while within 120 kpc it is about 20% smaller. The model velocity dispersion anisotropy β parameter for the globular clusters in M87 is small, varying from -0.2 at the center to 0.2 at ∼40 kpc, and gradually decreasing to zero at ∼120 kpc.

High-yield, single-step separation of metallic and semiconducting SWCNTs using block copolymers at low temperatures - Homenick, Christa M.; Rousina-Webb, Alexander; Cheng, Fuyong; Jakubinek, Michael B.; Malenfant, Patrick R. L.; Simard, Benoit (The Journal of Physical Chemistry C, 2014)
Electronic type separation of SWCNT material is necessary to facilitate the development of carbon nanotube electronics. A convenient, high-yield, single-step separation of metallic and semiconducting SWCNTs has been developed using block copolymers and density gradient ultracentrifugation. In particular by varying the centrifugation temperature and dissolved oxygen content under acidic conditions, extraction efficiencies of up to 65% were achieved with both metallic and semiconducting SWCNT electronic purity exceeding 99% as determined by absorption spectroscopy. It was demonstrated that lowering the temperature during the DGU separation, which is expected to increase the difference in densities between metallic and semiconducting nanotube complexes, results in higher purity and yield. Semiconducting and metallic bands are separated simply with a disposable pipet such that specialized fractioning equipment is not required for effective isolation of enriched SWCNTs.
Keywords: Centrifugation; Acidic conditions; Carbon nanotube electronics; Density gradients; Dissolved oxygen contents; Extraction efficiencies; Semi-conducting nanotubes; Semiconducting-SWCNTs; Ultracentrifugation; Block copolymers

Copper-catalysed cycloaddition reactions of nitrones and alkynes for bioorthogonal labelling of living cells - Sherratt, Allison R.; Chigrinova, Mariya; McKay, Craig S.; Beaulieu, Louis-Philippe B.; Rouleau, Yanouchka; Pezacki, John Paul (RSC Advances, 2014)
An adapted biocompatible version of the Kinugasa reaction, the copper-catalysed alkyne-nitrone cycloaddition followed by rearrangement (CuANCR), was developed for live-cell labelling. CuANCR labelling was demonstrated for both mammalian and bacterial cells. A method for metabolic incorporation of the nitrone group is also described. This journal is
Keywords: Bioorthogonal labelling; Cycloaddition reaction; Living cell; Nitrones

Phonon density of states and anharmonicity of UO2 - Pang, Judy W. L.; Chernatynskiy, Aleksandr; Larson, Bennett C.; Buyers, William J. L.; Abernathy, Douglas L.; McClellan, Kenneth J.; Phillpot, Simon R. (Physical Review B - Condensed Matter and Materials Physics, 2014)
Phonon density of states (PDOS) measurements have been performed on polycrystalline UO2 at 295 and 1200 K using time-of-flight inelastic neutron scattering to investigate the impact of anharmonicity on the vibrational spectra and to benchmark ab initio PDOS simulations performed on this strongly correlated Mott insulator. Time-of-flight PDOS measurements include anharmonic linewidth broadening, inherently, and the factor of ∼7 enhancement of the oxygen spectrum relative to the uranium component by the increased neutron sensitivity to the oxygen-dominated optical phonon modes. The first-principles simulations of quasiharmonic PDOS spectra were neutron weighted and anharmonicity was introduced in an approximate way by convolution with wave-vector-weighted averages over our previously measured phonon linewidths for UO2, which are provided in numerical form. Comparisons between the PDOS measurements and the simulations show reasonable agreement overall, but they also reveal important areas of disagreement for both high and low temperatures. The discrepancies stem largely from a ∼10 meV compression in the overall bandwidth (energy range) of the oxygen-dominated optical phonons in the simulations. A similar linewidth-convoluted comparison performed with the PDOS spectrum of Dolling et al. obtained by shell-model fitting to their historical phonon dispersion measurements shows excellent agreement with the time-of-flight PDOS measurements reported here. In contrast, we show by comparisons of spectra in linewidth-convoluted form that recent first-principles simulations for UO2 fail to account for the PDOS spectrum determined from the measurements of Dolling et al. These results demonstrate PDOS measurements to be stringent tests for ab inito simulations of phonon physics in UO2 and they indicate further the need for advances in theory to address the lattice dynamics of UO2.

Differences in lactococcal cell wall polysaccharide structure are major determining factors in bacteriophage sensitivity - Ainsworth, Stuart; Sadovskaya, Irina; Vinogradov, Evguenii; Courtin, Pascal; Guerardel, Yann; Mahony, Jennifer; Grard, Thierry; Cambillau, Christian; Chapot-Chartier, Marie-Pierre; van Sinderen, Douwe (mBio, 2014)
Analysis of the genetic locus encompassing a cell wall polysaccharide (CWPS) biosynthesis operon of eight strains of Lactococcus lactis, identified as belonging to the same CWPS type C genotype, revealed the presence of a variable region among the strains examined. The results allowed the identification of five subgroups of the C type named subtypes C1 to C5. This variable region contains genes encoding glycosyltransferases that display low or no sequence homology between the subgroups. In this study, we purified an acidic polysaccharide from the cell wall of L. lactis 3107 (subtype C2) and confirmed that it is structurally different from the previously established CWPS of subtype C1 L. lactis MG1363. The CWPS of L. lactis 3107 is composed of pentasaccharide repeating units linked by phosphodiester bonds with the structure 6-α-Glc-3-β-Galf-3-β-GlcNAc-2-β-Galf-6-α-GlcNAc-1-P. Combinations of genes from the variable region of subtype C2 were introduced into a mutant of subtype C1 L. lactis NZ9000 deficient in CWPS biosynthesis. The resulting recombinant mutant synthesized a polysaccharide with a composition characteristic of that of subtype C2 L. lactis 3107 and not wild-type C1 L. lactis NZ9000. By challenging the recombinant mutant with various lactococcal phages, we demonstrated that CWPS is the host cell surface receptor of tested bacteriophages of both the P335 and 936 groups and that differences between the CWPS structures play a crucial role in determining phage host range.
Keywords: bacterial polysaccharide; cell surface receptor; cell wall polysaccharide; pentasaccharide; unclassified drug; article; bacterial cell wall; bacterial genome; bacterial strain; bacteriophage; bacterium mutant; biochemical composition; biosynthesis; controlled study; gene cluster; genetic association; genetic complementation; genetic variability; host cell; host range; Lactococcus lactis; nonhuman; nucleotide sequence; priority journal; sensitivity analysis; structure analysis

A quantum particle swarm optimization and genetic algorithm approach to the correspondence problem - Hadavi, Hamid; Viktor, Herna L.; Paquet, Eric (INISTA 2014 - IEEE International Symposium on Innovations in Intelligent Systems and Applications, Proceedings, 2014)
Finding correspondences between deformable objects has wide application in many domains. In information retrieval, researchers may be interested in finding similar objects, while computer animation experts may be considering ways to morph shapes. The correspondence problem is especially challenging when the objects under consideration are suspect to non-rigid deformations, noise and/or distortions. In this paper, a novel method using Quantum Particle Swarm Optimization (QPSO) and Genetic Algorithms (GA) is presented to address this issue. In our QPSO-GA algorithm we formulate the problem of correspondence detection as an optimization problem over all possible mapping in between the geodesic distance matrices associated with two sets of point clouds. We proceed to identify the optimal mapping, by first applying Quantum Particle Swarm Optimization to the permutation matrices associated with their geodesic distance matrices and then employing Genetic Algorithms in order to guide the search. Experimental results suggest that our QPSO-GA algorithm is fast, scalable, and robust. Our method accurately identifies the correspondences between objects, even in the presence of noise and distortion.
Keywords: Algorithms; Animation; Deformation; Geodesy; Intelligent systems; Mapping; Particle swarm optimization (PSO); Correspondence; Deformable object; Isometry; Markovian process; Mutation; Genetic algorithms

Rotating ring-disk electrode method - Jia, Zheng; Yin, Geping; Zhang, Jiujun (Rotating Electrode Methods and Oxygen Reduction Electrocatalysts, 2014)
In this chapter, the importance of rotating ring-disk electrode (RRDE) fundamentals and practical usage in an oxygen reduction reaction (ORR) study is emphasized in terms of both the electron-transfer process on electrode surface, diffusion-convection kinetics near the electrode, and the ORR mechanism, particularly the detection of intermediate such as peroxide. One of most important parameters of RRDE, the collection efficiency, is extensively described including its concept, theoretical expression as well as experiment calibration. Its usage in evaluating the ORR kinetic parameters, the apparent electron transfer, and percentage of peroxide formation is also presented. In addition, the measurement procedure including RRDE preparation, current-potential curve recording, and the data analysis are also discussed in this chapter.

Experimental confirmation of micromotion shift cancellation via operation at trap magic frequency and reduction in evaluated systematic uncertainties for the 88Sr+ optical frequency standard at 445 THz - Madej, A. A.; Dubé, P.; Tibbo, M.; Bernard, J. E. (2014 Conference on Precision Electromagnetic Measurements (CPEM 2014), 2014)
We describe recent experiments and results which show the effective cancellation of micromotion induced systematic shifts for the 445-THz reference transition in a trapped and laser cooled 88Sr+ single ion reference. Using two different ion trap systems based on a Paul and endcap design, the critical or magic frequency at which micromotion effects cancel has been effectively measured at 14.4 MHz. This work also allows an improved determination of the polarizability difference of the ground and excited states and an improvement in the evaluated blackbody shifts to the low 10-17 level.
Keywords: Electric frequency control; Ions; Lasers; Spectroscopy; Stark effect; Strontium; Experimental confirmation; Laser stability; Micromotion; Optical frequency standard; Precision measurement; Systematic uncertainties; Clocks

Seeing red in M32 : constraints on the stellar content from near- and mid-infrared observations and applications for studies of more distant galaxies - Davidge, T. J. (The Astrophysical Journal, 2014)
The properties of asymptotic giant branch (AGB) stars in the Local Group galaxy M32 are investigated using ground- and space-based observations that span the 1-8 μm wavelength interval, with the goal of demonstrating the utility of infrared observations as probes of stellar content. Comparisons with isochrones indicate that the brightest resolved stars in M32 have ages of a few gigayears and are younger on average than AGB stars with the same intrinsic brightness in the outer disk of M31. Accounting for stellar variability is shown to be essential for modeling AGB luminosity functions (LFs). Model LFs that assume the star-forming history measured by Monachesi et al. and the variability properties of Galactic AGB stars match both the K and [5.8] LFs of M32. Models also suggest that the slope of the [5.8] LF between M [5.8] = -8.5 and -10.0 is sensitive to the mix of stellar ages, and a sizeable fraction of the stars in M32 must have an age older than 7 Gyr in order to match the [5.8] LF. The structural properties of M32 in the infrared are also investigated. The effective radii that are computed from near-infrared and mid-infrared isophotes are similar to those measured at visible wavelengths, suggesting that the stellar content of M32 is well mixed. However, isophotes at radii >16″ (>60 pc) in the near- and mid-infrared are flatter than those at visible wavelengths. The coefficient of the fourth-order cosine term in the Fourier expansion of isophotes changes from "boxy" values at r < 16″ to "disky" values at r > 48″in [3.6] and [4.5]. The mid-infrared colors near the center of M32 do not vary systematically with radius, providing evidence of a well mixed stellar content in this part of the galaxy.
Keywords: galaxies: dwarf; galaxies: evolution; galaxies: individual (M32); Local Group

Neurosurgical virtual reality simulation metrics to assess psychomotor skills during brain tumor resection - Azarnoush, Hamed; Alzhrani, Gmaan; Winkler-Schwartz, Alexander; Alotaibi, Fahad; Gelinas-Phaneuf, Nicholas; Pazos, Valérie; Choudhury, Nusrat; Fares, Jawad; DiRaddo, Robert; Del Maestro, Rolando F. (International Journal of Computer Assisted Radiology and Surgery, 2014)
Purpose Virtual reality simulator technology together with novel metrics could advance our understanding of expert neurosurgical performance and modify and improve resident training and assessment. This pilot study introduces innovative metrics that can be measured by the state-of-the-art simulator to assess performance. Such metrics cannot be measured in an operating room and have not been used previously to assess performance. Methods Three sets of performance metrics were assessed utilizing the NeuroTouch platform in six scenarios with simulated brain tumors having different visual and tactile characteristics. Tier 1 metrics included percentage of brain tumor resected and volume of simulated "normal" brain tissue removed. Tier 2 metrics included instrument tip path length, time taken to resect the brain tumor, pedal activation frequency, and sum of applied forces. Tier 3 metrics included sum of forces applied to different tumor regions and the force bandwidth derived from the force histogram. Results The results outlined are from a novice resident in the second year of training and an expert neurosurgeon. The three tiers of metrics obtained from the NeuroTouch simulator do encompass the wide variability of technical performance observed during novice/expert resections of simulated brain tumors and can be employed to quantify the safety, quality, and efficiency of technical performance during simulated brain tumor resection. Tier 3 metrics derived from force pyramids and force histograms may be particularly useful in assessing simulated brain tumor resections. Conclusion Our pilot study demonstrates that the safety, quality, and efficiency of novice and expert operators can be measured using metrics derived from the NeuroTouch platform, helping to understand how specific operator performance is dependent on both psychomotor ability and cognitive input during multiple virtual reality brain tumor resections.
Keywords: Performance metrics; Virtual reality neurosurgical simulation; Haptic feedback; Brain tumor resection; Neurosurgical oncology; NeuroTouch

High-density single nucleotide polymorphism (SNP) array mapping in Brassica oleracea : identification of QTL associated with carotenoid variation in broccoli florets - Brown, Allan F.; Yousef, Gad G.; Chebrolu, Kranthi K.; Byrd, Robert W.; Everhart, Koyt W.; Thomas, Aswathy; Reid, Robert W.; Parkin, Isobel A. P.; Sharpe, Andrew G.; Oliver, Rebekah; Guzman, Ivette; Jackson, Eric W. (Theoretical and Applied Genetics, 2014)
Key message A high-resolution genetic linkage map ofB. oleraceawas developed from aB. napusSNP array. The work will facilitate genetic and evolutionary studies inBrassicaceae. A broccoli population, VI-158 × BNC, consisting of 150 F2:3 families was used to create a saturated Brassica oleracea (diploid: CC) linkage map using a recently developed rapeseed (Brassica napus) (tetraploid: AACC) Illumina Infinium single nucleotide polymorphism (SNP) array. The map consisted of 547 non-redundant SNP markers spanning 948.1 cM across nine chromosomes with an average interval size of 1.7 cM. As the SNPs are anchored to the genomic reference sequence of the rapid cycling B. oleracea TO1000, we were able to estimate that the map provides 96 % coverage of the diploid genome. Carotenoid analysis of 2 years data identified 3 QTLs on two chromosomes that are associated with up to half of the phenotypic variation associated with the accumulation of total or individual compounds. By searching the genome sequences of the two related diploid species (B. oleracea and B. rapa), we further identified putative carotenoid candidate genes in the region of these QTLs. This is the first description of the use of a B. napus SNP array to rapidly construct high-density genetic linkage maps of one of the constituent diploid species. The unambiguous nature of these markers with regard to genomic sequences provides evidence to the nature of genes underlying the QTL, and demonstrates the value and impact this resource will have on Brassica research.

