bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antiarrhythmic Effects of JTV‐519, a Novel Cardioprotective Drug, on Atrial Fibrillation/Flutter in a Canine Sterile Pericarditis Model
Authors: Kumagai Koichiro , Nakashima Hideko , Gondo Naoki , Saku Keijiro 
Published: July 2003

Introduction: A new cardioprotective drug, JTV‐519, blocks Na+ current and inwardly rectifying K+ current and inhibits Ca2+ current. However, its role in atrial electrophysiology is unknown. We investigated the antiarrhythmic effects of JTV‐519 on atrial fibrillation/flutter in the canine sterile pericarditis model. Methods and Results: In nine dogs with sterile pericarditis, 38 episodes of sustained (>30 sec) atrial fibrillation (8 dogs) and 24 episodes of sustained atrial flutter (7 dogs) were induced by rapid atrial pacing. When atrial fibrillation or atrial flutter was sustained >15 minutes, it was cardioverted and reinduced. The inducibility of atrial fibrillation/flutter, the atrial effective refractory period, and the intra‐atrial conduction time were compared before and after the continuous infusion of JTV‐519 (0.03 mg/kg/min). JTV‐519 significantly decreased the mean number of sustained atrial fibrillation episodes (from 4.2 ± 2.9 to 0 ± 0, P < 0.01). In contrast, atrial flutter was still inducible in 4 dogs after JTV‐519 (from 2.7 ± 2.5 to 1.6 ± 2.1, P = NS). JTV‐519 significantly prolonged effective refractory period (from 123 ± 18 to 143 ± 14 msec, from 127 ± 18 to 151 ± 12 msec, and from 132 ± 13 to 159 ± 9 msec at basic cycle lengths of 200, 300, and 400 msec, respectively, P < 0.01), but it did not affect the intra‐atrial conduction time (from 47 ± 11 msec to 48 ± 11 msec, P = NS). Conclusion: JTV‐519 had significant protective effects on atrial fibrillation in the canine sterile pericarditis model, mainly by increasing effective refractory period, suggesting that it may have potential as a novel antiarrhythmic agent for atrial fibrillation. (J Cardiovasc Electrophysiol, Vol. 14, pp. 880‐884, August 2003)
Safety and Efficacy of Cryoablation of Accessory Pathways Adjacent to the Normal Conduction System
Authors: Gaita Fiorenzo , Riccardi Riccardo , Hocini Meleze , Haissaguerre Michel , Giustetto Carla , Jais Pierre , Grossi Stefano , Caruzzo Enrico , Bianchi Francesca , Richiardi Elena 
Published: July 2003

Introduction: Catheter ablation has become a routine treatment for patients with Wolff‐Parkinson‐White syndrome because of its low risk and high efficacy; however, radiofrequency ablation in the septum close to the AV node or His bundle still carries a definite risk for AV block. Cryoenergy catheter ablation has recently become available. This technique has specific features, such as the ability to create reversible loss of function to predict the effects of ablation (ice mapping) and the adherence of the catheter tip to the endocardium with freezing, which avoids the risk for dislodgment. Both of these characteristics may minimize the risk of complications. The aim of this study was to analyze the effectiveness and safety of catheter cryoablation in 20 patients with para‐Hisian or midseptal accessory pathways (AP). Methods and Results: Eleven patients with para‐Hisian and 9 patients with midseptal AP underwent catheter cryoablation. Ice mapping at −30°C was performed to ascertain the disappearance of AP conduction and the absence of impairment of AV nodal conduction. If the expected result was obtained, cryoablation was performed by lowering the temperature to −75°C for 4 minutes in order to create a permanent lesion. Cryoablation was successful in all patients using a mean of 1.2 ± 0.4 applications. Recurrences occurred in 4 patients (20%) who underwent a second successful cryoablation session. No complications were observed. Conclusion: Cryoablation appears to be a safe and effective technique for ablation of APs close to the AV node or His bundle because of the ability to predict the acute effects of ablation with ice mapping before creation of an irreversible lesion. (J Cardiovasc Electrophysiol, Vol. 14, pp. 825‐829, August 2003)
Heterogeneous Regional Endocardial Repolarization is Associated with Increased Risk for Ischemia‐Dependent Ventricular Fibrillation after Myocardial Infarction
Authors: Swann Michael H. , Nakagawa Hiroshi , Vanoli Emilio , Lazzara Ralph , Schwartz Peter J. , Adamson Philip B. 
Published: July 2003

