bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of gastrointestinal digestion and heating on the allergenicity of the kiwi allergens Act d 1, actinidin, and Act d 2, a thaumatin‐like protein
Authors: Bublin Merima , Radauer Christian , Knulst André , Wagner Stefan , Scheiner Otto , Mackie Alan R. , Mills E. N. Clare , Breiteneder Heimo 
Published: July 2008

AbstractKiwifruit is a significant elicitor of allergy both in children and adults. Digestibility of two kiwifruit allergens, actinidin (Act d 1) and thaumatin‐like protein (Act d 2), was assessed using an in vitro digestion system that approximates physiological conditions with respect to the passage of food through the stomach into the duodenum. Act d 1 precipitated in simulated gastric fluid at pH 2 and digestion of the aggregated protein proceeded slowly. The residual precipitate redissolved completely in simulated duodenal fluid at pH 6.5 and was partially digested. Forty percent of Act d 2 remained intact during gastric digestion and were cleaved by duodenal proteases into large fragments covalently linked by disulfide bonds. Both digested allergen samples displayed nearly unchanged IgE binding abilities. Circular dichroism spectra were used to analyze heat and acid‐induced unfolding. Thermal stability of both allergens was strongly pH dependent. While Act d 1 was irreversibly destabilized in acidic solutions, heat‐induced denaturation of Act d 2 at pH 2 was fully reversible. IgE binding to Act d 2 but not Act d 1 was detected in processed food products. The stability of Act d 1 and Act d 2 provides one explanation for the allergenic potency of kiwifruit.
Ketogenic diet‐fed rats have increased fat mass and phosphoenolpyruvate carboxykinase activity
Authors: Ribeiro Letícia C. , Chittó Ana L. , Müller Alexandre P. , Rocha Juliana K. , Castro da Silva Mariane , Quincozes‐Santos André , Nardin Patrícia , Rotta Liane N. , Ziegler Denize R. , Gonçalves Carlos‐Alberto , Da Silva Roselis S. M. , Perry Marcos L. S. , Gottfried Carmem 
Published: July 2008

AbstractThe ketogenic diet (KD), characterized by high fat and low carbohydrate and protein contents, has been proposed to be beneficial in children with epilepsy disorders not helped by conventional anti‐epileptic drug treatment. Weight loss and inadequate growth is an important drawback of this diet and metabolic causes are not well characterized. The aim of this study was to examine body weight variation during KD feeding for 6 wk of Wistar rats; fat mass and adipocyte cytosolic phosphoenolpyruvate carboxykinase (PEPCK) activity were also observed. PEPCK activity was determined based on the [H14CO3–]‐oxaloacetate exchange reaction. KD‐fed rats gained weight at a less rapid rate than normal‐fed rats, but with a significant increment in fat mass. The fat mass/body weight ratio already differed between ketogenic and control rats after the first week of treatment, and was 2.4×higher in ketogenic rats. The visceral lipogenesis was supported by an increment in adipocyte PEPCK, aiming to provide glycerol 3‐phosphate to triacylglycerol synthesis and this fat accumulation was accompanied by glucose intolerance. These data contribute to our understanding of the metabolic effects of the KD in adipose tissue and liver and suggest some potential risks of this diet, particularly visceral fat accumulation.
Uptake of grape anthocyanins into the rat kidney and the involvement of bilitranslocase
Authors: Vanzo Andreja , Terdoslavich Michela , Brandoni Anabel , Torres Adriana M. , Vrhovsek Urska , Passamonti Sabina 
Published: July 2008

AbstractAnthocyanins are among the most common flavonoids in the human diet. In spite of their very low bioavailability, anthocyanins are indicated as active in preventing the progress of cardiovascular and neurodegenerative diseases, obesity, inflammation, and cancer. Any piece of knowledge concerning absorption, tissue distribution, metabolism, and excretion of dietary anthocyanins is expected to help understanding the apparent paradox between their low concentrations in cells and their bioactivity. The aim of this work was to investigate the renal uptake of dietary anthocyanins and the underlying molecular mechanism. A solution containing anthocyanins extracted from grape (Vitis vinifera) was introduced into the isolated stomach of anesthetized rats; after both 10 and 30 min, plasma, liver, and kidney were analyzed for their anthocyanin contents. While anthocyanins in the liver were at apparent equilibrium with plasma both after 10 and 30 min, kidney anthocyanins were 3‐ and 2.3‐fold higher than in plasma, after 10 and 30 min, respectively. Since the transport activity of the bilitranslocase in kidney basolateral membrane vesicles was competitively inhibited by malvidin 3‐glucoside (Ki = 4.8 ± 0.2 μM), the anthocyanin uptake from blood into kidney tubular cells is likely to be mediated by the kidney isoform of this organic anion membrane transporter.
A power sparse approximate inverse preconditioning procedure for large sparse linear systems
Authors: Jia Zhongxiao , Zhu Baochen 
Published: July 2008

