bluuebunny/crossref_metadata_2025 huggingface dataset:
Ownership concentration, family control and performance of firms
Authors: Hamadi Malika
Published: July 2010

Abstract This paper explores the relationship between firm performance, measured by Tobin's Q and very powerful controlling shareholders in a sample of Belgian listed firms. The paper shows that overall the largest shareholders have a negative effect on firm performance. Nevertheless, in family firms the effect of large controlling shareholders on performance is positive except when they are organized in voting blocks. Firms related to coordination centers display higher performance associated with large shareholders. The paper shows that the presence of a second shareholder in the firm has no significant effect.
Rapid characterization of biomass using fluorescence spectroscopy coupled with multivariate data analysis. II. Northern red oak (Quercus rubra)
Authors: Nkansah K. , Dawson-Andoh B.
Published: July 2010

This paper is the final part of our study into the potential use of fluorescence spectrometer coupled with multivariate data analysis as a process analytical tool for rapid characterization of a variety of biomass residues and this study focuses on Northern red oak (Quercus rubra) as a bioenergy feedstock. The results of the study showed that with the exception of holocellulose content and ash content, fluorescence spectrometer can be used to predict some chemical and physical properties of biomass relevant to its biochemical conversion into bioenergy and bioproducts. Similar near infrared (NIR) spectra-based prediction models of the same properties and population from a previous study were compared with this study. The performance of the NIR spectra-based predictive models of each property was slightly superior over the fluorescence spectra-based models even though both can be used for the same purpose. Fluorescence spectra-based prediction models of estimated holocellulose content and ash content of Northern red oak were poorly predicted with a low R2 (<0.5).
Intersubband absorption in modulation doped heterostructures
Authors: Yao J. , Zheng W. , Opper H. , Cai J. , Taylor G. W.
Published: July 2010

Intersubband absorption is reported in a new modulation doped structure using strained InGaAs quantum wells (QWs) that support transistor operation. Well defined absorption peaks (1000 to 1700 cm−1) from 8 to 11.5 μm have been obtained using either n-type or p-type modulation doped wells. Both n and p well responses show strong polarization dependence with maximum values at incident angles of 65°–70° and peak positions which are adjusted by the QW parameters. The p well shows a double peaked response with a peak separation of about 1.5 μm which results from heavy and light hole contributions. The absorption data are compared with a theoretical model developed on the basis of variable k conservation and excellent agreement is obtained. It is shown that a mass difference between the upper and lower states is essential to predict a finite spectral width of the response.
On the phase formation of sputtered hafnium oxide and oxynitride films
Authors: Sarakinos K. , Music D. , Mráz S. , to Baben M. , Jiang K. , Nahif F. , Braun A. , Zilkens C. , Konstantinidis S. , Renaux F. , Cossement D. , Munnik F. , Schneider J. M.
Published: July 2010

Hafnium oxynitride films are deposited from a Hf target employing direct current magnetron sputtering in an Ar–O2–N2 atmosphere. It is shown that the presence of N2 allows for the stabilization of the transition zone between the metallic and the compound sputtering mode enabling deposition of films at well defined conditions of target coverage by varying the O2 partial pressure. Plasma analysis reveals that this experimental strategy facilitates control over the flux of the O− ions which are generated on the oxidized target surface and accelerated by the negative target potential toward the growing film. An arrangement that enables film growth without O− ion bombardment is also implemented. Moreover, stabilization of the transition sputtering zone and control of the O− ion flux without N2 addition is achieved employing high power pulsed magnetron sputtering. Structural characterization of the deposited films unambiguously proves that the phase formation of hafnium oxide and hafnium oxynitride films with the crystal structure of HfO2 is independent from the O− bombardment conditions. Experimental and theoretical data indicate that the presence of vacancies and/or the substitution of O by N atoms in the nonmetal sublattice favor the formation of the cubic and/or the tetragonal HfO2 crystal structure at the expense of the monoclinic HfO2 one.
Spheroidal nanoparticles as thermal near-field sensors
Authors: Biehs Svend-Age , Huth Oliver , Rüting Felix , Holthaus Martin
Published: July 2010

We suggest to exploit the shape-dependence of the near-field heat transfer for nanoscale thermal imaging. By utilizing strongly prolate or oblate nanoparticles as sensors one can assess individual components of the correlation tensors characterizing the thermal near field close to a nanostructured surface, and thus obtain directional information beyond the local density of states. Our theoretical considerations are backed by idealized numerical model calculations.
Effect of threading screw and edge dislocations on transport properties of 4H–SiC homoepitaxial layers
Authors: Maximenko S. I. , Freitas J. A. , Myers-Ward R. L. , Lew K.-K. , VanMil B. L. , Eddy C. R. , Gaskill D. K. , Muzykov P. G. , Sudarshan T. S.
Published: July 2010

Local recombination properties of threading screw and edge dislocations in 4H–SiC epitaxial layers have been studied using electron beam induced current (EBIC). The minority carrier diffusion length in the vicinity of dislocations was found to vary with dislocation type. Screw dislocations had a more pronounced impact on diffusion length than the edge dislocations, evidencing stronger recombination activity. Temperature dependence of EBIC contrast of dislocations suggests that their recombination activity is controlled by deep energy levels in the vicinity of dislocation cores. This paper shows that the type of dislocation (screw or edge) can be identified from analysis of EBIC contrast.
A high refractive index metamaterial at visible frequencies formed by stacked cut-wire plasmonic structures
Authors: Wei Xingzhan , Shi Haofei , Dong Xiaochun , Lu Yueguang , Du Chunlei
Published: July 2010

