bluuebunny/crossref_metadata_2025 huggingface dataset:
Extreme undercooling (down to 90K) of liquid metal nanoparticles
Authors: Parravicini G. B. , Stella A. , Ghigna P. , Spinolo G. , Migliori A. , d’Acapito F. , Kofman R.
Published: August 2006

Low-melting-point metal nanoparticles show remarkable undercoolings: exceptional values ΔT∕Tm≅0.5 were previously reported for confined Ga droplets in the 100–1000nm range. This was considered a characteristic limiting temperature for Ga. We here give evidence that Ga nanoparticles in the 3–15nm range can be undercooled at least down to 90K (ΔT∕Tm⩾0.7) without crystallization. Since computations and experiments on clusters with <50 atoms show on the contrary the signatures of melting at temperatures well above the bulk value, the result is particularly relevant in stressing the importance of interfacial and finite-size effects on the thermodynamics of the nanoscale.
Programmable optical wave form shaper on a microchip
Authors: Udeshi Kabir , Liao Kai-Hsiu , Que Long , Gianchandani Yogesh B. , Galvanauskas Almantas
Published: August 2006

This letter reports a device for in-fiber programmable optical pulse shaping, that consists of a chirped fiber grating and a micromachined array of Si actuators integrated on a 1×5mm2 chip. The pulse spectrum is longitudinally imaged inside a chirped fiber Bragg grating, thus permitting spectral components to be accessed inside the fiber by individual actuators. The demonstration of controlled optical pulse spectrum and temporal-width changes shows that the silicon microactuators, fabricated using a standard lithographic process, can tune the local refractive index of the grating by inducing localized fiber core strain gradients at a rate of >1μStrain per 1mW of actuator driving power.
On the validity of the continuum approximation in high Reynolds number turbulence
Authors: Moser Robert D.
Published: August 2006

It is shown that the inverse Kolmogorov-Knudsen number, defined as the ratio of the Kolmogorov length scale to the molecular mean-free path increases with turbulence Reynolds number, at constant turbulent Mach number. Despite the increasing range of turbulence spatial scales as the Reynolds number increases, in turbulence, the continuum assumption and the Navier-Stokes equations are an increasingly good approximation as the Reynolds number increases.
Characterization of the solvation dynamics of an ionic liquid via molecular dynamics simulation
Authors: Kobrak Mark N.
Published: August 2006

The solvation dynamics of ionic liquids have been the subject of intense experimental study but remain poorly understood. We present the results of molecular dynamics simulations of the solvation dynamics of the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate in response to photoexcitation of the fluorescent dye coumarin-153. We reproduce the time-resolved fluorescence Stokes shift using linear response theory, then use novel statistical techniques to analyze cation and anion contributions to the signal. We find that the solvation dynamics are dominated by collective ionic motion and characterize the time scale for various features of the collective response. Further, we use the Steele analysis [Mol. Phys. 61, 1031 (1987)] to characterize the contributions to the observed Stokes shift made by translational and rovibrational degrees of freedom. Our results indicate that in contrast to molecular liquids, the rovibrational response is trivial and the observed fluorescence response arises almost entirely from ionic translation. Our results resolve previously open questions in the literature about the nature of the rapid dynamics in room-temperature ionic liquids and offer insight into the physical principles governing ionic liquid behavior on longer time scales.
Effect of inertia on film flow over oblique and three-dimensional corrugations
Authors: Luo Haoxiang , Pozrikidis C.
Published: August 2006

The gravity-driven flow of a liquid film down an inclined plane wall with small-amplitude two-dimensional oblique or three-dimensional doubly periodic corrugations is investigated for finite Reynolds numbers. The film surface may exhibit constant or variable surface tension due to an insoluble surfactant. The key idea is to express the wall geometry as a Fourier series, and then reconstruct the three-dimensional flow in terms of the individual two-dimensional transverse and unidirectional flows over the constituent oblique two-dimensional corrugations. Three-dimensional corrugations may either reduce or amplify the surface deformation with respect to their two-dimensional counterparts due to the simultaneous effect of the constituent oblique components on the effective wave number, capillary number, and Reynolds number.
Organic inverter circuits employing ambipolar pentacene field-effect transistors
Authors: Singh Th. B. , Senkarabacak P. , Sariciftci N. S. , Tanda A. , Lackner C. , Hagelauer R. , Horowitz Gilles
Published: August 2006

Ambipolar transport has been observed in pentacene films grown on polyvinyl alcohol gate dielectric with hole and electron mobilities of 0.3 and 0.04cm2∕Vs, respectively. A simple device structure with Au as source-drain electrode can be used to operate a transistor in both p-channel and n-channel modes without employing low work function metal electrodes for ambipolar charge injection. Using ambipolar pentacene field-effect transistors, we construct a complementarylike inverter with voltage inversion gain of ∼10. These inverters are able to operate both in first and third quadrants of the voltage output to voltage input characteristics which is a unique feature of employing ambipolar transistors.
High-resolution x-ray photoelectron spectroscopy on oxygen-free amorphous Ge2Sb2Te5
Authors: Jung M.-C. , Shin H. J. , Kim K. , Noh J. S. , Chung J.
Published: August 2006

