bluuebunny/crossref_metadata_2025 huggingface dataset:
Developments in megavoltage cone beam CT with an amorphous silicon EPID: Reduction of exposure and synchronization with respiratory gating
Authors: Sillanpaa J. , Chang J. , Mageras G. , Riem H. , Ford E. , Todor D. , Ling C. C. , Amols H.
Published: March 2005

We have studied the feasibility of a low‐dose megavoltage cone beam computed tomography (MV CBCT) system for visualizing the gross tumor volume in respiratory gated radiation treatments of nonsmall‐cell lung cancer. The system consists of a commercially available linear accelerator (LINAC), an amorphous silicon electronic portal imaging device, and a respiratory gating system. The gantry movement and beam delivery are controlled using dynamic beam delivery toolbox, a commercial software package for executing scripts to control the LINAC. A specially designed interface box synchronizes the LINAC, image acquisition electronics, and the respiratory gating system. Images are preprocessed to remove artifacts due to detector sag and LINAC output fluctuations. We report on the output, flatness, and symmetry of the images acquired using different imaging parameters. We also examine the quality of three‐dimensional (3D) tomographic reconstruction with projection images of anthropomorphic thorax, contrast detail, and motion phantoms. The results show that, with the proper choice of imaging parameters, the flatness and symmetry are reasonably good with as low as three beam pulses per projection image. Resolution of 5% electron density differences is possible in a contrast detail phantom using 100 projections and 30 MU. Synchronization of image acquisition with simulated respiration also eliminated motion artifacts in a moving phantom, demonstrating the system's capability for imaging patients undergoing gated radiation therapy. The acquisition time is limited by the patient's respiration (only one image per breathing cycle) and is under 10 min for a scan of 100 projections. In conclusion, we have developed a MV CBCT system using commercially available components to produce 3D reconstructions, with sufficient contrast resolution for localizing a simulated lung tumor, using a dose comparable to portal imaging.
Investigating the effect of clonogen resensitization on the tumor response to fractionated external radiotherapy
Authors: Stavreva N. A. , Warkentin B. , Stavrev P. V. , Fallone B. G.
Published: March 2005

In this work we further develop the modeling of tumor dynamics by proposing a mechanism of tumor resensitization that is based on the process of reoxygenation. Reoxygenation is modeled using the concept of nonstationary diffusion of oxygen. This leads to the derivation of an explicit expression for the radiosensitivity parameter that predicts a radiosensitivity that increases with time. To account for the resensitization mechanism, the time‐dependent expression for the radiosensitivity is then incorporated within a tumor control probability (TCP) model that already includes tumor cell repopulation and repair. We fit a set of experimental animal TCP curves corresponding to several different fractionation regimes using both the modified (with resensitization) and unmodified (without resensitization) versions of the TCP model. In comparison to the unmodified model, the modified model produces statistically superior fits, and is able to describe an “inverse” dose‐fractionation behavior present in the data.
A novel extension of the parallel‐beam projection‐slice theorem to divergent fan‐beam and cone‐beam projections
Authors: Chen Guang‐Hong , Leng Shuai , Mistretta Charles A.
Published: March 2005

The general goal of this paper is to extend the parallel‐beam projection‐slice theorem to divergent fan‐beam and cone‐beam projections without rebinning the divergent fan‐beam and cone‐beam projections into parallel‐beam projections directly. The basic idea is to establish a novel link between the local Fourier transform of the projection data and the Fourier transform of the image object. Analogous to the two‐ and three‐dimensional parallel‐beam cases, the measured projection data are backprojected along the projection direction and then a local Fourier transform is taken for the backprojected data array. However, due to the loss of the shift invariance of the image object in a single view of the divergent‐beam projections, the measured projection data is weighted by a distance dependent weight before the local Fourier transform is performed. The variable in the weighting function is the distance from the backprojected point to the x‐ray source position. It is shown that a special choice of the weighting function, , will facilitate the calculations and a simple relation can be established between the Fourier transform of the image function and the local Fourier transform of the ‐weighted backprojection data array. Unlike the parallel‐beam cases, a one‐to‐one correspondence does not exist for a local Fourier transform of the backprojected data array and a single line in the two‐dimensional (2D) case or a single slice in the 3D case of the Fourier transform of the image function. However, the Fourier space of the image object can be built up after the local Fourier transforms of the ‐weighted backprojection data arrays are shifted and then summed in a laboratory frame. Thus the established relations Eq. (27) and Eq. (29) between the Fourier space of the image object and the Fourier transforms of the backprojected data arrays can be viewed as a generalized projection‐slice theorem for divergent fan‐beam and cone‐beam projections. Once the Fourier space of the image function is built up, an inverse Fourier transform could be performed to reconstruct tomographic images from the divergent beam projections. Due to the linearity of the Fourier transform, an image reconstruction step can be performed either when the complete Fourier space is available or in parallel with the building of the Fourier space. Numerical simulations are performed to verify the generalized projection‐slice theorem by using a disc phantom in the fan‐beam case.
Combined X–Y scanning magnet for conformal proton radiation therapy
Authors: Anferov Vladimir
Published: March 2005

