bluuebunny/crossref_metadata_2025_split huggingface dataset:
From 2‐D electrophoresis to proteomics
Authors: Klose Joachim 
Published: January 2010

AbstractAt first, a short history of the beginning of 2‐DE is provided. Based on the present state of the art at the time I developed a 2‐DE technique in 1975 that was able to resolve complex protein extracts from mouse tissues in hundreds of protein spots. My intention was to study proteins from a global point of view. Questions of interest were, how do proteins change during embryonic development, and what is the effect of induced mutations on the protein level. At that time protein chemistry was a matter of analyzing single proteins in detail. Therefore, my approach was frequently criticized as inappropriate because it would be impossible to identify and characterize the hundreds of proteins resolved. But soon it was realized that studying total proteins gives opportunities to answer many interesting questions. This led to a research field nowadays called “proteomics”. Already in the beginning of the 1980s the idea to analyze the total human proteins had come up. By entering the post‐genome era it became obvious that a human proteome project is needed in order to explain the human genome in terms of its functions. The problems in realizing such a project are considered.
Theory of electrophoresis: Fate of one equation
Authors: Gaš Bohuslav 
Published: January 2010

AbstractElectrophoresis utilizes a difference in movement of charged species in a separation channel or space for their spatial separation. A basic partial differential equation that results from the balance laws of continuous processes in separation sciences is the nonlinear conservation law or the continuity equation. Attempts at its analytical solution in electrophoresis go back to Kohlrausch's days. The present paper (i) reviews derivation of conservation functions from the conservation law as appeared chronologically, (ii) deals with theory of moving boundary equations and, mainly, (iii) presents the linear theory of eigenmobilities. It shows that a basic solution of the linearized continuity equations is a set of traveling waves. In particular cases the continuity equation can have a resonance solution that leads in practice to schizophrenic dispersion of peaks or a chaotic solution, which causes oscillation of electrolyte solutions.
DNA gel electrophoresis: The reptation model(s)
Authors: Slater Gary W. 
Published: January 2010

AbstractDNA gel electrophoresis has been the most important experimental tool to separate DNA fragments for several decades. The introduction of PFGE in the 1980s and capillary gel electrophoresis in the 1990s made it possible to study, map and sequence entire genomes. Explaining how very large DNA molecules move in a gel and why PFGE is needed to separate them has been an active field of research ever since the launch of the journal Electrophoresis. This article presents a personal and historical overview of the development of the theory of gel electrophoresis, focusing on the reptation model, the band broadening mechanisms, and finally the factors that limit the read length and the resolution of electrophoresis‐based sequencing systems. I conclude with a short discussion of some of the questions that remain unanswered.
From micro to macro: Conversion of capillary electrophoretic separations of biomolecules and bioparticles to preparative free‐flow electrophoresis scale
Authors: Kašička Václav 
Published: January 2010

AbstractThis invited contribution in the special issue of Electrophoresis published in celebration of the 30th Anniversary of this journal reflects the impact of our milestone paper [Prusík, Z., Kašička, V., Mudra, P., Štěpánek, J., Smékal, O., Hlaváček, J., Electrophoresis 1990, 11, 932–936] in the area of conversion of microscale analytical and micropreparative CE separations of biomolecules and bioparticles into (macro)preparative free‐flow electrophoresis (FFE) scale on the basis of a correlation between CE and FFE methods. In addition to the survey of advances in the relatively narrow field of CE‐FFE correlation and CE‐FFE conversion, a comprehensive review of the recent developments of micropreparative CE and (macro)preparative FFE techniques is also presented and applications of these techniques to micro‐ and (macro)preparative separations and purifications of biomolecules and bioparticles are demonstrated. The review covers the period since the year of publication of the above paper, i.e. ca. the last 20 years.
Combined use of mild oxidation and cutinase/lipase pretreatments for enzymatic processing of wool fabrics
Authors: Wang Ping , Cui Li , Wang Qiang , Fan Xuerong , Zhao Xianfei , Wu Jing 
Published: January 2010