A type of metamaterial composing of stacked cut-wire plasmonic structures has been designed, fabricated, and characterized. The excitation of electric resonance caused by the surface plasmons effect dominates the electric field states, so that the effective refractive index can behave as a dramatic increase at visible frequencies, which is intimately associated with the resonance strength and can be modulated by reasonably changing the structure geometries. The phenomenon has been demonstrated with the measured transmittances being in agreement with simulation results. And the effective parameters judged by Kramers–Kronig relations have been uniquely retrieved from the simulated transmission and reflection data.
Thermoelastic analysis of a silicon surface under x-ray free-electron-laser irradiation
Authors: de Castro A. R. B. , Vasconcellos Aurea R. , Luzzi Roberto
Published: July 2010

We present an analysis of the time evolution of a highly excited silicon substrate after partial absorption of a femtosecond soft x-ray pulse. The detailed time-dependent thermoelastic behavior of the substrate in terms of the displacements u(r,t) is derived for time delays for which the usual local thermodynamic variables, temperature T(r,t) and density n(r,t), become well-defined, namely, a few hundred femtoseconds after x-ray pulse absorption. For practical optical components under present conditions of operation with trains of pulses, we find that in a worst case scenario, already the second pulse in the train could be adversely affected by dynamic thermal distortion induced by the preceding pulse.
Interface defect-assisted single electron charging (and discharging) dynamics in Ge nanocrystals memories
Authors: de Sousa J. S. , Peibst R. , Farias G. A. , Leburton J.-P. , Hofmann K. R.
Published: July 2010

The charging and discharging dynamics of Ge nanocrystal memories is measured and compared with a realistic quantum mechanical model that is able to reproduce qualitatively the overall device behavior. Quantitatively, the charging (discharging) dynamics is faster (slower) than predicted by calculations. To explain the discrepancies, we propose the quantum confined nanocrystal states are responsible for collecting the incoming electrons, but some of them are captured by defects in the nanocrystal surface. The potential created by the filled defects modify the spatial distribution of the nanocrystal wave functions, enhancing their penetration in the tunneling oxide and increasing the incoming transition rates. In the discharging process, the electrons confined in the nanocrystal states escape initially, while the ones in the defects have to be thermally excited to the nanocrystals states in order to tunnel out, slowing down the escape of the last few electrons.
The role of quantum confinement and crystalline structure on excitonic lifetimes in silicon nanoclusters
Authors: Borrero-González L. J. , Nunes L. A. O. , Andreeta M. R. B. , Wojcik J. , Mascher P. , Pusep Y. A. , Comedi D. , Guimarães F. E. G.
Published: July 2010

The emission energy dependence of the photoluminescence (PL) decay rate at room temperature has been studied in Si nanoclusters (Si-ncl) embedded in Si oxide matrices obtained by thermal annealing of substoichiometric Si oxide layers SiyO1−y, y=(0.36,0.39,0.42), at various annealing temperatures (Ta) and gas atmospheres. Raman scattering measurements give evidence for the formation of amorphous Si-ncl at Ta=900 °C and of crystalline Si-ncl for Ta=1000 °C and 1100 °C. For Ta=1100 °C, the energy dispersion of the PL decay rate does not depend on sample fabrication conditions and follows previously reported behavior. For lower Ta, the rate becomes dependent on fabrication conditions and less energy dispersive. The effects are attributed to exciton localization and decoherence leading to the suppression of quantum confinement and the enhancement of nonradiative recombination in disordered and amorphous Si-ncl.
Dramatic mobility enhancements in doped SrTiO3 thin films by defect management
Authors: Kozuka Y. , Hikita Y. , Bell C. , Hwang H. Y.
Published: July 2010

We report bulk-quality n-type SrTiO3 (n-SrTiO3) thin films fabricated by pulsed laser deposition, with electron mobility as high as 6600 cm2 V−1 s−1 at 2 K and carrier density as low as 2.0×1018 cm−3 (∼0.02 at. %), far exceeding previous pulsed laser deposition films. This result stems from precise strontium and oxygen vacancy defect chemistry management, providing a general approach for defect control in complex oxide heteroepitaxy.
Evidence of atomic adsorption on TiO2 under plasma exposure and related C2H2 surface reactivity
Authors: Guaitella O. , Lazzaroni C. , Marinov D. , Rousseau A.
Published: July 2010

Adsorption/reaction kinetics of C2H2 on the surface of plasma-treated SiO2 and TiO2 catalysts is studied. The catalysts are pretreated with a dc discharge in Ar, O2, N2, or air. Then 950 ppm of C2H2 in air is introduced in the closed-volume reactor. It is found that TiO2 pretreated with O2 or air plasma catalyzes C2H2 removal from the gas phase without any UV activation. During 10 min after introduction the loss of C2H2 in the whole reactor is about 5×1015 molecules. Comparison between different pretreatment procedures shows that weakly bonded oxygen atoms may remain on TiO2 long after plasma exposure.
High performance atomic-layer-deposited LaLuO3/Ge-on-insulator p-channel metal-oxide-semiconductor field-effect transistor with thermally grown GeO2 as interfacial passivation layer
Authors: Gu J. J. , Liu Y. Q. , Xu M. , Celler G. K. , Gordon R. G. , Ye P. D.
Published: July 2010

