bluuebunny/crossref_metadata_2025 huggingface dataset:
Temperature-dependence of the internal efficiency droop in GaN-based diodes
Authors: Hader J. , Moloney J. V. , Koch S. W.
Published: November 2011

The temperature dependence of the measured internal efficiencies of green and blue emitting InGaN-based diodes is analyzed. With increasing temperature, a strongly decreasing strength of the loss mechanism responsible for droop is found which is in contrast to the usually assumed behavior of Auger losses. However, the experimental observations can be well reproduced assuming density activated defect recombination with a temperature independent recombination time.
Limits of elemental contrast by low energy electron point source holography
Authors: Livadaru Lucian , Mutus Josh , Wolkow Robert A.
Published: November 2011

Motivated by the need for less destructive imaging of nanostructures, we pursue point-source in-line holography (also known as point projection microscopy, or PPM) with very low energy electrons (∼100 eV). This technique exploits the recent creation of ultrasharp and robust nanotips, which can field emit electrons from a single atom at their apex, thus creating a path to an extremely coherent source of electrons for holography. Our method has the potential to achieve atom resolved images of nanostructures including biological molecules. We demonstrate a further advantage of PPM emerging from the fact that the very low energy electrons employed experience a large elastic scattering cross section relative to many-kV electrons. Moreover, the variation of scattering factors as a function of atom type allows for enhanced elemental contrast. The idea that one can obtain chemical information about a sample whereas imaging it by PPM is worth pursuing in more detail, and here we undertake simulations of this scheme to assess its feasibility to first order. Model results for small molecules and adatoms on graphene substrates, where very small damage is expected, indicate that a phase contrast is obtainable between elements with significantly different Z-numbers. For example, for typical setup parameters, atoms such as C and P are discernible, whereas C and N are not.
Atomic structure and transport properties of Cu50Zr45Al5 metallic liquids and glasses: Molecular dynamics simulations
Authors: Zhang Y. , Mattern N. , Eckert J.
Published: November 2011

We have simulated the atomic structure and the transport properties of Cu50Zr45Al5 metallic liquids and glasses within a wide cooling temperature range from 2000 to 300 K, using molecular dynamics simulations. High fractions of Cu- and Al-centered full icosahedra and Zr-centered icosahedra-like clusters have been detected in both supercooled liquids and glasses. The heat capacity and linear thermal expansion coefficients of both liquids and glasses are also calculated, which have not been reported for this off-eutectic composition previously. The critical temperature (Tc) of Cu50Zr45Al5 liquids is determined to be 874.7 K by investigating the self-diffusivity using the mode coupling theory. A dynamics cross-over is detected in the vicinity of Tc, which can be reflected by different diffusion mechanisms and a remarkable deviation from the Einstein-Stokes relation. The results further suggest a fragile to strong transition of Cu50Zr45Al5 liquids between 1500 K and 1300 K upon cooling, which may result from a drastic increase of stable clusters within this temperature range.
Magnetic field induced metal-insulator transition in a kagome nanoribbon
Authors: Dey Moumita , Maiti Santanu K. , Karmakar S. N.
Published: November 2011

In the present work, we investigate two-terminal electron transport through a finite width kagome lattice nanoribbon in presence of a perpendicular magnetic field. We employ a simple tight-binding (T-B) Hamiltonian to describe the system and obtain the transmission properties by using Green’s function technique within the framework of Landauer-Büttiker formalism. After presenting an analytical description of energy dispersion relation of a kagome nanoribbon in presence of the magnetic field, we investigate numerically the transmittance spectra together with the density of states and current-voltage characteristics. It is shown that for a specific value of the Fermi energy, the kagome network can exhibit a magnetic field induced metal-insulator transition, which is the central investigation of this communication. Our analysis may be inspiring in designing low-dimensional switching devices.
Modeling pulsed-laser melting of embedded semiconductor nanoparticles
Authors: Sawyer C. A. , Guzman J. , Boswell-Koller C. N. , Sherburne M. P. , Mastandrea J. P. , Bustillo K. C. , Ager J. W. , Haller E. E. , Chrzan D. C.
Published: November 2011

Pulsed-laser melting (PLM) is commonly used to achieve a fast quench rate in both thin films and nanoparticles. A model for the size evolution during PLM of nanoparticles confined in a transparent matrix, such as those created by ion-beam synthesis, is presented. A self-consistent mean-field rate equations approach that has been used successfully to model ion beam synthesis of germanium nanoparticles in silica is extended to include the PLM process. The PLM model includes classical optical absorption, multiscale heat transport by both analytical and finite difference methods, and melting kinetics for confined nanoparticles. The treatment of nucleation and coarsening behavior developed for the ion beam synthesis model is modified to allow for a nonuniform temperature gradient and for interacting liquid and solid particles with different properties. The model allows prediction of the particle size distribution after PLM under various laser fluences, starting from any particle size distribution including as-implanted or annealed simulated samples. A route for narrowing the size distribution of embedded nanoparticles is suggested, with simulated distribution widths as low as 15% of the average size.
Electronic band gap and transport in Fibonacci quasi-periodic graphene superlattice
Authors: Zhao Pei-Liang , Chen Xi
Published: November 2011

