bluuebunny/crossref_metadata_2025 huggingface dataset:
Single-conformation infrared spectra of model peptides in the amide I and amide II regions: Experiment-based determination of local mode frequencies and inter-mode coupling
Authors: Buchanan Evan G. , James William H. , Choi Soo Hyuk , Guo Li , Gellman Samuel H. , Müller Christian W. , Zwier Timothy S.
Published: September 2012

Single-conformation infrared spectra in the amide I and amide II regions have been recorded for a total of 34 conformations of three α-peptides, three β-peptides, four α/β-peptides, and one γ-peptide using resonant ion-dip infrared spectroscopy of the jet-cooled, isolated molecules. Assignments based on the amide NH stretch region were in hand, with the amide I/II data providing additional evidence in favor of the assignments. A set of 21 conformations that represent the full range of H-bonded structures were chosen to characterize the conformational dependence of the vibrational frequencies and infrared intensities of the local amide I and amide II modes and their amide I/I and amide II/II coupling constants. Scaled, harmonic calculations at the DFT M05-2X/6-31+G(d) level of theory accurately reproduce the experimental frequencies and infrared intensities in both the amide I and amide II regions. In the amide I region, Hessian reconstruction was used to extract local mode frequencies and amide I/I coupling constants for each conformation. These local amide I frequencies are in excellent agreement with those predicted by DFT calculations on the corresponding 13C = 18O isotopologues. In the amide II region, potential energy distribution analysis was combined with the Hessian reconstruction scheme to extract local amide II frequencies and amide II/II coupling constants. The agreement between these local amide II frequencies and those obtained from DFT calculations on the N–D isotopologues is slightly worse than for the corresponding comparison in the amide I region. The local mode frequencies in both regions are dictated by a combination of the direct H-bonding environment and indirect, “backside” H-bonds to the same amide group. More importantly, the sign and magnitude of the inter-amide coupling constants in both the amide I and amide II regions is shown to be characteristic of the size of the H-bonded ring linking the two amide groups. These amide I/I and amide II/II coupling constants remain similar in size for α-, β-, and γ-peptides despite the increasing number of C–C bonds separating the amide groups. These findings provide a simple, unifying picture for future attempts to base the calculation of both nearest-neighbor and next-nearest-neighbor coupling constants on a joint footing.
The effect of aqueous solutions of trimethylamine-N-oxide on pressure induced modifications of hydrophobic interactions
Authors: Sarma Rahul , Paul Sandip
Published: September 2012

To understand the mechanism of protein protection by the osmolyte trimethylamine-N-oxide (TMAO) at high pressure, using molecular dynamics (MD) simulations, solvation of hydrophobic group is probed in aqueous solutions of TMAO over a wide range of pressures relevant to protein denaturation. The hydrophobic solute considered in this study is neopentane which is a considerably large molecule. The concentrations of TMAO range from 0 to 4 M and for each TMAO concentration, simulations are performed at five different pressures ranging from 1 atm to 8000 atm. Potentials of mean force are calculated and the relative stability of solvent-separated state over the associated state of hydrophobic solute are estimated. Results suggest that high pressure reduces association of hydrophobic solutes. From computations of site-site radial distribution function followed by analysis of coordination number, it is found that water molecules are tightly packed around the nonpolar particle at high pressure and the hydration number increases with increasing pressure. On the other hand, neopentane interacts preferentially with TMAO over water and although hydration of neopentane reduces in presence of this osmolyte, TMAO does not show any tendency to prevent the pressure-induced dispersion of neopentane moieties. It is also observed that TMAO molecules prefer a side-on orientation near the neopentane surface, allowing its oxygen atom to form favorable hydrogen bonds with water while maintaining some hydrophobic contacts with neopentane. Analysis of hydrogen-bond properties and solvation characteristics of TMAO reveals that TMAO can form hydrogen bonds with water and it reduces the identical nearest neighbor water molecules caused by high hydrostatic pressures. Moreover, TMAO enhances life-time of water–water hydrogen bonds and makes these hydrogen bonds more attractive. Implication of these results for counteracting effect of TMAO against protein denaturation at high pressures are discussed.
Consistent schemes for non-adiabatic dynamics derived from partial linearized density matrix propagation
Authors: Huo Pengfei , Coker David F.
Published: September 2012

Powerful approximate methods for propagating the density matrix of complex systems that are conveniently described in terms of electronic subsystem states and nuclear degrees of freedom have recently been developed that involve linearizing the density matrix propagator in the difference between the forward and backward paths of the nuclear degrees of freedom while keeping the interference effects between the different forward and backward paths of the electronic subsystem described in terms of the mapping Hamiltonian formalism and semi-classical mechanics. Here we demonstrate that different approaches to developing the linearized approximation to the density matrix propagator can yield a mean-field like approximate propagator in which the nuclear variables evolve classically subject to Ehrenfest-like forces that involve an average over quantum subsystem states, and by adopting an alternative approach to linearizing we obtain an algorithm that involves classical like nuclear dynamics influenced by a quantum subsystem state dependent force reminiscent of trajectory surface hopping methods. We show how these different short time approximations can be implemented iteratively to achieve accurate, stable long time propagation and explore their implementation in different representations. The merits of the different approximate quantum dynamics methods that are thus consistently derived from the density matrix propagator starting point and different partial linearization approximations are explored in various model system studies of multi-state scattering problems and dissipative non-adiabatic relaxation in condensed phase environments that demonstrate the capabilities of these different types of approximations for treating non-adiabatic electronic relaxation, bifurcation of nuclear distributions, and the passage from nonequilibrium coherent dynamics at short times to long time thermal equilibration in the presence of a model dissipative environment.
Overlapping resonances interference-induced transparency: The S → S2/S1 photoexcitation spectrum of pyrazine
Authors: Grinev Timur , Shapiro Moshe , Brumer Paul
Published: September 2012

