bluuebunny/crossref_metadata_2025 huggingface dataset:
Theoretical predictions of red and near-infrared strongly emitting X-annulated rylenes
Authors: Peng Qian , Niu Yingli , Wang Zhaohui , Jiang Yuqian , Li Yan , Liu Yajun , Shuai Zhigang
Published: February 2011

The optical properties of rylenes are extremely interesting because their emission colors can be tuned from blue to near-infrared by simply elongating the chain length. However, for conjugated chains, the dipole-allowed odd-parity 1Bu excited state often lies above the dipole-forbidden even-parity 2Ag state as the chain length increases, thus preventing any significant luminescence according to Kasha's rule. We systemically investigated the 1Bu/2Ag crossover behaviors with respect to the elongating rylene chain length with various quantum chemistry approaches, such as time-depended density functional theory (TDDFT), complete active space self-consistent field theory (CASSCF/CASPT2), multireference configuration interaction (MRCI)/Zerner's intermediate neglect of diatomic overlap (ZINDO), and MRCI/modified neglect of differential overlap. The calculated results by CASSCF/CASPT2 and MRCI/ZINDO are completely coherent: the optical active 1Bu state lies below the dark B3g or 2Ag state for perylene and terrylene, which results in strong fluorescence; while a crossover to S1 = 2Ag occurs and leads to much weaker fluorescence for quaterrylene. Then we put forward a molecular design rule on how to recover fluorescence for the longer rylenes by introducing heteroatom bridges. Several heteroatom-annulated rylenes are designed theoretically, which are predicted to be strongly emissive in the red and near-infrared ranges. These are further confirmed by theoretical emission spectra as well as radiative and nonradiative decay rate calculations by using the vibration correlation function formalisms we developed earlier coupled with TDDFT.
Nanoscale switch based on interacting molecular dipoles: Cooperativity can improve the device characteristics
Authors: Mafé, Salvador , Manzanares, José A. , Reiss Howard
Published: February 2011

We propose a nanoscale switch, giving a nonlinear function with two conductive states separated by a sharp transition region, on the basis of an array of molecular dipoles. We show theoretically that the local interactions between dipoles result in cooperative phenomena that can significantly improve the switching characteristics. We demonstrate the general validity of the concept in the cases of (i) an electrical switch robust to the finite size and variability effects inherent to the nanoscale and (ii) a sensing layer based on the voltage and ligand concentration dependence of the dipole array conductance.
The reaction of Si(001) with magnesium and calcium
Authors: Pi T.-W. , Cheng C.-P. , Wertheim G. K.
Published: February 2011

We use a novel three-layer model function to assess the effect of the electron donors Mg and Ca on the Si(001) surface. The model shows that the previously unassigned C and D contributions of the Si 2p spectrum are due to the third surface layer. The layer-wise response of the Si(001) surface to the deposition of Mg atoms shows that the essential character of the dimer reconstruction initially remains in place, but is modified in discernible ways by charge donated to the dimer atoms. At larger coverage a new, well-organized silicide structure emerges which is identified as Mg2Si. A study of the reaction with Ca reveals a Ca2Si overlayer at room temperature, but CaSi2 overlayer at high temperature.
Compatible symplectic connections on a cotangent bundle and the Fedosov quantization
Authors: Tosiek Jaromir
Published: February 2011

A global construction of a family of symplectic connections on a cotangent bundle compatible with some linear symmetric connection on the base space is proposed. Examples of the compatible symplectic connections are given. A detailed analysis of an Abelian connection and of flat sections for this kind of symplectic connection in the Fedosov algorithm are presented. Some properties of the *–product determined by the compatible symplectic connection are shown.
Ultrafast exciton dynamics in ZnO: Excitonic versus electron-hole plasma lasing
Authors: Shih T. , Mazur E. , Richters J.-P. , Gutowski J. , Voss T.
Published: February 2011

The use of ZnO bulk and especially nanolayer and nanowire structures for novel device applications has led to a renewal of interest in high-electron-density processes in ZnO, such as those occurring during lasing in ZnO. Using a pump-probe reflectometry technique, we investigate the ultrafast exciton dynamics of bulk ZnO under femtosecond laser excitation close to lasing conditions. Under intense excitation by 266-nm femtosecond (fs) pump pulses, the exciton resonance becomes highly damped and does not recover for several picoseconds. This slow recovery indicates a significant screening of the Coulomb interaction. Even below the lasing thresholds typically found for ZnO nanolayers and nanowires, we observe damping of the exciton resonance for several picoseconds, which indicates that the primary mechanism for lasing in ZnO induced by femtosecond laser pumping is electron-hole plasma recombination.
Vibrational analysis of x-ray absorption fine structure thermal factors by ab initio molecular dynamics: The Zn(II) ion in aqueous solution as a case study
Authors: Rega Nadia , Brancato Giuseppe , Petrone Alessio , Caruso Pasquale , Barone Vincenzo
Published: February 2011

