bluuebunny/crossref_metadata_2025 huggingface dataset:
Regularized 13 moment equations for hard sphere molecules: Linear bulk equations
Authors: Struchtrup Henning , Torrilhon Manuel
Published: May 2013

The regularized 13 moment equations of rarefied gas dynamics are derived for a monatomic hard sphere gas in the linear regime. The equations are based on an extended Grad-type moment system, which is systematically reduced by means of the Order of Magnitude Method [H. Struchtrup, “Stable transport equations for rarefied gases at high orders in the Knudsen number,” Phys. Fluids 16(11), 3921–3934 (2004)]10.1063/1.1782751. Chapman-Enskog expansion of the final equations yields the linear Burnett and super-Burnett equations. While the Burnett coefficients agree with literature values, this seems to be the first time that super-Burnett coefficients are computed for a hard sphere gas. As a first test of the equations the dispersion and damping of sound waves is considered.
Observation of linear to planar structural transition in sulfur-doped gold clusters: AuxS− (x = 2–5)
Authors: Wen Hui , Liu Yi-Rong , Huang Teng , Xu Kang-Ming , Zhang Wei-Jun , Huang Wei , Wang Lai-Sheng
Published: May 2013

We report a joint experimental and theoretical study on the structures of a series of gold clusters doped with a sulfur atom, AuxS− (x = 2−5). Well-resolved photoelectron spectra are obtained and compared with theoretical results calculated using several density functional methods to elucidate the structures and bonding of AuxS− (x = 2−5). Au2S− is found to have an asymmetric linear global minimum structure with C∞v symmetry, while the most stable structure of neutral Au2S is bent with C2v symmetry, reminiscent of H2S. Au3S− is found to have an asymmetric bent structure with an Au–S–Au–Au connectivity. Two isomers are observed experimentally to co-exist for Au4S−: a symmetric bent 1D structure (C2v) and a 2D planar low-lying isomer (Cs). The global minimum of Au5S− is found to be a highly stable planar triangular structure (C2v). Thus, a 1D-to-2D structural transition is observed in the AuxS− clusters as a function of x at x = 4. Molecular orbital analyses are carried out to obtain insight into the nature of the chemical bonding in the S-doped gold clusters. Strong covalent bonding between S and Au is found to be responsible for the 1D structures of AuxS− (x = 2−4), whereas delocalized Au−Au interactions favor the 2D planar structure for the larger Au5S− cluster.
Excitation energy transfer efficiency: Equivalence of transient and stationary setting and the absence of non-Markovian effects
Authors: Jesenko Simon , Žnidarič Marko
Published: May 2013

We analyze efficiency of excitation energy transfer in photosynthetic complexes in transient and stationary setting. In the transient setting, the absorption process is modeled as an individual event resulting in a subsequent relaxation dynamics. In the stationary setting the absorption is a continuous stationary process, leading to the nonequilibrium steady state. We show that, as far as the efficiency is concerned, both settings can be considered to be the same, as they result in almost identical efficiency. We also show that non-Markovianity has no effect on the resulting efficiency, i.e., corresponding Markovian dynamics results in identical efficiency. Even more, if one maps dynamics to appropriate classical rate equations, the same efficiency as in quantum case is obtained.
Carbon monoxide adsorption on platinum-osmium and platinum-ruthenium-osmium mixed nanoparticles
Authors: Dimakis Nicholas , Navarro Nestor E. , Smotkin Eugene S.
Published: May 2013

Density functional calculations (DFT) on carbon monoxide (CO) adsorbed on platinum, platinum-osmium, and platinum-ruthenium-osmium nanoclusters are used to elucidate changes on the adsorbate internal bond and the carbon-metal bond, as platinum is alloyed with osmium and ruthenium atoms. The relative strengths of the adsorbate internal bond and the carbon-metal bond upon alloying, which are related to the DFT calculated C–O and C–Pt stretching frequencies, respectively, cannot be explained by the traditional 5σ-donation/2π*-back-donation theoretical model. Using a modified π-attraction σ-repulsion mechanism, we ascribe the strength of the CO adsorbate internal bond to changes in the polarization of the adsorbate-substrate hybrid orbitals towards carbon. The strength of the carbon-metal bond is quantitatively related to the CO contribution to the adsorbate-substrate hybrid orbitals and the sp and d populations of adsorbing platinum atom. This work complements prior work on corresponding slabs using periodic DFT. Similarities and differences between cluster and periodic DFT calculations are discussed.
Robust and efficient configurational molecular sampling via Langevin dynamics
Authors: Leimkuhler Benedict , Matthews Charles
Published: May 2013

A wide variety of numerical methods are evaluated and compared for solving the stochastic differential equations encountered in molecular dynamics. The methods are based on the application of deterministic impulses, drifts, and Brownian motions in some combination. The Baker-Campbell-Hausdorff expansion is used to study sampling accuracy following recent work by the authors, which allows determination of the stepsize-dependent bias in configurational averaging. For harmonic oscillators, configurational averaging is exact for certain schemes, which may result in improved performance in the modelling of biomolecules where bond stretches play a prominent role. For general systems, an optimal method can be identified that has very low bias compared to alternatives. In simulations of the alanine dipeptide reported here (both solvated and unsolvated), higher accuracy is obtained without loss of computational efficiency, while allowing large timestep, and with no impairment of the conformational exploration rate (the effective diffusion rate observed in simulation). The optimal scheme is a uniformly better performing algorithm for molecular sampling, with overall efficiency improvements of 25% or more in practical timestep size achievable in vacuum, and with reductions in the error of configurational averages of a factor of ten or more attainable in solvated simulations at large timestep.
A digital magnetic resonance imaging spectrometer using digital signal processor and field programmable gate array
Authors: Liang Xiao , Binghe Sun , Yueping Ma , Ruyan Zhao
Published: May 2013