The phenomenon of “overlapping resonances interference-induced transparency” (ORIT) is introduced and studied in detail for the S0 → S2/S1 photoexcitation of cold pyrazine (C4H4N2). In ORIT, a molecule becomes transparent at specific wavelengths due to interferences between envelopes of spectral lines displaying overlapping resonances. An example is the S2 ↔ S1 internal conversion in pyrazine where destructive interference between overlapping resonances causes the S0 → S2/S1 light absorption to disappear at certain wavelengths. ORIT may be of practical importance in multi-component mixtures where it would allow for the selective excitation of some molecules in preference to others. Interference-induced cross section enhancement is also shown.
Optical transition radiation used in the diagnostic of low energy and low current electron beams in particle accelerators
Authors: Silva T. F. , Bonini A. L. , Lima R. R. , Maidana N. L. , Malafronte A. A. , Pascholati P. R. , Vanin V. R. , Martins M. N.
Published: September 2012

Optical transition radiation (OTR) plays an important role in beam diagnostics for high energy particle accelerators. Its linear intensity with beam current is a great advantage as compared to fluorescent screens, which are subject to saturation. Moreover, the measurement of the angular distribution of the emitted radiation enables the determination of many beam parameters in a single observation point. However, few works deals with the application of OTR to monitor low energy beams. In this work we describe the design of an OTR based beam monitor used to measure the transverse beam charge distribution of the 1.9-MeV electron beam of the linac injector of the IFUSP microtron using a standard vision machine camera. The average beam current in pulsed operation mode is of the order of tens of nano-Amps. Low energy and low beam current make OTR observation difficult. To improve sensitivity, the beam incidence angle on the target was chosen to maximize the photon flux in the camera field-of-view. Measurements that assess OTR observation (linearity with beam current, polarization, and spectrum shape) are presented, as well as a typical 1.9-MeV electron beam charge distribution obtained from OTR. Some aspects of emittance measurement using this device are also discussed.
Particle size and density of a slurry from ultrasonic backscattering measurements at a solid interface
Authors: Greenwood Margaret Stautberg
Published: September 2012

The pivotal experiment was performed with a setup in which a plastic cylinder was mounted on the top of a horizontal Rexolite plate and a transducer mounted directly below the cylinder; a single layer of stationary 1588-μm acrylic spheres was placed in the cylinder filled with water. Two well-separated signals were received by the transducer operating in the pulse-echo mode: (1) a signal due to the reflection from water at the interface and (2) a time-delayed signal resulting from the backscattering from the spheres of diameter D. The important observation was that the time delay was equal to 2 D/c using standard notation. A method was developed to use the FFT phase difference between the incident and scattered signals at the interface to determine the time-delay as a function of frequency, the backscattering coefficient M versus frequency, a particle size distribution, and an average value of the diameter. Experimental average diameter results are shown in the square brackets for nominal particle sizes: (1) 1588-μm acrylic spheres [1564 μm], (2) polystyrene spheres for diameters from 200 μm to 500 μm [260 μm–536 μm], (3) suspended slurry of 250–300 μm polystyrene spheres at 2.25 MHz [253 μm], (4) 794 μm [759 μm] and 1588-μm [1623 μm] Teflon spheres, (5) 1588-μm stainless steel spheres [1674 μm], and (6) suspended slurry of 250–300 μm polystyrene spheres [275 μm] at 3.5 MHz for seven volume fractions. Density and particle size measurements were obtained for the latter. For the density measurement, the FFT amplitude of the scattered signal was summed from 2 to 4 MHz for each slurry. A plot of the square root of the FFT-amplitude-sum versus the volume fraction yields a straight line, passing through the origin. A calibration of the experimental setup is obtained by fitting a straight line through the data with error bars. Thus, the volume fraction for a slurry of unknown concentration can be determined by measuring the FFT-amplitude-sum. The density of the slurry is obtained from the volume fraction. These results make it feasible to develop an online and real-time pipeline sensor to measure particle size and slurry density.
Broadband ultrasonic linear array using ternary PIN-PMN-PT single crystal
Authors: Wang Wei , Zhao Xiangyong , Or Siu Wing , Ming Leung Chung , Zhang Yaoyao , Jiao Jie , Luo Haosu
Published: September 2012

