bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inhibitors of the Na+/H+ Exchanger Cannot Prevent Atrial Electrical Remodeling in the Goat
Authors: BLAAUW YURI , BEIER NORBERT , VAN DER VOORT PEPIJN , VAN HUNNIK ARNE , SCHOTTEN ULRICH , ALLESSIE MAURITS A. 
Published: April 2004

Introduction: It has been suggested that blockade of the Na+/H+ exchanger (NHE1) can prevent atrial fibrillation (AF)‐induced electrical remodeling and the development of AF. Methods and Results: AF was maintained by burst pacing in 10 chronically instrumented conscious goats. Intravenous and oral dosages of two NHE1 blockers (EMD87580 and EMD125021) resulted in plasma levels several magnitudes higher than required for effective NHE1 blockade. Shortening of atrial refractoriness immediately after 5 minutes of AF was not prevented by NHE1 blockade. In remodeled atria, increasing dosages of EMD87580 and EMD125021 did not reverse shortening of the atrial refractory period or reduce the duration of AF episodes. The cycle length during persistent AF also was not affected. Oral pretreatment with EMD87580 (8 mg/kg bid) starting 3 days before AF could not prevent electrical remodeling. After 24 and 48 hours of remodeling, the duration of AF paroxysms was 47 ± 32 seconds and 135 ± 63 seconds compared to 56 ± 17 seconds and 136 ± 52 seconds in placebo‐treated animals (P > 0.8), respectively. Conclusion: In the goat model of AF, the Na+/H+ exchanger inhibitors EMD87580 and EMD125021 did not prevent or revert AF‐induced electrical remodeling. This indicates that activation of the Na+/H+ exchanger is not involved in the intracellular pathways of electrical remodeling. This does not support the suggestion that blockers of the Na+/H+ exchanger may be beneficial for prevention and treatment of AF. (J Cardiovasc Electrophysiol, Vol. 15, pp. 440‐446, April 2004)
Low‐Affinity Nerve Growth Factor Receptor p75NTR Immunoreactivity in the Myocardium with Sympathetic Hyperinnervation
Authors: ZHOU SHENGMEI , CAO JI‐MIN , SWISSA MOSHE , GONZALEZ‐GOMEZ IGNACIO , CHANG CHE‐MING , CHIEN KAI , MIYAUCHI YASUSHI , FU KATHERINE J. , YI JOHNNY , ASOTRA KAMLESH , KARAGUEUZIAN HRAYR S. , FISHBEIN MICHAEL C. , CHEN PENG‐SHENG , CHEN LAN S. 
Published: April 2004

Introduction: We previously demonstrated the relationship between sympathetic nerve density in myocardium and the occurrences of ventricular arrhythmia. Nerve growth factor (NGF) regulates myocardial sympathetic innervation. However, it is unclear whether the NGF high‐affinity receptor tyrosine kinase A (TrkA) and the NGF low‐affinity receptor p75NTR are altered in the state of sympathetic hyperinnervation in the heart. The aim of this study was to determine the density and location of TrkA and p75NTR in canine ventricles with sympathetic hyperinnervation. Methods and Results: Myocardial sympathetic hyperinnervation was induced by local infusion of NGF into myocardium or left stellate ganglia, or chronic subthreshold electric stimulation to the left stellate ganglia. The results showed that TrkA immunoreactivity was absent in the myocardium. Low‐affinity receptor p75NTR immunoreactivity was present in axons, Schwann cells, and interstitial cells of sympathetic nerves, as well as in interstitial cells of the myocardium. The density of p75NTR immunolabeled myocardial interstitial cells at the NGF infusion site was lower than that at the site remote from NGF infusion, yet the sympathetic nerve density was higher at the infusion site than the remote area. The density of p75NTR also was lower in the myocardium with high sympathetic nerve density, induced by NGF infusion or chronic electric stimulation of the left stellate ganglia, compared to control groups. Conclusion: The data indicate that p75NTR may be the main NGF receptor in the myocardium, and p75NTR immunopositive interstitial cells may have a role in regulating sympathetic nerve growth in canine heart. (J Cardiovasc Electrophysiol, Vol. 15, pp. 430‐437, April 2004)
High‐Resolution Mapping Around the Crista Terminalis During Typical Atrial Flutter:
Authors: TAI CHING‐TAI , HUANG JIN‐LONG , LEE PI‐CHANG , DING YU‐AN , CHANG MAU‐SONG , CHEN SHIH‐ANN 
Published: April 2004