A digital spectrometer for low-field magnetic resonance imaging is described. A digital signal processor (DSP) is utilized as the pulse programmer on which a pulse sequence is executed as a subroutine. Field programmable gate array (FPGA) devices that are logically mapped into the external addressing space of the DSP work as auxiliary controllers of gradient control, radio frequency (rf) generation, and rf receiving separately. The pulse programmer triggers an event by setting the 32-bit control register of the corresponding FPGA, and then the FPGA automatically carries out the event function according to preset configurations in cooperation with other devices; accordingly, event control of the spectrometer is flexible and efficient. Digital techniques are in widespread use: gradient control is implemented in real-time by a FPGA; rf source is constructed using direct digital synthesis technique, and rf receiver is constructed using digital quadrature detection technique. Well-designed performance is achieved, including 1 μs time resolution of the gradient waveform, 1 μs time resolution of the soft pulse, and 2 MHz signal receiving bandwidth. Both rf synthesis and rf digitalization operate at the same 60 MHz clock, therefore, the frequency range of transmitting and receiving is from DC to ∼27 MHz. A majority of pulse sequences have been developed, and the imaging performance of the spectrometer has been validated through a large number of experiments. Furthermore, the spectrometer is also suitable for relaxation measurement in nuclear magnetic resonance field.
Room temperature magneto-birefringence in composites of stress-birefringence and magnetostriction
Authors: Luo X. B. , Wu D. , Zhang N.
Published: May 2013

Laminate composites that can show magneto-birefringence effect were suggested and fabricated based on the product effect of magnetostriction and stress-birefringence. Under a magnetic field no stronger than 1900 Oe, a phase difference of about 3.3π was observed for a trilayer composite Tb1−xDyxFe2−y/polycarbonate/Tb1−xDyxFe2−y with the polycarbonate layer in size of 5 × 2.75 × 20 mm3 at room temperature, resulting in a half-wave magnetic field of no greater than 270 Oe. Experiments and theoretical analysis showed that the magneto-birefringence effects in the laminate composites are wavelength-relative and high size-sensitive.
Measured hot-electron intensity thresholds quantified by a two-plasmon-decay resonant common-wave gain in various experimental configurations
Authors: Michel D. T. , Maximov A. V. , Short R. W. , Delettrez J. A. , Edgell D. , Hu S. X. , Igumenshchev I. V. , Myatt J. F. , Solodov A. A. , Stoeckl C. , Yaakobi B. , Froula D. H.
Published: May 2013

The fraction of laser energy converted into hot electrons by the two-plasmon-decay instability is found to have different overlapped intensity thresholds for various configurations on the Omega Laser Facility [T. R. Boehly et al., Opt. Commun. 133, 495 (1997); J. H. Kelly et al., J. Phys. IV 133, 75 (2006)]. A factor-of-2 difference in the overlapped intensity threshold is observed between two- and four-beam configurations. The overlapped intensity threshold increases by a factor of 2 between the 4- and 18-beam configurations and by a factor of 3 between the 4- and 60-beam configurations. This is explained by a linear common-wave model where multiple laser beams drive a common electron-plasma wave in a wavevector region that bisects the laser beams (resonant common-wave region in k-space). These experimental results indicate that the hot-electron threshold depends on the hydrodynamic parameters at the quarter-critical density surface, the configuration of the laser beams, and the sum of the intensity of the beams that share the same angle with the common-wave vector.
Wide-area scanner for high-speed atomic force microscopy
Authors: Watanabe Hiroki , Uchihashi Takayuki , Kobashi Toshihide , Shibata Mikihiro , Nishiyama Jun , Yasuda Ryohei , Ando Toshio
Published: May 2013

High-speed atomic force microscopy (HS-AFM) has recently been established. The dynamic processes and structural dynamics of protein molecules in action have been successfully visualized using HS-AFM. However, its maximum scan ranges in the X- and Y-directions have been limited to ∼1 μm and ∼4 μm, respectively, making it infeasible to observe the dynamics of much larger samples, including live cells. Here, we develop a wide-area scanner with a maximum XY scan range of ∼46 × 46 μm2 by magnifying the displacements of stack piezoelectric actuators using a leverage mechanism. Mechanical vibrations produced by fast displacement of the X-scanner are suppressed by a combination of feed-forward inverse compensation and the use of triangular scan signals with rounded vertices. As a result, the scan speed in the X-direction reaches 6.3 mm/s even for a scan size as large as ∼40 μm. The nonlinearity of the X- and Y-piezoelectric actuators’ displacements that arises from their hysteresis is eliminated by polynomial-approximation-based open-loop control. The interference between the X- and Y-scanners is also eliminated by the same technique. The usefulness of this wide-area scanner is demonstrated by video imaging of dynamic processes in live bacterial and eukaryotic cells.
Electrical and optical characterization of the metal-insulator transition temperature in Cr-doped VO2 thin films
Authors: Brown B. L. , Lee Mark , Clem P. G. , Nordquist C. D. , Jordan T. S. , Wolfley S. L. , Leonhardt D. , Edney C. , Custer J. A.
Published: May 2013

