bluuebunny/crossref_metadata_2025_split huggingface dataset:
Depassivation of steel reinforcement in case of pitting corrosion: detection techniques for laboratory studies
Authors: Bertolini L. , Redaelli E. 
Published: August 2009

AbstractMethods for service life prediction of reinforced concrete structures exposed to chloride‐bearing environments require, amongst other parameters, the knowledge of the chloride threshold for pitting corrosion initiation (Clth). Nowadays, although the main factors influencing the chloride threshold are well known, it is often difficult to quantify a value of the chloride threshold, partly because of its intrinsic high variability, and partly because of the different test methods that have been used to measure it. All the experimental tests rely on the detection of steel depassivation and simultaneous measurement of chloride content or steel potential. This paper deals with the methods that can be used to detect steel depassivation in relation with the determination of the chloride threshold. Tests in concrete‐pore‐simulating solutions as well as tests in concrete will be considered, and advantages and limitations will be discussed.
Release bias in accessing medical records in clinical trials: a STAR*D report
Authors: Kashner T. Michael , Trivedi Madhukar H. , Wicker Annie , Fava Maurizio , Shores‐Wilson Kathy , Wisniewski Stephen R. , Rush A. John 
Published: August 2009

AbstractClinical trials often require subjects to sign medical record releases to allow investigators to measure treatment fidelity, off‐protocol care use, and care costs. Little is known, however, if limiting samples to those willing to sign releases impacts external validity. Data came from outpatients with non‐psychotic major depressive disorder who enrolled in the multisite Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study. Differences between those who signed (n = 3116) and who did not sign (n = 925) releases were assessed using logistic regression and two‐part, three‐level log‐transformed regression models, corrected for site clustering and repeated measures. Patients who released records tended to believe care was helpful, were younger, and married. However, release status had little material or consistent associations with patient health outcomes or use of care. With appropriate adjustments to data, requiring patient medical records may pose only minimal challenges to external validity in cost‐outcome studies. Copyright © 2009 John Wiley & Sons, Ltd.
Psychometric properties of an interviewer‐administered version of the Kessler Psychological Distress scale (K10) among Dutch, Moroccan and Turkish respondents
Authors: Fassaert T. , De Wit M.A.S. , Tuinebreijer W.C. , Wouters H. , Verhoeff A.P. , Beekman A.T.F. , Dekker J. 
Published: August 2009

AbstractThe Kessler Psychological Distress scale (K10) is an instrument that is widely used to screen for mental disorders, but information is lacking on its psychometric qualities in non‐Western samples. This study used a population‐based sample (N = 725) to assess the reliability and validity of the K10 across ethnic groups in an urban area. The results were generally supportive of the K10 as a reliable and valid instrument to screen for anxiety and depression in all three groups. Cronbach's alpha was high (0.93) and the results indicated the existence of a solid single factor structure. Item bias in relation to ethnic background was minor. In each group, there was good criterion validity with respect to one‐month DSM‐IV diagnosis for depressive and/or anxiety disorder. The results nevertheless highlight the importance of cross‐cultural validation, as we found different cut‐off values for ethnic subgroups to obtain optimal sensitivity and specificity for detecting depressive and/or anxiety disorders. Copyright © 2009 John Wiley & Sons, Ltd.
Blinding in clozapine trials: a problem and a potential solution
Authors: Wohlfarth Tamar , Linszen Don , Van Den Brink Wim 
Published: August 2009

