bluuebunny/crossref_metadata_2025 huggingface dataset:
Solar energy trapping with modulated silicon nanowire photonic crystals
Authors: Demésy Guillaume , John Sajeev
Published: October 2012

We demonstrate the efficacy of nanostructured thin film silicon solar cells to trap and absorb approximately 75% of all sunlight incident (400 nm–1200 nm) with an equivalent bulk thickness of only 1 micron of silicon. This is achieved by sculpting the collection zone into a three-dimensional, simple-cubic-symmetry, photonic crystal consisting of modulated silicon nanowires embedded in SiO2 and sitting on a quartz substrate with no metallic mirrors. A specific modulation of the radius of nanowires provides antireflection, strong light trapping, and back-reflection mechanisms in targeted spectral regions. This modulation is linear at the top of the nano-rods leading to nanocones at the solar cell to air boundary. These silicon nanocones are very good absorbers at short wavelengths and act as broadband coupler to a light-trapping region below at longer wavelengths. In the light trapping region the modulation is periodic to form a simple cubic photonic crystal exhibiting a broad spectrum of strong parallel interface refraction resonances. Here, light incident from most angles is deflected into slow group velocity modes with energy flow nearly parallel to the interface, long dwell times, and strong light intensity enhancement (up to 150 times the incident intensity) in specific regions. Finally, a stronger and chirped modulation of the nanowire underneath provides back-reflection by means of a one-dimensional depth-dependent photonic stop-gap. The possibility of absorbing light at energies below the electronic band gap of silicon is illustrated using a graded index SixGe1−x alloy in the bottom section of each nanowire. Each nanowire is amenable to a radial P-N junction for proximal charge carrier separation and efficient collection of photo-generated current.
Stability and the continuum limit of the spin-polarized Thomas-Fermi-Dirac-von Weizsäcker model
Authors: E Weinan , Lu Jianfeng
Published: October 2012

The continuum limit of the spin-polarized Thomas-Fermi-Dirac-von Weizsäcker model in an external magnetic field is studied. An extension of the classical Cauchy-Born rule for crystal lattices is established for the electronic structure under sharp stability conditions on charge density and spin density waves. A Landau-Lifshitz type of micromagnetic energy functional is derived.
Building band structures for long finite chains in presence of an electric field
Authors: Vargas Jorge , Springborg Michael
Published: October 2012

At first, three different methods devoted to extracting the periodic-system band structures from the results of finite-system calculations are being discussed. Special emphasis is put on the performance of these methods for a system that is exposed to an external electrostatic field. Using model calculations we found that the three methods converge to the same results in the absence of the electrostatic field, but they lead to small differences when the field is included, which can be ascribed to distortions of the spatial extensions of the orbitals generated by the field. These small differences become important when addressing the issue whether it is possible to identify uniquely a set of band structures for the infinite, periodic system exposed to an electrostatic field. This question, related to the question whether the phases of the periodic-system orbitals are of physical importance, has so far not been answered. Applying the results of the first part we ultimately suggest that it is not possible to identify a unique set of band structures when the periodic system is exposed to an electrostatic field.
The motion of a single and multiple neutrally buoyant elliptical cylinders in plane Poiseuille flow
Authors: Chen Shih-Di , Pan Tsorng-Whay , Chang Chien-Cheng
Published: October 2012

In this article, we investigate the motion of neutrally buoyant elliptical cylinders in plane Poiseuille flow of a Newtonian fluid. The method of distributed Lagrange multiplier/fictitious domain was used to solve the Navier-Stokes equations as well as for the motion of elliptical cylinders. The motion of a single elliptical cylinder is shown to be dependent on the channel Reynolds number Re, the particle size ratio K = a*/H*, and the aspect ratio A = a*/b* of the cylinder, where H* is the half height of the channel, a* and b* are the lengths of the semi-major axis and semi-minor axis of the cylinder, respectively. It is found that there is a critical Reynolds number, Rec ∼ 3, which distinguishes the lateral migration of a single elliptical cylinder below and above it. As Re is increased, the equilibrium position of the elliptical cylinder shifts towards the wall when Re ≤ Rec or shifts closer to the central axis when Re ≥ Rec. Moreover, there are interesting correlations between the center-of-mass trajectories and the orientation dynamics, which depend on the ranges of K and Re. The motion of multiple elliptical cylinders is also affected by the total solid area fraction ϕT, which is defined to be the proportion of the area occupied by the cylinders in the domain of computation. For a few elliptical cylinders (the number of cylinders ND = 16 and the corresponding ϕT = 3.77%), the cylinders may scatter into several groups at lower Re (≤ 100), and each group fluctuates about an averaged position. At the higher Re (= 1000), the cylinders may converge to an equilibrium position on each side of the channel center. For a larger number of cylinders (ND = 36, 54, 72, 108, and the corresponding ϕT = 8.48%–25.45%), we observed a significant rheological behavior in the velocity profiles. In addition, there exists a particle-free layer next to each wall, and the thickness of the particle-free layers is increased as A (or K) or Re is increased.
Electronic effects on the melting of small gallium clusters
Authors: Steenbergen K. G. , Schebarchov D. , Gaston N.
Published: October 2012

