bluuebunny/crossref_metadata_2025 huggingface dataset:
Posttraumatic stress disorder and general health problems following myocardial infarction (Post‐MI PTSD) among older patients: the role of personality
Authors: Chung Man Cheung , Berger Zoë , Jones Rupert , Rudd Hannah
Published: September 2006

Objectives

This study aimed to: (1) investigate the degree to which older MI patients experienced post‐MI PTSD and general health problems, and to (2) identify the association between five personality traits, post‐MI PTSD and general health problems among these older people.

Methods

The sample comprised 96 older MI patients and were recruited from two general practices. They were interviewed using the Posttraumatic Stress Diagnostic Scale (PDS), the General Health Questionnaire‐28 (GHQ‐28) and the NEO‐Five Factor Inventory (NEO‐FFI). The control group comprised 92 older people who experienced no MI. They were assessed using the GHQ‐28.

Results

The older MI patients experienced hyperarousal the most, followed by avoidance and re‐experiencing symptoms. PDS revealed that 30% had full PTSD. The older patients were conscientious and agreeable individuals. They were also somewhat extraverted and open to experience. They also showed traits of neuroticism. Controlling for bypass surgery, heart failure, previous mental health difficulties, angina and angioplasty, regression analyses showed that neuroticism predicted re‐experiencing and avoidance symptoms and general health total. Neuroticism and less agreeableness predicted hyperarousal symptoms.

Conclusions

MI older patients could manifest PTSD symptoms and general health problems following their MI. Personality traits, particularly neuroticism and antagonism, played a role in the manifestation of these symptoms. Copyright © 2006 John Wiley & Sons, Ltd.
Subjective cognitive function and decline among older adults with psychometrically defined amnestic MCI
Authors: Crowe Michael , Andel Ross , Wadley Virginia , Cook Sarah , Unverzagt Frederick , Marsiske Michael , Ball Karlene
Published: September 2006

Objective

To examine the relationship between subjective cognitive function and subsequent cognitive decline among individuals with psychometrically defined amnestic mild cognitive impairment (MCI), and to determine whether the presence of depressive symptoms modifies this relationship.

Method

Fifty‐five individuals met psychometric criteria for amnestic mild cognitive impairment (MCI). Cognitive decline was measured using the Mini‐Mental State Examination (MMSE), which was administered at baseline and at follow‐up two years later. Subjective cognitive function was examined using two different one‐item memory complaints, as well as a scale focused on current level of cognitive function relative to past function and a scale focused on forgetting in specific everyday situations.

Results

In multiple regression analyses, the one‐item complaint of change in memory at baseline predicted future cognitive decline. There was a significant interaction effect whereby this association was stronger in participants who endorsed fewer symptoms of depression.

Conclusion

Individuals showing memory deficits consistent with amnestic MCI have at least some insight regarding cognitive decline and the extent to which subjective cognitive function is useful in predicting future decline may depend on what particular questions are asked as well as presence of depressive symptoms. Copyright © 2006 John Wiley & Sons, Ltd.
White matter lesion volumes and caudate volumes in late‐life depression
Authors: Hannestad Jonas , Taylor Warren D. , McQuoid Douglas R. , Payne Martha E. , Krishnan K. Ranga R. , Steffens David C. , MacFall James R.
Published: September 2006

Background

Decreased caudate volumes and increased white matter lesions (WMLs) are associated both with aging and late‐life depression, but the relationship between the two is unclear. We examined the association between WML and caudate volume, hypothesizing there would be a negative association, which would be stronger for WMLs located in anterior regions. We additionally hypothesized that this association would be stronger in depressed subjects.

Method

This MRI study included 182 elderly depressed and 64 elderly control subjects. Our imaging analysis procedures divided the brain into anterior and posterior halves. WML volume in each half was calculated, as were left and right caudate volumes. A statistical model incorporating WML volumes, age, total brain volume, diagnosis, and gender was used to examine caudate volumes.

Results

WML volume was negatively associated with total and right caudate volume. This association was stronger for WMLs in the anterior half of the brain. Anterior WML volume was additionally negatively associated with right caudate volume in depressed subjects, but not in controls.

Conclusions

Using unadjusted levels of significance, WML volume is negatively associated with right caudate volume in both older populations, but with left caudate volume only in depressed individuals. When statistical corrections for multiple comparisons are used, the finding is limited to a negative association between WML volume and right caudate volume, primarily in depressed subjects. This study demonstrates one mechanism by which WMLs may disrupt frontostriatal circuits. Copyright © 2006 John Wiley & Sons, Ltd.
Modelling crop canopy and residue rainfall interception effects on soil hydrological components for semi‐arid agriculture
Authors: Kozak Joseph A. , Ahuja Lajpat R. , Green Timothy R. , Ma Liwang
Published: September 2006