AbstractBackground: A methodological problem arises when efficacy of clozapine is compared with other antipsychotic medication in double blind randomized studies. Due to the risk of leucopenia and agranulocytosis, patients in the clozapine condition need to have regular blood testing. The problem is that in order to maintain blinding, patients in the comparison conditions need to undergo blood testing as well and this can lead to underestimation of treatment acceptability and efficacy of the comparators.Methods: A thought experiment considering all possible solutions for the methodological problem.Results: We propose a special study design that preserves randomization and blinding while at the same time prevents underestimation of the effect in the comparator treatments. In addition, the necessity for blood testing is limited to only a small number of patients who receive comparative treatments. The design involves initial randomization to a sub‐study including clozapine and a small comparator arm or to a sub‐study that includes only comparator arms. Blood testing is only necessary in the first sub‐study.Discussion: Limitations of the proposed design are discussed. It is noted that this study design may offer a solution to similar situations where blood testing or other types of monitoring (e.g. as with lithium) is required in one but not in all of the treatment arms of a double blind randomized study. Copyright © 2009 John Wiley & Sons, Ltd.
Line‐shape analysis of J‐resolved NMR spectra: application to metabolomics and quantification of intensity errors from signal processing and high signal congestion
Authors: Parsons Helen M. , Ludwig Christian , Viant Mark R. 
Published: August 2009

AbstractNMR spectroscopy remains one of the primary analytical approaches in metabolomics. Although 1D 1H NMR spectroscopy is versatile, highly reproducible and currently the most widely used technique in NMR metabolomics, analysis of complex biological samples typically yields highly congested spectra with severely overlapping signals making unambiguous metabolite identification and quantification almost impossible. Consequently there is a growing use of 2D NMR methods, in particular 1H J‐resolved (JRES) spectroscopy, which spreads the high signal density into a second dimension. One potentially powerful method to deconvolute these JRES spectra, facilitating metabolite quantification, is via line‐shape fitting. However, the mathematical functions describing the JRES NMR line‐shape, in particular after applying apodisation functions and JRES specific processing, including tilting and symmetrisation, remain uncharacterised. Furthermore, possible quantitation errors arising from processing JRES spectra have not been evaluated, nor have the potentially adverse quantitative effects of overlapping dispersive tails of closely spaced signals in the 2D spectrum. Here we address these issues and evaluate the suitability of the JRES experiment for accurate complex mixture analysis. Specifically, we have examined changes in NMR line‐shape and signal intensity after application of different apodisation functions (SINE and SEM) and JRES specific processing (tilting and symmetrising), comparing simulated and experimental data. We also report a significant quantitation error of up to 33%, dependent upon apodisation, due to overlap of the dispersive tails of closely spaced resonances. Finally, we have validated the use of these mathematical line‐shape functions for metabolite quantitation of 2D JRES spectra, by comparison to corresponding 1D NMR datasets, using both gravimetrically‐prepared chemically defined mixtures as well as biological tissue extracts. Copyright © 2009 John Wiley & Sons, Ltd.
Allocation of clearance assets in IED warfare
Authors: Washburn Alan , Lee Ewing LTC P. 
Published: August 2009

AbstractThis article deals with the optimal allocation of mine clearance resources to a network of roads that is continually being mined by an opponent. The motivating application is IED warfare as practiced in Iraq and Afghanistan. The situation differs from most mine warfare analyses in being protracted indefinitely in time, with the processes of mine placement by Red and mine clearance by Blue being intermixed. Each incident involving a Blue convoy and a Red mine removes the mine and possibly causes some damage to the convoy. Blue's object is to minimize the total damage rate by optimally deploying mine clearance forces to road segments. © 2009 Wiley Periodicals, Inc. Naval Research Logistics 58: 180–187, 2011
Convergence analysis and computational testing of the finite element discretization of the Navier–Stokes alpha model
Authors: Connors Jeffrey 
Published: August 2009

AbstractThis report performs a complete analysis of convergence and rates of convergence of finite element approximations of the Navier–Stokes‐α (NS‐α) regularization of the NSE, under a zero‐divergence constraint on the velocity, to the true solution of the NSE. Convergence of the discrete NS‐α approximate velocity to the true Navier–Stokes velocity is proved and rates of convergence derived, under no‐slip boundary conditions. Generalization of the results herein to periodic boundary conditions is evident. Two‐dimensional experiments are performed, verifying convergence and predicted rates of convergence. It is shown that the NS‐α‐FE solutions converge at the theoretical limit of O(h2) when choosing α = h, in the H1 norm. Furthermore, in the case of flow over a step the NS‐α model is shown to resolve vortex separation in the recirculation zone. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2010
Preparation of antimicrobial polycaprolactone‐silica composite films with nanosilver rods and triclosan using roll‐milling method
Authors: Olgun Uğursoy , Tunç Kenan , Özaslan Vildan 
Published: August 2009