AbstractMotivated by the Cayley–Hamilton theorem, a novel adaptive procedure, called a Power Sparse Approximate Inverse (PSAI) procedure, is proposed that uses a different adaptive sparsity pattern selection approach to constructing a right preconditioner M for the large sparse linear system Ax=b. It determines the sparsity pattern of M dynamically and computes the n independent columns of M that is optimal in the Frobenius norm minimization, subject to the sparsity pattern of M. The PSAI procedure needs a matrix–vector product at each step and updates the solution of a small least squares problem cheaply. To control the sparsity of M and develop a practical PSAI algorithm, two dropping strategies are proposed. The PSAI algorithm can capture an effective approximate sparsity pattern of A−1 and compute a good sparse approximate inverse M efficiently. Numerical experiments are reported to verify the effectiveness of the PSAI algorithm. Numerical comparisons are made for the PSAI algorithm and the adaptive SPAI algorithm proposed by Grote and Huckle as well as for the PSAI algorithm and three static Sparse Approximate Inverse (SAI) algorithms. The results indicate that the PSAI algorithm is at least comparable to and can be much more effective than the adaptive SPAI algorithm and it often outperforms the static SAI algorithms very considerably and is more robust and practical than the static ones for general problems. Copyright © 2008 John Wiley & Sons, Ltd.
Direct visualization of fluorescent signals in protein gels using a backlit blue light plate
Authors: Wu Szu‐Yu , Chin Li‐Te , Chen Li‐Ming , Chen Han‐Min 
Published: July 2008

AbstractThe visualization of fluorescently labeled protein gels is required for the analysis of electrophoretic results or manually picking protein bands or spots from gels. To accomplish this task, an UV light table is generally utilized, but may be hazardous to operators. The blue light transilluminator is another apparatus that may be used for this purpose, but is sometimes insufficient for revealing weak fluorescent signals. In this study, we invented a new setup utilizing a backlit blue light plate for illuminating fluorescently stained protein gels. This method employs Snell's law and allows for the direct visualization of fluorescent signals in protein gels without the use of a filter or filter glasses. This safe, convenient, economic, and effective setup was found to be an ideal alternative for illuminating fluorescent protein gels in proteomic experiments.
Glycoproteomics and glycomics investigation of membrane N‐glycosylproteins from human colon carcinoma cells
Authors: Vercoutter‐Edouart Anne‐Sophie , Slomianny Marie‐Christine , Dekeyzer‐Beseme Olivia , Haeuw Jean‐François , Michalski Jean‐Claude 
Published: July 2008

AbstractAberrant glycosylation of proteins is known to profoundly affect cellular adhesion or motility of tumoral cells. In this study, we used HT‐29 human colon epithelial cancer cells as a cellular model of cancer progression, as they can either proliferate or differentiate into enterocyte phenotype. A glycoproteomic approach based on Con A lectin‐affinity chromatography, SDS‐PAGE and MS analysis, allowed the identification of membrane N‐glycoproteins from Triton X‐100‐solubilized proteins from membrane preparation. Among them, 65% were membrane proteins, and 45% were known to be N‐glycosylated, such as α chains integrin and dipeptidyl isomerase IV. By lectin‐blot analysis, significant changes of α‐2,3‐ and α‐2,6‐sialylation of membrane glycoproteins were observed between proliferating and differentiated HT‐29 cells. From these results, nano‐LC‐MS/MS analysis of the tryptic digests of the corresponding bands was performed and led to the identification of several transmembrane glycoproteins, like members of the solute carrier family and adhesion proteins. Finally, we compared N‐glycans profiles and monosaccharide composition of proliferating and enterocyte‐like HT‐29 cells using MALDI‐MS and GC‐MS analyses of permethylated derivatives. This glycomic approach allowed to underscore significant changes in N‐glycans structure, in particular the expression of atypical N‐acetylglucosamine (GlcNAc)‐ended N‐glycans in enterocyte‐like HT‐29 cells.
Support needs and acceptability of psychological and peer consultation: attitudes of 108 women who had undergone or were considering prophylactic mastectomy
Authors: Patenaude Andrea F. , Orozco Sara , Li Xiaochun , Kaelin Carolyn M. , Gadd Michelle , Matory Yvedt , Mayzel Kathleen , Roche Constance A. , Smith Barbara L. , Farkas Walden , Garber Judy E. 
Published: July 2008

