bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new integrated statistical approach to the diagnostic use of two‐dimensional maps
Authors: Marengo Emilio , Robotti Elisa , Gianotti Valentina , Righetti Pier Giorgio , Cecconi Daniela , Domenici Enrico 
Published: March 2003

AbstractTwo‐dimensional (2‐D) electrophoresis is a very useful technique for the analysis of proteins in biological tissues. The complexity of the 2‐D maps obtained causes many difficulties in the comparison of different samples. A new method is proposed for comparing different 2‐D maps, based on five steps: (i) the digitalisation of the image; (ii) the transformation of the digitalised map in a fuzzy entity, in order to consider the variability of the 2‐D electrophoretic separation; (iii) the calculation of a similarity index for each pair of maps; (iv) the analysis by multidimensional scaling of the previously obtained similarity matrix; (v) the analysis by classification or cluster analysis techniques of the resulting map co‐ordinates. The method adopted was first tested on some simulated samples in order to evaluate its sensitivity to small changes in the spots position and size. The optimal setting of the method parameters was also investigated. Finally, the method was successfully applied to a series of real samples corresponding to the electrophoretic bidimensional analysis of sera from normal and nicotine‐treated rats. Multidimensional scaling allowed the separation of the two classes of samples without any misclassification.
Proteome analysis using isoelectric focusing in immobilized pH gradient gels followed by mass spectrometry
Authors: Giorgianni Francesco , Desiderio Dominic M. , Beranova‐Giorgianni Sarka 
Published: March 2003

AbstractOver the past several years, a large effort has been focused on improvements of two‐dimensional (2‐D) gel electrophoresis‐based proteomics technology, and on development of novel approaches for proteome analysis. Here, we describe the application of an alternative strategy for the analysis of complex proteomes. The strategy combines isoelectric focusing in immobilized pH gradient strips (in‐gel IEF), mass spectrometry (MS), and bioinformatics. A protein mixture is separated by in‐gel IEF, and the entire strip is cut into a set of gel sections. Proteins in each gel section are digested with trypsin, and the tryptic peptides are subjected to liquid chromatography‐nanoelectrospray‐quadrupole ion‐trap tandem mass spectrometry (LC‐ESI‐MS/MS). The LC‐ESI‐MS/MS data are used to identify the proteins through searches of a protein sequence database. Using this in‐gel IEF‐LC‐MS/MS strategy, we have identified 127 proteins from a human pituitary. This study demonstrates the potential of the in‐gel IEF‐LC‐MS/MS approach for analyses of complex mammalian proteomes.
Two‐dimensional protein map of human vastus lateralis muscle
Authors: Gelfi Cecilia , De Palma Sara , Cerretelli Paolo , Begum Shagn , Wait Robin 
Published: March 2003

AbstractProtein samples of human vastus lateralis muscle were analyzed by two‐dimensional gel electrophoresis, using immobilized pH gradients encompassing several pH regions in the first dimension and sodium dodecyl sulfate‐polyacrylamide gel electrophoresis in the second dimension. More than 500 protein spots on each gel were detected by silver staining, of which 150 were excised, digested in‐gel with trypsin and characterized by matrix assisted laser desorptioin/ionization‐mass spectrometry and tandem electrospray mass spectrometry. Using these techniques, 124 spots including contractile proteins and metabolic enzymes were identified. This database should provide a valuable resource for the definition of the functional properties of muscle fibres and for assessment of the influence of e.g., hypoxia, ischaemia and ageing on protein level.
Microchannel wall coatings for protein separations by capillary and chip electrophoresis
Authors: Doherty Erin A. S. , Meagher Robert J. , Albarghouthi Methal N. , Barron Annelise E. 
Published: March 2003

