bluuebunny/crossref_metadata_2025 huggingface dataset:
In situ preparation of cross‐linked polystyrene/poly(methyl methacrylate) blend foams with a bimodal cellular structure
Authors: Kohlhoff Dominik , Nabil Abacha , Ohshima Masahiro
Published: September 2011

In situ preparation of a cross‐linked poly(methyl methacrylate) (PMMA) and polystyrene (PS) blend and its foaming were investigated for creating a bimodal cellular structure in the foam. Methyl methacrylate (MMA) monomer was dissolved in PS under supercritical CO2 at a temperature of 60 °C and a pressure of 8 MPa, and the polymerization of MMA was conducted at 100 °C and 8 MPa CO2, with a cross‐linking agent in PS. The blend was successively foamed by depressurizing the CO2. CO2 played the roles of plasticizing the PS and enhancing the monomer dispersion in PS during the sorption process and as a physical blowing agent in the foaming process. The cross‐linking agent was used for controlling the elasticity of polymerized PMMA domains and differentiating their elasticity from that of the PS matrix. The difference in elasticity delayed the bubble nucleation in the PMMA domains from that in the PS and made the cell size bimodal distribution, in which the smaller cells ranging from 10 to 30 µm in diameter were located in the wall of large cells of 200–400 µm in diameter. The effects of the initial MMA content, the concentration of cross‐linking agent, and the depressurization rate on the bimodal cell structure and bulk foam density were investigated. Copyright © 2011 John Wiley & Sons, Ltd.
The use of silica gel coated with liquid paraffin as a stationary phase for chromatographic analysis of phytochemicals
Authors: Houghton P. J. , Osibogun I. M.
Published: September 2011

The development of the use of liquid paraffin as an impregnating agent for silica gel employed in chromatography is briefly reviewed. Its application to the isolation of polar chromone alkaloids and relatively non‐polar esters of long‐chain aliphatic acids and phenols is described.
The estimation of macromolecular synthesis in plant cell cultures
Authors: Mahady Gail B. , Beecher Christopher W. W.
Published: September 2011

A simple and relatively rapid technique is described which can be used to determine accurately the overall pattern of macromolecule biosynthesis in plant cells. Sanguinaria canadensis L. (Papaveraceae) suspension cells were used as the model system. The patterns of DNA, RNA and protein synthesis were determined through cellular incorporation of [methyl‐3H]‐thymidine, [5‐3H]‐uridine and [4,5‐3H]‐leucine, respectively. The method takes advantage of a one‐step filtering procedure, which simplifies the extraction methods normally used. The results are described and possible applications of this procedure in plant‐cell growth studies and biotechnology are discussed.
The application of high‐speed countercurrent chromatography to the semipreparative separation of vincamine and vincine
Authors: Zhou Jin‐Yun , Fang Qi‐Cheng , Lee Yu‐Wei
Published: September 2011

High‐speed countercurrent chromatography (HSCCC) has gained increasing popularity in the isolation of bioactive natural products. This paper reports its application to the separation of the alkaloids vincamine and vincine which differ only by a methoxy group. It is demonstrated in this study that the resolution and speed of HSCCC is comparable to high‐performance liquid chromatography (HPLC) and its capability in semi‐preparative purification via continuous sample injections can be a very useful application in phytochemical research·alkaloids; vincamine; vincine; high‐speed countercurrent chromatography
Ultradrawing properties of ultrahigh‐molecular weight polyethylene/functionalized carbon nanotube fibers and transmittance properties of their gel solutions
Authors: Yeh Jen‐Taut , Wu Tsong‐Wei , Lai Yu‐Ching , Li Qi‐Cheng , Zhou Huo‐Peng , Zhou Qin , Tsou Chi‐Hui , Shu Yao‐Chi , Huang Chi‐Yuan , Huang Kuo‐Shien
Published: September 2011

The influences of the dispersion level of carbon nanotubes (CNTs) and functionalized CNTs on the transmittance properties of ultrahigh‐molecular weight polyethylene (UHMWPE) gel solutions and on ultradrawing properties of their as‐prepared fibers are reported. The transmittance properties suggest that the dispersion level of functionalized CNTs in UHMWPE/functionalized CNTs gel solution is significantly better than plain CNTs in UHMWPE/CNTs gel solutions. The orientation factors, achievable draw ratios, tensile strength (σf), and modulus (E) values of UHMWPE/CNTs (FxCy) and UHMWPE/functionalized CNTs (FxCf‐y) as‐prepared fiber specimens reached a maximum value as their CNT and functionalized CNT contents approached optimum contents at 0.00015 and 0.0001 wt%, respectively. The σf and E values of both FxC0.0012 and FxCf‐0.001 series fiber specimens prepared at their optimum CNT and functionalized CNT contents reached another maximum as their UHMWPE approached optimum UHMWPE concentration of 1.7 wt%. Possible reasons accounting for these interesting properties are proposed. POLYM. ENG. SCI., 2011. © 2011 Society of Plastics Engineers
Polymerization of ethylene using amido functional half‐sandwich complexes of group 4 metals
Authors: Rajesh A. , Sivaram S.
Published: September 2011

