bluuebunny/crossref_metadata_2025_split huggingface dataset:
Finite‐element method simulation of rotating disk flow: effect of the transport of a chemical species
Authors: Pontes José , Rabello dos Anjos Gustavo , Mangiavacchi Norberto 
Published: August 2008

AbstractElectrochemical cells containing an iron rotating disk electrode which is dissolved in the electrolyte, an 1 M H2SO4 solution present a current instability in the plateau region, where the current is controlled by the mass transport. Dissolution of the electrode gives rise to a thin concentration boundary layer, due to a Schmidt number Sc = 2000. This boundary layer, together with the potential applied to the electrode, leads to an increase in the fluid viscosity and in a decrease in the diffusion coefficient, coupling the concentration and the chemical species field. Since the current is proportional to the concentration gradient at the interface, an instability of the coupled fields at Reynolds numbers attained in experimental conditions could be responsible for the current instability. Mangiavacchi [1] performed a linear stability analysis of the problem and showed that this is indeed the case. In this paper we review the main results of the stability analysis and present the main features of the FEM code recently developed in our group, to proceed with the investigation of the current instability observed in electrochemical cells. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Residual distribution schemes for Bondi‐Hoyle accretion
Authors: Rossmanith James A. 
Published: August 2008

AbstractBlack hole accretion is a key component in astrophysical phenomena such as gamma‐ray bursts and quasars. As a step towards understanding such phenomena, accurate and efficient computational methods for simulating gas dynamics in the presence of black holes must be developed. In this work a residual distribution scheme on unstructured grids is constructed for solving the general relativistic version of the compressible Euler equations. In particular, we simulate Bondi‐Hoyle accretion onto a Schwarzschild black hole. Presented here are preliminary results in a larger effort to develop high‐order methods on unstructured meshes for general relativistic flows. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Bayesian flux balance analysis applied to a skeletal muscle metabolic model
Authors: Calvetti Daniela , Heino Jenni , Somersalo Erkki , Tunyan Knarik 
Published: August 2008

AbstractThe steady state condition of two‐compartment skeletal muscle model is considered. The inverse problem is to estimate the reaction and transport fluxes, as well as the concentrations in venous blood when the stoichiometry and bound constraints for the fluxes and the concentrations are given. A new methodology based on a Bayesian statistical approach to the flux balance analysis (FBA) is proposed. We show how the bound constraints and optimality condition can be incorporated into the model in the Bayesian framework by proper construction of the prior densities. An effective Markov Chain Monte Carlo (MCMC) scheme to explore the posterior densities is proposed. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
SIMS and MALDI MS imaging of the spinal cord
Authors: Monroe Eric B. , Annangudi Suresh P. , Hatcher Nathan G. , Gutstein Howard B. , Rubakhin Stanislav S. , Sweedler Jonathan V. 
Published: August 2008

AbstractThe application of MS to imaging, or MS imaging (MSI), allows for the direct investigation of tissue sections to identify biological compounds and determine their spatial distribution. We present an approach to MSI that combines secondary ion MS (SIMS) and MALDI MS for the imaging and analysis of rat spinal cord sections, thereby enhancing the chemical coverage obtained from an MSI experiment. The spinal cord is organized into discrete, anatomically defined areas that include motor and sensory networks composed of chemically diverse cells. The MSI data presented here reveal the spatial distribution of multiple phospholipids, proteins, and neuropeptides obtained within single, 20 μm sections of rat spinal cord. Analyte identities are initially determined by primary mass match and confirmed in follow‐up experiments using LC MS/MS from extracts of adjacent spinal cord sections. Additionally, a regional analysis of differentially localized signals serves to rapidly screen compounds of varying intensities across multiple spinal regions. These MSI analyses reveal new insights into the chemical architecture of the spinal cord and set the stage for future imaging studies of the chemical changes induced by pain, anesthesia, and drug tolerance.
Protein and peptides in pictures: Imaging with MALDI mass spectrometry
Authors: Goodwin Richard J. A. , Pennington Stephen R. , Pitt Andrew R. 
Published: August 2008

