bluuebunny/crossref_metadata_2025 huggingface dataset:
Methicillin-Resistant Staphylococcus aureus in Geriatric Patients: Usefulness of Screening in a Chronic-Care Setting
Authors: Talon Daniel R. , Bertrand Xavier
Published: February 2006

Objective:

To evaluate the contribution of screening to the detection of cases of methicillin-resistant Staphylococcus aureus (MRSA) in a chronic-care facility.

Design:

Surveillance and laboratory observational study.

Methods:

During a 7-month period, we compared imported and acquired MRSA in a chronic-care center by screening patients for carriage of MRSA on admission and discharge, and by recording all cases of clinical specimens positive for MRSA

Setting:

The study was conducted in a 120-bed chronic-care center. This center admits approximately 850 patients per year. Approximately 90% of the patients were elderly and were admitted from other hospitals.

Results:

Of 519 patients admitted during the study period, 129 were positive for MRSA at some point during their residence, including 60 (11.6%) with MRSA found within 48 hours of admission and 69 (13.3%; 53% of all positives) with nosocomial MRSA Of the 519 admissions, 332 (64%) were discharged, of whom 62 (19%) were positive for MRSA. Of these 62, 43 (69%) acquired their MRSA during their stay in the center.

Conclusions:

Our study confirms the amplification effect of chronic-care facilities on MRSA propagation. It also shows that screening for MRSA carriage in a chronic-care center facilitates the early identification of a large proportion of patients with MRSA.
Influenza and Pneumococcal Vaccination Coverage Levels Among Hawaii Statewide Long-Term-Care Facilities
Authors: Cui Xiao Wei , Nagao Marcia M. , Effler Paul V.
Published: February 2006

Influenza and pneumococcal vaccination rates among Hawaii long-term-care facilities (LTCFs) statewide during the 1996/97 through the 1998/99 influenza seasons revealed that resident influenza vaccination rates remained over 89%, but pneumococcal vaccination was underutilized. LTCF staff influenza vaccination rates over the same time period were low.
Contamination of Gowns, Gloves, and Stethoscopes With Vancomycin-Resistant Enterococci
Authors: Zachary Kimon C. , Bayne Pamela S. , Morrison Victoria J. , Ford Dale S. , Silver Leah Christine , Hooper David C.
Published: February 2006

Objective:

To measure directly the rate of contamination, during routine patient examination, of gowns, gloves, and stethoscopes with vancomycin-resistant enterococci (VRE).

Setting:

A large, academic, tertiary-care hospital.

Patients:

Between January 1997 and December 1998, 49 patients colonized or infected with VRE were entered in the study.

Design:

After routine examination, the examiner's glove fingertips, gown (the umbilical region and the cuffs), and stethoscope diaphragm were pressed onto Columbia colistin-nalidixic acid (CNA) agar plates with 5% sheep blood plus vancomycin 6 ug/mL. The stethoscope diaphragm was sampled again after cleaning with a 70% isopropanol wipe.

Results:

VRE were isolated from at least 1 examiner site (gloves, gowns, or stethoscope) in 33 (67%) of 49 cases. Gloves were contaminated in 63%, gowns in 37%, and stethoscopes in 31%. All three items were positive for VRE in 24%. One case each had stethoscope and gown contamination without glove contamination. Only 1 (2%) of 49 stethoscopes was positive after wiping with an alcohol swab. Contamination at any site was more likely when the patient had a colostomy or ileostomy. Patients identified by rectal-swab culture alone were as likely to contaminate their examiners as were those identified by clinical specimens.

Conclusions:

Our study revealed a high rate of examiner contamination with VRE. The similar risk of contamination identified by surveillance and clinical cases reinforces concerns that patients not known to be colonized with VRE could serve as sources for dissemination. Wiping with alcohol is effective in decontaminating stethoscopes.
A Shared Vision of Healthcare Quality Improvement
Authors: Birnbaum David ,   Health Care Quality Special Interest Group
Published: February 2006

SHEA and the American Society for Quality's Health Care Division have been collaborating in areas of common concern to improve healthcare quality. We each possess a heritage of different but complementary approaches and stand a better chance of success together than apart. This presentation describes rapid growth of our interdisciplinary, international, special interest group and progress made thus far, as well as challenges facing hospital epidemiologists and quality improvement professionals.
Assessment of and Intervention for the Misuse of Aldehyde Disinfectants in Japan
Authors: Oie Shigeharu , Kamiya Akira
Published: February 2006

A survey of 145 Japanese hospitals revealed the use of 4 inappropriate aldehyde disinfection methods in 5.5% to 16.8%. Following education, there was discontinuation of 3 of these practices in 26 of 28 affected centers, but only 4 of 18 affected centers stopped the use of formaldehyde vapor cabinets. There is a need to inform hospitals about inappropriate disinfection methods that pose chemical risks to patients and staff.
Antimicrobial Use Prior to the Acquisition of Multiresistant Bacteria
Authors: Eveillard Matthieu , Schmit Jean-Luc , Eb François
Published: February 2006