In this work, we consider a new combination of vibrational analysis and normal-like mode decomposition of Debye–Waller factors of solvated ions entirely based on molecular dynamics data. Such a novel time-dependent analysis procedure provides a direct link between x-ray absorption fine structure parameters and normal mode contributions for an ion–solvent system. The potentialities of such a methodology rely on two fundamental aspects which distinguish it from already available tools. First, a general vibrational analysis that does not require any Gaussian or harmonic model for describing atomic fluctuations in liquids. Second, a very accurate sampling of the short range motions around the structural probe \documentclass[12pt]{minimal}\begin{document}$\it {\text{via}}$\end{document}via the recently developed atom centered density matrix propagation/general liquid optimized boundary method. This novel molecular dynamics methodology is based on an integrated ab initio/classical potential using localized basis functions and nonperiodic boundary conditions. As a case study we have chosen the Zn(II) ion in aqueous solution. The consistency of our results and the observed good agreement with experiments show how the key support to advanced structural techniques from molecular dynamics can be further expanded and investigated.
Renewal theory for single-molecule systems with multiple reaction channels
Authors: Berezhkovskii A. M.
Published: February 2011

Some single-molecule systems share a common feature: the system performs different cycles returning after each cycle to the same state. In such systems we deal with renewal processes. Examples include (1) single-molecule enzymatic reactions, (2) membrane transport through single-occupancy channels, (3) single-molecule fluorescence spectroscopy, and (4) motion of molecular motors. The paper is focused on the analysis of such systems by means of the renewal theory. To be more specific, the theory of renewal processes is used to study multivariate distribution functions of the numbers of different events in a given observation time. Our main results are simple formulas derived for the Laplace transforms of the distribution functions. General results are illustrated by consideration of several examples.
High efficiency multichannel collimator for structural studies of liquids and low-Z materials at high pressures and temperatures
Authors: Morard G. , Mezouar M. , Bauchau S. , Álvarez-Murga M. , Hodeau J.-L. , Garbarino G.
Published: February 2011

A high efficiency multichannel collimator (MCC) device has been developed at the high pressure beamline ID27 of the European Synchrotron Radiation Facility to drastically reduce the x-ray background from the sample environment in the Paris-Edinburgh press. The main technical difficulty, which resides in the minimum slits size achievable using the classical mono-bloc design, has been resolved using an original concept based on a set of independent slits. Then, a very small slit size of 50 μm was manufactured resulting in a great improvement of the signal to background ratio. In addition, the transfer function of the MCC has been measured using the x-ray diffusion signal of a metal doped glass and efficiently applied to correct the raw data. The potential of this new device is illustrated in two challenging examples: iron–sulfur liquid structures and C60 polymerization process at high pressure and high temperature.
Electronic structure of HgBa2Can−1CunO2n+2 (n = 1, 2, 3) superconductor parent compounds from periodic hybrid density functional theory
Authors: Moreira Ibério de P. R. , Rivero Pablo , Illas Francesc
Published: February 2011

The electronic structure of HgBa2Can−1CunO2n+2 (n = 1, 2, and 3) high Tc superconductor parent compounds has been investigated by means of periodic hybrid density functional theory. Similar to other cuprates, these materials are predicted to exhibit an antiferromagnetic ground state with well localized S = 1/2 magnetic centers at the Cu2+ sites. However, the presence of the HgO2 structural units largely defines the nature of states dominating the energy range around Fermi energy. This results in a complex charge transfer character of the insulating gap which decreases when increasing the number of CuO2 planes in the unit cell, to the point that in the HgBa2Ca2Cu3O8 compound it becomes so small that one can claim that the resulting material is metallic. Nevertheless, the metallic character arises from the HgO2 structural units and coexists with the antiferromagnetic order arising from the localized spins at the Cu2+ sites.
Note: Coherent detection of terahertz radiation employing a continuous wave optical parametric source
Authors: Kiessling Jens , Sowade Rosita , Mayorga Iván Cámara , Buse Karsten , Breunig Ingo
Published: February 2011

The combination of an all-optical terahertz source with a photoconductive antenna to achieve coherent detection is presented. This approach aims to overcome the frequency limits introduced by optoelectronic terahertz sources commonly used. Here the Gaussian-shaped and linearly polarized terahertz waves are generated by a continuous wave optical parametric oscillator with a power of 3 μW at 1.4 THz. The infrared signal light of the optical parametric oscillator can be used to coherently detect the generated terahertz wave with a photoconductive antenna. As a proof-of-principle experiment we determine the thickness profile of a plastic lens using phase shifting interferometry.
Resonant optical reflection by a periodic system of the quantum well excitons at the second quantum state
Authors: Chaldyshev V. V. , Chen Yuechao , Poddubny A. N. , Vasil’ev A. P. , Liu Zhiheng
Published: February 2011

A periodic multiple quantum well GaAs/AlGaAs structure was designed, grown, and characterized in order to reveal resonant features in optical spectra when the Bragg resonance was tuned to the second quantum state x(e2-hh2) of the heavy-hole exciton-polaritons in the multiple quantum wells. This double resonance was demonstrated by tuning the incident angle of the light as well as by comparison with a single quantum well structure. A significant enhancement of the light-matter interaction was observed, which manifests itself by strong resonant optical reflection and electroreflection.
An intermediate-band-assisted avalanche multiplication in InAs/InGaAs quantum dots-in-well infrared photodetector
Authors: Lin L. , Zhen H. L. , Zhou X. H. , Li N. , Lu W. , Liu F. Q.
Published: February 2011

