bluuebunny/crossref_metadata_2025 huggingface dataset:
Calculation of flip angles for echo trains with predefined amplitudes with the extended phase graph (EPG)‐algorithm: Principles and applications to hyperecho and TRAPS sequences
Authors: Hennig Juergen , Weigel Matthias , Scheffler Klaus
Published: December 2003

The article presents an algorithm for calculation of flip angles in multiecho experiments to generate echoes with predefined amplitudes based on the extended phase graph algorithm. The algorithm can be used to optimize the echo envelope and thus the point spread function (PSF) in hyperecho and TRAPS (transition into the pseudosteady state) experiments while minimizing the total RF power. Implementations at 3 T using echo trains with Gaussian and Lorentzian PSF demonstrate a reduction in RF power by a factor of 3–5 while maintaining high image quality. Magn Reson Med 51:68–80, 2004. © 2003 Wiley‐Liss, Inc.
Flow artifacts in steady‐state free precession cine imaging
Authors: Storey Pippa , Li Wei , Chen Qun , Edelman Robert R.
Published: December 2003

Steady‐state free precession (SSFP) cardiac cine images are frequently corrupted by dark flow artifacts, which can usually be eliminated by reshimming and retuning the scanner. A theoretical explanation for these artifacts is provided in terms of spins moving through an off‐resonant point in the magnetic field, and the theory is validated using phantom experiments. The artifacts can be reproduced in vivo by detuning the center frequency by an amount in the range of half the inverse repetition time (TR). Since this offset is similar in magnitude to the frequency difference between the water and lipid peaks, a likely cause of the artifacts in vivo is that the center frequency is tuned incorrectly to the lipid peak rather than the water peak. Magn Reson Med 51:115–122, 2004. © 2003 Wiley‐Liss, Inc.
Time‐optimal multidimensional gradient waveform design for rapid imaging
Authors: Hargreaves Brian A. , Nishimura Dwight G. , Conolly Steven M.
Published: December 2003

Magnetic resonance imaging (MRI) is limited in many cases by long scan times and low spatial resolution. Recent advances in gradient systems hardware allow very rapid imaging sequences, such as steady‐state free precession (SSFP), which has repetition times (TRs) of 2–5 ms. The design of these rapid sequences demands time‐optimal preparatory gradient waveforms to provide maximum readout duty‐cycle, and preserve spatial resolution and SNR while keeping TRs low. Time‐optimal gradient waveforms can be synthesized analytically for certain simple cases. However, certain problems, such as time‐optimal 2D and 3D gradient design with moment constraints, either may not have a solution or must be solved numerically. We show that time‐optimal gradient design is a convex‐optimization problem, for which very efficient solution methods exist. These methods can be applied to solve gradient design problems for oblique gradient design, spiral imaging, and flow‐encoding using either a constant slew rate or the more exact voltage‐limited gradient models. Ultimately, these methods provide a time‐optimal solution to many 2D and 3D gradient design problems in a sufficiently short time for interactive imaging. Magn Reson Med 51:81–92, 2004. © 2003 Wiley‐Liss, Inc.
Lumped‐element planar strip array (LPSA) for parallel MRI
Authors: Lee Ray F. , Hardy Christopher J. , Sodickson Daniel K. , Bottomley Paul A.
Published: December 2003

The recently introduced planar strip array (PSA) can significantly reduce scan times in parallel MRI by enabling the utilization of a large number of RF strip detectors that are inherently decoupled, and are tuned by adjusting the strip length to integer multiples of a quarter‐wavelength (λ/4) in the presence of a ground plane and dielectric substrate. In addition, the more explicit spatial information embedded in the phase of the signals from the strip array is advantageous (compared to loop arrays) for limiting aliasing artifacts in parallel MRI. However, losses in the detector as its natural resonance frequency approaches the Larmor frequency (where the wavelength is long at 1.5 T) may limit the signal‐to‐noise ratio (SNR) of the PSA. Moreover, the PSA's inherent λ/4 structure severely limits our ability to adjust detector geometry to optimize the performance for a specific organ system, as is done with loop coils. In this study we replaced the dielectric substrate with discrete capacitors, which resulted in both SNR improvement and a tunable lumped‐element PSA (LPSA) whose dimensions can be optimized within broad constraints, for a given region of interest (ROI) and MRI frequency. A detailed theoretical analysis of the LPSA is presented, including its equivalent circuit, electromagnetic fields, SNR, and g‐factor maps for parallel MRI. Two different decoupling schemes for the LPSA are described. A four‐element LPSA prototype was built to test the theory with quantitative measurements on images obtained with parallel and conventional acquisition schemes. Magn Reson Med 51:172–183, 2004. © 2003 Wiley‐Liss, Inc.
B0 dependence of the on‐resonance longitudinal relaxation time in the rotating frame (T1ρ) in protein phantoms and rat brain in vivo
Authors: Mäkelä Heidi I. , De Vita Enrico , Gröhn Olli H.J. , Kettunen Mikko I. , Kavec Martin , Lythgoe Mark , Garwood Michael , Ordidge Roger , Kauppinen Risto A.
Published: December 2003