Amorphous Ge2Sb2Te5 (a-GST) film, 100nm thick, was grown by cosputtering from GeTe and Sb2Te3 targets on a silicon wafer at room temperature. The native oxidized layer, which was formed in air and about 20nm thick measured by secondary ion mass spectroscopy, was removed by Ne+ ion sputtering for 1h with 0.6kV beam energy. Core-level spectra of the Te 3d and 4d, Sb 3d and 4d, and Ge 3d of the oxygen-free a-GST were obtained by high-resolution x-ray photoelectron spectroscopy with synchrotron radiation and compared with those from Ge and GeTe. The analysis implies that the a-GST is composed on the base of chemical states of GeTe.
Ferromagnetism and anomalous Hall effect in CoxGe1−x
Authors: Ko V. , Teo K. L. , Liew T. , Chong T. C.
Published: August 2006

We report the growth of Co-doped Ge (CoxGe1−x) thin films by low-temperature molecular-beam epitaxy and the ferromagnetic properties without any additional carrier doping. The as-grown Co0.02Ge0.98 has a Curie temperature, TC∼15K, while those CoxGe1−x with x⩾4.0at.% are ferromagnetic above room temperature. On the other hand, Co0.02Ge0.98 exhibit ferromagnetic ordering up to TC∼150±10K after a low-temperature annealing. A redshift in the Raman Ge–Ge mode was observed, indicating the substitution of Ge with Co atoms. The measured Co0.02Ge0.98 are of p type and exhibit pronounced anomalous Hall effects.
Giant tunneling magnetoresistance up to 410% at room temperature in fully epitaxial Co∕MgO∕Co magnetic tunnel junctions with bcc Co(001) electrodes
Authors: Yuasa Shinji , Fukushima Akio , Kubota Hitoshi , Suzuki Yoshishige , Ando Koji
Published: August 2006

Fully epitaxial Co(001)∕MgO(001)∕Co(001) magnetic tunnel junctions (MTJs) with metastable bcc Co(001) electrodes were fabricated with molecular beam epitaxy. The MTJs exhibited giant magnetoresistance (MR) ratios up to 410% at room temperature, the highest value reported to date. Temperature dependence of the MR ratio was observed to be very small compared with fully epitaxial Fe∕MgO∕Fe and textured CoFeB∕MgO∕CoFeB MTJs. The MR ratio of the Co∕MgO∕Co MTJ showed larger bias voltage dependence than that of the epitaxial Fe∕MgO∕Fe MTJs, which probably reflects the band structures of bcc Co and Fe for the k‖=0 direction.
Photoluminescence of oxygen-deficient defects in germanium oxides: A quantum chemical study
Authors: Zyubin A. S. , Mebel A. M. , Lin S. H.
Published: August 2006

The photoabsorption and photoluminescence (PL) properties of the surface E′ center, –GeX3, and the combined E′-center–oxygen vacancy, X3Ge–GeX2, defects in substoichiometric germanium oxides have been investigated by high-level ab initio calculations, including complete active space self-consistent field, multireference configuration interaction, and symmetry-adapted cluster configuration interaction methods. Both defects have been shown to give rise to photoabsorption bands between 4 and 6eV. Geometry relaxation is significant and the Stokes shifts are large for all calculated excited states. A removal of an electron from the Ge–Ge bond leads to its destruction, whereas the creation of an electron hole at lone pairs of O atoms results in elongations of the Ge–O–Ge bonds in the corresponding bridges. Most often, deexcitations of excited electronic states proceed radiationlessly, through crossing points of their potential energy surfaces with those of the lower states. The –GeX3 defect is able to generate several PL bands in the UV (∼3eV) and IR (1.2–1.4 and 0.5–0.6eV) spectral ranges, whereas the X3Ge–GeX2 defect gives only one red/orange PL band at 2.0–2.1eV. No intense PL band was found in the blue spectral region of 2.5–2.7eV, and the two defects are not likely to contribute to the intense blue photoluminescence observed for GeO2 nanowires.
Demonstration of two-dimensional fluidic lens for integration into microfluidic flow cytometers
Authors: Godin Jessica , Lien Victor , Lo Yu-Hwa
Published: August 2006

The focusing capabilities of a two-dimensional fluid-filled lens microfabricated in an optical polymer are demonstrated. The illumination path is visualized by localized scattering centers. Functionality for flow cytometry applications is demonstrated by localization of the excitation of large-angle scatter. Integrated in-plane optical systems offer simple, compact, and inexpensive alternatives to external optics, as well as the potential for increased detection efficiency and low-power operation.
Field electron emission from individual diamond cone formed by plasma etching
Authors: Wang Q. , Wang Z. L. , Li J. J. , Huang Y. , Li Y. L. , Gu C. Z. , Cui Z.
Published: August 2006

Field electron emission properties of individual diamond cone were investigated using a customized double-probe scanning electron microscope system. The diamond cone was formed by maskless ion sputtering process in bias-assisted hot filament chemical vapor deposition system. The as-formed sharp diamond cone coated with high-sp2-content amorphous carbon exhibited high emission current of about 80μA at an applied voltage of 100V. The field emission was stable and well in consistent with the conventional Fowler-Nordheim emission mechanism, due to a stabilization process in surface work function. It has demonstrated the possibility of using individual diamond cone as a point electron emission source, because of its high field electron emission ability and stable surface state after the process of work function stabilization.
Optical gain properties of InAs∕InAlGaAs∕InP quantum dash structures with a spectral gain bandwidth of more than 300nm
Authors: Somers A. , Kaiser W. , Reithmaier J. P. , Forchel A. , Gioaninni M. , Montrosset I.
Published: August 2006