The avalanche multiplication of photocurrent in InAs/InGaAs quantum dot infrared photodetectors (QDIPs) has been observed in the temperature range from 20 to 80 K. The avalanche onset voltage Vth, being larger than 1.2 V at T<55 K, is reduced to less than 0.8 V at T>60 K. This singularity of Vth indicates that intermediate-band-assisted avalanche multiplication is achieved in our dots-in-well structure, which benefits from the abrupt change of the electron occupation of the intermediate band at a temperature of approximately 55 K. The remarkable reduction of Vth for QDIP is a useful enhancement in the infrared detector’s performance.
Terahertz two-cylinder waveguide coupler for transverse-magnetic and transverse-electric mode operation
Authors: Theuer M. , Shutler A. J. , Harsha S. Sree , Beigang R. , Grischkowsky D.
Published: February 2011

We report the coupling and guiding of broadband terahertz radiation using a two-cylinder waveguide coupler. For the transverse electromagnetic TEM (TM0) geometry, the two opposing metal cylinders exhibit an amplitude transmission comparable to that of the cylindrical silicon lens coupled parallel-plate waveguide, but in the transverse-electric orientation the two-cylinder coupler shows much better amplitude transmission.
Gate capacitance of cylindrical nanowires with elliptical cross-sections
Authors: Majumdar Amlan , Lin Chung-Hsun
Published: February 2011

We investigate gate capacitance of cylindrical nanowires with elliptical cross-sections because most fabricated Si nanowires have elliptical cross-sections. We derive an exact result for the capacitance of confocal elliptical capacitors and an approximate expression for the capacitance of conformal elliptical capacitors. Using numerical simulations for conformal elliptical capacitors, we show that the analytical results for the confocal and conformal elliptical capacitors are within 5% of the numerical values for eccentricity <0.85. We also provide correction factors to the analytical results that match the numerical conformal elliptical capacitances to within 5% for all values of eccentricity.
Energy transfer between two crossed laser beams in a nonisothermal plasma
Authors: Tripathi Deepak , Uma R. , Tripathi V. K.
Published: February 2011

The energy transfer between two crossed lasers (a high frequency high amplitude pump and a low frequency low amplitude probe beam) through the coupling with a difference frequency electrostatic mode/quasimode in a plasma is examined. The electrostatic mode in an unmagnetized plasma is a linearly damped acoustic mode, while in a magnetized plasma it is also taken to be a lower hybrid mode. It is driven by the ponderomotive force due to the pump and probe beams. The electron density perturbation associated with the electrostatic mode beats with the oscillatory velocities due to the lasers to produce nonlinear current densities facilitating the energy transfer from the high frequency laser to the probe beam. Efficient energy transfer occurs when the phase matching conditions are satisfied. Even when a finite mismatch between the lasers and the low frequency mode/quasimode exists, a significant energy transfer is possible. The theoretical results for the unmagnetized plasma are in compliance with the published experimental results. In a magnetized plasma lower hybrid wave appears to be a potential contender for facilitating energy exchange between lasers.
Coupling of Kelvin–Helmholtz instability and buoyancy instability in a thermally laminar plasma
Authors: Ren Haijun , Cao Jintao , Dong Chao , Wu Zhengwei , Chu Paul K.
Published: February 2011

Thermal convective instability is investigated in a thermally stratified plasma in the presence of shear flow, which is known to give rise to the Kelvin–Helmholtz (KH) instability. We examine how the KH instability and magnetothermal instability (MTI) affect each other. Based on the sharp boundary model, the KH instability coupled with the MTI is studied. We present the growth rate and instability criteria. The shear flow is shown to significantly alter the critical condition for the occurrence of thermal convective instability.
Filamentation of laser in an inhomogeneous plasma
Authors: Singh Ranjeet , Tripathi V. K.
Published: February 2011

Filamentation of an intense short pulse laser in an inhomogeneous plasma is investigated when laser propagates along the direction of density gradient and nonlinearity arises due to the relativistic mass variation and ponderomotive force. The ion motion is neglected; however, the effect of dielectric swelling is included. The inhomogeneity in the density profile introduces dielectric swelling of the pump intensity enhancing the plasma permittivity and the growth rate of the instability. The perturbation in laser amplitude grows faster than exponential as the laser penetrates deeper into the denser plasma.
A method to compute probability current in generic coordinates
Authors: Nadal-Ferret Marc , Gelabert Ricard , Moreno Miquel , Lluch José M.
Published: February 2011

A method to compute probability current and its surface integral, the total flux, for systems of many particles of different masses is presented, based on transforming the wave function and its gradient onto a mass-weighted coordinate system. As a test for this methodology, it has been applied to a nontrivial 6-dimensional quantum dynamics study of a model of the operation of the proton-wire in Green Fluorescent Protein [O. Vendrell, R. Gelabert, M. Moreno, and J. M. Lluch, J. Phys. Chem. B, 112, 5500–5511 (2008)]. An adaptive Monte Carlo method is proposed, with favorable scaling properties for future applications, to solve the flux integral. Comparison of total reactive flux with the time derivative of the survival probability is satisfactory, corroborating the adequacy of the derivation. Using the new method the flux can quantitatively be divided into its positive and negative contributions, or more relevantly, into tunneling and classical parts.
Semianalytical study of hemispherical meniscus oscillation with an anchored edge on a conductive flat plate under an ac electric field
Authors: Tran Si Bui Quang , Byun Doyoung , Yudistira Hadi Teguh , Oh Je Hoon
Published: February 2011