Elucidating the surface chemistry of zinc phosphide nanoparticles through ligand exchange - Mobarok, Md Hosnay; Buriak, Jillian M. (Chemistry of Materials, 2014)
Zn3P2 nanoparticles, a potential earth abundant nanomaterial for photovoltaic applications, are prepared via a solution-based synthesis and end up capped with weakly bound phosphine ligands. These ligands are easily displaced from the nanoparticle surface, leading to an irreversible aggregation of particles. In this work, we elaborate the chemistry of Zn 3P2 nanoparticles both to elucidate the surface functionalities present after synthesis, and to enable the production of stable solutions of Zn3P2 colloidal solutions. Three different types of anionic type ligands, formed from their neutral precursors of oleic acid, n-decylphosphonic acid, and 1-octadecanethiol, were shown to be effective in yielding soluble functionalized nanoparticles. The functionalized Zn 3P2 nanoparticles were thoroughly characterized by electron microscopy, X-ray photoelectron spectroscopy, X-ray diffraction analyses, and FTIR spectroscopy. A combination of FTIR and multinuclear solution NMR spectroscopic studies on the starting agglomerated Zn3P 2 nanoparticles and the functionalized particle solutions reveals that the particle surface is terminated by Zn-CH3 and -PH x(SiMe3)3-x groups. Using oleic acid as the workhorse ligand, it was shown that addition of oleic acid to agglomerated nanoparticles led to a homogeneous dispersion of Zn3P2 nanoparticles, in toluene, along with production of CH4 and C 17H33COOSiMe3 as byproducts, as determined by 1H and 13C NMR spectroscopy. FTIR spectroscopy of the ligand-exchanged particles indicated oleate coordination, along with the appearance of what has been assigned as a P-H stretch. Similar reaction chemistry was observed during ligand exchange with n-decylphosphonic acid and 1-octadecanethiol. On the basis of these data, a general mechanism for ligand exchange chemistry on the Zn3P2 nanoparticle surface was proposed to enable both the production of zinc phosphide nanoparticle solutions and the determination of various routes to surface functionalization of this material.
Keywords: Agglomeration; Byproducts; Chelation; Fourier transform infrared spectroscopy; Ligands; Nanoparticles; Nuclear magnetic resonance spectroscopy; Oleic acid; Phosphorus compounds; Spectroscopic analysis; Surface chemistry; X ray diffraction; X ray diffraction analysis; X ray photoelectron spectroscopy; Zinc; Agglomerated nanoparticles; Functionalized nanoparticles; Functionalized particles; Homogeneous dispersions; Irreversible aggregation; Photovoltaic applications; Surface functionalities; Surface Functionalization; Synthesis (chemical)

Strain-promoted cycloadditions involving nitrones and alkynes-rapid tunable reactions for bioorthogonal labeling - MacKenzie, Douglas A.; Sherratt, Allison R.; Chigrinova, Mariya; Cheung, Lawrence L. W.; Pezacki, John Paul (Current Opinion in Chemical Biology, 2014)
The development and applications of strain-promoted alkyne-nitrone cycloaddition (SPANC) reactions have brought about new tools for rapid and specific functionalization of biomolecules in different settings. While a number of strain-promoted reactions have been successfully developed, SPANC reactions offer high reactivity with bimolecular rate constants of k2 that are as fast as 60M-1s-1. SPANC reactions also offer stability of starting materials, particularly in the case of endocyclic nitrones, as well as stereoelectronic tunability of the nitrone moiety to optimize reactivity towards different alkyne reaction partners. Herein we discuss recent advances in the development of SPANC reactions and their applications in bioorthogonal labeling.
Keywords: alkyne derivative; nitrone derivative; chemical reaction kinetics; cycloaddition; strain promoted alkyne nitrone cycloaddition

Establishment and validation of new complementing cells for production of E1-deleted adenovirus vectors in serum-free suspension culture - Gilbert, Rénald; Guilbault, Claire; Gagnon, David; Bernier, Alice; Bourget, Lucie; Elahi, Seyyed Mehdy; Kamen, Amine; Massie, Bernard (Journal of Virological Methods, 2014)
E1-deleted adenovirus vectors (AdV) are important gene transfer vehicles for gene therapy and vaccination. Amplification of AdV must take place in cells that express the adenovirus E1A and E1B genes. Sequence homology between AdV and the E1 genes integrated within the complementing cells should be minimal to reduce the odds of generating replication-competent adenovirus (RCA). The present study describes the establishment of AdV complementing cells constructed by stable transfection of the minimal E1A and E1B genes into human lung carcinoma (A549). Because some transgene products can be cytotoxic, the cells were engineered to stably express the repressor of the cumate-switch (CymR) to silence transgene transcription during vector growth. For regulatory compliance and to facilitate the scale-up, the resulting complementing cells (SF-BMAdR) were adapted to serum-free suspension culture. The best clone of SF-BMAdR produced AdV carrying an innocuous transgene to the same level as 293 cells, but titers were better for AdV carrying transgene for a cytotoxic product. Elevated titers were maintained for at least two months in suspension culture in the absence of selective agent and the cells did not produce RCA. Because of their advantageous properties, SF-BMAdR cells should become an important tool for developing large-scale production processes of AdV for research and clinical applications.
Keywords: Adenovirus vectors; Suspension culture; Serum-free medium; Cell line; Replication-competent adenovirus

A Star-forming shock front in radio galaxy 4C+41.17 resolved with laser-assisted adaptive optics spectroscopy - Steinbring, Eric (Astronomical Journal, 2014)
Near-infrared integral-field spectroscopy of redshifted [O III], Hβ, and optical continuum emission from the z = 3.8 radio galaxy 4C+41.17 is presented, obtained with the laser-guide-star adaptive optics facility on the Gemini North telescope. Employing a specialized dithering technique, a spatial resolution of 0″.10, or 0.7 kpc, is achieved in each spectral element, with a velocity resolution of ∼70 km s-1. Spectra similar to local starbursts are found for bright knots coincident in archival Hubble Space Telescope ( HST) rest-frame ultraviolet images, which also allows a key line diagnostic to be mapped together with new kinematic information. There emerges a clearer picture of the nebular emission associated with the jet in 8.3 GHz and 15 GHz Very Large Array maps, closely tied to a Lyα-bright shell-shaped structure seen with HST. This supports a previous interpretation of that arc tracing a bow shock, inducing ∼1010-11 M⊙ star formation regions that comprise the clumpy broadband optical/ultraviolet morphology near the core.
Keywords: active galaxies; galaxy jets; galaxy nuclei; starburst; adaptive optics

Electrocatalytic activity and stability of carbon nanotubes-supported Pt-on-Au, Pd-on-Au, Pt-on-Pd-on-Au, Pt-on-Pd, and Pd-on-Pt catalysts for methanol oxidation reaction - Shi, Ranran; Wang, Jianshe; Cheng, Niancai; Sun, Xueliang; Zhang, Lei; Zhang, Jiujun; Wang, Liucheng (Electrochimica Acta, 2014)
For optimizing both the activity and stability of Pt-based catalysts for methanol oxidation reaction (MOR), several carbon nanotubes(CNTs)-supported catalysts such as Pt-on-Au/CNTs, Pd-on-Au/CNTs, Pt-on-Pdon- Au/CNTs, Pt-on-Pd/CNTs, and Pd-on-Pt/CNTs catalysts are synthesized mainly through electrodeposition method. The activity and stability comparisons show that Pt-on-Au/CNTs has a higher MOR activity but a lower stability than Pd-on-Au/CNTs. To utilize the merits of the Pt and Pd components, Pt-on-Pd-on- Au/CNTs and Pt-on-Pd/CNTs catalysts are synthesized. The Pt-on-Pd-on-Au/CNTs and Pt-on-Pd/CNTs catalysts shows higher MOR activity than Pd-on-Au/CNTs and Pd/CNTs catalysts and higher stability than Pt-on-Au/CNTs, suggesting a synergistic interaction between Pt and Pd in catalyzing methanol oxidation reaction. Calculation shows that the total mass activity of Pt-on-Pd/CNTs with quite low Pt amount is on a similar level as that of Pt/CNTs for MOR oxidation, indicating the Pt-on-Pd catalyst could have promising potential as a low-Pt catalyst for MOR in alkaline media.
Keywords: methanol oxidation; low-Pt catalysts; stability; activity; Pt-on-Pd

Increased air velocity during exercise in the heat leads to equal reductions in hydration shifts and interleukin-6 with age - Wright-Beatty, Heather E.; Hardcastle, Stephen G.; Boulay, Pierre; Larose, Joanie; Kenny, Glen P. (European Journal of Applied Physiology, 2014)
Purpose The effectiveness of increased air velocity in reducing hydration shifts and physiological strain during work in the heat was examined in young and older males. Methods Ten young (mean ± SE, 24 ± 1 years) and 10 older (59 ± 1 years) males, matched for height, mass, and body surface area, cycled 4 × 15-min at moderate-to-heavy heat production (400 W), with 15-min rest separations between exercise bouts (final recovery 30 min), while wearing work clothing in humid heat (35 °C, 60 % relative humidity) under low (~0.5 m s-1) and high (~3.0 m s-1) air velocity. Rectal temperature (Tre) and heart rate were measured continuously, whereas hydration indices and interleukin (IL)-6 were measured at rest (PRE) and following the final recovery (POST). Results Young and older males experienced similar thermal and cardiovascular strain within the low (Tre end-exercise: young = 38.28 ± 0.11, older = 38.31 ± 0.08 °C) and high (Tre end-exercise: young = 37.94 ± 0.08, older = 37.87 ± 0.08 °C) air velocity conditions, with a reduced increase in both groups in high compared to low. Percent changes in plasma volume were similarly greater during the low (young = -10.9 ± 1.2, older = -10.8 ± 0.9 %) compared to high (young = -5.7 ± 0.6, older = -6.9 ± 0.7 %) condition for both groups. Despite elevated IL-6 at PRE in the older males, the IL-6 absolute change was similar between young (low = +4.10 ± 0.95, high = +0.99 ± 0.32 pg mL-1) and older (low = +3.58 ± 0.83, high = +1.24 ± 0.28 pg mL-1) males yet greater during the low compared to high condition. Conclusions Increased air velocity was effective in reducing the increase in hydration shifts and physiological strain (i.e. IL-6, thermal and cardiovascular strain) equally in young and older males.

Intramolecular charge transfer in di-tert-butylaminobenzonitriles and 2,4,6-tricyanoanilines : a computational TDDFT study - Zgierski, Marek Z.; Lim, Edward C.; Fujiwara, Takashige (Computational and Theoretical Chemistry, 2014)
The time-dependent DFT calculations for the low-lying excited electronic states of 4- and 3-di-tert-butylaminobenzonitrile, and 2,4,6-tricyano-N,N-dimethylaniline and 2,4,6-tricyanoaniline have been performed to investigate the mechanism of photo-induced intramolecular charge transfer (ICT). In addition, CC2-RI calculations were performed for TCDMA. For di-tert-butylaminobenzonitriles, we found evidence for the πσ *-state mediated mechanism associated with the sequential state-switches: ππ * → πσ * → ICT. It is predicted that 2,4,6-tricyano-N,N-dimethylaniline (TCDMA), but not 2,4,6-tricyanoaniline, possesses two ICT states, one of which shows the ICT-characterized quinoidal geometry and lies below the initially photo-excited S1(ππ *) state. The ππ * → ICT formation in TCDMA feasibly occurs in accord with the observed time-resolved excited-state absorption spectra and the biexponential fluorescence decay from the mixed S1(ππ *)/ICT state of TCDMA.
Keywords: Intramolecular charge transfer; TDDFT calculations; Di-tert-butylaminobenzonitriles; 2,4,6-Tricyanoanilines; CC2-RI calculations

Fabrication tolerant and broadband polarization splitter and rotator based on a taper-etched directional coupler - Xiong, Yule; Xu, Dan-Xia; Schmid, Jens H.; Cheben, Pavel; Janz, Siegfried; Ye, Winnie N. (Optics Express, 2014)
We propose a fabrication tolerant polarization splitter and rotator (PSR) on the silicon-on-insulator platform based on the mode-coupling mechanism. The PSR consists of a silicon wire waveguide coupled to a taper-etched waveguide. Compared to previously reported PSRs based on directional couplers which are sensitive to fabrication variations, the partially etched taper structure can compensate for fabrication inaccuracies. In addition, the taper-etched geometry breaks both the horizontal and vertical symmetries of the waveguide, introducing an additional degree of design freedom to accommodate different upper cladding layers. The proposed PSR can be readily integrated in a planar waveguide circuit using e.g. SiO2 cladding, making it compatible with typical metal back-end-ofline processes. Our simulation results show that the PSR has a low TM-to-TE polarization conversion loss of -0.09 dB in the C-band (or a conversion efficiency of 98%). A low TE-to-TE through insertion loss (-0.07 dB) and a very low polarization crosstalk (-30 dB) over a wide wavelength range exceeding 160 nm with a large fabrication tolerance (>50 nm) are numerically demonstrated.
Keywords: Directional couplers; Optical waveguides; Polarization; Silicon oxides; Waveguides; Fabrication tolerances; Planar waveguide circuit; Polarization conversion; Polarization crosstalk; Polarization splitters; Silicon wire waveguides; Silicon-on-insulator platforms; Upper cladding layers

Ursolic acid increases glucose uptake through the PI3K signaling pathway in adipocytes - He, Yonghan; Li, Wen; Li, Ying; Zhang, Shuocheng; Wang, Yanwen; Sun, Changhao (PLoS ONE, 2014)
Background: Ursolic acid (UA), a triterpenoid compound, is reported to have a glucose-lowering effect. However, the mechanisms are not fully understood. Adipose tissue is one of peripheral tissues that collectively control the circulating glucose levels.Objective: The objective of the present study was to determine the effect and further the mechanism of action of UA in adipocytes.Methods and Results: The 3T3-L1 preadipocytes were induced to differentiate and treated with different concentrations of UA. NBD-fluorescent glucose was used as the tracer to measure glucose uptake and Western blotting used to determine the expression and activity of proteins involved in glucose transport. It was found that 2.5, 5 and 10 μM of UA promoted glucose uptake in a dose-dependent manner (17%, 29% and 35%, respectively). 10 μM UA-induced glucose uptake with insulin stimulation was completely blocked by the phosphatidylinositol (PI) 3-kinase (PI3K) inhibitor wortmannin (1 μM), but not by SB203580 (10 μM), the inhibitor of mitogen-activated protein kinase (MAPK), or compound C (2.5 μM), the inhibitor of AMP-activated kinase (AMPK) inhibitor. Furthmore, the downstream protein activities of the PI3K pathway, phosphoinositide-dependent kinase (PDK) and phosphoinositide-dependent serine/threoninekinase (AKT) were increased by 10 μM of UA in the presence of insulin. Interestingly, the activity of AS160 and protein kinase C (PKC) and the expression of glucose transporter 4 (GLUT4) were stimulated by 10 μM of UA under either the basal or insulin-stimulated status. Moreover, the translocation of GLUT4 from cytoplasm to cell membrane was increased by UA but decreased when the PI3K inhibitor was applied.Conclusions: Our results suggest that UA stimulates glucose uptake in 3T3-L1 adipocytes through the PI3K pathway, providing important information regarding the mechanism of action of UA for its anti-diabetic effect.
Keywords: glucose; adipocytes; insulin; glucose metabolism; insulin resistance; adipocyte differentiation; membrane proteins; adipose tissue

Preface - Germer, Thomas A.; Zwinkels, Joanne C.; Tsai, Benjamin K. (Experimental Methods in the Physical Sciences, 2014)

Determining intrachain diffusion coefficients for biopolymer dynamics from single-molecule force spectroscopy measurements - Woodside, Michael T.; Lambert, John; Beach, Kevin S. D. (Biophysical Journal, 2014)
The conformational diffusion coefficient for intrachain motions in biopolymers, D, sets the timescale for structural dynamics. Recently, force spectroscopy has been applied to determine D both for unfolded proteins and for the folding transitions in proteins and nucleic acids. However, interpretation of the results remains unsettled. We investigated how instrumental effects arising from the force probes used in the measurement can affect the value of D recovered via force spectroscopy. We compared estimates of D for the folding of DNA hairpins found from measurements of rates and energy landscapes made using optical tweezers with estimates obtained from the same single-molecule trajectories via the transition path time. The apparent D obtained from the rates was much lower than the result found from the same data using transition time analysis, reflecting the effects of the mechanical properties of the force probe. Deconvolution of the finite compliance effects on the measurement allowed the intrinsic value to be recovered. These results were supported by Brownian dynamics simulations of the effects of force-probe compliance and bead size.