AbstractImaging using MS has the potential to deliver highly parallel, multiplexed data on the specific localization of molecular ions in tissue samples directly, and to measure and map the variations of these ions during development and disease progression or treatment. There is an intrinsic potential to be able to identify the biomarkers in the same experiment, or by relatively simple extension of the technique. Unlike many other imaging techniques, no a priori knowledge of the markers being sought is necessary. This review concentrates on the use of MALDI‐MS for MS imaging (MSI) of proteins and peptides, with an emphasis on mammalian tissue. We discuss the methodologies used, their potential limitations, overall experimental considerations and progress that has been made towards establishing MALDI‐MSI as a routine technique for the spatially resolved measurement of peptides and proteins. As well as determining the local abundance of individual molecular ions, there is the potential to determine their identity within the same experiment using relatively simple extensions of the basic techniques. In this way MSI offers an important opportunity for biomarker discovery and identification.
Iterative cluster‐NMA: A tool for generating conformational transitions in proteins
Authors: Schuyler Adam D. , Jernigan Robert L. , Qasba Pradman K. , Ramakrishnan Boopathy , Chirikjian Gregory S. 
Published: August 2008

AbstractComputational models provide insight into the structure–function relationship in proteins. These approaches, especially those based on normal mode analysis, can identify the accessible motion space around a given equilibrium structure. The large magnitude, collective motions identified by these methods are often well aligned with the general direction of the expected conformational transitions. However, these motions cannot realistically be extrapolated beyond the local neighborhood of the starting conformation. In this article, the iterative cluster‐NMA (icNMA) method is presented for traversing the energy landscape from a starting conformation to a desired goal conformation. This is accomplished by allowing the evolving geometry of the intermediate structures to define the local accessible motion space, and thus produce an appropriate displacement. Following the derivation of the icNMA method, a set of sample simulations are performed to probe the robustness of the model. A detailed analysis of β1,4‐galactosyltransferase‐T1 is also given, to highlight many of the capabilities of icNMA. Remarkably, during the transition, a helix is seen to be extended by an additional turn, emphasizing a new unknown role for secondary structures to absorb slack during transitions. The transition pathway for adenylate kinase, which has been frequently studied in the literature, is also discussed. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Evaluating spatial methods for investigating global clustering and cluster detection of cancer cases
Authors: Huang Lan , Pickle Linda W. , Das Barnali 
Published: August 2008

AbstractThere have been articles on comparing methods for global clustering evaluation and cluster detection in disease surveillance, but power and sample size (SS) requirements have not been explored for spatially correlated data in this area. We are developing such requirements for tests of spatial clustering and cluster detection for regional cancer cases. We compared global clustering methods including Moran'sI, Tango's and Besag–Newell'sRstatistics, and cluster detection methods including circular and elliptic spatial scan statistics (SaTScan), flexibly shaped spatial scan statistics, Turnbull's cluster evaluation permutation procedure, local indicators of spatial association, and upper‐level set scan statistics. We identified eight geographic patterns that are representative of patterns of mortality due to various types of cancer in the U.S. from 1998 to 2002. We then evaluated the selected spatial methods based on state‐ and county‐level data simulated from these different spatial patterns in terms of geographic locations and relative risks, and varying SSs using the 2000 population in each county. The comparison provides insight into the performance of the spatial methods when applied to varying cancer count data in terms of power and precision of cluster detection. Copyright © 2008 John Wiley & Sons, Ltd.
Analyses of cumulative incidence functions via non‐parametric multiple imputation
Authors: Ruan Ping K. , Gray Robert J. 
Published: August 2008