AbstractIn this study, antimicrobial polycaprolactone composite films containing 12.5% silica and 0.15% silver nanorods were prepared using the roll‐milling method. The destruction of E. coli and S. aureus on the surface of the composite films was evaluated after 6 hr of incubation at 37°C. For the E. Coli, no bacterial contamination was detected after 6 hr and the film surface was completely disinfected with 100% reduction of the microbial contamination. For the S. aureus, 94% reduction of the bacterial contamination was observed after 6 hr. The results were compared with the composite films containing triclosan, a broad‐spectrum antimicrobial agent. The antimicrobial activity tests with 0.25% triclosan incorporated polycaprolactone‐silica composite films showed only 70% reduction of E. coli and 95% reduction of S. aureus after 6 hr. The results demonstrated that the use of silver nanoparticles in the biopolymer industry has huge potential for the self‐cleaning applications. Copyright © 2009 John Wiley & Sons, Ltd.
Preparation and properties of polyethylene/montmorillonite nanocomposites formed via ethylene copolymerization
Authors: Guo Cun‐Yue , Ke Yucai , Liu Yuanxia , Mi Xia , Zhang Mingge , Hu Youliang 
Published: August 2009

AbstractBACKGROUND: In situ formation of polyethylene/clay nanocomposites is one of the prevalent preparation methods that include also solution blending and melt blending with regard to process simplification, economy in cost, environment protection and marked improvement in the mechanical properties of the polymeric matrix. In the work reported here, the preparation of linear low‐density polyethylene (LLDPE) and fabrication of polymer/clay nanocomposites were combined into a facile route by immobilizing pre‐catalysts for ethylene oligomerization on montmorillonite (MMT).RESULTS: [(2‐ArNC(Me))2C5H3N]FeCl2 (Ar = 2,4‐Me2(C6H3)) was supported on MMT treated using three different methods. The MMT‐supported iron complex together with metallocene compound rac‐Et(Ind)2ZrCl2 catalyzed ethylene to LLDPE/MMT nanocomposites upon activation with methylaluminoxane. The oligomer that was formed between layers of MMT promoted further exfoliation of MMT layers. The LLDPE/MMT nanocomposites were highly stable upon heating. Detailed scanning electron microscopy analysis revealed that the marked improvement in impact strength of the LLDPE/MMT nanocomposites originated from the dispersed MMT layers which underwent cavitation upon impact and caused plastic deformation to absorb most of the impact energy. In general, the mechanical properties of the LLDPE/MMT nanocomposites were improved as a result of the uniform dispersion of MMT layers in the LLDPE matrix.CONCLUSION: The use of the MMT‐supported iron‐based diimine complex together with metallocene led to ethylene copolymerization between layers of MMT to form LLDPE/MMT nanocomposites. The introduction of exfoliated MMT layers greatly improved the thermal stability and mechanical properties of LLDPE. Copyright © 2009 Society of Chemical Industry
Reproducibility, sensitivity and compatibility of the ProteoExtract® subcellular fractionation kit with saturation labeling of laser microdissected tissues
Authors: Sawhney Sonal , Stubbs Richard , Hood Kylie 
Published: August 2009