Motivated by experimental reports of higher-than-bulk melting temperatures in small gallium clusters, we perform first-principles molecular dynamics simulations of Ga20 and \documentclass[12pt]{minimal}\begin{document}${\rm Ga}_{20}^{+}$\end{document} Ga 20+ using parallel tempering in the microcanonical ensemble. The respective specific heat (CV) curves, obtained using the multiple histogram method, exhibit a broad peak centered at approximately 740 and 610 K—well above the melting temperature of bulk gallium (303 K) and in reasonable agreement with experimental data for \documentclass[12pt]{minimal}\begin{document}${\rm Ga}_{20}^+$\end{document} Ga 20+. Assessment of atomic mobility confirms the transition from solid-like to liquid-like states near the CV peak temperature. Parallel tempering molecular dynamics simulations yield low-energy isomers that are ∼0.1 eV lower in energy than previously reported ground state structures, indicative of an energy landscape with multiple, competing low-energy morphologies. Electronic structure analysis shows no evidence of covalent bonding, yet both the neutral and charged clusters exhibit greater-than-bulk melting temperatures.
Extreme statistics, Gaussian statistics, and superdiffusion in global magnitude fluctuations in turbulence
Authors: Labbé R. , Bustamante G.
Published: October 2012

Extreme value statistics, or extreme statistics for short, refers to the statistics that characterizes rare events of either unusually high or low intensity: climate disasters like floods following extremely intense rains are among the principal examples. Extreme statistics is also found in fluctuations of global magnitudes in systems in thermal equilibrium, as well as in systems far from equilibrium. A remarkable example in this last class is fluctuations of injected power in confined turbulence. Here we report results in a confined von Kármán swirling flow, produced by two counter-rotating stirrers, in which quantities derived from the same global magnitude—the rotation rate of the stirrers—can display both, extreme and Gaussian statistics. On the one hand, we find that underlying the extreme statistics displayed by the global shear of the flow, there is a nearly Gaussian process resembling a white noise, corresponding to the action of the normal stresses exerted by the turbulent flow, integrated on the flow-driving surfaces of the stirrers. On the other hand, the magnitude displaying Gaussian statistics is the global rotation rate of the fluid, which happens to be a realization of a 1D diffusion where the variance of the angular speed increments ΩR(t + Δt) − ΩR(t) scales as Δtν, while the power spectral density of the angular speed follows a 1/fα scaling law. These scaling exponents are found to be α ≈ 0.37 and ν ≈ 1.36, which implies that this process can be described as a 1D superdiffusion.
Diffusion in grid turbulence of isotropic macro-particles using a Lagrangian stochastic method: Theory and validation
Authors: Joly A. , Moulin F. , Violeau D. , Astruc D.
Published: October 2012

The prediction of solid bodies transport (such as algae, debris, sediment grains, or corrosion deposits) is a necessary requirement in many industrial or environmental processes. The physical processes involved cover a wide range of processes, from tidal flow to turbulent eddies and particle drag. A stochastic model was therefore developed to link the different scales of the physical processes where it was assumed that the particles are dilute enough that they do not affect the flow or the motion of other particles while being large enough that each particle does not follow exactly the fluid motions (i.e., macro-particles). The stochastic model is built in such a way that it uses Reynolds-averaged fluid properties to predict trajectories of individual particles. This model was then tested using experimental measurements obtained for isotropic particles released in semi-homogeneous turbulence. The turbulent flow was generated using a pair of oscillating grids and was characterized using particle image velocimetry measurements. The trajectories of the particles were measured using a pair of high resolution cameras. The comparison between the experimental data and different numerical models gives satisfactory results.
Crawling of a driven adherent membrane
Authors: Baumgaertner A.
Published: October 2012

We discuss motions of an elastic N × M membrane model whose constituents can bind reversibly with strength ɛ to adhesive sites of a flat substrate. One of the edges of the membrane (“front”) is driven in one direction at rate constant p by N stochastically treadmilling short parallel lines (“cortex”). The main conclusions derived from Monte Carlo studies of this model are the following: (a) Since the polymerizing cortex pushes only the leading edge of the membrane, the major part of the membranes is dragged behind. Therefore, the locomotion of the membrane can be described by frictional sliding processes which are asymmetrically distributed between front and rear of the membrane. A signature of this asymmetry is the difference between the life times of adhesion bonds at front and rear, τ1 and τM, respectively, where τ1 ≫ τM. (b) There are four characteristic times for the membrane motion: The first time, T0 ∼ τM ∼ eaɛ, is the resting time where the displacement of the membrane is practically zero. The second time, Tp ∼ τ1 ∼ M, is the friction time which characterizes the time between two consecutive ruptures of adhesion bonds at the front, and which signalizes the onset of drift (“protrusion”) at the leading edge. The third time, Tr ∼ Mγ(ɛ) (γ > 1), characterizes the “retraction” of the trailing edge, which is the retarded response to the pulling leading edge. The fourth time, TL ∼ M2, is the growth time for fluctuation of the end-to-end distance. (c) The separation of time scales, Tr/Tp ∼ Mγ(ɛ) − 1, leads to stretched fluctuations of the end-to-end distance, which are considered as stochastic cycles of protrusion and retraction on the time scale of TL. (d) The drift velocity v obeys anomalous scaling, \documentclass[12pt]{minimal}\begin{document}$\textrm {v} / p \sim f(p^{1/\gamma (\varepsilon )}M)$\end{document}v/p∼f(p1/γ(ɛ)M), where f (z) ∼ const. for small drag pM ≪ 1, and f (z) ∼ z−γ(ɛ) for pM ≫ 1, which implies \documentclass[12pt]{minimal}\begin{document}$\textrm {v} \sim M^{-\gamma (\varepsilon )}$\end{document}v∼M−γ(ɛ). These results may also turn out to be useful for the (more difficult) problem of understanding the protrusion-retraction cycle of crawling biological cells. We compare our model and our results to previous two-particle theories for membrane protrusion and to known stochastic friction models.
Modelling of electronic excitation and radiation in the Direct Simulation Monte Carlo Macroscopic Chemistry Method
Authors: Goldsworthy M. J.
Published: October 2012

