bluuebunny/crossref_metadata_2025 huggingface dataset:
Prediction of folding transition‐state position (βT) of small, two‐state proteins from local secondary structure content
Authors: Huang Ji‐Tao , Cheng Jin‐Pei
Published: April 2007

Folding kinetics of proteins is governed by the free energy and position of transition states. But attempts to predict the position of folding transition state on reaction pathway from protein structure have been met with only limited success, unlike the folding‐rate prediction. Here, we find that the folding transition‐state position is related to the secondary structure content of native two‐state proteins. We present a simple method for predicting the transition‐state position from their α‐helix, turn and polyproline secondary structures. The method achieves 81% correlation with experiment over 24 small, two‐state proteins, suggesting that the local secondary structure content, especially for content of α‐helix, is a determinant of the solvent accessibility of the transition state ensemble and size of folding nucleus. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Compounds from Ageratum conyzoides: isolation, structural elucidation and insecticidal activity
Authors: Moreira Márcio D , Picanço Marcelo C , Barbosa Luiz Cláudio A , Guedes Raul Narciso C , Barros Emerson C , Campos Mateus R
Published: April 2007

This work aimed at identifying plant compounds with insecticidal activity against Diaphania hyalinata (L.) (Lepidoptera: Pyralidae), Musca domestica (L.) (Diptera: Muscidae), Periplaneta americana (L.) (Blattodea: Blattidae) and Rhyzopertha dominica (F.) (Coleoptera: Bostrichidae). The plant species used were: basil (Ocimum selloi Benth.), rue (Ruta graveolens L.), lion's ear (Leonotis nepetaefolia L.), Jimson weed (Datura stramonium L.), ‘baleeira’ herb (Cordia verbenaceae L.), mint (Mentha piperita L.), wild balsam apple (Mormodica charantia L.) and billy goat weed (Ageratum conyzoides L.). Firstly, the insecticidal activities of hexane and ethanol plant extracts were evaluated against adults of R. dominica. Among them, only the hexane extract of A. conyzoides showed insecticidal activity. The hexane extract of this plant species was therefore fractionated by silica gel column chromatography to isolate and purify its bioactive chemical constituents. Three compounds were identified using IR spectra, 1H NMR, 13C NMR, HMBC and NOE after gel chromatography: 5,6,7,8,3′, 4′, 5′‐heptamethoxyflavone, 5,6,7,8,3′‐pentamethoxy‐4′, 5′‐methylenedioxyflavone and coumarin. The complete assignment of 13C NMR to 5,6,7,8,3′‐pentamethoxy‐4′, 5′‐methylenedioxyflavone was successfully made for the first time. 5,6,7,8,3′‐Pentamethoxy‐4′, 5′‐methylenedioxyflavone did not show any insecticidal activity against the four insect species tested. 5,6,7,8,3′, 4′, 5′‐Heptamethoxyflavone showed low activity against D. hyalinata and R. dominica and was not toxic to M. domestica or P. americana. In contrast, coumarin showed insecticidal activity against all four insect pest species tested, with the following order of susceptibility: R. dominica < P. americana < D. hyalinata < M. domestica after 24 h exposure. Copyright © 2007 Society of Chemical Industry
Use of pyrethroid analogues to identify key structural features for enhanced esterase resistance in Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae)
Authors: Gunning Robin V , Moores Graham D , Jewess Philip , Boyes Alastair L , Devonshire Alan L , Khambay Bhupinder PS
Published: April 2007

It has been reported previously that the major resistance mechanism to pyrethroid insecticides by the cotton bollworm Helicoverpa armigera (Hübner) in Australia is a consequence of overproduction of esterase isoenzymes. This paper reports structure–activity relationships that support such a view, based on in vivo bioassays conducted with a range of pyrethroid structures containing a variety of acid and alcohol moieties and the correlation with in vitro esterase inhibition assays against the same structures, and identifies the critical regions of the molecule with regard to esterase inhibition, and hence resistance. The implications of this work in terms of possible resistance management are evaluated and discussed. Copyright © 2007 Society of Chemical Industry
Photochemical etching of silicon by two photon absorption
Authors: Ouyang H. , Deng Y. , Knox W. H. , Fauchet P. M.
Published: April 2007

Photochemical etching of silicon assisted by two‐photon absorption (TPA) in the presence of hydrofluoric acid (HF) is demonstrated using a below‐bandgap femtosecond laser source. We investigate the morphology of the etched silicon as a function of the laser power, exposure time, as well as the substrate doping level. Self‐organized periodic silicon trenches with ∼150 nm spacing were observed at the etch front as the initial stage of the TPA photochemical etching process. Since the etching front can be precisely controlled by the focal point, this technique can be used for writing silicon microfluidic systems and for 3D micromachining. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Dependence of the singlet oxygen photosensitization efficiency on morphology of porous silicon
Authors: Ryabchikov Yu. V. , Belogorokhov I. A. , Vorontsov A. S. , Osminkina L. A. , Timoshenko V. Yu. , Kashkarov P. K.
Published: April 2007