We investigate electronic band gap and transport in Fibonacci quasi-periodic graphene superlattice. It is found that such structure can possess a zero-k¯ gap which exists in all Fibonacci sequences. Different from Bragg gap, zero-k¯ gap associated with Dirac point is less sensitive to the incidence angle and lattice constants. The defect mode appeared inside the zero-k¯ gap has a great effect on transmission, conductance, and shot noise, which can be applicable to control the electron transport.
Lyman-α radiation of a metastable hydrogen beam to measure electric fields
Authors: Lejeune A. , Chérigier-Kovacic L. , Doveil F.
Published: November 2011

The interaction between a metastable H(2s) atomic hydrogen beam and an external electric field leads to the emission of the Lyman-α line. It originates in the Stark mixing of the near-degenerate 2s1/2 and 2p1/2 levels separated by the Lamb shift. The quenched radiation proportional to the square of the electric field amplitude is recovered in vacuum by using such an atomic probe beam. We observe the strong enhancement of the signal when the field is oscillating at the Lamb shift frequency. This technique is applied in a plasma, offering an alternative way to measure weak electric fields by direct and non-intrusive means.
Accurate hyper-Rayleigh scattering polarization measurements
Authors: Shelton David P.
Published: November 2011

Apparatus and methods are described for measurement of the polarization dependence of hyper-Rayleigh scattering near 90° scattering angle with 0.1% accuracy for all four configurations where the incident and scattered light is linear polarized either parallel or perpendicular to the scattering plane. Measurements are made with large collection aperture and extrapolated to zero collection numerical aperture (NA = 0). Fiber coupling allows the system to be easily reconfigured for either polarization or spectral measurements.
Influence of Al/CuO reactive multilayer films additives on exploding foil initiator
Authors: Zhou Xiang , Shen Ruiqi , Ye Yinghua , Zhu Peng , Hu Yan , Wu Lizhi
Published: November 2011

An investigation on the influence of Al/CuO reactive multilayer films (RMFs) additives on exploding foil initiator was performed in this paper. Cu film and Cu/Al/CuO RMFs were produced by using standard microsystem technology and RF magnetron sputtering technology, respectively. Scanning electron microscopy characterization revealed the distinct layer structure of the as-deposited Al/CuO RMFs. Differential scanning calorimetry was employed to ascertain the amount of heat released in the thermite reaction between Al films and CuO films, which was found to be 2024 J/g. Electrical explosion tests showed that 600 V was the most matching voltage for our set of apparatus. The explosion process of two types of films was observed by high speed camera and revealed that compared with Cu film, an extra distinct combustion phenomenon was detected with large numbers of product particles fiercely ejected to a distance of about six millimeters for Cu/Al/CuO RMFs. By using the atomic emission spectroscopy double line technique, the reaction temperature was determined to be about 6000–7000 K and 8000–9000 K for Cu film and Cu/Al/CuO RMFs, respectively. The piezoelectricity of polyvinylidene fluoride film was employed to measure the average velocity of the slapper accelerated by the explosion of the films. The average velocities of the slappers were calculated to be 381 m/s and 326 m/s for Cu film and Cu/Al/CuO RMFs, respectively, and some probable reasons were discussed with a few suggestions put forward for further work.
Accurate and efficient characterization of streak camera using etalon and fitting method with constraints
Authors: Yang Dong , Wang Zhebin , Jiang Xiaohua , Liu Yonggang , Peng Xiaoshi , Zhu Tuo , Zhang Huan , Li Zhichao , Li Sanwei , Ding Yongkun
Published: November 2011

Streak camera is widely used in continuous time diagnostics in fast physical process. To produce accurate result, it requires delicate calibration and a reliable analysis method. High quality sweep-rate data with uncertainty smaller than 0.5% are obtained over the full record area by a constrained fitting method of peak position measurement, with a short pulse laser and an etalon as the fiducial source. The temporal response is linearized by this full-screen sweep-rate data, which eliminates errors in measurement due to nonlinearity and space-distortion inherent in streak camera.
Reversible and fast shift in reflection band of a cubic blue phase in a vertical electric field
Authors: Chen Hui-Yu , Chiou Ji-Yi , Yang Kai-Xian
Published: November 2011

Two electro-optical phenomena of liquid-crystal blue phase with cubic lattice structure—(1) a fast and reversible shift in reflection band and (2) a phase transition from blue phase to chiral nematic phase—are observed in this study. By increasing the magnitude of a vertical electric field, the reflected wavelength of the blue phase can be shifted to a longer wavelength in a range of 80 nm within a few ms. This reflection band shift is induced by the reorientation of liquid-crystal molecules constructing double twist cylinders, which induces lattice distortion of the blue phase.
Magnetic pinning of flux lattice in superconducting-nanomagnet hybrids
Authors: Perez de Lara D. , Castaño F. J. , Ng B. G. , Körner H. S. , Dumas R. K. , Gonzalez E. M. , Liu Kai , Ross C. A. , Schuller Ivan K. , Vicent J. L.
Published: November 2011

