bluuebunny/crossref_metadata_2025 huggingface dataset:
Very accurate potential energy curve of the ${\rm He}_2^+$ He 2+ ion
Authors: Tung Wei-Cheng , Pavanello Michele , Adamowicz Ludwik
Published: March 2012

A very accurate ground-state potential energy curve (PEC) of the ${\rm He}_2^+$ He 2+ molecule is calculated with 1200 explicitly correlated Gaussian functions with shifted centers in the range between 0.9 and 100 a0. The calculations include the adiabatic corrections determined for the 3He4He+, 3${\rm He}_2^+$ He 2+, and 4${\rm He}_2^+$ He 2+ isotopologues. The absolute accuracy of the PEC is better than 0.05 cm−1 and that of the adiabatic corrections is around 0.01 cm−1. The depths of the PECs augmented with the adiabatic corrections for the three isotopologues are: 19 956.708 cm−1 for 4${\rm He}_2^+$ He 2+, 19 957.054 cm−1 for 3He4He+, and 19 957.401 cm−1 for 3${\rm He}_2^+$ He 2+. The rovibrational energies are also determined. For 3He4He+ the computed rovibrational transitions corresponding to the ν = 1–0 band differ from the experiment by less than 0.005 cm−1. For the rovibrational transitions corresponding to the ν = 23–22 band the difference is around 0.012 cm−1. Presently, this represents the best agreement between theory and experiment for ${\rm He}_2^+$ He 2+.
Delay-driven spatial patterns in a plankton allelopathic system
Authors: Tian Canrong
Published: March 2012

Spatial patterns have received considerable attention in the physical, biological, and social sciences. Generally speaking, time delay is a prevailing phenomenon in aquatic environments, since the production of allelopathic substance by competitive species is not instantaneous, but mediated by some time lag required for maturity of species. A natural question is how delay affects the spatial patterns. Here, we consider a delayed plankton allelopathic system consisting of two competitive species and analytically investigate how the time delay affects the stability and spatial patterns. Based upon a stability analysis, we demonstrate that the delay can induce spatial patterns under some conditions. Moreover, by use of a series of numerical simulations performed with a finite difference scheme, we show that the delay plays an important role on pattern selection.
Excited states and electronic spectra of annulated dinuclear free-base phthalocyanines: A theoretical study on near-infrared-absorbing dyes
Authors: Fukuda Ryoichi , Ehara Masahiro
Published: March 2012

The electronic excited states and electronic absorption spectra of annulated dinuclear free-base phthalocyanine (C58H30N16) are studied through quantum chemical calculations using the symmetry-adapted cluster-configuration interaction (SAC-CI) method. Three tautomers are possible with respect to the position of the pyrrole protons; therefore, the SAC-CI calculations for these tautomers were performed. The structures of the Q-band states are discussed based on the character of their molecular orbitals. The lower energy shift of the Q-bands because of dimerization is explained by the decrease in the HOMO–LUMO gaps resulting from the bonding and antibonding interactions between the monomer units. The electronic dipole moments of the nonsymmetric tautomer were calculated, and the possibility of charge-separated excited states is discussed. The relative energies of these tautomers are examined using density functional theory (DFT) calculations for several peripheral substituents. The relative energies of these tautomers significantly depend on the substituents, and therefore, the abundance ratios of the three tautomers were affected by the substituents. The absorption spectra were simulated from the SAC-CI results weighted by the Boltzmann factors obtained from the DFT calculations. The SAC-CI spectra reproduce the experimental findings well. The thermal-averaged SAC-CI spectra could explain the observed substituent effect on the structure of the Q-bands in terms of the relative stabilities and the abundance ratios of the tautomers. The SAC-CI and time-dependent density functional theory calculations are also compared. The CAM-B3LYP results agreed with the trends of the SAC-CI results; however, the CAM-B3LYP calculation overestimated the excitation energies in comparison with the SAC-CI and experimental results.
Atomic structure variations of mechanically stable fcc-bcc interfaces
Authors: Kang K. , Wang J. , Beyerlein I. J.
Published: March 2012

It has recently been shown that under severe plastic deformation processing bi-metal fcc/bcc composites develop a mechanically stable heterophase interface that joins the {112}fcc//{112}bcc planes in the Kurdjumov-Sachs orientation relationship. In this article, we study variations in the relaxed equilibrium atomic structure of this interface with changes in fcc stacking fault energy (SFE) and lattice mismatch between the two crystals. Using molecular statics/dynamics simulations for three fcc/bcc systems, Cu-Nb, Al-Fe, and Al-Nb, we find that the number of distinct sets of intrinsic interfacial dislocations and their core structures vary significantly among these three systems. The impact of these atomic-scale structural differences on interfacial properties is demonstrated through their interactions with point defects. The interfaces studied here are shown to exhibit a wide variation in ability, ranging from being a poor to an excellent sink for vacancies.
Influence of environment induced correlated fluctuations in electronic coupling on coherent excitation energy transfer dynamics in model photosynthetic systems
Authors: Huo Pengfei , Coker David F.
Published: March 2012

