bluuebunny/crossref_metadata_2025 huggingface dataset:
Relativistic Weibel instability
Authors: Yoon Peter H.
Published: March 2007

The relativistic Weibel instability has received much attention because of its potential application to astrophysical problems. The purpose of this paper is to correct certain erroneous expressions in the author’s early paper on the subject [P. H. Yoon, Phys. Fluids B 1, 1336 (1989)], to discuss further properties of the relativistic Weibel instability, and to compare with its nonrelativistic counterpart.
Improved instrumentation for blood flow velocity measurements in the microcirculation of small animals
Authors: de Mesquita Jayme Alves , Bouskela Eliete , Wajnberg Eliane , de Melo Pedro Lopes
Published: March 2007

Microcirculation is the generic name of vessels with internal diameter less than 100μm of the circulatory system, whose main functions are tissue nutrition and oxygen supply. In microcirculatory studies, it is important to know the amount of oxyhemoglobin present in the blood and how fast it is moving. The present work describes improvements introduced in a classical hardware-based instrument that has usually been used to monitor blood flow velocity in the microcirculation of small animals. It consists of a virtual instrument that can be easily incorporated into existing hardware-based systems, contributing to reduce operator related biases and allowing digital processing and storage. The design and calibration of the modified instrument are described as well as in vitro and in vivo results obtained with electrical models and small animals, respectively. Results obtained in in vivo studies showed that this new system is able to detect a small reduction in blood flow velocity comparing arteries and arterioles (p<0.002) and a further reduction in capillaries (p<0.0001). A significant increase in velocity comparing capillaries and venules (p<0.001) and venules and veins (p<0.001) was also observed. These results are in close agreement with biophysical principles. Moreover, the improvements introduced in the device allowed us to clearly observe changes in blood flow introduced by a pharmacological intervention, suggesting that the system has enough temporal resolution to track these microcirculatory events. These results were also in close conformity to physiology, confirming the high scientific potential of the modified system and indicating that this instrument can also be useful for pharmacological evaluations.
Crystal structure and band gap determination of HfO2 thin films
Authors: Cheynet Marie C. , Pokrant Simone , Tichelaar Frans D. , Rouvière Jean-Luc
Published: March 2007

Valence electron energy loss spectroscopy (VEELS) and high resolution transmission electron microscopy (HRTEM) are performed on three different HfO2 thin films grown on Si (001) by chemical vapor deposition (CVD) or atomic layer deposition (ALD). For each sample the band gap (Eg) is determined by low-loss EELS analysis. The Eg values are then correlated with the crystal structure and the chemical properties of the films obtained by HRTEM images and VEELS line scans, respectively. They are discussed in comparison to both experimental and theoretical results published in literature. The HfO2 ALD film capped with poly-Si exhibits the largest band gap (Eg=5.9±0.5eV), as a consequence of its nanocrystallized orthorhombic structure. The large grains with a monoclinic structure formed in the HfO2 ALD film capped with Ge and the carbon contamination induced by the precursors in the HfO2 CVD film capped with Al2O3 are identified to be the main features responsible for lower band gap values (Eg=5.25±0.5 and 4.3±0.5eV respectively).
Arrays of magnetic nanoindentations with perpendicular anisotropy
Authors: Makarov D. , Baraban L. , Guhr I. L. , Boneberg J. , Schift H. , Gobrecht J. , Schatz G. , Leiderer P. , Albrecht M.
Published: March 2007

The authors report an approach to the fabrication of periodic magnetic patterns using spherical indentations. These troughs are shaped by an imprint technique, employing a self-assembled monolayer of particles. Well-defined structures with perpendicular magnetic anisotropy are obtained by deposition of Co∕Pd multilayer films onto the topographic array. The structures formed in the indentations can be magnetically exchange decoupled from their neighbors depending critically on their specific shape. The presented concept leads to a realization of a magnetic nanostructure medium, which offers advances in achieving high pattern densities combining a low cost nanoimprint approach with material functionalization.
Examination of flatband and threshold voltage tuning of HfO2∕TiN field effect transistors by dielectric cap layers
Authors: Guha S. , Paruchuri V. K. , Copel M. , Narayanan V. , Wang Y. Y. , Batson P. E. , Bojarczuk N. A. , Linder B. , Doris B.
Published: March 2007

The authors have examined the role of sub nanometer La2O3 and LaN cap layers interposed in Si∕HfO2∕TiN high-k gate dielectric stacks in tuning the flatband and threshold voltages of capacitors and transistors. High performance, band edge n metal oxide field effect transistors with channel lengths down to 60nm may be fabricated without significant compromise in mobility, electrical thickness, and threshold voltage. They have carried out a microstructural evaluation of these stacks and correlated these results with the electrical behavior of the devices.
Vortex shedding in confined swirling flow of polymer solutions
Authors: Tamano Shinji , Itoh Motoyuki , Ide Yuichiro , Yokota Kazuhiko
Published: March 2007