Introduction: The aim of this study was to delineate activation patterns around the crista terminalis (CT) using high‐resolution noncontact mapping. Methods and Results: Twenty‐six patients with typical atrial flutter (20 counterclockwise and 6 clockwise) were enrolled in the study. A noncontact mapping system was used to map atrial flutter. There were three activation patterns around the line(s) of block. Type I (n = 6) showed activation around a single complete line of block located in the CT. Type II (n = 17) showed activation around a single incomplete line of block with a conduction gap in the CT. Type III (n = 3) showed activation around double lines of block, one located in the CT and the other located in the sinus venosa region. Simultaneous activation around the tricuspid annulus and through the CT gap could result in double loop reentry (n = 12). After successful ablation of the cavotricuspid isthmus (CTI) in 24 patients, upper loop reentry was still induced in 12 patients with double loop reentry. Subsequent ablation of the CT gap was performed successfully in these 12 patients, and no arrhythmia was inducible thereafter. During the follow‐up period of 8.4 ± 4.1 months, there was no recurrence of atrial flutter in any patient. Conclusion: During typical atrial flutter, the CT might be an incomplete barrier. Simultaneous conduction through the CTI and CT gap could result in double loop reentry. Radiofrequency ablation of the CTI and CT gap was effective in eliminating this arrhythmia. (J Cardiovasc Electrophysiol, Vol. 15, pp. 406‐414, April 2004)
Effect of Uvulopalatopharyngoplasty and Genial and Hyoid Advancement on Swallowing in Patients with Obstructive Sleep Apnea Syndrome
Authors: Altman Jerald S. , Halpert Robert D. , Mickelson Samuel A. , Senior Brent A. 
Published: April 2004

OBJECTIVEUvulopalatopharyngoplasty (UPPP) and genial and hyoid advancement (GHA) are surgical techniques for the treatment of obstructive sleep apnea. These techniques enlarge the oropharyngeal and hypopharyngeal airway, reducing collapse at these levels. This study evaluated the effect of these procedures on swallowing.METHODSFifteen patients who had undergone UPPP and GHA were evaluated with a modified barium swallow to assess biomechanical changes in swallowing. Specifically, velopharyngeal insufficiency; changes in tongue‐base movement, laryngeal elevation, and closure; epiglottic movement; and pharyngoesophageal opening were examined. A brief swallowing questionnaire was administered to assess for subjective changes in swallowing.RESULTSNine of 15 patients demonstrated abnormal objective swallow, of whom 5 reported normal subjective swallowing. Six of 15 demonstrated normal objective swallowing. Of these, 5 reported subjective change.CONCLUSIONUPPP with GHA may alter biomechanical events during deglutition. However, little correlation exists between subjective symptoms and objective findings. Further studies that include preoperative and postoperative modified barium swallows are needed to identify a cause‐and‐effect relationship. (Otolaryngol Head Neck Surg 1999;120:454‐7.)
Direct Round Window Membrane Application of Gentamicin in the Treatment of Meniere's Disease
Authors: Silverstein Herbert , Arruda Johnny , Rosenberg Seth I. , Deems Daniel , Hester T. Oma 
Published: April 2004

OBJECTIVETo evaluate the effectiveness of the round window membrane (RWM) Gelfoam gentamicin technique in patients with Meniere's disease who were unresponsive to medical management or in whom surgical therapy failed.STUDY DESIGNProtocol 1, single intratympanic gentamicin infusion; protocol 2 (the best method), 2 infusions, 5 days apart with reevaluation at 1 month; and protocol 3, multiple infusions 1 to 4 weeks apart.PATIENTSIn total, 32 patients (19 male, 13 female) were enrolled in the study. The mean age was 65 years (range 34 to 94 years). Seven of these patients were surgical salvage cases.INTERVENTIONSLaser‐assisted otoendoscopy with a 1.7‐mm otoendoscope (Smith‐Nephew Richards, Memphis, TN) was performed first. If the RWM was obscured by mucosa or adhesions, these were cleared before placing a 2 × 3 mm piece of dry Gelfoam against the RWM. Buffered gentamicin (26.7 mg/mL) was then injected into the middle ear (0.2 to 0.3 mL).RESULTSOverall, vertigo was controlled in 75% of the patients after the completion of the treatment, with subtotal vestibular ablation in two thirds of patients. Hearing was preserved in 90% of the patients (within 15 dB pure‐tone average or 15% speech discrimination score), tinnitus improved in 48%, and aural pressure improved in 62.5%.
Pharyngeal pH Monitoring in Patients with Posterior Laryngitis
Authors: Ulualp Seckin O. , Toohill Robert J. , Hoffmann Raymond , Shaker Reza 
Published: April 2004