Ligands (C13H9)(2,6‐R2C6H3NH)SiPh2 [R = iPr (2a), Me (2b)] were synthesized by single deprotonation of the amino group in 2,6‐dialkylanilines with n‐BuLi at −78°C followed by reaction with fluorenyl diphenyl silyl chloride [FluSi(Ph2)Cl]. Single crystal X‐ray diffraction studies revealed different geometries around the nitrogen atom for the two compounds. Titanium and zirconium complexes (3a–3d) were prepared by double deprotonation of the ligands with n‐butyl lithium (n‐BuLi) followed by reaction with the respective metal chlorides, MCl4 (THF) 2. Polymerization of ethylene was performed using these complexes as catalyst precursors along with methylaluminoxane (MAO) as an activator at 5 bar pressure. Complexes 3a–3d/MAO exhibited moderate catalyst activities for polymerization of ethylene and resulted in high molecular weight linear poly(ethylene)s (Mv > 4 × 105 g/mol). Catalyst activities were much lower when compared to similar N‐alkyl substituted complexes presumably due to the resonance effect of the aromatic group on the amido nitrogen. POLYM. ENG.SCI., 2011. © 2011 Society of Plastics Engineers
Broadband dielectric spectroscopy studies of glassy‐state relaxations in annealed poly(2,5‐benzimidazole)
Authors: Nalawade Amol , Hassan Mohammad K. , Jarrett William A. , Mauritz Kenneth A. , Litt Morton H.
Published: September 2011

A broadband dielectric spectroscopic (BDS) study of poly(2,5‐benzimidazole) revealed three sub‐glass relaxations and the manner in which the time scales of these local molecular motions shift with annealing temperature and time. Also issuing from the BDS studies was a trend in the degree of connectivity of charge migration pathways and conductivity with annealing temperature and time. These studies were complemented with dynamic mechanical analysis, which showed the same relaxations, and solid state 1H and 13C NMR studies that showed hydrogen bonding group mobility versus temperature. Wide angle X‐ray diffraction investigations indicated an increase in chain‐packing efficiency that was used to rationalize the BDS and NMR results. Copyright © 2011 Society of Chemical Industry
Thermodynamically induced self‐assembled electrically conductive networks in carbon‐black‐filled ternary polymer blends
Authors: Shen Lie , Wang Fangquan , Jia Weican , Yang Hui
Published: September 2011

By calculating the surface tensions of the components, composites with innovative thermodynamically induced self‐assembled electrically conductive networks were designed, prepared and investigated. Carbon black (CB) was added into a ternary blend system comprised of poly(methyl methacrylate) (PMMA), ethylene–acrylic acid copolymer (EAA) and polypropylene (PP). Scanning electron microscopy images show that the PMMA/EAA/PP ternary blend forms a tri‐continuous phase structure like a sandwich, in which PMMA and PP form a co‐continuous phase while EAA spreads at the interface of the PMMA and PP phases as a sheath. The micrographs and resistivity–temperature characteristic curve results indicate that CB fillers are selectively located at the interface of the PMMA and PP phases, namely the EAA phase. The percolation threshold of PMMA/EAA‐CB/PP composites is 0.2 vol%, which is only one‐fifth of that of PP/CB composites. Copyright © 2011 Society of Chemical Industry
Rigorous optical modeling and optimization of thin‐film photovoltaic cells with textured transparent conductive oxides
Authors: Agrawal Mukul , Frei Michel
Published: September 2011

Typical thin‐film photovoltaic (PV) cells incorporate a textured transparent conductive oxide to enhance light trapping and efficiently harvest solar energy. Rigorous coherent optical simulations of these devices and a complete characterization of these textured films are a challenging problem because of the several orders of magnitude difference between the wavelengths of interest and the spatial dimension of the sample that needs to be evaluated. In this paper, a practical approach for rigorous and predictive modeling of optical properties of thin‐film PV cells incorporating a vast variety of light‐trapping structures including semi‐coherent textured films and patterned coherent structures is presented. In contrast to the existing semi‐empirical device models, it is demonstrated that the presented methodology can accurately predict the scattering properties of textured fluorine‐doped tin oxide and aluminum‐doped zinc oxide conductive transparent films. It is further shown that the optical response of single‐junction and tandem‐junction PV devices incorporating such films can also be predicted with good accuracy as compared with the measured results. Next, a methodology to identify the sufficient statistical fingerprints of semi‐coherent textured films that are needed to unambiguously predict the light propagation in thin‐film cells is presented. This comprehensive approach then lends itself to identifying the optimal surface morphology needed for strong light trapping. This rigorous approach automatically includes the effects of important loss mechanisms such as the surface plasmon‐enhanced absorption in textured metal surfaces that are otherwise very difficult to account for semi‐coherent approaches based on scalar scattering theory. Copyright © 2011 John Wiley & Sons, Ltd.
An improved method for the construction of decoy peptide MS/MS spectra suitable for the accurate estimation of false discovery rates
Authors: Ahrné Erik , Ohta Yuki , Nikitin Frederic , Scherl Alexander , Lisacek Frederique , Müller Markus
Published: September 2011

The relevance of libraries of annotated MS/MS spectra is growing with the amount of proteomic data generated in high‐throughput experiments. These reference libraries provide a fast and accurate way to identify newly acquired MS/MS spectra. In the context of multiple hypotheses testing, the control of the number of false‐positive identifications expected in the final result list by means of the calculation of the false discovery rate (FDR). In a classical sequence search where experimental MS/MS spectra are compared with the theoretical peptide spectra calculated from a sequence database, the FDR is estimated by searching randomized or decoy sequence databases. Despite on‐going discussion on how exactly the FDR has to be calculated, this method is widely accepted in the proteomic community. Recently, similar approaches to control the FDR of spectrum library searches were discussed. We present in this paper a detailed analysis of the similarity between spectra of distinct peptides to set the basis of our own solution for decoy library creation (DeLiberator). It differs from the previously published results in some key points, mainly in implementing new methods that prevent decoy spectra from being too similar to the original library spectra while keeping important features of real MS/MS spectra. Using different proteomic data sets and library creation methods, we evaluate our approach and compare it with alternative methods.
Large‐scale N‐glycoproteome map of rat brain tissue: Simultaneous characterization of insoluble and soluble protein fractions
Authors: Qiao Xiaoqiang , Tao Dingyin , Qu Yanyan , Sun Liangliang , Gao Liang , Zhang Xiaodan , Liang Zhen , Zhang Lihua , Zhang Yukui
Published: September 2011

