bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unconventional method based on circular dichroism to detect peanut DNA in food by means of a PNA probe and a cyanine dye
Authors: Sforza Stefano , Scaravelli Elena , Corradini Roberto , Marchelli Rosangela 
Published: September 2005

AbstractIn this paper we report an innovative and unconventional method based on circular dichroism for the identification of peanut DNA in food, which can be detected after PCR amplification at the nanomolar level by using an achiral PNA probe complementary to a tract of the peanut Ara h 2 gene and an achiral 3,3′‐diethylthiadicarbocyanine dye [DiSC2(5)]. Peanuts are one of the most common causes of severe allergic reactions to foods and are particularly dangerous when they are “hidden” (undeclared) in food. For better protection of consumers, detection methods are required to specifically detect the presence of hidden allergens in a wide variety of food items. Alternative to the detection of the proteins is the determination of species‐specific DNA, which is more resistant to technological treatments. PNAs are very specific probes able to recognize DNA sequences with high affinity and evidence for the binding can be obtained by using the DiSC2(5) dye, which aggregates onto the PNA–DNA duplex giving rise to a characteristic visibile band at 540 nm. Because the PNA–DNA duplex is in a right‐handed helical conformation, the aggregation of the dye to the duplex gives also rise to a strong CD signal in the 500–600 nm region with a strong exciton coupling due to the formation of multimeric species, since the handedness of the helix is transferred to the dye aggregate. The dye does not interact with the free single‐stranded DNA and although aggregating on the achiral PNA, this interaction is obviously not detectable by circular dichroism. Thus, only the formation of the PNA–DNA duplex, which takes place only upon specific Watson–Crick hydrogen binding between the PNA and the DNA bases, is detected, ensuring a very high specificity and sensitivity. The method has been optimized in a model system by using a synthetic oligonucleotide complementary to the PNA probe, showing that the intensity of the signal is linearly related to the amount of the DNA. The optimized method has been applied to the identification and quantitation of DNA extracted and amplified by PCR from peanuts and from peanut‐containing foods, allowing for a very sensitive detection at a very low level (few pmol). © 2005 Wiley‐Liss, Inc. Chirality 17:515–521, 2005.
Vectorization of Harungana madagascariensis Lam. ex Poir. (Hypericaceae) ethanolic leaf extract by using PLG‐nanoparticles: antibacterial activity assessment
Authors: Moulari B. , Lboutounne H. , Pellequer Y. , Guillaume Y.C. , Millet J. , Pirot F. 
Published: September 2005

AbstractThis study was undertaken to compare the in vitro and ex vivo antibacterial activity of an ethanolic Harungana madagascariensis leaf extract (HLE) incorporated into poly (D,L‐lactide‐co–glycolide) nanoparticles (HLE‐PLG‐NP). Two concentrations of HLE (500 and 1,000 µg/mL) for the in vitro study and one concentration (500 µg/mL) for the ex vivo study were compared using two gram‐positive bacterial strains (Micrococcus luteus and Staphylococcus epidermidis), and one gram‐negative bacterial strain (Moraxella sp.). The ex vivo antibacterial activity was evaluated on S. epidermidis CIP 55109 (SE) using an artificial contamination method. SE was inoculated for 12 h onto human skin fragment surfaces treated for 5 min either with HLE loaded, unloaded PLG‐NP, or HLE solution. In vitro, the two preparations inhibited completely the growth of all bacterial strains at 1,000 µg/mL. However, the HLE‐PLG‐NP had a significant antibacterial activity against SE (18.4±1.8–0.4±0.2 CFU/mL, P<0.05), and a marked antibacterial effect against M. luteus (ML) and Moraxella sp. (Msp) compared to HLE solution at 500 µg/mL. Ex vivo, HLE‐PLG‐NP at 500 µg/mL reduced viable bacteria (6.3–4.8 log10), compared to the HLE solution (6.3–5.5 log10) after 4 h artificial contamination (P<0.05). A thin layer chromatography study of both HLE solution and HLE‐PLG‐NP showed that among the seven components found on the chromatogram of the HLE solution, only two were present on the nanoparticles, one including a flavonoid heteroside fraction responsible for the antibacterial properties. The incorporation of the HLE into a colloidal carrier improved antibacterial performance. Drug Dev. Res. 65:26–33, 2005. © 2005 Wiley‐Liss, Inc.
Elevated vascular endothelial cell growth factor affects mesocardial morphogenesis and inhibits normal heart bending
Authors: Drake Christopher J. , Wessels Andy , Trusk Tom , Little Charles D. 
Published: September 2005