The unsteady swirling flow of an aqueous polymer solution due to a rotating disk in a cylindrical casing was investigated using the flow visualization technique. As the aqueous polymer solution, polyacrylamide solutions whose concentrations were 0.025, 0.1, 0.2, 0.5, 0.8, and 1.0wt% were used. The unsteady secondary flow patterns were classified using the Reynolds and elastic numbers. We found a new phenomenon of vortex shedding in which the ring vortex formed near the rotating disk was periodically shed away from the rotating disk in the unsteady flow regime. The nonaxisymmetric ring vortex was also observed for the higher Reynolds number compared to that of the axisymmetric ring vortex. The dependence of the period of vortex shedding on the Reynolds number was clarified.
Imaging of single infrared, optical, and ultraviolet photons using distributed tunnel junction readout on superconducting absorbers
Authors: Furlan Miha , Kirk Eugenie , Zehnder Alex
Published: March 2007

Single-photon imaging spectrometers of high quantum efficiency in the infrared to ultraviolet wavelength range, with good timing resolution and with a vanishing dark count rate, are on top of the wish list in earth-bound astronomy, material and medical sciences, or quantum information technologies. We review and present improved operation of a cryogenic detector system potentially offering all these qualities. It is based on a superconducting absorber strip read out with superconducting tunnel junctions. The detector performance is discussed in terms of responsivity, noise properties, and energy and position resolutions. Dynamic processes involved in the signal creation and detection are investigated for a basic understanding of the physics and for possible application-specific modifications of device characteristics.
Effects of electrical and thermal phenomena on the evolution of adhesion at contact interfaces of electrostatically activated surface microstructures
Authors: Timpe S. J. , Komvopoulos K.
Published: March 2007

A contact-mode microstructure fabricated by surface micromachining was used to study the development of adhesion at sidewall contact surfaces during electrical actuation. Temporary and permanent changes in the adhesion force were monitored for different voltages applied across the contact interface. Relatively low current flow across the interface yielded a significant increase in the adhesion force. A portion of the increase was attributed to thermal heating of the contacting asperities. Current flow through asperity contacts lead to the accumulation of trapped charges in the insulating oxide layer, resulting in electrostatic attraction that was maintained after surface separation and with grounded surfaces. High current flow across asperity contacts due to dielectric breakdown of the native oxide layer at a critical voltage resulted in interfacial bonding that caused permanent adhesion of the sidewall surfaces.
Fabrication of ultrathin magnetic structures by nanostencil lithography in dynamic mode
Authors: Gross L. , Schlittler R. R. , Meyer G. , Vanhaverbeke A. , Allenspach R.
Published: March 2007

The fabrication of magnetic elements containing constrictions is demonstrated using nanostencil lithography in dynamic mode, i.e., by a continuous translation of a shadow mask with respect to the sample. The authors quantify the current resolution limits of this technique, demonstrating edge profile widths of 120nm and thickness variations of 10%, and discuss prospects and challenges of dynamic nanostencil lithography.
Oscillatory thermal expansion of Pb thin films modulated by quantum size effects
Authors: Zhang Yan-Feng , Tang Zhe , Han Tie-Zhu , Ma Xu-Cun , Jia Jin-Feng , Xue Qi-Kun , Xun Kun , Wu Si-Cheng
Published: March 2007

Varied temperature photoemission study is performed to investigate the quantum size effects on the thermal property of atomically flat Pb films grown on Si(111). The binding energies of the quantum well states for the films with thicknesses from 10 to 24 ML exhibit a linear increase with increasing temperature from 75to270K. Under free electron approximation, thermal expansion coefficients of the thin films are determined, which manifest a large enhancement and oscillation behavior. The large enhancement is interpreted by a model based on the quantum confinement along the film normal direction. The oscillation is shown to be closely related to the structural instability and is a result of the formation of the quantized electronic states in thin films.
Fixed contact line helical interfaces in zero gravity
Authors: Lowry Brian J. , Thiessen David B.
Published: March 2007

Fluid interfaces supported in microgravity by a helical structure are shown to have a more robust stability than more common structures such as liquid bridges. In particular, helical interfaces can take the form of infinite right circular cylinders over a broad range of configurations. In the case of a single fixed contact line support, the infinite cylinder is stable for all cases in which the pitch to diameter ratio is less than π∕3 (more tightly coiled interfaces). When there are two or more equally spaced fixed contact line supports, the infinite cylinder is stable for all configurations. Furthermore, in the two support case (the double helix), stability persists for all volumes from the cylinder to zero volume, when the pitch to diameter ratio is greater than 2.082 (more loosely coiled interfaces). The equivalent to the axisymmetric Young-Laplace equation is derived for helical interfaces. Interfacial stability is determined from equilibrium branch structure following the application of Maddocks’ method by Lowry and Steen [Proc. R. Soc. London, Ser. A 449, 411 (1995)]. Perturbations to finite wavelength disturbances are considered for the case of a single helical support. Overall stability envelopes are presented for single and multiple support cases. Limited experimental results verify the infinite length stability limit for the single helical support case.
Effects of nitrogen incorporation in InSb1−xNx grown using radio frequency plasma-assisted molecular beam epitaxy
Authors: Pham H. T. , Yoon S. F. , Tan K. H. , Boning D.
Published: March 2007