Enhancement-mode p-channel metal-oxide-semiconductor field-effect transistor (MOSFET) on germanium-on-insulator substrate is fabricated with atomic-layer-deposited (ALD) LaLuO3 as gate dielectric. Significant improvement in both on-state current and effective hole mobility has been observed for devices with thermal GeO2 passivation. The negative threshold voltage (VT) shift in devices with GeO2 interfacial layer (IL) further demonstrates the effectiveness of surface passivation. Results from low temperature mobility characterization show that phonon scattering is the dominant scattering mechanism at a large inversion charge, indicating good interface quality. The combination of higher-k LaLuO3 and ultrathin GeO2 IL is a promising solution to the tradeoff between the aggressive equivalent oxide thickness scaling and good interface quality.
Infrared photovoltaic solar cells based on C60 fullerene encapsulated single-walled carbon nanotubes
Authors: Hatakeyama R. , Li Y. F. , Kato T. Y. , Kaneko T.
Published: July 2010

We have investigated the possibility of using single-walled carbon nanotubes (SWNTs) as the infrared energy conversion material based on the configuration of SWNT/Si heterojunction. The performance of solar cells based on SWNTs has been examined under illumination by the light with different wavelengths. Our experimental results confirm that SWNTs play a critical role in transforming the infrared light (1550 nm) into the electrical energy. The encapsulation of C60 fullerene inside SWNTs is found to significantly enhance the performance of solar cells through adjusting the Fermi level of SWNTs.
Spin-orbit coupling in double-sided doped InAs quantum well structures
Authors: Kim Kyung-Ho , Kim Hyung-jun , Koo Hyun Cheol , Chang Joonyeon , Han Suk-Hee
Published: July 2010

We have investigated Rashba spin-orbit interaction [Bychkov and Rashba, JETP Lett. 39, 78 (1984)] parameter (α) in double-sided doped InAs quantum well structures of different potential asymmetries created by introducing two separated carrier supply layers. The internal potential asymmetry is manipulated between negative and positive potential gradient by adjusting the relative doping concentrations of the two carrier supply layers. The larger potential asymmetry results in the more extensive variation in α with respect to gate electric field (Vg). The structures of the negative and positive potential gradients exhibit the opposite variation in α with respect to Vg which evidently supports the fact that the sign of α can be changed by the reversed potential asymmetry.
Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques
Authors: Satija R. , Hein J. , Lunter G. A.
Published: July 2010

Motivation: Comparative genomic sequence analysis is a powerful approach for identifying putative functional elements in silico. The availability of full-genome sequences from many vertebrate species has resulted in the development of popular tools, for example, the phastCons software package that search large numbers of genomes to identify conserved elements. While phastCons can analyze many genomes simultaneously, it ignores potentially informative insertion and deletion events and relies on a fixed, precomputed multiple sequence alignment.

Results: We have developed a new method, GRAPeFoot, which simultaneously aligns two full genomes and annotates a set of conserved regions exhibiting reduced rates of insertion, deletion and substitution mutations. We tested GRAPeFoot using the human and mouse genomes and compared its performance to a set of phastCons predictions hosted on the UCSC genome browser. Our results demonstrate that despite the use of only two genomes, GRAPeFoot identified constrained elements at rates comparable with phastCons, which analyzed data from 28 vertebrate genomes. This study demonstrates how integrated modelling of substitutions, indels and purifying selection allows a pairwise analysis to exhibit a sensitivity similar to a heuristic analysis of many genomes.

Availability: The GRAPeFoot software and set of genome-wide functional element predictions are freely available to download online at http://www.stats.ox.ac.uk/∼satija/GRAPeFoot/

Contact:  satija@stats.ox.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Fast overlapping of protein contact maps by alignment of eigenvectors
Authors: Di Lena Pietro , Fariselli Piero , Margara Luciano , Vassura Marco , Casadio Rita
Published: July 2010

Motivation: Searching for structural similarity is a key issue of protein functional annotation. The maximum contact map overlap (CMO) is one of the possible measures of protein structure similarity. Exact and approximate methods known to optimize the CMO are computationally expensive and this hampers their applicability to large-scale comparison of protein structures.

Results: In this article, we describe a heuristic algorithm (Al-Eigen) for finding a solution to the CMO problem. Our approach relies on the approximation of contact maps by eigendecomposition. We obtain good overlaps of two contact maps by computing the optimal global alignment of few principal eigenvectors. Our algorithm is simple, fast and its running time is independent of the amount of contacts in the map. Experimental testing indicates that the algorithm is comparable to exact CMO methods in terms of the overlap quality, to structural alignment methods in terms of structure similarity detection and it is fast enough to be suited for large-scale comparison of protein structures. Furthermore, our preliminary tests indicates that it is quite robust to noise, which makes it suitable for structural similarity detection also for noisy and incomplete contact maps.