Strong superconducting pinning effects are observed from magnetic landscapes produced by arrays of circular rings with varying magnetic remanent states. The collective and the background pinning of superconducting Nb films is strongly enhanced by the stray magnetic field produced by an array of circular Ni rings magnetized to form “onion” (bidomain) states. On the other hand, when the same rings are magnetized into vortex (flux-closed) states, or are randomly magnetized, the superconducting pinning is much smaller. The greatest pinning is produced when the superconducting vortex lattice motion is along a direction in which there is a strong magnetic field variation.
Local tunneling magnetoresistance probed by low-temperature scanning laser microscopy
Authors: Werner Robert , Weiler Mathias , Petrov Aleksandr Yu. , Davidson Bruce A. , Gross Rudolf , Kleiner Reinhold , Goennenwein Sebastian T. B. , Koelle Dieter
Published: November 2011

Tunneling magnetoresistance in a vertical manganite junction was investigated by low-temperature scanning laser microscopy (LTSLM) allowing to determine the local relative magnetization M orientation of the two electrodes as a function of magnitude and orientation of the external magnetic field H. Sweeping the field amplitude at fixed orientation revealed magnetic domain nucleation and propagation in the junction electrodes. For the high-resistance state, an almost single-domain antiparallel magnetization configuration was achieved, while in the low-resistance state the junction remained in a multidomain state. Calculated resistance Rcalc(H) based on the local M configuration obtained by LTSLM is in quantitative agreement with R(H) measured by magnetotransport.
Enhancement of the magnetization in the Fe3O4/BiFeO3 epitaxial heterostructures fabricated by magnetron sputtering
Authors: Liu X. F. , Li P. , Jin C. , Bai H. L.
Published: November 2011

Epitaxial Fe3O4/BiFeO3 heterostructures with different BiFeO3 thicknesses were deposited on (001) SrTiO3 substrates by magnetron sputtering. An unexpected enhancement in the magnetization measured with a high sensitivity of ∼10−7 emu magnetometer was observed, especially for the Fe3O4/BiFeO3 heterostructures with 22-nm-thick BiFeO3 layers. The magnetization of the heterostructures can be up to 133% of the sum of both single Fe3O4 and BiFeO3 layers deposited directly on the SrTiO3 substrate under the same conditions. The enhanced magnetization is considered to originate from the magnetic spin moments which interact and arrange ferromagnetically at the interface due to the strong interfacial coupling.
Negative ions: The overlooked species in thin film growth by pulsed laser deposition
Authors: Esposito M. , Bator M. , Döbeli M. , Lippert T. , Schneider C. W. , Wokaun A.
Published: November 2011

Plasma plume species from a ceramic La0.4Ca0.6MnO3 target were studied by plasma mass spectrometry as a function of laser fluence, background gas, and deposition pressure to understand the interplay between plasma composition and oxide thin film growth by pulsed laser deposition. The plume composition reveals a significant contribution of up to 24% of negative ions, most notably using a N2O background. The significance of negative ions for thin film growth is shown for La0.4Ca0.6MnO3 films grown in different background conditions where the best structural properties coincide with the largest amount of negative plasma species.
The efficient price: an opportunity for funding reform
Authors: Karnon Jonathan , Ben-Tovim David I. , Pham Clarabelle T. , Caffrey Orla , Hakendorf Paul H. , Crotty Maria , Phillips Paddy A.
Published: November 2011

Objective. Proposed Australian healthcare reforms describe a move towards partial Commonwealth funding of public hospitals, whereby hospitals will be paid an ‘efficient price’ for each separation, incorporating both the costs and benefits of services. This paper describes a potential approach to setting the efficient price using risk adjusted cost-effectiveness (RAC-E) analysis. Methods. RAC-E analysis uses a decision analytic framework to estimate lifetime costs and survival for individual patients, which are standardised by comparing observed and expected values. Analysis of standardised costs and effects at different hospitals identifies efficient hospitals, from which efficient prices can be defined. Results. A RAC-E analysis of services for stroke patients at the four main public hospitals in South Australia demonstrates the need to account for costs and benefits in identifying efficient hospitals. The hospital with the best patient outcomes incurred additional costs relative to less effective hospitals. If an investment of AU$14 760 to gain an additional life year in stroke patients is deemed to be a cost-effective use of resources, then the most effective hospital is also the most efficient hospital. Conclusions. The applied RAC-E analysis demonstrates a framework for comparing the economic efficiency of care provided at different hospitals, which provides a basis for defining the efficient price and appropriate funding incentives to achieve better patient outcomes. What is known about the topic? The efficient price is a recently introduced concept used in the context of the recent healthcare reforms produced by the Australian government. The stated objective in setting nationally efficient prices for public hospital services is to ‘strike an appropriate balance between reasonable access, clinical safety, efficiency and fiscal considerations’. There has been no explicit discussion to date about specific processes for estimating the efficient price. What does this paper add? This paper introduces risk adjusted cost-effectiveness (RAC-E) analysis as a framework for identifying hospitals that achieve the best balance between costs and outcomes in the provision of services for specific diagnostic groups, and hence provides the basis for estimating efficient prices. What are the implications for practitioners? The efficient price will determine a significant proportion of funding for public hospitals. Practitioners need to be aware of the rationale and potential consequences of the efficient price, and to be sure that the method used to estimate the efficient price is robust and transparent.
Searching for Fast Radio Transients with SKA Phase 1
Authors: Colegate T. M. , Clarke N.
Published: November 2011

