bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of active site loop amino acids of lactate dehydrogenase from Plasmodium vivax by site‐directed mutagenesis studies
Authors: Turgut‐Balik Dilek , Sadak Dilek , Celik Venhar
Published: June 2006

The spread of resistance of malaria parasites to conventional chemotherapies necessitates the development of new drugs. The present study analyzes the active site loop of the enzyme lactate dehydrogenase from Plasmodium vivax (PvLDH). A five–amino acids insertion was observed in the active site loop of PvLDH, as in other plasmodial LDHs, which is absent in human LDH and is therefore a potential novel target site for new antimalarial drugs. This study describes the mutagenic testing of overproduced Plasmodium vivax lactate dehydrogenase to evaluate the importance of the inserted amino acids in the active site loop, which were previously identified as important residues by crystal structure studies. Deletion of these 5 extra amino acids in the active site loop resulted in an inactive form of the protein, supporting the notion of using this site as a novel target for antimalarial drug design. Drug Dev. Res. 67:175–180, 2006 © 2006 Wiley‐Liss, Inc.
Prevalence of metabolic syndrome using WHO, ATPIII and IDF definitions in Asian Indians: the Chennai Urban Rural Epidemiology Study (CURES‐34)
Authors: Deepa M. , Farooq S. , Datta M. , Deepa R. , Mohan V.
Published: June 2006

Aim

To compare the prevalence of metabolic syndrome (MS) using the World Health Organisation (WHO), Adult Treatment Panel III (ATPIII) and International Diabetes Federation (IDF) criteria of MS in an urban south Indian population, and their ability to identify coronary artery disease (CAD) in males and females.

Methods

Chennai Urban Rural Epidemiology Study (CURES) is one of the largest epidemiological studies on diabetes carried out in India, in which 26 001 individuals aged ≥20 years were screened using systematic random sampling method. Every tenth subject recruited in Phase 1 of CURES was requested to participate in Phase 3, and the response rate was 90.4%. An oral glucose tolerance test (OGTT) was performed in all individuals except self‐reported diabetic subjects. Anthropometric measurements and lipid estimations were done in all subjects and the prevalence of MS estimated using the three criteria. Diagnosis of CAD, made by resting 12 lead ECG, was compared by the three criteria of MS.

Results

MS was identified in 546 subjects (23.2%) by WHO criteria, 430 subjects (18.3%) by ATPIII criteria and 607 subjects (25.8%) by IDF criteria. Only 224 of these subjects were identified by all the three criteria. There was an increased risk of probable CAD in MS subjects diagnosed by WHO criteria (odds ratio (OR) 3.86, 95% Confidence Interval (CI), 2.37–6.29, p < 0.001), compared to ATPIII criteria (OR 2.19, 95% CI 1.30–3.67, p < 0.05) and IDF criteria (OR 1.90, 95% CI 1.16–3.12, p < 0.05). The WHO criteria marked out a much higher population for CAD risk compared to ATPIII and IDF criteria in males, but not in females.

Conclusion

In Asian Indians, the WHO, ATPIII and IDF criteria of MS identify different individuals. The WHO criteria identify a greater number of CAD subjects in males, but not in females. Copyright © 2006 John Wiley & Sons, Ltd.
A diffusion model with cubic drift: statistical and computational aspects and application to modelling of the global CO2 emission in Spain
Authors: Gutiérrez R. , Gutiérrez‐Sánchez R. , Nafidi A. , Ramos E.
Published: June 2006

The aim of this work is the study of a new stochastic diffusion model with a cubic‐type drift coefficient. The model is considered as the solution of an Ito stochastic differential equation. Using the Ito's stochastic calculus and properties of the Kummer function, the trend functions and steady‐state distribution for the process are obtained. Statistical estimation and corresponding computational methodology are established. Finally, the model is applied to modelling and prediction of the global CO2 emission in Spain. Copyright © 2006 John Wiley & Sons, Ltd.
New approaches for predicting protein retention time in hydrophobic interaction chromatography
Authors: Lienqueo M. E. , Mahn A. , Navarro G. , Salgado J. C. , Perez‐Acle T. , Rapaport I. , Asenjo J. A.
Published: June 2006

Hydrophobic interaction chromatography (HIC) is an important technique for the purification of proteins. In this paper, we review three different approaches for predicting protein retention time in HIC, based either on a protein's structure or on its amino‐acidic composition, and we have extended one of these approaches. The first approach correlates the protein retention time in HIC with the protein average surface hydrophobicity. This methodology is based on the protein three‐dimensional structure data and considers the hydrophobic contribution of the exposed amino acid residues as a weighted average. The second approach, which we have extended, is based on the high correlation level between the average surface hydrophobicity of a protein's hydrophobic interacting zone and its retention time in HIC. Finally, a third approach carries out a prediction of the average surface hydrophobicity of a protein, using only its amino‐acidic composition, without knowing its three‐dimensional structure. These models would make it possible to test different operating conditions for the purification of a target protein by computer simulations, and thus make it easier to select the optimal conditions, contributing to the rational design and optimization of the process. Copyright © 2006 John Wiley & Sons, Ltd.
MR‐guided breast biopsy using an active marker: A phantom study
Authors: Werner Richard , Krueger Sascha , Winkel Axel , Albrecht Christoph , Schaeffter Tobias , Heller Martin , Frahm Christian
Published: June 2006

Purpose

To evaluate the advantages of using an active marker (active micro coil) for MR‐guided breast biopsy procedures.

