bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of multiexponential diffusion features as MRI cancer therapy response metrics
Authors: Hoff Benjamin A. , Chenevert Thomas L. , Bhojani Mahaveer S. , Kwee Thomas C. , Rehemtulla Alnawaz , Le Bihan Denis , Ross Brian D. , Galbán Craig J. 
Published: September 2010

AbstractThe aim of this study was to empirically test the effect of chemotherapy‐induced tissue changes in a glioma model as measured by several diffusion indices calculated from nonmonoexponential formalisms over a wide range of b‐values. We also compared these results to the conventional two‐point apparent diffusion coefficient calculation using nominal b‐values. Diffusion‐weighted imaging was performed over an extended range of b‐values (120–4000 sec/mm2) on intracerebral rat 9L gliomas before and after a single dose of 1,3‐bis(2‐chloroethyl)‐1‐nitrosourea. Diffusion indices from three formalisms of diffusion‐weighted signal decay [(a) two‐point analytical calculation using either low or high b‐values, (b) a stretched exponential formalism, and (c) a biexponential fit] were tested for responsiveness to therapy‐induced differences between control and treated groups. Diffusion indices sensitive to “fast diffusion” produced the largest response to treatment, which resulted in significant differences between groups. These trends were not observed for “slow diffusion” indices. Although the highest rate of response was observed from the biexponential formalism, this was not found to be significantly different from the conventional monoexponential apparent diffusion coefficient method. In conclusion, parameters from the more complicated nonmonoexponential formalisms did not provide additional sensitivity to treatment response in this glioma model beyond that observed from the two‐point conventional monoexponential apparent diffusion coefficient method. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Compressed sensing for chemical shift‐based water–fat separation
Authors: Doneva Mariya , Börnert Peter , Eggers Holger , Mertins Alfred , Pauly John , Lustig Michael 
Published: September 2010

AbstractMulti echo chemical shift‐based water–fat separation methods allow for uniform fat suppression in the presence of main field inhomogeneities. However, these methods require additional scan time for chemical shift encoding. This work presents a method for water–fat separation from undersampled data (CS‐WF), which combines compressed sensing and chemical shift‐based water–fat separation. Undersampling was applied in the k‐space and in the chemical shift encoding dimension to reduce the total scanning time. The method can reconstruct high quality water and fat images in 2D and 3D applications from undersampled data. As an extension, multipeak fat spectral models were incorporated into the CS‐WF reconstruction to improve the water–fat separation quality. In 3D MRI, reduction factors of above three can be achieved, thus fully compensating the additional time needed in three‐echo water–fat imaging. The method is demonstrated on knee and abdominal in vivo data. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Highly accelerated contrast‐enhanced MR angiography: Improved reconstruction accuracy and reduced noise amplification with complex subtraction
Authors: Koktzoglou Ioannis , Sheehan John J. , Dunkle Eugene E. , Breuer Felix A. , Edelman Robert R. 
Published: September 2010

AbstractContrast‐enhanced magnetic resonance angiography is routinely performed using parallel imaging to best capture the first pass of contrast material through the target vasculature, followed by digital subtraction to suppress the appearance of unwanted signal from background tissue. Both processes, however, amplify noise and can produce uninterpretable images when large acceleration factors are used. Using a phantom study of contrast‐enhanced magnetic resonance angiography, we show that complex subtraction processing prior to partially parallel reconstruction improves reconstruction accuracy relative to magnitude subtraction processing for reduction factors as large as 12. Time‐resolved contrast‐enhanced magnetic resonance angiographic data obtainedwith complex subtraction in volunteers supported the results of the phantom study and when compared with magnitude subtraction processing demonstrated reduced geometry factors as well as improved image quality at large reduction factors. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Dynamic contrast‐enhanced MRI of neuroendocrine hepatic metastases: A feasibility study using a dual‐input two‐compartment model
Authors: Koh T. S. , Thng C. H. , Hartono S. , Kwek J. W. , Khoo J. B. K. , Miyazaki K. , Collins D. J. , Orton M. R. , Leach M. O. , Lewington V. , Koh D.‐M. 
Published: September 2010