The effect of Cr doping on electrical and optical properties of CrxV1−xO2 thin films across the metal-insulator transition has been studied. Resistance, Hall effect, and infrared reflectance show that Cr doping systematically increases the transition temperature Tc from 59 °C at x = 0 to 70 °C at x = 0.11 with similar transition width and hysteresis from DC to infrared, but the effect appears to saturate. The conductance contrast between insulating and metallic phases decreases with Cr doping. The effects of carrier density and mobility changes across Tc will be discussed.
Nucleation rate reduction through stress relief of thermally annealed hydrogenated amorphous silicon films
Authors: Dabney M. S. , van Hest M. F. A. M. , Mahan A. H. , Ginley D. S.
Published: May 2013

The effect of film stress on crystallite nucleation is investigated in 0.11  μm thick, thermally annealed hydrogenated amorphous silicon films. Using a recently developed optical method, the crystallite density is measured as the films are isochronally annealed at 600 °C, which enables the determination of the crystallite nucleation rate. This rate is significantly suppressed around scratches, cleaved film edges, and laser ablated areas, extending laterally as much as 100–150 μm from these regions where the film connectivity is disrupted. μ-Raman measurements of the transverse optical mode of Si demonstrate an accompanying reduction in tensile stress in the regions where nucleation is suppressed. The first measurements of nucleation rate in stress and in stress relieved areas in the same film are presented.
Light-harvesting efficiency of a (6,5) carbon nanotube functionalized with a free-base tetraphenylporphyrin: Density functional theory calculations
Authors: Correa J. D. , Orellana W.
Published: May 2013

Using ab initio calculations, we study the optical absorption of a free-base tetraphenylporphyrin (TPP) noncovalently attached onto a (6,5) semiconducting carbon nanotube (CNT). The optical properties of the CNT-TPP assembly were obtained through the imaginary part of the dielectric function in the linear optical response, whereas the light-harvesting efficiency is estimated through adsorbed and delivered irradiance calculations on a CNT-TPP thin film. Our results suggest that the maximum efficiency could reach 40% for a 100 nm thick film, stabilizing in this value for thicker films. We also found a strong dipole-dipole interaction at the CNT-TPP interface not observed on achiral CNTs, suggesting that the high efficiency in the excitation energy transfer measured in this assembly would be originated in a resonance transfer process induced by the CNT chirality.
In-situ monitoring of molecular vibrations of two organic semiconductors in photovoltaic blends and their impact on thin film morphology
Authors: Tsoi Wing C. , Zhang Weimin , Razzell Hollis Joseph , Suh Minwon , Heeney Martin , McCulloch Iain , Kim Ji-Seon
Published: May 2013

We report in-situ simultaneous monitoring of molecular vibrations of two components in organic photovoltaic blends using resonant Raman spectroscopy. Blend films were composed of a low bandgap copolymer thieno[3,2-b]thiophene-diketopyrrolopyrrole (DPPTTT) and (6,6)-phenyl-C71-butyric acid ester (PC70BM). Changes in Raman spectra associated with crystallization processes of each component and their impact on thin film morphology were studied during thermal annealing and cooling processes. Transition temperatures to crystalline phases in blends were measured at ∼150 °C and ∼170 °C for DPPTTT and PC70BM, respectively. Such phase changes lead to modifications in local chemical composition reducing relative Raman peak intensities (IPC70BM/IDPPTTT) from ∼0.4 in PC70BM-rich domains to ∼0.15 in homogeneous areas.
Broadband vibration energy harvesting based on cantilevered piezoelectric bi-stable composites
Authors: Arrieta A. F. , Delpero T. , Bergamini A. E. , Ermanni P.
Published: May 2013

Bi-stable composites are considered for vibration based energy harvesting, thanks to the broadband nature of their dynamic response. In this letter, a cantilevered piezoelectric bi-stable composite concept is introduced for broadband energy harvesting. The proposed configuration allows for exploiting the large strains developed close to the clamped root, significantly enhancing the harvesting effectiveness in comparison to previous settings. A simple model is used for designing the dynamic response aiming to maximise broadband oscillations. Experimental results reveal wide bands of high power conversion. Additionally, a shunting circuit suitable for broadband conversion is employed, further increasing the effectiveness of the proposed concept.
Electric field-induced monodomain blue phase liquid crystals
Authors: Chen Yuan , Wu Shin-Tson
Published: May 2013

We demonstrate an electric field-induced monodomain blue phase liquid crystal and its application for polarizer-free reflective displays. Superior to multidomain structure, the monodomain exhibits a relatively high reflectance and narrow bandwidth (∼25 nm) so the reflected colors look vivid. As the applied voltage increases, the double-twist structure is gradually unwound so that Bragg reflection decreases leading to analogous grayscale. The submillisecond response time enables this reflective display to play videos without image blurs. Such a monodomain blue phase selectively reflects right-handed circularly polarized light when the employed chiral dopant is right-handed, and the reflected light is nearly circularly polarized.
On contribution and detection of higher eigenmodes during dynamic atomic force microscopy
Authors: Saraswat Govind , Salapaka Murti V.
Published: May 2013