AbstractThe necessity for microchannel wall coatings in capillary and chip‐based electrophoretic analysis of biomolecules is well understood. The regulation or elimination of EOF and the prevention of analyte adsorption is essential for the rapid, efficient separation of proteins and DNA within microchannels. Microchannel wall coatings and other wall modifications are especially critical for protein separations, both in fused‐silica capillaries, and in glass or polymeric microfluidic devices. In this review, we present a discussion of recent advances in microchannel wall coatings of three major classes – covalently linked polymeric coatings, physically adsorbed polymeric coatings, and small molecule additives. We also briefly review modifications useful for polymeric microfluidic devices. Within each category of wall coatings, we discuss those used to eliminate EOF, to tune EOF, to prevent analyte adsorption, or to perform multiple functions. The knowledgeable application of the most promising recent developments in this area will allow for the separation of complex protein mixtures and for the development of novel microchannel wall modifications.
Micropreparative capillary gel electrophoresis of DNA: Rapid expressed sequence tag library construction
Authors: Shi Liang , Khandurina Julia , Ronai Zsolt , Li Bi‐Yu , Kwan Wai King , Wang Xun , Guttman András 
Published: March 2003

AbstractA capillary gel electrophoresis based automated DNA fraction collection technique was developed to support a novel DNA fragment‐pooling strategy for expressed sequence tag (EST) library construction. The cDNA population is first cleaved by BsaJ I and EcoR I restriction enzymes, and then subpooled by selective ligation with specific adapters followed by polymerase chain reaction (PCR) amplification and labeling. Combination of this cDNA fingerprinting method with high‐resolution capillary gel electrophoresis separation and precise fractionation of individual cDNA transcript representatives avoids redundant fragment selection and concomitant repetitive sequencing of abundant transcripts. Using a computer‐controlled capillary electrophoresis device the transcript representatives were separated by their size and fractions were automatically collected in every 30 s into 96‐well plates. The high resolving power of the sieving matrix ensured sequencing grade separation of the DNA fragments (i.e., single‐base resolution) and successful fraction collection. Performance and precision of the fraction collection procedure was validated by PCR amplification of the collected DNA fragments followed by capillary electrophoresis analysis for size and purity verification. The collected and PCR‐amplified transcript representatives, ranging up to several hundred base pairs, were then sequenced to create an EST library.
Transcription factor binding study by capillary zone electrophoretic mobility shift assay
Authors: Ronai Zsolt , Wang Yan , Khandurina Julia , Budworth Paul , Sasvari‐Szekely Maria , Wang Xun , Guttman András 
Published: March 2003

AbstractRegulation of gene expression through interaction of proteins with specific DNA sequences is a central issue in functional genomics. Capillary electrophoretic mobility shift assay is an efficient novel method for the investigation of sequence specific protein‐DNA interactions, allowing rapid and sensitive quantification of the complex formation. In this paper, we present a pilot study on capillary zone electrophoretic mobility shift assay (CZEMSA) to investigate the interaction between the transcription factors of HeLa nuclear extract and Sp1‐specific fluorescein‐labeled oligonucleotide, using the unlabeled probe as competitor. The mobility shift assay was accomplished by CZE in coated capillaries without polymeric buffer additives. Specificity of the DNA protein complex formation was verified by competition experiments, as well as by supershift assay with an anti‐Sp1 antibody. The applied electric field strength did not affect the stability of DNA‐protein complex during the electrophoretic analysis, allowing rapid identification and quantification of the protein DNA interaction. A practical application to study the interaction between Oryza sativa MADS‐box transcription factor 4 (OsMADS4) and its consensus sequence is also reported.
Separation of peptides and proteins by capillary electrophoresis using acidic buffers containing tetraalkylammonium cations and cyclodextrins
Authors: Quang Changyu , Malek Amir , Khaledi Morteza G. 
Published: March 2003

AbstractA method for improving separations of peptides and other positively charged species in capillary zone electrophoresis with untreated capillaries using acidic buffers containing tetraalkylammonium cations is described. Tetramethylammonium and tetrabutylammonium cations dynamically modify the capillary surface, leading to a reversal in the direction of the electroosmotic flow. As a result, the adsorption of positively charged peptides and proteins is minimized, and resolution and peak capacity are improved as the migration of cationic analytes is counterbalanced by the electroosmotic flow. The combining effect of reversing electroosmotic flow and cyclodextrin inclusion complexation on separations of closely related peptides and a protein mixture, as well as tryptic digest of hemoglobin is demonstrated.
Attomole sensitivity for unlabeled proteins and polypeptides with on‐chip capillary electrophoresis and universal detection by interferometric backscatter
Authors: Wang Zhanling , Swinney Kelly , Bornhop Darryl J. 
Published: March 2003