AbstractNeuroendocrine hepatic metastases exhibit various contrast uptake enhancement patterns in dynamic contrast‐enhanced MRI. Using a dual‐input two‐compartment distributed parameter model, we analyzed the dynamic contrast‐enhanced MRI datasets of seven patient study cases with the aim to relate the tumor contrast uptake patterns to parameters of tumor microvasculature. Simulation studies were also performed to provide further insights into the effects of individual microcirculatory parameter on the tumor concentration‐time curves. Although the tumor contrast uptake patterns can be influenced by many parameters, initial results indicate that hepatic blood flow and the ratio of fractional vascular volume to fractional interstitial volume may potentially distinguish between the patterns of neuroendocrine hepatic metastases. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Mapping of redox status in a brain‐disease mouse model by three‐dimensional EPR imaging
Authors: Fujii Hirotada , Sato‐Akaba Hideo , Kawanishi Katsuya , Hirata Hiroshi 
Published: September 2010

AbstractElectron paramagnetic resonance imaging using nitroxides is a powerful method for visualizing the redox status modulated by oxidative stress in vivo. Typically, however, data acquisition times have been too slow to obtain a sufficient number of projections for three‐dimensional images, when using continuous wave‐electron paramagnetic resonance imager in small rodents, using nitroxides with comparatively short T2 and a half‐life values. Because of improvements in imagers that enable rapid data‐acquisition, the feasibility of three‐dimensional electron paramagnetic resonance imaging with good quality in mice was tested with nitroxides. Three‐dimensional images of mice were obtained at an interval of 15 sec under field scanning of 0.3 sec and with 46 projections in the case of strong electron paramagnetic resonance signals. Three‐dimensional electron paramagnetic resonance images of a blood brain barrier‐permeable nitroxide, 3‐hydroxymethyl‐2,2,5,5‐tetramethylpyrrolidine‐1‐oxyl, in the mouse head clearly showed that 3‐hydroxymethyl‐2,2,5,5‐tetramethylpyrrolidine‐1‐oxyl was distributed within brain tissues, and this was confirmed by MRI observations. Based on the pharmacokinetics of nitroxides in mice, half‐life mapping was demonstrated in an ischemia‐reperfusion model mouse brain. Inhomogeneous half‐lives were clearly mapped pixel‐by‐pixel in mouse head under oxidative stress by the improved continuous wave‐electron paramagnetic resonance imager noninvasively. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Influence of brain tumors on the MR spectra of healthy brain tissue
Authors: Busch M. , Liebenrodt K. , Gottfried S. , Weiland E. , Vollmann W. , Mateiescu S. , Winter S. , Lange S. , Sahinbas H. , Baier J. , van Leeuwen P. , Grönemeyer D. 
Published: September 2010

AbstractThe neurochemical environment of nontumorous white matter tissue was investigated in 135 single voxel spectra of “healthy” white matter regions of 43 tumor patients and 129 spectra of 52 healthy subjects. Spectra were acquired with short TE and TR values. With the data of tumor patients, it was examined whether differences were caused by the tumor itself or aggressive tumor therapies as confounding factors. Comparing the spectra of both classes, an excellent differentiation was possible based on the metabolite peak of N‐acetylaspartate (P ≈ 0) and myoinositol (P < 0.03). The area under curve of the receiver operating characteristic was calculated as 0.86 and 0.62, respectively. With linear discriminant analysis using combinations of integrals, a prediction was possible, whether a spectrum belonged to the patient or the healthy subject class with an overall accuracy above 80%. The confounding factors could be ruled out as source of the differences. The results show strong evidence for an influence of malignant growth on the biochemical environment of nontumorous white matter tissue. Because of the T1 weighting, the measured differences between both classes were most likely concentration changes interfered by T1 effects. The underlying processes will be subject of future studies. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Post‐processing correction of magnetization transfer effects in FENSI perfusion MRI data
Authors: Reynaud Olivier , Ciobanu Luisa 
Published: September 2010