Ternary Pb(In1/2Nb1/2)O3-Pb(Mg1/3Nb2/3)O3-PbTiO3 (PIN-PMN-PT) single crystal was investigated for potential application in ultrasonic linear array. Orientation and temperature dependences of height extensional electromechanical coupling coefficient k′33 for PIN-PMN-PT single crystal were studied. It was found that the [001] poled PIN-PMN-PT diced along the [100] direction would achieve a maximum k′33 (∼87%) and the service temperature was up to 110 °C. Ultrasonic linear arrays using PIN-PMN-PT single crystal and PZT ceramic were fabricated and compared. The bandwidth at −6 dB, two-way insertion loss and pulse length of the PIN-PMN-PT array were 98.6%, −45.1 dB, and 0.28 μs, respectively, which were about 25% broader, 3.7dB higher, and 0.08 μs shorter than those of the PZT array. The experimental results agreed well with the theoretical simulation. These superior performances were attributable to the excellent piezoelectric properties of PIN-PMN-PT single crystal.
Photopatternable nano-composite (SU-8/ZnO) thin films for piezo-electric applications
Authors: Kandpal Manoj , Sharan Chandrashekhar , Poddar Pankaj , Prashanthi K. , Apte Prakash R. , Ramgopal Rao V.
Published: September 2012

Photo-curable nanocomposite material was formulated by embedding ZnO nanoparticles into a SU-8 matrix and studied for its piezoelectric properties for low cost fabrication of self-powered nanodevices. The piezoelectric coefficient of ZnO nanoparticles was observed to be ranging between 15 and 23 pm/V, which is the highest reported. These experimental studies support the recent theoretical predictions where the piezoelectric coefficients in ZnO nanoparticles were found to be higher compared to the thin films because of the surface relaxation induced volume reductions in the nanometer scale. The photo-curable property of these polymer composite films is exploited to demonstrate fabrication of a micro-cantilever test structure.
Stable highly conductive ZnO via reduction of Zn vacancies
Authors: Look D. C. , Droubay T. C. , Chambers S. A.
Published: September 2012

Growth of Ga-doped ZnO by pulsed laser deposition at 200 °C in an ambient of Ar and H2 produces a resistivity of 1.5 × 10−4 Ω-cm, stable to 500 °C. The resistivity can be further reduced to 1.2 × 10−4 Ω-cm by annealing on Zn foil, which reduces the compensating Zn-vacancy acceptor concentration NA to 5 × 1019 cm−3, only 3% of the Ga-donor concentration ND of 1.6 × 1021 cm−3, with ND and NA determined from a degenerate mobility theory. The plasmon-resonance wavelength is only 1060 nm, further bridging the gap between metals and semiconductors.
Numerical modeling of flow control on a symmetric aerofoil via a porous, compliant coating
Authors: Venkataraman Divya , Bottaro Alessandro
Published: September 2012

A passive actuation technique, that entails covering the suction side of an aerofoil with a poro-elastic carpet, is presented. Numerical modeling of the coupled fluid-structure interaction problem is performed for a low Reynolds number regime, characteristic of micro aerial vehicles. The immersed boundary technique is employed, which offers the advantage of using Cartesian grids for complex geometries. By suitably selecting the characteristics of the carpet, to synchronise characteristic time scales of the fluid and the structural systems, significant drag reduction and/or lift enhancement can be achieved, associated with modifications of the length scales of the shed vortices and a mild intensification of their intensity. A parametric analysis shows that such a coating is able to affect the topology of the flow in the proximity of the rear of the aerofoil, by adapting spontaneously to the separated flow.
Carrier control and transport modulation in GaSb/InAsSb core/shell nanowires
Authors: Ganjipour Bahram , Ek Martin , Mattias Borg B. , Dick Kimberly A. , Pistol Mats-Erik , Wernersson Lars-Erik , Thelander Claes
Published: September 2012

We report transport studies of GaSb/InAs core/shell nanowires. It is shown that with increasing InAs shell thickness, it is possible to tune the carrier concentrations and transport in the structures from p-type (core-dominated) to n-type (shell dominated). For nanowires with an intermediate shell thickness (5–7 nm), we show that the transport is ambipolar, such that an applied top-gate potential can provide further control of carrier type and transport path. In this range, the nature of the GaSb-InAs junction also changes from broken gap (semimetal) to staggered (narrow bandgap) with a small decrease in shell thickness. From a device point of view, we demonstrate that the presence of a thin (<3 nm) InAs shell improves p-type GaSb nanowire transistor characteristics.
Acoustophoretic microfluidic chip for sequential elution of surface bound molecules from beads or cells
Authors: Augustsson Per , Malm Johan , Ekström Simon
Published: September 2012

An acoustophoresis-based microfluidic flow-chip is presented as a novel platform to facilitate analysis of proteins and peptides loosely bound to the surface of beads or cells. The chip allows for direct removal of the background surrounding the beads or cells, followed by sequential treatment and collection of a sequence of up to five different buffer conditions. During this treatment, the beads/cells are retained in a single flow by acoustic radiation force. Eluted peptides are collected from the outlets and subsequently purified by miniaturized solid-phase extraction and analyzed with matrix assisted laser desorption mass spectrometry. Fundamental parameters such as the system fluidics and dispersion are presented. The device was successfully applied for wash and sequential elution of peptides bound to the surface of microbeads and human spermatozoa, respectively.
Photonic assisted light trapping integrated in ultrathin crystalline silicon solar cells by nanoimprint lithography
Authors: Trompoukis Christos , El Daif Ounsi , Depauw Valérie , Gordon Ivan , Poortmans Jef
Published: September 2012