AbstractA universal detector based on backscatter interferometry has been developed to perform nanoliter volume refractive index measurements for on‐chip sodium dodecyl sulfate (SDS) gel based (polyethylene oxide gel) separations and quantification label‐free proteins. The on‐chip interferometric backscatter detector (OCIBD) system consists of a simple, folded optical train based on the interaction of a laser beam with an etched channel in the shape of half cylinder in a fused‐silica plate. The backscattered light from the channel takes on the form of a high‐contrast interference pattern that contains information related to the bulk properties of the fluid located within the probe or detection volume of 2.32×10−9 L. Depending on capillary electrophoresis (CE) injection method, the positional changes of the interference pattern extrema (fringes) allow for the quantification of unlabeled proteins at levels ranging from 11 to 310 amol (2.7×10−8 mol/L) with a linear dynamic range of 2.5 decades (egg albumin). Using OCIBD microchannel‐based SDS capillary gel electrophoresis (SDS/CGE), separation and detection of five label‐free proteins was achieved in less than 100 seconds with detection limits ranging from 0.95 pg (1.1×10−16 mol or 2.5×10−7 mol/L) of calmodulin to 7.0 pg (1.0×10−16 mol or 2.4×10−7 mol/L) for bovine serum albumin (BSA) without signal filtering or active thermal control. This development shows that a universal detector based on backscatter interferometry can be used effectively for on‐chip label‐free solute analysis.
Capillary electrophoresis coupled to time of flight‐mass spectrometry of therapeutic peptide hormones
Authors: Sanz‐Nebot Victoria , Benavente Fernando , Balaguer Elvira , Barbosa José 
Published: March 2003

AbstractWe have established a method for separation and characterization of a series of peptide hormones of pharmaceutical interest and wide therapeutical use by capillary electrophoresis‐electrospray‐mass spectrometry (CE‐ES‐MS) using a sheath flow interface. Several parameters were systematically investigated, such as concentration of the electrolyte, organic solvent and sheath liquid composition, gas flow rates and capillary position. Moreover, limits of detection, linearity, repeatability and day‐to‐day reproducibility of the proposed method were studied in order to obtain the main quality parameters.
Analysis of the performance of antibody capture methods using fluorescent peptides with capillary zone electrophoresis with laser‐induced fluorescence
Authors: Jackman Roy , Schmerr Mary Jo 
Published: March 2003

AbstractA method to analyze the performance of an antibody capture method using fluorescent peptides by capillary zone electrophoresis using laser‐induced fluorescence (CZE‐LIF) for detection has been developed. Fluorescent peptides from the prion protein were synthesized and the corresponding antibodies were produced in rabbits against these peptides. The antibodies were used to capture the fluorescent peptides. The antibodies were then bound to protein A Sepharose. After elution, the amount of fluorescent peptide that was captured vs. the total amount placed in the assay was evaluated by CZE‐LIF. Of the three peptides used in this evaluation, it was found that the recovery was approximately 25–35%. When the abnormal prion protein was prepared from scrapie‐infected brain samples from hamsters and a sheep using the previously described extraction method and this method, the amount of abnormal prion protein that was measured in the fluorescence immunoassay correlated with amounts estimated from Western blot. We conclude that this method can be used to detect abnormal prion protein in a tissue sample.
Asymmetric one‐storey elastic systems with non‐linear viscous and viscoelastic dampers: Earthquake response
Authors: Lin Wen‐Hsiung , Chopra Anil K. 
Published: March 2003