AbstractObjective: Prophylactic mastectomy (PM) offers 90% or greater reduction in risk of breast cancer to women at increased hereditary risk. Nonetheless, acceptance in North America is low (0–27%) and 25–50% of women electing surgery report psychological distress and/or difficulty adapting following PM. Most women also report reduced cancer worry postoperatively. Psychological consultation to aid decision‐making and post‐surgical coping is not routinely offered. This retrospective, cross‐sectional study explored interest in and acceptability of psychological consultation for issues related to PM among 108 women who had undergone or were considering surgery.Method: Qualitative interviews were conducted with 26 healthy women who had undergone prophylactic mastectomy of both (bilateral) breasts (BPM), 45 women who had undergone prophylactic mastectomy of one breast (unilateral contralateral) (UPM) after diagnosis of invasive breast cancer in the other breast or ductal carcinoma in situ (DCIS), and 37 women who were considering having PM surgery.Results: Of the women who had undergone PM, more than half felt pre‐surgical psychological consultation was advisable; nearly 2/3 thought post‐surgical psychological consultation would be helpful. All women currently considering PM believed psychological consultation would aid decision‐making and preparation for surgery. Strong support was reported in all groups for the emotional and informational value of speaking with a woman who had previously undergone PM.Conclusions: Narratives illustrate the nature and intensity of the need for psychological support and describe preferences for the role of the psychologist. Suggestions are offered for integration of psychological services for women deciding about or adapting to PM. Copyright © 2008 John Wiley & Sons, Ltd.
A randomized trial of a breast/ovarian cancer genetic testing decision aid used as a communication aid during genetic counseling
Authors: Wakefield Claire E. , Meiser Bettina , Homewood Judi , Taylor Alan , Gleeson Margaret , Williams Rachel ,   the AGenDA Collaborative Group, Tucker Kathy 
Published: July 2008

AbstractObjectives: To evaluate the impact of a decision aid for women considering genetic testing for breast/ovarian cancer risk given during genetic counseling.Methods: One hundred and forty‐eight women were randomized to receive the decision aid or a control pamphlet at the beginning of their first consultation with a genetic counselor. When the patient received the decision aid, it was used to complement consultation discussions about genetic testing. One hundred and ten (74.3%) women completed the first questionnaire designed to elicit information about women's levels of decisional conflict and knowledge about genetic testing. Of these, 105 (70.9%) completed a second questionnaire to assess longer‐term outcomes, 6 months postconsultation.Results: Results showed that women who received the decision aid felt more informed about genetic testing (χ2(1)=8.69; P=0.003), had clearer values (χ2(1)=6.90; P=0.009) and had higher knowledge levels (χ2(2)=6.49; P=0.039) than women who received the control pamphlet.Conclusions: The developed decision aid improved patient outcomes better than a control pamphlet when implemented during genetic counseling and given to the patient to take home. Copyright © 2008 John Wiley & Sons, Ltd.
A universal pathway for amyloid nucleus and precursor formation for insulin
Authors: Nayak Arpan , Sorci Mirco , Krueger Susan , Belfort Georges 
Published: July 2008

AbstractTo help identify the etiological agents for amyloid‐related diseases, attention is focused here on the fibrillar precursors, also called oligomers and protofibrils, and on modeling the reaction kinetics of the formation of the amyloid nucleus. Insulin is a favored model for amyloid formation, not only because amyloidosis can be a problem in diabetes, but also because aggregation and fibrillation causes problems during production, storage, and delivery. Small angle neutron scattering (SANS) is used to measure the temporal formation of insulin oligomers in H2O‐ and D2O‐based solvents and obtain consistent evidence of the composition of the insulin nucleus that comprised three dimers or six monomers similar to that recently proposed in the literature. A simple molecular structural model that describes the growth of oligomers under a wide range of environmental conditions is proposed. The model first involves lengthening or end‐on‐end association of dimers to form three‐dimer nuclei, and then exhibits broadening or side‐on‐side association of nuclei. Using different additives to demonstrate their influence on the kinetics of oligomer formation, we showed that, although the time required to form the nucleus was dependent on a specific system, they all followed a universal pathway for nucleus and precursor formation. The methods and analyses presented here provide the first experimental molecular size description of the details of amyloid nucleus formation and subsequent propagation to fibril precursors independent of kinetics. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Principles of flexible protein–protein docking
Authors: Andrusier Nelly , Mashiach Efrat , Nussinov Ruth , Wolfson Haim J. 
Published: July 2008