We report on the fabrication of two-dimensional periodic photonic nanostructures by nanoimprint lithography and dry etching and their integration into a 1-μm-thin mono-crystalline silicon solar cell. Thanks to the periodic nanopatterning, a better in-coupling and trapping of light is achieved, resulting in an absorption enhancement. The proposed light trapping mechanism can be explained as the superposition of a graded index effect and of the diffraction of light inside the photoactive layer. The absorption enhancement is translated into a 23% increase in short-circuit current, as compared to the benchmark cell, resulting in an increase in energy-conversion efficiency.
A few-electron quadruple quantum dot in a closed loop
Authors: Thalineau Romain , Hermelin Sylvain , Wieck Andreas D. , Bäuerle Christopher , Saminadayar Laurent , Meunier Tristan
Published: September 2012

We report the realization of a quadruple quantum dot device in a square-like configuration where a single electron can be transferred on a closed path free of other electrons. By studying the stability diagrams of this system, we demonstrate that we are able to reach the few-electron regime and to control the electronic population of each quantum dot with gate voltages. This allows us to control the transfer of a single electron on a closed path inside the quadruple dot system. This work opens the route towards electron spin manipulation using spin-orbit interaction by moving an electron on complex paths free of electrons.
Minimizing reflection losses from metallic electrodes and enhancing photovoltaic performance using the Si-micrograting solar cell with vertical sidewall electrodes
Authors: Yang Tien-Chung , Lee Bi-Shen , Yen Ta-Jen
Published: September 2012

Researchers have focused on the development of Si nano- or micro-structured solar cells (SCs) because of their enhanced optical absorption properties and their ability to decouple minority carrier diffusion and light absorption paths. We adopt a low-cost method to monolithically fabricate Si-micrograting SC (SiMG-SC) with vertical sidewall electrodes and a vertical multi-junction, which minimizes the reflection losses from conventional planar metallic electrodes and increases the minority carrier collection probability. We consequently intensified the photovoltaic properties, i.e., the current density, fill factor, and power conversion efficiency, by 11.2%, 23.7%, and 52.9%, respectively, compared to those of the control SCs.
The role of structural properties on deep defect states in Cu2ZnSnS4 studied by photoluminescence spectroscopy
Authors: Grossberg M. , Krustok J. , Raudoja J. , Raadik T.
Published: September 2012

In this study, we investigated the photoluminescence (PL) properties of Cu2ZnSnS4 polycrystals. Two PL bands at 1.27 eV and 1.35 eV at T = 10 K were detected. Similar behaviour with temperature and excitation power was found for both PL bands and attributed to the band-to-impurity recombination. Interestingly, the thermal activation energies determined from the temperature dependence of the PL bands coincide. With the support of the Raman results, we propose that the observed PL bands arise from the band-to-impurity-recombination process involving the same deep acceptor defect with ionization energy of around 280 meV but different Cu2ZnSnS4 phase with different bandgap energy.
Laser Doppler velocimetry based on the optoacoustic effect in a RF-excited CO2 laser
Authors: Lee Teaghee , Choi Jong Woon , Kim Yong Pyung
Published: September 2012

We present a compact optoacoustic laser Doppler velocimetry method that utilizes the self-mixing effect in a RF-excited CO2 laser. A portion of a Doppler-shifted laser beam, produced by irradiating a single wavelength laser beam on a moving object, is mixed with an originally existing laser beam inside a laser cavity. The fine change of pressure in the laser cavity modulated by the Doppler-shifted frequency is detected by a condenser microphone in the laser tube. In our studies, the frequency of the Doppler signal due to the optoacoustic effect was detected as high as 50 kHz. Our measurements also confirmed that the signal varied linearly with the velocity of the external scatterer (the moving object) and the cosine of the angle between the laser beam and the velocity vector of the object.
Effects of wild-type, AR1 and AR37 endophyte-infected perennial ryegrass on dairy production in Victoria, Australia
Authors: Moate P. J. , Williams S. R. O. , Grainger C. , Hannah M. C. , Mapleson D. , Auldist M. J. , Greenwood J. S. , Popay A. J. , Hume D. E. , Mace W. J. , Wales W. J.
Published: September 2012

A 3-year experiment compared the effects of wild-type ryegrass endophyte and two novel endophytes on milk production in dairy cattle. On three 9.9-ha farmlets in West Gippsland, Victoria, pasture swards were established that were dominant in perennial ryegrass (Lolium perenne) infected with either wild-type, AR1 or AR37 endophytes. Each farmlet was stocked with 25 spring-calving Holstein–Friesian cows, which rotationally grazed nine paddocks within their farmlet during three lactations over 3 years. The three endophytes are known to produce different alkaloids, with wild-type producing ergot alkaloids, lolitrems and peramine, AR1 producing peramine and AR37 producing epoxy-janthitrems. These alkaloids were present in fresh pasture as well as hay and silage made from that pasture. Grazed pasture comprised 53% of estimated annual DM intake. The proportion was least from December to March when the daily ration of 2 kg DM/cow.day cereal grain was increased to 6 kg/day and forage supplements were fed consisting of purchased lucerne (Medicago sativa) hay and pasture silage grown on the farmlets. There were no differences in pasture accumulation rates or nutritive characteristics of ryegrass pastures on the three farmlets and no differences in the production of milk, fat or protein by cows grazing pasture infected with the three endophytes. Ryegrass staggers was only observed in four cows consuming the wild-type-infected ryegrass in the first year when the highest concentrations of lolitrem B were recorded in pasture. Soil samples showed lower numbers of root aphids (Aploneura lentisci), mealybugs (Pseudococcidae) and pasture tunnel moths (Philobota spp.) beneath ryegrass infected with the AR37 endophyte compared with the other two endophytes. Numbers of redheaded (Adoryphorus couloni) and blackheaded (Aphodius tasmaniae) cockchafers did not differ between treatments. Under dairy management and supplementary feeding regimes common to south-eastern Australia, the novel endophytes AR1 and AR37 had no effect on the milk production compared with the wild-type endophyte, and did not cause ryegrass staggers.
Extreme weather-related health needs of people who are homeless
Authors: Cusack Lynette , van Loon Antonia , Kralik Debbie , Arbon Paul , Gilbert Sandy
Published: September 2012