The excellent wavelength tuning properties of InP-based quantum dash (QDash) layer structures were used to realize ultrawide-gain bandwidth lasers for applications in the 1.55μm telecommunication range. To expand the attainable gain bandwidth six QDash layers with three different emission wavelengths were combined in a laser structure. Broad area laser evaluation reveals good device performance. Within the optical telecommunication band at 1.55μm a gain bandwidth of more than 300nm could be experimentally confirmed, which is in good quantitative agreement with theoretical predictions by taking into account an inhomogeneous carrier distribution between the different dash layers.
Large area self-assembled masking for photonic applications
Authors: Nagy N. , Pap A. E. , Horváth E. , Volk J. , Bársony I. , Deák A. , Hórvölgyi Z.
Published: August 2006

Ordered porous structures for photonic application were fabricated on p- and n-type silicon by means of masking against ion implantation with Langmuir-Blodgett (LB) films. LB films from Stöber silica spheres [J. Colloid Interface Sci. 26, 62 (1968)] of 350nm diameter were applied in the boron and phosphorus ion-implantation step, thereby offering a laterally periodic doping pattern. Ordered porous silicon structures were obtained after performing an anodic etch and were then removed by alkaline etching resulting in the required two-dimensional photonic arrangement. The LB silica masks and the resulting silicon structures were studied by field emission scanning electron microscope analysis.
Cu-doped GaN: A dilute magnetic semiconductor from first-principles study
Authors: Wu R. Q. , Peng G. W. , Liu L. , Feng Y. P. , Huang Z. G. , Wu Q. Y.
Published: August 2006

First-principles calculations based on spin density functional theory are performed to study the spin-resolved electronic properties of GaN doped with 6.25% of Cu. The Cu dopants are found spin polarized and the calculated band structures suggest a 100% polarization of the conduction carriers. The Cu-doped GaN favors ferromagnetic ground state which can be explained in terms of p-d hybridization mechanism, and a Curie temperature around 350K can be expected. These results suggest that the Cu-doped GaN is a promising dilute magnetic semiconductor free of magnetic precipitates and may find applications in the field of spintronics.
Selective growth of Ge islands on nanometer-scale patterned SiO2∕Si substrate by molecular beam epitaxy
Authors: Yoon Tae-Sik , Zhao Zuoming , Liu Jian , Xie Ya-Hong , Ryu Du yeol , Russell Thomas P. , Kim Hyun-Mi , Kim Ki-Bum
Published: August 2006

The authors studied the selective growth of Ge islands by molecular beam epitaxy on Si(001) covered with nanometer-scale patterned SiO2 mask generated using self-assembled diblock copolymer. Selective growth is made possible by Ge adatoms desorbing from the SiO2 surface as well as diffusing into the exposed Si area. For the Ge coverage of 2nm, multiple islands are observed along the periphery of individual exposed Si areas. At 3.5nm coverage, the coalescence of small islands with significant strain relaxation becomes evident. The ramifications of the multiple islands morphology and their coalescence on potential device applications are discussed.
Vertical-cavity surface-emitting quantum-dot laser with low threshold current grown by metal-organic vapor phase epitaxy
Authors: Hopfer F. , Kaiander I. , Lochmann A. , Mutig A. , Bognar S. , Kuntz M. , Pohl U. W. , Haisler V. A. , Bimberg D.
Published: August 2006

Ground state lasing of electrically driven vertical-cavity surface-emitting lasers with a quantum-dot (QD) gain medium grown using metal-organic vapor phase epitaxy was realized. The devices use stacked InGaAs QD layers, placed in the field intensity antinodes of the cavity formed by selectively oxidized distributed Bragg reflectors. Devices with 3×3 QD layers demonstrate at 20°C a cw output power of 1.45mW at 1.1μm emission wavelength. The peak external efficiency was 45%, limited by lateral carrier spreading within the 4λ cavity and a reduction of the internal efficiency above 60°C. A minimum threshold current of 85μA was obtained from a device with a 1μm aperture.
The epidemiology and control of ascochyta blight in field peas: a review
Authors: Bretag T. W. , Keane P. J. , Price T. V.
Published: August 2006

Ascochyta blight is one of the most important diseases affecting field peas. The disease occurs in almost all pea-growing regions of the world and can cause significant crop losses when conditions are favourable for an epidemic. Here we review current knowledge of the epidemiology of the disease. Details are provided of disease symptoms, the disease cycle and the taxonomy of the causal fungi, Ascochyta pisi, Mycosphaerella pinodes and Phoma pinodella.
The importance of seed-, soil- and air-borne inoculum is discussed along with the factors that influence survival of the causal fungi in soil, on seed or associated with pea trash. Many studies have been reviewed to establish how the fungi responsible for the disease survives from year to year, how the disease becomes established in new crops and the conditions that favour disease development. Evidence is provided that crop rotation, destruction of infected pea trash and chemical seed treatments can significantly reduce the amount of primary inoculum. Later sowing of crops has been shown to reduce the incidence and severity of disease. Fungicides have been used successfully to control the disease, although the cost of their application can significantly reduce the profitability of the crop. The best long-term strategy for effective disease control appears to be the development of ascochyta blight resistant pea varieties. Reports of physiological specialisation in ascochyta blight fungi are also documented. Despite extensive screening of germplasm, relatively few sources of resistance to ascochyta blight fungi have been found in Pisum sativum. However, the discovery of much better sources of resistance in closely related species and the development of advanced breeding methods offer new possibilities for developing useful resistance.
Benchmarking water-use efficiency of rainfed wheat in dry environments
Authors: Sadras Victor O. , Angus John F.
Published: August 2006

