bluuebunny/crossref_metadata_2025 huggingface dataset:
Monte Carlo aided design of an improved well‐type ionization chamber for low energy brachytherapy sources
Authors: Bohm Tim D. , Micka John A. , DeWerd Larry A.
Published: April 2007

The determination of the air kerma strength of a brachytherapy seed is necessary for effective treatment planning. Well‐type ionization chambers are used on site at therapy clinics to determine the air kerma strength of seeds. In this work, an improved well‐type ionization chamber for low energy, low dose rate brachytherapy sources is designed using Monte Carlo transport calculations to aid in the design process. The design improvements are the elimination of the air density induced over‐response effect seen in other air‐communicating chambers for low energy photon sources, and a larger signal strength (response or current) for and based seeds. A prototype well chamber based on the Monte Carlo aided design but using graphite coated acrylic walls rather than the design basis air equivalent plastic (C‐552) walls was constructed and experimentally evaluated. The prototype chamber produced an 85% stronger signal when measuring a commonly used seed and a 26% stronger signal when measuring a commonly used seed when compared to another commonly used well chamber. The normalized corrected chamber response is, at most, 1.3% and 2.4% over unity for air densities/pressures corresponding to an elevation of above sea level for the commonly used and based seeds respectively. Comparing calculated and measured chamber responses for common and based brachytherapy seeds show agreement within 0.6% and 0.2%, respectively. We conclude that Monte Carlo transport calculations accurately model the response of this new well chamber and in general can be used to predict the response of well chambers. The prototype chamber built in this work responds as predicted by the Monte Carlo calculations.
Maximizing the potential of direct aperture optimization through collimator rotation
Authors: Milette Marie‐Pierre , Otto Karl
Published: April 2007

Intensity‐modulated radiation therapy (IMRT) treatment plans are conventionally produced by the optimization of fluence maps followed by a leaf sequencing step. An alternative to fluence based inverse planning is to optimize directly the leaf positions and field weights of multileaf collimator (MLC) apertures. This approach is typically referred to as direct aperture optimization (DAO). It has been shown that equivalent dose distributions may be generated that have substantially fewer monitor units (MU) and number of apertures compared to fluence based optimization techniques. Here we introduce a DAO technique with rotated apertures that we call rotating aperture optimization (RAO). The advantages of collimator rotation in IMRT have been shown previously and include higher fluence spatial resolution, increased flexibility in the generation of aperture shapes and less interleaf effects. We have tested our RAO algorithm on a complex C‐shaped target, seven nasopharynx cancer recurrences, and one multitarget nasopharynx carcinoma patient. A study was performed in order to assess the capabilities of RAO as compared to fixed collimator angle DAO. The accuracy of fixed and rotated collimator aperture delivery was also verified. An analysis of the optimized treatment plans indicates that plans generated with RAO are as good as or better than DAO while maintaining a smaller number of apertures and MU than fluence based IMRT. Delivery verification results show that RAO is less sensitive to tongue and groove effects than DAO. Delivery time is currently increased due to the collimator rotation speed although this is a mechanical limitation that can be eliminated in the future.
The trouble with
Authors: Boone John M.
Published: April 2007

The computed tomography dose index is typically measured using a long pencil ion chamber with cylindrical polymethyl methacrylate (PMMA) dosimetry phantoms. While this metric was useful in the era of single slice CT scanners with collimated slice thicknesses of or less, the efficiency of this metric in multi‐slice CT scanners with wide collimated x‐ray beams is unknown. Monte Carlo simulations were used to assess the efficiency of the parameter for wider beam collimations. The simulations utilized the geometry of a commercially available CT scanner, with modeled polyenergetic x‐ray spectra. Dose spread functions (DSFs) were computed along the length of diam rods placed at several radii in infinitely long diam (head) and diam (body) PMMA phantoms. The DSFs were used to compute radiation dose profiles for slice thicknesses from . efficiency was defined as the fraction of the dose along a PMMA rod collected in a length centered on the CT slice position, divided by the total dose deposited along an infinitely long PMMA rod. For a slice thickness, a x‐ray spectrum, and the PMMA head phantom, the efficiency of the was 82% and 90% for the center and peripheral holes, respectively. The corresponding efficiency values for the body phantom were 63% and 88%. These values are reduced by only 1% when a slice thickness was studied, so the use of for wide x‐ray beams is no less valid than its use for beam widths. However, these data illustrate that the efficiency of the measurement even with beam widths is low and, consequently, dose computations which are derived from this metric may not be as accurate as desirable.
An intercomparison between film dosimetry and diode matrix for IMRT quality assurance
Authors: Banci Buonamici F. , Compagnucci A. , Marrazzo L. , Russo S. , Bucciolini M.
Published: April 2007