To identify the extreme weather-related health needs of homeless people and the response by homeless service providers in Adelaide, South Australia, a five-phased qualitative interpretive study was undertaken. (1) Literature review, followed by semi-structured interviews with 25 homeless people to ascertain health needs during extreme weather events. (2) Identification of homeless services. (3) Semi-structured interviews with 16 homeless service providers regarding their response to the health needs of homeless people at times of extreme weather. (4) Gap analysis. (5) Suggestions for policy and planning. People experiencing homelessness describe adverse health impacts more from extreme cold, than extreme hot weather. They considered their health suffered more, because of wet bedding, clothes and shoes. They felt more depressed and less able to keep themselves well during cold, wet winters. However, homeless service providers were more focussed on planning for extra service responses during times of extreme heat rather than extreme cold. Even though a city may be considered to have a temperate climate with a history of very hot summers, primary homeless populations have health needs during winter months. The experiences and needs of homeless people should be considered in extreme weather policy and when planning responses.
Values and love styles in Turkey and Great Britain: An intercultural and intracultural comparison
Authors: Sanrı Çağla , Goodwin Robin
Published: September 2012

Little previous research has examined the relationship between values and love styles, and none has done so across cultures or intracultural regions. This research was the first attempt to explore the correlation between individual‐level values and love styles, and examined both within‐ and between‐cultural variations in love styles. In this study 224 participants from Turkey and Britain, from urban or rural locations, completed the Portrait Values Questionnaire and the Love Attitudes Scale measure of love styles. Pancultural analyses demonstrated significant correlations between certain value dimensions and love styles. In particular, agape (selfless love) was positively correlated with self‐transcendence, ludus (game‐playing love) was positively correlated with self‐enhancement, and pragma (realistic love) was positively correlated with conservation. The inclusion of location and nationality and their interactions with values in the multiple regression analyses significantly increased the variance explained by values for five of the six love styles. Multivariate analyses indicated that ludus, storge, mania, and pragma were all significantly higher among Turkish respondents; pragma, mania, and agape all higher amongst rural respondents. Eros was highest among rural British respondents; storge, pragma, and agape highest among rural Turks. When these culture effects were explored, conservation significantly mediated the relationship between the groups of more conservative rural Turks (versus other participants) and both pragmatic and storgic love styles. Findings are discussed in the light of disparities in values and relationship styles within cultures, and the need to include both intracultural and intercultural variations in cross cultural research.
Effects of Diets with 28% or 32% Protein and Meat and Bone Meal or Corn Gluten Feed on Performance of Golden Shiners in Pools
Authors: Lochmann R T , Phillips H
Published: September 2012

Alternative diets made without marine proteins and with more plant ingredients are being used in channel catfish Ictalurus punctatus with the goal of maintaining profitability. The potential to use similar diets for baitfish may be greater because they consume natural foods throughout production. We conducted a feeding trial in outdoor pools with golden shiners Notemigonus crysoleucas using four practical diets with 28% or 32% protein in formulas with porcine meat and bone meal (MBM) or corn gluten feed (CGF) and no animal protein. Groups of 200 fish with a total initial weight of 37.7 ± 0.9 g (mean ± SE) were stocked into each of four 4.1-m3static pools per treatment and fed daily to apparent satiation for 8 weeks. Diet effects were assessed by measuring growth, survival, feed conversion, condition index, and body composition. Chlorophyll a and zooplankton were sampled to gauge natural productivity. Individual weight and total length of golden shiners were greater in fish fed diets with 32% protein than in those fed diets with 28% protein and in fish fed diets with CGF than in those fed diets with MBM. However, the differences were not commercially relevant as all fish would grade into the “small crappie minnow” category. Mean individual weight gain (based on group initial and final weights), feed intake, feed conversion, and survival were similar in golden shiners fed diets with 28% or 32% protein and MBM or CGF. However, golden shiners fed diets with MBM had more body fat, higher Fulton's K index, and higher relative weight than those fed diets with CGF. These traits may indicate greater robustness, which is more important in baitfish than rapid growth. The 28%-protein diet with MBM was the least expensive option that increased body fat and condition of golden shiners. Natural productivity was positively correlated with fish growth, enhancing the potential to use less expensive diets in golden shiners in outdoor systems.
Koi ×Goldfish Hybrid Females Produce Triploid Progeny when Backcrossed to Koi Males
Authors: Gomelsky Boris , Schneider Kyle J , Plouffe Debbie A
Published: September 2012

