bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Petrov‐Galerkin method with quadrature for semi‐linear second‐order hyperbolic problems
Authors: Bialecki B. , Ganesh M. , Mustapha K. 
Published: January 2006

AbstractWe propose and analyze a Crank–Nicolson quadrature Petrov–Galerkin (CNQPG) ${\cal C}^2$‐spline method for solving semi‐linear second‐order hyperbolic initial‐boundary value problems. We prove second‐order convergence in time and optimal order H2 norm convergence in space for the CNQPG scheme that requires only linear algebraic solvers. We demonstrate numerically optimal order Hk, k = 0,1,2, norm convergence of the scheme for some test problems with smooth and nonsmooth nonlinearities. © 2006 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2006
Collagen/chitosan‐silicone membrane bilayer scaffold as a dermal equivalent
Authors: Shi Yanchao , Ma Lie , Zhou Jie , Mao Zhengwei , Gao Changyou 
Published: January 2006

AbstractA bilayer dermal equivalent was fabricated by combining the collagen/chitosan porous scaffold with a silicone membrane. The macroscopic shapes and microstructures of the collagen/chitosan scaffolds with or without silicone membrane were illustrated. Water‐uptake was characterized by the phosphate buffered saline (PBS)‐immersion test. It was found that the glutaraldehyde treated scaffold had a higher water‐uptake ratio than that of the thermal treatment. The water vapor permeability of the bilayer dermal equivalent was tested under different humidities at room temperature. The results proved that the water vapor permeability of this bilayer dermal equivalent was close to normal adult skin. Investigation of the mechanical performance found that the bilayer dermal equivalent had a tensile stress of 0.1 MPa and a strain of 30% in the wet state. In vitro cell culture demonstrated that the bilayer dermal equivalent presented in this study did not show any cytotoxicity. Copyright © 2006 John Wiley & Sons, Ltd.
Characterization on polystyrene/zinc oxide nanocomposites prepared from solution mixing
Authors: Chae Dong Wook , Kim Byoung Chul 
Published: January 2006

AbstractPolystyrene (PS)/zinc oxide (ZnO) nanocomposites were prepared by solution mixing, followed by film casting. The effects of ZnO nanoparticles on the physical properties of PS were investigated. Transmission electron microscopy (TEM) and field emission scanning electron microscopy (FESEM) showed that ZnO nanoparticles were homogeneously dispersed in the PS matrix. The introduction of 5 wt% ZnO increased slightly the glass transition temperature by 2.3°C. Thermal gravimetric analysis thermograms showed that the thermal stability of PS was enhanced with increasing ZnO content. Neither shift nor sharpening of absorption band was detected by infrared spectra. ZnO nanoparticles had little effect on the wide‐angle X‐ray diffraction (WAXD) pattern of PS. The transmittance of ultraviolet light was decreased with increasing ZnO content. PS/ZnO nanocomposites exhibited a small reduction in tensile strength and elongation to break. However, a significant enhancement in tensile modulus was achieved when 5 wt% ZnO was introduced. In the FESEM images of the tensile fractured surface, localized plastic deformation was observed for PS, while the site from which ZnO was pulled out was usually observed in the nanocomposites. Copyright © 2006 John Wiley & Sons, Ltd.
Preparation and characterization of optically active polymers containing pendent and terminal chiral units via atom transfer radical polymerization
Authors: Xu Wenjian , Zhu Xiulin , Zhu Jian , Cheng Zhenping 
Published: January 2006