The large‐scale N‐glycosylation analysis is critical for biomedical research, since a variety of diseases are found to be associated with glycoproteins. By a combination of glycoprotein analysis in insoluble protein fraction solubilized with 1% v/v 1‐butyl‐3‐methylimidazolium tetrafluoroborate (BMIM BF4) and those in soluble fraction, a total number of 462 non‐redundant N‐glycoprotein groups, including 316 transmembrane glycoproteins, were successfully identified. Correspondingly, 849 unique N‐glycosites were confidently recognized. The data set could provide a support for the further in‐depth research of brain N‐glycosylation, such as for the discovery of candidate drug targets and biomarkers.
Differential profiling studies of N‐linked glycoproteins in glioblastoma cancer stem cells upon treatment with γ‐secretase inhibitor
Authors: Dai Lan , Liu Yashu , He Jintang , Flack Callie G. , Talsma Caroline E. , Crowley Jessica G. , Muraszko Karin M. , Fan Xing , Lubman David M.
Published: September 2011

We have recently demonstrated that Notch pathway blockade by γ‐secretase inhibitor (GSI) depletes cancer stem cells (CSCs) in Glioblastoma Multiforme (GBM) through reduced proliferation and induced apoptosis. However, the detailed mechanism by which the manipulation of Notch signal induces alterations on post‐translational modifications such as glycosylation has not been investigated. Herein, we present a differential profiling work to detect the change of glycosylation pattern upon drug treatment in GBM CSCs. Rapid screening of differential cell surface glycan structures has been performed by lectin microarray on live cells followed by the detection of N‐linked glycoproteins from cell lysates using multi‐lectin chromatography and label‐free quantitative mass spectrometry analysis. A total of 51 and 52 glycoproteins were identified in the CSC‐ and GSI‐treated groups, respectively, filtered by a combination of decoy database searching and Trans‐Proteomic Pipeline (TPP) processing. Although no significant changes were detected from the lectin microarray experiment, 7 differentially expressed glycoproteins with high confidence were captured after the multi‐lectin column including key enzymes involved in glycan processing. Functional annotations of the altered glycoproteins suggest a phenotype transformation of CSCs toward a less tumorigenic form upon GSI treatment.
Proteomic profiling of oil bodies isolated from the unicellular green microalga Chlamydomonas reinhardtii: With focus on proteins involved in lipid metabolism
Authors: Nguyen Hoa M. , Baudet Mathieu , Cuiné Stéphan , Adriano Jean‐Marc , Barthe Damien , Billon Emmanuelle , Bruley Christophe , Beisson Fred , Peltier Gilles , Ferro Myriam , Li‐Beisson Yonghua
Published: September 2011

Oil bodies are sites of energy and carbon storage in many organisms including microalgae. As a step toward deciphering oil accumulation mechanisms in algae, we used proteomics to analyze purified oil bodies from the model microalga Chlamydomonas reinhardtii grown under nitrogen deprivation. Among the 248 proteins (≥2 peptides) identified by LC‐MS/MS, 33 were putatively involved in the metabolism of lipids (mostly acyl‐lipids and sterols). Compared with a recently reported Chlamydomonas oil body proteome, 19 new proteins of lipid metabolism were identified, spanning the key steps of the triacylglycerol synthesis pathway and including a glycerol‐3‐phosphate acyltransferase (GPAT), a lysophosphatidic acid acyltransferase (LPAT) and a putative phospholipid:diacylglycerol acyltransferase (PDAT). In addition, proteins putatively involved in deacylation/reacylation, sterol synthesis, lipid signaling and lipid trafficking were found to be associated with the oil body fraction. This data set thus provides evidence that Chlamydomonas oil bodies are not only storage compartments but also are dynamic structures likely to be involved in processes such as oil synthesis, degradation and lipid homeostasis. The proteins identified here should provide useful targets for genetic studies aiming at increasing our understanding of triacyglycerol synthesis and the role of oil bodies in microalgal cell functions.
Symbol nomenclature for representing glycan structures: Extension to cover different carbohydrate types
Authors: Harvey David J. , Merry Anthony H. , Royle Louise , Campbell Matthew P. , Rudd Pauline M.
Published: September 2011

This Viewpoint article addresses comments made on our original article describing a symbolic system for the depiction of N‐ and O‐linked carbohydrate structures and proposes a method for extending the symbol set to include monosaccharides commonly found in carbohydrates present in bacteria and plants. As before, basic monosaccharides are shown by shape with one or more additions such as solid fill or additions of lines, crosses or dots to represent functional groups. The use of colour to differentiate constituent monosaccharides is avoided, thus enabling the system to be used in a variety of formats. Linkage and anomericity are shown by the angle and type of line connecting the symbols. In this extended version, new symbols are proposed for additional hexoses and it is proposed that pyranose and furanose forms of the monosaccharides could be shown by solid or broken outlines to the symbols. Conventions for depicting the presence of multiple functional groups such as deoxy‐(NH2)2 are also discussed. It is hoped that these proposals will stimulate discussion so that a consensus can be reached as to how the glycobiology community can best convey complex information in a simple manner.
Protein recovery and identification from the gulf killifish, Fundulus grandis: Comparing snap‐frozen and RNAlater® preserved tissues
Authors: Abbaraju Naga V. , Cai Yang , Rees Bernard B.
Published: September 2011