Materials and Methods

An add‐on breast biopsy guidance device used with a standard breast coil was equipped with an active marker. The marker's position was determined with a dedicated MRI sequence. In combination with custom software, the biopsy planning process was reduced basically to defining the target in the diagnostic MR images. Automatic control scans verified the settings of the biopsy guidance device. To measure the targeting accuracy, x‐ray control of the needle placement was performed in phantoms containing 36 small titanium cylinders. The reliability of the procedure was evaluated in 24 core needle biopsies on phantoms. Workflow enhancements were analyzed.

Results

The root mean square deviation of the needle position from the target perpendicular to the needle axis was 1.25 mm, in three‐dimensions it was 1.35 mm. All targets were sampled successfully. The duration of a phantom biopsy was nine minutes.

Conclusion

The use of an active marker can offer advantages for MR‐guided breast biopsies in terms of handling and procedure time as well as accuracy. J. Magn. Reson. Imaging 2006. © 2006 Wiley‐Liss, Inc.
USPIO‐enhanced magnetic resonance imaging for nodal staging in patients with head and neck cancer
Authors: Curvo‐Semedo Luís , Diniz Mónica , Miguéis Jorge , Julião Maria‐José , Martins Paula , Pinto Alda , Caseiro‐Alves Filipe
Published: June 2006

Purpose

To determine the accuracy of ultrasmall superparamagnetic iron oxide (USPIO)‐enhanced magnetic resonance imaging (MRI) for nodal staging in patients with head and neck cancer.

Materials and Methods

Twenty patients with carcinomas of the upper aerodigestive tract were prospectively enrolled. MRI was performed before and 24–36 hours after intravenous infusion of an USPIO agent, ferumoxtran‐10 (Sinerem; Guerbet, France; and Combidex; Advanced Magnetics) at a dose of 2.6 mg Fe/kg using T2‐weighted spin‐echo and gradient‐echo sequences. Surgery was performed the same day or the day after the ferumoxtran‐10–enhanced MR examination. Based on MRI, selected nodes were surgically removed and directly correlated with pathology using hematoxylin‐eosin (H&E) and Perls stainings.

Results

A total of 63 nodes were studied; 36 were nonmetastatic, 25 metastatic, and two inflammatory. Ferumoxtran‐10–enhanced MRI allowed diagnosis of 24 metastatic and 30 nonmetastatic nodes, yielding a sensitivity of 96%, a specificity of 78.9%, a positive predictive value of 75%, and a negative predictive value of 96.8%, compared to 64%, 78.9%, 66.6%, and 76.9%, respectively, for nonenhanced MRI. Accuracy of ferumoxtran‐10–enhanced MRI was 85.7%. The gradient‐echo T2‐weighted sequence was the most accurate to detect signal loss in nonmetastatic nodes.

Conclusion

USPIO‐enhanced MRI is useful for nodal staging of patients with head and neck cancers. J. Magn. Reson. Imaging 2006. © 2006 Wiley‐Liss, Inc.
Prospective longitudinal proton magnetic resonance spectroscopic imaging in adult traumatic brain injury
Authors: Holshouser Barbara A. , Tong Karen A. , Ashwal Stephen , Oyoyo Udochukwu , Ghamsary Mark , Saunders David , Shutter Lori
Published: June 2006

Purpose

To investigate whether longitudinal magnetic resonance proton spectroscopic imaging (MRSI) demonstrates regional metabolite abnormalities after traumatic brain injury (TBI) that predict long‐term neurologic outcome.

Materials and Methods

Two‐dimensional‐MRSI (point resolved spectroscopy sequence [PRESS]; TR/TE = 3000/144 msec; 10 mm) was acquired prospectively in 42 adults with severe TBI through the level of the corpus callosum 7 ± 4 days after injury. Measurements were repeated in 31 patients six to 12 months after injury. Regional and pooled (all regions combined) mean ratios were compared with control values and then used to predict long‐term (six‐ to –12‐month) neurologic outcome (good vs. poor) using a logistic regression model.

Results

Initial pooled mean N‐acetylaspartate (NAA) ratios were lower (P < 0.01) and choline (Cho)/creatine (Cr) ratios higher (P < 0.01) in all TBI patients compared to controls. Ratios from the corpus callosum region were affected most and predicted long‐term dichotomized outcome with 83% accuracy. When repeated at six to 12 months after injury, pooled mean NAA/Cr remained lower (P = 0.03) and Cho/Cr remained higher (P = 0.01) in patients with poor outcomes.

Conclusion

The NAA/Cr ratio from the corpus callosum was most useful for outcome prediction. Chronic alterations of metabolite ratios are likely due to neuronal loss and glial proliferation long after injury. J. Magn. Reson. Imaging 2006. © 2006 Wiley‐Liss, Inc.
Raman spectroscopic study of the uranyl phosphate mineral dewindtite
Authors: Frost Ray L. , Čejka Jiří , Weier Matt , Ayoko Godwin A.
Published: June 2006