The Square Kilometre Array (SKA) provides an excellent opportunity for low-cost searches for fast radio transients. The increased sensitivity and field of view of the SKA compared with other radio telescopes will make it an ideal instrument to search for impulsive emission from high–energy density events. We present a high-level search ‘use case’ and propose event rate per unit cost as a figure of merit to compare transient survey strategies for radio telescope arrays; we use event rate per beam formed and searched as a first-order approximation of this measure. Key results are that incoherent (phase-insensitive) combination of antenna signals achieves the highest event rate per beam, and that 50–100 MHz processed bandwidth is sufficient for extragalactic searches with SKA Phase 1; the gain in event rate from using the full available bandwidth is small. Greater system flexibility will enable more effective searches, but need not drive the top-level system requirements beyond those already proposed for the SKA. The most appropriate search strategy depends on the observed sky direction and the source population; for SKA Phase 1, low-frequency aperture arrays tend to be more effective for extragalactic searches, and dishes more effective for directions of increased scatter broadening, such as near the Galactic plane.
Seasonal Patterns of Movement and Residency by Striped Bass within a Subestuary of the Chesapeake Bay
Authors: Wingate Rebecca L. , Secor David H. , Kraus Richard T.
Published: November 2011

Although often generalized as anadromous, striped bass Morone saxatilis show varying degrees of residency in natal estuaries and exhibit diverse seasonal migration patterns in estuarine and coastal waters. Most coastal striped bass originate from the Chesapeake Bay, but the bay and its subestuaries also harbor substantial numbers of striped bass throughout the year. The degree to which resident striped bass inhabit individual subestuaries was evaluated by use of acoustic telemetry. We investigated seasonal patterns of movement within and outside of the Patuxent River, a centrally located, intermediate‐size subestuary of the Chesapeake Bay. A fixed acoustic receiver array was deployed in the Patuxent River, and 42 acoustic‐tagged striped bass were monitored for a 2‐year period (2008–2009). Seasonal patterns of movement within the subestuary were similar between years and were generally consistent with overall anadromous behavior: striped bass moved downestuary during winter to points outside the Patuxent River, and they moved upestuary in spring, presumably for spawning, feeding, or both. However, a substantial fraction (∼40%) of individuals was present in the Patuxent River during summer months. Most of the tagged fish returned to the Patuxent River during fall. Striped bass were present in the Patuxent River for significant time periods (5–7 months), indicating that subestuaries like the Patuxent River are utilized by Chesapeake Bay striped bass during a major part of the year.
Long‐Term Shifts in the Lateral Distribution of Age‐0 Striped Bass in the San Francisco Estuary
Authors: Sommer Ted , Mejia Francine , Hieb Kathryn , Baxter Randall , Loboschefsky Erik , Loge Frank
Published: November 2011

Like several other fishes in the pelagic community of the upper San Francisco Estuary, age‐0 striped bass Morone saxatilis have shown a major decline based on a midwater trawl sampling program that has been conducted for over 40 years. We hypothesized that the apparent decline in age‐0 striped bass might be partially attributable to a behavioral shift away from the channels sampled by the trawls. We found no evidence of an upstream–downstream shift in age‐0 distribution. Instead, age‐0 striped bass distribution remains closely associated with the low‐salinity zone of the estuary. However, the survey data suggest a substantial long‐term distribution shift away from channels and toward shoal areas. The hypothesis that young striped bass are undersampled by midwater trawls is supported by modeling of demographic patterns, which showed that the decline in numbers of age‐0 fish was not consistent with increasing trends in age‐1 fish. We hypothesize that reduced food availability in pelagic habitat is a major cause of apparent behavioral shifts by age‐0 striped bass and some native fishes. Nonetheless, the magnitude of the shift toward shoal habitat does not appear to fully account for the extreme decline in age‐0 striped bass abundance.
The sports performance application of vibration exercise for warm‐up, flexibility and sprint speed
Authors: Cochrane Darryl
Published: November 2011

Since the turn of the 21st century, there has been a resurgence of vibration technology to enhance sport science especially for power and force development. However, vibration exercise has been trialled in other areas that are central to athlete performance such as warm‐up, flexibility and sprint speed. Therefore, the aim of this review was to attempt to gain a better understanding of how acute and short‐term vibration exercise may impact on warm‐up, flexibility and sprint speed. The importance of warming up for sporting performance has been well documented and vibration exercise has the capability to be included or used as a standalone warm‐up modality to increase intramuscular temperature at a faster rate compared to other conventional warm‐up modalities. However, vibration exercise does not provide any additional neurogenic benefits compared to conventional dynamic and passive warm‐up interventions. Vibration exercise appears to be a safe modality that does not produce any adverse affects causing injury or harm and could be used during interval and substitution breaks, as it would incur a low metabolic cost and be time‐efficient compared to conventional warm‐up modalities. Acute or short‐term vibration exercise can enhance flexibility and range of motion without having a detrimental effect on muscle power, however it is less clear which mechanisms may be responsible for this enhancement. It appears that vibration exercise is not capable of improving sprint speed performance; this could be due to the complex and dynamic nature of sprinting where the purported increase in muscle power from vibration exercise is probably lost on repeated actions of high force generation. Vibration exercise is a safe modality that produces no adverse side effects for injury or harm. It has the time‐efficient capability of providing coaches, trainers, and exercise specialists with an alternative modality that can be implemented for warm‐up and flexibility either in isolation or in conjunction with other conventional training methods.
Imaging atoms and molecules on surfaces by scanning tunnelling microscopy
Authors: Chiang Shirley
Published: November 2011