We assessed whether patients who acquired methicillin-resistantStaphylococcus aureus(MRSA) had less exposure to antimicrobial agents than did those who acquired Enterobacteriaceae that produced extended-spectrum β-lactamase (ESβL). In a 6-month, prospective study, ESβL carriers had received antimicrobial therapy more often than had MRSA carriers. Amoxicillin-clavulanic acid, fluoroquinolones, and third-generation cephalosporins, especially ceftazidime, had been prescribed more often for ESβL carriers than for MRSA carriers.
Pneumonia in the Long-Term-Care Facility
Authors: Marrie Thomas J.
Published: February 2006

Pneumonia is a common infection among residents of long-term-care facilities (LTCFs), with an incidence of 1.2 episodes per 1,000 patient-days. This rate is believed to be six- to tenfold higher than the rate of pneumonia among elderly individuals living in the community. The risk factors for pneumonia among residents of LTCFs are profound disability, bedridden state, urinary incontinence, difficulty swallowing, malnutrition, tube feedings, contractures, and use of benzodiazepines and anticholinergic medications. An elevated respiratory rate is often an early clue to pneumonia in this group of patients. Staphylococcus aureus (including methicillin-resistant S. aureus) and aerobic gram-negative bacilli (including multidrug-resistant isolates) are more frequent causes of pneumonia in this setting than in the community. Criteria have been developed that help identify patients for treatment in their LTCFs.
A Comparison of the Effect of Early Insertion of Standard Latex and Silver-Impregnated Latex Foley Catheters on Urinary Tract Infections in Burn Patients
Authors: Newton Terry , Still Joseph M. , Law Edward
Published: February 2006

A retrospective study was designed to compare the incidence of urinary tract infections during two different time periods in burn patients treated with two different types of Foley catheters. In time period 1, latex catheters present on admission were not changed. In time period 2, catheters were replaced on admission with silver alloy-impregnated catheters. In time period 1, the rate of symptomatic urinary tract infections was 7.2 per 1,000 catheter-days. In time period 2, the rate was 4.4 per 1,000 catheter-days. Results, compared using Fisher's exact test, revealed a statistically significant P value of .029. The use of silver-impregnated catheters significantly lowered the rate of urinary tract infection at our burn center.
An Outbreak Due to MultiresistantAcinetobacter baumanniiin a Burn Unit: Risk Factors for Acquisition and Management
Authors: Simor Andrew E. , Lee Mark , Vearncombe Mary , Jones-Paul Linda , Barry Clare , Gomez Manuel , Fish Joel S. , Cartotto Robert C. , Palmer Robert , Louie Marie
Published: February 2006

Objectives:

To describe the investigation and management of an outbreak due to multiresistantAcinetobacter baumanniiand to determine risk factors for acquisition of the organism.

Setting:

A 14-bed regional burn unit in a Canadian tertiary-care teaching hospital.

Design:

Case-control study with multivariate analysis of potential risk factors using logistic regression analysis. Surveillance cultures were obtained from the hospital environment, from noninfected patients, and from healthcare providers.

Results:

A total of 31 (13%) of 247 patients with acute burn injuries acquired multiresistantA. baumanniibetween December 1998 and March 2000; 18 (58%) of the patients were infected. The organism was recovered from the hospital environment and the hands of healthcare providers. Significant risk factors for acquisition of multiresistantA. baumanniiwere receipt of blood products (odds ratio [OR], 10.8; 95% confidence interval [CI95], 3.4 to 34.4;P< .001); procedures performed in the hydrotherapy room (OR, 4.1; CI95, 1.3 to 13.1;P= .02); and increased duration of mechanical ventilation (OR, 1.1 per day; CI95, 1.0 to 1.1;P=. 02).

Interventions:

Improved compliance with hand hygiene, strict patient isolation, meticulous environmental cleaning, and temporary closure of the unit to new admissions.

Conclusions:

Acquisition of multiresistantA. baumanniiwas likely multifactorial, related to environmental contamination and contact with transiently colonized healthcare providers. Control measures addressing these potential sources of multiresistantA. baumanniiwere successful in terminating the outbreak. Ongoing surveillance and continued attention to hand hygiene and adequate environmental cleaning are essential to prevent recurrent outbreaks due to antibiotic-resistant bacteria in burn units.
Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support
Authors: Canaran Payan , Stein Lincoln , Ware Doreen
Published: February 2006

Summary: We have developed Look-Align, an interactive web-based viewer to display pre-computed multiple sequence alignments. Although initially developed to support the visualization needs of the maize diversity website Panzea (), the viewer is a generic stand-alone tool that can be easily integrated into other websites.

Availability: Look-Align is written in Perl using open-source components and is available under an open-source license. Live installation and download information can be found at the Panzea website ().

Contact:  ware@cshl.edu

Supplementary information: The Supplementary information includes sample lists of multiple sequence alignment software and sample screenshots of the viewer.
A new summarization method for affymetrix probe level data
Authors: Hochreiter Sepp , Clevert Djork-Arné , Obermayer Klaus
Published: February 2006

Motivation: We propose a new model-based technique for summarizing high-density oligonucleotide array data at probe level for Affymetrix GeneChips. The new summarization method is based on a factor analysis model for which a Bayesian maximum a posteriori method optimizes the model parameters under the assumption of Gaussian measurement noise. Thereafter, the RNA concentration is estimated from the model. In contrast to previous methods our new method called ‘Factor Analysis for Robust Microarray Summarization (FARMS)’ supplies both P-values indicating interesting information and signal intensity values.