Two-dimensional photon-echo experiments indicate that excitation energy transfer between chromophores near the reaction center of the photosynthetic purple bacterium Rhodobacter sphaeroides occurs coherently with decoherence times of hundreds of femtoseconds, comparable to the energy transfer time scale in these systems. The original explanation of this observation suggested that correlated fluctuations in chromophore excitation energies, driven by large scale protein motions could result in long lived coherent energy transfer dynamics. However, no significant site energy correlation has been found in recent molecular dynamics simulations of several model light harvesting systems. Instead, there is evidence of correlated fluctuations in site energy-electronic coupling and electronic coupling-electronic coupling. The roles of these different types of correlations in excitation energy transfer dynamics are not yet thoroughly understood, though the effects of site energy correlations have been well studied. In this paper, we introduce several general models that can realistically describe the effects of various types of correlated fluctuations in chromophore properties and systematically study the behavior of these models using general methods for treating dissipative quantum dynamics in complex multi-chromophore systems. The effects of correlation between site energy and inter-site electronic couplings are explored in a two state model of excitation energy transfer between the accessory bacteriochlorophyll and bacteriopheophytin in a reaction center system and we find that these types of correlated fluctuations can enhance or suppress coherence and transfer rate simultaneously. In contrast, models for correlated fluctuations in chromophore excitation energies show enhanced coherent dynamics but necessarily show decrease in excitation energy transfer rate accompanying such coherence enhancement. Finally, for a three state model of the Fenna-Matthews-Olsen light harvesting complex, we explore the influence of including correlations in inter-chromophore couplings between different chromophore dimers that share a common chromophore. We find that the relative sign of the different correlations can have profound influence on decoherence time and energy transfer rate and can provide sensitive control of relaxation in these complex quantum dynamical open systems.
strange beta: An assistance system for indoor rock climbing route setting
Authors: Phillips C. , Becker L. , Bradley E.
Published: March 2012

This paper applies the mathematics of chaos to the task of designing indoor rock-climbing routes. Chaotic variation has been used to great advantage on music and dance, but the challenges here are quite different, beginning with the representation. We present a formalized system for transcribing rock climbing problems and then describe a variation generator that is designed to support human route-setters in designing new and interesting climbing problems. This variation generator, termed strange beta, uses chaos to introduce novelty. We validated this approach with a large blinded study in a commercial climbing gym, in cooperation with experienced climbers and expert route setters. The results show that strange beta can help a human setter produce routes that are at least as good as, and in some cases better than, those produced in the traditional manner.
Influence of inserting a thin fullerene layer on pentacene organic thin-film transistor
Authors: Li Yu-Chang , Lin Yu-Ju , Wei Chia-Yu , Chou Dei-Wei , Tsao Chun-Ho , Wang Yeong-Her
Published: March 2012

The performance of organic thin-film transistors (TFTs) with a pentacene/fullerene(C60)/pentacene (PCP) sandwich structure is presented. Using a 3.5 nm-thick C60 layer inserted between the pentacene films, the obtained hole mobility is improved by more than six times. By applying atomic force microscopy, x-ray diffraction, Raman spectrum, and transmission line method analysis, one can reasonably infer that the smoother surface of the pentacene film covered with thin C60 layer delays the phase transformation of the upper pentacene film, resulting in stronger intermolecular coupling and the reduction of channel resistance of the PCP TFTs from 3.03 to 1.72 MΩ, and, therefore, improving the device performance.
Theoretical studies on absorption, emission, and resonance Raman spectra of Coumarin 343 isomers
Authors: Wu Wenpeng , Cao Zexing , Zhao Yi
Published: March 2012

The vibrationally resolved spectral method and quantum chemical calculations are employed to reveal the structural and spectral properties of Coumarin 343 (C343), an ideal candidate for organic dye photosensitizers, in vacuum and solution. The results manifest that the ground-state energies are dominantly determined by different placements of hydrogen atom in carboxylic group of C343 conformations. Compared to those in vacuum, the electronic absorption spectra in methanol solvent show a hyperchromic property together with the redshift and blueshift for the neutral C343 isomers and their deprotonated anions, respectively. From the absorption, emission, and resonance Raman spectra, it is found that the maximal absorption and emission come from low-frequency modes whereas the high-frequency modes have high Raman activities. The detailed spectra are further analyzed for the identification of the conformers and understanding the potential charge transfer mechanism in their photovoltaic applications.
Thermomechanical stability of ultrananocrystalline diamond
Authors: Adiga Vivekananda P. , Suresh Sampath , Datta Arindom , Carlisle John A. , Carpick Robert W.
Published: March 2012

We have measured mechanical stiffness and dissipation in ultrananocrystalline diamond (UNCD) from 63 K to 450 K using microcantilever resonators in a custom ultrahigh vacuum (UHV) atomic force microscope. UNCD exhibits a temperature coefficient of modulus that is found to be extremely low: −26 ppm/K, which is close to the previously measured value of −24 ppm/K for single crystal diamond. The magnitude and the temperature dependence of dissipation are consistent with the behavior of disordered systems. The results indicate that defects, most likely at the grain boundaries, create the dominant contribution to mechanical dissipation. These measurements of modulus and dissipation versus temperature in this temperature range in UNCD establish the nanostructure’s effect on the thermomechanical stability and suggest routes for tailoring these properties.
Background-free imaging of plasmonic structures with cross-polarized apertureless scanning near-field optical microscopy
Authors: Esslinger M. , Dorfmüller J. , Khunsin W. , Vogelgesang R. , Kern K.
Published: March 2012