One of the most useful tools for modelling rarefied hypersonic flows is the Direct Simulation Monte Carlo (DSMC) method. Simulator particle movement and collision calculations are combined with statistical procedures to model thermal non-equilibrium flow-fields described by the Boltzmann equation. The Macroscopic Chemistry Method for DSMC simulations was developed to simplify the inclusion of complex thermal non-equilibrium chemistry. The macroscopic approach uses statistical information which is calculated during the DSMC solution process in the modelling procedures. Here it is shown how inclusion of macroscopic information in models of chemical kinetics, electronic excitation, ionization, and radiation can enhance the capabilities of DSMC to model flow-fields where a range of physical processes occur. The approach is applied to the modelling of a 6.4 km/s nitrogen shock wave and results are compared with those from existing shock-tube experiments and continuum calculations. Reasonable agreement between the methods is obtained. The quality of the comparison is highly dependent on the set of vibrational relaxation and chemical kinetic parameters employed.
Practical axial optical trapping
Authors: Mack A. H. , Schlingman D. J. , Regan L. , Mochrie S. G. J.
Published: October 2012

We describe a new method for calibrating optical trapping measurements in which tension is applied in the direction of the laser beam to a molecule tethered between a surface and an optically trapped bead. Specifically, we present a generally-applicable procedure for converting from the measured scattering intensity and the measured stage displacement to applied tension and bead-coverslip separation, using measurements of the light intensity scattered from an untethered, trapped bead. Our calibration accounts for a number of effects, including aberrations and the interference of forward-reflected bead-scattered light with the trapping beam. To demonstrate the accuracy of our method, we show measurements of the DNA force-versus-extension relation using a range of laser intensities, and show that these measurements match the expected extensible wormlike-chain (WLC) behavior. Finally, we also demonstrate a force-clamp, in which the tension in a tether is held fixed while the extension varies as a result of molecular events.
Stress and texture development during sputtering of yttria, zirconia, and yttria stabilized zirconia films on Si substrates
Authors: Narayanachari K. V. L. V. , Raghavan Srinivasan
Published: October 2012

Understanding and controlling growth stress is a requisite for integrating oxides with Si. Yttria stabilized zirconia (YSZ) is both an important functional oxide and a buffer layer material needed for integrating other functional oxides. Stress evolution during the growth of (100) and (111) oriented YSZ on Si (100) by radio frequency and reactive direct current sputtering has been investigated with an in-situ monitor and correlated with texture evolution. Films nucleated at rates <5 nm/min are found to be (111) oriented and grow predominantly under a compressive steady state stress. Films nucleated at rates >20 nm/min are found to be (100) oriented and grow under tension. A change in growth rate following the nucleation stage does not change the orientation. The value of the final steady state stress varies from −4.7 GPa to 0.3 GPa. The in-situ studies show that the steady state stress generation is a dynamic phenomenon occurring at the growth surface and not decided at film nucleation. The combination of stress evolution and texture evolution data shows that the adatom injection into the grain boundaries is the predominant source of compressive stress and grain boundary formation at the growth surface is the source of tensile stress.
Simultaneous measurement of external refractive index and temperature based on long-period-grating-inscribed Sagnac interferometer and fiber Bragg grating
Authors: Gao Peng , Chen Xiuyan , Feng Wenjiang
Published: October 2012

A compact Sagnac interferometer with a long-period grating (LPG) inscribed in a polarization-maintaining fiber (PMF-LPG) and a fiber Bragg grating (FBG) is proposed. The PMF-LPG is intrinsically sensitive to the external refractive index (ERI) and temperature, whereas the FBG is only sensitive to temperature. Simultaneous measurement of the ERI and temperature can be achieved by detecting wavelength shifts in the interference patterns of the Sagnac interferometer and the FBG. Because a Sagnac interference structure is used, a high ERI sensitivity of −21.07 nm/refractive index unit in measurement range 1.33–1.43 is obtained, which is about three times higher than for the normal LPG ERI sensor.
The origin of broad distribution of breakdown times in polycrystalline thin film dielectrics
Authors: Masuduzzaman Muhammad , Xie Sujing , Chung Jayhoon , Varghese Dhanoop , Rodriguez John , Krishnan Srikanth , Ashraful Alam Muhammad
Published: October 2012

