bluuebunny/crossref_metadata_2025 huggingface dataset:
Selective enrichment and ultrasensitive identification of trace peptides in proteome analysis using transient capillary isotachophoresis/zone electrophoresis coupled with nano‐ESI‐MS
Authors: An Yanming , Cooper Jonathan W. , Balgley Brian M. , Lee Cheng S.
Published: August 2006

Besides the complexity in protein samples of biological origin, probably the greatest challenge presently facing comprehensive proteome analysis is related to the large variation of protein relative abundances (>6 orders of magnitude), having potential biological significance in mammalian systems. As demonstrated in this work, transient capillary ITP/zone electrophoresis (CITP/CZE) provides selective analyte enrichment through electrokinetic stacking and extremely high resolving power toward protein and peptide mixtures. The result of the CITP process is that major components may be diluted, but trace compounds are concentrated. The on‐column transition of CITP to CZE minimizes additional band broadening while providing superior analyte resolution. Online coupling of transient CITP/CZE with nano‐ESI‐MS allows ultrasensitive detection of trace peptides at levels of subnanomolar concentration or subfemtomole mass in complex peptide mixtures. More importantly, selective enrichment of trace peptides enables the identification and sequence analysis of low‐abundance peptides co‐migrated with highly abundant species at a concentration ratio of 1:500 000. The combined CITP/CZE‐nano‐ESI‐MS system is demonstrated to be at least one to two orders of magnitude more sensitive than that attained in conventional electrophoretic and chromatographic‐based proteome technologies over a wide dynamic concentration range, potentially allowing comprehensive analysis of protein profiles within a small cell population and limited tissue samples using conventional mass spectrometers. Furthermore, the speed of CITP/CZE separation and the lack of column equilibration in CITP/CZE not only improve the throughput of proteome analysis, but also facilitate its seamless integration with other separation technologies in a multidimensional protein identification platform.
Capillary electrophoresis‐based separation techniques for the analysis of proteins
Authors: Huang Yu‐Fen , Huang Chih‐Chin , Hu Cho‐Chun , Chang Huan‐Tsung
Published: August 2006

CE offers the advantages of high speed, great efficiency, as well as the requirement of minimum amounts of sample and buffer for the analysis of proteins. In this review, we summarize the CE‐based techniques coupled with absorption, LIF, and MS detection systems for the analysis of proteins mostly within the past 5 years. The basic principle of each technique and its advantages and disadvantages for protein analysis are discussed in brief. Advanced CE techniques, including on‐column concentration techniques and high‐efficiency multidimensional separation techniques, for high‐throughput protein profiling of complex biological samples and/or of single cells are emphasized. Although the developed techniques provide improved peak capacity, they have not become practical tools for proteomics, mainly because of poor reproducibility, low‐sample lading capacity, and low throughput due to ineffective interfaces between two separation dimensions and that between separation and MS systems. In order to identify the complexities and dynamics of the proteomes expressed by cells, tissues, or organisms, techniques providing improved analytical sensitivity, throughput, and dynamic ranges are still demanded.

This paper is dedicated to the memory of a great mentor of H. T. Chang, Andreas Chrambach.
Dimethyl multiplexed labeling combined with microcolumn separation and MS analysis for time course study in proteomics
Authors: Hsu Jue‐Liang , Huang Sheng‐Yu , Chen Shu‐Hui
Published: August 2006

Stable‐isotope labeling coupled with liquid‐phase separation and MS analysis is a powerful technique for comparative proteomics. We developed a dimethyl labeling strategy (Anal. Chem. 2003, 75, 6843–6852 and J. Proteome Res. 2005, 4, 101–108) to label peptide N‐terminus and ε‐amino groups of Lys with water‐soluble formaldehyde via reductive methylation, and an isotopic pair of formaldehyde is used for binary labeling on two sets of samples. In this study, this approach is extended to a four sample labeling by combining the binary isotopic reagents of formaldehyde (d0, d2) and the binary isotopic reducing reagents, sodium cyanoborohydride (d0, d3). To ensure sufficient mass difference, this multiplexed labeling is coupled with endoproteinase Lys‐C instead of trypsin for digestion, resulting in at least two labeling sites with a mass difference of 4 Da for each pair of peptide digest. Moreover, multiplex dimethyl labeling was proved to have no significant isotopic effect during RP LC elution. This method was further applied for monitoring Lys‐C digestion using hemoglobin as a model. Dimethyl labeled digests derived from seven time points (1–30 h) were grouped into two sets of sample mixtures, separated by nano‐LC to reduce the complexity, and then analyzed by ESI‐MS/MS. The temporal study reveals that Lys‐C digestion was completed in 10–15 h for all detected peptides. The multiplex dimethyl method has not only provided a simultaneous detection mean for four sample sets but has also conserved all the advantages associated with the original binary method.
Microfluidic technologies for MALDI‐MS in proteomics
Authors: DeVoe Don L. , Lee Cheng S.
Published: August 2006