Attainable water-use efficiency relates attainable yield, i.e. the best yield achieved through skilful use of available technology, and seasonal evapotranspiration (ET). For wheat crops in south-eastern Australia, there is a common, often large gap between actual and attainable water-use efficiency. To evaluate whether this gap is only an Australian problem or a general feature of dry environments, we compared water-use efficiency of rainfed wheat in south-eastern Australia, the North American Great Plains, China Loess Plateau, and the Mediterranean Basin. A dataset of published data was compiled (n = 691); water-use efficiency (WUEY/ET) was calculated as the ratio between actual grain yield and seasonal ET. Maximum WUEY/ET was 22 kg grain/ha.mm. Average WUEY/ET (kg grain/ha.mm) was 9.9 for south-eastern Australia, 9.8 for the China Loess Plateau, 8.9 for the northern Great Plains of North America, 7.6 for the Mediterranean Basin, and 5.3 for the southern-central Great Plains; the variation in average WUEY/ET was largely accounted for by reference evapotranspiration around flowering. Despite substantial differences in important factors including soils, precipitation patterns, and management practices, crops in all these environments had similarly low average WUEY/ET, between 32 and 44% of attainable efficiency. We conclude that low water-use efficiency of Australian crops is not a local problem, but a widespread feature of dry environments. Yield gap analysis for crops in the Mallee region of Australia revealed low availability of phosphorus, late sowing, and subsoil chemical constraints as key factors reducing water-use efficiency, largely through their effects on soil evaporation.
Linkage between cellular communications, energy utilization, and proliferation in metastatic neuroendocrine cancers
Authors: Ippolito Joseph E. , Merritt Matthew E. , Bäckhed Fredrik , Moulder Krista L. , Mennerick Steven , Manchester Jill K. , Gammon Seth T. , Piwnica-Worms David , Gordon Jeffrey I.
Published: August 2006

To identify metabolic features that support the aggressive behavior of human neuroendocrine (NE) cancers, we examined metastatic prostate NE tumors and derived prostate NE cancer (PNEC) cell lines from a transgenic mouse model using a combination of magic angle spinning NMR spectroscopy,
in silico
predictions of biotransformations that observed metabolites may undergo, biochemical tests of these predictions, and electrophysiological/calcium imaging studies. Malignant NE cells undergo excitation and increased proliferation when their GABA
A
, glutamate, and/or glycine receptors are stimulated, use glutamate and GABA as substrates for NADH biosynthesis, and produce propylene glycol, a precursor of pyruvate derived from glycine that increases levels of circulating free fatty acids through extra-NE cell effects. Treatment of nude mice containing PNEC tumor xenografts with (
i
) amiloride, a diuretic that inhibits Abp1, an enzyme involved in NE cell GABA metabolism, (
ii
) carbidopa, an inhibitor of dopa decarboxylase which functions upstream of Abp1, plus (
iii
) flumazenil, a benzodiazepine antagonist that binds to GABA
A
receptors, leads to significant reductions in tumor growth. These findings may be generally applicable: GeneChip data sets from 471 human neoplasms revealed that components of GABA metabolic pathways, including ABP1, exhibit statistically significant increases in their expression in NE and non-NE cancers.
Glycoproteomic probes for fluorescent imaging of fucosylated glycans
in vivo
Authors: Sawa Masaaki , Hsu Tsui-Ling , Itoh Takeshi , Sugiyama Masakazu , Hanson Sarah R. , Vogt Peter K. , Wong Chi-Huey
Published: August 2006

Glycomics is emerging as a new field for the biology of complex glycoproteins and glycoconjugates. The lack of versatile glycan-labeling methods has presented a major obstacle to visualizing at the cellular level and studying glycoconjugates. To address this issue, we developed a fluorescent labeling technique based on the Cu(I)-catalyzed [3 + 2] cycloaddition, or click chemistry, which allows rapid, versatile, and specific covalent labeling of cellular glycans bearing azide groups. The method entails generating a fluorescent probe from a nonfluorescent precursor, 4-ethynyl-
N
-ethyl-1,8-naphthalimide, by clicking the fluorescent trigger, the alkyne at the 4 position, with an azido-modified sugar. Using this click-activated fluorescent probe, we demonstrate incorporation of an azido-containing fucose analog into glycoproteins via the fucose salvage pathway. Distinct fluorescent signals were observed by flow cytometry when cells treated with 6-azidofucose were labeled with the click-activated fluorogenic probe or biotinylated alkyne. The intracellular localization of fucosylated glycoconjugates was visualized by using fluorescence microscopy. This technique will allow dynamic imaging of cellular fucosylation and facilitate studies of fucosylated glycoproteins and glycolipids.
Experimental determination of particle range and dose distribution in thick targets through fragmentation reactions of stable heavy ions
Authors: Inaniwa Taku , Kohno Toshiyuki , Tomitani Takehiro , Urakabe Eriko , Sato Shinji , Kanazawa Mitsutaka , Kanai Tatsuaki
Published: August 2006