Reliable proteomic analysis of biological tissues requires sampling approaches that preserve proteins as close to their in vivo state as possible. In the current study, the patterns of protein abundance in one‐dimensional (1‐D) gels were assessed for five tissues of the gulf killifish, Fundulus grandis, following snap‐freezing tissues in liquid nitrogen or immersion of fresh tissues in RNAlater®. In liver and heart, the protein profiles in 1‐D gels were better preserved by snap‐freezing, while in gill, the 1‐D protein profile was better preserved by immersion in RNAlater®. In skeletal muscle and brain, the two approaches yielded similar patterns of protein abundance. LC‐MS/MS analyses and database searching resulted in the identification of 17 proteins in liver and 12 proteins in gill. Identified proteins include enzymes of energy metabolism, structural proteins, and proteins serving other biological functions. These protein identifications for a species without a sequenced genome demonstrate the utility of F. grandis as a model organism for environmental proteomic studies in vertebrates.
A kinetic investigation of surfactant‐free emulsion polymerization of styrene using laponite clay platelets as stabilizers
Authors: Sheibat‐Othman Nida , Cenacchi‐Pereira Ana‐Maria , Santos Amilton Martins Dos , Bourgeat‐Lami Elodie
Published: September 2011

We report the kinetics and mechanism of soap‐free emulsion polymerization of styrene using laponite platelets as stabilizers. The polymerization was initiated by potassium persulfate and the latex particles were stabilized by laponite platelets dispersed in water. Laponite adsorption on the polymer particles was enhanced by the addition of poly(ethylene glycol) monomethylether methacrylate (PEGMA). Particle nucleation can be described using the classical homogeneous nucleation mechanism followed by coagulation of unstable precursors. Oligomeric radicals formed in the water phase become insoluble and precipitate on the laponite surface leading to primary precursor particles composed of a few polymer chains and one or several clay platelets. Mature latex particles are then generated by coagulation and growth of the previously formed precursor particles. Both the nucleation and initial aggregation rates increased in the presence of PEGMA. Calorimetric monitoring of the polymerization allowed estimating the heat produced by the reaction and the monomer conversion. Hence, using the monomer material balance, the number of radicals in the polymer particles could be estimated precisely. The average number of radicals per particle,
, was found to be high in the range 3–6. This result was attributed to strong attractive interactions between the growing radicals and the clay surface. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011.
Modeling highly branched structures: Description of the solution structures of dendrimers, polyglycerol, and glycogen
Authors: Konkolewicz Dominik , Perrier Sébastien , Stapleton David , Gray‐Weale Angus
Published: September 2011

We show that Random Branching Theory (RBT) accurately describes the structures of various synthetic and natural highly branched polymers in solution. We test the theory against data taken from the literature, including radii of gyration of glycogen, hyperbranched polyglycerols, and polyamidoamine dendrimers and the small‐angle X‐ray scattering profiles of these same dendrimers. In particular, all these polymers can be described adequately by sequentially branching units, packed together in a random close packing arrangement. Combined with previous tests against experiments and computer simulations, the evidence presented here shows that RBT is a simple, but surprisingly useful, theory of highly branched polymers' solution structure. We suggest that it is sufficiently powerful to be useful in the design of new polymers. Our most surprising conclusion is that random attachment of component parts produces a good model of regularly branched polymers. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 1525–1538, 2011
Fear of recurrence and causal attributions in long‐term survivors of testicular cancer
Authors: Pedersen Anette Fischer , Rossen Philip , Olesen Frede , von der Maase Hans , Vedsted Peter
Published: September 2011

Background

The purpose was to examine the prevalence of fear of recurrence (FoR) in long‐term testicular cancer survivors (TCSs) and the association between FoR and causal attributions of cancer.

Methods

Testicular cancer survivors were sampled from a clinical register and were sent a questionnaire assessing FoR, depression using Beck Depression Inventory II (BDI‐II), physical symptoms (ototoxicity, neuropathy, and Raynaud‐like phenomena), and causal attributions of testicular cancer.

Results

There were 316 TCSs who completed the questionnaires (response rate, 65%). The mean age was 47.6 years (standard deviation (SD) = 10.9), and the mean time since diagnosis was 12.0 years (SD = 3.0). Among the TCSs, 27.9% reported FoR. Univariate analyses revealed that FoR was associated with a BDI‐II sum score of ≥19 (odds ratio (OR) = 7.07, p < 0.001) and attributing the cancer disease to psychological stress (OR = 2.57, p = 0.002). A multivariate analysis revealed associations between FoR and attributing the cancer disease to psychological stress (OR = 2.35, p = 0.010) and a BDI‐II sum score ≥19 (OR = 5.82, p = 0.002).