Dynamic mode operation of Atomic Force Microscopes relies on demodulation schemes to get information from different flexure modes of the cantilever while imaging a sample. In the article, we demonstrate that the conventional approach of discerning higher mode participation via amplitude and phase demodulation is not suitable for high bandwidth applications. Furthermore, we provide a method where the higher mode participation is reconstructed with high fidelity, and present a scheme for high bandwidth detection of higher modes when their participation becomes significant. These methods are shown to outperform the traditional amplitude-phase demodulation schemes in terms of speed, resolution, and fidelity. The framework developed is tested on simulations and the method's utility for first two modes is demonstrated experimentally.
Evidence of atomically resolved 6×6 buffer layer with long-range order and short-range disorder during formation of graphene on 6H-SiC by thermal decomposition
Authors: Hu T. W. , Ma F. , Ma D. Y. , Yang D. , Liu X. T. , Xu K. W. , Chu Paul K.
Published: May 2013

Scanning tunneling microscopy (STM) is performed to study the formation mechanism of graphene on 6H-SiC by thermal decomposition in situ and the evolution of an atomically resolved 6×6 structure in the buffer layer is revealed. The long-range order of the 6×6 structure is maintained during growth, but the short-range arrangement changes with temperature. Based on STM images acquired at different voltages, a structure consisting of triangular silicon clusters with the 6×6 structure and filled by amorphous carbon atoms is proposed. The 6×6 silicon clusters serve as the template and amorphous carbon atoms provide the carbon source for graphene growth.
Determination of stress, strain, and elemental distribution within In(Ga)As quantum dots embedded in GaAs using advanced transmission electron microscopy
Authors: Cherkashin N. , Reboh S. , Hÿtch M. J. , Claverie A. , Preobrazhenskii V. V. , Putyato M. A. , Semyagin B. R. , Chaldyshev V. V.
Published: May 2013

Non-truncated pyramidal In(Ga)As quantum dots (QDs) embedded in GaAs were obtained by a combination of low temperature/high rate GaAs covering of InAs QDs. We use advanced transmission electron microscopy to study the composition and mechanics of the objects. Results from the core region of a sliced QD, and from an entire object, are consistent and complementary allowing the development of accurate models describing the 3D shape, chemical distribution, elastic strains and stresses in the QD, wetting layer, and matrix. The measured structure develops an extremely compressive apex, reaching a vertical stress of −8 GPa and horizontal stress of −6.2 GPa.
Estimation of residual carrier density near the Dirac point in graphene through quantum capacitance measurement
Authors: Nagashio K. , Nishimura T. , Toriumi A.
Published: May 2013

We discuss the residual carrier density (n*) near the Dirac point (DP) in graphene estimated by quantum capacitance (CQ) and conductivity (σ) measurements. The CQ at the DP has a finite value and is independent of the temperature. A similar behavior is also observed for the conductivity at the DP, because their origin is residual carriers induced externally by charged impurities. The n* extracted from CQ, however, is often smaller than that from σ, suggesting that the mobility in the puddle region is lower than that in the linear region. The CQ measurement should be employed for estimating n* quantitatively.
Establishment, survival, and herbage production of novel, summer-active perennial pasture legumes in the low-rainfall cropping zone of Western Australia as affected by plant density and cutting frequency
Authors: Suriyagoda Lalith D. B. , Real Daniel , Renton Michael , Lambers Hans , Ryan Megan H.
Published: May 2013

Herbaceous perennial legumes that can provide forage in the summer–autumn dry period are urgently required in Mediterranean climates to complement annual pastures and the perennial legume lucerne (Medicago sativa). This study evaluated the establishment, survival, and herbage production of tedera (Bituminaria bituminosa var. albomarginata) and Cullen spp. native to Australia. Two experiments were replicated at Buntine (warmer site) and Newdegate (cooler site) in the low-rainfall cropping zone (<350 mm average annual rainfall) of Western Australia from June 2008 to September 2010. In the first experiment, established by transplanting seedlings, survival and herbage production of two accessions each of B. bituminosa and C. australasicum were studied under densities of 1, 2, 4, 8, and 16 plants/m2 with 0, 1, 2, or 3 cuts in summer–autumn in addition to a winter–spring cut. In the second experiment, established from seed, emergence and survival of several accessions of B. bituminosa, C. australasicum, and M. sativa were studied, along with C. pallidum and C. cinereum.
In the first experiment, B. bituminosa survived better than C. australasicum (70–80% v. 18–45%), especially at Buntine, but there was little impact of density or cutting frequency on survival. Plant death was highest during summer. Shoot dry weight (DW) accumulation varied greatly with site, year, and plant density. When rainfall was close to average, shoot DW was greater at Newdegate (B. bituminosa ≤7.4 t/ha, C. australasicum ≤4.5 t/ha) than at Buntine (≤2.3 t/ha), and both species produced much of their shoot DW in summer–autumn (e.g. 6 t/ha for B. bituminosa and 3 t/ha for C. australasicum at Newdegate). An early-summer cut reduced the DW that could be harvested later in summer–autumn. In the second experiment, emergence of B. bituminosa was either similar to, or higher than, emergence of the other species, being 43% at Buntine and 44% at Newdegate. Survival of B. bituminosa, compared with M. sativa, was similar at Buntine (13%) and slightly lower at Newdegate (14%). Emergence and survival of Cullen spp. varied among species and accessions, with survival of the best performing accession of C. australasicum (SA4966) similar to that of B. bituminosa and M. sativa at both sites. We conclude that B. bituminosa shows promise as a perennial summer forage for low-rainfall zones, with a density of 8–16 plants/m2 and cutting frequency of 3 cuts/year (i.e. cut twice in summer–autumn), while C. australasicum and C. pallidum warrant further study.
Genetic profile of dingoes (Canis lupus dingo) and free-roaming domestic dogs (C. l. familiaris) in the Tanami Desert, Australia
Authors: Newsome Thomas M. , Stephens Danielle , Ballard Guy-Anthony , Dickman Christopher R. , Fleming Peter J. S.
Published: May 2013