Electrode kinetics of electron-transfer reaction and reactant transport in electrolyte solution - Cai, Weiwei; Zhao, Xiao; Liu, Changpeng; Xing, Wei; Zhang, Jiujun (Rotating Electrode Methods and Oxygen Reduction Electrocatalysts, 2014)
In this chapter, to facilitate understanding and preparing the basic knowledge for rotating electrode theory, both the electron-transfer and reactant transport theories at the interface of electrode/electrolyte are presented. Regarding the reactant transport, three transportation modes such as diffusion, migration, and convection are described. A focusing discussion is given to the reactant diffusion near the electrode surface using both Fick's first and second laws. In addition, based on the approach in literature, the kinetics of reactant transport near and within a porous matrix electrode layer and its effect on the electron-transfer process is also presented using a simple equivalent electrode/electrolyte interface.

High field solid state 13C NMR spectroscopy of cucurbituril materials - Bardelang, David; Brinkmann, Andreas; Ratcliffe, Christopher I.; Ripmeester, John A.; Terskikh, Victor V.; Udachin, Konstantin A. (CrystEngComm, 2014)
Solid state 13C NMR spectra of several cucurbituril materials, CB[n] where n = 5, 6, 7 and 8, have been analysed in detail. Where crystal structures are known the complex splitting patterns for the CO, CH and CH 2 resonances can be directly related to the different site symmetries imposed on the CB molecule by the crystal. Conversely, where the structure is not known the NMR splitting patterns can be used to suggest possible symmetries for the CB, and these could conceivably aid in solving crystal structures. The fact that each structure produces a uniquely different 13C NMR splitting pattern makes it a useful fingerprinting tool which can be used to detect new phases.

Early osmotic adjustment responses in drought-resistant and drought-sensitive oilseed rape - Hatzig, Sarah; Zaharia, L. Irina; Abrams, Suzanne; Hohmann, Marie; Legoahec, Laurie; Bouchereau, Alain; Nesi, Nathalie; Snowdon, Rod J. (Journal of Integrative Plant Biology, 2014)
The impact of osmotic stress on growth, physiology, and metabolism of winter oilseed rape (Brassica napus L.) was investigated by detailed analysis of biomass traits, hormone metabolites and osmolytes in two genetically unrelated drought-tolerant genotypes and two unrelated drought-sensitive genotypes. Seedlings were grown in vitro under controlled conditions and osmotic stress was simulated by applying a gradual treatment with polyethylene glycol (PEG 6000), followed by hypo-osmotic treatment of variants used for metabolite determination. The results provide a basis for the identification of reliable selection criteria for drought resistance in oilseed rape. The in vitro cultivation system established during this study enabled effective discrimination of early osmotic stress responses between drought-resistant and -susceptible oilseed rape genotypes that also show large differences in relative seed yield under drought conditions in the field. Clear physiological and metabolic differences were observed between the drought-resistant and drought-sensitive genotypes, suggesting that osmotic adjustment is a key component of drought response in oilseed rape. Unexpectedly, however, the drought-resistant genotypes did not show typical hormonal adjustment and osmolyte accumulation, suggesting that they possess alternative physiological mechanisms enabling avoidance of stress symptoms.
Keywords: Abscisic acid; Brassica napus; Drought; Hormones; Metabolites

Control of multiphoton and avalanche ionization using an ultraviolet-infrared pulse train in femtosecond laser micro/nano-machining of fused silica - Yu, Xiaoming; Bian, Qiumei; Chang, Zenghu; Corkum, P. B.; Lei, Shuting (Laser-based Micro- and Nanoprocessing VIII, 2014)
We report on the experimental results of micro- and nanostructures fabricated on the surface of fused silica by a train of two femtosecond laser pulses, a tightly focused 266 nm (ultraviolet, UV) pulse followed by a loosely focused 800 nm (infrared, IR) pulse. By controlling the fluence of each pulse below the damage threshold, micro- and nanostructures are fabricated using the combined beams. The resulting damage size is defined by the UV pulse, and a reduction of UV damage threshold is observed when the two pulses are within ∼ 1 ps delay. The effects of IR pulse duration on the UV damage threshold and shapes are investigated. These results suggest that the UV pulse generates seed electrons through multiphoton absorption and the IR pulse utilizes these electrons to cause damage by avalanche process. A single rate equation model based on electron density can be used to explain these results. It is further demonstrated that structures with dimensions of 124 nm can be fabricated on the surface of fused silica using 0.5 NA objective. This provides a possible route to XUV (or even shorter wavelength) laser nano-machining with reduced damage threshold.
Keywords: Fabrication; Multiphoton processes; Nanostructures; Ultrafast lasers; Ultrashort pulses; Avalanche ionization; Avalanche process; Damage threshold; Micro and nanostructures; Multi-photon absorption; On-electron density; Shorter wavelength; Ultraviolet , uv; Pulse generators

Controllable hydrothermal synthesis of Cu-doped δ-MnO2 films with different morphologies for energy storage and conversion using supercapacitors - Su, Xiaohui; Yu, Lin; Cheng, Gao; Zhang, Huanhua; Sun, Ming; Zhang, Lei; Zhang, Jiujun (Applied Energy, 2014)
The δ-MnO2 and Cu-doped δ-MnO2 grown on Ni foams are synthesized by a simple hydrothermal method for supercapacitor electrode application. The samples are characterized by XRD, ICP-AES, SEM, and BET for its composition, structure/morphology, and BET surface area. The electrochemical properties of the electrodes are studied by cyclic voltammetry (CV), galvanostatic charge/discharge and electrochemical impedance spectroscopy (EIS) in 1M Na2SO4 solution. The results show that copper addition can vary the self-assembly of δ-MnO2 nanosheets, inducing the formation of flower-like structure. The morphology and electrochemical performance of the formed δ-MnO2 electrodes can be controlled by simply tuning the copper doping concentration. The 2at.% Cu-doped δ-MnO2 film obtains the maximum specific capacitance as high as 296Fg-1 at 1Ag-1, which is 80% higher than that of the pure δ-MnO2 film. Furthermore, it also shows a better cyclic stability than undoped δ-MnO2 film. The enhanced electrochemical properties may be attributed to its optimized hybrid nanosheet network and flow-like structure. A possible explanation for such enhancement in electrochemical properties of Cu-doped δ-MnO2 films has been discussed in this paper.
Keywords: Copper doping; Flow-like structure; Birnessite MnO2 (d-MnO2); Supercapacitor; Electrochemical properties

Importance of Rhodococcus strains in a bacterial consortium degrading a mixture of hydrocarbons, gasoline, and diesel oil additives revealed by metatranscriptomic analysis - Auffret, Marc. D.; Yergeau, Étienne; Labbé, Diane; Fayolle-Guichard, Francoise; Greer, Charles W. (Applied Microbiology and Biotechnology, 2014)
A bacterial consortium (Mix3) composed of microorganisms originating from different environments (soils and wastewater) was obtained after enrichment in the presence of a mixture of 16 hydrocarbons, gasoline, and diesel oil additives. After addition of the mixture, the development of the microbial composition of Mix3 was monitored at three different times (35, 113, and 222 days) using fingerprinting method and dominant bacterial species were identified. In parallel, 14 bacteria were isolated after 113 days and identified. Degradation capacities for Mix3 and the isolated bacterial strains were characterized and compared. At day 113, we induced the expression of catabolic genes in Mix3 by adding the substrate mixture to resting cells and the metatranscriptome was analyzed. After addition of the substrate mixture, the relative abundance of Actinobacteria increased at day 222 while a shift between Rhodococcus and Mycobacterium was observed after 113 days. Mix3 was able to degrade 13 compounds completely, with partial degradation of isooctane and 2-ethylhexyl nitrate, but tert-butyl alcohol was not degraded. Rhodococcus wratislaviensis strain IFP 2016 isolated from Mix3 showed almost the same degradation capacities as Mix3: these results were not observed with the other isolated strains. Transcriptomic results revealed that Actinobacteria and in particular, Rhodococcus species, were major contributors in terms of total and catabolic gene transcripts while other species were involved in cyclohexane degradation. Not all the microorganisms identified at day 113 were active except R. wratislaviensis IFP 2016 that appeared to be a major player in the degradation activity observed in Mix3.
Keywords: Bacterial consortium; Diesel oil; Metatranscriptomic analysis; Mixture of hydrocarbons; Rhodococcus; Dynamics of gene expression; Bacterial enrichment

A current-comparator-based high-voltage reference inductor - So, Eddy; Bennett, David (2014 Conference on Precision Electromagnetic Measurements (CPEM 2014), 2014)
The development of a current-comparator-based high-voltage reference inductor at the National Research Council of Canada (NRC) for calibrating loss measurement systems of large high voltage shunt reactors is presented. The high voltage reference inductor features an adjustable loss angle equivalent to a power factor from zero to 0.01. It has an uncertainty of less than 10Ã—10-6 in both magnitude and phase.
Keywords: Current-comparator-based; High-voltages; Loss angle; reference inductor; Shunt reactors; uncertainty

Quantum confinement in Si and Ge nanostructures: Theory and experiment - Barbagiovanni, Eric G.; Lockwood, David J.; Simpson, Peter J.; Goncharova, Lyudmila V. (Applied Physics Reviews, 2014)
The role of quantum confinement (QC) in Si and Ge nanostructures (NSs) including quantum dots, quantum wires, and quantum wells is assessed under a wide variety of fabrication methods in terms of both their structural and optical properties. Structural properties include interface states, defect states in a matrix material, and stress, all of which alter the electronic states and hence the measured optical properties. We demonstrate how variations in the fabrication method lead to differences in the NS properties, where the most relevant parameters for each type of fabrication method are highlighted. Si embedded in, or layered between, SiO2, and the role of the sub-oxide interface states embodies much of the discussion. Other matrix materials include Si3N4 and Al2O3. Si NSs exhibit a complicated optical spectrum, because the coupling between the interface states and the confined carriers manifests with varying magnitude depending on the dimension of confinement. Ge NSs do not produce well-defined luminescence due to confined carriers, because of the strong influence from oxygen vacancy defect states. Variations in Si and Ge NS properties are considered in terms of different theoretical models of QC (effective mass approximation, tight binding method, and pseudopotential method). For each theoretical model, we discuss the treatment of the relevant experimental parameters.
Keywords: Fabrication; Interface states; Interfaces (materials); Optical properties; Quantum confinement; Semiconducting germanium; Effective mass approximation; Experimental parameters; Fabrication method; Oxygen vacancy defects; Pseudopotential method; Structural and optical properties; Theoretical modeling; Tight binding methods; Silicon

The establishment of high current DC shunt calibration system at KRISS and comparison with NRC - Kim, Kyu-Tae; Jung, Jae Kap; Lee, YoungSup; So, Eddy (2014 Conference on Precision Electromagnetic Measurements (CPEM 2014), 2014)
The application of a simple binary step up method for possible calibration of high current DC shunts up to a few thousand amperes in which a pair of HCDC shunts are used to evaluate the current dependence of the shunt resistance. It was found that a complex exponential linear model can be applied to separate the drifts in voltage measurements from the contribution of the current coefficient of the shunt. This approach allows one to extract the information on the current coefficient of the shunt and together with low current measurement of the shunt resistance to calibrate the current output of HCDC source, which in turn can be used as a reference for calibration of customer's shunts. In order to validate the step up method, the calibrated HCDC source was used to obtain DC current ratios which is to be compared with NRC's high current ratio measurements of a multi-ratio 3000 A reference DC CT.
Keywords: Voltage measurement; Calibration system; comparison; Current ratios; High currents; Calibration

Failure mechanisms and damage model of ductile cast iron under low-cycle fatigue conditions - Wu, Xijia; Quan, Guangchung; MacNeil, Ryan; Zhang, Zhong; Sloss, Clayton (Metallurgical and Materials Transactions A: Physical Metallurgy and Materials Science, 2014)
Strain-controlled low-cycle fatigue (LCF) tests were conducted on ductile cast iron (DCI) at strain rates of 0.02, 0.002, and 0.0002/s in the temperature range from room temperature to 1073 K (800 °C). A constitutive-damage model was developed within the integrated creep-fatigue theory (ICFT) framework on the premise of strain decomposition into rate-independent plasticity and time-dependent creep. Four major damage mechanisms: (i) plasticity-induced fatigue, (ii) intergranular embrittlement (IE), (iii) creep, and (iv) oxidation were considered in a nonlinear creep-fatigue interaction model which represents the overall damage accumulation process consisting of oxidation-assisted fatigue crack nucleation and propagation in coalescence with internally distributed damage (e.g., IE and creep), leading to final fracture. The model was found to agree with the experimental observations of the complex DCI-LCF phenomena, for which the linear damage summation rule would fail.
Keywords: Cracks; Creep; Failure (mechanical); Plasticity; Strain rate; Creep-fatigue interactions; Damage accumulation; Ductile cast irons; Fatigue-crack nucleation; Intergranular embrittlement; Low cycle fatigues; Rate-independent plasticities; Time-dependent creeps; Fatigue damage

Uncertainty of measurements of podded propulsor performance characteristics - Islam, Mohommed; Veitch, Brian; Liu, Pengfei (Ocean Engineering, 2014)
One of the fundamental aspects of any physical experiment is the uncertainty or error limits of the measurement. Unfortunately, majority of published model experimental results do not come with the much needed error analysis. It is imperative that a fundamental and rigorous uncertainty assessment is carried out for all measurements, especially for measurements using a newly designed apparatus. This paper presents the uncertainty analysis methodology and results for a newly designed fully functional podded propulsor performance measurement apparatus. The measurements include propeller thrust, torque, rotation rate and advance speed as well as global forces and moments of a pod unit. The facility and measurement systems are briefly described, and detailed uncertainty assessment methodologies with examples for each measurement are provided with descriptions of bias and precision limits and total uncertainties. The generalized methodology can also be used for other relevant measurements.
Keywords: Uncertainty analysis; Error limits; Bias error; Precision error; Podded propulsors; Measurement uncertainty

Methanogen community composition and rates of methane consumption in Canadian High Arctic permafrost soils - Allan, J.; Ronholm, J.; Mykytczuk, N. C. S.; Greer, C. W.; Onstott, T. C.; Whyte, L. G. (Environmental Microbiology Reports, 2014)
Increasing permafrost thaw, driven by climate change, has the potential to result in organic carbon stores being mineralized into carbon dioxide (CO2) and methane (CH4) through microbial activity. This study examines the effect of increasing temperature on community structure and metabolic activity of methanogens from the Canadian High Arctic, in an attempt to predict how warming will affect microbially controlled CH4 soil flux. In situCO2 and CH4 flux, measured in 2010 and 2011 from ice-wedge polygons, indicate that these soil formations are a net source of CO2 emissions, but a CH4 sink. Permafrost and active layer soil samples were collected at the same sites and incubated under anaerobic conditions at warmer temperatures, with and without substrate amendment. Gas flux was measured regularly and indicated an increase in CH4 flux after extended incubation. Pyrosequencing was used to examine the effects of an extended thaw cycle on methanogen diversity and the results indicate that in situ methanogen diversity, based on the relative abundance of the 16S ribosomal ribonucleic acid (rRNA) gene associated with known methanogens, is higher in the permafrost than in the active layer. Methanogen diversity was also shown to increase in both the active layer and permafrost soil after an extended thaw. This study provides evidence that although High Arctic ice-wedge polygons are currently a sink for CH4, higher arctic temperatures and anaerobic conditions, a possible result of climate change, could result in this soil becoming a source for CH4 gas flux.
Keywords: methane; Arctic; chemistry; classification; isolation and purification; kinetics; metabolism; microbiology; soil; temperature; bacteria; soil microbiology