AbstractA cutinase from Thermobifida fusca WSH04 and two lipases, L3126 and Lipex 100L, were applied to the enzymatic pretreatment of wool fabrics followed by protease treatment, aiming at hydrolyzing the outmost bound lipids on the wool surface. A mild oxidation with 2 g/L hydrogen peroxide (30%) was selectively carried out before the enzymatic treatments. The cooperative actions of mild oxidation, cutinase and lipase pretreatments during wool processing were investigated. The results showed that lipase pretreatment alone had less impact on the wettability and anti‐felting ability of wool fabrics than cutinase treatment. Combined use of cutinase and lipase pretreatments did not evidently improve the properties of the wool fabric compared with the individual cutinase pretreatment. By contrast, mild oxidation slightly enhanced the activity of cutinase toward the wool surface and promoted the subsequent proteolytic reactions. The wetting time and contact angle of the protease‐treated fabric deceased to 1.2 min and 55°, respectively; the area shrinkage decreased to 3.1%, with an acceptable strength loss from 489 to 418 N. The changes in the cuticle scales of the wool fibers, confirmed by scanning electron microscopy, further proved the cooperative actions of mild oxidation and cutinase pretreatment during enzymatic wool processing.
Chondrogenesis of articular chondrocytes in hydroxyapatite/chitin/chitosan scaffolds supplemented with pituitary extract
Authors: Kuo Yung‐Chih , Leou Sho‐Noen 
Published: January 2010

AbstractThis study analyzes the effects of pituitary extract supplement on the cultivation of bovine knee chondrocytes (BKCs) in three‐dimensional chitin/chitosan biomaterials. Transforming growth factor‐β1 (TGF‐β1) in the supplement was identified by Western blot near 23 kDa, and the immunoassayed concentration of TGF‐β1 in the supplement was about 33 ng/mL. The typical pore diameter of the chitin/chitosan scaffolds was 250 μm, indicating an apposite void space for chondrocyte growth. The characteristic width of needlelike hydroxyapatite crystals was 85 nm after chemical co‐precipitation of hydroxyapatite on the pore surfaces of the scaffolds. Over 4‐wk cultivation, the amounts of proliferated BKCs, secreted glycosaminoglycans and produced collagen were improved with the concentration of TGF‐β1 in culture medium. In addition, the cultivated constructs revealed mature neocartilage with lacunas enclosing BKCs, demonstrating chondrogenesis. Pituitary extract supplement was more efficient in the synthesis of extracellular matrix than pure TGF‐β1. Hence, an appropriate addition of the supplement can enhance the formation of cartilaginous components in the scaffolds to regenerate articular cartilage.
Daily morphological changes determined by high‐energy events on an embayed beach: a qualitative model
Authors: Martins Cristina Celia , de Mahiques Michel Michaelovitch , Dias João Manuel Alveirinho 
Published: January 2010

AbstractThis paper examines the daily morphological responses of Sununga Beach, an embayed beach located on the south‐eastern Brazilian coast, to storms in the South Atlantic Ocean. The main mechanisms and timing of beach erosion and accretion, the relationship between wave height and direction, and beach volume changes are considered, to establish a qualitative model for short‐term embayed beach morphological changes.The methodology consisted of daily topographic surveys during the month of May in 2001, 2002, and 2003, using an RTK‐GPS (real‐time kinematics – global positioning system). Weather and wave model results were used to correlate hydrodynamics and beach morphology.The results indicate that the morphodynamics of Sununga Beach are characterized by a process of beach rotation, which occurred more or less clearly during all three surveys. Unlike what has been commonly described in the literature for longer time intervals and alternations of fair and stormy weather, the beach rotation processes on Sununga Beach occurred under conditions of moderate‐to‐high wave energy change (wave heights greater than 2 m).An integrated evaluation of the behaviour of the meteorological aspects, together with beach morphology, enabled us to recognize that extra‐tropical cyclones were the most important agent in remobilizing the beach planform, whether in beach rotation or in cross‐shore erosion. Copyright © 2010 John Wiley & Sons, Ltd.
Dynamics of suspended sediment transport and yield in a large agricultural catchment, southwest France
Authors: Oeurng Chantha , Sauvage Sabine , Sánchez‐Pérez José‐Miguel 
Published: January 2010

