bluuebunny/crossref_metadata_2025 huggingface dataset:
Least‐squares solutions of matrix inverse problem for bi‐symmetric matrices with a submatrix constraint
Authors: Liao An‐ping , Lei Yuan
Published: February 2007

An n × n real matrix A = (aij)n × n is called bi‐symmetric matrix if A is both symmetric and per‐symmetric, that is, aij = aji and aij = an+1−1,n+1−i (i, j = 1, 2,..., n). This paper is mainly concerned with finding the least‐squares bi‐symmetric solutions of matrix inverse problem AX = B with a submatrix constraint, where X and B are given matrices of suitable sizes. Moreover, in the corresponding solution set, the analytical expression of the optimal approximation solution to a given matrix A* is derived. A direct method for finding the optimal approximation solution is described in detail, and three numerical examples are provided to show the validity of our algorithm. Copyright © 2007 John Wiley & Sons, Ltd.
Remarks on the efficiency of POD for model reduction in non‐linear dynamics of continuous elastic systems
Authors: Sampaio Rubens , Soize Christian
Published: February 2007

The first objective of this paper is to analyse the efficiency of the reduced models constructed using the proper orthogonal decomposition (POD)‐basis and the LIN‐basis in non‐linear dynamics for continuous elastic systems. The POD‐basis is the Hilbertian basis constructed with the POD method while the LIN‐basis is the Hilbertian basis derived from the generalized continuous eigenvalue problem associated with the underlying conservative part of the continuous elastic system and usually called the eigenmodes of vibration. The efficiency of the POD‐basis or the LIN‐basis is related to the rate of convergence in the frequency domain of the solution constructed with the reduced model with respect to its dimension. A basis will be more efficient than another if the reduced‐order solution of the Galerkin projection converges to the solution of the dynamical system more rapidly than the reduced‐order solution of the other.

As a second objective of this paper, we present the usual results concerning the POD method using a continuous formulation, with respect to both time and space variables, and then deriving the numerical approximations. Such a presentation allows convergence discussions to be treated.

Six examples in non‐linear elastodynamics problems are presented in order to analyse the efficiency of the POD‐basis and the LIN‐basis. It is concluded that the POD‐basis is not more efficient than the LIN‐basis for the examples treated in non‐linear elastodynamics. Copyright © 2007 John Wiley & Sons, Ltd.
A new plate bending element based on orthogonal polynomials expansion of the curvature field
Authors: Pitacco I.
Published: February 2007

A new approach to derive finite elements for the thin plate model is presented. The proposed method approximates compatible Kirchhoff formulations by means of orthogonal polynomials expansion of the curvature field depending only on the element boundary traces. With respect to the compatible formulation the proposed method produces elements that beneficially underestimate the deformation energy. A simple triangular element is developed and investigated from both the theoretical and the numerical point of view and numerically compared with other two well‐known elements. Copyright © 2007 John Wiley & Sons, Ltd.
Evolutionary optimization for passive gamma tomography reconstruction of circular inclusions in nuclear waste vaults
Authors: Mera N. S.
Published: February 2007

In this study we investigate numerically the possibility of reconstructing the interior details of a nuclear waste vault using photon flux measurements. The passive gamma ray tomography method is employed in order to simultaneously retrieve the intensity and the location of strongly radioactive components. After reformulating the problem as an optimization problem the objective functional obtained is found to have a multi‐modal non‐smooth structure. Therefore, evolutionary algorithms are used in order to minimize the objective functional in order to determine the radioactive components. Circular inclusions are considered and detailed numerical results are presented for both exact and noisy data. Copyright © 2007 John Wiley & Sons, Ltd.
Extension of LMS formulations for L‐stable optimal integration methods with U0–V0 overshoot properties in structural dynamics: the level‐symmetric (LS) integration methods
Authors: Leontiev V. A.
Published: February 2007

In the present article a new family of linear multi‐step (LMS) optimal integration methods for stiff structural dynamic problems is synthesized. Developing the ideas following the original works in References (Int. J. Numer. Meth. Engng 2004; 59:597–668, Int. J. Numer. Meth. Engng 2004; 60:1699–1740, Int. J. Numer. Meth. Engng 2006; 66:1738–1790) of design of optimal and controllable dissipation, extensions are made in this paper to a class of optimal integration methods with maximum possible damping of high frequencies separately from the degree of damping of low frequencies. Generalized single step single solve (GSSSS) optimal algorithm recently developed and basic well‐known ‘weighted‐residual’ methods are compared with ‘level‐symmetric’ (LS) integration methods proposed. These LS methods are created as symmetric variants of extended three‐level (3L‐LMS) integration algorithm with direct use of dynamic equations to obtain algorithmically simple integration methods, which belong to [U0–V0] L‐stable optimal class without overshoots and have the maximum damping of high‐frequency modes. General formulas for L‐stable family of multi‐step LS‐N methods are obtained. Standard two‐level representation (2L‐LMS) of 3L‐LMS integration algorithm is also obtained, and L‐stable second‐order accurate LS‐BDF integration method for the stiff first‐order ordinary differential equations is proposed. Roots, dissipation and dispersion properties of LS‐1 integration method (second‐order accurate in displacement) and of other obtained LS‐2, LS‐3, LS‐4 methods (third‐order accurate in displacement) are analysed and demonstrated. Comparison with some up‐to‐date integration methods is considered in three numerical examples. Copyright © 2007 John Wiley & Sons, Ltd.
A high‐order generalized FEM for through‐the‐thickness branched cracks
Authors: Duarte C. A. , Reno L. G. , Simone A.
Published: February 2007