We present advances in experimental techniques of apertureless scanning near-field optical microscopy (aSNOM). The rational alignment procedure we outline is based upon a phase singularity that occurs while scanning polarizers around the nominal cross-polarized configuration of s-polarized excitation and p-polarized detection. We discuss the theoretical origin of this topological feature of the setup, which is robust against small deviations, such as minor tip misalignment or shape variations. Setting the polarizers to this singular configuration point eliminates all background signal, allowing for reproducible plasmonic eigenmode mapping with optimal signal-to-noise ratio.
Efficient evaluation of Coulomb integrals in a mixed Gaussian and plane-wave basis using the density fitting and Cholesky decomposition
Authors: Čársky Petr , Čurík Roman , Varga Štefan
Published: March 2012

The objective of this paper is to show that the density fitting (resolution of the identity approximation) can also be applied to Coulomb integrals of the type (k1(1)k2(1)|g1(2)g2(2)), where k and g symbols refer to plane-wave functions and gaussians, respectively. We have shown how to achieve the accuracy of these integrals that is needed in wave-function MO and density functional theory-type calculations using mixed Gaussian and plane-wave basis sets. The crucial issues for achieving such a high accuracy are application of constraints for conservation of the number electrons and components of the dipole moment, optimization of the auxiliary basis set, and elimination of round-off errors in the matrix inversion.
Optical investigation of degradation mechanisms in AlGaN/GaN high electron mobility transistors: Generation of non-radiative recombination centers
Authors: Hodges C. , Killat N. , Kaun S. W. , Wong M. H. , Gao F. , Palacios T. , Mishra U. K. , Speck J. S. , Wolverson D. , Kuball M.
Published: March 2012

Degradation mechanisms in AlGaN/GaN high electron mobility transistors have been studied under pinch-off conditions. Sites of localized emission of electroluminescence (EL) in the form of hotspots, known to be related to gate leakage currents, are shown to be the result of the generation of non-radiative recombination centers in the AlGaN device layer during device stress. EL from the hotspot site contains both hot-carrier emission from the acceleration of charge carriers in the device channel and defect-related transitions. Gate leakage through the generated centers is the most likely mechanism for the observation of EL hotspots.
X-ray absorption spectroscopy of doped ZrO2 systems
Authors: Basu S. , Varma Salil , Shirsat A. N. , Wani B. N. , Bharadwaj S. R. , Chakrabarti A. , Jha S. N. , Bhattacharyya D.
Published: March 2012

ZrO2 samples with 11% Nd and La doping and with 7, 9, 11, and 13% Gd doping have been prepared by co-precipitation route followed by sintering at 700 °C and 1100 °C, for potential application as high conductivity electrolytes in solid oxide fuel cells. The samples have been characterized by x-ray diffraction with laboratory x-ray source of Cu Kα radiation and extended x-ray absorption fine structure (EXAFS) spectroscopy measurement at Zr K edge with synchrotron radiation. The XRD spectra have been analyzed to determine the structure of the samples and the EXAFS data have been analyzed to find out relevant local structure parameters of the Zr-O and Zr-Zr shells, viz., bond distances, co-ordinations, and disorder parameters. The effect of change in ionic radius as well as concentration of the dopants on the above parameters has been thoroughly studied. The experimental results, in some cases, have also been corroborated by first principle calculations of the energetics of the systems.
Dynamic Monte Carlo simulations of double crystallization accelerated in microdomains of diblock copolymers
Authors: Li Yuan , Ma Yu , Li Juan , Jiang Xiaoming , Hu Wenbing
Published: March 2012

We report dynamic Monte Carlo simulations of microphase separated diblock copolymers, to investigate how crystallization of one species could accelerate the subsequent crystallization of another species. Although the lattice copolymer model brings a boundary constraint to the long periods of microdomains, the single-molecular-level force balance between two blocks and its change can be revealed in this simple approach. We found two contrastable acceleration mechanisms: (1) the metastable lamellar crystals of one species become thicker at higher crystallization temperatures, sacrificing its microphase interfacial area to make a larger coil-stretching of another amorphous species and hence to accelerate subsequent crystallization of the latter with a more favorable conformation. (2) While in the case allowing chain-sliding in the crystal, the equilibrated lamellar crystals of one species become thinner at higher temperatures, sacrificing its thermal stability to gain a higher conformational entropy of another amorphous species and hence to accelerate subsequent crystallization of the latter with a stronger tension at the block junction. Parallel situations of experiments have been discussed.
Light-induced electron paramagnetic resonance evidence of charge transfer in electrospun fibers containing conjugated polymer/fullerene and conjugated polymer/fullerene/carbon nanotube blends
Authors: Shames Alexander I. , Bounioux Céline , Katz Eugene A. , Yerushalmi-Rozen Rachel , Zussman Eyal
Published: March 2012

Electrospun sub-micron fibers containing conjugated polymer (poly(3-hexylthiophene), P3HT) with a fullerene derivative, phenyl-C61-butyric acid methylester (PCBM) or a mixture of PCBM and single-walled carbon nanotubes (SWCNTs) were studied by light-induced electron paramagnetic resonance spectroscopy. The results provide experimental evidence of electron transfer between PCBM and P3HT components in both fiber systems and suggest that the presence of a dispersing block-copolymer, which acts via physical adsorption onto the PCBM and SWCNT moieties, does not prevent electron transfer at the P3HT-PCBM interface. These findings suggest a research perspective towards utilization of fibers of functional nanocomposites in fiber-based organic optoelectronic and photovoltaic devices. The latter can be developed in the textile-type large area photovoltaics or individual fiber-based solar cells that will broaden energy applications from macro-power tools to micro-nanoscale power conversion devices and smart textiles.
Graphene-lead zirconate titanate optothermal field effect transistors
Authors: Hsieh Chun-Yi , Chen Yung-Ting , Tan Wei-Jyun , Chen Yang-Fang , Shih Wan Y. , Shih Wei-Heng
Published: March 2012