Light‐ion beams have several features that make them very effective in radiation therapy applications. These include favorable depth dose distribution, finite penetration range, and high radio‐biological efficiency. Moreover, magnetic scanning methods allow one to spread an ion beam to an exact image of a complex tumor shape. The ion scanning system usually consists of two magnets, each scanning horizontal and vertical directions independently. This paper discusses the design for a novel combined X–Y beam scanning magnet which is under development for the Midwest Proton Radiotherapy Institute.
Dosimetric evaluation of a commercial 3D treatment planning system using the AAPM Task Group 23 test package
Authors: Casanova Borca Valeria , Pasquino Massimo , Bresciani Sara , Catuzzo Paola , Ozzello Franca , Tofani Santi
Published: March 2005

The accuracy of the dose calculation algorithm is one of the most critical steps in assessing the radiotherapy treatment to achieve the 5% accuracy in dose delivery, which represents the suggested limit to increase the complication‐free local control of tumor. We have used the AAPM Task Group 23 (TG‐23) test package for clinical photon external beam therapy to evaluate the accuracy of the new version of the PLATO TPS algorithm. The comparison between tabulated values and calculated ones has been performed for 266 and 297 dose values for the 4 and photon beams, respectively. Dose deviations less than 2% were found in the 98.5%‐ and 90.6% analyzed dose points for the two considered energies, respectively. Larger deviations were obtained for both energies, in large dose gradients, such as the build‐up region or near the field edges and blocks. As far as the radiological field width is concerned, 64 points were analyzed for both the energies: 53 points (83%) and 64 points (100%) were within for the 4 and photon beams, respectively. The results show the good accuracy of the algorithm either in simple geometry beam conditions or in complex ones, in homogeneous medium, and in the presence of inhomogeneities, for low and high energy beams. Our results fit well the data reported by several authors related to the calculation accuracy of different treatment planning systems (TPSs) (within a mean value of 0.7% and 1.2% for 4 and respectively). The TG‐23 test package can be considered a powerful instrument to evaluate dose calculation accuracy, and as such may play an important role in a quality assurance program related to the commissioning of a new TPS.
An antidote to the emerging two tier organ donation policy in Canada: the Public Cadaveric Organ Donation Program
Authors: Giles S
Published: March 2005

In Canada, as in many other countries, there exists an organ procurement/donation crisis. This paper reviews some of the most common kidney procurement and allocation programmes, analyses them in terms of public and private administration, and argues that privately administered living donor models are an inequitable stopgap measure, the good intentions of which are misplaced and opportunistic. Focusing on how to improve the publicly administered equitable cadaveric donation programme, and at the same time offering one possible explanation for its current failure, it is suggested that the simple moral principle of “give and you shall receive”, already considered by some, be extended further. This would allow for those who are willing to sign up to be a public cadaveric donor be given a priority for receiving an organ donation should they ever require it. It is argued that this priority may provide the motivation to give that is so far lacking in Canada. This model is called the Public Cadaveric Organ Donation Program.
How should we measure informed choice? The case of cancer screening: Table 1
Authors: Jepson R G , Hewison J , Thompson A G H , Weller D
Published: March 2005

Informed choice is increasingly recognised as important in supporting patient autonomy and ensuring that people are neither deceived nor coerced. In cancer screening the emphasis has shifted away from just promoting the benefits of screening to providing comprehensive information to enable people to make an informed choice. Cancer screening programmes in the UK now have policies in place which state that it is their responsibility to ensure that individuals are making an individual informed choice. There is a need to evaluate whether such policies mean that those people invited for screening are making informed choices, and how comprehensive information affects other variables such as uptake, cost effectiveness, and satisfaction. At the present time, there is no validated measure of informed choice in cancer screening. Such a measure could be used to evaluate the effectiveness of interventions to increase informed choice and levels of informed choice in a population invited for screening. It could encourage health professionals to be accountable. Factors important when measuring informed choice in cancer screening include an individual’s understanding of the limitations of screening, the ability to make an autonomous choice, and the difference between choice and behaviour.
Therapeutic optimism in the consent forms of phase 1 gene transfer trials: an empirical analysis
Authors: Kimmelman J , Palmour N
Published: March 2005

Background:“Therapeutic misconception” arises when human subjects interpret a clinical trial as aimed primarily at therapy rather than producing knowledge. Therapeutic misconceptions may be more prevalent in trials enrolling gravely ill subjects or involving novel and well publicised investigational agents.

Objective:To examine the extent to which investigators express therapeutic optimism in phase 1 human gene transfer consent documents, whether highly active gene transfer researchers are more prone to expressing therapeutic optimism, and whether consent forms have grown more optimistic in their descriptions of personal benefit over the last decade.

Design:Content analysis was performed on 277 consent documents to measure the number of sentences describing possibility of benefit, terminology used for experimental agents, the proportion of statements describing personal versus societal benefits, and whether investigators attempted to thwart therapeutic misconceptions.

