bluuebunny/crossref_metadata_2025 huggingface dataset:
The immersed/fictitious element method for fluid–structure interaction: Volumetric consistency, compressibility and thin members
Authors: Wang Hongwu , Chessa Jack , Liu Wing K. , Belytschko Ted
Published: September 2007

A weak form and an implementation are given for fluid–structure interaction by the immersed/fictitious element method for compressible fluids. The weak form is applicable to models where the fluid is described by Eulerian coordinates while the solid is described by Lagrangian coordinates, which suits their intrinsic characteristics. A unique feature of the method is the treatment of the fictitious fluid by a Lagrangian description,
which simplifies the interface conditions. Methods for enforcing volumetric consistency between the fluid and solid and treating thin members are given. Although a compressible viscous fluid is considered here, the new developments can be applied to incompressible fluids. Copyright © 2007 John Wiley & Sons, Ltd.
A mixed stress model for linear elastodynamics of arbitrarily curved beams
Authors: Cannarozzi M. , Molari L.
Published: September 2007

This work presents a mixed stress finite element for linear elastodynamics of arbitrarily curved beams based on a modified Hellinger–Reissner functional. A rational approach to choose the stress approximation is proposed. In particular, the self‐equilibrated stress is augmented by some stress modes obtained from the lower‐order displacement approximation using the equilibrium equations, in such a way that the total number of stress modes is equal to the number of strain modes. The rationale is to preserve all the interactions among the stresses, proper of a curved structure without compromising the flexibility of the element. An arbitrarily curved geometry is described using a parametric Hermitian interpolation scheme tuned by minimizing the initial curvature of the arch. The effectiveness of the present approach is numerically demonstrated. Copyright © 2007 John Wiley & Sons, Ltd.
Meshfree and finite element nodal integration methods
Authors: Puso M. A. , Chen J. S. , Zywicz E. , Elmer W.
Published: September 2007

Nodal integration can be applied to the Galerkin weak form to yield a particle‐type method where stress and material history are located exclusively at the nodes and can be employed when using meshless or finite element shape functions. This particle feature of nodal integration is desirable for large deformation settings because it avoids the remapping or advection of the state variables required in other methods. To a lesser degree, nodal integration can be desirable because it relies on fewer stress point evaluations than most other methods. In this work, aspects regarding stability, consistency, efficiency and explicit time integration are explored within the context of nodal integration. Both small and large deformation numerical examples are provided. Copyright © 2007 John Wiley & Sons, Ltd.
Effect of temperature, pressure, and composition on DC resistivity and AC conductivity of conductive styrene–butadiene rubber–particulate metal alloy nanocomposites
Authors: Mohanraj G.T. , Dey P.K. , Chaki T.K. , Chakraborty A. , Khastgir D.
Published: September 2007

Conductive nanocomposites were prepared using styrene butadiene rubber as the polymer matrix and nanosized powder of copper–nickel (Cu–Ni) alloy as the filler. The filler loading was varied from 0 to 40 phr. The electrical conductivity of filled polymer composites is due to the formation of some continuous conductive networks in the polymer matrix. Atomic force microscopy was used to determine the particle size of the nanofiller and its nature of dispersion in the rubber matrix. The DC volume resistivity was measured against the loading of the nanofiller to check the percolation limit. The effect of temperature, applied pressure, time duration under constant compressive stress on the DC resistivity and AC conductivity of the composites with different filler loading were investigated. The change in DC resistivity and AC conductivity against temperature of these composites exhibited positive coefficient of temperature. With the change in applied pressure and time duration under constant compressive stress the DC resistivity undergoes an exponential decrease. The effect of AC field frequency on the AC conductivity was investigated. POLYM. COMPOS. 28:696–704, 2007. © 2007 Society of Plastics Engineers
Extracellular matrix regenerated: tissue engineering via electrospun biomimetic nanofibers
Authors: Sell Scott , Barnes Catherine , Smith Matthew , McClure Michael , Madurantakam Parthasarathy , Grant Joshua , McManus Michael , Bowlin Gary
Published: September 2007

While electrospinning had seen intermittent use in the textile industry from the early twentieth century, it took the explosion of the field of tissue engineering, and its pursuit of biomimetic extracellular matrix (ECM) structures, to create an electrospinning renaissance. Over the past decade, a growing number of researchers in the tissue engineering community have embraced electrospinning as a polymer processing technique that effectively and routinely produces non‐woven structures of nanoscale fibers (sizes of 80 nm to 1.5 µm). These nanofibers are of physiological significance as they closely resemble the structure and size scale of the native ECM (fiber diameters of 50 to 500 nm). Attempts to replicate the many roles of native ECM have led to the electrospinning of a wide array of polymers, both synthetic (poly(glycolic acid), poly(lactic acid), polydioxanone, polycaprolactone, etc.) and natural (collagen, fibrinogen, elastin, etc.) in origin, for a multitude of different tissue applications. With various compositions, fiber dimensions and fiber orientations, the biological, chemical and mechanical properties of the electrospun materials can be tailored. In this review we highlight the role of electrospinning in the engineering of different tissues and applications (skin/wound healing, cartilage, bone, vascular tissue, urological tissues, nerve, and ligament), and discuss its potential role in future work. Copyright © 2007 Society of Chemical Industry
Apparatus for preparing electrospun nanofibers: designing an electrospinning process for nanofiber fabrication
Authors: Park SuA , Park Koeun , Yoon Hyeon , Son JoonGon , Min Teijin , Kim GeunHyung
Published: September 2007

