bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

AbstractMotivation: 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 fromContact: hochreit@bioinf.jku.atSupplementary information:
Non-linear tests for identifying differentially expressed genes or genetic networks
Authors: Xiong Hao 
Published: February 2006

AbstractMotivation: 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.eduSupplementary 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

Abstract
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

Abstract
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

AbstractMotivation: 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

Abstract
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

Abstract
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

Abstract
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
Double-Strand Break Repair in Plants Is Developmentally Regulated
Authors: Boyko Alexander , Zemp Franz , Filkowski Jody , Kovalchuk Igor 
Published: February 2006

Abstract
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

AbstractTemperature 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

AbstractArabidopsis 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

AbstractShoot 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

AbstractThe 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.