bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transmural myocardial strain in mouse: Quantification of high‐resolution MR tagging using harmonic phase (HARP) analysis
Authors: Zhong Jia , Liu Wei , Yu Xin 
Published: March 2009

AbstractMR tagging allows noninvasive examination of regional myocardial function with high accuracy and reproducibility. The current tagging method is limited by low tagging resolution for accurate transmural strain quantification. Previously, a spatial modulation of magnetization (SPAMM)‐based method was proposed to increase the tagging resolution by combining two or more tagged images with different tagging grid positions. However, there has been limited application due to the challenge in image processing of multiple data sets. In the current study, we propose a harmonic phase (HARP)‐based method for automated and fast analysis of high tagging resolution images. First‐order harmonic peaks from low tagging resolution images were combined to generate the composite second‐order harmonic peak for strain computation. The combined images reached a tagging resolution of 0.3 mm. The proposed method was applied to the quantification of transmural myocardial wall strain in seven normal C57BL/6 mice. Principal strains, as well as radial and circumferential strains, were quantified using the current method. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Strategies for reducing respiratory motion artifacts in renal perfusion imaging with arterial spin labeling
Authors: Robson Philip M. , Madhuranthakam Ananth J. , Dai Weiying , Pedrosa Ivan , Rofsky Neil M. , Alsop David C. 
Published: March 2009

AbstractArterial spin labeling (ASL) perfusion measurements may have many applications outside the brain. In the abdomen, severe image artifacts can arise from motions between acquisitions of multiple signal averages in ASL, even with single‐shot image acquisition. Background suppression and respiratory motion synchronization techniques can be used to ameliorate these artifacts. Two separate in vivo studies of renal perfusion imaging using pulsed continuous ASL (pCASL) were performed. The first study assessed various combinations of background suppression and breathing strategies. The second investigated the retrospective sorting of images acquired during free breathing based on respiratory position. Quantitative assessments of the test‐retest repeatability of perfusion measurements and the image quality scored by two radiologists were made. Image quality was most significantly improved by using background suppression schemes and controlled breathing when compared to other combinations without background suppression or with free breathing, assessed by test‐retests (5% level, F‐test), and by radiologists' scores (5% level, Mann‐Whitney U‐test). Under free breathing, retrospectively sorting images based on respiratory position showed significant improvement. Both radiologists found 100% of the images had preferable image sharpness after sorting. High‐quality renal perfusion measurements with reduced respiratory motion artifacts have been demonstrated using ASL when appropriate background suppression and breathing strategies are applied. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
MR spectroscopy of the human brain with enhanced signal intensity at ultrashort echo times on a clinical platform at 3T and 7T
Authors: Mekle Ralf , Mlynárik Vladimír , Gambarota Giulio , Hergt Martin , Krueger Gunnar , Gruetter Rolf 
Published: March 2009

AbstractRecently, the spin‐echo full‐intensity acquired localized (SPECIAL) spectroscopy technique was proposed to unite the advantages of short TEs on the order of milliseconds (ms) with full sensitivity and applied to in vivo rat brain. In the present study, SPECIAL was adapted and optimized for use on a clinical platform at 3T and 7T by combining interleaved water suppression (WS) and outer volume saturation (OVS), optimized sequence timing, and improved shimming using FASTMAP. High‐quality single voxel spectra of human brain were acquired at TEs below or equal to 6 ms on a clinical 3T and 7T system for six volunteers. Narrow linewidths (6.6 ± 0.6 Hz at 3T and 12.1 ± 1.0 Hz at 7T for water) and the high signal‐to‐noise ratio (SNR) of the artifact‐free spectra enabled the quantification of a neurochemical profile consisting of 18 metabolites with Cramér‐Rao lower bounds (CRLBs) below 20% at both field strengths. The enhanced sensitivity and increased spectral resolution at 7T compared to 3T allowed a two‐fold reduction in scan time, an increased precision of quantification for 12 metabolites, and the additional quantification of lactate with CRLB below 20%. Improved sensitivity at 7T was also demonstrated by a 1.7‐fold increase in average SNR (= peak height/root mean square [RMS]‐of‐noise) per unit‐time. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Numerical simulation of double‐wave vector experiments investigating diffusion in randomly oriented ellipsoidal pores
Authors: Koch Martin A. , Finsterbusch Jürgen 
Published: March 2009