This paper presents an experimental observation and a semianalytical simulation of the oscillations of an anchored hemispherical liquid meniscus on a conductive flat plate under an ac electric field. For the simulation, the liquid is assumed to be an incompressible, inviscid, and perfectly conductive fluid in a zero-gravity environment. The mutual interaction between the electric field and the hydrodynamics is iteratively solved. As a result, the simulation can follow the oscillating meniscus shapes and contours of the electric field outside the meniscus according to the applied frequency. The velocity profile of the liquid inside the meniscus is also presented. The present theory can be used to predict the oscillation shape of a liquid droplet on a plate with a certain applied frequency. The simulated oscillation shape is in agreement with the experimental result. The effects of the liquid density, the liquid surface tension, and the radius of the hemispherical meniscus on the oscillation are investigated. Then the oscillation of the drop on hydrophobic and hydrophilic substrates is also experimentally studied. Furthermore, we investigated the effects of the applied electric field on the coffee stain effect while the droplet is drying.
Photo-induced magnetoresistance enhancement in manganite heterojunction at room temperature
Authors: Yue Z J , Zhao K , Ni H , Zhao S Q , Kong Y C , Wong H K , Wang A J
Published: February 2011

The enhanced magnetoresistance (MR) effect has been discovered under laser illumination in the La2/3Ca1/3MnO3 film on the n-Si substrate at room temperature. The MR ratio dramatically increases from 0.54% to as large as 18% by irradiating with a 808 nm CW laser in 6.4 kOe magnetic field. Our results have potential applications to develop novel photo-magnetic functional devices operated at room temperature, and even possible multifunctional devices with tunable optical and magnetic properties.
Photoluminescence properties of erbium-doped europium thiosilicate
Authors: Sugiyama Mitsuharu , Nanai Yasushi , Okada Yuu , Okuno Tsuyoshi
Published: February 2011

Photoluminescence properties of erbium-doped europium thiosilicate (Eu2SiS4 : Er) are reported. The material is fabricated in powder and on silicon substrates. The luminescence at 1.54 µm corresponding to the 4
I
13/2–4
I
15/2 transition of Er3+ is observed. Broad absorption of the 4f7–4f65d transition of Eu2+ in the host matrix in 350–500 nm region is used for the excitation of Er3+. Efficient energy transfer from the host to erbium is realized.
Matrix localizations of 𝑛-firs. I
Authors: Malcolmson Peter
Published: February 2011

An

n
n

-fir is an associative ring in which every

n
n

-generator right ideal is free of unique rank. Matrix localization of a ring involves the adjunction of universal inverses to certain matrices over the ring, so that a new ring results over which the matrices have inverses, but so that the minimum of additional relations is imposed. A full matrix is a square matrix which, when considered as an endomorphism of a free module, cannot be factored through a free module of smaller rank. The main result of this paper is that if the original ring is an

n
n

-fir with

n
>
2
k

n > 2k

and if we form a matrix localization by adjoining universal inverses to all full matrices of size

k
k

, then the resulting ring is an

(
n
−
2
k
)

(n - 2k)

-fir. This generalizes an announced result of V. N. Gerasimov. There are related results on the structure of the universal skew field of fractions of a semifir.
Noncommutative topological dynamics. I
Authors: Avitzour Daniel
Published: February 2011

Ergodicity and minimality are defined for

C

∗

C^{\ast }

-flows

(
G
,
A
)

(G,A)

where

G
G

is a group acting on a

C

∗

C^{\ast }

-algebra

A
A

by *-automorphisms. Elementary properties are proved and several examples are given. In particular, an example shows that there are arbitrarily large

C

∗

C^{\ast }

-algebras admitting a minimal action of the integers.
Summability of Hermite expansions. I
Authors: Thangavelu S.
Published: February 2011

We study the summability of one-dimensional Hermite expansions. We prove that the critical index for the Riesz summability is

1

/

6

1/6

. We also prove analogues of the Fejér-Lebesgue theorem and Riemann’s localisation principle.
FIMO: scanning for occurrences of a given motif
Authors: Grant Charles E. , Bailey Timothy L. , Noble William Stafford
Published: February 2011

Summary: A motif is a short DNA or protein sequence that contributes to the biological function of the sequence in which it resides. Over the past several decades, many computational methods have been described for identifying, characterizing and searching with sequence motifs. Critical to nearly any motif-based sequence analysis pipeline is the ability to scan a sequence database for occurrences of a given motif described by a position-specific frequency matrix.

Results: We describe Find Individual Motif Occurrences (FIMO), a software tool for scanning DNA or protein sequences with motifs described as position-specific scoring matrices. The program computes a log-likelihood ratio score for each position in a given sequence database, uses established dynamic programming methods to convert this score to a P-value and then applies false discovery rate analysis to estimate a q-value for each position in the given sequence. FIMO provides output in a variety of formats, including HTML, XML and several Santa Cruz Genome Browser formats. The program is efficient, allowing for the scanning of DNA sequences at a rate of 3.5 Mb/s on a single CPU.

Availability and Implementation: FIMO is part of the MEME Suite software toolkit. A web server and source code are available at http://meme.sdsc.edu.

