bluuebunny/crossref_metadata_2025_split huggingface dataset:
Peristaltic flow of a Carreau fluid in a channel with different wave forms
Authors: Hayat T. , Saleem Najma , Ali N. 
Published: December 2009

AbstractThis investigation deals with the peristaltic motion of a Carreau fluid in a planar channel by employing long wavelength approximation. Five wave forms are chosen. Explicit solutions of longitudinal velocity and pressure gradient are derived. The pumping and trapping phenomena are properly examined. Comparison is made for the flow characteristics of the various selected wave forms. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 2010
Effect of wall properties on the magnetohydrodynamic peristaltic flow of a Maxwell fluid with heat transfer and porous medium
Authors: Hayat T. , Hina S. , Ali N. 
Published: December 2009

AbstractThe elastic effect of the flexible walls is analyzed on the peristaltic motion of Maxwell fluid in a channel with heat transfer. An incompressible and magnetohydrodynamic (MHD) fluid fills the porous space. The series solution of the modeled problem is derived by considering small wave number. The influence of pertinent parameters is shown and discussed with the help of graphs. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 2010
Structural estimation of particle arrays at air–water interface based on silica particles with well‐defined and highly grafted poly(methyl methacrylate)
Authors: Moon Jung‐Min , Kim Bong‐Soo , Paik Hyun‐Jong , Lee Jang‐Oo , Mouri Emiko , Yoshinaga Kohji 
Published: December 2009

AbstractSilica nanoparticles with well‐defined, highly grafted dense poly(methyl methacrylate) (MMA) were prepared by surface‐initiated activators regenerated by electron transfer for atom transfer radical polymerization (ARGET ATRP) of methyl methacrylate with an initiator‐fixed silica particle in the presence of air. Two different polymerizations of MMA were carried out under the same conditions using tris[2‐(dimethylamino)ethyl]amine (Me6TREN) and N,N,N′,N′,N″‐pentamethyldiethylene‐triamine (PMDETA) as the ligand, respectively. In the CuCl2/PMDETA system, polymerization appeared to be more controlled with a lower polydisperisty compared with the CuCl2/Me6TREN system. The monolayer of these particles was formed at the air–water interface using Langmuir‐Blodgett (LB) technique. Multilayers of the particles were fabricated by repetition of LB depositing. A surface pressure–area (π–A) measurement and SEM observation were used to characterize the particle arrays. POLYM. ENG. SCI., 2010. © 2009 Society of Plastics Engineers
The differential effects of two self‐managed math instruction procedures: Cover, Copy, and Compare versus Copy, Cover, and Compare
Authors: Grafman Joel M. , Cates Gary L. 
Published: December 2009

AbstractThis study compared the fluency and error rates produced when using the Cover, Copy, and Compare (CCC) and a modified CCC procedure (MCCC) called Copy, Cover, and Compare to complete subtraction math problems. Two second‐grade classrooms consisting of 47 total students participated in the study. The following items were administered to participants: (a) a timed pretest, (b) a timed CCC worksheet, (c) a timed MCCC worksheet, and (d) a timed posttest. Then the participants were asked which procedure they liked best. Results revealed significantly higher digits correct per minute (i.e., fluency scores) on the posttest when compared with the pretest scores. Likewise, students' fluency scores were significantly higher under the CCC condition when compared to the MCCC condition. There were no significant differences in accuracy from pretest to posttest nor between the CCC and MCCC conditions. Discussion focuses on implications for modifying instructional strategies, measuring student progress, implications for practice, and directions for future research. © 2009 Wiley Periodicals, Inc.
Die Kanalbeobachter
Authors: Loos Andreas 
Published: December 2009

AbstractAls der Science‐Fiction Autor Kurd Lasswitz 1897 sein Bild vom Mars entwirft, weiß er genau, was die Leser erwarten: Zwanzig Jahre zuvor hat der Italiener Giovanni Schiaparelli mit seiner Entdeckung von “Canali” auf dem Mars für Furor in den Medien gesorgt. Marskanäle dürfen jetzt in keinem Science‐Fiction‐Roman mehr fehlen. Doch fast zur selben Zeit will ein amerikanischer Geschäftsmann der Sache wissenschaftlich auf den Grund gehen.
Der Knall im Lawinenhang. Die Ursache von Schneebrettlawinen
Authors: Heierli Joachim , Zaiser Michael , Gumbsch Peter 
Published: December 2009

