bluuebunny/crossref_metadata_2025_split huggingface dataset:
B0 mapping with multi‐channel RF coils at high field
Authors: Robinson Simon , Jovicich Jorge 
Published: May 2011

AbstractMapping the static magnetic field via the phase evolution over gradient echo scans acquired at two or more echo times is an established method. A number of possibilities exist, however, for combining phase data from multi‐channel coils, denoising and thresholding field maps for high field applications. Three methods for combining phase images when no body/volume coil is available are tested: (i) Hermitian product, (ii) phase‐matching over channels, and (iii) a new approach based on calculating separate field maps for each channel. The separate channel method is shown to yield field maps with higher signal‐to‐noise ratio than the Hermitian product and phase‐matching methods and fewer unwrapping errors at low signal‐to‐noise ratio. Separate channel combination also allows unreliable voxels to be identified via the standard deviation over channels, which is found to be the most effective means of denoising field maps. Tests were performed using multichannel coils with between 8 and 32 channels at 3 T, 4 T, and 7 T. For application in the correction of distortions in echo‐planar images, a formulation is proposed for reducing the local gradient of field maps to eliminate signal pile‐up or swapping artifacts. Field maps calculated using these techniques, implemented in a freely available MATLAB toolbox, provide the basis for an effective correction for echo‐planar imaging distortions at high fields. Magn Reson Med, 2011. © 2011 Wiley‐Liss, Inc.
Sparse‐CAPR: Highly accelerated 4D CE‐MRA with parallel imaging and nonconvex compressive sensing
Authors: Trzasko Joshua D. , Haider Clifton R. , Borisch Eric A. , Campeau Norbert G. , Glockner James F. , Riederer Stephen J. , Manduca Armando 
Published: May 2011

AbstractCartesian Acquisition with Projection‐Reconstruction‐like sampling is a SENSE‐type parallel 3DFT acquisition paradigm for 4D contrast‐enhanced magnetic resonance angiography that has been demonstrated capable of providing high spatial and temporal resolution, diagnostic‐quality images at very high acceleration rates. However, Cartesian Acquisition with Projection–Reconstruction‐like sampling images are typically reconstructed online using Tikhonov regularization and partial Fourier methods, which are prone to exhibit noise amplification and undersampling artifacts when operating at very high acceleration rates. In this work, a sparsity‐driven offline reconstruction framework for Cartesian Acquisition with Projection‐Reconstruction‐like sampling is developed and demonstrated to consistently provide improvements over the currently‐employed reconstruction strategy against these ill‐effects. Moreover, the proposed reconstruction strategy requires no changes to the existing Cartesian Acquisition with Projection–Reconstruction‐like sampling acquisition protocol, and an efficient numerical optimization and hardware system are described that allow for a 256 × 160 × 80 volume contrast‐enhanced magnetic resonance angiography volume to be reconstructed from an eight‐channel data set in less than 2 min. Magn Reson Med, 2011. © 2011 Wiley‐Liss, Inc.
Amide proton transfer imaging with improved robustness to magnetic field inhomogeneity and magnetization transfer asymmetry using saturation with frequency alternating RF irradiation
Authors: Scheidegger Rachel , Vinogradov Elena , Alsop David C. 
Published: May 2011

AbstractAmide proton transfer (APT) imaging has shown promise as an indicator of tissue pH and as a marker for brain tumors. Sources of error in APT measurements include direct water saturation, and magnetization transfer (MT) from membranes and macromolecules. These are typically suppressed by postprocessing asymmetry analysis. However, this approach is strongly dependent on B0 homogeneity and can introduce additional errors due to intrinsic MT asymmetry, aliphatic proton features opposite the amide peak and radiation damping‐induced asymmetry. Although several methods exist to correct for B0 inhomogeneity, they tremendously increase scan times and do not address errors induced by asymmetry of the z‐spectrum. In this article, a novel saturation scheme—saturation with frequency alternating RF irradiation (SAFARI)—is proposed in combination with a new magnetization transfer ratio (MTR) parameter designed to generate APT images insensitive to direct water saturation and MT, even in the presence of B0 inhomogeneity. The feasibility of the SAFARI technique is demonstrated in phantoms and in the human brain. Experimental results show that SAFARI successfully removes direct water saturation and MT contamination from APT images. It is insensitive to B0 offsets up to 180 Hz without using additional B0 correction, thereby dramatically reducing scanning time. Magn Reson Med, 2011. © 2011 Wiley Periodicals, Inc.
2H2O incorporation into hepatic acetyl‐CoA and de novo lipogenesis as measured by Krebs cycle‐mediated 2H‐enrichment of glutamate and glutamine
Authors: Silva Ana Maria , Martins Fatima , Jones John G. , Carvalho Rui 
Published: May 2011