We have developed a pyroelectric field effect transistor (FET) based on a graphene-lead zirconate titanate (PZT) system. Under the incidence of a laser beam, the drain current can be increased or decreased depending on the direction of the polarization of the PZT substrate. The drain current sensitivity of the optothermal FET can reach up to 360 nA/mW at a drain field of 6.7 kV/m more than 5 orders of magnitude higher than that of the photogating transistors based on carbon nanotube on SiO2/Si substrate. Graphene is an excellent component for pyroelectric FET due to its high optical transparency and conductance.
Investigation and compensation of the nonlinear response in photomultiplier tubes for quantitative single-shot measurements
Authors: Knappe C. , Lindén J. , Abou Nada F. , Richter M. , Aldén M.
Published: March 2012

A concept for time-sensitive optical detectors is described that shows how to confirm whether the detection device is operating in the linear response regime. By evaluating the recorded time decay of a thermographic phosphor, even weak saturation effects far from obvious situations can be identified and further related to either optical or electrical saturation. The concept has been validated by running a PMT detector close to saturation and exposing it to the optical signal decay of two different thermographic phosphors, La2O2S:Eu and CdWO4. It was confirmed that short but intense light exposures at the beginning of an individual time decay influence the detector response for the rest of the decaying signal including temporal areas, where the anode current has dropped well below the manufacturer specified current limit. Such situations are common when applying, e.g., phosphor thermometry where it is necessary to retrieve the full decay curve from a single-shot event, i.e., standard techniques based on single-photon counting are omitted. Finally, means of compensation are introduced in order to facilitate the retrieval of useful information from the measurement data when operation in the non-linear response regime is inevitable.
Thermally induced van der Waals rupture of thin viscous fluid sheets
Authors: Bowen Mark , Tilley B. S.
Published: March 2012

We consider the dynamics of a thin symmetric fluid sheet subject to an initial temperature profile, where inertia, viscous stresses, disjoining pressures, capillarity, and thermocapillarity are important. We apply a long-wave analysis in the limit where deviations from the mean sheet velocity are small, but thermocapillary stresses and heat transfer from the sheet to the environment are significant and find a coupled system of partial differential equations that describe the sheet thickness, the mean sheet velocity, and the mean sheet temperature. From a linear stability analysis, we find that a stable thermal mode couples the velocity to the interfacial dynamics. This coupling can be utilized to delay the onset of rupture or to promote an earlier rupture event. In particular, rupture can be induced thermally even in cases when the heat transfer to the surrounding environment is significant, provided that the initial phase shift between the initial velocity and temperature disturbances is close to ϕ = π/2. These effects suggest a strategy that uses phase modulation in the initial temperature perturbation related to the initial velocity perturbation that assigns priority of the rupture events at particular sites over several spatial periods.
Gas flow and heat transfer in nanotube and nanowire arrays
Authors: Martin Michael J.
Published: March 2012

Gas flow through arrays of nanotube or nanowire structures is modeled by combining the one-dimensional equations for conservation of mass, momentum, and energy with the linearized free-molecular drag and heat transfer for a cylinder. The results show that the pressure gradient, temperature, and local velocity of the gas are governed by coupled ordinary differential equations. Three cases are considered: an isothermal system, a constant wall temperature, and a constant wall heat flux. While the coupled momentum, heat transfer, and continuity equations are nonlinear, the relatively low velocities encountered in these systems cause the nonlinear portions of pressure drops and thermal phenomena to be relatively small.
Fabrication of microgrooves on a curved surface by the confocal measurement system using pulse laser and continuous laser
Authors: Noh Jiwhan , Cho Ilhwan , Lee Seungwoo , Na Suckjoo , Lee Jae-Hoon
Published: March 2012

In order to fabricate microgrooves on a curved surface, the curved surface was measured with a confocal system and then it was used for laser microprocessing. This paper proposes a new method of using a pulse laser for the confocal system to measure the curved surface. It also compares the conventional way of using a continuous laser and a new way of using the pulse laser with the confocal system. Using the data measured with the pulse laser for fabrication, microgrooves were fabricated on a curved surface. The width of the fabricated microgroove was 10 μm and the depth was 27 μm. The microgroove fabricated on a curved surface as a part of this study can be used in injection molding to manufacture a micropatterned plastic surface at a low cost. This plastic surface can be applied for a superhydrophobic surface, a self-cleaning surface, or a biochip.
Soliton interactions in some semidiscrete integrable systems
Authors: Zhou Tong , Zhu Zuo-nong
Published: March 2012