AbstractThe dynamics of suspended sediment transport were monitored continuously in a large agricultural catchment in southwest France from January 2007 to March 2009. The objective of this paper is to analyse the temporal variability in suspended sediment transport and yield in that catchment. Analyses were also undertaken to assess the relationships between precipitation, discharge and suspended sediment transport, and to interpret sediment delivery processes using suspended sediment‐discharge hysteresis patterns. During the study period, we analysed 17 flood events, with high resolution suspended sediment data derived from continuous turbidity and automatic sampling. The results revealed strong seasonal, annual and inter‐annual variability in suspended sediment transport. Sediment was strongly transported during spring, when frequent flood events of high magnitude and intensity occurred. Annual sediment transport in 2007 yielded 16 614 tonnes, representing 15 t km−2 (85% of annual load transport during floods for 16% of annual duration), while the 2008 sediment yield was 77 960 tonnes, representing 70 t km−2 (95% of annual load transport during floods for 20% of annual duration). Analysis of the relationships between precipitation, discharge and suspended sediment transport showed that there were significant correlations between total precipitation, peak discharge, total water yield, flood intensity and sediment variables during the flood events, but no relationship with antecedent conditions. Flood events were classified in relation to suspended sediment concentration (SSC)–discharge hysteretic loops, complemented with temporal dynamics of SSC–discharge ranges during rising and falling flow. The hysteretic shapes obtained for all flood events reflected the distribution of probable sediment sources throughout the catchment. Regarding the sediment transport during all flood events, clockwise hysteretic loops represented 68% from river deposited sediments and nearby source areas, anticlockwise 29% from distant source areas, and simultaneity of SSC and discharge 3%. Copyright © 2010 John Wiley & Sons, Ltd.
Predicting wetted width in any river at any discharge
Authors: Booker D.J. 
Published: January 2010

AbstractCoefficients describing at‐a‐station power‐law relationships between discharge and width were calculated by applying multilevel models to field data collected during routine hydrological monitoring at 326 gauging stations across New Zealand. These hydraulic geometry coefficients were then estimated for each of these stations using standard stepwise multiple‐linear regression models. Analysis was carried out to quantify how the relationship between width and discharge changed in relation to several available explanatory variables. All coefficients describing the at‐a‐station hydraulic geometry were found to have statistically significant relationships with catchment area. Statistically significant relationships between each of the coefficients were also found with the addition of catchment climate as an explanatory variable. Further statistically significant relationships were found when station elevation and channel slope, as well as hydrological source of flow and landcover of the upstream catchment were added to the explanatory variables. The level of confidence that can be associated with estimates of width at ungauged sites, and sites with limited data availability, was then assessed by comparing model predictions with independent paired data on observed width and discharge from 197 sites. When compared against these independent data, model predictions of width were improved with the addition of predictor variables of the hydraulic geometry coefficients. The greatest improvements were made when climate was added to catchment area as predictor variables. Minor improvements were made when all available information was used to predict width at these independent sites. Although the analysis was purely empirical, results describing relationships between hydraulic geometry coefficients and catchment characteristics corresponded well with knowledge of the processes controlling at‐a‐station hydraulic geometry of river width. Copyright © 2010 John Wiley & Sons, Ltd.
A numerical investigation of side‐loads resulting from rigid body motions of an overexpanded engine nozzle
Authors: Lefrançois E. 
Published: January 2010

AbstractA numerical model for fluid–structure interactions is presented. Its purpose, within the context of 2D overexpanded engine nozzles, is to improve understanding of interactions between side‐loads and rigid body rotations, and more generally of the underlying physics between a shock in motion and nozzle movements. The model is based on three different solvers, for fluid, structure and mesh deformation respectively, which are linked to a coupling scheme in a parallel environment. In particular it is shown that the nozzle has a natural torsional frequency for which the measured side‐loads are the greatest. This phenomenon is associated with a transversal wave in the flow between the two internal walls of the nozzle. For free coupling cases, our calculations go some way to explain how the mechanical energy is dissipated with a transfer of energy to the shock that encounters the largest motions to dissipate it. It has also been observed that the compression shock may adopt a quasi‐steady state response with regard to nozzle rotations at low frequencies, whereas this will no longer be the case at higher frequencies, where a phase shift may occur between side‐loads and rotational position. This study is aimed at enhancing the only current aeroelastic stability model for overexpanded nozzles (AIAA, 29th Joint Propulsion Conference and Exhibit, Monterey, CA, 28–30 June 1993). Copyright © 2010 John Wiley & Sons, Ltd.
Conditional and syllogistic deductive tasks dissociate functionally during premise integration
Authors: Reverberi Carlo , Cherubini Paolo , Frackowiak Richard S.J. , Caltagirone Carlo , Paulesu Eraldo , Macaluso Emiliano 
Published: January 2010