AbstractWe describe a non‐parametric multiple imputation method that recovers the missing potential censoring information from competing risks failure times for the analysis of cumulative incidence functions. The method can be applied in the settings of stratified analyses, time‐varying covariates, weighted analysis of case‐cohort samples and clustered survival data analysis, where no current available methods can be readily implemented. The method uses a Kaplan–Meier imputation method for the censoring times to form an imputed data set, so cumulative incidence can be analyzed using techniques and software developed for ordinary right censored survival data. We discuss the methodology and show from both simulations and real data examples that the method yields valid estimates and performs well. The method can be easily implemented via available software with a minor programming requirement (for the imputation step). It provides a practical, alternative analysis tool for otherwise complicated analyses of cumulative incidence of competing risks data. Copyright © 2008 John Wiley & Sons, Ltd.
Long‐term survivor model with bivariate random effects: Applications to bone marrow transplant and carcinoma study data
Authors: Lai Xin , Yau Kelvin K. W. 
Published: August 2008

AbstractCured patients (or the so‐called long‐term survivors) are increasingly being observed in clinical trial studies. As exemplified in two data sets, the bone marrow transplantation study for leukaemia patients and the multi‐centre study for patients with carcinoma in the oropharynx, a considerable portion of the patients in these studies are deemed to be cured. With the presence of random hospital/centre effects, a long‐term survivor model with bivariate random effects is proposed to analyse clustered survival data with a possible portion of cured patients. This model extends earlier work by allowing random effects in both the cured fraction and the hazard function parts to follow a bivariate normal distribution, which gives a generalized model with an additional correlation parameter governing the relationship between the recovery probability and the instantaneous failure rate due to the hospital/centre effects. By adopting the GLMM formulation, random effects are incorporated in the model via the linear predictor terms. REML estimation of parameters is achieved via the EM algorithm. Application to the two sets of data illustrates the usefulness of the proposed model. A simulation study is conducted to assess the performance of the estimators, under the proposed numerical estimation scheme. Copyright © 2008 John Wiley & Sons, Ltd.
Improving the efficiency of inductive logic programming systems
Authors: Fonseca Nuno A. , Costa Vítor Santos , Rocha Ricardo , Camacho Rui , Silva Fernando 
Published: August 2008

AbstractInductive logic programming (ILP) is a sub‐field of machine learning that provides an excellent framework for multi‐relational data mining applications. The advantages of ILP have been successfully demonstrated in complex and relevant industrial and scientific problems. However, to produce valuable models, ILP systems often require long running times and large amounts of memory. In this paper we address fundamental issues that have direct impact on the efficiency of ILP systems. Namely, we discuss how improvements in the indexing mechanisms of an underlying logic programming system benefit ILP performance. Furthermore, we propose novel data structures to reduce memory requirements and we suggest a new lazy evaluation technique to search the hypothesis space more efficiently. These proposals have been implemented in the April ILP system and evaluated using several well‐known data sets. The results observed show significant improvements in running time without compromising the accuracy of the models generated. Indeed, the combined techniques achieve several order of magnitudes speedup in some data sets. Moreover, memory requirements are reduced in nearly half of the data sets. Copyright © 2008 John Wiley & Sons, Ltd.
ISTA13—International interlaboratory comparative evaluation of microbial assay for risk assessment (MARA)
Authors: Wadhia K. 
Published: August 2008

AbstractThe microbial assay for risk assessment (MARA) is an innovative system based on an array of 11 different microbial species freeze‐dried in a 96‐well micro‐titer plate. Developed for testing the toxicity of chemicals, mixtures, and environmental samples, the assay employs species of a taxonomically diverse range. In addition to 10 prokaryotic species, a eukaryote (yeast) is included in the range. The MARA's innate scope of a multi‐dimensional test allows determination of toxicity based on a unique assay fingerprint or index, numerically expressed as the mean microbial toxic concentration (MTC). The most significant potential of the test is in the additional inference that can be conveyed to the toxicity evaluation because of the presence of each of the constituent species. The performance of MARA was evaluated to ascertain its capability and potential scope in an intralaboratory trial. Sensitivity to toxicants and different environmental samples was assessed. Evaluation included comparison with other tests; namely Microtox®, invertebrate (Daphnia magna and Thamnocephalus platyurus) microbiotests, and respiration‐ and nitrification‐inhibition tests. MARA's performance was further assessed with the implementation of an international interlaboratory trial. This involved the participation of 13 laboratories ranging from academic establishments to regulatory agencies. The results of the testing will be presented with assessment of the extent of variability and specific assay components. The trial evaluation indicated that performance of the assay was satisfactory and the results were within the acceptable range. MARA is a robust multispecies assay offering scope for toxicity assessment of a diverse range of samples. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2008.
Differential Dynamic Logic for Hybrid Systems
Authors: Platzer André 
Published: August 2008