Raman spectra of two samples of the uranyl mineral dewindtite are presented and interpreted. The observed bands are attributed to the stretching and bending vibrations of the (UO2)2+ and (PO4)3− units and water molecules. The hydrogen‐bonding network in the dewindtite crystal structure is briefly mentioned. The UO bond lengths in uranyls were calculated with empirical relations and wavenumbers of the (UO2)2+ stretching vibrations. These calculations are in agreement with the X‐ray single crystal structure data. Copyright © 2006 John Wiley & Sons, Ltd.
Beneficial effect of yam on the amyloid β‐protein, monoamine oxidase B and cognitive deficit in mice with accelerated senescence
Authors: Chan Yin‐Ching , Hsu Cheng‐Kuang , Wang Ming‐Fu , Liao Jiunn‐Wang , Su Ting‐Ya
Published: June 2006

This study was designed to evaluate the effect of yam tuber material [Dioscorea alata L. var. purpurea (M.) Pouch.] on the amyloid β‐protein (Aβ) accumulation, monoamine oxidase (MAO) activity, cognitive ability and antioxidative defense system in senescence‐accelerated mice (SAMP8). Three‐month‐old male mice were fed with four different diets for 12 weeks: a casein diet (control group) and a casein diet supplemented with either 100, 200 or 400 g kg−1 lyophilized yam. The results of the active shuttle avoidance test showed that the mice fed with the yam‐containing diets had significantly better learning and memory ability than the control group. All yam‐containing diet groups had lower Aβ levels and MAO B activities than the control, whereas the MAO A activity did not differ among the four diet groups. At the 400 g kg−1 level, the yam‐containing diet group showed significantly lower concentration of thiobarbituric acid‐reactive substances (TBARS), higher total thiol level and superoxide dismutase (SOD) activity in the hippocampus than the control, but these values were not altered by the 100 and 200 g kg−1 yam‐containing diet groups. The addition of 200 or 400 g kg−1 yam also lowered the triglyceride levels but not the total cholesterol concentration. These results indicate that lyophilized yam could reduce brain Aβ accumulation, MAO B activity and cognitive deficits and promote the antioxidative defense system in SAMP8 mice. The improvements were in a dose‐dependent manner, possibly because the 400 g kg−1 yam‐containing diet might contain more antioxidative phytochemicals. Copyright © 2006 Society of Chemical Industry
Time of flight mass spectrometry applied to the liquid chromatographic analysis of pesticides in water and food
Authors: Lacorte Sílvia , Fernandez‐Alba Amadeo R.
Published: June 2006

Liquid chromatography coupled to mass spectrometry (LC‐MS) is an excellent technique to determine trace levels of polar and thermolabile pesticides and their degradation products in complex matrices. LC‐MS can be equipped with several mass analyzers, each of which provides unique features capable to identify, quantify, and resolve ambiguities by selecting appropriate ionization and acquisition parameters. We discuss in this review the use of LC coupled to (quadrupole) time‐of‐flight mass spectrometry (LC‐(Q)ToF‐MS) to determine the presence of target and non‐target pesticides in water and food. This technique is characterized by operating at a resolving power of 10,000 or more. Therefore, it gives accurate masses for both parent and fragment ions and enables the measurement of the elemental formula of a compound achieving compound identification. In addition, the combination of quadrupole‐ToF permits tandem mass spectrometry, provides more structural information, and enhances selectivity. The purpose of this article is to provide an overview on the state of art and applicability of liquid chromatography time‐of‐flight mass spectrometry (LC‐ToF‐MS), and liquid chromatography quadrupole time‐of‐flight mass spectrometry (LC‐QToF‐MS) for the analysis of pesticides in environmental matrices and food. The performance of such techniques is depicted in terms of accurate mass measurement, fragmentation, and selectivity. The final section is devoted to describing the applicability of LC‐(Q)ToF‐MS to routine analysis of pesticides in food matrices, indicating those operational conditions and criteria used to screen, quantify, and identify target and “suspected” pesticides and their degradation products in water, fruits, and vegetables. The potential and future trends as well as limitations of LC‐(Q)ToF‐MS for pesticide monitoring are highlighted. © 2006 Wiley Periodicals, Inc.
Excellent response to apomorphine in Parkinsonism with optic atrophy unresponsive to oral antiparkinsonian medication
Authors: Deutschländer Angela , Asmus Friedrich , Marelli Elena , Klopstock Thomas , Gasser Thomas , Bötzel Kai
Published: June 2006

Two patients presented with the cardinal symptoms of Parkinson's disease (PD), which had developed slowly and progressively. One patient underwent brain imaging of the dopaminergic system, the results of which were compatible with PD. However, both patients showed no response to L‐dopa or oral dopaminergic medication. They also had optic nerve atrophy of unknown etiology. The severe motor symptoms of both patients were conspicuously alleviated by apomorphine delivered subcutaneously. One patient underwent bilateral subthalamic nucleus deep brain stimulation, which also proved effective. © 2006 Movement Disorder Society
Heterozygous PINK1 mutations: A susceptibility factor for Parkinson disease?
Authors: Djarmati Ana , Hedrich Katja , Svetel Marina , Lohnau Thora , Schwinger Eberhard , Romac Stanka , Pramstaller Peter P. , Kostić Vladimir , Klein Christine
Published: June 2006

PINK1 mutations cause recessively inherited early‐onset Parkinson's disease (EOPD). We comprehensively tested 75 Serbian and 17 South Tyrolean EOPD patients for mutations in this gene and found three heterozygous mutation carriers. Two of these patients shared mutations with their affected relatives, further suggesting that heterozygous PINK1 mutations may act as a susceptibility factor for EOPD.
Diffusion tensor imaging in presymptomatic and early Huntington's disease: Selective white matter pathology and its relationship to clinical measures
Authors: Rosas H. Diana , Tuch David S. , Hevelone Nathanael D. , Zaleta Alexandra K. , Vangel Mark , Hersch Steven M. , Salat David H.
Published: June 2006