The evaluation of the agreement between measured and calculated dose plays an essential role in the quality assurance (QA) procedures for intensity modulated radiation therapy (IMRT). Film dosimetry has been widely adopted for this purpose due to excellent film characteristics in terms of spatial resolution; unfortunately, it is a time‐consuming procedure and requires great care if film has to be used as an absolute dosimeter. If this is not the case, then an independent ionimetric measurement is mandatory to assess the absolute dose agreement. Arrays of detectors are now replacing films for routine IMRT QA, since they permit very simple verification procedures. They show excellent characteristics in terms of linearity, repeatability, and independence of the response from the dose rate, but at the same time present a poor spatial resolution, due to the limited number of detectors available. In our institution, a diode matrix (MapCHECK™, provided by Sun Nuclear) is adopted for routine QA. The aim of this work is to compare the performances of absolute film dosimetry with this matrix in QA procedures and to investigate the origin of possible discrepancies between the two methods. The results we present show a very good agreement between the two detectors when used to assess the mean dose deviation between calculated and measured doses (in both cases 0.2%). If the matrix method is adopted, MapCHECK™ response shows a slightly better agreement with computed dose distribution than film dosimetry (mean percentage of points satisfying the constraint : 96% versus 94%). This difference is shown not to depend on the different field sampling, but on the detectors’ capabilities. Moreover, we show that the diode matrix is able to identify eventual delivery errors as well as film. Our conclusion is that the diode matrix may effectively replace both film dosimetry and ionimetric measurements in routine IMRT QA.
The impact of breathing motion versus heterogeneity effects in lung cancer treatment planning
Authors: Rosu Mihaela , Chetty Indrin J. , Tatro Daniel S. , Ten Haken Randall K.
Published: April 2007

The purpose of this study is to investigate the effects of tissue heterogeneity and breathing‐induced motion/deformation on conformal treatment planning for pulmonary tumors and to compare the magnitude and the clinical importance of changes induced by these effects. Treatment planning scans were acquired at normal exhale/inhale breathing states for fifteen patients. The internal target volume (ITV) was defined as the union of exhale and inhale gross tumor volumes uniformly expanded by . Anterior/posterior opposed beams (AP/PA) and three‐dimensional (3D)‐conformal plans were designed using the unit‐density exhale (“static”) dataset. These plans were further used to calculate (a) density‐corrected (“heterogeneous”) static dose and (b) heterogeneous cumulative dose, including breathing deformations. The DPM Monte Carlo code was used for dose computations. For larger than coin‐sized tumors, relative to unit‐density plans, tumor and lung doses increased in the heterogeneity‐corrected plans. In comparing cumulative and static plans, larger normal tissue complication probability changes were observed for tumors with larger motion amplitudes and uncompensated breathing‐induced hot/cold spots in lung. Accounting for tissue heterogeneity resulted in average increases of 9% and 7% in mean lung dose (MLD) for the and photon beams, respectively. Breathing‐induced effects resulted in approximately 1% and 2% average decreases in MLD from the static value, for the 6 and photon beams, respectively. The magnitude of these effects was not found to correlate with the treatment plan technique, i.e., AP/PA versus 3D‐CRT. Given a properly designed ITV, tissue heterogeneity effects are likely to have a larger clinical significance on tumor and normal lung treatment evaluation metrics than four‐dimensional respiratory‐induced changes.
Quality assurance of HDR sources using a Fricke dosimeter
Authors: Austerlitz C. , Mota H. , Almeida C. E. , Allison R. , Sibata C.
Published: April 2007

A prototype of a Fricke dosimetry system consisting of a water phantom made of Plexiglas® and a Pyrex balloon fitted with a thick Pyrex sleeve in its center was created to assess source strength and treatment planning algorithms for use in high dose rate (HDR) afterloading units. In routine operation, the radioactive source is positioned at the end of a sleeve, which coincides with the center of the spherical balloon that is filled with Fricke solution, so that the solution is nearly isotropically irradiated. The Fricke system was calibrated in terms of source strength against a reference well‐type ionization chamber, and in terms of radial dose by means of an existing algorithm from the HDR's treatment planning system. Because the system is based on the Fricke dosimeter itself, for a given type and model of source, the system needs initial calibration but no recalibration. The results from measurements made over a period, including source decay and source substitutions, have shown the feasibility of using such a system for quality control (QC) of HDR afterloading equipment, including both the source activity and treatment planning parameters. The benefit of a large scale production and the use of this device for clinical HDR QC audits via mail are also discussed.
Effects of Hounsfield number conversion on CT based proton Monte Carlo dose calculations
Authors: Jiang Hongyu , Seco Joao , Paganetti Harald
Published: April 2007

The Monte Carlo method provides the most accurate dose calculations on a patient computed tomography (CT) geometry. The increase in accuracy is, at least in part, due to the fact that instead of treating human tissues as water of various densities as in analytical algorithms, the Monte Carlo method allows human tissues to be characterized by elemental composition and mass density, and hence allows the accurate consideration of all relevant electromagnetic and nuclear interactions. On the other hand, the algorithm to convert CT Hounsfield numbers to tissue materials for Monte Carlo dose calculation introduces uncertainties. There is not a simple one to one correspondence between Hounsfield numbers and tissue materials. To investigate the effects of Hounsfield number conversion for proton Monte Carlo dose calculations, clinical proton treatment plans were simulated using the Geant4 Monte Carlo code. Three Hounsfield number to material conversion methods were studied. The results were compared in forms of dose volume histograms of gross tumor volume and clinical target volume. The differences found are generally small but can be dosimetrically significant. Further, different methods may cause deviations in the predicted proton beam range in particular for deep proton fields. Typically, slight discrepancies in mass density assignments play only a minor role in the target region, whereas more significant effects are caused by different assignments in elemental compositions. In the presence of large tissue inhomogeneities, for head and neck treatments, treatment planning decisions could be affected by these differences because of deviations in the predicted tumor coverage. Outside the target area, differences in elemental composition and mass density assignments both may play a role. This can lead to pronounced effects for organs at risk, in particular in the spread‐out Bragg peak penumbra or distal regions. In addition, the significance of the elemental composition effect (dose to water vs. dose to tissue) is tissue‐type dependent and is also affected by nuclear reactions.
Fetal cortisol response to intrauterine microbial colonisation identified by the polymerase chain reaction and fetal inflammation
Authors: Miralles R , Hodge R , Kotecha S
Published: April 2007

Objective:

To determine the fetal cortisol response to intrauterine infection.