Introduction: The aim of this study was to investigate whether the characteristics of endocardial ventricular repolarization are associated with differential risk for sudden death. Prolonged surface QT interval is associated with increased arrhythmic risk after myocardial infarction (MI), but the underlying mechanism of QT prolongation and its relation to lethal arrhythmias are unclear. Methods and Results: Ventricular fibrillation (VF) risk was assessed in 12 dogs 1 month after anterior MI during an exercise test coupled with brief circumflex coronary occlusion. Susceptible dogs (n = 5) developed VF during the brief ischemic episode, whereas resistant dogs did not (n = 7). Surface QT interval was measured at rest. Endocardial electroanatomic catheter maps of left ventricular repolarization were obtained in four unique regions identified by echocardiography and compared between groups. Compared to resistant dogs, susceptible dogs were characterized by prolonged surface QT intervals (240 ± 10 msec vs 222 ± 7 msec, P = 0.04). In addition, they had lower baroreflex sensitivity (9.7 ± 1.5 msec/mmHg vs 28 ± 9.8 msec/mmHg, P < 0.01) and a tachycardic response to acute ischemia suggesting higher propensity for stronger sympathetic reflexes. Surface QT interval prolongation in susceptible dogs was due to a marked heterogeneity of endocardial left ventricular repolarization (239 ± 42 msec, basal anterior wall vs 197 ± 35, lateral wall; P < 0.001). Resistant animals had no regional differences in endocardial repolarization. Conclusion: Sympathetic activation following MI not only produces adverse structural remodeling but also contributes to adverse electrophysiologic remodeling resulting in heterogeneous ventricular repolarization and in a myocardial substrate conducive to lethal reentrant arrhythmias. (J Cardiovasc Electrophysiol, Vol. 14, pp. 873‐879, August 2003)
Clinical usefulness of head-up tilt test in patients with syncope and intraventricular conduction defect
Authors: Sagristà-Sauleda J. , Romero B. , Permanyer-Miralda G. , Moya A. , Rius-Gelabert T. , Mont Girbau L. , Soler-Soler J. 
Published: July 2003

Abstract
Head-up tilt test was performed in 99 patients with syncope of unknown origin and intraventricular conduction defect. Twenty-five per cent had a positive response to tilt with reproduction of spontaneous clinical symptoms. Holter recording revealed paroxysmal atrioventricular (AV) block in three patients. Carotid sinus massage was positive in four patients. An electrophysiological study was performed in 76 patients with abnormal findings in 17 (22%). Thus, vasovagal syncope was the discharge diagnosis in 25 patients (25%). Therefore, tilt test should be considered in patients with intraventricular conduction defect presenting with syncope of unknown origin, especially if clinical findings suggest the possibility of a vasovagal mechanism, or if the results of the electrophysiological study are inconclusive.
Quantitative quality control in microarray
experiments and the application in data filtering,
normalization and false positive rate prediction
Authors: Wang Xujing , Hessner Martin J. , Wu Yan , Pati Nirupma , Ghosh Soumitra 
Published: July 2003

Abstract
Abstract: Data preprocessing including proper normalization and adequate quality control before complex data mining is crucial for studies using the cDNA microarray technology. We have developed a simple procedure that integrates data filtering and normalization with quantitative quality control of microarray experiments. Previously we have shown that data variability in a microarray experiment can be very well captured by a quality score qcom that is defined for every spot, and the ratio distribution depends on qcom. Utilizing this knowledge, our data-filtering scheme allows the investigator to decide on the filtering stringency according to desired data variability, and our normalization procedure corrects the qcom-dependent dye biases in terms of both the location and the spread of the ratio distribution. In addition, we propose a statistical model for false positive rate determination based on the design and the quality of a microarray experiment. The model predicts that a lower limit of 0.5 for the replicate concordance rate is needed in order to be certain of true positives. Our work demonstrates the importance and advantages of having a quantitative quality control scheme for microarrays.
Contact: xujing@mcw.edu
* To whom correspondence should be addressed.
ESTprep: preprocessing cDNA sequence reads
Authors: Scheetz Todd E. , Trivedi Nishank , Roberts Chad A. , Kucaba Tamara , Berger Brian , Robinson Natalie L. , Birkett Clayton L. , Gavin Allen J. , O’Leary Brian , Braun Terry A. , Bonaldo Maria F. , Robinson John P. , Sheffield Val C. , Soares Marcelo B. , Casavant Thomas L. 
Published: July 2003