AbstractInvestigated are earthquake responses of one‐way symmetric‐plan, one‐storey systems with non‐linear fluid viscous dampers (FVDs) attached in series to a linear brace (i.e. Chevron or inverted V‐shape braces).Thus, the non‐linear damper is viscous when the brace is considered rigid or viscoelastic (VE) when the brace is flexible. The energy dissipation capacity of a non‐linear FVD is characterized by an amplitude‐dependent damping ratio for an energy‐equivalent linear FVD, which is determined assuming the damper undergoes harmonic motion. Although this formulation is shown to be advantageous for single‐degree‐of‐freedom (SDF) systems, it is difficult to extend its application to multi‐degree‐of‐freedom (MDF) systems for two reasons: (1) the assumption that dampers undergo harmonic motion in parameterizing the non‐linear damper is not valid for its earthquake‐induced motion of an MDF system; and (2) ensuring simultaneous convergence of all unknown amplitudes of dampers is difficult in an iterative solution of the non‐linear system. To date, these limitations have precluded the parametric study of the dynamics of MDF systems with non‐linear viscous or VE dampers. However, they are overcome in this investigation using concepts of modal analysis because the system is weakly non‐linear due to supplemental damping. It is found that structural response is only weakly affected by damper non‐linearity and is increased by a small amount due to bracing flexibility. Thus, the effectiveness of supplemental damping in reducing structural responses and its dependence on the planwise distribution of non‐linear VE dampers were found to be similar to that of linear FVDs documented elsewhere. As expected, non‐linear viscous and VE dampers achieve essentially the same reduction in response but with much smaller damper force compared to linear dampers. Finally, the findings in this investigation indicate that the earthquake response of the asymmetric systems with non‐linear viscous or VE dampers can be estimated with sufficient accuracy for design applications by analysing the same asymmetric systems with all non‐linear dampers replaced by energy‐equivalent linear viscous dampers. Copyright © 2003 John Wiley & Sons, Ltd.
Exact computation of input‐energy spectra from Fourier amplitude spectra
Authors: Ordaz Mario , Huerta Benjamin , Reinoso Eduardo 
Published: March 2003

AbstractA theoretically exact relation is presented between the Fourier amplitude spectrum and the elastic input‐energy spectrum. This energy spectrum is computed from the Fourier acceleration amplitude spectrum and the real part of the relative velocity transfer function of the single‐degree‐of‐freedom elastic oscillator. Some accelerometric records collected worldwide are used to prove the solution. It is shown that the relation presented in this work opens the door for a better understanding of the relationship between the input‐energy spectrum and other seismological variables, such as magnitude and focal distance. Copyright © 2003 John Wiley & Sons, Ltd.
Inelastic dynamic analysis of RC bridges accounting for spatial variability of ground motion, site effects and soil–structure interaction phenomena. Part 1: Methodology and analytical tools
Authors: Sextos Anastasios G. , Pitilakis Kyriazis D. , Kappos Andreas J. 
Published: March 2003

AbstractDuring strong ground motion it is expected that extended structures (such as bridges) are subjected to excitation that varies along their longitudinal axis in terms of arrival time, amplitude and frequency content, a fact primarily attributed to the wave passage effect, the loss of coherency and the role of local site conditions. Furthermore, the foundation interacts with the soil and the superstructure, thus significantly affecting the dynamic response of the bridge. A general methodology is therefore set up and implemented into a computer code for deriving sets of appropriately modified time histories and spring–dashpot coefficients at each support of a bridge with account for spatial variability, local site conditions and soil–foundation–superstructure interaction, for the purposes of inelastic dynamic analysis of RC bridges. In order to validate the methodology and code developed, each stage of the proposed procedure is verified using recorded data, finite‐element analyses, alternative computer programs, previous research studies, and closed‐form solutions wherever available. The results establish an adequate degree of confidence in the use of the proposed methodology and code in further parametric analyses and seismic design. Copyright © 2003 John Wiley & Sons, Ltd.
Inelastic dynamic analysis of RC bridges accounting for spatial variability of ground motion, site effects and soil–structure interaction phenomena. Part 2: Parametric study
Authors: Sextos Anastasios G. , Kappos Andreas J. , Pitilakis Kyriazis D. 
Published: March 2003

