bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractIn 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

AbstractThis 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

AbstractA 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

AbstractObjectiveClinical 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.MethodsA 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.ResultsThe 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.ConclusionThis 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

AbstractObjectivesTo study the role of selected cytokines and growth factors involved in the pathogenesis of fetal chylous pleural effusion.MethodsSeventeen 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).ResultsNo 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.ConclusionOur 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

AbstractPerformance 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

AbstractThere 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

AbstractIn 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

AbstractPsychological 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

AbstractThe 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

AbstractA 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

AbstractGlomerular 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

AbstractAluminum (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

AbstractPhenolic 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

AbstractThe 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.