Context Many rare and endangered species are threatened by the effects of hybridisation with their domesticated and often numerically dominant relatives. However, factors that influence interactions between hybridising species are poorly understood, thus limiting our ability to develop ameliorative strategies. Aims Here, we identify family groups and investigate patterns of gene flow between dingoes (Canis lupus dingo) and domestic dogs (C. l. familiaris) in the Tanami Desert of central Australia. We aimed to determine whether human-provided resources facilitate hybridisation or alter typical patterns of dingo breeding and social behaviour. We also ask whether remote townships are arenas for dingo–dog hybridisation. Methods Tissue samples and morphological details were collected from dingo-like animals around two mine sites where humans provide abundant supplementary food and water. Using molecular DNA analyses, we assigned animals to population clusters, determined kinship and the numbers of family groups. Rates of hybridisation were assessed around the mines and in two nearby townships. Key results Of 142 samples from mine sites, ‘pure’ dingoes were identified genetically in 89% of cases. This predominance of dingoes was supported by our observations on coat colour and body morphology. Only 2 of 86 domestic dogs sampled at the two townships showed evidence of dingo ancestry. Around the mine sites, there were two distinct population clusters, including a large family group of 55 individuals around a refuse facility. Conclusions Where superabundant and consistent food, and reliable water, was available, dingo packs were much larger and co-existed with others, contrary to expectations derived from previous research. Dingo sociality and pack structures can therefore be altered where human-provided food and water are constantly available, and this could facilitate accelerated rates of hybridisation. Implications The development of appropriate domestic-waste management strategies should be a high priority in remote areas to ensure only normal rates of population increase by dingoes, and other canids more broadly. It will also potentially impede hybridisation rates if typical canid social and behavioural traits remain intact. Additionally, areas surrounding remote human settlements are likely arenas for accentuated dingo–domestic dog interactions and should be a target for future studies.
Measuring tuberculosis immune responses in the lung - the correct target?
Authors: Breen R. , Lipman M.
Published: May 2013

This chapter discusses how the immune response in tuberculosis has been studied in the lungs. It focuses on tuberculosis pathogenesis as well as diagnosis, and evaluates the status of current research. Finally, it reflects on the value gained from lung-based work and reviews future directions in tuberculosis lung immunology programmes.
Molecular tools for fast identification of resistance and characterization of MDR/XDR-TB.
Authors: Cadmus S. , Soolingen D. van
Published: May 2013

This chapter discusses the principles of drug resistance and the advantages and limitations of novel methods for rapid molecular detection of multiple/extensive drug resistance in Mycobacterium tuberculosis (e.g., line probe assays and semi-automated real-time polymerase chain reaction).
Monitoring therapy by bacterial load.
Authors: O'Sullivan D. M.
Published: May 2013

This chapter reviews the use of microscopy, culture, molecular tools (e.g., polymerase chain reaction) and immunological assays in the determination of bacterial to monitor treatment of tuberculosis.
Modelling responses to tuberculosis treatment.
Authors: Davies G. R.
Published: May 2013

This chapter describes the conceptualization of tuberculosis treatment response and the problem of surrogate end points. It provides an overview of the challenges this problem poses for the development of new drugs, summarizes the state of current efforts to overcome them and gives some insight into future developments.
Transcriptomic approaches to mapping responses to drug therapy for tuberculosis.
Authors: Waddell S. J. , Butcher P. D.
Published: May 2013

This chapter focuses on the applications of gene expression profiling, derived predominantly from microarray analyses, towards the development of novel compounds and a greater understanding of drug action in Mycobacterium tuberculosis, as well as characterizing the molecular mechanisms of drug resistance and tolerance.
Therapy of the XDR-TB patient with thioridazine - an old drug with new applications.
Authors: Amaral L. , Martins M. , Couto I. , Viveiros M.
Published: May 2013

This chapter provides the rationale and experimental basis for considering thioridazine (an inexpensive neuroleptic drug used for over 40 years) as a new effective drug for treatment of extensively drug-resistant tuberculosis (XDR-TB). The development of antibiotic resistance in Mycobacterium tuberculosis, the criteria for an effective anti-MDR/XDR-TB, anti-latent M. tuberculosis agent, and the antituberculosis activity of phenothiazines are described.
The 2-blocks of defect 4
Authors: Külshammer Burkhard , Sambale Benjamin
Published: May 2013