The field of microfluidics continues to offer great promise as an enabling technology for advanced analytical tools. For biomolecular analysis, there is often a critical need to couple on‐chip microfluidic sample manipulation with back‐end MS. Though interfacing microfluidics to MS has been most often reported through the use of direct ESI‐MS, there are compelling reasons for coupling microfluidics to MALDI‐MS as an alternative to ESI‐MS for both online and offline analysis. The intent of this review is to provide a summary of recent developments in the integration of microfluidic systems with MALDI‐MS, with an emphasis on applications in proteomics. Key points are summarized, followed by a review of relevant technologies and a discussion of outlook for the field.
Analyzing wildfire threat counts using a negative binomial regression model
Authors: Quintanilha J. A. , Ho L. L.
Published: August 2006

The fire‐monitoring program managed by the Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis collected fire pixel counts from 1998 to 2002 and used them as a measure of wildfire threats for the Amazon region. The objective of the study was to identify the most relevant explanatory variables related to the frequency of fire pixel occurrence. The sample unit was the municipality, the dependent variable was a function of fire pixel counts, and the explanatory variables were related to land management, census, and agricultural data. A generalized longitudinal linear model was used. The most relevant explanatory variables were administrative limits, year, type of region, season, percentages of deforested area and male population, extent of unpaved road, and density of cattle. Approximately 95% of the standardized residuals resulting from fitting the model were in the interval [−2, +2]. Copyright © 2006 John Wiley & Sons, Ltd.
Sampling and variance estimation on continuous domains
Authors: Cooper Cynthia
Published: August 2006

This paper explores fundamental concepts of design‐ and model‐based approaches to sampling and estimation for a response defined on a continuous domain. The paper discusses the concepts in design‐based methods as applied in a continuous domain, the meaning of model‐based sampling, and the interpretation of the design‐based variance of a model‐based estimate. A model‐assisted variance estimator is examined for circumstances for which a direct design‐based estimator may be inadequate or not available. The alternative model‐assisted variance estimator is demonstrated in simulations on a realization of a response generated by a process with exponential covariance structure. The empirical results demonstrate that the model‐assisted variance estimator is less biased and more efficient than Horvitz–Thompson and Yates–Grundy variance estimators applied to a continuous‐domain response. Copyright © 2006 John Wiley & Sons, Ltd.
A Bayesian hierarchical extreme value model for lichenometry
Authors: Cooley Daniel , Naveau Philippe , Jomelli Vincent , Rabatel Antoine , Grancher Delphine
Published: August 2006

Currently, there is a tremendous scientific research effort in the area of climate change. In this paper, our motivation is to improve the understanding of historical climatic events such as the Little Ice Age (LIA), a period of relatively cold weather around 1450–1850 AD. Although the LIA is well documented in Europe, its extent and timing are not known in areas of the globe where climatological records were not kept during this period.

To study the climate, which predates historical records, proxy climate records must be used. A proxy record for the timing of climatic cooling events are the ages of the moraines left behind by glacial advances. Unfortunately, to determine the ages of these moraines in alpine environments there is little material available but lichens. Hence, lichenometry was developed to determine the ages of glacial landforms by using lichen measurements. To our knowledge, this article provides the first attempt at deriving a comprehensive statistical model for lichenometry. Our model foundation is based on extreme value theory because only the largest lichens are measured in lichenometry studies. This application is novel to extreme value theory because the quantities of interest (the ages of climatic events) are not the measured quantities (lichen diameters), i.e., it is a inverse problem.

We model the lichen measurements with the generalized extreme value (GEV) distribution, upon which a Bayesian hierarchical model is built. The hierarchical model enables estimation of the hidden covariate ages of the moraines. The model also allows for pooling of data from different locations and evaluation of spatial differences in lichen growth. Parameter inference is obtained using a straightforward Markov Chain Monte Carlo method. Our procedure is applied to data gathered from the Cordillera Real region in Bolivia. Copyright © 2006 John Wiley & Sons, Ltd.
Network design for verification of ceiling and visibility forecasts
Authors: Gilleland Eric , Fowler Tressa L.
Published: August 2006

Cloud ceiling height and visibility forecasts are of importance for use in flight planning. This is particularly true for the general aviation community, where pilots who are not instrument rated must avoid flying in areas with poor visibility conditions. These forecasts rely on data obtained from Aviation Routine Weather Report (METAR) stations. Two issues arise in the verification of ceiling and visibility forecasts: (i) forecasts with short‐to‐no lead time (i.e., nowcasts) require use of the same METAR observations for forecast creation and verification, and (ii) placement of reporting stations may introduce bias in the verification analysis. Independent data is necessary for an accurate verification, but because the same data are used to verify the nowcasts as are used to create the nowcasts, the data are not independent. A common strategy is to divide the data into testing and training sets to obtain quasi‐independent data. The second issue arises from the fact that the METAR stations are unevenly spaced so that a forecast verification is potentially biased for areas with numerous stations; thereby giving little or no information on forecast performance elsewhere. In this paper, we present a network thinning strategy to obtain a reasonable subset network of METAR stations that is more ‘regularly’ spaced. The strategy involves three steps: (i) an initial inspection of graphs of pair‐wise agreement between stations by distance, (ii) a coverage design algorithm, and finally (iii) inspection of the distributions of verification scores among various designs and the original network. We give test examples for two different regions in the United States. In each case, it seems reasonable to reduce the network size by nearly half of the original number of stations. The resulting designs are regularly spaced, and verification results for the original network are very similar to those for the thinned networks. Copyright © 2006 John Wiley & Sons, Ltd.
Landscape‐based geostatistics: a case study of the distribution of blue crab in Chesapeake Bay
Authors: Jensen Olaf P. , Christman Mary C. , Miller Thomas J.
Published: August 2006