AbstractMagnetization transfer effects induced by repetitive saturation pulses employed in flow enhancement of signal intensity imaging sequences currently prevent quantitative, in vivo, cerebral perfusion studies. This study investigates the magnitude of these effects and introduces a post‐processing correction protocol. The study shows that the magnetization transfer effect is consistent across individuals, which enables the derivation of a correction factor to be applied in post‐acquisition. Our results, obtained for cerebral flux in white and gray matter in rodent brains, are in agreement with cerebral blood flow measurements previously reported in the literature. Magn Reson Med, 2011. © 2010 Wiley‐Liss, Inc.
Measuring perfusion and bioenergetics simultaneously in mouse skeletal muscle: a multiparametric functional‐NMR approach
Authors: Baligand C. , Wary C. , Ménard J. C. , Giacomini E. , Hogrel J.‐Y. , Carlier P. G. 
Published: September 2010

AbstractA totally noninvasive set‐up was developed for comprehensive NMR evaluation of mouse skeletal muscle function in vivo. Dynamic pulsed arterial spin labeling‐NMRI perfusion and blood oxygenation level‐dependent (BOLD) signal measurements were interleaved with 31P NMRS to measure both vascular response and oxidative capacities during stimulated exercise and subsequent recovery. Force output was recorded with a dedicated ergometer. Twelve exercise bouts were performed. The perfusion, BOLD signal, pH and force–time integral were obtained from mouse legs for each exercise. All reached a steady state after the second exercise, justifying the pointwise summation of the last 10 exercises to compensate for the limited 31P signal. In this way, a high temporal resolution of 2.5 s was achieved to provide a time constant for phosphocreatine (PCr) recovery (τPCr). The higher signal‐to‐noise ratio improved the precision of τPCr measurement [coefficient of variation (CV) = 16.5% vs CV = 49.2% for a single exercise at a resolution of 30 s]. Inter‐animal summation confirmed that τPCr was stable at steady state, but shorter (89.3 ± 8.6 s) than after the first exercise (148 s, p < 0.05). This novel experimental approach provides an assessment of muscle vascular response simultaneously to energetic function in vivo. Its pertinence was illustrated by observing the establishment of a metabolic steady state. This comprehensive tool offers new perspectives for the study of muscle pathology in mice models. Copyright © 2010 John Wiley & Sons, Ltd.
A novel approach for anionic bulk polymerization of 1,3,5‐tris(trifluoropropylmethyl)cyclotrisiloxane
Authors: Gao Yajuan , Jiang Wei , Guan Yong , Yang Peng , Zheng Anna 
Published: September 2010

AbstractPresent work gave a new method for preparing polymethyl(3,3,3‐trifluoropropyl)siloxane (PMTFPS) in the mixing chamber of a torque rheometer using sodium silanolate as initiator, and ethyl acetate (EA) and dimethyl sulfoxide (DMSO) as promoters. The promoting effect of EA in the anionic bulk polymerization of 1,3,5‐tris(trifluoropropylmethyl) cyclotrisiloxane (F3) was investigated in comparison with DMSO, a common promoter. Results showed that EA exhibited an effective promoting effect as DMSO did. When the polymerization was carried out for 4.0 min at 120°C in the presence of 0.30 mol L−1 EA, the maximum of number average molecular weight (Mn = 2.45 × 105 g mol−1) of PMTFPS was obtained with high yield (89.2 wt%). The back‐biting reactions during the polymerization were almost suppressed and less than 0.75 wt% cyclic by‐products were obtained by matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry (MALDI‐TOF‐MS) for EA promoter system. Investigations of differential scanning calorimetry and thermogravimetic analysis showed that PMTFPS could be used in a wide range of operational temperatures. POLYM. ENG. SCI., 2010. © 2010 Society of Plastics Engineers
Manufacturing and testing of long basalt fiber reinforced thermoplastic matrix composites
Authors: Deák Tamás , Czigány Tibor , Maršálková Miroslava , Militký Jiří 
Published: September 2010

