bluuebunny/crossref_metadata_2025 huggingface dataset:
Kinetic Modeling of the Molecular Architecture of Cross‐Linked Copolymers Synthesized by Controlled Radical Polymerization Techniques
Authors: Gonçalves Miguel AD. , Trigo Ivone MR. , Dias Rolando CS. , Costa Mário Rui PFN.
Published: June 2010

A recently developed general kinetic approach, based on population balances in terms of generating functions, is applied to the modeling of the molecular architecture of branched copolymers produced through controlled radical polymerization (CRP) techniques, namely nitroxide‐mediated radical polymerization (NMRP) and atom‐transfer radical polymerization (ATRP). Thanks to this method, it is possible to carry out dynamic predictions of distributions of molecular weights, sequence lengths and z‐average mean square radius of gyration of the products, both before and after gelation (whenever it occurs) with consideration of complex kinetic schemes. The model chemical systems styrene + divinylbenzene (S/DVB) and methyl methacrylate + ethylene glycol dimethacrylate (MMA/EGDMA) are experimentally investigated in order to assess the prediction capabilities of the aforementioned approach. Measurements of absolute molecular weights and z‐average radius of gyration of the copolymers are performed for different times of polymerization using a SEC system with a refractive index detector coupled with MALLS. It is shown that the proposed computational tool can enhance the possibility of better design of these complex materials but additional studies concerning the impact of intramolecular cyclizations on the structure of materials synthesized at diluted conditions are needed.
Forced Gelation in an Off‐Stoichiometric Copolymerization of A2 and B3 Monomers
Authors: Lechowicz Jaromir B. , Galina Henryk
Published: June 2010

A step‐growth alternating copolymerization of monomers A2 and B3 was studied by an off‐lattice Monte‐Carlo simulation. In the random systems, i.e. with no substitution effect, the polymerization leads to gel formation provided the molar ratio of monomers is not very far from the stoichiometric one (A2: B3 ≈ 3: 2) and the reaction is carried out in one batch. A substantial deviation from the stoichiometric ratio may halt gelation altogether, even at conversions of the minority functional groups approaching unity. We demonstrate that in these non‐gelling off‐stoichiometric systems, one can force the system to gel, after all, without altering the kinetics or diffusion parameters of the reaction. The clue is to carry out the reaction in steps.
Bioapplications of Networks Based on Photo‐Cross‐Linked Hyperbranched Polymers
Authors: Pedrón Sara , Anseth Kristi , Benton Julie A. , Bosch Paula , Peinado Carmen
Published: June 2010

This article deals with some of the most recent developments in the use of hyperbranched polymers in biomedical applications. Some examples have been selected to show their potential in drug delivery, tissue engineering, imaging technologies and molecular imprinting. Moreover, the preparation of methacrylic networks using chemically‐modified hyperbranched polymers as multifunctional macromonomers by photopolymerization is described. The capability to support valve interstitial cell culture was demonstrated and the adhesion and functionality of the cells was related to the mechanical properties of these materials.
Cell Adhesion to Polymethacrylate Networks Prepared by Photopolymerization and Functionalized with GRGDS Peptide or Fibrinogen
Authors: Johnson C. , Perlin L. , Wyman P. , Zhao B. , Fullwood N. J. , MacNeil S. , Rimmer S.
Published: June 2010

Polymethacrylate hydrogels are useful scaffolds for tissue engineering and cell‐based therapies provided they can be modified to give good cell adhesion characteristics. They have advantages over non‐swollen materials, such as good diffusion properties, tunable moduli and porosities. However, conventional non‐charged hydrogels are essentially non‐adhesive for cells and they are poor substrates for cell culture. In a previous volume in this series of symposia from the Polymer Networks Group, we described how both amphiphilic conetworks and alkyl‐aminated hydrogels were excellent substrates for cell culture.1 In this article we report our most recent work on understanding how to modify hydrogels for cell attachment. We report how the choice of photoinitiator affects the viability of human dermal fibroblasts (HDFs). Next, we provide further results involving the use of an enzyme deprotection strategy that can be carried out after copolymerization of a GRGDS methacrylate monomer. We show that the peptide enhanced the culture of HDFs in serum when the peptide was attached to poly(1,2‐propane diol methacrylate‐co‐ethane diol dimethacrylate). On the other hand, poly(n‐butyl methacrylate‐co‐ethane diol dimethacrylate) networks adsorb larger amounts of protein non‐specifically, and they are reasonable substrates for adhesion of HDFs without peptide modification. Attachment of GRGDS to an example of these networks did not increase the attachment and proliferation of HDFs in serum containing media. We also describe the attachment of fibrinogen/fibrin coatings by the transglutaminase mediated reaction of alkyl amines attached to a poly(1,2‐propane diol methacrylate‐co‐ethane diol dimethacrylate‐co‐dodecyl methacrylate) network. This work illustrates the reactivity of alkyl‐aminated hydrogels in transglutaminase catalyzed reactions, although the addition of the fibrin coating did not improve the performance of the material for cell culture which was already good on these hydrogels.
Alginate Oligoguluronates as a Tool for Tailoring Properties of Ca‐Alginate Gels
Authors: Sletmoen Marit , Draget Kurt I. , Stokke Bjørn T.
Published: June 2010