We investigate the effect of oxygen molecule adsorption on the photoluminescence of porous silicon films of different porosity. The experimental results are explained by the photosensitization of singlet oxygen generation due to the energy transfer from excitons confined in Si nanocrystals to O2 molecules adsorbed on the Si nanocrystal surface. The energy transfer time and photosensitization efficiency are found to depend on porosity of the samples. The singlet oxygen generation efficiency increases strongly for porous silicon with high (>80%) porosity. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electrochemical pore etching in Ge – An overview
Authors: Fang C. , Föll H. , Carstensen J. , Langa S.
Published: April 2007

While electrochemical pore etching in semiconductors has become a thriving field for research (and applications) in the past 15 years or so, little work has been done in Ge. Besides Si, Ge is the only semiconductor with a diffusion length large enough to enable the use of backside illumination, which has proved to be the decisive “trick” for the formation of excellent macropores in Si, and experiments in this vein have been conducted. However, Ge proved to behave in rather unexpected ways – the large body of pore etching knowledge obtained with Si and the III–V's was not directly applicable to Ge. While no good pores could be produced in most previous endeavours including our own, we finally succeeded in producing deep pores in n‐type but also in p‐type Ge of various doping levels and crystal orientations. A host of new and not yet totally understood phenomena was discovered. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Carbon nanofibers encapsulated in macropores in silicon
Authors: Starkov V. , Red'kin A.
Published: April 2007

This work reports on the development of fuel cells electrodes with a porous silicon structure and carbon nanofibers encapsulated in macropores in silicon. It is demonstrated that decomposition of carbon on a Ni catalyst deposited on the pore walls can be used to create a homogeneous carbon nanotube layer that dramatically increases the specific surface area while simultaneously reducing the resistivity of the macroporous silicon layer. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Porous silicon as an internal reflector in thin epitaxial solar cells
Authors: Kuzma‐Filipek I. , Duerinckx F. , Van Nieuwenhuysen K. , Beaucarne G. , Poortmans J. , Mertens R.
Published: April 2007

Thin film epitaxial silicon solar cells are considered a near future alternative to bulk silicon solar cells. However due to the limited thickness of the active layer they require efficient light trapping. Therefore we propose the development and implementation of such light confinement by means of a porous silicon (PS) intermediate reflector at the epi/substrate interface. The formation of the reflector is done by electrochemical etching of a highly doped Si substrate into a multilayer stack (Bragg‐optical reflector), and is followed by epitaxial deposition of the active layer. The implementation of the PS reflector however requires detailed analysis of many problematic issues, foremost the optical optimisation of the stack for internal reflection at the Si/PS/Si interface. Other topics include the pore rearrangement during high‐temperature CVD as well as the quality of the epitaxial layer grown on porous silicon. Another challenge is the resistance within the PS layers. For that purpose, SRP (Spreading Resistance Probe) and resistance measurements were performed to determine the conductive properties of rearranged PS. First cells with a 9‐layer porous silicon reflector gave a very promising efficiency of 13.5% which is 1.5% higher compared to cells without internal reflector. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Vapor control of resonant Zener tunneling of light in a photonic crystal
Authors: Ghulinyan M. , Gaburro Z. , Wiersma D. S. , Pavesi L.
Published: April 2007

We show a vapor controlled one‐dimensional photonic crystal built with a silicon‐based dielectric mesoporous material, in which the refractive index can be continuously tuned by flowing organic vapors through the pores. Exposure of the crystal to vapors induces an inhomogeneous change in the refractive index through the depth and results in a tilted photonic band structure. We drive the photonic crystal to the optical Zener breakdown condition, introducing an enhanced transmission channel through the crystal. This phenomenon closely resembles the electronic Zener breakdown in a reverse‐biased p–n junction. The effect is reversible and opens new perspectives for physics in photonic crystals and novel device concepts based on sensing, switching and processing of light. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Dynamics of photogenerated carriers in porous silicon probed by microwave absorption
Authors: Porteanu H. E.
Published: April 2007

We report on dynamics of photogenerated carriers in porous silicon using contactless investigation tools. A comparison of two theoretical models: the simple point charge description versus degenerate gas model is presented. The temperature dependence reveals the dominant role of surface states below 70 K. Light intensity dependences evidence Auger processes. The optical and chemical properties can be indirectly improved using the microwave conductivity by studying the surface states of porous materials. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
p+–n diodes with a lateral porous layer as gas sensors
Authors: Barillaro G. , Diligenti A. , Strambini L. M.
Published: April 2007