Results:Consent forms generally used therapeutic terminology to describe study agents, devoted more sentences to describing possible personal benefits than to describing benefits to society, and infrequently explained that a particular benefit was unlikely. Consent documents used by highly active gene transfer researchers tended to portray significantly greater optimism about personal benefit than less active investigators, though they were also significantly more cautious with agent terminology. Finally, therapeutic optimism expressed in consent forms has declined over the past decade.

Conclusions:Consent documents used in phase 1 gene transfer trials, although increasingly attentive to possible therapeutic misconceptions, are inappropriately optimistic about direct benefits of trial participation. Such optimism is expressed more emphatically in trials involving highly active gene transfer researchers as principal investigators.
Effect of Pb and Cd on Cu adsorption by sand–bentonite liners
Authors: Kaoser Saleh , Barrington Suzelle , Elektorowicz Maria , Wang Li
Published: March 2005

The mobility of Cu alone and in the presence of Cd (compatible) and Pb (incompatible) was studied using laboratory columns packed with a 95 wt.% sand and 5 wt.% bentonite mixture. The liner material was subjected to one of four heavy metal solutions using a pressure head of 7 kPa: 2.0 cmol(+) Cu/L solution; 1.0 cmol(+) Cu and 1.0 cmol(+) Cd/L solution for a total of 2.0 cmol(+)/L solution; and 1.0 cmol(+) Cu and 1.0 cmol(+) Pb/L solution for a total of 2.0 cmol(+)/L solution. The effluents and the liner samples were analyzed for Cu, Pb, and Cd. The breakthrough curves indicated that Cd was the most mobile of the metal cations, whereas Pb was the least. Total metal adsorption was greatest for Cu with Pb, followed by that of Cu with Cd, and then that of Cu alone, showing that Cu is compatible with Cd but not Pb. The selective sequential extraction analysis indicated that most of the Cu was precipitated by the carbonate and hydroxide fractions.Key words: Cd, Pb, Cu, sand–bentonite liners, adsorption, leaching.
Developing sustainability criteria for urban infrastructure systems
Authors: Sahely Halla R , Kennedy Christopher A , Adams Barry J
Published: March 2005

Research in the area of sustainable urban infrastructure reflects the need to design and manage engineering systems in light of both environmental and socioeconomic considerations. A principal challenge for the engineer is the development of practical tools for measuring and enhancing the sustainability of urban infrastructure over its life cycle. The present study develops such a framework for the sustainability assessment of urban infrastructure systems. The framework focuses on key interactions and feedback mechanisms between infrastructure and surrounding environmental, economic, and social systems. One way of understanding and quantifying these interacting effects is through the use of sustainability criteria and indicators. A generic set of sustainability criteria and subcriteria and system-specific indicators is put forward. Selected indicators are quantified in a case study of the urban water system of the City of Toronto, Ontario, Canada.Key words: sustainable infrastructure, sustainability criteria and indicators, energy use, urban water systems.
Ductility and linear analysis with moment redistribution in reinforced high-strength concrete beams
Authors: do Carmo Ricardo N.F , Lopes Sérgio M.R
Published: March 2005

The evaluation of the ductility of reinforced concrete beams is very important, since it is essential to avoid a fragile collapse of the structure by ensuring adequate deformation at the ultimate limit state. One of the procedures used to quantify ductility is based on deformations, namely, the plastic rotation capacity. Knowledge of the plastic rotation capacity of certain regions of the structure is important for a plastic analysis or a linear analysis with moment redistribution. An experimental program is described in this article. It is composed of 10 tests designed to study the moment redistribution and ductility of continuous high-strength concrete beams. Particular care was given to analysing how the tensile reinforcement ratio and the transverse reinforcement ratio influence the plastic rotation capacity of the beams. A comparative study was carried out on several codes related to the moment redistribution permitted and the experimental findings. It was found that some of the recommendations are unsafe. It was also found that high-strength concrete beams, when properly designed, have enough deformation capacity to be used in plastic analysis.Key words: structural concrete, plastic rotation, moment redistribution, high-strength concrete.
Continuous primary dynamic pavement response system using piezoelectric axle sensors
Authors: Huff Rebecca , Berthelot Curtis , Daku Brian
Published: March 2005

Increasing commercial traffic over recent years is inflicting increased damage to roadways. As a result, road engineers are adopting more mechanistic performance-based road-modeling techniques to assist in the design, construction, and preservation of road assets. One such common mechanistic analysis technique is dynamic deflection pavement response induced under typical commercial truck loading. This paper presents an investigation of piezoelectric axle sensors as a possible tool for obtaining dynamic pavement deflection data under commercial truck loadings. One of the primary benefits to using piezoelectric axle sensors is that there are thousands of piezoelectric sensors already installed in roads world wide currently measuring the dynamic weights of commercial vehicles. Specifically, this research investigated the potential to use several different types and orientations of commercially available piezoelectric axle sensors to measure pavement deflection response under heavy truck loading. This research found that data from certain piezoelectric sensors and configurations could potentially predict deflection characteristics of a typical flexible pavement system. Based on these findings, there is the potential to use piezoelectric axle sensors for primary response modeling of road structures.Key words: piezoelectric sensors, deflection bowl, weigh-in-motion, mechanistic road modeling.
Traffic load modelling and factors influencing the accuracy of predicted extremes
Authors: O'Connor Alan , O'Brien Eugene J
Published: March 2005