Conclusions

Fear of recurrence is prevalent in long‐term TCSs. The observed relationship between FoR and a psychological causal attribution is probably complex and the direction of causality may be twofold: attributing the disease to a factor that is perceived as uncontrollable in nature could induce loss of control, and high levels of FoR may increase the need to gain control over the situation by pointing out factors that could be responsible for the disease such as psychological stress. Copyright © 2011 John Wiley & Sons, Ltd.
Communication about standard treatment options and clinical trials: can we teach doctors new skills to improve patient outcomes?
Authors: Bernhard Jürg , Butow Phyllis , Aldridge Julie , Juraskova Ilona , Ribi Karin , Brown Richard
Published: September 2011

Background

The International Breast Cancer Study Group conducted a phase III trial in Australian/New Zealand (ANZ) and Swiss/German/Austrian (SGA) centres on training doctors in clear and ethical information delivery about treatment options and strategies to encourage shared decision making.

Methods

Medical, surgical, gynaecological and radiation oncologists, and their patients for whom adjuvant breast cancer therapy was indicated, were eligible. Doctors were randomised to participate in a workshop with standardised teaching material and role playing. Patients were recruited in the experimental and control groups before and after the workshop.

Results

In ANZ centres, 21 eligible doctors recruited a total of 304 assessable patients. In SGA centres, 41 doctors recruited 390 patients. The training was well accepted. There was no overall effect on patient decisional conflict (primary endpoint) 2 weeks after the consultation. Overall, patients were satisfied with their treatment decision, their consultation and their doctors' consultation skills. Considerable variation was observed in patient outcomes between SGA and ANZ centres; the effect sizes of the intervention were marginal (<0.2).

Conclusions

Shared decision making remains a challenge. A sustained training effect may require more intensive training tailored to the local setting. Cross‐cultural differences need attention in conducting trials on communication interventions. Copyright © 2011 John Wiley & Sons, Ltd.
Study of Plastic Explosives based on Attractive Cyclic Nitramines Part I. Detonation Characteristics of Explosives with PIB Binder
Authors: Elbeih Ahmed , Pachman Jiři , Trzciński Waldemar A. , Zeman Svatopluk , Akštein Zbyněk , Šelešovský Jakub
Published: September 2011

Four plastic explosives based on energetic nitramines and a non‐energetic binder were prepared and studied. The nitramines were RDX (1,3,5‐trinitro‐1,3,5‐triazine), HMX (1,3,5,7‐tetranitro‐1,3,5,7‐tetrazine), BCHMX (cis‐1,3,4,6‐tetranitro‐octahydroimidazo‐[4,5‐d]imidazole) and HNIW (ε‐2,4,6,8,10,12‐hexanitro‐2,4,6,8,10,12‐hexaazaisowurtzitane, ε‐CL‐20). The binder was in all cases polyisobutylene (PIB) as in the standard composition C‐4. These powerful plastic explosives were compared to standard PETN‐based commercially available explosives Semtex 1A and Sprängdeg m/46. The detonation velocities were experimentally measured and compared to the ones calculated by the Kamlet–Jacobs method, CHEETAH and EXPLO5 Codes. The experimental detonation velocities as well as the calculated detonation parameters decrease in the following order: HNIW‐PIB>HMX‐PIB≥BCHMX‐PIB>RDX‐PIB>Sprändeg m/46≥Semtex 1A. Urizar coefficients for the various binders were calculated from experimental data.
A Process of Subgroup Identification in Non‐specific Low Back Pain Using a Standard Clinical Examination and Cluster Analysis
Authors: McCarthy Christopher James , Roberts Christopher , Gittins Matthew , Oldham Jacqueline Ann
Published: September 2011

Background and Purpose

Non‐specific low back pain (NSLBP) accounts for over 85% of all low back pain. Homogenous subgroups may exist within this diagnosis. This study derived a clinical examination and evaluated the examination's ability to identify homogenous subgroups in NSLBP.

Methods

Patients with NSLBP were examined using a standardized clinical examination. Each patient was examined by two physiotherapists. Data were analysed for item reliability and the presence of distinct subgroups using cluster analysis. Cross‐validation of the clusters identified was conducted.

Results

Three hundred and one patients were examined. The inter‐tester reliability of the majority of items was moderate to substantial (52% of items with kappa > 0.40). A K‐means cluster analysis of the two data sets revealed agreement on the presence of two subgroups. One group (n = 47, 16%) had higher fear avoidance beliefs, anxiety and disability. They were more likely to be provoked by pain provocative tests. They were also more likely to be judged as having central sensitization and a dominant psychosocial component to their presentation.

Conclusion

The identification of a group of hypervigilant NSLBP patients should allow the interventions to be targeted towards this group. A valid, standardized clinical examination does contribute to the diagnostic management of NSLBP. Copyright © 2011 John Wiley & Sons, Ltd.
High‐resolution structure prediction of a circular permutation loop
Authors: Correia Bruno E. , Holmes Margaret A. , Huang Po‐Ssu , Strong Roland K. , Schief William R.
Published: September 2011

Methods for rapid and reliable design and structure prediction of linker loops would facilitate a variety of protein engineering applications. Circular permutation, in which the existing termini of a protein are linked by the polypeptide chain and new termini are created, is one such application that has been employed for decreasing proteolytic susceptibility and other functional purposes. The length and sequence of the linker can impact the expression level, solubility, structure and function of the permuted variants. Hence it is desirable to achieve atomic‐level accuracy in linker design. Here, we describe the use of RosettaRemodel for design and structure prediction of circular permutation linkers on a model protein. A crystal structure of one of the permuted variants confirmed the accuracy of the computational prediction, where the all‐atom rmsd of the linker region was 0.89 Å between the model and the crystal structure. This result suggests that RosettaRemodel may be generally useful for the design and structure prediction of protein loop regions for circular permutations or other structure‐function manipulations.
Evaluation of disorder predictions in CASP9
Authors: Monastyrskyy Bohdan , Fidelis Krzysztof , Moult John , Tramontano Anna , Kryshtafovych Andriy
Published: September 2011