Contact:  t.bailey@imb.uq.edu.au; t.bailey@imb.uq.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
Defining an informativeness metric for clustering gene expression data
Authors: Mar Jessica C. , Wells Christine A. , Quackenbush John
Published: February 2011

Motivation: Unsupervised ‘cluster’ analysis is an invaluable tool for exploratory microarray data analysis, as it organizes the data into groups of genes or samples in which the elements share common patterns. Once the data are clustered, finding the optimal number of informative subgroups within a dataset is a problem that, while important for understanding the underlying phenotypes, is one for which there is no robust, widely accepted solution.

Results: To address this problem we developed an ‘informativeness metric’ based on a simple analysis of variance statistic that identifies the number of clusters which best separate phenotypic groups. The performance of the informativeness metric has been tested on both experimental and simulated datasets, and we contrast these results with those obtained using alternative methods such as the gap statistic.

Availability: The method has been implemented in the Bioconductor R package attract; it is also freely available from http://compbio.dfci.harvard.edu/pubs/attract_1.0.1.zip.

Contact:  jess@jimmy.harvard.edu; johnq@jimmy.harvard.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Analysis of Dynamic Intratidal Compliance in a Lung Collapse Model
Authors: Schumann Stefan , Vimlati László , Kawati Rafael , Guttmann Josef , Lichtwarck-Aschoff Michael
Published: February 2011

Background

For mechanical ventilation to be lung-protective, an accepted suggestion is to place the tidal volume (V(T)) between the lower and upper inflection point of the airway pressure-volume relation. The drawback of this approach is, however, that the pressure-volume relation is assessed under quasistatic, no-flow conditions, which the lungs never experience during ventilation. Intratidal nonlinearity must be assessed under real (i.e., dynamic) conditions. With the dynamic gliding-SLICE technique that generates a high-resolution description of intratidal mechanics, the current study analyzed the profile of the compliance of the respiratory system (C(RS)).

Methods

In 12 anesthetized piglets with lung collapse, the pressure-volume relation was acquired at different levels of positive end-expiratory pressure (PEEP: 0, 5, 10, and 15 cm H(2)O). Lung collapse was assessed by computed tomography and the intratidal course of C(RS) using the gliding-SLICE method.

Results

Depending on PEEP, C(RS) showed characteristic profiles. With low PEEP, C(RS) increased up to 20% above the compliance at early inspiration, suggesting intratidal recruitment; whereas a profile of decreasing C(RS), signaling overdistension, occurred with V(T) > 5 ml/kg and high PEEP levels. At the highest volume range, C(RS) was up to 60% less than the maximum. With PEEP 10 cm H(2)O, C(RS) was high and did not decrease before 5 ml/kg V(T) was delivered.

Conclusions

The profile of dynamic C(RS) reflects nonlinear intratidal mechanics of the respiratory system. The SLICE analysis has the potential to detect intratidal recruitment and overdistension. This might help in finding a combination of PEEP and V(T) level that is protective from a lung-mechanics perspective.
Determinants of the human infant intestinal microbiota after the introduction of first complementary foods in infant samples from five European centres
Authors: Fallani Matteo , Amarri Sergio , Uusijarvi Agneta , Adam Rüdiger , Khanna Sheila , Aguilera Marga , Gil Angel , Vieites Jose M. , Norin Elisabeth , Young David , Scott Jane A. , Doré Joël , Edwards Christine A. ,   the INFABIO team
Published: February 2011

Although it is well established that early infant feeding has a major influence on the establishment of the gut microbiota, very little is understood about how the introduction of first solid food influences the colonization process. This study aimed to determine the impact of weaning on the faecal microbiota composition of infants from five European countries (Sweden, Scotland, Germany, Italy and Spain) which have different lifestyle characteristics and infant feeding practices. Faecal samples were collected from 605 infants approximately 4 weeks after the introduction of first solid foods and the results were compared with the same infants before weaning (6 weeks of age) to investigate the association with determining factors such as geographical origin, mode of delivery, previous feeding method and age of weaning. Samples were analysed by fluorescencein situhybridization and flow cytometry using a panel of 10 rRNA targeted group- and species-specific oligonucleotide probes. The genusBifidobacterium(36.5 % average proportion of total detectable bacteria),Clostridium coccoidesgroup (14 %) andBacteroides(13.6 %) were predominant after weaning. Similar to pre-weaning, northern European countries were associated with a higher proportion of bifidobacteria in the infant gut microbiota while higher levels ofBacteroidesand lactobacilli characterized southern European countries. As before weaning, the initial feeding method influenced theClostridium leptumgroup andClostridium difficile+Clostridium perfringensspecies, and bifidobacteria still dominated the faeces of initially breast-fed infants. Formula-fed babies presented significantly higher proportions ofBacteroidesand theC. coccoidesgroup. The mode of birth influenced changes in the proportions of bacteroides and atopobium. Although there were significant differences in the mean weaning age between countries, this was not related to the populations of bifidobacteria or bacteroides. Thus, although the faecal microbiota of infants after first complementary foods was different to that before weaning commenced, many of the initial influences on microbiota composition were still evident.
Comparison of toxin and spore production in clinically relevant strains of Clostridium difficile
Authors: Vohra Prerna , Poxton Ian R.
Published: February 2011