AbstractOptically active homopolymers and copolymers, bearing chiral units at the side chain and end chain, were prepared via atom transfer radical polymerization (ATRP) techniques. The well‐defined optically active polymers were obtained via the ATRP of pregnenolone methacrylate (PR‐MA), β‐cholestanol acrylate (CH‐A), and 20‐(hydroxymethyl)‐pregna‐1,4‐dien‐3‐one acrylate (HPD‐A) with ethyl 2‐bromopropionate as the initiator and CuBr/N,N,N′,N″,N″‐pentamethyldiethylenetriamine as the catalytic system. The experimental results showed that the polymerizations of PR‐MA, CH‐A, and HPD‐A proceeded in a living fashion, providing pendent chiral group polymers with low molecular weight distributions and predetermined molecular weights that increased linearly with the monomer conversion. Furthermore, the copolymers poly(pregnenolone methacrylate)‐b‐poly[(dimethylamino)ethyl methacrylate] and poly(pregnenolone methacrylate‐co‐methyl methacrylate) were synthesized and characterized with 1H NMR, transmission electron microscopy, and polarimetric analysis. In addition, when optically active initiators estrone 2‐bromopropionate and 20‐(hydroxymethyl)‐pregna‐1,4‐dien‐3‐one 2‐bromopropionate were used for ATRPs of methyl methacrylate and styrene, terminal optically active poly(methyl methacrylate) and polystyrene were obtained. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 1502–1513, 2006
Organizational factors that influence safety
Authors: Killimett Patrick 
Published: January 2006

AbstractFor the past 20 years the author and his associates have worked with over 1600 organizations to improve safety performance. In the course of this work, we have discovered that organizations optimize their efforts when they provide and support strong roles at each of three levels: the front‐line employee, supervisory, and senior manager levels. These three roles, when appropriately engaged, make up a cord of three strands that is not easily broken.Of these three areas, the leadership role has proved not only to have the greatest impact on safety improvement but also the most complex to understand and influence. One striking example of this is seen in the study of sites using the same improvement methodology. Even when compared by industry, site size, and systems, some organizations achieve steady improvement whereas others consistently struggle. More than any other factor, the quality of the organization's leadership—in particular its influence on the organizational culture—determined the level of success achieved. By organizational culture we mean the shared common values that drive organizational performance, more commonly defined as “the way we do things here.” Culture applies to many areas of functioning, is generally unstated, in the background, and slow to change.Even though it is generally recognized that leadership is important to performance, the “how” of that leadership is often debated. What makes a leader effective at influencing and improving safety? What are the qualities of such a leader? What are the key tasks that a leader must perform to generate desired results?Although this paper focuses on these questions with respect to senior leaders, the principles discussed are applicable to all levels in the organization. © 2006 Behavior Science Technology, Inc. (BST), 2006
A time‐saving approach for separating and focusing on human factors checklist discussion questions
Authors: Vaughen Bruce K. 
Published: January 2006

AbstractThe approach proposed in this report saves valuable process hazards analysis (PHA) team meeting time by quantifying and helping to separate a usually nonquantifiable subject: important process safety–related human factors issues. A human factors checklist modeled after the CCPS checklist is used and analyzed in three steps. First, operations, maintenance, engineering, and management personnel fill out responses to a 106‐question human factors checklist, using numbers ranging from 1 (“Okay As Is”) to 5 (“Needs Work”). Second, simple analysis on each question provided question‐related averages and standard deviations. Third, histograms on these results help to identify the ranges and to reduce the number of questions discussed by the team. The questions that showed general agreement had either high or low relative scores with low standard deviations; the questions that showed either diverse interpretations or opinions had high standard deviations. This approach saves the costs associated with longer PHA team meeting times because the discussion focuses on specific questions (issues) instead of all of the checklist questions. © 2006 American Institute of Chemical Engineers Process Saf Prog, 2006
Engineering supply chains as systems
Authors: Hassan Mohsen M. D. 
Published: January 2006

AbstractIn recent years companies in various fields form supply chains to support them manage their products and services during their life‐cycles. A supply chain usually extends from the source of raw material to end customers, consists of many components, and performs many functions. The components and functions have to be integrated in order to manage the flow of material, information, and finances from the source of raw material to end customers efficiently and at minimum cost. Further, a supply chain has a life‐cycle that is associated with the life‐cycle of the product(s) it supports, exists in an environment that impacts it, is dynamic, and has a purpose and objectives. With such aspects, a supply chain might better realize its potentials if it is viewed and treated as a system. This paper demonstrates the characteristics of systems inherent in supply chains and their implications on their design, and the ability of the systems engineering approach to the design of systems to benefit their formation. © 2006 Wiley Periodicals, Inc. Syst Eng 9: 73–89, 2006
A study of valley winds using the MIUU meso‐scale model
Authors: Bergström Hans , Juuso Nikolaus 
Published: January 2006