Results: We compare FARMS on Affymetrix's spike-in and Gene Logic's dilution data to established algorithms like Affymetrix Microarray Suite (MAS) 5.0, Model Based Expression Index (MBEI), Robust Multi-array Average (RMA). Further, we compared FARMS with 43 other methods via the ‘Affycomp II’ competition. The experimental results show that FARMS with default parameters outperforms previous methods if both sensitivity and specificity are simultaneously considered by the area under the receiver operating curve (AUC). We measured two quantities through the AUC: correctly detected expression changes versus wrongly detected (fold change) and correctly detected significantly different expressed genes in two sets of arrays versus wrongly detected (P-value). Furthermore FARMS is computationally less expensive then RMA, MAS and MBEI.

Availability: The FARMS R package is available from

Contact:  hochreit@bioinf.jku.at

Supplementary information:
Non-linear tests for identifying differentially expressed genes or genetic networks
Authors: Xiong Hao
Published: February 2006

Motivation: One of the recently developed statistics for identifying differentially expressed genetic networks is Hotelling T2 statistic, which is a quadratic form of difference in linear functions of means of gene expressions between two types of tissue samples, and so their power is limited.

Results: To improve the power of test statistics, a general statistical framework for construction of non-linear tests is presented, and two specific non-linear test statistics that use non-linear transformations of means are developed. Asymptotical distributions of the non-linear test statistics under the null and alternative hypothesis are derived. It has been proved that under some conditions the power of the non-linear test statistics is higher than that of the T2 statistic. Besides theory, to evaluate in practice the performance of the non-linear test statistics, they are applied to two real datasets. The preliminary results demonstrate that the P-values of the non-linear statistics for testing differential expressions of the genetic networks are much smaller than those of the T2 statistic. And furthermore simulations show the Type I errors of the non-linear statistics agree with the threshold used and the statistics fit the χ2 distribution.

Contact:  hxiong@cs.tamu.edu

Supplementary information: Supplementary data are available on Bioinformatics online.
CFinder: locating cliques and overlapping modules in biological networks
Authors: Adamcsek Balázs , Palla Gergely , Farkas Illés J. , Derényi Imre , Vicsek Tamás
Published: February 2006

Summary: Most cellular tasks are performed not by individual proteins, but by groups of functionally associated proteins, often referred to as modules. In a protein assocation network modules appear as groups of densely interconnected nodes, also called communities or clusters. These modules often overlap with each other and form a network of their own, in which nodes (links) represent the modules (overlaps). We introduce CFinder, a fast program locating and visualizing overlapping, densely interconnected groups of nodes in undirected graphs, and allowing the user to easily navigate between the original graph and the web of these groups. We show that in gene (protein) association networks CFinder can be used to predict the function(s) of a single protein and to discover novel modules. CFinder is also very efficient for locating the cliques of large sparse graphs.

Availability: CFinder (for Windows, Linux and Macintosh) and its manual can be downloaded from .

Supplementary information: Supplementary data are available on Bioinformatics online.

Contact:  cfinder@angel.elte.hu
Generation of 3D templates of active sites of proteins with rigid prosthetic groups
Authors: Nebel Jean-Christophe
Published: February 2006

Motivation: With the increasing availability of protein structures, the generation of biologically meaningful 3D patterns from the simultaneous alignment of several protein structures is an exciting prospect: active sites could be better understood, protein functions and protein 3D structures could be predicted more accurately. Although patterns can already be generated at the fold and topological levels, no system produces high-resolution 3D patterns including atom and cavity positions. To address this challenge, our research focuses on generating patterns from proteins with rigid prosthetic groups. Since these groups are key elements of protein active sites, the generated 3D patterns are expected to be biologically meaningful.

Results: In this paper, we present a new approach which allows the generation of 3D patterns from proteins with rigid prosthetic groups. Using 237 protein chains representing proteins containing porphyrin rings, our method was validated by comparing 3D templates generated from homologues with the 3D structure of the proteins they model. Atom positions were predicted reliably: 93% of them had an accuracy of 1.00 Å or less. Moreover, similar results were obtained regarding chemical group and cavity positions. Results also suggested our system could contribute to the validation of 3D protein models. Finally, a 3D template was generated for the active site of human cytochrome P450 CYP17, the 3D structure of which is unknown. Its analysis showed that it is biologically meaningful: our method detected the main patterns of the cytochrome P450 superfamily and the motifs linked to catalytic reactions. The 3D template also suggested the position of a residue, which could be involved in a hydrogen bond with CYP17 substrates and the shape and location of a cavity. Comparisons with independently generated 3D models comforted these hypotheses.

Availability: Alignment software (Nestor3D) is available at

Contact:  j.nebel@kingston.ac.uk
Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations
Authors: Kel A. , Konovalova T. , Waleev T. , Cheremushkin E. , Kel-Margoulis O. , Wingender E.
Published: February 2006

Motivation: Functionally related genes involved in the same molecular-genetic, biochemical or physiological process are often regulated coordinately. Such regulation is provided by precisely organized binding of a multiplicity of special proteins [transcription factors (TFs)] to their target sites (cis-elements) in regulatory regions of genes. Cis-element combinations provide a structural basis for the generation of unique patterns of gene expression.

Results: Here we present a new approach for defining promoter models based on the composition of TF binding sites and their pairs. We utilize a multicomponent fitness function for selection of the promoter model that fits best to the observed gene expression profile. We demonstrate examples of successful application of the fitness function with the help of a genetic algorithm for the analysis of functionally related or co-expressed genes as well as testing on simulated and permutated data.