Nanofibers are widely used in a range of material applications, such as filter media, biosensors, military protective coatings, three‐dimensional tissue scaffolds, composites, drug delivery, wound dressings and electronic devices. To fabricate nanofibers with desired physical and chemical functions, a variety of electrospinning processes have been introduced using specially designed collectors, microelectromechanical system (MEMS) nozzle tips and auxiliary electrodes to stabilize the spin jets. However, the development of new electrospinning processes continues in the search for ‘tailor‐made’ nanofibers, in which parameters such as the fiber orientation and three‐dimensional structure are ultimately controllable. This paper discusses recently suggested electrospinning methods that are designed to impart specific functionality. It also details the correlations between applied processing parameters and the obtained physical properties of electrospun fibers. Finally, future design directions are suggested for developing an electrospinning apparatus capable of producing optimally structured nanofibers. Copyright © 2007 Society of Chemical Industry
Alternative and effective proteomic analysis inArabidopsis
Authors: Espagne Christelle , Martinez Aude , Valot Benoît , Meinnel Thierry , Giglione Carmela
Published: September 2007

Various functional genomics platforms are required to define the phenotype associated with a mutant. Global protein analyses may be included in any study. We describe here a rapid method of protein sample preparation and analysis, suitable for all laboratories and usingArabidopsisplantlets as the starting material. This reliable and reproducible method for high yield protein extraction from small amounts of material can be used on even the most recalcitrant tissues. The proteins extracted are suitable for many types of protein analysis, including nondenaturing investigations. This method was validated by a rigorous 2‐DE approach, coupled with unambiguous LC‐MS/MS identifications featuring strong sequence coverage (average of 26% with eight different peptides/spot protein). The reproducibility of the method was demonstrated by multiple protein identifications from identical series of spots. An interactive map (http://www.isv.cnrsgif.fr/gel2d/), including 435 protein variants showed that (i) 38% of the proteins were yet unreported, (ii) reduced subfractionation, (iii) had frequent protein modifications (average of two spots/protein entry), and (iv) underwent no major proteolytic events other than leader peptide cleavage. Finally, a simple mobility shift method for the large subunit of RuBisCo (LS) in the first dimension made it possible to characterize previously masked protein spots.
Analysis of membrane microdomain‐associated proteins in the insular cortex of post‐mortem human brain
Authors: Behan Áine T. , Foy Martina , Wynne Kieran , Clarke Michael , Sullivan Matthew , Cotter David R. , Maguire Patricia B.
Published: September 2007

Membrane microdomains (MM) are membrane rafts within the cell membrane enriched in cholesterol and glycosphingolipids that have been implicated in the trafficking and sorting of membrane proteins, secretory and endocytotic pathways, and signal transduction. To date, MM have not been characterised in the human brain. We reason that by identifying MM in the normal human cortex, we may better understand the molecular mechanisms of human brain dysfunction. To characterize the protein composition of MM in the human brain, we have carried out a comprehensive proteomic analysis of detergent resistant membranes (DRMs) associated proteins derived from human postmortem insular cortex using 1‐DE separation prior to LC coupled to MS/MS or GeLC‐MS/MS. Eighty five proteins were identified including 57 unique to human brain cortex DRMs (by comparison with DRM proteins reported in other cell types). High levels of signal transduction, cell adhesion, cell transport and cell trafficking proteins were identified including synaptic proteins such as synapsin II and synaptic vesicle membrane protein, mitochondrial proteins such as ATPase subunits and metabolic enzymes such as malate dehydrogenase. This data will facilitate our understanding of protein expression changes within membranes in candidate brain regions in human brain diseases such as schizophrenia, bipolar disorder and other psychiatric and neurodegenerative disorders.
Markers of breast and gynecological malignancies: The clinical approach of proteomics‐based studies
Authors: Lomnytska Marta , Souchelnytskyi Serhiy
Published: September 2007

Breast, ovarian, endometrial and cervical cancers are diseases with a relatively high lethal outcome, despite recent development of surgical, chemotherapeutic, radiotherapeutic and anti‐hormonal treatments. The mortality of women with breast cancer is at the level of 20%, while for ovarian cancer it is up to 75%. For cervical cancer it is 38% and for endometrial cancer 17%. To enhance survival of patients, better diagnostics of these cancers in early and non‐invasive stages is essential. Proteomics allows a comprehensive analysis of hundreds of proteins in clinical samples. Studies of tissue samples and body fluids, e.g., blood and plasma, have shown their usefulness in discovery of markers of cancers at early stages. Searches for markers of breast and ovarian cancers have been performed with promising results. Studies of endometrial and cervical cancer markers have been less extensive. This review describes recent reports of markers for early detection of breast, ovarian, endometrial and cervical cancers. A clinical evaluation of the markers discovered with the use of proteomics techniques is discussed.
Towards stable diagnostic setups in clinical proteomics: Absolute quantitation of peptide biomarkers using MALDI‐TOF‐MS
Authors: Baechle Daniel , Sparbier Katrin , Dihazi Hassan , Blaschke Sabine , Mueller Gerhard‐Anton , Kostrzewa Markus , Flad Thomas
Published: September 2007