In this work an integrated p+–n diode, diffused on a crystalline substrate and provided with a thin adsorbing porous layer, is proposed as gas sensor. The sensor can be easily integrated by using an industrial CMOS process due to the fact that the porous film formation is the last process step. The sensitivity to isopropanol vapors has been investigated by measuring both the forward and reverse current of the diode as a function of the vapor concentration. The current variations, up to two orders of magnitude, could be explained by assuming that the adsorption of molecules in the porous layer and their interaction with localized states modify the band structure of the crystalline diode at the interface with the porous silicon, and in turn its current. Another sensor feature is that the value of the reverse current variation, induced by isopropanol vapors, depends on the voltage, so that the sensitivity can be settled by simply changing the reverse voltage itself. The fabrication process, the static and dynamic behavior of the sensor are presented and discussed. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Influence of Pd layer on the sensitivity of CHx/PS/Si as structure for H2 sensing
Authors: Gabouze N. , Cheraga H. , Belhousse S. , Ghellai N. , Zouadi N. , Ouadah Y. , Chabane‐Sari N.‐E.
Published: April 2007

In this work, a hydrogen sensor based on Palladium/hydrocarbons (CHx )/Porous silicon/Silicon structure has been studied in presence of hydrogen gas. Current–voltage characterizations show that the sensitivity of the sensor is improved by more than two orders of magnitude compared with the uncoated CHx /PS/Si device. In addition, a rapid response time of the sensor of about 10 s is measured. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
CMOS‐compatible fabrication of porous silicon gas sensors and their readout electronics on the same chip
Authors: Barillaro G. , Bruschi P. , Pieri F. , Strambini L. M.
Published: April 2007

In this work, integration on the same chip of porous silicon gas sensors along with their driving/readout electronic circuits by using an industrial microelectronic process is demonstrated. To ensure maximum compatibility, the porous silicon formation is performed after the integrated circuit fabrication flow is completed. The chip contains three CMOS operational amplifiers, a band‐gap voltage reference, an integrated temperature sensor and several porous silicon‐based NO2 sensors. The simultaneous functionality of the electronics and the sensor is demonstrated by using various circuit blocks to implement a simple driving/readout electronic interface for the sensor. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electrochemical fabrication of buried folded microchannels into silicon substrates
Authors: Barillaro G. , Nannini A. , Piotto M.
Published: April 2007

In this work an original process for buried folded silicon microchannel fabrication is reported. Electrochemical micromachining is exploited to etch high aspect ratio meander‐shaped trenches into a silicon substrate. Thermal oxidation is then employed to seal the top of etched trenches and obtain buried microchannels at the bottom. The process is straightforward and allows the integration of buried folded channels into silicon substrates with a high density. Experimental results are reported and advantages and drawbacks of the proposed process are discussed. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electrically enhanced erosion of porous Si material in electrolyte by pH modulation and its application in chronotherapy
Authors: Leong W. Y. , Loni A. , Canham L. T.
Published: April 2007

We have studied the enhanced erosion of porous Si material in the vicinity of a cathodic electrode during electrolysis of tap water and simulated gastric or intestinal fluids. This enhanced erosion is attributed to the pH increase (more alkaline) near the cathode due to a local depletion of the [H+] species during the electrolysis of water. The effect provides a means of electrically controlling drug release from the porous Si structures useful in chrono‐therapeutic applications. We have described the concept and prototype of a self‐contained electronic time‐controlled drug delivery capsule system suitable for oral administration or implantation into the body. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Waveguiding, absorption and emission properties of dye‐impregnated oxidized porous silicon
Authors: Navarro‐Urrios D. , Ghulinyan M. , Capuj N. E. , Oton C. J. , Riboli F. , Martín I. R. , Pavesi L.
Published: April 2007

The waveguiding, absorption and emission properties of oxidised porous silicon waveguides when impregnated with Nile Blue have been studied. We present m‐line measurements before and after the impregnation showing that the effective indices of the modes remain the same. When performing guided luminescence experiments, a structured emission band is measured. Using the refractive index profile extracted from m‐line measurements it has been possible to simulate the emission lineshape assuming the observation of an interference pattern formed across the waveguide. We demonstrate that these oscillations appear because in the first hundreds of nanometers the dye concentration is several orders of magnitude higher than in the rest of the sample. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Cathodoluminescence and photoluminescence of individual silicon nanowires
Authors: Dovrat M. , Arad N. , Zhang X. H. , Lee S. T. , Sa'ar A.
Published: April 2007

Photoluminescence (PL) spectroscopy and Cathodoluminescence (CL) spectroscopy and imaging have been utilized to resolve red and blue emission bands from silicon nanowires. We have found that the blue emission band comes from local defects in the silicon dioxide shell of the wires while the red band comes from interfaces between the silicon dioxide shell and the crystalline silicon core. Time‐resolved PL spectroscopy of hydrogen‐ and oxygen‐terminated silicon nanowires, indicates that surface chemistry plays an essential role in determining the luminescence properties of the nanowires. We suggest that the PL lifetime should be related to nonradiative relaxation processes that take place at the interface of the silicon core and the clad material of the nanowires. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Luminescence properties of the porphyrin/porous silicon composites
Authors: Chirvony V. S. , Bolotin V. L. , Ovejero J. , Matveeva E. S. , Dzhagarov B. M. , Albella J. , Parkhutik V. P.
Published: April 2007