Crop canopies and residues have been shown to intercept a significant amount of rainfall. However, rainfall or irrigation interception by crops and residues has often been overlooked in hydrologic modelling. Crop canopy interception is controlled by canopy density and rainfall intensity and duration. Crop residue interception is a function of crop residue type, residue density and cover, and rainfall intensity and duration. We account for these controlling factors and present a model for both interception components based on Merriam's approach. The modified Merriam model and the current modelling approaches were examined and compared with two field studies and one laboratory study. The Merriam model is shown to agree well with measurements and was implemented within the Agricultural Research Service's Root Zone Water Quality Model (RZWQM). Using this enhanced version of RZWQM, three simulation studies were performed to examine the quantitative effects of rainfall interception by corn and wheat canopies and residues on soil hydrological components. Study I consisted of 10 separate hypothetical growing seasons (1991–2000) for canopy effects and 10 separate non‐growing seasons (1991–2000) for residue effects for eastern Colorado conditions. For actual management practices in a no‐till wheat–corn–fallow cropping sequence at Akron, Colorado (study II), a continuous 10‐year RZWQM simulation was performed to examine the cumulative changes on water balance components and crop growth caused by canopy and residue rainfall interception. Finally, to examine a higher precipitation environment, a hypothetical, no‐till wheat–corn–fallow rotation scenario at Corvallis, Oregon, was simulated (study III). For all studies, interception was shown to decrease infiltration, runoff, evapotranspiration from soil, deep seepage of water and chemical transport, macropore flow, leaf area index, and crop/grain yield. Because interception decreased both infiltration and soil evapotranspiration, no significant change in soil water storage was simulated. Nonetheless, these findings and the new interception models are significant new contributions for hydrologists. Published in 2006 John Wiley & Sons, Ltd.
Effects of TGF‐β1 and triiodothyronine on cartilage maturation: In vitro analysis using long‐term high‐density micromass cultures of chick embryonic limb mesenchymal cells
Authors: Mello Maria A. , Tuan Rocky S.
Published: September 2006

Endochondral ossification is initiated by differentiation of mesenchymal cells into chondrocytes, which produce a cartilaginous matrix, proliferate, mature, and undergo hypertrophy, followed by matrix calcification, and substitution of cartilage by bone. A number of hormones and growth factors have been implicated in this process. Using in vitro, long‐term, high‐density, micromass cultures of chick embryonic mesenchyme, that recapitulate the process of chondrogenesis, chondrocyte maturation, and hypertrophy, we have investigated the importance of a balance between proliferation and apoptosis in cartilage maturation, focusing specifically on the effects of transforming growth factor‐β1 (TGF‐β1) and the thyroid hormone, triiodothyronine (T3). Our results showed that TGF‐β1 stimulates proliferation, by week 2 of culture, and T3 inhibits proliferation by week 3. Cell size increases in cultures treated with T3. Collagen type X is expressed in all culture, and delay in matrix deposition is seen only in the cultures treated with TGF‐β1. T3 stimulates alkaline phosphatase activity, but not calcification. T3 enhances apoptosis, as seen by TUNEL staining, and internucleosomal DNA fragmentation. The results support the roles of T3 and TGF‐β in cartilage maturation, i.e., TGF‐β stimulates proliferation and suppresses hypertrophy, while T3 stimulates hypertrophy and apoptosis. © 2006 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 24:2095–2105, 2006
Linear and non‐linear stability thresholds for thermal convection in a box
Authors: Hill A. A. , Straughan B.
Published: September 2006

We analyse the problem of finding instability thresholds and global non‐linear stability bounds for thermal convection in a linearly viscous fluid in a finite box. The vertical walls are maintained at different temperatures which gives rise to a non‐uniform temperature field in steady state. This problem was previously analysed by Georgescu and Mansutti (Int. J. Non‐Linear Mech. 1999; 34:603–613). In our work we determine the linear instability threshold to be well above the global stability boundary found by an energy method. Since the perturbed system is not symmetric we expect this to be the case, and our analysis yields a parameter region where possible sub‐critical instabilities may be found. Copyright © 2006 John Wiley & Sons, Ltd.
Cadherin in developing and maturing cysts of Torpedo Marmorata Testis
Authors: Prisco Marina , Liguoro Annamaria , Ricchiari Loredana , Angelini Francesco , Andreuccetti Piero
Published: September 2006

We investigated the presence of cadherins, Ca++ dependent cell–cell adhesion molecules, during the development and maturation of cysts in the testis of the spotted ray Torpedo marmorata. Using different anti‐cadherin antibodies, we provide evidence by means of immunohistochemistry and immunoblotting that cadherins are involved in the interaction between Sertoli and germ cells. During the development and maturation of cysts, in fact, cadherins occur between Sertoli and germ cells when they begin to interact to build a cyst. Later on, the presence of cadherins between Sertoli and germ cells persists; furthermore, during the formation of spermatoblast, it is also evident at the level of indentations, arising from Sertoli cells and encompassing germ cells. Finally, the present findings strongly suggest that cadherins are also involved in the spermiogenesis as germ cells, when male gamete differentiation starts, are intensively stained, while, when spermiation is completed, the spermatozoa appear unlabeled. Mol. Reprod. Dev. © 2006 Wiley‐Liss, Inc.
Insulin‐like growth factor‐I promotes resistance of bovine preimplantation embryos to heat shock through actions independent of its anti‐apoptotic actions requiring PI3K signaling
Authors: Jousan F. Dean , Hansen Peter J.
Published: September 2006