The distribution of breakdown times of thin film dielectrics, stressed in a constant voltage mode, is generally interpreted in terms of percolation theory of dielectric breakdown. The percolation model suggests that relative distribution of failure times (normalized to the mean) should narrow down considerably for thicker dielectrics. Explicitly contradicting this prediction, we find a larger distribution of failure times even for relatively thick polycrystalline oxides. We use atomic force microscopy and conductive AFM measurements to confirm that breakdown in these films are primarily localized in the grain boundaries, decorated with large number of pre-existing defects. The classical percolation model—adapted to this specific situation of spatially localized trap generation—offers an intuitive explanation of the breadth of the failure time distribution in thick polycrystalline dielectric. The theory offers an opportunity to optimize the intrinsic trade-off between variability and reliability in polycrystalline films.
Nonadiabatic fiber taper-based Mach-Zehnder interferometer for refractive index sensing
Authors: Xu Linlin , Li Ying , Li Baojun
Published: October 2012

A Mach-Zehnder interferometer based on a nonadiabatic fiber taper is proposed for refractive index (RI) sensing. Only the first order cladding guided mode is excited in the down-taper. The radius of the fiber core in the interference region is too thin (<1.64 μm) to confine the fundamental mode in the fiber core, the fundamental core guided mode is converted to the fundamental cladding guided mode and interference occurs between it and the first order cladding guided mode. The sensitivity of the sensor is 980 nm per refractive index unit for the surrounding refractive index ranging from 1.332 to 1.392.
Crystal structure of 0.96(Na0.5Bi0.5TiO3)–0.04(BaTiO3) from combined refinement of x-ray and neutron diffraction patterns
Authors: Usher T.-M. , Forrester J. S. , dela Cruz C. R. , Jones J. L.
Published: October 2012

High-resolution x-ray and neutron diffraction of (0.96)Na0.5Bi0.5TiO3–(0.04)BaTiO3 (NBT-4BT) reveal subtle structural distortions that evidence lower symmetry than allowed in the R3c space group. The combined refinement that best models the diffraction patterns is a two phase mixture of a monoclinic Cc phase and a minor fraction of a metrically cubic Pm3¯m phase (13 wt. %). The cubic phase is utilized to account for nanometer-scale regions whose local deviations from the long-range symmetry are not observed, such as polar nano-regions or tetragonal platelets. This suggests that the low symmetry found in the NBT-rich phases extends from 0 at. % to at least 4 at. % BT.
Study of Nb epitaxial growth on Cu(111) at sub-monolayer level
Authors: Clavero Cesar , Guisinger Nathan P. , Srinivasan Srivilliputhur G. , Lukaszew Rosa A.
Published: October 2012

The epitaxial growth of Nb on Cu(111) is experimentally and theoretically investigated at submonolayer level since the early stages of growth for this system remain unexplored despite its interest in superconducting thin film applications. The growth conditions were optimized to obtain crystalline nanoisland ordering on the first subatomic layer. Interestingly, we observe that Nb atoms arrange forming a hexagonal lattice on Cu(111) in contrast with the expected tetragonal pseudomorphic growth observed in other systems such as Nb on Pd (111). The correlation between annealing temperature and Cu-Nb intermixing was experimentally and theoretically investigated.
Passively Q-switching induced by gold nanocrystals
Authors: Jiang Tao , Xu Yang , Tian Qijun , Liu Lai , Kang Zhe , Yang Renyuan , Qin Guanshi , Qin Weiping
Published: October 2012

Passive Q-switching was experimentally demonstrated in an erbium-doped fiber laser (EDFL) by using gold nanocrystals (GNCs). The GNCs were mixed with sodium carboxymethylcellulose (NaCMC) to form GNCs-NaCMC films. The films exhibited a broad absorption band in the range of 400–1750 nm. By placing the GNCs-NaCMC film in an EDFL cavity pumped by a 980 nm laser diode, stable passive Q-switching was achieved for a threshold pump power of ∼30 mW, and 3.2 μs pulses at 1560 nm with a repetition rate of 24.2 kHz were obtained for a pump power of ∼125 mW.
Emission wavelength of multilayer distributed feedback dye lasers
Authors: Vannahme Christoph , Smith Cameron L. C. , Brøkner Christiansen Mads , Kristensen Anders
Published: October 2012

Precise emission wavelength modeling is essential for understanding and optimization of distributed feedback (DFB) lasers. An analytical approach for determining the emission wavelength based on setting the propagation constant of the Bragg condition and solving for the resulting slab waveguide mode is reported. The method is advantageous to established methods as it predicts the wavelength precisely with reduced complexity. Four-layered hybrid polymer-TiO2 first order DFB dye lasers with different TiO2 layer thicknesses are studied. Varying the TiO2 thickness from 0 nm to 30 nm changes the emission wavelength by 7 nm with compelling agreement of modeling results to experimental measurements.
A study of solitary wave trains generated by injection of a blob into plasmas
Authors: Choi C.-R. , Rha K.-C. , Ryu C.-M. , Choi E.-J. , Min K.-W. , Lee E. , Parks G. K.
Published: October 2012

We have investigated the evolution of consecutive electrostatic solitary waves (ESWs) generated upon injection of a finite-sized blob into plasmas using one-dimensional electrostatic particle-in-cell simulations. Strong charge separation developed at the leading edge of the blob, producing a huge electrostatic potential in which electrons were trapped and heated. Ions were reflected from the boundaries of the blob, forming fast, cold ion beams in the forward and backward directions. The forward ion beams interacted with the hot electrons, which were escaping from the potential developed at the leading edge of the blob, to produce successive ESWs. On the other hand, the backward ion beams formed ion phase space holes as a result of the ion two-stream instability. The present study demonstrates that localized density perturbations in plasmas can be a viable source of consecutive ESWs observed in space.
Observation of spin dependent photocoductivity in InSb quantum well nanowires
Authors: Li Juerong , Gilbertson A. M. , Litvinenko K. L. , Cohen L. F. , Clowes S. K.
Published: October 2012