In Sb 1 − x N x was grown by radio frequency plasma-assisted molecular beam epitaxy. The effect of nitrogen plasma power (200–500W) and growth temperature (330–420°C) on nitrogen incorporation was investigated. A combined analysis involving x-ray diffraction, x-ray photoelectron spectroscopy, and secondary ion mass spectroscopy measurements indicates that the dominant nitrogen defect is interstitial N–Sb. Increasing the plasma power resulted in increase in the interstitial N–Sb amount rather than the substitutional NSb amount. For fixed plasma power, decreasing the growth temperature helped reduce the interstitial N–Sb defect. Under the experimental conditions, the average value of substitutional N is approximately 1.6%–2%.
Reduction of ac transport and magnetization loss of a high-Tc superconducting tape by placing soft ferromagnetic materials at the edges
Authors: Gömöry F. , Šouc J. , Vojenčiak M. , Alamgir A. K. M. , Han Z. , Gu Ch.
Published: March 2007

Reduction of dissipation at the transport of alternating current as well as when exposed to a time varying magnetic field has been observed in the tape from high-temperature superconductor Bi2Sr2Ca2Cu3O10 covered by a Ni sheath at the edges. The improvement of critical current can explain this achievement only in part. Analysis of experimental data shows that also a more favorable pattern of the magnetic flux penetration should take place.
Phase structures and electrical properties of new lead-free (Na0.5K0.5)NbO3–(Bi0.5Na0.5)TiO3 ceramics
Authors: Zuo Ruzhong , Fang Xusheng , Ye Chun
Published: March 2007

Highly dense (1−x)(Na0.5K0.5)NbO3–x(Bi0.5Na0.5)TiO3 (NKN-BST) solid solution piezoelectric ceramics have been fabricated by ordinary sintering. All compositions show pure perovskite structures, showing room-temperature symmetries of orthorhombic at x⩽0.02, of tetragonal at 0.03⩽x⩽0.09, of cubic at 0.090.20. A morphotropic phase boundary (MPB) between orthorhombic and tetragonal ferroelectric phases was identified in the composition range of 0.02<x<0.03. The materials near the MPB exhibit a strong compositional dependence, owning peak values of the planar electromechanical coupling factor kp∼43%, the piezoelectric constant d33∼195pC∕N, and the Curie temperature of 375°C comparable to that of commercial lead zinconate titanate ceramics. The results indicate that NKN-BST ceramic is a promising lead-free piezoelectric candidate material.
Very narrow-band ultraviolet photodetection based on strained M-plane GaN films
Authors: Ghosh Sandip , Rivera C. , Pau J. L. , Muñoz E. , Brandt O. , Grahn H. T.
Published: March 2007

The authors demonstrate a photodetection configuration where the responsivity in the ultraviolet spectral region is limited to a few nanometers, representing high-quality-factor, narrow-band detection together with polarization sensitivity. Both features are obtained by utilizing a polarization-sensitive photodectector in combination with a polarization filter made from two identical M-plane GaN films on γ-LiAlO2 (100) substrate. The optical band gap of these films depends on the direction of the in-plane polarization vector of the incident light beam with respect to the c axis. Electronic-band-structure calculations show that the naturally present anisotropic in-plane strain in these films is the crucial parameter to achieve both a high responsivity and a high polarization contrast.
Microarray blob-defect removal improves array analysis
Authors: Song Jun S. , Maghsoudi Kaveh , Li Wei , Fox Edward , Quackenbush John , Shirley Liu X.
Published: March 2007

Motivation: New generation Affymetrix oligonucleotide microarrays often have blob-like image defects that will require investigators to either repeat their hybridization assays or analyze their data with the defects left in place. We investigated the effect of analyzing a spike-in experiment on Affymetrix ENCODE tiling arrays in the presence of simulated blobs covering between 1 and 9% of the array area. Using two different ChIP-chip tiling array analysis programs (Affymetrix tiling array software, TAS, and model-based analysis of tiling arrays, MAT), we found that even the smallest blob defects significantly decreased the sensitivity and increased the false discovery rate (FDR) of the spike-in target prediction.

Results: We introduced a new software tool, the microarray blob remover (MBR), which allows rapid visualization, detection and removal of various blob defects from the .CEL files of different types of Affymetrix microarrays. It is shown that using MBR significantly improves the sensitivity and FDR of a tiling array analysis compared to leaving the affected probes in the analysis.

Availability: The MBR software and the sample array .CEL files used in this article are available at: http://liulab.dfci.harvard.edu/Software/MBR/MBR.htm

Contact:  xsliu@jimmy.harvard.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
NucPred—Predicting nuclear localization of proteins
Authors: Brameier Markus , Krings Andrea , MacCallum Robert M.
Published: March 2007

Summary: NucPred analyzes patterns in eukaryotic protein sequences and predicts if a protein spends at least some time in the nucleus or no time at all. Subcellular location of proteins represents functional information, which is important for understanding protein interactions, for the diagnosis of human diseases and for drug discovery. NucPred is a novel web tool based on regular expression matching and multiple program classifiers induced by genetic programming. A likelihood score is derived from the programs for each input sequence and each residue position. Different forms of visualization are provided to assist the detection of nuclear localization signals (NLSs). The NucPred server also provides access to additional sources of biological information (real and predicted) for a better validation and interpretation of results.