On‐resonance longitudinal relaxation time in the rotating frame (T1ρ) has been shown to provide unique information during the early minutes of acute stroke. In the present study, the contributions of the different relaxation mechanisms to on‐resonance T1ρ relaxation were assessed by determining relaxation rates (R1ρ) in both protein phantoms and in rat brain at 2.35, 4.7, and 9.4 T. Similar to transverse relaxation rate (R2), R1ρ increased substantially with increasing magnetic field strength (B0). The B0 dependence was more pronounced at weak spin‐lock fields. In contrast to R1ρ, longitudinal relaxation rate (R1) decreased as a function of increasing B0 field. The present data argue that dipole–dipole interaction forms only one pathway for T1ρ relaxation and the contributions from other physicochemical factors need to be considered. Magn Reson Med 51:4–8, 2004. © 2003 Wiley‐Liss, Inc.
FASCINATE: A pulse sequence for simultaneous acquisition of T2‐weighted and fluid‐attenuated images
Authors: Takeo Kazuhiro , Ishikawa Akihiro , Okazaki Masato , Kohno Satoru , Shimizu Koji
Published: December 2003

A pulse sequence that enables simultaneous acquisition of T2‐weighted and fluid‐attenuated images is presented. This sequence is referred to as FASCINATE (Fluid‐Attenuated Scan Combined with Interleaved Non‐ATtEnuation). In this new technique, the inversion pulse of conventional fast fluid‐attenuated inversion recovery (FLAIR) is replaced with a fast spin echo (FSE) acquisition that has an additional 180(y)–90(x) pulse train for driven inversion. By using appropriate scan parameters, the first part of the sequence provides T2‐weighted images and the second part provides fluid‐attenuated images, thus allowing simultaneous acquisition in a single scan time comparable to that of fast FLAIR. FASCINATE was compared with conventional scanning techniques using a normal volunteer and a patient. A signal simulation was also conducted. In the human study, both T2‐weighted and fluid‐attenuated images from FASCINATE showed the same image quality as conventional images, suggesting the potential for this technique to replace the combination of fast FLAIR and T2‐weighted FSE for scan time reduction. Magn Reson Med 51:205–211, 2004. © 2003 Wiley‐Liss, Inc.
Signal‐to‐noise ratio and parallel imaging performance of a 16‐channel receive‐only brain coil array at 3.0 Tesla
Authors: de Zwart Jacco A. , Ledden Patrick J. , van Gelderen Peter , Bodurka Jerzy , Chu Renxin , Duyn Jeff H.
Published: December 2003

The performance of a 16‐channel receive‐only RF coil for brain imaging at 3.0 Tesla was investigated using a custom‐built 16‐channel receiver. Both the image signal‐to‐noise ratio (SNR) and the noise amplification (g‐factor) in sensitivity‐encoding (SENSE) parallel imaging applications were quantitatively evaluated. Furthermore, the performance was compared with that of hypothetical coils with one, two, four, and eight elements (n) by combining channels in software during image reconstruction. As expected, both the g‐factor and SNR improved substantially with n. Compared to an equivalent (simulated) single‐element coil, the 16‐channel coil showed a 1.87‐fold average increase in brain SNR. This was mainly due to an increase in SNR in the peripheral brain (an up to threefold SNR increase), whereas the SNR increase in the center of the brain was 4%. The incremental SNR gains became relatively small at large n, with a 9% gain observed when n was increased from 8 to 16. Compared to the (larger) product birdcage head coil, SNR increased by close to a factor of 2 in the center, and by up to a factor of 6 in the periphery of the brain. For low SENSE acceleration (rate‐2), g‐factors leveled off for n > 4, and improved only slightly (1.4% averaged over brain) going from n = 8 to n = 16. Improvements in g for n > 8 were larger for higher acceleration rates, with the improvement for rate‐3 averaging 12.0%. Magn Reson Med 51:22–26, 2004. Published 2003 Wiley‐Liss, Inc.
Optimizing the sequence parameters for double‐quantum CRAZED imaging
Authors: Marques J.P. , Bowtell R.
Published: December 2003

The evolution of magnetization during repeated application of the double‐quantum‐(DQ)‐CRAZED sequence is analyzed, with the aim of identifying sequence parameters that maximize sensitivity to signal produced by the distant dipole field (DDF). Phase cycling schemes that allow cancellation of signals following undesired coherence pathways are also described. Simulations and imaging experiments carried out at 3 T on phantoms and the human head were used to verify the analysis. The results indicate that in the absence of phase cycling, the DDF‐related signal‐to‐noise ratio (SNR) per unit time is maximized using TR = 2.05 T1, along with values of the RF flip angles (α ≈ 90° and β ≈ 60°), and echo time (TE = T2) that have previously been shown to maximize the DDF‐related signal at long TR. However, with TR = 2.05 T1 there can also be a significant signal contribution due to stimulated echo effects (up to 40% of the signal for water at 3 T and TE = 70 ms). Using a two‐step phase cycle, the stimulated echo signal is eliminated and the maximum SNR per unit time occurs for TR = 2.76 T1. It is also demonstrated that sensitivity to signal changes caused by small variations in T2 is maximized by setting TE = 2T2. Magn Reson Med 51:148–157, 2004. © 2003 Wiley‐Liss, Inc.
Grafting sulfobetaine monomer onto silicone surface to improve haemocompatibility
Authors: Yuan Youling , Zang Xiaopeng , Ai Fei , Zhou Jun , Shen Jian , Lin Sicong
Published: December 2003

