bluuebunny/crossref_metadata_2025 huggingface dataset:
Setup for the in situ monitoring of the irradiation-induced effects in optical fibers in the ultraviolet-visible optical range
Authors: Sporea D. G. , Sporea R. A.
Published: November 2005

The paper describes a setup for in situ monitoring of the radiation-induced optical absorption and the radiation-induced luminescence, in the UV-visible spectral range (200–800 nm), for large diameter (400μm) optical fibers. Silica and sapphire optical fibers were irradiated, at room temperature, with gamma rays (dose rate of 0.33kGy∕h, total dose of 34.5 kGy) and protons (dose rate of 100Gy∕s, total dose of 1.8 MGy). At several moments, the irradiation was interrupted and the annealing of the radiation-induced optical absorption was observed at room temperature. The setup also makes possible the monitoring of the optical radiation-induced recovery of the optical absorption (the effect of photobleaching), as the optical fiber can be exposed at the same time to both the ionizing radiation (gamma or protons) and to the radiation of a broadband optical source. The optical absorption and radioluminescence were measured with an optical fiber multichannel spectrometer coupled to an optical fiber multiplexer. The equipment control as well as the data collection and processing were performed using the graphical programming environment LabVIEW. The paper includes several graphs illustrating the evolution of the optical absorption and radiation-induced luminescence during gamma and proton irradiation of optical fibers.
Slender body method for slender prolate spheroids and hemispheroids on planes in linearized oscillatory flow
Authors: Shatz Lisa F.
Published: November 2005

This paper extends the slender body theory of Stokes flow [G. K. Batchelor, J. Fluid Mech. 44, 419 (1970)] to slender prolate hemispheroids on infinite planes that are undergoing rotational or translational oscillatory motion. Unsteady stokeslets and doublets are placed along the focal length axis to represent the hydrodynamics, with strengths or weightings that are determined numerically from the boundary conditions. The hydrodynamic torque is determined using two different methods. Method 1 uses Green’s functions for torque that are derived from unsteady stokeslets and doublets. Method 2 uses the stokeslet weightings, the boundary velocity, and the spheroidal shape to compute the torque, in a similar way as was done [C. Pozrikidis, Phys. Fluids A 1, 1508 (1989)] in computing the force on a prolate spheroid undergoing translational oscillatory motion. The results agree with those of the singularity- and boundary element methods.
X-ray imaging of cryogenic deuterium-tritium layers in a beryllium shell
Authors: Kozioziemski B. J. , Sater J. D. , Moody J. D. , Sanchez J. J. , London R. A. , Barty A. , Martz H. E. , Montgomery D. S.
Published: November 2005

Solid deuterium-tritium (D-T) fuel layers inside copper-doped beryllium shells are robust inertial confinement fusion fuel pellets. This paper describes the first characterization of such layers using phase-contrast x-ray imaging. Good agreement is found between calculation and experimental contrast at the layer interfaces. Uniform solid D-T layers and their response to thermal asymmetries were measured in the Be(Cu) shell. The solid D-T redistribution time constant was measured to be 28 min in the Be(Cu) shell.
Cross calibration of new x-ray films against direct exposure film from 1 to 8keV using the X-pinch x-ray source
Authors: Chandler K. M. , Pikuz S. A. , Shelkovenko T. A. , Mitchell M. D. , Hammer D. A. , Knauer J. P.
Published: November 2005

A cross calibration of readily available x-ray sensitive films has been carried out against the calibrated direct exposure film (DEF) which is no longer being manufactured by Kodak. Four-wire X pinches made from various metal wires were used as x-ray sources for this purpose. Tests were carried out for the Kodak films Biomax MS, Biomax XAR, M100, Technical Pan, and T-Max over the energy range of 1–8keV (12.4–1.5Å wavelength). The same hand-development procedures as described by Henke et al. [J. Opt. Soc. Am. B 3, 1540 (1986)] were followed for all films in every test. Sensitivity curves as a function of wavelength for these films relative DEF are presented. These relative calibrations show that Biomax MS is likely to be the best replacement film for DEF for most purposes over the energy range tested here.
Efficient rainbow color luminescence from InxGa1−xN single quantum wells fabricated on {112¯2} microfacets
Authors: Nishizuka K. , Funato M. , Kawakami Y. , Narukawa Y. , Mukai T.
Published: November 2005

Rainbow color luminescence from InxGa1−xN single quantum wells (SQWs) is achieved and almost covers the entire visible range when the layers are fabricated on {112¯2} facets with a few micron-width using a regrowth technique on striped GaN templates. These facets are tilted 56° with respect to the (0001) facets and border the (0001) and {112¯0} facets. The emission wavelength on the {112¯2} facets is redshifted from the {112¯0} side to (0001) side due to the variations of the In composition, which leads to the color contrast with the rainbow geometry. The temperature dependence of the photoluminescence intensity shows that the internal quantum efficiency at room temperature is 33% due to the very small internal electric fields and a small threading dislocation density compared to that in conventional (0001) InxGa1−xN SQWs. Since the emission efficiency does not show a noticeable emission wavelength dependence, this type of structure has potential as light-emitting devices with multiwavelengths that perform numerous color controllability such as pastel and white colors.
Electromagnetic solitons produced by stimulated Brillouin pulsations in plasmas
Authors: Weber S. , Lontano M. , Passoni M. , Riconda C. , Tikhonchuk V. T.
Published: November 2005

