bluuebunny/crossref_metadata_2025_split huggingface dataset:
Autonomous protein sample processing on‐chip using solid‐phase microextraction, capillary force pumping, and microdispensing
Authors: Wallman Lars , Ekström Simon , Marko‐Varga György , Laurell Thomas , Nilsson Johan 
Published: November 2004

AbstractA capillary force filling microsystem consisting of a chip‐integrated solid‐phase microextraction (SMEC) array and a microdispenser for sample purification and trace enrichment of peptides is described. The microextraction array was loaded with solid‐phase media (50 μm Poros R2 beads) for purification and enrichment of proteomic samples. Samples bound to the SMEC were eluted in a volume of 200 nL. A piezo‐electric microdispenser was docked to the array and the samples bound to the SMEC were eluted in a volume of 200 nL using capillary forces. The purified and enriched samples were dispensed onto the matrix‐assisted laser desorption/ionization (MALDI) target, providing quality data from samples in the picomolar range. The nanoproteomic platform was compared to corresponding commercial preparation protocols, showing higher mass spectrometry (MS) signal intensities for peptides generated from an α‐casein digest. The platform was also elvaluated with regards to two‐dimensional (2‐D) gel‐derived protein digests from both fibroblast and epithelial target cells.
Microbead‐based affinity chromatography chip using RNA aptamer modified with photocleavable linker
Authors: Cho Suhyung , Lee Sang‐Ho , Chung Woo‐Jae , Kim Yong‐Kweon , Lee Yoon‐Sik , Kim Byung‐Gee 
Published: November 2004

AbstractA microbead‐based affinity chromatography chip (μ‐BACC) controlling hundreds of nanoliters of reaction volume was developed to separate and analyze hepatitis C virus (HCV) RNA polymerase protein by immobilization of an RNA aptamer on beads. A photocleavable linker was conjugated in between the beads and the aptamer to elute the bound RNA polymerase from the RNA aptamer in one step by UV irradiation, resulting in an efficient method to elute and identify the target molecule bound on RNA using a mass spectrometer. This linker showed a cleavage activity over 70% upon UV irradiation at 1050 mW/cm2 for more than 5 min. The photoelution method could prevent the target molecule from contaminations in affinity chromatography caused by elution solutions of high salt concentration, extreme pH and detergent, respectively. In this chip, sample reagents up to 800 nL could be metered quantitatively into the bead chamber using a nanoliter dispenser working, based on surface‐guided flow control and pneumatic control by external air pressure on the chip. RNA polymerase eluted after UV irradiation was successfully analyzed by trypsin treatment without additional purification. As a result, using the aptamer, we could detect RNA polymerase from 800 nL hepatitis C patient serum containing 96 fmol HCV RNA polymerase. The detection limit of this system was estimated to be 9.6 fmol HCV RNA polymerase.
Exploiting the benefits of miniaturization for the enhancement of DNA microarrays
Authors: Vanderhoeven Johan , Pappaert Kris , Dutta Binita , Vanhummelen Paul , Baron Gino V. , Desmet Gert 
Published: November 2004

AbstractThe present study demonstrates that the best way to enhance DNA microarray assays, both in terms of analysis speed and in final spot intensity, is to dissolve the available molar amount of sample in the smallest possible buffer volume and to subsequently convect this solution continuously across the surface of the array. The presently proposed shear‐driven flow system is pre‐eminently suited for this task, as it allows to induce strongly enhanced lateral transport rates, independently of the degree of miniaturization of the hybridization chamber. This transport enhancement method, however, only increases the hybridization rate and not the final spot intensity, as neither can any of the other transport enhancement methods already proposed in literature. A series of experiments with synthetic single‐stranded (ssDNA) samples and an accompanying mass balance analysis are presented to demonstrate these points.
High‐power blue/UV light‐emitting diodes as excitation sources for sensitive detection
Authors: Kuo Jason S. , Kuyper Christopher L. , Allen Peter B. , Fiorini Gina S. , Chiu Daniel T. 
Published: November 2004

