bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational biology in the study of cardiac ion channels and cell electrophysiology
Authors: Rudy Yoram , Silva Jonathan R. 
Published: July 2006

1. Prologue 582. The Hodgkin–Huxley formalism for computing the action potential 592.1 The axon action potential model 592.2 Cardiac action potential models 623. Ion-channel based formulation of the action potential 653.1 Ion-channel structure 653.2 Markov models of ion-channel kinetics 663.3 Role of selected ion channels in rate dependence of the cardiac action potential 713.4 Physiological implications of IKs subunit interaction 773.5 Mechanism of cardiac action potential rate-adaptation is species dependent 784. Simulating ion-channel mutations and their electrophysiological consequences 814.1 Mutations in SCN5A, the gene that encodes the cardiac sodium channel 824.1.1 The ΔKPQ mutation and LQT3 824.1.2 SCN5A mutation that underlies a dual phenotype 874.2 Mutations in HERG, the gene that encodes IKr: re-examination of the ‘gain of function/loss of function’ concept 944.3 Role of IKs as ‘repolarization reserve’ 1005. Modeling cell signaling in electrophysiology 1025.1 CaMKII regulation of the Ca2+ transient 1025.2 The β-adrenergic signaling cascade 1056. Epilogue 1077. Acknowledgments 1088. References 109The cardiac cell is a complex biological system where various processes interact to generate electrical excitation (the action potential, AP) and contraction. During AP generation, membrane ion channels interact nonlinearly with dynamically changing ionic concentrations and varying transmembrane voltage, and are subject to regulatory processes. In recent years, a large body of knowledge has accumulated on the molecular structure of cardiac ion channels, their function, and their modification by genetic mutations that are associated with cardiac arrhythmias and sudden death. However, ion channels are typically studied in isolation (in expression systems or isolated membrane patches), away from the physiological environment of the cell where they interact to generate the AP. A major challenge remains the integration of ion-channel properties into the functioning, complex and highly interactive cell system, with the objective to relate molecular-level processes and their modification by disease to whole-cell function and clinical phenotype. In this article we describe how computational biology can be used to achieve such integration. We explain how mathematical (Markov) models of ion-channel kinetics are incorporated into integrated models of cardiac cells to compute the AP. We provide examples of mathematical (computer) simulations of physiological and pathological phenomena, including AP adaptation to changes in heart rate, genetic mutations in SCN5A and HERG genes that are associated with fatal cardiac arrhythmias, and effects of the CaMKII regulatory pathway and β-adrenergic cascade on the cell electrophysiological function.
Editorial
Authors:   WTE/JWS
Published: July 2006

COURT, MEET THY PUBLICThe public stir caused by recent rulings of the European Court of Justice opens a new window on the EU judiciary's condition and especially on its relations with the public. In the Pupino judgment, the Court ordered Italian colleagues to align domestic rules of criminal procedure with the EU ones by way of construction, whenever possible. The Environmental Framework decision ruling was about a legislative act meant to have states protect the environment by the use of criminal sanctions.
Programme factors that influence completion of residential treatment
Authors: MEIER PETRA S. , BEST DAVID 
Published: July 2006

AbstractThe aim of this study was to predict retention in residential rehabilitation (RR) services for drug users, focusing on service provider factors. A national postal survey of RR services in England and Wales was carried out and information was obtained from 57 of 87 services identified (65.5%). Service managers were asked to complete a questionnaire asking about treatment philosophy, treatments provided, staff characteristics and staffing levels, as well as overall service size and funding. Services also provided information on the number of clients admitted and the number who had completed, dropped out and been asked to leave in the past year. Completion rates varied widely, from 3% to 92%, with an average of 48%. Higher completion rates were associated with lower counsellor caseloads, fewer beds, single rooms, shorter scheduled treatment durations, higher fees per client and provision of what could be termed a balanced treatment programme containing adequate amounts of individual counselling and programme‐free time, and with only moderate demands for domestic duties. Programmes with more drug than alcohol users had lower completion rates, but the proportion of dual diagnosis or criminal justice referred clients did not appear to affect retention. Completion rates varied as a function of a number of service factors that are amenable to manipulation. To retain clients successfully, programmes should not be too large and should have adequate levels of therapeutic staff, a well‐developed treatment schedule which is not too demanding for the client in terms of duties or overall time spent in structured activities, and which incorporates sufficient levels of individual counselling.
Sampling Within Households in Household Surveys
Authors: Clark Robert G. , Steel David G. 
Published: July 2006