Study design:

16s ribosomal RNA genes or the urease genes ofUreaplasmaspp were identified by the polymerase chain reaction in intrauterine samples. Cord blood cortisol, interleukin 6 (IL6) and IL8 were measured in samples from 31 infants born at <32 weeks gestation.

Results:

13 infants (median gestation 30 weeks, birth weight 1350 g) had at least one positive intrauterine sample for microbial genes and 18 infants (31 weeks, 1320 g) did not. The cord blood cortisol concentration was significantly higher in fetuses exposed to intrauterine infection and significantly increased in fetuses/mothers presenting in preterm labour with intact membranes compared with infants delivered by elective prelabour caesarean section (p<0.05). The cord blood cortisol concentration was increased in the mothers with prelabour premature rupture of membranes but this was not significant compared with the caesarean section group. The cord blood cortisol concentration was significantly increased in the presence of chorioamnionitis or funisitis and was moderately correlated with cord blood IL6 (r = 0.64, p<0.01) and IL8 (r = 0.52, p<0.01).

Conclusions:

In this study, cord blood cortisol was increased in the colonised group compared with non-colonised infants. It is unclear if infants born following prelabour premature rupture of the membranes mount an adequate anti-inflammatory response.
MANAGED FLOAT EXCHANGE RATE SYSTEM: THE SINGAPORE EXPERIENCE
Authors: KHOR HOE EE , LEE JASON , ROBINSON EDWARD , SUPAAT SAKTIANDI
Published: April 2007

This paper examines the key characteristics of Singapore's exchange rate-centered monetary policy; in particular, its managed float regime which incorporates key features of the basket, band and crawl system popularized by Williamson (1998, 1999). We assess how the flexibility accorded by this framework has been advantageous in facilitating adjustment to various shocks to the economy. A characterization of the countercyclical nature of Singapore's exchange rate policy is also offered, with reference to recent work on the monetary policy reaction function and estimates of Singapore's behavioral equilibrium exchange rate. We also review previous econometric analysis which provides evidence that Singapore's managed float system may have helped to mitigate the spillover effects of such increased volatility into the real economy. The track record of Singapore's managed float regime over the past two decades suggests that intermediate regimes are a viable alternative to the so-called "corner solutions", especially when supported by consistent macroeconomic and microeconomic policies as well as strong institutions.
TO PEG OR NOT TO PEG?
Authors: MAKIN ANTHONY J.
Published: April 2007

This paper presents a simple framework for analyzing the macroeconomic effects of internal and external shocks under polar exchange rate regimes. It highlights the significance of fluctuations in competitiveness and real income for exchange rate policy, revealing that positive (negative) real shocks increase (decrease) national income and strengthen (weaken) the balance of payments and exchange rate. It also shows that, ceteris paribus, pegged exchange rates facilitate real income growth for emerging economies while lowering its variability when exports and productivity are improving and monetary shocks predominate. Alternatively, a floating exchange rate system may be most appropriate for less open advanced economies with relatively stable monetary sectors that frequently experience negative real shocks.
ESTIMATING THE EMPLOYMENT PERFORMANCE INDICATOR: THE CASE OF UNIVERSITI UTARA MALAYSIA GRADUATES
Authors: LIM HOCK-EAM
Published: April 2007

This paper proposes an alternate method of estimating the employment performance indicator using the Cox Proportional Hazard model with competing risk framework. Simple aggregation and the logit model have also been used in the estimating for comparison purpose. Using the data of Universiti Utara Malaysia graduates, the study finds that the Bachelor of Accounting degree has the highest employment performance indicator. There are significant differences found in the employment performance ranking as constructed by the proportional hazard model, logit model and simple aggregation.
A COMPARATIVE STUDY OF EXCHANGE RATE REGIMES AND MACRO-INSTABILITIES IN THE TWIN ECONOMIES OF SINGAPORE AND HONG KONG
Authors: MA YUE , KUEH Y. Y. , NG RAYMOND C. W.
Published: April 2007

Based on a small, open-economy IS-LM prototype model, this paper examines the sources of macroeconomic instabilities in Hong Kong and Singapore operating under two different currency board arrangements. The empirical findings suggest that in general, both external and internal factors contribute to the macroeconomic volatilities observed in the two economies. There is evidence of a tradeoff between exchange rate and interest rate targeting for the stability of money supply in Singapore. Our findings have important implications for Mainland China's monetary authorities in the transition from a hard-peg exchange rate regime like Hong Kong to a basket-link system like the one in Singapore.
DOES MONEY TELL US ANYTHING ABOUT INFLATION IN NIGERIA?
Authors: ADEBIYI MICHAEL ADEBAYO
Published: April 2007

This paper seeks to establish whether or not monetary aggregates M1 and M2 have useful information for forecasting inflation, other than that provided by inflation itself. The study is approached in two ways. First, it conducts forecasting experiments, using mean absolute percentage errors (MAPEs). It then evaluates whether each monetary variable improves the forecasts of a simple autoregressive (AR) (1) model of inflation or not. The study reveals that the MAPEs for all the variables are less than that of the benchmark AR (1) model. This implies that all the variables examined serve as important information variables for price movements.