A study of luminescence properties of water‐soluble and hydrophobic porphyrin and chlorin molecules immobilized in oxidized (i.e. non‐luminescent) and as‐prepared (i.e. luminescent) porous silicon (porSi) layers is carried out. It is found that the oxidized porSi matrix itself does not introduce any quenching effect on the porphyrin fluorescence, but the fluorescence is subjected to the concentration quenching. At maximum porphyrin/chlorin concentration used (ca. 10–3 M in impregnation solutions) the quenching is strong in case of hydrophobic porphyrins and sufficiently moderate for water‐soluble ones, especially for cationic porphyrin TMPyP4. A concentration of the latter in porSi layer is determined by direct measurements. Both hydrophobic and water‐soluble porphyrins immobilized on the surface of as‐prepared porSi are found to quench the luminescence of the latter. In case of hydrophobic porphyrins the quenched porSi luminescence is regained almost to the initial value on the time scale of tens of hours, whereas in case of water‐soluble porphyrins the fluorescence spectrum of the latter builds up in course of time. Possible mechanisms responsible for these effects are discussed. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Theoretical study of acoustic band‐gap structures made of porous silicon
Authors: Reinhardt A. , Snow P. A.
Published: April 2007

In this paper, we discuss the acoustic properties of porous silicon and outline the differences and similarities of the behaviour of elastic and light waves in mesoporous porous silicon etched in p+‐type silicon wafers. We then investigate the expected acoustic characteristics of distributed Bragg mirrors and rugate filters obtained by a modulation of porosity with depth. In particular, we emphasize some features these mirrors exhibit when compared to the optical equivalents in pSi. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Anisotropic and inhomogeneous Coulomb screening in the Thomas–Fermi approximation: Application to quantum dot–wetting layer system and Auger relaxation
Authors: Even J. , Cornet C. , Doré F.
Published: April 2007

A model for anisotropic and inhomogeneous Coulomb screening due to 2D and 3D carriers, is proposed in the Thomas–Fermi approximation. Analytical expressions for the screened interaction potentials and scattering matrix elements are obtained. This model is applied to the Auger relaxation of carriers in an InAs/InP quantum dot (QD) – wetting layer (WL) system. The influences of the QD morphology and carriers densities on screening and Auger effects are studied. 2D–2D scattering is found to be the most important process, depending especially on QD morphology. A smearing effect is associated to the wetting layer wavefunction extension along the growth axis. The screened potential is similar to a potential screened by 3D carriers. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Monte Carlo calculation of Ising model with single‐site anisotropy energy in ferromagnetic iron nitride system
Authors: Liu Junyou , Zhang Lanting , Shan Aidang
Published: April 2007

The magnetic behavior of a mixed Ising ferromagnetic system on Fe4N expended face‐center cubic lattice, with single‐site anisotropy, has been studied with Monte Carlo Simulation. The expended face‐center cubic lattice was divided into one simple cubic lattice composed of Fe(I) at the corner site and three inhomogeneous simple cubic lattices composed of Fe(II) at the face‐centered one. The two sublattices have spin‐3/2 and spin‐1, respectively. The model includes nearest interactions and single‐site anisotropy terms. By studying magnetization, internal energy, specific heat of this model at different temperatures, we found that the absolute zero value of magnetization is changed by existence of Fe(I)'s and Fe(II)'s crystal‐field interactions (D1,D2). The final value of internal energy is different for differentD1andD2. Curie temperature is increasing with the increase ofD1andD2. Especially, equal point of sublattice magnetization was recognized, whenD1was changed. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electron orderings in the (hard‐core) boson–fermion model
Authors: Sidowski M. , Robaszkiewicz S.
Published: April 2007

The system of coexisting local pairs and itinerant electrons described by the (hard‐core) boson–fermion model is analysed, taking into account both the intersubsystem charge exchange coupling I0 as well as the density–density interaction V0. In our preliminary report [Acta Phys. Pol. A 109, 647 (2006)] we have shown within an extended mean‐field approach that at T = 0 the model considered can exhibit not only the superconducting (SC) but also the charge density wave (CDW) phases as well as the so called charge Kondo state (CKS), which is characterised by a compensation of a local charge moment (isospin singlet). Here we shortly conclude those findings and present several new results concerning this subject. In particular the mutual stability of various phases, including the mixed ordered state (SC‐CKS) is analysed and the effects of the deviation from half‐filling on the properties of the system are discussed. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Structural transition control of laterally overgrown c‐GaN and h‐GaN on stripe‐patterned GaAs (001) substrates by MOVPE
Authors: Sanorpim S. , Takuma E. , Ichinose H. , Katayama R. , Onabe K.
Published: April 2007