Silicone rubber has been used as a biomaterial for more than two decades and displays good mechanical and optical properties, but its chemical nature, poor antithrombogenicity, as well as its hydrophobicity, prevents its use in many demanding biomedical applications. In order to provide modified silicone with enhanced haemocompatibility, surface modification techniques were used. Ozonization was used to introduce active peroxide groups onto the silicone film surface and, subsequently, graft polymerization of N,N′‐dimethyl‐N‐methacryloyloxyethyl‐N‐(3‐sulfopropyl) ammonium (DMMSA), a zwitterionic sulfobetaine structure, onto the ozone activated silicone surface was conducted. Surface analysis was accomplished by means of attenuated total reflectance‐Fourier‐transform infrared (ATR‐FTIR), and X‐ray photoelectron spectra (XPS), and scanning electron microscopy (SEM) and contact angle measurement. ATR‐FTIR and XPS investigation confirmed the graft polymerization. The grafted film possessed a relatively hydrophilic surface as indicated by contact angle measurement. The blood compatibility of the grafted films was evaluated by platelet adhesion in platelet‐rich plasma (PRP) and protein adsorption in bovine fibrinogen using silicone film as the reference. No platelet adhesion was observed for the grafted films incubated in PRP for 120 min. The protein adsorption was reduced on the grafted films after incubated in bovine fibrinogen for 120 min. These results confirmed that the improved blood compatibility was obtained by grafting this new zwitterronic sulfobetaine structure onto silicone film. Copyright © 2003 Society of Chemical Industry
Determination of radial structural properties and spectral dispersion curves of poly(aryl ether ether ketone) fibre
Authors: El‐Bakary MA
Published: December 2003

Poly(aryl ether ether ketone) (PEEK) fibre was studied using a variable wavelength interferometric technique (VAWI). This technique was used in conjunction with a Pluta polarizing interference microscope to determine the spectral dispersion curves of fibre refractive indices and birefringence fibre. The results were used to calculate the dispersion properties of the fibre, ie dispersion and oscillation energies, Cauchy's constants of dispersion relation and the natural wavelength of the fibre. The radial refractive index and birefringence profiles were also determined, taking into consideration the refraction of light beam by the fibre, and some radial structural profiles were then calculated using a ring‐zonal model. The measurements of these radial profiles are required for optimizing the spinning and processing of manufactured textile fibres. The Fraunhofer diffraction pattern of a He–Ne laser beam was used to determine the average thickness of the fibre. Microinterferograms are presented for illustration. Copyright © 2003 Society of Chemical Industry
Poly(4‐methyl‐1‐pentene)/clay nanocomposites: effect of organically modified layered silicates
Authors: Wanjale Santosh D , Jog Jyoti P
Published: December 2003

The preparation and properties of poly(4‐methyl‐1‐pentene) (PMP)/clay nanocomposites are reported. Melt intercalation of PMP is carried out with organoclays of different cation/charge exchange capacities and modifiers to facilitate intercalation of the polymer into the silicate layers. The effect of modifiers on the structure and properties of PMP/clay nanocomposites is explored. XRD patterns confirm the intercalation of polymer in the layered silicates as evidenced by the increase in the inter‐layer spacing which is dependent on the type of modifier used. Dynamic mechanical analysis shows increments in the storage modulus over the temperature range studied for all of the three clays, but the extent depends on the type of clay modifier used. The coefficient of thermal expansion is lower for all of the nanocomposites, as compared to the pristine polymer, indicating improved dimensional stability Copyright © 2003 Society of Chemical Industry
Toughening of epoxy resin systems using low‐viscosity additives
Authors: Varley Russell J
Published: December 2003

This study has evaluated three low‐viscosity epoxy additives as potential tougheners for two epoxy resin systems. The systems used were a lower‐reactive resin based upon the diglycidyl ether of bisphenol A (DGEBA) and the amine hardener diethyltoluene diamine, while the second epoxy resin was based upon tetraglycidyl methylene dianiline (TGDDM) and a cycloaliphatic diamine hardener. The additives evaluated as potential tougheners were an epoxy‐terminated aliphatic polyester hyperbranched polymer, a carboxy‐terminated butadiene rubber and an aminopropyl‐terminated siloxane. This work has shown that epoxy‐terminated hyperbranched polyesters can be used effectively to toughen the lower cross‐linked epoxy resins, i.e. the DGEBA‐based systems, with the main advantage being that they have minimal effect upon processing parameters such as viscosity and the gel time, while improving the fracture properties by about 54 % at a level of 15 wt% of additive and little effect upon the Tg. This result was attributed to the phase‐separation process producing a multi‐phase particulate morphology able to initiate particle cavitation with little residual epoxy resin dissolved in the continuous epoxy matrix remaining after cure. The rubber additive was found to impart similar levels of toughness improvement but was achieved with a 10–20 °C decrease in the Tg and a 30 % increase in initial viscosity. The siloxane additive was found not to improve toughness at all for the DGEBA‐based resin system due to the poor dispersion within the epoxy matrix. The TGDDM‐based resin systems were found not to be toughened by any of the additives due to the lack of plastic deformation of the highly cross‐linked epoxy network Copyright © 2003 Society of Chemical Industry
On the fractal character of polymer spherulites: an ultra‐small‐angle X‐ray scattering study of poly[(R)‐3‐hydroxybutyrate]
Authors: Owen Anthony , Bergmann Antje
Published: December 2003