We report on the electrical detection of spin dependent photoconductivity in 500 nm wide InSb quantum well nanowires using the optical orientation of electron spins. By applying weak magnetic fields (≈200 mT), we observe a spin filtering effect of classical origin caused by spin dependent back scattering of electrons from the sidewalls. Spin dependent features in the longitudinal photovoltage decay with temperature and disappears at characteristic energy (≈50 K) consistent with the theoretical spin splitting and the thermal level broadening. We show that the observed signal is due to the inversion asymmetry of the quantum well, with an additional Zeeman contribution.
Phenotypic variation for productivity and drought tolerance is widespread in germplasm collections of Australian Cullen species
Authors: Bennett R. G. , Colmer T. D. , Real D. , Renton M. , Ryan M. H.
Published: October 2012

Cullen australasicum is a legume species from Australia that holds promise for development as a drought-tolerant perennial pasture species, yet only a few accessions have been evaluated for agronomic traits. Several Cullen species aside from C. australasicum may also have potential for use as perennial pastures. We compared the field survival and aboveground biomass production of 100 germplasm accessions from 9 Cullen species, 2 lucerne (Medicago sativa) cultivars and 2 perennial Lotus species over 18 months in a low-rainfall region of the wheatbelt of Western Australia. Nutritive value of selected Cullen accessions was also compared with lucerne and L. australis. Several accessions of C. australasicum demonstrated good survival, productivity and nutritional value, and some accessions of C. discolor, C. lachnostachys, C. pallidum and C. pustulatum also showed promise in some or all of these traits. Significant phenotypic variation was seen among accessions of C. australasicum, C. pallidum, C. cinereum and C. tenax for some agronomic traits. We discuss the implications of this variation for further experiments or development of Cullen species. While survival and productivity of many Cullen accessions was similar to lucerne, only a few C. australasicum accessions were more productive than lucerne. We conclude that C. australasicum is currently the best prospect among Cullen species for cultivar development as a perennial pasture legume, and our analysis has highlighted accessions of particular interest. In addition, further work on C. discolor, C. lachnostachys, C. pallidum and C. pustulatum may also, in the longer term, provide useful pasture species.
A comparison of two online cognitive‐behavioural interventions for symptoms of depression in a student population: The role of therapist responsiveness
Authors: Richards Derek , Timulak Ladislav , Hevey David
Published: October 2012

Objectives: The study aimed to compare the efficacy of eight weekly sessions of a self‐administered online CBT treatment (cCBT; n=51) to a therapist‐assisted email CBT treatment (eCBT; n=50) in University students. Design: The design was a randomised parallel group trial. The study randomised participants with symptoms of depression to one of two available treatments. Method: Participants were offered eight weekly sessions of either cCBT or eCBT. Participants completed the Beck Depression Inventory‐II (BDI‐II) and the Clinical Outcomes in Routine Evaluation – Outcome Measure (CORE‐OM) at pre‐and post‐treatment, at weeks 16 and 32 follow‐up. The Working Alliance Inventory‐Short Form (WAI‐SR) was completed at weeks 2, 4, and 6. Results: For both groups, pre‐post within group effect sizes reported were large for the BDI‐II and the CORE‐OM and these were maintained at follow‐up. Perceptions of working alliance were similar in each group, but Bond was significantly stronger for the eCBT condition. WAI scores correlated more positively with the outcome on BDI‐II for those in the eCBT condition than the cCBT condition, but not significantly. Conclusion: There were no significant differences between the two online treatments, both reduced depressive symptoms and improved general functioning. Similarly, at post‐treatment and follow‐up, clinical improvement and recovery was demonstrated for both groups equally. The study demonstrates the possibility for cCBT in a university setting that may contribute to addressing the shortcomings in meeting increasing demands that mental health services presently face.
Notes on the phenomenology of interiority and the foundations of psychology
Authors: Brooke Roger
Published: October 2012

Interiority and any reference to an inner life have been radically deconstructed by the philosophical anthropologists, who find in the psychological constructions of the self and the theories of mental life the legacy of Descartes and Galileo. This critique is argued in some detail. However, the language of interiority is not merely an epistemological error on the part of the speaker. Psychoanalysis and psychopathology have documented the developmental significance of interiority and its absence. A phenomenological analysis of interiority, based in part on a clinical example, reveals several interrelated themes: temporal continuity; imagination; responsibility and ownership; privacy; self-reflection. Each of these themes is interpreted existentially in terms of being in the world. A critical discussion of interiority in Giegerich's work concludes the paper. It is argued paradoxically that the dialectical tension between interiority and exteriority – psyche and its grounding in events and relations to others – is a dimension within interiority itself.
ON ABSORPTION BY CIRCUMSTELLAR DUST, WITH THE PROGENITOR OF SN 2012aw AS A CASE STUDY
Authors: Kochanek C. S. , Khan R. , Dai X.
Published: October 2012

