bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effects of disease severity, use of corticosteroids and social factors on neuropsychiatric complaints in severe acute respiratory syndrome (SARS) patients at acute and convalescent phases
Authors: Sheng Bun , Wing Cheng Sammy Kin , Lau Kwok Kwong , Li Ho Lun , Yiu Chan Eric Lok 
Published: September 2004

AbstractObjectiveTo evaluate the effects of disease severity, corticosteroids and social factors on neuropsychiatric complaints in severe acute respiratory syndrome (SARS) patients, both during acute and convalescent phases.MethodsSelf-administered mail questionnaires survey to 308 SARS patients after discharging from hospital. Both patients and their families were asked about symptoms related to various neuropsychiatric domains, and the questions covered both acute and convalescent phases.ResultsAmong the 102 (33%) valid replies, 65% had strong symptoms in convalescent phase as indicated by GHQ28 score ≥ 5. In multiple linear regression analysis, use of pulse steroid and total dosages of pulse steroid during hospitalisation were predictive for anxiety-depression, psychosis and behavioural symptoms in acute phase, the effects persisted in convalescent phase. Disease severity had direct correlation with symptoms in all neuropsychiatric domains at acute phase and anxiety-depression and cognition at convalescent phase. Health care workers had more neuropsychiatric complaints in both phases. Severity of symptoms, corticosteroids and social factors explained about half of the variances (R2 = 52) in anxiety-depression at acute phase and 33% at convalescent phase.ConclusionsSevere disease, high dose corticosteroids and being health care workers were independent predictors of neuropsychiatric complaints in both acute and convalescent phases.
Patellofemoral joint contact area increases with knee flexion and weight‐bearing
Authors: Besier Thor F. , Draper Christine E. , Gold Garry E. , Beaupré Gary S. , Delp Scott L. 
Published: September 2004

AbstractPatellofemoral pain is a common and debilitating disorder. Elevated cartilage stress of the patellofemoral joint is hypothesized to play a role in the onset of pain. Estimating cartilage stress requires accurate measurements of contact area. The purpose of this study was to estimate patellofemoral joint contact areas in a group of healthy, pain‐free subjects during upright, weight‐bearing conditions. Sixteen subjects (8 female, 8 male) were scanned in a GE Signa SP open configuration MRI scanner, which allowed subjects to stand or squat while reclining 25° from vertical with the knee positioned at 0°, 30°, or 60° of flexion. A custom‐built backrest enabled subjects to be scanned without motion artifact in both weight‐bearing (0.45 body weight per leg) and reduced loading conditions (‘unloaded’ at 0.15 body weight) at each knee flexion posture. Male subjects displayed mean unloaded patellofemoral joint contact areas of 210, 414, and 520mm2 at 0°, 30° and 60° of knee flexion, respectively. Female subjects' unloaded contact areas were similar at full extension (0°), but significantly smaller at 30° and 60° (p < 0.01), with mean values of 269 and 396 mm2, respectively. When normalized by patellar dimensions (height × width), contact areas were not different between genders. Under weight‐bearing conditions, contact areas increased by an average of 24% (p < 0.05). This study highlights the differences in patellofemoral joint contact area between gender, knee flexion postures, and physiologic loading conditions. © 2004 Orthopaedic Research Society. Published by Elsevier Ltd. All rights reserved.
The Los Alamos hepatitis C sequence database
Authors: Kuiken Carla , Yusim Karina , Boykin Laura , Richardson Russell 
Published: September 2004

Abstract
Motivation: The hepatitis C virus (HCV) is a significant threat to public health worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for vaccine and drug design. At present, some 30 000 HCV sequences have been published. A central website that provides annotated sequences and analysis tools will be helpful to HCV scientists worldwide.
Results: The HCV sequence database collects and annotates sequence data and provides them to the public via a website that contains a user-friendly search interface and a large number of sequence analysis tools, based on the model of the highly regarded Los Alamos HIV database. The HCV sequence database was officially launched in September 2003. Since then, its usage has steadily increased and is now at an average of ∼280 visits per day from distinct IP addresses.
Availability: The HCV website can be accessed via http://hcv.lanl.gov and http://hcv-db.org
Contact: hcv-info@lanl.gov
SNPP: automating large-scale SNP genotype data management
Authors: Zhao Lan-Juan , Li Miao-Xin , Guo Yan-Fang , Xu Fu-Hua , Li Jin-Long , Deng Hong-Wen 
Published: September 2004