Availability: The web interface to the NucPred tool is provided at http://www.sbc.su.se/~maccallr/nucpred. In addition, the Perl code is made freely available under the GNU Public Licence (GPL) for simple incorporation into other tools and web servers.

Contact:  brameier@birc.au.dk, r.maccallum@imperial.ac.uk
COBALT: constraint-based alignment tool for multiple protein sequences
Authors: Papadopoulos Jason S. , Agarwala Richa
Published: March 2007

Motivation: A tool that simultaneously aligns multiple protein sequences, automatically utilizes information about protein domains, and has a good compromise between speed and accuracy will have practical advantages over current tools.

Results: We describe COBALT, a constraint based alignment tool that implements a general framework for multiple alignment of protein sequences. COBALT finds a collection of pairwise constraints derived from database searches, sequence similarity and user input, combines these pairwise constraints, and then incorporates them into a progressive multiple alignment. We show that using constraints derived from the conserved domain database (CDD) and PROSITE protein-motif database improves COBALT's alignment quality. We also show that COBALT has reasonable runtime performance and alignment accuracy comparable to or exceeding that of other tools for a broad range of problems.

Availability: COBALT is included in the NCBI C++ toolkit. A Linux executable for COBALT, and CDD and PROSITE data used is available at: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/cobalt

Contact:  richa@helix.nih.gov
Maintenance of a Drosophila Laboratory: General Procedures
Authors: Ashburner Michael , Roote John
Published: March 2007

INTRODUCTION

This article provides a general introduction to keeping Drosophila stocks, making and scoring crosses, mutagenesis, and controlling diseases in the laboratory.
Cleavage at Tryptophan by ο-Iodosobenzoic Acid
Authors: Simpson Richard J.
Published: March 2007

INTRODUCTION

Chemical reagents that selectively cleave at tryptophan residues have contributed greatly to the elucidation of protein structure and function. This protocol uses ο-iodosobenzoic acid for specific cleavage at tryptophan residues.
Preparing Cytoplasmic Extracts from Drosophila Embryos
Authors: Moritz Michelle
Published: March 2007

INTRODUCTION

In recent years, Drosophila has been an excellent source for biochemical quantities of proteins involved in a variety of cellular processes, such as cytoskeletal function and RNA binding. It is relatively simple to obtain a high-quality Drosophila embryonic cytoplasmic extract for protein purification or biochemistry, if population cages are used that produce at least 5 g of embryos during a 3-hour period. Smaller quantities of embryos can be used to produce extracts for in vitro biochemical assays. This protocol describes the collection and dechorionation of Drosophila embryos and the preparation of cytoplasmic extracts.
Persistent pain is associated with substance use after detoxification: a prospective cohort analysis
Authors: Larson Mary Jo , Paasche‐Orlow Michael , Cheng Debbie M. , Lloyd‐Travaglini Christine , Saitz Richard , Samet Jeffrey H.
Published: March 2007

Aims  To test the hypothesis that persistent pain is associated with an increased odds of substance use after detoxification.

Design  Analysis of data from a prospective cohort enrolled in a randomized controlled trial (RCT) to improve linkage with primary medical care.

Setting  An urban residential detoxification program.

Participants  Adults (n = 397) enrolled in the RCT with heroin, alcohol or cocaine as a substance of choice and at least one follow‐up interview.

Measurements  The key independent variable was pain status: persistent pain (moderate to very severe pain at all available interviews), no pain (mild pain or less at all available interviews) and intermittent pain (all others). There were four outcomes of interest: self‐reported use of any substance; heroin/opioid use; heavy alcohol use; and cocaine use 24 months after detoxification. Multivariable logistic regression controlled for several covariates including demographics, physical/sexual abuse, depressive symptoms, duration of follow‐up and addiction severity at study entry.

Findings  Pain in detoxification patients was common; 16% had persistent pain and 54% had intermittent pain. Persistent pain was associated with an increased odds for use of any substance [adjusted odds ratio (AOR) 4.2, 95% confidence interval (CI) 1.9–9.3], heroin/opioid use (AOR 5.4, 95% CI 2.1–13.8) and heavy alcohol use (AOR 2.2, 95% CI 1.0–4.5) at the 24‐month follow‐up. A statistically non‐significant increase in the odds of cocaine use (AOR 2.0, 95% CI 0.9–4.6) was also observed.

Conclusions  Among individuals leaving residential detoxification, chronic pain is a common problem and is associated independently with long‐term substance use after detoxification. Addressing pain as a treatable chronic condition among adults receiving detoxification presents a potential opportunity to improve long‐term clinical outcomes and warrants further intervention research.
A randomized, controlled trial to assess the efficacy and safety of a transdermal delivery system of nicotine/mecamylamine in cigarette smokers
Authors: Glover Elbert D. , Laflin Molly T. , Schuh Kory J. , Schuh Leslie M. , Nides Mitch , Christen Arden G. , Glover Penny N. , Strnad Julia V.
Published: March 2007

Aims  To determine the efficacy and safety of nicotine transdermal therapy co‐administered with the nicotine antagonist, mecamylamine, compared to a nicotine transdermal patch alone (21 mg nicotine + 6 mg mecamylamine, 21 mg nicotine + 3 mg mecamylamine, and 21 mg nicotine + 0 mg mecamylamine).