13C metabolic flux analysis shows that resistin impairs the metabolic response to insulin in L6E9 myotubes - Guzmán, Shirley; Marin, Silvia; Miranda, Anibal; Selivanov, Vitaly A.; Centelles, Josep J.; Harmancey, Romain; Smih, Fatima; Turkieh, Annie; Durocher, Yves; Zorzano, Antonio; Rouet, Philippe; Cascante, Marta (BMC Systems Biology, 2014)
Background: It has been suggested that the adipokine resistin links obesity and insulin resistance, although how resistin acts on muscle metabolism is controversial. We aimed to quantitatively analyse the effects of resistin on the glucose metabolic flux profile and on insulin response in L6E9 myotubes at the metabolic level using a tracer-based metabolomic approach and our in-house developed software, Isodyn.Results: Resistin significantly increased glucose uptake and glycolysis, altering pyruvate utilisation by the cell. In the presence of resistin, insulin only slightly increased glucose uptake and glycolysis, and did not alter the flux profile around pyruvate induced by resistin. Resistin prevented the increase in gene expression in pyruvate dehydrogenase-E1 and the sharp decrease in gene expression in cytosolic phosphoenolpyruvate carboxykinase-1 induced by insulin.Conclusions: These data suggest that resistin impairs the metabolic activation of insulin. This impairment cannot be explained by the activity of a single enzyme, but instead due to reorganisation of the whole metabolic flux distribution.
Keywords: Resistin; Insulin resistance; Glucose metabolism; Fluxomics; Bioinformatics; Tracer-based metabolomics

The hot core towards the intermediate-mass protostar NGC 7129 FIRS 2: Chemical similarities with Orion KL - Fuente, A.; Cernicharo, J.; Caselli, P.; McCoey, C.; Johnstone, D.; Fich, M.; Van Kempen, T.; Palau, A.; Yildiz, U. A.; Tercero, B.; López, A. (Astronomy and Astrophysics, 2014)
Context. This paper is dedicated to the study of the chemistry of the intermediate-mass (IM) hot core NGC 7129 FIRS 2, probably the most compact warm core found in the 2-8 M⊙ stellar mass range. Aims. Our aim is to determine the chemical composition of the IM hot core NGC 7129 FIRS 2, and to provide new insights on the chemistry of hot cores in a more general context. Methods. NGC 7129 FIRS 2 (hereafter, FIRS 2) is located at a distance of 1250 pc and high spatial resolution observations are required to resolve the hot core at its center. We present a molecular survey from 218 200 MHz to 221 800 MHz carried out with the IRAM Plateau de Bure Interferometer (PdBI). These observations were complemented with a long integration single-dish spectrum taken with the IRAM 30 m telescope in Pico de Veleta (Spain). We used a local thermodynamic equilibrium (LTE) single temperature code to model the whole dataset. Results. The interferometric spectrum is crowded with a total of 300 lines from which a few dozen remain unidentified. The spectrum has been modeled with a total of 20 species and their isomers, isotopologues, and deuterated compounds. Complex molecules like methyl formate (CH3OCHO), ethanol (CH3CH2OH), glycolaldehyde (CH2OHCHO), acetone (CH3COCH3), dimethyl ether (CH3OCH 3), ethyl cyanide (CH3CH2CN), and the aGg' conformer of ethylene glycol (aGg'-(CH2OH)2) are among the detected species. The detection of vibrationally excited lines of CH 3CN, CH3OCHO, CH3OH, OCS, HC3N, and CH3CHO proves the existence of gas and dust at high temperatures. The gas kinetic temperature estimated from the vibrational lines of CH 3CN, ∼405-67 +100 K, is similar to that measured in massive hot cores. Our data allow an extensive comparison of the chemistry in FIRS 2 and the Orion hot core. Conclusions. We find a quite similar chemistry in FIRS 2 and Orion. Most of the studied fractional molecular abundances agree within a factor of 5. Larger differences are only found for the deuterated compounds D2CO and CH2DOH and a few molecules (CH3CH2CN, SO2, HNCO and CH3CHO). Since the physical conditions are similar in both hot cores, only different initial conditions (warmer pre-collapse and collapse phase in the case of Orion) and/or different crossing times of the gas in the hot core can explain this behavior. We discuss these two scenarios.
Keywords: Acetone; Deuterium; Ethylene glycol; Fuels; Isomers; Molecules; Sulfur dioxide; Astrochemistry; Chemical compositions; High spatial resolution; ISM: individual objects: NGC 7129; Kinetic temperatures; Local thermodynamic equilibrium; Stars: formation; Stars

Oxygen solubility, diffusion coefficient, and solution viscosity - Xing, Wei; Yin, Min; Lv, Qing; Hu, Yang; Liu, Changpeng; Zhang, Jiujun (Rotating Electrode Methods and Oxygen Reduction Electrocatalysts, 2014)
In this chapter, the necessary parameters for both rotating disk electrode/rotating ring-disk electrode analysis in oxygen reduction reaction study, such as O2 solubility, O2 diffusion coefficient and the viscosity of the aqueous electrolyte solutions are discussed in depth in terms of their definitions, theoretical background, and experiment measurements. The effects of type/concentration of electrolyte, temperature, and pressure on values of these parameters are also discussed. To provide the readers with useful information, the values of these parameters are collected from literature, and summarized in several tables. In addition, the values of both the O2 solubility and diffusion coefficient in Nafion® membranes or ionomers are also listed in the tables. Hopefully, this chapter would be able to serve as a data source for the later chapters of this book, and also the readers could find it useful in their experimental data analysis.
Keywords: Oxygen reduction reaction(ORR); Rotating disk electrode(RDE); Rotating ring-disk electrode(RRDE); temperature; Nafion film ionomer; Pressure and pH; diffusion coefficient; electrolyte type/concentration; kinematic viscosity; oxygen solubility

Polylactic acid (PLA) biomedical foams for tissue engineering - Shah Mohammadi, M.; Bureau, M. N.; Nazhat, S. N. (Biomedical Foams for Tissue Engineering Applications, 2014)
Porous scaffolds based on polylactic acid (PLA) and its copolymers have been extensively used as templates for potential tissue regeneration applications. This chapter discusses the techniques involved in creating PLA-based foams, focusing on gas foaming. It also covers the structure, physical and mechanical properties of the scaffolds. It then reviews some of the applications of PLA-based foams for the engineering of soft and hard tissues. It also provides an insight into future trends in the design of PLA foams for biomedical applications. © 2014 Woodhead Publishing Limited. All rights reserved.

Identification and distribution of oxygenated fatty acids in Plantago seed lipids - Smith, Mark A.; Zhang, Haixia; Purves, Randy W. (JAOCS, Journal of the American Oil Chemists' Society, 2014)
Plant oils rich in oxygenated fatty acids (FAs) are of interest as renewable raw materials for industry. Previous studies reported unusual oxygenated FAs in the seed lipids of Plantago major and P. ovata. To determine if oxygenated FAs are a common component of Plantago seed oils, seed fatty acyl quality and quantity were determined for 23 Plantago species. Fatty acyl content, as a percentage of dry weight, ranged from 4.9 % in P. sempervirens to 18.8 % in P. coronopus. Oxygenated FAs were a frequent, but not ubiquitous component of Plantago seed lipids, reaching a level of almost 15 % in the seeds of P. nivalis. The oxygenated FAs were identified as isoricinoleic acid (9-hydroxy-cis-12-octadecenoic acid, IR) and 9-oxo-cis-12-octadecenoic acid (OX). When present, most species contained both IR and OX. FAs containing oxo groups have not been reported as components of the seed oil of other plant species that synthesize IR or ricinoleic acid (12-hydroxy-cis-9-octadecenoic acid), suggesting unique aspects to the pathway of oxygenated FA biosynthesis in Plantago. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) demonstrated that IR and OX are components of triacylglycerol, and triacylglycerol estolides are a minor component of the seed oil of P. lanceolata with secondary acylation by oxygenated FAs.
Keywords: Fatty acid methyl ester mass spectra; Isoricinoleic acid; MALDI-TOF MS; Oxo-fatty acid; Plantago lanceolata; Seed oil; Triacylglycerol estolide

Evanescent field waveguide sensing with subwavelength grating structures in silicon-on-insulator - Wangüemert-Pérez, J. Gonzalo; Cheben, Pavel; Ortega-Moñux, Alejandro; Alonso-Ramos, Carlos; Pérez-Galacho, Diego; Halir, Robert; Molina-Fernández, Iñigo; Xu, Dan-Xia; Schmid, Jens H. (Optics Letters, 2014)
We explore, to the best of our knowledge, the potential of diffractionless subwavelength grating waveguides for sensing applications. We show that by subwavelength patterning of silicon-wire waveguides the field delocalization can be engineered to increase the sensitivity. Fully vectorial 3D-FDTD simulations confirm the sensitivity enhancement, achieving sensitivities of 0.83 RIU/RIU and 1.5 · 10-3 RIU/nm for bulk and surface sensing, respectively, which compare favorably to state-of-the-art sensing waveguides.
Keywords: Waveguides; Delocalizations; Evanescent field waveguides; Sensing applications; Sensitivity enhancements; Sub-wave length grating; Sub-wavelength; Subwavelength grating waveguides; Surface sensing; Diffraction gratings

Monte Carlo calculations of electron beam quality conversion factors for several ion chamber types - Muir, B. R.; Rogers, D. W. O. (Medical Physics, 2014)
Purpose: To provide a comprehensive investigation of electron beam reference dosimetry using Monte Carlo simulations of the response of 10 plane-parallel and 18 cylindrical ion chamber types. Specific emphasis is placed on the determination of the optimal shift of the chambers' effective point of measurement (EPOM) and beam quality conversion factors.Methods: The EGSnrc system is used for calculations of the absorbed dose to gas in ion chamber models and the absorbed dose to water as a function of depth in a water phantom on which cobalt-60 and several electron beam source models are incident. The optimal EPOM shifts of the ion chambers are determined by comparing calculations of R50 converted from I50 (calculated using ion chamber simulations in phantom) to R50 calculated using simulations of the absorbed dose to water vs depth in water. Beam quality conversion factors are determined as the calculated ratio of the absorbed dose to water to the absorbed dose to air in the ion chamber at the reference depth in a cobalt-60 beam to that in electron beams.Results: For most plane-parallel chambers, the optimal EPOM shift is inside of the active cavity but different from the shift determined with water-equivalent scaling of the front window of the chamber. These optimal shifts for plane-parallel chambers also reduce the scatter of beam quality conversion factors, kQ, as a function of R50. The optimal shift of cylindrical chambers is found to be less than the 0.5 rcav recommended by current dosimetry protocols. In most cases, the values of the optimal shift are close to 0.3 rcav. Values of kecal are calculated and compared to those from the TG-51 protocol and differences are explained using accurate individual correction factors for a subset of ion chambers investigated. High-precision fits to beam quality conversion factors normalized to unity in a beam with R50 = 7.5 cm (k′Q) are provided. These factors avoid the use of gradient correction factors as used in the TG-51 protocol although a chamber dependent optimal shift in the EPOM is required when using plane-parallel chambers while no shift is needed with cylindrical chambers. The sensitivity of these results to parameters used to model the ion chambers is discussed and the uncertainty related to the practical use of these results is evaluated.Conclusions: These results will prove useful as electron beam reference dosimetry protocols are being updated. The analysis of this work indicates that cylindrical ion chambers may be appropriate for use in low-energy electron beams but measurements are required to characterize their use in these beams.
Keywords: electron beam reference dosimetry; EGSnrc; kQ; kecal; beam quality conversion factors; EPOM; dosimetry protocols

Biosensor systems and applications in genomics, proteomics and metabolomics: A review - Mackay, Scott; Chen, Jie (Proceedings - IEEE International Symposium on Circuits and Systems, 2014)
This article provides a brief overview and background on current biosensor designs for applications in genomics, proteomics and metabolomics. As research continues in many different aspects of biosensor design, new and better ways to recognize and detect low concentrations of a wide variety of different biomolecules are being developed for various applications. Biosensors can offer a simpler, faster and cheaper alternative to the testing that is often required to collect the large amounts of data for genomic, proteomic and metabolomic sensing. Recognition elements such as DNA aptamers make detecting very different types of biomolecules in the same system possible, while the use of signal-enhancing nanoparticle probes and microfabricated sensor arrays make it possible to test for a large number of different target biomolecules quickly and effectively.
Keywords: Antibodies; Biomolecules; Carbon nanotubes; Chemical detection; Aptamers; ELectrochemical detection; Genomics; Metabolomics; Optical detection; SELEX; Biosensors

Polyploid evolution of the Brassicaceae during the Cenozoic era - Kagale, Sateesh; Robinson, Stephen J.; Nixon, John; Xiao, Rong; Huebert, Terry; Condie, Janet; Kessler, Dallas; Clarke, Wayne E.; Edger, Patrick P.; Links, Matthew G.; Sharpe, Andrew G.; Parkin, Isobel A. P. (Plant Cell, 2014)
The Brassicaceae (Cruciferae) family, owing to its remarkable species, genetic, and physiological diversity as well as its significant economic potential, has become a model for polyploidy and evolutionary studies. Utilizing extensive transcriptome pyrosequencing of diverse taxa, we established a resolved phylogeny of a subset of crucifer species. We elucidated the frequency, age, and phylogenetic position of polyploidy and lineage separation events that have marked the evolutionary history of the Brassicaceae. Besides the well-known ancient α (47 million years ago [Mya]) and β (124 Mya) paleopolyploidy events, several species were shown to have undergone a further more recent (~7 to 12 Mya) round of genome multiplication. We identified eight whole-genome duplications corresponding to at least five independent neo/mesopolyploidy events. Although the Brassicaceae family evolved from other eudicots at the beginning of the Cenozoic era of the Earth (60 Mya), major diversification occurred only during the Neogene period (0 to 23 Mya). Remarkably, the widespread species divergence, major polyploidy, and lineage separation events during Brassicaceae evolution are clustered in time around epoch transitions characterized by prolonged unstable climatic conditions. The synchronized diversification of Brassicaceae species suggests that polyploid events may have conferred higher adaptability and increased tolerance toward the drastically changing global environment, thus facilitating species radiation.

CIR modulation of the X-ray flux from the O7.5 III(n)((f)) star ξ Persei? - Massa, D.; Oskinova, L.; Fullerton, A. W.; Prinja, R. K.; Bohlender, D. A.; Morrison, N. D.; Blake, M.; Pych, W. (Monthly Notices of the Royal Astronomical Society, 2014)
We analyse a 162 ks high energy transmission grating Chandra observation of the O7.5 III(n)((f)) star ξ Per, together with contemporaneous Hα observations. The X-ray spectrum of this star is similar to other single O stars, and not pathological in any way. Its UV wind lines are known to display cyclical time variability, with a period of 2.086 d, which is thought to be associated with corotating interaction regions (CIRs). We examine the Chandra and Hα data for variability on this time-scale. We find that the X-rays vary by ~15 per cent over the course of the observations and that this variability is out of phase with variable absorption on the blue wing of the Hα profiles (assumed to be a surrogate for the UV absorption associated with CIRs). While not conclusive, both sets of data are consistent with models where the CIRs are either a source of X-rays or modulate them.