We use the progenitor of SN 2012aw to illustrate the consequences of modeling circumstellar dust using Galactic (interstellar) extinction laws that (1) ignore dust emission in the near-IR and beyond, (2) average over dust compositions, and (3) mischaracterize the optical/UV absorption by assuming that scattered photons are lost to the observer. The primary consequences for the progenitor of SN 2012aw are that both the luminosity and the absorption are significantly overestimated. In particular, the stellar luminosity is most likely in the range 104.8 < L
*/L
☉ < 105.0 and the star was not extremely massive for a Type IIP progenitor, with M
* < 15 M
☉. Given the properties of the circumstellar dust and the early X-ray/radio detections of SN 2012aw, the star was probably obscured by an ongoing wind with

to 10−5.0 
M
☉ yr−1 at the time of the explosion, roughly consistent with the expected mass-loss rates for a star of its temperature (T
* ≃ 3600+300
− 200 K) and luminosity. In the spirit of Galactic extinction laws, we supply simple interpolation formulae for circumstellar extinction by dusty graphitic and silicate shells as a function of wavelength (λ ⩾ 0.3 μm) and total (absorption plus scattering) V-band optical depth (τ
V
⩽ 20). These do not include the contributions of dust emission, but provide a simple, physical alternative to incorrectly using interstellar extinction laws.
Gαs promotes EEA1 endosome maturation and shuts down proliferative signaling through interaction with GIV (Girdin)
Authors: Beas Anthony O. , Taupin Vanessa , Teodorof Carmen , Nguyen Lien T. , Garcia-Marcos Mikel , Farquhar Marilyn G.
Published: October 2012

The organization of the endocytic system into biochemically distinct subcompartments allows for spatial and temporal control of the strength and duration of signaling. Recent work has established that Akt cell survival signaling via the epidermal growth factor receptor (EGFR) occurs from APPL early endosomes that mature into early EEA1 endosomes. Less is known about receptor signaling from EEA1 endosomes. We show here that EGF-induced, proliferative signaling occurs from EEA1 endosomes and is regulated by the heterotrimeric G protein Gαs through interaction with the signal transducing protein GIV (also known as Girdin). When Gαs or GIV is depleted, activated EGFR and its adaptors accumulate in EEA1 endosomes, and EGFR signaling is prolonged, EGFR down-regulation is delayed, and cell proliferation is greatly enhanced. Our findings define EEA1 endosomes as major sites for proliferative signaling and establish that Gαs and GIV regulate EEA1 but not APPL endosome maturation and determine the duration and strength of proliferative signaling from this compartment.
Sec1/Munc18 protein Vps33 binds to SNARE domains and the quaternary SNARE complex
Authors: Lobingier Braden T. , Merz Alexey J.
Published: October 2012

Soluble N-ethylmaleimide–sensitive factor attachment protein receptor (SNARE) proteins catalyze membrane fusion events in the secretory and endolysosomal systems, and all SNARE-mediated fusion processes require cofactors of the Sec1/Munc18 (SM) family. Vps33 is an SM protein and subunit of the Vps-C complexes HOPS (homotypic fusion and protein sorting) and CORVET (class C core vacuole/endosome tethering), which are central regulators of endocytic traffic. Here we present biochemical studies of interactions between Saccharomyces cerevisiae vacuolar SNAREs and the HOPS holocomplex or Vps33 alone. HOPS binds the N-terminal Habc domain of the Qa-family SNARE Vam3, but Vps33 is not required for this interaction. Instead, Vps33 binds the SNARE domains of Vam3, Vam7, and Nyv1. Vps33 directly binds vacuolar quaternary SNARE complexes, and the affinity of Vps33 for SNARE complexes is greater than for individual SNAREs. Through targeted mutational analyses, we identify missense mutations of Vps33 that produce a novel set of defects, including cargo missorting and the loss of Vps33-HOPS association. Together these data suggest a working model for membrane docking: HOPS associates with N-terminal domains of Vam3 and Vam7 through Vps33-independent interactions, which are followed by binding of Vps33, the HOPS SM protein, to SNARE domains and finally to the quaternary SNARE complex. Our results also strengthen the hypothesis that SNARE complex binding is a core attribute of SM protein function.
SCYL1BP1 modulates neurite outgrowth and regeneration by regulating the Mdm2/p53 pathway
Authors: Liu Yonghua , Chen Ying , Lu Xiang , Wang Youhua , Duan Yinong , Cheng Chun , Shen Aiguo
Published: October 2012

SCY1-like 1–binding protein 1 (SCYL1BP1) is a newly identified transcriptional activator domain containing a protein with many unknown biological functions. Recently emerging evidence has revealed that it is a novel regulator of the p53 pathway, which is required for neurite outgrowth and regeneration. Here we present evidence that SCYL1BP1 inhibits nerve growth factor–mediated neurite outgrowth in PC12 cells and affects morphogenesis of primary cortical neurons by strongly decreasing the p53 protein level in vitro, all of which depends on SCYL1BP1's transcriptional activator domain. Exogenous p53 rescues neurite outgrowth and neuronal morphogenesis defects caused by SCYL1BP1. Furthermore, SCYL1BP1 can directly induce Mdm2 transcription, whereas inhibiting the function of Mdm2 by specific small interfering RNAs results in partial rescue of neurite outgrowth and neuronal morphogenesis defects induced by SCYL1BP1. In vivo experiments show that SCYL1BP1 can also depress axonal regeneration, whereas inhibiting the function of SCYL1BP1 by specific short hairpin RNA enhances it. Taken together, these data strongly suggested that SCYL1BP1 is a novel transcriptional activator in neurite outgrowth by directly modulating the Mdm2/p53-dependent pathway, which might play an important role in CNS development and axonal regeneration after injury.
Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads
Authors: Li Wei , Jiang Tao
Published: October 2012