This paper presents high‐order implementations of a generalized finite element method for through‐the‐thickness three‐dimensional branched cracks. This approach can accurately represent discontinuities such as triple joints in polycrystalline materials and branched cracks, independently of the background finite element mesh. Representative problems are investigated to illustrate the accuracy of the method in combination with various discretizations and refinement strategies. The combination of local refinement at crack fronts and high‐order continuous and discontinuous enrichments proves to be an excellent combination which can deliver convergence rates close to that of problems with smooth solutions. Copyright © 2007 John Wiley & Sons, Ltd.
Multi‐step tangential versus transversal linearizations in non‐linear dynamics
Authors: Ghosh S. , Roy D.
Published: February 2007

A family of multi‐step tangential linearization (MTnL) techniques is developed for numeric–analytic and geometric integration of non‐linear oscillators under deterministic loading. A family of multi‐step transversal linearization (MTrL) schemes is also explored and a comparison between the two linearization families is provided with a view of bringing out their relative advantages and deficiencies. The MTnL methodology essentially works through an application of the concept of MTrL to non‐linear rate equations. Different variants of the MTnL are obtained and it turns out that they are specific cases of a generalized MTnL method. Local error estimates are also provided. Moreover, higher order MTrL and MTnL methods are successfully implemented through Chebyshev nodes instead of equidistant nodes. This helps to improve accuracy even with larger step sizes. A comparison of relative errors through the MTrL and MTnL techniques consistently indicates a superior quality of approximations via the MTrL route. Whilst the usage of the tangential linearization is very common in non‐linear computational mechanics, it is demonstrated that the transversal version offers, in addition to higher numerical accuracy, an easier implementation and avoids computation of Jacobian matrices. This allows the MTrL family to be applicable even to non‐linear oscillators having C0 vector fields. Copyright © 2007 John Wiley & Sons, Ltd.
Sacrococcygeal teratoma in a fetus with prenatally diagnosed partial trisomy 10q (10q24.3→qter) and partial monosomy 17p (p13.3→pter)
Authors: Batukan Cem , Ozgun Mahmut Tuncay , Basbug Mustafa , Caglayan Okay , Dundar Munis , Murat Nurcan
Published: February 2007

Objective

Clinical features of the distal 10q trisomy syndrome consist of mental retardation, facial dysmorphism and renal and cardiac anomalies. The presence of a sacrococcygeal teratoma (SCT) in a fetus with distal 10q trisomy has not been reported yet.

Methods

A 33‐year‐old, G5, P2 woman with a singleton pregnancy was referred to our clinic at 24 weeks of gestation for further evaluation of a fetal sacral exophytic mass. Detailed fetal sonographic examination together with chromosomal analysis by amniocentesis was performed.

Results

The scan revealed a large SCT together with a persistent right umbilical vein, cardiomegaly, bilateral mild hydronephrosis and intrauterine growth retardation. The fetal karyotype showed distal 10q trisomy (10q24.3→qter) distal monosomy 17 (p13→pter). The fetus died after a preterm delivery at 28 weeks of gestation. Postnatal examination confirmed the prenatal findings and added the typical facial features of this syndrome, which consisted of prominent forehead, small nose with depressed nasal bridge, micrognathia and bow‐shaped mouth.

Conclusion

This case provides further evidence of a possible association between chromosomal aberrations in SCTs. Copyright © 2007 John Wiley & Sons, Ltd.
Proinflammatory macrophage migratory inhibition factor and interleukin‐6 are concentrated in pleural effusion of human fetuses with prenatal chylothorax
Authors: Chen Ming , Hsieh Chang‐Yao , Shih Jin‐Chung , Chou Chia‐Hung , Ma Gwo‐Chin , Chen Tze‐Ho , Lee Tsung‐Hsien , Tsai Horng‐Der , Cameron Alan D. , Chen Chih‐Ping
Published: February 2007

Objectives

To study the role of selected cytokines and growth factors involved in the pathogenesis of fetal chylous pleural effusion.

Methods

Seventeen fetuses with prenatal chylothorax at gestational age (GA) 17–29 weeks were enrolled as the study group during the period 2003–2005. Their pleural effusion (n = 17) and amniotic fluid (n = 17) were drawn when disease set in. Eleven fetuses received cordocentesis because of suspected fetal anemia. Forty‐one normal fetuses without adverse perinatal outcome at GA 17‐29 weeks received amniocentesis and were enrolled in the reference group. Levels of hepatocyte growth factor (HGF), stromal‐derived factor‐1(SDF‐1), vascular endothelial growth factor (VEGF), interleukin‐8 (IL‐8), macrophage migratory inhibition factor (MIF), and interleukin‐6 (IL‐6) were determined in the samples from both groups (amniotic fluid, pleural fluid, and cord blood from the study group and amniotic fluid from the reference group) by enzyme‐linked immunoassay (EIA).