Growth mechanisms and material quality of the laterally overgrown cubic‐phase gallium nitride (c‐GaN) and hexagonal‐phase gallium nitride (h‐GaN) on stripe‐patterned GaAs (001) substrates were investigated using transmission electron microscopy (TEM). Investigational results show that h‐GaN is only laterally overgrown along the (111)B facets of the c‐GaN stripes with the growth direction of (0001)h‐GaN//(111)B c‐GaN for all the mask stripe orientations. Dislocation density in the laterally overgrown h‐GaN regions for the [110]‐stripe pattern is reduced to be lower than 104 cm–2, which is six orders of magnitude smaller than that in the conventionally grown h‐GaN films. On the other hand, the laterally overgrown c‐GaN with lower planar defect (stacking faults and twins) density presents in the region just above the stripe windows for the [1$ \bar 1 $0]‐stripe pattern. In addition, a large reduction of planar defect density was found in the laterally overgrown c‐GaN regions for the [100] stripe direction. Also, a model is used to describe the cubic‐to‐hexagonal structural transition in lateral‐overgrown GaN on patterned GaAs (001) substrates for the purpose of lower dislocation and lower planar defect densities in the laterally overgrown h‐GaN and c‐GaN, respectively. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Temperature dependencies of high‐temperature reduction on conversion products and their isotopic signatures
Authors: Leuenberger Markus C. , Filot Marc S.
Published: April 2007

High‐temperature reduction (HTR) is widely used for oxygen and hydrogen isotope determination. Decomposition of cellulose, sucrose and polyethylene foil by HTR is quantitative for temperatures around 1450°C. For lower reaction temperature production of CO2, water and the deposition of carbon inside the reactor are significant and thus the element of interest for isotopic analysis is split into different pools, leading to isotope fractionation. After reduction of cellulose or sucrose at 1125°C less than 60% of the oxygen is found as CO, which is monitored with the isotope ratio mass spectrometer to determine the δ18O value. The remaining oxygen is unevenly distributed between CO2 and H2O, preferentially as CO2. Raising the reaction temperature to 1425°C yields almost quantitative conversion of oxygen into CO and results in a 3‰ more positive δ18O value. Similarly, only 40–50% of the carbon of cellulose and sucrose is transformed into CO in the HTR reactor at 1125°C. This is far from the stoichiometric expected value of 83% for quantitative carbon transfer for cellulose and 92% for sucrose. Of the carbon 40–50% is deposited in the reactor and the remainder can be found as CO2. Based on the comparison of carbon isotope results from HTR and those obtained from combustion, we hypothesize that CO produced during the HTR originates partly from sample carbon and glassy carbon. A combined combustion and HTR carbon isotope determination may provide an insight into the intramolecular carbon distribution of organic substances. These results suggest that HTR should be carried out at temperatures above 1450°C to make sure that fractionations associated with the reduction process are minimal. If this is not possible frequent calibration is required using reference materials of the same structure as the sample. Copyright © 2007 John Wiley & Sons, Ltd.
Understanding the building blocks of dynamic systems
Authors: Cronin Matthew A. , Gonzalez Cleotilde
Published: April 2007

We report three empirical studies intended to clarify why individuals misperceive the relationships between stocks and flows. We tested whether familiarity with the problem type, motivation to solve the problem, or the graphical presentation of the problem affected participants' understanding of stock and flow relationships. We conclude that the misperceptions of stocks and flows are a pervasive and important problem in human reasoning. Neither the domain familiarity nor increased motivation helped individuals improve their perception of stock and flow relationships; but it seems that the graphical representation directs attention to flows and not stocks, setting the stage for subsequent mistakes. Individuals attend to the most salient points of a graph rather than comprehending the overall accumulation over time. Future research needs to investigate several aspects of the problem representations, such as the use of physical or textual rather than graphical representations. Copyright © 2007 John Wiley & Sons, Ltd.
Dynamics of climate policy
Authors: Fiddaman Thomas
Published: April 2007

This article is based on the talk I delivered at the 2006 International System Dynamics Conference in Nijmegen, upon receiving the Jay W. Forrester Award for Exploring policy options with a behavioral climate–economy model (Fiddaman, 2002). Here I attempt to step back from modeling particulars, to talk about the global policy context of climate change. In particular, it appears to me that a great deal of effort is misdirected toward policies that are unlikely to achieve significant mitigation of climate change. Redirecting that effort toward practical policies requires a shift in the regulatory paradigm of policymakers and the mental models of the public. System dynamics is well positioned to contribute some of the innovations needed to make that shift happen. Copyright © 2007 John Wiley & Sons, Ltd.
Statistical validation of intermediate endpoints for chronic diseases
Authors: Freedman Laurence S. , Graubard Barry I. , Schatzkin Arthur
Published: April 2007