Ultra‐small‐angle X‐ray scattering (USAXS) and small‐angle X‐ray scattering (SAXS) measurements are presented for poly[(R)‐3‐hydroxybutyrate] (PHB) crystallized at room temperature. The USAXS patterns indicated that the spherulites had a radially orientated fibrillar nanostructure with fractal geometry over a length scale ranging from 12 nm up to at least 300 nm, with a mass fractal dimension of approximately 2.7 in aged samples. The SAXS patterns indicated that the fibrils themselves were built up of bundles of crystalline lamellae separated by layers of disordered material, with a period length of approximately 6 nm. The SAXS measurements during primary crystallization gave an initial fractal dimension of 4 during spherulite growth, due to the sharp phase boundary between the spherulites and the melt. Copyright © 2004 Society of Chemical Industry
Finite element simulation of mechanical property evolvement of silicone rubber in the hot vulcanizing process
Authors: Jia Yuxi , Sun Sheng , Liu Lili , Ji Zhong
Published: December 2003

The technical outline of integrated research on the mechanical properties, the crosslinked structure and the hot vulcanizing technology of silicone rubber materials is formulated. From the statistics of rubber elasticity, the relationship of stored energy function and crosslinked structure parameters is constructed. Following the stress–strain theory of elastomers, related expressions for the mechanical properties and the crosslinked structure are deduced. On the basis of previous research findings, numerical expressions of the mechanical properties of silicone rubber in hot vulcanizing process are obtained. Consequently, the properties of silicone rubber can be predicted and the crosslinked structure can be controlled based on a forward simulation method, or the processing parameters and the initial polymeric material can be optimized on the basis of a backward simulation method Copyright © 2003 Society of Chemical Industry
Design of lactide copolymers as biomaterials
Authors: Ouchi Tatsuro , Ohya Yuichi
Published: December 2003

A very important goal of researchers today is providing poly(L‐lactide) (PLA)‐based polymers with controllable degradation profiles, various (soft or elastic) mechanical properties, reactivity for chemical modification, and other functionalities while keeping the favorable characteristics of PLA. This article concerns the synthetic methods and properties of the following novel lactide copolymers: (1) random and block copolymers of depsipeptide and L‐lactide with reactive (ionic) side‐chain groups, (2) comb‐type PLA and branched PLA, and (3) PLA‐grafted polysaccharide and PLA with terminal saccharide residues. Poly(depsipeptide‐random‐L‐lactide)s and polydepsipeptide‐block‐poly(L‐lactide)s with reactive (ionic) side‐chain groups should be useful for the preparation of matrices and microspheres with reactive surfaces because of their amphiphilic structures. Comb‐type PLA and branched PLA show lower crystallinities than linear PLA. PLA‐grafted polysaccharide should be useful for the preparation of matrices with various microstructures and mechanical and degradation properties through the introduction of hydrophilic segments. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 453–462, 2004
Synthesis and characterization of linear tetrablock quarterpolymers of styrene, isoprene, dimethylsiloxane, and 2‐vinylpyridine
Authors: Fragouli Panagiota G. , Iatrou Hermis , Hadjichristidis Nikos
Published: December 2003

A series of five tetrablock quarterpolymers of styrene, isoprene, dimethylsiloxane, and 2‐vinylpyridine with molecular weights varying from 117 × 103 to 177 × 103 and having different compositions were synthesized. The synthesis was based on recent advances in the controlled high‐vacuum anionic polymerization of hexamethylcyclotrisiloxane and on the selective linking of poly(dimethylsiloxane)lithium with the chlorosilane group of the heterofunctional linking agent chloromethylphenylethylene dimethylchlorosilane. Combined characterization results by size exclusion chromatography, membrane osmometry, and NMR spectroscopy suggested that the synthesized multiblock multicomponent polymers had a high degree of structural and compositional homogeneity. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 514–519, 2004
New photocleavable structures. II. α‐Cleavable photoinitiators based on pyridines
Authors: Liska R. , Herzog D.
Published: December 2003

A series of novel pyridine‐based type I photoinitiators were synthesized. UV spectroscopy revealed absorption characteristics very similar to those of a commercially available hydroxyalkylphenone [2‐hydroxy‐2‐methyl‐1‐phenyl propan‐1‐one (1b)]. Photo‐differential scanning calorimetry was used to study the polymerization kinetics of lauryl acrylate photoinitiated by the new pyridines. Under a nitrogen atmosphere, a 3‐substituted derivative [2‐hydroxy‐2‐methyl‐1‐pyridin‐3‐yl‐propan‐1‐one (3b)] gave results comparable to those obtained with 1b. Measurements under air indicated decreased sensitivity toward oxygen quenching reactions. Additionally, pyridine derivatives showed good water solubility (4.9 g/100 mL). Preliminary steady‐state photolysis experiments with 2,2,6,6‐tetramethyl‐1‐piperidinyloxy as a radical scavenger were carried out, and the α‐cleavage mechanism was found to be the main reaction pathway. The quantum yields of α‐cleavage were approximately 0.30 ± 0.04 for 3b and 0.18 ± 0.03 for 1b. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 752–764, 2004
Controlling the water content of never dried and reswollen bacterial cellulose by the addition of water‐soluble polymers to the culture medium
Authors: Seifert Marit , Hesse Stephanie , Kabrelian Vasken , Klemm Dieter
Published: December 2003