Lack of stable three‐dimensional structure, or intrinsic disorder, is a common phenomenon in proteins. Naturally, unstructured regions are proven to be essential for carrying function by many proteins, and therefore identification of such regions is an important issue. CASP has been assessing the state of the art in predicting disorder regions from amino acid sequence since 2002. Here, we present the results of the evaluation of the disorder predictions submitted to CASP9. The assessment is based on the evaluation measures and procedures used in previous CASPs. The balanced accuracy and the Matthews correlation coefficient were chosen as basic measures for evaluating the correctness of binary classifications. The area under the receiver operating characteristic curve was the measure of choice for evaluating probability‐based predictions of disorder. The CASP9 methods are shown to perform slightly better than the CASP7 methods but not better than the methods in CASP8. It was also shown that capability of most CASP9 methods to predict disorder decreases with increasing minimum disorder segment length. Proteins 2011;. © 2011 Wiley‐Liss, Inc.
Prots: A fragment based protein thermo‐stability potential
Authors: Li Yunqi , Zhang Jian , Tai David , Russell Middaugh C. , Zhang Yang , Fang Jianwen
Published: September 2011

Designing proteins with enhanced thermo‐stability has been a main focus of protein engineering because of its theoretical and practical significance. Despite extensive studies in the past years, a general strategy for stabilizing proteins still remains elusive. Thus effective and robust computational algorithms for designing thermo‐stable proteins are in critical demand. Here we report PROTS, a sequential and structural four‐residue fragment based protein thermo‐stability potential. PROTS is derived from a nonredundant representative collection of thousands of thermophilic and mesophilic protein structures and a large set of point mutations with experimentally determined changes of melting temperatures. To the best of our knowledge, PROTS is the first protein stability predictor based on integrated analysis and mining of these two types of data. Besides conventional cross validation and blind testing, we introduce hypothetical reverse mutations as a means of testing the robustness of protein thermo‐stability predictors. In all tests, PROTS demonstrates the ability to reliably predict mutation induced thermo‐stability changes as well as classify thermophilic and mesophilic proteins. In addition, this white‐box predictor allows easy interpretation of the factors that influence mutation induced protein stability changes at the residue level. Proteins 2012; © 2011 Wiley Periodicals, Inc.
BSP‐SLIM: A blind low‐resolution ligand‐protein docking approach using predicted protein structures
Authors: Lee Hui Sun , Zhang Yang
Published: September 2011

We developed BSP‐SLIM, a new method for ligand–protein blind docking using low‐resolution protein structures. For a given sequence, protein structures are first predicted by I‐TASSER; putative ligand binding sites are transferred from holo‐template structures which are analogous to the I‐TASSER models; ligand–protein docking conformations are then constructed by shape and chemical match of ligand with the negative image of binding pockets. BSP‐SLIM was tested on 71 ligand–protein complexes from the Astex diverse set where the protein structures were predicted by I‐TASSER with an average RMSD 2.92 Å on the binding residues. Using I‐TASSER models, the median ligand RMSD of BSP‐SLIM docking is 3.99 Å which is 5.94 Å lower than that by AutoDock; the median binding‐site error by BSP‐SLIM is 1.77 Å which is 6.23 Å lower than that by AutoDock and 3.43 Å lower than that by LIGSITECSC. Compared to the models using crystal protein structures, the median ligand RMSD by BSP‐SLIM using I‐TASSER models increases by 0.87 Å, while that by AutoDock increases by 8.41 Å; the median binding‐site error by BSP‐SLIM increase by 0.69Å while that by AutoDock and LIGSITECSC increases by 7.31 Å and 1.41 Å, respectively. As case studies, BSP‐SLIM was used in virtual screening for six target proteins, which prioritized actives of 25% and 50% in the top 9.2% and 17% of the library on average, respectively. These results demonstrate the usefulness of the template‐based coarse‐grained algorithms in the low‐resolution ligand–protein docking and drug‐screening. An on‐line BSP‐SLIM server is freely available at http://zhanglab.ccmb.med.umich.edu/BSP‐SLIM. Proteins 2012. © 2011 Wiley Periodicals, Inc.
The impact of altered herbicide residues in transgenic herbicide‐resistant crops on standard setting for herbicide residues
Authors: Kleter Gijs A , Unsworth John B , Harris Caroline A
Published: September 2011

The global area covered with transgenic (genetically modified) crops has rapidly increased since their introduction in the mid‐1990s. Most of these crops have been rendered herbicide resistant, for which it can be envisaged that the modification has an impact on the profile and level of herbicide residues within these crops. In this article, the four main categories of herbicide resistance, including resistance to acetolactate‐synthase inhibitors, bromoxynil, glufosinate and glyphosate, are reviewed. The topics considered are the molecular mechanism underlying the herbicide resistance, the nature and levels of the residues formed and their impact on the residue definition and maximum residue limits (MRLs) defined by the Codex Alimentarius Commission and national authorities. No general conclusions can be drawn concerning the nature and level of residues, which has to be done on a case‐by‐case basis. International residue definitions and MRLs are still lacking for some herbicide–crop combinations, and harmonisation is therefore recommended. Copyright © 2011 Society of Chemical Industry
Ultra‐smooth single crystal diamond surfaces resulting from implantation and lift‐off processes
Authors: Thi T. N. Tran , Fernandez B. , Eon D. , Gheeraert E. , Härtwig J. , Lafford T. , Perrat‐Mabilon A. , Peaucelle C. , Olivero P. , Bustarret E.
Published: September 2011