Atrophy of cortical and subcortical gray matter is apparent in Huntington's disease (HD) before symptoms manifest. We hypothesized that the white matter (WM) connecting cortical and subcortical regions must also be affected early and that select clinical symptoms were related to systems degeneration. We used diffusion tensor magnetic resonance imaging (DTI) to examine the regional nature of WM abnormalities in early HD, including the preclinical period, and to determine whether regional changes correlated with clinical features. We studied individuals in early stages (HD), presymptomatic individuals known to carry the genetic mutation that causes HD (Pre‐HD), and matched healthy controls. DTI indices of tissue integrity were obtained from several regions of interest, including the corpus callosum (CC), internal capsule (IC), and basal ganglia, were compared across groups by t tests, and were correlated to cognitive and clinical measures. WM alterations were found throughout the CC, in the anterior and posterior limbs of the IC, and in frontal subcortical WM in HD subjects, supporting the selective involvement of the pyramidal tracts in HD; a similar distribution of changes was seen in Pre‐HD subjects, supporting presymptomatic alterations. There was a significant relationship between select DTI measures and cognitive performance. Alterations in diffusion indices were also seen in the striatum that were independent of atrophy. Our findings support that WM alterations occur very early in HD. The distribution of the changes suggests that these changes contribute to the disruption of pyramidal and extrapyramidal circuits and also support a role of compromised cortical circuitry in early cognitive and subtle motor impairment during the preclinical stages of HD. © 2006 Movement Disorder Society
Controlled withdrawal of pramipexole after 6 months of open‐label treatment in patients with restless legs syndrome
Authors: Trenkwalder Claudia , Stiasny‐Kolster Karin , Kupsch Andreas , Oertel Wolfgang H. , Koester Juergen , Reess Juergen
Published: June 2006

Although dopamine agonists are becoming first‐line therapy for restless legs syndrome (RLS), few reports describe treatment periods exceeding 12 weeks. Here, 150 RLS patients who had responded to pramipexole during a 6‐month run‐in period (mean dose, 0.50 mg) were randomly assigned to receive placebo or continue receiving pramipexole at an individually optimized dose of 0.125 to 0.75 mg/day for a further 3 months. Patients switched to placebo reached the primary endpoint (a predefined worsening on both the Clinical Global Impressions‐Global Improvement scale and the International RLS Study Group Rating Scale) significantly more often than patients who continued to receive pramipexole (85.5% vs. 20.5%; P < 0.0001). They also reached the primary endpoint faster, in 5 versus 42 days to a Kaplan–Meier survival estimate of 0.85 and 7 versus > 84 days to an estimate of 0.5. Over the total 9 months, clinician and patient ratings of symptoms, sleep, and quality of life identified no decline in pramipexole's benefit or tolerability. The great majority of adverse events (AEs) were mild or moderate, and of expected types. Augmentation was considered an AE, but in this population of responders it did not occur. © 2006 Movement Disorder Society
Rhythmic cortical myoclonus in Niemann–Pick disease type C
Authors: Canafoglia Laura , Bugiani Marianna , Uziel Graziella , Dalla Bernardina Bernardo , Ciano Claudia , Scaioli Vidmer , Avanzini Giuliano , Franceschetti Silvana , Panzica Ferruccio
Published: June 2006

We here describe a patient with late‐infantile Niemann–Pick disease type C (NPC) presenting with worsening myoclonus, seizures, cerebellar symptoms, mild mental impairment, and gaze palsy. Electroencephalographic (EEG) –polymyographic examinations showed abnormally high and diffuse background alpha‐activity, enhanced by intermittent photic stimulation. The electromyographic (EMG) showed quasirhythmic myoclonic jerks during motor activation. EEG–EMG frequency analysis (better than jerk‐locked back‐averaging) demonstrated the cortical origin of the myoclonus. Our observations indicate that cortical myoclonus may occur as the main symptom of NPC. © 2006 Movement Disorder Society
Coordinating outcomes measurement in ataxia research: Do some widely used generic rating scales tick the boxes?
Authors: Riazi Afsane , Cano Stefan J. , Cooper J. Mark , Bradley Jane L. , Schapira Anthony H.V. , Hobart Jeremy C.
Published: June 2006

The objective of this study was to examine the psychometric properties of four widely used generic health status measures in Friedreich's ataxia (FA), to determine their suitability as outcome measures. Fifty‐six people with genetically confirmed FA completed the Barthel Index (BI), General Health Questionnaire (GHQ‐12), EuroQol (EQ‐5D), and Medical Outcomes Study 36‐item Short Form Health Survey (SF‐36) by means of postal survey. Six psychometric properties (data quality, scaling assumptions, acceptability, reliability, validity, and responsiveness) were examined. The response rate was 97%. In general, the psychometric properties of the four measures satisfied recommended criteria. However, closer examination highlighted limitations restricting their use for treatment trials. For example, the BI had high levels of missing data, EQ‐5D had poor discriminant ability, and five SF‐36 scales had high floor and/or ceiling effects. Most scale scores did not span the entire scale range, had means that differed notably from the scale mid‐point, and had wide confidence intervals. Effect sizes (ES) were small for all four measures raising questions about their ability to detect clinically significant change. Results highlight the potential limitations of these four scales for evaluating health outcomes in FA and suggest the need for new disease‐specific patient‐based measures of its impact. © 2006 Movement Disorder Society
Drugs modulating the biological effects of peroxynitrite and related nitrogen species
Authors: Olmos Ana , Giner Rosa M. , Máñez Salvador
Published: June 2006