Numerical simulations and their theoretical interpretation of the formation of standing electromagnetic solitons produced in a regime of pulsating stimulated Brillouin scattering are presented. The localized field structures are stable, long-living entities and their physical properties are in very good agreement with theoretical predictions of electromagnetic solitons in a hot and dense plasma. They are the final outcome of a specific mode-coupling regime that can be attained for high laser intensities via the transient excitation of kinetic electrostatic nonlinear electron modes.
One-step growth of ZnO from film to vertically well-aligned nanorods and the morphology-dependent Raman scattering
Authors: Cong G. W. , Wei H. Y. , Zhang P. F. , Peng W. Q. , Wu J. J. , Liu X. L. , Jiao C. M. , Hu W. G. , Zhu Q. S. , Wang Z. G.
Published: November 2005

We observed a transition from film to vertically well-aligned nanorods for ZnO grown on sapphire (0001) substrates by metalorganic chemical vapor deposition. A growth mechanism was proposed to explain such a transition. Vertically well-aligned homogeneous nanorods with average diameters of ∼30, 45, 60, and 70nm were grown with the c-axis orientation. Raman scattering showed that the E2 (high) mode shifted to high frequency with the decrease of nanorod diameters, which revealed the dependence of nanorod diameters on the stress state. This dependence suggests a stress-driven diameter-controlled mechanism for ZnO nanorod arrays grown on sapphire (0001) substrates.
Control of the active site structure of giant bilayer hemoglobin from the Annelid Eisenia foetida using hierarchic assemblies
Authors: Girasole Marco , Arcovito Alessandro , Marconi Augusta , Davoli Camilla , Congiu-Castellano Agostina , Bellelli Andrea , Amiconi Gino
Published: November 2005

The active site structure of the oxygenated derivative of the main subassemblies (whole protein, dodecamers, and trimers) of the giant haemoglobin from Eisenia foetida has been characterized by x-ray absorption near edge structure spectroscopy. The data revealed a remarkable effect of the hierarchic assemblies on the active site of the subunit. Specifically, the whole protein has the same site structure of the dodecamer, while a sharp conformational transition occurs when the dodecamer is disassembled into trimers (and monomers) revealing that constraints due to the protein matrix determine the active site geometry and, consequently, the protein function in these large complexes.
Comparison of extended x-ray absorption fine structure and Scherrer analysis of x-ray diffraction as methods for determining mean sizes of polydisperse nanoparticles
Authors: Calvin S. , Luo S. X. , Caragianis-Broadbridge C. , McGuinness J. K. , Anderson E. , Lehman A. , Wee K. H. , Morrison S. A. , Kurihara L. K.
Published: November 2005

Curve fitting of extended x-ray absorption fine structure (EXAFS) spectra, transmission electron microscopy (TEM) imaging, and Scherrer analysis of x-ray diffraction (XRD) are compared as methods for determining the mean crystallite size in polydisperse samples of platinum nanoparticles. By applying the techniques to mixtures of pure samples, it is found that EXAFS correctly determines the relative mean sizes of these polydisperse samples, while XRD tends to be weighted more toward the largest crystallites in the sample. Results for TEM are not clear cut, due to polycrystallinity and aggregation, but are consistent with the other results.
Intraband magnetoabsorption as a probing tool for the quantum dot charge
Authors: López-Richard V. , Alcalde A. M. , Prado S. J. , Marques G. E. , Trallero-Giner C.
Published: November 2005

A method of characterizing the quantum dot charge buildup in a magnetic field is proposed based on the far-infrared magneto-optical response properties. The inherent topological symmetry of the nanostructure and several optical configurations are analyzed as key factors determining the appropriate use of intraband transitions as a probing tool for the quantum dot charge buildup.
Quantum well behavior of single stacking fault 3C inclusions in 4H-SiC p-i-n diodes studied by ballistic electron emission microscopy
Authors: Park K.-B. , Pelz J. P. , Grim J. , Skowronski M.
Published: November 2005

We show that “single” stacking fault 3C inclusions formed in 4H-SiC p-i-n diodes behave as electron quantum wells (QWs) with the QW energy depth of ∼0.25eV below 4H-SiC conduction band minimum, by measuring the Schottky barriers on and away from inclusions with ballistic electron emission microscopy (BEEM). The Schottky barrier on the 4H area ([11-20] oriented) is measured to be essentially the same as (0001) plane studied previously, indicating that the interface pinning effects on both crystal faces are almost identical. Additionally, BEEM current amplitude is observed to be very sensitive to subsurface damage induced by polishing.
High-resolution differential thermography of integrated circuits with optical feedback laser scanning microscopy
Authors: Blanca Carlo Mar , Cemine Vernon Julius , Sastine Vera Marie , Saloma Caesar
Published: November 2005