We discuss the implementation of a criterion due to Prentice for the statistical validation of intermediate endpoints for chronic disease. The criterion involves examining in a cohort or intervention study whether an exposure or intervention effect, adjusted for the intermediate endpoint, is reduced to zero. For example, to examine whether serum cholesterol level is an intermediate endpoint for coronary heart disease (CHD), we may investigate the effect of the cholesterol lowering drug cholestyramine on CHD incidence adjusted for serum cholesterol levels. We show that use of this criterion will usually demand some form of model selection. When the unadjusted exposure or treatment effect is less than four times its standard error, the analysis can usually lead only to a weak form of validation, a conclusion that the data are not inconsistent with the validation criterion. More significant unadjusted exposure effects offer the potential for stronger types of validation statement such as ‘the intermediate endpoint explains at least 50 per cent (or 75 per cent) of the exposure effect’.
A note on the effect of the intraclass correlation in the multiple reading procedure with a unanimity rule
Authors: Lui Kung‐Jong
Published: April 2007

The use of multiple reading procedures to improve the performance of a diagnostic test occurs often in practice. Evaluation of the utility of multiple reading procedures, however, usually ignores the effect of the intraclass correlation. This paper provides a quantitative assessment of this effect in the multiple reading procedure with a unanimity rule with respect to sensitivity, specificity, positive and negative predictive values. We have found that when the disease prevalence is rare or moderate (≤ 0·20), use of the multiple reading procedure with a unanimity rule is effective in increasing the positive predictive value of a single reading procedure for the situation in which the variation of responses among different subjects and the intraclass correaltion among repeated tests are small. This is, however, not true for the situation in which the disease is rare and the variation of responses among different subjects is large, even when the intraclass correlation is small or 0. Furthermore, when the disease is rare and the variation of responses among subjects is small, a small or moderate intraclass correlation can substantially decrease the positive predictive value that one calculates under the assumption that the intraclass correlation is equal to 0. In general, when the disease is rare or moderate (≤ 0.20), the intraclass correlation between repeated tests and the variation of responses among subjects have little effect on the negative predictive value.
Stochastic progression of new states in psychotherapy
Authors: Badalamenti Anthony F. , Langs Robert J. , Kessler Marc
Published: April 2007

This paper presents a study of the stochastic behaviour of the entry of a 5‐dimensional, 2400 state, system into new states. Each state consists of five measurements on variables that are sensitive measures of the degree of activated unconscious communication. The data come from six psychotherapy consultation sessions. The study sought to investigate the manner in which patient and therapist progress into new configurations (new states) of the five variables, and the way tension accumulates to the point of overcoming the inertia in the patient/therapist system. We show that the time series that consists of the time intervals between successive new states is a generalized Poisson process. That is, the process is inherently governed by a Poisson parameter that is a continuous piecewise linear function of time. It increases rapidly in the opening moments of an interview and decreases slowly thereafter. This non‐linear, non‐stationary Markov model fits the data well according to the Kolmogorov–Smirnoff criterion. We discuss the model's implications for the nature of psychotherapy and its participants.
A random coefficient growth curve analysis of mental development in low‐birth‐weight infants
Authors: Carter Randy L. , Resnick Michael B. , Ariet Mario , Shieh Gwowen , Vonesh Edward F.
Published: April 2007

In many medical studies, longitudinal data are collected on each of a sample of patients. The objectives of such studies often are: to estimate and test bivariate or multivariate relationships within each of several groups of patients from these repeated measures data; to compare these relationships among groups; and to test for the effects of baseline covariates on the relationships. This paper illustrates the use of statistical methods for growth curve analysis recently proposed by Vonesh and Carter for achieving these goals by relating a measure of preschool cognitive development to age in four race by sex groups of low‐birth‐weight infants. Significant declines in Bayley's Mental Development Index (MDI) with increasing age were found in all groups. Birth‐weight did not significantly influence the rate of decline but did influence the overall level of performance. Even so, in the group most comparable to Bayley's normative population, predicted MDI was near the norm even for extremely low‐birth‐weight infants (that is, 1000 grams). Although there is some risk of mental deficit associated with prematurity, eventual developmental delays in low‐birth‐weight infants frequently are acquired with age. The rate of decline in MDI was significantly associated with race and mother's education. Assumptions required for the valid application of these methods are discussed and tested in the setting of this applied problem. The assumptions appeared valid in this application. We conclude with a brief discussion of available alternatives when the assumptions are violated and point to areas for future research.
Model‐based screening by risk with application to down's syndrome
Authors: Royston Patrick , Thompson Simon G.
Published: April 2007

Screening for a disorder may be carried out by assessing the risk that an individual is affected given the values of variables whose distributions alter when the disorder is present. An optimal screening policy is obtained by identifying those individuals whose risk is greater than some cut‐off value. This paper summarizes the way in which risk is derived from the likelihood ratio of being affected by the disorder, and compares three different methods of estimating the likelihood ratio, namely direct estimation, logistic regression and distribution modelling. For continuous variables that have a multivariate normal distribution, screening by risk is equivalent to the use of quadratic discrimination. The paper shows how estimates of the risk and associated detection and false positive rates can be derived for a screening policy which uses specified risk cut‐offs. Screening by risk has the counter‐intuitive property that as the separation in the distribution of screening variables between affected and unaffected individuals increases, the detection and false positive rates may both increase. The approach is explored using data on antenatal screening for Down's syndrome. The method of choice is model‐based; the model is described and tested for goodness of fit. Complications arising from outliers and non‐normality must be overcome before an appropriate assessment of risk can be made. The concept of shrinkage is used to estimate the detection and false positive rates that may be expected in a new data set.
Predicting the prevalence of a disease in a cohort at risk
Authors: Mackisack M. , Dobson A. J. , Heathcote C. R.
Published: April 2007