We show that the major counting conjectures of modular representation theory are satisfied for

2
2

-blocks of defect at most

4
4

except one possible case. In particular, we determine the invariants of such blocks.
Targeting anti‐beta‐1‐adrenergic receptor antibodies for dilated cardiomyopathy
Authors: Patel Priyesh A. , Hernandez Adrian F.
Published: May 2013

Anti‐beta‐1‐adrenergic receptor antibodies (anti‐β1AR Abs) have long been implicated in the pathogenesis of dilated cardiomyopathy (DCM). It is believed that these autoantibodies bind to and constitutively stimulate the β1AR to promote pathological cardiac remodelling and β1AR desensitization and downregulation. The prevalence of anti‐β1AR Abs in patients with DCM ranges from 26% to 60%, and the presence of these autoantibodies correlates with a poor prognosis. Several small studies have shown improvements in functional status, haemodynamics, and biomarkers of heart failure upon removal or neutralization of these antibodies from the sera of affected patients. Traditionally, removal of anti‐β1AR Abs required immunoadsorption therapy with apheresis columns directed against human immunoglobulins (Igs) and subsequent i.v. Ig infusion, thereby essentially performing a plasma exchange transfusion. However, recent advances have allowed the development of small peptides and nucleotide sequences that specifically target and neutralize anti‐β1AR Abs, providing a hopeful avenue for future drug development to treat DCM. Herein, we briefly review the clinical literature of therapy directed against anti‐β1AR Abs and highlight the opportunity for further research and development in this area.
Microtopography of the eye surface of the crab
Carcinus maenas
: an atomic force microscope study suggesting a possible antifouling potential
Authors: Greco G. , Lanero T. Svaldo , Torrassa S. , Young R. , Vassalli M. , Cavaliere A. , Rolandi R. , Pelucchi E. , Faimali M. , Davenport J.
Published: May 2013

Marine biofouling causes problems for technologies based on the sea, including ships, power plants and marine sensors. Several antifouling techniques have been applied to marine sensors, but most of these methodologies are environmentally unfriendly or ineffective. Bioinspiration, seeking guidance from natural solutions, is a promising approach to antifouling. Here, the eye of the green crab
Carcinus maenas
was regarded as a marine sensor model and its surface characterized by means of atomic force microscopy. Engineered surface micro- and nanotopography is a new mechanism found to limit biofouling, promising an effective solution with much reduced environmental impact. Besides giving a new insight into the morphology of
C. maenas
eye and its characterization, our study indicates that the eye surface probably has antifouling/fouling-release potential. Furthermore, the topographical features of the surface may influence the wettability properties of the structure and its interaction with organic molecules. Results indicate that the eye surface micro- and nanotopography may lead to bioinspired solutions to antifouling protection.
Curved pleat folding for smooth wrapping
Authors: Lee Nicolas , Close Sigrid
Published: May 2013

A technique is presented to minimize the packaged size of a flat sheet by folding it into a strip that can be wrapped around a hub. This is difficult to accomplish using regular straight creases, because of the thickness of the sheet. A curved crease pattern is used to address this problem of non-zero thickness. A mathematical formulation is developed in order to compute the required crease pattern for coiling a folded strip to any desired curvature, and specifically for coiling it into a tight spiral around a hub. This method is demonstrated with paper models. The crease computation algorithm is then extended to provide a folding strategy to efficiently package a square sheet around a central hub such that it can easily unfold or deploy. This development has applications particularly for deployable structures on small spacecraft.
Multivariate sexual selection in a rapidly evolving speciation phenotype
Authors: Oh Kevin P. , Shaw Kerry L.
Published: May 2013

Estimating the fitness surface of rapidly evolving secondary sexual traits can elucidate the origins of sexual isolation and thus speciation. Evidence suggests that sexual selection is highly complex in nature, often acting on multivariate sexual characters that sometimes include non-heritable components of variation, thus presenting a challenge for predicting patterns of sexual trait evolution.
Laupala
crickets have undergone an explosive species radiation marked by divergence in male courtship song and associated female preferences, yet patterns of sexual selection that might explain this diversification remain unknown. We used female phonotaxis trials to estimate the fitness surface for acoustic characters within one population of
Laupala cerasina
, a species with marked geographical variation in male song and female preferences. Results suggested significant directional sexual selection on three major song traits, while canonical rotation of the matrix of nonlinear selection coefficients (
γ
) revealed the presence of significant convex (stabilizing) sexual selection along combinations of characters. Analysis of song variation within and among males indicated significantly higher repeatability along the canonical axis of greatest stabilizing selection than along the axis of greatest linear selection. These results are largely consistent with patterns of song divergence that characterize speciation and suggest that different song characters have the potential to indicate distinct information to females during courtship.
Sex allocation pattern of the diatomCyclotella meneghiniana
Authors: Shirokawa Y. , Shimada M.
Published: May 2013