In radiation therapy with highly energetic heavy ions, the conformal irradiation of a tumour can be achieved by using their advantageous features such as the good dose localization and the high relative biological effectiveness around their mean range. For effective utilization of such properties, it is necessary to evaluate the range of incident ions and the deposited dose distribution in a patient's body. Several methods have been proposed to derive such physical quantities; one of them uses positron emitters generated through projectile fragmentation reactions of incident ions with target nuclei. We have proposed the application of the maximum likelihood estimation (MLE) method to a detected annihilation gamma-ray distribution for determination of the range of incident ions in a target and we have demonstrated the effectiveness of the method with computer simulations. In this paper, a water, a polyethylene and a polymethyl methacrylate target were each irradiated with stable12C,14N,16O and20Ne beams. Except for a few combinations of incident beams and targets, the MLE method could determine the range of incident ionsRMLEwith a difference betweenRMLEand the experimental range of less than 2.0 mm under the circumstance that the measurement of annihilation gamma rays was started just after the irradiation of 61.4 s and lasted for 500 s. In the process of evaluating the range of incident ions with the MLE method, we must calculate many physical quantities such as the fluence and the energy of both primary ions and fragments as a function of depth in a target. Consequently, by using them we can obtain the dose distribution. Thus, when the mean range of incident ions is determined with the MLE method, the annihilation gamma-ray distribution and the deposited dose distribution can be derived simultaneously. The derived dose distributions in water for the mono-energetic heavy-ion beams of four species were compared with those measured with an ionization chamber. The good agreement between the derived and the measured distributions implies that the deposited dose distribution in a target can be estimated from the detected annihilation gamma-ray distribution with a positron camera.
Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information
Authors: Capriotti E. , Calabrese R. , Casadio R.
Published: August 2006

Motivation: Human single nucleotide polymorphisms (SNPs) are the most frequent type of genetic variation in human population. One of the most important goals of SNP projects is to understand which human genotype variations are related to Mendelian and complex diseases. Great interest is focused on non-synonymous coding SNPs (nsSNPs) that are responsible of protein single point mutation. nsSNPs can be neutral or disease associated. It is known that the mutation of only one residue in a protein sequence can be related to a number of pathological conditions of dramatic social impact such as Altzheimer's, Parkinson's and Creutzfeldt-Jakob's diseases. The quality and completeness of presently available SNPs databases allows the application of machine learning techniques to predict the insurgence of human diseases due to single point protein mutation starting from the protein sequence.

Results: In this paper, we develop a method based on support vector machines (SVMs) that starting from the protein sequence information can predict whether a new phenotype derived from a nsSNP can be related to a genetic disease in humans. Using a dataset of 21 185 single point mutations, 61% of which are disease-related, out of 3587 proteins, we show that our predictor can reach more than 74% accuracy in the specific task of predicting whether a single point mutation can be disease related or not. Our method, although based on less information, outperforms other web-available predictors implementing different approaches.

Availability: A beta version of the web tool is available at

Contact:  casadio@alma.unibo.it
Group testing for pathway analysis improves comparability of different microarray datasets
Authors: Manoli Theodora , Gretz Norbert , Gröne Hermann-Josef , Kenzelmann Marc , Eils Roland , Brors Benedikt
Published: August 2006

Motivation: The wide use of DNA microarrays for the investigation of the cell transcriptome triggered the invention of numerous methods for the processing of microarray data and lead to a growing number of microarray studies that examine the same biological conditions. However, comparisons made on the level of gene lists obtained by different statistical methods or from different datasets hardly converge. We aimed at examining such discrepancies on the level of apparently affected biologically related groups of genes, e.g. metabolic or signalling pathways. This can be achieved by group testing procedures, e.g. over-representation analysis, functional class scoring (FCS), or global tests.

Results: Three public prostate cancer datasets obtained with the same microarray platform (HGU95A/HGU95Av2) were analyzed. Each dataset was subjected to normalization by either variance stabilizing normalization (vsn) or mixed model normalization (MMN). Then, statistical analysis of microarrays was applied to the vsn-normalized data and mixed model analysis to the data normalized by MMN. For multiple testing adjustment the false discovery rate was calculated and the threshold was set to 0.05. Gene lists from the same method applied to different datasets showed overlaps between 42 and 52%, while lists from different methods applied to the same dataset had between 63 and 85% of genes in common. A number of six gene lists obtained by the two statistical methods applied to the three datasets was then subjected to group testing by Fisher's exact test. Group testing by GSEA and global test was applied to the three datasets, as well. Fisher's exact test followed by global test showed more consistent results with respect to the concordance between analyses on gene lists obtained by different methods and different datasets than the GSEA. However, all group testing methods identified pathways that had already been described to be involved in the pathogenesis of prostate cancer. Moreover, pathways recurrently identified in these analyses are more likely to be reliable than those from a single analysis on a single dataset.

Contact:  b.brors@dkfz.de

Supplementary Information:  Supplementary Figure 1 and Supplementary Tables 1–4 are available at Bioinformatics online.
Cosecretion of Protease Inhibitor Stabilizes Antibodies Produced by Plant Roots
Authors: Komarnytsky Slavko , Borisjuk Nikolai , Yakoby Nir , Garvey Alison , Raskin Ilya
Published: August 2006

A plant-based system for continuous production of monoclonal antibodies based on the secretion of immunoglobulin complexes from plant roots into a hydroponic medium (rhizosecretion) was engineered to produce high levels of single-chain and full-size immunoglobulins. Replacing the original signal peptides of monoclonal antibodies with a plant-derived calreticulin signal increased the levels of antibody yield 2-fold. Cosecretion of Bowman-Birk Ser protease inhibitor reduced degradation of the immunoglobulin complexes in the default secretion pathway and further increased antibody production to 36.4 μg/g root dry weight per day for single-chain IgG1 and 21.8 μg/g root dry weight per day for full-size IgG4 antibodies. These results suggest that constitutive cosecretion of a protease inhibitor combined with the use of the plant signal peptide and the antibiotic marker-free transformation system offers a novel strategy to achieve high yields of complex therapeutic proteins secreted from plant roots.
A Versatile and Reliable Two-Component System for Tissue-Specific Gene Induction in Arabidopsis
Authors: Brand Lukas , Hörler Mirjam , Nüesch Eveline , Vassalli Sara , Barrell Philippa , Yang Wei , Jefferson Richard A. , Grossniklaus Ueli , Curtis Mark D.
Published: August 2006