AbstractHigh winds are sometimes found in low‐altitude terrain in mountain valleys. The reasons for this and the possibilities to find such sites from modelled wind fields are investigated. The higher‐order closure MIUU model developed at Uppsala University is used for a general study of channelling of winds in mountain valleys. The importance of length, width and depth of the valley is investigated. Comparisons are made with wind measurements. Copyright © 2006 John Wiley & Sons, Ltd.
Analytical modelling of wind speed deficit in large offshore wind farms
Authors: Frandsen Sten , Barthelmie Rebecca , Pryor Sara , Rathmann Ole , Larsen Søren , Højstrup Jørgen , Thøgersen Morten 
Published: January 2006

AbstractThe proposed model for the wind speed deficit in wind farms is analytical and encompasses both small wind farms and wind farms extending over large areas. As is often the need for offshore wind farms, the model handles a regular array geometry with straight rows of wind turbines and equidistant spacing between units in each row and equidistant spacing between rows. Firstly, the case with the flow direction being parallel to rows in a rectangular geometry is considered by defining three flow regimes. Secondly, when the flow is not in line with the main rows, solutions are suggested for the patterns of wind turbine units corresponding to each wind direction. The presentation is an outline of a model complex that will be adjusted and calibrated with measurements in the near future. Copyright © 2006 John Wiley & Sons, Ltd.
Cavum septum pellucidum and adhesio interthalamica in schizophrenia: an MRI study
Authors: Crippa José Alexandre de Souza , Zuardi Antonio Waldo , Busatto Geraldo F. , Sanches Rafael Faria , Santos Antonio Carlos , Araújo David , Amaro Edson , Hallak Jaime Eduardo Cecílio , Ng Virginia , McGuire Philip K. 
Published: January 2006

AbstractSeveral studies have independently suggested that patients with schizophrenia are more likely to have an enlarged cavum septum pellucidum (CSP) and an absent adhesio interthalamica (AI), respectively. However, neither finding has been consistently replicated and it is unclear whether there is an association between these two midline brain abnormalities. Thus, we compared the prevalence of absent AI and the prevalence, size and volume of CSP in 38 patients with schizophrenia and 38 healthy controls using magnetic resonance imaging (MRI). There were no between group differences in the presence or volume of CSP; however, an enlarged CSP was commoner among patients than controls. There was also a positive correlation between CSP ratings and volumes. No differences in the presence or absence of the AI were found between patients and controls; however, an absent AI was commoner in male patients with schizophrenia than females. There was absolutely no overlap between the presence of a large CSP and an absence of AI. In conclusion, our findings are in line with several case series and other MRI investigations that have shown a higher incidence of putatively developmental brain abnormalities in patients with schizophrenia, particularly in males, and support the neurodevelopmental model of this disorder.
Inferring global levels of alternative splicing isoforms using a generative model of microarray data
Authors: Shai Ofer , Morris Quaid D. , Blencowe Benjamin J. , Frey Brendan J. 
Published: January 2006

AbstractMotivation: Alternative splicing (AS) is a frequent step in metozoan gene expression whereby the exons of genes are spliced in different combinations to generate multiple isoforms of mature mRNA. AS functions to enrich an organism's proteomic complexity and regulates gene expression. Despite its importance, the mechanisms underlying AS and its regulation are not well understood, especially in the context of global gene expression patterns. We present here an algorithm referred to as the Generative model for the Alternative Splicing Array Platform (GenASAP) that can predict the levels of AS for thousands of exon skipping events using data generated from custom microarrays. GenASAP uses Bayesian learning in an unsupervised probability model to accurately predict AS levels from the microarray data. GenASAP is capable of learning the hybridization profiles of microarray data, while modeling noise processes and missing or aberrant data. GenASAP has been successfully applied to the global discovery and analysis of AS in mammalian cells and tissues.Results: GenASAP was applied to data obtained from a custom microarray designed for the monitoring of 3126 AS events in mouse cells and tissues. The microarray design included probes specific for exon body and junction sequences formed by the splicing of exons. Our results show that GenASAP provides accurate predictions for over one-third of the total events, as verified by independent RT–PCR assays.Contact: ofer@psi.toronto.eduSupplementary information:
Copying nodes versus editing links: the source of the difference between genetic regulatory networks and the WWW
Authors: Louzoun Yoram , Muchnik Lev , Solomon Sorin 
Published: January 2006

