bluuebunny/crossref_metadata_2025 huggingface dataset:
Atmospheric moisture budget in the Arctic based on the ERA‐40 reanalysis
Authors: Jakobson Erko , Vihma Timo
Published: October 2009

The atmospheric moisture budget in the Arctic in 1979–2001 was analysed on the basis of the ERA‐40 reanalysis. Zonal variations in the profiles of specific humidity mainly occur at altitudes below 5 km. The moisture transport peaks at altitudes lower than previously suggested; the median peak level of meridional moisture flux (MMF) across 70°N is in winter at 930 hPa pressure level and in other seasons at 970–990 hPa level. Mean precipitable water for the polar cap (70–90°N) ranges from 2.4 mm in winter to 12.3 mm in summer. Transient eddies (TE) are responsible for most of the water vapour transport across 70°N by providing from 81% of MMF in winter to 92% of MMF in summer. The contribution by stationary eddies (SE) ranges from 5 to 9%, whereas the contribution of mean meridional circulation (MMC) ranges from 1% in summer to 12% in winter. Relative inter‐annual variation in MMF components is highest for SE (standard deviation/mean = 133%), second highest for the MMC (61%) and smallest for TE (4%). The MMF across 70°N accounts for 59% of the annual precipitation. Averaged for the polar cap, the mean annual moisture flux convergence (192 mm) and net precipitation (179 mm) are close to each other, but local differences exceeding 200 mm occur at several places. Over the open ocean, the moisture flux convergence is considered more reliable. The Arctic Oscillation (AO) index correlates with MMF in spring and winter (correlation coefficient r = 0.75) and with net precipitation in spring (r = 0.61) and winter (r = 0.50). The AO and precipitable water correlate in Canada and Greenland in winter and spring (r = − 0.7) and in Europe in winter (r = 0.8). Copyright © 2009 Royal Meteorological Society
Determination of paclitaxel and its analogues in the needles of Taxus species by using negative pressure cavitation extraction followed by HPLC‐MS‐MS
Authors: Li Shuangming , Fu Yujie , Zu Yuangang , Zu Baishi , Wang Ying , Efferth Thomas
Published: October 2009

A new separation method, negative pressure cavitation (NPC) extraction followed by HPLC‐MS‐MS for the determination of paclitaxel and its analogues in the needles of Taxus species is described in this study. Compared with three conventional extraction methods, NPC is a more effective, economical, and facile method for the separation of nature compounds from herbal plants. In contrast to high‐temperature extraction, NPC at low temperature can minimize undesirable reactions such as thermal decomposition or degradation. In addition, the extraction mechanism of NPC was also illuminated. The effects of vacuum degree, extraction solvent, ratio of solid to liquid, time, and times extraction were studied and optimized. The optimum extraction conditions were as follows: vacuum degree –0.03 MPa, solvent 80% v/v alcohol, ratio of material to liquid 1:15 (g/mL), extraction time 60 min, extraction (×3). Using these conditions, the recoveries of 10‐deacetyl‐7‐xylosylpaclitaxel, 10‐deacetylpaclitaxel, cephalomannine, and paclitaxel were higher than 95.88, 95.82, 94.85, and 96.18%, respectively. The contents of paclitaxel, 10‐deacetyl‐7‐xylosylpaclitaxel, 10‐deacetylpaclitaxel, and cephalomannine for Taxus chinensis were 0.0053, 0.0467, 0.0132, and 0.0076%, and 0.0067, 0.0153, 0.0047, and 0.0064% for Taxus cuspidata, respectively. Furthermore, a comparison of SEM images observed the morphological changes of microstructures and cellular damage in yew needles.
Soot–additive interactions in engine oils
Authors: Uy Dairene , O'Neill A. E. , Simko Steven J. , Gangopadhyay Arup K.
Published: October 2009

Soot is known to cause engine wear. In this work, we focus on how engine oil formulation affects soot‐related wear, and how the lubricant‐derived anti‐wear film changes when soot is present. Friction and wear experiments of fully and partially formulated diesel engine oils (containing basestock, dispersants and viscosity modifiers) are conducted with a ball‐on‐disk rig in the presence of carbon black (CB) as a soot surrogate. The friction coefficient was largely unaffected by CB dispersed in the oils, but electrically insulating film formation, an indication of the formation of anti‐wear films, was decreased. Wear on the disk was found to either remain the same or decrease when CB was present, depending on the oil formulation. An examination of the lubricant‐derived films using Raman and Auger electron spectroscopies found that the presence of more abundant amorphous carbon and lesser amounts of anti‐wear film components on the surface was associated with higher wear. Copyright © 2009 John Wiley & Sons, Ltd.
Chemical Binding of Unsaturated Fluorenes to Poly(2‐chloroxylylene) Thin Films
Authors: Bolognesi Alberto , Botta Chiara , Andicsova Anita , Giovanella Umberto , Arnautov Sergey , Charmet Jérôme , Laux Edith , Keppner Herbert
Published: October 2009

A series of substituted fluorenes with vinyl groups as reactive sites were synthesized and characterized. Fluorene‐based polymers with vinyl groups as end chains and side chains functionalities were also prepared. In both cases, successful preparation of functionalized Parylene C films (modylayers) was achieved. The set of spectral methods used has allowed us to conclude that such functionalization is based on the chemical reaction of double bonds with xylylene radicals during deposition process. Parylene C films chemically modified with specially synthesized polyfluorenes showed PL quantum efficiency comparable with neat polyfluorenes.