Also, from the inflation equation, the paper reveals that monetary aggregate (M2), Treasury bill rate, deposit rate and exchange rates are significant in the equation, therefore concluding that these variables provide useful information in predicting inflation in Nigeria.
INFLUENCE OF ENVIRONMENTAL NOISE ON THE DYNAMICS OF A REALISTIC ECOLOGICAL MODEL
Authors: UPADHYAY R. K. , MUKHOPADHYAY A. , IYENGAR S. R. K.
Published: April 2007

The present paper investigates the influence of environmental noise on a fairly realistic three-species food chain model based on the Leslie-Gower scheme. The self- growth parameter for the prey species is assumed to be perturbed by white noise characterized by a Gaussian distribution with mean zero and unit spectral density. Using tools borrowed from the nonlinear dynamical system theory, we study the dynamical behavior of the model system. The behavior of the stochastic system (perturbed one) is studied and the fluctuations in the populations are measured both analytically (for the linearized system) and numerically by computer simulation. Varying one of the control parameters in its range, while keeping all the others constant, we monitor the changes in the dynamical behavior of the model system, thereby fixing the regimes in which the system exhibits chaotic dynamics. Our study suggests that the trophic level (top, middle or bottom) at which a population is positioned, the amplitude of environmental noise and the population's susceptibility to environmental noise play key roles in how noise affects the population dynamics.
SYNTHESIS OF MOLECULAR GOLD CLUSTERS WITH LUMINESCENCE PROPERTIES BY MERCAPTIDE THERMOLYSIS IN POLYMER MATRICES
Authors: CAROTENUTO G. , LONGO A. , DE PETROCELLIS L. , DE NICOLA S. , REPETTO P. , PERLO P. , AMBROSIO L.
Published: April 2007

Highly fluorescent Au /polystyrene nanocomposite films have been prepared by thermal decomposition at 250°C of gold mercaptide molecules (dodecyl-mercaptide of gold(I), C 12 H 25 SAu ) dissolved in polystyrene. Owing to a continuous nucleation of metallic phase generated by the thermolysis reaction, molecular gold clusters, which are characterized by fluorescence properties because of the very small size, can be obtained by this very simple technique.
MEASUREMENT OF NANOMECHANICAL PROPERTIES OF THIN FILMS BY INTEGRATING NANOINDENTATION SYSTEM AND ATOMIC FORCE MICROSCOPE
Authors: CHAO LU-PING , HSU JOING-SHIUN , LAU YUNG-DONG
Published: April 2007

In this paper, the nanoindentation system and atomic force microscope (AFM) are integrated to improve the limitation of the present area function of nanoindentation test used for shallow depth. The projected areas under the shallow contact depth are modified through scanning directly the immediate vinicity of indenter tip. The results indicate that both indentation hardness and reduced modulus obtained from the proposed method are better than those of the present area function as well as the perfect geometry relation.
EFFECT OF CHLORINATION ON PHOTOLUMINESCENCE PROPERTIES OF POROUS SILICON
Authors: NATARAJAN B. , RAMAKRISHNAN V. , VASU V. , RAMAMURTHY S.
Published: April 2007

The surface passivation of porous silicon plays a significant role in emission efficiency of the material. Photoluminescence (PL) studies were carried out for p-type porous silicon and chlorinated porous silicon to understand the effect of surface passivation on porous silicon. Visible photoluminescence was observed at 625 nm for both porous silicon and chlorinated porous silicon. The whole sample exhibits a PL band at red region and intensity decreased in chlorinated porous silicon. This paper presents an analytical solution that covers contributions from the components of silicon tetra chloride interface, silicon backbone, and voids using a serial–parallel capacitance method. Simulation study indicates that there is a good correlation between theory and observed PL.
INCORPORATION OF IRON INTO NANO HYDROXYAPATITE PARTICLES SYNTHESIZED BY THE MICROWAVE PROCESS
Authors: PON-ON WEERAPHAT , MEEJOO SIWAPORN , TANG I-MING
Published: April 2007

This research focuses on understanding the nature of the Fe ions substituted in hydroxyapatite ((HAP) Ca 10-x Fe x( PO 4)6( OH )2-xÿx: x = 0, 0.2 and 0.4) powder synthesized at temperatures between 500°C and 1000°C and their crystallization. The DSC scan indicates a solid state phase transition at about 757°C for the as-prepared powder HAP. The transformation of HAP to β-tricalcium phosphate (β- TCP , β- Ca 3( PO 4)2) is seen when the powder were heated to 750°C. The sizes of the crystallites were determined to be about 46–51 nm, 33–40 nm and 33–59 nm for Fe content of 0, 0.2 and 0.4 mol%, respectively. The ESR parameters for the Fe 3+ ions, g = 4.23 and 8.93 indicated that the ions were subjected to a rhombic ion crystal field within the HAP structures. The g values of ~2.01 indicated that the particles were super-paramagnetic and ferromagnetic iron nanoparticles, having an average size about 0.2–0.5 μm in length.
THE EFFECT OF ANNEALING ON THE THERMAL PROPERTIES OF NANO-CdS BY PHOTOACOUSTICS
Authors: RAJI P. , RAMACHANDRAN K.
Published: April 2007

Nano- CdS samples are synthesized by precipitation method and are annealed at 50°C, 82°C and 110°C for 5 h in air. The particle size of these annealed samples is measured by photoacoustic technique and the influence of annealing on the thermal properties are measured and discussed.
EFFECTIVE THERMAL CONDUCTIVITY OF NANOFLUIDS CONTAINING CYLINDRICAL NANOPARTICLES
Authors: SABBAGHZADEH JAMSHID , EBRAHIMI SADOLLAH
Published: April 2007