Abstract
We study two kinds of networks: genetic regulatory networks and the World Wide Web. We systematically test microscopic mechanisms to find the set of such mechanisms that optimally explain each networks' specific properties. In the first case we formulate a model including mainly random unbiased gene duplications and mutations. In the second case, the basic moves are website generation and rapid surf-induced link creation (/destruction). The different types of mechanisms reproduce the appropriate observed network properties. We use those to show that different kinds of networks have strongly system-dependent macroscopic experimental features. The diverging properties result from dissimilar node and link basic dynamics. The main non-uniform properties include the clustering coefficient, small-scale motifs frequency, time correlations, centrality and the connectivity of outgoing links. Some other features are generic such as the large-scale connectivity distribution of incoming links (scale-free) and the network diameter (small-worlds). The common properties are just the general hallmark of autocatalysis (self-enhancing processes), while the specific properties hinge on the specific elementary mechanisms.
Contact: louzouy@math.biu.ac.il
Supplementary information: Supplementary data are available at Bioinformatics Online.
Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression
Authors: Boeva Valentina , Regnier Mireille , Papatsenko Dmitri , Makeev Vsevolod 
Published: January 2006

Abstract
Motivation: Genomic sequences are highly redundant and contain many types of repetitive DNA. Fuzzy tandem repeats (FTRs) are of particular interest. They are found in regulatory regions of eukaryotic genes and are reported to interact with transcription factors. However, accurate assessment of FTR occurrences in different genome segments requires specific algorithm for efficient FTR identification and classification.
Results: We have obtained formulas for P-values of FTR occurrence and developed an FTR identification algorithm implemented in TandemSWAN software. Using TandemSWAN we compared the structure and the occurrence of FTRs with short period length (up to 24 bp) in coding and non-coding regions including UTRs, heterochromatic, intergenic and enhancer sequences of Drosophila melanogaster and Drosophila pseudoobscura. Tandems with period three and its multiples were found in coding segments, whereas FTRs with periods multiple of six are overrepresented in all non-coding segment. Periods equal to 5–7 and 11–14 were characteristic of the enhancer regions and other non-coding regions close to genes.
Availability: TandemSWAN web page, stand-alone version and documentation can be found at
Contacts: valeyo@imb.ac.ru
Supplementary information: Supplementary data are available at Bioinformatics online.
Using a state-space model with hidden variables to infer transcription factor activities
Authors: Li Zheng , Shaw Stephen M. , Yedwabnick Matthew J. , Chan Christina 
Published: January 2006

Abstract
Motivation: In a gene regulatory network, genes are typically regulated by transcription factors (TFs). Transcription factor activity (TFA) is more difficult to measure than gene expression levels are. Other models have extracted information about TFA from gene expression data, but without explicitly modeling feedback from the genes. We present a state-space model (SSM) with hidden variables. The hidden variables include regulatory motifs in the gene network, such as feedback loops and auto-regulation, making SSM a useful complement to existing models.
Results: A gene regulatory network incorporating, for example, feed-forward loops, auto-regulation and multiple-inputs was constructed with an SSM model. First, the gene expression data were simulated by SSM and used to infer the TFAs. The ability of SSM to infer TFAs was evaluated by comparing the profiles of the inferred and simulated TFAs. Second, SSM was applied to gene expression data obtained from Escherichia coli K12 undergoing a carbon source transition and from the Saccharomyces cerevisiae cell cycle. The inferred activity profile for each TF was validated either by measurement or by activity information from the literature. The SSM model provides a probabilistic framework to simulate gene regulatory networks and to infer activity profiles of hidden variables.
Availability: Supplementary data and Matlab code will be made available at the URL below.
Contact: krischan@egr.msu.edu
Supplementary information:
Optimized multilayer perceptrons for molecular classification and diagnosis using genomic data
Authors: Wang Zuyi , Wang Yue , Xuan Jianhua , Dong Yibin , Bakay Marina , Feng Yuanjian , Clarke Robert , Hoffman Eric P. 
Published: January 2006