For the bovine preimplantation embryo, insulin‐like growth factor‐I (IGF‐I) is a survival factor that blocks the induction of apoptosis and reduces the decrease in development caused by heat shock. The first objective was to determine the signaling pathways whereby IGF‐I acts to increase embryo cell number while inhibiting heat‐shock induced apoptosis. Exposure of embryos to heat shock reduced cell number and increased percent apoptosis, but IGF‐I increased cell number and blocked induction of apoptosis caused by heat shock. Actions of IGF‐I to increase cell number were blocked by treatment with the mitogen activated protein kinase kinase (MAPKK) inhibitor PD 98059 whereas the phosphatidylinositol 3‐kinase (PI3K) inhibitor LY 294002 had no effect. Conversely, LY 294002 but not PD 98059 blocked actions of IGF‐I to inhibit induction of apoptosis caused by heat shock. The second objective was to determine whether IGF‐I blocks effects of heat shock on development to the blastocyst stage by preventing apoptosis. Culture of embryos with IGF‐I was effective in blocking the reduction in blastocyst development caused by heat shock—this action occurred even in the presence of LY 294002. Addition of another inhibitor of apoptosis, the caspase‐3 inhibitor z‐DEVD‐fmk, did not mimic the protective effects of IGF‐I on blastocyst development. Surprisingly, IGF‐I was not effective in blocking the reduction in blastocyst development caused by heat shock when cultured with z‐DEVD‐fmk. In conclusion, the anti‐apoptotic actions of IGF‐I require PI3K signaling while actions to promote proliferation require MAPKK signaling. Moreover, actions of IGF‐I to allow heat‐shocked embryos to continue development to the blastocyst stage are independent of its anti‐apoptotic effects. Mol. Reprod. Dev. © 2006 Wiley‐Liss, Inc.
Maturation medium supplements affect transcript level of apoptosis and cell survival related genes in bovine blastocysts produced in vitro
Authors: Warzych E. , Wrenzycki C. , Peippo J. , Lechniak D.
Published: September 2006

The aim of the present study was to investigate whether protein or macromolecule supplements to in vitro maturation media affect transcript abundance of seven genes (Bax, Bcl2, Hsp70, IGF1, IGF1R, IGF2, and IGF2R) in oocytes and blastocysts. Cumulus–oocyte complexes aspirated from slaughterhouse ovaries were matured in TCM199 medium supplemented either with 10% FBS, 6% fatty acid free BSA (fafBSA) or 4% PVP40, then inseminated and cultured in vitro for 9 days. Transcript abundance analysis was carried out on immature and in vitro matured oocytes, as well as on blastocysts. Total RNA was isolated from pools of oocytes and embryos, reverse transcribed into cDNA and subjected to transcript analysis by real‐time PCR. No transcript of IGF1 gene was detected either in oocytes or in blastocysts. Maturation conditions significantly affected transcript levels of investigated loci in blastocysts but not in matured oocytes, with one exception. Only relative abundance (RA) of IGF2 gene was higher in oocytes matured with fafBSA. Moreover, oocyte maturation with fafBSA elevated transcript abundance of IGF1R, IGF2, and IGF2R genes in resulting blastocysts, whereas Hsp70 transcription was stimulated by FBS supplementation. Thus, under described conditions, fafBSA may be the optimal supplement to IVM medium due to higher transcript level of growth factor coding genes accompanied by a lower transcript level of Hsp70. Mol. Reprod. Dev. © 2006 Wiley‐Liss, Inc.
Stimulated jitter in the masseter muscle: Normative values
Authors: Rousseff Rossen T. , Khuraibet Adnan J. , Al‐Shubaili Asmahan F. , Tzvetanov Plamen
Published: September 2006

Nineteen healthy volunteers (median age, 25; range, 18–51 years) were enrolled in a study to obtain normative values for stimulated jitter in the masseter muscle. Axonal microstimulation was performed via a monopolar needle electrode introduced in the masseter 2–2.5 cm above the mandibular angle on the line connecting it with the lateral canthus. The recording single‐fiber electromyography (SFEMG) electrode was inserted anteriorly in the twitching area of the muscle. The mean consecutive difference (MCD) values for the 426 endplates studied followed a distribution skewed to the left, with a minimum value of 4.3 μs, maximal 44.7 μs, and a maximum of distribution at 11 μs. Mean pooled MCD measured 16.0 μs, and the mean of mean MCD per study was 13.6 μs. The value of the 95th upper percentile for an individual fiber was 29.3 μs. We suggest an upper normal limit for mean MCD per study of 21 μs and upper normal limit of MCD for individual fibers of 30 μs. The stimulated jitter study of masseter muscle is easy and reliable. Muscle Nerve, 2006
Is exercise necessary with repetitive nerve stimulation in evaluating patients with suspected myasthenia gravis?
Authors: Rubin Devon I. , Hentschel Kenneth
Published: October 2006

We retrospectively evaluated the effect of exercise on the degree of decrement in ulnar, spinal accessory, and facial repetitive nerve stimulation (RNS) in 179 patients with myasthenia gravis (MG) to assess whether exercise increases the diagnostic yield of identifying significant decrements. The mean worsening of decrement following exercise was 1.9% (ulnar nerve), 1.9% (spinal accessory nerve), and 1.3% (facial nerve). Abnormal (≥10%) decrement solely following exercise occurred in the ulnar nerve in 7% of patients, accessory nerve in 5%, and facial nerve in 7%. When analyzed according to Myasthenia Gravis Foundation of America class of disease, the likelihood of producing ≥10% decrement only after exercise was greatest in class I MG with facial RNS and in class II and III generalized MG with ulnar and spinal accessory RNS. In all other disease stages, the likelihood of producing ≥10% decrement only after exercise was ≤7%. This study suggests that exercise increases the yield of diagnosis of MG by RNS in only a small percent of patients. Therefore, in most patients with suspected MG, RNS at rest is sufficient and the additional time required for prolonged postexercise RNS may be better spent in examining other muscle–nerve combinations. Muscle Nerve, 2006
A m‐parallel crane scheduling problem with a non‐crossing constraint
Authors: Lim Andrew , Rodrigues Brian , Xu Zhou
Published: September 2006