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Non‐Fouling Character of Poly[2‐(methacryloyloxy)ethyl Phosphorylcholine]‐Modified Gold Surfaces Fabricated by the ‘Grafting to’ Method: Comparison of its Protein Resistance with Poly(ethylene glycol)‐Modified Gold Surfaces
Authors: Yoshimoto Keitaro , Hirase Takumi , Madsen Jeppe , Armes Steven P. , Nagasaki Yukio
Published: October 2009

Poly[2‐(methacryloyloxy)ethyl phosphorylcholine] ‐modified gold surfaces, which have been newly prepared by a ‘grafting to’ method using a series of monosulfanyl‐terminated PMPC, are characterized by protein adsorption experiments based on surface plasmon resonance spectroscopy and ellipsometry measurements. The extent of BSA adsorption on PMPC‐modified surfaces was systematically reduced for thicker PMPC layers, thus the number of MPC units on the gold surface appears to be an important factor for the excellent protein resistance offered by PMPC‐modified gold surfaces fabricated by the ‘grafting to’ method, which is sharp contrast to that of PEG tethered chains.

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Normative decision making with multiattribute performance targets
Authors: Abbas Ali E. , Matheson James E.
Published: October 2009

Many companies set multiple performance targets for their managers and reward them on meeting a threshold value for each target or goal. Examples of such incentive structures abide in the managerial literature and in organizational settings. We show that this incentive structure, while popular, has two main problems: (i) it can induce managers who try to maximize the probability of meeting their performance targets to make decisions that are not compatible with expected utility maximizing decisions, and (ii) it may lead to trade‐offs among the performance objectives that are inconsistent with the corporate value function. In this paper, we propose a method to remedy these two problems, while retaining a target‐based incentive scheme. We define a multiattribute target as a deterministic region in the space of multiattribute outcomes that has two properties: (1) the probability that the outcome of a multiattribute lottery lies within the target region is equal to the expected utility of the lottery, and (2) all outcomes within the target region are preferred to all outcomes outside it. These two properties lead to a new quantity; which we call the ‘value aspiration equivalent’ that leads managers who maximize the probability of meeting their targets to simultaneously maximize the expected utility, and it also induces trade‐offs that are consistent with the decision maker's value function. Copyright © 2009 John Wiley & Sons, Ltd.
Paramedical treatment in primary dystonia: A systematic review
Authors: Delnooz Cathérine C.S. , Horstink Martin W.I.M. , Tijssen Marina A. , van de Warrenburg Bart P.C.
Published: October 2009

Dystonia is a disabling movement disorder with a significant impact on quality of life. The current therapeutic armamentarium includes various drugs, botulinum toxin injections, and occasionally (neuro)surgery. In addition, many patients are referred for paramedical (including allied health care) interventions. An enormous variation in the paramedical treatment is provided, largely because evidence‐based, accepted treatment regimes are not available. We have conducted a systematic review of studies that explored the effect of various paramedical interventions in primary dystonia. Only studies that have used clinical outcome measures were included. There were no class A1 or A2 studies and therefore, level 1 or 2 practice recommendations for a specific intervention could not be deducted. Many papers were case reports, mostly with a very limited number of patients and a clear publication bias for beneficial effects of a particular paramedical intervention. Some potentially interesting interventions come from class B studies, which include physical therapy in addition to botulinum toxin injections (BoNT‐A) in cervical dystonia; sensorimotor training and transcutaneous electrical nerve stimulation (TENS) in writer's cramp; and speech therapy added to BoNT‐A injections in laryngeal dystonia. Good quality clinical studies are therefore warranted, which should have the aim to be generally applicable. A design in which the paramedical intervention is added to a current gold standard, for example, BoNT‐A injections in cervical dystonia, is recommended. © 2009 Movement Disorder Society
Three‐dimensional finite element study of arching behavior in slope/drilled shafts system
Authors: Liang Robert Y. , Yamin Mohammad
Published: October 2009

Two‐dimensional slope stability analysis for a slope with a row of drilled shafts needs a mechanism to take into account the three‐dimensional effect of the soil arching due to the spaced drilled shafts on slope. To gain a better understanding of the arching mechanisms in a slope with evenly spaced drilled shafts socketed into a stable stratum (or a rock layer), the three‐dimensional finite element modelling technique was used for a comprehensive parametric study, where the nonlinear and plastic nature of the soil and the elastic behavior of the drilled shafts as well as the interface frictions were modelled. Various factors were varied in the parametric study to include (1) the rigidity of the drilled shafts as influenced by its diameter, modulus of elasticity, and total length; (2) shafts spacing and location on the slope; (3) the material properties of rock and the socket length of shaft; and (4) the soil movement and strength parameters. Evidences of soil arching and reduction in the stresses and displacements through the load transfer mechanisms due to the presence of the drilled shafts were elucidated through the finite element method (FEM) simulation results. Design charts based on regression analysis of FEM simulation results were created to obtain a numerical value of the load transfer factor for the arching mechanism provided by the drilled shafts on the slope. Observations of the arching behavior learned from the FEM simulations provide an insight into the behavior of drilled shafts stabilized slope. Copyright © 2009 John Wiley & Sons, Ltd.
Metabolic correlatives of brain activity in a FOS epilepsy patient
Authors: Peca Stefano , Carnì Marco , Di Bonaventura Carlo , Aprile Teresa , Hagberg Gisela E. , Giallonardo Anna Teresa , Manfredi Mario , Mangia Silvia , Garreffa Girolamo , Maraviglia Bruno , Giove Federico
Published: October 2009

