bluuebunny/crossref_metadata_2025 huggingface dataset:
Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects
Authors: Rocklin Gabriel J. , Mobley David L. , Dill Ken A. , Hünenberger Philippe H.
Published: November 2013

The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges −5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol−1) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non-periodic PB calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol−1). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pKa and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning.
Robofurnace: A semi-automated laboratory chemical vapor deposition system for high-throughput nanomaterial synthesis and process discovery
Authors: Oliver C. Ryan , Westrick William , Koehler Jeremy , Brieland-Shoultz Anna , Anagnostopoulos-Politis Ilias , Cruz-Gonzalez Tizoc , Hart A. John
Published: November 2013

Laboratory research and development on new materials, such as nanostructured thin films, often utilizes manual equipment such as tube furnaces due to its relatively low cost and ease of setup. However, these systems can be prone to inconsistent outcomes due to variations in standard operating procedures and limitations in performance such as heating and cooling rates restrict the parameter space that can be explored. Perhaps more importantly, maximization of research throughput and the successful and efficient translation of materials processing knowledge to production-scale systems, relies on the attainment of consistent outcomes. In response to this need, we present a semi-automated lab-scale chemical vapor deposition (CVD) furnace system, called “Robofurnace.” Robofurnace is an automated CVD system built around a standard tube furnace, which automates sample insertion and removal and uses motion of the furnace to achieve rapid heating and cooling. The system has a 10-sample magazine and motorized transfer arm, which isolates the samples from the lab atmosphere and enables highly repeatable placement of the sample within the tube. The system is designed to enable continuous operation of the CVD reactor, with asynchronous loading/unloading of samples. To demonstrate its performance, Robofurnace is used to develop a rapid CVD recipe for carbon nanotube (CNT) forest growth, achieving a 10-fold improvement in CNT forest mass density compared to a benchmark recipe using a manual tube furnace. In the long run, multiple systems like Robofurnace may be linked to share data among laboratories by methods such as Twitter. Our hope is Robofurnace and like automation will enable machine learning to optimize and discover relationships in complex material synthesis processes.
Full dimensional potential energy surface for the ground state of $\mathbf {H_4^+}$H4+ system based on triatomic-in-molecules formalism
Authors: Sanz-Sanz Cristina , Roncero Octavio , Paniagua Miguel , Aguado Alfredo
Published: November 2013

In this work, we present a global potential energy surface for the ground electronic state of the ${\rm H}_4^+$H4+ based on ab initio calculations. The final fit is based on triatomics-in-molecules (TRIM) approximation and it includes extra four-body terms for the better description of some discrepancies found on the TRIM model. The TRIM method itself allows a very accurate description of the asymptotic regions. The global fit uses more than 19 000 multireference configuration interaction ab initio points. The global potential energy surface has an overall root mean square error of 0.013 eV for energies up to 2 eV above the global minimum. This work presents an analysis of the stationary points, reactant and product channels, and crossing between the two lowest TRIM adiabatic states. It is as well included a brief description of the two first excited states of the TRIM matrix, concluding that TRIM method is a very good approximation not only for the ground state but also for at least two of the excited states of ${\rm H}_4^+$H4+ system.
Phase behavior of the modified-Yukawa fluid and its sticky limit
Authors: Schöll-Paschinger Elisabeth , Valadez-Pérez Néstor E. , Benavides Ana L. , Castañeda-Priego Ramón
Published: November 2013

Simple model systems with short-range attractive potentials have turned out to play a crucial role in determining theoretically the phase behavior of proteins or colloids. However, as pointed out by D. Gazzillo [J. Chem. Phys. 134, 124504 (2011)], one of these widely used model potentials, namely, the attractive hard-core Yukawa potential, shows an unphysical behavior when one approaches its sticky limit, since the second virial coefficient is diverging. However, it is exactly this second virial coefficient that is typically used to depict the experimental phase diagram for a large variety of complex fluids and that, in addition, plays an important role in the Noro-Frenkel scaling law [J. Chem. Phys. 113, 2941 (2000)], which is thus not applicable to the Yukawa fluid. To overcome this deficiency of the attractive Yukawa potential, D. Gazzillo has proposed the so-called modified hard-core attractive Yukawa fluid, which allows one to correctly obtain the second and third virial coefficients of adhesive hard-spheres starting from a system with an attractive logarithmic Yukawa-like interaction. In this work we present liquid-vapor coexistence curves for this system and investigate its behavior close to the sticky limit. Results have been obtained with the self-consistent Ornstein-Zernike approximation (SCOZA) for values of the reduced inverse screening length parameter up to 18. The accuracy of SCOZA has been assessed by comparison with Monte Carlo simulations.
Electric force microscopy of semiconductors: Theory of cantilever frequency fluctuations and noncontact friction
Authors: Lekkala Swapna , Marohn John A. , Loring Roger F.
Published: November 2013