In routine clinical diagnostics, peptide biomarkers are most commonly quantified using immunological techniques but these methods often lack sensitivity and/or specificity. Hence, quantitative mass spectrometry detection is desirable as an alternative diagnostic tool. To date, quantitative mass spectrometry is mostly based on ESI‐MS coupled to LC, requiring highly sophisticated instrumentation and knowledge and is time consuming and expensive. In contrast, MALDI‐TOF‐MS is a very simple, sensitive and rapid method for the detection of peptide biomarkers. However, the infeasibility of absolute quantification has been a tremendous handicap to the use of MS in stable clinical diagnostics. Here, we describe the development of a technical platform based on ClinProt particles and heavy‐isotope internal peptide standards for the fast and reliable preparation of samples. This combines the advantages of MALDI‐TOF as a read‐out system with absolute quantitation of peptide biomarkers. As a proof‐of‐concept, this platform was successfully employed for the absolute determination of the concentration of the highly abundant serum peptide des‐Ala‐Fibrinopeptide A in 45 serum samples from healthy donors. Such technology essentially contributes to the development of a stable MALDI‐TOF‐MS‐based clinical assay.
Epitope mapping and structural analysis of an anti‐ErbB2 antibody A21: Molecular basis for tumor inhibitory mechanism
Authors: Hu Siyi , Zhu Zhiqiang , Li Liangwei , Chang Liang , Li Weifang , Cheng Liansheng , Teng Maikun , Liu Jing
Published: September 2007

Anti‐ErbB2 antibodies targeting distinct epitopes can have different biological functions on cancer cells. A21 prepared by surface epitope masking (SEM) method is a tumor‐inhibitory anti‐ErbB2 monoclonal antibody. Previously we engineered a single chain chimeric antibody chA21 with potential for therapy of ErbB2‐overexpressing tumors. Here, we mapped the A21 epitope on ErbB2 extracellular domain (ECD) by screening a combinatorial phage display peptide library, serial subdomain deletion, and mutagenesis scanning. X‐ray crystal structure of the A21 scFv fragment at 2.1 Å resolution was also determined. A molecular model of Ag‐Ab complex was then constructed based on the crystal structures of the A21 scFv and ErbB2 ECD. Some of biological functions of the A21 mAb and its derivative antibodies including their tumor cell growth inhibition and effects on the expression, internalization, and phosphorylation of ErbB2 receptor were also investigated. The results showed that A21 recognized a conformational epitope comprising a large region mostly from ErbB2 extracellular subdomain I with several surface‐exposed residues important for the binding affinity. These data provide unique functional properties of A21 that are quite different from two broadly used anti‐ErbB2 mAbs, Herceptin and 2C4. It suggested that the A21 epitope may be another valuable target for designing new anti‐ErbB2 therapeutics. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Distance dependent centroid to centroid force fields using high resolution decoys
Authors: Rajgaria R. , McAllister S. R. , Floudas C. A.
Published: September 2007

Simplified force fields play an important role in protein structure prediction and de novo protein design by requiring less computational effort than detailed atomistic potentials. A side chain centroid based, distance dependent pairwise interaction potential has been developed. A linear programming based formulation was used in which non‐native “decoy” conformers are forced to take a higher energy compared with the corresponding native structure. This model was trained on an enhanced and diverse protein set. High quality decoy structures were generated for ∼1400 nonhomologous proteins using torsion angle dynamics along with restricted variations of the hydrophobic cores of the native structure. The resulting decoy set was used to train the model yielding two different side chain centroid based force fields that differ in the way distance dependence has been used to calculate energy parameters. These force fields were tested on an independent set of 148 test proteins with 500 decoy structures for each protein. The side chain centroid force fields were successful in correctly identifying ∼86% native structures. The Z‐scores produced by the proposed centroid–centroid distance dependent force fields improved compared with other distance dependent Cα‐Cα or side chain based force fields. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Water penetration in the low and high pressure native states of ubiquitin
Authors: Day Ryan , García Angel E.
Published: September 2007

Theoretical studies on the solvation of methane molecules in water have shown that the effect of increased pressure is to stabilize solvent separated contacts relative to direct contacts. This suggests that high pressure stabilizes waters that have penetrated into a protein's core, indicating a mechanism for the high pressure denaturation of proteins. We test this theory on a folded protein by studying the penetration of water into the native state of ubiquitin at low and high pressures, using molecular dynamics. An ensemble of conformations sampled in the folded state of ubiquitin has been determined by NMR at two pressures below the protein's denaturation pressure, 30 atm and 3000 atm. We find that 1–5 more waters penetrate the high pressure conformations than the low pressure conformations. Low volume configurations of the system are favored at high pressures, but different components of the system may experience increases or decreases in their specific volumes. We find that penetrating waters have a higher volume per water than bulk waters, but that the volume per protein residue may be lowered by solvation. Furthermore, we find that penetration of the protein by water at high pressures is driven by the difference in the pressure dependence of the probability of cavity opening in the protein and pressure dependence of the probability of cavity opening in the bulk solvent. The volume changes associated with cavity opening and closing indicate that each penetrating water reduces the volume of the system by about 12 mL/mol. The experimental volume change going from the low pressure to the high pressure native state of ubiquitin is 24 mL/mol. Our results indicate that this volume change can be explained by penetration of the protein by two water molecules. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single‐point mutation of a β‐sheet miniprotein
Authors: Muff Stefanie , Caflisch Amedeo
Published: September 2007