AbstractDeuterated water is widely used for measuring de novo lipogenesis on the basis of quantifying lipid 2H‐enrichment relative to that of body water. However, incorporation of 2H‐enrichment from body water into newly synthesized lipid molecules is incomplete therefore the true lipid precursor enrichment differs from that of body water. We describe a novel measurement of de novo lipogenesis that is based on a true precursor‐product analysis of hepatic acetyl‐CoA and triglyceride methyl enrichments from deuterated water. After deuterated water administration to seven in situ and seven perfused livers, acetyl‐CoA methyl enrichment was inferred from 2H nuclear magnetic resonance analysis of hepatic glutamate/glutamine (Glx) enrichment and triglyceride methyl enrichment was directly determined by 2H nuclear magnetic resonance of triglycerides. Acetyl‐CoA 2H‐enrichment was 71% ± 1% that of body water for in situ livers and 53% ± 2% of perfusate water for perfused livers. From the ratio of triglyceride‐methyl/acetyl‐CoA enrichments, fractional de novo lipogenesis rates of 0.97% ± 0.09%/2 hr and 7.92% ± 1.47%/48 hr were obtained for perfused and in situ liver triglycerides, respectively. Our method reveals that acetyl‐CoA enrichment is significantly less than body water both for in situ and perfused livers. Furthermore, the difference between acetyl‐CoA and body water enrichments is sensitive to the experimental setting. Magn Reson Med, 2011. © 2011 Wiley Periodicals, Inc.
Discrete differential operators on irregular nodes (DDIN)
Authors: Isshiki H. 
Published: May 2011

AbstractA previous research made an integral mathematical contribution for obtaining local function interpolation using neighboring nodal values of the solution function. Subsequent researchers developed mesh‐free methods for Finite Element Method (FEM). This principle can also be used to obtain discrete differential operators on irregular nodes. They may be successfully applied to Finite Difference method, Moving Particle Semi‐implicit (MPS) method and Random Collocation Method (RCM). In this paper, we obtain discrete differential operators on irregular nodes and successfully apply them to solve differential equations using the RCM. We also discuss mathematical aspects of the MPS method. Copyright © 2011 John Wiley & Sons, Ltd.
The dynamic protein partnership of RNA polymerase inBacillus subtilis
Authors: Delumeau Olivier , Lecointe François , Muntel Jan , Guillot Alain , Guédon Eric , Monnet Véronique , Hecker Michael , Becher Dörte , Polard Patrice , Noirot Philippe 
Published: May 2011

AbstractIn prokaryotes, transcription results from the activity of a 400 kDa RNA polymerase (RNAP) protein complex composed of at least five subunits (2α, β, β′, ω). To ensure adequate responses to changing environmental cues, RNAP activity is tightly controlled by means of interacting regulatory proteins. Here, we report the affinity‐purification of the Bacillus subtilis RNAP complexes from cells in different growth states and stress conditions, and the quantitative assessment by mass spectrometry of the dynamic changes in the composition of the RNAP complex. The stoichiometry of RNA polymerase was determined by a comparison of two mass spectrometry‐based quantification methods: a label‐based and a label‐free method. The validated label‐free method was then used to quantify the proteins associated with RNAP. The levels of sigma factors bound to RNAP varied during growth and exposure to stress. Elongation factors, helicases such as HelD and PcrA, and novel unknown proteins were also associated with RNAP complexes. The content in 6S RNAs of purified RNAP complexes increased at the onset of the stationary phase. These quantitative variations in the protein and RNA composition of the RNAP complexes well correlate with the known physiology of B. subtilis cells under different conditions.
Combined proteomic and transcriptomic analysis of the response of Bacillus anthracis to oxidative stress
Authors: Pohl Susanne , Tu Wang Y. , Aldridge Phillip D. , Gillespie Colin , Hahne Hannes , Mäder Ulrike , Read Timothy D. , Harwood Colin R. 
Published: May 2011