SummaryThe number of people to select within selected households has significant consequences for the conduct and output of household surveys. The operational and data quality implications of this choice are carefully considered in many surveys, but the effect on statistical efficiency is not well understood. The usual approach is to select all people in each selected household, where operational and data quality concerns make this feasible. If not, one person is usually selected from each selected household. We find that this strategy is not always justified, and we develop intermediate designs between these two extremes. Current practices were developed when household survey field procedures needed to be simple and robust; however, more complex designs are now feasible owing to the increasing use of computer-assisted interviewing. We develop more flexible designs by optimizing survey cost, based on a simple cost model, subject to a required variance for an estimator of population total. The innovation lies in the fact that household sample sizes are small integers, which creates challenges in both design and estimation. The new methods are evaluated empirically by using census and health survey data, showing considerable improvement over existing methods in some cases.
A Multivariate Regression Model for Continuous Genetic Traits
Authors: Yuan Ao , Bonney George E. 
Published: July 2006

Summary
In many commonly used models for multivariate traits, the likelihood is specified as a mixture of nested sums of products over the unobserved genotypes of all the family members, in which the familial covariance matrices vary in size and structure for different families, and their sizes can be immense for large family units. These issues pose computational difficulties in many applications. Bonney’s compound regressive model for univariate traits simplifies the familial covariance structure and reduces the mixture of nested sums only to the parent–offspring level, thus enhancing computation significantly. This model has been extended to the multivariate case in the absence of unobserved genotypes. Here, we further extend this model to incorporate major genes, covariates and multiple loci. As is typical in practice, this causes new computational difficulties. We study the computational issues and explore the behaviour of this extended model.
Willingness to consume and produce transgenic bananas in Costa Rica
Authors: Aguilar Francisco X. , Kohlmann Bert 
Published: July 2006

AbstractAn exploratory study of the willingness to produce and consume transgenic bananas was carried out in Costa Rica. Transgenic crops are plants with novel genes incorporated into their genome through the use of genetic engineering techniques. Farm managers’ opinions were gathered using faxed questionnaires while final consumers’ opinions were obtained through personal intercept interviews. Consumers expressed a lack of knowledge about transgenic crops and had received non‐favour but also non‐negative information through the media about their adoption. The results of a probit regression model show that, other things being equal, younger, wealthier consumers, with higher levels of education, with smaller households are more likely to consume transgenic bananas. All producers included in the study consider they would adopt a new transgenic variety. Producers’ willingness to pay for such a variety would depend on its capacity to reduce pest management costs and is estimated to range between $500 and $999 per hectare. This study stresses the potential for development and adoption of a new transgenic variety that would alleviate the current issues faced by banana farmers. On the other hand, final consumers should be better informed on the nature of such products, their benefits and risks.
Explaining consumers’ willingness to be environmentally friendly
Authors: Abdul‐Muhmin Alhassan G. 
Published: July 2006

AbstractTheoretical and empirical evidence from the environmental psychology and related literatures are used to develop a model for explaining consumers’ willingness to perform environmentally friendly behaviour. Environmental concern and perceived psychological consequences of environmentally friendly behaviour are posited as key determinants of willingness. Hypothesized antecedents of these are also included in the model, which is tested using structural equation modelling on data from a sample of 232 consumers collected in the Eastern Province of Saudi Arabia. The results indicate that the key determinant of willingness is perceived psychological consequences, which in turn is significantly determined by past behaviour. A hypothesized effect of environmental concern on willingness is not significant, although concern is itself significantly determined by perceived psychological consequences. Other positive determinants of concern are environmental knowledge and perceived seriousness of threats to the global environment. Substantive and methodological implications of the findings are outlined and discussed.
Vital pulp therapy of mandibular incisors: a case report with 11‐year follow up
Authors: Parirokh Masoud , Kakoei Shahla 
Published: July 2006