The effects of a single‐point mutation on folding thermodynamics and kinetics are usually interpreted by focusing on the native structure and the transition state. Here, the entire conformational spaces of a 20‐residue three‐stranded antiparallel β‐sheet peptide (double hairpin) and of its single‐point mutant W10V are sampled close to the melting temperature by equilibrium folding–unfolding molecular dynamics simulations for a total of 40 μs. The folded state as well as the most populated free energy basins in the denatured state are isolated by grouping conformations according to fast relaxation at equilibrium. Such kinetic analysis provides more detailed and useful information than a simple projection of the free energy. The W10V mutant has the same native structure as the wild type peptide, and similar folding rate and stability. In the denatured state, the N‐terminal hairpin is about 20% more structured in W10V than the wild type mainly because of van der Waals interactions. Notably, the W10V mutation influences also the van der Waals energy at the transition state ensemble causing a shift in the ratio of fluxes between two different transition state regions on parallel folding pathways corresponding to nucleation at either of the two β‐hairpins. Previous experimental studies have focused on the effects of denaturant‐dependent or temperature‐dependent changes in the structure of the denatured state. The atomistic simulations show that a single‐point mutation in the central strand of a β‐sheet peptide results in remarkable changes in the topography of the denatured state ensemble. These changes modulate the relative accessibility of parallel folding pathways because of kinetic partitioning of the denatured state. Therefore, the observed dependence of the folding process on the starting ensemble raises questions on the biological significance of in vitro folding studies under strongly denaturing conditions. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Predicting transmembrane helix pair configurations with knowledge‐based distance‐dependent pair potentials
Authors: Wendel Christina , Gohlke Holger
Published: September 2007

As a first step toward a novel de novo structure prediction approach for α‐helical membrane proteins, we developed coarse‐grained knowledge‐based potentials to score the mutual configuration of transmembrane (TM) helices. Using a comprehensive database of 71 known membrane protein structures, pairwise potentials depending solely on amino acid types and distances between Cα‐atoms were derived. To evaluate the potentials, they were used as an objective function for the rigid docking of 442 TM helix pairs. This is by far the largest test data set reported to date for that purpose. After clustering 500 docking runs for each pair and considering the largest cluster, we found solutions with a root mean squared (RMS) deviation <2 Å for about 30% of all helix pairs. Encouragingly, if only clusters that contain at least 20% of all decoys are considered, a success rate >71% (with a RMS deviation <2 Å) is obtained. The cluster size thus serves as a measure of significance to identify good docking solutions. In a leave‐one‐protein‐family‐out cross‐validation study, more than 2/3 of the helix pairs were still predicted with an RMS deviation <2.5 Å (if only clusters that contain at least 20% of all decoys are considered). This demonstrates the predictive power of the potentials in general, although it is advisable to further extend the knowledge base to derive more robust potentials in the future. When compared to the scoring function of Fleishman and Ben‐Tal, a comparable performance is found by our cross‐validated potentials. Finally, well‐predicted “anchor helix pairs” can be reliably identified for most of the proteins of the test data set. This is important for an extension of the approach towards TM helix bundles because these anchor pairs will act as “nucleation sites” to which more helices will be added subsequently, which alleviates the sampling problem. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Protonless 13C direct detection NMR: Characterization of the 37 kDa trimeric protein CutA1
Authors: Bertini Ivano , Jiménez Beatriz , Pierattelli Roberta , Wedd Anthony G. , Xiao Zhiguang
Published: September 2007

The major limitation of nuclear magnetic resonance spectroscopy arises from the increase of nuclear transverse relaxation rates with increasing molecular mass. This causes reduction in spectral resolution and coherence transfer efficiency. The use of 2H‐labeling to eliminate 1H‐mediated relaxation pathways and the constructive use of cross correlation effects (TROSY, CRINEPT) alleviate the phenomenon. An alternative approach is to use direct detection of heteronuclei. Specifically designed 13C direct detection experiments can complement the set of 1H‐based NMR experiments commonly used for structure determination providing an additional source of information less affected by the detrimental transverse relaxation effect. We applied this novel methodology to the study of the CutA1 protein (12.3 kDa) from E. coli that forms a homotrimer in solution with a total molecular mass of 37 kDa. In this work we demonstrate that the information available from 13C direct detection experiments makes it possible to completely assign the NMR resonances of the backbone of this 37 kDa trimeric protein without the need of deuteration. The structural and dynamical knowledge obtained for this system may contribute to understand its biological role. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Proton pathways in a [NiFe]‐hydrogenase: A theoretical study
Authors: Teixeira Vitor H. , Soares Cláudio M. , Baptista António M.
Published: September 2007