Availability: Available at http://bioinformatics.cs.unibo.it/Al-Eigen

Contact:  dilena@cs.unibo.it

Supplementary information:  Supplementary data are available at Bioinformatics online.
Methods to Study PAMP-Triggered Immunity Using Tomato andNicotiana benthamiana
Authors: Nguyen Hanh P. , Chakravarthy Suma , Velásquez André C. , McLane Heather L. , Zeng Lirong , Nakayashiki Hitoshi , Park Duck-Hwan , Collmer Alan , Martin Gregory B.
Published: July 2010

Understanding the molecular basis of plant responses to pathogen-associated molecular patterns (PAMPs) is an active area of research in the field of plant–microbe interactions. A growing number of plant genes involved in various steps of PAMP-triggered immunity (PTI) pathways and microbial factors involved in the elicitation or suppression of PTI have been identified. These studies have largely relied on Arabidopsis thaliana and, therefore, most of the PTI assays have been developed and optimized for that model plant system. Although PTI is a conserved feature among plants, the response spectra vary across different species. Thus, there is a need for robust PTI assays in other pathosystems, such as those involving Solanaceae plant–pathogen interactions, which include many economically important plants and their diseases. We have optimized molecular, cellular, and whole-plant methods to measure PTI responses in two widely studied solanaceous species, tomato (Solanum lycopersicum) and Nicotiana benthamiana. Here, we provide detailed protocols for measuring various PTI-associated phenotypes, including bacterial populations after pretreatment of leaves with PAMPs, induction of reporter genes, callose deposition, activation of mitogen-activated protein kinases, and a luciferase-based reporter system. These methods will facilitate limited genetic screens and detailed characterization of potential PTI-related genes in model and economically important Solanaceae spp.–pathogen interactions.
β-Aminobutyric Acid Primes an NADPH Oxidase–Dependent Reactive Oxygen Species Production During Grapevine-Triggered Immunity
Authors: Dubreuil-Maurizi Carole , Trouvelot Sophie , Frettinger Patrick , Pugin Alain , Wendehenne David , Poinssot Benoît
Published: July 2010

The molecular mechanisms underlying the process of priming are poorly understood. In the present study, we investigated the early signaling events triggered by β-aminobutyric acid (BABA), a well-known priming-mediated plant resistance inducer. Our results indicate that, in contrast to oligogalacturonides (OG), BABA does not elicit typical defense-related early signaling events nor defense-gene expression in grapevine. However, in OG-elicited cells pretreated with BABA, production of reactive oxygen species (ROS) and expression of the respiratory-burst oxidase homolog RbohD gene were primed. In response to the causal agent of downy mildew Plasmopara viticola, a stronger ROS production was specifically observed in BABA-treated leaves. This process was correlated with an increased resistance. The NADPH oxidase inhibitor diphenylene iodonium (DPI) abolished this primed ROS production and reduced the BABA-induced resistance (BABA-IR). These results suggest that priming of an NADPH oxidase–dependent ROS production contributes to BABA-IR in the Vitis-Plasmopara pathosystem.
PsSAK1, a Stress-Activated MAP Kinase of Phytophthora sojae, Is Required for Zoospore Viability and Infection of Soybean
Authors: Li Aining , Wang Yonglin , Tao Kai , Dong Suomeng , Huang Qian , Dai Tingting , Zheng Xiaobo , Wang Yuanchao
Published: July 2010

Mitogen-activated protein kinase (MAPK) pathways are universal and evolutionarily conserved signal transduction modules in all eukaryotic cells. In this study, PsSAK1, which encodes a stress-activated MAPK of Phytophthora sojae, was identified. PsSAK1 is highly conserved in oomycetes, and it represents a novel group of MAPK due to its pleckstrin homology domain. Reverse-transcription polymerase chain reaction analysis showed that PsSAK1 expression was upregulated in zoospores and cysts and during early infection. In addition, its expression was induced by osmotic and oxidative stress mediated by NaCl and H2O2, respectively. To elucidate the function, the expression of PsSAK1 was silenced using stable transformation of P. sojae. The silencing of PsSAK1 did not impair hyphal growth, sporulation, or oospore production but severely hindered zoospore development, in that the silenced strains showed quicker encystment and a lower germination ratio than the wild type. PsSAK1-silenced mutants produced much longer germ tubes and could not colonize either wounded or unwounded soybean leaves. Our results indicate that PsSAK1 is an important regulator of zoospore development and pathogenicity in P. sojae.
Experimental evidence for real-time song frequency shift in response to urban noise in a passerine bird
Authors: Bermúdez-Cuamatzin Eira , Ríos-Chelén Alejandro A. , Gil Diego , Garcia Constantino Macías
Published: July 2010

Research has shown that bird songs are modified in different ways to deal with urban noise and promote signal transmission through noisy environments. Urban noise is composed of low frequencies, thus the observation that songs have a higher minimum frequency in noisy places suggests this is a way of avoiding noise masking. Most studies are correlative and there is as yet little experimental evidence that this is a short-term mechanism owing to individual plasticity. Here we experimentally test if house finches (
Carpodacus mexicanus
) can modulate the minimum frequency of their songs in response to different noise levels. We exposed singing males to three continuous treatments: low–high–low noise levels. We found a significant increase in minimum frequency from low to high and a decrement from high to low treatments. We also found that this was mostly achieved by modifying the frequency of the same low-frequency syllable types used in the different treatments. When different low-frequency syllables were used, those sung during the noisy condition were longer than the ones sang during the quiet condition. We conclude that house finches modify their songs in several ways in response to urban noise, thus providing evidence of a short-term acoustic adaptation.
Clock
polymorphism in Pacific salmon: evidence for variable selection along a latitudinal gradient
Authors: O'Malley Kathleen G. , Ford Michael J. , Hard Jeffrey J.
Published: July 2010