Geostatistical techniques have gained widespread use in ecology and environmental science. Variograms are commonly used to describe and examine spatial autocorrelation, and kriging has become the method of choice for interpolating spatially‐autocorrelated variables. To date, most applications of geostatistics have defined the separation between sample points using simple Euclidean distance. In heterogeneous environments, however, certain landscape features may act as absolute or semi‐permeable barriers. This effective separation may be more accurately described by a measure of distance that accounts for the presence of barriers. Here we present an approach to geostatistics based on a lowest‐cost path (LCP) function, in which the cost of a path is a function of both the distance and the type of terrain crossed. The modified technique is applied to 13 years of survey data on blue crab abundance in Chesapeake Bay. Use of this landscape‐based distance metric significantly changed estimates of all three variogram parameters. In this case study, although local differences in kriging predictions were apparent, the use of the landscape‐based distance metric did not result in consistent improvements in kriging accuracy. Copyright © 2006 John Wiley & Sons, Ltd.
Probabilistic risk assessment for wildfires
Authors: Brillinger D. R. , Preisler H. K. , Benoit J. W.
Published: August 2006

Forest fires are an important societal problem. They cause extensive damage and substantial funds are spent preparing for and fighting them. This work develops a stochastic model useful for probabilistic risk assessment, specifically to estimate chances of fires at a future time given explanatory variables. Questions of interest include: Are random effects needed in the risk model? and if yes, How is the analysis to be implemented? An exploratory data analysis approach is taken using both fixed and random effects models for data concerning the Federal Lands in the state of California during the period 2000–2003. Published in 2006 by John Wiley & Sons, Ltd.
Adolescent inpatient treatment for anorexia nervosa: a qualitative study exploring young adults' retrospective views of treatment and discharge
Authors: Offord Abaigh , Turner Hannah , Cooper Myra
Published: August 2006

Objective

To explore young adults' views regarding: the inpatient treatment they received for anorexia nervosa during their adolescences; their experiences of discharge; and the impact their admission had on issues of control and low self‐esteem.

Method

Semi‐structured interviews were conducted with seven young adults treated in general adolescent psychiatric units. Data were analysed using Interpretative Phenomenological Analysis.

Results

Four super‐ordinate themes emerged from participants' accounts: (1) Removal from normality versus connecting with the outside world; (2) Treated as another anorexic versus a unique individual in distress; (3) Control and collaboration; (4) The importance of peer relationships.

Discussion

Findings unique to this study concerned a sense of feeling removed and disconnected from ‘normality’; a feeling that one's developmental needs were not always addressed; and the importance placed on supportive relationships with fellow patients. It was also found that authoritarian approaches may compound patients' feelings of ineffectiveness, worthlessness and isolation. Copyright © 2006 John Wiley & Sons, Ltd and Eating Disorders Association.
The relationship between two‐dimensional self‐esteem and problem solving style in an anorexic inpatient sample
Authors: Paterson Gillian , Power Kevin , Yellowlees Alex , Park Katy , Taylor Louise
Published: August 2006

Objective

Research examining cognitive and behavioural determinants of anorexia is currently lacking. This has implications for the success of treatment programmes for anorexics, particularly, given the high reported dropout rates. This study examines two‐dimensional self‐esteem (comprising of self‐competence and self‐liking) and social problem‐solving in an anorexic population and predicts that self‐esteem will mediate the relationship between problem‐solving and eating pathology by facilitating/inhibiting use of faulty/effective strategies.

Method

Twenty‐seven anorexic inpatients and 62 controls completed measures of social problem solving and two‐dimensional self‐esteem.

Results

Anorexics scored significantly higher than the non‐clinical group on measures of eating pathology, negative problem orientation, impulsivity/carelessness and avoidance and significantly lower on positive problem orientation and both self‐esteem components. In the clinical sample, disordered eating correlated significantly with self‐competence, negative problem‐orientation and avoidance. Associations between disordered eating and problem solving lost significance when self‐esteem was controlled in the clinical group only. Self‐competence was found to be the main predictor of eating pathology in the clinical sample while self‐liking, impulsivity and negative and positive problem orientation were main predictors in the non‐clinical sample.