AbstractDeduction allows us to draw consequences from previous knowledge. Deductive reasoning can be applied to several types of problem, for example, conditional, syllogistic, and relational. It has been assumed that the same cognitive operations underlie solutions to them all; however, this hypothesis remains to be tested empirically. We used event‐related fMRI, in the same group of subjects, to compare reasoning‐related activity associated with conditional and syllogistic deductive problems. Furthermore, we assessed reasoning‐related activity for the two main stages of deduction, namely encoding of premises and their integration. Encoding syllogistic premises for reasoning was associated with activation of BA 44/45 more than encoding them for literal recall. During integration, left fronto‐lateral cortex (BA 44/45, 6) and basal ganglia activated with both conditional and syllogistic reasoning. Besides that, integration of syllogistic problems additionally was associated with activation of left parietal (BA 7) and left ventro‐lateral frontal cortex (BA 47). This difference suggests a dissociation between conditional and syllogistic reasoning at the integration stage. Our finding indicates that the integration of conditional and syllogistic reasoning is carried out by means of different, but partly overlapping, sets of anatomical regions and by inference, cognitive processes. The involvement of BA 44/45 during both encoding (syllogisms) and premise integration (syllogisms and conditionals) suggests a central role in deductive reasoning for syntactic manipulations and formal/linguistic representations. Hum Brain Mapp, 2010. © 2010 Wiley‐Liss, Inc.
Effective functional mapping of fMRI data with support‐vector machines
Authors: Lee Sangkyun , Halder Sebastian , Kübler Andrea , Birbaumer Niels , Sitaram Ranganatha 
Published: January 2010

AbstractThere is a growing interest in using support vector machines (SVMs) to classify and analyze fMRI signals, leading to a wide variety of applications ranging from brain state decoding to functional mapping of spatially and temporally distributed brain activations. Studies so far have generated functional maps using the vector of weight values generated by the SVM classification process, or alternatively by mapping the correlation coefficient between the fMRI signal at each voxel and the brain state determined by the SVM. However, these approaches are limited as they do not incorporate both the information involved in the SVM prediction of a brain state, namely, the BOLD activation at voxels and the degree of involvement of different voxels as indicated by their weight values. An important implication of the above point is that two different datasets of BOLD signals, presumably obtained from two different experiments, can potentially produce two identical hyperplanes irrespective of their differences in data distribution. Yet, the two sets of signal inputs could correspond to different functional maps. With this consideration, we propose a new method called Effect Mapping that is generated as a product of the weight vector and a newly computed vector of mutual information between BOLD activations at each voxel and the SVM output. By applying this method on neuroimaging data of overt motor execution in nine healthy volunteers, we demonstrate higher decoding accuracy indicating the greater efficacy of this method. Hum Brain Mapp, 2010. © 2010 Wiley‐Liss, Inc.
Promoter hypomethylation and upregulation of trefoil factors in prostate cancer
Authors: Vestergaard Else Marie , Nexø Ebba , Tørring Niels , Borre Michael , Ørntoft Torben Falck , Sørensen Karina Dalsgaard 
Published: January 2010