Design  Multi‐center (n = 4), double‐blind, randomized, parallel group, repeat‐dose study.

Setting  Clinical laboratory.

Participants  A total of 540 subjects were enrolled into the study—135 from each of four sites; 180 patients in each of three treatment arms.

Intervention  Treatment was administered for the first 6 weeks of the 8‐week study. Patients were instructed to continue smoking for the first 2 weeks of treatment.

Measurements  The primary efficacy parameter was 4‐week continuous abstinence after the quit date, confirmed with an expired carbon monoxide of < 10 parts per million.

Findings  Analysis of the 4‐week continuous abstinence for the intent‐to‐treat population showed overall rates of 29% (nicotine + 6 mg mecamylamine), 29% (nicotine + 3 mg mecamylamine) and 23% (nicotine only) using the slip definition which allows smoking in the first 2 weeks after the quit date. Statistical analyses revealed no significant treatment differences. Analyses using the strict definition (no smoking after the quit date) yielded similar non‐significant group differences (29%, 27%, 26%).

Conclusion  If adding mecamylamine to nicotine replacement therapy (NRT) improves the chances of success at stopping smoking, the results of this study suggest that the effect is very small.
Dihydropyrimidine dehydrogenase activity and the IVS14+1G>A mutation in patients developing 5FU‐related toxicity
Authors: Magné Nicolas , Etienne‐Grimaldi Marie‐Christine , Cals Laurent , Renée Nicole , Formento Jean‐Louis , Francoual Mireille , Milano Gérard
Published: March 2007

What is already known about this subject

• Dihydropyrimidine dehydrogenase (DPD) deficiency is known to be a major cause of severe 5FU‐related toxicity.

• A link has been previously shown between 5FU toxicity and either low enzyme activity measured in peripheral blood mononuclear cells (PMNC) or germinal DPD mutations.

• The link between the most common DPD mutation (IVS14+1G>A) and PMNC enzyme activity is poorly documented.

What this study adds

• This paper provides the largest series of case‐reports (n = 131) with 5FU‐related toxicity, analyzed for both PMNC‐DPD activity and the IVS14+1G>A mutation.

• A very low incidence of the IVS14+1G>A mutation (2.2%) was observed in this selected Caucasian population.

• Present data suggest that IVS14+1 mutation screening has limited effectiveness in identifying patients at risk for severe 5FU toxicity. Also, patients with normal PMNC‐DPD activity may develop life‐threatening toxicity.

Aims

To examine retrospectively the relationship between DPD phenotype/genotype and the intensity of 5FU toxicity.

Methods

One hundred and thirty‐one case‐reports (81 women, 50 men) with 5FU‐related toxicity were analyzed.

Results

The lower the DPD activity (10–504 pmol min−1 mg−1), the higher the toxicity grade was scored (P < 0.01). Toxicity‐related deaths occurred in nine patients (eight women) who significantly expressed lower DPD activity than other patients. Two of the deceased patients had normal DPD activity. The IVS14+1G>A mutation, analyzed in 93 patients, was detected in two patients (nonlethal toxicity).

Conclusions

The IVS14+1G>A mutation may not help prevent toxicity and patients with normal DPD activity may develop life‐threatening 5FU toxicity.
Frequent epigenetic silencing of protocadherin 10 by methylation in multiple haematologic malignancies
Authors: Ying Jianming , Gao Zifen , Li Hongyu , Srivastava Gopesh , Murray Paul G. , Goh Hwee Koon , Lim Chai Yen , Wang Yajun , Marafioti Teresa , Mason David Y. , Ambinder Richard F. , Chan Anthony T. C. , Tao Qian
Published: March 2007

Epigenetic silencing of tumour suppressor genes (TSG) inactivates TSG functions. Previously, we identified PCDH10 as a methylated TSG in carcinomas. Here, we detected its frequent silencing and methylation in lymphoma cell lines including 100% Burkitt, 100% diffuse large B cell, 86% Hodgkin, 100% nasal natural killer/T‐cell lymphoma and 1/3 of leukaemia cell lines, and in primary tumours but not in normal peripheral blood mononuclear cells or lymph nodes. PCDH10 silencing could be reversed by demethylation with 5‐aza‐2′‐deoxycytidine. Methylation was further detected in 14% of Hodgkin lymphoma sera. Thus, PCDH10 methylation is frequently involved in lymphomagenesis and could serve as a tumour‐specific biomarker.
Touch cytology in diagnosing Helicobacter pylori: comparison of four staining methods
Authors: Hashemi M. R. , Rahnavardi M. , Bikdeli B. , Dehghani Zahedani M. , Iranmanesh F.
Published: March 2007

Objectives:  Helicobacter pylori (Hp), a major cause of peptic ulcer disease and an important risk factor for gastric malignancy, can be diagnosed by several methods. Touch cytology (TC) of the gastric mucosa has been noted to give good results and has been found to be very simple, inexpensive and rapid. However, evidence regarding the accuracy of different staining methods of TC is lacking. The present study aims at defining the diagnostic accuracy of four different staining methods of TC.