Availability: The CMA program is freely available for non-commercial users. URL . It is also a part of the commercial system ExPlain™ () designed for causal analysis of gene expression data.

Contact:  alexander.kel@biobase-international.com
Comparison of P-RnaPredict and mfold—algorithms for RNA secondary structure prediction
Authors: Wiese Kay C. , Hendriks Andrew
Published: February 2006

Motivation: Ribonucleic acid is vital in numerous stages of protein synthesis; it also possesses important functional and structural roles within the cell. The function of an RNA molecule within a particular organic system is principally determined by its structure. The current physical methods available for structure determination are time-consuming and expensive. Hence, computational methods for structure prediction are sought after. The energies involved by the formation of secondary structure elements are significantly greater than those of tertiary elements. Therefore, RNA structure prediction focuses on secondary structure.

Results: We present P-RnaPredict, a parallel evolutionary algorithm for RNA secondary structure prediction. The speedup provided by parallelization is investigated with five sequences, and a dramatic improvement in speedup is demonstrated, especially with longer sequences. An evaluation of the performance of P-RnaPredict in terms of prediction accuracy is made through comparison with 10 individual known structures from 3 RNA classes (5S rRNA, Group I intron 16S rRNA and 16S rRNA) and the mfold dynamic programming algorithm. P-RnaPredict is able to predict structures with higher true positive base pair counts and lower false positives than mfold on certain sequences.

Availability:  P-RnaPredict is available for non-commercial usage. Interested parties should contact Kay C. Wiese (wiese@cs.sfu.ca).

Contact:  wiese@cs.sfu.ca
Development and validation of a consistency based multiple structure alignment algorithm
Authors: Ebert Jessica , Brutlag Douglas
Published: February 2006

Summary: We introduce an algorithm that uses the information gained from simultaneous consideration of an entire group of related proteins to create multiple structure alignments (MSTAs). Consistency-based alignment (CBA) first harnesses the information contained within regions that are consistently aligned among a set of pairwise superpositions in order to realign pairs of proteins through both global and local refinement methods. It then constructs a multiple alignment that is maximally consistent with the improved pairwise alignments. We validate CBA's alignments by assessing their accuracy in regions where at least two of the aligned structures contain the same conserved sequence motif.

Results: CBA correctly aligns well over 90% of motif residues in superpositions of proteins belonging to the same family or superfamily, and it outperforms a number of previously reported MSTA algorithms.

Availability: CBA is available at and the source code is freely available at

Contact:  brutlag@stanford.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
CellML2SBML: conversion of CellML into SBML
Authors: Schilstra Maria J. , Li Lu , Matthews Joanne , Finney Andrew , Hucka Michael , Le Novère Nicolas
Published: February 2006

Summary: CellML and SBML are XML-based languages for storage and exchange of molecular biological and physiological reaction models. They use very similar subsets of MathML to specify the mathematical aspects of the models. CellML2SBML is implemented as a suite of XSLT stylesheets that, when applied consecutively, convert models expressed in CellML into SBML without significant loss of information. The converter is based on the most recent stable versions of the languages (CellML version 1.1; SBML Level 2 Version 1), and the XSLT used in the stylesheets adheres to the XSLT version 1.0 specification. Of all 306 models in the CellML repository in April 2005, CellML2SBML converted 91% automatically into SBML. Minor manual changes to the unit definitions in the originals raised the percentage of successful conversions to 96%.

Availability:  

Contact:  m.j.1.schilstra@herts.ac.uk

Supplementary information: Instructions for use and further documentation available on
EFFICIENCY ANALYSIS OF THE TURKISH BANKING SECTOR IN PRECRISIS AND CRISIS PERIOD: A DEA APPROACH
Authors: OZKAN‐GUNAY E. NUR , TEKTAS ARZU
Published: February 2006

Structural weaknesses and recent crises increased the fragility of the Turkish banking system. Consequently, 25% of the domestic commercial banks were taken by SDIF between 1997 and 2001. This study assesses the technical efficiency of nonpublic commercial banks between 1990 and 2001 following the DEA model. The study reports a declining trend in the number of efficient banks and the mean efficiency of bank subgroups. It analyzes sensitivity to the output variables and depicts consistency between the model proposals and supervisory agent decisions. Thus the DEA model can be a tool to detect and improve the sources of inefficiency by bank management and supervisory agents. (JEL G15, G21, G28)
Allied Breweries and the Development of the Area Manager in British Brewing, 1950–1984
Authors: Mutch Alistair
Published: February 2006

Brewing in the United Kingdom in the years following 1950 saw a shift from a production to a retailing orientation. As part of this shift, the role of the area manager started to move from production and sales discipline to retail development. This article explores the job of the area manager during the period, seeking to demonstrate the weakness in recent accounts that suggest that area managers serve only as an “information relay” between senior managers and unit managers. Although the evidence is limited, because of problems with the survival of records, it suggests a more complex picture, which has implications for area managers in retail and service industries more generally.
Double-Strand Break Repair in Plants Is Developmentally Regulated
Authors: Boyko Alexander , Zemp Franz , Filkowski Jody , Kovalchuk Igor
Published: February 2006