AbstractSignaling by means of vascular endothelial cell growth factor (VEGF) and its receptors (VEGFRs) is required for cardiovascular development. To examine how VEGF/VEGFR receptor signaling affects early endocardial cell behavior, embryonic quail hearts were subjected to elevated VEGF165 levels (five‐ to nine‐somite stage). Primitive embryonic hearts microinjected with recombinant human (rh)VEGF165 exhibit several distinct malformations compared with hearts in untreated embryos: the endocardial tube is malformed with tortuous cords and folds surrounded by a diminished cardiac jelly space, and the lumens of affected hearts are conspicuously reduced. Furthermore, the embryonic heart fails to loop properly. Inhibition of bending is accompanied by an apparent failure of the dorsal mesocardium to atrophy—an event thought to be necessary for heart bending. Instead of atrophy, VEGF‐treated mesocardia exhibit a marked increased in the number of resident endothelial cells. Collectively, the data suggest that the abnormally robust mesocardia in VEGF‐treated hearts impede the mechanical deformation required for normal heart bending. We conclude that the excessive VEGF signaling culminates in a physical or biomechanical mechanism that acts over a wide, tissue‐level, length scale to cause a severe developmental defect—failure of heart bending. Developmental Dynamics 235:10–18, 2006. © 2005 Wiley‐Liss, Inc.
Collagen XVIII/endostatin is associated with the epithelial–mesenchymal transformation in the atrioventricular valves during cardiac development
Authors: Carvalhaes Lorenza S. , Gervásio Othon L. , Guatimosim Cristina , Heljasvaara Ritva , Sormunen Raija , Pihlajaniemi Taina , Kitten Gregory T. 
Published: September 2005

AbstractType XVIII collagen is a multidomain protein that contains cleavable C‐terminal NC1 and endostatin fragments, which have been shown to either induce or inhibit cell migration. Endostatin is being intensely studied because of its anti‐angiogenic activity. Three variants of type XVIII collagen have been reported to be distributed in epithelial and endothelial basement membranes in a tissue‐specific manner. The single gene encoding collagen XVIII is on chromosome 21 within the region associated with the congenital heart disease phenotype observed in Down's syndrome. In this study, we investigated the expression pattern of collagen XVIII in embryonic mouse hearts during formation of the atrioventricular (AV) valves. We found that collagen XVIII is localized not only in various basement membranes but is also highly expressed throughout the connective tissue core of the endocardial cushions and forming AV valve leaflets. It was closely associated with the epithelial–mesenchymal transformation of endothelial cells into mesenchymal cushion tissue cells and was localized around these cells as they migrated into the cardiac jelly to form the initial connective tissue elements of the valve leaflets. However, after embryonic day 17.5 collagen XVIII expression decreased rapidly in the connective tissue and thereafter remained detectable only in the basement membranes of the endothelial layer covering the leaflets. The staining pattern observed within the AV endocardial cushions suggests that collagen XVIII may have a role in cardiac valve morphogenesis. These results may help us to better understand normal heart development and the aberrant mechanisms that cause cardiac malformations in Down's syndrome. Developmental Dynamics 235:132–142, 2006. © 2005 Wiley‐Liss, Inc.
Vascular endothelial growth factor receptor signaling is required for cardiac valve formation in zebrafish
Authors: Lee You Mie , Cope John J. , Ackermann Gabriele E. , Goishi Katsutoshi , Armstrong Ehrin J. , Paw Barry H. , Bischoff Joyce 
Published: September 2005