We present here a theoretical study to investigate possible proton pathways in the [NiFe]‐hydrogenase from Desulfovibrio gigas. The approach used in this study consists of a combination of Poisson–Boltzmann and Monte Carlo simulations together with a distance‐based network analysis to find possible groups involved in the proton transfer. Results obtained at different pH values show a reasonable number of proton active residues distributed by the protein interior and surface, with a concentration around the metal centres. The electrostatic interactions in this protein are strong, as shown by the unusual shape of the titration curves of several sites. Some residue pairs show strongly correlated protonations, indicating the sharing and probably exchange of a proton between them. The conjugation of the PB and MC simulations with the distance‐based analysis allows a detailed characterization of the possible proton pathways. We discuss previous suggestions and propose a new complete pathway for the proton transfer between the active site and the surface. This pathway is mainly composed of histidines and glutamic acid residues. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Dopamine transporter comparative molecular modeling and binding site prediction using the LeuTAaleucine transporter as a template
Authors: Indarte Martín , Madura Jeffry D. , Surratt Christopher K.
Published: September 2007

Pharmacological and behavioral studies indicate that binding of cocaine and the amphetamines by the dopamine transporter (DAT) protein is principally responsible for initiating the euphoria and addiction associated with these drugs. The lack of an X‐ray crystal structure for the DAT or any other member of the neurotransmitter:sodium symporter (NSS) family has hindered understanding of psychostimulant recognition at the atomic level; structural information has been obtained largely from mutagenesis and biophysical studies. The recent publication of a crystal structure for the bacterial leucine transporter LeuTAa, a distantly related NSS family homolog, provides for the first time a template for three‐dimensional comparative modeling of NSS proteins. A novel computational modeling approach using the capabilities of the Molecular Operating Environment program MOE 2005.06 in conjunction with other comparative modeling servers generated the LeuTAa‐directed DAT model. Probable dopamine and amphetamine binding sites were identified within the DAT model using multiple docking approaches. Binding sites for the substrate ligands (dopamine and amphetamine) overlapped substantially with the analogous region of the LeuTAacrystal structure for the substrate leucine. The docking predictions implicated DAT side chains known to be critical for high affinity ligand binding and suggest novel mutagenesis targets in elucidating discrete substrate and inhibitor binding sites. The DAT model may guide DAT ligand QSAR studies, and rational design of novel DAT‐binding therapeutics. Proteins 2008. © 2007 Wiley‐Liss, Inc.
HingeProt: Automated prediction of hinges in protein structures
Authors: Emekli Ugur , Schneidman‐Duhovny Dina , Wolfson Haim J. , Nussinov Ruth , Haliloglu Turkan
Published: September 2007

Proteins are highly flexible molecules. Prediction of molecular flexibility aids in the comprehension and prediction of protein function and in providing details of functional mechanisms. The ability to predict the locations, directions, and extent of molecular movements can assist in fitting atomic resolution structures to low‐resolution EM density maps and in predicting the complex structures of interacting molecules (docking). There are several types of molecular movements. In this work, we focus on the prediction of hinge movements. Given a single protein structure, the method automatically divides it into the rigid parts and the hinge regions connecting them. The method employs the Elastic Network Model, which is very efficient and was validated against a large data set of proteins. The output can be used in applications such as flexible protein–protein and protein–ligand docking, flexible docking of protein structures into cryo‐EM maps, and refinement of low‐resolution EM structures. The web server of HingeProt provides convenient visualization of the results and is available with two mirror sites at http://www.prc.boun.edu.tr/appserv/prc/HingeProt3 and http://bioinfo3d.cs.tau.ac.il/HingeProt/. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Structural analysis of substance P using molecular dynamics and NMR spectroscopy
Authors: Corcho Francesc J. , Salvatella Xavier , Canto Josep , Giralt Ernest , Perez Juan J.
Published: September 2007

The present work is a combined structural study, using Nuclear Magnetic Resonance (NMR) and Molecular Dynamics(MD), of the amidated and the free acid forms of substance P in water and methanol. The results obtained using both approaches were compared in order to characterize the structural features of both peptides in solution. From the NMR experiments it was derived that the free acid form adopts an extended conformation at the N‐terminus and a helical conformation at the C‐terminal segment of the peptide in both water and methanol; these structural features are in qualitative agreement with the results of the MD simulations. No significant differences in behavior were observed between the amidated and the free acid forms of the peptide in the simulations and in the experiments carried out in water, suggesting that the different activities of these analogs are due to their different mode of interaction with the receptor rather than to their structural preferences. Finally, we propose that the structure of substance P can be partially inferred from its sequence due to the presence of a Pro‐X‐Pro motif on the N‐terminus and a Gly–Leu sequence on the C‐terminus. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
A relatively stable antifungal peptide from buckwheat seeds with antiproliferative activity toward cancer cells
Authors: Leung Edwin H. W. , Ng T. B.
Published: September 2007