In this study, we analyzed double-strand break (DSB) repair in Arabidopsis (Arabidopsis thaliana) at various developmental stages. To analyze DSB repair, we used a homologous recombination (HR) and point mutation reversion assays based on nonfunctional β-glucuronidase reporter genes. Activation of the reporter gene through HR or point mutation reversion resulted in the appearance of blue sectors after histochemical staining. Scoring of these sectors at 3-d intervals from 2 to 31 d post germination (dpg) revealed that, although there was a 100-fold increase in the number of genomes per plant, the recombination frequency only increased 30-fold. This translates to a recombination rate at 31 dpg (2.77 × 10−8) being only 30% of the recombination rate at 2 dpg (9.14 × 10−8). Conversely, the mutation frequency increased nearly 180-fold, resulting in a 1.8-fold increase in mutation rate from 2 to 31 dpg. Additional analysis of DSBs over the early developmental stages revealed a substantial increase in the number of strand breaks per unit of DNA. Furthermore, RNA analysis of Ku70 and Rad51, two key enzymes in two different DSB repair pathways, and further protein analysis of Ku70 revealed an increase in Ku70 levels and a decrease of Rad51 levels in the developing plants. These data suggest that DSB repair mechanisms are developmentally regulated in Arabidopsis, whereby the proportion of breaks repaired via HR substantially decreases as the plants mature.
FLOWERING LOCUS CMediates Natural Variation in the High-Temperature Response of theArabidopsisCircadian Clock
Authors: Edwards Kieron D. , Anderson Paul E. , Hall Anthony , Salathia Neeraj S. , Locke James C.W. , Lynn James R. , Straume Martin , Smith James Q. , Millar Andrew J.
Published: February 2006

Temperature compensation contributes to the accuracy of biological timing by preventing circadian rhythms from running more quickly at high than at low temperatures. We previously identified quantitative trait loci (QTL) with temperature-specific effects on the circadian rhythm of leaf movement, including a QTL linked to the transcription factor FLOWERING LOCUS C (FLC). We have now analyzed FLC alleles in near-isogenic lines and induced mutants to eliminate other candidate genes. We showed that FLC lengthened the circadian period specifically at 27°C, contributing to temperature compensation of the circadian clock. Known upstream regulators of FLC expression in flowering time pathways similarly controlled its circadian effect. We sought to identify downstream targets of FLC regulation in the molecular mechanism of the circadian clock using genome-wide analysis to identify FLC-responsive genes and 3503 transcripts controlled by the circadian clock. A Bayesian clustering method based on Fourier coefficients allowed us to discriminate putative regulatory genes. Among rhythmic FLC-responsive genes, transcripts of the transcription factor LUX ARRHYTHMO (LUX) correlated in peak abundance with the circadian period in flc mutants. Mathematical modeling indicated that the modest change in peak LUX RNA abundance was sufficient to cause the period change due to FLC, providing a molecular target for the crosstalk between flowering time pathways and circadian regulation.
ArabidopsisPEN3/PDR8, an ATP Binding Cassette Transporter, Contributes to Nonhost Resistance to Inappropriate Pathogens That Enter by Direct Penetration
Authors: Stein Mónica , Dittgen Jan , Sánchez-Rodríguez Clara , Hou Bi-Huei , Molina Antonio , Schulze-Lefert Paul , Lipka Volker , Somerville Shauna
Published: February 2006

Arabidopsis thaliana is a host to the powdery mildew Erysiphe cichoracearum and nonhost to Blumeria graminis f. sp hordei, the powdery mildew pathogenic on barley (Hordeum vulgare). Screening for Arabidopsis mutants deficient in resistance to barley powdery mildew identified PENETRATION3 (PEN3). pen3 plants permitted both increased invasion into epidermal cells and initiation of hyphae by B. g. hordei, suggesting that PEN3 contributes to defenses at the cell wall and intracellularly. pen3 mutants were compromised in resistance to the necrotroph Plectosphaerella cucumerina and to two additional inappropriate biotrophs, pea powdery mildew (Erysiphe pisi) and potato late blight (Phytophthora infestans). Unexpectedly, pen3 mutants were resistant to E. cichoracearum. This resistance was salicylic acid–dependent and correlated with chlorotic patches. Consistent with this observation, salicylic acid pathway genes were hyperinduced in pen3 relative to the wild type. The phenotypes conferred by pen3 result from the loss of function of PLEIOTROPIC DRUG RESISTANCE8 (PDR8), a highly expressed putative ATP binding cassette transporter. PEN3/PDR8 tagged with green fluorescent protein localized to the plasma membrane in uninfected cells. In infected leaves, the protein concentrated at infection sites. PEN3/PDR8 may be involved in exporting toxic materials to attempted invasion sites, and intracellular accumulation of these toxins in pen3 may secondarily activate the salicylic acid pathway.
Arabidopsis REGULATOR OF AXILLARY MERISTEMS1Controls a Leaf Axil Stem Cell Niche and Modulates Vegetative Development
Authors: Keller Thomas , Abbott Jessica , Moritz Thomas , Doerner Peter
Published: February 2006