In this paper, soliton interactions in three semidiscrete integrable systems are studied. It will be shown that in some cases the solitary waves of the semidiscrete integrable systems can interact elastically, i.e., the shapes, the amplitudes, and the velocities of waves preserve after undergoing collision. However, soliton interactions in the semidiscrete integrable systems possess different properties from the continuous solitons, for example, the shorter waves can travel faster than the taller ones. We also find that two stable solitary waves can be destroyed after interaction, and the elastic properties of collisions between two solitary waves are sensitively dependent on the choices of some parameters in solution. We therefore conclude that soliton interactions in semidiscrete integrable systems are richer than the ones in continuous soliton systems.
Ferroelectricity-induced resistive switching in Pb(Zr0.52Ti0.48)O3/Pr0.7Ca0.3MnO3/Nb-doped SrTiO3 epitaxial heterostructure
Authors: Md. Sadaf Sharif , Mostafa Bourim El , Liu Xinjun , Hasan Choudhury Sakeb , Kim Dong-Wook , Hwang Hyunsang
Published: March 2012

We investigated the effect of a ferroelectric Pb(Zr0.52Ti0.48)O3 (PZT) thin film on the generation of resistive switching in a stacked Pr0.7Ca0.3MnO3 (PCMO)/Nb-doped SrTiO3 (Nb:STO) heterostructure forming a p-n junction. To promote the ferroelectric effect, the thin PZT active layer was deposited on an epitaxially grown p-type PCMO film on a lattice-matched n-type Nb:STO single crystal. It was concluded that the observed resistive switching behavior in the all-perovskite Pt/PZT/PCMO/Nb:STO heterostructure was related to the modulation of PCMO/Nb:STO p-n junction’s depletion width, which was caused either by the PZT ferroelectric polarization field effect, the electrochemical drift of oxygen ions under an electric field, or both simultaneously.
Enhancing gas induced charge doping in graphene field effect transistors by non-covalent functionalization with polyethyleneimine
Authors: Sabri Shadi S. , Guillemette Jonathan , Guermoune Abdelaadim , Siaj Mohamed , Szkopek Thomas
Published: March 2012

We demonstrate that large-area, graphene field effect transistors with a passive parylene substrate and a polyethyleneimine functional layer have enhanced sensitivity to CO2 gas exposure. The electron doping of graphene, caused by protonated amine groups within the polyethyleneimine, is modulated by the formation of negatively charged species generated by CO2 adsorption. The charge doping mechanism is general, and quantitative doping density changes can be determined from the graphene field effect transistor characteristics.
Subwavelength optical absorber with an integrated photon sorter
Authors: Le Perchec J. , Desieres Y. , Rochat N. , Espiau de Lamaestre R.
Published: March 2012

We provide the experimental and theoretical evidence that several nano-patch antennas assembled within a wavelength-scale region may constitute an efficient and easily tunable multi-band photodetector. The system uses highly confined localization states of light and exhibits a robust spectral sorting capability, paving the way to highly integrated hyperspectral imaging.
A new way to describe the transition characteristics of a rotating-disk boundary-layer flow
Authors: Imayama Shintaro , Alfredsson P. Henrik , Lingwood R. J.
Published: March 2012

A new method of graphically representing the transition stages of a rotating-disk flow is presented. The probability density function contour map of the fluctuating azimuthal disturbance velocity is used to show the characteristics of the boundary-layer flow over the rotating disk as a function of Reynolds numbers. Compared with the variation of the disturbance amplitude (rms) or spectral distribution, this map more clearly shows the changing flow characteristics through the laminar, transitional, and turbulent regions. This method may also be useful to characterize the different stages in the transition process not only for the rotating-disk flow but also for other flows.
Electronic structures of graphane with vacancies and graphene adsorbed with fluorine atoms
Authors: Wu Bi-Ru , Yang Chih-Kai
Published: March 2012

We investigate the electronic structure of graphane with hydrogen vacancies, which are supposed to occur in the process of hydrogenation of graphene. A variety of configurations is considered and defect states are derived by density functional calculation. We find that a continuous chain-like distribution of hydrogen vacancies will result in conduction of linear dispersion, much like the transport on a superhighway cutting through the jungle of hydrogen. The same conduction also occurs for chain-like vacancies in an otherwise fully fluorine-adsorbed graphene. These results should be very useful in the design of graphene-based electronic circuits.
Vitamin E and fatty acid content of lamb meat from perennial pasture or annual pasture systems with supplements
Authors: Ponnampalam E. N. , Burnett V. F. , Norng S. , Warner R. D. , Jacobs J. L.
Published: March 2012

The present study investigated the effect of a perennial lucerne and phalaris pasture, or annual pasture with lucerne hay and a range of supplements provided as pellets (700 g/day) on Vitamin E and fatty acid content of skeletal muscle and oxidative stability of lamb meat post-farm gate. Treatments were lambs grazing perennial pasture only (PP); lambs grazing annual pasture with lucerne hay and oat grain pellet supplement (AP); AP with cracked flaxseed (AP+FS); and AP with flaxmeal (AP+FM). After 7 weeks of feeding, lambs were slaughtered after an overnight fast. At 24 h post-slaughter, samples of muscle longissimus lumborum (LL) were collected for determination of fatty acid profile and antioxidant status, as measured by Vitamin E content. Samples were also collected for retail colour assessment of fresh meat at 24 h, 48 h, 72 h and 96 h of post-slaughter. Vitamin E content of the LL from lambs grazing PP was higher (5.9 v. 3.4 mg α-tocopherol/kg, P < 0.01) than that of lambs grazing other treatments. Long-chain n-3 and total n-3 fatty acid contents in the muscle were similar among treatment groups and adequate to claim as a source of n-3. Inclusion of oat grain at 245 g (AP) or at 175 g with flaxseed (AP+FS) or 175 g with flaxmeal (AP+FM) per day in the diet of lambs increased the linoleic acid content (P < 0.05) and the ratio of n-6 : n-3 (P < 0.007) in the LL, compared with lambs grazing PP. Oxidative stability of fresh meat evaluated by retail shelf life (retention of redness) and formation of lipid oxidative substance showed no differences among treatment groups and, as indicated by redness (a*-value) over a 96-h display, all values were within the range (>9.5) for quality meat over the time frame used in the present study. The results provided some evidence that inclusion of PP in the diets of lambs during dry seasons (late summer to autumn) is an effective tool of improving the Vitamin E content of muscle tissues at slaughter.
Whole lifespan microscopic observation of budding yeast aging through a microfluidic dissection platform
Authors: Lee Sung Sik , Vizcarra Ima Avalos , Huberts Daphne H. E. W. , Lee Luke P. , Heinemann Matthias
Published: March 2012