AbstractVascular endothelial growth factor‐receptors (VEGF‐Rs) are pivotal regulators of vascular development, but a specific role for these receptors in the formation of heart valves has not been identified. We took advantage of small molecule inhibitors of VEGF‐R signaling and showed that blocking VEGF‐R signaling with receptor selective tyrosine kinase inhibitors, PTK 787 and AAC 787, from 17–21 hr post‐fertilization (hpf) in zebrafish embryos resulted in a functional and structural defect in cardiac valve development. Regurgitation of blood between the two chambers of the heart, as well as a loss of cell‐restricted expression of the valve differentiation markers notch 1b and bone morphogenetic protein‐4 (bmp‐4), was readily apparent in treated embryos. In addition, microangiography revealed a loss of a definitive atrioventricular constriction in treated embryos. Taken together, these data demonstrate a novel function for VEGF‐Rs in the endocardial endothelium of the developing cardiac valve. Developmental Dynamics 235:29–37, 2006. © 2005 Wiley‐Liss, Inc.
Mechanism of Taurine: α‐Ketoglutarate Dioxygenase (TauD) from Escherichia coli
Authors: Bollinger J. Martin , Price John C. , Hoffart Lee M. , Barr Eric W. , Krebs Carsten 
Published: September 2005

AbstractThe iron(II)‐ and α‐ketoglutarate‐dependent dioxygenases comprise enzymes that catalyze a variety of important reactions in biology, including steps in the biosynthesis of collagen and antibiotics, the degradation of xenobiotics, the repair of alkylated DNA, and the sensing of oxygen and response to hypoxia. In these reactions, the reductive activation of oxygen is coupled to hydroxylation of the substrate and decarboxylation of the co‐substrate, α‐ketoglutarate. It is believed that a single, conserved mechanistic pathway for formation of a high‐valent iron intermediate that attacks the substrate is operant in all members of this family. Application of a combination of rapid kinetic and spectroscopic techniques to the reaction of taurine/α‐ketoglutarate dioxygenase (TauD), one member of this large enzyme family, has led to the detection of two reaction intermediates. The first intermediate, which is termed J, is a high‐spin FeIV‐oxo complex. Decay of J exhibits a large, normal C1 deuterium kinetic isotope effect, demonstrating that it is the species activating the C–H bond for hydroxylation. The second intermediate is an FeII‐containing product(s) complex. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
Lattice models of peptide aggregation: Evaluation of conformational search algorithms
Authors: Oakley Mark T. , Garibaldi Jonathan M. , Hirst Jonathan D. 
Published: September 2005

AbstractWe present a series of conformational search calculations on the aggregation of short peptide fragments that form fibrils similar to those seen in many protein mis‐folding diseases. The proteins were represented by a face‐centered cubic lattice model with the conformational energies calculated using the Miyazawa–Jernigan potential. The searches were performed using algorithms based on the Metropolis Monte Carlo method, including simulated annealing and replica exchange. We also present the results of searches using the tabu search method, an algorithm that has been used for many optimization problems, but has rarely been used in protein conformational searches. The replica exchange algorithm consistently found more stable structures then the other algorithms, and was particularly effective for the octamers and larger systems. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1638–1646, 2005
Systematic sparse matrix error control for linear scaling electronic structure calculations
Authors: Rubensson Emanuel H. , Sałek Paweł 
Published: September 2005

AbstractEfficient truncation criteria used in multiatom blocked sparse matrix operations for ab initio calculations are proposed. As system size increases, so does the need to stay on top of errors and still achieve high performance. A variant of a blocked sparse matrix algebra to achieve strict error control with good performance is proposed. The presented idea is that the condition to drop a certain submatrix should depend not only on the magnitude of that particular submatrix, but also on which other submatrices that are dropped. The decision to remove a certain submatrix is based on the contribution the removal would cause to the error in the chosen norm. We study the effect of an accumulated truncation error in iterative algorithms like trace correcting density matrix purification. One way to reduce the initial exponential growth of this error is presented. The presented error control for a sparse blocked matrix toolbox allows for achieving optimal performance by performing only necessary operations needed to maintain the requested level of accuracy. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1628–1637, 2005
Oxidation of metronidazole with sodium N‐bromo‐p‐toluenesulfonamide in acid and alkaline media: A kinetic and mechanistic study
Authors: Puttaswamy  , Jagadeesh R. V. , Gowda N. M. Made 
Published: September 2005