AbstractWith advances in III‐V nitride manufacturing processes, high‐power light‐emitting diode (LED) chips in the blue and UV wavelengths are now commercially available at reasonable cost and can be used as excitation sources in optical sensing. We describe the use of these high‐power blue and UV LEDs for sensitive fluorescence detection, including chip‐based flow cytometry, capillary electrophoresis (CE), and single‐molecule imaging. By using a blue LED with a focusable power of ∼40 mW as the excitation source for fluorescent beads, we demonstrate a simple chip‐based bead sorter capable of enriching the concentration of green fluorescent beads from 63% to 95%. In CE experiments, we show that a mixture of analyte solution containing 30 nM 6‐carboxyrhodamine 6G and 10 nM fluorescein can be separated and detected with excellent signal‐to‐noise ratio (∼17 for 10 nM fluorescein) using the collimated emission from a blue LED; the estimated mass detection limit was ∼200 zmol for fluorescein. We also demonstrated ultrasensitive fluorescence imaging of single rhodamine 123 molecules and individual λ‐DNA molecules. At a small fraction of the cost of an Ar+ laser, high‐power blue and UV LEDs are effective alternatives for lasers and arc lamps in fluorescence applications that demand portability, low cost, and convenience.
Noninvasive fluid flow measurements in microfluidic channels with backscatter interferometry
Authors: Markov Dmitry A. , Dotson Stephen , Wood Scott , Bornhop Darryl J. 
Published: November 2004

AbstractThe ability to measure fluid velocity within picoliter volumes or on‐chip noninvasively, is important toward fully realizing the potential of microfluidics and micrototal analysis systems, particularly in applications such as micro‐high‐performance liquid chromatography (HPLC) or in metering mixing where the flow rate must be quantified. Additionally, these measurements need to be performed directly on moving fluids in a noninvasive fashion. We presented here the proof of principle experiments showing nonintrusive fluid flow measurements can be accomplished on‐chip using a pump and probe configuration with backscattering interferometry. The on‐chip interferometric backscatter detector (OCIBD) is based on a fiber‐coupled HeNe laser that illuminates a portion of an isotropically etched 40 μm radius channel and a position sensitive transducer to measure fringe pattern shifts. An infrared laser with a mechanical shutter is used to heat a section of a flowing volume and the resulting refractive index (RI) change is detected with the OCIBD downstream as a time‐dependent RI perturbation. Fluid velocity is quantified as changes in the phase difference between the shutter signal and the OCIBD detected signal in the Fourier domain. The experiments are performed in the range of 3–6 μL/h with 3σ detection limits determined to be 0.127 nL/s. Additionally, the RI response of the system is calibrated using temperature changes as well as glycerol solutions.
DNA sequencing and genotyping in miniaturized electrophoresis systems
Authors: Kan Cheuk‐Wai , Fredlake Christopher P. , Doherty Erin A. S. , Barron Annelise E. 
Published: November 2004

AbstractAdvances in microchannel electrophoretic separation systems for DNA analyses have had important impacts on biological and biomedical sciences, as exemplified by the successes of the Human Genome Project (HGP). As we enter a new era in genomic science, further technological innovations promise to provide other far‐reaching benefits, many of which will require continual increases in sequencing and genotyping efficiency and throughput, as well as major decreases in the cost per analysis. Since the high‐resolution size‐ and/or conformation‐based electrophoretic separation of DNA is the most critical step in many genetic analyses, continual advances in the development of materials and methods for microchannel electrophoretic separations will be needed to meet the massive demand for high‐quality, low‐cost genomic data. In particular, the development (and commercialization) of miniaturized genotyping platforms is needed to support and enable the future breakthroughs of biomedical science. In this review, we briefly discuss the major sequencing and genotyping techniques in which high‐throughput and high‐resolution electrophoretic separations of DNA play a significant role. We review recent advances in the development of technology for capillary electrophoresis (CE), including capillary array electrophoresis (CAE) systems. Most of these CE/CAE innovations are equally applicable to implementation on microfabricated electrophoresis chips. Major effort is devoted to discussing various key elements needed for the development of integrated and practical microfluidic sequencing and genotyping platforms, including chip substrate selection, microchannel design and fabrication, microchannel surface modification, sample preparation, analyte detection, DNA sieving matrices, and device integration. Finally, we identify some of the remaining challenges, and some of the possible routes to further advances in high‐throughput DNA sequencing and genotyping technologies.
The revived Bretton Woods system
Authors: Dooley Michael P. , Folkerts‐Landau David , Garber Peter 
Published: November 2004