Design and assessment of highway bridges requires accurate prediction of the extreme load effects expected during the proposed or remaining life of the structure. Traditionally these effects are calculated using conservative codified deterministic loading models. While this conservatism is relatively insignificant in design, it may be critical in assessment. Advances in weigh-in-motion (WIM) technology, i.e., the process of weighing trucks travelling at full highway speeds, have increased the availability of accurate and unbiased site-specific traffic records. Assessments performed using WIM data are generally accepted as less conservative than those performed using generalized codified loading models. This paper briefly describes traffic simulation using WIM statistics. The implications of the accuracy of the recorded data and the duration of recording and of the sensitivity of the extreme to the method of prediction are investigated. Traffic evolution with time is also explored. The conclusions are of interest to engineers performing assessment of existing bridges.Key words: bridge, load effects, characteristic values, simulation, traffic flow, Monte Carlo, weigh-in-motion.
Indicators and framework for assessing sustainable infrastructure
Authors: Dasgupta Shovini , Tam Edwin K.L
Published: March 2005

Much of the focus on sustainable infrastructure has concentrated on buildings and construction processes. To advance this thinking for other civil infrastructure systems (CIS), this paper outlines a framework that uses a set of proposed indicators to measure the sustainability of chosen infrastructure options and help select the preferred alternative in a multiobjective decision approach. Physically implementing "sustainable infrastructure" involves three life stages for any project: preproject planning, project implementation, and ongoing operations. It is critical to evaluate the sustainability of chosen options in each of these life stages. This research develops two categories of indicators, mandatory screening indicators (MSI) and judgment indicators (JI), and a multilayer approach for incorporating these indicators. A normalization procedure has been adapted to work within the framework to help compare alternatives across a range of indicators and different orders of data magnitude. A hypothetical example using a transmission line corridor is presented to illustrate how the framework can be applied.Key words: indicators, infrastructure, sustainable, environment, decision making, alternatives.
Assessing the performance of sustainable technologies for building projects
Authors: Nelms Cheryl , Russell Alan D , Lence Barbara J
Published: March 2005

At present, the performance of sustainable technologies in buildings is generally not assessed holistically, but rather from a primarily single issue perspective, e.g., only financially or environmentally. Such an approach is limited in that it ignores the interaction of the technologies within the physical facility itself as expressed through life cycle costs, the impact on the surrounding environment, design objectives of the project and its stakeholders whose value systems may conflict. This work identifies the primary cause-and-effect relationships of selected sustainable building technologies and illustrates elements of a framework for the systematic assessment of their performance from an environmental, social, economic, and technical perspective. Rooftop garden technology is used to demonstrate application of the framework. The primary goal of this work is to improve the understanding and decision-making capabilities of the building industry and government when faced with decisions regarding investment and policy regarding sustainable building technologies. A secondary goal is to identify knowledge gaps in our understanding of sustainable technologies.Key words: risk identification, sustainable technology, knowledge management, infrastructure projects, sustainable buildings.
Current situation with the production and use of supplementary cementitious materials (SCMs) in concrete construction in Canada
Authors: Bouzoubaâ Nabil , Fournier Benoît
Published: March 2005

The data gathered on the current situation of supplementary cementing materials (SCMs) in Canada have shown that around 524 000, 347 000, and 37 000 t of fly ash, ground granulated blast furnace slag (GGBFS), and silica fume were used in cement and concrete applications in 2001, respectively, which represents 11%, 90%, and 185% of the quantity produced. The remaining 10% of GGBFS produced was used in the US, and 17 000 t of silica fume were imported from the US and Norway to meet market demand. Fly ash appears to be the only material that is underused and that represents a potential for increased use of SCMs in Canada. For the GGBFS, the quantity produced can be increased if the demand increases. This investigation has shown, however, that there are policy, technical, and economic barriers to the increased use of SCMs in Canada. Some solutions were proposed to overcome these barriers and are summarized in the conclusions of the paper.Key words: fly ash, slag, silica fume, concrete, blended cement.
Apport de la technique du krigeage avec dérive externe pour une cartographie raisonnée de l'équivalent en eau de la neige : Application aux bassins de la rivière Gatineau
Authors: Tapsoba Dominique , Fortin Vincent , Anctil François , Haché Mario
Published: March 2005

The geostatistical algorithm of kriging with external drift (KED) is applied to the spatial estimation of snow water equivalent measured at single points. A digital elevation model with a 10-km resolution is used as external drift. Over the dense network of the period of interest (mid-March 1982), which corresponds to the maximum snow accumulation and the beginning of the snow melt in the Gatineau River basin, the KED technique is compared to the univariate ordinary kriging (OK). The results indicate a significant estimation precision improvement when the KED technique is used, notably in the under-sampled and extrapolated zones. A quantitative performance barometer — the root-mean-square (RMS) error — of this method with regards to the various degradation levels of the snow depth measurement network is proposed.Key words: snow water equivalent, kriging with external drift, root-mean-square errors, digital elevation model.[Journal translation]
Toward sustainable neighbourhoods: the need to consider infrastructure interactions
Authors: Engel-Yan Joshua , Kennedy Chris , Saiz Susana , Pressnail Kim
Published: March 2005