The term “reactive nitrogen species” includes nitrogen monoxide, commonly called nitric oxide, and some other remarkable chemical entities (peroxynitrite, nitrosoperoxycarbonate, etc.) formed mostly from nitrogen monoxide itself in biological environments. Regardless of the specific mechanisms implicated in their effects, however, it is clear that an integrated pharmacological approach to peroxynitrite and related species is only just beginning to take shape. The array of affected chemical and pathological processes is extremely broad. One of the most conspicuous mechanisms observed thus far has been the scavenging of the peroxynitrite anion by molecules endowed with antioxidant activity. This discovery has in turn lent great significance to several naturally occurring and synthetic antioxidants, which usually protect not only against oxidative reactions, but also from nitrating ones, bothin vitroandin vivo. This has proven to be beneficial in different tissues, especially within the central nervous system. Taking these results and those of other biochemical investigations into account, many research lines are currently in progress to establish the true potential of reactive nitrogen species deactivators in the therapy of neurological diseases, ischemia‐reperfusion damage, renal failure, and lung injury, among others. © 2006 Wiley Periodicals, Inc. Med Res Rev, 27, No. 1, 1–64, 2007
Retrospective measurement of the diffusion tensor eigenvalues from diffusion anisotropy and mean diffusivity in DTI
Authors: Hasan Khader M. , Narayana Ponnada A.
Published: June 2006

A simple theoretical framework to compute the eigenvalues of a cylindrically symmetric prolate diffusion tensor (D) from one of the rotationally‐invariant diffusion anisotropy indices and average diffusivity is presented and validated. Cylindrical or axial symmetry assumes a prolate ellipsoid shape (λ∥ = λ1 > λ⟂ = (λ2 + λ3)/2; λ2 = λ3). A prolate ellipsoid with such symmetry is largely satisfied in a number of white matter (WM) structures, such as the spinal cord, corpus callosum, internal capsule, and corticospinal tract. The theoretical model presented is validated using in vivo DTI measurements of rat spinal cord and human brain, where eigenvalues were calculated from both the set of diffusion coefficients and a tensor analysis. This method was used to retrospectively analyze literature data that reported tensor‐derived average diffusivity, anisotropy, and eigenvalues, and similar eigenvalue measurements were obtained. The method provides a means to retrospectively reanalyze literature data that do not report eigenvalues. Other potential applications of this method are also discussed. Magn Reson Med, 2006. © 2006 Wiley‐Liss, Inc.
Using ISO 17799: 2005 information security management: a STOPE view with six sigma approach
Authors: Saleh Mohammad Saad , Alrabiah Abdullah , Bakry Saad Haj
Published: June 2006

This paper is concerned with supporting the use of ISO 17799: 2005 information security management standard for the purpose of providing a ‘common safe environment’ for information services. The paper introduces a STOPE view of the standard, integrating its parts and protection measures around the basic domains of ‘strategy, technology, organization, people, and environment’. The paper also presents an approach for the application of the standard, considering the STOPE view, in a way that emphasizes continuous improvement. The phases of the approach are based on the phases of six sigma DMAIC approach of ‘define, measure, analyze, improve, and control’; the team proposed for the implementation of the work is also based on six sigma principles. The paper concludes with some suggestions for future related and needed work. Copyright © 2006 John Wiley & Sons, Ltd.
Finite element response sensitivity analysis using three‐field mixed formulation: general theory and application to frame structures
Authors: Barbato M. , Zona A. , Conte J. P.
Published: June 2006

This paper presents a method to compute response sensitivities of finite element models of structures based on a three‐field mixed formulation. The methodology is based on the direct differentiation method (DDM), and produces the response sensitivities consistent with the numerical finite element response. The general formulation is specialized to frame finite elements and details related to a newly developed steel–concrete composite frame element are provided. DDM sensitivity results are validated through the forward finite difference method (FDM) using a finite element model of a realistic steel–concrete composite frame subjected to quasi‐static and dynamic loading. The finite element model of the structure considered is constructed using both monolithic frame elements and composite frame elements with deformable shear connection based on the three‐field mixed formulation. The addition of the analytical sensitivity computation algorithm presented in this paper extends the use of finite elements based on a three‐field mixed formulation to applications that require finite element response sensitivities. Such applications include structural reliability analysis, structural optimization, structural identification, and finite element model updating. Copyright © 2006 John Wiley & Sons, Ltd.
Incorporation of multipoint constraints into the balancing domain decomposition method and its parallel implementation
Authors: Miyamura Tomoshi
Published: June 2006