The first CMOS LNA on a radio telescope - Belostotski, Lenoid; Haslett, James W.; Veidt, Bruce; Landecker, Thomas L.; Gray, Andrew D.; Hovey, Gary J.; Sheehan, Ev; Messing, Rob. (Proceedings - ANTEM 2014: 2014 16th International Symposium on Antenna Technology and Applied Electromagnetics, 2014)
This paper reports on the world's first CMOS low noise amplifier (LNA) operating successfully on a radio telescope since October 15th, 2010. The radio telescope used in this work is the Synthesis Telescope operated by the Dominion Radio Astrophysical Observatory, NRC, and located near Penticton, BC, Canada. This paper describes the work that led to the installation of the LNA on the telescope and shows measurement results obtained with the telescope.
Keywords: Astrophysics; CMOS integrated circuits; Observatories; Radio frequency amplifiers; Radio telescopes; Aperture synthesis; Astrophysical observatory; CMOS LNA; CMOS low noise amplifiers; Square Kilometre Array (SKA); Low noise amplifiers

The GALEX ultraviolet virgo cluster survey (GUViCS) : III. The ultraviolet source catalogs - Voyer, E. N.; Boselli, A.; Boissier, S.; Heinis, S.; Cortese, L.; Ferrarese, L.; Cote, P.; Cuillandre, J.-C.; Gwyn, S. D. J.; Peng, E. W.; Zhang, H.; Liu, C. (Astronomy and Astrophysics, 2014)
In this paper we introduce the deepest and most extensive ultraviolet extragalactic source catalogs of the Virgo Cluster area to date. Archival and targeted GALEX imaging is compiled and combined to provide the deepest possible coverage over 120 deg2 in the NUV (eff = 231 6 Å) and ~40 deg2 in the FUV (eff = 1539 Å) between 180= RA =195 and 0° =Dec = 20°. We measure the integrated photometry of 1770 extended UV sources of all galaxy types anduse GALEX pipeline photometry for 1230855 point-like sources in the foreground, within, and behind the cluster. Extended source magnitudes are reliable to mUV ~ 22 showing a = ~ 0.01 = s difference from their asymptotic magnitudes. Point-like source magnitudes have a 1 = s standard deviation within = ~ 0.2 mag down to muv ~ 23. The point-like source catalog is cross-matched with large optical databases and surveys including the SDSS DR9 (> 1 million Virgo Cluster sources), the Next Generation Virgo Cluster Survey (NGVS; > 13 million Virgo Cluster sources),and the NED (~ 30000 sources in the Virgo Cluster). We find that 69% of the entire UV point-like source catalog has a unique optical counterpart, 11% of which are stars and 0.01% (129) are Virgo cluster members that are neither in the VCC nor part of the bright CGCG galaxy catalog (i.e., mpg < 14.5). These data are collected in three catalogs containing the UV extended sources, the UV point-like sources, and the most relevant optical parameters of UV-optically matched point-like sources for further studies from SDSS. The GUViCS catalogs provide a unique set of data for future work on UV and multiwavelength studies in the cluster and background environments.
Keywords: Catalogs; Galaxies: clusters: individual: Virgo; Galaxies: photometry; Galaxies: star formation; Ultraviolet: galaxies

G141.2+5.0, a new pulsar wind nebula discovered in the Cygnus arm of the Milky Way - Kothes, R.; Sun, X. H.; Reich, W.; Foster, T. J. (The Astrophysical Journal Letters, 2014)
We report the discovery of the new pulsar wind nebula (PWN) G141.2+5.0 in data observed with the Dominion Radio Astrophysical Observatory's Synthesis Telescope at 1420 MHz. The new PWN has a diameter of about 3.′5, which translates to a spatial extent of about 4 pc at a distance of 4.0 kpc. It displays a radio spectral index of α ≈ -0.7, similar to the PWN G76.9+1.1. G141.2+5.0 is highly polarized up to 40% with an average of 15% in the 1420 MHz data. It is located in the center of a small spherical H I bubble, which is expanding at a velocity of 6 km s-1 at a systemic velocity of v LSR = -53 km s-1. The bubble could be the result of the progenitor star's mass loss or the shell-type supernova remnant (SNR) created by the same supernova explosion in a highly advanced stage. The systemic LSR velocity of the bubble shares the velocity of H I associated with the Cygnus spiral arm, which is seen across the second and third quadrants and an active star-forming arm immediately beyond the Perseus arm. A kinematical distance of 4 ± 0.5 kpc is found for G141.2+5.0, similar to the optical distance of the Cygnus arm (3.8 ± 1.1 kpc). G141.2+5.0 represents the first radio PWN discovered in 17 years and the first SNR discovered in the Cygnus spiral arm, which is in stark contrast with the Perseus arm's overwhelming population of shell-type remnants.

Reproductive impacts and physiological adaptations of zebrafish to elevated dietary nickel - Alsop, Derek; Lall, Santosh P.; Wood, Chris M. (Comparative Biochemistry and Physiology Part - C: Toxicology and Pharmacology, 2014)
Nickel (Ni) concentrations in the environment can rise due to human industrial activities. The toxicity of waterborne Ni to aquatic animals has been examined in a number of previous studies; however, little is known about the impacts of elevated dietary Ni. In the present study, zebrafish were chronically fed diets containing two concentrations of Ni [3.7 (control) and 116 μg Ni/g diet]. Ni-exposed males, but not females, were significantly smaller (26%) compared to controls at 80 days. In addition, total egg production was decreased by 65% in the Ni treatment at 75-78 days of the experiment. Ni was ubiquitously distributed in control animals (similar to previous studies), and concentrations varied between tissues by 15-fold. Ni exposure resulted in modest but significant Ni accumulation in some tissues (increases were highest in brain, vertebrae and gut; 44%, 34% and 25%, respectively), an effect observed only at 80 days. The limited Ni accumulation may be due to (1) the lack of an acidified stomach in zebrafish and/or (2) the efficient upregulation of Ni transport and excretion mechanisms, as indicated by the 4.5-fold increase in waterborne 63Ni uptake by Ni-exposed fish. Eggs from Ni-exposed adults had Ni concentrations that were 5.2-fold higher than controls. However, by 4 days post fertilization, larvae had similar Ni concentrations as controls, demonstrating a capacity for rapid Ni depuration. Larvae from Ni-exposed adults were also more resistant to waterborne Ni (35% increase in the 96-h LC50 over controls). In conclusion, elevated dietary Ni significantly affected zebrafish reproduction despite only modest tissue Ni accumulation. There were also indications of adaptation, including increased Ni uptake rates and increased Ni tolerance of offspring from Ni-exposed adults. Ni concentrations were particularly elevated in the brain with exposure; possible relations to growth and reproductive impacts require further study.
Keywords: estradiol; hydrocortisone; nickel; adaptation; animal experiment; animal tissue; brain; controlled study; dietary intake; egg production; environmental exposure; excretion; growth; intestine; larva; male; metabolic rate; nonhuman; ovary follicle; reproduction; survival; upregulation; zebra fish

Design and development of copper coatings for long term storage of used nuclear fuel - Keech, P.G.; Vo, P.; Ramamurthy, S.; Chen, J.; Jacklin, R.; Shoesmith, D. W. (Corrosion Engineering Science and Technology, 2014)
Within ongoing work, Canada's Nuclear Waste Management Organization (NWMO) is demonstrating that copper coatings can be developed as viable corrosion barriers for used fuel nuclear containers, emplaced in a deep geological repository. As a means of assessing container design and feasibility, coated samples, manufactured via cold spray and electro-deposition have been produced and characterised. Corrosion testing for coated samples and wrought samples reveals that cold spray samples behave similar to wrought samples in 3 mol L21NaCl solution at room temperature. When oxygen is absent, corrosion has not been observed.
Keywords: Electrodeposition; Radioactive wastes; Cold spray; Copper coatings; Deep geological repository; Design and Development; Long-term storage; Copper corrosion

Efficient Raman generation in a waveguide: A route to ultrafast quantum random number generation - England, D. G.; Bustard, P. J.; Moffatt, D. J.; Nunn, J.; Lausten, R.; Sussman, B. J. (Applied Physics Letters, 2014)
The inherent uncertainty in quantum mechanics offers a source of true randomness which can be used to produce unbreakable cryptographic keys. We discuss the development of a high-speed random number generator based on the quantum phase fluctuations in spontaneously initiated stimulated Raman scattering (SISRS). We utilize the tight confinement and long interaction length available in a Potassium Titanyl Phosphate waveguide to generate highly efficient SISRS using nanojoule pulse energies, reducing the high pump power requirements of the previous approaches. We measure the random phase of the Stokes output using a simple interferometric setup to yield quantum random numbers at 145 Mbps.
Keywords: Optical pumping; Quantum theory; Waveguides; Cryptographic key; Interaction length; Potassium titanyl phosphate; Pulse energies; Quantum phase fluctuations; Raman generation; Random number generators

Eremophilane glucosides from petasites japonicus - Wang, Guangyin; Zhang, Junzeng; Kulka, Marianna; Guo, Fujiang; Li, Yiming (Helvetica Chimica Acta, 2014)
Three new eremophilane glucosides, namely, petasitosides A-C, and seven known eremophilane-type sesquiterpenoids were isolated from the roots of Petasites japonicus. Their structures were elucidated by spectroscopic techniques including 1D- and 2D-NMR spectroscopy and mass spectrometry. This is the first report on eremophilane glycosides from the genus Petasites.
Keywords: Eremophilane glucosides; Petasites japonicus; Petasitosides AC; Sesquiterpenoids

Electrochemical synthesis of highly ordered polypyrrole on copper modified aluminium substrates - Siddaramanna, Ashoka; Saleema, N.; Sarkar, D. K. (Applied Surface Science, 2014)
Fabrication of highly ordered conducting polymers on metal surfaces has received a significant interest owing to their potential applications in organic electronic devices. In this context, we have developed a simple method for the synthesis of highly ordered polypyrrole (PPy) on copper modified aluminium surfaces via electrochemical polymerization process. A series of characteristic peaks of PPy evidenced on the infrared spectra of these surfaces confirm the formation of PPy. The X-ray diffraction (XRD) pattern of PPy deposited on copper modified aluminium surfaces also confirmed the deposition of PPy as a sharp and intense peak at 2θ angle of 23° attributable to PPy is observed while this peak is absent on PPy deposited on as-received aluminium surfaces. An atomic model of the interface of PPy/Cu has been presented based on the inter-atomic distance of copper-copper of (1 0 0) plane and the inter-monomer distance of PPy, to describe the ordering of PPy on Cu modified Al surfaces.
Keywords: Electrodeposition; Ordered polypyrrole; X-ray diffraction; Infrared spectroscopy; Copper films; Aluminium alloy surface

Long-range spin transfer in triple quantum dots - Sánchez, R.; Granger, G.; Gaudreau, L.; Kam, A.; Pioro-Ladrière, M.; Studenikin, S.A.; Zawadzki, P.; Sachrajda, A.S.; Platero, G. (Physical Review Letters, 2014)
Tunneling in a quantum coherent structure is not restricted to only nearest neighbors. Hopping between distant sites is possible via the virtual occupation of otherwise avoided intermediate states. Here we report the observation of long-range transitions in the transport through three quantum dots coupled in series. A single electron is delocalized between the left and right quantum dots, while the center one remains always empty. Superpositions are formed, and both charge and spin are exchanged between the outermost dots. The delocalized electron acts as a quantum bus transferring the spin state from one end to the other. Spin selection is enabled by spin correlations. The process is detected via the observation of narrow resonances which are insensitive to Pauli spin blockade. © 2014 American Physical Society.
Keywords: Atomic physics; Physics; Coherent structure; Delocalized electron; Intermediate state; Narrow resonances; Nearest neighbors; Single electron; Spin correlations; Spin selection; Semiconductor quantum dots

Amino acid derivatives as bitter taste receptor (T2R) blockers - Pydi, Sai P.; Sobotkiewicz, Tyler; Billakanti, Rohini; Bhullar, Rajinder P.; Loewen, Michele C.; Chelikani, Prashen (Journal of Biological Chemistry, 2014)
In humans, the 25 bitter taste receptors (T2Rs) are activated by hundreds of structurally diverse bitter compounds. However, only five antagonists or bitter blockers are known. In this study, using molecular modeling guided site-directed mutagenesis, we elucidated the ligand-binding pocket of T2R4. We found seven amino acids located in the extracellular side of transmembrane 3 (TM3), TM4, extracellular loop 2 (ECL2), and ECL3 to be involved in T2R4 binding to its agonist quinine. ECL2 residues Asn-173 and Thr-174 are essential for quinine binding. Guided by a molecular model of T2R4, a number of amino acid derivatives were screened for their ability to bind to T2R4. These predictions were tested by calcium imaging assays that led to identification of γ-aminobutryic acid (GABA) and Nα,Nα-bis(carboxymethyl)-L-lysine (BCML) as competitive inhibitors of quinine-activated T2R4 with an IC50of 3.2 ± 0.3 μM and 59 ± 18 nM, respectively. Interestingly, pharmacological characterization using a constitutively active mutant of T2R4 reveals that GABA acts as an antagonist, whereas BCML acts as an inverse agonist on T2R4. Site-directed mutagenesis confirms that the two novel bitter blockers share the same orthosteric site as the agonist quinine. The signature residues Ala-90 and Lys-270 play important roles in interacting with BCML and GABA, respectively. This is the first report to characterize a T2R endogenous antagonist and an inverse agonist. The novel bitter blockers will facilitate physiological studies focused on understanding the roles of T2Rs in extraoral tissues.
Keywords: Amino acid derivatives; Bitter blockers; Bitter taste receptors; Calcium imaging; G protein-coupled receptor (GPCR); Molecular modeling; Receptor structure-function; Site-directed mutagenesis; Taste receptors

Excited state dynamics in SO2. I. Bound state relaxation studied by time-resolved photoelectron-photoion coincidence spectroscopy - Wilkinson, Iain; Boguslavskiy, Audrey E.; Mikosch, Jochen; Bertrand, Julien B.; Wörner, Hans Jakob; Villeneuve, David M.; Spanner, Michael; Patchkovskii, Serguei; Stolow, Albert (Journal of Chemical Physics, 2014)
The excited state dynamics of isolated sulfur dioxide molecules have been investigated using the time-resolved photoelectron spectroscopy and time-resolved photoelectron-photoion coincidence techniques. Excited state wavepackets were prepared in the spectroscopically complex, electronically mixed (B̃)1B1/(Ã)1A2, Clements manifold following broadband excitation at a range of photon energies between 4.03 eV and 4.28 eV (308 nm and 290 nm, respectively). The resulting wavepacket dynamics were monitored using a multiphoton ionisation probe. The extensive literature associated with the Clements bands has been summarised and a detailed time domain description of the ultrafast relaxation pathways occurring from the optically bright (B̃)1B1 diabatic state is presented. Signatures of the oscillatory motion on the (B̃) 1B1/(Ã)1A2 lower adiabatic surface responsible for the Clements band structure were observed. The recorded spectra also indicate that a component of the excited state wavepacket undergoes intersystem crossing from the Clements manifold to the underlying triplet states on a sub-picosecond time scale. Photoelectron signal growth time constants have been predominantly associated with intersystem crossing to the (c̃)3B2 state and were measured to vary between 750 and 150 fs over the implemented pump photon energy range. Additionally, pump beam intensity studies were performed. These experiments highlighted parallel relaxation processes that occurred at the one- and two-pump-photon levels of excitation on similar time scales, obscuring the Clements band dynamics when high pump beam intensities were implemented. Hence, the Clements band dynamics may be difficult to disentangle from higher order processes when ultrashort laser pulses and less-differential probe techniques are implemented.
Keywords: Dynamics; Excited states; Photoelectron spectroscopy; Photoelectrons; Probes; Sulfur dioxide; Ultrashort pulses; Wave packets; Excited-state dynamics; Inter-system crossings; Multiphoton ionisation; Photoelectron signals; Photoelectron-photoion coincidence; Time domain description; Time-resolved photoelectron spectroscopy; Ultrafast relaxation; Photons

Abscisic acid flux alterations result in differential abscisic acid signaling responses and impact assimilation efficiency in barley under terminal drought stress - Seiler, Christiane; Harshavardhan, Vokkaliga T.; Reddy, Palakolanu Sudhakar; Hensel, Götz; Kumlehn, Jochen; Eschen-Lippold, Lennart; Rajesh, Kalladan; Korzun, Viktor; Wobus, Ulrich; Lee, Justin; Selvaraj, Gopalan; Sreenivasulu, Nese (Plant Physiology, 2014)
Abscisic acid (ABA) is a central player in plant responses to drought stress. How variable levels of ABA under short-term versus long-term drought stress impact assimilation and growth in crops is unclear. We addressed this through comparative analysis, using two elite breeding lines of barley (Hordeum vulgare) that show senescence or stay-green phenotype under terminal drought stress and by making use of transgenic barley lines that express Arabidopsis (Arabidopsis thaliana) 9-cis-epoxycarotenoid dioxygenase (AtNCED6) coding sequence or an RNA interference (RNAi) sequence of ABA 8'-hydroxylase under the control of a drought-inducible barley promoter. The high levels of ABA and its catabolites in the senescing breeding line under long-term stress were detrimental for assimilate productivity, whereas these levels were not perturbed in the stay-green type that performed better. In transgenic barley, drought-inducible AtNCED expression afforded temporal control in ABA levels such that the ABA levels rose sooner than in wild-type plants but also subsided, unlike as in the wild type, to near-basal levels upon prolonged stress treatment due to down-regulation of endogenous HvNCED genes. Suppressing of ABA catabolism with the RNA interference approach of ABA 89-hydroxylase caused ABA flux during the entire period of stress. These transgenic plants performed better than the wild type under stress to maintain a favorable instantaneous water use efficiency and better assimilation. Gene expression analysis, protein structural modeling, and protein-protein interaction analyses of the members of the PYRABACTIN RESISTANCE1/PYRABACTIN RESISTANCE1-LIKE/REGULATORY COMPONENT OF ABA RECEPTORS, TYPE 2C PROTEIN PHOSPHATASE Sucrose nonfermenting1- related protein kinase2, and ABA-INSENSITIVE5/ABA-responsive element binding factor family identified specific members that could potentially impact ABA metabolism and stress adaptation in barley.