This paper details the role of infrastructure in promoting sustainability at the neighbourhood scale. A sustainable neighbourhood design process is outlined and the importance of adopting a systems perspective and considering infrastructure interconnections is emphasized. The performance of local infrastructure systems (e.g., buildings and local transportation network) is influenced by interactions with the greater urban region and with other local infrastructure. Through a broad review of the literature on transportation, water, building, and urban forestry systems, this paper identifies many of these extra- and inter-neighbourhood interactions. The paper concludes that it is difficult to achieve neighbourhood sustainability objectives without infrastructure systems at the urban scale that support these micro-scale goals. Furthermore, interactions between local infrastructure systems can have a positive or negative impact on infrastructure performance and environmental impacts. Careful consideration of these relationships during neighbourhood design could yield significant improvements in infrastructure resource efficiency as well as reductions in pollutant emissions and overall costs.Key words: sustainable neighbourhood design, infrastructure systems, transportation, water, buildings, urban forestry.
Creative destruction: building toward sustainability
Authors: Hartshorn James , Maher Michael , Crooks Jack , Stahl Richard , Bond Zoë
Published: March 2005

The engineering community at large, and the civil engineering community in particular, has the opportunity and arguably the obligation to promote a development agenda that considers not only the economics of development, but also the health of the environment and society at large. In this paper, we contemplate the challenge of sustainable development and its effect on project scale and scope. We discuss the inherent opportunity to drive the "creative destruction" of the development industry, using innovation to exploit inefficiencies in the planning and management of engineering systems to create a range of "future" products and services that challenge existing practice. We review the impact of procurement policy, contract pricing, prescriptive codes, and public policy on innovation. Several examples of innovative design and sustainable development introduced into the planning and management of Canadian civil engineering projects are provided. We assert that the most effective means of promoting the sustainability of built environment and civil infrastructure systems will be through inter- and intra-industry collaboration with the support of public policy-makers.Key words: sustainable development, civil, engineering, infrastructure, innovation, creative destruction, environment, collaboration.
SOLUTIONS OF DEFORMED THREE-DIMENSIONAL GRAVITY
Authors: MIGNEMI S.
Published: March 2005

We investigate the gauging of a three-dimensional deformation of the anti-de Sitter algebra, which accounts for the existence of an invariant energy scale. By means of the Poisson sigma model formalism, we obtain explicit solutions of the field equations, which reduce to the BTZ black hole in the undeformed limit.
SO(10)À LA PATI–SALAM
Authors: AULAKH CHARANJIT S. , GIRDHAR AARTI
Published: March 2005

To facilitate explicit analysis of SO (10) GUT's we present rules for rewriting SO (10) tensor and spinor invariants in terms of invariants of its "Pati–Salam" maximal subgroup ( SU (4)× SU (2) L × SU (2) R ) supplemented by the discrete symmetry called D parity. Explicit decompositions of quadratic and cubic invariants relevant to GUT model building are presented and the role of D parity in organizing the terms explained. Our rules provide a complete and explicit method for obtaining the "Clebsch–Gordon" coefficients for SO (10)↔ SU (4)× SU (2) L × SU (2) R in a notation appropriate for field theory models. We illustrate the usefulness our methods by calculating previously unavailable mass matrices and couplings of the SU (2) L doublets and SU (3)c triplets in the minimal SUSY SO (10) GUT which are essential to specify the phenomenology of this model. We also present the bare effective potential for baryon number violation in this model and show that it receives novel contributions from exchange of triplet Higgsinos contained the in "neutrino mass" Higgs submultiplets [Formula: see text]. This further tightens the emerging connection between neutrino mass and proton decay.
OPTICAL BISTABILITY SWITCHING PROPERTY IN ONE-DIMENSIONAL NONLINEAR PHOTONIC CRYSTAL
Authors: CHEN MING , LI CHUNFEI , MA SHAOJIE , XU MAI , WANG WEIBIAO , XIA YUXUE
Published: March 2005

Optical bistability device based on nonlinear one-dimensional photonic crystals is designed and manufactured. The device has 20 periods and is made from ZnS and ZnSe layers alternately. When the incident power density reach threshold power density 1.0 × 105 W/cm2, the Ar ion laser, whose wavelength is 514.5 nm, is shifted out of the optical band gap of the one-dimensional nonlinear photonic crystals, so an optical switch is made. It also can be made into an optical bistability device. The threshold power density of the optical bistability is 1.38 × 105 W/cm2 and its switching time is about 100 ps in experiment. The experimental results are in good accordance with the theoretical ones.
HIGHER ORDER COEFFICIENT MEASUREMENTS IN NONLINEAR ABSORPTION PROCESS
Authors: CHERUKULAPPURATH S. , GODET J. L. , BOUDEBS G.
Published: March 2005