Abstract
Motivation: High accuracy of data always governs the large-scale gene discovery projects. The data should not only be trustworthy but should be correctly annotated for various features it contains. Sequence errors are inherent in single-pass sequences such as ESTs obtained from automated sequencing. These errors further complicate the automated identification of EST-related sequencing. A tool is required to prepare the data prior to advanced annotation processing and submission to public databases.
Results: This paper describes ESTprep, a program designed to preprocess expressed sequence tag (EST) sequences. It identifies the location of features present in ESTs and allows the sequence to pass only if it meets various quality criteria. Use of ESTprep has resulted in substantial improvement in accurate EST feature identification and fidelity of results submitted to GenBank.
Availability: The program is freely available for download from http://genome.uiowa.edu/pubsoft/software.html
Contact: tscheetz@eng.uiowa.edu
* To whom correspondence should be addressed.
Design and assessment of a fast algorithm for
identifying specific probes for human and mouse genes
Authors: Chang Pei-chin , Peck Konan 
Published: July 2003

Abstract
Motivation: Mammalian genomes are highly complex. To identify the unique sequences of each gene in a mammalian gene database containing tens of thousands of DNA sequences is a computation intensive task. With the advent of parallel genetic analysis methods such as microarrays and the availability of more and more whole genome sequences of organisms, an algorithm allowing speedy identification of the unique gene probes for functional studies of individual genes will be a very useful tool.
Results: We have developed a fast algorithm as well as a software program based on the algorithm for identifying gene specific probes of complex organisms. The algorithm was applied to the assemblies of gene sequences and was highly efficient for large databases such as the TIGR human THC and mouse TC databases. The results were assessed with the BLAST sequence alignment software. Two probe data sets have been compiled to contain specific probes for around 100 000 putative human gene transcripts and 70 000 putative mouse gene transcripts.
Availability: The gene specific probes for the putative human and mouse genes referenced in the TIGR gene indices are available at: ftp://genestamp.ibms.sinica.edu.tw/pub/SpecificP/. The software program and the source codes are available upon request.
Contact: konan@ibms.sinica.edu.tw
* To whom correspondence should be addressed.
Noise sampling method: an ANOVA approach
allowing robust selection of differentially regulated
genes measured by DNA microarrays
Authors: Draghici Sorin , Kulaeva Olga , Hoff Bruce , Petrov Anton , Shams Soheil , Tainsky Michael A. 
Published: July 2003

Abstract
Motivation: A crucial step in microarray data analysis is the selection of subsets of interesting genes from the initial set of genes. In many cases, especially when comparing a specific condition to a reference, the genes of interest are those which are differentially expressed. Two common methods for gene selection are: (a) selection by fold difference (at least n fold variation) and (b) selection by altered ratio (at least n standard deviations away from the mean ratio).
Results: The novel method proposed here is based on ANOVA and uses replicate spots to estimate an empirical distribution of the noise. The measured intensity range is divided in a number of intervals. A noise distribution is constructed for each such interval. Bootstrapping is used to map the desired confidence levels from the noise distribution corresponding to a given interval to the measured log ratios in that interval. If the method is applied on individual arrays having replicate spots, the method can calculate an overall width of the noise distribution which can be used as an indicator of the array quality. We compared this method with the fold change and unusual ratio method. We also discuss the relationship with an ANOVA model proposed by Churchill et al.
In silico experiments were performed while controlling the degree of regulation as well as the amount of noise. Such experiments show the performance of the classical methods can be very unsatisfactory. We also compared the results of the 2-fold method with the results of the noise sampling method using pre and post immortalization cell lines derived from the MDAH041 fibroblasts hybridized on Affymetrix GeneChip arrays. The 2-fold method reported 198 genes as upregulated and 493 genes as downregulated. The noise sampling method reported 98 gene upregulated and 240 genes downregulated at the 99.99% confidence level. The methods agreed on 221 genes downregulated and 66 genes upregulated. Fourteen genes from the subset of genes reported by both methods were all confirmed by Q-RT-PCR. Alternative assays on various subsets of genes on which the two methods disagreed suggested that the noise sampling method is likely to provide fewer false positives.
Contact: sod@cs.wayne.edu
* To whom correspondence should be addressed.
† The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
A comparison of physical mapping algorithms
based on the maximum likelihood model
Authors: Huang Jinling , Bhandarkar Suchendra M. 
Published: July 2003