An antifungal peptide with a molecular mass of approximately 4 kDa was isolated from buckwheat seeds by using ion‐exchange chromatography on SP‐Sepharose and Q‐Sepharose, and gel filtration on Superdex peptide. The peptide was adsorbed on SP‐Sepharose in 10 mM NH4OAc buffer (pH 4.5) and on Q‐Sepharose in 10 mM NH4HCO3 buffer (pH 9.4), and appeared to be highly purified after these two steps. It inhibited mycelial growth in Fusarium oxysporum and Mycosphaerella arachidicola with an IC50 of 35 and 40 µM, respectively. Its antifungal activity was stable between 0 and 70 °C, and between pH 1.0/2.0 and 13. It inhibited proliferation of Hep G2 (hepatoma) cells, L1210 (leukemia) cells, breast cancer (MCF‐7) cells, and liver embryonic WRL 68 cells with an IC50 of 33, 4, 25, and 37 µM, respectively. On the other hand, the peptide was unable to evoke a mitogenic response from splenocytes or induce nitric oxide production by macrophages. It inhibited HIV‐1 reverse transcriptase with an IC50 of 5.5 µM. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
QSAR modeling and computer‐aided design of antimicrobial peptides
Authors: Jenssen HÅvard , Fjell Christopher D. , Cherkasov Artem , Hancock Robert E. W.
Published: September 2007

The drastic increase in multi‐drug‐resistant bacteria has created an urgent need for new therapeutic interventions, including antimicrobial peptides, an interesting template for novel drug development. However, the process of optimizing peptide antimicrobial activity and specificity using large peptide libraries is both tedious and expensive. Here we confirm the use of a mathematical model for prediction, prior to synthesis, of peptide antibacterial activity toward the antibiotic resistant pathogen Pseudomonas aeruginosa. By the use of novel descriptors quantifying the contact energy between neighboring amino acids, as well as a set of inductive and conventional QSAR descriptors, we were able to model the antibacterial activity of peptides. Cross‐correlation and optimization of the implemented descriptor values enabled us to build two models, using very limited sets of peptides, which were able to correctly predict the activity of 85 or 71% of the tested peptides, within a twofold deviation window of the corresponding previously assessed IC50 values, measured earlier. Though these two models were significantly different in size, they demonstrated no significant difference in their predictive power, implying that it is possible to build powerful predictive models using even small sets of structurally different peptides, when using contact‐energy descriptors and inductive and conventional QSAR descriptors in the model design. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd.
Thermoelectric properties of p‐type Mg2Si0.6Ge0.4 fabricated by bulk mechanical alloying and hot pressing
Authors: Song R. B. , Liu Y. Z. , Aizawa T.
Published: September 2007

Bulk mechanical alloying (BMA) followed by hot pressing (HP) was used to prepare Mg2Si0.6Ge0.4 thermoelectric material with high densification. Starting from the elemental power mixture, the Mg2Si0.6Ge0.4 solid solution was solid‐state synthesized via BMA. In fact, the peaks for the cubic‐structured Mg2Si0.6Ge0.4 solid solution phase were detected after 300 cycles in BMA. The single phase of Mg2Si0.6Ge0.4 was synthesized at 600 cycles in BMA. Mg2Si0.6Ge0.4 showed p‐type semiconduction without doping. Effects of hot pressing conditions on thermoelectric properties were investigated. With increasing hot pressing temperature from 673 to 773 K and pressure from 500 MPa to 1 GPa, the electrical conductivity increased and the Seebeck coefficient decreased. The maximum figure of merit was obtained with the processing parameter of 600 cycles BMA and hot pressing at 773 K, 1 GPa for 1 h. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Conditional approval: discussion points from the PSI conditional approval expert group
Authors: Carroll Kevin , Ross Hilary Chaudri , Evans Dan , France Lesley , Hemmings Rob , Hughes Sara , Lynn Frances , Mahoney Paul , Phillips Alan
Published: September 2007

The European Agency for the Evaluation of Medicinal Products has recently completed the consultation of a draft guidance on how to implement conditional approval. This route of application is available for orphan drugs, emergency situations and serious debilitating or life‐threatening diseases. Although there has been limited experience in implementing conditional approval to date, PSI (Statisticians in the Pharmaceutical Industry) sponsored a meeting of pharmaceutical statisticians with an interest in the area to discuss potential issues. This article outlines the issues raised and resulting discussions, based on the group's interpretation of the legislation. Conditional approval seems to fit well with the accepted regulatory strategy in HIV. In oncology, conditional approval may be most likely when (a) compelling phase II data are available using accepted clinical outcomes (e.g. progression/recurrence‐free survival or overall survival) and Phase III has been planned or started, or (b) when data are available using a surrogate endpoint for clinical outcome (e.g. response rate or biochemical measures) from a single‐arm study in rare tumours with high response, compared with historical data. The use of interim analyses in Phase III for supporting conditional approval raises some challenging issues regarding dissemination of information, maintenance of blinding, potential introduction of bias, ethics, switching, etc. Copyright © 2007 John Wiley & Sons, Ltd.
Precolumn derivatization of cysteine residues for quantitative analysis of five major cytochrome P450 isoenzymes by liquid chromatography/tandem mass spectrometry
Authors: Duan Xiaotao , Chen Xiaoyan , Yang Yiming , Zhong Dafang
Published: September 2007