For the modification of medically useful biomaterials from bacterially synthesized cellulose, fleeces of Acetobacter xylinum have been produced in the presence of 0.5, 1.0, and 2.0% (m/v) carboxymethylcellulose (CMC), methylcellulose (MC), and poly(vinyl alcohol) (PVA), respectively, in the Hestrin‐Schramm culture medium. The incorporation of the water‐soluble polymers into cellulose and their influence on the structure, crystal modifications, and material properties are described. With IR and solid‐state 13C NMR spectroscopy of the fleeces, the presence of the cellulose ethers and an increase in the amorphous parts of the cellulose modifications (NMR results) have been detected. The incorporation is represented by a higher product yield, too. As demonstrated by scanning electron microscopy, a porelike cellulose network structure forms in the presence of CMC and MC. This modified structure increases the water retention ability (expressed as the water content), the ion absorption capacity, and the remaining nitrogen‐containing residues from the culture medium or bacteria cells. The water content of bacterial cellulose (BC) in the never dried state and the freeze‐dried, reswollen state can be controlled by the CMC concentration in the culture solution. The freeze‐dried, reswollen BC‐CMC (2.0%) contains 96% water after centrifugation, whereas standard BC has only 73%. About 98% water is included in a BC‐MC composite in the wet state, and about 93% is included in the reswollen state synthesized in the presence of 0.5, 1.0, or 2.0% MC. These biomaterial composites can be stored in the dried state and reswollen before use, reaching a higher water absorption than pure, never dried BC. The copper ion capacity of BC‐CMC composites increases proportionally with the added amount of CMC. BC‐CMC (0.5%) can absorb 3 times more copper ions than original BC. In the case of 0.5 and 1.0% PVA additions to the culture solution, this polymer cannot be detected in the cellulose fleeces after they are washed. Nevertheless the presence of PVA in the culture medium effects a decreased product yield, a retention of nitrogen‐containing residues in the material during purification, a reduced water absorption ability, and a slightly higher copper ion capacity in comparison with original BC. The water content of freeze‐dried, reswollen BC‐PVA (0.5%) is only 62%. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 463–470, 2004
Analysis of surface mobility in polystyrene films with monodisperse and bimodal molecular weights by lateral force microscopy
Authors: Kajiyama Tisato , Tanaka Keiji , Takahara Atsushi
Published: December 2003

The surface glass‐transition temperature (T) in monodisperse polystyrene (PS) films was examined on the basis of the temperature dependence of the lateral force at a given scanning rate. T of the PS films was found to be markedly lower than the corresponding bulk glass‐transition temperature over the entire molecular weight range (4900–1,460,000). Also, the apparent activation energy of the surface segmental motion in the PS films was 230 ± 10 kJ mol−1, significantly smaller than that for bulk PS. Finally, T measurement by lateral force microscopy was applied to binary PS mixtures with different molecular weights. On the basis of the Gordon–Taylor equation, the surface composition of the shorter component in the blend films was successfully obtained. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 639–647, 2004
Synthesis of block copolymers by combined ultrasonic irradiation and reverse atom transfer radical polymerization processes
Authors: Degirmenci Mustafa , Catalgil‐Giz Huceste , Yagci Yusuf
Published: December 2003

A two‐step procedure based on ultrasonic irradiation and reverse atom transfer radical polymerization (RATRP) for the synthesis of block copolymers is described. In the first step of the procedure, a stable chlorine‐end‐capped polymer is formed upon the ultrasonic irradiation of poly(methyl methacrylate) (PMMA) in dry benzene in the presence of a copper chloride/2,2′‐bipyridine catalyst. Heating the system to 110 °C initiates the polymerization of the second monomer, styrene, and this results in the formation of the block copolymers. The degradation behavior of PMMA under ultrasonic irradiation has also been studied. The agreement of the experimentally obtained molecular weights and theoretical molecular weights and the unimodal shapes of the gel permeation chromatography curves of the block copolymers indicate the controlled nature of the RATRP process initiated by polymeric radicals formed by sonication. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 534–540, 2004
Sequence and structural analysis of cellular retinoic acid‐binding proteins reveals a network of conserved hydrophobic interactions
Authors: Gunasekaran Kannan , Hagler Arnold T. , Gierasch Lila M.
Published: December 2003

Abstract Proteins in the intracellular lipid‐binding protein (iLBP) family show remarkably high structural conservation despite their low‐sequence identity. A multiple‐sequence alignment using 52 sequences of iLBP family members revealed 15 fully conserved positions, with a disproportionately high number of these (n=7) located in the relatively small helical region. The conserved positions displayed high structural conservation based on comparisons of known iLBP crystal structures. It is striking that the β‐sheet domain had few conserved positions, despite its high structural conservation. This observation prompted us to analyze pair‐wise interactions within the β‐sheet region to ask whether structural information was encoded in interacting amino acid pairs. We conducted this analysis on the iLBP family member, cellular retinoic acid‐binding protein I (CRABP I), whose folding mechanism is under study in our laboratory. Indeed, an analysis based on a simple classification of hydrophobic and polar amino acids revealed a network of conserved interactions in CRABP I that cluster spatially, suggesting a possible nucleation site for folding. Significantly, a small number of residues participated in multiple conserved interactions, suggesting a key role for these sites in the structure and folding of CRABP I. The results presented here correlate well with available experimental evidence on folding of CRABPs and their family members and suggest future experiments. The analysis also shows the usefulness of considering pair‐wise conservation based on a simple classification of amino acids, in analyzing sequences and structures to find common core regions among homologues. Proteins 2003. © 2003 Wiley‐Liss, Inc.
Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation
Authors: Oostenbrink Chris , van Gunsteren Wilfred F.
Published: December 2003