Methods:  Biopsy specimens were taken from the antral mucosa of one hundred consecutive patients referred for upper gastrointestinal endoscopy (UGIE) for various indications. TC slides were processed by four staining methods: Wright, Giemsa, Papanicolaou and Gram. Rapid urease test (RUT) and histological examination of specimens were also performed. The same experienced pathologist evaluated the coded samples. A patient's Hp status was established by minimum concordance of the three tests, including histology, RUT, and ‘Touch mean’. The latter was defined positive when at least three of the four TC staining methods were positive.

Results:  Forty‐six patients (46%) were positive for Hp according to Hp status. TC stained by Wright had excellent agreement with both histology (κ = 0.80, P < 0.001) and RUT (κ = 0.84, P < 0.001). Regarding Hp status, histology was 100% sensitive and RUT was 100% specific. Wright‐stained TC (88.89%) was significantly more specific than both Giemsa‐ (74.07%; P < 0.05) and Papanicolaou‐stained (70.37%; P < 0.05) TC.

Conclusions:  RUT should still be acknowledged as the primary test in diagnosing Hp following UGIE. If RUT is negative and Hp detection is intended only, Wright‐stained TC can safely substitute for histology. However, when assessment for severity of mucosal damage or cell atypias is meant, histology cannot be neglected.
Adsorption and transport of nitrate and potassium in an Andosol under banana (Guadeloupe, French West Indies)
Authors: Sansoulet J. , Cabidoche Y. M. , Cattan P.
Published: March 2007

A series of batch, soil column and field experiments was carried out in order to study nitrate and potassium transport and to improve fertilizer practices in an Andosol under a banana plantation. The focus of the study was on the influence of the substantial variable charge of the soil on ion transport. Leaching of both K+ and NO3−‐N through the Andosol were both retarded, as expected, because of the soil’s cation and anion exchange capacities (CEC and AEC). Under acidic conditions, the B horizon, with the greater allophane content, developed preferential affinity for nitrate. The A horizon, with both organic and mineral adsorption sites, exhibited a stronger affinity for potassium than the B horizon when the soil solution pH was below the zero point of charge (ZPC). Fast leaching of nutrients occurred under the banana stem due to the abundant stemflow derived from rainfall interception by the banana plant. Intensive leaching under the plant questions the concept of fertilizer application at the plant stem.
Biogeographic barriers, connectivity and homogenization of freshwater faunas: it's a small world after all
Authors: RAHEL FRANK J.
Published: March 2007

1. Historically, biogeographic barriers to the movement of aquatic organisms existed at multiple spatial scales and contributed to the development of unique regional faunas. At increasing spatial scales, these barriers consisted of waterfalls and cascades; catchment divides; major mountain ranges and oceans. This hierarchy of movement barriers produced increasingly distinct aquatic biotas at larger drainage units.

2. Humans have provided a variety of pathways by which aquatic species can circumvent historical biogeographic barriers. These include both authorised and unauthorised stocking, construction of canals and water conveyance systems, transport in ship ballast water, fishing and angling gear (including boats) transferred among water bodies and intentional release of ornamental and other captive species.

3. One consequence of human‐aided breaching of biogeographic barriers has been the spread of noxious species that have altered aquatic ecosystems and fisheries in ways that are undesirable to humans.

4. Another consequence of human‐aided breaching of biogeographic barriers has been the homogenization of aquatic biotas. Homogenization occurs when a few cosmopolitan species come to dominate communities at the expense of unique native species. Among aquatic organisms this phenomenon is best documented for fish faunas where a small set of species introduced for sport fishing, aquaculture, or ornamental purposes have become widespread throughout the world.

5. Slowing biotic homogenization will require slowing the rate at which species breach biogeographic barriers. This will involve implementing regulations that limit stocking opportunities; increasing the public's awareness about the consequences of releasing non‐native species and developing technological solutions that prevent movement of aquatic organisms or eliminate them before they become established.

6. River restoration can influence homogenization of aquatic biotas through two major mechanisms: by removing barriers to movement and by restoring natural habitat conditions. Removal of movement barriers may facilitate the spread of non‐native species and thus contribute to biotic homogenization. Restoration of natural flow regimes and habitat conditions may reduce biotic homogenization by favouring regional native species over cosmopolitan, non‐native species.
Hyporheic rehabilitation in rivers: restoring vertical connectivity
Authors: BOULTON ANDREW J.
Published: March 2007

1. The hyporheic zone below the channel and banks of many rivers where surface water and ground water exchanges plays a crucial functional role in the biogeochemical transformation of water, mediated by active microbial biofilms. This zone also harbours assemblages of invertebrates that graze biofilms, contribute to secondary production, and can alter the porosity of the hyporheic zone through their movement or burrowing activities.

2. Many human activities cause interstitial sedimentation or disrupt surface–groundwater hydrological linkages, impacting upon ecological processes in the hyporheic zone. However, strategies for river rehabilitation seldom explicitly consider the hyporheic zone or seek to restore lost vertical linkages with groundwater. Instead, restoration goals target surface, riparian or floodplain features even though current river ecosystem theory emphasises the three dimensions of hydrological connectivity. To guide effective, holistic river restoration, scientists and managers therefore need information on the mechanisms by which energy and material are transferred in the hyporheic zone and which ecosystem services are thus provided.