The domain decomposition method (DDM) is a major solution algorithm that is used to parallelize the finite element method. In the case of implicit structural analysis using the DDM, the substructuring‐based iterative linear solver is a powerful tool when an effective preconditioner such as the balancing domain decomposition (BDD) method is used. In the present study, a method by which to incorporate a set of linear multipoint constraints (MPC) into the BDD method is proposed. In this method, when an MPC is enforced on the internal degrees of freedom (DOFs) in some subdomains, the DOFs are converted into interface DOFs, that is, all of the DOFs constrained by MPCs become interface DOFs. Then, the interface problem with the set of MPCs for the interface DOFs is solved by the conjugate projected gradient method. In order to combine the above procedure with the preconditioner used in the BDD method, the effect of the MPCs for the interface DOFs is also imposed on the coarse grid problem of the BDD method using the penalty method. A parallel implementation of the present method is also described. Some illustrative examples are solved and good convergence and parallel performance of the present method are demonstrated. Copyright © 2006 John Wiley & Sons, Ltd.
Numerical evaluation of harmonic Green's functions for triclinic half‐space with embedded sources—Part II: a 3D model
Authors: Chen Zhengxiang , Dravinski Marijan
Published: June 2006

The displacement and stress Green's functions for a 3D triclinic half‐space with embedded harmonic point load is considered. The resulting displacement and stress fields are expressed in terms of triple Fourier integrals. The first integral was evaluated using contour integration and the 3D Green's functions were obtained as a superposition of 2D results over the azimuthal angle. The resulting algorithm developed for evaluation of the Green's functions avoids repeated calculations of the same quantities and it utilizes the vectorized manipulation within MATLAB environment. The algorithm places no restriction on material properties, frequency and location of source and observation points. Extensive testing of the numerical results was performed for both displacement and stress. The tests confirm the accuracy of the numerical results. Copyright © 2006 John Wiley & Sons, Ltd.
Numerical approximation of optimal control for distributed diffusion Hopfield neural networks
Authors: Wang Q.‐F.
Published: June 2006

This work presents a numerical approximation of optimal control problems for non‐linear distributed Hopfield Neural Network equations with diffusion term. For one spatial dimensional case, a semi‐discrete numerical algorithm was constructed to find optimal control variable using finite element discretization, updated conjecture gradient iteration method. Furthermore, experiments demonstration will be implemented to show the effectiveness and stability through 3D graphics simulations. Copyright © 2006 John Wiley & Sons, Ltd.
The cohesive element approach to dynamic fragmentation: the question of energy convergence
Authors: Molinari J. F. , Gazonas G. , Raghupathy R. , Rusinek A. , Zhou F.
Published: June 2006

The cohesive element approach is getting increasingly popular for simulations in which a large amount of cracking occurs. Naturally, a robust representation of fragmentation mechanics is contingent to an accurate description of dissipative mechanisms in form of cracking and branching. A number of cohesive law models have been proposed over the years and these can be divided into two categories: cohesive laws that are initially rigid and cohesive laws that have an initial elastic slope. This paper focuses on the initially rigid cohesive law, which is shown to successfully capture crack branching mechanisms in simulations. The paper addresses the issue of energy convergence of the finite‐element solution for high‐loading rate fragmentation problems, within the context of small strain linear elasticity. These results are obtained in an idealized one‐dimensional setting, and they provide new insight for determining proper cohesive zone spacing as function of loading rate. The findings provide a useful roadmap for choosing mesh sizes and mesh size distributions in two and three‐dimensional fragmentation problems. Remarkably, introducing a slight degree of mesh randomness is shown to improve by up to two orders of magnitude the convergence of the fragmentation problem. Copyright © 2006 John Wiley & Sons, Ltd.
1‐Norm‐based regularization scheme for system identification of structures with discontinuous system parameters
Authors: Park Hyun Woo , Park Man Woo , Ahn Byeong Kyu , Lee Hae Sung
Published: June 2006

This paper presents a new class of regularization functions and the associated regularization scheme for structural system identification. In particular, 1‐norm regularization functions are investigated to overcome the smearing effect of 2‐norm regularization functions for the identification of discontinuous system parameters of structures. The truncated singular value decomposition is employed to filter out noise‐polluted solution components and to impose the 1‐norm regularization function on SI. The bilinear fitting method is proposed for selecting an optimal truncation number of the truncated singular value decomposition. The validity of the proposed method is demonstrated through the identification of an inclusion in a square plate and damaged members in a two‐span truss. Copyright © 2006 John Wiley & Sons, Ltd.
Peripheral chondrosarcoma progression is accompanied by decreased Indian Hedgehog signalling
Authors: Hameetman L , Rozeman LB , Lombaerts M , Oosting J , Taminiau AHM , Cleton‐Jansen A‐M , Bovée JVMG , Hogendoorn PCW
Published: June 2006

Hedgehog (HH) signalling is important for specific developmental processes, and aberrant, increased activity has been described in various tumours. Disturbed HH signalling has also been implicated in the hereditary syndrome, Multiple Osteochondromas. Indian Hedgehog (IHH), together with parathyroid hormone‐like hormone (PTHLH), participates in the organization of growth plates in long bones. PTHLH signalling is absent in osteochondromas, benign tumours arising adjacent to the growth plate, but is reactivated when these tumours undergo malignant transformation towards secondary peripheral chondrosarcoma. We describe a gradual decrease in the expression ofPatched(PTCH) andglioma‐associated oncogene homologue 1(GLI1) (both transcribed upon IHH activity), andGLI2with increasing malignancy, suggesting that IHH signalling is inactive and PTHLH signalling is IHH independent in secondary peripheral chondrosarcomas. cDNA expression profiling and immunohistochemical studies suggest that transforming growth factor‐β (TGF‐β)‐mediated proliferative signalling is active in high‐grade chondrosarcomas since TGF‐β downstream targets were upregulated in these tumours. This is accompanied by downregulation of energy metabolism‐related genes and upregulation of the proto‐oncogenejun B. Thus, the tight regulation of growth plate organization by IHH signalling is still seen in osteochondroma, but gradually lost during malignant transformation to secondary peripheral chondrosarcoma and subsequent progression. TGF‐β signalling is stimulated during secondary peripheral chondrosarcoma progression and could potentially regulate the retained activity of PTHLH. Copyright © 2006 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Paediatric Kikuchi–Fujimoto disease: A benign cause of fever and lymphadenopathy
Authors: Lazzareschi Ilaria , Barone Giuseppe , Ruggiero Antonio , Liotti Lucia , Maurizi Palma , Larocca Luigi Maria , Riccardi Riccardo
Published: June 2006