Results

No significant differences were observed in the amniotic fluids between the study group and the reference group regarding levels of IL‐6, IL‐8, MIF, SDF‐1, HGF and VEGF. In the study group, levels of IL‐8, VEGF and SDF‐1 (all pro‐angiogenic) showed no significant differences between the amniotic fluid, cord blood and pleural effusion. The level of HGF (proangiogenic) was significantly higher in the amniotic fluid than in the cord blood or the pleural effusion, but there were no significant differences between the levels in the pleural fluid and in the cord blood. Interestingly, the levels of MIF and IL‐6 (both are proinflammatory) in the amniotic fluid and in the pleural effusion were much higher than the levels in the cord blood.

Conclusion

Our study demonstrated that the levels of pro‐inflammatory proteins (MIF and IL‐6) that we tested were higher in the fetal pleural effusion than in the fetal circulation, a phenomenon not observed in the levels of proangiogenic proteins (HGF, SDF‐1, VEGF, IL‐8). This result implies that inflammation‐related proteins may be more relevant than the angiogenesis‐related proteins in the local environment of accumulating pleural effusion, a prominent feature of prenatal chylothorax. Copyright © 2007 John Wiley & Sons, Ltd.
Culturally competent school assessment: Performance measures of personality
Authors: Dana Richard
Published: February 2007

Performance measures of personality—narratives, Rorschach, and drawing techniques—provide continuing comprehensive assessment resources for school psychologists. These measures are examined for assets, limitations, and applications consistent with a new practice model for culturally competent school‐based services. Cultural competency is informed by a generic training model and illustrated by contents of a public sector California training program. Expanding cultural competency training opportunities in all school psychology programs can integrate assessment, intervention, and outcome evaluations using performance measures within a context of guidelines and ethical responsibilities. © 2007 Wiley Periodicals, Inc. Psychol Schs 44: 229–241, 2007.
Integration of psychological assessment approaches in school psychology
Authors: Riccio Cynthia A. , Rodriguez Olga L.
Published: February 2007

There are multiple existing and emerging models and methods of psychological assessment derived from a variety of theoretical or empirical perspectives. Integration of information relating to personality, behavior, and social‐emotional competence as part of the psychological assessment with psychoeducational data can better inform service delivery and the outcomes of the children and families served. The various models and methods of psychological assessment used by school psychologists are reviewed in this article. The advantages and complexities of integrating information using actuarial and clinical judgment are explored. Finally, a discussion and model of how psychological and psychoeducational data can be used to aid in the understanding of the child and facilitate intervention planning is provided. © 2007 Wiley Periodicals, Inc. Psychol Schs 44: 243–255, 2007.
Current status of Rorschach assessment: Implications for the school psychologist
Authors: Hughes Tammy L. , Gacono Carl B. , Owen Patrick F.
Published: February 2007

In this article we examine the current status of Rorschach assessment. School psychologists are provided with an introduction to the Rorschach Inkblot Method (RIM), the types of information that the test provides, and guidelines for evaluating the RIM. We also address criticisms that have served to discourage the use of the RIM. When administered, coded, and interpreted within guidelines provided by Exner's Comprehensive System, the Rorschach clearly meets ethical and professional standards for psychological test usage. The RIM can provide unique and important information concerning the emotional and social functioning of children and adolescents that aids in developing individualized educational programming including behavior intervention plans. © 2007 Wiley Periodicals, Inc. Psychol Schs 44: 281–291, 2007.
Therapeutic assessment with a child as a family intervention: A clinical and research case study
Authors: Tharinger Deborah J. , Finn Stephen E. , Wilkinson Alison D. , Schaber Pamela McDonald
Published: February 2007

Psychological assessment has the potential to impact positively both those individuals being assessed and the systems in which they are embedded (e.g., families and schools). Therapeutic Assessment (TA) is a relatively new paradigm that uses collaborative psychological assessment to address consumers' questions of interest and promote positive change. TA with children aims to impact the parents, the child, and their relationship and to date has been used primarily in clinics and independent practices, with some auxiliary involvement of schools. This article draws from the first research project investigating the efficacy of TA with children and families. Clients were referred from the waiting list of a community mental health center, and TA was provided in a university clinic setting. First, excerpts from a TA “report” with a child are presented. Next, the theoretical underpinnings and research on TA are discussed, as well as the protocol for using TA with children and families. Finally, a detailed clinical case study is presented, with outcome measures indicating high acceptability and satisfaction, decreased child symptomatology, improved hope and self‐esteem, and enhanced parental efficacy. Yet to be explored is the effectiveness of comprehensive TA in the schools, where the target of intervention could also include teachers, organizational aspects of schools, and parent‐school collaboration. Until that time, suggestions are provided for implementing techniques of TA—as currently conceptualized—within schools. © 2007 Wiley Periodicals, Inc. Psychol Schs 44: 293–309, 2007.
Quantitative proteomic analysis of rat liver for carcinogenicity prediction in a 28‐day repeated dose study
Authors: Yamanaka Hidenori , Yakabe Yoshikuni , Saito Koichi , Sekijima Masaru , Shirai Tomoyuki
Published: February 2007