The correlation and the interactions between neuronal activity and underlying metabolic dynamics are still a matter of debate, especially in pathological conditions. This study reports findings obtained on a subject suffering from fixation‐off sensitivity (FOS) epilepsy, exploited as a model system of triggerable anomalous electrical activity. Functional Magnetic Resonance Spectroscopy was used to investigate the metabolic response to visual spike‐inducing stimuli in a single voxel placed in the temporo‐occipital lobe of a FOS epilepsy patient. MRS measurements were additionally performed on a control group of five healthy volunteers. The FOS patient also underwent an EEG session with the same stimulus paradigm. Uniquely in the FOS patient, glutamate and glutamine concentration increased during the first 10 min of stimulation and then returned to baseline. On the other hand, FOS‐induced epileptic activity (spiking) endured throughout all the stimulation epoch. The observed metabolic dynamics may be likely linked to a complex interplay between alterations of the metabolic pathways of glutamate and modulation of the neuronal activity. Copyright © 2009 John Wiley & Sons, Ltd.
A two‐stage vehicle routing model for large‐scale bioterrorism emergencies
Authors: Shen Zhihong , Dessouky Maged M. , Ordóñez Fernando
Published: October 2009

In this article, we are interested in routing vehicles to service a large‐scale bioterrorism emergency. We describe the specifics of routing vehicles in such a large‐scale emergency and decompose the problem into two stages: a planning stage and an operational stage. In the planning stage, we generate the routes well in advance of any emergency. In the operational stage, we take into account the planned routes and the information revealed at the time of the emergency, to decide the delivery quantity and any adjustments to the routes. We propose mathematical formulations and solution approaches for both stages. Lastly, we demonstrate the effectiveness of our formulations and solution procedures in developing robust routes through numerical experiments. © 2009 Wiley Periodicals, Inc. NETWORKS, 2009
Recent results on Arc Routing Problems: An annotated bibliography
Authors: Corberán Angel , Prins Christian
Published: October 2009

Arc routing problems are vehicle routing problems in which the tasks to be performed are located on some arcs or edges of a network, e.g., spreading salt on a road or collecting municipal refuse in a street. They have been much less studied than node routing problems but impressive developments have been achieved in the last decade. The objective of this article is to survey these recent results and to provide an annotated bibliography. Except for a few references, the period surveyed starts from the publication of the book “Arc routing: theory, solutions and applications”, edited by Dror in 2000. The article is made up of two main parts: one on uncapacitated (single vehicle) problems derived from the Chinese Postman Problem, the Rural Postman Problem, and the General Routing Problem; and one on multivehicle or capacitated problems such as the Capacitated Arc Routing Problem. © 2009 Wiley Periodicals, Inc. NETWORKS, 2010
New periodic wave solutions for nonlinear evolution equations with variable coefficients via mapping method
Authors: Abdou M.A. , Abd ElGawad S.S.
Published: October 2009

An extended mapping method with a computerized symbolic computation is used for constructing a new exact travelling wave solutions for nonlinear evolution equations arising in physics, namely, generalized Zakharov Kuznetsov equation with variable coefficients. As a result, many exact travelling wave solutions are obtained which include new periodic wave solution, trigonometric function solutions and rational solutions. The method is straightforward and concise, and it can also be applied to other nonlinear evolution equations with variable coefficients arising in mathematical physics. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2010
Variational iteration method for solving three‐dimensional Navier–Stokes equations of flow between two stretchable disks
Authors: Rashidi M.M. , Shahmohamadi H. , Domairry G.
Published: October 2009

The similarity transform for the steady three‐dimensional Navier–Stokes equations of flow between two stretchable disks gives a system of nonlinear ordinary differential equations. In this article, the variational iteration method was used for solving these equations. The results have been compared with the numerical results. This article depicts that the VIM is an efficient and powerful method for solving nonlinear differential equations. This method is applicable to strongly and weakly nonlinear problems. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2011
Stagnation slip flow and heat transfer over a nonlinear stretching sheet
Authors: Abbas Z. , Hayat T.
Published: October 2009

Stagnation slip flow and heat transfer characteristics of a viscous fluid over a nonlinear stretching surface has been investigated. The governing partial differential equations are transformed to nonlinear ordinary differential equations using similarity transformations. The analytical solution of the nonlinear system is obtained in series form using the very efficient homotopy analysis method (HAM). Convergence of the series solution is shown explicitly. Important features of flow and heat transfer characteristics are plotted and discussed. Comparison is made with existing numerical results when the stagnation‐point and slip effects are excluded. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2011
Convergence of the interpolated coefficient finite element method for the two‐dimensional elliptic sine‐Gordon equations
Authors: Wang Cheng
Published: October 2009