Abstract
Motivation: Multilayer perceptrons (MLP) represent one of the widely used and effective machine learning methods currently applied to diagnostic classification based on high-dimensional genomic data. Since the dimensionalities of the existing genomic data often exceed the available sample sizes by orders of magnitude, the MLP performance may degrade owing to the curse of dimensionality and over-fitting, and may not provide acceptable prediction accuracy.
Results: Based on Fisher linear discriminant analysis, we designed and implemented an MLP optimization scheme for a two-layer MLP that effectively optimizes the initialization of MLP parameters and MLP architecture. The optimized MLP consistently demonstrated its ability in easing the curse of dimensionality in large microarray datasets. In comparison with a conventional MLP using random initialization, we obtained significant improvements in major performance measures including Bayes classification accuracy, convergence properties and area under the receiver operating characteristic curve (Az).
Supplementary information: The Supplementary information is available on
Contact: yuewang@vt.edu
Host-Mediated Phosphorylation of Type III Effector AvrPto PromotesPseudomonasVirulence and Avirulence in Tomato
Authors: Anderson Jeffrey C. , Pascuzzi Pete E. , Xiao Fangming , Sessa Guido , Martin Gregory B. 
Published: January 2006

AbstractThe AvrPto protein from Pseudomonas syringae pv tomato is delivered into plant cells by the bacterial type III secretion system, where it either promotes host susceptibility or, in tomato plants expressing the Pto kinase, elicits disease resistance. Using two-dimensional gel electrophoresis, we obtained evidence that AvrPto is phosphorylated when expressed in plant leaves. In vitro phosphorylation of AvrPto by plant extracts occurs independently of Pto and is due to a kinase activity that is conserved in tomato (Solanum lycopersicum), tobacco (Nicotiana tabacum), and Arabidopsis thaliana. Three Ser residues clustered in the C-terminal 18 amino acids of AvrPto were identified in vitro as putative phosphorylation sites, and one site at S149 was directly confirmed as an in vivo phosphorylation site by mass spectrometry. Substitution of Ala for S149 significantly decreased the ability of AvrPto to enhance disease symptoms and promote growth of P. s. tomato in susceptible tomato leaves. In addition, S149A significantly decreased the avirulence activity of AvrPto in resistant tomato plants. Our observations support a model in which AvrPto has evolved to mimic a substrate of a highly conserved plant kinase to enhance its virulence activity. Furthermore, residues of AvrPto that promote virulence are also monitored by plant defenses.
ArabidopsisRibonucleotide Reductases Are Critical for Cell Cycle Progression, DNA Damage Repair, and Plant Development
Authors: Wang Chunxin , Liu Zhongchi 
Published: January 2006

AbstractRibonucleotide reductase (RNR), comprising two large (R1) and two small (R2) subunits, catalyzes a rate-limiting step in the production of deoxyribonucleotides needed for DNA replication and repair. Previous studies in yeast and mammals indicated that defective RNR often led to cell cycle arrest, growth retardation, and p53-dependent apoptosis, whereas abnormally increased RNR activities led to higher mutation rates. Because plants are constantly exposed to environmental mutagens and plant cells are totipotent, an understanding of RNR function in plants is important. We isolated and characterized mutations in all three R2 genes (TSO2, RNR2A, and RNR2B) in Arabidopsis thaliana. tso2 mutants had reduced deoxyribonucleoside triphosphate (dNTP) levels and exhibited developmental defects, including callus-like floral organs and fasciated shoot apical meristems. tso2 single and tso2 rnr2a double mutants were more sensitive to UV-C light, and tso2 rnr2a seedlings exhibited increased DNA damage, massive programmed cell death, and release of transcriptional gene silencing. Analyses of single and double r2 mutants demonstrated that a normal dNTP pool and RNR function are critical for the plant response to mutagens and proper plant development. The correlation between DNA damage accumulation and the subsequent occurrence of apoptotic nuclei in tso2 rnr2a double mutants suggests that perhaps plants, like animals, can initiate programmed cell death upon sensing DNA damage.