In this paper, we study a m‐parallel machine scheduling problem with a non‐crossing constraint motivated by crane scheduling in ports. We decompose the problem to allow time allocations to be determined once crane assignments are known and construct a backtracking search scheme that manipulates domain reduction and pruning strategies. Simple approximation heuristics are developed, one of which guarantees solutions to be at most two times the optimum. For large‐scale problems, a simulated annealing heuristic that uses random neighborhood generation is provided. Computational experiments are conducted to test the algorithms. © 2006 Wiley Periodicals, Inc. Naval Research Logistics, 2007.
Large‐scale topology optimization using preconditioned Krylov subspace methods with recycling
Authors: Wang Shun , Sturler Eric de , Paulino Glaucio H.
Published: September 2006

The computational bottleneck of topology optimization is the solution of a large number of linear systems arising in the finite element analysis. We propose fast iterative solvers for large three‐dimensional topology optimization problems to address this problem. Since the linear systems in the sequence of optimization steps change slowly from one step to the next, we can significantly reduce the number of iterations and the runtime of the linear solver by recycling selected search spaces from previous linear systems. In addition, we introduce a MINRES (minimum residual method) version with recycling (and a short‐term recurrence) to make recycling more efficient for symmetric problems. Furthermore, we discuss preconditioning to ensure fast convergence. We show that a proper rescaling of the linear systems reduces the huge condition numbers that typically occur in topology optimization to roughly those arising for a problem with constant density. We demonstrate the effectiveness of our solvers by solving a topology optimization problem with more than a million unknowns on a fast PC. Copyright © 2006 John Wiley & Sons, Ltd.
Calibration of a class of non‐linear viscoelasticity models with sensitivity assessment based on duality
Authors: Johansson Håkan , Runesson Kenneth
Published: September 2006

The calibration of constitutive models is based on the solution of an optimization problem, whereby the sought parameter values minimize an objective function that measures the discrepancy between experimental observations and the corresponding simulated response. By the introduction of an appropriate adjoint problem, the resulting formulation becomes well suited for a gradient‐based optimization scheme. A class of viscoelastic models is studied, where a discontinuous Galerkin method is used to integrate the governing evolution equation in time. A practical solution algorithm, which utilizes the time‐flow structure of the underlying evolution equation, is presented. Based on the proposed formulation it is convenient to estimate the sensitivity of the calibrated parameters with respect to measurement noise. The sensitivity is computed using a dual method, which compares favourably with the conventional primal method. The strategy is applied to a viscoelasticity model using experimental data from a uniaxial compression test. Copyright © 2006 John Wiley & Sons, Ltd.
Umbrella spherical integration: a stable meshless method for non‐linear solids
Authors: Kucherov L. , Tadmor E. B. , Miller R. E.
Published: September 2006

A stable meshless method for studying the finite deformation of non‐linear three‐dimensional (3D) solids is presented. The method is based on a variational framework with the necessary integrals evaluated through nodal integration. The method is truly meshless, requiring no 3D meshing or tessellation of any form. A local least‐squares approximation about each node is used to obtain necessary deformation gradients. The use of a local field approximation makes automatic grid refinement and the application of boundary conditions straightforward. Stabilization is achieved through the use of special ‘umbrella’ shape functions that have discontinuous derivatives at the nodes. Novel efficient algorithms for constructing the nodal stars and computing the nodal volumes are presented. The method is applied to four test problems: uniaxial tension, simple shear and bending of a bar, and cylindrical indentation. Convergence studies at infinitesimal strain show that the method is well‐behaved and converges with the number of nodes for both uniform and non‐uniform grids. Typical of meshless methods employing nodal integration, the total energy can be underestimated due to the approximate integration. At finite deformation the method reproduces known exact solutions. The bending example demonstrates an interesting example of torsional buckling resulting from the bending. Copyright © 2006 John Wiley & Sons, Ltd.
A numerical approach for limit analysis of orthotropic composite laminates
Authors: Pisano A. A. , Fuschi P.
Published: September 2006

A numerical approach for limit analysis of structures whose constituent material exhibits orthotropic behaviour is presented and discussed. Attention is focused on orthotropic composite laminates under plane stress conditions. The proposed approach is an extension, in the context of orthotropic materials, of the linear matching method (LMM). The latter is based on a sequence of linear analyses performed on the analysed structure made of a fictitious linear viscous material with spatially varying moduli. Here the LMM is applied to structures made of materials obeying the Tsai–Wu criterion. An appropriate choice of the fictitious material, which in this case is assumed linear, viscous, orthotropic and suffering a distribution of assigned initial stresses, reduces the number of parameters to be spatially varied thus rendering the whole procedure applicable and reliable. The results obtained are highly promising as witnessed by a number of numerical examples which are carried out to verify the effectiveness of the proposed approach. Copyright © 2006 John Wiley & Sons, Ltd.
Weighted radial basis collocation method for boundary value problems
Authors: Hu H. Y. , Chen J. S. , Hu W.
Published: September 2006