Sex allocation is one of the most successful applications of evolutionary game theory. This theory has usually been applied to multicellular organisms; however, conditional sex allocation in unicellular organisms remains an unexplored field of research. Observations at the cellular level are indispensable for an understanding of the phenotypic sex allocation strategy among individuals within clonal unicellular organisms. The diatomCyclotella meneghiniana, in which the sexes are generated from vegetative cells, is suitable for investigating effects of phenotypic plasticity factors on sex allocation while excluding genetic differences. We designed a microfluidic system that allowed us to trace the fate of individual cells. Sex allocation by individual mother cells was affected by cell lineage, cell size and cell density. Sibling cell pairs tended to differentiate into the same fates (split sex ratio). We found a significant negative correlation between the cell area of the mother cell and sex ratio of the two sibling cells. The male-biased sex ratio declined with higher local cell population density, supporting the fertility insurance hypothesis. Our results characterize multiple non-genetic factors that affect the phenotypic single cell-level sex allocation. Sex allocation in diatoms may provide a model system for testing evolutionary game theory in unicellular organisms.
The evolution of mutation rate in an antagonistic coevolutionary model with maternal transmission of parasites
Authors: Greenspoon Philip B. , M'Gonigle Leithen K.
Published: May 2013

By constantly selecting for novel genotypes, coevolution between hosts and parasites can favour elevated mutation rates. Models of this process typically assume random encounters. However, offspring are often more likely to encounter their mother's parasites. Because parents and offspring are genetically similar, they may be susceptible to the same parasite strains and thus, in hosts, maternal transmission should select for mechanisms that decrease intergenerational genetic similarity. In parasites, however, maternal transmission should select for genetic similarity. We develop and analyse a model of host and parasite mutation rate evolution when parasites are maternally inherited. In hosts, we find that maternal transmission has two opposing effects. First, it eliminates coevolutionary cycles that previous work shows select for higher mutation. Second, it independently selects for higher mutation rates, because offspring that differ from their mothers are more likely to avoid infection. In parasites, however, the two effects of maternal transmission act in the same direction. As for hosts, maternal transmission eliminates coevolutionary cycles, thereby reducing selection for increased mutation. Unlike for hosts, however, maternal transmission additionally selects against higher mutation by favouring parasite offspring that are the same as their mothers.
High prevalence of occult hepatitis C virus infection in patients with chronic hepatitis B virus infection
Authors: Castillo Inmaculada , Bartolomé Javier , Quiroga Juan Antonio , Carreño Vicente
Published: May 2013

Hepatitis C virus (HCV) infection in the absence of detectable antibodies against HCV and of viral RNA in serum is called occult HCV infection. Its prevalence and clinical significance in chronic hepatitis B virus (HBV) infection is unknown. HCV RNA was tested for in the liver samples of 52 patients with chronic HBV infection and 21 (40 %) of them were positive for viral RNA (occult HCV infection). Liver fibrosis was found more frequently and the fibrosis score was significantly higher in patients with occult HCV than in negative ones, suggesting that occult HCV infection may have an impact on the clinical course of HBV infection.
Responses to Light Intensity in a Genome-Scale Model of Rice Metabolism
Authors: Poolman Mark G. , Kundu Sudip , Shaw Rahul , Fell David A.
Published: May 2013

We describe the construction and analysis of a genome-scale metabolic model representing a developing leaf cell of rice (Oryza sativa) primarily derived from the annotations in the RiceCyc database. We used flux balance analysis to determine that the model represents a network capable of producing biomass precursors (amino acids, nucleotides, lipid, starch, cellulose, and lignin) in experimentally reported proportions, using carbon dioxide as the sole carbon source. We then repeated the analysis over a range of photon flux values to examine responses in the solutions. The resulting flux distributions show that (1) redox shuttles between the chloroplast, cytosol, and mitochondrion may play a significant role at low light levels, (2) photorespiration can act to dissipate excess energy at high light levels, and (3) the role of mitochondrial metabolism is likely to vary considerably according to the balance between energy demand and availability. It is notable that these organelle interactions, consistent with many experimental observations, arise solely as a result of the need for mass and energy balancing without any explicit assumptions concerning kinetic or other regulatory mechanisms.
A Change inSHATTERPROOFProtein Lies at the Origin of a Fruit Morphological Novelty and a New Strategy for Seed Dispersal inMedicagoGenus
Authors: Fourquin Chloé , del Cerro Carolina , Victoria Filipe C. , Vialette-Guiraud Aurélie , de Oliveira Antonio C. , Ferrándiz Cristina
Published: May 2013

Angiosperms are the most diverse and numerous group of plants, and it is generally accepted that this evolutionary success owes in part to the diversity found in fruits, key for protecting the developing seeds and ensuring seed dispersal. Although studies on the molecular basis of morphological innovations are few, they all illustrate the central role played by transcription factors acting as developmental regulators. Here, we show that a small change in the protein sequence of a MADS-box transcription factor correlates with the origin of a highly modified fruit morphology and the change in seed dispersal strategies that occurred in Medicago, a genus belonging to the large legume family. This protein sequence modification alters the functional properties of the protein, affecting the affinities for other protein partners involved in high-order complexes. Our work illustrates that variation in coding regions can generate evolutionary novelties not based on gene duplication/subfunctionalization but by interactions in complex networks, contributing also to the current debate on the relative importance of changes in regulatory or coding regions of master regulators in generating morphological novelties.
The Pseudomonas syringae Type III Effector AvrRpt2 Promotes Pathogen Virulence via Stimulating Arabidopsis Auxin/Indole Acetic Acid Protein Turnover
Authors: Cui Fuhao , Wu Shujing , Sun Wenxian , Coaker Gitta , Kunkel Barbara , He Ping , Shan Libo
Published: May 2013