We demonstrate a noninvasive technique for generating differential thermal maps of semiconductor edifices in integrated circuits (IC) at diffraction-limited resolution. An inexpensive optical feedback laser-scanning microscope detects changes in the optical beam-induced currents (OBIC) that are produced in the active layer in response to variations in the IC package temperature. The OBIC yield of a semiconductor normally increases with temperature. A differential thermal map derived from the OBIC output variations, shows locations of high thermal activity in the active layer including anomalous regions where the OBIC outputs decrease with increasing temperature. Anomalous regions are loci of accumulating semiconductor electrical resistance that are highly susceptible to device failure. They provide the best jump-off points for efficient and accurate IC fault analysis procedure.
Parallel Search for Conjunctions with Stimuli in Apparent Motion
Authors: Casco Clara , Ganis Giorgio
Published: November 2005

A series of experiments was conducted to determine whether apparent motion tends to follow the similarity rule (ie is attribute-specific) and to investigate the underlying mechanism. Stimulus duration thresholds were measured during a two-alternative forced-choice task in which observers detected either the location or the motion direction of target groups defined by the conjunction of size and orientation. Target element positions were randomly chosen within a nominally defined rectangular subregion of the display (target region). The target region was presented either statically (followed by a 250 ms duration mask) or dynamically, displaced by a small distance (18 min of arc) from frame to frame. In the motion display, the position of both target and background elements was changed randomly from frame to frame within the respective areas to abolish spatial correspondence over time. Stimulus duration thresholds were lower in the motion than in the static task, indicating that target detection in the dynamic condition does not rely on the explicit identification of target elements in each static frame. Increasing the distractor-to-target ratio was found to reduce detectability in the static, but not in the motion task. This indicates that the perceptual segregation of the target is effortless and parallel with motion but not with static displays. The pattern of results holds regardless of the task or search paradigm employed. The detectability in the motion condition can be improved by increasing the number of frames and/or by reducing the width of the target area. Furthermore, parallel search in the dynamic condition can be conducted with both short-range and long-range motion stimuli. Finally, apparent motion of conjunctions is insufficient on its own to support location decision and is disrupted by random visual noise. Overall, these findings show that (i) the mechanism underlying apparent motion is attribute-specific; (ii) the motion system mediates temporal integration of feature conjunctions before they are identified by the static system; and (iii) target detectability in these stimuli relies upon a nonattentive, cooperative, directionally selective motion mechanism that responds to high-level attributes (conjunction of size and orientation).
Gestalt Theory Reconfigured: Max Wertheimer's Anticipation of Recent Developments in Visual Neuroscience
Authors: Westheimer Gerald
Published: November 2005

In the 1920s Max Wertheimer enunciated a credo of Gestalt theory: the properties of any of the parts are governed by the structural laws of the whole. Intense efforts at the time to discover these laws had only very limited success. Psychology was in the grips of the Fechnerian tradition to seek exact relationships between the material and the mental and, because the Gestalt movement could not deliver these, it never attained a major standing among students of perception. However, as neurophysiological research into cortical processing of visual stimuli progresses the need for organizing principles is increasingly making itself felt. Concepts like contour salience and figure segregation, once the province of Gestalt psychology, are now taking on renewed significance as investigators combine neural modeling and psychophysical approaches with electrophysiological ones to characterize neural mechanisms of cognition. But it would be perilous not to take heed of some of the lessons that the history of the Gestalt movement teaches.
The extracytoplasmic adaptor protein CpxP is degraded with substrate by DegP
Authors: Isaac Daniel D. , Pinkner Jerome S. , Hultgren Scott J. , Silhavy Thomas J.
Published: November 2005

In
Escherichia coli
, the CpxR/A two-component system senses various types of extracytoplasmic stresses and responds by activating the expression of genes encoding periplasmic protein folding and trafficking factors that clear such stresses to ensure the organism's survival. The
cpxP
gene encodes a small, stress-combative periplasmic protein and is the most strongly induced member of the Cpx regulon. We demonstrate that the Cpx stress response suppresses the toxicity associated with two misfolded proteins derived from the P pilus of uropathogenic
E. coli
and that mutations in either
cpxP
or the gene for the periplasmic protease DegP prevent suppression by preventing the degradation of these proteins. Strikingly, the presence of a periplasmic misfolded protein substrate significantly enhances the proteolysis of CpxP by DegP. Our data suggest that CpxP functions as a periplasmic adaptor protein that is required for the effective proteolysis of a subset of misfolded substrates by the DegP protease.
Within-host evolution of CD8+-TL epitopes encoded by overlapping and non-overlapping reading frames of simian immunodeficiency virus
Authors: Hughes Austin L. , Piontkivska Helen , Krebs Kendall C. , O'Connor David H. , Watkins David I.
Published: November 2005

Summary: In order to understand the impact of overlapping reading frames on natural selection by host CD8+ T lymphocytes (CD8+-TL), we analyzed the pattern of nucleotide substitution in simian immunodeficiency virus (SIV) genomes sampled from populations at time of death in 35 rhesus monkeys. Both the mean number of nonsynonymous nucleotide substitutions per nonsynonymous site (dN) and the mean number of synonymous nucleotide substitutions per synonymous site (dS) were elevated in overlap regions in comparison to non-overlap regions. Mean dN exceeded mean dS in CD8+-TL epitopes restricted by the host's class I major histocompatibility complex molecules. This pattern, which is indicative of positive Darwinian selection favoring amino acid changes in these epitopes, was seen in both overlap and non-overlap regions; but mean dN was particularly elevated in restricted CD8+-TL epitopes encoded in overlap regions. Amino acid changes from the inoculum were defined as parallel if the same amino acid change occurred at the same site independently in two or more monkeys, and a surprisingly high proportion (71.9%) of observed amino acid changes throughout the SIV genome occurred in parallel in different monkeys. The proportion of parallel changes in restricted epitopes encoded by overlapping reading frames was still higher (80%), supporting the hypothesis that the interaction of positive selection and overlapping reading frames enhances the probability of convergent or parallel amino acid change.