Hybrids of koi (an ornamental variant of the common carp Cyprinus carpio) and goldfish Carassius auratus auratus were produced by artificial spawning. All 3-year-old F1 hybrid males examined were sterile, whereas some F1 hybrid females were fertile and produced eggs after hormonal injection. Backcross progeny were obtained by using intact koi sperm to inseminate eggs from F1 hybrid females; gynogenetic progeny were obtained by inseminating eggs from F1 hybrid females with koi sperm that was genetically inactivated by ultraviolet irradiation. Flow cytometric analysis of DNA content indicated that the backcross progeny were triploid, while the gynogenetic progeny, pure koi, pure goldfish, and F1 hybrids were all diploid. The triploidy of backcross progeny obtained without application of any treatment to the eggs demonstrates that the koi × goldfish hybrid females produce diploid eggs.
An Ultrastructure Study of Diet-Related Changes in Epithelial Tissue of Hybrid Striped Bass Larvae
Authors: Gallagher Margie L
Published: September 2012

This study characterized the ultrastructure of normal epidermal and gastrointestinal epithelial cells of larval hybrid striped bass (white bass Morone chrysops × striped bass M. saxatilis) that were fed live prey (brine shrimp Artemia spp. nauplii) or an artificial dry diet. Scanning electron microscopy of larvae that were given live feed revealed normal epidermal cells with microridge structures and proliferation of neuromasts along the lateral line. Cell junctions had double microridge structures. Transmission electron microscopy of the gut showed keratinized epithelial cells with underlying mucous cells in the foregut, while the midgut was characterized by columnar epithelial cells with extensive pinocytotic activity. The hindgut had columnar epithelial cells with centrally located nuclei, regularly spaced microvilli, and numerous tubular mitochondria surrounded by rough endoplasmic reticulum. Larvae that received live feed reached metamorphosis by 27 d posthatch (dph), and clearly identifiable gastric glands were present. Larvae that were given the artificial diet did not develop; both epidermal and gastrointestinal cells showed apparent osmotic stress by 10 dph, and the condition worsened through 24 dph. Stress was indicated by loss of microridges in epidermal cells and eventual necrosis. Increased keratinization and reduced pinocytotic activity were observed in midgut cells, whereas hindgut epithelial cells showed dissociation of the rough endoplasmic reticulum and reduced numbers of mitochondria. However, tight cell junctions, desmosomes, and double microridges at cell junctions persisted.
TRAF-interacting protein (TRIP) negatively regulates IFN-β production and antiviral response by promoting proteasomal degradation of TANK-binding kinase 1
Authors: Zhang Meng , Wang Lijuan , Zhao Xueying , Zhao Kai , Meng Hong , Zhao Wei , Gao Chengjiang
Published: September 2012

TANK-binding kinase 1 (TBK1) plays an essential role in Toll-like receptor (TLR)– and retinoic acid–inducible gene I (RIG-I)–mediated induction of type I interferon (IFN; IFN-α/β) and host antiviral responses. How TBK1 activity is negatively regulated remains largely unknown. We report that TNF receptor-associated factor (TRAF)–interacting protein (TRIP) promotes proteasomal degradation of TBK1 and inhibits TLR3/4- and RIG-I–induced IFN-β signaling. TRIP knockdown resulted in augmented activation of IFN regulatory factor 3 (IRF3) and enhanced expression of IFN-β in TLR3/4- and RIG-I–activated primary peritoneal macrophages, whereas overexpression of TRIP had opposite effects. Consistently, TRIP impaired Sendai virus (SeV) infection–induced IRF3 activation and IFN-β production and promoted vesicular stomatitis virus (VSV) replication. As an E3 ubiquitin ligase, TRIP negatively regulated the cellular levels of TBK1 by directly binding to and promoting K48-linked polyubiquitination of TBK1. Therefore, we identified TRIP as a negative regulator in TLR3/4- and RIG-I–triggered antiviral responses and suggested TRIP as a potential target for the intervention of diseases with uncontrolled IFN-β production.
Reduced TCR signaling potential impairs negative selection but does not result in autoimmune disease
Authors: Hwang SuJin , Song Ki-Duk , Lesourne Renaud , Lee Jan , Pinkhasov Julia , Li LiQi , El-Khoury Dalal , Love Paul E.
Published: September 2012

Negative selection and regulatory T (T reg) cell development are two thymus-dependent processes necessary for the enforcement of self-tolerance, and both require high-affinity interactions between the T cell receptor (TCR) and self-ligands. However, it remains unclear if they are similarly impacted by alterations in TCR signaling potential. We generated a knock-in allele (6F) of the TCR ζ chain gene encoding a mutant protein lacking signaling capability whose expression is controlled by endogenous ζ regulatory sequences. Although negative selection was defective in 6F/6F mice, leading to the survival of autoreactive T cells, 6F/6F mice did not develop autoimmune disease. We found that 6F/6F mice generated increased numbers of thymus-derived T reg cells. We show that attenuation of TCR signaling potential selectively impacts downstream signaling responses and that this differential effect favors Foxp3 expression and T reg cell lineage commitment. These results identify a potential compensatory pathway for the enforcement of immune tolerance in response to defective negative selection caused by reduced TCR signaling capability.
Evidence of weak plasma series resonance heating in the H-mode of neon and neon/argon inductively coupled plasmas
Authors: Boffard John B , Jung R O , Lin Chun C , Aneskavich L E , Wendt A E
Published: September 2012