Intensity-dependent two-photon absorption in chalcogenide glasses has been experimentally observed. Analytical solution of the basic differential equation giving the intensity at the output of the sample is difficult to obtain in this case. A quasi-analytical solution is provided. Second and third-order nonlinear coefficients are deduced from experimental data using Runge–Kutta numerical integration on data obtained via Z-scan technique. Results of the measured higher-order nonlinear coefficients are given. Comparison of these results with those obtained by various approximate analytical solutions of the differential equation is made.
NOISE AND TRANSPORT IN MESOSCOPICS: PHYSICS BEYOND THE LANDAUER–BÜTTIKER FORMALISM
Authors: GREEN FREDERICK , DAS MUKUNDA P.
Published: March 2005

The standard physical model of contemporary mesoscopic noise and transport consists in a phenomenologically based approach, proposed originally by Landauer and since continued and amplified by Büttiker, Imry and others. Throughout all the years of its gestation and growth, it is surprising that the Landauer–Büttiker approach to mesoscopics has matured with scant attention to the conserving properties lying at its roots: that is, at the level of actual microscopic principles. We systematically apply the sum rules for the electron gas to clarify the issue of conservation within the standard model of mesoscopic conduction. Noise, as observed in quantum point contacts, provides the vital clue.
ON THE STABILITY OF NONLINEAR CONSERVATION LAWS IN THE HAUSDORFF METRIC
Authors: PINTO MARTIN CAMPOS , COHEN ALBERT , DAHMEN WOLFGANG , DEVORE RONALD
Published: March 2005

The mapping properties of the time evolution operator E(t) of nonlinear hyperbolic scalar conservation laws is investigated. It is shown that this operator is Lipschitz in the Hausdorff metric in one space dimension whenever the flux is convex and one of the initial conditions satisfies a one-sided Lipschitz condition. The Hausdorff distance between the graphs of the solutions measures the closeness in L∞ in the regions where the solutions are smooth, as well as the closeness between the locations of shocks. A similar result on Hausdorff stability is proved with respect to a perturbation of the flux function. These results complement the well known L1 contractivity of the solution operator. They are used in a subsequent paper to prove new smoothness results for solutions to such conservation laws. Negative results are proved in the case of non-convex and genuinely multidimensional fluxes.
A REMARK ON LONG RANGE SCATTERING FOR THE NONLINEAR KLEIN–GORDON EQUATION
Authors: LINDBLAD HANS , SOFFER AVY
Published: March 2005

We consider the scattering problem for the nonlinear Klein–Gordon Equation with long range nonlinearity in one dimension. We prove that for all prescribed asymptotic solutions there is a solution of the equation with such behavior, for some choice of initial data. In the case the nonlinearity has the good sign (repulsive) the result hold for arbitrary size asymptotic data. The method of proof is based on reducing the long range phase effects to an ODE; this is done via an appropriate ansatz. We also find the complete asymptotic expansion of the solutions.
AB INITIO QUANTUM CHEMICAL AND MIXED QUANTUM MECHANICS/MOLECULAR MECHANICS (QM/MM) METHODS FOR STUDYING ENZYMATIC CATALYSIS
Authors: Friesner Richard A. , Guallar Victor
Published: March 2005

▪ Abstract  We describe large scale ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic reactions. First, technical aspects of the methodology are reviewed, including the hybrid density functional theory (DFT) methods that are typically employed for the QM aspect of the calculations, and various approaches to defining the interface between the QM and MM regions in QM/MM approaches. The modeling of the enzymatic catalytic cycle for three examples—methane monooxygenase, cytochrome P450, and triose phosphate isomerase—are discussed in some depth, followed by a brief summary of other systems that have been investigated by ab initio methods over the past several years. Finally, a discussion of the qualitative and quantitative conclusions concerning enzymatic catalysis that are available from modern ab initio approaches is presented, followed by a conclusion briefly summarizing future prospects.
TIME-RESOLVED SPECTROSCOPY OF ORGANIC DENDRIMERS AND BRANCHED CHROMOPHORES
Authors: Goodson T.
Published: March 2005

▪ Abstract  Organic dendrimers have been considered for a number of optical applications and are now of great interest for the purpose of enhanced nonlinear optical effects. In order to understand the mechanism of the enhanced effects in branched structures it is important to probe the fundamental excitations and the degree of intramolecular interactions utilizing various spectroscopic techniques. In this review, the nonlinear optical and excited state dynamics of different dendritic and other branching chromophore structures are discussed. The methods of two-photon absorption, time-resolved fluorescence, transient absorption, and three-pulse photon echo peak shift are discussed in regards to the degree of intramolecular coupling in the macromolecular systems. These techniques are also used for a comparison of the dynamics in the linear molecular analog systems as well. Thus, this review focuses on the aspect of intramolecular interactions in a branched system and its importance to enhanced nonlinear optical effects useful for modern optical devices.
HEAT CAPACITY IN PROTEINS
Authors: Prabhu Ninad V. , Sharp Kim A.
Published: March 2005