Developmental progression and differentiation of distinct cell types depend on the regulation of gene expression in space and time. Tools that allow spatial and temporal control of gene expression are crucial for the accurate elucidation of gene function. Most systems to manipulate gene expression allow control of only one factor, space or time, and currently available systems that control both temporal and spatial expression of genes have their limitations. We have developed a versatile two-component system that overcomes these limitations, providing reliable, conditional gene activation in restricted tissues or cell types. This system allows conditional tissue-specific ectopic gene expression and provides a tool for conditional cell type- or tissue-specific complementation of mutants. The chimeric transcription factor XVE, in conjunction with Gateway recombination cloning technology, was used to generate a tractable system that can efficiently and faithfully activate target genes in a variety of cell types. Six promoters/enhancers, each with different tissue specificities (including vascular tissue, trichomes, root, and reproductive cell types), were used in activation constructs to generate different expression patterns of XVE. Conditional transactivation of reporter genes was achieved in a predictable, tissue-specific pattern of expression, following the insertion of the activator or the responder T-DNA in a wide variety of positions in the genome. Expression patterns were faithfully replicated in independent transgenic plant lines. Results demonstrate that we can also induce mutant phenotypes using conditional ectopic gene expression. One of these mutant phenotypes could not have been identified using noninducible ectopic gene expression approaches.
Self‐Control of Smoking: When Does Narrowed Attention Help?1
Authors: Westling Erika , Mann Traci , Ward Andrew
Published: August 2006

Two studies examined the capacity of cognitive load to enhance or disrupt the self‐control of smoking in the presence of situational pressures that either promote or discourage the behavior. In Study 1, participants who were exposed to cues encouraging smoking smoked more under high cognitive load than under low cognitive load. In Study 2, participants who were exposed to cues discouraging smoking smoked less under high load than under low load. Cognitive load appears to narrow attention, resulting in a state of attentional myopia, which leads to disinhibited smoking behavior when pressures to smoke are disproportionately salient and enhanced control of smoking when pressures not to smoke are disproportionately salient. Implications for smoking cessation are discussed.
Racial Bias in Juridic Judgment at Private and Public Levels
Authors: Bothwell Robert K. , Pigott Melissa A. , Foley Linda A. , McFatter Robert M.
Published: August 2006

Mock jurors (college students and prospective jurors) made individual decisions regarding liability and damages (before and after deliberation) in response to a case of sexual harassment. There were no significant differences in damage awards from college students and prospective jurors. There was evidence of racial bias among White mock jurors against plaintiffs who accused a Black supervisor of sexual harassment: Lower damages were recommended for plaintiffs who accepted an offer to meet for drinks in a Black supervisor's room than for plaintiffs who accepted the same offer from a White supervisor. There was also evidence of racial bias among White mock jurors against Black plaintiffs: Lower damages were recommended for Black plaintiffs than for White plaintiffs. These effects were present in the individual judgments of college students and prospective jurors. However, these forms of racial bias did not carry over into the decisions made by juries comprised of college students or prospective jurors. Subtle racial biases operating primarily at a subconscious level may get washed out in the complex task of coming to agreement on an appropriate award. The effects of manipulated variables on damage awards probably are overestimated in general in mock juror studies that do not examine group verdicts.
Olfactory Comfort: Smelling a Partner's Clothing During Periods of Separation1
Authors: McBurney Donald H. , Shoup Melanie L. , Streeter Sybil A.
Published: August 2006

We demonstrate for the first time that most women, and some men, deliberately smell their partners' clothing when they are apart. We asked undergraduate men and women who were, or who had ever been, in a committed heterosexual relationship if they had ever slept with an article of a partner's clothing or deliberately smelled a partner's clothing during periods of separation. Both men and women reported that smelling an absent partner's clothing made them feel happy, comfortable, and secure. We suggest that olfactory comfort is a significant component of attachment and is likely to involve family members other than partners.
Randomized controlled trial of melatonin for children with autistic spectrum disorders and sleep problems
Authors: Garstang J. , Wallis M.
Published: August 2006

Background  Melatonin is often used for autistic children with sleep disorders, despite a lack of published evidence in this population.

Methods  A randomized, placebo‐controlled double‐blind crossover trial of melatonin was undertaken in 11 children with autistic spectrum disorder (ASD).

Results  Seven children completed the trial. Sleep latency was 2.6 h [95% confidence intervals (CI) 2.28–2.93] baseline, 1.91 h (95% CI 1.78–2.03) with placebo and 1.06 h (95% CI 0.98–1.13) with melatonin. Wakings per night were 0.35 (95% CI 0.18–0.53) baseline, 0.26 (95% CI 0.20–0.34) with placebo and 0.08 (95% CI 0.04–0.12) with melatonin. Total sleep duration was 8.05 h (95% CI 7.65–8.44) baseline, 8.75 h (95% CI 8.56–8.98) with placebo and 9.84 h (95% CI 9.68–9.99) with melatonin.