Alginates represent a family of structural polysaccharides derived from either seaweeds or bacteria. They readily form ionotropically‐induced physcial gels in aqueous solution in the presence of multivalent ions. In this study, the homogeneous release of Ca2+ from Ca‐ethylene glycol tetraacetic acid (Ca‐EGTA) within an alginate solution is utilized to prepare homogeneous gelation conditions. The pH‐dependence of the multiple equilibria involved, i.e. between Ca2+, the various states of EGTA, the alginate and its protonation and ion binding, is modeled and used as a basis for designing the glucono‐δ‐lactone concentration to reduce the pH. This method is used for the perturbation of the Ca‐induced gelation of alginates in the presence of oligoguluronate oligomers. These oligoguluronate oligomers are able to be involved in the binding of Ca2+, but sufficiently short not to mediate connectivity through their chains. The results indicate that the oligoguluronate oligomers perturb the gelation of alginate differently in the Ca2+‐limited and non‐Ca2+‐limited regimes. In the calcium limited regime, the oligoguluronate oligomers appear to sequester calcium either by binding to oligoguluronate sequences of the network, or between the free oligoguluronates, yielding an overall net effect of reduced gel strength. In the non‐Ca2+ limited regime, the experimental data shows increased gel strength in the presence of oligoguluronate blocks. These results show that oligoguluronates can be used as modulators of gelation kinetics as well as local network structure formation and equilibrium properties in alginate gels.
Effect of interface properties on the effective properties of biopolymer composite materials
Authors: Rjafiallah S. , Benseddiq N. , Guessasma S.
Published: June 2010

Weak adhesion between constituents in starch‐zein composites has been proven using nanoindentation experiments. In order to quantify the effect of imperfect interface on the elastic properties of the composite, a Finite Element (FE) model is presented. Starting from the generation of typical 2D microstructures representing the result of a thermomoulding process, circular zein particles are embedded in a starch matrix. Particles are allowed to overlap in order to represent flowability of the filler into the matrix. Zein fraction in the composite is varied in the full range (0–100%). The generated microstructures are converted into a finite element model, where the influence of the interface is modelled thanks to a cohesive zone model. The predicted results show that Young's modulus of the composite is significantly affected by the spatial distribution of the interfaces. When the phase ratio is small enough, the interface effect is localized around filler clusters. Increasing further more the phase ratio leads to a percolation of the interface. In particular, interface percolation perpendicular to the loading direction predicts the lowest modulus. When the filler phase becomes predominant, the interface effect weakens. Based on the former discussion, an effective law is suggested using a simple non‐linear function between the effective modulus and the phase ratio.
A lattice Monte Carlo analysis on thermal diffusion in syntactic hollow‐sphere structures
Authors: Farnsworth J. , Murch G. E. , Belova I. V. , Öchsner A. , Fiedler T.
Published: June 2010

The Lattice Monte Carlo method [1] is a computationally intensive approach towards the study of thermal material properties. The Lattice Monte Carlo method has previously been used in the area of mass diffusion, and has more recently been applied towards the analysis of thermal diffusion in materials. Whilst previous studies have focused on two‐phase material consisting of component material and pore geometry only, this study applies the Lattice Monte Carlo method towards the investigation of three‐phase Metallic Hollow Sphere Structures (MHSS). MHSS consist of high‐conducting metallic shells, low‐conducting adhesive and non‐conducting pores. In the present study, three‐dimensional computerised models of the MHSS are built up from analysis of computed tomography (CT) scans. The results of this numerical analysis indicate a spatial variation of the thermal conductivity. However, MHSS can be considered as being isotropic to a good approximation.

Die ‘Lattice Monte Carlo’ Methode [1] ist ein rechenintensiver Ansatz zur Bestimmung thermischer Materialeigenschaften. Die ‘Lattice Monte Carlo’ Methode hat sich für die Simulation der Diffusion in Festkörpern etabliert und wird seit kurzem auch für die Analyse thermischer Diffusion in Werkstoffen eingesetzt. Vorhergehende Studien konzentrierten sich auf Zwei‐Phasen‐Materialien bestehend aus Grundmaterial und Pooren. Die jetzige Analyse nutzt die ‘Lattice Monte Carlo’ Methode für die Untersuchung drei‐phasiger metallischer Hohlkugelstrukturen (abgekürzt aus dem Englischen ‘Metallic Hollow Sphere Structures’ als MHSS). MHSS bestehen aus hoch‐leitfähigen metallischen Schalen, thermisch‐isolierenden Kunststoff und nicht‐leitfähigen Poren. Drei‐dimensionale Rechenmodelle wurden in der vorliegenden Studie von computer‐tomographischen Daten abgeleitet. Die Ergebnisse der numerischen Analyse deuten eine räumliche Streuung der thermsichen Leitfähigkeit an. Die lokalen thermischen Leitfähigkeiten sind jedoch isotrop.
Static and fatigue behaviour of room temperature vulcanising silicone adhesives for high temperature aerospace applications
Authors: Banea M. D. , da Silva L. F. M.
Published: June 2010