▪ Abstract   Heat capacity (Cp) is one of several major thermodynamic quantities commonly measured in proteins. With more than half a dozen definitions, it is the hardest of these quantities to understand in physical terms, but the richest in insight. There are many ramifications of observed Cp changes: The sign distinguishes apolar from polar solvation. It imparts a temperature (T) dependence to entropy and enthalpy that may change their signs and which of them dominate. Protein unfolding usually has a positive ΔCp, producing a maximum in stability and sometimes cold denaturation. There are two heat capacity contributions, from hydration and protein-protein interactions; which dominates in folding and binding is an open question. Theoretical work to date has dealt mostly with the hydration term and can account, at least semiquantitatively, for the major Cp-related features: the positive and negative Cp of hydration for apolar and polar groups, respectively; the convergence of apolar group hydration entropy at T ≈ 112°C; the decrease in apolar hydration Cp with increasing T; and the T-maximum in protein stability and cold denaturation.
VIBRATIONAL AUTOIONIZATION IN POLYATOMIC MOLECULES
Authors: Pratt S.T.
Published: March 2005

▪ Abstract  The vibrationally autoionizing Rydberg states of small polyatomic molecules provide a fascinating laboratory in which to study fundamental nonadiabatic processes. In this review, recent results on the vibrational mode dependence of vibrational autoionization are discussed. In general, autoionization rates depend strongly on the character of the normal mode driving the process and on the electronic character of the Rydberg electron. Although quantitative calculations based on multichannel quantum defect theory are available for some polyatomic molecules, including H3, only qualitative information exists for most molecules. This review shows how qualitative information, such as Walsh diagrams along different normal coordinates of the molecule, can provide insight into the vibrational autoionization rates.
MICROFLUIDIC TOOLS FOR STUDYING THE SPECIFIC BINDING, ADSORPTION, AND DISPLACEMENT OF PROTEINS AT INTERFACES
Authors: Holden Matthew A. , Cremer Paul S.
Published: March 2005

▪ Abstract  A combination of temperature and concentration gradient microfluidic devices were employed to study the mechanistic details of biomacromolecule interactions at oxide interfaces. These lab-on-a-chip techniques allowed high-throughput, multiplexed data collection using only nanoliters of analyte. The three examples presented demonstrate rapid data acquisition relative to standard methods. First, we show ligand-receptor binding data for multivalent binding between membrane-bound ligands and incoming aqueous proteins with several binding pockets. A model is described for obtaining both the first and second dissociation constant for the reaction. The second example employs temperature gradient microfluidics to study the thermoresponsive properties of polymers and proteins. Both the folding mechanism and subsequent formation of an aqueous two-phase system were followed. Finally, these microfluidic techniques were combined with fluorescence microscopy and nonlinear optical spectroscopy to elucidate the mechanism of fibrinogen displacement from silica surfaces. This combination of methods enabled both direct and indirect observation of protein conformational changes.
PROBING TRANSIENT MOLECULAR STRUCTURES IN PHOTOCHEMICAL PROCESSES USING LASER-INITIATED TIME-RESOLVED X-RAY ABSORPTION SPECTROSCOPY
Authors: Chen Lin X.
Published: March 2005

▪ Abstract  Molecular structures during chemical processes are crucial for predicting molecular reactivity and reaction mechanisms. Using a laser pulse as an internal clock for starting fundamental chemical processes, molecular structural dynamics can be characterized by coherent vibrational motions and by incoherent transitions between different intermediate states. Recent developments in pulsed X-ray facilities allow structural determination of discrete excited states and reaction intermediates using laser-initiated time-resolved X-ray absorption spectroscopy (LITR-XAS). Moreover, femtosecond X-ray sources have begun making significant contributions in monitoring coherent molecular motions. This review summarizes recent developments in the field, including technical and scientific challenges as well as several examples involving excited state molecular structure and electronic configuration determinations. Future applications of this technique with high time resolution will enable visualization of fundamental chemical events in many systems and further our understanding in photochemistry.
Alterations in carbohydrate metabolism in response to short-term dietary carbohydrate restriction
Authors: Harber Matthew P. , Schenk Simon , Barkan Ariel L. , Horowitz Jeffrey F.
Published: March 2005