Contact:  austin@biol.sc.edu
Four-helix bundle: a ubiquitous sensory module in prokaryotic signal transduction
Authors: Ulrich Luke E. , Zhulin Igor B.
Published: November 2005

Motivation: Transmembrane chemoreceptors in Escherichia coli utilize ligand-binding domains for detecting various external signals. The structure of this domain in the E.coli aspartate receptor, Tar, is known and its signal transduction mechanism is under investigation. Current domain models for this important sensory module are inaccurate and, therefore, cannot reveal the distribution of this domain within the current genomic landscape.

Results: We carried out sensitive and exhaustive PSI-BLAST searches initiated with the sequence corresponding to a known structure of the four-helix, ligand-binding domain of the aspartate chemoreceptor. From the resulting sequences, we built a multiple sequence alignment for this domain family, which confirmed that the current TarH model is erroneous and fails to detect most of the domain homologs. In the process, we developed a technique that visualizes the secondary structure prediction of each protein sequence in order to improve the multiple sequence alignment. We found that the four-helix up-and-down bundle represents a large domain family and includes representatives of all major classes of prokaryotic signal transduction, namely histidine kinases, di-guanylate cyclases and chemotaxis receptors.

Contact:  gtg209d@mail.gatech.edu

Supplementary Information: Supplementary data are available on Bioinformatics online.
Incorporation of splice site probability models for non-canonical introns improves gene structure prediction in plants
Authors: Sparks Michael E. , Brendel Volker
Published: November 2005

Motivation: The vast majority of introns in protein-coding genes of higher eukaryotes have a GT dinucleotide at their 5′-terminus and an AG dinucleotide at their 3′ end. About 1–2% of introns are non-canonical, with the most abundant subtype of non-canonical introns being characterized by GC and AG dinucleotides at their 5′- and 3′-termini, respectively. Most current gene prediction software, whether based on ab initio or spliced alignment approaches, does not include explicit models for non-canonical introns or may exclude their prediction altogether. With present amounts of genome and transcript data, it is now possible to apply statistical methodology to non-canonical splice site prediction. We pursued one such approach and describe the training and implementation of GC-donor splice site models for Arabidopsis and rice, with the goal of exploring whether specific modeling of non-canonical introns can enhance gene structure prediction accuracy.

Results: Our results indicate that the incorporation of non-canonical splice site models yields dramatic improvements in annotating genes containing GC–AG and AT–AC non-canonical introns. Comparison of models shows differences between monocot and dicot species, but also suggests GC intron-specific biases independent of taxonomic clade. We also present evidence that GC–AG introns occur preferentially in genes with atypically high exon counts.

Availability: Source code for the updated versions of GeneSeqer and SplicePredictor (distributed with the GeneSeqer code) isavailable at . Web servers for Arabidopsis, rice and other plant species are accessible at , and , respectively. A SplicePredictor web server is available at . Software to generate training data and parameterizations for Bayesian splice site models is available at

Contact:  vbrendel@iastate.edu

Supporting information:
Maximum significance clustering of oligonucleotide microarrays
Authors: de Ridder Dick , Staal Frank J. T. , van Dongen Jacques J. M. , Reinders Marcel J. T.
Published: November 2005

Motivation: Affymetrix high-density oligonucleotide microarrays measure the expression of DNA transcripts using probesets, i.e. multiple probes per transcript. Usually, these multiple measurements are transformed into a single probeset expression level before data analysis proceeds; any information on variability is lost. In this paper we demonstrate how individual probe measurements can be used in a statistic for differential expression. Furthermore, we show how this statistic can serve as a criterion for clustering microarrays.

Results: A novel clustering algorithm using this maximum significance criterion is demonstrated to be more efficient with the measured data than competing techniques for dealing with repeated measurements, especially when the sample size is small.

Availability: MATLAb source code can be found at

Contact:  D.deRidder@ewi.tudelft.nl
Detecting periodic patterns in unevenly spaced gene expression time series using Lomb–Scargle periodograms
Authors: Glynn Earl F. , Chen Jie , Mushegian Arcady R.
Published: November 2005

Motivation: Periodic patterns in time series resulting from biological experiments are of great interest. The commonly used Fast Fourier Transform (FFT) algorithm is applicable only when data are evenly spaced and when no values are missing, which is not always the case in high-throughput measurements. The choice of statistic to evaluate the significance of the periodic patterns for unevenly spaced gene expression time series has not been well substantiated.