An interpolated coefficient finite element method is presented and analyzed for the two‐dimensional elliptic sine‐Gordon equations with Dirichlet boundary conditions. It is proved that the discretization scheme admits at least one solution, and that a subsequence of the approximation solutions converges to an exact solution in L2‐norm as the mesh size tends to zero. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2011
Finite element approximation of coupled seismic and electromagnetic waves in fluid‐saturated poroviscoelastic media
Authors: Santos Juan E.
Published: October 2009

This work presents a collection of global and iterative finite element procedures for the numerical approximation of coupled seismic and electromagnetic waves in 2D bounded fluid‐saturated porous media, with absorbing boundary conditions at the artificial boundaries. The equations being analyzed are the coupled Biot's equations of motion and Maxwell equations in the diffusive range. Both seismoelectric and electroseismic coupling are simultaneously included and analyzed in the model. The case of compressional and vertically polarized shear waves coupled with the transverse magnetic polarization (PSVTM‐mode) is analyzed in detail, including the derivation of a priori error estimates on the global finite element procedure and results on the convergence of a domain decomposition iterative algorithm. Later, the corresponding results for the case of horizontally polarized shear waves coupled with the transverse electric polarization (SHTE‐mode) are stated. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2011
Integrated fast and high‐accuracy computation of convection diffusion equations using multiscale multigrid method
Authors: Wang Yin , Zhang Jun
Published: October 2009

We present an explicit sixth‐order compact finite difference scheme for fast high‐accuracy numerical solutions of the two‐dimensional convection diffusion equation with variable coefficients. The sixth‐order scheme is based on the well‐known fourth‐order compact (FOC) scheme, the Richardson extrapolation technique, and an operator interpolation scheme. For a particular implementation, we use multiscale multigrid method to compute the fourth‐order solutions on both the coarse grid and the fine grid. Then, an operator interpolation scheme combined with the Richardson extrapolation technique is used to compute a sixth‐order accurate fine grid solution. We compare the computed accuracy and the implementation cost of the new scheme with the standard nine‐point FOC scheme and Sun–Zhang's sixth‐order method. Two convection diffusion problems are solved numerically to validate our proposed sixth‐order scheme. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2011
An improved compact finite difference scheme for solving an N‐carrier system with Neumann boundary conditions
Authors: Dai Weizhong
Published: October 2009

Recently, we have developed a higher‐order and unconditionally stable compact finite difference scheme for solving a model of energy exchanges in an N‐carrier system with Neumann boundary conditions, which extends the concept of the well‐known parabolic two‐step model for microheat transfer. However, the combined compact finite difference scheme for the boundary is second‐order accurate. Unfortunately, our statement in (Dai and Tzou, Numer Methods Partial Differential Equation, Zhao et al., Numer Methods Partial Differential Equations 23 (2007), 949–959.), that it is a fourth‐order scheme is inaccurate, because the scheme was multiplied by Δx2 in the derivation. In this article, we develop a new combined compact finite difference scheme for the boundary, which is third‐order accurate. Using the exact same proof for stability analysis as in (Dai and Tzou, Numer Methods Partial Differential Equations), the new scheme is unconditionally stable with respect to the initial conditions and source terms. The improved compact scheme is then tested by a numerical example. Results show that the convergence rate with respect to the spatial variable from the new scheme is higher and the solution is much more accurate, when compared with those obtained using our previous compact scheme in (Dai and Tzou, Numer Methods Partial Differential Equations). © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2011
Ultraviolet‐induced crosslinking of poly(butylene succinate) and its thermal property, dynamic mechanical property, and biodegradability
Authors: Huang Xi , Li Chuncheng , Zhu Wenxiang , Zhang Dong , Guan Guohu , Xiao Yaonan
Published: October 2009

Crosslinking is an effective way to improve polymer properties. This paper focuses on ultraviolet‐induced crosslinking of poly(butylene succinate) (PBS) in the presence of a photoinitiator and a crosslinking agent at ambient temperature. The effects of the concentration of photoinitiator, the crosslinking agent content, and the irradiation time on the crosslink behavior were investigated. To obtain an appropriate gel fraction in different irradiation times, 3.0 wt% of photoinitiator and 10.0 wt% of crosslinking agent were proved to be the optimum choice. Furthermore, properties such as thermal properties, dynamic mechanical property, and enzymatic degradation of PBS before and after crosslinking were examined. Differential scanning calorimetry (DSC) analysis revealed that glass transition temperature (Tg) increased with increase in gel fraction, while melting temperature (Tm) and the degree of crystallinity decreased. This may be caused by the reduced molecular chain mobility and inhibited molecular motion for crystallization in crosslinked samples. The crosslinked polymer also showed improved thermal stability and dynamic mechanical property. In addition, the introduction of crosslinking retarded the enzymatic degradation rate of PBS, but it was still biodegradable. The improved properties of crosslinked PBS will extend the application of PBS. Copyright © 2009 John Wiley & Sons, Ltd.
Preparation of biocompatible multi‐walled carbon nanotubes as potential tracers for sentinel lymph nodes
Authors: Li Junjun , Yang Feng , Guo Guiquan , Yang Dong , Long Jiang , Fu Deliang , Lu Jennifer , Wang Changchun
Published: October 2009