AbstractThe endospore‐forming Gram‐positive pathogen Bacillus anthracis is responsible for the usually fatal disease, inhalational anthrax. The success of this pathogen is dependent on its ability to subvert elements of the innate immune system of its animal hosts. B. anthracis spores, which are the main infective agent, are engulfed and germinate in patrolling alveolar macrophages. In order for the infection to progress, the resulting vegetative cells must resist the antimicrobial oxidative burst mounted by the host NADPH oxidase complex. The response of B. anthracis to this and other macrophage‐related stresses is therefore of major importance to the success of this pathogen, and consequently we have analysed the superoxide and peroxide stress stimulons of B. anthracis strain UM23C1‐2 by means of a combined transcriptomics and proteomics approach. The results show distinct patterns of expression in response to paraquat (endogenous superoxide) and hydrogen peroxide stress. While the main response to paraquat is the induction of iron uptake pathways, the response to peroxide predominantly involves the induction of protection and repair mechanisms. Comparisons between the responses of B. anthracis and related soil bacterium, B. subtilis, reveal differences that are likely to be relevant to their respective habitats.
Synthesis and properties of mesogen‐jacketed liquid crystalline polymers containing biphenyl mesogen with asymmetric substitutions
Authors: Zhang Lanying , Wu Hongliang , Shen Zhihao , Fan Xinghe , Zhou Qifeng 
Published: May 2011

AbstractThis work focuses on the design, synthesis, and characterization of a series of mesogen‐jacketed liquid crystalline polymers (MJLCPs), poly(alkyl 4′‐(octyloxy)‐2‐vinylbiphenyl‐4‐carboxylate) (pVBP(m,8), m = 1, 2, 4, 6, 8, 10, 12). For the first time, we realized asymmetric substitutions in the mesogens of MJLCPs. The polymers obtained by conventional free radical polymerization were investigated in detail by a combination of various techniques, such as differential scanning calorimetry, wide‐angle X‐ray diffraction, and polarized light microscopy. Our results showed that all the polymers were thermally stable, and their glass transition temperatures decreased when m increased. The liquid crystalline (LC) phases that developed at high temperatures and disappeared at low temperatures were strongly dependent on the difference in lengths of alkyl groups on the 4 and 4′ substitution positions of the side‐chain biphenyl. While polymer pVBP(1,8) was not liquid crystalline, columnar liquid crystalline phases were observed for all other pVBP(m,8) (m = 2, 4, 6, 8, 10, 12) polymers. Polymer pVBP(8,8) showed a tetragonal columnar nematic liquid crystalline phase, and the other LC polymers exhibited columnar nematic phases. In additions, the smaller the difference in the lengths of the terminal alkyls, the easier the development of the liquid crystalline phase. Birefringence measurements showed that solution‐cast polymer films exhibited moderately high positive birefringence values, indicating potential applications as optical compensation films for liquid crystal displays. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Synthesis strategies to incorporate acrylic acid into N‐vinylcaprolactam‐based microgels
Authors: Imaz Ainara , Forcada Jacqueline 
Published: May 2011

AbstractTwo different synthesis strategies were used to synthesize N‐vinylcaprolactam (VCL)‐acrylic acid (AA)‐based temperature‐ and pH‐sensitive microgels under the adequate conditions to avoid possible hydrolysis of VCL due to the presence of carboxylic groups provided by AA. Polymeric and colloidal features of the microgels were analyzed: the partial conversion evolutions of each comonomer were determined by 1H NMR and the swelling/deswelling behavior by means of Photon Correlation Spectroscopy. Considering that microgels are porous soft nanoparticles, conductimetric titrations at the swollen state were carried out to calculate the volumetric charge density. The results indicate that the addition of AA after 30 minutes of reaction time helped to incorporate higher amounts of AA into microgels and as a result, to obtain both temperature‐ and pH‐sensitive nanoparticles. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Influence of polymer backbone branching on liquid crystal mesomorphous in nonequimolar complexes of poly(ethyleneimine) and dendritic amphiphiles
Authors: Cheng Zhiyu , Ren Biye , Li Chongqing , Liu Xinxing , Tong Zhen 
Published: May 2011