AbstractLaser microdissection (LMD), a method of isolating specific microscopic regions of interest from a tissue that has been sectioned, is increasingly being applied to study proteomics. LMD generally requires tissues to be fixed and histologically stained, which can interfere with protein recovery and subsequent analysis. We evaluated the compatibility and reproducibility of protein extractions from laser microdissected human colon mucosa using a subcellular fractionation kit (ProteoExtract®, Calbiochem). Four protein fractions corresponding to cytosol (fraction 1), membrane/organelle (fraction 2), nucleus (fraction 3) and cytoskeleton (fraction 4) were extracted, saturation labeled with Cy5 and 5 μg separated by both acidic (pH 4–7) and basic (pH 6–11) 2‐DE. The histological stains and fixation required for LMD did not interfere with the accurate subcellular fractionation of proteins into their predicted fraction. The combination of subcellular fractionation and saturation CyDye labeling produced very well resolved, distinct protein spot maps by 2‐DE for each of the subcellular fractions, and the total number of protein spots consistently resolved between three independent extractions for each fraction was 893, 1128, 1245 and 1577 for fractions 1, 2, 3 and 4, respectively. Although significant carryover of protein did occur between fractions, this carryover was consistent between experiments, and very low inter‐experimental variation was observed. In summary, subcellular fractionation kits are very compatible with saturation labeling DIGE of LMD tissues and provide greater coverage of proteins from very small amounts of microdissected material.
Proteomics of mouse liver microsomes: Performance of different protein separation workflows for LC‐MS/MS
Authors: Zgoda Victor G. , Moshkovskii Sergei A. , Ponomarenko Elena A. , Andreewski Timofey V. , Kopylov Arthur T. , Tikhonova Olga V. , Melnik Stanislav A. , Lisitsa Andrei V. , Archakov Alexander I. 
Published: August 2009

AbstractThe mouse liver microsome proteome was investigated using ion trap MS combined with three separation workflows including SDS‐PAGE followed by reverse‐phase LC of in‐gel protein digestions (519 proteins identified); 2‐D LC of protein digestion (1410 proteins); whole protein separation on mRP heat‐stable column followed by 2‐D LC of protein digestions from each fraction (3‐D LC; 3703 proteins). The higher number of proteins identified in the workflow corresponded to the lesser percentage of run‐to‐run reproducibility. Gel‐based method yielded a number of predicted membrane proteins similar to LC‐based workflows.
p35 interacts with α‐tubulin and organelle proteins: Nuclear translocation of p35 in dying cells
Authors: Son Yonghae , Kim Sunmi , Choi Kyungha , Park Youngchul , Eo Seongkug , Kim Youngkook , Rhim Byungyong , Kim Koanhoi 
Published: August 2009

AbstractWe identified heterogeneous nuclear ribonucleoprotein (hnRNP) C1/C2, hnRNP A1, the translocase of the transporter outer membrane 40 (TOM40), and α‐tubulin as new interaction partners of anti‐apoptotic protein p35 using MS‐based functional proteomics with GST‐p35 fusion protein as a bait, and using a pull‐down assay with p35‐6His followed by Western blot analysis. p35 was localized in the cytoplasm and in distinct organelles such as the nucleus and mitochondria. p35 was more abundant in the cytoplasm than it was in the nucleus. It co‐localized with α‐tubulin in the cytoplasm in the absence of a death stimulus. However, while cells were undergoing death induced by actinomycin D, cytoplasmic p35 was translocated into the nucleus; this process was inhibited by deletions of the N‐ and C‐terminal domains containing leucine‐rich motifs. Gene delivery of p35 using recombinant adenoviruses inhibited cytoplasmic compartmentalization of hnRNP C1/C2 and hnRNP A1 in dying cells. This study demonstrated translocation of p35 into the nuclei, as well as protection of the hnRNPs from redistribution in cells undergoing death. We propose an active role for p35 in maintaining the integrity of nuclear proteins during cell death.
A kinetic assessment of the C. elegans amyloid disaggregation activity enables uncoupling of disassembly and proteolysis
Authors: Bieschke Jan , Cohen Ehud , Murray Amber , Dillin Andrew , Kelly Jeffery W. 
Published: August 2009