The potential of quantitative proteomic analysis to predict carcinogenicity of chemical compounds was investigated. Using 2D‐DIGE, we analyzed the effects of 63 chemical compounds on protein expression in the rat liver after 28 daily doses. Types of carcinogens were categorized depending on the species and organ specificity. The carcinogen characteristic proteins for each classification were identified by Welch's t value. For evaluation of the predictive concordance we used support vector machines. The rat hepatic carcinogen‐specific classification gave higher concordance than the other classification. The generalization performance was measured by leave‐one‐out cross‐validation. For genotoxic and non‐genotoxic compounds, a concordance of 79.3 and 76.5%, respectively, was obtained by the top 30 ranked proteins with Welch's t value. Furthermore, we found that the increase of the expression level of the stress response proteins as the common feature of poorly predicted chemical compounds in the leave‐20%‐out cross‐validation. Quantitative proteomics could be promising technique for developing biomarker panels that can be used for carcinogenicity prediction. The list of proteins identified in this study and the zoomed gel images of the top ranked proteins in statistic analysis are provided in Supplementary Data.
Development and validation of a spectral library searching method for peptide identification from MS/MS
Authors: Lam Henry , Deutsch Eric W. , Eddes James S. , Eng Jimmy K. , King Nichole , Stein Stephen E. , Aebersold Ruedi
Published: February 2007

A notable inefficiency of shotgun proteomics experiments is the repeated rediscovery of the same identifiable peptides by sequence database searching methods, which often are time‐consuming and error‐prone. A more precise and efficient method, in which previously observed and identified peptide MS/MS spectra are catalogued and condensed into searchable spectral libraries to allow new identifications by spectral matching, is seen as a promising alternative. To that end, an open‐source, functionally complete, high‐throughput and readily extensible MS/MS spectral searching tool, SpectraST, was developed. A high‐quality spectral library was constructed by combining the high‐confidence identifications of millions of spectra taken from various data repositories and searched using four sequence search engines. The resulting library consists of over 30 000 spectra for Saccharomyces cerevisiae. Using this library, SpectraST vastly outperforms the sequence search engine SEQUEST in terms of speed and the ability to discriminate good and bad hits. A unique advantage of SpectraST is its full integration into the popular Trans Proteomic Pipeline suite of software, which facilitates user adoption and provides important functionalities such as peptide and protein probability assignment, quantification, and data visualization. This method of spectral library searching is especially suited for targeted proteomics applications, offering superior performance to traditional sequence searching.
A proteomic investigation of glomerular podocytes from a Denys‐Drash Syndrome patient with a mutation in the Wilms tumour suppressor gene WT1
Authors: Viney Rebecca L. , Morrison Avril A. , van den Heuvel Lambert P. , Ni Lan , Mathieson Peter W. , Saleem Moin A. , Ladomery Michael R.
Published: February 2007

Glomerular podocytes are essential for blood filtration in the kidney underpinned by their unique cytoskeletal morphology. An increasing number of kidney diseases are being associated with key podocyte abnormalities. The Wilms tumour suppressor gene (WT1) encodes a zinc finger protein with a crucial role in normal kidney development; and in the adult, WT1 is required for normal podocyte function. Denys‐Drash Syndrome (DDS) results from mutations affecting the zinc finger domain of WT1. The aim of this study was to undertake, for the first time, a proteomic analysis of cultured human podocytes; and to analyse the molecular changes in DDS podocytes. The morphology of DDS podocytes was highly irregular, reminiscent of a fibroblastic appearance. A reference 2‐D gel was generated, and 75 proteins were identified of which 43% involved in cytoskeletal architecture. The DDS and wild‐type proteomes were compared by 2‐D DIGE. The level of 95.6% of proteins was unaltered; but 4.4% were altered more than two‐fold. A sample of proteins involved in cytoskeletal architecture appeared to be misexpressed in DDS podocytes. Consistent with this finding, overall levels of filamentous actin also appeared reduced in DDS podocytes. We conclude that one of WT1 functions in podocytes is to regulate the expression of key components and regulators of the cytoskeleton.
Identification of aluminum‐responsive proteins in rice roots by a proteomic approach: Cysteine synthase as a key player in Al response
Authors: Yang Qiaosong , Wang Yuqi , Zhang Jianjun , Shi Weiping , Qian Chunmei , Peng Xinxiang
Published: February 2007

Aluminum (Al) toxicity is a serious limitation to worldwide crop production. Rice is one of the most Al‐tolerant crops and also serves as an important monocot model plant. This study aims to identify Al‐responsive proteins in rice, based on evidence that Al resistance is an inducible process. Two Al treatment systems were applied in the study: Al3+‐containing simple Ca solution culture and Al3+‐containing complete nutrient solution culture. Proteins prepared from rice roots were separated by 2‐DE. The 2‐DE patterns were compared and the differentially expressed proteins were identified by MS. A total of 17 Al‐responsive proteins were identified, with 12 of those being up‐regulated and 5 down‐regulated. Among the up‐regulated proteins are copper/zinc superoxide dismutase (Cu‐Zn SOD), GST, and S‐adenosylmethionine synthetase 2, which are the consistently known Al‐induced enzymes previously detected at the transcriptional level in other plants. More importantly, a number of other identified proteins including cysteine synthase (CS), 1‐aminocyclopropane‐1‐carboxylate oxidase, G protein β subunit‐like protein, abscisic acid‐ and stress‐induced protein, putative Avr9/Cf‐9 rapidly elicited protein 141, and a 33 kDa secretory protein are novel Al‐induced proteins. Most of these proteins are functionally associated with signaling transduction, antioxidation, and detoxification. CS, as consistently detected in both Al stress systems, was further validated by Western blot and CS activity assays. Moreover, the metabolic products of CS catalysis, i.e. both the total glutathione pool and reduced glutathione, were also significantly increased in response to Al stress. Taken together, our results suggest that antioxidation and detoxification ultimately related to sulfur metabolism, particularly to CS, may play a functional role in Al adaptation for rice.
The proteome and transcriptome analysis of Bacillus subtilis in response to salicylic acid
Authors: Van Duy Nguyen , Mäder Ulrike , Tran Ngoc Phuong , Cavin Jean‐François , Tam Le Thi , Albrecht Dirk , Hecker Michael , Antelmann Haike
Published: February 2007