Discussion

Findings support the two‐dimensional self‐esteem theory with self‐competence only being relevant to the anorexic population and support the hypothesis that self‐esteem mediates the relationship between disordered eating and problem solving ability in an anorexic sample. Treatment implications include support for programmes emphasising increasing self‐appraisal and self‐efficacy. Copyright © 2006 John Wiley & Sons, Ltd and Eating Disorders Association.
Using fully implicit conservative statements to close open boundaries passing through recirculations
Authors: Darbandi Masoud , Vakilipour Shidvash
Published: August 2006

The numerical solution of the fluid flow governing equations requires the implementation of certain boundary conditions at suitable places to make the problem well‐posed. Most of numerical strategies exhibit weak performance and obtain inaccurate solutions if the solution domain boundaries are not placed at adequate locations. Unfortunately, many practical fluid flow problems pose difficulty at their boundaries because the required information for solving the PDE's is not available there. On the other hand, large solution domains with known boundary conditions normally need a higher number of mesh nodes, which can increase the computational cost. Such difficulties have motivated the CFD workers to confine the solution domain and solve it using artificial boundaries with unknown flow conditions prevailing there. In this work, we develop a general strategy, which enables the control‐volume‐based methods to close the outflow boundary at arbitrary locations where the flow conditions are not known prior to the solution. In this regard, we extend suitable conservative statements at the outflow boundary. The derived statements gradually detect the correct boundary conditions at arbitrary boundaries via an implicit procedure using a finite element volume method. The extended statements are validated by solving the truncated benchmark backward‐facing step problem. The investigation shows that the downstream boundary can pass through a recirculation zone without deteriorating the accuracy of the solution either in the domain or at its boundaries. The results indicate that the extended formulation is robust enough to be employed in solution domains with unknown boundary conditions. Copyright © 2006 John Wiley & Sons, Ltd.
An operator splitting scheme for the stream‐function formulation of unsteady Navier–Stokes equations
Authors: Christov C. I. , Tang X.‐H.
Published: August 2006

A fictitious time is introduced into the unsteady equation of the stream function rendering it into a higher‐order ultra‐parabolic equation. The convergence with respect to the fictitious time (we call the latter ‘internal iterations’) allows one to obtain fully implicit nonlinear scheme in full time steps for the physical‐time variable. For particular choice of the artificial time increment, the scheme in full time steps is of second‐order of approximation. For the solution of the internal iteration, a fractional‐step scheme is proposed based on the splitting of the combination of the Laplace, bi‐harmonic and advection operators. A judicious choice for the time staggering of the different parts of the nonlinear advective terms allows us to prove that the internal iterations are unconditionally stable and convergent. We assess the number of operations needed per time step and show computational effectiveness of the proposed scheme. We prove that when the internal iterations converge, the scheme is second‐order in physical time and space, nonlinear, implicit and absolutely stable. The performance of the scheme is demonstrated for the flow created by oscillatory motion of the lid of a square cavity. All theoretical findings are demonstrated practically. Copyright © 2006 John Wiley & Sons, Ltd.
Multigrid third‐order least‐squares solution of Cauchy–Riemann equations on unstructured triangular grids
Authors: Nishikawa H.
Published: August 2006

In this paper, a multigrid algorithm is developed for the third‐order accurate solution of Cauchy–Riemann equations discretized in the cell‐vertex finite‐volume fashion: the solution values stored at vertices and the residuals defined on triangular elements. On triangular grids, this results in a highly overdetermined problem, and therefore we consider its solution that minimizes the residuals in the least‐squares norm. The standard second‐order least‐squares scheme is extended to third‐order by adding a high‐order correction term in the residual. The resulting high‐order method is shown to give sufficiently accurate solutions on relatively coarse grids. Combined with a multigrid technique, the method then becomes a highly accurate and efficient solver. We present some results to demonstrate its accuracy and efficiency, including both structured and unstructured triangular grids. Copyright © 2006 John Wiley & Sons, Ltd.
A robust numerical method for flow through a pipe driven by an oscillating pressure gradient
Authors: Ansari Ali R. , Miller John J. H. , Shishkin Grigori I.
Published: August 2006

The problem of periodic flow of an incompressible fluid through a pipe, which is driven by an oscillating pressure gradient (e.g. a reciprocating piston), is investigated in the case of a large Reynolds number. This process is described by a singularly perturbed parabolic equation with a periodic right‐hand side, where the singular perturbation parameter is the viscosity ν. The periodic solution of this problem is a solution of the Navier–Stokes equations with cylindrical symmetry. We are interested in constructing a parameter‐robust numerical method for this problem, i.e. a numerical method generating numerical approximations that converge uniformly with respect to the parameter ν and require a bounded time, independent of the value of ν, for their computation. Our method comprises a standard monotone discretization of the problem on non‐standard piecewise uniform meshes condensing in a neighbourhood of the boundary layer. The transition point between segments of the mesh with different step sizes is chosen in accordance with the behaviour of the analytic solution in the boundary layer region. In this paper we construct the numerical method and discuss the results of extensive numerical experiments, which show experimentally that the method is parameter‐robust. Copyright © 2006 John Wiley & Sons, Ltd.
Computational study of the axial instability of rimming flow using Arnoldi method
Authors: Bae Sun Hyuk , Kim Do Hyun
Published: August 2006