Methods: The Lomb–Scargle periodogram approach is used to search time series of gene expression to quantify the periodic behavior of every gene represented on the DNA array. The Lomb–Scargle periodogram analysis provides a direct method to treat missing values and unevenly spaced time points. We propose the combination of a Lomb–Scargle test statistic for periodicity and a multiple hypothesis testing procedure with controlled false discovery rate to detect significant periodic gene expression patterns.

Results: We analyzed the Plasmodium falciparum gene expression dataset. In the Quality Control Dataset of 5080 expression patterns, we found 4112 periodic probes. In addition, we identified 243 probes with periodic expression in the Complete Dataset, which could not be examined in the original study by the FFT analysis due to an excessive number of missing values. While most periodic genes had a period of 48 h, some had a period close to 24 h. Our approach should be applicable for detection and quantification of periodic patterns in any unevenly spaced gene expression time-series data.

Availability: The computations were performed in R. The R code is available from

Contact:  chenj@umkc.edu

Supplementary information: The online supplement is available at
Statistical estimation of gene expression using multiple laser scans of microarrays
Authors: Khondoker Mizanur R. , Glasbey Chris A. , Worton Bruce J.
Published: November 2005

Summary: We propose a statistical model for estimating gene expression using data from multiple laser scans at different settings of hybridized microarrays. A functional regression model is used, based on a non-linear relationship with both additive and multiplicative error terms. The function is derived as the expected value of a pixel, given that values are censored at 65 535, the maximum detectable intensity for double precision scanning software. Maximum likelihood estimation based on a Cauchy distribution is used to fit the model, which is able to estimate gene expressions taking account of outliers and the systematic bias caused by signal censoring of highly expressed genes. We have applied the method to experimental data. Simulation studies suggest that the model can estimate the true gene expression with negligible bias.

Availability: FORTRAN 90 code for implementing the method can be obtained from the authors.

Contact:  mizanur@bioss.ac.uk
A bi-dimensional regression tree approach to the modeling of gene expression regulation
Authors: Ruan Jianhua , Zhang Weixiong
Published: November 2005

Motivation: The transcriptional regulation of a gene depends on the binding of cis-regulatory elements on its promoter to some transcription factors and the expression levels of the transcription factors. Most existing approaches to studying transcriptional regulation model these dependencies separately, i.e. either from promoters to gene expression or from the expression levels of transcription factors to the expression levels of genes. Little effort has been devoted to a single model for integrating both dependencies.

Results: We propose a novel method to model gene expression using both promoter sequences and the expression levels of putative regulators. The proposed method, called bi-dimensional regression tree (BDTree), extends a multivariate regression tree approach by applying it simultaneously to both genes and conditions of an expression matrix. The method produces hypotheses about the condition-specific binding motifs and regulators for each gene. As a side-product, the method also partitions the expression matrix into small submatrices in a way similar to bi-clustering. We propose and compare several splitting functions for building the tree. When applied to two microarray datasets of the yeast Saccharomyces cerevisiae, BDTree successfully identifies most motifs and regulators that are known to regulate the biological processes underlying the datasets. Comparing with an existing algorithm, BDTree provides a higher prediction accuracy in cross-validations.

Availability: The software is available upon request from the authors.

Contact:  zhang@cse.wustl.edu

Supplementary information:
REDfly: a Regulatory Element Database for Drosophila
Authors: Gallo Steven M. , Li Long , Hu Zihua , Halfon Marc S.
Published: November 2005

Summary: Bioinformatics studies of transcriptional regulation in the metazoa are significantly hindered by the absence of readily available data on large numbers of transcriptional cis-regulatory modules (CRMs). Even the richly annotated Drosophila melanogaster genome lacks extensive CRM information. We therefore present here a database of Drosophila CRMs curated from the literature complete with both DNA sequence and a searchable description of the gene expression pattern regulated by each CRM. This resource should greatly facilitate the development of computational approaches to CRM discovery as well as bioinformatics analyses of regulatory sequence properties and evolution.

Availability:  

Contact:  mshalfon@buffalo.edu
Tilt and acoustic instabilities in ABX
4, A
2
BX
4 and ABX
3 perovskite structure types: their role in the incommensurate phases of the organic–inorganic perovskites
Authors: Swainson Ian Peter
Published: November 2005

An examination of the tilt modes and other low-frequency modes is made for an isolated, untilted perovskite layer, which maps very simply to the ABX
4 perovskites. A sheet of pure tilts exists at the Brillouin Zone boundary at {ξ, ½, ζ}. An instability is also found at all wavevectors which can be described as continuously varying from pure tilts to pure layer displacements as a function of the wavevector. Analysis is extended by considering the stacking of layers in the I-centered A
2
BX
4-layer perovskites. The effect of freezing in the commensurate tilt required to generate the Cmca tilt system, pertinent to the modulated phases of propylammonium salts, is examined. The zero-frequency modes are restricted to two planes in the Brillouin Zone. All of the observed wavevectors associated with modulated phases, and the commensurately tilted propylammonium tetrachlorocadmate, are consistent with this calculation. The effect of full three-dimensional connectivity is briefly reviewed for the true ABX
3 perovskites. While pure tilt incommensurates appear to be hypothetically possible, they do not appear to have been observed to date.
Validation of techniques to detect illicit heroin use in patients prescribed pharmaceutical heroin for the management of opioid dependence
Authors: Paterson S. , Lintzeris N. , Mitchell T. B. , Cordero R. , Nestor L. , Strang J.
Published: November 2005

Background  The clinical implementation and evaluation of heroin substitution programmes have been confounded by the lack of objective and validated biomarkers for illicit heroin use in patients prescribed pharmaceutical heroin. This study examined the capacity to detect illicit heroin use by gas chromatography–mass spectrometry (GC‐MS) analysis of urine samples for the presence of opium impurities common to illicit, but not pharmaceutical heroin.