An electric force microscope employs a charged atomic force microscope probe in vacuum to measure fluctuating electric forces above the sample surface generated by dynamics of molecules and charge carriers. We present a theoretical description of two observables in electric force microscopy of a semiconductor: the spectral density of cantilever frequency fluctuations (jitter), which are associated with low-frequency dynamics in the sample, and the coefficient of noncontact friction, induced by higher-frequency motions. The treatment is classical-mechanical, based on linear response theory and classical electrodynamics of diffusing charges in a dielectric continuum. Calculations of frequency jitter explain the absence of contributions from carrier dynamics to previous measurements of an organic field effect transistor. Calculations of noncontact friction predict decreasing friction with increasing carrier density through the suppression of carrier density fluctuations by intercarrier Coulomb interactions. The predicted carrier density dependence of the friction coefficient is consistent with measurements of the dopant density dependence of noncontact friction over Si. Our calculations predict that in contrast to the measurement of cantilever frequency jitter, a noncontact friction measurement over an organic semiconductor could show appreciable contributions from charge carriers.
Phase behaviors of supramolecular graft copolymers with reversible bonding
Authors: Zhang Xu , Wang Liquan , Jiang Tao , Lin Jiaping
Published: November 2013

Phase behaviors of supramolecular graft copolymers with reversible bonding interactions were examined by the random-phase approximation and real-space implemented self-consistent field theory. The studied supramolecular graft copolymers consist of two different types of mutually incompatible yet reactive homopolymers, where one homopolymer (backbone) possesses multifunctional groups that allow second homopolymers (grafts) to be placed on. The calculations carried out show that the bonding strength exerts a pronounced effect on the phase behaviors of supramolecular graft copolymers. The length ratio of backbone to graft and the positions of functional groups along the backbone are also of importance to determine the phase behaviors. Phase diagrams were constructed at high bonding strength to illustrate this architectural dependence. It was found that the excess unbounded homopolymers swell the phase domains and shift the phase boundaries. The results were finally compared with the available experimental observations, and a well agreement is shown. The present work could, in principle, provide a general understanding of the phase behaviors of supramolecular graft copolymers with reversible bonding.
Transversal thermal transport in single-walled carbon nanotube bundles: Influence of axial stretching and intertube bonding
Authors: Gharib-Zahedi Mohammad Reza , Tafazzoli Mohsen , Böhm Michael C. , Alaghemandi Mohammad
Published: November 2013

Using reverse nonequilibrium molecular dynamics simulations the influence of intermolecular bridges on the thermal conductivity (λ) in carbon nanotube (CNT) bundles has been investigated. The chosen cross linkers (CH2, O, CO) strengthen the transversal energy transport relative to the one in CNT bundles without bridges. The results showed that λ does not increase linearly with the linker density. The efficiency of the heat transport is determined by the number of linkers in the direction of the heat flux, the type of the linker, and their spatial ordering. The influence of a forced axial stress on the transversal λ has been also studied. The observed λ reduction with increasing axial stretching in a neat CNT bundle can be (over)compensated by cross linkers. The present computational data emphasize the contribution of phonons to the transversal heat transport in CNT bundles with intertube bonds.
Electromagnetic fluctuations and normal modes of a drifting relativistic plasma
Authors: Ruyer C. , Gremillet L. , Bénisti D. , Bonnaud G.
Published: November 2013

We present an exact calculation of the power spectrum of the electromagnetic fluctuations in a relativistic equilibrium plasma described by Maxwell-Jüttner distribution functions. We consider the cases of wave vectors parallel or normal to the plasma mean velocity. The relative contributions of the subluminal and supraluminal fluctuations are evaluated. Analytical expressions of the spatial fluctuation spectra are derived in each case. These theoretical results are compared to particle-in-cell simulations, showing a good reproduction of the subluminal fluctuation spectra.
Shielding of the electromagnetic field of a coplanar waveguide by a metal film: Implications for broadband ferromagnetic resonance measurements
Authors: Bailleul Matthieu
Published: November 2013

We show that the propagation of microwave fields along a planar transmission line is strongly modified when a conducting film is brought close to it. The effect is attributed to the shielding of the electrical and/or magnetic microwave fields which is shown to occur over a wide range of parameters (microwave frequency, film square resistance, transverse dimensions of the waveguide). This is illustrated by finite-element electromagnetic simulations and interpreted using a distributed impedance model. We discuss the implications of this phenomenon for broadband measurements of ferromagnetic resonance realized by placing a ferromagnetic metal film above a coplanar waveguide.
Morphology, electrical, and optical properties of heavily doped ZnTe:Cu thin films
Authors: El Akkad Fikry , Abdulraheem Yaser
Published: November 2013