This work introduces the weighted radial basis collocation method for boundary value problems. We first show that the employment of least‐squares functional with quadrature rules constitutes an approximation of the direct collocation method. Standard radial basis collocation method, however, yields a larger solution error near boundaries. The residuals in the least‐squares functional associated with domain and boundary can be better balanced if the boundary collocation equations are properly weighted. The error analysis shows unbalanced errors between domain, Neumann boundary, and Dirichlet boundary least‐squares terms. A weighted least‐squares functional and the corresponding weighted radial basis collocation method are then proposed for correction of unbalanced errors. It is shown that the proposed method with properly selected weights significantly enhances the numerical solution accuracy and convergence rates. Copyright © 2006 John Wiley & Sons, Ltd.
Fast frequency sweep computations using a multi‐point Padé‐based reconstruction method and an efficient iterative solver
Authors: Avery Philip , Farhat Charbel , Reese Garth
Published: September 2006

Problems of the form Z(σ) u(σ)=f(σ), where Z is a given matrix, f is a given vector, and σ is a circular frequency or circular frequency‐related parameter arise in many applications including computational structural and fluid dynamics, and computational acoustics and electromagnetics. The straightforward solution of such problems for fine increments of σ is computationally prohibitive, particularly when Z is a large‐scale matrix. This paper discusses an alternative solution approach based on the efficient computation of u and its successive derivatives with respect to σ at a few sample values of this parameter, and the reconstruction of the solution u(σ) in the frequency band of interest using multi‐point Padé approximants. This computational methodology is illustrated with applications from structural dynamics and underwater acoustic scattering. In each case, it is shown to reduce the CPU time required by the straightforward approach to frequency sweep computations by two orders of magnitude. Copyright © 2006 John Wiley & Sons, Ltd.
Conductive polymer composites obtained from recycled poly(carbonate) and rubber blends for heating and sensing applications
Authors: Zribi K. , Feller J. F. , Elleuch K. , Bourmaud A. , Elleuch B.
Published: September 2006

Conductive polymer composites (CPCs) can be obtained by blending an insulating polymer matrix with conductive fillers. When the percolation of the dispersed particles is achieved, it is possible to obtain a sensible material for self‐regulated heating by the Joule effect. To fit the durable development concept only recycled materials have been used to design CPCs, i.e. poly(carbonate) (PC) pellets cut out from signal panels and crushed rubber particles from car tires. The conductive properties of the CPCs have been investigated to determine the percolation conditions and the conductivity level with regard to heating and sensing applications. High amplitude positive temperature coefficient (PTC) effects are obtained with [poly(carbonate)‐carbon black]80%/crushed rubber 20% CPC, i.e. (PC‐CB)80/CR20 m/m, over 120°C allowing self‐regulated heating. This result is noteworthy as there are no other results reported in the literature for amorphous thermoplastic matrices like PC. A positive synergy is found between carbon black (CB) and crushed rubber (CR) particles, which act as a PTC booster. Nevertheless, rubber particles already conductive must be doped by the addition of at least 5% v/v CB to achieve higher conductivities. The response amplitudes obtained with (PC‐CB)/CR CPC are large enough to allow sensing and have a good selectivity towards the studied vapors (toluene and dichloromethane); large CR particles are found to be more suitable for this application. Copyright © 2006 John Wiley & Sons, Ltd.
Chemokine receptor expression profiles in nasopharyngeal carcinoma and their association with metastasis and radiotherapy
Authors: Ou D‐L , Chen C‐L , Lin S‐B , Hsu C‐H , Lin L‐I
Published: September 2006

Nasopharyngeal carcinoma (NPC) is an epithelial cancer that metastasizes predictably to cervical lymph nodes or distant organs. To assess whether the chemokine receptors of NPC cells play important roles in metastasis and are associated with radiotherapy history, the significance of various chemokine receptors (CCR1–10, CXCR1–6, XCR1, and CX3CR1) in NPC cell lines (TW01, TW04, HONE1, BM1, and AS1) and 52 NPC tumour biopsies from 48 patients with NPC was evaluated by mRNA and cytometric analyses, chemotaxis and actin polymerization assays, and immunohistochemical staining. Quantitative real‐time reverse transcription‐polymerase chain reaction revealed substantial expression of CCR7, CCR9, CXCR4, and CXCR6 mRNA in all the NPC cell lines. Of these, however, only CCR7, CXCR4, and CXCR6 were functional in NPC cells. Negative immunoreactivity for CCR7, CXCR4, and CXCR6 was demonstrated in almost all nasopharyngeal (NP) specimens from patients with primary NPC (n = 12) and in those with regional metastatic NPC (n = 15). However, expression of two or three of these chemokine receptors was demonstrated in NP specimens from patients with liver metastasis. Strong positivity was demonstrated for all three of these chemokine receptors in almost all of the regional and distant metastasis specimens. Significant differences in the expression of CCR7, CXCR4, and CXCR6 were found between primary tumours and metastases (p < 0.001, p < 0.001, and p < 0.002, respectively). This observation was further confirmed by laser capture microdissection of freshly frozen tumours from primary (n = 5) and metastatic (n = 8) NPC sites (p = 0.04, 0.03, and 0.03 for CCR7, CXCR4, and CXCR6, respectively). Finally, significant differences in CXCR4 expression were demonstrated between de novo and post‐radiotherapy groups (1/22 vs. 5/8; p < 0.003). It appears reasonable to conclude, therefore, that CCR7, CXCR4, and CXCR6 are expressed and active in human NPC metastases, while CXCR4 expression is associated with radiotherapy history. Copyright © 2006 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Risk minimization practices for pregnancy prevention: understanding risk, selecting tools
Authors: Uhl Kathleen , Trontell Anne , Kennedy Dianne
Published: September 2006