AbstractThis report describes a case of a young patient in whom all the mandibular incisor teeth suffered complicated crown fractures because of a car accident. For all mandibular incisors, pulpotomy with calcium hydroxide were performed in order to achieve apexogenesis and the teeth were restored with a double‐seal of glass ionomer cement and composite resin. The patient was reviewed over 11 years. All the mandibular incisor teeth showed continued root development and complete apex formation. Pulp canal obliteration was observed in only the mandibular right central incisor.
Molecular diagnosis of lyssaviruses and sequence comparison of Australian bat lyssavirus samples
Authors: FOORD AJ , HEINE HG , PRITCHARD LI , LUNT RA , NEWBERRY KM , ROOTES CL , BOYLE DB 
Published: July 2006

Objective  To evaluate and implement molecular diagnostic tests for the detection of lyssaviruses in Australia.Design  A published hemi‐nested reverse transcriptase polymerase chain reaction (RT‐PCR) for the detection of all lyssavirus genotypes was modified to a fully nested RT‐PCR format and compared with the original assay. TaqMan assays for the detection of Australian bat lyssavirus (ABLV) were compared with both the nested and hemi‐nested RT‐PCR assays. The sequences of RT‐PCR products were determined to assess sequence variations of the target region (nucleocapsid gene) in samples of ABLV originating from different regions.Results  The nested RT‐PCR assay was highly analytically specific, and at least as analytically sensitive as the hemi‐nested assay. The TaqMan assays were highly analytically specific and more analytically sensitive than either RT‐PCR assay, with a detection level of approximately 10 genome equivalents per µl. Sequence of the first 544 nucleotides of the nucleocapsid protein coding sequence was obtained from all samples of ABLV received at Australian Animal Health Laboratory during the study period.Conclusion  The nested RT‐PCR provided a means for molecular diagnosis of all tested genotypes of lyssavirus including classical rabies virus and Australian bat lyssavirus. The published TaqMan assay proved to be superior to the RT‐PCR assays for the detection of ABLV in terms of analytical sensitivity. The TaqMan assay would also be faster and cross contamination is less likely. Nucleotide sequence analyses of samples of ABLV from a wide geographical range in Australia demonstrated the conserved nature of this region of the genome and therefore the suitability of this region for molecular diagnosis.
Daughter Cell Separation by Penicillin-Binding Proteins and Peptidoglycan Amidases in
Escherichia coli
Authors: Priyadarshini Richa , Popham David L. , Young Kevin D. 
Published: July 2006

ABSTRACT

As one of the final steps in the bacterial growth cycle, daughter cells must be released from one another by cutting the shared peptidoglycan wall that separates them. In
Escherichia coli
, this delicate operation is performed by several peptidoglycan hydrolases, consisting of multiple amidases, lytic transglycosylases, and endopeptidases. The interactions among these enzymes and the molecular mechanics of how separation occurs without lysis are unknown. We show here that deleting the endopeptidase PBP 4 from strains lacking AmiC produces long chains of unseparated cells, indicating that PBP 4 collaborates with the major peptidoglycan amidases during cell separation. Another endopeptidase, PBP 7, fulfills a secondary role. These functions may be responsible for the contributions of PBPs 4 and 7 to the generation of regular cell shape and the production of normal biofilms. In addition, we find that the
E. coli
peptidoglycan amidases may have different substrate preferences. When the
dd
-carboxypeptidase PBP 5 was deleted, thereby producing cells with higher levels of pentapeptides, mutants carrying only AmiC produced a higher percentage of cells in chains, while mutants with active AmiA or AmiB were unaffected. The results suggest that AmiC prefers to remove tetrapeptides from peptidoglycan and that AmiA and AmiB either have no preference or prefer pentapeptides. Muropeptide compositions of the mutants corroborated this latter conclusion. Unexpectedly, amidase mutants lacking PBP 5 grew in long twisted chains instead of straight filaments, indicating that overall septal morphology was also defective in these strains.
Incidence and predictors of subacute thrombosis in patients undergoing primary angioplasty for an acute myocardial infarction
Authors: Smit Jaap Jan , de Boer Menko , Hoorntje Jan , Dambrink Jan Henk , Gosselink A. T. , Ottervanger Jan , Kolkman J. J. , Suryapranata Harry , van ’t Hof Arnoud 
Published: July 2006