Seasonal timing of life-history events is often under strong natural selection. The
Clock
gene is a central component of an endogenous circadian clock that senses changes in photoperiod (day length) and mediates seasonal behaviours. Among Pacific salmonids (
Oncorhynchus
spp.), seasonal timing of migration and breeding is influenced by photoperiod. To expand a study of 42 North American Chinook salmon (
Oncorhynchus tshawytscha
) populations, we tested whether duplicated
Clock
genes contribute to population differences in reproductive timing. Specifically, we examined geographical variation along a similar latitudinal gradient in the polyglutamine domain (PolyQ) of
OtsClock1a
and
OtsClock1b
among 53 populations of three species: chum (
Oncorhynchus keta
), coho (
Oncorhynchus kisutch
) and pink salmon (
Oncorhynchus gorbuscha
). We found evidence for variable selection on
OtsClock1b
that corresponds to latitudinal variation in reproductive timing among these species. We evaluated the contribution of day length and a freshwater migration index to
OtsClock1b
PolyQ domain variation using regression trees and found that day length at spawning explains much of the variation in
OtsClock1b
allele frequency among chum and Chinook, but not coho and pink salmon populations. Our findings suggest that
OtsClock1b
mediates seasonal adaptation and influences geographical variation in reproductive timing in some of these highly migratory species.
Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles
Authors: Eo Soo Hyung , DeWoody J. Andrew
Published: July 2010

Rates of biological diversification should ultimately correspond to rates of genome evolution. Recent studies have compared diversification rates with phylogenetic branch lengths, but incomplete phylogenies hamper such analyses for many taxa. Herein, we use pairwise comparisons of confamilial sauropsid (bird and reptile) mitochondrial DNA (mtDNA) genome sequences to estimate substitution rates. These molecular evolutionary rates are considered in light of the age and species richness of each taxonomic family, using a random-walk speciation–extinction process to estimate rates of diversification. We find the molecular clock ticks at disparate rates in different families and at different genes. For example, evolutionary rates are relatively fast in snakes and lizards, intermediate in crocodilians and slow in turtles and birds. There was also rate variation across genes, where non-synonymous substitution rates were fastest atATP8and slowest atCO3. Family-by-gene interactions were significant, indicating that local clocks vary substantially among sauropsids. Most importantly, we find evidence that mitochondrial genome evolutionary rates are positively correlated with speciation rates and with contemporary species richness. Nuclear sequences are poorly represented among reptiles, but the correlation between rates of molecular evolution and species diversification also extends to 18 avian nuclear genes we tested. Thus, the nuclear data buttress our mtDNA findings.
How many species of flowering plants are there?
Authors: Joppa Lucas N. , Roberts David L. , Pimm Stuart L.
Published: July 2010

We estimate the probable number of flowering plants. First, we apply a model that explicitly incorporates taxonomic effort over time to estimate the number of as-yet-unknown species. Second, we ask taxonomic experts their opinions on how many species are likely to be missing, on a family-by-family basis. The results are broadly comparable. We show that the current number of species should grow by between 10 and 20 per cent. There are, however, interesting discrepancies between expert and model estimates for some families, suggesting that our model does not always completely capture patterns of taxonomic activity. The as-yet-unknown species are probably similar to those taxonomists have described recently—overwhelmingly rare and local, and disproportionately in biodiversity hotspots, where there are high levels of habitat destruction.
Is parasite pressure a driver of chemical cue diversity in ants?
Authors: Martin Stephen J. , Helanterä Heikki , Drijfhout Falko P.
Published: July 2010

Parasites and pathogens are possibly key evolutionary forces driving recognition systems. However, empirical evidence remains sparse. The ubiquitous pioneering ant
Formica fusca
is exploited by numerous socially parasitic ant species. We compared the chemical cue diversity, egg and nest mate recognition abilities in two Finnish and two UK populations where parasite pressure is high or absent, respectively. Finnish populations had excellent egg and nest mate discrimination abilities, which were lost in the UK populations. The loss of discrimination behaviour correlates with a loss in key recognition compounds (C
25
-dimethylalkanes). This was not owing to genetic drift or different ecotypes since neutral gene diversity was the same in both countries. Furthermore, it is known that the cuticular hydrocarbon profiles of non-host ant species remain stable between Finland and the UK. The most parsimonious explanation for the striking difference in the cue diversity (number of C
25
-dimethylalkanes isomers) between the UK and Finland populations is the large differences in parasite pressure experienced by
F. fusca
in the two countries. These results have strong parallels with bird (cuckoo) studies and support the hypothesis that parasites are driving recognition cue diversity.
High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection
Authors: Cooper Sara J. , Finney Gregory L. , Brown Shauna L. , Nelson Sven K. , Hesselberth Jay , MacCoss Michael J. , Fields Stanley
Published: July 2010