Dietary carbohydrate restriction (CR) presents a challenge to glucose homeostasis. Despite the popularity of CR diets, little is known regarding the metabolic effects of CR. The purpose of this study was to examine changes in whole body carbohydrate oxidation, glucose availability, endogenous glucose production, and peripheral glucose uptake after dietary CR, without the confounding influence of a negative energy balance. Postabsorptive rates of glucose appearance in plasma (Ra; i.e., endogenous glucose production) and disappearance from plasma (Rd; i.e., glucose uptake) were measured using isotope dilution methods after a conventional diet [60% carbohydrate (CHO), 30% fat, and 10% protein; kcals = 1.3 × resting energy expenditure (REE)] and after 2 days and 7 days of CR (5% CHO, 60% fat, and 35% protein; kcals = 1.3 × REE) in eight subjects (means ± SE; 29 ± 4 yr; BMI 24 ± 1 kg/m2) during a 9-day hospital visit. Postabsorptive plasma glucose concentration was reduced ( P = 0.01) after 2 days but returned to prediet levels the next day and remained at euglycemic levels throughout the diet (5.1 ± 0.2, 4.3 ± 0.3, and 4.8 ± 0.4 mmol/l for prediet, 2 days and 7 days, respectively). Glucose Ra and glucose Rd were reduced to below prediet levels (9.8 ± 0.6 μmol·kg−1·min−1) after 2 days of CR (7.9 ± 0.3 μmol·kg−1·min−1) and remained suppressed after 7 days (8.3 ± 0.4 μmol·kg−1·min−1; both P < 0.001). A greater suppression in carbohydrate oxidation, compared with the reduction in glucose Rd, led to an increased (all P ≤ 0.05) rate of nonoxidative glucose disposal at 7 days (5.2 ± 0.5 μmol·kg−1·min−1), compared with 2 days (2.7 ± 0.5 μmol·kg−1·min−1) and prediet (1.6 ± 0.8 μmol·kg−1·min−1). In response to eucaloric CR, a marked increase in nonoxidative glucose disposal may help maintain systemic glucose availability.
Regulated expression of renal and intestinal UT-B urea transporter in response to varying urea load
Authors: Inoue Hideki , Kozlowski Shelley D. , Klein Janet D. , Bailey James L. , Sands Jeff M. , Bagnasco Serena M.
Published: March 2005

Production, recycling, and elimination of urea are important to maintain nitrogen balance. Adaptation to varying loads of urea due to different protein intake or in renal failure may involve changes in urea transport and may possibly affect urea transporters. In this study, we examined the expression of the UT-B urea transporter in rats fed a low-protein diet (LPD), a high-protein diet (HPD), and a 20% urea-supplemented diet. In the kidney, UT-B protein abundance increased in the outer medulla of both LPD-fed rats and 20% urea-fed rats, without changes in the inner medulla of either group compared with controls. In HPD-fed rats, UT-B protein decreased significantly in both the outer and inner medulla. We identified expression of UT-B in the rat colon, as a 2-kb mRNA transcript and as an ∼45-kDa protein, with apical localization in superficial colon epithelial cells. UT-B also is expressed in rat small intestine. In rat colon, UT-B protein abundance was mildly, but significantly, decreased in LPD-fed and 20% urea-fed rats. UT-B abundance also was examined in the colon of 7/8 nephrectomized, uremic rats and in HPD-fed rats and was not significantly different from that in control rats. These findings indicate that UT-B expression is regulated in response to different loads of urea, with a pattern that suggests involvement of tissue-specific regulatory mechanism in kidney and colon.
WT1-interacting protein and ZO-1 translocate into podocyte nuclei after puromycin aminonucleoside treatment
Authors: Rico Maribel , Mukherjee Amitava , Konieczkowski Martha , Bruggeman Leslie A. , Miller R. Tyler , Khan Shenaz , Schelling Jeffrey R. , Sedor John R.
Published: March 2005

Podocyte differentiation is required for normal glomerular filtration barrier function and is regulated by the transcription factor WT1. We identified WT1-interacting protein (WTIP) and hypothesized that it functions as both a scaffold for slit diaphragm proteins and a corepressor of WT1 transcriptional activity by shuttling from cell-cell junctions to the nucleus after injury. Endogenous WTIP colocalizes with zonula occludens-1 (ZO-1) in cultured mouse podocyte adherens junctions. To model podocyte injury in vitro, we incubated differentiated podocytes with puromycin aminonucleoside (PAN; 100 μg/ml) for 24 h, which disassembled cell-cell contacts, rearranged actin cytoskeleton, and caused process retraction. Podocyte synaptopodin expression diminished after PAN treatment, consistent with podocyte dedifferentiation in some human glomerular diseases. To assess podocyte function, we measured albumin flux across differentiated podocytes cultured on collagen-coated Transwell filters. Albumin transit across PAN-treated cells increased to levels observed with undifferentiated podocytes. Consistent with our hypothesis, WTIP, as well as ZO-1, translocated from podocyte adherens junctions to nuclei in PAN-treated cells. Because WTIP is a transcriptional corepressor for WT1, we examined the effect of PAN on expression of retinoblastoma binding protein Rbbp7 (also known as RbAp46), a WT1 target gene expressed in S-shaped bodies during nephrogenesis. Rbbp7 expression in PAN-treated podocytes was reduced compared with untreated cells. In conclusion, WTIP translocates from cell-cell junctions to the nucleus in PAN-treated podocytes. We suggest that WTIP monitors slit diaphragm protein assembly and shuttles into the nucleus after podocyte injury, translating changes in slit diaphragm structure into altered gene expression and a less differentiated phenotype.
Periodicity in a ratio‐dependent predator‐prey system with stage structure for predator
Authors: Chen Fengde
Published: March 2005

With the help of a continuation theorem based on Gaines and Mawhin′s coincidence degree, easily verifiable criteria are established for the global existence of positive periodic solutions of a delayed ratio‐dependent predator‐prey system with stage structure for predator. The approach involves some new technique of priori estimate. For the system without delay, by constructing a suitable Lyapunov function, some sufficient conditions which guarantee the existence of a unique global attractive positive periodic solution are obtained. Those results have further applications in population dynamics.