Important insights into aging have been generated with the genetically tractable and short-lived budding yeast. However, it is still impossible today to continuously track cells by high-resolution microscopic imaging (e.g., fluorescent imaging) throughout their entire lifespan. Instead, the field still needs to rely on a 50-y-old laborious and time-consuming method to assess the lifespan of yeast cells and to isolate differentially aged cells for microscopic snapshots via manual dissection of daughter cells from the larger mother cell. Here, we are unique in achieving continuous and high-resolution microscopic imaging of the entire replicative lifespan of single yeast cells. Our microfluidic dissection platform features an optically prealigned single focal plane and an integrated array of soft elastomer-based micropads, used together to allow for trapping of mother cells, removal of daughter cells, monitoring gradual changes in aging, and unprecedented microscopic imaging of the whole aging process. Using the platform, we found remarkable age-associated changes in phenotypes (e.g., that cells can show strikingly differential cell and vacuole morphologies at the moment of their deaths), indicating substantial heterogeneity in cell aging and death. We envision the microfluidic dissection platform to become a major tool in aging research.
Protein misinteraction avoidance causes highly expressed proteins to evolve slowly
Authors: Yang Jian-Rong , Liao Ben-Yang , Zhuang Shi-Mei , Zhang Jianzhi
Published: March 2012

The tempo and mode of protein evolution have been central questions in biology. Genomic data have shown a strong influence of the expression level of a protein on its rate of sequence evolution (E-R anticorrelation), which is currently explained by the protein misfolding avoidance hypothesis. Here, we show that this hypothesis does not fully explain the E-R anticorrelation, especially for protein surface residues. We propose that natural selection against protein–protein misinteraction, which wastes functional molecules and is potentially toxic, constrains the evolution of surface residues. Because highly expressed proteins are under stronger pressures to avoid misinteraction, surface residues are expected to show an E-R anticorrelation. Our molecular-level evolutionary simulation and yeast genomic analysis confirm multiple predictions of the hypothesis. These findings show a pluralistic origin of the E-R anticorrelation and reveal the role of protein misinteraction, an inherent property of complex cellular systems, in constraining protein evolution.
Common genetic variants in the
PSCA
gene influence gene expression and bladder cancer risk
Authors: Fu Yi-Ping , Kohaar Indu , Rothman Nathaniel , Earl Julie , Figueroa Jonine D. , Ye Yuanqing , Malats Núria , Tang Wei , Liu Luyang , Garcia-Closas Montserrat , Muchmore Brian , Chatterjee Nilanjan , Tarway McAnthony , Kogevinas Manolis , Porter-Gill Patricia , Baris Dalsu , Mumy Adam , Albanes Demetrius , Purdue Mark P. , Hutchinson Amy , Carrato Alfredo , Tardón Adonina , Serra Consol , García-Closas Reina , Lloreta Josep , Johnson Alison , Schwenn Molly , Karagas Margaret R. , Schned Alan , Diver W. Ryan , Gapstur Susan M. , Thun Michael J. , Virtamo Jarmo , Chanock Stephen J. , Fraumeni Joseph F. , Silverman Debra T. , Wu Xifeng , Real Francisco X. , Prokunina-Olsson Ludmila
Published: March 2012

Genome-wide association studies have identified a SNP, rs2294008, on 8q24.3 within the prostate stem cell antigen (
PSCA
) gene, as a risk factor for bladder cancer. To fine-map this region, we imputed 642 SNPs within 100 Kb of rs2294008 in addition to 33 markers genotyped in one of the reported genome-wide association study in 8,652 subjects. A multivariable logistic regression model adjusted for rs2294008 revealed a unique signal, rs2978974 (
r
2
= 0.02, D′ = 0.19 with rs2294008). In the combined analysis of 5,393 cases and 7,324 controls, we detected a per-allele odds ratio (OR) = 1.11 [95% confidence interval (CI) = 1.06–1.17,
P
= 5.8 × 10
−5
] for rs2294008 and OR = 1.07 (95% CI = 1.02–1.13,
P
= 9.7 × 10
−3
) for rs2978974. The effect was stronger in carriers of both risk variants (OR = 1.24, 95% CI = 1.08–1.41,
P
= 1.8 × 10
−3
) and there was a significant multiplicative interaction (
P
= 0.035) between these two SNPs, which requires replication in future studies. The T risk allele of rs2294008 was associated with increased
PSCA
mRNA expression in two sets of bladder tumor samples (
n
= 36,
P
= 0.0007 and
n
= 34,
P
= 0.0054) and in normal bladder samples (
n
= 35,
P
= 0.0155), but rs2978974 was not associated with
PSCA
expression. SNP rs2978974 is located 10 Kb upstream of rs2294008, within an alternative untranslated first exon of
PSCA
. The non-risk allele G of rs2978974 showed strong interaction with nuclear proteins from five cell lines tested, implying a regulatory function. In conclusion, a joint effect of two
PSCA
SNPs, rs2294008 and rs2978974, suggests that both variants may be important for bladder cancer susceptibility, possibly through different mechanisms that influence the control of mRNA expression and interaction with regulatory factors.
DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees
Authors: Foret Sylvain , Kucharski Robert , Pellegrini Matteo , Feng Suhua , Jacobsen Steven E. , Robinson Gene E. , Maleszka Ryszard
Published: March 2012