Aims  To characterize the diagnostic properties of the metabolites of noscapine and papaverine in comparison to morphine as a gold‐standard marker of illicit heroin use; and to examine the relationships between the self‐reported time since most recent heroin use and the detection of these opioids in urine.

Design  A cross‐sectional study of 52 opioid‐dependent patients in treatment (not prescribed heroin), who self‐reported illicit heroin use within the preceding 2 weeks. Self‐report data regarding recent drug use and a urine sample were collected. GC‐MS analyses of urines were conducted and reported by laboratory staff blinded to self‐report data.

Findings  The metabolites of papaverine (hydroxypapaverine and dihydroxypapeverine) were found to have high sensitivity, specificity and negative predictive values as markers for illicit heroin use compared to the ‘gold‐standard’ morphine. Other opioids, including 6‐mono‐acetylmorphine (6‐MAM), codeine and noscapine metabolites (e.g. meconine) were less adequate in detecting heroin use.

Conclusions  GC‐MS detection of papaverine metabolites in urine appears to be suitable method of identifying illicit heroin use for clinical and research purposes.
Gender‐specific mortality associated with alcohol consumption in Poland in transition*
Authors: Wojtyniak Bogdan , Moskalewicz Jacek , Stokwiszewski Jakub , Rabczenko Daniel
Published: November 2005

Aims  To show the impact of rapid political and economic transitions on alcohol consumption and associated mortality in different socio‐demographic segments of the Polish society, with particular focus on gender differences. Two causes of death associated with drinking (liver diseases and alcohol poisoning) are investigated.

Design  Mortality time series 1986–2002 are analysed against consumption estimates and population drinking survey data.

Setting  Poland 1986–2002.

Participants  General adult population.

Measurement  Age‐standardized annual and 3‐year death rates were calculated for age, gender and place of residence subgroups. For education, age‐standardized relative frequency of deaths or proportional mortality in four basic educational levels was calculated.

Findings  Alcohol‐related mortality shows great variability in response to substantial changes in alcohol consumption. Patterns of mortality and their magnitude of change correspond with average alcohol consumption and are therefore different for men and women, for different age and educational groups and in urban and rural areas. Level of education, however, may affect alcohol‐related mortality more strongly than overall alcohol intake, particularly with regard to acute consequences of drinking.

Conclusion  The Polish experience illustrates that the impact of rapid political and economic transitions on alcohol consumption and associated mortality is highly differentiated and specific to gender and social class.
Alcohol and the economic crisis in Argentina: recent findings*
Authors: Munné Myriam I.
Published: November 2005

Aims  In 2002 Argentina participated in the GENACIS project (Gender, Alcohol, and Culture: An International Study) as one of the countries funded by the World Health Organization. Four questions about the current economic crisis in Argentina were added to the original GENACIS questionnaire in order to find out the opinions of the general population in relation to alcohol and the economic crisis.

Methods  Gender differences in the answers to these questions were examined. Logistic regression was used to identify demographic, drinking pattern and drinking problems variables related significantly to responses to the economic crisis questions.

Findings  During the economic crisis people stopped or reduced going to bars and instead drank at home or at friends’ homes. A large number of respondents also reported that people had changed to cheaper or lower‐quality alcoholic drinks. Women were more likely to agree with statements that the economic crisis had increased ‘escape’ drinking and required reductions in money spent on alcohol; men were more likely to agree that the crisis had led to less drinking in bars and to the purchase of cheaper or lower‐quality alcoholic beverages. Respondents who reported having significant others with drinking‐related problems were more likely to endorse all four statements about effects of the economic crisis on drinking behaviour. A qualitative approach was used to discuss themes in the general comments that were recorded by the interviewers while collecting data. A strongly moralistic attitude towards alcohol was present in these comments, especially among women.

Conclusion  The findings suggest that the economic crisis in Argentina led to major changes in patterns of drinking that differed according to gender roles and other demographic variables. The long‐term effects of these changes remain to be determined as economic circumstances improve.
Developments in alcohol consumption in reunited Germany
Authors: Bloomfield Kim , Grittner Ulrike , Kramer Stephanie
Published: November 2005

Aims  To investigate changes in measures of frequency of general alcohol and beverage‐specific alcohol drinking in eastern and western Germany between 1991 and 1998.