Kikuchi–Fujimoto disease (KFD) is a rare and benign disease that typically affects the cervical lymph nodes. Its aetiology is unknown and a role of the autoimmune system in the pathogenesis is hypothesized. This self‐limiting disease is often confused with malignancies. No specific management is generally required but long‐term follow‐up should be planned despite the low risk of recurrence, as recurrences have been described many years after the first episode and there is a high risk of development of an autoimmune disease or even lymphoma. We review the clinical and histological features of KFD and report an unusual case presenting with cervical and supraclavicular lymphadenopathy, and persistent fever. Pediatr Blood Cancer 2008;50:119–123. © 2006 Wiley‐Liss, Inc.
α‐helix stabilization by alanine relative to glycine: Roles of polar and apolar solvent exposures and of backbone entropy
Authors: López‐Llano J. , Campos L.A. , Sancho J.
Published: June 2006

The energetics of α‐helix formation are fairly well understood and the helix content of a given amino acid sequence can be calculated with reasonable accuracy from helix‐coil transition theories that assign to the different residues specific effects on helix stability. In internal helical positions, alanine is regarded as the most stabilizing residue, whereas glycine, after proline, is the more destabilizing. The difference in stabilization afforded by alanine and glycine has been explained by invoking various physical reasons, including the hydrophobic effect and the entropy of folding. Herein, the contribution of these two effects and that of hydrophilic area burial is evaluated by analyzing Ala and Gly mutants implemented in three helices of apoflavodoxin. These data, combined with available data for similar mutations in other proteins (22 Ala/Gly mutations in α‐helices have been considered), allow estimation of the difference in backbone entropy between alanine and glycine and evaluation of its contribution and that of apolar and polar area burial to the helical stabilization typically associated to Gly→Ala substitutions. Alanine consistently stabilizes the helical conformation relative to glycine because it buries more apolar area upon folding and because its backbone entropy is lower. However, the relative contribution of polar area burial (which is shown to be destabilizing) and of backbone entropy critically depends on the approximation used to model the structure of the denatured state. In this respect, the excised‐peptide model of the unfolded state, proposed by Creamer and coworkers (1995), predicts a major contribution of polar area burial, which is in good agreement with recent quantitations of the relative enthalpic contribution of Ala and Gly residues to α‐helix formation. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Multiple imputation for interval censored data with auxiliary variables
Authors: Hsu Chiu‐Hsieh , Taylor Jeremy M. G. , Murray Susan , Commenges Daniel
Published: June 2006

We propose a non‐parametric multiple imputation scheme, NPMLE imputation, for the analysis of interval censored survival data. Features of the method are that it converts interval‐censored data problems to complete data or right censored data problems to which many standard approaches can be used, and that measures of uncertainty are easily obtained. In addition to the event time of primary interest, there are frequently other auxiliary variables that are associated with the event time. For the goal of estimating the marginal survival distribution, these auxiliary variables may provide some additional information about the event time for the interval censored observations. We extend the imputation methods to incorporate information from auxiliary variables with potentially complex structures. To conduct the imputation, we use a working failure‐time proportional hazards model to define an imputing risk set for each censored observation. The imputation schemes consist of using the data in the imputing risk sets to create an exact event time for each interval censored observation. In simulation studies we show that the use of multiple imputation methods can improve the efficiency of estimators and reduce the effect of missing visits when compared to simpler approaches. We apply the approach to cytomegalovirus shedding data from an AIDS clinical trial, in which CD4 count is the auxiliary variable. Copyright © 2006 John Wiley & Sons, Ltd.
A test for publication bias in meta‐analysis with sparse binary data
Authors: Schwarzer Guido , Antes Gerd , Schumacher Martin
Published: June 2006

A new test for the detection of publication bias in meta‐analysis with sparse binary data is proposed. The test statistic is based on observed and expected cell frequencies, and the variance of the observed cell frequencies. These quantities are utilized in a rank correlation test. Type I error rate and power of the test are evaluated in simulations; results are compared to those of two other commonly used test procedures. Sample sizes were generated according to findings in a survey of eight German medical journals. Simulation results indicate that, in contrast to existing test procedures, the new test holds the prescribed significance level when data are sparse. However, the power of all tests is low in many situations of practical importance. Copyright © 2006 John Wiley & Sons, Ltd.
On the analysis of count data of birth‐and‐death process type: with application to molecularly targeted cancer therapy
Authors: Liu Hao , Beckett Laurel A. , DeNardo Gerald L.
Published: June 2006