The development of a novel method for absolute quantification of the five most clinically relevant CYP450 isoenzymes is described based on chemical derivatization of cysteine residues. The sulfhydryl‐reactive reagents, 2‐bromo‐4′‐chloroacetophenone (p‐CPB) and 2‐bromo‐4′‐bromoacetophenone (p‐BPB), are proposed for use in quantitative proteomics. After reducing and denaturing, the P450s are derivatized with p‐CPB for sulfhydryl alkylation then subjected to trypsin digestion. The resulting p‐CPB‐attached peptides are enriched using a phenyl resin solid‐phase cartridge, then separated on a Zorbax 300SB reversed‐phase column, and detected under positive electrospray ionization in the multiple reaction monitoring mode. Quantification is achieved using p‐BPB‐modified peptides as internal standards. Validation results demonstrated that this method showed good linearity between the concentration range of 10 fmol/µg to 5 pmol/µg for the six selected peptides in a complex matrix (rat liver microsomal protein). Intra‐day and inter‐day precision, expressed by relative standard deviation, were all less than 18%. Assay accuracy was within ± 20% in terms of relative error. The quantitative derivatization approach proved to be reproducible, cost‐effective and readily suitable for high‐throughput assays. The reliability of this method for quantification of intact P450s was demonstrated through comparing with the well‐applied isotope‐coded affinity tag (ICAT) method. Copyright © 2007 John Wiley & Sons, Ltd.
Simultaneous determination of aflatoxins, ochratoxin A andFusariumtoxins in maize by liquid chromatography/tandem mass spectrometry after multitoxin immunoaffinity cleanup
Authors: Lattanzio Veronica Maria Teresa , Solfrizzo Michele , Powers Steve , Visconti Angelo
Published: September 2007

A liquid chromatography/tandem mass spectrometry method was developed for the simultaneous determination of aflatoxins (B1, B2, G1, G2), ochratoxin A, fumonisins (B1, B2), deoxynivalenol, zearalenone, T‐2 and HT‐2 toxins in maize. A double extraction approach, using a phosphate‐buffered solution followed by methanol, was applied to achieve effective co‐extraction of the 11 mycotoxins under investigation having quite different polarities and chemical structures. A new multitoxin immunoaffinity column containing antibodies for all these mycotoxins was used to clean up the extract. Detection and quantification of the 11 mycotoxins were performed by reversed‐phase liquid chromatography coupled with electrospray ionization triple quadrupole mass spectrometry (LC/ESI‐MS/MS) using, as chromatographic mobile phase, a linear gradient of methanol/water containing 0.5% acetic acid and 1 mM ammonium acetate. Method performances were quite satisfactory for all tested mycotoxins at contamination levels close to or below the relevant EU maximum permitted or recommended levels. Limits of detection in maize ranged from 0.3 to 4.2 µg/kg. Recoveries higher than 79% were obtained for all tested mycotoxins with relative standard deviations less than 13%. Copyright © 2007 John Wiley & Sons, Ltd.
Tests for the homogeneity of two binomial proportions in extremely unbalanced 2 × 2 contingency tables
Authors: Kang Seung‐Ho , Ahn Chul W.
Published: September 2007

Asymptotic tests such as the Pearson chi‐square test are unreliable for testing the homogeneity of two binomial probabilities in extremely unbalanced cases. Two exact tests (conditional and unconditional) are available as alternatives and can be implemented easily in StatXact 6.0. In equal sample cases it is well known that the unconditional exact test is more powerful than the conditional exact test. However, in this paper, we show that the opposite result holds in extremely unbalanced cases. The reason is that the peaks of the type I error occur at the extremes of the nuisance parameter when the imbalance among the sample sizes becomes severe. After we show that the conditional exact test is more powerful than the unconditional exact test in extremely unbalanced cases whose sample ratio is greater than 20, we compare the conditional exact test with the Berger and Boos approach (J. Amer. Stat. Assoc. 1994; 89:1012–1016) in which the supremum is taken over a confidence interval for the nuisance parameter. The Berger and Boos approach turns out to be slightly more powerful than the conditional exact test in extremely unbalanced data. A real example is provided. Copyright © 2007 John Wiley & Sons, Ltd.
Influence of Soluble Polymer Residues in Crosslinked Carboxymethyl Starch on some Physical Properties of its Hydrogels
Authors: Heß Christoph , Hartmann Brigitte , Lechner M. Dieter , Nierling Wolfgang , Seidel Christian , Kulicke Werner‐Michael
Published: September 2007

Crosslinked carboxymethyl starch (CMS) was synthesized from potato starch in a single‐step procedure with mono‐ (MCA) and dichloroacetic acid (DCA), using the well‐known Williamson reaction. The products varied in their degree of substitution DS (average number of carboxymethyl groups per monomer unit) and crosslinker ratio Fz (number of crosslinker molecules offered per monomer unit). After neutralizing and removal of the formed salt, one part of the synthesized CMS networks was pre‐swollen in water in an additional purification step in order to wash out unlinked, soluble polymer chains. The rest of the product remained unwashed. Different swelling experiments were performed with the two samples, before being dried and ground. Both, the Free Swelling Capacity (FSC) and the Absorption Capacity Under Mechanical Load (AUL) of the hydrogels were strongly influenced by chemically unlinked CMS chains that were only physically entangled in the network structure. These mobile polymer segments were responsible for a significant weight loss of the swollen, unwashed hydrogels over the course of time. Rheological oscillatory experiments showed that, in order to achieve comparable values for the storage and loss moduli (G′ and G′′), the polymer content of an unwashed hydrogel had to be more than twice as high as that of the corresponding purified product. By using a special rheological test procedure with a cyclic temperature program, the long‐term stability of CMS gels could be measured and verified.
Analysis of the Material and Tablet Formation Properties of four Dioscorea Starches
Authors: Odeku Oluwatoyin A. , Picker‐Freyer Katharina M.
Published: September 2007