This paper focuses on the mechanical properties of room temperature vulcanising (RTV) silicone adhesives for aerospace applications. In view of the very limited amount of published data on this subject, we analyzed the performances of two RTV silicone rubber adhesives through adhesive joint tests. The standard Thick Adherend Shear Test (TAST) was performed in order to measure the shear properties of the adhesives. Single lap joints (SLJs) were fabricated and tested to assess the adhesive performance in a joint. The influence of temperature on the lap‐shear strength of the adhesives was investigated. It is shown that the lap‐shear strength of both adhesives decreased with increasing of temperature. The effect of bondline thickness and overlap length on the lap‐shear strength of the adhesives was also studied. The reduction of failure load with an increase of the bondline thickness is a very common situation when dealing with structural adhesives. However, for the tested RTV silicone adhesives the failure loads increased as the bondline was made thicker. Also, the failure loads of RTV silicone adhesive joints increased almost proportionally with increasing the overlap length. Fatigue tests were also performed and show a low dispersion of the results.
Optimal design of rear chassis components for lightweight automobile using design of experiment
Authors: Park J.‐H. , Kim S.‐K. , Choi B.‐I. , Lee H.‐J. , Lee Y.‐H. , Kim J.‐S. , Kim K.‐J.
Published: June 2010

With growing public concerns on the rising price of fossil fuel and the greenhouse gas emissions, the automotive industry is once again faced with the increased demand to develop more fuel‐efficient vehicles. Savings in weight using lightweight materials such as aluminum can lead to increased fuel economy and reduction in pollution. Aluminum material has a weak point compared to the steel material in strength for life cycle. In this study, to design a lighter and more reliable chassis component using aluminum material as compared with existing steel chassis components, a new link shape was suggested by adding vertical ribs to an existing I‐beam type link and to investigate how each design parameter makes an effect on the reliability and component weight. The design of experiment (DOE) was performed with six design parameters and two levels. Through the analysis of variance, three parameters which were the most influential on weight were selected. And then the response surface analysis was performed with two levels to find out the optimal dimensions. The weight of the aluminum link was 64% that of the steel link. The stiffness of the optimized aluminum link under all loads was more than 100% that of the steel link. The maximum von Mises stresses of the optimized aluminum link under all loads was equal or less than 20% of the ultimate tensile strength (58 MPa).
Transcriptomic analysis of tubular carcinomas of the breast reveals similarities and differences with molecular subtype‐matched ductal and lobular carcinomas
Authors: Lopez‐Garcia Maria A , Geyer Felipe C , Natrajan Rachael , Kreike Bas , Mackay Alan , Grigoriadis Anita , Reis‐Filho Jorge S , Weigelt Britta
Published: June 2010

Tubular carcinoma (TC) is an uncommon special type of breast cancer characterized by an indolent clinical course. Although described as part of a spectrum of related lesions named ‘low‐grade breast neoplasia family’ due to immunophenotypical and genetic similarities, TCs, low‐grade invasive ductal carcinomas of no special type (IDC‐NSTs), and classic invasive lobular carcinomas (ILCs) significantly differ in terms of histological features and clinical outcome. The aim of this study was to investigate whether pure TCs constitute an entity distinct from low‐grade IDC‐NSTs and from classic ILCs. To define the transcriptomic differences between TCs and IDC‐NSTs and ILCs whilst minimizing the impact of histological grade and molecular subtype on their profiles, we subjected a series of grade‐ and molecular subtype‐matched TCs and IDC‐NSTs and molecular subtype‐matched TCs and classic ILCs to genome‐wide gene expression profiling using oligonucleotide microarrays. Unsupervised and supervised analysis revealed that TCs are similar at the transcriptomic level to grade‐ and molecular subtype‐matched IDC‐NSTs. However, subtle yet significant differences were detected and validated by quantitative reverse transcriptase‐PCR, which may in part explain the reported more favourable outcome of TCs. Transcriptomic differences between TCs and molecular subtype‐matched classic ILCs were more overt, predominantly due to lower expression of proliferation and cell cycle genes in TCs and down‐regulation of cell adhesion/extracellular matrix‐related genes in classic ILCs. Our results support the existence of a ‘low‐grade breast neoplasia family’; however, the transcriptomes of these lesions display small, yet important differences, which, together with their distinct biological behaviour, warrant their separation as discrete entities. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
The biological and clinical value of p53 expression in pelvic high‐grade serous carcinomas
Authors: Köbel Martin , Reuss Alexander , Bois Andreas du , Kommoss Stefan , Kommoss Friedrich , Gao Dongxia , Kalloger Steve E , Huntsman David G , Gilks C Blake
Published: June 2010