To accomplish successful infection, pathogens deploy complex strategies to interfere with host defense systems and subvert host physiology to favor pathogen survival and multiplication. Modulation of plant auxin physiology and signaling is emerging as a common virulence strategy for phytobacteria to cause diseases. However, the underlying mechanisms remain largely elusive. We have previously shown that the Pseudomonas syringae type III effector AvrRpt2 alters Arabidopsis (Arabidopsis thaliana) auxin physiology. Here, we report that AvrRpt2 promotes auxin response by stimulating the turnover of auxin/indole acetic acid (Aux/IAA) proteins, the key negative regulators in auxin signaling. AvrRpt2 acts additively with auxin to stimulate Aux/IAA turnover, suggesting distinct, yet proteasome-dependent, mechanisms operated by AvrRpt2 and auxin to control Aux/IAA stability. Cysteine protease activity is required for AvrRpt2-stimulated auxin signaling and Aux/IAA degradation. Importantly, transgenic plants expressing the dominant axr2-1 mutation recalcitrant to AvrRpt2-mediated degradation ameliorated the virulence functions of AvrRpt2 but did not alter the avirulent function mediated by the corresponding RPS2 resistance protein. Thus, promoting auxin response via modulating the stability of the key transcription repressors Aux/IAA is a mechanism used by the bacterial type III effector AvrRpt2 to promote pathogenicity.
Cecropia peltataAccumulates Starch or Soluble Glycogen by Differentially Regulating Starch Biosynthetic Genes
Authors: Bischof Sylvain , Umhang Martin , Eicke Simona , Streb Sebastian , Qi Weihong , Zeeman Samuel C.
Published: May 2013

The branched glucans glycogen and starch are the most widespread storage carbohydrates in living organisms. The production of semicrystalline starch granules in plants is more complex than that of small, soluble glycogen particles in microbes and animals. However, the factors determining whether glycogen or starch is formed are not fully understood. The tropical tree Cecropia peltata is a rare example of an organism able to make either polymer type. Electron micrographs and quantitative measurements show that glycogen accumulates to very high levels in specialized myrmecophytic structures (Müllerian bodies), whereas starch accumulates in leaves. Compared with polymers comprising leaf starch, glycogen is more highly branched and has shorter branches—factors that prevent crystallization and explain its solubility. RNA sequencing and quantitative shotgun proteomics reveal that isoforms of all three classes of glucan biosynthetic enzyme (starch/glycogen synthases, branching enzymes, and debranching enzymes) are differentially expressed in Müllerian bodies and leaves, providing a system-wide view of the quantitative programming of storage carbohydrate metabolism. This work will prompt targeted analysis in model organisms and cross-species comparisons. Finally, as starch is the major carbohydrate used for food and industrial applications worldwide, these data provide a basis for manipulating starch biosynthesis in crops to synthesize tailor-made polyglucans.
Thermal expansion and enhanced heat transfer in high-entropy alloys
Authors: Lu Chieh-Lien , Lu Sheng-Yi , Yeh Jien-Wei , Hsu Wen-Kuang
Published: May 2013

Alloys made from equimolar mixtures of more than five elements exhibit an improved thermal diffusivity at elevated temperatures, and the improvement reaches 20% at 423 K and 50% at 573 K. This phenomenon is identified from the lengthened mean free path upon thermal expansion, and lengthening scales with lattice dilation over a wide range of temperatures.
Isoelectronic and isolobal O, CH2, CH3+and BH3as electron pairs; similarities between molecular and solid-state chemistry
Authors: Vegas Ángel , Notario Rafael , Chamorro Eduardo , Pérez Patricia , Liebman Joel F.
Published: May 2013

A topological analysis of the electron localization function (ELF) of a molecule of hexamethyldisiloxane, (H3C)3–Si–O–Si–(CH3)3, has been carried out, drawing a consistent picture of Si—O—Si bonding both in the linear and angular geometries. The ELF analysis confirms the idea that the O atom, in the linear geometry of (H3C)3—Si—O—Si—(CH3)3, is isolobal with the isoelectronic —CH_3^+— and —BH3— groups, the bonding in the Si—O—Si group being described as a two-electron, three-center (2e, 3c) bond. At the same time, the three oxygen lone pairs mirror the three C—H and B—H bonds, respectively. On the contrary, in the angular geometry the same O atoms form two Si—O bonds and its lone pairs mimic the geometry of the —CH2— group. In this model the O atoms would play the same role as the formally present O2−anions in the `so-called' ionic solids, such as in the skeletons of aluminate and silicate polyanions, thereby connecting molecular and solid-state chemistry as formulated by the `fragment formalism' or the `molecular unit-cell approach'. This unifying concept as well as the calculations we have carried out fully agree and also give support to earlier ideas developed by Bragg and Bent, among other authors. Bonding in the series of compounds P4, P4O6, P4O10, N4(CH2)6(hexamethylenetetramine) and (CH)4(CH2)6(adamantane) is discussed in the context of the isolobal model.