Pathological mechanism for delayed hyperenhancement of chronic scarred myocardium in contrast agent enhanced magnetic resonance imaging - Wang, Jian; Xiang, Bo; Lin, Hung-Yu; Liu, Hongyu; Freed, Darren; Arora, Rakesh C.; Tian, Ganghong (PLoS ONE, 2014)
Objectives: To evaluate possible mechanism for delayed hyperenhancement of scarred myocardium by investigating the relationship of contrast agent (CA) first pass and delayed enhancement patterns with histopathological changes. Materials and Methods: Eighteen pigs underwent 4 weeks ligation of 1 or 2 diagonal coronary arteries to induce chronic infarction. The hearts were then removed and perfused in a Langendorff apparatus. The hearts firstly experienced phosphorus 31 MR spectroscopy. The hearts in group I (n = 9) and II (n = 9) then received the bolus injection of Gadolinium diethylenetriamine pentaacetic acid (0.05 mmol/kg) and gadolinium-based macromolecular agent (P792, 15 mmol/kg), respectively. First pass T2* MRI was acquired using a gradient echo sequence. Delayed enhanced T1 MRI was acquired with an inversion recovery sequence. Masson's trichrome and anti- von Willebrand Factor (vWF) staining were performed for infarct characterization. Results: Wash-in of both kinds of CA caused the sharp and dramatic T2* signal decrease of scarred myocardium similar to that of normal myocardium. Myocardial blood flow and microvessel density were significantly recovered in 4-week-old scar tissue. Steady state distribution volume (ΔR1 relaxation rate) of Gd-DTPA was markedly higher in scarred myocardium than in normal myocardium, whereas ΔR1 relaxation rate of P792 did not differ significantly between scarred and normal myocardium. The ratio of extracellular volume to the total water volume was significantly greater in scarred myocardium than in normal myocardium. Scarred myocardium contained massive residual capillaries and dilated vessels. Histological stains indicated the extensively discrete matrix deposition and lack of cellular structure in scarred myocardium. Conclusions: Collateral circulation formation and residual vessel effectively delivered CA into scarred myocardium. However, residual vessel without abnormal hyperpermeability allowed Gd-DTPA rather than P792 to penetrate into extravascular compartment. Discrete collagen fiber meshwork and loss of cellularity enlarged extracellular space accessible to Gd-DTPA, resulting in the delayed hyper-enhanced scar. © 2014 Wang et al.
Keywords: collagen fiber; contrast medium; gadolinium pentetate; gadomelitol; von Willebrand factor; animal experiment; animal model; animal tissue; article; capillary density; cardiovascular magnetic resonance; contrast enhancement; controlled study; coronary artery ligation; domestic pig; extracellular space; heart disease; heart infarction; heart muscle blood flow; histopathology; isolated heart; nonhuman; phosphorus nuclear magnetic resonance; scarred myocardium

Detection of single graves by airborne hyperspectral imaging - Leblanc, G.; Kalacska, M.; Soffer, R. (Forensic Science International, 2014)
Airborne hyperspectral imaging (HSI) was assessed as a potential tool to locate single grave sites. While airborne HSI has shown to be useful to locate mass graves, it is expected the location of single graves would be an order of magnitude more difficult due to the smaller size and reduced mass of the targets. Two clearings were evaluated (through a blind test) as potential sites for containing at least one set of buried remains. At no time prior to submitting the locations of the potential burial sites from the HSI were the actual locations of the sites released or shared with anyone from the analysis team.The two HSI sensors onboard the aircraft span the range of 408-2524. nm. A range of indicators that exploit the narrow spectral and spatial resolutions of the two complimentary HSI sensors onboard the aircraft were calculated. Based on the co-occurrence of anomalous pixels within the expected range of the indicators three potential areas conforming to our underlying assumptions of the expected spectral responses (and spatial area) were determined. After submission of the predicted burial locations it was revealed that two of the targets were located within GPS error (10. m) of the true burial locations. Furthermore, due to the history of the TPOF site for burial work, investigation of the third target is being considered in the near future. The results clearly demonstrate promise for hyperspectral imaging to aid in the detection of buried remains, however further work is required before these results can justifiably be used in routine scenarios.
Keywords: Hyperspectral; Grave detection; Single burial; Airborne remote sensing

Progress toward development of low-temperature microwave refractive index gas thermometry at NRC - Rourke, P. M. C.; Hill, K. D. (International Journal of Thermophysics, 2014)
Progress toward the development of a low-temperature microwave refractive index gas thermometry implementation for primary thermometry at NRC is reported. A prototype quasi-spherical copper resonator has been integrated into a cryogenic system with a 5 K base temperature, and preliminary microwave measurements in vacuum have been completed to characterize the resonator between 5 K and 297 K. The dependence of experimental results on spectral fitting background terms, 1st- and 2nd-order shape corrections, and waveguide corrections has also been explored. The current NRC results agree with previous room-temperature measurements on the same resonator at NIST, and indicate no significant change in resonator shape between room temperature and low temperature. The temperature dependences of the resonator electrical conductivity and linear thermal expansion coefficient, as obtained from the microwave resonances, agree with published literature values for oxygen-free high-conductivity copper measured using other techniques.
Keywords: Electromagnetic resonance; Gas thermometers; Low temperatures; Microwave refractive index; Microwaves

Investigating the antiviral role of cell death-inducing DFF45-like effector B in HCV replication - Singaravelu, Ragunath; Delcorde, Julie; Lyn, Rodney K.; Steenbergen, Rineke H.; Jones, Daniel M.; Tyrrell, David Lorne; Russell, Rodney S.; Pezacki, John P. (FEBS Journal, 2014)
Cell-death-inducing DFF45-like effector B (CIDEB) is an apoptotic host factor, which was recently found to also regulate hepatic lipid homeostasis. Herein we delineate the relevance of these dual roles of CIDEB in apoptosis and lipid metabolism in the context of hepatitis C virus (HCV) replication. We demonstrate that HCV upregulates CIDEB expression in human serum differentiated hepatoma cells. CIDEB overexpression inhibits HCV replication in HCV replicon expressing Huh7.5 cells, while small interfering RNA knockdown of CIDEB expression in human serum differentiated hepatoma cells promotes HCV replication and secretion of viral proteins. Furthermore, we characterize a CIDEB mutant, KRRA, which is deficient in lipid droplet clustering and fusion and demonstrate that CIDEB-mediated inhibition of HCV is independent of the protein's lipid droplet fusogenic role. Our results suggest that higher levels of CIDEB expression, which favour an apoptotic role for the host factor, inhibit HCV. Collectively, our data demonstrate that CIDEB can act as an anti-HCV host factor and contribute to altered triglyceride homeostasis. Here, we illustrate that hepatitis C virus (HCV) replication activates the expression of the liver abundant host factor CIDEB with known regulatory roles in hepatic lipid homeostasis and apoptosis. We demonstrate that siRNA mediated knockdown CIDEB overexpression increase HCV replication and CIDEB knockdown inhibits HCV replication and this inhibition is independent of CIDEB's role in lipid droplet clustering and fusion.
Keywords: cell death inducing DFF45 like effector b; host factor; small interfering RNA; unclassified drug; virus protein; apoptosis; controlled study; hepatitis C; lipid metabolism; nucleotide sequence; protein expression; protein function; protein secretion; replicon; upregulation; virus inhibition; virus replication; CARS microscopy; cell-inducing DFF45 like effector; lipid droplet; Apoptosis Regulatory Proteins; Caspase 3; Caspase 7; Caspases; Cell Line, Tumor; Hepacivirus; Homeostasis; Host-Pathogen Interactions; Lipid Metabolism; Triglycerides

Rotating disk electrode method - Du, Chunyu; Tan, Qiang; Yin, Geping; Zhang, Jiujun (Rotating Electrode Methods and Oxygen Reduction Electrocatalysts, 2014)
In this chapter, to give readers the knowledge how to appropriately use rotating disk electrode (RDE) in their oxygen reduction reaction (ORR) study, fundamentals of both the electron transfer process on electrode surface and diffusion-convection kinetics near the rotating electrode are presented. Two kinds of RDE and their associated theories of the diffusion-convection kinetics and its coupling with the electron-transfer process are presented, one is the smooth electrode surface, and the other is the catalyst-layer-coated electrode. For measurements using the RDE method, the apparatus of RDE and its associated devices such as rotator and electrochemical cell are described to give the readers the basic sense about this technique. The measurement procedure including RDE preparation, catalyst layer fabrication, current-potential curve recording, the data analysis, as well as the cautions in RDE measurements are also discussed in this chapter.

Hosting various guests including fullerenes and free radicals in versatile organic paramagnetic bTbk open frameworks - Bardelang, David; Giorgi, Michel; Hornebecq, Virginie; Stepanov, Anatoli; Hardy, Micael; Rizzato, Egon; Monnier, Valerie; Zaman, Md. Badruz; Chan, Gordon; Udachin, Konstantin; Enright, Gary; Tordo, Paul; et al. (Crystal Growth and Design, 2014)
The dinitroxide bis(TEMPO) bisketal (bTbk) was shown to crystallize into open frameworks whose structures were determined by single-crystal X-ray diffraction. We show that bTbk can be used as a supramolecular building block for the hosting of a plethora of guests inside the 1D channels of its paramagnetic framework, including other radicals such as TEMPO or 2-azaadamantane-N-oxyl. C60 and C70 were also found to be easily included in this open framework during its crystallization. This resulted in well-defined, nanostructured assemblies of composite radical crystals (bTbk/toluene/C60 or C70) or (bTbk/toluene/TEMPO) by a very simple dissolution/crystallization process with tunable guest content. Selective C60 extraction was also demonstrated directly from fullerene soot.
Keywords: Building blockes; Fullerene soot; Nanostructured assembly; Open frameworks; Single crystal x-ray diffraction; Free radicals; Fullerenes; X ray diffraction; Paramagnetism

Analytical method for the determination of trace toxic elements in milk based on combining Fe3O4 nanoparticles accelerated UV fenton-like digestion and solid phase extraction - Ai, Xi; Wu, Li; Zhang, Mengni; Hou, Xiandeng; Yang, Lu; Zheng, Chengbin (Journal of Agricultural and Food Chemistry, 2014)
A UV Fenton-like digestion method was developed first time for a complete digestion of milk samples by using 1.6 g L-1 Fe3O 4 magnetic nanoparticles, 0.2% (v/v) nitric acid, and 6% (w/w) H 2O2. During the digestion, the liberated As-, Sb-, and Bi-containing species were preconcentrated onto the surface of Fe 3O4 magnetic nanoparticles, which were conveniently separated with a hand-held magnet and subsequently dissolved in hydrochloric acid prior to hydride generation atomic fluorescence spectrometric detection. Owing to the integration of UV Fenton-like digestion, solid phase extraction, and magnetic separation into a single step, the developed method significantly simplifies sample preparation steps and reduces chemical consumption and hazardous waste. Limits of detection of 0.0015, 0.0022, and 0.0025 μg L -1 were obtained for As, Sb, and Bi, respectively, using a 50 mL milk sample. The method was applied to the determination of these elements in a Certified Reference Material and milk samples.
Keywords: Antimony; Bismuth; Effluent treatment; Hydrides; Magnetic separation; Nanoparticles; Phase separation; Certified reference materials; Chemical consumption; Fenton reactions; Hydride generations; Magnetic nano-particles; Sample pretreatment; Solid-phase extraction; Spectrometric detection; Trace elements

Hybrid cryogenic low noise amplifier for the MeetKAT array - Jiang, Frank; Claude, Stéphane; Garcia, Dominic (Proceedings - ANTEM 2014: 2014 16th International Symposium on Antenna Technology and Applied Electromagnetics, 2014)
Hybrid microwave integrated circuit technology is used to design and develop an L-band (900-2100 MHz) ultra-low noise amplifier for the MeerKAT array. This low noise amplifier achieved 2 K noise temperature, more than 40 dB gain, S11 & S22 better than -11 & -15 dB at 15 K ambient. Linearity and gain compression is verified. The noise performance is explored as the cooling temperature changes from 15 to 85 K.
Keywords: Amplifiers (electronic); Antenna arrays; Cryogenics; Microwave amplifiers; Microwave integrated circuits; Cooling temperature; Cryogenic low noise amplifiers; Hybrid microwave integrated circuits; MeerKAT array; Noise amplifiers; Noise performance; Noise temperature; SKA; Low noise amplifiers

Continuous slow and fast light generation using a silicon-on-insulator microring resonator incorporating a multimode interference coupler - Shahoei, Hiva; Xu, Dan-Xia.; Schmid, Jens H.; Yao, Jianping (Journal of Lightwave Technology, 2014)
Continuously tunable slow and fast light generation using a silicon-on-insulator microring resonator (MRR) incorporating a multimode interference (MMI) coupler is proposed and experimentally demonstrated. The MMI coupler is optimized for the transverse-magnetic mode. By changing the input polarization state, the self-coupling coefficient and the loss factor of the MRR are changed. The depth and the bandwidth of the MRR are tunable by tuning the self-coupling coefficient and the loss factor; thus, a tunable phase shift can be achieved at the resonance wavelength, which leads to the generation of a tunable slow and fast light. The proposed scheme is experimentally evaluated. A tunable slow light with a maximum time delay of 35 ps and a slow-to-fast light with a continuously tunable range of 102 ps are achieved for a 13.5-GHz Gaussian optical pulse by using a double-MMI coupler MRR and a single-MMI coupler MRR, respectively.
Keywords: Microring resonator; Microring Resonator (MRR); Multimode interference couplers; Silicon photonics; Slow and fast light

Silicon photonic integration with subwavelength gratings - Schmid, J. H.; Cheben, P.; Lapointe, J.; Xu, D. -X.; Janz, S.; Vachon, M.; Wang, S.; Bock, P.; Benedikovič, D.; Halir, R.; Ortega-Moñux, A.; Ramos, C. A.; et al. (International Conference on Transparent Optical Networks, 2014)
Subwavelength grating structures with a pitch smaller than the Bragg resonance length can be used for engineering the refractive index in silicon photonic waveguides. We discuss the principles, design, fabrication and applications of subwavelength nanostructures in silicon photonics and review our recent results on fiber-chip coupling structures, surface grating couplers, waveguide crossings, and athermal waveguides with a polymersilicon hybrid core.
Keywords: Photonics; Refractive index; Transparent optical networks; Waveguides; Athermal waveguides; Fiber chip coupling; Grating couplers; Silicon photonics; Sub-wave length grating; Subwavelength nanostructures; Surface grating couplers; Waveguide crossings; Photonic devices

Effect of pre- and post-weld heat treatments on linear friction welded Ti-5553 - Wanjara, Priti; Dalgaard, Elvi; Gholipour, Javad; Cao, Xinjin; Cuddy, Jonathan; Jonas, John J. (Metallurgical and Materials Transactions A: Physical Metallurgy and Materials Science, 2014)
Linear friction welding allows solid-state joining of near-beta (β) titanium alloy Ti-5553 (Ti-5Al-5V-5Mo-3Cr). In the as-welded condition, the weld zone (WZ) exhibits β grain refinement and marked softening as compared with Ti-5553 in the solution heat treated and aged condition. The softening of the weldment is attributed to the depletion of the strengthening alpha (α) phase in the WZ and the adjacent thermo-mechanically affected zone (TMAZ). Specifically, in near-β titanium alloys, the strength of the material mainly depends on the shape, size, distribution, and fraction of the primary α and other decomposition products of the β phase. Hence, a combination of pre- and post-weld heat treatments were applied to determine the conditions that allow mitigating the α phase depletion in the WZ and TMAZ of the welds. The mechanical response of the welded samples to the heat treatments was determined by performing microhardness measurements and tensile testing at room temperature with an automated 3D deformation measurement system. It was found that though the joint efficiency in the as-welded condition was high (96 pct), strain localization and failure occurred in the TMAZ. The application of post-weld solution heat treatment with aging was effective in restoring α, increasing the joint efficiency (97 to 99 pct) and inducing strain localization and failure in the parent material region.
Keywords: Friction welding; Grain refinement; Heat treatment; Strength of materials; Tensile testing; Welding; 3D deformation measurements; Decomposition products; Linear friction welding; Microhardness measurement; Post weld heat treatment; Solution heat treated; Solution heat treatment; Thermomechanically affected zones; Titanium alloys