The measurement of small molecule metabolites on a large scale offers the opportunity for a more complete understanding of cellular metabolism. We developed a high-throughput method to quantify primary amine-containing metabolites in the yeast Saccharomyces cerevisiae by the use of capillary electrophoresis in combination with fluorescent derivatization of cell extracts. We measured amino acid levels in the yeast deletion collection, a set of ∼5000 strains each lacking a single gene, and developed a computational pipeline for data analysis. Amino acid peak assignments were validated by mass spectrometry, and the overall approach was validated by the result that expected pathway intermediates accumulate in mutants of the arginine biosynthetic pathway. Global analysis of the deletion collection was carried out using clustering methods. We grouped strains based on their metabolite profiles, revealing clusters of mutants enriched for genes encoding mitochondrial proteins, urea cycle enzymes, and vacuolar ATPase functions. One of the most striking profiles, common among several strains lacking ribosomal protein genes, accumulated lysine and a lysine-related metabolite. Mutations in the homologous ribosomal protein genes in the human result in Diamond-Blackfan anemia, demonstrating that metabolite data may have potential value in understanding disease pathology. This approach establishes metabolite profiling as capable of characterizing genes in a large collection of genetic variants.
Mortality from peptic ulcer bleeding: the impact of comorbidity and the use of drugs that promote bleeding
Authors: Åhsberg K. , Höglund P. , Staël von Holstein C.
Published: July 2010

Background  Use of drugs promoting peptic ulcer bleed has increased several folds.

Aim  To make a time‐trend analysis of peptic ulcer bleed patients and evaluate the impact of age, gender, comorbidity and use of drugs promoting peptic ulcer bleed on outcome.

Methods  Retrospective review of hospitalizations for peptic ulcer bleed at Lund University Hospital during 1984, 1994 and 2004. Univariate analyses between years and multivariable logistic regression for risk factors of fatal outcome.

Results  Incidence decreased from 62.0 to 32.1 per 100 000 inhabitants between 1984 and 2004. Mortality rates were stable. Median age (70–77 years; P = 0.001), number of comorbidities (mean ± s.d.: 0.88 ± 0.96 to 1.16 ± 0.77; P = 0.021), use of aspirin (16–57%; P < 0.001) and warfarin (5–17%; P = 0.02) increased. Pharmacological and endoscopic therapy improved. Age above 65 years (OR: 1.11, 95% CI: 1.02–1.23) and number of comorbidities (OR: 6.00, 95% CI: 2.56–17.4) were independent risk factors for in‐hospital mortality. Bleeding promoting drugs did not influence outcome negatively. Aspirin decreased the risk of fatal outcome (OR: 0.12, 95% CI: 0.012–0.67).

Conclusions  Incidence of peptic ulcer bleed decreased despite higher prescription rates of bleeding promoting drugs. The in‐hospital mortality remained unchanged. The effect of improved therapy against peptic ulcer bleed is probably outweighed by older and more comorbid patients. The decreased risk of fatal outcome in aspirin users warrants further investigations.
The extension of epidural blockade for emergency Caesarean section: a survey of current UK practice*
Authors: Regan K. J. , O'Sullivan G.
Published: July 2010

The conversion of epidural analgesia during labour to surgical anaesthesia for Caesarean section can have important medical and medicolegal implications. This survey sought to establish the current management for extending epidural blockade for emergency Caesarean section. A postal questionnaire was sent to the lead obstetric anaesthetist in all maternity units in the UK (n = 254). The response rate was 82% (n = 209). Of those surveyed, 68% (136) give the full dose of the local anaesthetic mixture in the delivery room, whilst 12.5% (25) initiate the top‐up in the delivery room and give the remainder of the dose in theatre. Fifteen per cent (30) transfer the woman to theatre before commencing anaesthesia and 34% (68) give a test dose before the full anaesthetic dose. Guidelines for converting labour analgesia to anaesthesia for emergency Caesarean section were available in 64% (128) units. Bupivacaine 0.5% was the most commonly used agent, being used as the sole agent by 41.5% (81) units and in combination by a further 18% (36). Adrenaline was added to the chosen local anaesthetic by 30% (60) whilst 12% (24) added bicarbonate. In all, 13 combinations of local anaesthetics and adjuncts were used. The mode time to transfer the patient to theatre was 1 min. Of the 161 respondents who commenced anaesthesia in the delivery room, 71% (114) did not monitor the patient during transfer, whilst 87% (140) had ephedrine immediately available. Thirty‐three respondents reported a total of 43 adverse incidents associated with the extension of epidural blockade. These included high blocks, inadequate blocks and possible intravascular injections, the latter resulting in two seizures and one cardiac arrest.
Point‐of‐care testing in haemostasis
Authors: Perry David J. , Fitzmaurice David A. , Kitchen Steve , Mackie Ian J. , Mallett Sue
Published: July 2010

Point‐of‐care testing (POCT) in haematology has seen a significant increase in both the spectrum of tests available and the number of tests performed annually. POCT is frequently undertaken with the belief that this will reduce the turnaround time for results and so improve patient care. The most obvious example of POCT in haemostasis is the out‐of‐hospital monitoring of the International Normalized Ratio in patients receiving a vitamin K antagonist, such as warfarin. Other areas include the use of the Activated Clotting Time to monitor anticoagulation for patients on cardio‐pulmonary bypass, platelet function testing to identify patients with apparent aspirin or clopidogrel resistance and thrombelastography to guide blood product replacement during cardiac and hepatic surgery. In contrast to laboratory testing, POCT is frequently undertaken by untrained or semi‐trained individuals and in many cases is not subject to the same strict quality control programmes that exist in the central laboratory. Although external quality assessment programmes do exist for some POCT assays these are still relatively few. The use of POCT in haematology, particularly in the field of haemostasis, is likely to expand and it is important that systems are in place to ensure that the generated results are accurate and precise.
Tanespimycin monotherapy in relapsed multiple myeloma: results of a phase 1 dose‐escalation study
Authors: Richardson Paul G. , Chanan‐Khan Asher A. , Alsina Melissa , Albitar Maher , Berman David , Messina Marianne , Mitsiades Constantine S. , Anderson Kenneth C.
Published: July 2010