AbstractTreating flexibility in molecular docking is a major challenge in cell biology research. Here we describe the background and the principles of existing flexible protein–protein docking methods, focusing on the algorithms and their rational. We describe how protein flexibility is treated in different stages of the docking process: in the preprocessing stage, rigid and flexible parts are identified and their possible conformations are modeled. This preprocessing provides information for the subsequent docking and refinement stages. In the docking stage, an ensemble of pre‐generated conformations or the identified rigid domains may be docked separately. In the refinement stage, small‐scale movements of the backbone and side‐chains are modeled and the binding orientation is improved by rigid‐body adjustments. For clarity of presentation, we divide the different methods into categories. This should allow the reader to focus on the most suitable method for a particular docking problem. Proteins 2008. Published Wiley‐Liss, Inc.
Molecular simulations enlighten the binding mode of quercetin to lipoxygenase‐3
Authors: Fiorucci Sébastien , Golebiowski Jérôme , Cabrol‐Bass Daniel , Antonczak Serge 
Published: July 2008

AbstractInhibition of lipoxygenases (LOXs) by flavonoid compounds is now well documented, but the description of the associated mechanism remains controversial due to a lack of information at the molecular level. For instance, X‐ray determination of quercetin/LOX‐3 system has led to a structure where the enzyme was cocrystallized with a degradation product of the substrate, which rendered the interpretation of the reported interactions between this flavonoid compound and the enzyme difficult. Molecular modeling simulations can in principle allow obtaining precious insights that could fill this lack of structural information. Thus, in this study, we have investigated various binding modes of quercetin to LOX‐3 enzyme in order to understand the first step of the inhibition process, that is the association of the two entities. Molecular dynamics simulations and free energy calculations suggest that quercetin binds the metal center via its 3‐hydroxychromone function. Moreover, enzyme/substrate interactions within the cavity impose steric hindrances to quercetin that may activate a direct dioxygen addition on the substrate. Proteins 2008;73:290–298. © 2008 Wiley‐Liss, Inc.
Characterization of preferred orientated vanadium dioxide film on muscovite (001) substrate
Authors: Yan Jiazhen , Huang Wanxia , Zhang Yue , Liu Xiaojie , Tu Mingjin 
Published: July 2008

AbstractIn this paper, a natural muscovite slice is used as the substrate for deposition of the vanadium dioxide films. Vanadium oxide gel films are fabricated on the muscovite (001) cleavage plane by an aqueous sol–gel method, then the films are crystallized and reduced to vanadium dioxide by annealing in static N2 atmosphere at a temperature of 480 °C. The X‐ray patterns of the reduced films exhibit the unique diffraction peak of the monoclinic VO2(011) plane. The result indicates that the films are perfectly (011) orientated on muscovite (001) plane. The optic and electrical properties of the films are investigated below and above the metal‐to‐isolator phase‐transition temperature. The thermochromic VO2 films on muscovite exhibit changes in electrical resistivity more than three orders of magnitude, while infrared transmittance switches more than 60% in the wave number range of 4000–2000 cm–1. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
An EQCM study of ultrasonically assisted electrodeposition of Co/CeO2 and Ni/CeO2 composites for fuel cell applications
Authors: Argirusis Chr. , Matić S. , Schneider O. 
Published: July 2008

AbstractThe electrodeposition of Co/CeO2 and Ni/CeO2 composites from electrolytes containing suspended nanoparticles of gadolinia doped ceria under the influence of power ultrasound was studied using the electrochemical quartz crystal microbalance technique (EQCM). The amount of oxide incorporation into the layers was determined by electron probe microanalysis. From 0.1 M cobalt electrolytes rough Co layers with ceria contents of up to 8% were deposited, and a strong increase in the damping of the quartz was observed. In the case of Ni deposition an increase of the deposition rate enhanced the current efficiency and lead to larger ceria contents. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Introduction of metal dopants and/or Ag nanoparticles into direct‐patternable ZnO thin films formed by photochemical solution deposition
Authors: Kim Hyuncheol , Park Hyeong‐Ho , Sivasankar Reddy A. , Park Hyung‐Ho , Choi Se‐Young 
Published: July 2008