In honey bees (Apis mellifera), the development of a larva into either a queen or worker depends on differential feeding with royal jelly and involves epigenomic modifications by DNA methyltransferases. To understand the role of DNA methylation in this process we sequenced the larval methylomes in both queens and workers. We show that the number of differentially methylated genes (DMGs) in larval head is significantly increased relative to adult brain (2,399 vs. 560) with more than 80% of DMGs up-methylated in worker larvae. Several highly conserved metabolic and signaling pathways are enriched in methylated genes, underscoring the connection between dietary intake and metabolic flux. This includes genes related to juvenile hormone and insulin, two hormones shown previously to regulate caste determination. We also tie methylation data to expressional profiling and describe a distinct role for one of the DMGs encoding anaplastic lymphoma kinase (ALK), an important regulator of metabolism. We show thatalkis not only differentially methylated and alternatively spliced inApis, but also seems to be regulated by acis-acting, anti-sense non–protein-coding transcript. The unusually complex regulation of ALK inApissuggests that this protein could represent a previously unknown node in a process that activates downstream signaling according to a nutritional context. The correlation between methylation and alternative splicing ofalkis consistent with the recently described mechanism involving RNA polymerase II pausing. Our study offers insights into diet-controlled development inApis.
Ultraviolet detection using TiO2 nanowire array with Ag Schottky contact
Authors: Chinnamuthu P , Dhar J C , Mondal A , Bhattacharyya A , Singh N K
Published: March 2012

The glancing angle deposition technique has been employed to synthesize TiO2 nanowire (NW) arrays which have been characterized by x-ray diffraction, field emission-scanning electron microscopy and high resolution transmission electron microscopy. Optical absorption measurements show the absorption edge at 3.42 eV and 3.48 eV for TiO2 thin film (TF) and NW, respectively. The blue shift in absorption band is attributed to quantum confinement in NW structures. Photoluminescence measurement revealed oxygen-defect-related emission at 425 nm (∼2.9 eV). Ag/TiO2 (NW) and Ag/TiO2 (TF) contacts exhibit Schottky behaviour, and a higher turn-on voltage (∼6.5 V) was observed for NW devices than that of TF devices (∼5.25 V) under dark condition. In addition, TiO2-NW-based devices show twofold improvement in photodetection efficiency in the UV region, compared with TiO2-TF-based devices.
Low-pressure water vapour plasma treatment of surfaces for biomolecules decontamination
Authors: Fumagalli F , Kylián O , Amato L , Hanuš J , Rossi F
Published: March 2012

Decontamination treatments of surfaces are performed on bacterial spores, albumin and brain homogenate used as models of biological contaminations in a low-pressure, inductively coupled plasma reactor operated with water-vapour-based gas mixtures. It is shown that removal of contamination can be achieved using pure H2O or Ar/H2O mixtures at low temperatures with removal rates comparable to oxygen-based mixtures. Particle fluxes (Ar+ ions, O and H atomic radicals and OH molecular radicals) from water vapour discharge are measured by optical emission spectroscopy and Langmuir probe under several operating conditions. Analysis of particle fluxes and removal rates measurements illustrates the role of ion bombardment associated with O radicals, governing the removal rates of organic matter. Auxiliary role of hydroxyl radicals is discussed on the basis of experimental data. The advantages of a water vapour plasma process are discussed for practical applications in medical devices decontamination.
Self-irradiation of thin SiC nanowires with low-energy ions: a molecular dynamics study
Authors: Sun Lixin , Lan Chune , Zhao Shijun , Xue Jianming , Wang Yugang
Published: March 2012

Irradiation of ultra-thin silicon carbide nanowires (SiC NWs) with low-energy ions was investigated with the molecular dynamics (MD) method. The energies of the incident Si and C ions varied from 0.2 to 5.0 keV. Simulation results show that the ion range predicted by the SRIM code is a little shorter than that obtained from the MD simulation when the incident energy is low and the implanted ions can form a peak-like distribution inside the NW. Compared with bulk material, the sputtering yield of the SiC NW is much higher as a result of the NW's larger surface-to-volume ratio, and for a high ion energy, the sputtering yields show a different dependence to the nuclear stopping power because the NW's limited volume stops the collision cascade from fully evolving. Moreover, the calculated short-range order values indicate that the amorphous degree for most irradiated samples is acceptable and repairable. For a high ion energy range, the SiC NW is more difficult to amorphize compared with bulk SiC. By carefully optimizing the implantation parameters, a desirable distribution of dopants can be achieved in the thin SiC NW while the irradiation damage is kept at an acceptable level.
Myosin-X functions in polarized epithelial cells
Authors: Liu Katy C. , Jacobs Damon T. , Dunn Brian D. , Fanning Alan S. , Cheney Richard E.
Published: March 2012