Studies on the p53 expression and outcome for women with ovarian carcinoma have produced conflicting results. The observed heterogeneity may be due to the range of cut‐offs used to define overexpression and the mix of histotypes of the study cohorts. We aimed to examine the association between p53 expression and biological properties of tumours as well as outcome in 502 pelvic high‐grade serous carcinomas (HGSCs) derived from two population‐based cohorts from British Columbia representing cases with or without residual tumour after initial surgery, respectively, and one clinical trial cohort from Germany (AGO‐OVAR‐3). p53 expression was assessed on tissue microarrays by immunohistochemistry using the DO‐7 antibody. p53 expression was scored in three tiers as complete loss of expression, focal expression or overexpression (defined as more than 50% positive tumour cell nuclei) and correlated with survival using multivariate Cox regression models. p53 was completely absent in 30.3%, focally expressed in 12.0%, and overexpressed in 57.7% of HGSCs, which was an inverse pattern compared to clear cell and endometrioid types of ovarian carcinomas, where 76% and 69% of cases showed focal expression, respectively (p < 0.001, chi square test). Pelvic HGSCs show either complete absence of p53 expression or p53 overexpression in 88% of cases; thus, aberrant p53 expression is a ubiquitous feature of HGSCs. HGSCs with p53 overexpression were associated with a reduced risk of recurrence compared to cases with complete absence of p53 in the British Columbia cohort with residual tumour (HR = 0.71, 95% CI 0.51–0.99) and for a combination of all three cohorts (HR = 0.70, 95% CI 0.55–0.89) in multivariate analysis including age, stage, residual tumour, and stratification by cohort. The association of complete absence of p53 expression with unfavourable outcome suggests functional differences of TP53 mutations underlying overexpression, compared to those underlying complete absence of expression. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
How do executive functions fit with the Cattell–Horn–Carroll model? Some evidence from a joint factor analysis of the Delis–Kaplan Executive Function System and the Woodcock–Johnson III tests of cognitive abilities
Authors: Floyd Randy G. , Bergeron Renee , Hamilton Gloria , Parra Gilbert R.
Published: June 2010

This study investigated the relations among executive functions and cognitive abilities through a joint exploratory factor analysis and joint confirmatory factor analysis of 25 test scores from the Delis–Kaplan Executive Function System and the Woodcock–Johnson III Tests of Cognitive Abilities. Participants were 100 children and adolescents recruited from general education classrooms. Principal axis factoring followed by an oblique rotation yielded a six‐factor solution. The Schmid–Leiman transformation was then used to examine the relations between specific cognitive ability factors and a general factor. A variety of hypothesis‐driven models were also tested using confirmatory factor analysis. Results indicated that all tests measure the general factor, and 24 tests measure at least one of five broad cognitive ability factors outlined by the Cattell–Horn–Carroll theory of cognitive abilities. These results, with limitations considered, add to the body of evidence supporting the confluence of measures of executive functions and measures of cognitive abilities derived from individual testing. © 2010 Wiley Periodicals, Inc.
Thermal state of permafrost in Russia
Authors: Romanovsky V. E. , Drozdov D. S. , Oberman N. G. , Malkova G. V. , Kholodov A. L. , Marchenko S. S. , Moskalenko N. G. , Sergeev D. O. , Ukraintseva N. G. , Abramov A. A. , Gilichinsky D. A. , Vasiliev A. A.
Published: June 2010

The results of the International Permafrost Association's International Polar Year Thermal State of Permafrost (TSP) project are presented based on field measurements from Russia during the IPY years (2007–09) and collected historical data. Most ground temperatures measured in existing and new boreholes show a substantial warming during the last 20 to 30 years. The magnitude of the warming varied with location, but was typically from 0.5°C to 2°C at the depth of zero annual amplitude. Thawing of Little Ice Age permafrost is ongoing at many locations. There are some indications that the late Holocene permafrost has begun to thaw at some undisturbed locations in northeastern Europe and northwest Siberia. Thawing of permafrost is most noticeable within the discontinuous permafrost domain. However, permafrost in Russia is also starting to thaw at some limited locations in the continuous permafrost zone. As a result, a northward displacement of the boundary between continuous and discontinuous permafrost zones was observed. This data set will serve as a baseline against which to measure changes of near‐surface permafrost temperatures and permafrost boundaries, to validate climate model scenarios, and for temperature reanalysis. Copyright © 2010 John Wiley & Sons, Ltd.
Potential remobilization of belowground permafrost carbon under future global warming
Authors: Kuhry P. , Dorrepaal E. , Hugelius G. , Schuur E. A. G. , Tarnocai C.
Published: June 2010

Research on permafrost carbon has dramatically increased in the past few years. A new estimate of 1672 Pg C of belowground organic carbon in the northern circumpolar permafrost region more than doubles the previous value and highlights the potential role of permafrost carbon in the Earth System. Uncertainties in this new estimate remain due to relatively few available pedon data for certain geographic sectors and the deeper cryoturbated soil horizons, and the large polygon size in the soil maps used for upscaling. The large permafrost carbon pool is not equally distributed across the landscape: peat deposits, cryoturbated soils and the loess‐like deposits of the yedoma complex contain disproportionately large amounts of soil organic matter, often exhibiting a low degree of decomposition. Recent findings in Alaska and northern Sweden provide strong evidence that the deeper soil carbon in permafrost terrain is starting to be released, supporting previous reports from Siberia. The permafrost carbon pool is not yet fully integrated in climate and ecosystem models and an important objective should be to define typical pedons appropriate for model setups. The thawing permafrost carbon feedback needs to be included in model projections of future climate change. Copyright © 2010 John Wiley & Sons, Ltd.
The thermal state of permafrost in the nordic area during the international polar year 2007–2009
Authors: Christiansen H. H. , Etzelmüller B. , Isaksen K. , Juliussen H. , Farbrot H. , Humlum O. , Johansson M. , Ingeman‐Nielsen T. , Kristensen L. , Hjort J. , Holmlund P. , Sannel A. B. K. , Sigsgaard C. , Åkerman H. J. , Foged N. , Blikra L. H. , Pernosky M. A. , Ødegård R. S.
Published: June 2010