AbstractProtein aggregation is a common feature of late onset neurodegenerative disorders, including Alzheimer's disease. In Alzheimer's disease, misassembly of the Aβ peptide is genetically linked to proteotoxicity associated with disease etiology. A reduction in Aβ proteotoxicity is accomplished, in part, by the previously reported Aβ disaggregation and proteolysis activities–under partial control of heat shock factor 1, a transcription factor regulating proteostasis in the cytosol and negatively regulated by insulin growth factor signaling. Herein, we report an improved in vitro assay to quantify recombinant fibrillar Aβ disaggregation kinetics accomplished by the exogenous application of C.elegans extracts. With this assay we demonstrate that the Aβ disaggregation and proteolysis activities of C.elegans are separable. The disaggregation activity found in C.elegans preparations is more heat resistant than the proteolytic activity. Aβ disaggregation in the absence of proteolysis was found to be a reversible process. Future discovery of the molecular basis of the disaggregation and proteolysis activities offers the promise of delaying the age‐onset proteotoxicity that leads to neurodegeneration in a spectrum of maladies.
Assessment of disorder predictions in CASP8
Authors: Noivirt‐Brik Orly , Prilusky Jaime , Sussman Joel L. 
Published: August 2009

AbstractThe interest in intrinsically disordered proteins has greatly increased, as it has become clear that they are very widespread, especially in eukaryotic organisms. Functionally, they appear to play a significant role in the control of many cellular processes and signalling pathways and have been, also, associated with a number of diseases ranging from cancer to Alzheimer's. Thus, there is enormous interest in attempts to predict disordered regions in proteins solely from knowledge of their amino acid sequences. In this study, we assess the quality of predictions for 25 groups on predicting disordered regions in 122 target proteins. In addition, we suggest the need of a “knowledge‐independent” measure that would enable one to normalize the results of the different CASP experiments and to determine whether the disorder prediction field had improved across the years. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Critical assessment of methods of protein structure prediction—Round VIII
Authors: Moult John , Fidelis Krzysztof , Kryshtafovych Andriy , Rost Burkhard , Tramontano Anna 
Published: August 2009

AbstractThis article is an introduction to the special issue of the journal Proteins, dedicated to the eighth CASP experiment to assess the state of the art in protein structure prediction. The article describes the conduct of the experiment, the categories of prediction included, and outlines the evaluation and assessment procedures. Highlights are the first blind assessment of model refinement methods showing that under some circumstances substantial model improvements are possible; improvements in the performance of methods for determining the accuracy of a model; and some progress in the accuracy of comparative models in regions not present in a principal template. Against these advances must be stacked the fact that there is no detectable progress in model quality compared with CASP7 in either template‐based or template free modeling, using the established CASP measures. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Modeling reaction routes from rhodopsin to bathorhodopsin
Authors: Khrenova M. G. , Bochenkova A. V. , Nemukhin A. V. 
Published: August 2009

AbstractThe quantum mechanical–molecular mechanical (QM/MM) theory was applied to calculate accurate structural parameters, vibrational and optical spectra of bathorhodopsin (BATHO), one of the primary photoproducts of the functional cycle of the visual pigment rhodopsin (RHO), and to characterize reaction routes from RHO to BATHO. The recently resolved crystal structure of BATHO (PDBID: 2G87) served as an initial source of coordinates of heavy atoms. Protein structures in the ground electronic state and vibrational frequencies were determined by using the density functional theory in the PBE0/cc‐pVDZ approximation for the QM part and the AMBER force field parameters in the MM part. Calculated and assigned vibrational spectra of both model protein systems, BATHO and RHO, cover three main regions referring to the hydrogen‐out‐of‐plan (HOOP) motion, the CC ethylenic stretches, and the CC single‐bond stretches. The S0–S1electronic excitation energies of the QM part, including the chromophore group in the field of the protein matrix, were estimated by using the advanced quantum chemistry methods. The computed structural parameters as well as the spectral bands match perfectly the experimental findings. A structure of the transition state on the S0potential energy surface for the ground electronic state rearrangement from RHO to BATHO was located proving a possible route of the thermal protein activation to the primary photoproduct. Proteins 2010. © 2009 Wiley‐Liss, Inc.