Phenolic acids that are present in plant–soil ecosystems can be considered as toxins which induce specific stress responses in microorganisms. In this paper, we have analyzed the global response of the soil bacterium Bacillus subtilis to salicylic acid using proteomics and transcriptomics. The results demonstrate that salicylic acid caused predominantly the induction of the SigmaB‐dependent general stress response in B. subtilis which is not related to the acidic conditions. Treatment of B. subtilis with growth‐inhibitory concentrations of 4 mM salicylic acid caused protein damage in B. subtilis as reflected by the induction of the CtsR and Spx regulons. Both phenolic acid decarboxylases (pads) of B. subtilis padC and bsdBCD (yclBCD) were induced by 4 mM salicylic acid that were previously shown to be involved in decarboxylation and detoxification of different phenolic acids. Deletion of the putative LysR‐type regulator encoded by the divergently transcribed bsdA (yclA) gene upstream of the bsdBCD operon revealed that BsdA is the transcriptional activator of bsdBCD expression in response to salicylic acid. Phenotype analysis of bsdA and padC single and double mutants demonstrated that both pads confer resistance to salicylic acid in B. subtilis.
Automated reporting from gel‐based proteomics experiments using the open source Proteios database application
Authors: Levander Fredrik , Krogh Morten , Wårell Kristofer , Gärdén Per , James Peter , Häkkinen Jari
Published: February 2007

The assembly of data from different parts of proteomics workflow is often a major bottleneck in proteomics. Furthermore, there is an increasing demand for the publication of details about protein identifications due to the problems with false‐positive and false‐negative identifications. In this report, we describe how the open‐source Proteios software has been expanded to automate the assembly of the different parts of a gel‐based proteomics workflow. In Proteios it is possible to generate protein identification reports that contain all the information currently required by proteomics journals. It is also possible for the user to specify maximum allowed false positive ratios, and reports are automatically generated with the corresponding score cut‐offs calculated. When protein identification is conducted using multiple search engines, the score thresholds that correlate to the predetermined error rate are also explicitly calculated for proteins that appear on the result lists of more than one search engine.
Comparison of cytochromes b5 from insects and vertebrates
Authors: Wang Lijun , Cowley Aaron B. , Terzyan Simon , Zhang Xuejun , Benson David R.
Published: February 2007

We report a 1.55 Å X‐ray crystal structure of the heme‐binding domain of cytochrome b5 from Musca domestica (house fly; HF b5), and compare it with previously published structures of the heme‐binding domains of bovine microsomal cytochrome b5 (bMc b5) and rat outer mitochondrial membrane cytochrome b5 (rOM b5). The structural comparison was done in the context of amino acid sequences of all known homologues of the proteins under study. We show that insect b5s contain an extended hydrophobic patch at the base of the heme binding pocket, similar to the one previously shown to stabilize mammalian OM b5s relative to their Mc counterparts. The hydrophobic patch in insects includes a residue with a bulky hydrophobic side chain at position 71 (Met). Replacing Met71 in HF b5 with Ser, the corresponding residue in all known mammalian Mc b5s, is found to substantially destabilize the holoprotein. The destabilization is a consequence of two related factors: (1) a large decrease in apoprotein stability and (2) extension of conformational disruption in the apoprotein beyond the empty heme binding pocket (core 1) and into the heme‐independent folding core (core 2). Analogous changes have previously been shown to accompany replacement of Leu71 in rOM b5 with Ser. That the stabilizing role of Met71 in HF b5 is manifested primarily in the apo state is highlighted by the fact that its crystallographic Cα B factor is modestly larger than that of Ser71 in bMc b5, indicating that it slightly destabilizes local polypeptide conformation when heme is in its binding pocket. Finally, we show that the final unit of secondary structure in the cytochrome b5 heme‐binding domain, a 310 helix known as α6, differs substantially in length and packing interactions not only for different protein isoforms but also for given isoforms from different species. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Analysis of chameleon sequences and their implications in biological processes
Authors: Guo Jun‐Tao , Jaromczyk Jerzy W. , Xu Ying
Published: February 2007