The material and tablet formation properties of starches from four different Dioscorea species, namely White (D. rotundata), Bitter (D. dumetorum), Chinese (D. oppositifolia) and Water yam (D. alata), was characterized to determine their applicability as direct compression excipient. The physicochemical, thermal, morphological and material properties of the starches were investigated. The tablet formation properties were assessed using the 3‐D modeling parameters, the Heckel equation and the force‐displacement profiles. The tablet properties were evaluated using the elastic recovery and compactibility plots. The results indicate that the chemical composition, thermal and material properties of the starches varied considerably among the four species. The sorption isotherms show that the relative humidity (RH) during tablet production and storage should be carefully controlled. The tableting results show that all four starches exhibit similar time dependent deformation (d). The ranking for pressure plasticity (e) was Water > Chinese > White > Bitter, which indicates that Water deforms more easily and Bitter less easily. The ranking for fast elastic decompression was White > Water ≥ Chinese > Bitter. The amylose content, size and shape of the starch granules and specific surface area appears to play a significant role in the compressibility. Thus, White and Water with larger granules and high amylose content exhibited poor compressibility and did not form compacts except at high ρrel,max, while Bitter and Chinese with polygonal shape, small particle size and high specific surface area were more compressible and formed tablets of acceptable crushing force. Thus, Chinese and Bitter could be useful as excipient in direct compression.
Characteristics of Novel Starch‐based Hydrogels Prepared by UV Photopolymerization of Acryloylated Starch and A Zwitterionic Monomer
Authors: Li Jie‐Mei , Zhang Li‐Ming
Published: September 2007

New starch‐based hydrogels were prepared by the UV‐induced polymerization of acryloylated starch with the zwitterionic monomer 3‐dimethyl(methacryloyloxyethyl) ammonium propane sulfonate (DMAPS). The swelling kinetics of the resultant hydrogels in distilled water and their equilibrium swelling ratios in aqueous NaCl and CaCl2 solutions were investigated. With increasing amount of incorporated DMAPS, the formed hydrogel had an enhanced swelling ability in distilled water and in aqueous salt solutions. In particular, antipolyelectrolyte swelling behavior of the hydrogel was observed in aqueous salt solutions.
Combined heat and mass transfer in magneto‐micropolar fluid flow from radiate surface with variable permeability in slip‐flow regime
Authors: Chaudhary R.C. , Jain P.
Published: September 2007

An analysis is presented to study the effects of radiation on the hydromagnetic free convection flow (set up due to temperature as well as species concentration) of an electrically conducting micropolar fluid past a vertical porous plate through porous medium in slip‐flow regime. A uniform magnetic field acts perpendiculary to the porous surface which absorbs the micropolar fluid with variable suction velocity. The Rosseland approximation is used to describe the radiative heat flux in energy equation. The numerical results of velocity distribution of micropolar fluids are compared with the corresponding flow problems for a Newtonian fluid. Assuming variable permeability of the medium, numerical results are presented graphically in the form of velocity, micro rotation, and temperature profiles for different material parameters entering into the analysis. Also, the results of the skin‐friction coefficient, the couple stress coefficient, the rate of heat and mass transfers at the wall are discussed with the help of figures.
An interior point method for a parabolic optimal control problem with regularized pointwise state constraints
Authors: Prüfert U. , Tröltzsch F.
Published: September 2007

A primal‐dual interior point method for state‐constrained parabolic optimal control problems is considered. By a Lavrentiev type regularization, the state constraints are transformed to mixed control‐state constraints which, after a simple transformation, can be handled as control constraints. Existence and convergence of the central path are shown. Moreover, the convergence of a short step interior point algorithm is proven in a function space setting. The theoretical properties of the algorithm are confirmed by numerical examples.
Existence results for a contact problem with varying friction coefficient and nonlinear forces
Authors: Schmid F. , Mielke A.
Published: September 2007

We consider the rate‐independent problem of a particle moving in a three‐dimensional half space subject to a time‐dependent nonlinear restoring force having a convex potential and to Coulomb friction along the flat boundary of the half space, where the friction coefficient may vary along the boundary. Our existence result allows for solutions that may switch arbitrarily often between unconstrained motion in the interior and contact where the solutions may switch between sticking and frictional sliding. However, our existence result is local and guarantees continuous solutions only as long as the convexity of the potential is strong enough to compensate the variation of the friction coefficient times the contact force. By simple examples we show that our sufficient conditions are also necessary.

Our method is based on the energetic formulation of rate‐independent systems as developed in [MTL02, MiT04]. We generalize the time‐incremental minimization procedure of [MiR06] for the present situation of a non‐associative flow rule.