This review discusses nearly 30 years of scanning tunnelling microscopy (STM) work on high resolution imaging of numerous materials systems, giving a historical perspective on the field through the author's work. After a brief discussion of early STM and atomic force microscope (AFM) instrumentation development, the review discusses high resolution STM imaging on semiconductors, metals on semiconductors, Au(1 1 1), metal on metals including surface alloys, oxygen on metals, molecules adsorbed on metals, and AFM measurements of friction on graphite and mica.
High-resolution mapping of plasmonic modes: photoemission and scanning tunnelling luminescence microscopies
Authors: Douillard Ludovic , Charra Fabrice
Published: November 2011

Photonic properties of dense metal nanostructures are currently under intense investigation because of the possible local enhancements of electromagnetic fields induced by plasmonic excitations. In this review paper, we present examples of plasmonic-field mappings based on multiphoton photoemission or STM-induced light emission, two techniques among those which offer today's best spatial resolutions for plasmon microscopy. By imaging the photoemitted electrons, using well-established electron optics, two-dimensional intensity maps reflecting the actual distribution of the optical near-field are obtained. The imaging technique involves no physical probe altering the measure. This approach provides full field spectroscopic images with a routine spatial resolution of the order of 20 nm (down to 2 nm with recent aberration corrected instruments). Alternatively, an unfamiliar property of the junction of scanning tunnelling microscope is its ability to behave as a highly localized source of light. It can be exploited to probe opto-electronic properties, in particular plasmonic fields, with ultimate subnanometre spatial resolution, an advantage balanced by a sometimes delicate deconvolution of local-probe influence.
LT-STM studies on substrate-dependent self-assembly of small organic molecules
Authors: Huang Han , Wong Swee Liang , Chen Wei , Wee Andrew Thye Shen
Published: November 2011

Low temperature scanning tunnelling microscopy is widely used to image and manipulate individual atoms and molecules on surfaces, as well as to investigate surface molecular processes such as diffusion, desorption, and configuration switching, at the atomic scale. The aim of this contribution is to highlight our recent progress in understanding the interface between small organic molecules and different substrates, focusing on two model systems: copper hexadecafluorophthalocyanine (F16CuPc) on HOPG, Ag(1 1 1), Bi/Ag(1 1 1), and copper(II) phthalocyanine (CuPc) on perylene-3,4,9,10-tetracarboxylic-3,4,9,10-dianhydride (PTCDA) and C60 pre-covered surfaces. The influence of the underlying substrates on the molecular packing is discussed.
STM and MBE: one of the best combinations
Authors: Jia Jin-Feng , Ma Xucun , Chen Xi , Sakurai T , Xue Qi-Kun
Published: November 2011

It has been 30 years since the scanning tunnelling microscope (STM) was invented by G Binnig and H Rohrer. Rapid developments have made STM increasingly powerful as an extremely versatile technique for many disciplines in condensed matter physics, chemistry, biology and other areas. As a state-of-the-art growth method, molecular beam epitaxy (MBE) is a gifted technique for epitaxial growth with atomic-level control. In this paper, by giving several examples, we will show that an STM–MBE combined system is more powerful and unique for studies on low-dimensional and new functional materials.
Atomic magnetism revealed by spin-resolved scanning tunnelling spectroscopy
Authors: Wiebe Jens , Zhou Lihui , Wiesendanger Roland
Published: November 2011

This review focuses on recent advances in the magnetic imaging of atoms adsorbed on a nonmagnetic solid surface (adatoms) by means of spin-resolved scanning tunnelling spectroscopy (SP-STS). Magnetic field dependent spectroscopy using magnetically stable spin-polarized tips has been pushed to enable magnetometry on the single atomic-spin limit. We give a detailed review of the technique for the example of Co adatoms on Pt(1 1 1). We discuss the issues concerning the basic magnetic properties of individual adatoms as well as concerning their substrate mediated interactions that have been addressed.
Effect of molecular spatial configuration on the photovoltaic properties of triphenylamine-containing D–A structured organic molecules
Authors: Zhang Jing , Yang Yi , He Chang , Deng Dan , Li Zhibo , Li Yongfang
Published: November 2011