Motivation: RNA-Seq uses the high-throughput sequencing technology to identify and quantify transcriptome at an unprecedented high resolution and low cost. However, RNA-Seq reads are usually not uniformly distributed and biases in RNA-Seq data post great challenges in many applications including transcriptome assembly and the expression level estimation of genes or isoforms. Much effort has been made in the literature to calibrate the expression level estimation from biased RNA-Seq data, but the effect of biases on transcriptome assembly remains largely unexplored.

Results: Here, we propose a statistical framework for both transcriptome assembly and isoform expression level estimation from biased RNA-Seq data. Using a quasi-multinomial distribution model, our method is able to capture various types of RNA-Seq biases, including positional, sequencing and mappability biases. Our experimental results on simulated and real RNA-Seq datasets exhibit interesting effects of RNA-Seq biases on both transcriptome assembly and isoform expression level estimation. The advantage of our method is clearly shown in the experimental analysis by its high sensitivity and precision in transcriptome assembly and the high concordance of its estimated expression levels with quantitative reverse transcription–polymerase chain reaction data.

Availability: CEM is freely available at http://www.cs.ucr.edu/~liw/cem.html.

Contact:  liw@cs.ucr.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches
Authors: Mendes Nuno D. , Heyne Steffen , Freitas Ana T. , Sagot Marie-France , Backofen Rolf
Published: October 2012

Motivation: The computational search for novel microRNA (miRNA) precursors often involves some sort of structural analysis with the aim of identifying which type of structures are prone to being recognized and processed by the cellular miRNA-maturation machinery. A natural way to tackle this problem is to perform clustering over the candidate structures along with known miRNA precursor structures. Mixed clusters allow then the identification of candidates that are similar to known precursors. Given the large number of pre-miRNA candidates that can be identified in single-genome approaches, even after applying several filters for precursor robustness and stability, a conventional structural clustering approach is unfeasible.

Results: We propose a method to represent candidate structures in a feature space, which summarizes key sequence/structure characteristics of each candidate. We demonstrate that proximity in this feature space is related to sequence/structure similarity, and we select candidates that have a high similarity to known precursors. Additional filtering steps are then applied to further reduce the number of candidates to those with greater transcriptional potential. Our method is compared with another single-genome method (TripletSVM) in two datasets, showing better performance in one and comparable performance in the other, for larger training sets. Additionally, we show that our approach allows for a better interpretation of the results.

Availability and Implementation: The MinDist method is implemented using Perl scripts and is freely available at http://www.cravela.org/?mindist=1.

Contact:  backofen@informatik.uni-freiburg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
An ensemble correlation-based gene selection algorithm for cancer classification with gene expression data
Authors: Piao Yongjun , Piao Minghao , Park Kiejung , Ryu Keun Ho
Published: October 2012

Motivation: Gene selection for cancer classification is one of the most important topics in the biomedical field. However, microarray data pose a severe challenge for computational techniques. We need dimension reduction techniques that identify a small set of genes to achieve better learning performance. From the perspective of machine learning, the selection of genes can be considered to be a feature selection problem that aims to find a small subset of features that has the most discriminative information for the target.

Results: In this article, we proposed an Ensemble Correlation-Based Gene Selection algorithm based on symmetrical uncertainty and Support Vector Machine. In our method, symmetrical uncertainty was used to analyze the relevance of the genes, the different starting points of the relevant subset were used to generate the gene subsets and the Support Vector Machine was used as an evaluation criterion of the wrapper. The efficiency and effectiveness of our method were demonstrated through comparisons with other feature selection techniques, and the results show that our method outperformed other methods published in the literature.

Availability: By request from the author.

Contact:  pyz@dblab.chungbuk.ac.kr; khryu@dblab.cbnu.ac.kr
Aragonite-associated biomineralization proteins are disordered and contain interactive motifs
Authors: Evans John Spencer
Published: October 2012

Motivation: The formation of aragonite mineral in the mollusk shell or pearl nacre requires the participation of a diverse set of proteins that form the mineralized extracellular matrix. Although self-assembly processes have been identified for several nacre proteins, these proteins do not contain known globular protein–protein binding domains. Thus, we hypothesize that other sequence features are responsible for nacre matrix protein–protein assembly processes and ultimately aragonite biosynthesis.

Results: Of 39 mollusk aragonite-associated protein sequences, 100% contain at least one region of intrinsic disorder or unfolding, with the highest percentages found in framework and pearl-associated proteins relative to the intracrystalline proteins. In some instances, these intrinsically disordered regions were identified as bind/fold sequences, and a limited number correlate with known biomineral-relevant sequences. Interestingly, 95% of the aragonite-associated protein sequences were found to contain at least one occurrence of amyloid-like or cross-β strand aggregation-prone supersecondary motifs, and this correlates with known aggregation and aragonite formation functions in three experimentally tested protein sequences. Collectively, our findings indicate that aragonite-associated proteins have evolved signature sequence traits of intrinsic disorder and aggregation-prone regions that are important for their role(s) in matrix assembly and mineralization.