Shoot branching is a major determinant of variation in plant stature. Branches, which form secondary growth axes, originate from stem cells activated in leaf axils. The initial steps by which axillary meristems (AMs) are specified and their stem cells organized are still poorly understood. We identified gain- and loss-of-function alleles at the Arabidopsis thaliana  REGULATOR OF AXILLARY MERISTEMS1 (RAX1) locus. RAX1 is encoded by the Myb-like transcription factor MYB37 and is an Arabidopsis homolog of the tomato (Solanum lycopersicum) Blind gene. RAX1 is transiently expressed in a small central domain within the boundary zone separating shoot apical meristem and leaf primordia early in leaf primordium development. RAX1 genetically interacts with CUP-SHAPED COTYLEDON (CUC) genes and is required for the expression of CUC2 in the RAX1 expression domain, suggesting that RAX1 acts through CUC2. We propose that RAX1 functions to positionally specify a stem cell niche for AM formation. RAX1 also affects the timing of developmental phase transitions by negatively regulating gibberellic acid levels in the shoot apex. RAX1 thus defines a novel activity that links the specification of AM formation with the modulation of the rate of progression through developmental phases.
TheArabidopsis-mei2-LikeGenes Play a Role in Meiosis and Vegetative Growth inArabidopsis
Authors: Kaur Jagreet , Sebastian Jose , Siddiqi Imran
Published: February 2006

The Arabidopsis-mei2-Like (AML) genes comprise a five-member gene family related to the mei2 gene, which is a master regulator of meiosis in Schizosaccharomyces pombe and encodes an RNA binding protein. We have analyzed the AML genes to assess their role in plant meiosis and development. All five AML genes were expressed in both vegetative and reproductive tissues. Analysis of AML1-AML5 expression at the cellular level indicated a closely similar expression pattern. In the inflorescence, expression was concentrated in the shoot apical meristem, young buds, and reproductive organ primordia. Within the reproductive organs, strong expression was observed in meiocytes and developing gametes. Functional analysis using RNA interference (RNAi) and combinations of insertion alleles revealed a role for the AML genes in meiosis, with RNAi lines and specific multiple mutant combinations displaying sterility and a range of defects in meiotic chromosome behavior. Defects in seedling growth were also observed at low penetrance. These results indicate that the AML genes play a role in meiosis as well as in vegetative growth and reveal conservation in the genetic mechanisms controlling meiosis in yeast and plants.
TheArabidopsisSOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE1 Protein Complex Includes BRASSINOSTEROID-INSENSITIVE1
Authors: Karlova Rumyana , Boeren Sjef , Russinova Eugenia , Aker José , Vervoort Jacques , de Vries Sacco
Published: February 2006

Arabidopsis thaliana SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE1 (SERK1) is a leucine-rich repeat receptor-like kinase (LRR-RLK) involved in the acquisition of embryogenic competence and in male sporogenesis. To determine the composition of the SERK1 signaling complex in vivo, we generated plants expressing the SERK1 protein fused to cyan fluorescent protein under SERK1 promoter control. The membrane receptor complex was immunoprecipitated from seedlings, and the coimmunoprecipitating proteins were identified using liquid chromatography/matrix-assisted laser desorption ionization–time of flight/mass spectrometry of the trypsin-released peptides. This approach identified two other LRR-RLKs, the BRASSINOSTEROID-INSENSITIVE1 (BRI1) receptor and its coreceptor, the SERK3 or BRI1-ASSOCIATED KINASE1 protein. In addition, KINASE-ASSOCIATED PROTEIN PHOSPHATASE, CDC48A, and 14-3-3ν were found. Finally, the MADS box transcription factor AGAMOUS-LIKE15 and an uncharacterized zinc finger protein, a member of the CONSTANS family, were identified as part of the SERK1 complex. Using blue native gel electrophoresis, we show that SERK1 and SERK3 are part of BRI1-containing multiple protein complexes with relative masses between 300 and 500 kD. The SERK1 mutant allele serk1-1 enhances the phenotype of the weak BRI1 allele bri1-119. Collectively, these results suggest that apart from SERK3, SERK1 is also involved in the brassinolide signaling pathway.
SUGAR-DEPENDENT1Encodes a Patatin Domain Triacylglycerol Lipase That Initiates Storage Oil Breakdown in GerminatingArabidopsisSeeds
Authors: Eastmond Peter J.
Published: February 2006

Triacylglycerol hydrolysis (lipolysis) plays a pivotal role in the life cycle of many plants by providing the carbon skeletons and energy that drive postgerminative growth. Despite the physiological importance of this process, the molecular mechanism is unknown. Here, a genetic screen has been used to identify Arabidopsis thaliana mutants that exhibit a postgerminative growth arrest phenotype, which can be rescued by providing sugar. Seventeen sugar-dependent (sdp) mutants were isolated, and six represent new loci. Triacylglycerol hydrolase assays showed that sdp1, sdp2, and sdp3 seedlings are deficient specifically in the lipase activity that is associated with purified oil bodies. Map-based cloning of SDP1 revealed that it encodes a protein with a patatin-like acyl-hydrolase domain. SDP1 shares this domain with yeast triacylglycerol lipase 3 and human adipose triglyceride lipase. In vitro assays confirmed that recombinant SDP1 hydrolyzes triacylglycerols and diacylglycerols but not monoacylglycerols, phospholipids, galactolipids, or cholesterol esters. SDP1 is expressed predominantly in developing seeds, and a SDP1–green fluorescent protein fusion was shown to associate with the oil body surface in vivo. These data shed light on the mechanism of lipolysis in plants and establish that a central component is evolutionarily conserved among eukaryotes.
Persistence despite omnivory: benthic communities and the discrepancy between theory and observation
Authors: HilleRisLambers Reinier , Van De Koppel Johan , Herman Peter M. J.
Published: February 2006