Chameleon sequences have been implicated in amyloid related diseases. Here we report an analysis of two types of chameleon sequences, chameleon‐HS (Helix vs. Strand) and chameleon‐HE (Helix vs. Sheet), based on known structures in Protein Data Bank. Our survey shows that the longest chameleon‐HS is eight residues while the longest chameleon‐HE is seven residues. We have done a detailed analysis on the local and global environment that might contribute to the unique conformation of a chameleon sequence. We found that the existence of chameleon sequences does not present a problem for secondary structure prediction programs, including the first generation prediction programs, such as Chou–Fasman algorithm, and the third generation prediction programs that utilize evolution information. We have also investigated the possible implication of chameleon sequences in structural conservation and functional diversity of alternatively spliced protein isoforms. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Possible anxiolytic effect of two extracts of Passiflora quadrangularis L. in experimental models
Authors: de Castro Pollyanna Celso F. , Hoshino Alberto , Silva Jair Campos da , Mendes Fúlvio Rieli
Published: February 2007

Several species of the genus Passiflora, known in Brazil as ‘maracujá’, have widespread use in folk medicine as sedatives and anxiolytics. The anxiolytic activities of aqueous and hydroalcohol extracts of Passiflora quadrangularis leaves were evaluated using the elevated plus‐maze, open field and holeboard tests. The hydroalcohol extract presented results suggestive of anxiolytic activity in dosages around 100, 250 and 500 mg/kg, as expressed by elevation of the time spent on the open arms in the plus‐maze; a decrease of freezing and an increase of deambulation and rearing in the open field test. The hydroalcohol extract showed results similar to diazepam on the holeboard. No positive results were found for the aqueous extract. Copyright © 2007 John Wiley & Sons, Ltd.
Shilajit: a review
Authors: Agarwal Suraj P. , Khanna Rajesh , Karmarkar Ritesh , Anwer Md. Khalid , Khar Roop K.
Published: February 2007

Shilajit is a pale‐brown to blackish‐brown exudation, of variable consistency, exuding from layers of rocks in many mountain ranges of the world, especially the Himalayas and Hindukush ranges of the Indian subcontinent. It has been found to consist of a complex mixture of organic humic substances and plant and microbial metabolites occurring in the rock rhizospheres of its natural habitat. Shilajit has been used as a rejuvenator and an adaptogen for thousands of years, in one form or another, as part of traditional systems of medicine in a number of countries. Many therapeutic properties have been ascribed to it, a number of which have been verified by modern scientific evaluation. Shilajit has been attributed with many miraculous healing properties. Copyright © 2007 John Wiley & Sons, Ltd.
New approach in asthma treatment using excitatory modulator
Authors: Hoang Ba X. , Shaw D. Graeme , Levine Stephen , Hoang Cuong , Pham Phuong
Published: February 2007

The impact of a herbal extract with excitatory modulator activity in the management of asthma was studied. An open and selective 3‐year follow‐up of 14 chronic refractory asthmatics aged between 22 and 70 was used. Participants received an extract of Sophora flavescens Ait. Medication use, a diary card of symptoms and respiratory function were recorded. The study was retrospective and all patients gave written informed consent. The quality of life, clinical symptoms and respiratory function improved during all periods of measurement. The use of inhaled corticosteroid and β‐agonists were reduced or eliminated. There were no significant adverse reactions reported. Therefore the extract of S. flavescens as an excitatory modulator appears to be a safe and may be an effective alternative treatment for refractory chronic asthma. Copyright © 2007 John Wiley & Sons, Ltd.
Ursolic acid: a potent Inhibitor of superoxides produced in the cellular system
Authors: Ali Muhammad S. , Ibrahim Syed A. , Jalil Saima , Choudhary Muhammad I.
Published: February 2007

Triterpenoids of ursane class: ursolic acid, ilelatifol D, corosolic acid and euscaphic acid were isolated for the first time from Leonurus cardiaca, a member of the family Lamiaceae. The isolated compounds were tested for their cell‐based antiinflammatory potential by suppressing respiratory burst activity and superoxide scavenging property by using xanthine/xanthine oxidase system to produce superoxides in the cell‐free system. Ursolic acid was found to be an excellent inhibitor for the superoxides produced in the cellular system, while the same was inactive in the superoxide scavenging activity in cell‐free system. Copyright © 2007 John Wiley & Sons, Ltd.
Wound healing activity of root extracts of Berberis lyceum royle in rats
Authors: Asif A. , Kakub G. , Mehmood S. , Khunum R. , Gulfraz M.
Published: February 2007

The wound healing activities of the aqueous and methanol extracts of the root of Berberis lyceum were assessed using incision, excision and dead wound space models of wound repair in rats. After application of both extracts it was observed that the area of epithelialization increased, followed by an increase in wound contraction, skin breaking strength, tissue granulation, dry weight and hydroxyproline content. Histopathological studies of the granulation tissue also indicated that there was an increase in collagen formation in those rats treated with the methanol extract, compared with the control group animals. The methanol extract was more effective than the aqueous extract, but both showed significant results compared with the control. Copyright © 2007 John Wiley & Sons, Ltd.
Method development aspects for the quantitation of pharmaceutical compounds in human plasma with a matrix‐assisted laser desorption/ionization source in the multiple reaction monitoring mode
Authors: Kovarik Peter , Grivet Chantal , Bourgogne Emmanuel , Hopfgartner Gérard
Published: February 2007