AbstractThe methodology for dealing with spatial variability of ground motion, site effects and soil–structure interaction phenomena in the context of inelastic dynamic analysis of bridge structures, and the associated analytical tools established and validated in a companion paper are used herein for a detailed parametric analysis, aiming to evaluate the importance of the above effects in seismic design. For a total of 20 bridge structures differing in terms of structural type (fundamental period, symmetry, regularity, abutment conditions, pier‐to‐deck connections), dimensions (span and overall length), and ground motion characteristics (earthquake frequency content and direction of excitation), the dynamic response corresponding to nine levels of increasing analysis complexity was calculated and compared with the ‘standard’ case of a fixed base, uniformly excited, elastic structure for which site effects were totally ignored. It is concluded that the dynamic response of RC bridges is indeed strongly affected by the coupling of the above phenomena that may adversely affect displacements and/or action effects under certain circumstances. Evidence is also presented that some bridge types are relatively more sensitive to the above phenomena, hence a more refined analysis approach should be considered in their case. Copyright @ 2003 John Wiley & Sons, Ltd.
Seismic test of a full‐scale model of a five‐storey stone pagoda
Authors: Kim Jae Kwan , Ryu Hyeuk 
Published: March 2003

AbstractA moderate size earthquake of magnitude 5 occurred at Whagae‐Myun, Hadong‐Gun, Kyongsangnam‐Do, Korea on 4 July 1936. It caused severe damage to the buildings and other structures in Sang‐Gye‐Sa, a famous and beautiful Buddhist temple. A five‐storey stone pagoda was standing in front of Keumdang, the main building. The top component of the pagoda was tipped over and fell down to the ground during the earthquake. In order to have a quantitative estimate of the intensity of the earthquake, a full‐scale model was constructed through a rigorous verification process. The completed model was mounted on a shaking table and subjected to two kinds of dynamic test: exploratory test and fragility test. The exploratory test was performed with low intensity shaking. In the fragility test, the failure modes of the model were investigated while increasing the shaking intensity. The construction details of the model are described and test procedures are reported. Important relations between failure modes and characteristics of ground motion were obtained from the tests. The intensity of the 1936 earthquake was estimated from the examination of test results. Copyright © 2003 John Wiley & Sons, Ltd.
Close range digital photogrammetric analysis of experimental drainage basin evolution
Authors: Brasington J. , Smart R. M. A. 
Published: March 2003

AbstractDespite the difficulties of establishing formal hydraulic and geometric similarity, small‐scale models of drainage basins have often been used to investigate the evolution and dynamics of larger‐scale landforms. Historically, this analysis has been restricted to planform basin characteristics and only in the last decade has the topographic similarity of experimental landscapes been explored through explicitly three‐dimensional parameters such as the distributions of cumulative drainage area, area–slope and catchment elevation. The current emphasis on three‐dimensional morphometry reflects a growing awareness of the descriptive paucity of planform data and the need for more robust analysis of spatial scaling relationships. This paradigm shift has been significantly facilitated by technological developments in topographic survey and digital elevation modelling (DEM) which now present the opportunity to acquire and analyse high‐resolution, distributed elevation data. Few studies have, however, attempted to use topographic modelling to provide information on the changing pattern and rate of sediment transport though an evolving landscape directly by using multitemporal DEM differencing techniques. This paper reports a laboratory study in which digital photogrammetry was employed to derive high‐resolution DEMs of a simulated landscape in declining equilibrium at 15 minute frequency through a 240 minute simulation. Detailed evaluation of the DEMs revealed a vertical precision of 1·2 mm and threshold level of change detection between surfaces of ±3 mm at the 95 per cent confidence level. This quality assurance set the limits for determining the volumetric change between surfaces, which was used to recover the sediment budget through the experiment and to examine local ‐ and basin‐scale rates of sediment transport. A comparison of directly observed and morphometric estimates of sediment yield at the basin outlet was used to quantify the closure of the sediment budget over the simulation, and revealed an encouragingly small 6·2 per cent error. The application of this dynamic morphological approach has the potential to offer new insights into the controls on landform development, as demonstrated here by an analysis of the changing pattern of the basin sediment delivery ratio during network growth. Copyright © 2003 John Wiley & Sons, Ltd.