3. Other gaps in our understanding of hyporheic zone rehabilitation include recruitment processes of the hyporheos and the relative importance of groups of hyporheic invertebrates in rivers differing in substratum size, disturbance frequency and groundwater linkages. Carefully designed experiments that assess responses to hyporheic rehabilitation strategies will provide valuable data at varying scales (e.g. distribution of hyporheic habitat types at the reach scale) for management as well as providing insights into the mechanisms controlling hyporheic invertebrate assemblages and ecological processes. Fully successful river rehabilitation must include restoration of vertical linkages between the river and its shallow groundwater aquifers.
Changes in habitat structure, benthic invertebrate diversity, trout populations and ecosystem processes in restored forest streams: a boreal perspective
Authors: MUOTKA TIMO , SYRJÄNEN JUKKA
Published: March 2007

1. Most Finnish streams were channelised during the 19th and 20th century to facilitate timber floating. By the late 1970s, extensive programmes were initiated to restore these degraded streams. The responses of fish populations to restoration have been little studied, however, and monitoring of other stream biota has been negligible. In this paper, we review results from a set of studies on the effects of stream restoration on habitat structure, brown trout populations, benthic macroinvertebrates and leaf retention.

2. In general, restoration greatly increased stream bed heterogeneity. The cover of mosses in channelised streams was close to that of unmodified reference sites, but after restoration moss cover declined to one‐tenth of the pre‐restoration value.

3. In one stream, densities of age‐0 trout were slightly lower after restoration, but the difference to an unmodified reference stream was non‐significant, indicating no effect of restoration. In another stream, trout density increased after restoration, indicating a weakly positive response. The overall weak response of trout to habitat manipulations probably relates to the fact that restoration did not increase the amount of pools, a key winter habitat for salmonids.

4. Benthic invertebrate community composition was more variable in streams restored 4–6 years before sampling than in unmodified reference streams or streams restored 8 years before sampling. Channelised streams supported a distinctive set of indicator species, most of which were filter‐feeders or scrapers, while most of the indicators in streams restored 8 years before sampling were shredders.

5. Leaf retentiveness in reference streams was high, with 60–70% of experimentally released leaves being retained within 50 m. Channelised streams were poorly retentive (c. 10% of leaves retained), and the increase in retention following restoration was modest (+14% on average). Aquatic mosses were a key retentive feature in both channelised and natural streams, but their cover was drastically reduced through restoration.

6. Mitigation of the detrimental impacts of forestry (e.g. removal of mature riparian forests) is a major challenge to the management of boreal streams. This goal cannot be achieved by focusing efforts only on restoration of physical structures in stream channels, but also requires conservation and ecologically sound management of riparian forests.
Evaluation of the oral health situation of a group of Egyptian haemophilic children and their re‐evaluation following an oral hygiene and diet education programme
Authors: KABIL N. , EL ALFY M. , METWALLI N.
Published: March 2007

Summary.  Haemophilic children in Egypt have received minimal dental intervention and their dental needs required assessment. The purpose of this study was to assess the oral health needs of a sample (n = 60) of Egyptian haemophilic children (6–12 years), so as to develop, implement and evaluate an oral hygiene education programme over an 8‐month period on the experimental group (n = 30) vs. the control group (n = 30). The oral hygiene index simplified (OHI‐S) index was used for baseline data and at the end of the study, while DMFS and defs were used to collect caries experience baseline data on each subject. The results showed that the DMFT and deft were significantly higher than those of the non‐haemophilic population in Egypt and also higher than those of haemophilic children in developed countries and that the decayed component represented most of the index values. At phase I, the mean value of the OHI‐S of experimental and the control groups was 2.67 ± 0.45 and 2.53 ± 0.53, respectively, but the difference was not significant (P > 0.05), both values were in the ‘fair’ category (1.3–3.0). At phase II, the end of the 8 months follow‐up period and after the application of a strict oral care programme in the experimental group, there was a significant decrease from 2.67 to 1.20 (P < 0.001), a shift of values occurred from the ‘fair’ category to the ‘good’ category (0.1–1.2) while there was no significant difference in the control group. It can be concluded that professional plaque control, education and access to oral hygiene aids is paramount to improve oral health of these children.
Attributing recovery from depression. Perceptions of people cared for in primary care
Authors: Badger Frances , Nolan Peter
Published: March 2007

Aims and objectives.  The aim of the study was to understand how people treated for depression in primary care perceived the care they received. The focus was specifically on ascertaining their perceptions of what had helped during their treatment, their understanding of the factors to which they attributed their recovery, and their reflections on their experience of depression.

Background.  Although knowledge of the factors that promote recovery from depression is growing, personal accounts of attributions of recovery are largely absent from the literature. Identifying and understanding people's accounts of their recovery is particularly important for practitioners involved in medication management and prescribing.

Method.  A purposeful sample of 60 people who had accessed primary care and been prescribed medication because of depressive symptoms was interviewed using a semistructured approach. Interviews explored people's experiences of accessing and using primary care, their assessments of care offered, experiences of medication management and their attributions of recovery.

Results.  Recovery from depression was characterized by its multifactorial nature, and two‐thirds of the participants felt that medication had contributed to their recovery. Factors in recovery changed with the passage of time and many perceived personal strengths as important to recovery. Practitioners who acknowledged and encouraged people's roles in recovery and supported multifaceted care were perceived by users as caring and offering holistic, individualized care.