Relative free energies of binding to the ligand‐binding domain of the estrogen receptor have been calculated for a series of 17 hydroxylated polychlorinated biphenyls. Because traditional thermodynamic integration or perturbation approaches are hardly feasible for these numbers of compounds, the one‐step perturbation approach is applied and is shown to yield accurate results based on only two 2‐ns molecular dynamics simulations of an unphysical, judiciously chosen, reference state. The mean absolute difference between the calculated and experimental binding free energies for the 17 compounds is 3.4 kJ/mol, which illustrates the accuracy of the GROMOS biomolecular force field used. Excluding the three largest ligands from the comparison reduces the deviation to 2.0 kJ/mol (i.e., < kBT). Apart from the relative free energy, structural information about the binding mode and binding orientation for every compound can also be extracted from the simulation, showing that a ligand bound to its receptor cannot be represented by a single conformation, but it samples an ensemble of different orientations. Proteins 2004;54:000–000. © 2003 Wiley‐Liss, Inc.
Phenomenological similarities between protein denaturation and small‐molecule dissolution: Insights into the mechanism driving the thermal resistance of globular proteins
Authors: Ragone Raffaele
Published: December 2003

This article shows that the stability profiles of thermophilic proteins are significantly displaced toward higher temperatures as compared to those of mesophilic proteins. A similar trend characterizes the aqueous transfer of N‐alkyl amides. In fact, as a general feature of transfer processes, liquid dissolution profiles are centered at temperatures higher than those of solid ones. This behavior is governed by packing contributions. A partition of the unfolding thermodynamics based on the analysis of phenomenological temperatures common to dissolution and unfolding phenomena provides a clue to understanding the mechanism of thermal stabilization. In fact, the position of stability profiles along the temperature axis does not appear to depend on solvation of internal residues. Instead, it is notably affected by solidlike components, whose progressive decrease appears to drive the heat denaturation temperature increase of most thermostable proteins. As a corollary, it is shown that there are actually two limiting mechanisms of thermal stabilization. Proteins 2004. © 2003 Wiley‐Liss, Inc.
Novel protein and Mg2+ configurations in the Mg2+GDP complex of the SRP GTPase ffh
Authors: Focia Pamela J. , Alam Hena , Lu Thanh , Ramirez Ursula D. , Freymann Douglas M.
Published: December 2003

Ffh is the signal sequence recognition and targeting subunit of the prokaryotic signal recognition particle (SRP). Previous structural studies of the NG GTPase domain of Ffh demonstrated magnesium‐dependent and magnesium‐independent binding conformations for GDP and GMPPNP that are believed to reflect novel mechanisms for exchange and activation in this member of the GTPase superfamily. The current study of the NG GTPase bound to Mg2+GDP reveals two new binding conformations—in the first the magnesium interactions are similar to those seen previously, however, the protein undergoes a conformational change that brings a conserved aspartate into its second coordination sphere. In the second, the protein conformation is similar to that seen previously, but the magnesium coordination sphere is disrupted so that only five oxygen ligands are present. The loss of the coordinating water molecule, at the position that would be occupied by the oxygen of the γ‐phosphate of GTP, is consistent with that position being privileged for exchange during phosphate release. The available structures of the GDP‐bound protein provide a series of structural snapshots that illuminate steps along the pathway of GDP release following GTP hydrolysis. Proteins 2004;54:000–000. © 2003 Wiley‐Liss, Inc.
Semiempirical QM/MM method for studying HCl adsorption on ice
Authors: Bolton Kim
Published: December 2003

The combined QM/MM method, where the QM forces are obtained from a fitted PM3 semiempirical Hamiltonian, is used to study HCl adsorption at an ice surface ledge defect site. The PM3‐SSP (PM3 with system‐specific parameters) Hamiltonian allows for multidimensional molecular dynamics simulations that are computationally inexpensive while still providing valid reaction dynamics. The simulations reveal that, depending on the initial position of the HCl above the ledge and the number and positions of dangling surface hydrogens, adsorption may be molecular or dissociative. HCl binding energies and geometries at the ice defect site are similar to those for adsorption at crystalline hexagon sites. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Ab initio description of the structure and dynamics of the nitrosomethane molecule in the first excited singlet and triplet electronic states
Authors: Dolgov Eugeniy K. , Bataev Vadim A. , Pupyshev Vladimir I. , Godunov Igor A.
Published: December 2003

Electronic structure of the low‐lying excited states of the CH3NO molecule is considered. The detailed analysis of the first excited triplet and singlet states of this molecule is performed by different ab initio methods to estimate equilibrium geometry, barriers to internal rotation, harmonic frequencies, and adiabatic transition energies. Anharmonic vibrational approximations are also considered. The multidimensional VibSCF scheme and the 1‐D variational method for the section of the potential energy surface along the torsion coordinate are used. Theoretical results are found to be in good agreement with experimental data. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Possibility of a pressure‐induced 2N2 → N4 reaction
Authors: Evangelisti Stefano
Published: December 2003