We report on a study of the physical properties of ZnTe:Cu films with Cu content up to ∼12 at. % prepared using rf magnetron sputtering. The composition and lateral homogeneities are studied using X-ray photoelectron spectroscopy (XPS). Atomic force microscopy measurements on films deposited at different substrate temperatures (up to 325 °C) yielded activation energy of 12 kJ/mole for the grains growth. The results of XPS and electrical and optical measurements provide evidence for the formation of the ternary zinc copper telluride alloy in films containing Cu concentration above ∼4 at. %. The XPS results suggest that copper is incorporated in the alloy with oxidation state Cu1+ so that the alloy formula can be written Zn1−yCuy Te with y = 2−x, where x is a parameter measuring the stoichiometry in the Cu site. The formation of this alloy causes appreciable shift in the binding energies of the XPS peaks besides an IR shift in the energy band gap. Detailed analysis of the optical absorption data revealed the presence of two additional transitions, besides the band gap one, originating from the Γ8 and Γ7 (spin-orbit) valence bands to a donor level at ∼0.34 eV below the Γ6 conduction band. This interpretation yields a value for the valence band splitting energy Δ ≅ 0.87 eV independent of copper concentration. On the other hand, the mechanism of formation of the alloy is tentatively explained in terms of a point defect reaction in which substitutional Cu defect CuZn is also created. Assuming that substitutional Cu is the dominant acceptor in the Zn rich alloy as in ZnTe, its formation energy was determined to be 1.7 eV close to the theoretical value (1.41 eV) in ZnTe.
Communication: A Jastrow factor coupled cluster theory for weak and strong electron correlation
Authors: Neuscamman Eric
Published: November 2013

We present a Jastrow-factor-inspired variant of coupled cluster theory that accurately describes both weak and strong electron correlation. Compatibility with quantum Monte Carlo allows for variational energy evaluations and an antisymmetric geminal power reference, two features not present in traditional coupled cluster that facilitate a nearly exact description of the strong electron correlations in minimal-basis N2 bond breaking. In double-ζ treatments of the HF and H2O bond dissociations, where both weak and strong correlations are important, this polynomial cost method proves more accurate than either traditional coupled cluster or complete active space perturbation theory. These preliminary successes suggest a deep connection between the ways in which cluster operators and Jastrow factors encode correlation.
Dynamic plasmonic tweezers enabled single-particle-film-system gap-mode Surface-enhanced Raman scattering
Authors: Shen Junfeng , Wang Jian , Zhang Cuijiao , Min Changjun , Fang Hui , Du Luping , Zhu Siwei , Yuan X.-C.
Published: November 2013

Based on numerical simulation and experiment, we demonstrate a dynamic single-particle-film Surface-enhanced Raman scattering (SERS) system enabled by manipulation of a single gold nanoparticle by plasmonic nano-tweezers (PNT). A corresponding dynamic plasmonic gap-mode is induced by the hybridization of the surface plasmon polaritons (SPPs) on the film and the localized surface plasmon of the particle. This gap-mode produces an additional enhancement of ∼104 compared to the bare SPPs without the particle, reaching a final SERS enhancement factor of ∼109. Enabled by nano-manipulation with PNT, this dynamic single-particle-film-system provides a promising route to controllable SERS detection in aqueous environments.
Evidence of enhanced electron-phonon coupling in ultrathin epitaxial copper films
Authors: Timalsina Yukta P. , Shen Xiaohan , Boruchowitz Grant , Fu Zhengping , Qian Guoguang , Yamaguchi Masashi , Wang Gwo-Ching , Lewis Kim M. , Lu Toh-Ming
Published: November 2013

Electron phonon (el-ph) coupling is a fundamental quantity that controls the electron transport through a conductor. We experimentally determined the el-ph coupling strength of epitaxial copper (Cu) films ranging from 5 to 1000 nm thick using both ultra-fast, optical pump-probe reflectivity and temperature-dependent resistivity measurements. An enhancement of the el-ph coupling strength was observed when the thickness of the films was reduced to below 50 nm. We suggest that this unexpected enhancement of the el-ph coupling strength is partially responsible for the observed increase of resistivity in the films below 50 nm thick.
Light-induced anodisation of silicon for solar cell passivation
Authors: Cui J. , Wang X. , Opila R. , Lennon A.
Published: November 2013

This paper reports a new method for forming anodic oxides on silicon surfaces using the light-induced current of pn-junction solar cells to make p-type silicon surfaces anodic. The light-induced anodisation process enables anodic oxide layers as thick as 79 nm to be formed at room temperature in a faster, more uniform, and controllable manner compared to previously reported clip-based anodisation methods. Although the effective minority carrier lifetime decreased immediately after light-induced anodisation from initial values measured with an 17 nm thermally grown oxide on both wafer surfaces, the 1-sun implied open circuit voltage of wafers on which the thermally grown oxide on the p-type surface was replaced by an anodic oxide of the same thickness could be returned to its initial value of ∼635 mV (for 3–5 Ω-cm Cz silicon wafers) after a 400 °C anneal in oxygen and then forming gas. The passivation of the formed anodic oxide layers was stable for a period of 50 days providing the oxide was protected by a 75 nm thick silicon nitride capping layer.
Note: Design and development of an integrated three-dimensional scanner for atomic force microscopy
Authors: Rashmi T. , Dharsana G. , Sriramshankar R. , Sri Muthu Mrinalini R. , Jayanth G. R.
Published: November 2013