Conclusion.  People with depression are keen to regard their recovery as multifactorial and to have their own roles in recovery acknowledged. Preferences for a ‘portfolio’ of care, the components of which change as recovery progresses, were evident.

Relevance to clinical practice.  Practitioners involved in prescribing and medication management for depression must aim to explore patients’ beliefs about appropriate treatments and recovery. Addressing these can potentially promote treatment concordance and enhance recovery from depression by establishing and sustaining therapeutic relationships.
Non‐finite loss and emotional labour: family caregivers’ experiences of living with motor neurone disease
Authors: Ray Robin A , Street Annette F
Published: March 2007

Aim and objectives.  This paper aims to add to nurses’ knowledge concerning the losses and emotional labour family caregivers face caring for people living with neurodegenerative, life‐limiting illnesses such as motor neurone disease.

Background.  Motor neurone disease is a relentless, progressive illness resulting in progressive loss of voluntary muscle mass and function. Previous caregiver research presents the salient losses such as social, financial and relationship loss. However, the non‐finite, unpredictable losses faced every day by caregivers and the emotional labour experienced are not effectively represented and have not been explored for caregivers of adult patients with life‐limiting, degenerative, illness.

Design/methods.  Semi‐structured interviews, ecomaps of social support networks and field notes were used to collect data for this ethnographic case study. Data were attained at three time points over a 10‐month period from 18 primary caregivers and once from six peripheral caregivers.

Results.  Data revealed new information about the psychosocial and emotional losses experienced daily, when living with motor neurone disease. The impact of the constancy of voluntary muscle degeneration and the uncertainty of the illness progression in terms of available time and functional loss, threatened people's understanding and expectations of life, their relationships, their personal identity and their future. Managing their relationship with the patient and their reactions to the devastation of motor neurone disease is consistent with the concept of emotional labour.

Conclusions.  Family caregivers living with relentless, life‐limiting illness experience non‐finite losses and emotional labour on a daily basis. While each individual's experience of loss is unique, nurses need to include caregivers as well as patients, in their spectrum of supportive care.

Relevance to clinical practice.  Nurses can be independent confidants who share the emotional labour and work with caregivers to develop interventions to assist them to manage their losses and their changing needs for psychological and emotional support.
The process of developing audiovisual patient information: challenges and opportunities
Authors: Hutchison Catherine , McCreaddie May
Published: March 2007

Aim.  The aim of this project was to produce audiovisual patient information, which was user friendly and fit for purpose. The purpose of the audiovisual patient information is to inform patients about randomized controlled trials, as a supplement to their trial‐specific written information sheet.

Background.  Audiovisual patient information is known to be an effective way of informing patients about treatment. User involvement is also recognized as being important in the development of service provision. The aim of this paper is (i) to describe and discuss the process of developing the audiovisual patient information and (ii) to highlight the challenges and opportunities, thereby identifying implications for practice. A future study will test the effectiveness of the audiovisual patient information in the cancer clinical trial setting.

Methods.  An advisory group was set up to oversee the project and provide guidance in relation to information content, level and delivery. An expert panel of two patients provided additional guidance and a dedicated operational team dealt with the logistics of the project including: ethics; finance; scriptwriting; filming; editing and intellectual property rights.

Results.  Challenges included the limitations of filming in a busy clinical environment, restricted technical and financial resources, ethical needs and issues around copyright. There were, however, substantial opportunities that included utilizing creative skills, meaningfully involving patients, teamworking and mutual appreciation of clinical, multidisciplinary and technical expertise.

Conclusion.  Developing audiovisual patient information is an important area for nurses to be involved with. However, this must be performed within the context of the multiprofessional team. Teamworking, including patient involvement, is crucial as a wide variety of expertise is required.

Relevance to clinical practice.  Many aspects of the process are transferable and will provide information and guidance for nurses, regardless of specialty, considering developing this format of patient information.
Predictors of change in satisfaction with chewing ability: a 24‐month study of dentate adults
Authors: MENG X. , GILBERT G. H.
Published: March 2007

Summary  People's satisfaction with chewing ability is not determined entirely by their mechanical chewing function. Instead, it is a complex measure that embraces broad physical, social and psychological components. Using data from the Florida Dental Care Study, a prospective longitudinal study of oral health and dental care, this current study aimed to identify the longitudinal relationships between changes in satisfaction with chewing ability and changes in other dimensions of oral health and oral health‐related quality of life (OHRQoL). A multidimensional conceptual model of oral health and OHRQoL was applied to guide the analysis. Most dentate people were satisfied with their chewing ability. However, changes in satisfaction with chewing ability were common: nearly 11–22% of subjects experienced improved satisfaction, depending on the interval; while about 12–18% of subjects experienced deteriorated satisfaction by the end of the interval. Changes in satisfaction with chewing ability were significantly associated with changes in other aspects of oral health and OHRQoL. Onset of certain oral health problems/conditions or constantly having such problems was associated with a lower probability of reporting improvement in satisfaction and a higher probability of experiencing deterioration. In contrast, recovery from certain oral health problems/conditions or not having such problems was associated with a higher probability of improvement and a lower probability of deterioration.