We present a theoretical model for explaining the enhancement in the effective thermal conductivity of nanotubes (cylindrical shape particles) for use in nanotube-in-fluid suspensions. Our theoretical model shows that the effective thermal conductivity is decreased with cylindrical nanoparticle diameter, which agrees with experimental results. We also show that with the decrease of nanotube diameter, the thermal conductivity increases if the thickness of nanolayers increases. We provide a good estimation for the nanolayer's thickness which plays an important role in increasing the thermal conductivity.
ELECTROPHORETIC FRACTIONATION OF CARBON NANOTUBE DISPERSIONS ON AGAROSE GELS
Authors: VETCHER ALEXANDRE A. , FAN JUN-HUEI , VETCHER IVAN A. , LIN TIFFANY , ABRAMOV SEMEN M. , DRAPER ROCKFORD , KOZLOV MIKHAIL E. , BAUGHMAN RAY H. , LEVENE STEPHEN D.
Published: April 2007

We show that various aqueous suspensions of single-walled and multi-walled carbon nanotubes, dispersed using either common surfactants or DNA, can be separated into components using agarose gel electrophoresis. In a DC electric field, carbon nanotubes and nanotube–DNA complexes migrate in the gel in the direction of positive potential to form well-defined bands. Raman spectroscopy as a function of band position shows that nanotubes having different spectroscopic properties have distinct electrophoretic mobilities. The results suggest that the separation of nanotubes according to structure can be achieved by this procedure. We discuss the factors affecting the mobility of the nanotube complexes and propose analytical applications of this technique.
ELECTRONIC CONDUCTANCE AND CURRENT DISTRIBUTION OF A PENTACENE MOLECULAR TAP
Authors: WANG LI-GUANG , CHEN LEI , WONG TERENCE KIN SHUN , YU DING-WEN , LI YONG
Published: April 2007

The electronic conductance characteristics of a pentacene molecular tap has been investigated theoretically by a Green's function approach based on an empirical tight-binding theory in which only one π orbital electron per carbon atom is considered. The quantum transmission probability for electrons through the pentacene tap from an input to three other outputs is obtained. A strong dependence of the transmission probability on the incident electron energy and the molecular energy levels is evident for all three input–output combinations. The electronic current distributions inside the pentacene tap are calculated by a current density method based on the Fisher–Lee formula for two electron energies (E = ± 0.68 and ±1.31 eV) at which the transmission spectra peaks. The current distributions are in good agreement with the Kirchhoff quantum current momentum conservation law.
THEORETICAL STUDIES ON THE REACTION MECHANISM OF HNCS WITH CH2CH RADICAL
Authors: XU JIAN-HUA , LI LAI-CAI , ZHENG YAN , LIU JUN-LING , WANG XIN
Published: April 2007

The reaction mechanisms of HNCS with CH 2 CH radical have been investigated by density functional theory (DFT). The geometries and harmonic frequencies of the reactants, intermediates, transition states and products have been calculated at the B3LYP/6-311++G(d,p) level. The results show that the reaction is very complicated. Nine possible reaction pathways were identified. The results show that the most feasible reaction channel is the hydrogen-transfer pathway CH 2 CH + HNCS → IMA1 → TSA1 → CH 2 CHH + NCS . The pathway VIC C-S addition channel ( CH 2 CH + HNCS → TSD5 → IMD4 → TSD9 → CH 2 CHS + CNH ) can also occur easily. Ethene and radical NCS is the main product of the studied reaction, and product P8 ( CH 2 CHS and CNH ) may also be observed. Compared with our previous study on the reaction HNCS + CH 2 CH , the present reaction is easier to proceed.
COMPARISON OF THREE 3D-QSAR METHODS USING A NOVEL CLASS OF MURF INHIBITORS
Authors: KONG DE-XIN , ZHU WEI-LIANG , WU DA-LEI , SHEN XU , JIANG HUA-LIANG
Published: April 2007

MurF was considered as an attractive target for new antibacterial discovery. In this paper, three QSAR methods were employed, viz. comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) and hologram QSAR (HQSAR), to derive highly predictive QSAR models for designing novel MurF inhibitors and comparing different 3D-QSAR/alignment methods. QSAR models with high predictive ability for MurF inhibitors were successfully constructed in terms of cross-validation q2, standard error and predictive coefficient r2, which were around 0.70, 0.55 and 0.99, respectively. All the models from different methods were in good agreement with each other. Compounds with indeterminate activities were used as a test set; results showed that CoMSIA had the best predictive ability, followed by HQSAR and CoMFA. Based on these models, some key features for designing new MurF inhibitors were identified. A virtual database screen process was proposed based on the combination of these models.
HOMOLOGY MODELING AND MOLECULAR DYNAMICS STUDY OF HUMAN INOSINE TRIPHOSPHATE PYROPHOSPHATASE
Authors: ZHENG QING-CHUAN , SUN CHIA-CHUNG
Published: April 2007

With homology-modeling techniques, molecular mechanics and molecular dynamics methods, a 3D structure model of the human inosine triphosphatase (ITPase; EC 3.6.1.19) is created and refined. This model is further assessed by Profile-3D and ProStat, which confirm that the refined model is reliable. With this model, a flexible docking study is performed, and the results indicate that Arg178, Lys19 and Glu44 are three important determinant residues in substrate binding because they have prominent interaction energies with ITP and form strong hydrogen bonds with ITP. In addition, we further find that the P32T substitution alters the α-helices of ITPase but the β-sheets are almost not changed, and the mutation induces the interaction energy between ITPase and ITP to increase, which are consistent with the conclusion predicted by Sumi et al.8 The results from the mutagenesis imply that Pro32 is vital for the catalytic activity.
AB INITIO MOLECULAR DYNAMICS STUDY OF DISSOLVED SiO2 IN SUPERCRITICAL WATER
Authors: DOLTSINIS N. L. , BURCHARD M. , MARESCH W. V. , BOESE A. D. , FOCKENBERG T.
Published: April 2007