Abstract
Summary: To manage high-throughput single nucleotide polymorphism (SNP) genotyping data efficiently, we developed a dynamic general database management system—SNPP (SNP Processor). It provides several functions, including data importing with comparison, Mendelian inheritance check within pedigrees, data compiling and exporting. Furthermore, SNPP may generate files for repeat genotyping and transform them into files that can be executed by a liquid handling system.
Availability: http://orclinux.creighton.edu/snpp/
Contact: lanjuanzhao@creighton.edu
A simple and fast secondary structure prediction method using hidden neural networks
Authors: Lin Kuang , Simossis Victor A. , Taylor Willam R. , Heringa Jaap 
Published: September 2004

Abstract
Motivation: In this paper, we present a secondary structure prediction method YASPIN that unlike the current state-of-the-art methods utilizes a single neural network for predicting the secondary structure elements in a 7-state local structure scheme and then optimizes the output using a hidden Markov model, which results in providing more information for the prediction.
Results: YASPIN was compared with the current top-performing secondary structure prediction methods, such as PHDpsi, PROFsec, SSPro2, JNET and PSIPRED. The overall prediction accuracy on the independent EVA5 sequence set is comparable with that of the top performers, according to the Q3, SOV and Matthew's correlations accuracy measures. YASPIN shows the highest accuracy in terms of Q3 and SOV scores for strand prediction.
Availability: YASPIN is available on-line at the Centre for Integrative Bioinformatics website (http://ibivu.cs.vu.nl/programs/yaspinwww/) at the Vrije University in Amsterdam and will soon be mirrored on the Mathematical Biology website (http://www.mathbio.nimr.mrc.ac.uk) at the NIMR in London.
Contact: kxlin@nimr.mrc.ac.uk
RALEE—RNA ALignment Editor in Emacs
Authors: Griffiths-Jones Sam 
Published: September 2004

AbstractSummary: Production of high quality multiple sequence alignments of structured RNAs relies on an iterative combination of manual editing and structure prediction. An essential feature of an RNA alignment editor is the facility to mark-up the alignment based on how it matches a given secondary structure prediction, but few available alignment editors offer such a feature. The RALEE (RNA ALignment Editor in Emacs) tool provides a simple environment for RNA multiple sequence alignment editing, including structure-specific colour schemes, utilizing helper applications for structure prediction and many more conventional editing functions. This is accomplished by extending the commonly used text editor, Emacs, which is available for Linux, most UNIX systems, Windows and Mac OS.Availability: The ELISP source code for RALEE is freely available from http://www.sanger.ac.uk/Users/sgj/ralee/ along with documentation and examples.Contact: sgj@sanger.ac.uk
RDP2: recombination detection and analysis from sequence alignments
Authors: Martin D. P. , Williamson C. , Posada D. 
Published: September 2004

Abstract
Summary: RDP2 is a Windows 95/XP program that examines nucleotide sequence alignments and attempts to identify recombinant sequences and recombination breakpoints using 10 published recombination detection methods, including GENECONV, BOOTSCAN, MAXIMUM χ2, CHIMAERA and SISTER SCANNING. The program enables fast automated analysis of large alignments (up to 300 sequences containing 13 000 sites), and interactive exploration, management and verification of results with different recombination detection and tree drawing methods.
Availability: RDP2 is available free from the RDP2 website (http://darwin.uvigo.es/rdp/rdp.html)
Contact: darren@science.uct.ac.za
Supplementary information: Detailed descriptions of RDP2 and the methods it implements are included in the program manual, which can be downloaded from the RDP2 website.
Predicting protein functions with message passing algorithms
Authors: Leone Michele , Pagnani Andrea 
Published: September 2004