Design, setting and participants  Data come from two nationally representative health surveys, one conducted in 1991/1992 and the other in 1998. The earlier sample comprises two separate surveys, a 1991 western German survey (n = 5255) and a 1992 eastern German survey (n = 2211); the sample from 1998 contains information from 5463 people. The two 1991/1992 samples were merged to produce a single data set, comprising 7466 cases. The 1998 sample was limited to people aged 25–69 years, the age range of the 1991/1992 surveys.

Measurements  The surveys included measures of current drinking, current beverage‐specific drinking, weekly drinking, daily drinking, heavy drinking and mean amount consumed per day.

Findings  The prevalence of almost all measures of drinking frequency declined in both regions of Germany and for both genders. Decreases were larger in the East and especially for frequency of current spirits drinking and daily drinking. Despite the decreases, western women consistently consumed at higher levels than eastern women, as did eastern men in relation to western men. Moreover, gender and regional differences within the country decreased.

Conclusions  Overall frequency of consumption has declined in Germany in the 1990s and drinking behaviour in the two regions has become more similar.
Pattern of drinking and fatal injury: a population‐based follow‐up study of Finnish men
Authors: Paljärvi Tapio , Mäkelä Pia , Poikolainen Kari
Published: November 2005

Aim  To find out how the frequency of drinking one to two drinks, three to four drinks and five or more drinks of alcohol per drinking occasion predicts injury mortality in 16 years of follow‐up among the Finnish 15–69‐year‐old male population.

Design  Three alcohol surveys conducted in 1969, 1976 and 1984 were pooled and linked with mortality information from the national cause of death register.

Method  Cox proportional hazard models were used for analysing the survival time data.

Findings  Drinking at the level of one to two drinks, regardless of frequency, did not elevate the risk of fatal injury, nor did drinking at the level of three to four drinks. Drinking five or more drinks at a time significantly increased the risk of fatal injury in graded relation, compared with those who never drank at that level. The risk was highest for those who drank five or more drinks at a time at least weekly (RR = 5.78, 95% CI = 2.80–11.94), when adjusted for possible confounders.

Conclusions  We found that besides the total volume of consumption, a drinking pattern that involves drinking occasions when consumption exceeds four drinks of alcohol at a time leads to a significant increase in the risk of fatal injury among Finnish men. The risk is highest among those who have the highest annual number of heavy drinking occasions. The finding does not support the hypothesis that alcohol tolerance would lower the risk of fatal injuries among frequent heavy drinkers.
A comparison of buprenorphine and lofexidine for community opiate detoxification: results from a randomized controlled trial
Authors: Raistrick Duncan , West David , Finnegan Olwyn , Thistlethwaite Gill , Brearley Roger , Banbery Jo
Published: November 2005

Objective  To investigate whether a buprenorphine opiate detoxification regimen can be considered to be at least as clinically effective as a lofexidine regimen.

Design  An open‐label randomized controlled trial (RCT) using a non‐inferiority approach. Non‐inferiority is demonstrated if, within a 95% confidence interval, buprenorphine performs within a preset tolerance limit of clinically acceptable difference in outcomes and completion rates between the two treatments.

Methods  Individuals ready for heroin detoxification were given information about the trial and invited to participate. Consenting participants (n = 210) were then randomized to one of the two treatments. Detoxification was undertaken in a specialist out‐patient clinic according to predefined protocols. The primary outcome was whether or not an individual completed the detoxification. Abstinence at 1‐month follow‐up was used as a secondary outcome measure. Additional secondary outcome measures were substance use, dependence, psychological health, social satisfaction, and treatment satisfaction. Data were also collected for individuals who declined randomization and instead chose their treatment (n = 271).

Results  A total of 46% of those on lofexidine and 65% of those on buprenorphine completed detoxification. Of these, 35.7% of the lofexidine and 45.9% of the buprenorphine groups reported abstinence at 1 month. Of those not completing detoxification abstinence was reported at 27.5% and 29.0%, respectively; 271 individuals who opted not to be allocated randomly and instead chose one of the two treatments produced similar results

Conclusions  Buprenorphine is at least as effective as lofexidine detoxification treatment. Whether or not individuals were randomized to, or chose, a treatment appeared not to affect the study's outcome.
Cytological and molecular analyses of non‐host resistance of Arabidopsis thaliana to Alternaria alternata
Authors: NARUSAKA YOSHIHIRO , NARUSAKA MARI , SEKI MOTOAKI , ISHIDA JUNKO , SHINOZAKI KAZUO , NAN YOH , PARK PYOYUN , SHIRAISHI TOMONORI , KOBAYASHI MASATOMO
Published: November 2005

When challenged with the necrotrophic fungal pathogen Alternaria alternata Japanese pear pathotype, all tested ecotypes of Arabidopsis plants failed to show hypersensitive cell death, accumulation of detectable levels of reactive oxygen species or accumulation of phytoalexin. We operationally define A. alternata as a non‐host pathogen for Arabidopsis plants and show that the protection against A. alternata demonstrated in this study is a non‐host penetration resistance. To characterize non‐host penetration resistance, we examined the expression patterns of c. 7000 genes by cDNA microarray analysis in Arabidopsis Col‐0 plants after inoculation with A. alternata. After inoculation with A. alternata, the transcript levels of 48 genes increased in Col‐0 plants. The expression of genes associated with hypersensitive reaction was induced in the non‐host penetration resistance to A. alternata, despite the fact that A. alternata had no visible effect on the plants. The non‐host penetration resistance to A. alternata was clearly associated with activation of the jasmonate‐ and ethylene‐signalling pathways. In addition, analysis using histochemical staining of GUS activity suggests that defence reactions in non‐host penetration resistance are activated locally. The characterization of non‐host pathosystem involving Arabidopsis and A. alternata offers an overview of non‐host penetration resistance.
Review article: immediate‐release proton‐pump inhibitor therapy – potential advantages
Authors: HOWDEN C. W.
Published: November 2005