SummarySubacute thrombosis (SAT) is a major concern in patients undergoing percutaneous coronary intervention (PCI). So far, only little data has been available on characteristics and outcome of patients with SAT after primary PCI for ST elevation myocardial infarction (STEMI). From 1997–2001, 1,548 unselected consecutive patients underwent primary PCI for STEMI as part ofa randomized controlled trial stenting vs. balloon angioplasty. All patients received acetylsalicylic acid (500 mg i. v.) and heparin (5,000 IU) before the procedure. After stenting, all patients received ticlopidine 250 mg daily (before July 1999) or clopidogrel 75 mg daily (after July 1999) for one month. Five percent of patients received glycoprotein IIb/IIIa blockers. We prospectively recorded incidence and characteristics of patients with SAT during one year follow-up. SAT occurred in 4. 1% (63/1548) and reinfarction in 6. 0% of patients. The incidence of SAT did not change over time (1997: 8/175[4. 6%],1998: 8/325 [2.5%],1999: 13/358 [3.6%], 2000: 22/426 [5.2%], 2001: 12/264 [4.5%]). SAT occurred in 39/63(62%) patients during hospital stay. The incidence did not differ between patients after ticlopidine 23/681 (3.4%) or clopidogrel 40/867 (4. 6%, p=0. 222). Univariate predictors of SAT were: patients with an LAD stenosis (5.4% vs. 2.9%, p=0. 016), with Killip class>1 at presentation (8.6% vs. 3.7%, p=0.007) and in patients who received a stent (5.1% vs. 2.7%, p=0. 022). After multivariate analysis, Killip class>1 on admission was the only independent predictor of SAT(OR 2.26, 95% CI 1.14–4.47, p=0.019). SAT was associated with a higher mortality at long-term follow-up (15% vs. 7%, p=0. 026). In a prospectively recorded, unselected consecutive series of patients undergoing PCI for STEMI, SAT occurred in 4. 1% of patients at oneyear follow-up. Signs of heart failure on admission, anterior myocardial infarction and stenting were predictors of SAT.
Exchange transfusion activates coagulation and alters the coagulation profile in newborn infants
Authors: Wartiovaara-Kautto Ulla , Andersson Sture , Heikinheimo Markku , Petäjä Jari , Långström Satu 
Published: July 2006

SummaryExchange transfusion (ET) with adult blood is a standard procedure for neonates with severe hyperbilirubinemia. How ET affects newborn coagulation system remains, however, largely unknown. Thus, we prospectively evaluated the effect of ET on thrombin formation and coagulation profile in 18 newborns (22 ETs). Prothrombin fragment F1+2 and thrombin-antithrombin complexes increased considerably during ET while platelets were significantly reduced. Protein C increased less (p<0.001) and factorVIIIc more (p<0.001) than expected based on their levels in the infused blood. Further, in vitro thrombin generation initiated by5 pM tissue factor was analysed. Before the first ET, newborn endogenous thrombin potential (ETP) and thrombin peak remained at ≈60% of adult control plasma levels, but the lag time to thrombin burst in newborn plasma was ≈45% shorter than the lag time in adult plasma. At the end of the first ET, the thrombin burst still started ≈35% earlier in newborn than adult plasma, whereas ETP and thrombin peak were increased to >90% of adult levels. ETP and peak remained elevated at adult levels until the beginning of the second ET. APC-induced reductions in newborn ETP remained unaltered throughout the first ET. The reductions of ETP by APC were less pronounced in newborn than adult plasma (p<0.0001).We conclude that ET is associated with multiple procoagulant changes and increased in vivo thrombin formation. This ET-induced procoagulant challenge may be of clinical significance in sick newborns already prone to bleeding and thrombotic complications.
Hurricane Juan (2003). Part II: Forecasting and Numerical Simulation
Authors: McTaggart-Cowan Ron , Bosart Lance F. , Gyakum John R. , Atallah Eyad H. 
Published: July 2006