Ab initio molecular dynamics simulations of SiO 2 in supercritical water at temperatures of 900 K and 1200 K and a pressure of 1.5 GPa at concentrations of 5 wt% and 16 wt% have been carried out. The different polymeric forms SiO 4 H 4, Si 2 O 7 H 6, and Si 3 O 10 H 8 are found to be energetically similar within the statistical error, suggesting that all three polymeric forms play an important role in solutions at the above conditions. However, neither spontaneous polymerization nor depolymerization has been observed during the 10-ps time span of the simulations. The dynamic and structural properties of the supercritical solutions have been analyzed in terms of diffusion coefficients, vibrational spectra, and radial pair distribution functions.
EXPLORING THE POTENTIAL ENERGY SURFACE OF THE CATALYZED ISOMERIZATION OF NITROSOMETHANE TO FORMALDOXIME
Authors: LIANG GUO-MING , REN YI , CHU SAN-YAN , WONG NING-BEW
Published: April 2007

The mechanism of the isomerization of nitrosomethane to formaldoxime catalyzed by neutral molecule ( H 2 O and HCOOH ) has been investigated at the level of B3LYP/6-311+G**. Calculated results indicate that the rearrangement from nitrosomethane to more stable trans-formaldoxime can proceed via two different reaction channels, but the favorable reaction pathway catalyzed by water and formic acid is different from the one in the catalyst-free reaction. It is more favorable that the tautomeric reaction involves the formation of cis-formaldoxime and a subsequent rotation about the N – O bond to form trans-formaldoxime in the catalyzed reaction. The activation energy of rate-determining step was reduced from 197.9 kJ/mol to 138.7 kJ/mol in the water-catalyzed reaction and 79.6 kJ/mol in the formic acid-catalyzed reaction, respectively, due to the catalysis of hydroxylic groups, but the catalysis of more acidic hydroxyl group in the latter system has been shown to be more efficient.
A DFT INVESTIGATION OF SULFUR ADSORPTION ON Ir(100)
Authors: HUANG WUYING , LAI WENZHEN , XIE DAIQIAN
Published: April 2007

The adsorptions of sulfur atom on the Ir (100) surface at p (2 × 2) and c (2 × 2) phases were investigated by the density functional calculations within the generalized gradient approximation. The adsorption energy, adsorption geometry, work function change, and charge density distribution were analyzed. The hollow site was found to be the most stable, followed by the bridge and the top sites. The calculated adsorption geometries were in good agreement with the observed results. Particularly, it was found that the adsorption of S on Ir (100) caused a work function decrease. A charge accumulation at the interface between the S layer and the Ir substrate, which centered closer to the S atom, suggests a polar covalent bonding. Density of states (DOS) analysis showed that the adsorption of S induces a reduction of the surface Ir d-orbital DOS around the Fermi level.
ELECTRONIC STRUCTURES OFS-DOPED ANATASE AND RUTILETiO2
Authors: MA XIN-GUO , TANG CHAO-QUN , YANG XIAO-HUA
Published: April 2007

The electronic structures of S -doped TiO2have been carried out by first-principles calculations based on density functional theory with plane-wave ultrasoft pseudopotential method. Comparing anion doping with cation doping in anatase and rutile, we found different energy band structures and origins of photoactivity of S -doped TiO2. For anion-doped TiO2, new S –3p bands appear and which lie slightly above the top of the O –2p valence band. It plays a significant role in increasing absorbance in the visible region, resulting in improvement in photocatalytic activity under visible-light irradiation. For cation-doped TiO2, the potential of the O –2p valence band shift much downwards, yielding the stronger oxidative power than that of undoped and S anion-doped TiO2. Nevertheless, the deep impurity states in BG (bond gap) that originate from the S -dopant have negative effects on the recombination of the photoexcited electrons and holes. From our calculated results, we can explain their differences in photocatalytic activity under visible-light irradiation.
Antidiabetic sulfonylurea stimulates insulin secretion independently of plasma membrane KATPchannels
Authors: Geng Xuehui , Li Lehong , Bottino Rita , Balamurugan A. N. , Bertera Suzanne , Densmore Erik , Su Anjey , Chang Yigang , Trucco Massimo , Drain Peter
Published: April 2007