Omnivory is omnipresent in natural communities. However, most theoretical models predict that omnivory should be rare, especially at high basal productivity. To address this incongruity, we consider as an example benthic food webs with omnivory. We present a mathematical analysis of simple benthic food webs in which a number of mechanisms promote persistence of omnivory. As a model system, we focus on the interaction between detritus, bacteria and deposit feeders that feed on both bacteria and detritus. Biomass patterns change with increasing basal productivity, triggering mechanisms that weaken the interactions between components of omnivorous interactions. Consequently, these mechanisms extend the range of organic input rates at which omnivorous interactions persist, and prevent exclusion, promoting omnivorous interactions in productive environments. These mechanisms give potential explanations for the high incidence of omnivory in benthic communities and shed insight on the persistence of omnivory in other communities.
Conditional outcomes in plant–herbivore interactions: neighbours matter
Authors: Baraza Elena , Zamora Regino , A. Hódar José
Published: February 2006

Spatial distribution of palatable and unpalatable plants can influence the foraging behaviour of herbivores, thereby changing plant‐damage probabilities. Moreover, the immediate proximity to certain plants can benefit other plants that grow below them, where toxicity or spines act as a physical barrier or concealment against herbivores. This paper presents the results of a multi‐scale experiment performed to test the effect of shrubs as protectors of tree saplings against herbivores and the mechanism involved in Mediterranean ecosystems. We performed a factorial design in two mountain ranges, similar in physiognomy and vegetation, planting saplings of a palatable tree, the maple (Acer opalus subsp. granatense), and an unpalatable tree, the black pine (Pinus nigra), under three different types of shrubs. We considered four experimental microhabitats: highly palatable shrub (Amelanchier ovalis), palatable but spiny shrub (Crataegus monogyna or Prunus ramburii), unpalatable spiny shrub (Berberis vulgaris subsp. australis) and control (gaps of bare soil without shrubs). Three main factors were found to determine the probability of sapling attack: sapling palatability, experimental microhabitat and plot. Palatable saplings (maples) were browsed much more than unpalatable ones (pines). The degree of protection provided by the shrub proved greater as its palatability decreased with respect to sapling palatability, the unpalatable spiny shrub being the safest microhabitat for palatable saplings and bare soil for unpalatable ones. The differences found in number of attacked saplings between plots may be attributable to differences in herbivore pressure. The community context in which interaction takes place, namely the characteristics of the neighbours and the intensity of herbivore pressure, are determining factors for understanding and predicting the damage undergone by a target plant species. The mechanism that best explains these results is associational avoidance of saplings that grow near to unpalatable shrubs. It is necessary to introduce this neighbour effect in theoretical models and food‐web approaches that analyse the plant–herbivore relationships, since it can strongly determine not only the intensity of the interaction, but also the spatial distribution and diversity of the plant community.
Review article: intragastric and oesophageal pH monitoring in patients with gastro‐oesophageal reflux disease
Authors: KATZ P. O.
Published: February 2006

Treatment of gastro‐oesophageal reflux disease with acid suppressive therapy is based on the principle that effective control of intragastric pH (a marker of acid control) leads to healing of erosive oesophagitis and relief of gastro‐oesophageal reflux disease‐associated symptoms.

Most patients with gastro‐oesophageal reflux disease can be managed successfully with current antisecretory therapy. In difficult‐to‐treat patients, oesophageal pH monitoring is a useful technique to assess pH control and to investigate the association of reflux with refractory symptoms.

Intragastric pH monitoring allows direct assessment of acid suppression achieved with an agent, and is the most useful for head‐to‐head comparisons of antisecretory therapies, evaluating variability in individual gastric pH response, assessing dose timing and food effect, and determining alternate dosing strategies; as such, it is useful in the research laboratory, and may be useful clinically to guide clinicians in dose titration and in evaluating the effect of switching agents.

This article reviews these and other uses of these tests in an effort to explore the question of how to optimally use oesophageal pH monitoring and gastric pH monitoring in patient management.
Review article: physiologic and clinical effects of proton pump inhibitors on non‐acidic and acidic gastro‐oesophageal reflux
Authors: MINER P. B.
Published: February 2006

The control of oesophageal acid exposure through gastric acid inhibition, as the basis for gastro‐oesophageal reflux disease (GERD) treatment, arose from the apparent pH dependency of erosive oesophagitis and relationship to GERD symptoms.

The current perception is that reflux disease is an entirely acid‐mediated condition, and antisecretory therapies, particularly proton pump inhibitors, are the treatment of choice for patients with erosive and non‐erosive reflux disease. A positive patient response to an empiric trial of proton pump inhibitor (PPI) therapy, or the ‘PPI test’, is commonly suggested as a method of GERD diagnosis.

Recent studies have modified our understanding of the relationship between oesophageal acid exposure and GERD pathology, manifestations and symptoms. Whereas the use of PPIs to reduce oesophageal acid exposure in patients with erosions is associated with increased healing rates, non‐erosive reflux disease patients are less likely to have an abnormal oesophageal pH profile. Patterns of oesophageal acid exposure, particularly nocturnal oesophageal acid exposure, have been linked to increased disease severity. Non‐acidic reflux and the effect of PPIs on this parameter, including bile reflux and the toxicity of bile acids, may also be an important factor in GERD.