Myosin-X (Myo10) is an unconventional myosin that localizes to the tips of filopodia and has critical functions in filopodia. Although Myo10 has been studied primarily in nonpolarized, fibroblast-like cells, Myo10 is expressed in vivo in many epithelia-rich tissues, such as kidney. In this study, we investigate the localization and functions of Myo10 in polarized epithelial cells, using Madin-Darby canine kidney II cells as a model system. Calcium-switch experiments demonstrate that, during junction assembly, green fluorescent protein–Myo10 localizes to lateral membrane cell–cell contacts and to filopodia-like structures imaged by total internal reflection fluorescence on the basal surface. Knockdown of Myo10 leads to delayed recruitment of E-cadherin and ZO-1 to junctions, as well as a delay in tight junction barrier formation, as indicated by a delay in the development of peak transepithelial electrical resistance (TER). Although Myo10 knockdown cells eventually mature into monolayers with normal TER, these monolayers do exhibit increased paracellular permeability to fluorescent dextrans. Importantly, knockdown of Myo10 leads to mitotic spindle misorientation, and in three-dimensional culture, Myo10 knockdown cysts exhibit defects in lumen formation. Together these results reveal that Myo10 functions in polarized epithelial cells in junction formation, regulation of paracellular permeability, and epithelial morphogenesis.
The fission yeast septation initiation network (SIN) kinase, Sid2, is required for SIN asymmetry and regulates the SIN scaffold, Cdc11
Authors: Feoktistova Anna , Morrell-Falvey Jennifer , Chen Jun-Song , Singh N. Sadananda , Balasubramanian Mohan K. , Gould Kathleen L.
Published: March 2012

The Schizosaccharomyces pombe septation initiation network (SIN) is an Spg1-GTPase–mediated protein kinase cascade that triggers actomyosin ring constriction, septation, and cell division. The SIN is assembled at the spindle pole body (SPB) on the scaffold proteins Cdc11 and Sid4, with Cdc11 binding directly to SIN signaling components. Proficient SIN activity requires the asymmetric distribution of its signaling components to one of the two SPBs during anaphase, and Cdc11 hyperphosphorylation correlates with proficient SIN activity. In this paper, we show that the last protein kinase in the signaling cascade, Sid2, feeds back to phosphorylate Cdc11 during mitosis. The characterization of Cdc11 phosphomutants provides evidence that Sid2-mediated Cdc11 phosphorylation promotes the association of the SIN kinase, Cdc7, with the SPB and maximum SIN signaling during anaphase. We also show that Sid2 is crucial for the establishment of SIN asymmetry, indicating a positive-feedback loop is an important element of the SIN.
Identification of a novel ADAMTS9/GON-1 function for protein transport from the ER to the Golgi
Authors: Yoshina Sawako , Sakaki Kenjiro , Yonezumi-Hayashi Aki , Gengyo-Ando Keiko , Inoue Hideshi , Iino Yuichi , Mitani Shohei
Published: March 2012

A disintegrin-like and metalloprotease with thrombospondin type I motif (ADAMTS9) is a member of the secreted metalloprotease family that is believed to digest extracellular matrix (ECM) proteins outside of cells. Its Caenorhabditis elegans orthologue, GON-1, is involved in ECM degradation and is required for gonad morphogenesis. ADAMTS9 and GON-1 have similar domain structures, and both have a unique C-terminal domain called the “GON domain,” whose function remains unknown. Here we show that down-regulation of human ADAMTS9 and C. elegans GON-1 results in the inhibition of protein transport from the endoplasmic reticulum (ER) to the Golgi. This phenotype was rescued by the expression of the GON domain localizing in the ER in human cells and C. elegans. We propose a novel function of ADAMTS9 and GON-1 in the ER that promotes protein transport from the ER to the Golgi. This function is GON-domain dependent but protease activity independent.
Biogenesis of the preprotein translocase of the outer mitochondrial membrane: protein kinase A phosphorylates the precursor of Tom40 and impairs its import
Authors: Rao Sanjana , Schmidt Oliver , Harbauer Angelika B. , Schönfisch Birgit , Guiard Bernard , Pfanner Nikolaus , Meisinger Chris
Published: March 2012

The preprotein translocase of the outer mitochondrial membrane (TOM) functions as the main entry gate for the import of nuclear-encoded proteins into mitochondria. The major subunits of the TOM complex are the three receptors Tom20, Tom22, and Tom70 and the central channel-forming protein Tom40. Cytosolic kinases have been shown to regulate the biogenesis and activity of the Tom receptors. Casein kinase 2 stimulates the biogenesis of Tom22 and Tom20, whereas protein kinase A (PKA) impairs the receptor function of Tom70. Here we report that PKA exerts an inhibitory effect on the biogenesis of the β-barrel protein Tom40. Tom40 is synthesized as precursor on cytosolic ribosomes and subsequently imported into mitochondria. We show that PKA phosphorylates the precursor of Tom40. The phosphorylated Tom40 precursor is impaired in import into mitochondria, whereas the nonphosphorylated precursor is efficiently imported. We conclude that PKA plays a dual role in the regulation of the TOM complex. Phosphorylation by PKA not only impairs the receptor activity of Tom70, but it also inhibits the biogenesis of the channel protein Tom40.