AbstractTrefoil factors, mucin‐associated peptides, are overexpressed in prostate cancer (PC). We hypothesized that promoter methylation contributes to the regulation of trefoil factors (TFF1, TFF2 and TFF3) in human prostate cells. Here we show hypomethylation of promoter regions of TFF1 and TFF3 in PC cell lines with significant TFF expression as compared to benign immortalized prostate cell lines and PC cell lines not expressing trefoil factor. The most striking difference was observed for CpG sites located close to the AUG start codon overlapping several putative binding sites for cellular transcription factors. TFF2 was hypermethylated and had no or very low expression in all prostate cell lines investigated. Treatment of methylated cell lines with 5‐aza‐2′‐deoxycytidine restored TFF expression in cell lines not expressing TFF and increased expression significantly in low‐expressing cell lines. In clinical samples, methylation of the promoter/enhancer regions of TFF1 and TFF3 was significantly lower in PC compared to benign prostatic hyperplasia. The present study shows an inverse relation between promoter methylation and expression of trefoil factors. Preliminary analysis on clinical samples suggests that this regulatory mechanism is responsible for the increased levels of TFF1 and TFF3 observed in PC. The overexpression and promoter hypomethylation of trefoil factors may serve as biomarkers in PC.
Flavokawain B, a kava chalcone, induces apoptosis via up‐regulation of death‐receptor 5 and Bim expression in androgen receptor negative, hormonal refractory prostate cancer cell lines and reduces tumor growth
Authors: Tang Yaxiong , Li Xuesen , Liu Zhongbo , Simoneau Anne R. , Xie Jun , Zi Xiaolin 
Published: January 2010

AbstractLimited success has been achieved in extending the survival of patients with metastatic and hormone‐refractory prostate cancer (HRPC). There is a strong need for novel agents in the treatment and prevention of HRPC. We have shown that flavokawain B (FKB), a kava chalcone, is about 4‐ to 12‐fold more effective in reducing the cell viabilities of androgen receptor (AR)‐negative, HRPC cell lines DU145 and PC‐3 than AR‐positive, hormone‐sensitive prostate cancer cell lines LAPC4 and LNCaP, with minimal effect on normal prostatic epithelial and stromal cells. FKB induces apoptosis with an associated increased expression of proapoptotic proteins: death receptor‐5, Bim and Puma and a decreased expression of inhibitors of apoptosis protein: XIAP and survivin. Among them, Bim expression was significantly induced by FKB as early as 4 hr of the treatment. Knockdown of Bim expression by short‐hairpin RNAs attenuates the inhibitory effect on anchorage‐dependent and ‐independent growth and caspase cleavages induced by FKB. These findings suggest that the effect of FKB, at least in part, requires Bim expression. In addition, FKB synergizes with TRAIL for markedly enhanced induction of apoptosis. Furthermore, FKB treatment of mice bearing DU145 xenograft tumors results in tumor growth inhibition and increases Bim expression in tumor tissues. Together, these results suggest robust mechanisms for FKB induction of apoptosis preferentially for HRPC and the potential usefulness of FKB for prevention and treatment of HRPC in an adjuvant setting.
The health and economic effects of HPV DNA screening in The Netherlands
Authors: Berkhof Johannes , Coupé Veerle M. , Bogaards Johannes A. , van Kemenade Folkert J. , Helmerhorst Theo J. , Snijders Peter J. , Meijer Chris J. 
Published: January 2010

AbstractWe studied the health and economic effects of human papillomavirus (HPV) DNA testing in cervical screening using a simulation model. The key data source was a Dutch longitudinal screening trial. We compared cytological testing with repeat cytology (for borderline/mildly abnormal smears) to HPV testing with cytology triage (for HPV‐positive smears), combination testing (combined HPV and cytology) and cytological testing with HPV triage (for borderline/mildly abnormal smears). We varied the screening interval from 5 to 10 years. The main outcome measures were the number of cervical cancer cases, the number of quality‐adjusted life years (QALYs), and the incremental cost‐effectiveness ratio (ICER). The base‐case estimates were accompanied with ranges across 118 calibrated parameter settings (calibration criteria: cervical intraepithelial neoplasia 2/3, cancer and mortality rates). In comparison to 5‐yearly cytology, 5‐yearly HPV testing with cytology triage gave a reduction in the number of cancer cases of 23% (range, 9–27%). The reduction was 26% (range, 10–29%) for combination testing and 3% (range, −1 to 8%) for cytology with HPV triage. For strategies with primary HPV testing, the model also estimated a reduction in cancer cases when the screening interval was extended to 7.5 years. Five‐yearly cytology with HPV triage and 5 to 7.5‐yearly HPV testing with cytology triage were cost effective for the base‐case settings and the majority of calibrated parameter settings (ICER below Dutch willingness‐to‐pay threshold of €20,000/QALY). Our model indicates that HPV testing with cytology triage is likely to be cost effective. An extension of the screening interval may be considered to control costs.