AbstractThe economic emergence of a fixed exchange rate periphery in Asia has re‐established the United States as the centre country in the Bretton Woods international monetary system. We argue that the normal evolution of the international monetary system involves the emergence of a periphery for which the development strategy is export‐led growth supported by undervalued exchange rates, capital controls and official capital outflows in the form of accumulation of reserve asset claims on the centre country. The success of this strategy in fostering economic growth allows the periphery to graduate to the centre. Financial liberalization, in turn, requires floating exchange rates among the centre countries. But there is a line of countries waiting to follow the Europe of the 1950s/60s and Asia today, sufficient to keep the system intact for the foreseeable future. Copyright © 2004 John Wiley & Sons, Ltd.
How do UK‐based foreign exchange dealers think their market operates?
Authors: Cheung Yin‐Wong , Chinn Menzie D. , Marsh Ian W. 
Published: November 2004

AbstractThis paper summarizes the results of a survey of UK‐based foreign exchange dealers conducted in 1998. It addresses topics in three main areas: the microeconomic operation of the foreign exchange market; the beliefs of dealers regarding the importance, or otherwise, of observable macroeconomic fundamental factors in affecting exchange rates; microstructure factors in FX. We find that heterogeneity of traders' beliefs is evident from the results but that it is not possible to explain such disagreements in terms of institutional detail, rank or trading technique (e.g. technical analysts versus fundamentalists). As expected, non‐observable fundamental factors are thought to dominate short horizon changes in exchange rates, but observable fundamentals are deemed important over much shorter horizons than the mainstream empirical literature would suggest. Finally, market ‘norms’ and behavioural phenomena are very strong in the FX market and appear to be key determinants of the bid–ask spread. Copyright © 2004 John Wiley & Sons, Ltd.
Impact of genotype and micronutrient applications on nitrate reductase activity of tea leaves
Authors: Venkatesan Selvaraj 
Published: November 2004

AbstractTea flush shoots comprising three leaves and a bud were collected from various clones (cultivars) from different experimental fields and analysed for nitrate reductase (NR) activity. Most of the cultivars of Assam type had higher NR activity, followed by Cambod and China types. NR activity was maximum in the clone UPASI‐9. It was found that NR activity could be used as a biochemical tool to predict the yield potential of cultivars at the initial stage of selection for a breeding programme. The activity was higher in the youngest part of the tea plant. With the existing methodology it was not possible to measure the NR activity in stem portions of the tea plant. There was a strong positive correlation between NR activity and amino acid contents of tea shoots. Inclusion of molybdenum in the foliar applied micronutrient mixture was found helpful in triggering the NR activity in a few clones and seedlings. Copyright © 2004 Society of Chemical Industry
Carotenoid composition of kale as influenced by maturity, season and minimal processing
Authors: de Azevedo Cristiane H , Rodriguez‐Amaya Delia B 
Published: November 2004

AbstractThe principal carotenoids of kale were identified by chemical reactions, high‐performance liquid chromatography/mass spectrometry and high‐performance liquid chromatography/photodiode array detection and were quantified by the last technique. In kale taken from conventional farms, the β‐carotene and lutein contents were significantly higher in the mature leaves, violaxanthin was at an unusually high level in the young leaves, and neoxanthin had practically the same concentration at both stages of maturity. In samples taken from an organic farm, the carotenoid contents were essentially the same in the young and the mature leaves. Except for β‐carotene, which did not differ with season, the carotenoid concentrations of marketed minimally processed kale were found to be significantly higher in the summer than in the winter, reflecting seasonal rather than processing effects. In minimally processed kale monitored during 5 days of storage at 7–9 °C, β‐carotene, lutein, violaxanthin and neoxanthin were reduced by 14, 27, 20 and 31% respectively. Thus minimal processing, seasonal and maturity factors were found to have an influence on the carotenoid content of kale. Copyright © 2004 Society of Chemical Industry
Comparison of biological and chemical methods, and internal and external standards, for assaying tannins in Spanish shrub species
Authors: del Pino María C Álvarez , Hervás Gonzalo , Mantecón Ángel R , Giráldez F Javier , Frutos Pilar 
Published: November 2004