Contact:  jse1@nyu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Tools for mapping high-throughput sequencing data
Authors: Fonseca Nuno A. , Rung Johan , Brazma Alvis , Marioni John C.
Published: October 2012

Motivation: A ubiquitous and fundamental step in high-throughput sequencing analysis is the alignment (mapping) of the generated reads to a reference sequence. To accomplish this task, numerous software tools have been proposed. Determining the mappers that are most suitable for a specific application is not trivial.

Results: This survey focuses on classifying mappers through a wide number of characteristics. The goal is to allow practitioners to compare the mappers more easily and find those that are most suitable for their specific problem.

Availability: A regularly updated compendium of mappers can be found at http://wwwdev.ebi.ac.uk/fg/hts_mappers/.

Contact:  nf@ebi.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Olorin: combining gene flow with exome sequencing in large family studies of complex disease
Authors: Morris James A. , Barrett Jeffrey C.
Published: October 2012

Motivation: The existence of families with many individuals affected by the same complex disease has long suggested the possibility of rare alleles of high penetrance. In contrast to Mendelian diseases, however, linkage studies have identified very few reproducibly linked loci in diseases such as diabetes and autism. Genome-wide association studies have had greater success with such diseases, but these results explain neither the extreme disease load nor the within-family linkage peaks, of some large pedigrees. Combining linkage information with exome or genome sequencing from large complex disease pedigrees might finally identify family-specific, high-penetrance mutations.

Results: Olorin is a tool, which integrates gene flow within families with next generation sequencing data to enable the analysis of complex disease pedigrees. Users can interactively filter and prioritize variants based on haplotype sharing across selected individuals and other measures of importance, including predicted functional consequence and population frequency.

Availability:  http://www.sanger.ac.uk/resources/software/olorin

Contact:  olorin@sanger.ac.uk
Association between diabetes mellitus and post‐discharge outcomes in patients hospitalized with heart failure: findings from the EVEREST trial
Authors: Sarma Satyam , Mentz Robert J. , Kwasny Mary J. , Fought Angela J. , Huffman Mark , Subacius Haris , Nodari Savina , Konstam Marvin , Swedberg Karl , Maggioni Aldo P. , Zannad Faiez , Bonow Robert O. , Gheorghiade Mihai ,   on behalf of the EVEREST investigators
Published: October 2012

Aims

We evaluated the impact of diabetes mellitus (DM) and diabetic therapy on outcomes in patients with reduced ejection fraction (EF) after hospitalization for heart failure (HF). DM is prevalent in patients hospitalized with HF, yet inconclusive data exist on the post‐discharge outcomes of this patient population.

Methods and results

Post‐hoc analysis was performed on the EVEREST (Efficacy of Vasopressin Antagonism in Heart Failure Outcome Study with Tolvaptan) study, a randomized trial of patients hospitalized with HF (n = 4133) with median follow‐up of 9.9 months. DM status was determined from intake questionnaires and cross‐verified by medication history. Univariate relationships were examined using χ test, t‐test, and Wilcoxon tests. The two primary outcomes of (i) all‐cause mortality (ACM) and (ii) cardiovascular mortality or HF hospitalization (CVM + HFH) were assessed for those with and without DM and by diabetic treatment strategy using log rank tests and multivariable Cox regression models. DM was present in 40% of participants. Patients with DM were more likely to have hypertension, coronary artery disease, and chronic kidney disease. Diabetes was associated with ACM and CVM + HFH (both P < 0.001). Following multivariate risk adjustment, DM was associated with ACM, but this estimate was imprecise [hazard ratio (HR) 1.16; 95% confidence interval (CI) 1.00–1.34] and remained associated with CVM or HFH (HR 1.17; 95% CI 1.04–1.31). Diabetic control strategy did not independently affect outcomes.

Conclusion

Diabetes is common in patients hospitalized for heart failure with a reduced EF. These patients have a higher post‐discharge CVM and higher HF hospitalizations compared with patients with no diabetes. Different diabetic treatment regimens did not appear to influence post‐discharge outcomes.
‘Vividness’ in english natural history and anatomy, 1650–1700
Authors: Wragge-Morley Alexander
Published: October 2012

This article concerns the use of rhetorical strategies in the natural historical and anatomical works of the seventeenth-century Royal Society. Choosing representative works, it argues that naturalists such as Nehemiah Grew, John Ray and the neuroanatomist Thomas Willis used the rhetorical device known as ‘comparison’ to make their descriptions of natural things vivid. By turning to contemporary works of neurology such as Willis's
Cerebri Anatome
and contemporary rhetorical works inspired by other such descriptions of the brain and nerves, it is argued that the effects of these strategies were taken to be wide-ranging. Contemporaries understood the effects of rhetoric in terms inflected by anatomical and medical discourse—the brain was physically altered by powerful sense impressions such as those of rhetoric. I suggest that the rhetoric of natural history could have been understood in the same way and that natural history and anatomy might therefore have been understood to cultivate the mind, improving its capacity for moral judgements as well as giving it knowledge of nature.