A compact scanning head for the Atomic Force Microscope (AFM) greatly enhances the portability of AFM and facilitates easy integration with other tools. This paper reports the design and development of a three-dimensional (3D) scanner integrated into an AFM micro-probe. The scanner is realized by means of a novel design for the AFM probe along with a magnetic actuation system. The integrated scanner, the actuation system, and their associated mechanical mounts are fabricated and evaluated. The experimentally calibrated actuation ranges are shown to be over 1 μm along all the three axes.
Single photon emission from site-controlled InGaN/GaN quantum dots
Authors: Zhang Lei , Teng Chu-Hsiang , Hill Tyler A. , Lee Leung-Kway , Ku Pei-Cheng , Deng Hui
Published: November 2013

Single photon emission was observed from site-controlled InGaN/GaN quantum dots. The single-photon nature of the emission was verified by the second-order correlation function up to 90 K, the highest temperature to date for site-controlled quantum dots. Micro-photoluminescence study on individual quantum dots showed linearly polarized single exciton emission with a lifetime of a few nanoseconds. The dimensions of these quantum dots were well controlled to the precision of state-of-the-art fabrication technologies, as reflected in the uniformity of their optical properties. The yield of optically active quantum dots was greater than 90%, among which 13%–25% exhibited single photon emission at 10 K.
Coherent phase control of resonance-mediated two-photon absorption in rare-earth ions
Authors: Zhang Shian , Lu Chenhui , Jia Tianqing , Qiu Jianrong , Sun Zhenrong
Published: November 2013

We theoretically and experimentally demonstrate the quantum coherent control of the resonance-mediated two-photon absorption in rare-earth ions by the phase-shaped femtosecond laser pulse. Our theoretical results show that the resonance-mediated two-photon absorption can be effectively controlled, but the control efficiency depends on the laser repetition rate in real experiment due to the long lifetime and the short decoherence time of the excited state, and the larger laser repetition rate yields the lower control efficiency. These theoretical results are experimentally confirmed in glass sample doped with Er3+ by utilizing the femtosecond lasers with low repetition rate of 1 kHz and high repetition rate of 80 MHz.
Against Better Knowledge: The Magical Force of Amodal Volume Completion
Authors: Ekroll Vebjørn , Sayim Bilge , Wagemans Johan
Published: November 2013

In a popular magic routine known as “multiplying billiard balls”, magicians fool their audience by using an empty shell that the audience believes to be a complete ball. Here, we present some observations suggesting that the spectators do not merely entertain the intellectual belief that the balls are all solid, but rather automatically and immediately perceive them as such. Our observations demonstrate the surprising potency and genuinely perceptual origin of amodal volume completion.
Ecology and movement of urban koalas adjacent to linear infrastructure in coastal south-east Queensland
Authors: de Oliveira S. M. , Murray P. J. , de Villiers D. L. , Baxter G. S.
Published: November 2013

In Redland City, koalas (Phascolarctos cinereus) are in rapid decline as they are exposed to anthropogenic threats such as habitat clearing, dog attacks, vehicle collisions and disease. This study investigated the influence of linear infrastructure on the movement and habitat use of urban koalas. Seven koalas were tracked for up to 28 weeks during the breeding season. Home ranges were calculated for 95% Minimum Convex Polygon (MCP95%) and 95% fixed Kernel Density (FK95%). Koalas responded to the landscape in different ways. Linear infrastructure did not restrict the movements of most koalas. Home ranges varied from 1.1 to 31.5 ha MCP95% and from 5 to 55 ha for FK95%. Koalas mainly used Eucalyptus tereticornis throughout the study site. A variety of non-regionally endemic and regionally endemic trees in urban and remnant vegetation areas were used, suggesting that all trees are potentially koala habitat. At the completion of the study, four koalas remained alive, two were killed by trains and one died from a dog attack. Despite the small sample size and short duration, our results suggest that koalas are able to navigate linear infrastructure; however, the high rates of mortality associated with these movements puts the long-term viability of urban koala populations in doubt.
High-throughput, cost-effective verification of structural DNA assembly
Authors: Dharmadi Yandi , Patel Kedar , Shapland Elaine , Hollis Daniel , Slaby Todd , Klinkner Nicole , Dean Jed , Chandran Sunil S.
Published: November 2013