A non‐homogeneous Markov chain model is used to describe the evolution of a progressive chronic disease. Transition probabilities are estimated from data on coronary heart disease in Australia. By varying the transition probabilities, the effects of changes in medical management or in the natural history of the disease are examined. For reducing rates of fatal and non‐fatal acute myocardial infarction a multifaceted strategy of primary and secondary prevention and improved acute care is found most effective. Primary prevention reducing the risk of early stages of the disease has the potential to yield the highest proportion of disease‐free people. By contrast, intensive medical treatment of acute disease would reduce mortality but increase the total burden of disease in the population.
Strengthening some common multiple test procedures for discrete data
Authors: Rom Dror M.
Published: April 2007

This paper proposes modification of some commonly used multiple test procedures for testing problems that arise when the underlying distributions are discrete. These procedures have been shown as conservative beeause the exact nominal levels are unattainable. The amended procedures can achieve actual type I errors much closer to the nominal levels, thus giving rise to more powerful tests.
Using an autoregressive model to detect departures from steady states in unequally spaced tumour biomarker data
Authors: Schlain Brian R. , Lavin Philip T. , Hayden Cheryl L.
Published: April 2007

A new method, based on a continuous time autoregressive [CAR(1)] model of time series data, is provided for detecting departures of tumour markers from steady states in breast cancer patients following surgery. A Kalman filter recursive algorithm is used to calculate the likelihood function arising from the CAR(1) model and to calculate recursive residuals, which are monitored by a Shewhart–Cusum scheme. This approach can be used to monitor the serial marker data of large numbers of patients even when the series are short and the data are serially correlated and unequally spaced. Further, the methodology can be used to recommend appropriate testing intervals.
Analysis of the incubation period for measles in the epidemic in greenland in 1951 using a variance components model
Authors: Kronborg Dorte , Hansen Bettina , Aaby Peter
Published: April 2007

This paper presents a model for analysing the incubation period of highly infectious diseases in populations where almost all susceptibles become infected during an epidemic. The model leads to a simple method for estimating the variance of the duration of the incubation period without any distributional assumptions. Further, the influence of covariates on the duration of the incubation period can be analysed. Data from the epidemic of measles in Greenland in 1951 are analysed and it is found that intersymptom times are correlated within households, suggesting that secondary cases are infected almost simultaneously. This result is inconsistent with a variation in the times of infection of secondary cases within a household which is often assumed when analysing data on measles. Prophylactic treatment did not prevent infection in the epidemic in Greenland, but it is found that the incubation period tended to be shorter for persons not receiving prophylactic treatment.
Effects of different parametric estimates of seroconversion time on analysis of progression to aids among Italian HIV‐positive haemophiliacs
Authors: Chiarotti Flavia , Palombi Massimo , Schinaia Nicola , Ghirardini Alessandro , Prospero Luca
Published: April 2007

The purpose of this study was to estimate seroconversion time using different parametric methods and to assess their influence on the estimation of the incubation time between HIV infection and onset of AIDS. Study subjects were 712 HIV‐positive haemophiliacs enrolled in the Italian National Registry of patients with congenital coagulation disorders. Seroconversion time was estimated using the mid‐point of each seroconversion interval (MID), the median of each interval under an estimated uniform distribution with cutpoints at December 1981 and December 1985 (MUU), the median of each interval under an estimated Weibull distribution (MUW), and the median of three random values drawn from each interval under the Weibull distribution (RUW). Kaplan‐Meier survival analysis showed that the cumulative incidence of AIDS over a 7‐year period was 11·6 per cent (SE 1·3 per cent) when using the MID estimate of seroconversion time, 10·8 per cent (1·2 per cent) with the MUU estimate, and 13·4 per cent (1·3 per cent) and 12·3 per cent (1·3 per cent) when using MUW and RUW estimates, respectively. This study demonstrates that the estimate of seroconversion time does not seem to be a major factor affecting estimates of AIDS incidence since the different techniques for estimating HIV seroconversion time yielded very similar results.
Closed‐form estimates for missing counts in two‐way contingency tables
Authors: Baker Stuart G. , Rosenberger William F. , Dersimonian Rebecca
Published: April 2007

One method for analyzing contingency tables with missing observations is to model the missing‐data mechanism using log‐linear models. Previous methods for obtaining estimates (of missing counts and parameters) have required an iterative algorithm. In many cases, however, one can obtain estimates by use of a simple algebraic formula. We illustrate the method with data on smoking and birth weight.
Mathematical models of complex dose‐response relationships: Implications for experimental design in psychopharmacologic research
Authors: Faraone Stephen V. , Simpson John C. , Brown Walter A.
Published: April 2007