Abstract
Motivation: Physical mapping of chromosomes using the maximum likelihood (ML) model is a problem of high computational complexity entailing both discrete optimization to recover the optimal probe order as well as continuous optimization to recover the optimal inter-probe spacings. In this paper, two versions of the genetic algorithm (GA) are proposed, one with heuristic crossover and deterministic replacement and the other with heuristic crossover and stochastic replacement, for the physical mapping problem under the maximum likelihood model. The genetic algorithms are compared with two other discrete optimization approaches, namely simulated annealing (SA) and large-step Markov chains (LSMC), in terms of solution quality and runtime efficiency.
Results: The physical mapping algorithms based on the GA, SA and LSMC have been tested using synthetic datasets and real datasets derived from cosmid libraries of the fungus Neurospora crassa. The GA, especially the version with heuristic crossover and stochastic replacement, is shown to consistently outperform the SA-based and LSMC-based physical mapping algorithms in terms of runtime and final solution quality. Experimental results on real datasets and simulated datasets are presented. Further improvements to the GA in the context of physical mapping under the maximum likelihood model are proposed.
Availability: The software is available upon request from the first author.
Contact: tupistra@yahoo.com
* To whom correspondence should be addressed.
† Present address: Center for Tropical and Emerging Global Diseases, 623 Biological Science Building, University of Georgia, Athens, GA 30602, USA.
On the use of permutation in and the performance
of a class of nonparametric methods to detect
differential gene expression
Authors: Pan Wei 
Published: July 2003

Abstract
Motivation: Recently a class of nonparametric statistical methods, including the empirical Bayes (EB) method, the significance analysis of microarray (SAM) method and the mixture model method (MMM), have been proposed to detect differential gene expression for replicated microarray experiments conducted under two conditions. All the methods depend on constructing a test statistic Z and a so-called null statistic z. The null statistic z is used to provide some reference distribution for Z such that statistical inference can be accomplished. A common way of constructing z is to apply Z to randomly permuted data. Here we point our that the distribution of z may not approximate the null distribution of Z well, leading to possibly too conservative inference. This observation may apply to other permutation-based nonparametric methods. We propose a new method of constructing a null statistic that aims to estimate the null distribution of a test statistic directly.
Results: Using simulated data and real data, we assess and compare the performance of the existing method and our new method when applied in EB, SAM and MMM. Some interesting findings on operating characteristics of EB, SAM and MMM are also reported. Finally, by combining the idea of SAM and MMM, we outline a simple nonparametric method based on the direct use of a test statistic and a null statistic.
Contact: weip@biostat.umn.edu
2HAPI: a microarray data analysis system
Authors: Fink J. Lynn , Drewes Scott , Patel Hiren , Welsh John B. , Masys Daniel R. , Corbeil Jacques , Gribskov Michael 
Published: July 2003

Abstract
Summary: 2HAPI (version 2 of High density Array Pattern Interpreter) is a web-based, publicly-available analytical tool designed to aid researchers in microarray data analysis. 2HAPI includes tools for searching, manipulating, visualizing, and clustering the large sets of data generated by microarray experiments. Other features include association of genes with NCBI information and linkage to external data resources. Unique to 2HAPI is the ability to retrieve upstream sequences of co-regulated genes for promoter analysis using MEME (Multiple Expectation-maximization for Motif Elicitation)
Availability: 2HAPI is freely available at http://array.sdsc.edu. Users can try 2HAPI anonymously with pre-loaded data or they can register as a 2HAPI user and upload their data.
Contact: gribskov@sdsc.edu
* To whom correspondence should be addressed.
GeneTRACE–reconstruction of gene content of ancestral species
Authors: Kunin Victor , Ouzounis Christos A. 
Published: July 2003