DNA ‘assembly’ from ‘building blocks’ remains a cornerstone in synthetic biology, whether it be for gene synthesis (∼1 kb), pathway engineering (∼10 kb) or synthetic genomes (>100 kb). Despite numerous advances in the techniques used for DNA assembly, verification of the assembly is still a necessity, which becomes cost-prohibitive and a logistical challenge with increasing scale. Here we describe for the first time a comprehensive, high-throughput solution for structural DNA assembly verification by restriction digest using exhaustive in silico enzyme screening, rolling circle amplification of plasmid DNA, capillary electrophoresis and automated digest pattern recognition. This low-cost and robust methodology has been successfully used to screen over 31 000 clones of DNA constructs at <$1 per sample.
Distribution of Xylella fastidiosa in Blueberry Stem and Root Sections in Relation to Disease Severity in the Field
Authors: Holland R. M. , Christiano R. S. C. , Gamliel-Atinsky E. , Scherm H.
Published: November 2013

Xylella fastidiosa causes bacterial leaf scorch, a new disease of southern highbush blueberry in the southeastern United States. Infections occlude the xylem of affected plants, causing drought-like symptoms and, eventually, plant death. To assess the likelihood of mitigation of bacterial leaf scorch through cultural practices such as pruning or hedging of affected plants, we determined the localization and population density of X. fastidiosa in naturally infected blueberry plants with varying levels of bacterial leaf scorch severity. Stem segments were sampled from the current season's growth down to the base of the plant, as were root segments on plants that were either asymptomatic or had light, moderate, or severe symptoms in three plantings affected by the disease. Stem sap was extracted from each segment and population densities of X. fastidiosa were determined using real-time polymerase chain reaction with species-specific primers. Detection frequencies were lowest (but non-zero) in sap from asymptomatic plants and highest in plants with severe symptoms. In asymptomatic plants, detection was generally least frequent (0 to 20.0%) in top and root sections and highest (4.6 to 55.6%) in middle and base stem sections. As disease severity increased, detection frequencies in roots increased to >80% in two plantings and to 60% in the third planting. Overall, detection frequencies were highest (>80%) in middle and base stem sections of plants from the moderate and severe disease classes. The lowest bacterial titers (averaging 0 to 2.1 × 101 CFU per 50 μl of sap) were observed in top and root sections of asymptomatic plants, whereas the highest titers (generally between 104 and 105 CFU per 50 μl of sap) were obtained from middle, base, and root sections of plants from the moderate and severe classes. The presence of the bacterium in middle and base stem sections at low disease severity indicates rapid distribution of X. fastidiosa in affected plants. Because the pathogen accumulates in the roots at moderate and high disease severity levels, management strategies such as pruning and mowing are unlikely to be effective in curing affected plants from bacterial leaf scorch.
Identification of Dickeya zeae as a Causal Agent of Bacterial Soft Rot in Banana in China
Authors: Zhang Jingxin , Shen Huifang , Pu Xiaoming , Lin Birun , Hu John
Published: November 2013

Bacterial soft rot of banana was first noticed in 2009 in Guangzhou city, China. The disease also was observed on various banana cultivars of different genotypes in several other cities. Symptoms of the disease included leaf wilting, collapse of pseudostems, and unusual odor. Five isolated strains that fulfilled Koch's postulates were used for biochemical testing. The five strains were most similar to Dickeya dadantii or D. zeae, but were much less similar to D. paradisiaca when using several phenotype characteristics. Sequence analysis of 16S rDNA, dnaX, gryB, and recA of a reference strain revealed a similarity of 99% with the sequences of D. zeae, rather than D. paradisiaca. Phylogenic analysis of concatenated sequences of dnaX, gryB, and recA indicated that the banana strain constituted a distinguishable clade with several D. zeae strains involving rice pathogens D. zeae EC1 and ZJU1202 from Guangdong province, but the banana pathogen had several characteristics that distinguished it from the rice pathogens. Therefore, the banana pathogen was determined to be D. zeae. This is the first report of banana soft rot caused by D. zeae in China; however, the pathogen can infect other important crops.
Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability
Authors: Akagi Keiko , Li Jingfeng , Broutian Tatevik R. , Padilla-Nash Hesed , Xiao Weihong , Jiang Bo , Rocco James W. , Teknos Theodoros N. , Kumar Bhavna , Wangsa Danny , He Dandan , Ried Thomas , Symer David E. , Gillison Maura L.
Published: November 2013