We develop a mathematical model to account for the complex relationship between drug dose and clinical response in psychopharmacologic research. The model specifies relationships among drug dose, drug bioavailability, pharmacokinetic factors, course moderators, clinical response and the heterogeneity of the disorder, and allows for the derivation of results that have implications for experimental design in psychopharmacologic research. These results form the basis for computer simulations which indicate that random assignment to two fixed doses is more powerful and less sensitive to heterogeneity than assignment to clinically determined doses. Fixed dose designs, however, tend to overestimate the magnitude of drug bioavailability–clinical response relationships. Clinically determined dose designs are useful in some experimental situations; their effectiveness is enhanced by systematically reducing the clinically determined dose. Larger dose reductions improve the ability to detect bioavailability–clinical response relationships.
On identifying a positive dose‐response surface for combination agents
Authors: Hung H. M. James
Published: April 2007

This article concerns construction of a confidence surface for tangential slopes of the dose‐response surface of a combination therapy to identify where response increases as a function of drug dosage. This approach extends to the assessment of the effectiveness of the combination therapy.
Estimating the number of clusters for the analysis of correlated binary response variables from unbalanced data
Authors: Shoukri M. M. , Martin S. W.
Published: April 2007

Dominating the literature on sample size determination are papers concerned with observations collected from independent responses. We discuss in this paper, under the common correlation model for binary responses, the issue of estimating the number of groups when the sampling units are clusters of variable sizes.
k‐ratio t tests for multiple comparisons involving several treatments and a control
Authors: Brant Larry J. , Duncan David B. , Dixon Dennis O.
Published: April 2007

We consider the problem of simultaneously comparing several treatment means with a control mean and also with one another. Following an elementary decision‐theoretic Bayesian approach requiring the choice of a type‐I to type‐II error‐seriousness ratio k, a posteriori t tests are derived for testing both treatment versus control (TvC) and treatment versus treatment (TvT) differences. These k‐ratio t tests are strictly comparisonwise in nature. That is, the test applied to any TvC or TvT difference d, depends in no way at all on whether the other differences are being tested. The test for d, however, does depend on the sizes of the other differences through tG, the standardized average of the observed TvC differences, and through FT, the observed between‐treatments F ratio. From these adaptive dependences on tG and FT, the critical t values can be large or small, thus avoiding the intuitive objections of under‐ or over‐conservatism in classical comparisonwise or experimentwise level testing rules.
Estimation of time since exposure for a prevalent cohort
Authors: Muñoz Alvaro , Carey Vincent , Taylor Jeremy M. G. , Chmiel Joan S. , Kingsley Lawrence , van Raden Mark , Hoover Donald R.
Published: April 2007

In natural history studies of human immunodeficiency virus type 1 (HIV‐1) infection a substantial proportion of participants are seropositive at time of enrolment in the study. These participants form aprevalent subcohort.Estimation of the unknown times since exposure to HIV‐1 in the prevalent subcohort is of primary importance for estimation of the incubation time of AIDS. The subset of the cohort that tested negative for antibody to HIV‐1 at study entry and was observed to seroconvert forms theincident subcohortthat provides longitudinal data on markers of maturity (that is, duration) of infection. We use parametric life table regression models incorporating truncation to describe the conditional distribution (imputing model) of the times since seroconversion given a vector of the markers of maturity. Using the fitted model and the values of the markers of maturity of infection provided by the seroprevalent subcohort at entry into the study, we can impute the unknown times since seroconversion for the prevalent subcohort. We implement multiple imputation based on a model‐robust estimate of the covariance matrix of parameters of the imputing model to provide confidence intervals for the geometric mean of the time since seroconversion in the prevalent subcohort, and to compare maturity of infection of cohorts recruited in different cities. The accuracy of imputation is further validated by comparisons of imputation‐based estimates of AIDS incubation distribution in the seroprevalent subcohort with more direct estimates obtained from the seroincident subcohort.
Assessing response bias in random‐digit dialling surveys: The telephone‐prefix method
Authors: Diehr Paula , Koepsell Thomas D. , Cheadle Allen , Psaty Bruce M.
Published: April 2007

Knowledge of the characteristics of survey non‐respondents is important to determine generalizability to the population of interest. In a recent random‐digit dialling survey of health behaviours only 73 per cent of the households contacted provided any information about household composition, and only 74 per cent of those actually completed the extended interview, for an overall response rate of 54 per cent. To identify possible biases we grouped all attempted phone numbers by their prefix, and looked for the association between the response rate for that prefix and other summary variables known about the prefix. A simulation study showed that the method can identify non‐response biases if certain assumptions are correct. The analysis suggested that our survey data under‐represent older people and those with a college education. We found no significant biases in health behaviours, possibly because the basic assumptions did not hold. This method may assist in identification of non‐response bias in other studies.