Conclusions  Although the study was small owing to recruitment difficulties, it still provides evidence of effectiveness of melatonin in children with sleep difficulties and ASD, which we predict a larger study would confirm.
Oestradiol stimulates prolactin secretion in women through oestrogen receptors
Authors: Garas A. , Trypsianis G. , Kallitsaris A. , Milingos S. , Messinis I. E.
Published: August 2006

Objective  To examine the effects of clomiphene and raloxifene on basal and GnRH‐induced prolactin (PRL) secretion in postmenopausal women.

Design  Postmenopausal women participated in two experimental procedures a month apart. In one experiment they received raloxifene (180 mg/day) (R‐Exp) and in the other clomiphene (150 mg/day) (Cl‐Exp). In Group 1, the women (n = 8) received raloxifene or clomiphene for 30 days plus oestradiol via skin patches (100 µg/24 h) for the last 10 days. In Group 2, the women (n = 8) received oestradiol for 30 days plus raloxifene (R‐Exp) or clomiphene (Cl‐Exp) for the last 10 days. The pituitary response to GnRH (100 µg i.v.) was investigated in all women on days 0, 10, 20 and 30 of each experiment.

Patients  The study included 16 healthy postmenopausal volunteer women aged 56–60 years.

Measurements  Basal levels of PRL and the area under the curve (AUC) of ΔPRL response to GnRH were calculated.

Results  In Group 1, basal levels of PRL and the area under the curve (AUC) of PRL response to GnRH did not change significantly in both experiments. In Group 2, during both experiments basal levels of PRL and the AUC of PRL increased significantly on days 10 (P < 0·05) and 20 (P < 0·05) as compared to day 0 and then they decreased significantly on day 30 as compared to day 20 (P < 0·05).

Conclusions  Our study demonstrates for the first time that raloxifene and clomiphene affect the secretion of PRL in postmenopausal women in a similar manner. It is suggested that oestradiol stimulates the secretion of PRL in women by acting through oestrogen receptors.
In vivoand mechanistic evidence of nuclear receptor CAR induction by artemisinin
Authors: Simonsson U. S. H. , Lindell M. , Raffalli‐Mathieu F. , Lannerbro A. , Honkakoski P. , Lang M. A.
Published: August 2006

Background Artemisinin (a sesquiterpene lactone endoperoxide) has become important in multi‐drug treatment of malaria. There is evidence that artemisinin induces drug metabolism which could result in drug–drug interactions. The objective of this study was to characterize the inductive properties of artemisinin on drug‐metabolizing cytochrome P450 (CYP450) enzymes.

Materials and methods The possibility of artemisinin to induce CYP450 was studied in artemisinin‐treated (orally for four days) and vehicle‐treated rats using reverse transcriptase polymerase chain reaction (RT‐PCR). The effect on enzymatic activities in mouse microsomes from multiple artemisinin administration (intraperitonally) to mice were also studied as well as the effect on the expression in mouse primary hepatocytes and HEK293 cells.

Results Increased CYP2B1 mRNA levels in rats could be seen after artemisinin treatment as well as a weak but reproducible increase in the intensity of CYP1A2. Administration of artemisinin to mice up‐regulated hepatic CYP2B10‐dependent, and to a lesser extent, CYP2A5‐dependent enzyme activities. In primary hepatocyte culture, artemisinin significantly increased the CYP2B10 mRNA levels whereas the CYP2A5 mRNA levels were increased to a lesser extent. No significant changes were seen in the levels of other CYP enzymes. Artemisinin was an activator of constitutive androstane receptor (CAR) but not pregnane X receptor (PXR) in HEK293 cells.

Conclusions The results demonstrate that the drug exerts its effects on drug metabolism via the CAR receptor that results in up‐regulation of genes such as theCyp2b. The weaker up‐regulation of CYP2A5 might also be CAR‐dependent or alternatively, a consequence of artemisinin toxicity. The results of this study are of importance when predicting potential drug–drug interactions in multi‐drug therapies with artemisinin.
Agalsidase alpha and hearing in Fabry disease: data from the Fabry Outcome Survey
Authors: Hajioff D. , Hegemannn S. , Conti G. , Beck M. , Sunder‐Plassmann G. , Widmer U. , Mehta A. , Keilmann A.
Published: August 2006

Background  Fabry disease is an X‐linked lysosomal storage disorder characterized by multi‐organ dysfunction, including hearing loss – mainly sensorineural. The recent introduction of enzyme replacement therapy (ERT) has resulted in improvements in renal and cardiac function, pain and quality of life. One study has also suggested small improvements in high‐frequency hearing. In this paper, we study the effect of ERT on hearing in patients in the Europe‐wide database – the Fabry Outcome Survey (FOS).

Materials and methods  Twenty‐six patients in FOS had pure‐tone audiometry performed up to 6 months before starting ERT with agalsidase alpha and after a median of 12 months of treatment. We assessed changes in hearing thresholds, expressed as deviations from the 50th centile of the normal population (International Organization for Standardization ISO 7029) to correct for age‐related non‐specific hearing deterioration.

Results  Hearing did not change significantly in ears with normal hearing (less than 10 dB deviation from the 50th centile of ISO 7029) or those with severe hearing loss (more than 40 dB deviation from the 50th centile of ISO 7029) at baseline. In ears with a mild or moderate hearing loss at baseline, hearing thresholds, expressed as deviations from the normal 50th centile, improved significantly by 4–7 dB at most frequencies (P < 0·05).