Genomic instability is a hallmark of human cancers, including the 5% caused by human papillomavirus (HPV). Here we report a striking association between HPV integration and adjacent host genomic structural variation in human cancer cell lines and primary tumors. Whole-genome sequencing revealed HPV integrants flanking and bridging extensive host genomic amplifications and rearrangements, including deletions, inversions, and chromosomal translocations. We present a model of “looping” by which HPV integrant-mediated DNA replication and recombination may result in viral–host DNA concatemers, frequently disrupting genes involved in oncogenesis and amplifying HPV oncogenes E6 and E7. Our high-resolution results shed new light on a catastrophic process, distinct from chromothripsis and other mutational processes, by which HPV directly promotes genomic instability.
Characterization and Identification of cis-Regulatory Elements in Arabidopsis Based on Single-Nucleotide Polymorphism Information
Authors: Korkuć Paula , Schippers Jos H.M. , Walther Dirk
Published: November 2013

Identifying regulatory elements and revealing their role in gene expression regulation remains a central goal of plant genome research. We exploited the detailed genomic sequencing information of a large number of Arabidopsis (Arabidopsis thaliana) accessions to characterize known and to identify novel cis-regulatory elements in gene promoter regions of Arabidopsis by relying on conservation as the hallmark signal of functional relevance. Based on the genomic layout and the obtained density profiles of single-nucleotide polymorphisms (SNPs) in sequence regions upstream of transcription start sites, the average length of promoter regions in Arabidopsis could be established at 500 bp. Genes associated with high degrees of variability of their respective upstream regions are preferentially involved in environmental response and signaling processes, while low levels of promoter SNP density are common among housekeeping genes. Known cis-elements were found to exhibit a decreased SNP density than sequence regions not associated with known motifs. For 15 known cis-element motifs, strong positional preferences relative to the transcription start site were detected based on their promoter SNP density profiles. Five novel candidate cis-element motifs were identified as consensus motifs of 17 sequence hexamers exhibiting increased sequence conservation combined with evidence of positional preferences, annotation information, and functional relevance for inducing correlated gene expression. Our study demonstrates that the currently available resolution of SNP data offers novel ways for the identification of functional genomic elements and the characterization of gene promoter sequences.
exo-1,7-Dimethyl-4-phenyl-10-oxa-4-azatricyclo[5.2.1.02,6]dec-8-ene-3,5-dione
Authors: Pineda-Contreras Armando , Vázquez-Vuelvas Oscar Fernando , Negrete-López Laura Edith , García-Ortega Héctor , Flores-Alamo Marcos
Published: November 2013

The title compound, C16H15NO3, consists of an oxabicycle fused to anN-phenyl-substituted pyrrolidine ringantito the double bond, affording theexoisomer. In the oxabicycle system, the six-membered ring presents a boat conformation, while the heterocyclic rings show envelope conformations with the O atom projected out of the plane. In the crystal, adjacent molecules are linkedviaweak C—H...O hydrogen bonds, forming chains propagating along thea-axis direction. The chains are linked by C—H...π interactions, forming two-dimensional networks lying parallel to theacplane.
Ethyl 4-anilino-2-methyl-5-oxo-1-phenyl-2,5-dihydro-1H-pyrrole-2-carboxylate
Authors: Akkurt Mehmet , Mohamed Shaaban K. , Elremaily Mahmoud A. A. , Santoyo-Gonzalez Francisco , Albayati Mustafa R.
Published: November 2013

In the title compound, C20H20N2O3, the central 2,5-dihydro-1H-pyrrole ring [r.m.s. deviation = 0.014 (1) Å] is oriented at dihedral angles of 77.81 (6) and 25.33 (6)°, respectively, to the attached phenyl ring and the aniline phenyl ring. An intramolecular N—H...O hydrogen bond occurs. In the crystal, molecules are linked through pairs of N—H...O hydrogen bonds, forming inversion dimers with anR22(10) ring motif. Two weak C—H...π interactions are also observed.
(μ3-Hydrido)[μ3-2-(trimethylsilyl)ethylidyne-κ3C1:C1:C1]tetrakis[(η5-cyclopentadienyl)cobalt(II)]
Authors: Haehnel Martin , Spannenberg Anke , Rosenthal Uwe
Published: November 2013

In the title compound, [Co4(C5H5)4(μ3-CCH2SiMe3)(μ3-H)], the Co atoms form a distorted tetrahedron with the ethylidyne moiety bridging three of the Co atoms as well as the hydrido ligand also bridging three of the Co atoms. The Co—Co bond lengths in the Co4tetrahedron vary from 2.3844 (4) to 2.4608 (4) Å. Each Co atom is additionally η5-bonded to a cyclopentadienyl (Cp) anion.
Assessing governance and learning lessons
Authors: Geddes Louise , Shand Rory
Published: November 2013

Purpose

– The purpose of this paper is to examine the role of tiers of governance and discuss the findings from research into a crime policy's implementation focusing on resourcing, community engagement, accountability and leadership. The paper examines the shift from partnership delivery to the Big Society.

Design/methodology/approach

– 18 in-depth semi-structured interviews with partnership managers from a range of organisations combined with non-participant semi-structured of ten partnership meetings and documentary analysis were undertaken, in tandem with the policy networks framework.