Abstract
The landfall of Hurricane Juan (September 2003) in the Canadian Maritimes represents an ideal case in which to study the performance of operational forecasting of an intense, predominantly tropical feature entering the midlatitudes. A hybrid cyclone during its genesis phase, Juan underwent a tropical transition as it drifted slowly northward 1500 km from the east coast of the United States. Shortly after reaching its peak intensity as a category-2 hurricane, the storm accelerated rapidly northward and made landfall near Halifax, Nova Scotia, Canada, with maximum sustained winds of 44 m s−1. Although the forecasts and warnings produced by the U.S. National Hurricane Center and the Canadian Hurricane Centre were of high quality throughout Hurricane Juan’s life cycle, guidance from numerical weather prediction models became unreliable as the storm accelerated toward the coast. The short-range, near-surface forecasts from eight operational models during the crucial prelandfall portion of Juan’s track are investigated in this study. Despite continued improvements to operational numerical forecasting systems, it is shown that those systems not employing advanced tropical vortex initialization techniques were unable to provide forecasters with credible near-surface guidance in this case. A pair of regional forecasts, one successful and one from the failed model set, are compared in detail. Spurious asymmetries in the initial vortex of the deficient model are shown to hamper structural predictions and to cause nonnegligible track perturbations from the trajectory implied by the well-described deep-layer mean flow. The Canadian Mesoscale Compressible Community model is rerun with an improved representation of the hurricane’s vortex in the initial state. The hindcast produced following the tropical cyclone initialization contains reduced track, structure, and intensity errors compared with those generated by the model in real time. The enhanced initial intensity produces a direct improvement in the forecast storm strength throughout the period, and the symmetrization of the vortex eliminates the interactions that plague the operational system. The southeastward relocation of the implanted vortex to Juan’s observed location eliminates a significant northwestward track bias under the influence of a broad area of southerly steering flow. The study concludes that the initialization of Hurricane Juan’s structure and position adds value to numerical guidance even as the storm accelerates poleward at a latitude where the implantation of a quasi-symmetric vortex may not be generally valid.
The Impact of Satellite-Derived Atmospheric Motion Vectors on Mesoscale Forecasts over Hawaii*
Authors: Cherubini T. , Businger S. , Velden C. , Ogasawara R. 
Published: July 2006

Abstract
Tropospheric motions can be inferred from geostationary satellites by tracking clouds and water vapor in sequential imagery. These atmospheric motion vectors (AMV) have been operationally assimilated into global models for the past three decades, with positive forecast impacts. This paper presents results from a study to assess the impact of AMV derived from Geostationary Operational Environmental Satellite (GOES) imagery on mesoscale forecasts over the conventional data-poor central North Pacific region. These AMV are derived using the latest automated processing methodologies by the University of Wisconsin—Cooperative Institute for Meteorological Satellite Studies (CIMSS). For a test case, a poorly forecast subtropical cyclone (kona low) that occurred over Hawaii on 23–27 February 1997 was chosen. The Local Analysis and Prediction System (LAPS) was used to assimilate GOES-9 AMV data and to produce fifth-generation Pennsylvania State University–NCAR Mesoscale Model (MM5) initial conditions. The satellite wind assimilation is carried out on the 27-km-resolution domain covering the central Pacific area. The MM5 was run with three two-way nested domains (27, 9, and 3 km), with the innermost domain moving with the kona low. The AMV data are found to influence the cyclone’s development, improving the prediction of the cyclone’s central pressure and the track of the low’s center. Since September 2003, GOES-10 AMV data have been routinely accessed from CIMSS in real time and assimilated into the University of Hawaii (UH) LAPS, providing high-resolution initial conditions for twice-daily runs of MM5 at the Mauna Kea Weather Center collocated at the UH. It is found that the direct assimilation of AMV data into LAPS has a positive impact on the forecast accuracy of the UH LAPS/MM5 operational forecasting system when validated with observations in Hawaii. The implications of the results are discussed.