The photovoltaic properties of four triphenylamine (TPA)-containing organic molecules were studied by fabricating bulk-heterojunction organic solar cells (OSCs) with the organic molecules as the donor and [6,6]-phenyl-C71-butyric acid methyl ester (PC70BM) as the acceptor. The molecules possess a D–A structure with TPA as the donor unit and benzothiadiazole (BT) as the acceptor unit, and have different spatial configurations with TPA as the core and with single-armed configuration (linear molecule TPA-BT), two-armed configuration (bi-armed molecule b-TPA-BT) and three-armed configuration (tri-armed molecules t-TPA-BT and S(TPA-BT)). The OSCs based on TPA-BT, b-TPA-BT, t-TPA-BT and S(TPA-BT) display power conversion efficiencies of 1.33%, 2.33%, 3.14% and 3.37%, respectively, under the illumination of AM 1.5G, 100 mW cm−2. The results indicate that the spatial configuration of the molecules influenced the photovoltaic properties significantly and the star-shaped molecules are superior to the linear and two-armed molecules in the application as donor materials in solution-processed OSCs.
Elastic (stress–strain) halo associated with ion-induced nano-tracks in lithium niobate: role of crystal anisotropy
Authors: Rivera A , Garcia G , Olivares J , Crespillo M L , Agulló-López F
Published: November 2011

The elastic strain/stress fields (halo) around a compressed amorphous nano-track (core) caused by a single high-energy ion impact on LiNbO3 are calculated. A method is developed to approximately account for the effects of crystal anisotropy of LiNbO3 (symmetry 3m) on the stress fields for tracks oriented along the crystal axes (X, Y or Z). It only considers the zero-order (axial) harmonic contribution to the displacement field in the perpendicular plane and uses effective Poisson moduli for each particular orientation. The anisotropy is relatively small; however, it accounts for some differential features obtained for irradiations along the crystallographic axes X, Y and Z. In particular, the irradiation-induced disorder (including halo) and the associated surface swelling appear to be higher for irradiations along the X- or Y-axis in comparison with those along the Z-axis. Other irradiation effects can be explained by the model, e.g. fracture patterns or the morphology of pores after chemical etching of tracks. Moreover, it offers interesting predictions on the effect of irradiation on lattice parameters.
Virtual normalization and virtual fundamental classes
Authors: Martín Alberto
Published: November 2011

In this paper, we compare the virtual fundamental classes of the stacks of

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-stable ramified maps

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-log stable ramified maps

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. For that we will see how they are identified via virtual normalization and then apply Costello’s push-forward formula.
The homology of surface diffeomorphism groups and a question of Morita
Authors: Bowden Jonathan
Published: November 2011

We answer a question posed by Morita concerning the non-trivial- ity of certain secondary characteristic classes for surface bundles. In doing so we are naturally led to show that a form of Harer stability holds for surface diffeomorphism groups in homology of small degree.
deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns
Authors: Langenberger David , Pundhir Sachin , Ekstrøm Claus T. , Stadler Peter F. , Hoffmann Steve , Gorodkin Jan
Published: November 2011

Motivation: High-throughput sequencing methods allow whole transcriptomes to be sequenced fast and cost-effectively. Short RNA sequencing provides not only quantitative expression data but also an opportunity to identify novel coding and non-coding RNAs. Many long transcripts undergo post-transcriptional processing that generates short RNA sequence fragments. Mapped back to a reference genome, they form distinctive patterns that convey information on both the structure of the parent transcript and the modalities of its processing. The miR-miR* pattern from microRNA precursors is the best-known, but by no means singular, example.

Results:  deepBlockAlign introduces a two-step approach to align RNA-seq read patterns with the aim of quickly identifying RNAs that share similar processing footprints. Overlapping mapped reads are first merged to blocks and then closely spaced blocks are combined to block groups, each representing a locus of expression. In order to compare block groups, the constituent blocks are first compared using a modified sequence alignment algorithm to determine similarity scores for pairs of blocks. In the second stage, block patterns are compared by means of a modified Sankoff algorithm that takes both block similarities and similarities of pattern of distances within the block groups into account. Hierarchical clustering of block groups clearly separates most miRNA and tRNA, and also identifies about a dozen tRNAs clustering together with miRNA. Most of these putative Dicer-processed tRNAs, including eight cases reported to generate products with miRNA-like features in literature, exhibit read blocks distinguished by precise start position of reads.

Availability: The program deepBlockAlign is available as source code from http://rth.dk/resources/dba/.

Contact:  gorodkin@rth.dk; studla@bioinf.uni-leipzig.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
AMPA: an automated web server for prediction of protein antimicrobial regions
Authors: Torrent Marc , Di Tommaso Paolo , Pulido David , Nogués M. Victòria , Notredame Cedric , Boix Ester , Andreu David
Published: November 2011

Summary: AMPA is a web application for assessing the antimicrobial domains of proteins, with a focus on the design on new antimicrobial drugs. The application provides fast discovery of antimicrobial patterns in proteins that can be used to develop new peptide-based drugs against pathogens. Results are shown in a user-friendly graphical interface and can be downloaded as raw data for later examination.

Availability: AMPA is freely available on the web at http://tcoffee.crg.cat/apps/ampa. The source code is also available in the web.