A method for obtaining a smooth, single crystal diamond surface is presented, whereby a sacrificial defective layer is created by implantation of a regular (4 nm roughness) Ib diamond plate. This was then graphitized by annealing before being selectively etched. We have used O+ at 240 keV, the main process variables being the ion fluence (ranging from 3 × 1015 to 3 × 1017 cm−2) and the final etching process (wet etch, H2 plasma, and annealing in air). The substrates were characterized by atomic force microscopy, optical profilometry and white beam X‐ray topography. The influence of the various process parameters on the resulting lift‐off efficiency and final surface roughness is discussed. An O+ fluence of 2 × 1017 cm−2 was found to result in sub‐nanometer roughness over tens of µm2.
Creation of colour centres in diamond by collimated ion‐implantation through nano‐channels in mica
Authors: Pezzagna S. , Rogalla D. , Becker H.‐W. , Jakobi I. , Dolde F. , Naydenov B. , Wrachtrup J. , Jelezko F. , Trautmann C. , Meijer J.
Published: September 2011

The fabrication of scalable quantum devices in diamond relies on the ability to produce optical centres with a high spatial resolution. Ion implantation is the most powerful technique for placing impurity atoms in a diamond matrix. Even though shallow optical centres can be produced with a resolution below 20 nm, deep centres may be preferred for generally better overall properties. However, the focusing of ion beams in the MeV range can hardly be achieved below 1 µm. We present here a novel approach by implanting ions through a mask with high‐aspect‐ratio nano‐channels and improve the collimation to below 50 nm. The mask contains parallel oriented channels of a few tens of nanometres in diameter. They are produced by exposing mica sheets to GeV heavy ion projectiles and subsequent track etching. We demonstrate the high‐resolution creation of deep nitrogen‐vacancy (NV) centres in diamond by implanting nitrogen ions through the nano‐channels. Transmission rates and energy distribution of the nitrogen ions transmitted through the nano‐channels were also analysed.
Nanotextured crystalline silicon solar cells
Authors: Dimitrov Dimitre Z. , Lin Ching‐Hsi , Du Chen‐Hsun , Lan Chung‐Wen
Published: September 2011

Nano‐scale textures are formed on crystalline silicon surfaces by using a two‐step electroless wet‐chemical method consisting of a treatment in an activated Na2S2O8 (K2S2O8) solution for localized oxidation/surface reaction and silver nanoparticles deposition. The oxidation/reaction products are etched in an aqueous solution of HF and H2O2 assisted by the presence of silver nanoparticles. The reflectance of the nanotextured silicon wafer surfaces less than 5% in the spectral interval 300–900 nm is observed. It was found that the surface texture can withstand without significantly changing the high‐temperature solar cell processing. A weighted reflectance of 9.5% and 16.43% efficiency are obtained on nanotextured mc‐Si solar cells with an active area of 146 mm2 prepared using the standard screen‐printing technique.
Growth of aligned multi‐walled carbon nanotubes: First in situ and time‐resolved X‐ray diffraction analysis
Authors: Landois Périne , Rouziére Stéphan , Pinault Mathieu , Porterat Dominique , Mocuta Cristian , Elkaim Erik , Mayne‐L'Hermite Martine , Launois Pascale
Published: September 2011

Catalytic chemical vapour deposition has become a method of choice to produce carbon nanotubes (CNT), particularly for the synthesis of aligned nanotube forests. But a thorough understanding of the mechanisms for CNT nucleation, growth and alignment is still missing. In situ and time resolved experiments allowing to study these processes in real conditions are required. We have developed a specific reactor and furnace to perform such experiments using X‐ray diffraction (XRD). Experiments were performed at synchrotron SOLEIL. XRD patterns were recorded as a function of time, during nucleation and growth. We present here our first results, discussing the interest of the XRD method with respect to other existing in situ methods.

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The study of thermal and electrical properties of Fe‐based amorphous alloys Fe80‐xCox P12B4Si4
Authors: Chen Lingshan , Zhang Hongguang , Chen Yuanyuan , Liu Hao , Li Yongtao , Dong Xueguang , Chen Kai , Li Qi
Published: September 2011

The effects of disordered structure on the thermal and electrical properties of Fe‐Co‐P‐B‐Si amorphous alloy are presented. From the X‐ray diffraction (XRD) pattern of series of Fe‐based amorphous ribbon alloys Fe80‐xCox P12B4Si4(x = 20, 25, 30, 35), all samples show amorphous structure. The good glass forming ability of those series samples is detected by differential scanning calorimeter (DSC) measurements. The electrical resistivity and its temperature dependence behaviour have also been measured by four probe method, which shows that an electron‐phonon interaction of disordered structure plays an important role on the resistance changes. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effect of magnetic field on phase morphology transformation of MnO2 nanostructures in a hydrothermal process
Authors: Zhu Mingyuan , Hu Yemin , Li Ying , Jin Hongming , Zhu Zhenzhen
Published: September 2011