AbstractA kinetic study of oxidation of metronidazole (Met) with sodium N‐bromo‐p‐toluenesulfonamide or bromamine‐T (BAT) has been carried out in HClO4 (30°C) and NaOH (40°C) media. The experimental rate laws obtained are –d[BAT]/dt=k[BAT][Met]x [H+]y in acid medium and –d[BAT]/dt=k[BAT][Met]x [OH−]y/[PTS]z in alkaline medium, where x, y, and z are less than unity and PTS is p‐toluenesulfonamide. The reaction was subjected to changes in (a) ionic strength, (b) concentration of added reduction product PTS, (c) concentration of added neutral salts, (d) dielectric permittivity, and (e) solvent isotope effect. In both media, the stoichiometry of the reaction was found to be 1:1, and the oxidation product of metronidazole was identified as its aldehyde. The reaction was studied at different temperatures, and the activation parameters have been evaluated. The reaction constants involved in the proposed schemes were deduced. The reaction was found to be faster in acid medium in comparison with alkaline medium, which is attributed to the involvement of different oxidizing species. Mechanisms proposed and the rate laws derived are consistent with the observed kinetics. © 2005 Wiley Periodicals, Inc. Int J Chem Kinet 37: 700–709, 2005
The production of organic nitrates from various anthropogenic volatile organic compounds
Authors: Espada Cyntia , Grossenbacher John , Ford Kevin , Couch Tara , Shepson Paul B. 
Published: September 2005

AbstractProduction of organic nitrates from OH reaction with cyclohexane, cyclohexene, n‐butane, 1‐bromopropane, and p‐xylene in the presence of NO was studied. The total organic nitrate yields for cyclohexane and n‐butane were determined to be 17 ± 4 and 7 ± 2% respectively, which is in good agreement with previous determinations. Total yields for cyclohexene, 1‐bromopropane, and p‐xylene were 2.5 ± 0.5, 1.2 ± 0.3, and 3.2 ± 0.7 respectively. The yield for cyclohexene was five times smaller than that for cyclohexane. The 1‐bromopropane yield is three times smaller that that for n‐propane, but similar to that for propene, indicating that the effect of Br substitution in the reactant may be similar to that for OH substitution. The only nitrooxy product detected for p‐xylene was 4‐methylbenzylnitrate, which was formed following H abstraction from either methyl group. No organic nitrate was detected for peroxy radicals produced from OH addition to the ring, which accounts for 90% of the OH oxidation of p‐xylene. The calculated k3b/k3 value for p‐methyl benzyl peroxy radicals (0.32) was slightly smaller than for n‐octyl peroxy radicals (0.39). These data imply that substituent inductive effects impact the k3b/k3 ratios. We found no significant difference in the k3b/k3 ratios for primary vs. secondary peroxy radicals of the same carbon chain. © 2005 Wiley Periodicals, Inc. Int J Chem Kinet 37: 675–685, 2005
Rechnerischer Festigkeitsnachweis der Ermüdungstragfähigkeit von vergüteten und einsatzgehärteten Stirnrädern
Authors: Höhn B.‐R. , Oster P. , Hertter T. 
Published: September 2005

AbstractThe work presents a calculative proof of strength for compensated and case hardened spur gears taking into account the different stress conditions in the tooth root and on the tooth flank. The basis of the proof of stregth is the local comparision of the occured stresses and the allowed stresses in the spur gear. The complex stress condition on the tooth flank is illustrated. On the flank occours a three dimensional stress condition with turnig principial stress systems. Furthermore the influences on this stress condition of residual stresses and of the contact of technical surfaces are discussed. Especially the described complex stress condition on the tooth flank asks for a calculation with an adequate criterion of failure. For this purpose a variant of the Schubspannungsintensitätshypothese (SIH) is proposed. The applicability of the proposed model is verified with numerous results of experiments. Some of the calculations are presented here. Altogether there is a good conformity between the test results and the calculated results especially for the ammount of the fatigue limit, the kind of damage (e.g. tooth root breackage, pitting, tooth breackage in the region of the flank) and the position of the beginning of the damage.
The effect of psychological motivation on volumes voided during uroflowmetry in healthy aged male volunteers
Authors: Tong Yat‐Ching 
Published: September 2005