Abstract
Motivation: In the last few years, a growing interest in biology has been shifting toward the problem of optimal information extraction from the huge amount of data generated via large-scale and high-throughput techniques. One of the most relevant issues has recently emerged that of correctly and reliably predicting the functions of a given protein with that of functions exploiting information coming from the whole network of proteins physically interacting with the functionally undetermined one. In the present work, we will refer to an ‘observed’ protein as the one present in the protein–protein interaction networks published in the literature.
Methods: The method proposed in this paper is based on a message passing algorithm known as Belief Propagation, which accepts the network of protein's physical interactions and a catalog of known protein's functions as input, and returns the probabilities for each unclassified protein of having one chosen function. The implementation of the algorithm allows for fast online analysis, and can easily be generalized into more complex graph topologies taking into account hypergraphs, i.e. complexes of more than two interacting proteins.
Results: Benchmarks of our method are the two Saccharomyces cerevisiae protein–protein interaction networks and the Database of Interacting Proteins. The validity of our approach is successfully tested against other available techniques.
Contact: leone@isiosf.isi.it
Supplementary information: http://isiosf.isi.it/~pagnani
Delayed administration may improve entacapone effects in parkinsonian patients non‐responding to the drug
Authors: Brusa L. , Bassi A. , Lunardi G. , Fedele E. , Peppe A. , Stefani A. , Pasqualetti P. , Stanzione P. , Pierantozzi M. 
Published: September 2004

Background:  Entacapone is a COMT inhibitor used in Parkinson's disease (PD) patients, as an adjunctive therapy to l‐dopa in order to prolong its bioavailability and thus its clinical effect. However, previous studies reported entacapone‐induced l‐dopa to have lower Cmax and delayed tmax values, coupled with a delayed onset of the clinical effect, possibly suggesting an interference between the two drugs. The aim of our study was to evaluate whether a delayed entacapone administration in association with standard l‐dopa/carbidopa, may in some subjects improve the entacapone effects on l‐dopa AUC and thus on the clinical ‘on time’ duration.Methods:  Twenty‐eight idiopathic advanced PD patients were blindly evaluated in three different test days, following administration of carbidopa/l‐dopa or carbidopa/l‐dopa plus co‐administered entacapone or plus entacapone administered with 30 min of delay.Results:  The AUC, the ‘on time’ and UPDRS score of the whole group were improved by both modalities of entacapone administration. An ex post analysis showed that the delayed entacapone administration produced a significant improvement in a subgroup of 10 non‐responding patients to the co‐administration.Conclusion:  We suggest that the delayed administration should be attempted in the subjects not improved by entacapone co‐administration.
Sulfide consumption by mussel gill mitochondria is not strictly tied to oxygen reduction: measurements using a novel polarographic sulfide sensor
Authors: Kraus David W. , Doeller Jeannette E. 
Published: September 2004

SUMMARYSome organisms that survive in environments rich in hydrogen sulfide possess specific metabolic pathways for sulfide oxidation and subsequent use of reducing equivalents in oxidative phosphorylation, a process called chemolithoheterotrophy. This process is dependent on ambient oxygen partial pressure and environmental sulfide exposure. To define accurately the kinetics of sulfide metabolism and its dependence on cellular conditions, we have developed a polarographic sulfide sensor (PSS) to measure sulfide concentrations directly and continuously under physiological conditions.The ribbed mussel Geukensia demissa, an inhabitant of sulfide-rich coastal sediments, consumes sulfide in a chemolithoheterotrophic metabolic strategy. Gill mitochondria use sulfide as respiratory substrate for ATP production, and sulfide consumption is sufficiently rapid and so kinetically complex that only continuous real-time detection captures these events. Under normoxic conditions, oxygen and sulfide consumption are matched. Under hypoxic to anoxic conditions, however, sulfide consumption continues without commensurate oxygen consumption, and these results can be duplicated at higher oxygen conditions by selective blockade of terminal oxidases. These metabolic capabilities depend on prior environmental sulfide exposure, which suggests substantial mitochondrial metabolic plasticity. The recent finding that endogenous sulfide is a critical cell signaling molecule in all organisms suggests that the metabolic pathways that tightly control cellular sulfide levels are widespread. Sensors that accurately report sulfide concentrations under physiologically relevant conditions are valuable tools with which to explore the expanding role of sulfide in biological systems.
Producing H2‐rich gas from simulated biogas and applying the gas to a 50w PEFC stack
Authors: Xu Guangwen , Chen Xin , Honda Kazunori , Zhang Zhan‐Guo 
Published: September 2004