Abstract
While current computational methods allow the reconstruction of individual ancestral protein sequences, reconstruction of complete gene content of ancestral species is not yet an established task. In this paper, we describe GeneTrace, an efficient linear-time algorithm that allows the reconstruction of evolutionary history of individual protein families as well as the complete gene content of ancestral species. The performance of the method was validated with a simulated evolution program called SimulEv. Our results indicate that given a set of correct phylogenetic profiles and a correct species tree, ancestral gene content can be reconstructed with sensitivity and selectivity of more than 90%. SimulEv simulations were also used to evaluate performance of the reconstruction of gene content-based phylogenetic trees, suggesting that these trees may be accurate at the terminal branches but suffer from long branch attraction near the root of the tree.
Contact: ouzounis@ebi.ac.uk
* To whom correspondence should be addressed.
POAVIZ: a Partial Order Multiple Sequence Alignment Visualizer
Authors: Grasso Catherine , Quist Michael , Ke Kevin , Lee Christopher 
Published: July 2003

Abstract
Summary: POAVIZ creates a visualization of a multiple sequence alignment that makes clear the overall structure of how sequences match and diverge in the alignment. POAVIZ can construct visualizations from any multiple sequence alignment source (e.g. PIR and CLUSTAL formats), and is valuable for revealing complex branching structure (such as domains, large-scale insertions / deletions or recombinations), especially in partnership with the Partial Order Alignment (POA) multiple sequence alignment program.
Availability: The Partial Order multiple sequence Alignment Visualizer (POAVIZ) program is available at http://www.bioinformatics.ucla.edu/poa
Contact: leec@mbi.ucla.edu
* To whom correspondence should be addressed.
Estimation of transformation parameters for microarray data
Authors: Durbin Blythe , Rocke David M. 
Published: July 2003

Abstract
Motivation and Results: Durbin et al. (2002), Huber et al. (2002) and Munson (2001) independently introduced a family of transformations (the generalized-log family) which stabilizes the variance of microarray data up to the first order. We introduce a method for estimating the transformation parameter in tandem with a linear model based on the procedure outlined in Box and Cox (1964). We also discuss means of finding transformations within the generalized-log family which are optimal under other criteria, such as minimum residual skewness and minimum mean-variance dependency.
Availability: R and Matlab code and test data are available from the authors on request.
Contact: bpdurbin@ucdavis.edu
* To whom correspondence should be addressed.
Teacher‐pupil dialogue in the guided reading session
Authors: Skidmore David , Perez‐Parent Montserrat , Arnfield Simon 
Published: July 2003

AbstractDrawing on the findings of an ESRC‐funded project, this article concerns the quality of teacher‐pupil dialogue in the guided reading session of the Literacy Hour and its relationship to pupils' powers of comprehension. We recorded and analysed examples of discussions during the guided reading session in four primary schools, visiting each of them three times. On each school visit, we recorded the same group of six Year 6 children (10–11‐year‐olds) working with their class teacher. The results of the study suggest that talk in this context is teacher‐dominated. The teacher: usually asks questions to which s/he already knows the answer; normally selects which pupil is going to speak next; keeps a tight grip on the topic of conversation; and does most of the talking. We argue that there is a case for making time available during the guided reading session for a period of discussion in which pupils are invited to play a more leading role in shaping the topic of conversation.
Face‐to‐face talk to support computer‐mediated discussion in a primary school literacy practice
Authors: Staarman Judith Kleine 
Published: July 2003

AbstractIn this study, Dutch primary school children used a computer‐mediated discussion forum to discuss the concept of horror stories. In such discussion forums children often write their contributions individually. This paper presents an ongoing empirical study in which the contributions to an electronic discussion forum from children working individually were compared to contributions from children working in dyads. Preliminary results indicated that children working in dyads around the computer wrote more contributions to the computer‐mediated discussion and were more attentive to the collaborative process, than children who wrote their contributions individually.