bluuebunny/crossref_metadata_2025_split 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

AbstractBesides 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

AbstractCE 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

AbstractStable‐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

AbstractThe 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

AbstractThe 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

AbstractThis 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

AbstractCurrently, 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

AbstractCloud 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

AbstractGeostatistical 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

AbstractForest 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

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

AbstractObjectiveResearch 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.MethodTwenty‐seven anorexic inpatients and 62 controls completed measures of social problem solving and two‐dimensional self‐esteem.ResultsAnorexics 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.DiscussionFindings 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

AbstractThe 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

AbstractA 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

AbstractIn 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.