AbstractIn this work, long basalt fiber reinforced composites were investigated and compared with short basalt fiber reinforced compounds. The results show that long fiber reinforced thermoplastic composites are particularly advantageous in the respects of dynamic mechanical properties and injection molding shrinkage. The fiber orientation in long basalt fiber reinforced products fundamentally differs from short basalt fiber reinforced ones. This results in more isotropic molding shrinkage in case of long basalt fiber reinforced composites. The main advantage of the used long fiber thermoplastic technology is that the special long fiber reinforced pellet can be processed by most conventional injection molding machines. During extrusion compounding the fibers in the compound containing 30 wt% fibers are fragmented to an average length of 0.48 mm (typical of short fiber reinforced thermoplastic compounds), this length decreases further during injection molding to 0.20 mm. Contrarily using long fiber reinforced pellets and cautious injection molding parameters, an average fiber length of 1.8 mm can be achieved with a conventional injection molding machine, which increased the average length/diameter ratio from 14 to 130. POLYM. ENG. SCI., 2010. © 2010 Society of Plastics Engineers
Influence of processing condition and HA content on the crystallization behavior of HA‐filled EVA biocomposite
Authors: Wang Yanying , Zhang Li , Zhou Song , Huang Di , Gao Shibo , Gong Mei , Li Yubao 
Published: September 2010

AbstractHydroxyapatite/ethylene‐vinyl acetate (HA/EVA) composites with a HA content of 30 and 50 wt% were prepared by injection molding. The crystallization behaviors of EVA under different injection pressure, annealing temperature, and HA content were investigated. Fourier transform infrared spectroscopy (FTIR), X‐ray diffraction (XRD), differential scanning calorimetry (DSC), and scanning electron microscope were used to evaluate the composites. The result of FTIR analysis infers the occurrence of hydrogen bonding between HA and EVA. XRD and DSC analyses show that the increasing injection pressure can accelerate the crystallization rate of EVA but it tends to decrease the crystallization degree slightly, which may be caused by the increase of EVA segmental activity and the loss of EVA crystallization order with the increase of pressure. The EVA crystallization degree can be improved by the annealing process. It is found that HA can induce more nucleation sites of EVA, but the crystallization degree of EVA decreases with the increase of HA content. The large content of HA acts to reduce the mobility of EVA crystallizable chain segments and inhibits the crystal growth of EVA. POLYM. ENG. SCI., 2011. © 2010 Society of Plastics Engineers
Structural determinants of tobacco vein mottling virus protease substrate specificity
Authors: Sun Ping , Austin Brian P. , Tözsér József , Waugh David S. 
Published: September 2010

AbstractTobacco vein mottling virus (TVMV) is a member of the Potyviridae, one of the largest families of plant viruses. The TVMV genome is translated into a single large polyprotein that is subsequently processed by three virally encoded proteases. Seven of the nine cleavage events are carried out by the NIa protease. Its homolog from the tobacco etch virus (TEV) is a widely used reagent for the removal of affinity tags from recombinant proteins. Although TVMV protease is a close relative of TEV protease, they exhibit distinct sequence specificities. We report here the crystal structure of a catalytically inactive mutant TVMV protease (K65A/K67A/C151A) in complex with a canonical peptide substrate (Ac‐RETVRFQSD) at 1.7‐Å resolution. As observed in several crystal structures of TEV protease, the C‐terminus (∼20 residues) of TVMV protease is disordered. Unexpectedly, although deleting the disordered residues from TEV protease reduces its catalytic activity by ∼10‐fold, an analogous truncation mutant of TVMV protease is significantly more active. Comparison of the structures of TEV and TVMV protease in complex with their respective canonical substrate peptides reveals that the S3 and S4 pockets are mainly responsible for the differing substrate specificities. The structure of TVMV protease suggests that it is less tolerant of variation at the P1′ position than TEV protease. This conjecture was confirmed experimentally by determining kinetic parameters kcat and Km for a series of oligopeptide substrates. Also, as predicted by the cocrystal structure, we confirm that substitutions in the P6 position are more readily tolerated by TVMV than TEV protease.
Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit
Authors: Skjaerven Lars , Martinez Aurora , Reuter Nathalie 
Published: September 2010