Findings

– Despite the expectations placed on crime partnerships by New Labour, governance has continued to be driven by professionals and dominated by the large public sector organisations, rather than the community they serve or their service users, and with little involvement from the business sector in delivery. The focus upon voluntarism, enterprise and business in the Big Society vision will mean rapid adaptation in the sector if it is to fit the Big Society agenda successfully.

Originality/value

– The paper serves to set out the relationships between key actors in governance in this policy area and the relevance of this to the Big Society idea. Its findings and lessons can be used to compare the policy sector across countries and for practical use by policy makers.
Multicultural markets and acculturation: implications for service firms
Authors: Poulis Konstantinos , Poulis Efthimios , Yamin Mo
Published: November 2013

Purpose

– The purpose is to construct an analytical framework that encapsulates implications for the marketing offering of service firms as a result of observed intra-national ethnic diversity in these firms' markets of operation.

Design/methodology/approach

– This is a conceptual approach which promotes the idea that acculturation matters for service firms operating in multicultural markets and adopts relevant propositions related to service firms' strategy in such markets.

Findings

– Integrating fragmented insights from consumer behaviour and multicultural marketing, the study suggests that the various interactions and contacts between ethnic groups in a multicultural country can generate acculturation outcomes that lend themselves to novel avenues for empirical research. These avenues move beyond a research focus on the presence of ethnic groups as stand-alone entities of intra-ethnic uniformity.

Practical implications

– Firms with a broader market horizon in a multicultural market can employ acculturation in their marketing strategy since an exclusive focus on ethnicity as a basis of segmenting the market reveals shortcomings. Otherwise, a myopic approach that ignores cross-ethnic interactions may lead to bypassing opportunities for more considerate market responses by a service firm.

Originality/value

– To the best of the authors' knowledge, this is the only acculturation study in a services context that offers an analytical framework and propositions that can be used as a guide for multicultural, services marketing researchers and practitioners that see the market in a holistic fashion.
Religious influences on consumers' high-involvement purchasing decisions
Authors: Siala Haytham
Published: November 2013

Purpose

– This aim of this paper is to investigate the impact that religious factors have on a consumer's perception of brand loyalty in the context of the services industry. Specifically, the study focuses on the attitudinal/affective form of brand loyalty. An empirical investigation was conducted to test whether the religiosity and religious centrism of Muslim consumers can instill attitudinal brand loyalty towards an insurer selling a religiously-conforming high-involvement indemnity service.

Design/methodology/approach

– An online survey was conducted with 208 Muslim consumers, and structural equation modeling (SEM) analysis was used to test the relationships between the exogenous and endogenous variables.

Findings

– The results shows that there is a positive relationship between the exogenous religiosity and religious centrism constructs, and the endogenous attitudinal brand loyalty, price tolerance and word-of-mouth constructs.

Practical implications

– The findings of this research study suggest that religion can have a significant impact on consumers' choice when purchasing an indemnity service such as a car insurance service. Given the fact that religious values are persistent over time, there are some potential long-term benefits for companies that can identify the lucrative religious consumer segments that are present in the local and global markets.

Originality/value

– This study provides valuable insight into the UK Muslim consumer behavior by exploring the religious factors that can influence consumers' brand loyalty toward buying high-involvement religiously-compliant products and services. The findings of this study also indicate that the existing TRA and TRB models in the social sciences literature may need to incorporate a new ritualistic/religious dimension to the existing attitude-intention relationship saga.
The influence of social undermining on the service employee's customer-oriented boundary-spanning behavior
Authors: Yoo Jaewon
Published: November 2013

Purpose

– This study aims to investigate the effect of social undermining on the service employees' boundary-spanning behavior though perceived fit with job (P-J fit). This study also aims to examine the moderating role of ethical climate in the relationship between service employees' perceived fit with job (P-J fit) and boundary-spanning behavior.

Design/methodology/approach

– Using a sample of 469 Korean bank and insurance employees, research model and hypotheses were tested. Data analysis was performed using structural equation modeling and the hierarchical regression model.

Findings

– The results showed that supervisor and co-worker undermining have detrimental influences on the service employee's perceived fit with job. P-J fit has a positive effect on employees' boundary-spanning behavior and this relationship was positively moderated by the employee's prevailing perception of organizational practices and procedures that have ethical content.

Research limitations/implications

– This research should be evaluated in light of limitations, one of which is the reliance on cross-sectional data. The generalizability of this research model across settings and across outcome variables is still an open question. The measures of social undermining were based on participant perceptions, and in each case, participants make judgments about their negative behaviors retrospectively. Furthermore, the data were collected in Korea, so generalizing the hypothesized model beyond this setting is limited. Since Korea represents a distinct cultural and economic context, future research could examine the model in different countries.