Tanespimycin, a heat shock protein 90 (HSP90) inhibitor, induces apoptosis in drug‐sensitive and ‐resistant MM cell lines and in tumour cells from patients with relapsed MM. In this phase 1 dose‐escalation study, the safety, plasma pharmacokinetics, and biological/antitumour activity of tanespimycin were evaluated in heavily pretreated patients with relapsed/refractory MM. Tanespimycin (150–525 mg/m2) was given on days 1, 4, 8, and 11 of each 3‐week cycle for up to 8 cycles. Non‐haematological AEs included diarrhoea (59%), back pain (35%), fatigue (38%), and nausea (35%); haematological AEs included anaemia (24%) and thrombocytopenia (21%). One patient (3%) achieved minimal response (MR), with a progression‐free survival (PFS) of 3 months, a 41% decrease from baseline in urine M protein, and a 33% decrease from baseline in serum M protein. Fifteen patients (52%) achieved SD with a median PFS of 2·1 months; 5/15 had reductions in serum M protein ranging from 7% to 38% and in urine M protein ranging from 6% to 91%. Mean HSP70 levels increased from day 1 h 0 to day 1 h 4 with further increases on day 11 h 0 and day 11 h 4, consistent with a therapeutic treatment effect. Tanespimycin monotherapy was well tolerated and demonstrated activity across all doses tested.
Dendritic cells pulsed with antigen-specific apoptotic bodies prevent experimental type 1 diabetes
Authors: Marin-Gallen S , Clemente-Casares X , Planas R , Pujol-Autonell I , Carrascal J , Carrillo J , Ampudia R , Verdaguer J , Pujol-Borrell R , Borràs F E , Vives-Pi M
Published: July 2010

Dendritic cells (DCs) are powerful antigen-presenting cells capable of maintaining peripheral tolerance. The possibility to generate tolerogenic DCs opens new therapeutic approaches in the prevention or remission of autoimmunity. There is currently no treatment inducing long-term tolerance and remission in type 1 diabetes (T1D), a disease caused by autoimmunity towards β cells. An ideal immunotherapy should inhibit the autoimmune attack, avoid systemic side effects and allow islet regeneration. Apoptotic cells – a source of autoantigens – are cleared rapidly by macrophages and DCs through an immunologically silent process that contributes to maintaining tolerance. Our aims were to prevent T1D and to evaluate the re-establishment of peripheral tolerance using autologous DCs pulsed in vitro with apoptotic bodies from β cells. Immature DCs derived from bone marrow of non-obese diabetic (NOD) mice were obtained and pulsed with antigen-specific apoptotic bodies from the β cell line NIT-1. Those DCs that phagocytosed apoptotic cells diminished the expression of co-stimulatory molecules CD40 and CD86 and reduced secretion of proinflammatory cytokines. Moreover, these cells were resistant to increase the expression of co-stimulatory molecules after lipopolysaccharide activation. The administration of these cells to NOD transgenic mice expressing interferon-β in their insulin-producing cells, a model of accelerated autoimmune diabetes, decreased diabetes incidence significantly and correlated positively with insulitis reduction. DCs pulsed with apoptotic cells that express disease-associated antigens constitutes a promising strategy to prevent T1D.
Minerals controlling arsenic distribution in floodplain soils
Authors: Ackermann J. , Vetterlein D. , Kuehn T. , Kaiser K. , Jahn R.
Published: July 2010

As a consequence of intensive mining of the western Erzgebirge since medieval times, floodplain soils of the Mulde river contain large concentrations of arsenic (As) (>50 mg kg−1). Arsenic in soil is often bound to poorly crystalline Fe and Mn (hydr)oxides, which may dissolve under reducing conditions. Part of the As may also exist in primary minerals, predominately sulphides, or in secondary minerals formed upon weathering. In order to better understand the impact of seasonal flooding, we surveyed As‐bearing mineral phases, especially of iron (Fe) (hydr)oxides. Because Fe (hydr)oxides are clay‐sized, soil samples were fractionated into six particle‐size fractions. The fractions were digested with aqua regia for determination of total element concentrations, extracted with hydroxylammonium chloride (NH3OHCl; selective for Mn (hydr)oxides and NH4 oxalate), and analysed by X‐ray diffraction and scanning electron microscopy. The largely similar distribution of As and lead (Pb) suggested the potential co‐existence of the two elements in primary or secondary mineral phases. However, neither As–Pb minerals nor any other As mineral were detected. Association with Mn oxides was negligible. The predominant As‐bearing phases were poorly crystalline Fe (hydr)oxides, which also incorporated large amounts of Pb and were affected by redox dynamics.
Functional differences between native and alien species: a global‐scale comparison
Authors: Ordonez Alejandro , Wright Ian J. , Olff Han
Published: July 2010

1. A prevalent question in the study of plant invasions has been whether or not invasions can be explained on the basis of traits. Despite many attempts, a synthetic view of multi‐trait differences between alien and native species is not yet available.