AbstractTwo kinds of ionic self‐assembled complexes of linear or branched poly(ethyleneimine) (lPEI or bPEI) with Percec‐type dendrons [(3,4,5)16G1‐COOH] were prepared as lPEI‐(3,4,5)16G1‐x and bPEI‐(3,4,5)16G1‐x, where x is the mole ratio of the carboxyl groups of the dendritic amphiphile to the amino groups at the PEI chain. The crystal and mesomorphous structures and thermal properties of these complexes were investigated with X‐ray diffraction (XRD), Fourier transform infrared (FTIR), differential scanning calorimetry (DSC), and polarized optical microscope (POM). Both the lPEI and bPEI complexes exhibited the same αH crystal phase and similar lamellar mesomorphous phase, irrespective of the branching of the polymer backbone and the binding degree. The lPEI series complexes lPEI‐(3,4,5)16G1‐x, however, had more ordered lamellar stacking than that of the bPEI‐(3,4,5)16G1‐x complexes, so the thermotropic liquid crystal phase SmA was formed only in the lPEI‐(3,4,5)16G1‐x complexes beyond the melting point of the tail crystal of the dendritic amphiphile. No liquid crystalline phase was found from the bPEI‐(3,4,5)16G1‐x complexes. The results suggest that the branching of polymer backbone plays a key role to the formation of thermotropic liquid crystal in the polymer–dendritic amphiphile complex. The present finding is significant for the design of functional nanostructures based on the ionic complexation of polymers and amphiphiles. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011
Biochemical and structural studies on the high affinity of Hsp70 for ADP
Authors: Arakawa Akihiko , Handa Noriko , Shirouzu Mikako , Yokoyama Shigeyuki 
Published: May 2011

AbstractThe molecular chaperone 70‐kDa heat shock protein (Hsp70) is driven by ATP hydrolysis and ADP–ATP exchange. ADP dissociation from Hsp70 is reportedly slow in the presence of inorganic phosphate (Pi). In this study, we investigated the interaction of Hsp70 and its nucleotide‐binding domain (NBD) with ADP in detail, by isothermal titration calorimetry measurements and found that Mg2+ ion dramatically elevates the affinity of Hsp70 for ADP. On the other hand, Pi increased the affinity in the presence of Mg2+ ion, but not in its absence. Thus, Pi enhances the effect of the Mg2+ ion on the ADP binding. Next, we determined the crystal structures of the ADP‐bound NBD with and without Mg2+ ion. As compared with the Mg2+ ion‐free structure, the ADP‐ and Mg2+ ion‐bound NBD contains one Mg2+ ion, which is coordinated with the β‐phosphate group of ADP and associates with Asp10, Glu175, and Asp199, through four water molecules. The Mg2+ ion is also coordinated with one Pi molecule, which interacts with Lys71, Glu175, and Thr204. In fact, the mutations of Asp10 and Asp199 reduced the affinity of the NBD for ADP, in both the presence and the absence of Pi. Therefore, the Mg2+ ion‐mediated network, including the Pi and water molecules, increases the affinity of Hsp70 for ADP, and thus the dissociation of ADP is slow. In ADP–ATP exchange, the slow ADP dissociation might be rate‐limiting. However, the nucleotide‐exchange factors actually enhance ADP release by disrupting the Mg2+ ion‐mediated network.
Micro‐machined fluidic devices for terahertz time‐domain spectroscopy
Authors: Baragwanath Adam J. , Swift G. Peter , Dai DeChang , Zeze Dagou , Gallant Andrew J. , Chamberlain J. Martyn 
Published: May 2011

AbstractHere we present a silicon based, micro‐machined fluidic device for terahertz frequencies, fabricated using standard lithographic and micro‐machining processes in a cleanroom environment. Designed for use in a conventional transmission terahertz time‐domain spectroscopy (THz‐TDS) arrangement, we present a possible solution to the ‘water problem’ currently hampering the analysis of aqueous and biological systems at THz frequencies. We detail results from a range of experiments, highlighting the device sensitivity and potential, wide‐ranging applications. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Spectral features of specular reflection from nanoparticle films
Authors: Fokine M. , Jang Hoon , Gouvêa P. M. P. , Braga A. M. B. , Carvalho I. C. S. 
Published: May 2011

AbstractIn this work we analyze the internal reflection (Fresnel reflection) from Au nanoparticles on the end face of optical fibers. We demonstrate that changes in the refractive index of the surrounding medium can be detected by shifts in the reflection spectra associated with changes in the Localized Surface Plasmon Resonance of the Au‐Nanoparticles. The spectral response is simulated using a model based on the interference in multilayer structures and can be described by transfer‐matrix method. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optical properties of amorphous hydrogenated and microcrystalline silicon films prepared by plasma enhanced chemical vapor deposition and re‐crystallized at moderate temperatures
Authors: Netrvalova Marie , Prusakova Lucie , Mullerova Jarmila , Sutta Pavol 
Published: May 2011