Clostridium difficile is a major cause of nosocomial diarrhoea. The toxins that it produces (TcdA and TcdB) are responsible for the characteristic pathology of C. difficile infection (CDI), while its spores persist in the environment, causing its widespread transmission. Many different strains of C. difficile exist worldwide and the epidemiology of the strains is ever-changing: in Scotland, PCR ribotype 012 was once prevalent, but currently ribotypes 106, 001 and 027 are endemic. This study aimed to identify the differences among these ribotypes with respect to their growth, and toxin and spore production in vitro. It was observed that the hypervirulent ribotype 027 produces significantly more toxin than the other ribotypes in the exponential and stationary phases of growth. Further, the endemic strains produce significantly more toxins and spores than ribotype 012. Of note was the observation that tcdC expression did not decrease into the stationary phase of growth, implying that it may have a modulatory rather than repressive effect on toxin production. Further, the increased expression of tcdE in ribotype 027 suggests its importance in the release of the toxins. It can thus be concluded that several genotypic and phenotypic traits might synergistically contribute to the hypervirulence of ribotype 027. These observations might suggest a changing trend towards increased virulence in the strains currently responsible for CDI.
Structure–function relationships of the competence lipoprotein ComL and SSB in meningococcal transformation
Authors: Benam Afsaneh V. , Lång Emma , Alfsnes Kristian , Fleckenstein Burkhard , Rowe Alexander D. , Hovland Eirik , Ambur Ole Herman , Frye Stephan A. , Tønjum Tone
Published: February 2011

Neisseria meningitidis, the meningococcus, is naturally competent for transformation throughout its growth cycle. The uptake of exogenous DNA into the meningococcus cell during transformation is a multi-step process. Beyond the requirement for type IV pilus expression for efficient transformation, little is known about the neisserial proteins involved in DNA binding, uptake and genome integration. This study aimed to identify and characterize neisserial DNA binding proteins in order to further elucidate the multi-factorial transformation machinery. The meningococcus inner membrane and soluble cell fractions were searched for DNA binding components by employing 1D and 2D gel electrophoresis approaches in combination with a solid-phase overlay assay with DNA substrates. Proteins that bound DNA were identified by MS analysis. In the membrane fraction, multiple components bound DNA, including the neisserial competence lipoprotein ComL. In the soluble fraction, the meningococcus orthologue of the single-stranded DNA binding protein SSB was predominant. The DNA binding activity of the recombinant ComL and SSB proteins purified to homogeneity was verified by electromobility shift assay, and the ComL–DNA interaction was shown to be Mg2+-dependent. In 3D models of the meningococcus ComL and SSB predicted structures, potential DNA binding sites were suggested. ComL was found to co-purify with the outer membrane, directly interacting with the secretin PilQ. The combined use of 1D/2D solid-phase overlay assays with MS analysis was a useful strategy for identifying DNA binding components. The ComL DNA binding properties and outer membrane localization suggest that this lipoprotein plays a direct role in neisserial transformation, while neisserial SSB is a DNA binding protein that contributes to the terminal part of the transformation process.
MicroRNAs Regulate the Timing of Embryo Maturation in Arabidopsis
Authors: Willmann Matthew R. , Mehalick Andrew J. , Packer Rachel L. , Jenik Pablo D.
Published: February 2011

The seed is a key evolutionary adaptation of land plants that facilitates dispersal and allows for germination when the environmental conditions are adequate. Mature seeds are dormant and desiccated, with accumulated storage products that are to be used by the seedling after germination. These properties are imposed on the developing embryo by a maturation program, which operates during the later part of embryogenesis. A number of “master regulators” (the “LEC genes”) required for the induction of the maturation program have been described, but it is not known what prevents this program from being expressed during early embryogenesis. Here, we report that Arabidopsis (Arabidopsis thaliana) embryos mutant for strong alleles of DICER-LIKE1, the enzyme responsible for the biosynthesis of microRNAs (miRNAs), mature earlier than their wild-type counterparts. This heterochronic phenotype indicates that miRNAs are key regulators of the timing of the maturation program. We demonstrate that miRNAs operate in part by repressing the master regulators LEAFY COTYLEDON2 and FUSCA3 and identify the trihelix transcription factors ARABIDOPSIS 6B-INTERACTING PROTEIN1-LIKE1 (ASIL1) and ASIL2 and the histone deacetylase HDA6/SIL1 as components that act downstream of miRNAs to repress the maturation program early in embryogenesis. Both ASIL1 and HDA6/SIL1 are known to act to prevent the expression of embryonic maturation genes after germination, but to our knowledge, this is the first time they have been shown to have a role during embryogenesis. Our data point to a common negative regulatory module of maturation during early embryogenesis and seedling development.
RNAi‐mediated resistance to Cassava brown streak Uganda virus in transgenic cassava
Authors: YADAV JITENDER S. , OGWOK EMMANUEL , WAGABA HENRY , PATIL BASAVAPRABHU L. , BAGEWADI BASAVARAJ , ALICAI TITUS , GAITAN‐SOLIS ELIANA , TAYLOR NIGEL J. , FAUQUET CLAUDE M.
Published: February 2011