Carbon nanotubes (CNTs) are capable of traversing cellular membranes by endocytosis and are therefore promising materials for use in imaging and drug delivery. Unfortunately, pristine CNTs are practically insoluble and tend to accumulate inside cells, organs and tissues. To overcome the poor dispersibility and toxicity of pristine CNTs, hydrophilic functionalization of CNTs has been intensively investigated. Water‐soluble multi‐walled carbon nanotubes (MWCNTs) were prepared by in situ polymerization of acrylic acid in a poor solvent for poly(acrylic acid) (PAA). The solvent type influenced the grafted density and chain length of PAA. MWCNTs with a high grafted density of PAA (22 wt%) could be well dispersed in water, NaCl aqueous solution (0.9 wt%) and cell culture media. The in vitro cytotoxicity of these MWCNTs for endothelial cells is reasonably low even at high concentration of PAA‐g‐MWCNT (70 µg mL−1). The experimental results show that the biocompatibility of these MWCNTs is sufficient for biological applications. PAA‐g‐MWCNTs were successfully utilized for lymph node tracing. Experimental results suggest that PAA‐g‐MWCNTs have potential to be used as a vital staining dye, which may simplify the identification of lymph nodes during surgery. Copyright © 2009 Society of Chemical Industry
Thermal and morphological properties of high‐density polyethylene/ethylene–vinyl acetate copolymer composites with polyhedral oligomeric silsesquioxane nanostructure
Authors: Scapini Patrícia , Figueroa Carlos A , Amorim Cíntia LG , Machado Giovanna , Mauler Raquel S , Crespo Janaina S , Oliveira Ricardo VB
Published: October 2009

The demand for improved properties of common polymers keeps increasing, and several new approaches have been investigated. In the study reported here, composites with a polymer matrix comprising a blend of high‐density polyethylene with ethylene–vinyl acetate copolymer (EVA), and with polyhedral oligomeric silsesquioxane (POSS) as a nanostructure, were processed and characterized in terms of their thermal and morphological properties. For the preparation of the composites, the concentrations of the blend components (0, 50 and 100 wt%) and of the POSS (0, 1 and 5 wt%) were varied. X‐ray diffraction results indicated that the presence of EVA in the composites led to the appearance of crystalline domains at lower POSS concentrations. Transmission and scanning electron microscopy showed that samples with 1 wt% of POSS had a homogeneous distribution in the polymer matrix with average dimensions of ca 150 nm. However, the formation of aggregates occurred in samples with 5 wt% of POSS. Differential scanning calorimetry and thermogravimetic analyses indicated that the POSS did not affect the melt and degradation temperatures of the polymer matrix. POSS underwent aggregation at higher concentrations during the composite processing, indicating a solubility limit of around 1 wt%. The presence of EVA in the composite favors POSS aggregation due to an increase in the polarity of the polymer matrix. Copyright © 2009 Society of Chemical Industry
DynaDock: A new molecular dynamics‐based algorithm for protein–peptide docking including receptor flexibility
Authors: Antes Iris
Published: October 2009

Molecular docking programs play an important role in drug development and many well‐established methods exist. However, there are two situations for which the performance of most approaches is still not satisfactory, namely inclusion of receptor flexibility and docking of large, flexible ligands like peptides. In this publication a new approach is presented for docking peptides into flexible receptors. For this purpose a two step procedure was developed: first, the protein–peptide conformational space is scanned and approximate ligand poses are identified and second, the identified ligand poses are refined by a new molecular dynamics‐based method, optimized potential molecular dynamics (OPMD). The OPMD approach uses soft‐core potentials for the protein–peptide interactions and applies a new optimization scheme to the soft‐core potential. Comparison with refinement results obtained by conventional molecular dynamics and a soft‐core scaling approach shows significant improvements in the sampling capability for the OPMD method. Thus, the number of starting poses needed for successful refinement is much lower than for the other methods. The algorithm was evaluated on 15 protein–peptide complexes with 2–16mer peptides. Docking poses with peptide RMSD values <2.10 Å from the equilibrated experimental structures were obtained in all cases. For four systems docking into the unbound receptor structures was performed, leading to peptide RMSD values <2.12 Å. Using a specifically fitted scoring function in 11 of 15 cases the best scoring poses featured a peptide RMSD ≤2.10 Å. Proteins 2010. © 2009 Wiley‐Liss, Inc.
On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins
Authors: Kahraman Abdullah , Morris Richard J. , Laskowski Roman A. , Favia Angelo D. , Thornton Janet M.
Published: October 2009

Most function prediction methods that identify cognate ligands from binding site analyses work on the assumption of molecular complementarity. These approaches build on the conjectured complementarity of geometrical and physicochemical properties between ligands and binding sites so that similar binding sites will bind similar ligands. We found that this assumption does not generally hold for protein–ligand interactions and observed that it is not the chemical composition of ligand molecules that dictates the complementarity between protein and ligand molecules, but that the ligand's share within the functional mechanism of a protein determines the degree of complementarity. Here, we present for a set of cognate ligands a descriptive analysis and comparison of the physicochemical properties that each ligand experiences in various nonhomologous binding pockets. The comparisons in each ligand set reveal large variations in their experienced physicochemical properties, suggesting that the same ligand can bind to distinct physicochemical environments. In some protein ligand complexes, the variation was found to correlate with the electrochemical characteristic of ligand molecules, whereas in others it was disclosed as a prerequisite for the biochemical function of the protein. To achieve binding, proteins were observed to engage in subtle balancing acts between electrostatic and hydrophobic interactions to generate stabilizing free energies of binding. For the presented analysis, a new method for scoring hydrophobicity from molecular environments was developed showing high correlations with experimental determined desolvation energies. The presented results highlight the complexities of molecular recognition and underline the challenges of computational structural biology in developing methods to detect these important subtleties. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Turning the growth hormone receptor on: Evidence that hormone binding induces subunit rotation
Authors: Poger David , Mark Alan E.
Published: October 2009