The absorption of most oral proton‐pump inhibitors is delayed by the enteric coating required to protect the acid‐labile proton‐pump inhibitor from degradation in the stomach and, as a result, antisecretory effect is also delayed.

This article provides an overview of the pharmacokinetics and pharmacodynamics of a new immediate‐release omeprazole [(IR‐OME) Zegerid power for oral suspension; Santarus Inc., San Diego, CA, USA] and its potential advantages over delayed‐release proton‐pump inhibitors.

Immediate‐release omeprazole has a higher mean peak plasma omeprazole concentration (Cmax) and a significantly shorter mean time to reach Cmax (tmax) than delayed‐release omeprazole. Immediate‐release omeprazole 40 mg has a prolonged antisecretory effect with median intragastric pH above 4.0 for 18.6 h/day at steady‐state, after 7 days of once daily dosing. The sodium bicarbonate in immediate‐release omeprazole protects the uncoated omeprazole from degradation by gastric acid. The accelerated antisecretory action of immediate‐release omeprazole compared with delayed‐release omeprazole may be due to the activation of proton pumps by the rapid neutralization of intragastric acid by the sodium bicarbonate. The faster onset of action seen with immediate‐release omeprazole is not achieved by using an antacid with a delayed‐release proton‐pump inhibitor, because administering antacids with conventional delayed‐release proton‐pump inhibitors does not significantly enhance absorption of the proton‐pump inhibitor.

In conclusion, immediate‐release omeprazole is associated with rapid absorption of omeprazole and rapid onset of antisecretory effect, without compromising the duration of acid suppression.
Review article: oesophageal pH monitoring – technologies, interpretation and correlation with clinical outcomes
Authors: KAHRILAS P. J. , PANDOLFINO J. E.
Published: November 2005

Using a simple ‘test’ to diagnose gastro‐oesophageal reflux disease is difficult because accurately measuring gastric refluxate and correlating reflux events with symptom episodes is complex. This paper reviews the safety, tolerability and diagnostic accuracy of Bravo (Medtronic, Shoreview, MN, USA), ambulatory oesophageal pH monitoring technology.

Catheter‐based pH electrodes inhibit patients’ normal activity, and can yield erroneous results because of placement or subsequent migration of the probe or errors in the thermal compensation algorithm that is requisite for antimony pH electrodes. Bravo pH studies reliably discriminated oesophagitis patients from controls, but are less discriminatory in endoscopy‐negative gastro‐oesophageal reflux disease patients. The Bravo system can be accurately placed using endoscopic landmarks and pH studies demonstrated more accurate in vivo pH recording than with a catheter‐based system. The Bravo system detected fewer reflux events of short duration compared with a catheter‐based system. Studies examining the correlation between reflux events and symptoms have not yet been conducted using the Bravo system.

In conclusion, the Bravo system offers a more user‐friendly ambulatory pH monitoring technique that more accurately records pH compared with a catheter‐based system. More research is needed to determine whether the detection of reflux events with Bravo will provide a good correlation with symptom episodes.
Review article: alternative approaches to the long‐term management of GERD
Authors: FENNERTY M. B.
Published: November 2005

Although proton‐pump inhibitors are highly effective for the treatment of gastro‐oesophageal reflux disease, there are issues with long‐term maintenance therapy: not all patients require full daily dose for maintenance treatment, some patients are reluctant to take long‐term daily medication, and long‐term PPI therapy is inadequate for some patients.

This article aims to review alternatives to daily proton‐pump inhibitor therapy for the long‐term management of gastro‐oesophageal reflux disease, including intermittent or on‐demand proton‐pump inhibitor use, as well as endoscopic and surgical options.

On‐demand proton‐pump inhibitor therapy has demonstrated efficacy in achieving acceptable symptom control, healing and maintenance of quality of life for a proportion of patients with gastro‐oesophageal reflux disease. Endoscopic antireflux procedures can reduce the need for proton‐pump inhibitor therapy, but safety and durability of these procedures require more study. Surgical treatment of gastro‐oesophageal reflux disease in properly selected patients has demonstrated efficacy in reducing symptoms and the need for proton‐pump inhibitor therapy; however, long‐term follow‐up suggests that it is not a permanent solution for many patients.

While daily proton‐pump inhibitor therapy remains the main treatment regimen option for most patients with gastro‐oesophageal reflux disease, on‐demand therapy may prove effective for many patients. Endoscopic anti‐reflux therapies and surgery are options for patients who prefer nonpharmacological treatment, but experience is limited at this point in time for the former.