AbstractDer Scherbruch gilt allgemein als Ursache für Schneebrettlawinen. Scherbrüche können sich allerdings in einer wenig geneigten Schneedecke nicht ausbreiten, da keine ausreichenden Scherkräfte vorliegen. Dennoch wird Bruchausbreitung im flachen Gelände oft beobachtet und führt auch zu zahlreichen Lawinenunfällen durch Fernauslösung. Dieser Widerspruch wurde von der Schneeforschung bisher nicht erkannt. Ein Ansatz aus der Materialforschung erklärt nun diesen Zusammenhang: Beim Bruchprozess eines kohäsiv‐granularen Materials wie Schnee werden die abgebrochenen Schneekörner in die porösen Zwischenräume gepresst, so dass die ungewöhnliche Versagensform des Antirisses zum Tragen kommt. Es lässt sich erklären, warum sich Antirisse selbst bei beliebig großer Bruchflächenreibung durch eine horizontale Schneedecke ausbreiten können.
Psychosocial effects of mastectomy on married African women in Northwestern Nigeria
Authors: Odigie V. I. , Tanaka Rika , Yusufu L. M. D. , Gomna A. , Odigie E. C. , Dawotola D. A. , Margaritoni Marko 
Published: December 2009

AbstractObjectives: Few studies have examined the psychosocial impact of breast cancer and its treatment on African women who come from a poverty‐stricken, uneducated background in a developing country. The purpose of this study was to describe the specific psychosocial effects of breast cancer on married African women in order to help physicians educate and counsel future women and their families in Northwestern Nigeria.Methods: Two semi‐structured, self‐report questionnaires were given to 81 consenting married African women treated with unilateral total mastectomy secondary to operable breast cancer at the Ahmadu Bello University Teaching Hospital. Questionnaires were answered at the time of the diagnosis and treatment consultation and at 6 months postmastectomy and included questions about demographics, frequency of conjugal relations and how the woman's sense of femininity was affected. Marital status was also tracked up to 3 years.Results: Six months after surgery, the survey responses revealed that 67.9% of women felt inadequate as a woman because of the mastectomy and that 79.0% experienced a decrease in frequency of conjugal relations. Three years after primary breast cancer treatment, 61.7% of the participants were still married while 38.3% reported being divorced/separated from their husbands.Conclusions: These results indicated that married African women face significant physical, emotional and social changes and difficulties following primary breast cancer treatment. Culturally sensitive therapeutic groups and interventions should be established to help Nigerian women with breast cancer and their spouses and families understand and cope with the disease and its long‐term health and quality‐of‐life implications. Copyright © 2009 John Wiley & Sons, Ltd.
Post‐traumatic growth: finding positive meaning in cancer survivorship moderates the impact of intrusive thoughts on adjustment in younger adults
Authors: Park Crystal L. , Chmielewski Jennifer , Blank Thomas O. 
Published: December 2009

AbstractObjective: We examined whether post‐traumatic growth would moderate the impact of intrusive thoughts on a range of dimensions of well‐being in a sample of younger adult survivors of various types of cancer.Methods: 167 participants completed questionnaires regarding intrusive thoughts, post‐traumatic growth, mental and physical health‐related quality of life, positive and negative affect, life satisfaction, and spiritual well‐being. Multiple regression analyses controlling for relevant background and cancer‐related variables tested the interaction effects of post‐traumatic growth and intrusive thoughts.Results: Intrusive thoughts were related to poorer adjustment on all indices except physical health‐related quality of life. However, post‐traumatic growth moderated the effects of intrusive thoughts on positive and negative affect, life satisfaction, and spiritual well‐being in a protective fashion. That is, for those higher in post‐traumatic growth, higher levels of intrusive thoughts were related to better adjustment.Conclusions: The positive meaning that individuals assign to their cancer experience as reflected in their reports of post‐traumatic growth appears to be important in determining the impact of intrusive thoughts on post‐cancer adjustment. Copyright © 2009 John Wiley & Sons, Ltd.
Cyclic voltammetry: A new strategy for the evaluation of oxidative damage to bovine insulin
Authors: Zong Wansong , Liu Rutao , Sun Feng , Wang Meijie , Zhang Pengjun , Liu Yihong , Tian Yanmin 
Published: December 2009