Intra-pixel response of the new JWST infrared detector arrays - Hardy, T.; Willot, C.; Pazder, J. (SPIE - International Society for Optical Engineering. Proceedings, 2014)
We have repeated some of our previous measurements of the intra-pixel response of the infrared detector arrays for the Fine Guidance Sensor (FGS) instrument on the James Webb Space Telescope (JWST). This set of tests was performed on a 5 micron cutoff substrate-removed HAWAII-1RG from the new batch of devices produced for JWST. The measurements were done at wavelengths from 650 nm to 1550 nm. The results from these tests indicate that there are no significant differences in the intra-pixel response between the older JWST devices and the new ones. Modeling suggests that the primary contributor to the response profile is diffusion in the bulk detector material.
Keywords: Diffusion; Infrared detectors; Space telescopes; 1550 nm; Detector materials; Fine guidance sensors; Intra-pixel response; James Webb space telescope; Response profile; Astronomy

An investigation on bio-based polyurethane foam insulation for building construction - Mukhopadhyaya, Phalguni; Ton-That, Minh-Tan; Ngo, Tri-Dung; Legros, Nathalie; Masson, J. -F.; Bundalo-Perc, Sladana; van Reenen, David (ASTM Special Technical Publication, 2014)
Bio-based renewable construction material is an old concept. Wood, straw, and other products of nature have been used for millennia around the world. However, in modern construction, the ratio of bio-based to non-renewable building materials is very low. This is primarily due to performance requirements. Purely bio-based construction materials sometimes have performance levels not quite equal to modern construction materials. The biggest challenge for the development of bio-based construction materials is to bring environmental friendliness and high engineering performance together in a single material. This paper presents results from a laboratory screening study on the development and the assessment of rigid partially bio-based polyurethane (PU) foams (seven different formulations) that contain lignin-based polyols, up to 20 % of polyol weight. The formulation strategy, morphology, and hygrothermal performance of rigid bio-based PU foams are presented and compared with the traditional petroleum-based reference PU foam. This study demonstrates that partially bio-based rigid PU foam with appropriate formulation can have characteristics that may be suitable for the construction industry applications. For market acceptance, further investigation is needed on long-term performance and durability.
Keywords: Alcohols; Construction industry; Industrial applications; Rigid foamed plastics; Thermal insulation; Bio-based; Bio-foam; Engineering performance; Environmental friendliness; Hygrothermal performance; Modern construction materials; Performance requirements; Polyurethane Foam; Building materials

Far-IR spectra of small neutral gold clusters in the gas phase - Gruene, Philipp; Butschke, Burkhard; Lyon, Jonathan T.; Rayner, David M.; Fielicke, André (Zeitschrift fur Physikalische Chemie, 2014)
Vibrational spectra of small neutral gold clusters containing up to 8 Au atoms are measured in the far-infrared (46-222 cm-1) via photodissociation of their complexes with krypton atoms. Comparisons with calculated IR spectra for bare Au n clusters using density functional theory allow for structural assignment. For these small sizes, all clusters are found to be planar and of comparably high symmetry. For Au6 no data is available, as this cluster size is not detected in the photoionization mass spectra due to its high ionization energy. The structures assigned are for n = 4: rhombus (D2h); 5: trapezoid (C2v); 7: edge-capped triangle (Cs), 8: 4-fold edge-capped square (D4h).

Flow control in an aggressive interturbine transition duct using low profile vortex generators - Zhang, Yanfeng; Hu, Shuzhen; Zhang, Xue-Feng; Benner, Michael; Mahallati, Ali; Vlasic, Edward (Journal of Engineering for Gas Turbines and Power, 2014)
This paper presents an experimental investigation of the flow mechanisms in an aggressive interturbine transition duct with and without low-profile vortex generators flow control. The interturbine duct had an area ratio of 1.53 and a mean rise angle of 35deg. Measurements were made inside the annulus at a Reynolds number of 150,000. At the duct inlet, the background turbulence intensity was raised to 2.3% and a uniform swirl angle of 20deg was established with a 48-airfoil vane ring. Results for the baseline case (no vortex generators) showed the flow structures within the duct were dominated by counter-rotating vortices and boundary layer separation in both the casing and hub regions. The combination of the adverse pressure gradient at the casing's first bend and upstream low momentum wakes caused the boundary layer to separate on the casing. The separated flow on the casing appears to reattach at the second bend. Counter-rotating and corotating vortex generators were installed on the casing. While both vortex generators significantly decreased the casing boundary layer separation with consequential reduction of overall pressure losses, the corotating configuration was found to be more effective.
Keywords: Boundary layers; Flow control; Reynolds number; Transport aircraft; Adverse pressure gradient; Boundary-layer separation; Casing boundary layer; Co-rotating vortices; Counter-rotating vortices; Experimental investigations; Overall pressure loss; Turbulence intensity; Ducts

Alma observations of the Orion proplyds - Mann, Rita K.; Di Francesco, James; Johnstone, Doug; Andrews, Sean M.; Williams, Jonathan P.; Bally, John; Ricci, Luca; Hughes, A. Meredith; Matthews, Brenda C. (The Astrophysical Journal, 2014)
We present Atacama Large Millimeter/submillimeter Array (ALMA) observations of protoplanetary disks ("proplyds") in the Orion Nebula Cluster. We imaged five individual fields at 856 μm containing 22 Hubble Space Telescope (HST)-identified proplyds and detected 21 of them. Eight of those disks were detected for the first time at submillimeter wavelengths, including the most prominent, well-known proplyd in the entire Orion Nebula, 114-426. Thermal dust emission in excess of any free-free component was measured in all but one of the detected disks, and ranged between 1 and 163 mJy, with resulting disk masses of 0.3-79 M jup. An additional 26 stars with no prior evidence of associated disks in HST observations were also imaged within the 5 fields, but only 2 were detected. The disk mass upper limits for the undetected targets, which include OB stars, θ1 Ori C, and θ1 Ori F, range from 0.1 to 0.6 M jup. Combining these ALMA data with previous Submillimeter Array observations, we find a lack of massive (≳3 M jup) disks in the extreme-UV-dominated region of Orion, within 0.03 pc of θ1 Ori C. At larger separations from θ1 Ori C, in the far-UV-dominated region, there is a wide range of disk masses, similar to what is found in low-mass star forming regions. Taken together, these results suggest that a rapid dissipation of disk masses likely inhibits potential planet formation in the extreme-UV-dominated regions of OB associations, but leaves disks in the far-UV-dominated regions relatively unaffected.

Crystal engineering the clathrate hydrate lattice with NH4F - Shin, Kyuchul; Moudrakovski, Igor L.; Davari, Mehdi D.; Alavi-Shoushtari, Saman; Ratcliffe, Christophe I.; Ripmeester, John A. (CrystEngComm, 2014)
There have been very few attempts to apply crystal engineering approaches to modify the clathrate lattice with the aim of modifying structure and properties. To this end, solutions of ammonium fluoride in water were used to prepare clathrate hydrates with ammonium fluoride replacing water molecules in the hydrate lattice. Both modified structure I Xe and structure II tetrahydrofuran/Xe hydrates were prepared, with the hydrate lattices consisting of NH4F-water solid solutions containing up to ~19 and 25 mole% NH4F, respectively. The lattice constants for both hydrates decreased with increase of the amount of NH4F incorporated, and guest positions and cage occupancies were determined from the PXRD patterns with direct space methods and Rietveld analysis. The 129Xe NMR spectra for Xe in the small cavities of each hydrate showed NH4F concentration-dependent fine structure, not evident in the pure water clathrates, and characteristic of the presence of cage configurations with different distributions of ions. Analysis of the spectra along with density functional theory calculations of the chemical shifts allowed reasonable assignments to be made of the ion distribution. As a test of the altered function of the clathrate upon modification, a clathrate of methanol was prepared, something which has not been possible to do with a pure water clathrate. Structural analysis of the PXRD pattern by direct space methods showed that the methanol OH was hydrogen-bonded to one or both of the NH 4 + and F- ions in the lattice, a conclusion corroborated by the absence of molecular motion (except for methyl group rotation) of the methanol guest in the clathrate cages, as determined by static 2H NMR and molecular dynamics simulations. The stability of the modified methanol clathrate can be attributed to the strong methanol CH 3OH⋯F- or CH3OH⋯NH 4 + hydrogen bonding which leaves the water-water hydrogen bonding network intact, as opposed to the situation in a pure water clathrate where the methanol-water hydrogen bonding disrupts the lattice and a stable clathrate cannot be made.

Molecular mechanisms in the selective basal activation of pyrabactin receptor 1: Comparative analysis of mutants - Dorosh, Lyudmyla; Rajagopalan, Nandhakishore; Loewen, Michele C.; Stepanova, Maria (FEBS Open Bio, 2014)
Pyrabactin receptors (PYR) play a central role in abscisic acid (ABA) signal transduction; they are ABA receptors that inhibit type 2C protein phosphatases (PP2C). Molecular aspects contributing to increased basal activity of PYR against PP2C are studied by molecular dynamics (MD) simulations. An extensive series of MD simulations of the apo-form of mutagenized PYR1 as a homodimer and in complex with homology to ABA-insensitive 1 (HAB1) phosphatase are reported. In order to investigate the detailed molecular mechanisms mediating PYR1 activity, the MD data was analyzed by essential collective dynamics (ECD), a novel approach that allows the identification, with atomic resolution, of persistent dynamic correlations based on relatively short MD trajectories. Employing the ECD method, the effects of select mutations on the structure and dynamics of the PYR1 complexes were investigated and considered in the context of experimentally determined constitutive activities against HAB1. Approaches to rationally design constitutively active PYR1 constructs to increase PP2C inhibition are discussed.
Keywords: abscisic acid; homodimer; mutant protein; pyrabactin receptor 1; in vitro study; molecular dynamics; mutation; protein analysis; protein function; protein structure; signal transduction; simulation

Thickness measurements using photonic modes in monochromated electron energy-loss spectroscopy - Yurtsever, Aycan; Couillard, Martin M.; Hyun, Jerome K.; Muller, David A. (Microscopy and Microanalysis, 2014)
Characteristic energies of photonic modes are a sensitive function of a nanostructures' geometrical parameters. In the case of translationally invariant planar waveguides, the eigen-energies reside in the infrared to ultraviolet parts of the optical spectrum and they sensitively depend on the thickness of the waveguide. Using swift electrons and the inherent Cherenkov radiation in dielectrics, the energies of such photonic states can be effectively probed via monochromated electron energy-loss spectroscopy (EELS). Here, by exploiting the strong photonic signals in EELS with 200 keV electrons, we correlate the energies of waveguide peaks in the 0.5-3.5 eV range with planar thicknesses of the samples. This procedure enables us to measure the thicknesses of cross-sectional transmission electron microscopy samples over a 1-500 nm range and with best-case accuracies below ±2%. The measurements are absolute with the only requirement being the optical dielectric function of the material. Furthermore, we provide empirical formulation for rapid and direct thickness estimations for a 50-500 nm range. We demonstrate the methodology for two semiconducting materials, silicon and gallium arsenide, and discuss how it can be applied to other dielectrics that produce strong optical fingerprints in EELS. The asymptotic form of the loss function for two-dimensional materials is also discussed.

Particle filter-based method for prognostics with application to auxiliary power unit - Yang, Chunsheng; Lou, Qingfeng; Liu, Jie; Yang, Yubin; Bai, Yun (Modern Advances in Applied Intelligence : 27th International Conference on Industrial Engineering and Other Applications of Applied Intelligent Systems, IEA/AIE 2014, Kaohsiung, Taiwan, June 3-6, 2014, Proceedings, Part I, 2014)
Particle filter (PF)-based method has been widely used for machinery condition-based maintenance (CBM), in particular, for prognostics. It is employed to update the nonlinear prediction model for forecasting system states. In this work, we applied PF techniques to Auxiliary Power Unit (APU) prognostics for estimating remaining useful cycle to effectively perform APU health management. After introducing the PF-based prognostic method and algorithms, the paper presents the implementation for APU Starter prognostics along with the experimental results. The results demonstrated that the developed PF-based method is useful for estimating remaining useful cycle for a given failure of a component or a subsystem.
Keywords: Intelligent systems; Machinery; Maintenance; Monte Carlo methods; Systems engineering; APU Starter prognostics; Condition-based maintenance (CBM); Data-driven prognostics; Particle filter (PF); remaining useful cycle (RUC); Auxiliary power systems

Structure of CbpA J-domain bound to the regulatory protein CbpM explains its specificity and suggests evolutionary link between CbpM and transcriptional regulators - Sarraf, Naghmeh S.; Shi, Rong; McDonald, Laura; Baardsnes, Jason; Zhang, Linhua; Cygler, Miroslaw; Ekiel, Irena (PLoS ONE, 2014)
CbpA is one of the six E. coli DnaJ/Hsp40 homologues of DnaK co-chaperones and the only one that is additionally regulated by a small protein CbpM, conserved in γ-proteobacteria. CbpM inhibits the co-chaperone and DNA binding activities of CbpA. This regulatory function of CbpM is accomplished through reversible interaction with the N-terminal Jdomain of CbpA, which is essential for the interaction with DnaK. CbpM is highly specific for CbpA and does not bind DnaJ despite the high degree of structural and functional similarity between the J-domains of CbpA and DnaJ. Here we report the crystal structure of the complex of CbpM with the J-domain of CbpA. CbpM forms dimers and the J-domain of CbpA interacts with both CbpM subunits. The CbpM-binding surface of CbpA is highly overlapping with the CbpA interface for DnaK, providing a competitive model for regulation through forming mutually exclusive complexes. The structure also provides the explanation for the strict specificity of CbpM for CbpA, which we confirmed by making mutants of DnaJ that became regulated by CbpM. Interestingly, the structure of CbpM reveals a striking similarity to members of the MerR family of transcriptional regulators, suggesting an evolutionary connection between the functionally distinct bacterial cochaperone regulator CbpM and the transcription regulator HspR.
Keywords: CbpA protein; CbpM protein; chaperone; heat shock protein 40; MerR like family; protein DnaJ; protein DnaK; unclassified drug; article; binding competition; binding site; complex formation; controlled study; crystal structure; enzyme specificity; nonhuman; protein binding; protein domain; protein protein interaction; protein subunit; regulatory mechanism

Estimation of human body shape and posture under clothing - Wuhrer, Stefanie; Pishchulin, Leonid; Brunton, Alan; Shu, Chang; Lang, Jochen (Computer Vision and Image Understanding, 2014)
Estimating the body shape and posture of a dressed human subject in motion represented as a sequence of (possibly incomplete) 3D meshes is important for virtual change rooms and security. To solve this problem, statistical shape spaces encoding human body shape and posture variations are commonly used to constrain the search space for the shape estimate. In this work, we propose a novel method that uses a posture-invariant shape space to model body shape variation combined with a skeleton-based deformation to model posture variation. Our method can estimate the body shape and posture of both static scans and motion sequences of human body scans with clothing that fits relatively closely to the body. In case of motion sequences, our method takes advantage of motion cues to solve for a single body shape estimate along with a sequence of posture estimates. We apply our approach to both static scans and motion sequences and demonstrate that using our method, higher fitting accuracy is achieved than when using a variant of the popular SCAPE model [2,18] as statistical model.
Keywords: Virtual reality; Fitting accuracy; Geometry processing; Human subjects; Motion sequences; Posture modeling; Search spaces; Statistical modeling; Statistical shapes; Hosiery manufacture