Contact:  marc.torrent@upf.edu; david.andreu@upf.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Characterization of the Gene Encoding Pisatin Demethylase (FoPDA1) in Fusarium oxysporum
Authors: Coleman Jeffrey J. , Wasmann Catherine C. , Usami Toshiyuki , White Gerard J. , Temporini Esteban D. , McCluskey Kevin , VanEtten Hans D.
Published: November 2011

The pea pathogen Fusarium oxysporum f. sp. pisi is able to detoxify pisatin produced as a defense response by pea, and the gene encoding this detoxification mechanism, FoPDA1, was 82% identical to the cytochrome P450 pisatin demethylase PDA1 gene in Nectria haematococca. A survey of F. oxysporum f. sp. pisi isolates demonstrated that, as in N. haematococca, the PDA gene of F. oxysporum f. sp. pisi is generally located on a small chromosome. In N. haematococca, PDA1 is in a cluster of pea pathogenicity (PEP) genes. Homologs of these PEP genes also were found in the F. oxysporum f. sp. pisi isolates, and PEP1 and PEP5 were sometimes located on the same small chromosomes as the FoPDA1 homologs. Transforming FoPDA1 into a pda– F. oxysporum f. sp. lini isolate conferred pda activity and promoted pathogenicity on pea to some transformants. Different hybridization patterns of FoPDA1 were found in F. oxysporum f. sp. pisi but these did not correlate with the races of the fungus, suggesting that races within this forma specialis arose independently of FoPDA1. FoPDA1 also was present in the formae speciales lini, glycines, and dianthi of F. oxysporum but they had mutations resulting in nonfunctional proteins. However, an active FoPDA1 was present in F. oxysporum f. sp. phaseoli and it was virulent on pea. Despite their evolutionary distance, the amino acid sequences of FoPDA1 of F. oxysporum f. sp. pisi and F. oxysporum f. sp. phaseoli revealed only six amino acid differences, consistent with a horizontal gene transfer event accounting for the origin of these genes.
Reduced Carbohydrate Diet to Improve Metabolic Outcomes and Decrease Adiposity in Obese Peripubertal African American Girls
Authors: Casazza Krista , Cardel Michelle , Dulin‐Keita Akilah , Hanks Lynae J. , Gower Barbara A. , Newton Anna L. , Wallace Stephenie
Published: November 2011

Objective:

Obesity prevalence among African American (AA) girls is higher than that in other groups. Because typical energy‐restriction obesity treatment strategies have had limited success, alterations in macronutrient composition may effectively improve metabolic outcomes in this population and affect future body composition trajectories. The objective was to evaluate the efficacy of a moderately restricted carbohydrate (CHO) versus a standard CHO diet on weight/fat loss and metabolic parameters in overweight/obese AA girls ages 9 to 14 years.

Methods:

A total of 26 AA girls (ranging from 92nd body mass index percentile and above) were assigned to either a reduced‐ (SPEC: 42% energy from CHO, n = 12) or a standard‐ (STAN: 55% of energy from CHO, n = 14) CHO diet (protein held constant) for 16 weeks. All of the meals were provided and clinically tailored to meet the estimated energy requirements (resting energy expenditure × 1.2 in eucaloric phase and resting energy expenditure × 1.2 − 1000 kcal in energy deficit phase). The first 5 weeks encompassed a eucaloric phase evaluating metabolic changes in the absence of weight change. The subsequent 11 weeks were hypocaloric (1000 kcal/day deficit) to promote weight/fat loss. Meal tests were performed during the eucaloric phase for metabolic analyses. Dual‐energy x‐ray absorptiometry was used to evaluate body composition.

Results:

Both groups experienced reductions in weight/adiposity, but the difference did not reach significance. The solid meal test indicated improved glucose/insulin homeostasis on the SPEC diet up to 3 hours postingestion. In addition, significantly lower triglycerides (P < 0.001) were observed on the SPEC diet.

Conclusions:

Dietary CHO reduction favorably influences metabolic parameters but did not result in greater weight/fat loss relative to a standard diet in obese AA girls. Future research is needed to determine long‐term effectiveness of a reduced CHO diet on glucose and insulin homeostasis and how it may apply to weight maintenance/fat loss during development alone and/or in combination with additional weight loss/metabolic improvement strategies.
A versatile gene trap to visualize and interrogate the function of the vertebrate proteome
Authors: Trinh Le A. , Hochgreb Tatiana , Graham Matthew , Wu David , Ruf-Zamojski Frederique , Jayasena Chathurani S. , Saxena Ankur , Hawk Rasheeda , Gonzalez-Serricchio Aidyl , Dixson Alana , Chow Elly , Gonzales Constanza , Leung Ho-Yin , Solomon Ilana , Bronner-Fraser Marianne , Megason Sean G. , Fraser Scott E.
Published: November 2011

We report a multifunctional gene-trapping approach, which generates full-length Citrine fusions with endogenous proteins and conditional mutants from a single integration event of the FlipTrap vector. We identified 170 FlipTrap zebrafish lines with diverse tissue-specific expression patterns and distinct subcellular localizations of fusion proteins generated by the integration of an internal citrine exon. Cre-mediated conditional mutagenesis is enabled by heterotypic lox sites that delete Citrine and “flip” in its place mCherry with a polyadenylation signal, resulting in a truncated fusion protein. Inducing recombination with Cerulean-Cre results in fusion proteins that often mislocalize, exhibit mutant phenotypes, and dramatically knock down wild-type transcript levels. FRT sites in the vector enable targeted genetic manipulation of the trapped loci in the presence of Flp recombinase. Thus, the FlipTrap captures the functional proteome, enabling the visualization of full-length fluorescent fusion proteins and interrogation of function by conditional mutagenesis and targeted genetic manipulation.
Large drought‐induced aboveground live biomass losses in southernRockyMountain aspen forests
Authors: Huang Cho‐Ying , Anderegg William R. L.
Published: November 2011