This paper provides a snapshot of the permafrost thermal state in the Nordic area obtained during the International Polar Year (IPY) 2007–2009. Several intensive research campaigns were undertaken within a variety of projects in the Nordic countries to obtain this snapshot. We demonstrate for Scandinavia that both lowland permafrost in palsas and peat plateaus, and large areas of permafrost in the mountains are at temperatures close to 0°C, which makes them sensitive to climatic changes. In Svalbard and northeast Greenland, and also in the highest parts of the mountains in the rest of the Nordic area, the permafrost is somewhat colder, but still only a few degrees below the freezing point. The observations presented from the network of boreholes, more than half of which were established during the IPY, provide an important baseline to assess how future predicted climatic changes may affect the permafrost thermal state in the Nordic area. Time series of active‐layer thickness and permafrost temperature conditions in the Nordic area, which are generally only 10 years in length, show generally increasing active‐layer depths and rising permafrost temperatures. Copyright © 2010 John Wiley & Sons, Ltd.
Permafrost thermal state in the polar Northern Hemisphere during the international polar year 2007–2009: a synthesis
Authors: Romanovsky Vladimir E. , Smith Sharon L. , Christiansen Hanne H.
Published: June 2010

The permafrost monitoring network in the polar regions of the Northern Hemisphere was enhanced during the International Polar Year (IPY), and new information on permafrost thermal state was collected for regions where there was little available. This augmented monitoring network is an important legacy of the IPY, as is the updated baseline of current permafrost conditions against which future changes may be measured. Within the Northern Hemisphere polar region, ground temperatures are currently being measured in about 575 boreholes in North America, the Nordic region and Russia. These show that in the discontinuous permafrost zone, permafrost temperatures fall within a narrow range, with the mean annual ground temperature (MAGT) at most sites being higher than −2°C. A greater range in MAGT is present within the continuous permafrost zone, from above −1°C at some locations to as low as −15°C. The latest results indicate that the permafrost warming which started two to three decades ago has generally continued into the IPY period. Warming rates are much smaller for permafrost already at temperatures close to 0°C compared with colder permafrost, especially for ice‐rich permafrost where latent heat effects dominate the ground thermal regime. Colder permafrost sites are warming more rapidly. This improved knowledge about the permafrost thermal state and its dynamics is important for multidisciplinary polar research, but also for many of the 4 million people living in the Arctic. In particular, this knowledge is required for designing effective adaptation strategies for the local communities under warmer climatic conditions. Copyright © 2010 John Wiley & Sons, Ltd.
Fold homology detection using sequence fragment composition profiles of proteins
Authors: Solis Armando D. , Rackovsky Shalom R.
Published: June 2010

The effectiveness of sequence alignment in detecting structural homology among protein sequences decreases markedly when pairwise sequence identity is low (the so‐called “twilight zone” problem of sequence alignment). Alternative sequence comparison strategies able to detect structural kinship among highly divergent sequences are necessary to address this need. Among them are alignment‐free methods, which use global sequence properties (such as amino acid composition) to identify structural homology in a rapid and straightforward way. We explore the viability of using tetramer sequence fragment composition profiles in finding structural relationships that lie undetected by traditional alignment. We establish a strategy to recast any given protein sequence into a tetramer sequence fragment composition profile, using a series of amino acid clustering steps that have been optimized for mutual information. Our method has the effect of compressing the set of 160,000 unique tetramers (if using the 20‐letter amino acid alphabet) into a more tractable number of reduced tetramers (∼15–30), so that a meaningful tetramer composition profile can be constructed. We test remote homology detection at the topology and fold superfamily levels using a comprehensive set of fold homologs, culled from the CATH database that share low pairwise sequence similarity. Using the receiver‐operating characteristic measure, we demonstrate potentially significant improvement in using information‐optimized reduced tetramer composition, over methods relying only on the raw amino acid composition or on traditional sequence alignment, in homology detection at or below the “twilight zone”. Proteins 2010. © 2010 Wiley‐Liss, Inc.
An integrated suite of fast docking algorithms
Authors: Mashiach Efrat , Schneidman‐Duhovny Dina , Peri Aviyah , Shavit Yoli , Nussinov Ruth , Wolfson Haim J.
Published: June 2010

The CAPRI experiment (Critical Assessment of Predicted Interactions) simulates realistic and diverse docking challenges, each case having specific properties that may be exploited by docking algorithms. Motivated by the different CAPRI challenges, we developed and implemented a comprehensive suite of docking algorithms. These were incorporated into a dynamic docking protocol, consisting of four main stages: (1) Biological and bioinformatics research aiming to predict the binding site residues, to define distance constraints between interface atoms and to analyze the flexibility of molecules; (2) Rigid or flexible docking, performed by the PatchDock or FlexDock method, which utilizes the information gathered in the previous step. Symmetric complexes are predicted by the SymmDock method; (3) Flexible refinement and reranking of the rigid docking solution candidates, performed by FiberDock; and finally, (4) clustering and filtering the results based on energy funnels. We analyzed the performance of our docking protocol on a large benchmark and on recent CAPRI targets. The analysis has demonstrated the importance of biological information gathering prior to docking, which significantly increased the docking success rate, and of the refinement and rescoring stage that significantly improved the ranking of the rigid docking solutions. Our failures were mostly a result of mishandling backbone flexibility, inaccurate homology modeling, or incorrect biological assumptions. Most of the methods are available at http://bioinfo3d.cs.tau.ac.il/. Proteins 2010. © 2010 Wiley‐Liss, Inc.
A review of nanomaterial safety concerns
Authors: Lavoie Joseph H.
Published: June 2010