2. We compiled a database of three ecologically important traits (specific leaf area, typical maximum canopy height, individual seed mass) for 4473 species sampled over 95 communities (3784 species measured in their native range, 689 species in their introduced range, 207 in both ranges).

3. Considering each trait separately, co‐occurring native and alien species significantly differed in their traits. These differences, although modest, were expressed in a combined 15% higher specific leaf area, 16% lower canopy height and 26% smaller seeds.

4. Using three novel multi‐trait metrics of functional diversity, aliens showed significantly smaller trait ranges, larger divergences and a consistent differentiation from the median trait combination of co‐occurring natives.

5. We conclude that the simultaneous evaluation of multiple traits is an important novel direction in understanding invasion success. Our results support the phenotypic divergence hypothesis that predicts functional trait differences contribute to the success of alien species.
‘A local habitation and a name’: how narrative evidence‐based medicine transforms the translational research paradigm
Authors: Goyal Rishi K. , Charon Rita , Lekas Helen‐Maria , Fullilove Mindy T. , Devlin Michael J. , Falzon Louise , Wyer Peter C.
Published: July 2010

Rationale We propose narrative evidence‐based medicine as a necessary elaboration of the NIH translational research roadmap. The roadmap defined two complex obstacles, T1 and T2, to the progress of research from the ‘bench’ or basic laboratory science to the ‘bedside’ or clinical application, the traversal of which requires emergence of complex transformative relationships between the parties and stakeholders. It fails to encompass patient interactions, hesitancies and alliances with medical care.

Aims and Objectives We suggest a third transformative or translational step, T3, that begins at the point that practitioners have themselves elected to adopt and recommend strategies and interventions based on high‐level evidence and guidelines. In our model, T3 encompasses all aspects of care that converge on the practitioner–patient relationship and ultimately determine what therapies and choices patients actually make regarding their care.

Results Learning from the biopsychosocial model, patient‐centred care and shared decision making while attending to the ethical injunction of Emmanuel Levinas to know the other, we have developed a medical practice and theory that unites the local and specific concerns of narrative medicine with the generalizability and power of evidence‐based medicine.

Conclusions We offer innovative approaches to study, teach and improve the therapeutic intimacy and integrative effectiveness of the practitioner–patient relationship.
The applicability of the Kaufman Assessment Battery for Children (K‐ABC) with older adults (50+ years) with moderate, severe and profound intellectual impairment
Authors: Hogg J. , Moss S.
Published: July 2010

To define the intellectual characteristics of a population of older people (50+ years) with severe intellectual impairment who were the focus of a wider demographic study, participants were assessed on the Kaufman Assessment Battery for Children (K‐ABC). Test material was modified to make it age‐appropriate and culturally suitable. Of the 122 people in the population [chronological age (CA) = 63·5 years; range 50–90 years], 61 were successfully tested on the K‐ABC (CA = 60·9 years; range 51–81 years). Factor analysis closely replicated the factorial structure demonstrated for younger children. Separate Sequential and Simultaneous Mental Processing factors were identified, with subtests from the Achievement Scale loading on these factors and not constituting a separate factor. Application of hierarchical cluster analysis confirmed the factor structures. Inferences in relation to cognitive development from a Piagetian perspective are drawn, and the utility of information on mental processing for educational intervention with older persons with severe intellectual impairment is noted.
Psychotherapeutic approaches in the treatment of mental illness and behavioural disorders in mentally retarded people: the significance of a psychoanalytic perspective
Authors: Gaedt C.
Published: July 2010

As a result of the increasing preoccupation with pre‐oedipal disturbances, psychoanalytic theory has had to expand its basis. Through this new interpretation, better possibilities for the explanation and treatment of the various forms of psychopathology associated with mental retardation emerge. In this connection, the notion of a ‘persisting developmental deficit’ plays an important role based on ego‐psychology which includes object‐relation theory and psychoanalytic developmental psychology. Four specific issues illustrate the significance of a psychoanalytically orientated approach, namely: (1) the transformation of organic brain deficits into mental disorders; (2) ‘secondary psychosocial deficit'; (3) the significance of the therapeutic relationship; and (4) re‐enactments as expression of a pathological identity.
A small antisense RNA downregulates expression of an essential replicase protein of an Agrobacterium tumefaciens Ti plasmid
Authors: Chai Yunrong , Winans Stephen C.
Published: July 2010

Tumour‐inducing (Ti) plasmids of Agrobacterium tumefaciens replicate via the products of the repABC genes, which are highly conserved among plasmids of the alpha‐Proteobacteria. RepA and RepB direct stable partitioning of daughter plasmids, while the RepC directs replicative DNA synthesis. We have identified a new gene (repE) within the repB–repC intergenic region of an octopine‐type Ti plasmid. This gene encodes a small, non‐translated RNA that is transcribed in the direction opposite to the repABC mRNA. Increased expression of repE blocked plasmid replication of a repABC‐dependent miniplasmid, while decreased repE expression increased plasmid copy number. Direct RNA measurements and repC–lacZ fusions demonstrated that RepE inhibits the expression of RepC at the transcriptional level and possibly also at the translational level. Based on our experimental results and an RNA folding algorithm, we predict that RepE binding to the repABC mRNA would promote termination of the repABC transcript near the start codon of repC. Sequence analysis suggests that this phenomenon may be widespread among plasmids of this family.