Atomistic molecular dynamics simulations have been used to investigate the conformational changes associated with the binding of human growth hormone (hGH) to the extracellular domains (ECD) of the human growth hormone receptor (hGHR), thereby shedding light on the mechanism of activation. It is shown that the removal of hGH from the hormone‐bound receptor complex results in a counter‐clockwise rotation of the twosubunits relative to each other by 30°–64° (average 45° ± 14°), in close agreement in terms of both the magnitude and direction of the rotation with that proposed based on mutagenesis experiments. In addition to providing evidence to support a rotational activation mechanism, the simulations have enabled the nature of the interaction interfaces in both the cytokine‐bound and unliganded hGHR states to be analyzed in detail. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Pressure perturbation calorimetry of apolipoproteins in solution and in model lipoproteins
Authors: Benjwal Sangeeta , Gursky Olga
Published: October 2009

High‐density lipoproteins (HDLs) are complexes of lipids and proteins (termed apolipoproteins) that remove cell cholesterol and protect from atherosclerosis. Apolipoproteins contain amphipathic α‐helices that have high content (≥1/3) and distinct distribution of charged and apolar residues, adopt molten globule‐like conformations in solution, and bind to lipid surfaces. We report the first pressure perturbation calorimetry (PPC) study of apolipoproteins. In solution, the main HDL protein, apoA‐I, shows relatively large volume contraction, ΔVunf = −0.33%, and an apparent reduction in thermal expansivity upon unfolding, Δαunf ≤ 0, which has not been observed in other proteins. We propose that these values are dominated by increased charged residue hydration upon α‐helical unfolding, which may result from disruption of multiple salt bridges. At 5°C, apoA‐I shows large thermal expansion coefficient, α(5°) = 15·10−4 K−1, that rapidly declines upon heating from 5 to 40°C, α(40°) − α(5°) = −4·10−4 K−1; apolipoprotein C‐I shows similar values of α(5°) and α(40°). These values are larger than in globular proteins. They indicate dominant effect of charged residue hydration, which may modulate functional apolipoprotein interactions with a broad range of their protein and lipid ligands. The first PPC analysis of a protein–lipid complex is reported, which focuses on the chain melting transition in model HDL containing apoA‐I or apoC‐I, dimyristoyl phosphatidylcholine, and 0–20% cholesterol. The results may provide new insights into volumetric properties of HDL that modulate metabolic lipoprotein remodeling during cholesterol transport. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Is Asp‐His‐Ser/Thr‐Trp tetrad hydrogen‐bond network important to WD40‐repeat proteins: A statistical and theoretical study
Authors: Wu Xian‐Hui , Zhang Hui , Wu Yun‐Dong
Published: October 2009

WD40‐repeat proteins are abundant and play important roles in forming protein complexes. The domain usually has seven WD40 repeats, which folds into a seven β‐sheet propeller with each β‐sheet in a four‐strand structure. An analysis of 20 available WD40‐repeat proteins in Protein Data Bank reveals that each protein has at least one Asp‐His‐Ser/Thr‐Trp (D‐H‐S/T‐W) hydrogen‐bonded tetrad, and some proteins have up to six or seven such tetrads. The relative positions of the four residues in the tetrads are also found to be conserved. A sequence alignment analysis of 560 WD40‐repeat protein sequences in human reveals very similar features, indicating that such tetrad may be a general feature of WD40‐repeat proteins. We carried out density functional theory and found that these tetrads can lead to significant stabilization including hydrogen‐bonding cooperativity. The hydrogen bond involving Trp is significant. These results lead us to propose that the tetrads may be critical to the stability and the mechanism of folding of these proteins. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Detection of multiscale pockets on protein surfaces using mathematical morphology
Authors: Kawabata Takeshi
Published: October 2009

Detection of pockets on protein surfaces is an important step toward finding the binding sites of small molecules. In a previous study, we defined a pocket as a space into which a small spherical probe can enter, but a large probe cannot. The radius of the large probes corresponds to the shallowness of pockets. We showed that each type of binding molecule has a characteristic shallowness distribution. In this study, we introduced fundamental changes to our previous algorithm by using a 3D grid representation of proteins and probes, and the theory of mathematical morphology. We invented an efficient algorithm for calculating deep and shallow pockets (multiscale pockets) simultaneously, using several different sizes of spherical probes (multiscale probes). We implemented our algorithm as a new program, ghecom (grid‐based HECOMi finder). The statistics of calculated pockets for the structural dataset showed that our program had a higher performance of detecting binding pockets, than four other popular pocket‐finding programs proposed previously. The ghecom also calculates the shallowness of binding ligands, Rinaccess (minimum radius of inaccessible spherical probes) that can be obtained from the multiscale molecular volume. We showed that each part of the binding molecule had a bias toward a specific range of shallowness. These findings will be useful for predicting the types of molecules that will be most likely to bind putative binding pockets, as well as the configurations of binding molecules. The program ghecom is available through the Web server (http://biunit.naist.jp/ghecom). Proteins 2010. © 2009 Wiley‐Liss, Inc.
Symmetry‐based analysis of the electron–phonon interaction in graphene
Authors: Milošević I. , Kepčija N. , Dobardžić E. , Mohr M. , Maultzsch J. , Thomsen C. , Damnjanović M.
Published: October 2009