According to the March of Dimes, approximately 4% (1/28) of babies are born in the US each year with a birth defect. For the majority of birth defects the etiology is unknown, although chemicals, including drug exposures, probably account for less than 1% of all birth defects. The identification of potential human teratogenicity during drug development is important because drug‐induced adverse fetal effects are potentially preventable with the application of risk assessment strategies and risk minimization tools and programs to minimize risk of pregnancy exposure while preserving access to drug benefits; risk assessment and risk minimization together comprise risk management. It is important that risk minimization programs intended to limit fetal exposure use a consistent approach and are tailored to the product‐specific risk concerns in order to optimize the benefit–risk balance for a particular drug. This paper highlights general considerations in developing specific risk minimization programs to prevent fetal drug exposure including the relative advantages and disadvantages of each strategy. Published in 2006 by John Wiley and Sons Ltd.
Differential AC‐chip calorimeter for glass transition measurements in ultrathin films
Authors: Huth H. , Minakov A. A. , Schick C.
Published: September 2006

A differential AC‐chip calorimeter capable of measuring the step in heat capacity at the glass transition in nanometer‐thin films is described. Because of the differential setup, pJ/K sensitivity is achieved. Heat capacity can be measured for sample masses below 1 ng in broad temperature range as needed for the study of the glass transition in nanometer‐thin polymeric films. Relative accuracy is sufficient to investigate the changes in heat capacity as the step at the glass transition of polystyrene. The step is about 25% of the total heat capacity of polystyrene. The calorimeter allows for the frequency dependent measurement of complex heat capacity in the frequency range from 1 Hz to 1 kHz. The glass transition in thin polystyrene films (50–4 nm) was determined at well‐defined experimental time scales. No thickness dependency of the glass transition temperature was observed within the error limits (±3 K)—neither at constant frequency (40 Hz) nor for the trace in the activation diagram (1 Hz–1 kHz). © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 2996–3005, 2006
Interpreting the dynamics of nano‐confined glass‐formers and thin polymer films: Importance of starting from a viable theory for the bulk
Authors: Ngai K.L.
Published: September 2006

The changes of the dynamic properties of the nanoconfined materials vary greatly depending on the nature of the interfaces, the chemical structure of the nanoconfined glass‐former, the experimental methods used, and, in the case of polymers, the length‐scale of the dynamics probed. Just for the glass transition temperature (Tg) alone, it can decrease, increase, or remain the same depending upon the experimental or simulation conditions. The conventional theories of Tg are unable to explain the range of behaviors seen at the nanometer size scale, and some of the theories give even conflicting predictions on the effect of small size or nanoconfinement on Tg. These problems of conventional theories orginate from the neglect or inadaquate treatment of the many‐molecule relaxation, showing up already when applied to the bulk for not being able to explain some general properties of glass transition. Thus, it is not surprising to find the conventional theories fail to explain the range of behaviors of the more complicated case of materials in nanoconfinement. On the other hand, based on concepts and parameters that capture the essentials of many‐molecule relaxation, the Coupling Model is not only consistent with the general properties of bulk glass‐formers but can also explain the range of behaviors found in materials subjected to nanoconfinement. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 2980–2995, 2006
Physicochemical descriptors to discriminate protein–protein interactions in permanent and transient complexes selected by means of machine learning algorithms
Authors: Block Peter , Paern Juri , Hüllermeier Eyke , Sanschagrin Paul , Sotriffer Christoph A. , Klebe Gerhard
Published: September 2006

Analyzing protein–protein interactions at the atomic level is critical for our understanding of the principles governing the interactions involved in protein–protein recognition. For this purpose, descriptors explaining the nature of different protein–protein complexes are desirable. In this work, the authors introduced Epic Protein Interface Classification as a framework handling the preparation, processing, and analysis of protein–protein complexes for classification with machine learning algorithms. We applied four different machine learning algorithms: Support Vector Machines, C4.5 Decision Trees, K Nearest Neighbors, and Naïve Bayes algorithm in combination with three feature selection methods, Filter (Relief F), Wrapper, and Genetic Algorithms, to extract discriminating features from the protein–protein complexes. To compare protein–protein complexes to each other, the authors represented the physicochemical characteristics of their interfaces in four different ways, using two different atomic contact vectors, DrugScore pair potential vectors and SFCscore descriptor vectors. We classified two different datasets: (A) 172 protein–protein complexes comprising 96 monomers, forming contacts enforced by the crystallographic packing environment (crystal contacts), and 76 biologically functional homodimer complexes; (B) 345 protein–protein complexes containing 147 permanent complexes and 198 transient complexes. We were able to classify up to 94.8% of the packing enforced/functional and up to 93.6% of the permanent/transient complexes correctly. Furthermore, we were able to extract relevant features from the different protein–protein complexes and introduce an approach for scoring the importance of the extracted features. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Thermal versus mechanical unfolding of ubiquitin
Authors: Irbäck Anders , Mitternacht Simon
Published: September 2006