The present work investigates various method development aspects for the quantitative analysis of pharmaceutical compounds in human plasma using matrix‐assisted laser desorption/ionization and multiple reaction monitoring (MALDI‐MRM). Talinolol was selected as a model analyte. Liquid‐liquid extraction (LLE) and protein precipitation were evaluated regarding sensitivity and throughput for the MALDI‐MRM technique and its applicability without and with chromatographic separation. Compared to classical electrospray liquid chromatography/mass spectrometry (LC/ESI‐MS) method development, with MALDI‐MRM the tuning of the analyte in single MS mode is more challenging due to interfering matrix background ions. An approach is proposed using background subtraction. With LLE and using a 200 µL human plasma aliquot acceptable precision and accuracy could be obtained in the range of 1 to 1000 ng/mL without any LC separation. Approximately 3 s were required for one analysis. A full calibration curve and its quality control samples (20 samples) can be analyzed within 1 min. Combining LC with the MALDI analysis allowed improving the linearity down to 50 pg/mL, while reducing the throughput potential only by two‐fold. Matrix effects are still a significant issue with MALDI but can be monitored in a similar way to that used for LC/ESI‐MS analysis. Copyright © 2007 John Wiley & Sons, Ltd.
Mass spectral studies of native and mass‐labeled perfluorooctanesulfonamides
Authors: Arsenault Gilles , Chittim Brock , McAlees Alan , McCrindle Robert , Potter Dave , Tashiro Colleen , Yeo Brian
Published: February 2007

This work examines the mass spectra of several environmentally relevant amides, perfluorooctanesulfonamide (FOSA), NMeFOSA, NEtFOSA, and NMe2FOSA, under electron ionization conditions. A previous mass spectral study of FOSA and NEtFOSA led the authors to propose possible structures for some of the fragment ions and fragmentation pathways that might explain their formation. In the present communication, further fragment ions are identified for these two compounds and alternative fragmentation pathways proposed. Mass spectral analyses of NMeFOSA and NMe2FOSA and of mass‐labeled NMeFOSA and NEtFOSA reinforce our conclusions about potential fragmentation pathways for these amides and the fragment ions expected. The mass spectral data presented here will help chemists to identify signals found in a gas chromatographic/mass spectrometric (GC/MS) analysis that stem from these perfluoroalkylsulfonamides. Copyright © 2007 John Wiley & Sons, Ltd.
Comparison of a two‐dimensional liquid chromatography/mass spectrometry approach with a chip‐based nanoelectrospray device for structural elucidation of metabolites in a human ADME study using a quadrupole time‐of‐flight mass spectrometer
Authors: Trunzer Markus , Graf Daniel , Kiffe Michael
Published: February 2007

The study of the metabolic fate of drugs is essential for the safety assessment of new compounds in the drug development process. However, the characterization and structural elucidation of metabolites from in vivo experiments is still a very challenging task. In this paper, we compare a two‐dimensional liquid chromatography/mass spectrometry (LC/MS) approach using either a capillary LC/MS system or the recently introduced chip‐based nanoelectrospray/MS system (Nanomate®) as the second dimension for structural elucidation of metabolites by MS. More than 30 radioactive fractions of a chromatographic separation from a human urine sample were analyzed and 54 metabolites could be identified. The long persisting and stable nanoelectrospray enabled the search for unknown metabolites by precursor‐ion scanning experiments followed by product‐ion scanning experiments of potential metabolites using a quadrupole time‐of‐flight (qTOF) mass spectrometer. The number of fragments produced by nanoelectrospray with product‐ion scanning was significantly higher compared to LC/MS experiments with in‐source fragmentation. Therefore, the assignment of possible modifications in metabolites to certain moieties of the drug could be investigated with higher accuracy. The capillary LC/MS system for the second dimension was more sensitive in the case of low abundant metabolites. These metabolites could not be detected by direct nanoelectrospray infusion, which limits the application of the Nanomate for trace metabolites. Copyright © 2007 John Wiley & Sons, Ltd.
Understanding HSV‐1 entry glycoproteins
Authors: Reske Adi , Pollara Gabriele , Krummenacher Claude , Chain Benjamin M. , Katz David R.
Published: February 2007

Herpes Simplex Virus‐1 is a common infectious agent, but the precise detail of entry and infection of cells has only now begun to be clarified. Four viral surface glycoproteins (gB, gD, gH and gL) are required. This review summarises the known structure and function of each of these essential viral envelope glycoproteins, and explores what is known about their close cooperation with each other in mediating cellular membrane fusion. It is suggested that, following gD binding to one of its entry receptors, membrane fusion is mediated by gB and the heterodimer gH/gL. Significantly, these four entry glycoproteins also play a key role in the interaction between HSV and the host immune system. The glycoproteins serve an important role as targets of adaptive immunity. However, recent studies have demonstrated that the same proteins also play a key role in initiating the early innate immune response to HSV. Understanding the complex functions of these HSV proteins may be essential for successful development of vaccines for HSV. Copyright © 2007 John Wiley & Sons, Ltd.
A Self‐Consistent Bathymetric Mapping Algorithm
Authors: Roman Chris , Singh Hanumant
Published: February 2007