Symmetry‐based analysis of the electron–phonon interaction in graphene is performed. Some nontrivial physical properties of graphene are shown to be direct consequence of symmetry, independent on the applied dynamical model. Namely, it is found that there are vibronically uncoupled non symmetric modes which thus might be responsible for the stability of the honeycomb lattice. Symmetry also predicts vanishing of the electron–phonon interaction for quite a number of the normal displacements. Consequently, lattice dynamics along these degrees of freedom is governed by the ion repulsion which leads to the anharmonic terms, being linear in absolute elongation. In particular, this effect is attributed to the K and Γ points of the Brillouin zone, giving insight into origin of the Kohn anomaly. The results are further numerically confirmed within full and tight‐binding density functional calculations and force constants model.
AFM induced electrostatic charging of nanocrystalline diamond on silicon
Authors: Verveniotis E. , Čermák J. , Kromka A. , Rezek B.
Published: October 2009

A nanocrystalline diamond (NCD) thin film (80 nm) is deposited on a p‐type Si substrate and oxygen terminated by r.f. oxygen plasma. An atomic force microscope (AFM) is used to induce electrostatically charged micrometer‐sized areas on the diamond film by applying a bias voltage on the AFM tip during contact mode scan. Trapped charge is detected by Kelvin force microscopy showing a potential difference of up to 1.4 V. The potential amplitude and spatial distribution are controlled by the bias voltage applied on the tip (±30 V) and scan speed (2–20 µm/s). Contribution of diamond bulk and grain boundaries to the charging effects shows no significant variations. We compare the results with the charging of bare Si substrate.
Donor–acceptor nanocomposite structures for organic photovoltaic applications
Authors: Fostiropoulos Konstantinos , Schindler Wolfram
Published: October 2009

We investigated the effect of substrate temperature TS on the growth of 80 nm donor–acceptor nanocomposite (DAN) layers consisting of co‐evaporated Zn‐phthalocyanine (ZnPc) and C60 as absorber materials in organic solar cells. High temperature devices show lower series resistances RS but also reduced VOC. Both effects are diminished when the upper 20 nm of the blend are deposited at room temperature (RT). Moreover, the temperature profile improves the photocurrent density JSC. Best efficiencies (up to 2.1%) were achieved applying a 90 °C/RT profile. Transmission electron microscopy studies on the corresponding DAN revealed the temperature‐dependent formation of crystalline C60 phases (already at low TS) and crystalline ZnPc phases (at highest TS). The strong phase separation at 90 °C results in less compact and mechanical unstable films. Such devices exhibit low parallel resistance RP. When the cold cover layer is applied RP doubles.
Mass separation of metallic and semiconducting single‐wall carbon nanotubes using agarose gel
Authors: Tanaka Takeshi , Jin Hehua , Miyata Yasumitsu , Fujii Shunjiro , Nishide Daisuke , Kataura Hiromichi
Published: October 2009

Metallic and semiconducting single‐wall carbon nanotubes (SWCNTs) were separated using agarose gel. When the SWCNTs isolated with sodium dodecyl sulfate (SDS) were embedded in agarose gel, the metallic SWCNTs were eluted from the gel by applying electronic field or mechanical stress, for example, centrifugation etc., and semiconducting SWCNTs remained in the gel. The purities for metallic and semiconducting SWCNTs were ∼70% and ∼95%, respectively. One of the simplest methods was freeze, thaw and squeeze the SWCNTs containing gel. These methods can separate various kinds of SWCNTs. By using centrifugation method, we could separate about 10 mg of SWCNTs with a 500 ml bottle.
Atoms, elements, molecules, and matter: An investigation into the congenitally blind adolescents' conceptual frameworks on the nature of matter
Authors: Smothers Sinikka M. , Goldston M. Jenice
Published: October 2009

