bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractBackgroundThe 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.MethodsTesticular 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.ResultsThere 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).ConclusionsFear 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

AbstractBackgroundThe 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.MethodsMedical, 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.ResultsIn 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).ConclusionsShared 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

AbstractFour 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

AbstractBackground and PurposeNon‐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.MethodsPatients 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.ResultsThree 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.ConclusionThe 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

AbstractMethods 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

AbstractLack 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

AbstractDesigning 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

AbstractWe 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

AbstractThe 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

AbstractA 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

AbstractThe 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

AbstractNano‐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

AbstractCatalytic 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.magnified image
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

AbstractThe 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

AbstractMnO2 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

AbstractRetrospective 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