AbstractTannin contents of stems, flowers and leaves of four shrub species (Erica arborea, Erica australis, Cytisus cantabricus and Genista occidentalis) were chemically assessed using two colorimetric assays (butanol–HCl and Folin–Ciocalteu) and several standards (tannic acid, purified quebracho condensed tannins (CT) and purified CT extracted from each species). A method based on the biological activity of tannins in the rumen was also used for assaying tannins. Depending on the species, the use of quebracho tannin as standard over‐ or underestimated CT contents, in comparison to the use of the respective internal standard. However, the high correlationship observed between in vitro gas production in the presence or absence of polyethylene glycol (PEG) and CT contents estimated from quebracho suggests that this standard could be used for a quicker estimate of the nutritive value of tannin‐containing plants. Tannin contents obtained by the Folin–Ciocalteu method, using tannic acid as standard, were also related to their activity on rumen fermentation. The use of the in vitro gas production technique, in the absence or presence of PEG, may provide more useful information than the chemical assays when the final aim of tannin analysis is to assess the nutritive value of feedstuffs for ruminants. Copyright © 2004 Society of Chemical Industry
Influence of drying mode on iridoid bitter constituent levels in gentian root
Authors: Carnat Andrée , Fraisse Didier , Carnat André‐Paul , Felgines Catherine , Chaud Denis , Lamaison Jean‐Louis 
Published: November 2004

AbstractRoot samples of wild gentian (Gentiana lutea L) were harvested from six localities (altitude 970 m to 1350 m) from May to November 2000. Each batch of roots was split into three: fresh roots, naturally dried roots (ambient air) and artificially dried roots (40 °C). In all the samples, levels of iridoid bitter constituents and of xanthone coloured compounds were determined by HPLC. The mean total iridoid content in the fresh roots was 102.4 g kg−1 in dry matter (DM). The mean level of the principal bitter compound gentiopicroside was particularly high at 81 g kg−1 DM. Loganic acid, not previously reported in G lutea, was the second most abundant bitter compound at a mean level of 14.3 g kg−1 DM. Swertiamarin was present at 5.4 g kg−1, with another minor unidentified iridoid. Levels of iridoid compounds were strongly dependent of the drying mode. These amounts were 88.5 g kg−1 DM in artificially dried roots and 62.5 g kg−1 DM in naturally dried roots, mostly owing to a marked decrease in gentiopicroside. The temperature of 40 °C preserved the bitter compounds and the bitterness of fresh gentian roots. The amount of coloured xanthones was relatively low at 3.3 g kg−1 and did not change with the drying mode. Copyright © 2004 Society of Chemical Industry
Prediction of protein supply to ruminants from concentrates: comparison of the NRC‐2001 model with the DVE/OEB system
Authors: Yu Peiqiang 
Published: November 2004

AbstractThe objective of this study was to compare the DVE/OEB system (DVE = truly absorbed protein in the small intestine; OEB = degraded protein balance) and the NRC‐2001 model in the prediction of supply of protein to dairy cows from 46 selected concentrates: malting‐type barley (cv Harrington), feed‐type barley (cv Valier), field tick beans (Vicia faba), white albus lupins (Lupinus albus), whole soybeans and horse beans (Vicia faba cv Alfred). The two barleys were processed by coarse (roller miller, 0.533 mm gap) and fine (hammer mill, 2 mm screen) processing. The field tick beans and white albus lupins were dry roasted at various conditions at the University of Melbourne. The soybeans and horse beans were pressure‐toasted at 100, 118 and 136 °C for 3, 7, 15 and 30 min at Wageningen Feed Processing Centre. Comparisons were made in terms of (1) ruminally synthesized microbial protein, (2) truly absorbed protein in the small intestine and (3) degraded protein balance, based on 46 samples. The results showed that the predicted values from the DVE/OEB system and the NRC‐2001 model had significant correlations. However, using the DVE/OEB system, the overall average microbial protein supply based on available energy was 10% lower and the truly absorbed protein in the small intestine was 8% lower than that predicted by the NRC‐2001 model. A difference was also found in the prediction of the degraded protein balances, which was 16% higher than that estimated from the NRC‐2001 model. These differences are due to factors used in calculations in the two models, although both are based on similar principles. This indicates that further refinement is needed for a modern protein evaluation and prediction system. Copyright © 2004 Society of Chemical Industry
Micellar electrokinetic capillary chromatography of methylxanthines‐containing beverages: discussion of the molecular species involved
Authors: Pomilio Alicia B , Trajtemberg Silvia P , Vitale Arturo A 
Published: November 2004