AbstractSince 2000, a technical program was developed to convert biogas into hydrogen‐rich gas, and to demonstrate the possibility of applying the acquired hydrogenous gas to the polymer electrolyte fuel cell (PEFC). The gas conversion was accomplished in two steps, successively, in a desulfurizer that removes the hydrogen sulfide in biogas and in a hydrogen‐rich gas producer that converts the desulfurized biogas into hydrogen‐rich gas containing CO less than the PEFC‐tolerable value of 10 ppm. The gas producer consisted of four catalytic reactors, in succession, a steam reformer, two water‐gas‐shift reactors, and a selective CO oxidizer. Determining the necessary conditions for all such reactors and the applicability of the produced hydrogen‐rich gas to a 50‐watt model PEFC stack is examined. Experiments were conducted using clean model biogas over commercial catalysts. A successful production of the PEFC‐usable hydrogen‐rich gas was fulfilled, and the gas showed a composition of about 70 vol. % H2, 30 vol. % CO2, and residual CH4 (<1.0 vol. %). Directly applying the gas to the downstream model PEFC stack generated stable powers higher than 50 watts, provided the equivalent hydrogen feed was sufficient. Nonetheless, the CO2 in the gas obviously reduced the stack performance. Compared to the case running on pure hydrogen, the stack exhibited not only a lower voltage (power) at a given current, but also a smaller limit current that restricts the maximal output from the stack at each specified hydrogen feed rate. © 2004 American Institute of Chemical Engineers AIChE J, 50: 2467–2480, 2004
A case of Adams–Oliver syndrome with associated brain and pulmonary involvement: Further evidence of vascular pathology?
Authors: Piazza Anthony Joseph , Blackston Dwain , Sola Augusto 
Published: September 2004

AbstractWe report on a case of Adams–Oliver syndrome (AOS) with typical skin and limb defects along with the unique findings of pulmonary hypertension and central nervous system (CNS) involvement. Adams–Oliver syndrome has a wide spectrum of physical anomalies ranging from characteristic aplasia cutis congenita (ACC), transverse limb defects, and cutis marmorata telangiectica to extensive lethal anomalies. While pulmonary hypertension is usually not associated with AOS, the abnormal endothelial regulation of vascular tone seen in the pulmonary vasculature may enhance current pathophysiologic concepts of vascular abnormalities in AOS. There is accumulating evidence of significant CNS defects in AOS. This infant had hypoplastic corpus callosum and focal findings in the periventricular white matter. Evaluation for pulmonary hypertension and CNS anomalies in patients suspected to have AOS, can help identify those who are at risk for acute morbidities and associated developmental delays. © 2004 Wiley‐Liss, Inc.
Recreating the biological pacemaker
Authors: Rosen Michael R. , Robinson Richard B. , Brink Peter , Cohen Ira S. 
Published: September 2004

AbstractIn recent years, several groups have reported a variety of strategies for developing biological pacemakers whose ultimate function would be to supplement/replace electronic pacemakers. Strategies have included gene therapy using naked plasmids or viral vectors and cell therapy for which both adult human mesenchymal stem cells (hMSCs) and human embryonic stem cells have been employed. This article reviews the various approaches and summarizes our own research in which the pacemaker gene, HCN2, is administered via viral vector or in an hMSC platform to produce pacemaker function in the intact canine heart. © 2004 Wiley‐Liss, Inc.
Functional imaging of the embryonic pacemaking and cardiac conduction system over the past 150 years: Technologies to overcome the challenges
Authors: Rothenberg Florence , Efimov Igor R. , Watanabe Michiko 
Published: September 2004