AbstractPrincipal component analysis (PCA) and normal mode analysis (NMA) have emerged as two invaluable tools for studying conformational changes in proteins. To compare these approaches for studying protein dynamics, we have used a subunit of the GroEL chaperone, whose dynamics is well characterized. We first show that both PCA on trajectories from molecular dynamics (MD) simulations and NMA reveal a general dynamical behavior in agreement with what has previously been described for GroEL. We thus compare the reproducibility of PCA on independent MD runs and subsequently investigate the influence of the length of the MD simulations. We show that there is a relatively poor one‐to‐one correspondence between eigenvectors obtained from two independent runs and conclude that caution should be taken when analyzing principal components individually. We also observe that increasing the simulation length does not improve the agreement with the experimental structural difference. In fact, relatively short MD simulations are sufficient for this purpose. We observe a rapid convergence of the eigenvectors (after ca. 6 ns). Although there is not always a clear one‐to‐one correspondence, there is a qualitatively good agreement between the movements described by the first five modes obtained with the three different approaches; PCA, all‐atoms NMA, and coarse‐grained NMA. It is particularly interesting to relate this to the computational cost of the three methods. The results we obtain on the GroEL subunit contribute to the generalization of robust and reproducible strategies for the study of protein dynamics, using either NMA or PCA of trajectories from MD simulations. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Mapping mouse IL‐13 binding regions using structure modeling, molecular docking, and high‐density peptide microarray analysis
Authors: Madala Satish K. , Dolan Michael A. , Sharma Deepak , Ramalingam Thirumalai R. , Wilson Mark S. , Mentink‐Kane Margaret M. , Masison Daniel C. , Wynn Thomas A. 
Published: September 2010

AbstractInterleukin‐13 is a Th2‐associated cytokine responsible for many pathological responses in allergic asthma including mucus production, inflammation, and extracellular matrix remodeling. In addition, IL‐13 is required for immunity to many helminth infections. IL‐13 signals via the type‐II IL‐4 receptor, a heterodimeric receptor of IL‐13Rα1 and IL‐4Rα, which is also used by IL‐4. IL‐13 also binds to IL‐13Rα2, but with much higher affinity than the type‐II IL‐4 receptor. Binding of IL‐13 to IL‐13Rα2 has been shown to attenuate IL‐13 signaling through the type‐II IL‐4 receptor. However, molecular determinants that dictate the specificity and affinity of mouse IL‐13 for the different receptors are largely unknown. Here, we used high‐density overlapping peptide arrays, structural modeling, and molecular docking methods to map IL‐13 binding sequences on its receptors. Predicted binding sequences on mouse IL‐13Rα1 and IL‐13Rα2 were in agreement with the reported human IL‐13 receptor complex structures and site‐directed mutational analysis. Novel structural differences were identified between IL‐13 receptors, particularly at the IL‐13 binding interface. Notably, additional binding sites were observed for IL‐13 on IL‐13Rα2. In addition, the identification of peptide sequences that are unique to IL‐13Rα1 allowed us to generate a monoclonal antibody that selectively binds IL‐13Rα1. Thus, high‐density peptide arrays combined with molecular docking studies provide a novel, rapid, and reliable method to map cytokine‐receptor interactions that may be used to generate signaling and decoy receptor‐specific antagonists. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Improved identification of outer membrane beta barrel proteins using primary sequence, predicted secondary structure, and evolutionary information
Authors: Mizianty Marcin J. , Kurgan Lukasz 
Published: September 2010

AbstractMembrane proteins (MPs) are difficult to identify in genomes and to crystallize, making it hard to determine their tertiary structures. MPs could be categorized into α‐helical (AMP) and outer membrane proteins which mostly include beta barrel folds (OMBBs). The AMPs are relatively easy to predict from a protein sequence because they usually include several long membrane‐spanning hydrophobic α‐helices. The OMBBs play important roles in cell biology, they are targeted by multiple drugs, and they are more challenging to identify as they have shorter membrane‐spanning regions which lack a folding patern, that is, as consistent as in the case of the AMPs. Hence, accurate in silico methods for prediction of OMBBs from their primary sequences are needed. We present an accurate sequence‐based predictor of OMBBs, called OMBBpred, which utilizes a Support Vector Machine classifier and a custom‐designed set of 34 novel numerical descriptors derived from predicted secondary structures, hydrophobicity, and evolutionary information. Our method outperforms modern existing OMBB predictors and achieves accuracy of above 98% when tested on two existing benchmark datasets and 96% on a new large dataset. OMBBpred reduces the error rates of the second best method, depending on the dataset used, by between 13 and 65%, and generates predictions with high specificity of above 96%. Our solution is a useful tool for high‐throughput discovery of the OMBBs on a genome scale and can be found at http://biomine.ece. ualberta.ca/OMBBpred/OMBBpred.htm. Proteins 2010. © 2010 Wiley‐Liss, Inc.