AbstractAmorphous hydrogenated silicon films different in thickness (600 – 2400 nm) were deposited by plasma enhanced chemical vapour deposition on Corning glass substrates at 250 °C using silan 10% / argon 90% gas mixture. The samples were consequently isothermally heated in a high temperature vacuum chamber at 0.1 Pa and at temperatures from 580 to 620 °C. In order to evaluate structural and optical properties of the films X‐ray diffraction analysis, Raman spectrometry and optical spectrophotometry were used. Crystalline state (amorphous or microcrystalline), optical band gaps, refractive indices, extinction coefficients, absorption coefficients were determined. X‐ray diffraction analysis indicated that originally deposited films were amorphous with different degree of homogeneity depending on the film thickness. After the heat treatment the films became polycrystalline with crystallite sizes 40‐50 nm without particular dependence on the recrystallization process used. Raman spectrometry confirmed the results obtained from X‐ray diffraction and furthermore revealed the residual amorphous phase 20–25% in volume. Optical spectrophotometry has shown that the values of refractive indices of thermally treated films approach the mono‐crystalline silicon refractive index. Extinction coefficients of the thermally treated films are slightly higher than those for monocrystalline silicon. Absorption coefficients for thermally treated films reached quite high values near the absorption edge of the original amorphous material, which can be advantageous for tandem solar cell technologies. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Efficient second harmonic generation green light in RTP planar waveguides
Authors: Cugat Jaume , Solé Rosa Maria , Pujol Maria Cinta , Carvajal Joan Josep , Mateos Xavier , Díaz Francesc , Aguiló Magdalena 
Published: May 2011

AbstractIn this paper, epitaxial layers of Rb1‐xBaxTi1‐y‐zYbyNbzOPO4 have been successfully grown on (001) oriented RbTiOPO4 substrates. Although the Ba2+ contents in these layers was very low, the contrasts in refractive indices between the epitaxial layer and the substrate were high enough to allow the propagation of one TE and three TM modes, at the wavelength of 632.8 nm, using a 5 μm thickness epilayer. These light propagation modes were first simulated, using the refractive indices of the layer and the substrate measured previously. The TE and TM dark‐mode spectra obtained experimentally, using the prism coupler method and a He‐Ne laser beam, agree well with the simulation results. Finally, type II Second Harmonic Generation experiments were carried out with pumping at 1130 nm and obtaining green light at 565 nm. The experimental efficiency in the Second Harmonic Generation experiments was of 69%/mWcm2. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Tropical cyclone convection: the effects of ambient vertical vorticity
Authors: Wissmeier Ulrike , Smith Roger K. 
Published: May 2011

AbstractWe present idealized numerical model experiments to isolate and quantify the influence of ambient vertical vorticity on the dynamics of deep convection, such as that in the inner‐core region of a tropical depression. The vertical vorticity is represented either by a uniform horizontal shear, a uniform solid‐body rotation, or a combination of both. We show that the growing convective cells amplify locally the ambient rotation at low levels by more than an order of magnitude and that this vorticity, which is produced by the stretching of existing ambient vorticity, persists long after the initial updraught has decayed. Significant amplification of vorticity occurs even for a background rotation rate typical of the undisturbed tropical atmosphere and even for clouds of only moderate vertical extent. This finding has important implications for tropical cyclogenesis and provides a basis for a unified theory of tropical cyclogenesis and tropical cyclone intensification.The presence of ambient vertical vorticityreducesthe updraught strength, slightly more when the vorticity is associated with horizontal shear than when it is associated with solid‐body rotation on account of enhanced entrainment. The reduction of the updraught strength can be attributed to the reduction of the lateral inflow by the centrifugal and Coriolis forces. Despite the significant amplification of vorticity, the sum of the centrifugal and Coriolis forces is mostly small compared with the lateral pressure gradient. Thus, at the level of background rotation studied, the Rossby elasticity effects in the updraught postulated by Montgomeryet al.are not large, but may be important for higher levels of background rotation. The simulations ignore several processes that are likely to be important in reality, such as ambient vertical shear and surface friction, but they provide important benchmark calculations for interpreting the additional complexity arising from the inclusion of these effects. Copyright © 2011 Royal Meteorological Society