Cassava brown streak disease (CBSD), caused by Cassava brown streak Uganda virus (CBSUV) and Cassava brown streak virus (CBSV), is of new epidemic importance to cassava (Manihot esculenta Crantz) production in East Africa, and an emerging threat to the crop in Central and West Africa. This study demonstrates that at least one of these two ipomoviruses, CBSUV, can be efficiently controlled using RNA interference (RNAi) technology in cassava. An RNAi construct targeting the near full‐length coat protein (FL‐CP) of CBSUV was expressed constitutively as a hairpin construct in cassava. Transgenic cassava lines expressing small interfering RNAs (siRNAs) against this sequence showed 100% resistance to CBSUV across replicated graft inoculation experiments. Reverse transcriptase‐polymerase chain reaction (RT‐PCR) analysis showed the presence of CBSUV in leaves and some tuberous roots from challenged controls, but not in the same tissues from transgenic plants. This is the first demonstration of RNAi‐mediated resistance to the ipomovirus CBSUV in cassava.
The SLT2 mitogen‐activated protein kinase‐mediated signalling pathway governs conidiation, morphogenesis, fungal virulence and production of toxin and melanin in the tangerine pathotype of Alternaria alternata
Authors: YAGO JONAR INGAN , LIN CHING‐HSUAN , CHUNG KUANG‐REN
Published: February 2011

Fungi respond and adapt to different environmental stimuli via signal transduction systems. We determined the function of a yeast SLT2 mitogen‐activated protein (MAP) kinase homologue (AaSLT2) in Alternaria alternata, the fungal pathogen of citrus. Analysis of the loss‐of‐function mutant indicated that AaSLT2 is required for the production of a host‐selective toxin, and is crucial for fungal pathogenicity. Moreover, the A. alternata slt2 mutants displayed hypersensitivity to cell wall‐degrading enzymes and chemicals such as Calcofluor white and Congo red. This implicates an important role of AaSLT2 in the maintenance of cell wall integrity in A. alternata. The A. alternata slt2 mutants were also hypersensitive to a heteroaromatic compound, 2‐chloro‐5‐hydroxypyridine, and a plant growth regulator, 2,3,5‐triiodobenzoic acid. Developmentally, the AaSLT2 gene product was shown to be critical for conidial formation and hyphal elongation. Compared with the wild‐type, the mutants produced fewer but slightly larger conidia with less transverse septae. The mutants also accumulated lower levels of melanin and chitin. Unlike the wild‐type progenitor, the A. alternata slt2 mutants produced globose, swollen hyphae that did not elongate in a straight radial direction. All defective phenotypes in the mutant were restored by transformation and expression of a wild‐type copy of AaSLT2 under the control of its endogenous promoter. This study highlights an important role of the AaSLT2 MAP kinase‐mediated signalling pathway, regulating diverse physiological, developmental and pathological functions, in the tangerine pathotype of A. alternata.
Mapping studies of the Peach latent mosaic viroid reveal novel structural features
Authors: DUBÉ AUDREY , BOLDUC FRANÇOIS , BISAILLON MARTIN , PERREAULT JEAN‐PIERRE
Published: February 2011

Knowledge of the structure of a viroid is critically important to elucidate the roles played by the various RNA motifs in the steps of the viroid's life cycle. A new technique, RNA‐selective 2′‐hydroxyl acylation analysed by primer extension (SHAPE), has recently been shown to be fast, reliable and applicable to the study of various RNA molecules. Consequently, this method was used to probe sequence variants of Peach latent mosaic viroid (PLMVd). Initially, probing data from RNA strands of both polarities of the Siberian C variant confirmed the secondary structures previously determined using both conventional and fastidious approaches. Subsequently, analysis of an Alberta variant showed an identical structure for the strand of (−) polarity, but the (+) polarity strand exhibited two differences from the Siberian C variant: the P11–L11 stem–loop domain formed a cruciform structure, and nucleotides from loops L1 and L11 were involved in the formation of a pseudoknot. The existence of both of these motifs was confirmed by site‐directed mutagenesis. The subsequent probing of 12 natural sequence variants led to the elucidation of the criteria governing the formation of this novel pseudoknot. Importantly, this study revealed that the heterogeneity of a viroid is not limited to its nucleotide sequence, but may also occur at the structural level.
Everyday clinical experience of alitretinoin in the treatment of severe chronic hand eczema: seven case studies
Authors: English J. , Graham-Brown R. , de Sica Chapman A. , Alexandroff A. B.
Published: February 2011

Chronic hand eczema (CHE) is a debilitating and distressing disease for patients, the physical symptoms of which are compounded by psychosocial problems. Alitretinoin is an endogenously occurring physiological vitamin A derivative (retinoid) that possesses strong anti-inflammatory and immunomodulatory activity. It is currently the only licensed product for severe CHE unresponsive to treatment with potent topical corticosteroids, and has been proven to be highly effective in clinical trials with two-thirds of patients who responded to treatment remaining in remission at 6 months. For those that did relapse, a second study showed they could be successfully retreated with a further 3–6 month course of alitretinoin. Seven case studies of alitretinoin have been provided by consultant dermatologists showing its use in normal UK clinical practice. The cases chosen demonstrate the efficacy of alitretinoin across several different subtypes of CHE, and the positive effects the treatment brought to patients’ quality of life.
Investigating the contribution of community nurses to anticipatory care: a qualitative exploratory study
Authors: Kennedy Catriona , Harbison Jean , Mahoney Catherine , Jarvis Alison , Veitch Linda
Published: February 2011

kennedy c., harbison j., mahoney c., jarvis a. & veitch l. (2011) Investigating the contribution of community nurses to anticipatory care: a qualitative exploratory study. Journal of Advanced Nursing67(7), 1558–1567.