AbstractThe introduction of metal dopants and nanoparticles into ZnO films influences film conductivity and transparency but the effects of dopants and nanoparticles are not always predictable. The incorporation of Ag nanoparticles into a ZnO film enhanced film conductivity. Less than 1% donor‐doping into the ZnO film induced a decrease in film resistance when using both interstitial and substitutional metal‐dopants. When a metal‐dopant and Ag nanoparticles were introduced into ZnO film simultaneously, the Ag nanoparticles acted as an electron scattering center in the case of Ag or Cd doped ZnO films (interstitially doped). A decrease in the sheet resistance was observed in the case of In or Sn doped ZnO films (substitutionally doped). The transmittance tended to decrease with the incorporation of Ag nanoparticles. This was caused by light absorption from the surface plasmon resonance of the Ag nanoparticles in the film. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Identification and structural characterization of steroidal glycosides in Hoodia gordonii by ion‐trap tandem mass spectrometry and liquid chromatography coupled with electrospray ionization time‐of‐flight mass spectrometry
Authors: Avula Bharathi , Wang Yan‐Hong , Pawar Rahul S. , Shukla Yatin J. , Smillie Troy J. , Khan Ikhlas A. 
Published: July 2008

AbstractElectrospray ion‐trap tandem mass spectrometry (ESI‐MS/MS) and high‐performance liquid chromatography coupled with electrospray ionization time‐of‐flight mass spectrometry (LC/ESI‐TOFMS) were used to identify and characterize eight C‐21 steroidal glycosides in Hoodia gordonii. A generalized fragmentation pathway was proposed by comparing the spectra acquired for eight C‐21 steroidal glycosides. The steroidal glycosides in Hoodia gordonii have been classified into two major core groups: hoodigenin A and calogenin. Using the ESI‐TOF method, the major core peak ions generated by hoodigenin A glycosides are m/z 313 and 295 and by calogenin glycosides are m/z 479, 461, 299 and 281, respectively. In the MS/MS spectra, fragmentation reactions of the [M+Na]+ ion were recorded to provide structural information about the glycosyl and aglycone moieties. The data illustrates the ability of positive mode ESI for the identification of hoodigenin A and calogenin glycosides, including the nature of the hoodigenin A and calogenin core, the number of sugar residues and the type of saccharide moiety. Copyright © 2008 John Wiley & Sons, Ltd.
A combinatorial approach to jumping particles: The parallel TASEP
Authors: Duchi Enrica , Schaeffer Gilles 
Published: July 2008

AbstractIn this article, we continue the combinatorial study of models of particles jumping on a row of cells which we initiated with the standard totally asymmetric simple exclusion process or TASEP (Duchi and Schaeffer, Journal of Combinatorial Theory, Series A, 110(2005), 1–29). We consider here the parallel TASEP, in which particles can jump simultaneously. On the one hand, the interest in this process comes from highway traffic modeling: it is the only solvable special case of the Nagel‐Schreckenberg automaton, the most popular model in that context. On the other hand, the parallel TASEP is of some theoretical interest because the derivation of its stationary distribution, as appearing in the physics literature, is harder than that of the standard TASEP.We offer here an elementary derivation that extends the combinatorial approach we developed for the standard TASEP. In particular, we show that this stationary distribution can be expressed in terms of refinements of Catalan numbers. © 2008 Wiley Periodicals, Inc. Random Struct. Alg., 2008
Visual Cocaine Detection with Gold Nanoparticles and Rationally Engineered Aptamer Structures
Authors: Zhang Juan , Wang Lihua , Pan Dun , Song Shiping , Boey Freddy Y. C. , Zhang Hua , Fan Chunhai 
Published: July 2008

AbstractA novel bioassay strategy is designed to detect small‐molecule targets such as cocaine, potassium, and adenosine, based on gold nanoparticles (AuNPs) and engineered DNA aptamers. In this design, an aptamer is engineered to be two pieces of random, coil‐like single‐stranded DNA, which reassembles into the intact aptamer tertiary structure in the presence of the specific target. AuNPs can effectively differentiate between these two states via their characteristic surface‐plasmon resonance‐based color change. Using this method, cocaine in the low‐micromolar range is selectively detected within minutes. This strategy is also shown to be generic and applicable to the detection of several other small‐molecule targets.