AbstractAimsTo study the effect of psychological motivation on the voided volume during uroflowmetry in aged‐male volunteers.MethodsAn open contest of free‐flow rate was held for the elderly community. People over 60 years old with no prior history of lower urinary tract symptoms were invited to compete. Participants were given the suggestion to void only when strong desire was experienced because greater the volume, faster the flow. One month later, 20 of the male participants were asked to come back for an office uroflowmetry, given the instruction to hold until strong desire was experienced. The results of the maximum flow rate, mean flow rate, and voided volume were compared between these two tests.ResultsIn the first uroflowmetry, the average voided volume for the 20 participants was 532 ± 109 ml; maximum flow rate and average flow rate were 27.1 ± 9.4, and 17.2 ± 6.4 ml/sec, respectively. The voided volume decreased significantly in the second uroflowmetry (338 ± 82 ml, P < 0.01); the maximum and average flow rates did not changed significantly (24.2 ± 9.5 and 14.9 ± 6.9 ml/sec, respectively). No participant had a shift of more than one standard deviation between the two tests on the Siroky's flow‐rate nomogram.ConclusionsWith psychological motivation to win the contest, the participants showed greater tolerance to bladder filling. This suggests that the state of mind can affect the perception on bladder sensation. On the other, the performance on emptying function is not significantly improved by motivation. Neurourol. Urdynam. © 2005 Wiley‐Liss, Inc.
Characterization of proton‐conducting organic–inorganic polymeric materials by ASAXS
Authors: Prado Luís A. S. de A. , Goerigk G. , Ponce M. L. , Garamus V. M. , Wittich H. , Willumeit R. , Schulte K. , Nunes S. P. 
Published: September 2005

AbstractThe distribution of ZrO2 and phosphotungstic acid (PTA) in a matrix of sulfonated polyether ketone was investigated by anomalous small‐angle X‐ray scattering (ASAXS). Scattering curves were obtained using X‐ray energies near the Zr and W absorption edges, allowing the independent analysis of the distribution of ZrO2 and PTA in the sample. The interaction between both inorganic components improved their dispersion considerably when compared with films containing just one of the additives. The synergism was correlated to previous investigations concerning proton conductivity and permeability of the membranes developed for direct methanol fuel cell. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 2981–2992, 2005
Prediction of disulfide connectivity from protein sequences
Authors: Chen Yu‐Ching , Hwang Jenn‐Kang 
Published: September 2005

AbstractThe difficulties in predicting disulfide connectivity from protein sequences lie in the nonlocal properties of the disulfide bridges that involve cysteine pairs at large sequence separation. Though some progress has been recently made in the prediction of disulfide connectivity, the current methods predict less than half of the disulfide patterns for the data set sharing less than 30% sequence identity. In this report, we use the support vector machines based on sequence features such as the coupling between the local sequence environments of cysteine pair, the cysteines sequence separations, and the global sequence descriptor, such as amino acid content. Our approach is able to predict 55% of the disulfide patterns of proteins with two to five disulfide bridges, which is 11–26% higher than other methods in the literature. Proteins 2005. © 2005 Wiley‐Liss, Inc.
3D domain‐swapped human cystatin C with amyloidlike intermolecular β‐sheets
Authors: Janowski Robert , Kozak Maciej , Abrahamson Magnus , Grubb Anders , Jaskolski Mariusz 
Published: September 2005

AbstractOligomerization of human cystatin C (HCC) leads to amyloid deposits in brain arteries, and this process is greatly accelerated with a naturally occurring L68Q variant. The crystal structures of N‐truncated and full‐length HCC (cubic form) showed dimer formation via three‐dimensional (3D) domain swapping, and this observation has led to the suggestion that an analogous domain‐swapping mechanism, but propagated in an open‐ended fashion, could be the basis of HCC fibril formation. Here we report that full‐length HCC, when crystallized in a new, tetragonal form, dimerizes by swapping the same secondary structure elements but with a very different overall structure generated by the flexibility of the hinge linking the moveable elements. The β‐strands of the β‐cores of the two folding units of the present dimer are roughly parallel, while they formed an angle of about 100° in the previous two structures. The dimers pack around a crystallographic dyad by extending their molecular β‐sheets in an intermolecular context. At the other edge of the molecular β‐sheet, side‐chain–side‐chain hydrogen bonds propagate the β‐structure in the same direction. In consequence, a supramolecular crystal structure is generated, with all the β‐strands of the domain‐swapped dimers being perpendicular to one crystallographic direction. This observation is relevant to amyloid aggregation of HCC, as X‐ray diffraction studies of amyloid fibrils show them to have ordered, repeating structure, consistent with the so‐called cross‐β structure, in which extended polypeptide chains are perpendicular to the fiber axis and form infinite β‐sheets that are parallel to this axis. Proteins 2005. © 2005 Wiley‐Liss, Inc.