This qualitative multiple case study explored the conceptual frameworks of two congenitally blind male adolescents on the nature of matter. We examined participants' responses on four tactile investigations focused on concepts and processes associated with matter changes. The matter changes investigated were dissolution, chemical change, expansion, and condensation. Individual interview and model‐making sessions comprised the primary data collection, whereas journal writing and focus group interviews provided additional, secondary data. Participants' responses during matter activities were analyzed by using three data frames: structural views of matter, types of understanding of matter changes, and conceptual consistency of students' explanatory schemes. Coding of the responses identified macro‐ (physically observable) and microparticulate (invisible) views of matter and both scientifically accurate and alternate understandings of matter changes coexisting within one response set. Data analysis led to the development of individual meandering mind maps as an analytical tool that illustrates the shifting of each participant's thinking between the macro‐ and microparticulate views of matter. A meandering mind map utilized in the study consists of a macroparticulate outer layer, microparticulate inner layer, and an interface layer that includes lynchpin concepts compound, molecule, atom, and element. The lynchpin concepts are perceived to mediate and scaffold cognitive shifts between the macroparticulate and the microparticulate views of matter. During individual interviews, each participant's responses were coded to one of the three categories, plotted in clockwise sequence and connected with a line. The findings include that congenitally blind participants hold (a) both macro‐ and microparticulate views of the nature of matter, (b) scientifically accepted and scientifically alternative understandings about matter concepts, and (c) conceptually inconsistent explanatory schemes of matter across the four data collection activities. © 2009 Wiley Periodicals, Inc. Sci Ed 94:448–477, 2010
Generation of Human-Induced Pluripotent Stem Cells in the Absence of Exogenous Sox2
Authors: Li Wenlin , Zhou HongYan , Abujarour Ramzey , Zhu Saiyong , Young Joo Jin , Lin Tongxiang , Hao Ergeng , Schöler Hans R. , Hayek Alberto , Ding Sheng
Published: October 2009

Induced pluripotent stem cell technology has attracted enormous interest for potential application in regenerative medicine. Here, we report that a specific glycogen synthase kinase 3 (GSK-3) inhibitor, CHIR99021, can induce the reprogramming of mouse embryonic fibroblasts transduced by only two factors, Oct4 and Klf4. When combined with Parnate (also named tranylcypromine), an inhibitor of lysine-specific demethylase 1, CHIR99021 can cause the reprogramming of human primary keratinocyte transduced with the two factors, Oct4 and Klf4. To our knowledge, this is the first time that human iPS cells have been generated from somatic cells without exogenous Sox2 expression. Our studies suggest that the GSK-3 inhibitor might have a general application to replace transcription factors in both mouse and human reprogramming.

Disclosure of potential conflicts of interest is found at the end of this article.
Requirement of α4β1 and α5β1 Integrin Expression in Bone-Marrow-Derived Progenitor Cells in Preventing Endotoxin-Induced Lung Vascular Injury and Edema in Mice
Authors: Wary Kishore K. , Vogel Stephen M. , Garrean Sean , Zhao Yidan D. , Malik Asrar B.
Published: October 2009

The goal of this study was to determine the role of integrin-mediated adhesion of bone-marrow-derived progenitor cells (BMPCs) as a requirement for the endothelial barrier protection in a lung injury model. C57BL mice were used as the source for BMPCs, which were characterized as CD34+ and fetal liver kinase-1 (Flk1)+ and also an expression of a repertoire of integrins. We used a mouse model of bacterial lipopolysaccharide (LPS)-induced lung vascular injury and edema formation to test the effects of BMPC integrin expression in preventing endothelial barrier injury. Adhesion of BMPCs to purified extracellular matrix proteins induced focal adhesion kinase (Fak) phosphorylation and formation of branching point structures in a α4 and α5 integrin-dependent manner. BMPCs expressing red fluorescent protein (RFP) were administered via the retro-orbital venous route in mice treated intraperitonially with LPS (7.5 mg/kg body weight). We observed increased retention of RFP-labeled Flk1+ and CD34+ BMPCs for up to 8 weeks in mice injured with LPS. BMPC transplantation increased survival by 50% (at 72–96 hours after LPS) and reduced lung vascular injury and extravascular water content induced by LPS. However, blocking with anti-α4 or anti-α5 integrin antibody or shRNA-mediated silencing of α4 or α5 integrins in donor BMPCs failed to prevent the vascular injury or edema formation and mortality. Thus, α4 and α5 integrin-dependent adhesion of BMPCs in lung tissue plays a critical role in preventing lung vascular injury and increasing survival in a mouse model of LPS-induced acute lung injury.

Disclosure of potential conflicts of interest is found at the end of this article.
Performance‐based plastic design (PBPD) method for earthquake‐resistant structures: an overview
Authors: Goel Subhash C. , Liao Wen‐Cheng , Reza Bayat M. , Chao Shih‐Ho
Published: October 2009

This paper presents a brief overview of performance‐based plastic design method as applied to the seismic design of building structures. The method uses pre‐selected target drift and yield mechanisms as key performance criteria. The design base shear for a selected hazard level is calculated by equating the work needed to push the structure monotonically up to the target drift to that required by an equivalent single degree of freedom to achieve the same state. Plastic design is performed to detail the frame members and connections in order to achieve the targeted yield mechanism and behaviour. The method has been successfully applied to a variety of common steel framing systems and, more recently, to Reinforced Concrete (RC) moment frames. Results of extensive inelastic static and dynamic analyses showed that the frames developed desired strong column‐sway mechanisms, and the storey drifts and ductility demands were well within the target values, thus meeting the desired performance objectives. The examples of 20‐storey steel and RC moment frames, as presented in the paper, showed that the method is especially advantageous for tall frames, where cumbersome and lengthy iterative design work in current practice can be completely eliminated, while leading to excellent performance as targeted. The basic work‐energy equation can also be used for seismic evaluation of existing structures. The results, as presented in this paper, showed excellent agreement with those obtained from more elaborate inelastic time‐history analyses. Copyright © 2009 John Wiley & Sons, Ltd.