Axial instability of rimming flow has been investigated by solving a linear generalized eigenvalue problem that governs the evolution of perturbations of two‐dimensional base flow. Using the Galerkin finite element method, full Navier–Stokes equations were solved to calculate base flow and this base flow was perturbed with three‐dimensional disturbances. The generalized eigenproblem formulated from these equations was solved by the implicitly restarted Arnoldi method using shift‐invert technique. This study presents instability curves to identify the critical wavelength of the neutral mode and the critical β, which measures the importance of gravity relative to viscosity. The axial instability of rimming flow is examined and three‐dimensional flow was reconstructed by using eigenvector and growth rate at a critical wave number. The critical β value in the axial instability analysis was observed to be comparable to the onset β value of the transition between the bump and the homogeneous film state in 2‐D base flow calculations. Copyright © 2006 John Wiley & Sons, Ltd.
Adaptive wall functions for the v2‐f turbulence model
Authors: Kalitzin Georgi , Medic Gorazd
Published: August 2006

Adaptive wall functions for the v2‐f turbulence model have been derived for the flow over a flat plate at zero pressure gradient. These wall functions were implemented via tables for the turbulence quantities and the friction velocity uτ. A special treatment for the ε and f boundary conditions is proposed. On fine grids (y+<1) this approach yields results consistent with the wall integration solution. Detailed numerical results are presented for a zero pressure gradient boundary layer and separated flow over a ramp. Copyright © 2006 John Wiley & Sons, Ltd.
A two‐phase flow interface capturing finite element method
Authors: Devals C. , Heniche M. , Bertrand F. , Tanguy P. A. , Hayes R. E.
Published: August 2006

A new interface capturing algorithm is proposed for the finite element simulation of two‐phase flows. It relies on the solution of an advection equation for the interface between the two phases by a streamline upwind Petrov–Galerkin (SUPG) scheme combined with an adaptive mesh refinement procedure and a filtering technique. This method is illustrated in the case of a Rayleigh–Taylor two‐phase flow problem governed by the Stokes equations. Copyright © 2006 John Wiley & Sons, Ltd.
Comparison of derivative free Newton‐based and evolutionary methods for shape optimization of flow problems
Authors: Harth Zerrin , Sun Hongtao , Schäfer Michael
Published: August 2006

The object of this study is to investigate two derivative free optimization techniques, i.e. Newton‐based method and an evolutionary method for shape optimization of flow geometry problems. The approaches are compared quantitatively with respect to efficiency and quality by using the minimization of the pressure drop of a pipe conjunction which can be considered as a representative test case for a practical three‐dimensional flow configuration. The comparison is performed by using CONDOR representing derivative free Newton‐based techniques and SIMPLIFIED NSGA‐II as the representative of evolutionary methods (EM).

For the shape variation the computational grid employed by the flow solver is deformed. To do this, the displacement fields are scaled by design variables and added to the initial grid configuration. The displacement vectors are calculated once before the optimization procedure by means of a free form deformation (FFD) technique.

The simulation tool employed is a parallel multi‐grid flow solver, which uses a fully conservative finite‐volume method for the solution of the incompressible Navier–Stokes equations on a non‐staggered, cell‐centred grid arrangement. For the coupling of pressure and velocity a pressure‐correction approach of SIMPLE type is used. The possibility of parallel computing and a multi‐grid technique allow for a high numerical efficiency. Copyright © 2006 John Wiley & Sons, Ltd.
Unsteady simulations of the flow around a short surface‐mounted cylinder
Authors: Pattenden R. J. , Bressloff N. W. , Turnock S. R. , Zhang X.
Published: August 2006

The flow around a surface‐mounted circular cylinder, of height/diameter ratio 1 with a free end, is simulated using large‐eddy simulation (LES) and detached‐eddy simulation (DES) at a Reynolds number based on diameter of 200 000. A comparison is made between the abilities of the two models to capture flow features observed in particle image velocimetry (PIV) experiments carried out by the authors. The flow contains three interacting features formed from the junction flow between the cylinder and the ground, separation from the cylinder wall and resultant turbulent wake, and the flow over the free‐end of the cylinder. Both LES and DES overpredict the length of the recirculation region by 30%, but the turbulence quantities are close to the measured values. The topology of the flow over the free‐end is confirmed as consisting of an arch or ‘mushroom’ vortex. Due to the high Reynolds number the grid resolution is insufficient to resolve the approaching ground‐plane boundary layer flow with LES, leading to inaccuracies in the horseshoe vortex system. The DES model improves this area, though still has grid induced separation effects. Copyright © 2006 John Wiley & Sons, Ltd.
Numerical identification of flow‐induced oscillation modes in rectangular cavities using large eddy simulation
Authors: Rubio G. , De Roeck W. , Baelmans M. , Desmet W.
Published: August 2006