The authors studied the temperature‐induced unfolding of ubiquitin by all‐atom Monte Carlo simulations. The unfolding behavior is compared with that seen in previous simulations of the mechanical unfolding of this protein, based on the same model. In mechanical unfolding, secondary‐structure elements were found to break in a quite well‐defined order. In thermal unfolding, the authors saw somewhat larger event‐to‐event fluctuations, but the unfolding pathway was still far from random. Two long‐lived secondary‐structure elements could be identified in the simulations. These two elements have been found experimentally to be the thermally most stable ones. Interestingly, one of these long‐lived elements, the first β‐hairpin, was found to break early in the mechanical unfolding simulations. Their combined simulation results thus enable the authors to predict in detail important differences between the thermal and mechanical unfolding behaviors of ubiquitin. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Theoretical study of the reaction of alkynes with furan catalyzed by AuCl3 and AuCl
Authors: Rabaâ Hassan , Engels Bernd , Hupp Thomas , Hashmi A. Stephen K.
Published: September 2006

A general scheme for the endo‐ and exo‐cyclization of furan reactivity with [L‐AuIII, IClx] with (x = 3, 1 and L‐acetylene and vinylidene) complexes is investigated using density functional theory (DFT) code. Two conceivable mechanisms via a [4 + 2] Diels–Alder process or carbene complex are analyzed. According to the activation energy values of the gold (III and I) catalyst, the first mechanism, which implies the Diels–Alder reaction of AuIII, is thermodynamically favored and gives more evidence of the intramolecular addition of the furan with the alkynes. The second mechanism, presumably assisted by the spontaneous formation of the exo‐vinylidene complexes and intermediates of gold (III, I) by forming the carbene complex, is kinetically favored. Additionally, we compare our results with other structures with intramolecular additions that exhibit the quasi‐similarity of gold analogue structures. Differences in activation energies are observed, according to the functional used. Finally, we probe the solvent effects, which decrease the energy barrier in the path. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Resistance distance and Kirchhoff index in circulant graphs
Authors: Zhang Heping , Yang Yujun
Published: September 2006

The resistance distance rij between vertices i and j of a connected (molecular) graph G is computed as the effective resistance between nodes i and j in the corresponding network constructed from G by replacing each edge of G with a unit resistor. The Kirchhoff index Kf(G) is the sum of resistance distances between all pairs of vertices. In this work, closed‐form formulae for Kirchhoff index and resistance distances of circulant graphs are derived in terms of Laplacian spectrum and eigenvectors. Special formulae are also given for four classes of circulant graphs (complete graphs, complete graphs minus a perfect matching, cycles, Möbius ladders Mp). In particular, the asymptotic behavior of Kf(Mp) as p → ∞ is obtained, that is, Kf(Mp) grows as ⅙p3 as p → ∞. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Theoretical study of molecular interaction between tirapazamine enzymatic catalysis metabolites and water
Authors: Li Lai‐Cai , Zha Dong , Zheng Yan , Wang Xin , Tian An‐Min , Wong Ning‐Bew
Published: September 2006

The weakly hydrogen‐bonded complexes, between tirapazamine enzymatic catalysis metabolites and water, have been investigated by density functional theory (DFT), using the B3LYP hybrid functional. The geometries of these complexes have been fully optimized at the B3LYP/6‐31G(d) and B3LYP/6‐311+G(d) levels. The stabilization energies and charge changes of some atoms have been calculated and analyzed. The results indicate that the catalysis metabolites and water can form stable hydrogen‐bonded complexes. Nine complexes are identified. It is important and necessary to add zero‐point vibrational energy (ZPVE) and basis set superposition error (BSSE) corrections for calculating stabilization energy. The results also reveal an important relationship between the relative stabilities of hydrogen‐bonded complexes and the final products of tirapazamine medication. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Finite element investigation of the ground states of the helium trimers 4He3 and 4He2–3He
Authors: Salci Moses , Yarevsky Evgeny , Levin Sergey B. , Elander Nils
Published: September 2006

A three‐dimensional finite element method is applied to the ground states of the symmetric and asymmetric atomic helium trimers 4He3 and 4He2–3He. Three different He–He interaction potentials of hard‐core nature were studied. Two extrapolation procedures based on the convergence properties of the finite element method are investigated. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Theoretical studies of mechanisms of cycloaddition reaction between difluoromethylene carbene and acetone
Authors: Lu Xiu Hui , Yu Hai Bin , Wu Wei Rong , Xu Yue Hua
Published: September 2006