AbstractResearch on protein oxidative damage may give insight into the nature of protein functions and pathological conditions. In this work, the oxidative damage of bovine insulin on Au electrode was investigated by cyclic voltammetry (CV). The experimental results show that there are two anodic peaks for the oxidative damage of bovine insulin, which arise from the oxidation of the exposed disulfide bond SSCYS7A,CYS7B, forming sulfenic acid RSOH (1.20 V, vs. SCE), sulfinic acid RSO2H and sulfonic acid RSO3H (1.35 V, vs. SCE). These in vitro findings not only demonstrate the applicability of CV in simulating/evaluating the oxidative damage of nonredox proteins but also find two promising candidates (two anodic peaks) for measuring insulin.
Amyloidogenic sequences in native protein structures
Authors: Tzotzos Susan , Doig Andrew J. 
Published: December 2009

AbstractNumerous short peptides have been shown to form β‐sheet amyloid aggregates in vitro. Proteins that contain such sequences are likely to be problematic for a cell, due to their potential to aggregate into toxic structures. We investigated the structures of 30 proteins containing 45 sequences known to form amyloid, to see how the proteins cope with the presence of these potentially toxic sequences, studying secondary structure, hydrogen‐bonding, solvent accessible surface area and hydrophobicity. We identified two mechanisms by which proteins avoid aggregation: Firstly, amyloidogenic sequences are often found within helices, despite their inherent preference to form β structure. Helices may offer a selective advantage, since in order to form amyloid the sequence will presumably have to first unfold and then refold into a β structure. Secondly, amyloidogenic sequences that are found in β structure are usually buried within the protein. Surface exposed amyloidogenic sequences are not tolerated in strands, presumably because they lead to protein aggregation via assembly of the amyloidogenic regions. The use of α‐helices, where amyloidogenic sequences are forced into helix, despite their intrinsic preference for β structure, is thus a widespread mechanism to avoid protein aggregation.
Mobile loop mutations in an archaeal inositol monophosphatase: Modulating three‐metal ion assisted catalysis and lithium inhibition
Authors: Li Zheng , Stieglitz Kimberly A. , Shrout Anthony L. , Wei Yang , Weis Robert M. , Stec Boguslaw , Roberts Mary F. 
Published: December 2009

AbstractThe inositol monophosphatase (IMPase) enzyme from the hyperthermophilic archaeon Methanocaldococcus jannaschii requires Mg2+ for activity and binds three to four ions tightly in the absence of ligands: KD = 0.8 μM for one ion with a KD of 38 μM for the other Mg2+ ions. However, the enzyme requires 5–10 mM Mg2+ for optimum catalysis, suggesting substrate alters the metal ion affinity. In crystal structures of this archaeal IMPase with products, one of the three metal ions is coordinated by only one protein contact, Asp38. The importance of this and three other acidic residues in a mobile loop that approaches the active site was probed with mutational studies. Only D38A exhibited an increased kinetic KD for Mg2+; D26A, E39A, and E41A showed no significant change in the Mg2+ requirement for optimal activity. D38A also showed an increased Km, but little effect on kcat. This behavior is consistent with this side chain coordinating the third metal ion in the substrate complex, but with sufficient flexibility in the loop such that other acidic residues could position the Mg2+ in the active site in the absence of Asp38. While lithium ion inhibition of the archaeal IMPase is very poor (IC50∼250 mM), the D38A enzyme has a dramatically enhanced sensitivity to Li+ with an IC50 of 12 mM. These results constitute additional evidence for three metal ion assisted catalysis with substrate and product binding reducing affinity of the third necessary metal ion. They also suggest a specific mode of action for lithium inhibition in the IMPase superfamily.
Crystal structure of a super leucine zipper, an extended two‐stranded super long coiled coil
Authors: Diao Jiasheng 
Published: December 2009