Exploration of a new approach for calibrating grinding power model - Shi, Zhongde; Guo, Changsheng; Attia, Helmi (ASME 2014 International Manufacturing Science and Engineering Conference, MSEC 2014 Collocated with the JSME 2014 International Conference on Materials and Processing and the 42nd North American Manufacturing Research Conference, 2014)
This paper is concerned with the reliable calibration of the grinding power model. The power model used in the present paper is expressed by formulae with grinding parameters as input arguments, and a number of model constants representing a given wheel, workpiece, and grinding fluid combination. The model constants are calibrated using measured grinding forces and power, taking into consideration of the chip formation, sliding, and plowing components of the power. These correspond to the constants of specific chip formation energy uch, the coefficient of friction μ and average contact pressure pa, and the plowing force per unit width F'pl, respectively. A new generalized experimental approach was developed in this study to reflect the physical meaning of the model. Compared with other approaches, this approach does not require a preknowledge of the wheel wear flat area value and the regime of the average contact pressure. The proposed approach includes measurements of forces and power from surface grinding tests with a fixed set of grinding parameters conducted at different wheel dullness levels for calibrating the constant μ, as well as tests with variable workspeeds at each of the wheel dullness level for calibrating the other constants. As an application example, it was applied to calibrating the power model for grinding of a nickel-based alloy with oil as grinding fluid and electroplated CBN wheels. The calibrated model was then validated through tests under different grinding conditions.
Keywords: Grinding power; New approaches

Observation of mixed acetylene - Nitrous oxide trimers: Infrared spectra of C2H2-(N2O)2 and (C2H2)2-N2O - Sheybani-Deloui, S.; Yousefi, M.; Norooz Oliaee, J.; McKellar, A. R. W.; Moazzen-Ahmadi, N. (Journal of Molecular Spectroscopy, 2014)
Infrared spectra of the lowest energy isomers of C2H2-(N2O)2 and (C2H2)2-N2O were observed in the region of the ν1 fundamental band of the N2O monomer (∼2224 cm-1) using a tunable diode laser and/or a CW quantum cascade laser to probe a pulsed supersonic slit jet expansion. One infrared band was measured for each trimer. The band for C2H2-(N2O)2 corresponds to the out-of-phase vibrations of the pair of equivalent N2O monomers. It is blue shifted by about 10 cm-1 with respect to the free N2O monomer. The band for (C2H2)2-N2O is slightly less blue shifted (centered at 2232.81 cm-1). It can be simulated as a predominately a-type band. In addition to the normal isotopologues, the corresponding bands for C2D2-(N2O)2 and (C2D2)2-N2O were also observed. The structures of these trimers are similar to those of the lowest energy isomers of the analogous OCS - acetylene trimers reported previously, that is, a twisted barrel with C2 symmetry for C2H2-(N2O)2 and a distorted T-shaped acetylene dimer with a coplanar N2O beside the stem of the T for (C2H2)2-N2O. Here, we present our observation and experimental results, which agree well with calculations based on distributed multipole pair potentials.
Keywords: Infrared spectrum; Nitrous oxide; Van der Waals clusters

Detecting low concentration bacterial cells in complex media using a microchip-based flow cytometer - Mu, Canjun; Zhang, Zhiyi; Lin, Min; Du, Yan; Cao, Xudong (Sensors and Actuators, B: Chemical, 2014)
Rapid detection of pathogenic bacteria in real-world samples, in which low concentration target bacteria usually coexist with a large quantity of interfering particles, is very important in many areas related to public health. In this study, we present our recent efforts in detecting low concentration bacteria in complex media that contain interfering particles and background noise using a microchip-based flow cytometer (i.e., microcytometer). To achieve this goal, low concentration 1.00 μm YG fluorescent beads, model particles for bacteria, were first detected in the presence of both a great number of polystyrene beads and fluorescence background noise using a microcytometer developed in this study. The microcytometer was further used to detect low concentrations of FITC labeled bacteria E. coli DH5α in the presence of a large quantity of interfering beads and FITC fluorescence background noise. We show that the FITC labeled E. coli DH5α cells at concentrations as low as 431 cells/mL were detected by the microcytometer with efficiencies of over 86% in complex media that contained high concentration (i.e., 4.89 × 10 7 particles/mL) blank interfering beads (d = 4.50 μm) with 0.5 μM FITC fluorescein as fluorescence background. This translates to detection of one target bacterial cell from approximately 1 × 105 interfering particles. Unlike other reports, this is the first report that studied detection of low concentration bacteria by a microcytometer in complex sample media. The outstanding detection performances of the microcytometer demonstrated by this study strongly suggest that microcytometers are indeed very promising candidate for detection of pathogenic bacteria in real-world samples.
Keywords: Bacteria detection; Microcytometer; Real-world samples; Food safety

Unraveling interactions in molecular crystals using dispersion corrected density functional theory : the case of the epoxydihydroarsanthrene molecules - Otero de la Roza, A.; Luana, Victor; Tiekink, Edward R. T.; Zukerman-Schpector, Julio (Journal of Chemical Theory and Computation, 2014)
Noncovalent interactions are prevalent in crystal packing and supramolecular chemistry. Directional noncovalent interactions such as donor-acceptor bonds (e.g., hydrogen, chalcogen, and pnictogen bonds) as well as nondirectional forces (such as dispersion) come together to stabilize supramolecular assemblies by striking a delicate energetic balance. Typically, a two-pronged approach employing experimental X-ray structures and gas phase quantum chemical modeling has been used to understand and design supramolecular architectures. Drawing from recent advances in molecular crystal modeling with dispersion corrected density functional theory (DFT), we propose in this article a combination of qualitative noncovalent index (NCI) analysis and periodic and gas phase DFT calculations on substitutional crystal analogues to unravel the dominant interactions in a particular crystal packing. We illustrate the possibilities of this approach by studying three crystal packings of epoxydihydroarsanthrene analogues that present a complex combination of donor-acceptor interactions including pnictogen-pnictogen, pnictogen-π, and pnictogen-chalcogen. We show that, in these crystals, the chalcogen-pnictogen interaction dominates over the pnictogen-pnictogen and pnictogen-π. In the latter, the role of donor and acceptor is reversed depending on the interacting moieties. Multiple chalcogen-pnictogen interactions necessitate larger donor atoms, such as sulfur. These observations explain and rationalize the experimentally observed crystal structures.

Improved catalytic reactor for the electrochemical promotion of highly dispersed Ru nanoparticles with CeO2 support - Dole, Holly A. E.; Safady, Luis F.; Ntais, Spyridon; Couillard, Martin; Baranova, Elena A. (ECS Transactions, 2014)
An improved design for a catalytic reactor for electrochemical promotion of highly dispersed catalysts was presented and compared to that of a plug flow-type reactor for the model reaction of ethylene oxidation. Electrochemical cells were prepared with low particle size (1.1 nm) Ru nanoparticles (RuNPs) which were supported on a mixed ionic-electronic conductor, CeO2, with a low metal loading (1 wt%), interfaced with a YSZ electrolyte. Comparable catalytic performance between the two reactors was observed for both open-circuits measurements. However, the rate enhancement ratio in the single-chamber capsule (SCC) reactor was found to be 1.6 compared to 1.4 for the plug flow-type reactor for an applied current of -5μA. These results were attributed to better electrical contact to the isolated RuNPs. Furthermore, the SCC reactor is simple to assemble and provides an intimate contact between the RuNPs/CeO2 catalyst and the current collector (i.e., gold mesh).
Keywords: Catalysts; Catalytic oxidation; Ethylene; Metal nanoparticles; Catalytic performance; Catalytic reactor; Current collector; Electrical contacts; Electrochemical promotion; Ethylene oxidation; Flow-type reactor; Mixed ionic-electronic conductors; Ruthenium

Genome wide SNP identification in chickpea for use in development of a high density genetic map and improvement of chickpea reference genome assembly - Deokar, Amit A.; Ramsay, Larissa; Sharpe, Andrew G.; Diapari, Marwan; Sindhu, Anoop; Bett, Kirsten; Warkentin, Thomas D.; Tar'an, Bunyamin (BMC Genomics, 2014)
Background: In the whole genome sequencing, genetic map provides an essential framework for accurate and efficient genome assembly and validation. The main objectives of this study were to develop a high-density genetic map using RAD-Seq (Restriction-site Associated DNA Sequencing) genotyping-by-sequencing (RAD-Seq GBS) and Illumina GoldenGate assays, and to examine the alignment of the current map with the kabuli chickpea genome assembly.Results: Genic single nucleotide polymorphisms (SNPs) totaling 51,632 SNPs were identified by 454 transcriptome sequencing of Cicer arietinum and Cicer reticulatum genotypes. Subsequently, an Illumina GoldenGate assay for 1,536 SNPs was developed. A total of 1,519 SNPs were successfully assayed across 92 recombinant inbred lines (RILs), of which 761 SNPs were polymorphic between the two parents. In addition, the next generation sequencing (NGS)-based GBS was applied to the same population generating 29,464 high quality SNPs. These SNPs were clustered into 626 recombination bins based on common segregation patterns. Data from the two approaches were used for the construction of a genetic map using a population derived from an intraspecific cross. The map consisted of 1,336 SNPs including 604 RAD recombination bins and 732 SNPs from Illumina GoldenGate assay. The map covered 653 cM of the chickpea genome with an average distance between adjacent markers of 0.5 cM. To date, this is the most extensive genetic map of chickpea using an intraspecific population. The alignment of the map with the CDC Frontier genome assembly revealed an overall conserved marker order; however, a few local inconsistencies within the Cicer arietinum pseudochromosome 1 (Ca1), Ca5 and Ca8 were detected. The map enabled the alignment of 215 unplaced scaffolds from the CDC Frontier draft genome assembly. The alignment also revealed varying degrees of recombination rates and hotspots across the chickpea genome. Conclusions: A high-density genetic map using RAD-Seq GBS and Illumina GoldenGate assay was developed and aligned with the existing kabuli chickpea draft genome sequence. The analysis revealed an overall conserved marker order, although some localized inversions between draft genome assembly and the genetic map were detected. The current analysis provides an insight of the recombination rates and hotspots across the chickpea genome.
Keywords: Cicer arietinum; Genotyping-by-sequencing; Illumina GoldenGate and Genetic mapping; Restriction site associated DNA (RAD) markers

Recent improvements of the NRC watt balance - Sanchez, C. A.; Wood, B. M. (2014 Conference on Precision Electromagnetic Measurements (CPEM 2014), 2014)
We describe the modifications and improvements that have been made over the past two years to reduce the uncertainty of the NRC watt balance.
Keywords: Electronic kilogram; Measurement uncertainty; Planck's constants; Watt balance

Electrochemically enhanced metal-support interaction of highly dispersed Ru nanoparticles with a CeO2 support - Dole, H. A. E.; Safady, L. F.; Ntais, S.; Couillard, M.; Baranova, E. A. (Journal of Catalysis, 2014)
Small particle size (1.1 nm) Ru nanoparticles were supported on a mixed ionic-electronic conductor, CeO2, with a low metal loading (1 wt%), interfaced with a YSZ electrolyte. A pronounced enhancement (up to about 2.5 times) of the catalytic rate for the complete oxidation of ethylene was observed for negative polarization. The opposite effect was observed for positive polarization. Apparent Faradaic efficiencies up to 96 were determined, indicating a non-Faradaic effect. The modification of the cerium oxidation state (i.e., reduction from Ce4+ to Ce3+) is proposed to enhance the catalytic performance of the Ru nanoparticles. XPS analysis was performed to confirm this reduction of ceria. The enhancement of catalytic activity is attributed to the presence of more oxygen vacancies in the ceria interlayer causing a stronger metal-support interaction. Results demonstrate the feasibility of in-situ modification of the metal support-interaction between Ru nanoparticles and CeO2 catalytic support by a small current (-2 μA) application.
Keywords: Catalyst activity; Catalytic oxidation; Cerium compounds; Ethylene; Metal nanoparticles; Metals; Oxidation; Polarization; Reduction; Yttria stabilized zirconia; Catalytic performance; Electrochemical promotion; Ethylene oxidation; Faradaic efficiencies; Metal-support interactions; Mixed ionic-electronic conductors; Negative polarization; Ru nanoparticles; Ruthenium

Symbiosis with Frankia sp. Benefits the establishment of Alnus viridis ssp. Crispa and Alnus incana ssp. Rugosa in tailings sand from the Canadian oil sands industry - Bissonnette, C.; Fahlman, B.; Peru, K. M.; Khasa, D. P.; Greer, C. W.; Headley, J. V.; Roy, S. (Ecological Engineering, 2014)
Canada's oil sands reserves found in an area of about 142,000km2 in Northern Alberta are estimated to be about 170 billion barrels. Extraction procedures generates oil sands process-affected materials (OSPM), a high pH, high salt and low nutrient residue which contains phytotoxic hydrocarbons. Efficient methods are needed to revegetate impacted landscapes in line with governmental standards. Actinorhizal alders could be used to provide nitrogen in a reclamation program as they are early successional species that naturally colonize harsh habitats and improve the soil conditions. In order to evaluate the extent to which alders can withstand OSPM-generated stress, the growth and development of both green (Alnus viridis (Chaix) DC. ssp. crispa) and speckled (Alnus incana (L.) Moench ssp. rugosa) alders in varying proportions of OSPM mixed with pristine sand (from 0 to 100%) was assessed both in the presence and the absence of their symbiont, Frankia sp. Alder survival was not impaired by the presence of OSPM, although symbiosis establishment was less efficient when the alders grew in pure OSPM residue. Actinorhizal alders are very tolerant to OSPM: when grown in pure OSPM (100%), their dry biomass was 15 times greater than that of non-nodulated alders. Moreover, symbiotic alders allocated a higher proportion of their biomass to aerial parts, regardless of the OSPM percentage, whereas non-symbiotic alders showed a greater biomass investment in roots. When symbiosis was present, the alders thrived and produced a large amount of biomass that was highly correlated to the total nodule biomass. The pre-inoculation of alder seedlings in commercial greenhouses prior to their outplanting on OSPM-affected reclamation sites could significantly accelerate their growth and development.
Keywords: Actinorhizal symbiosis; Alder; Early-successional; Extraction procedure; Frankia; Naphthenic acid; Oil sands industry; bacterium; biomass allocation; ecological engineering; growth rate; host-symbiont interaction; inoculation; reclaimed land; restoration ecology; revegetation; root system; symbiosis; tailings

Histological assessment of angiogenesis in the hypoxic central nervous system - Freitas-Andrade, Moises; Slinn, Jacqueline; Charlebois, Claudie; Moreno, Maria J. (Methods in Molecular Biology, 2014)
Angiogenesis, the sprouting of new capillaries from preexisting vessels, is an integral part of both normal development and numerous pathological conditions such as tumor growth, inflammation, and stroke. The development of angiogenesis assays has been critical in understanding this process in both the context of disease and normal physiology. With the growing availability of antibodies against angiogenic markers as well as advances in microscopy and imaging analysis software, a more comprehensive assessment of the angiogenesis process is beginning to take form (Milner et al., Stroke 39:191-197, 2008; Freitas-Andrade et al., J Cereb Blood Flow Metab 32:663-675, 2012; Li et al., Glia 58:1157-1167, 2010; Dore-Duffy and LaManna, Antioxid Redox Signal 9:1363-1371, 2007). This chapter describes an in vivo method of inducing brain angiogenesis in mice by chronic exposure to mild hypoxia. In addition, a detailed procedure of quantifying angiogenesis using multiple immunofluorescent labeling of mouse brain tissue sections is also presented.
Keywords: angiogenesis; animal cell; animal tissue; antibody labeling; brain tissue; central nervous system; confocal laser scanning microscope; controlled study; female; fluorescence; hypoxia; image analysis; immunofluorescence; in vivo study; mouse; quantitative analysis; tissue section; Brain; Cell Hypoxia; Cerebrovascular Circulation; Cryoultramicrotomy; Fluorescent Antibody Technique, Indirect; Mice; Microscopy, Fluorescence; Neovascularization, Physiologic