Nanomaterials are quickly moving from research benches to the manufacturing environment and into product lines. These materials pose unique safety concerns, which should be made clear to both the workers and the consumers who are exposed to them. The following is a summary of documents concerning the dangers posed by a wide variety of nanomaterials as well as references, which may be useful to practicing process engineers and EHS professionals. © 2010 American Institute of Chemical Engineers Process Saf Prog, 2010
ZnO nanoparticles prepared by an electroexploding wire technique
Authors: Singh N. Kamal , Alqudami A. , Annapoorni S.
Published: June 2010

Zinc oxide (ZnO) nanoparticles have been successfully prepared by an electroexploding wire (EEW) technique from pure zinc (Zn). The system comprises of a wire‐plate and a series of 12 V batteries. The formation of ZnO and nature of the crystallinity have been studied using X‐ray diffraction (XRD) and Raman analyses. The polycrystalline nature of the prepared nanoparticles is confirmed from the XRD studies. The time‐dependent UV–Visible absorption and photoluminescence (PL) studies confirm the evolution of ZnO nanoparticles from Zn obtained by the EEW technique. The sizes of the as‐prepared and annealed nanoparticles as estimated using the effective mass theory from the UV–Visible absorption are 8.9 and 22.0 nm, respectively. These are in agreement with those obtained from TEM micrographs. A broad and intense PL emission centered about 508 nm that is in the green region is observed. It is characteristic of the presence of defect energy states due to oxygen deficiency. From the energy‐dependent analysis of the PL emission, the green emission observed is concluded to be due to the bulk contribution rather than surface defects.
Initial rise of transient electroluminescence in doped Alq3 films
Authors: Uddin A. , Lee C. B. , Andersson T. G.
Published: June 2010

The doping effect on initial rise of transient electroluminescence (EL) in organic light emitting diodes (OLEDs) is investigated. The dopants red light emitter 5,6,11,12‐tetraphenylnaphthacene (Rb) and 4‐(diacynomethylene)‐2‐methyl‐6‐(p‐dimethylaminostyryl)‐4H‐pyan (DCM), and yellow light emitter 3‐(2′‐benzothiazolyl)‐7‐diethylaminocoumarin (C‐6) were used in green light emitter tris‐(8‐hydroxyquinoline) aluminum (Alq3) film with various concentrations from 0.5 to 24 wt%. The increase of EL delay time and the slower rise of EL saturation were observed with doping concentrations. The values of EL delay time was found from 0.78 to 1.86 µs in doped OLED compared to 0.74 µs in pure Alq3 device. The EL saturation time was found from 1.2 to 2.8 µs for different doping concentration. We have also estimated the carrier mobility from the transient EL measurements. The charge‐carrier mobility was found as 0.5–1.2 × 10−5 cm2 V−1 s−1 in doped Alq3 films.
Gate voltage and structure parameter modulated spin splitting in AlGaN/GaN quantum wells
Authors: Li M. , Zhang R. , Zhang Z. , Liu B. , Fu Deyi , Zhao C. Z. , Xie Z. L. , Xiu X. Q. , Zheng Y. D.
Published: June 2010

In this paper, considerable magnitude of spin splitting for the conduction subband at the Fermi energy is obtained in AlGaN quantum wells (QWs) grown along the c‐axis. We have analyzed how the magnitude of spin splitting of the first electron subband in AlGaN QWs with different sheet carrier concentration changes as a function of applied gate voltage, well width, and Al content in the barrier. It is also found that the contribution to spin splitting from Dresselhaus term is much larger than that from Rashba term, the contribution of Dresselhaus term to the total spin splitting depends greatly on the carrier concentrations, the change of well width has little effect on total spin splitting, and the magnitude of spin splitting can be greatly modulated by Al content in the barrier, gate voltage, and sheet carrier concentration. The internal polarized electric field is crucial for considerable spin splitting in III‐nitride QWs. Moreover, the magnitude of total spin splitting calculated here is comparable with other theoretical and experimental values observed in III‐nitride heterostructures.
Surface enhanced infrared spectroscopy using gold nanoantennas
Authors: Pucci A. , Neubrech F. , Weber D. , Hong S. , Toury T. , de la Chapelle M. Lamy
Published: June 2010

The sensitivity of infrared (IR) vibration spectroscopy can be enhanced by several orders of magnitude if plasmonic electromagnetic nearfield enhancement is exploited. For maximum enhancement the plasmonic resonance needs to be strong, which cannot be achieved by randomly grown metal island films that on average may show already signal enhancement of the order of 1000. Metal nanowires may give sufficiently strong antenna‐like plasmonic resonances in the IR that can be adjusted to the molecular vibration frequencies of interest via the wire length. With individual gold nanowires we obtained vibration‐signal enhancement up to 500,000 for molecular monolayers adsorbed on gold nanowires. The already obtained enhancement is not a limit. Since antennae coupled via nanogaps should enable strong electromagnetic nearfield enhancement in these gaps, respective arrays would be ideal for surface enhanced IR spectroscopy. First experiments prove the tendency of increasing vibration‐signal enhancement with decreasing gap size.
FP‐LAPW calculations of structural and elastic properties of tantalum under high pressure
Authors: Liu Zhong‐Li , Li Xiao‐Feng , Cai Ling‐Cang , Jing Fu‐Qian
Published: June 2010