Self‐sustained oscillations are present in a wide variety of flows. For flows passing cavities, acoustics can play a role in the physical mechanisms triggering and maintaining the oscillation phenomena. This is the case for the flow over rectangular cavities, which is studied in this paper. The compressible LES Navier–Stokes equations are solved for cavities with an upstream laminar boundary layer. The flow passing rectangular cavities is computed, varying two different parameters related to the physics of the problem, Mach number and length of the cavity divided by the momentum thickness of the boundary layer at the leading edge. This paper intends to prove that the switch between shear‐layer oscillation mode, characterized by an acoustic feedback process, and wake oscillation mode, characterized by a large‐scale vortex shedding with Strouhal number independent of Mach number, can be identified using large eddy simulation, and consequently, with much less computational effort than in other studies in literature, where direct numerical simulation has been applied. Copyright © 2006 John Wiley & Sons, Ltd.
A methodology for high performance computation of fully inhomogeneous turbulent flows
Authors: You Donghyun , Wang Meng , Mittal Rajat
Published: August 2006

A large‐eddy simulation methodology for high performance parallel computation of statistically fully inhomogeneous turbulent flows on structured grids is presented. Strategies and algorithms to improve the memory efficiency as well as the parallel performance of the subgrid‐scale model, the factored scheme, and the Poisson solver on shared‐memory parallel platforms are proposed and evaluated. A novel combination of one‐dimensional red–black/line Gauss–Seidel and two‐dimensional red–black/line Gauss–Seidel methods is shown to provide high efficiency and performance for multigrid relaxation of the Poisson equation. Parallel speedups are measured on various shared‐distributed memory systems. Validations of the code are performed in large‐eddy simulations of turbulent flows through a straight channel and a square duct. Results obtained from the present solver employing a Lagrangian dynamic subgrid‐scale model show good agreements with other available data. The capability of the code for more complex flows is assessed by performing a large‐eddy simulation of the tip‐leakage flow in a linear cascade. Copyright © 2006 John Wiley & Sons, Ltd.
Efficiency of a POD‐based reduced second‐order adjoint model in 4D‐Var data assimilation
Authors: Daescu D. N. , Navon I. M.
Published: August 2006

Order reduction strategies aim to alleviate the computational burden of the four‐dimensional variational data assimilation by performing the optimization in a low‐order control space. The proper orthogonal decomposition (POD) approach to model reduction is used to identify a reduced‐order control space for a two‐dimensional global shallow water model. A reduced second‐order adjoint (SOA) model is developed and used to facilitate the implementation of a Hessian‐free truncated‐Newton (HFTN) minimization algorithm in the POD‐based space. The efficiency of the SOA/HFTN implementation is analysed by comparison with the quasi‐Newton BFGS and a nonlinear conjugate gradient algorithm. Several data assimilation experiments that differ only in the optimization algorithm employed are performed in the reduced control space. Numerical results indicate that first‐order derivative methods are effective during the initial stages of the assimilation; in the later stages, the use of second‐order derivative information is of benefit and HFTN provided significant CPU time savings when compared to the BFGS and CG algorithms. A comparison with data assimilation experiments in the full model space shows that with an appropriate selection of the basis functions the optimization in the POD space is able to provide accurate results at a reduced computational cost. The HFTN algorithm benefited most from the order reduction since computational savings were achieved both in the outer and inner iterations of the method. Further experiments are required to validate the approach for comprehensive global circulation models. Copyright © 2006 John Wiley & Sons, Ltd.
A piecewise linear approach to volume tracking a triple point
Authors: Choi Benjamin Y. , Bussmann Markus
Published: August 2006

An approach to volume tracking three materials is presented that, in contrast with the so‐called ‘onion‐skin’ methodology, assumes the existence of a ‘triple point’ at which two interfaces between three materials intersect. The reconstruction of any cell that contains three materials is iterative: the approach is to locate a point of intersection between two interfaces that minimizes a given error expression. The advantages and limitations of the algorithm are presented via a series of advection tests that demonstrate that triple points can be reconstructed and advected just as well as simpler interfaces in typical applications. Copyright © 2006 John Wiley & Sons, Ltd.
Tumor necrosis factor and its p55 and p75 receptors are not required for axonal lesion‐induced microgliosis in mouse fascia dentata
Authors: Fenger Christina , Drojdahl Nina , Wirenfeldt Martin , Sylvest Lene , Jorgensen Ole Steen , Meldgaard Michael , Lambertsen Kate L. , Finsen Bente
Published: August 2006

Tumor necrosis factor (TNF) is a potent pro‐inflammatory and neuromodulatory cytokine. In the CNS it is produced primarily by microglia and considered to regulate microglial activation. On the basis of previous observations of increased microglial TNF mRNA synthesis in areas of anterograde axonal and terminal degeneration in mice, we studied the effect of TNF and its p55 and p75 receptors on axonal lesion‐induced microglial activation in fascia dentata following transection of the perforant path (PP) projection. Unexpectedly, cell counting showed that the axonal lesion‐induced microglial response in TNF and TNF‐p55p75 receptor knock out mice and C57BL/6 mice was similar 5 days after the lesion. In addition, the microglial expression of the lysosomal‐associated antigen CD68, and the clearance of MBP+ myelin debris appeared similar in TNF and TNF‐p55p75 receptor knock out mice compared to C57BL/6 mice. Quantitative PCR and in situ hybridization showed the expression of TNF mRNA to be maximally upregulated 6 h after the lesion, and confirmed that TNF mRNA was still upregulated 5 days after lesion when microglial numbers, CD11b mRNA level, and cellular TNF‐p55 and ‐p75 receptor mRNA level reached maximum. However, in spite of the induction of TNF mRNA, TNF protein level remained at base‐line in fascia dentata using immunohistochemistry and ELISA. In conclusion, the results showed a lower than expected lesion‐induced increase in TNF protein, and that neither TNF nor its receptors were required for the axonal lesion‐induced microglial morphological transformation and proliferation or for the initial clearance of degenerated myelin in the PP‐deafferented fascia dentata. © 2006 Wiley‐Liss, Inc.
Rafts in oligodendrocytes: Evidence and structure–function relationship
Authors: Gielen Ellen , Baron Wia , Vandeven Martin , Steels Paul , Hoekstra Dick , Ameloot Marcel
Published: August 2006