Conclusions  Agalsidase alpha stabilizes, and possibly improves, hearing in Fabry patients who have not already progressed to severe hearing loss. Further follow‐up of these patients will determine the longer‐term effects of ERT.
The importance of independent risk‐factors for long‐term mortality prediction after cardiac surgery
Authors: Toumpoulis I. K. , Anagnostopoulos C. E. , Ioannidis J. P. , Toumpoulis S. K. , Chamogeorgakis T. , Swistel D. G. , DeRose J. J.
Published: August 2006

Background The purpose of the present study was to determine independent predictors for long‐term mortality after cardiac surgery. The European System for Cardiac Operative Risk Evaluation (EuroSCORE) was developed to score in‐hospital mortality and recent studies have shown its ability to predict long‐term mortality as well. We compared forecasts based on EuroSCORE with other models based on independent predictors.

Methods Medical records of patients with cardiac surgery who were discharged alive (n = 4852) were retrospectively reviewed. Their operative surgical risks were calculated according to EuroSCORE. Patients were randomly divided into two groups: training dataset (n = 3233) and validation dataset (n = 1619). Long‐term survival data (mean follow‐up 5·1 years) were obtained from the National Death Index. We compared four models: standard EuroSCORE (M1); logistic EuroSCORE (M2); M2 and other preoperative, intra‐operative and post‐operative selected variables (M3); and selected variables only (M4). M3 and M4 were determined with multivariable Cox regression analysis using the training dataset.

Results The estimated five‐year survival rates of the quartiles in compared models in the validation dataset were: 94·5%, 87·8%, 77·1%, 64·9% for M1; 95·1%, 88·0%, 80·5%, 64·4% for M2; 93·4%, 89·4%, 80·8%, 64·1% for M3; and 95·8%, 90·9%, 81·0%, 59·9% for M4. In the four models, the odds of death in the highest‐risk quartile was 8·4‐, 8·5‐, 9·4‐ and 15·6‐fold higher, respectively, than the odds of death in the lowest‐risk quartile (P < 0·0001 for all).

Conclusions EuroSCORE is a good predictor of long‐term mortality after cardiac surgery. We developed and validated a model using selected preoperative, intra‐operative and post‐operative variables that has better discriminatory ability.
Natural strontium isotope composition as a tracer of weathering patterns and of exchangeable calcium sources in acid leached soils developed on loess of central Belgium
Authors: Drouet Th. , Herbauts J. , Gruber W. , Demaiffe D.
Published: August 2006

The natural Sr isotope composition of acid leached soils developed on loess, under beech forest, in central Belgium was used as a tracer of soil forming processes, in conjunction with physico‐chemical and quantitative mineralogical investigations. Attention was focused on weathering and exchange processes, with special emphasis on the origin of the current soil exchangeable fraction and the influence of the atmospheric deposition and biological cycling on the calcium exchangeable pool (Sr acts as a proxy for Ca). The determination of 87Sr/86Sr ratios was made on the bulk soil, on the clay‐ and silt‐size soil separates, on 0.1 m HCl extracts, on the labile pool, on the soil solution and on the bulk precipitation. The acid leached soil profiles are characterized by a sequence of weathering processes that is highlighted by both mineralogical and isotopic changes. From the calcareous unweathered loess (pH 7.5) to the uppermost soil horizons (pH < 4.0) the evolution of the 87Sr/86Sr isotope ratio clearly reflects: (i) the selective weathering of Ca‐plagioclase (small 87Sr/86Sr ratio) and the increasing proportion of resistant K‐ and Rb‐rich minerals (large 87Sr/86Sr ratio) in the uppermost soil horizons; and (ii) a downward translocation of clay minerals with a large isotopic ratio, a physical breakdown of muscovite and a non‐congruent chemical weathering of K‐feldspar. The influence of organic restitutions or atmospheric deposition is not significant. The comparison between the Sr isotopic signature of the soil solution, and the exchangeable and HCl‐extractible soil fractions provides information about cation exchange efficiency, soil–water interaction and the origin of the exchangeable pool.
Interactions between CD8αβ and the TCRαβ/CD3‐receptor Complex
Authors: Rubin B. , Riond J. , Leghait J. , Gairin J. E.
Published: August 2006

CD8+ T cells recognize antigenic peptides bound to major histocompatibility complex (MHC) class I molecules on normal antigen‐presenting cells (APC), as well as on virus‐infected cells or tumour cells (pMHC). At least two receptor types participate in recognition of these complexes: T‐cell receptor (TCR) αβ heterodimers and CD8αβ molecules. The former molecules react with antigenic peptide and variable regions of MHC class I molecules, whereas the latter molecules react with constant α3 regions of MHC class I molecules. As the avidity of both receptor‐MHC interactions is low, it is believed that TCRαβ and CD8αβ heterodimers collaborate in T‐cell recognition. We have established a TCR/CD3–CD8 capture ELISA, which can measure the interaction of pMHC with CD8αβ molecules and with TCR/CD3 complexes. The major findings are: (1) TCR/CD3 complexes derived from in vitro activated T cells and captured by anti‐CD3 MoAb, do bind specific pMHC and (2) CD8+ T cells express at least three forms of CD8αβ molecules: single CD8αβ, CD3–CD8 and TCR/CD3–CD8 complexes. Only the latter complexes are associated with CD3ζ homodimers, and the quantity of TCR/CD3–CD8 complexes relative to total CD8αβ molecules appears to increase and to be selected into sucrose‐gradient microdomains as a function of TCRαβ‐mediated T‐cell activation.