The achievable accuracy of bathymetric mapping in the deep ocean using robotic systems is most often limited by the available guidance or navigation information used to combine the measured sonar ranges during the map making process. This paper presents an algorithm designed to mitigate the affects of poor ground referenced navigation by applying the principles of map registration and pose filtering commonly used in simultaneous localization and mapping (SLAM) algorithms. The goal of the algorithm is to produce a self‐consistent point cloud representation of the bottom terrain with errors that are on a scale similar to the sonar range resolution rather than any direct positioning measurement. The presented algorithm operates causally and utilizes sensor data that are common to instrumented underwater robotic vehicles used for mapping and scientific explorations. Real world results are shown for data taken on several expeditions with the JASON remotely operated vehicle (ROV). Comparisons are made between more standard mapping approaches and the proposed method is shown to significantly improve the map quality and reveal scene information that would have otherwise been obscured due to poor direct navigation information. © 2007 Wiley Periodicals, Inc.
Real‐Time SLAM with Octree Evidence Grids for Exploration in Underwater Tunnels
Authors: Fairfield Nathaniel , Kantor George , Wettergreen David
Published: February 2007

We describe a simultaneous localization and mapping (SLAM) method for a hovering underwater vehicle that will explore underwater caves and tunnels, a true three‐dimensional (3D) environment. Our method consists of a Rao‐Blackwellized particle filter with a 3D evidence grid map representation. We describe a procedure for dynamically adjusting the number of particles to provide real‐time performance. We also describe how we adjust the particle filter prediction step to accommodate sensor degradation or failure. We present an efficient octree data structure that makes it feasible to maintain the hundreds of maps needed by the particle filter to accurately model large environments. This octree structure can exploit spatial locality and temporal shared ancestry between particles to reduce the processing and storage requirements. To test our SLAM method, we utilize data collected with manually deployed sonar mapping vehicles in the Wakulla Springs cave system in Florida and the Sistema Zacato´n in Mexico, as well as data collected by the DEPTHX vehicle in the test tank at the Austin Applied Research Laboratory. We demonstrate our mapping and localization approach with these real‐world datasets. © 2007 Wiley Periodicals, Inc.
Dense 3D Map Construction for Indoor Search and Rescue
Authors: Ellekilde Lars‐Peter , Huang Shoudong , Valls Miró Jaime , Dissanayake Gamini
Published: February 2007

The main contribution of this paper is a new simultaneous localization and mapping (SLAM) algorithm for building dense three‐dimensional maps using information acquired from a range imager and a conventional camera, for robotic search and rescue in unstructured indoor environments. A key challenge in this scenario is that the robot moves in 6D and no odometry information is available. An extended information filter (EIF) is used to estimate the state vector containing the sequence of camera poses and some selected 3D point features in the environment. Data association is performed using a combination of scale invariant feature transformation (SIFT) feature detection and matching, random sampling consensus (RANSAC), and least square 3D point sets fitting. Experimental results are provided to demonstrate the effectiveness of the techniques developed. © 2007 Wiley Periodicals, Inc.
Graphical SLAM for Outdoor Applications
Authors: Folkesson John , Christensen Henrik I.
Published: February 2007

Application of SLAM outdoors is challenged by complexity, handling of nonlinearities, and flexible integration of a diverse set of features. A graphical approach to SLAM is introduced that enables flexible data‐association. The method allows for handling of nonlinearities. The method also enables easy introduction of global constraints. Computational issues can be addressed as a graph reduction problem. A complete framework for graphical based SLAM is presented. The framework is demonstrated for a number of outdoor experiments using an ATRV robot equipped with a SICK laser scanner and a Cross‐Bow Inertial Unit. The experiments include handling of large outdoor environments with loop closing. The presented system operates at 5 Hz on a 800 MHz computer. © 2007 Wiley Periodicals, Inc.
SLAM with Panoramic Vision
Authors: Lemaire Thomas , Lacroix Simon
Published: February 2007

This article presents an approach to SLAM that takes advantage of panoramic images. Landmarks are interest points detected and matched in the images and mapped according to a bearings‐only SLAM approach. As they are acquired and processed, the panoramic images are also indexed and stored into a database. A database query procedure, independent of the robot and landmark position estimates, is able to detect loop closures by retrieving memorized images that are close to the current robot position. The bearings‐only estimation process is described, and results over a trajectory of a few hundreds of meters are presented and discussed. © 2007 Wiley Periodicals, Inc.
Building a Robust Implementation of Bearing‐only Inertial SLAM for a UAV
Authors: Bryson Mitch , Sukkarieh Salah
Published: February 2007

This paper presents the on‐going design and implementation of a robust inertial sensor based simultaneous localization and mapping (SLAM) algorithm for an unmanned aerial vehicle (UAV) using bearing‐only observations. A single color vision camera is used to observe the terrain from which image points corresponding to features in the environment are extracted. The SLAM algorithm estimates the complete six degrees‐of‐freedom motion of the UAV along with the three‐dimensional position of the features in the environment. An extended Kalman filter approach is used where a technique of delayed initialization is performed to initialize the three‐dimensional position of features from bearing‐only observations. Data association is achieved using a multihypothesis innovation gate based on the spatial uncertainty of each feature. Results are presented by running the algorithm off‐line using inertial sensor and vision data collected during a flight test of a UAV. © 2007 Wiley Periodicals, Inc.