AbstractMicellar electrokinetic capillary chromatography (MECC) experimental conditions were applied to 12 samples of methylxanthine‐containing infusions of different commercial brands of yerba mate, coffee, tea and cocoa as well as two cola drinks. The best resolution in this mode of automated high‐performance capillary electrophoresis (HPCE) was achieved here when using 15 kV voltage in an uncoated fused‐silica capillary of 45 cm length (40 cm effective length), 50 mM sodium dodecylsulfate, 90 mM pH 8.5 borate buffer and UV detection. Theobromine, caffeine and theophylline were separated, and the peak splitting due to tautomeric species was observed. Experimental conditions were controlled, keeping constant the size of the elution window in each analysis. The limit of detection was less than 1 mg l−1, the limit of quantitation was 2.5 mg l−1 and the work range was 2.5–300 mg l−1. This HPCE–MECC system has proved suitable for the analysis/quality control of xanthines in beverages for consumption. Roles of various parameters as well as distinctly charged species of each xanthine and the origin of peak splitting in this MECC system are discussed. Copyright © 2004 Society of Chemical Industry
Validation of alternative methods of data normalization in gene co-expression studies
Authors: Reverter Antonio , Barris Wes , McWilliam Sean , Byrne Keren A. , Wang Yong H. , Tan Siok H. , Hudson Nick , Dalrymple Brian P. 
Published: November 2004

AbstractMotivation: Clusters of genes encoding proteins with related functions, or in the same regulatory network, often exhibit expression patterns that are correlated over a large number of conditions. Protein associations and gene regulatory networks can be modelled from expression data. We address the question of which of several normalization methods is optimal prior to computing the correlation of the expression profiles between every pair of genes.Results: We use gene expression data from five experiments with a total of 78 hybridizations and 23 diverse conditions. Nine methods of data normalization are explored based on all possible combinations of normalization techniques according to between and within gene and experiment variation. We compare the resulting empirical distribution of gene × gene correlations with the expectations and apply cross-validation to test the performance of each method in predicting accurate functional annotation. We conclude that normalization methods based on mixed-model equations are optimal.Contact: tony.reverter-gomez@csiro.au
Aphid suppression by natural enemies in mulched cereals
Authors: Schmidt Martin H. , Thewes Ulrich , Thies Carsten , Tscharntke Teja 
Published: November 2004

AbstractLarge populations of natural enemies are the basis for natural pest control. Effects of mulch on predator–prey interactions in arable fields are poorly known, despite its potential to enhance ground‐dwelling predators and thereby reduce pest infestations. We studied the densities of predators and parasitoids, and their impact on cereal aphids in the presence and absence of mulch. Released populations of the bird cherry aphid,Rhopalosiphum padi(L.) (Homoptera: Aphididae), and two naturally occurring aphid species, were monitored under experimentally reduced densities of: (i) ground‐dwelling predators, (ii) flying predators and parasitoids, and (iii) with straw mulch. The three treatments were applied in a 2 × 2 × 2 factorial design in a field of spring wheat (Triticum aestivumL.). The exclusion of ground‐dwelling predators increased aphid populations by 55% in June and 40% in July, respectively. Mulched plots had 25% lower aphid densities in June. This was presumably due to enhanced densities of spiders (Araneida) in mulched plots. The exclusion of flying predators and parasitoids led to 94% higher aphid populations in late July (109 vs. 56 individuals per 100 shoots), irrespective of mulch or ground predator manipulation. This was attributed to the larvae of gall midgesAphidoletescf.aphidimyza(Rondani) (Diptera: Cecidomyiidae) and hoverflies (Diptera: Syrphidae). The results indicate that a scarcity of predators and a bare soil surface renders crops more susceptible to arthropod pests. Farming schemes should aim at enhancing both ground‐dwelling and flying predators for elevated levels of natural pest control.