The CAS‐SCF energy of an N4 cluster for a fixed value of the system volume (constrained to a D2d symmetry) is studied. It is shown that, for a wide range of volumes, two minima exist: one corresponding to two separated N2 molecules and one to an N4 cluster with tetrahedric shape. For small values of the volume, the energy of the tetrahedric form becomes lower than the energy of the two N2 molecules. This suggests the possibility that, at high densities, tetrahedric N4 might be more stable than two N2 molecules, with a pressure‐drive phase transition between the two forms occurring at a very high pressure. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Extrapolation methods and scaled perturbation theory for determining intermolecular potential energy surfaces
Authors: Hodges Matthew P. , Bichoutskaia Elena , Tulegenov Akyl S. , Wheatley Richard J.
Published: December 2003

We construct potential energy curves for six rare‐gas dimers and several 1‐D cuts through two H2 … rare‐gas potential energy surfaces using two methods. The first is based on supermolecule dimer calculations at a low level of theory, extrapolated using monomer calculations at higher levels of theory. The second is based on perturbation theory calculations, where the effects of intramolecular electron correlation on different interaction terms are treated using approximate scaling relationships. Both methods are competitive with supermolecule dimer calculations at higher levels of theory and provide computationally efficient means of studying weakly bound systems. The methods are therefore suitable for calculations on larger systems for which accurate supermolecule methods would be computationally expensive. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Quantum vs. semiclassic initial value representation probabilities for nonreactive systems
Authors: Lago N. Faginas , Laganà A. , Riganelli A.
Published: December 2003

The initial value representation (IVR) of the semiclassic (SC) formulation of the probability of inelastic transitions have been investigated for collinear atom–diatom systems. An analysis of the convergence and accuracy of the calculated probabilities is performed by comparing SC‐IVR values calculated using an increasing number of trajectories with exact quantum results. Both far and near the threshold behaviors are considered. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Validating the PSL/Sugar Semantics Using Automated Reasoning
Authors: Gordon Michael J. C.
Published: December 2003

The Accellera organisation selected Sugar, IBM’s formal specification language, as the basis for a standard to ‘drive assertion-based verification’ in the electronics industry. Sugar combines regular expressions, Linear Temporal Logic (LTL) and Computation Tree Logic (CTL) into a property language intended for both static verification (e.g. model checking) and dynamic verification (e.g. simulation). In 2003 Accellera decided to rename the evolving standard to ‘Accellera Property Specification Language’ (or ‘PSL’ for short). We motivate and describe a deep semantic embedding of PSL in the version of higher-order logic supported by the HOL 4 theorem-proving system. The main goal of this paper is to demonstrate that mechanised theorem proving can be a useful aid to the validation of the semantics of an industrial design language.
Actors and their Composition
Authors: Janneck Jörn W.
Published: December 2003

Modern environments for modelling and designing concurrent computational systems increasingly supportheterogeneoussystem models, which are characterised by different coordination mechanisms governing the interaction between concurrent components in different parts or at different levels of the model. These interaction semantics, also calledmodels of computation, pose a major challenge to the definition of the meaning of heterogeneous models, especially if such a definition is to be independent of any specific set of models of computation, ways of describing actors, or notations for describing models. This paper makes three main contributions. (1) It presents a framework for describing the semantics of actors and models of computation. Its central notion is the concept of a model of computation as a program transformation that composes actor descriptions into a description of a composite actor. This framework is entirely independent of any specific syntax for describing actors, or any particular modelling language. (2) It uses this framework to describe properties of actor compositions and models of computation, and to classify and analyse them. (3) Finally, it discusses the implications of this theory for the design of languages for describing actors and models of computation.
Impas 1 possesses endoproteolytic activity against multipass membrane protein substrate cleaving the presenilin 1 holoprotein
Authors: Moliaka Yuri K , Grigorenko Anastasia , Madera Dmitri , Rogaev Evgeny I
Published: December 2003

Presenilins (PS1 and PS2) are supposed to be unusual aspartic proteases and components of the γ‐secretase complex regulating cleavage of type I proteins. Multiple mutations in PS1 are a major cause of familial early‐onset Alzheimer's disease (AD). We and others recently identified PS‐related families of proteins (IMPAS/PSH/signal peptide peptidases (SPP)). The functions of these proteins are yet to be determined. We found that intramembrane protease‐associated or intramembrane protease aspartic protein Impas 1 (IMP1)/SPP induces intramembranous cleavage of PS1 holoprotein in cultured cells coexpressing these proteins. Mutations in evolutionary invariant sites in hIMP1 or specific γ‐secretase inhibitors abolish the hIMP1‐mediated endoproteolysis of PS1. In contrast, neither AD‐like mutations in hIMP1 nor in PS1 substrate abridge the PS1 cleavage. The data suggest that IMP1 is a bi‐aspartic polytopic protease capable of cleaving transmembrane precursor proteins. These data, to our knowledge, are a first observation that a multipass transmembrane protein or the integral protease per se may be a primary substrate for an intramembranous proteolysis.
Mitochondrial functional interactions between frataxin and Isu1p, the iron–sulfur cluster scaffold protein, in Saccharomyces cerevisiae
Authors: Ramazzotti Anna , Vanmansart Vincent , Foury Françoise
Published: December 2003