Understanding mechanisms by which glibenclamide stimulates insulin release is important, particularly given recent promising treatment by glibenclamide of permanent neonatal diabetic subjects. Antidiabetic sulfonylureas are thought to stimulate insulin secretion solely by inhibiting their high-affinity ATP-sensitive potassium (KATP) channel receptors at the plasma membrane of β-cells. This normally occurs during glucose stimulation, where ATP inhibition of plasmalemmal KATPchannels leads to voltage activation of L-type calcium channels for rapidly switching on and off calcium influx, governing the duration of insulin secretion. However, growing evidence indicates that sulfonylureas, including glibenclamide, have additional KATPchannel receptors within β-cells at insulin granules. We tested nonpermeabilized β-cells in mouse islets for glibenclamide-stimulated insulin secretion mediated by granule-localized KATPchannels by using conditions that bypass glibenclamide action on plasmalemmal KATPchannels. High-potassium stimulation evoked a sustained rise in β-cell calcium level but a transient rise in insulin secretion. With continued high-potassium depolarization, addition of glibenclamide dramatically enhanced insulin secretion without affecting calcium. These findings support the hypothesis that glibenclamide, or an increased ATP/ADP ratio, stimulates insulin secretion in part by binding at granule-localized KATPchannels that functionally contribute to sustained second-phase insulin secretion.
6-Fluoro-6-deoxy-d-glucose as a tracer of glucose transport
Authors: Landau Bernard R. , Spring-Robinson Chandra L. , Muzic Raymond F. , Rachdaoui Nadia , Rubin Darrell , Berridge Marc S. , Schumann William C. , Chandramouli Visvanathan , Kern Timothy S. , Ismail-Beigi Faramarz
Published: April 2007

Glucose transport rates are estimated noninvasively in physiological and pathological states by kinetic imaging using PET. The glucose analog most often used is18F-labeled 2FDG. Compared with glucose, 2FDG is poorly transported by intestine and kidney. We examined the possible use of 6FDG as a tracer of glucose transport. Lacking a hydroxyl at its 6th position, 6FDG cannot be phosphorylated as 2FDG is. Prior studies have shown that 6FDG competes with glucose for transport in yeast and is actively transported by intestine. Its uptake by muscle has been reported to be unresponsive to insulin, but that study is suspect. We found that insulin stimulated 6FDG uptake 1.6-fold in 3T3-L1 adipocytes and azide stimulated the uptake 3.7-fold in Clone 9 cells. Stimulations of the uptake of 3OMG, commonly used in transport assays, were similar, and the uptakes were inhibited by cyclochalasin B. Glucose transport is by GLUT1 and GLUT4 transporters in 3T3-L1 adipocyte and by the GLUT1 transporter in Clone 9 cells. Cytochalasin B inhibits those transporters. Rats were also imaged in vivo by PET using 618FDG. There was no excretion of18F into the urinary bladder unless phlorizin, an inhibitor of active renal transport, was also injected.18F activity in brain, liver, and heart over the time of scanning reached a constant level, in keeping with the 6FDG being distributed in body water. In contrast,18F from 218FDG was excreted in relatively large amounts into the bladder, and18F activity rose with time in heart and brain in accord with accumulation of 218FDG-6-P in those organs. We conclude that 6FDG is actively transported by kidney as well as intestine and is insulin responsive. In trace quantity, it appears to be distributed in body water unchanged. These results provide support for its use as a valid tracer of glucose transport.
Differential body weight and feeding responses to high-fat diets in rats and mice lacking cholecystokinin 1 receptors
Authors: Bi Sheng , Chen Jie , Behles R. Ryan , Hyun Jayson , Kopin Alan S. , Moran Timothy H.
Published: April 2007

Prior data demonstrated differential roles for cholecystokinin (CCK)1 receptors in maintaining energy balance in rats and mice. CCK1 receptor deficiency results in hyperphagia and obesity of Otsuka Long-Evans Tokushima Fatty (OLETF) rats but not in mice. To ascertain the role of CCK1 receptors in high-fat-diet (HFD)-induced obesity, we compared alterations in food intake, body weight, fat mass, plasma glucose, and leptin levels, and patterns of hypothalamic gene expression in OLETF rats and mice lacking CCK1 receptors in response to a 10-wk exposure to HFD. Compared with Long-Evans Tokushima Otsuka (LETO) control rats, OLETF rats on HFD had sustained overconsumption over the 10-wk period. High fat feeding resulted in greater increases in body weight and plasma leptin levels in OLETF than in LETO rats. In situ hybridization determinations revealed that, while HFD reduced neuropeptide Y (NPY) mRNA expression in both the arcuate nucleus (Arc) and the dorsomedial hypothalamus (DMH) of LETO rats, HFD resulted in decreased NPY expression in the Arc but not in the DMH of OLETF rats. In contrast to these results in OLETF rats, HFD increased food intake and induced obesity to an equal degree in both wild-type and CCK1 receptor−/− mice. NPY gene expression was decreased in the Arc in response to HFD, but was not detectable in the DMH in both wild-type and CCK1 receptor−/− mice. Together, these data provide further evidence for differential roles of CCK1 receptors in the controls of food intake and body weight in rats and mice.
Renal responses to the κ-opioid-receptor agonist U-50488H in conscious lambs
Authors: Qi Wei , Ebenezar K. Kumar , Samhan Mohamed A. , Smith Francine G.
Published: April 2007

In adult animals and humans, activation of κ-opioid receptors results in a diuresis. The aim of the present study was to investigate whether κ-opioids are also diuretic early in life and whether this is altered during postnatal maturation. Therefore, the renal effects of the κ-opioid-receptor agonist U-50488H were measured in two separate age groups of conscious lambs at two stages of postnatal maturation (∼1 wk and ∼6 wk) under physiological conditions. To evaluate whether the renal responses to U-50488H resulted from receptor-dependent effects, responses to U-50488H were also tested in the presence of the specific κ-opioid-receptor antagonist 5′-guanidinonaltrindole (GNTI). Urinary flow rate, free water clearance, and electrolyte excretions and clearances were measured for 30 min before and for 90 min after intravenous injection of U-50488H or vehicle. An increase in urinary flow rate accompanied by an increase in free water clearance occurred in response to administration of U-50488H but not vehicle. There were no effects of U-50488H on electrolyte excretions or clearances at either 1 or 6 wk of postnatal life. Although there were no effects of GNTI on any of the measured or calculated variables, the aforementioned diuretic response to U-50488H was abolished by pretreatment with GNTI in both age groups. We conclude that κ-opioid receptors are diuretic early in life and that this response does not appear to be altered as postnatal maturation proceeds. Therefore, these data provide evidence that activation of κ-opioid receptors early in life may lead to alterations in fluid balance.
Activity-Dependent Depression of Local Excitatory Connections in the CA1 Region of Mouse Hippocampus
Authors: Fink Ann E. , Sariñana Joshua , Gray Erin E. , O'Dell Thomas J.
Published: April 2007