MnO2 nanostructures with various phases and morphologies were successfully synthesized by a magnetic‐field‐assisted hydrothermal approach. By applying a pulsed magnetic field to the reaction system, the phase and morphology transformation progress, i.e. urchin‐like α‐ and γ‐MnO2 nanostructures converting to β‐MnO2 nanowires was interfered comparing with those reacted without magnetic field. The effect of pulsed magnetic field on the growth of MnO2 was investigated by tracking the evolution of phase and morphology of the samples at different reaction stages by using X‐ray diffraction (XRD) and field emission scanning electron microscopy (FESEM) techniques. It is found that the pulsed magnetic field obviously affects the nucleation and growth of MnO2 nanostructures and therefore influences the phase and morphology transformation of MnO2. The transformation mechanism for the MnO2 nanostructures in hydrothermal treatment is the well‐known “Ostwald ripening process”. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Improvement of retrospective optimal interpolation by incorporating eigen‐decomposition and covariance inflation
Authors: Song Hyo‐Jong , Lim Gyu‐Ho
Published: September 2011

Retrospective optimal interpolation (ROI) is a method that is used to minimize cost functions with multiple minima without using adjoint models. We address two weaknesses associated with the cost‐effective formulation of ROI and offer possible solutions. The first weakness of the cost‐effective ROI formulation is that the error tolerance would become large in practical application due to computation costs. When the error tolerance is large, accuracy‐saturated modes do not extract information from new incoming observations even though they are likely to be flawed. To address this problem, we modify the existing ‘reduced‐resolution’ formulation by using eigen‐decomposition of the background error covariance at each analysis step. We refer to the modified algorithm as a ‘reduced‐rank’ algorithm. This modification allows us to deal with larger error variances while analysing the same number of control variables, because eigen‐decomposition steeply reorders the error variance in descending order. As a result, when the reduced‐rank algorithm is applied, the number of analysed control variables becomes smaller than when the reduced‐resolution algorithm is used with the same error tolerance. The second weakness is the underestimation of the trailing mode of background error covariance that is projected onto the future observation space. This originates from errors in control variables extracted from analysis procedures. To prevent the occurrence of filter divergence due to this underestimation, we reduce the weighting of the observational increments in the analysis. By implicitly assuming that the rate of being projected onto the future observation space of the trailing eigenmodes is similar to that of the leading eigenmodes, we develop a method that inflates the observation error covariance and consequently improves analysis quality in the Lorenz 40‐variable and the 960‐variable model experiments. Copyright © 2011 Royal Meteorological Society
Bayesian Analysis of Step‐Stress Accelerated Life Test with Exponential Distribution
Authors: Lee Jinsuk , Pan Rong
Published: September 2011

In this article, we propose a general Bayesian inference approach to the step‐stress accelerated life test with type II censoring. We assume that the failure times at each stress level are exponentially distributed and the test units are tested in an increasing order of stress levels. We formulate the prior distribution of the parameters of life‐stress function and integrate the engineering knowledge of product failure rate and acceleration factor into the prior. The posterior distribution and the point estimates for the parameters of interest are provided. Through the Markov chain Monte Carlo technique, we demonstrate a nonconjugate prior case using an industrial example. It is shown that with the Bayesian approach, the statistical precision of parameter estimation is improved and, consequently, the required number of failures could be reduced. Copyright © 2011 John Wiley & Sons, Ltd.
Thermodynamic and kinetic analysis on the reaction of dimethyl sulfide radical with oxygen
Authors: Jin Fei , Asatryan Rubik , Bozzelli Joseph W.
Published: September 2011

Thermochemical properties of methylthiol‐methylhydroperoxide, CH3SCH2OOH and its two terminal radicals resulting from the loss of hydrogen atoms, viz. CH3SCH2OO· and C·H2SCH2OOH, are important to understand the stability, reaction paths, and kinetics of the reactions of dimethyl sulfide and related sulfur‐containing hydrocarbons in the atmosphere and the combustion processes. Thermochemical properties ΔHof, S(T) and Cp(T) and internal rotation potentials for reactants, intermediates, and transition states in the methylthiomethyl (CH3SC·H2) radical + O2 reaction system are analyzed to evaluate reaction paths and kinetics versus temperature and pressure. Isodesmic reaction analysis is used to determine the enthalpies of formation (ΔHof298) using density functional B3LYP/6‐311G(d,p) and complete basis set extrapolation CBS‐QB3 computational methods. Entropy and heat capacities Cp(T) are determined using geometric parameters and vibration frequencies obtained at B3LYP/6‐311G(d,p) level of calculation. ΔHfo298 values estimated at the CBS‐QB3 level (units: kcal mol−1) are CH3SC·H2 (32.7), CH3SCH2OOH (–29.1), CH3SCH2OO· (5.2), C·H2SCH2OOH (11.5). Quantum Rice–Ramsperger–Kassel analysis is used to calculate energy‐dependent rate constants, k(E), and master equation is used to account for collisional stabilization of peroxy adduct and the hydroperoxide isomer. The methylthiomethyl radical associates with O2 to form a methylthiomethyl peroxy radical with a well depth of 27.49 kcal mol−1. The peroxy radical can dissociate back to reactants, isomerize via hydrogen shift to form a hydroperoxide methyl radical C·H2SCH2OOH, decompose via hydrogen transfer, and undergo subsequent low‐energy beta scission to form CH3SC(O)H and OH radical. The peroxy radical can also attack the sulfur atom via TS3 to form CH3S(O) + CH2O product set. The C·H2SCH2OOH isomer can decompose via an elimination transition state to CH2S + CH2O + OH, or through a four‐member ring transition state to 1,3‐Oxathietane + OH products. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011