AbstractCoiled coil is a ubiquitous structural motif in proteins, with two to seven alpha helices coiled together like the strands of a rope, and coiled coil folding and assembly is not completely understood. A GCN4 leucine zipper mutant with four mutations of K3A, D7A, Y17W, and H18N has been designed, and the crystal structure has been determined at 1.6 Å resolution. The peptide monomer shows a helix trunk with short curved N‐ and C‐termini. In the crystal, two monomers cross in 35° and form an X‐shaped dimer, and each X‐shaped dimer is welded into the next one through sticky hydrophobic ends, thus forming an extended two‐stranded, parallel, super long coiled coil rather than a discrete, two‐helix coiled coil of the wild‐type GCN4 leucine zipper. Leucine residues appear at every seventh position in the super long coiled coil, suggesting that it is an extended super leucine zipper. Compared to the wild‐type leucine zipper, the N‐terminus of the mutant has a dramatic conformational change and the C‐terminus has one more residue Glu 32 determined. The mutant X‐shaped dimer has a large crossing angle of 35° instead of 18° in the wild‐type dimer. The results show a novel assembly mode and oligomeric state of coiled coil, and demonstrate that mutations may affect folding and assembly of the overall coiled coil. Analysis of the formation mechanism of the super long coiled coil may help understand and design self‐assembling protein fibers.
Docking of insulin to a structurally equilibrated insulin receptor ectodomain
Authors: Vashisth Harish , Abrams Cameron F. 
Published: December 2009

AbstractThe insulin receptor (IR) is a homo‐dimeric, disulfide‐linked, membrane‐spanning tyrosine kinase. IR displays negative cooperativity in insulin binding to its two pockets, suggesting “see‐sawing” between symmetry‐inverted conformations. The crystal structure of the dimeric IR ectodomain, IRΔβ [PDB code 2DTG (McKern et al., Nature 2006 443:218–221)], provides structural bases for this speculation. Unfortunately, neither binding pocket of the crystallographic IRΔβ structure allows steric accommodation of insulin. During almost 70‐ns of all‐atom, explicit‐water MD simulation (∼0.5 million atoms), IRΔβ undergoes significant asymmetric interdomain and intersubunit conformational fluctuations that do not alter its quaternary structure. Subtle variations in intersubunit buried surface area coincide with these conformational fluctuations, resulting in one easily‐accessible insulin binding pocket with the other blocked. We use a combination of Metropolis Monte‐Carlo and MD simulations to dock both T‐ and R‐state insulin into the open binding pocket. Both complexes remain stable during 30‐ns of MD simulation. In these complexes, “hexamer interface” residues on insulin directly contact the “site‐2” epitope on the first type‐III fibronectin domain (F1) of IR. Our results support the hypothesis that intersubunit flexibility of IR, governed by alternating modulation of buried intersubunit surface area, is the physical mechanism underlying a “see‐saw” model of negative cooperativity. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Circular permuted proteins in the universe of protein folds
Authors: Schmidt‐Goenner Tobias , Guerler Aysam , Kolbeck Bjoern , Knapp Ernst Walter 
Published: December 2009

AbstractFinding and identifying circular permuted protein pairs (CPP) is one of the harder tasks for structure alignment programs, because of the different location of the break in the polypeptide chain connectivity. The protein structure alignment tool GANGSTA+ was used to search for CPPs in a database of nearly 10,000 protein structures. It also allows determination of the statistical significance of the occurrence of circular permutations in the protein universe. The number of detected CPPs was found to be higher than expected, raising questions about the evolutionary processes leading to CPPs. The GANGSTA+ protein structure alignment tool is available online via the web server at http://gangsta.chemie.fu‐berlin.de. On the same webpage the complete data base of similar protein structure pairs based on the ASTRAL40 set of protein domains is provided and one can select CPPs specifically. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Studying pressure denaturation of a protein by molecular dynamics simulations
Authors: Sarupria Sapna , Ghosh Tuhin , García Angel E. , Garde Shekhar 
Published: December 2009