AbstractDouble‐wave vector diffusion weighting is expected to represent a possibility to acquire information on cell size and shape. In numerical simulations, a theoretical description of the double wave vector‐weighted signal is tested in a situation where the approximating assumptions (infinitely short gradient pulses, infinitely long diffusion time, infinitely long or zero delay between diffusion weightings, small gradient moment) are not strictly met. It is shown how the dependence of the signal on the angle between the diffusion gradient directions changes upon varying the delay between the second and the third gradient pulse, and how the measures of pore geometry derived from signal differences between two angles depend on the duration, temporal separation, and amplitude of the gradient pulses. The results indicate that a violation of the approximation conditions due to finite gradient pulse duration and separation generally leads to an underestimation of pore size and pore eccentricity. It is also concluded from the simulations that for pore sizes on the order of 10 μm the investigated effects are in a range that is observable even with whole‐body gradient systems. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Controlled experimental study depicting moving objects in view‐shared time‐resolved 3D MRA
Authors: Mostardi Petrice M. , Haider Clifton R. , Rossman Phillip J. , Borisch Eric A. , Riederer Stephen J. 
Published: March 2009

AbstractVarious methods have been used for time‐resolved contrast‐enhanced magnetic resonance angiography (CE‐MRA), many involving view sharing. However, the extent to which the resultant image time series represents the actual dynamic behavior of the contrast bolus is not always clear. Although numerical simulations can be used to estimate performance, an experimental study can allow more realistic characterization. The purpose of this work was to use a computer‐controlled motion phantom for study of the temporal fidelity of three‐dimensional (3D) time‐resolved sequences in depicting a contrast bolus. It is hypothesized that the view order of the acquisition and the selection of views in the reconstruction can affect the positional accuracy and sharpness of the leading edge of the bolus and artifactual signal preceding the edge. Phantom studies were performed using dilute gadolinium‐filled vials that were moved along tabletop tracks by a computer‐controlled motor. Several view orders were tested using view‐sharing and Cartesian sampling. Compactness of measuring the k‐space center, consistency of view ordering within each reconstruction frame, and sampling the k‐space center near the end of the temporal footprint were shown to be important in accurate portrayal of the leading edge of the bolus. A number of findings were confirmed in an in vivo CE‐MRA study. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Time‐efficient fast spin echo imaging at 4.7 T with low refocusing angles
Authors: Lebel R. Marc , Wilman Alan H. 
Published: March 2009

AbstractAn implementation of fast spin echo at 4.7 T designed for versatile and time‐efficient T2‐weighted imaging of the human brain is presented. Reduced refocusing angles (α < 180°) were employed to overcome specific absorption rate (SAR) constraints and their effects on image quality assessed. Image intensity and tissue contrast variations from heterogeneous RF transmit fields and incidental magnetization transfer effects were investigated at reduced refocusing angles. We found that intraslice signal variations are minimized with refocusing angles near 180°, but apparent gray/white matter contrast is independent of refocusing angle. Incidental magnetization transfer effects from multislice acquisitions were shown to attenuate white matter intensity by 25% and gray matter intensity by 15% at 180°; less than 5% attenuation was seen in all tissues at flip angles below 60°. We present multislice images acquired without excess delay time for SAR mitigation using a variety of protocols. Subsecond half Fourier acquisition single‐shot turbo spin echo (HASTE) images were obtained with a novel variable refocusing angle echo train (20° < α < 58°) and high‐resolution scans with a voxel volume of 0.18 mm3 were acquired in 6.5 min with refocusing angles of 100°. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Meshfree co‐rotational formulation for two‐dimensional continua
Authors: Yaw L. L. , Sukumar N. , Kunnath S. K. 
Published: March 2009