Friedreich's ataxia is caused by a deficit in the mitochondrial protein frataxin. The present work demonstrates that in vivo yeast frataxin Yfh1p and Isu1p, the mitochondrial scaffold protein for the Fe–S cluster assembly, have tightly linked biological functions, acting in concert to promote the Fe–S cluster assembly. A synthetic lethal screen on high iron media with the mild G107D yfh1 mutant has specifically identified Isu1p. Analysis of the cellular phenotypes resulting from pairwise combinations of yfh1 and isu1 mutations, and cross‐linking experiments in isolated mitochondria provide evidence for a direct interaction between Yfh1p and Isu1p.
RECENT WORK ON FRENCH RURAL HISTORY
Authors: JONES P. M.
Published: December 2003

The purpose of this review is to take stock as the historiography of rural France pauses for breath following the headlong expansion of the post-Second World War decades. It examines some of the themes that continue to exert an attraction on scholars, and also some of the most recent attempts to challenge and reformulate the research agendas inherited from the Annales historians. The works discussed below raise questions concerning growth and stagnation in the rural economy, the basic characteristics of the rural community, and the role of quantification in rural history.
Islamization, Gentrification and Domestication: ‘A Girls’ Islamic Course' and Rural Muslims in Western Uttar Pradesh
Authors: Jeffery Patricia , Jeffery Roger , Jeffrey Craig
Published: December 2003

Girls' education has been enduringly controversial in north India, and the disputes of the
second half of the nineteenth century and early twentieth century still echo in debates about
girls' education in contemporary India. In this paper, we reflect on the education of rural Muslim
girls in contemporary western Uttar Pradesh (UP), by examining an Islamic course for girls
[Larkiyon kā Islālmī Course], written in Urdu and widely used in
madrasahs there. First, we summarize the central themes in the Course:
purifying religious practice; distancing demure, self-controlled, respectable woman from the lower
orders; and the crucial role of women as competent homemakers. Having noted the conspicuous
similarities between these themes and those in the nineteenth and early twentieth-century
textbooks and advice manuals for girls and women, the second section examines the context in which
the earlier genre emerged. Finally, we return to the present day. Particularly since September 11th
2001, madrasahs have found themselves the focus of hostile allegations that bear little or no
relationship to the activities of the madrasahs that we studied. Nevertheless,
madrasah education does have problematic implications. The special curricula for girls
exemplifies how a particular kind of élite project has been sustained and transformed, and
we aim to shed light on contemporary communal and class issues as well as on gender politics.
An outbreak of pertussis among young Israeli soldiers
Authors: KLEMENT E. , ULIEL L. , ENGEL I. , HASIN T. , YAVZORI M. , ORR N. , DAVIDOVITZ N. , LAHAT N. , SRUGO I. , ZANGVIL E. , COHEN D.
Published: December 2003

In winter 2001, an outbreak of pertussis involving an estimated 75 people occurred among soldiers serving in an infantry regiment of the Israeli Defense Forces (IDF). Nasopharyngeal swabs were obtained from patients and contacts for culture and PCR. Serum samples were obtained and assayed by ELISA for the presence of IgA, IgM and IgG antibodies to a lysate antigen of Bordetella pertussis. The calculated attack rate was 21% based on clinical signs alone (cough lasting 30 days or longer) and 9·5% based on clinical signs with laboratory confirmation (by PCR, IgA or IgM). A high carriage rate was observed; 20% of the asymptomatic and previously symptomatic subjects were PCR-positive for B. pertussis. These findings emphasize the importance of B. pertussis as a causative agent of epidemic respiratory infections in young adults and reveal the occurrence of a significant proportion of pertussis transient carriers during an outbreak of the disease.
Fresh garlic: a possible vehicle for Salmonella Virchow
Authors: BENNETT C. M. , DALTON C. , BEERS-DEEBLE M. , MILAZZO A. , KRAA E. , DAVOS D. , PUECH M. , TAN A. , HEUZENROEDER M. W.
Published: December 2003

A sustained increase in Salmonella enterica serovar Virchow notifications in South Eastern Australia between September 1997 and May 1998 instigated a case-control study and environmental investigations. Cases were defined as having locally acquired culture-confirmed S. Virchow phage-type 8 infection and diarrhoeal disease. Matched controls were selected by progressive digit dialling based on cases' telephone numbers. An exposure and food history questionnaire was administered by telephone. Phage typing and pulse field gel electrophoresis were performed on case and environmental isolates. Thirty-two notifications of S. Virchow infection met the case definition, 37% reported bloody diarrhoea and S. Virchow was isolated from blood in 13% of cases. Twelve patients were admitted to hospital and one died. Fresh garlic (OR 4·1, 95% CI 1·3–12·8) and semi-dried tomatoes (OR 12·6, 95% CI 1·5–103·1) were associated with these cases. The associations remained significant after adjusting for sex and age. S. Virchow (PT 8) was cultured from two brands of semi-dried tomatoes associated with cases in two different states. We provide sufficient evidence for semi-dried tomatoes and fresh garlic to be considered as potential risk foods in future Salmonella outbreak investigations.