AbstractEarly analyses of cardiac pacemaking and conduction system (CPCS) development relied on classic histology and visual inspection of the beating heart. Current techniques that facilitate delineation of the CPCS include the use of specific antibody markers and transgenic mouse lines specifically expressing reporter genes. Assaying the function of tiny embryonic hearts required an increase in the level of spatial and temporal resolution. Current methods for such analyses include the use of intracellular and extracellular microelectrodes, echocardiography, rapid optical imaging using fluorescent dyes, and most recently optical coherence tomography. This review will focus on methods developed to investigate the functional emergence of the embryonic cardiac conduction system. Where appropriate, the methods used to delineate the anatomic pathways will also be discussed. The combination of techniques to capture both morphological and functional data from the CPCS will further improve with continued interdisciplinary collaboration. © 2004 Wiley‐Liss, Inc.
Transitions in ventricular activation revealed by two‐dimensional optical mapping
Authors: Chuck Emil Thomas , Meyers Kathleen , France David , Creazzo Tony L. , Morley Gregory E. 
Published: September 2004

AbstractWhile cardiac function in the mature heart is dependent on a properly functioning His‐Purkinje system, the early embryonic tubular heart efficiently pumps blood without a distinct specialized conduction system. Although His‐Purkinje system precursors have been identified using immunohistological techniques in the looped heart, little is known whether these precursors function electrically. To address this question, we used high‐resolution optical mapping and fluorescent dyes with two CCD cameras to describe the motion‐corrected activation patterns of 76 embryonic chick hearts from tubular stages (stage 10) to mature septated hearts (stage 35). Ventricular activation in the tubular looped heart (stages 10–17) using both calcium‐sensitive fluo‐4 and voltage‐sensitive di‐4‐ANEPPS shows sequentially uniform propagation. In late looped hearts (stages 18–22), domains of the dorsal and lateral ventricle are preferentially activated before spreading to the remaining myocardium and show alternating regions of fast and slow propagation. During stages 22–26, action potentials arise from the dorsal ventricle. By stages 27–29, action potential breakthrough is also observed at the right ventricle apex. By stage 31, activation of the heart proceeds from foci at the apex and dorsal surface of the heart. The breakthrough foci correspond to regions where putative conduction system precursors have been identified immunohistologically. To date, our study represents the most detailed electrophysiological characterization of the embryonic heart between the looped and preseptated stages and suggests that ventricular activation undergoes a gradual transformation from sequential to a mature pattern with right and left epicardial breakthroughs. Our investigation suggests that cardiac conduction system precursors may be electrophysiologically distinct and mature gradually throughout cardiac morphogenesis in the chick. © 2004 Wiley‐Liss, Inc.
Nature, significance, and mechanisms of electrical heterogeneities in ventricle
Authors: Poelzing Steven , Rosenbaum David S. 
Published: September 2004

AbstractPreviously, dispersion of repolarization (DOR) has been extensively linked to the development of arrhythmias and sudden cardiac death. The electrical heterogeneities that cause DOR between transmural myocyte layers have been reported in a wide variety of animals and humans. The underlying causes of transmural electrical heterogeneities are in part due to heterogeneous functional expression of proteins responsible for ion handling. Recently, we found that electrophysiologic heterogeneities between subepicardial and midmyocardial cells can form a substrate for reentrant ventricular arrhythmias. However, cell‐to‐cell coupling through gap junctions is expected to attenuate transmural heterogeneities between cell types spanning the ventricular wall. In this article we review a hypothesis that regional uncoupling resulting from expression patterns of gap junctions across the ventricular wall underlies DOR, and DOR can be amplified under disease conditions which remodel gap junctions. We find the principle gap junction protein, connexin43 (Cx43), is selectively reduced in the subepicardium (by 24%) compared to deeper layers of normal canine left ventricle. Additionally, the greatest DOR occurs within the subepicardial‐midmyocardial interface, precisely where Cx43 expression is reduced. The present data suggests that ion channel and gap junction heterogeneities act in conjunction to form and maintain transmural DOR. Importantly, both ion channel and gap junction remodeling occurs during many disease states such as heart failure. Importantly, in the absence of ion channel remodeling, pharmacological uncoupling increases transmural DOR, particularly within the epicardial‐midmyocardial interface, to values observed in heart failure. Therefore, these data suggest that heterogeneous Cx43 expression produces functionally significant electrophysiologic heterogeneities across the ventricular wall and may be a mechanism for promoting DOR which underlie arrhythmias in heart failure. © 2004 Wiley‐Liss, Inc.