AbstractIn this paper, a meshfree co‐rotational formulation for two‐dimensional continua is proposed. In a co‐rotational formulation, the motion of a body is separated into rigid motion and strain‐producing deformation. Traditionally, this has been done in the setting of finite elements for beams and shell‐type elements. In the present work every node in a meshfree discretized domain has its own co‐rotating coordinate system. Three key ingredients are established in order to apply the co‐rotational formulation: (i) the relationship between global and local variables, (ii) the angle of rotation of a typical co‐rotating coordinate system, and (iii) a variationally consistent tangent stiffness matrix. An algorithm for the co‐rotational formulation based on load control is provided. Maximum‐entropy basis functions are used to discretize the domain and stabilized nodal integration is implemented to construct the global system of equations. Numerical examples are presented to demonstrate the validity of the meshfree co‐rotational formulation. Copyright © 2009 John Wiley & Sons, Ltd.
It's a choice to move forward: women's perceptions about treatment decision making in recurrent ovarian cancer
Authors: Elit L. , Charles C. , Dimitry S. , Tedford‐Gold S. , Gafni A. , Gold I. , Whelan T. 
Published: March 2009

AbstractObjective: This research explores the treatment decision‐making (TDM) experiences of women with recurrent ovarian cancer (ROC) with regard to treatment options; their understanding of risks and benefits of various treatment options; the decision‐making role they want for themselves and for their oncologist; and the social context of the consultation as it pertains to the decision.Methods: We conducted semi‐structured interviews with 26 women at the time of first recurrence. Through inductive data analysis key themes were identified.Results: Many women describe self‐identifying the cancer recurrence fairly quickly due to new symptoms. Many feel that the goal for treating their recurrence is to control versus cure the cancer. They describe the subsequent process of diagnosis and TDM for ROC as quick and straightforward with all women accepting the oncologists' treatment recommendation. They feel that the type and number of treatment options are limited. They have a strong desire for physician continuity in their care. Participants feel that their doctor's recommendations as well as their previous experience with ovarian cancer are strong factors influencing their current TDM process.Conclusions: Shared decision making is based on a simultaneous participation of both the physician and patient in TDM. When faced with ROC, women feel that their doctor's recommendation and their past experience with treatment and TDM are prominent factors influencing the current TDM process. Copyright © 2009 John Wiley & Sons, Ltd.
Comprehensive secondary‐structure analysis of disulfide variants of lysozyme by synchrotron‐radiation vacuum‐ultraviolet circular dichroism
Authors: Matsuo Koichi , Watanabe Hidenori , Tate Shin‐ichi , Tachibana Hideki , Gekko Kunihiko 
Published: March 2009

AbstractTo elucidate the effects of specific disulfide bridges (Cys6‐Cys127, Cys30‐Cys115, Cys64‐Cys80, and Cys76‐Cys94) on the secondary structure of hen lysozyme, the vacuum‐ultraviolet circular dichroism (VUVCD) spectra of 13 species of disulfide‐deficient variants in which Cys residues were replaced with Ala or Ser residues were measured down to 170 nm at pH 2.9 and 25°C using a synchrotron‐radiation VUVCD spectrophotometer. Each variant exhibited a VUVCD spectrum characteristic of a considerable amount of residual secondary structures depending on the positions and numbers of deleted disulfide bridges. The contents of α‐helices, β‐strands, turns, and unordered structures were estimated with the SELCON3 program using the VUVCD spectra and PDB data of 31 reference proteins. The numbers of α‐helix and β‐strand segments were also estimated from the VUVCD data. In general, the secondary structures were more effectively stabilized through entropic forces as the number of disulfide bridges increased and as they were formed over larger distances in the primary structure. The structures of three‐disulfide variants were similar to that of the wild type, but other variants exhibited diminished α‐helices with a border between the ordered and disordered structures around the two‐disulfide variants. The sequences of the secondary structures were predicted for all the variants by combining VUVCD data with a neural‐network method. These results revealed the characteristic role of each disulfide bridge in the formation of secondary structures. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Solution structure of the DNA binding domain of AraC protein
Authors: Rodgers Michael E. , Schleif Robert 
Published: March 2009