OBJECTIVETo evaluate the diagnostic value of 3‐site 24‐hour ambulatory pH monitoring in patients with posterior laryngitis (PL) and the prevalence of esophageal abnormalities in this patient group.METHODSTwenty patients with PL and 17 healthy volunteers were studied as controls. Control subjects had transnasal esophagogastroduodenoscopy (T‐EGD) and ambulatory pH monitoring. Patients underwent T‐EGD, ambulatory pH monitoring, and barium esophagram.RESULTST‐EGD documented no abnormality in controls. Esophagitis was present in 2 PL patients, and hiatal hernia in 3. Ambulatory pH monitoring showed that 15 PL patients and 2 controls exhibited pharyngeal acid reflux. Barium esophagram documented gastroesophageal reflux in 5 PL patients. However, none of these barium reflux events reached the pharynx. All PL patients with barium esophagram evidence of gastroesophageal reflux also showed pharyngeal acid reflux by pH monitoring.CONCLUSIONPharyngeal acid reflux is more prevalent in patients with PL than in healthy controls. Patients with PL infrequently have esophageal sequelae of reflux disease. Ambulatory 24‐hour simultaneous 3‐site pharyngoesophageal pH monitoring detects gastroesophagopharyngeal acid reflux events in most patients with PL.
Stage Grouping Reliability: TNM '97 versus TANIS in Laryngeal Cancer
Authors: Carinci Francesco , Farina Antonio , Pelucchi Stefano , Pastore Antonio , Longhini Luca , Urso Richard G. , Calearo Carlo 
Published: April 2004

PURPOSETo compare the correlation of TANIS and TNM '97 with the survival rate in laryngeal cancer.METHODS AND MATERIALFrom 1970 to 1990, 599 patients at the ENT Clinic, University of Ferrara, had a complete follow‐up and met the criteria of enrollment. Data were analyzed by means of survival analyses (Kaplan‐Meier and Cox algorithms).RESULTSBoth systems showed a significant correlation with the survival rate. TANIS advanced subcategories were better correlated with the mortality rate than TNM stages IVa and IVb. Again, in the final statistical model, TANIS was more highly correlated with survival rate than TNM.
Constructing an enzyme-centric view of metabolism
Authors: Horne A. B. , Hodgman T. C. , Spence H. D. , Dalby A. R. 
Published: April 2004

Abstract
Motivation: The current paradigm for viewing metabolism, such as the Boehringer Chart or KEGG, takes a metabolite-centric view that is not ideal for genomics analysis because the same enzyme can appear in multiple places. Therefore an enzyme-centric view is also required.
Results: We have eliminated synonymous compound names taken from the ENZYME database ensuring that it is computationally parseable at all levels. Based on these results, we have written a software to create enzyme-centric graphs from reaction data, and we have created a second dataset with hub molecules removed, allowing a greater depth of information to be extracted from these graphs. We also present a detailed analysis of the various stages of the reconditioning process and the characteristics of the subgraphs resulting from the application of our software to the revised datasets.
Availability: Complete datasets and supplementary material may be downloaded from http://helix.ex.ac.uk/metabolism. The software for the creation of enzyme-centric graphs from reaction data is available on request from the authors.
Web-based kinetic modelling using JWS Online
Authors: Olivier Brett G. , Snoep Jacky L. 
Published: April 2004

Abstract
Summary: JWS Online is a repository of kinetic models, describing biological systems, which can be interactively run and interrogated over the Internet. It is implemented using a client–server strategy where the clients, in the form of web browser based Java applets, act as a graphical interface to the model servers, which perform the required numerical computations.
Availability: The JWS Online website is publicly accessible at http://jjj.biochem.sun.ac.za/ with mirrors at http://www.jjj.bio.vu.nl/ and http://jjj.vbi.vt.edu/
Speeding up whole-genome alignment by indexing frequency vectors
Authors: Kahveci Tamer , Ljosa Vebjorn , Singh Ambuj K. 
Published: April 2004