AbstractMany globular proteins unfold when subjected to several kilobars of hydrostatic pressure. This “unfolding‐up‐on‐squeezing” is counter‐intuitive in that one expects mechanical compression of proteins with increasing pressure. Molecular simulations have the potential to provide fundamental understanding of pressure effects on proteins. However, the slow kinetics of unfolding, especially at high pressures, eliminates the possibility of its direct observation by molecular dynamics (MD) simulations. Motivated by experimental results—that pressure denatured states are water‐swollen, and theoretical results—that water transfer into hydrophobic contacts becomes favorable with increasing pressure, we employ a water insertion method to generate unfolded states of the protein Staphylococcal Nuclease (Snase). Structural characteristics of these unfolded states—their water‐swollen nature, retention of secondary structure, and overall compactness—mimic those observed in experiments. Using conformations of folded and unfolded states, we calculate their partial molar volumes in MD simulations and estimate the pressure‐dependent free energy of unfolding. The volume of unfolding of Snase is negative (approximately −60 mL/mol at 1 bar) and is relatively insensitive to pressure, leading to its unfolding in the pressure range of 1500–2000 bars. Interestingly, once the protein is sufficiently water swollen, the partial molar volume of the protein appears to be insensitive to further conformational expansion or unfolding. Specifically, water‐swollen structures with relatively low radii of gyration have partial molar volume that are similar to that of significantly more unfolded states. We find that the compressibility change on unfolding is negligible, consistent with experiments. We also analyze hydration shell fluctuations to comment on the hydration contributions to protein compressibility. Our study demonstrates the utility of molecular simulations in estimating volumetric properties and pressure stability of proteins, and can be potentially extended for applications to protein complexes and assemblies. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Dimerization of protein G B1 domain at low pH: A conformational switch caused by loss of a single hydrogen bond
Authors: Tomlinson Jennifer H. , Craven C. Jeremy , Williamson Mike P. , Pandya Maya J. 
Published: December 2009

AbstractA number of signals in the NMR spectrum of the B1 domain of staphylococcal protein G (GB1) show a chemical shift dependence on the concentration of the protein at pH 3 but not at neutral pH, implying the existence of self‐association at low pH. NMR backbone relaxation experiments show that GB1 undergoes a slow conformational exchange at pH 3, which is not seen at higher pH. Analysis of relaxation dispersion experiments yields a self‐association constant of 50 mM, and shows that 15N chemical shift changes in the dimer interface are up to 3 ppm. The shift changes measured from concentration‐dependent HSQC spectra and from relaxation dispersion show good consistency. Measurements of chemical shifts as a function of pH show that a hydrogen bond between the sidechains of Asp44 and Gln40 is broken when Asp44 is protonated, and that loss of this hydrogen bond leads to the breaking of the (i, i + 4) backbone helical hydrogen bond from Asp44 HN to Gln40 O, and therefore to a loss of two residues from the C‐terminal end of the helix. This weakens the helix structure and facilitates the loss of further helical structure thus permitting dimerization, which is suggested to occur in the same way as observed for the A42F mutant of GB1 (Jee et al., Proteins 2007;71:1420–1431), by formation of an antiparallel β‐sheet between the edge strands 2 in two monomers. The monomer/dimer ratio is thus a finely balanced equilibrium even in the wild type protein. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Piezoresistive cantilever array sensor for consolidated bioprocess monitoring
Authors: Kim Seonghwan , Rahman Touhidur , Senesac Larry R. , Davison Brian H. , Thundat Thomas 
Published: December 2009

AbstractCellulolytic microbes occur in diverse natural niches and are being screened for industrial modification and utility. A microbe for consolidated bioprocessing (CBP) development can rapidly degrade pure cellulose and then ferment the resulting sugars into fuels. To identify and screen for novel microbes for CBP, we have developed a piezoresistive cantilever array sensor which is capable of simultaneous monitoring of glucose and ethanol concentration changes in a phosphate buffer solution. 4‐mercaptophenylboronic acid and polyethyleneglycol‐thiol are employed to functionalize each piezoresistive cantilever for glucose and ethanol sensing, respectively. Successful concentration measurements of glucose and ethanol with minimal interferences are obtained with our cantilever array sensor. SCANNING 31: 204–210, 2009. © 2009 Wiley Periodicals, Inc.