Practical implications

– The findings of this study confirm the crucial role of managers in creating an ethical climate where decisions are based on formally stated ethical guidelines. Such guidelines help service employees solve the ethical dilemmas that are common to their positions. These research findings demonstrate that creating an ethical climate is not only the right thing to do but also has significant benefits for both the service employees and the organization.

Originality/value

– Considering the boundary-spanning role of the service employee, not only the organizational side (supervisor and co-worker undermining), but also the customer is specified as a major source of social undermining.
Comparative analysis of passive defences in spiders (Araneae)
Authors: Pekár Stano
Published: November 2013

Being frequent prey of many predators, including especially wasps and birds, spiders have evolved a variety of defence mechanisms. Here I studied patterns of passive defences, namely anachoresis, crypsis, masquerade, aposematism and Batesian mimicry, in spiders.

Using published information pertaining more than 1000 spider species, the phylogenetic pattern of different passive defences (i.e. defences that decrease the risk of an encounter with the predator) was investigated. Furthermore, I studied the effect of foraging guild, geographical distribution and diel activity on the frequency of defences as these determine the predators diversity, presence and perception.

I found that crypsis (background matching) combined with anachoresis (hiding) was the most frequent defence confined mainly to families/genera at the base of the tree. Aposematism (warning coloration) and Batesian mimicry (imitation of noxious/dangerous model) were found in taxa that branched later in the tree, and masquerade (imitation of inedible objects) was confined to families at intermediate positions of the tree. Aposematism and Batesian mimicry were restricted to a few lineages.

Masquerade was used particularly by web‐building species with nocturnal activity. Aposematism was rare but mainly used by web‐building diurnal species. Batesian mimicry was frequently observed in cursorial species with diurnal activity. Cryptic species were more common in temperate zones, whereas aposematic and mimetic species were more common in the tropics.

Here I show that the evolution of passive defences in spiders was influenced by the ecology of species. Then, I discuss the evolutionary significance of the particularly defences.
Eighty‐seven cases of a nail gun injury to the extremity
Authors: Ling Shi‐Neng James , Ong Natalie Chuen‐Ying , North John Bevan
Published: November 2013

Objectives

The aims of this research were to characterise the injury patterns associated with nail guns, highlight their potential complications and review treatment options.

Methods

A retrospective case series was conducted of all patients with a nail gun injury to the upper or lower limb who presented to the Princess Alexandra Hospital from 1 January 2007 to 30 July 2012.

Results

Young men in the work environment were at most risk of sustaining a nail gun injury to their non‐dominant hand. Out of 87 cases identified, 29% were intra‐articular, 16% had evidence of neurovascular injury, 24% involved bone and 37% had evidence of tendon injury. Fifty‐eight per cent underwent operative management, 32% were treated solely in the ED and 10% were transferred to a private facility. At the time of operation, 14% of cases had tendon, joint or neurovascular involvement and 20% had retained foreign material. The median length of operation was 17 min and no anaesthetic complications were identified. Four (13%) patients had ongoing pain, paraesthesia or stiffness at the time of follow up.

Conclusions

The present study characterises the injury patterns caused by nail guns. Treatment of these injuries should be based on clinical findings; however, the majority of cases should undergo surgical treatment. The required operation is a short and safe treatment modality that might allow a thorough assessment of the injury, removal of embedded material, repair of structural damage and a sterile washout to be performed.
Characteristics of Aboriginal and Torres Strait Islander presentations to three Victorian emergency departments
Authors: Martin Catherine , Smith Tammy , Graudins Andis , Braitberg George , Chapman Rose
Published: November 2013

Objectives

Aboriginal and Torres Strait Islander (ATSI) people have significant health disparity compared with other Australians. The present study examines the characteristics of ATSI patients presenting to three EDs of a single healthcare network to determine whether any healthcare disadvantages exist.

Methods

This is a retrospective audit of 179 795 presentations to the ED from 1 July 2011 to 30 June 2012. Measures included socioeconomic status, general practitioner nomination, triage category status, primary diagnosis recorded, length of stay and the outcome of stay, including numbers leaving before and after medical treatment was commenced.

Results

ATSI people were found to live in the lower socioeconomic regions of the network's catchment area, were more likely to attend the ED (135.5 non‐ATSI persons presenting per 1000 non‐ATSI persons and 210.4 ATSI persons presenting per 1000 ATSI persons), less likely to nominate a general practitioner (73.3 vs 82.1%; OR 0.60, 95% CI 0.51–0.71), more likely to leave before (5.5 vs 4.0%; OR 1.40, 95% CI 1.09–1.80) or after treatment had commenced (3.2 vs 2.3%; OR 1.43, 95% CI 1.03–1.97), and were more likely to re‐attend the ED than non‐ATSI people (OR 1.24, 95% CI 1.06–1.46).

Conclusion

ATSI people living in Melbourne's south‐east have social and health utilisation inequities, which might have an impact on their health status.