Mechanisms of the cycloaddition reaction between singlet difluoromethylene carbene and acetone have been investigated with the second‐order Møller–Plesset (MP2)/6‐31G* method, including geometry optimization and vibrational analysis. Energies for the involved stationary points on the potential energy surface (PES) are corrected by zero‐point energy (ZPE) and CCSD(T)/6‐31G* single‐point calculations. From the PES obtained with the CCSD(T)//MP2/6‐31G* method for the cycloaddition reaction between singlet difluoromethylene carbene and acetone, it can be predicted that path B of reactions 2 and 3 should be two competitive leading channels of the cycloaddition reaction between difluoromethylene carbene and acetone. The former consists of two steps: (i) the two reactants first form a four‐membered ring intermediate, INT2, which is a barrier‐free exothermic reaction of 97.8 kJ/mol; (ii) the intermediate INT2 isomerizes to a four‐membered product P2b via a transition state TS2b with an energy barrier of 24.9 kJ/mol, which results from the methyl group transfer. The latter proceeds in three steps: (i) the two reactants first form an intermediate, INT1c, through a barrier‐free exothermic reaction of 199.4 kJ/mol; (ii) the intermediate INT1c further reacts with acetone to form a polycyclic intermediate, INT3, which is also a barrier‐free exothermic reaction of 27.4 kJ/mol; and (iii) INT3 isomerizes to a polycyclic product P3 via a transition state TS3 with an energy barrier of 25.8 kJ/mol. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Single‐electron halogen bond: Ab initio study
Authors: Wang Yan‐Hua , Zou Jian‐Wei , Lu Yun‐Xiang , Yu Qing‐Sen , Xu Hui‐Ying
Published: September 2006

Ab initio calculations have been performed on single‐electron halogen bonds between methyl radical and bromine‐containing molecules to gain a deeper insight into the nature of such noncovalent interactions. Bader's atoms in molecules (AIM) theory have also been applied to the analysis of the linking of the single‐electron halogen bond. Various characteristics of the RBr…CH3 interaction, i.e., binding energies, geometrical parameters and topological properties of the electron density have been determined. The presence of the bond critical points (BCPs) between the bromine atom and methyl radical and the values of electron density and Laplacian of electron density at these BCPs indicate the closed‐shell interactions in the complexes. The single‐electron halogen bonds, which are significantly weaker than the normal halogen bonds, exhibit equally bond strength as compared to the single‐electron hydrogen bond. It has been also found that plotting of the binding energies versus topological properties of the electron density at the BCPs gives two straight lines. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Modeling η5‐C5Me4SiMe3 with η3‐C3H5 for DFT study of a tetranuclear yttrium polyhydrido complex [(η5‐C5Me4SiMe3)YH2]4
Authors: Luo Yi , Hou Zhaomin
Published: September 2006

π‐Allyl (η3‐C3H5), a four‐electron donor, was used as a ligand model to replace η5‐C5Me4SiMe3 in DFT calculations on the tetranuclear yttrium polyhydrido complex (η5‐C5Me4SiMe3)4Y4H8 containing a Y4H8 tetrahedral core structure, which may separate the four π‐allyl groups and hence suppress the allyl ligand coupling during the computation. In terms of the calculated core geometry, isomerization energy barrier, charge population, and frontier orbital features of the complex, the η3‐C3H5 ligand model is comparable to η5‐C5H5. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Parameterization of AZT—A widely used nucleoside inhibitor of HIV‐1 reverse transcriptase
Authors: Carvalho Alexandra T. P. , Fernandes Pedro A. , Ramos Maria J.
Published: September 2006

Seven nucleoside reverse transcriptase (RT) inhibitors are currently used in the clinical treatment of acquired immunodeficiency syndrome (AIDS). These substrate analogues block DNA synthesis by the viral enzyme RT. However, the emergence of resistant variants of RT allied to their long‐term toxicity requires the design of new and better RT inhibitors, with long‐term in vivo efficacy. In this work we used density functional theory (DFT) calculations to develop a set of molecular mechanics (MM) parameters committed to the AMBER force field for one of the most used in the clinic nucleoside reverse transcriptase inhibitors (NRTIs): zidovudine (AZT). These parameters were tested by comparing the optimized geometries of AZT at both the DFT and MM levels of theory. The ability of the new parameters to reproduce the torsional energy of the azide group was also verified by scanning the surface in MM with the new parameters and comparing the results with the same potential energy surface (PES) at the DFT level. Finally, the parameters were validated through classical MD simulations of AZT in aqueous environment. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Hot spot computational identification: Application to the complex formed between the hen egg white lysozyme (HEL) and the antibody HyHEL‐10
Authors: Moreira I. S. , Fernandes P. A. , Ramos M. J.
Published: September 2006

The definition and comprehension of the hot spots in an interface is a subject of primary interest for a variety of fields, including structure‐based drug design. Therefore, to achieve an alanine mutagenesis computational approach that is at the same time accurate and predictive, capable of reproducing the experimental mutagenesis values is a major challenge in the computational biochemistry field. Antibody/protein antigen complexes provide one of the greatest models to study protein–protein recognition process because they have three fundamentally features: specificity, high complementary association and a small epitope restricted to the diminutive complementary determining regions (CDR) region, while the remainder of the antibody is largely invariant. Thus, we apply a computational mutational methodological approach to the study of the antigen–antibody complex formed between the hen egg white lysozyme (HEL) and the antibody HyHEL‐10. A critical evaluation that focuses essentially on the limitations and advantages between different computational methods for hot spot determination, as well as between experimental and computational methodological approaches, is presented. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007