Abstract
Motivation: Many biological applications require the comparison of large genome strings. Current techniques suffer from high computational and I/O costs.
Results: We propose an efficient technique for local alignment of large genome strings. A space-efficient index is computed for one string, and the second string is compared with this index in order to prune substring pairs that do not contain similar regions. The remaining substring pairs are handed to a hash-table-based tool, such as BLAST, for alignment. A dynamic strategy is employed to optimize the number of disk seeks needed to access the hash table. Additionally, our technique provides the user with a coarse-grained visualization of the similarity pattern, quickly and before the actual search. The experimental results show that our technique aligns genome strings up to two orders of magnitude faster than BLAST. Our technique can be used to accelerate other search tools as well.
Availability: A web-based demo can be found at http://bioserver.cs.ucsb.edu/. Source code is available from the authors on request.
GeConT: gene context analysis
Authors: Ciria R. , Abreu-Goodger C. , Morett E. , Merino E. 
Published: April 2004

Abstract
Summary: The fact that adjacent genes in bacteria are often functionally related is widely known. GeConT (Gene Context Tool) is a web interface designed to visualize genome context of a gene or a group of genes and their orthologs in all the completely sequenced genomes. The graphical information of GeConT can be used to analyze genome annotation, functional ortholog identification or to verify the genomic context congruence of any set of genes that share a common property.
Availability: http://www.ibt.unam.mx/biocomputo/gecont.html
An examination of the conservation of surface patch polarity for proteins
Authors: Shanahan H. P. , Thornton J. M. 
Published: April 2004

Abstract
Motivation: The solubility of a protein is crucial for its function and is therefore an evolutionary constraint. As the solubility of a protein is related to the distribution of polar and hydrophobic residues on its solvent accessible surface, such a constraint should provide a valuable insight into the evolution of protein surfaces. We examine how the surfaces of proteins have evolved by considering how the average hydrophobicities of patches of surface residues vary across homologous proteins. We derive distributions for the average hydrophobicity/philicity of surface patches at a residue-based level—which we refer to as the residue hydrophobic density. This is computed for a set of 28 monomeric proteins and their homologues. The resulting distributions are compared with a set of randomized sequences, with the same residue content.
Results: We find that the patches, involving typically more than 10 residues, maintain a more hydrophilic surface than one would expect from a random substitution model, indicating a cooperative behaviour for these surfaces residues in terms of this single variable.
Supplementary information: Additional plots for all of the proteins examined in this paper can be found at: http://www.ebi.ac.uk/~shanahan/PCon/index.html
Probabilistic representation of gene regulatory networks
Authors: Mao Linyong , Resat Haluk 
Published: April 2004

Abstract
Motivation: Recent experiments have established unambiguously that biological systems can have significant cell-to-cell variations in gene expression levels even in isogenic populations. Computational approaches to studying gene expression in cellular systems should capture such biological variations for a more realistic representation.
Results: In this paper, we present a new fully probabilistic approach to the modeling of gene regulatory networks that allows for fluctuations in the gene expression levels. The new algorithm uses a very simple representation for the genes, and accounts for the repression or induction of the genes and for the biological variations among isogenic populations simultaneously. Because of its simplicity, introduced algorithm is a very promising approach to model large-scale gene regulatory networks. We have tested the new algorithm on the synthetic gene network library bioengineered recently. The good agreement between the computed and the experimental results for this library of networks, and additional tests, demonstrate that the new algorithm is robust and very successful in explaining the experimental data.
Availability: The simulation software is available upon request.
Supplementary information: Supplementary material will be made available on the OUP server.
An interactive triple-helical collagen builder
Authors: Rainey Jan K. , Goh M. Cynthia 
Published: April 2004

Abstract
Summary: To facilitate the building of triple-helical polypeptide structures, we provide an interactive, platform-independent Tcl/Tk script. User specified amino acid sequences are parsed to obtain localized melting temperature estimates corresponding to helical propensity. These propensities may be graphically examined prior to their automated use in combination with two separate statistical parameter sets to build the complete polypeptide backbone and, if desired, predict side-chain terminal atom locations.
Availability: The Tcl/Tk Triple Helical collagen Building Script (THe BuScr) and full documentation is freely available under the terms of the GNU General Public License at www.pence.ca/~jrainey/ or www.chem.utoronto.ca/staff/MCG/
Supplementary information: www.pence.ca/~jrainey
PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR
Authors: Marshall Owen J. 
Published: April 2004