AbstractHybrid systems are models for complex physical systems and are defined as dynamical systems with interacting discrete transitions and continuous evolutions along differential equations. With the goal of developing a theoretical and practical foundation for deductive verification of hybrid systems, we introduce a dynamic logic for hybrid programs, which is a program notation for hybrid systems. As a verification technique that is suitable for automation, we introduce a free variable proof calculus with a novel combination of real-valued free variables and Skolemisation for lifting quantifier elimination for real arithmetic to dynamic logic. The calculus is compositional, i.e., it reduces properties of hybrid programs to properties of their parts. Our main result proves that this calculus axiomatises the transition behaviour of hybrid systems completely relative to differential equations. In a case study with cooperating traffic agents of the European Train Control System, we further show that our calculus is well-suited for verifying realistic hybrid systems with parametric system dynamics.
Grade of adiposity affects the impact of fat mass on resting energy expenditure in women
Authors: Bosy-Westphal Anja , Müller Manfred J. , Boschmann Michael , Klaus Susanne , Kreymann Georg , Lührmann Petra M. , Neuhäuser-Berthold Monika , Noack Rudolf , Pirke Karl M. , Platte Petra , Selberg Oliver , Steiniger Jochen 
Published: August 2008

Body fat mass (FM) adds to the variance in resting energy expenditure (REE). However, the nature and extent of this relationship remains unclear. Using a database of 1306 women and a linear regression model, we systematically analysed the contribution of FM to the total variance in REE at different grades of adiposity (ranges of body %FM). After adjusting for age, the relative contribution of FM on REE variance increased from low ( ≤ 10 %FM) to normal (>10– ≤ 30 %FM) and moderately elevated (>30– ≤ 40 %FM) grades of adiposity but decreased sharply at high (>40– ≤ 50 %FM) and very high (>50 %FM) grades of adiposity according to the ratio between regression coefficients. These data suggest that the specific metabolic rate of fat tissue is reduced at high adiposity. This should be considered when REE is normalized for FM in obesity.
Consumption of mate tea (Ilex paraguariensis) decreases the oxidation of unsaturated fatty acids in mouse liver
Authors: Martins Fernanda , Suzan Amanda Janaína , Cerutti Suzete Maria , Arçari Demétrius Paiva , Ribeiro Marcelo Lima , Bastos Débora Helena Markowicz , Carvalho Patrícia de Oliveira 
Published: August 2008

Mate (Ilex paraguariensis) is rich in polyphenolic compounds, which are thought to contribute to the health benefits of tea. Mate tea was administered orally to mice at a dose of 0·5, 1·0 or 2·0 g/kg for 60 d, and changes both in serum lipid concentration and fatty acid composition of liver and kidney were examined. The effects of mate tea on serum and tissue lipid peroxidation were assessed by the evaluation of thiobarbituric acid-reactive substances (TBARS). In tea-consuming mice, both MUFA (18 : 1n-9) and PUFA (18 : 2n-6 and 20 : 4n-6) were increased (P < 0·05) in the liver lipid (approximately 90 and 60 %, respectively), whereas only MUFA (approximately 20 %) were increased in the kidney lipid. The most altered PUFA class wasn-6 PUFA, which increased by approximately 60–75 % (P < 0·05). This difference in the fatty acid profile in the liver is reflected in the increased PUFA:SFA ratio. Consistent with these results, mice fed with mate tea had much lower TBARS in the liver. No differences (P>0·05) were found in the levels of serum cholesterol, HDL-cholesterol and TAG under the conditions of the present study. These results suggest that treatment with mate tea was able to protect unsaturated fatty acids from oxidation and may have selective protective effects within the body, especially on the liver.
The effects of a reduced-sodium, high-potassium salt substitute on food taste and acceptability in rural northern China
Authors: Li Nicole , Prescott John , Wu Yangfeng , Barzi Federica , Yu Xuequn , Zhao Liancheng , Neal Bruce ,   for the China Salt Substitute Study Collaborative Group
Published: August 2008