Widespread drought‐induced forest mortality has been documented across multiple tree species inNorthAmerica in recent decades, but it is a poorly understood component in terrestrial carbon (C) budgets. Recent severe drought in concert with elevated temperature likely triggered widespread forest mortality of trembling aspen (Populus tremuloides), the most widely distributed tree species inNorthAmerica. The impact on the regional C budgets and spatial pattern of this drought‐induced tree mortality, which has been termed ‘sudden aspen decline (SAD)’, is not well known and could contribute to increased regional C emissions, an amplifying feedback to climate change. We conducted a regional assessment of drought‐induced live aboveground biomass (AGB) loss fromSADacross 915 km2of southwesternColorado,USA, and investigated the influence of topography on the severity of mortality by combining field measures, remotely sensed nonphotosynthetically active vegetation and a digital elevation model. Mean [± standard deviation (SD)] remote sensing estimate of liveAGBloss was 60.3 ± 37.3 Mg ha−1, which was 30.7% of field measuredAGB, totaling 2.7 Tg of potential C emissions from this dieback event. Aspen forest health could be generally categorized as healthy (0–30% field measured canopy dieback), intermediate (31–50%), andSAD(51–100%), with the remote sensing estimated mean (± SD) liveAGBlosses of 26.4 ± 15.1, 64.5 ± 9.2, and 108.5 ± 24.0 Mg ha−1, respectively. There was a pronounced clustering pattern ofSADon south‐facing slopes due to relatively drier and warmer conditions, but no apparent spatial gradient was found for elevation and slope. This study demonstrates the feasibility of utilizing remote sensing to assess the ramification of climate‐induced forest mortality on ecosystems and suggests promising opportunities for systematic large‐scale C dynamics monitoring of tree dieback, which would improve estimates of C budgets ofNorthAmerica with climate change.
Ocean acidification and seaweed reproduction: increased CO2 ameliorates the negative effect of lowered pH on meiospore germination in the giant kelp Macrocystis pyrifera (Laminariales, Phaeophyceae)
Authors: Roleda Michael Y. , Morris Jaz N. , McGraw Christina M. , Hurd Catriona L.
Published: November 2011

The worldwide effects of ocean acidification (OA) on marine species are a growing concern. In temperate coastal seas, seaweeds are dominant primary producers that create complex habitats and supply energy to higher trophic levels. Studies on OA and macroalgae have focused on calcifying species and adult stages, but critically, they have overlooked the microscopic stages of the reproductive life cycle, which, for other anthropogenic stressors, e.g., UV‐B radiation, are the most susceptible life‐history phase. Also, environmental cues and stressors can cause changes in the sex ratio, which has implications for the mating system and recruitment success. Here, we report the effects of pH (7.59–8.50) on meiospore germination and sex determination for the giant kelp, Macrocystis pyrifera (Laminariales), in the presence and absence of additional dissolved inorganic carbon (DIC). Lowered pH (7.59–7.60, using HCl‐only) caused a significant reduction in germination, whereas added DIC had the opposite effect, indicating that increased CO2 at lower pH ameliorates physiological stress. This finding also highlights the importance of appropriate manipulation of seawater carbonate chemistry when testing the effects of OA on photosynthetic organisms. The proportion of male to female gametophytes did not vary significantly between treatments, suggesting that pH was not a primary environmental modulator of sex. Relative to the baseline (pH 8.19), gametophytes were 32% larger under moderate OA (pH 7.86) and 10% larger under extreme OA (pH 7.61). We suggest that metabolically active cells can compensate for the acidification of seawater. This homeostatic function minimizes the negative effects of lower pH (high H+ ions) on cellular activity. The 6–9% reduction in germination success under extreme OA suggests that meiospores of M. pyrifera may be resistant to future OA.
A maxillary lateral incisor with four root canals
Authors: Kottoor J. , Murugesan R. , Albuquerque D. V.
Published: November 2011

Kottoor J, Murugesan R, Albuquerque DV. A maxillary lateral incisor with four root canals. International Endodontic Journal, 45, 393–397, 2012.

Aim  To describe the successful non‐surgical endodontic management of a permanent maxillary lateral incisor tooth with four root canals.

Summary  Aberrant morphology of root canals can occur in any tooth, including maxillary lateral incisors. In the presented case, clinical examination and radiographs clearly depicted the presence of four root canals in a right maxillary lateral incisor. The differential diagnosis included fusion, gemination, dens invaginatus or a combination of these. The report emphasises the need for attention during root canal treatment of maxillary lateral incisors.

Key learning points 

 Clinicians should be aware of the variable root canal anatomy in maxillary lateral incisor teeth.

 Careful examination of radiographs and the internal anatomy of teeth are essential prerequisites for successful root canal treatment.

 Four root canals in maxillary lateral incisors is a possibility.