The existence of recurrent excitatory synapses between pyramidal cells in the hippocampal CA1 region has been known for some time yet little is known about activity-dependent forms of plasticity at these synapses. Here we demonstrate that under certain experimental conditions, Schaffer collateral/commissural fiber stimulation can elicit robust polysynaptic excitatory postsynaptic potentials due to recurrent synaptic inputs onto CA1 pyramidal cells. In contrast to CA3 pyramidal cell inputs, recurrent synapses onto CA1 pyramidal cells exhibited robust paired-pulse depression and a sustained, but rapidly reversible, depression in response to low-frequency trains of Schaffer collateral fiber stimulation. Blocking GABAB receptors abolished paired-pulse depression but had little effect on low-frequency stimulation (LFS)-induced depression. Instead, LFS-induced depression was significantly attenuated by an inhibitor of A1 type adenosine receptors. Blocking the postsynaptic effects of GABAB and A1 receptor activation on CA1 pyramidal cell excitability with an inhibitor of G-protein-activated inwardly rectifying potassium channels had no effect on either paired-pulse depression or LFS-induced depression. Thus activation of presynaptic GABAB and adenosine receptors appears to have an important role in activity-dependent depression at recurrent synapses. Together, our results indicate that CA3-CA1 and CA1-CA1 synapses exhibit strikingly different forms of short-term synaptic plasticity and suggest that activity-dependent changes in recurrent synaptic transmission can transform the CA1 region from a sparsely connected recurrent network into a predominantly feedforward circuit.
Activation of Pedunculopontine Tegmental PKA Prevents GABAB Receptor Activation–Mediated Rapid Eye Movement Sleep Suppression in the Freely Moving Rat
Authors: Datta Subimal
Published: April 2007

The pedunculopontine tegmental (PPT) GABAergic system plays a crucial role in the regulation of rapid eye movement (REM) sleep. I recently reported that the activation of PPT GABAB receptors suppressed REM sleep by inhibiting REM-on cells. One of the important mechanisms for GABAB receptor activation–mediated physiological action is the inhibition of the intracellular cAMP-dependent protein kinase A (cAMP-PKA) signaling pathway. Accordingly, I hypothesized that the PPT GABAB receptor activation–mediated REM sleep suppression effect could be mediated through inhibition of cAMP-PKA activation. To test this hypothesis, a GABAB receptor selective agonist, baclofen hydrochloride (baclofen), cAMP-PKA activator, Sp-adenosine 3′,5′-cyclic monophosphothioate triethylamine (SpCAMPS), and vehicle control were microinjected into the PPT in selected combinations to determine effects on sleep-waking states of chronically instrumented, freely moving rats. Microinjection of SpCAMPS (1.5 nmol) induced REM sleep within a short latency (12.1 ± 3.6 min) compared with vehicle control microinjection (60.0 ± 6.5 min). On the contrary, microinjection of baclofen (1.5 nmol) suppressed REM sleep by delaying its appearance for ∼183 min; however, the suppression of REM sleep by baclofen was prevented by a subsequent microinjection of SpCAMPS. These results provide evidence that the activation of cAMP-PKA within the PPT can successfully block the GABAB receptor activation–mediated REM sleep suppression effect. These findings suggest that the PPT GABAB receptor activation–mediated REM sleep regulating mechanism involves inactivation of cAMP-PKA signaling in the freely moving rat.
Interval Coding. II. Dendrite-Dependent Mechanisms
Authors: Doiron Brent , Oswald Anne-Marie M. , Maler Leonard
Published: April 2007

The rich temporal structure of neural spike trains provides multiple dimensions to code dynamic stimuli. Popular examples are spike trains from sensory cells where bursts and isolated spikes can serve distinct coding roles. In contrast to analyses of neural coding, the cellular mechanics of burst mechanisms are typically elucidated from the neural response to static input. Bridging the mechanics of bursting with coding of dynamic stimuli is an important step in establishing theories of neural coding. Electrosensory lateral line lobe (ELL) pyramidal neurons respond to static inputs with a complex dendrite-dependent burst mechanism. Here we show that in response to dynamic broadband stimuli, these bursts lack some of the electrophysiological characteristics observed in response to static inputs. A simple leaky integrate-and-fire (LIF)-style model with a dendrite-dependent depolarizing afterpotential (DAP) is sufficient to match both the output statistics and coding performance of experimental spike trains. We use this model to investigate a simplification of interval coding where the burst interspike interval (ISI) codes for the scale of a canonical upstroke rather than a multidimensional stimulus feature. Using this stimulus reduction, we compute a quantization of the burst ISIs and the upstroke scale to show that the mutual information rate of the interval code is maximized at a moderate DAP amplitude. The combination of a reduced description of ELL pyramidal cell bursting and a simplification of the interval code increases the generality of ELL burst codes to other sensory modalities.