The plasma membrane of eukaryotic cells exhibits lateral inhomogeneities, mainly containing cholesterol and sphingomyelin, which provide liquid‐ordered microdomains (lipid “rafts”) that segregate membrane components. Rafts are thought to modulate the biological functions of molecules that become associated with them, and as such, they appear to be involved in a variety of processes, including signal transduction, membrane sorting, cell adhesion and pathogen entry. Although still a matter of ongoing debate, evidence in favor of the presence of these microdomains is gradually accumulating but a consensus on issues like their size, lifetime, composition, and biological significance has yet to be reached. Here, we provide an overview of the evidence supporting the presence of rafts in oligodendrocytes, the myelin‐producing cells of the central nervous system, and discuss their functional significance. The myelin membrane differs fundamentally from the plasma membrane, both in lipid and protein composition. Moreover, since myelin membranes are unusually enriched in glycosphingolipids, questions concerning the biogenesis and functional relevance of microdomains thus appear of special interest in oligodendrocytes. The current picture of rafts in oligodendrocytes is mainly based on detergent methods. The robustness of such data is discussed and alternative methods that may provide complementary data are indicated. © 2006 Wiley‐Liss, Inc.
The impact of the CERAD‐NP on diagnosis of cognitive deficiencies in late onset depression and Alzheimer's disease
Authors: Künig Gabriella , Jäger Michael , Stief Volker , Kaldune Andreas , Urbaniok Frank , Endrass Jerome
Published: August 2006

Objectives

To identify the most appropriate test combination for distinguishing between late onset depression (LOD) and Alzheimer's disease (AD). To achieve this objective, the Consortium to Establish a Register for Alzheimer's Disease‐Neuropsychological Battery (CERAD‐NP) data of patients diagnosed with these two conditions were analyzed using multiple regression analysis.

Methods

In the first regression analysis, the following CERAD‐NP subtests were included: verbal fluency, Boston naming test, word list learning, constructional praxis, word list recall, and constructional praxis recall. In a second regression analysis, only CERAD‐NP memory parameters were included: word list learning, word list recall, word list intrusions, word list savings, word list recognition, word list false positive errors, constructional praxis recall, and constructional praxis savings.

Results

The combination of word list recall and constructional praxis recall best distinguished between LOD and AD, with a ROC of 0.91. In the stepwise regression of memory measures, word list recall, word list savings, and constructional praxis recall was the best combination, resulting in a ROC of 0.92.

Conclusion

The most efficacious combination of the CERAD‐NP battery for discriminating between LOD and AD consisted of word list recall and constructional praxis recall. Of the CERAD‐NP memory measures, word list recall, word list savings, and constructional praxis recall represented the best diagnostic combination. Copyright © 2006 John Wiley & Sons, Ltd.
Validation of a memory inventory for the assessment of awareness of memory deficits in Alzheimer's disease in Chinese elderly
Authors: Cheong Lui Victor Wing , Wa Lam Linda Chiu , Kum Chiu Helen Fung
Published: August 2006

Background

This paper describes the development and validation of the Memory Inventory for Chinese (MIC), for measuring the awareness of memory deficits in the Chinese population with Alzheimer's disease (AD).

Methods

A combination of qualitative and quantitative approaches was adopted. The MIC was developed with focus group discussion and pilot testing. It has a patient and a caregiver version. A consecutive series of 79 new out‐patients with the National Institute of Neurological and Communicative Disorders and Stroke and the Alzheimer's Disease and Related Disorder Association (NINCDS‐ADRDA) criteria of probable and possible AD and 20 non‐demented elderly subjects were recruited.

Results

A high internal consistency was found, with Cronbach alpha of 0.89 for the patient version and 0.90 for the caregiver version of MIC. The inter‐rater reliability was satisfactory. For validity assessment, the caregiver score of the MIC correlated significantly with cognitive score of the subject as assessed by the Mini‐Mental State Examination (rp = −0.37; p < 0.01). The Memory Deficit Awareness Score, calculated by subtracting the patient score from the caregiver score, correlated significantly with clinician ratings of awareness of memory impairment (rs = −0.67; p < 0.01).