This article explores some of these assumptions, practices and relationships, including: the association between oesophageal acid exposure and erosive and non‐erosive gastro‐oesophageal reflux disease; the effect of PPIs on oesophageal acid exposure in erosive oesophagitis patients; the influence of nocturnal acid secretion in GERD and the use of PPIs to control this parameter; the relevance of the PPI test for reflux disease diagnosis; and PPI influence on non‐acidic reflux.
Comparison of conventional and polymerase chain reaction diagnostic techniques for leishmaniasis in the endemic region of Adana, Turkey
Authors: Culha Gulnaz , Uzun Soner , Ozcan Kadri , Memisoglu Hamdi R. , Chang Kwang‐Poo
Published: February 2006

Background  Cutaneous leishmaniasis (CL) has long been reported in the Cukurova region. We have compared the sensitivity of the conventional methods of diagnosis by microscopy and cultivation of lesion aspirates against polymerase chain reaction (PCR) amplification of parasite‐specific DNA from these samples.

Methods  The samples (n = 25) were obtained from patients clinically diagnosed with CL at the regional dermatology clinic. Aliquots of the samples were stained with Giemsa for microscopy and cultured in Novy‐Nicolle‐McNeal (NNN) blood agar for promastigote growth. The remainder were subjected to DNA extraction for PCR amplification of the conserved region of kinetoplast minicircle DNA. PCR products of the expected size (120 bp) were observed after agarose gel electrophoresis, followed by staining with ethidium bromide.

Results  The positive rates from 25 samples were 44%, 68%, and 100% for cultivation, microscopy, and PCR, respectively.

Conclusions  The PCR method used appears to be the most sensitive for the diagnosis of CL in this region.
Acute cognitive dysfunction after hip fracture: frequency and risk factors in an optimized, multimodal, rehabilitation program
Authors: Bitsch M. S. , Foss N. B. , Kristensen B. B. , Kehlet H.
Published: February 2006

Background:  Patients undergoing hip fracture surgery often experience acute post‐operative cognitive dysfunction (APOCD). The pathogenesis of APOCD is probably multifactorial, and no single intervention has been successful in its prevention. No studies have investigated the incidence of APOCD after hip fracture surgery in an optimized, multimodal, peri‐operative rehabilitation regimen.

Methods:  One hundred unselected hip fracture patients treated in a well‐defined, optimized, multimodal, peri‐operative rehabilitation regimen were included. Patients were tested upon admission and on the second, fourth and seventh post‐operative days with the Mini Mental State Examination (MMSE) score.

Results:  Thirty‐two per cent of patients developed a significant post‐operative cognitive decline, which was associated with several pre‐fracture patient characteristics, including age and cognitive function, but also the number of peri‐operative transfusions. The development of APOCD was also associated with impaired post‐operative rehabilitation and an increased length of stay. APOCD was associated with the development of a major medical complication in 35% of all patients. In 65% of patients developing APOCD without a concomitant medical complication, the only risk factors were cognitive level and regular anti‐psychotic treatment.

Conclusion:  On the basis of current evidence, APOCD is prevalent amongst hip fracture patients despite multimodal intervention; future research should therefore focus on defining subgroups of hip fracture patients amenable to specific prophylactic or interventional measures against APOCD.
Neuropathic pain is enhanced in δ‐opioid receptor knockout mice
Authors: Nadal Xavier , Baños Josep‐Eladi , Kieffer Brigitte L. , Maldonado Rafael
Published: February 2006

We have evaluated the possible involvement of δ‐opioid receptor (DOR) in the development and expression of neuropathic pain. For this purpose, partial ligation of the sciatic nerve was performed in DOR knockout mice and wild‐type littermates. The development of mechanical and thermal allodynia, as well as thermal hyperalgesia was evaluated by using the von Frey filament model, the cold‐plate test and the plantar test, respectively. In wild‐type and DOR knockout mice, sciatic nerve injury led to a neuropathic pain syndrome revealed in these nociceptive behavioural tests. However, the development of mechanical and thermal allodynia, and thermal hyperalgesia was significantly enhanced in DOR knockout mice. These results reveal the involvement of DOR in the control of neuropathic pain and suggest a new potential therapeutic use of DOR agonists.
Localization of a vocal pattern generator in the pontine brainstem of the squirrel monkey
Authors: Hage Steffen R. , Jürgens Uwe
Published: February 2006

Very little is known about the coordination of muscles involved in mammalian vocalization at the level of single neurons. In the present study, a telemetric single‐unit recording technique was used to explore the ventrolateral pontine brainstem for vocalization‐correlated activity in the squirrel monkey during vocal communication. We found a discrete area in the reticular formation just above the superior olivary complex showing vocalization‐correlated activity. These neurons showed an increase in neuronal activity exclusively just before and during vocalization; none of them was active during mastication, swallowing or quiet respiration. Furthermore, the neuronal activity of these neurons reflected acoustic features, such as call duration or syllable structure of frequency‐modulated vocalization, directly. Based on these findings and previously reported anatomical data, we propose that this area serves as a vocal pattern generator for frequency‐modulated call types.