Aims.  To investigate how one aspect of anticipatory care is understood and delivered in practice. ‘Anticipatory care’ in this context can be understood as proactive care, which is oriented towards prevention of adverse events.

Background.  Scotland has identified the intention to move away from a preoccupation with acute care and invest in health improvement and anticipatory care. Community nurses are the key, yet little is known about how they understand and deliver anticipatory care.

Methods.  A qualitative case study design using individual in‐depth interviews (n = 10), observation (n = 9) and focus groups (n = 5) was selected. Five focus group interviews were carried out with district nurses, practice nurses and health visitors. Subsequently, nine observation events took place, each focused on a single nurse/client encounter. Data were collected during 2008 and 2009 in one Community Health Partnership in Scotland.

Findings.  Two approaches to anticipatory care emerged; these were influenced by participants’ roles and responsibilities. Approach 1 derives from Government policy agenda and is focused on protocol‐focused management of long‐term illness. Approach 2 is synonymous with long‐standing nursing activity focused on holistic care of individual patients. Both approaches are proactive in nature.

Conclusions.  There is scope to develop a more conceptually complex model of anticipatory care, building on this initial exploration, within which all aims, roles, practices and methods of evaluation can be located and clearly visible. This offers the potential to enable practitioners to interpret and apply policy – otherwise change may be limited and result in service gaps.
Exploring and comparing the experience and coping behaviour of men and women with colorectal cancer at diagnosis and during surgery
Authors: McCaughan Eilis , Prue Gillian , Parahoo Kader , McIlfatrick Sonja , McKenna Hugh
Published: February 2011

mccaughan e., prue g., parahoo k., mcilfatrick s. & mckenna h. (2011) Exploring and comparing the experience and coping behaviour of men and women with colorectal cancer at diagnosis and during surgery. Journal of Advanced Nursing67(7), 1591–1600.

Aim.  This paper is a report of a study exploring and comparing the experience of men and women with colorectal cancer at diagnosis and during surgery.

Background.  Men have higher incidence and mortality rates for nearly all cancers and frequently use health behaviours that reflect their masculinity. There has been minimal investigation into the influence of gender on the experience of a ‘shared’ cancer.

Methods.  From November 2006 to November 2008, a qualitative study was conducted involving 38 individuals (24 men, 14 women) with colorectal cancer. Data were generated using semi‐structured interviews at four time points over an 18‐month period. This paper reports the participants’ experience at diagnosis and during surgery (time point 1) with the purpose of examining the impact of gender on this experience.

Findings.  In general, men appeared more accepting of their diagnosis. The majority of females seemed more emotional and more affected by the physical side effects. However, there was variation in both gender groups, with some men and women portraying both ‘masculine’ and ‘feminine’ traits. There was also individual variation in relation to context.

Conclusions.  It appears that many men may have been experiencing side effects and/or psychological distress that they were reluctant to discuss, particularly as some men portrayed typical ‘masculine’ traits in public, but felt able to open up in private. Nurses should not make assumptions based on the traditional view of masculinity, and should determine how each man wants to deal with their diagnosis and not presume that all men need to ‘open up’ about their illness.
The accuracy of using integrated electronic health care data to identify patients with undiagnosed diabetes mellitus
Authors: Ho Michael L. , Lawrence Nadine , van Walraven Carl , Manuel Doug , Keely Erin , Malcolm Janine , Reid Robert D. , Forster Alan J.
Published: February 2011

Rationale, aims and objectives  Diabetes mellitus is a growing health and economic burden. Identification of patients with unrecognized diabetes, or those at high risk for diabetes, provides an opportunity for timely intervention. This study assessed the accuracy of using electronic health care data to identify patients with undiagnosed diabetes.

Methods  The study was conducted at a tertiary‐care teaching facility in Ottawa, Canada. The study cohort was a stratified random sample of hospitalizations between 1 January 2003 and 31 December 2008. We used diagnostic codes, pharmacy orders and serum glucose tests to classify patients into six groups: ‘recognized diabetes’ (a diabetes diagnostic code or any diabetes medication), ‘probable diabetes’ (maximum glucose ≥ 11.1 mmol L−1), ‘possible diabetes’ (maximum glucose between 7.8 and 11.1 mmol L−1), ‘unlikely diabetes’ (maximum glucose between 6.0 and 7.8 mmol L−1), ‘no diabetes’ (maximum glucose < 6.0 mmol L−1) and ‘unknown diabetes status’ (no glucose test). We compared this electronic classification to a reference standard chart review performed by a blinded abstractor.

Results  A total of 500 hospitalizations were included. The prevalence of each diabetes group was: recognized – 17%; probable – 4%; possible – 15%; unlikely – 20%; none – 15%; and unknown – 29%. Our electronic algorithm correctly classified 88.8% (95% confidence interval 85.7–91.3) of hospitalizations (weighted‐Kappa = 0.885; 95% confidence interval 0.851–0.919). The sensitivity, specificity and positive predictive values of our algorithm for ‘known diabetes’ was 0.842, 0.988 and 0.941, respectively. For patients at a ‘high risk for diabetes’ (maximum glucose > 7.8 mmol L−1), the corresponding values were 0.921, 0.971 and 0.872.

Conclusions  Patients with diagnosed and undiagnosed diabetes can be accurately identified using electronic health care data.