Phase-resolved optical emission spectroscopy measurements in argon and neon inductively coupled plasmas (ICPs) have revealed a surplus of high-energy electrons in neon-containing plasmas. Differences between results of emission model analyses using neon and argon lines (as well as probe measurements) also indicate a high-energy enhancement in neon-containing plasmas. The abundance of these extra high-energy electrons is correlated with the sheath thickness near the rf antenna and can be reduced by either adding a Faraday shield (external shielding) or increasing the plasma density. A comparison of modelled and experimental values of the 13.56 MHz time modulation of select neon emission lines strongly suggests plasma series resonance heating adjacent to the ICP antenna as the source of the extra heating.
Interaction of the dual effects triggered by AlN interlayers in thick GaN grown on 3C-SiC/Si substrates
Authors: Fang H , Takaya Y , Miyake H , Hiramatsu K , Asamura H , Kawamura K
Published: September 2012

In this work, the stress distribution of a thick GaN layer, which was realized with multiple AlN interlayers (ILs) on a 3C-SiC/Si (1 1 1) substrate, was mapped by low-temperature cathodoluminescence spectroscopy. A relaxation of compressive stress was distinguished in the top GaN layers above the AlN ILs by the inhomogeneous luminescent property. Through cross-sectional transmission electron microscopy, misfit dislocations (MDs) transformed from threading dislocations were observed. Analysis confirmed that the transformation process of dislocations should account for a part of compressive stress relaxation. As a result, a trade-off between compressive stress induction and dislocation transformation effects, both of which were induced by the AlN ILs, was proposed. In this model, the mean length of MDs in the GaN/AlN multi-layer structure was evaluated as L = 84 nm.
An electrical detection of the fluctuating plasma of laser welding with a passive probe
Authors: Bi Chao , Yang Lijun , Xu Wenhao , Wang Langping
Published: September 2012

A laser-induced plasma is an important physical phenomenon that plays an important role in the laser welding process and the quality of the weld. The objective of this study is to obtain a fundamental knowledge of this physical process. A new detecting method of using a passive probe to detect the electric signals of the plasma plume is proposed and developed. This is demonstrated to be a feasible method for the measurement of electron temperature referring to the electron temperature calculated from the synchronous spectral signal. From an analysis of the wave patterns of the electric signal, the signal can reflect the eruption moment of the fluctuating plasma. The experimental results demonstrate that if the probe is placed appropriately, the designed electric probe can be used to reflect the real-time fluctuation of electron temperature of the generated plasma.
Effects of numerical and physical anisotropic diffusion on branching phenomena of negative-streamer dynamics
Authors: Eichwald O , Bensaad H , Ducasse O , Yousfi M
Published: September 2012

This paper is a contribution to the fluid modelling and simulation of the spontaneous branching of an initial mono-filamentary negative streamer propagating in molecular nitrogen at atmospheric pressure. The effects of both numerical diffusion and physical anisotropic diffusion on the branching structure are studied. We used MUSCL-type flux limiters where an artificial amount of numerical diffusion can be introduced through the choice of the value of a characteristic slope parameter. It was shown that a small amount of numerical diffusion can inhibit the spontaneous streamer branching. This means that the use of a high-order numerical scheme preventing the numerical diffusion and dispersion is a major parameter that must be taken into account in the interpretation of the simulated streamer development and splitting. This paper also clearly shows that the consideration of the anisotropy of electron diffusion affects the streamer head structure in comparison with the isotropic diffusion case. This especially occurs for electrons in gases presenting a large difference between the longitudinal and transversal diffusion coefficients as in N2 or in air.
Solar absorption and microstructure of C-doped and H-co-doped TiO2 thin films
Authors: Buha J
Published: September 2012

This work examined the effect of different levels of C doping on the microstructure and optical properties of TiO2 thin films consisting of mostly rutile and amorphous phases. The increase in the substitutional C doping from 0.32 to 8.57 at% was found to reduce the long-range order through the refinement of the crystalline phase, and increases in the concentration of the extended defects and fraction of the disordered phase, where C gets segregated due to its low solubility in the crystalline phase. As expected, the main absorption threshold red-shifted with the increase in C doping (from 3.22 to 2.48 eV) and additional thresholds existed in the visible and NIR ranges. However, at the same time only a small reduction in the separation between the extended states (by up to 0.27 eV) was achieved. The significant increase in the visible absorption originated mostly from the C-induced spread of localized states within the band gap. Higher levels of C doping introduce localized states deeper into the band gap, which may increase the carrier recombination as well. Co-doping with hydrogen nearly fills the band gap with localized states and further increases the visible and NIR absorption.
Effect of reoxidation annealing on the PTCR behaviour of multilayer Nb5+-doped BaTiO3 ceramics with a Ni internal electrode
Authors: Cheng Xuxin , Zhou Dongxiang , Fu Qiuyun , Gong Shuping , Qin Yuxiang
Published: September 2012