A potassium chloride-containing salt substitute lowers blood pressure levels, but its overall acceptability has been of concern due to its potential adverse effects on food taste. In a large-scale, blinded randomised trial evaluating the comparative effects of a salt substitute (65 % sodium chloride, 25 % potassium chloride and 10 % magnesium sulphate) and a normal salt (100 % sodium chloride) on blood pressure, we collected data on the saltiness, flavour and overall acceptability of food. We performed this at baseline, 1, 6 and 12 months post-randomisation using 100 mm visual analogue scales for assessments of both home-cooked foods and a standard salty soup. The mean age of the 608 participants from rural northern China was 60 years and 56 % of them were females. In the primary analyses, the changes in the saltiness, flavour and overall acceptability of both home-cooked foods and a standard salty soup were not different between the randomised groups (all P>0·08). In the secondary analyses, weighting each of the data points according to the lengths of the respective follow-up intervals, the flavour of both home-cooked foods (mean difference = − 1·8 mm, P = 0·045) and a standard salty soup (mean difference = − 1·9 mm, P = 0·03) was slightly weaker in the salt substitute group. We conclude that salt substitution is both an effective and an acceptable means of blood pressure control. Possible small differences in flavour did not importantly deter the use of the salt substitute in this study group, although the acceptability of the salt substitute by a more general population group would need to be confirmed.
Effects of dietary supplementation with the green tea polyphenol epigallocatechin-3-gallate on insulin resistance and associated metabolic risk factors: randomized controlled trial
Authors: Brown A. Louise , Lane Joan , Coverly Jacqueline , Stocks Janice , Jackson Sarah , Stephen Alison , Bluck Les , Coward Andy , Hendrickx Hilde 
Published: August 2008

Animal evidence indicates that green tea may modulate insulin sensitivity, with epigallocatechin-3-gallate (EGCG) proposed as a likely health-promoting component. The purpose of this study was to investigate the effect of dietary supplementation with EGCG on insulin resistance and associated metabolic risk factors in man. Overweight or obese male subjects, aged 40–65 years, were randomly assigned to take 400 mg capsules of EGCG (n46) or the placebo lactose (n42), twice daily for 8 weeks. Oral glucose tolerance testing and measurement of metabolic risk factors (BMI, waist circumference, percentage body fat, blood pressure, total cholesterol, LDL-cholesterol, HDL-cholesterol, TAG) was conducted pre- and post-intervention. Mood was evaluated weekly using the University of Wales Institute of Science and Technology mood adjective checklist. EGCG treatment had no effect on insulin sensitivity, insulin secretion or glucose tolerance but did reduce diastolic blood pressure (mean change: placebo − 0·058 (se0·75) mmHg; EGCG − 2·68 (se0·72) mmHg;P = 0·014). No significant change in the other metabolic risk factors was observed. The EGCG group also reported feeling in a more positive mood than the placebo group across the intervention period (mean score for hedonic tone: EGCG, 29·11 (se0·44); placebo, 27·84 (se0·46);P = 0·048). In conclusion, regular intake of EGCG had no effect on insulin resistance but did result in a modest reduction in diastolic blood pressure. This antihypertensive effect may contribute to some of the cardiovascular benefits associated with habitual green tea consumption. EGCG treatment also had a positive effect on mood. Further studies are needed to confirm the findings and investigate their mechanistic basis.