For molecularly targeted cancer therapy, potency of a novel monoclonal antibody is typically studiedin vitroin order to observe directly the effect of the antibody on a malignant tumour cell population. Numbers of viable cells of the population are counted over time to evaluate how the antibody may change the population growth pattern. Usually, such count data is analysed by a log‐linear model to estimate the average antibody effects, but it is based on a Poisson‐like process and is not appropriate for modelling the growth pattern of the tumour cells. In this paper, we propose to analyse the count data from the point of view of a birth‐and‐death process, which is a more natural description of the biological process in these experiments. Assuming a simple birth‐and‐death process and a naïve regression model for the birth rate and death rate, we show that the log‐linear relationship still holds for the average count and the covariates, although the linear predictor needs to satisfy a specific functional form. The estimation can be based on the quasi‐likelihood method. The variance is not a simple function of the mean, but can be adequately approximated by a function of mean of either quadratic form or linear form, available in most standard statistical packages. We perform a simulation study to show that the proposed method provides consistent and robust estimations. The utility of the method is demonstrated by the analysis of a data set for experiment for anti‐lymphoma monoclonal antibodies. Copyright © 2006 John Wiley & Sons, Ltd.
Mass spectrometry of hydrogen/deuterium exchange in 70S ribosomal proteins from E. coli
Authors: Yamamoto Tatsuya , Izumi Shunsuke , Gekko Kunihiko
Published: June 2006

The 70S ribosome from Escherichia coli is a supermacro complex (MW: 2.7 MDa) comprising three RNA molecules and more than 50 proteins. We have for the first time successfully analyzed the flexibility of 70S ribosomal proteins in solution by detecting the hydrogen/deuterium exchange with mass spectrometry. Based on the deuterium incorporation map of the X‐ray structure obtained at the time of each exchange, we demonstrate the structure–flexibility–function relationship of ribosome focusing on the deuterium incorporation of the proteins binding ligands (tRNA, mRNA, and elongation factor) and the relation with structural assembly processes.
Acceleration of α‐synuclein aggregation by homologous peptides
Authors: Du Hai-Ning , Li Hong-Tao , Zhang Feng , Lin Xiao-Jing , Shi Jia-Hao , Shi Yan-Hong , Ji Li-Na , Hu Jun , Lin Dong-Hai , Hu Hong-Yu
Published: June 2006

α‐Synuclein (α‐Syn), amyloid β‐protein and prion protein are among the amyloidogenic proteins that are associated with the neurodegenerative diseases. These three proteins share a homologous region with a consensus sequence mainly consisting of glycine, alanine and valine residues (accordingly named as the GAV motif), which was proposed to be the critical core for the fibrillization and cytotoxicity. To understand the role of the GAV motif in protein amyloidogenesis, we studied the effects of the homologous peptides corresponding to the sequence of GAV motif region (residues 66–74) on α‐Syn aggregation. The result shows that these peptides can promote fibrillization of wild‐type α‐Syn and induce that of the charge‐incorporated mutants but not the GAV‐deficient α‐Syn mutant. The acceleration of α‐Syn aggregation by the homologous peptides is under a sequence‐specific manner. The interplay between the GAV peptide and the core regions in α‐Syn may accelerate the aggregation process and stabilize the fibrils. This finding provides clues for developing peptide mimics that could promote transforming the toxic oligomers or protofibrils into the inert mature fibrils.
Pregnancy outcome in gestational diabetes
Authors: Fan Zitian , Yang Huixia , Gao Xuelian , Lintu Hanna , Sun Weijie
Published: June 2006

Objective: To assess maternal and neonatal outcomes of gestational diabetes mellitus (GDM) following glycemic screening and diabetic management, with special focus on concurrent GDM and pre‐eclampsia.

Methods: A retrospective chart review of 782 women diagnosed with and treated for GDM at a Chinese university teaching hospital. Data on maternal and neonatal outcome, glycemic control, concurrent pre‐eclampsia, and diabetic management were collected and analyzed.

Results: The incidence of GDM was 3.8%. Of the affected women, 62.9% were managed with diet only and the remainder received insulin treatment. Overall, 80.7% had good glycemic control. Poor glycemic control and concurrent pre‐eclampsia correlated with maternal and neonatal complications.

Conclusion: Aggressive management for tight glycemic control improves maternal and neonatal outcomes in women with GDM.
On Greek VSO again!
Authors: ROUSSOU ANNA , TSIMPLI IANTHI-MARIA
Published: June 2006

In the present paper we provide an account of VSO in Greek and its (relative) absence in Italian, despite the fact that both languages allow for postverbal subjects. We argue that this parametric difference reduces to different lexicalisation options regarding the D-system of the two grammars. We assume that the clause structure divides into three basic domains (V, T, and C), and that nominal (clitic) positions are available in each of these domains, which, as we argue, can be lexicalised not only by clitics but also by full DPs. On this basis, we argue that the subject and object DP in Greek can appear in the same domain (V), as they spell out different features depending on their grammatical function, while this is not so in Italian, given that DPs spell out the same set of features irrespective of their grammatical function. This basic difference is responsible for the presence of VSO in Greek but not in Italian. We also consider the implications of our approach for the interpretation of subjects and arguments in general.
Proper names and the theory of metaphor
Authors: WEE LIONEL
Published: June 2006

Metaphorical expressions involving proper names have been discussed only sporadically. This paper demonstrates that there are in fact interesting things to be said about such metaphors, and makes two key points, one general and one specific. The general point is that their behavior accords more with the class-inclusion model of metaphor than the correspondence model. Having established this, I make the more specific point that there are cultural dimensions to these metaphors that pose particular problems for the kind of correspondence model proposed by Lakoff and his associates.