The effects of reoxidation annealing on the electrical properties and the positive temperature coefficient of resistance (PTCR) effects of multilayer Ba1.005(Ti1−x
Nb
x
)O3 (BTN) ceramics sintered at different temperatures from 1100 to 1160 °C for 2 h in a reducing atmosphere and reoxidized at various temperatures in the range 500–900 °C were investigated. The results indicated that the room-temperature (RT) resistance of the BTN ceramics reoxidized at different temperatures first increased slowly and then quickly with the increase in the reoxidation temperature. Meanwhile, the resistance jump of the samples increased first and then decreased with the increase in the reoxidation temperature. In addition, the PTCR effect could be improved by prolonging the reoxidation time. Finally, the samples reoxidized at a low temperature of 600 °C after sintering at 1160 °C in a reducing atmosphere exhibited a significant PTCR effect, with a resistance jump of 3.5 orders of magnitude, along with a low RT resistance of 0.38 Ω. Additionally, the influences of the reoxidation temperature and time on the grain resistance and grain-boundary resistance were investigated using complex-impedance spectroscopy.
Surface plasmons in metallic nanoparticles: fundamentals and applications
Authors: Garcia M A
Published: September 2012

The full text of this corrigendum is available in the PDF.
Sums of products of positive operators and spectra of Lüders operators
Authors: Magajna Bojan
Published: September 2012

Each bounded operator

T
T

on an infinite dimensional Hilbert space

H

\mathcal {H}

is a sum of three operators that are similar to positive operators; two such operators are sufficient if

T
T

is not a compact perturbation of a scalar. The spectra of Lüders operators (elementary operators on

B

(

H

)

\mathrm {B}(\mathcal {H})

with positive coefficients) of lengths at least three are not necessarily contained in

B

(

H

)
+

\mathrm {B}(\mathcal {H})^+

. On the other hand, the spectra of such operators of lengths (at most) two are contained in

B

(

H

)
+

\mathrm {B}(\mathcal {H})^+

if the coefficients on one side commute.
Updating annotations with the distributed annotation system and the automated sequence annotation pipeline
Authors: Speier William , Ochs Michael F.
Published: September 2012

Summary: The integration between BioDAS ProServer and Automated Sequence Annotation Pipeline (ASAP) provides an interface for querying diverse annotation sources, chaining and linking results, and standardizing the output using the Distributed Annotation System (DAS) protocol. This interface allows pipeline plans in ASAP to be integrated into any system using HTTP and also allows the information returned by ASAP to be included in the DAS registry for use in any DAS-aware system. Three example implementations have been developed: the first accesses TRANSFAC information to automatically create gene sets for the Coordinated Gene Activity in Pattern Sets (CoGAPS) algorithm; the second integrates annotations from multiple array platforms and provides unified annotations in an R environment; and the third wraps the UniProt database for integration with the SPICE DAS client.

Availability: Source code for ASAP 2.7 and the DAS 1.6 interface is available under the GNU public license. Proserver 2.20 is free software available from SourceForge. Scripts for installation and configuration on Linux are provided at our website: http://www.rits.onc.jhmi.edu/dbb/custom/A6/

Contact: Speier@mii.ucla.edu or mfo@jhu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Interaction-based feature selection and classification for high-dimensional biological data
Authors: Wang Haitian , Lo Shaw-Hwa , Zheng Tian , Hu Inchi
Published: September 2012

Motivation: Epistasis or gene–gene interaction has gained increasing attention in studies of complex diseases. Its presence as an ubiquitous component of genetic architecture of common human diseases has been contemplated. However, the detection of gene–gene interaction is difficult due to combinatorial explosion.

Results: We present a novel feature selection method incorporating variable interaction. Three gene expression datasets are analyzed to illustrate our method, although it can also be applied to other types of high-dimensional data. The quality of variables selected is evaluated in two ways: first by classification error rates, then by functional relevance assessed using biological knowledge. We show that the classification error rates can be significantly reduced by considering interactions. Secondly, a sizable portion of genes identified by our method for breast cancer metastasis overlaps with those reported in gene-to-system breast cancer (G2SBC) database as disease associated and some of them have interesting biological implication. In summary, interaction-based methods may lead to substantial gain in biological insights as well as more accurate prediction.

Contact:  imichu@ust.hk; slo@stat.columnbia.edu

Supplementary information:  Supplementary data are available at the Bioinformatics online.
Why No Feeding Frenzy? Mechanisms of Nutrient Acquisition and Utilization During Infection by the Rice Blast Fungus Magnaporthe oryzae
Authors: Fernandez J. , Wilson R. A.
Published: September 2012

Magnaporthe oryzae is a devastating pathogen of rice and wheat. It is a hemibiotroph that exhibits symptomless biotrophic growth for the first 4 to 5 days of infection of susceptible cultivars before becoming necrotrophic. Here, we review recent advances in our understanding of how M. oryzae is able to grow, acquire nutrients, and interact with the plant cell during infection. In particular, we describe direct mechanisms (such as the integration of carbon and nitrogen metabolism by trehalose-6-phospate synthase 1) and indirect mechanisms (such as the suppression of host responses) that allow M. oryzae to utilize available host nutrient. We contrast the ability of M. oryzae to voraciously metabolize a wide range of carbon and nitrogen sources in vitro with the carefully orchestrated development it displays during the biotrophic phase of in planta growth and ask how the two observations can be reconciled. We also look at how nutrient acquisition and effector biology might be linked in order to facilitate rapid colonization of the plant host.