We have revisited and refined the high‐pressure elastic properties of body‐centered‐cubic Ta using the accurate all‐electron full potential linearized augmented plane wave method (FP‐LAPW) within the framework of density functional theory (DFT). Based on the total energy calculations, we first deduced the accurate static equation of state (EOS) of Ta. Then we derived the elastic constants, C11, C12, and C44 under pressure up to 500 GPa using the pressure‐correction method which corrected the previous method theoretically, and the calculated elastic constants agree well with experiment under high pressure. From the accurately determined elastic constants, we also discussed the elastic anisotropy and the sound velocities of Ta at high pressure. The predicted Debye temperature at 0 GPa and 0 K is in good agreement with experiment, and the Debye temperature increases monotonously as pressure increases.
Zero temperature coefficient of frequency crystal cuts in monoclinic NdCa4O(BO3)3piezoelectric crystals
Authors: Yu Fapeng , Zhang Shujun , Zhao Xian , Yuan Duorong , Wang Qing‐Ming , Shrout Thomas R.
Published: June 2010

The temperature coefficient of frequency (TCF) was investigated in monoclinic NdCa4O(BO3)3(NdCOB) piezoelectric crystals over the temperature range of –140 °C to 200 °C. A zero TCF characteristic was achieved for the (ZXw) 15° crystal cut, with turnover point at 20 °C. The electromechanical couplingk26and piezoelectric coefficientd26, in shear vibration mode, were determined to be 25% and 13.5 pC/N, respectively. The zero TCF crystal cut, large coupling factor and high piezoelectric coefficient, together with a high mechanical quality factor (Q> 10,000), demonstrate NdCOB crystals promising candidates for bulk acoustic wave resonators over a wide temperature range. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Floodplain management strategies for flood attenuation in the river Po
Authors: Castellarin A. , Di Baldassarre G. , Brath A.
Published: June 2010

This paper analyses the effects of different floodplain management policies on flood hazard using a 350 km reach of the river Po (Italy) as a case study. The river Po is the longest Italian river, and the largest in terms of streamflow. The middle‐lower Po flows East some 350 km in the Pianura Padana (Po Valley), a very important agricultural region and industrial heart of Northern Italy. This portion of the river consists of a main channel (200–500 m wide) and a floodplain (overall width from 200 m to 5 km) confined by two continuous artificial embankments. Floodplains are densely cultivated, and a significant portion of these areas is protected against frequent flooding by a system of minor dykes, which impacts significantly the hydraulic behaviour of the middle‐lower Po during major flood events. This study aims at investigating the effects of the adoption of different floodplain management strategies (e.g. raising, lowering or removing the minor dyke system) on the hydrodynamics of the middle‐lower Po and, in particular, on flood‐risk mitigation. This is a crucial task for institutions and public bodies in charge of formulating robust flood risk management strategies for the river Po. Furthermore, the results of this study are of interest for other European water‐related public bodies managing large river basins, in the light of the recent European Directive 2007/60/EC on the assessment and management of flood risks. The analysis is performed by means of a quasi‐2D hydraulic model, which has been developed on the basis of a laser‐scanning DTM and a large amount of calibration data recorded during the significant flood event of October 2000. Copyright © 2010 John Wiley & Sons, Ltd.
Learning from dam removal monitoring: Challenges to selecting experimental design and establishing significance of outcomes
Authors: Kibler K. M. , Tullos D. D. , Kondolf G. M.
Published: June 2010

As the decommissioning of dams becomes a common restoration technique, decisions about dam removals must be based on sound predictions of expected outcomes. Results of past and ongoing dam removal monitoring are an important source of information that practitioners may utilize to evolve predictive and decision‐making tools, emphasizing the need for thorough and defensible documentation of dam removal outcomes. However, as dam removals challenge many basic assumptions of conventional experimental designs and data analysis techniques, the quality of information available to aid decision‐making may be questionable or misleading.

Nevertheless, some study design principles and analysis procedures may be robust to the challenges presented by dam removal research. To assist managers in undertaking dam removal monitoring, this article discusses the assets and limitations of monitoring and analysis options available for dam removal studies, with emphasis on selecting a rigorous experimental design and determining significance of results.

As the chosen monitoring design will influence the appropriateness of applying standard analytical methods, particularly statistical hypothesis testing, researchers should carefully consider constraints inherent to dam removal studies when designing a monitoring plan and assigning significance to observed changes. Ecological significance is often the most justifiable method for framing significance of dam removal outcomes, though it may be complicated by identification of environmentally significant thresholds. Another alternative is evaluation of the practical significance of results, when observed changes exceed measurement error and background variability. Establishing practical significance may be informative when statistical and ecological significance is inappropriate or impossible to determine. Copyright © 2010 John Wiley & Sons, Ltd.
The impact of dams on flood flows in the United States
Authors: FitzHugh Thomas W. , Vogel Richard M.
Published: June 2010