Abstract
Summary: PerlPrimer is a cross-platform graphical user interface application for the design of primers for standard, bisulphite and real-time PCR, and sequencing. The program incorporates highly accurate melting-temperature and primer–dimer prediction algorithms with powerful tools such as sequence retrieval from Ensembl and the ability to BLAST search primer pairs. It aims to automate and simplify the process of primer design.
Availability: Open-source and freely available from http://perlprimer.sourceforge.net
PUNS: transcriptomic- and genomic-in silico PCR for enhanced primer design
Authors: Boutros Paul C. , Okey Allan B. 
Published: April 2004

Abstract
Summary: We developed a CGI/Perl-based web server to perform in silico polymerase chain reaction (PCR) on PCR primer sequences. The PUNS (Primer-UniGene Selectivity) server simulates PCR reactions by running BLASTN analysis on user-entered primer pairs against both the transcriptome and the genome to assess primer specificity. PUNS is particularly suited for the identification of highly selective primers for quantitative microarray validation.
Availability: Both system access and source-code are freely available at http://okeylabimac.med.utoronto.ca/PUNS
G-PRIMER: greedy algorithm for selecting minimal primer set
Authors: Wang Jiren , Li Kuo-Bin , Sung Wing-Kin 
Published: April 2004

Abstract
Summary: G-PRIMER, a web-based primer design program, has been developed to compute a minimal primer set specifically annealed to all the open reading frames in a given microbial genome. This program has been successfully used in the microarray experiment for analyzing the expression of genes in the Xanthomonas campestris genome.
Availability: It is available at http://mammoth.bii.a-star.edu.sg/gprimer/. Its source code is available upon request.
Monomer topology defines folding speed of heptamer
Authors: Bascos Neil , Guidry Jesse , Wittung‐Stafshede Pernilla 
Published: April 2004

AbstractSmall monomeric proteins often fold in apparent two‐state processes with folding speeds dictated by their native‐state topology. Here we test, for the first time, the influence of monomer topology on the folding speed of an oligomeric protein: the heptameric cochaperonin protein 10 (cpn10), which in the native state has seven β‐barrel subunits noncovalently assembled through β‐strand pairing. Cpn10 is a particularly useful model because equilibrium‐unfolding experiments have revealed that the denatured state in urea is that of a nonnative heptamer. Surprisingly, refolding of the nonnative cpn10 heptamer is a simple two‐state kinetic process with a folding‐rate constant in water (2.1 sec−1; pH 7.0, 20°C) that is in excellent agreement with the prediction based on the native‐state topology of the cpn10 monomer. Thus, the monomers appear to fold as independent units, with a speed that correlates with topology, although the C and N termini are trapped in β‐strand pairing with neighboring subunits. In contrast, refolding of unfolded cpn10 monomers is dominated by a slow association step.
Deciphering the function of an ORF: Salmonella enterica DeoM protein is a new mutarotase specific for deoxyribose
Authors: Assairi Liliane , Bertrand Thomas , Ferdinand Joëlle , Slavova‐Azmanova Neli , Christensen Mette , Briozzo Pierre , Schaeffer Francis , Craescu Constantin T. , Neuhard Jan , Bârzu Octavian , Gilles Anne‐Marie 
Published: April 2004

AbstractWe identified in Salmonella enterica serovar Typhi a cluster of four genes encoding a deoxyribokinase (DeoK), a putative permease (DeoP), a repressor (DeoQ), and an open reading frame encoding a 337 amino acid residues protein of unknown function. We show that the latter protein, called DeoM, is a hexamer whose synthesis is increased by a factor over 5 after induction with deoxyribose. The CD spectrum of the purified recombinant protein indicated a dominant contribution of βtype secondary structure and a small content of α‐helix. Temperature and guanidinium hydrochloride induced denaturation of DeoM indicated that the hexamer dissociation and monomer unfolding are coupled processes. DeoM exhibits 12.5% and 15% sequence identity with galactose mutarotase from Lactococcus lactis and respectively Escherichia coli, which suggested that these three proteins share similar functions. Polarimetric experiments demonstrated that DeoM is a mutarotase with high specificity for deoxyribose. Site‐directed mutagenesis of His183 in DeoM, corresponding to a catalytically active residue in GalM, yielded an almost inactive deoxyribose mutarotase. DeoM was crystallized and diffraction data collected for two crystal systems, confirmed its hexameric state. The possible role of the protein and of the entire gene cluster is discussed in connection with the energy metabolism of S. enterica under particular growth conditions.