AbstractWe report the solution structure of the DNA binding domain of the Escherichia coli regulatory protein AraC determined in the absence of DNA. The 20 lowest energy structures, determined on the basis of 1507 unambiguous nuclear Overhauser restraints and 180 angle restraints, are well resolved with a pair wise backbone root mean square deviation of 0.7 Å. The protein, free of DNA, is well folded in solution and contains seven helices arranged in two semi‐independent sub domains, each containing one helix‐turn‐helix DNA binding motif, joined by a 19 residue central helix. This solution structure is discussed in the context of extensive biochemical and physiological data on AraC and with respect to the DNA‐bound structures of the MarA and Rob homologs. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Combining interface core and whole interface descriptors in postscan processing of protein‐protein docking models
Authors: Kowalsman Noga , Eisenstein Miriam 
Published: March 2009

AbstractComputational protein‐protein docking scans commonly produce correct and nearly correct interaction models, but sometimes these models are ranked low. We present here postscan processing procedures that dramatically enhance the distinction between nearly correct and false predictions. The procedures employ propensity descriptors calculated for the interface core, an interface‐core clusters count, solvation energy, and a geometric‐electrostatic‐hydrophobic complementarity score. The various descriptors rank high different selections of false models (shuffling effect), and therefore, are used as Boolean yes/no classifiers in “soft intersection” filters, which eliminate large proportions of false models. Furthermore, the standardized descriptors are used in new scoring functions that highlight nearly correct models (NCMs). All the tests are performed on unbound docking models produced with MolFit without use of external data. We find that the discrimination between nearly correct and false models by the various descriptors is class dependent; hence, our postscan processing is class specific. The filters reduce the number of putative models from 10,726, 12,517, and 11,054 to 758, 157, and 1218 for enzyme‐inhibitor, antibody‐antigen, and nonclassified systems. When combined with the new scoring functions, they improve the average rank of the highest ranking NCMs from 673 to 122. Application to 23 CAPRI targets demonstrates the effectiveness of the postscan procedures in cases where external information is used in the production of the putative models. Our new per‐molecule residue propensity descriptors show that interacting interfaces are enriched with high propensity residues except for antigenic sites, which resemble more the noninteracting regions of protein surfaces. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Potential for microbial diuron mineralisation in a small wine‐growing watershed: from treated plots to lotic receiver hydrosystem
Authors: Pesce Stéphane , Martin‐Laurent Fabrice , Rouard Nadine , Montuelle Bernard 
Published: March 2009

AbstractBACKGROUND: Since biological degradation processes are known to be a major driver of the natural attenuation of pesticide residues in the environment, microbial communities adapted to pesticide biodegradation are likely to play a key environmental role in reducing pesticide exposure in contaminated ecosystems. The aim of this study was to assess the diuron‐mineralising potential of microbial communities at a small‐scale watershed level, including a diuron‐treated vineyard (pollution source), its associated grass buffer strip (as a river protection area against pesticide runoff) and the lotic receiver hydrosystem (sediments and epilithon), by using radiorespirometry.RESULTS: Comparison of results obtained at different sampling sites (in both soil and aquatic systems) revealed the importance of diuron exposure in the adaptation of microbial communities to rapid diuron mineralisation in the vineyard but also in the contaminated grass strip and in downstream epilithic biofilms and sediments.CONCLUSION: This study provides strong suggestive evidence for high diuron biodegradation potential throughout its course, from the pollution source to the final receiving hydrosystem, and suggests that, after microbial adaptation, grass strips may represent an effective environmental tool for mineralisation and attenuation of intercepted pesticides. Copyright © 2009 Society of Chemical Industry
Anderson localization: 2‐D system in an external magnetic field and the generalized diffusion approach
Authors: Kuzovkov V. N. 
Published: March 2009