Natural flood regimes provide a wide array of important ecological functions. Our goal is to assess the hydrologic impact of dams on flood flows throughout the United States. Regional regression models of the median annual 1‐day maximum flow were developed as a function of natural watershed characteristics, dam storage, and population density. Most of the regressions have adjusted R2 values in excess of 0.80, and overall the models covered 78% of the area of the continental U.S. Alteration of flood flows is present in every region of the country, and is more severe west of the Mississippi and especially in the southern Great Plains, desert Southwest, and northern California. The percent of U.S. rivers with greater than a 25% reduction in the median annual flood is 55% for large rivers, 25% for medium rivers, and 10% for small rivers. The majority of freshwater ecoregions in the country have at least 10% of their rivers with 25% or greater alteration in all three river size classes. A simple model based on the ratio of dam storage to mean annual runoff was developed for assessing alteration in ungauged rivers, and was found to be generally useful for classifying rivers into categories of potential alteration. Overall, we document the alteration of natural flood flows across the U.S. in more detail than has been previously accomplished, and demonstrate the efficacy of multivariate regional regression models and other indicators for assessing hydrologic alteration. Copyright © 2010 John Wiley & Sons, Ltd.
Mathematical model to identify nitrogen variability in large rivers
Authors: Ani E.‐C. , Hutchins M. , Kraslawski A. , Agachi P. S.
Published: June 2010

The river Swale in Yorkshire, northern England has been the subject of many studies concerning water quality. This paper builds on existing data resources and previous 1D river water quality modelling applications at daily resolution (using QUESTOR) to provide a different perspective on understanding pollution, through simulation of the short‐term dynamics of nutrient transport along the river. The two main objectives are (1) building, calibration and evaluation of a detailed mathematical model (Advection‐Dispersion Model: ADModel), for nutrient transport under unsteady flow conditions and (2) the development of methods for estimating key parameters characterizing pollutant transport (velocity, dispersion coefficient and transformation rates) as functions of hydrological parameters and/or seasonality.

The study of ammonium and nitrate has highlighted temporal variability in processes, with maximum nitrification and denitrification rates during autumn. Results show that ADModel is able to predict the main trend of measured concentration with reasonable accuracy and accounts for temporal changes in water flow and pollutant load along the river. Prediction accuracy could be improved through more detailed modelling of transformation processes by taking into account the variability of factors for which existing data were insufficient to allow representation. For example, modelling indicates that interactions with bed sediment may provide an additional source of nutrients during high spring flows. Copyright © 2010 John Wiley & Sons, Ltd.
The control of surface segregation of blend films using stereocomplex formation between enantiomeric polylactide chains
Authors: Lee Won‐Ki , Wells David D. , Goacher Robyn E. , Gardella Joseph A.
Published: June 2010

This study investigated the stereocomplex‐induced surface structure of enantiomeric poly(lactide) (PLA) blend films by time‐of‐flight secondary ion mass spectrometry (TOF‐SIMS). The design of the blend systems was based on the principle of surface segregation of a modified component with a low surface energy, fluorine‐end‐capped PLLA (F‐PLLA). Analysis of F‐PLLA/PDLA and F‐PLLA/PLLA blends, yielded a difference in the ion beam‐induced behavior between fluorine and lactide groups. In addition, a completely phase‐separated sample of PLLA with the fluorine end‐capping agent cast onto the surface was used for a real analysis of peak intensities from the two components, simulating bulk compositions. The two blend systems, uncomplexed (F‐PLLA/PLLA) and complexed (F‐PLLA/PDLA) blends, showed quite different surface structures: namely, a higher fluorine concentration was observed in the uncomplexed blends while the complexed blends showed a wider range of fluorine concentrations, depending on the degree of complexation. This indicates that the complexed blends offer a greater level of control over the surface fluorine concentration because this concentration changes more significantly with the blend composition (or the degree of complexation). Copyright © 2010 John Wiley & Sons, Ltd.
SIMS and thermal evolution analysis of oxygen in Zr‐1%Nb alloy after high‐temperature transitions
Authors: Lorincik J. , Klouc̆ek V. , Negyesi M. , Kabátová J. , Novotný L. , Vrtilkova V.
Published: June 2010

The concentration of oxygen in the primary β‐phase of Zr‐1%Nb alloy was investigated using SIMS and thermal evolution analysis (TEA). The specimens were as‐received or preoxidized in water vapor (425 °C/10,7 MPa) to simulate the reactor conditions. Then the specimens were exposed to hot water vapor (0,1 MPa) and high temperatures (950–1200 °C) for variable time intervals, which simulated the Loss of Coolant Accident (LOCA). The specimens were quenched in water with ice. Both SIMS and TEA quantitative results were in good agreement and were correlated with the mechanical properties (microhardness, residual ductility), which depend on the oxygen concentration and are important for the safety analyses assessment. The ceiling concentration of oxygen in the β‐phase was established based on the experimental results of SIMS and TEA. Copyright © 2010 John Wiley & Sons, Ltd.
Spin‐resolved photoemission microscopy and magnetic imaging in applied magnetic fields
Authors: Kronast F. , Schlichting J. , Radu F. , Mishra S.K. , Noll T. , Dürr H.A.
Published: June 2010

We describe a novel experimental facility at the BESSY II synchrotron, aiming at probing element‐specific magnetic properties at the nm‐length scale. It consists of a novel photoemission electron microscope with photoelectron spin analysis combined with a microfocus beamline and full X‐ray polarization control. The facility is capable of magnetic imaging in applied fields allowing the observation of magnetic switching phenomena on a 30‐nm‐length scale. Copyright © 2010 John Wiley & Sons, Ltd.