Conclusions

The MIC appears to be a culturally appropriate and valid instrument for the measurement of awareness of memory deficits in Chinese patients with AD. Potential applications of the MIC should be further explored in other subtypes of dementia and in prospective studies. Copyright © 2006 John Wiley & Sons, Ltd.
Subjective complaints and self‐evaluation of memory test performance in Questionable dementia
Authors: Wong Candy Ho Yan , Lam Linda Chiu Wa , Lui Victor Wing Cheong , Chiu Helen Fung Kum , Chan Sandra Sau Man , Tam Cindy Woon Chi
Published: August 2006

Background

The clinical significance of subjective memory complaints in elderly subjects has been an area of active research. In this study, we evaluated subjective complaints and self‐evaluation of memory test performance in subjects with Questionable dementia (QD) and mild Alzheimer's disease (AD).

Methods

Ninety‐two subjects (35 cognitively intact normal controls NC, 33 QD, and 24 mild AD) were assessed. Subjective memory complaints were evaluated using a memory inventory for the Chinese (MIC); objective assessment of awareness was assessed by the self‐evaluation of own memory test performance. Cognitive function was assessed with the Alzheimer's Disease Assessment Scale—Cognitive subscale (ADAS‐Cog), Category Verbal Fluency Test (CVFT) and Executive Interview (EXIT‐25). Depressive symptoms were evaluated with the Cornell Scale for Depression in Dementia (CSDD).

Results

The total number of subjective memory complaints (MI‐tol) were significantly different between different subject groups (Kruskal Wallis test, χ2 = 13.19, p = 0.001). Significant correlations between scores of the MI‐tol and CSDD (r = 0.33, p < 0.001), CMMSE (r = −0.33, p < 0.001), CDR (r = 0.36, p < 0.001) were found. In self‐evaluation of memory test performance, the NC group tended to under‐estimate while the AD subjects tended to over‐estimate their performance. Group differences in the discrepancies of self‐evaluation of memory performance were significant for both the immediate (Kruskal Wallis test, χ2 = 9.86, p = 0.007) and delayed recall (Kruskal Wallis test, χ2 = 10.55, p < 0.001) trials.

Conclusions

Subjects with QD and mild AD showed higher frequency of subjective memory complaints, reflecting that the subjects still retain some ability to appreciate own memory function. However, the trend for over‐estimation of performance in AD subjects suggests that the precision of estimation may be suboptimal. Moreover, depressive symptoms may affect the presentation of memory complaints and this factor should be carefully considered in future prospective studies. Copyright © 2006 John Wiley & Sons, Ltd.
Sleep duration during the 24‐hour day is associated with the severity of dementia in nursing home patients
Authors: Fetveit Arne , Bjorvatn Bjørn
Published: August 2006

Study objectives

To describe the characteristics of 24‐h sleep patterns in nursing home patients with dementia, and to determine whether various degrees of dementia have any influence on total sleep duration.

Design and setting

Cross‐sectional study in a nursing home population (n = 23) consisting of patients with varying degree of dementia. Sleep was measured with actigraphy for a consecutive period of 14 days, based on individual bed and rising time, which was registered by nursing home staff.

Measurements and results

Mean age ± standard deviation was 86.1 ± 7.0 (range 72–96) and mean Mini‐Mental Status Examination Score (MMSE) was 13.4 ± 5.3 (range 1–21). Ten patients had MMSE ≤ 12. Sleep was extremely fragmented, with frequent wake bouts during nighttime and frequent naps during daytime. During the 24‐h period, patients spent nearly 13 h asleep, distributed as more than 9 h of nighttime sleep and more than 3 h of daytime sleep. Patients with severe degree of dementia (MMSE ≤ 12) slept significantly longer during the 24‐h day than patients with lesser degree of dementia (MMSE > 12). There was no significant difference in age between the dementia sub‐groups.

Conclusion

Sleep duration during the 24‐h day was positively correlated with the severity of dementia in nursing home patients. This is in contrast with total sleep time seen in healthy elderly, which shows a gradually decline with age. Changes in sleep patterns in dementia could be explained by co‐morbid and environmental factors, as well as unknown pathological changes related to dementing illnesses. Copyright © 2006 John Wiley & Sons, Ltd.
Diagnosing Aspergers syndrome in the elderly: a series of case presentations
Authors: James Ian Andrew , Mukaetova‐Ladinska Elizabeta , Reichelt F. Katharina , Briel Ruth , Scully Ann
Published: August 2006

Background

There are over 200 000 people in the UK diagnosed with Aspergers Syndrome (AS). Most of these are children and young adults, owing to the fact the disorder was established relatively recently. It can be argued, therefore, that there are many older adults who may have met the criteria for AS as children, but never received such a diagnosis due to the fact it had yet to be established. What happended to these people as they aged?

Method

This paper examines this issue in detail and presents five case studies of elderly individuals who the authors believe meet the criteria of AS.

Results

The work illustrates AS presentation in old age, the assessment problems and tools required to assess older people, and the implications of such formulations for clinical practice.

Conclusion

Older patients with undiagnosed AS may currently be receiving inappropriate treatments. Greater awareness of AS in the older population would enable better management of such patients. Copyright © 2006 John Wiley & Sons, Ltd.