AbstractThe analytical approach developed by us for the calculation of the phase diagram for the Anderson localization via disorder [J. Phys.: Condens. Matter 14, 13777 (2002)] is generalized here to the case of a strong magnetic field when q subbands (q = 1, 2, 3) arise. It is shown that in a line with the generally accepted point of view, each subband is characterized by a critical point with a divergent localization length ξ which reveals anomaly in energy and disorder parameters. These critical points belong to the phase coexistence area which cannot be interpreted by means of numerical investigations. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Mn and Si influence on the hyperfine properties of the fcc and hcp phases in the Fe–Mn and Fe–Mn–Si systems
Authors: Martínez Javier , Cotes Sonia M. , Desimoni Judith 
Published: March 2009

AbstractA study of the hyperfine properties of the fcc and hcp phases of the Fe–Mn and Fe–Mn–Si systems, performed on a systematic and accurate set of samples belonging to the 15 at% to 30 at% Mn and 0 at% to 12 at% Si composition ranges, is presented. The samples were characterized using Conversion Electron Mössbauer Spectroscopy. The evolution with the Mn and Si contents of the hyperfine parameters of both phases has been determined. A constancy of the isomer shift parameter of the hcp phase with both constituents of the alloy was observed. While constancy and a linear decrease of the isomer shift values of the fcc phase with Mn and Si, respectively, were determined. The magnetic hyperfine field of the fcc phase presents two different values depending on the Mn content in the binary system and a decrease with the addition of Si when the ternary alloy is considered. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Lost in space, the sequel: spatial sampling issues with 1‐D PHABSIM
Authors: Williams John G. 
Published: March 2009

AbstractThe Physical Habitat Simulation System (PHABSIM) is a popular method for evaluating the habitat value of a stream in terms of a statistic, weighted usable area (WUA). Usually, PHABSIM is used with one‐dimensional (1‐D) hydraulic models, and curves of WUA over discharge are calculated at transects and combined to produce a composite curve. Curves of WUA over discharge are often presented as evidence in proceedings to determine instream flow requirements, so the reliability of these curves is important. Representing a reach of stream with transects introduces ordinary statistical questions: is the sample of transects unbiased, and is it large enough to produce usefully precise estimates? Unfortunately, these questions are seldom considered in PHABSIM studies, even though most PHABSIM studies characterize streams with fewer than 15 transects. Moreover, transect locations usually are selected deliberately, so estimates of WUA will usually be biased. This paper extends an earlier analysis of the uncertainty in composite WUA curves with a much larger set of transect curves, with more analysis of uncertainty in the shape of the WUA curves, and with a different method for simulating errors in estimates of WUA at the transects. The results show that even with larger than usual numbers of transect curves, the precision of composite WUA curves is likely to be poor, especially if there are errors in the transect WUA curves. I also offer suggestions regarding sampling, and for estimating the number of transects that might be needed to achieve a given level of precision in WUA estimates. Copyright © 2009 John Wiley & Sons, Ltd.
Comparative toxicity of bentazon and molinate on growth, photosynthetic pigments, photosynthesis, and respiration of the Portuguese ricefield cyanobacterium Nostoc muscorum
Authors: Galhano Victor , Peixoto Francisco , Gomes‐Laranjo José , Fernández‐Valiente Eduardo 
Published: March 2009

AbstractBentazon and molinate are selective herbicides recommended for integrated weed management in rice. Their toxicity on growth and some biochemical and physiological parameters of Nostoc muscorum, an abundant cyanobacterium in Portuguese rice fields, was evaluated under laboratory conditions during time‐ and concentration‐dependent exposure for 72 h. Results showed that toxic concentrations (0.75–2 mM) of both herbicides have pleiotropic effects on the cyanobacterium. Molinate was more toxic than bentazon to growth, respiration, chlorophyll‐a, carotenoids, and phycobiliproteins contents. Protein content was increased by both herbicides although the effect was particularly evident with higher concentrations of molinate (1.5–2 mM). The herbicides had contrasting effects on carbohydrates content: molinate increased this organic fraction whereas bentazon decreased it. Photosynthesis and respiration were inhibited by both herbicides. © 2009 Wiley Periodicals, Inc. Environ Toxicol, 2010.