bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photoluminescence of bridged polysilsesquioxanes containing urea groups: Doping with Safranine‐O to generate red‐light emission
Authors: Gómez M. L. , Fasce D. P. , Williams R. J. J. , Montejano H. A. , Previtali C. M. 
Published: December 2007

AbstractBridged polysilsesquioxanes containing urea groups (ureasils) exhibit a broad photoluminescent emission in the visible spectrum. For a particular bridged polysilsesquioxane synthesized by the hydrolytic condensation of a precursor prepared by reaction of 4,4′‐[1,3 phenylenebis‐(1‐methylethylidene)]bis(aniline) (BSA) with 3‐(isocyanatepropyl)triethoxysilane (IPTES), we show that the broad photoluminescent band could be transformed into a relatively narrow emission band located in the red region of the spectra, by doping with Safranine‐O. The spectral overlap between the host emission and the dye absorption generated an efficient energy transfer process (antenna effect). Absorption, emission, and triplet–triplet absorption spectra revealed an efficient dispersion of the dye in the ureasil as well as the presence of strong host‐guest specific interactions. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 289–296, 2008
The polycomb group protein EZH2 regulates actin polymerization in human prostate cancer cells
Authors: Bryant R.J. , Winder S.J. , Cross S.S. , Hamdy F.C. , Cunliffe V.T. 
Published: December 2007

AbstractBACKGROUNDThe Polycomb Group protein EZH2 is implicated in prostate cancer progression. EZH2 promotes prostate cancer cell proliferation and invasiveness. We describe a link between EZH2 function and actin polymerization in prostate cancer cells.METHODSNuclear and cytoplasmic EZH2 expression in benign and malignant prostate tissue samples was assessed. An association between EZH2 function and actin polymerization in prostate cancer cells was investigated using siRNA‐mediated knock‐down of EZH2. Effects of EZH2 knock‐down on actin polymerization dynamics were analyzed biochemically using immunoblot analysis of cell lysate fractions, and morphologically using immunocytochemistry.RESULTSCytoplasmic EZH2 is expressed at low levels in benign prostate epithelial cells and over‐expressed in prostate cancer cells. Cytoplasmic EZH2 expression levels correlate with nuclear EZH2 expression in prostate cancer samples. Knock‐down of EZH2 in PC3 prostate cancer cells increases the amount of F‐actin polymerization, cell size, and formation of actin‐rich filaments.CONCLUSIONSCytoplasmic EZH2 is over‐expressed in prostate cancer cells. EZH2 function promotes a reduction in the pool of insoluble F‐actin in invasive prostate cancer cells. EZH2 may regulate actin polymerization dynamics and thereby promote prostate cancer cell motility and invasiveness. Prostate 68: 255–263, 2008. © 2007 Wiley‐Liss, Inc.
Prostate‐Specific genes and their regulation by dihydrotestosterone
Authors: Ci Ma , Mayumi Yoshioka , André Boivin , Pascal Belleau , Lin Gan , Yasukazu Takase , Fernand Labrie , Jonny St‐Amand 
Published: December 2007

AbstractBACKGROUNDProstate is a well‐known androgen‐dependent tissue.METHODSBy sequencing 4,294,186 serial analysis of gene expression (SAGE) tags, we have investigated the transcriptomes of normal mouse prostate, liver, testis, lung, brain, femur, skin, adipose tissue, skeletal muscle, vagina, ovary, mammary gland, and uterus in order to identify the most abundant and tissue‐specific transcripts in the prostate, as well as to target the androgen responsive transcripts specifically regulated in the prostate. Small interference RNA (siRNA) in LNCaP cells was applied to validate the roles of prostate‐specific/enriched ARGs in the growth of human prostate cancer cells.RESULTSThe most abundant transcripts were involved in prostatic secretion, energy metabolism and immunity. Previously well‐known prostate‐specific transcripts, including many transcripts involved in prostatic secretion, polyamine biosynthesis and transport, and immunity were specific/enriched in the prostate. Only 22 transcripts among 114 androgen‐regulated genes (ARGs) in the mouse prostate were modulated by dihydrotestosterone (DHT) in two or more tissues. The siRNA results showed that inhibition of HSPA5 and MAT2A gene expression repressed growth of human cancer LNCaP cells.ConclusionsThe current study globally assessed the transcriptome of the prostate and revealed the most abundant and tissue‐specific transcripts which are responsible for the unique functions of this organ. These prostate‐specific ARGs might be used as targets to develop safe and effective gene‐based therapy for the prevention and treatment of prostate cancer. Prostate 68: 241–254, 2008. © 2007 Wiley‐Liss, Inc.
Characterization of bovine surfactant proteins B and C by electrospray ionization mass spectrometry
Authors: Liu Suya , Zhao Lin , Manzanares Dahis , Doherty‐Kirby Amanda , Zhang Cunjie , Possmayer Fred , Lajoie Gilles A. 
Published: December 2007

AbstractBovine surfactant proteins B (SP‐B) and C (SP‐C) were analyzed by nano‐electrospray ionization mass spectrometry (nano‐ESI‐MS). The observed molecular masses showed discrepancies compared to the calculated molecular masses using the published amino acid sequences. The number of cysteine residues in the published bovine SP‐B amino acid sequences also failed to match the observed mass shift upon reduction of the SP‐B dimer. To determine the amino acid sequences of two proteins, SP‐B was first digested with trypsin and analyzed by liquid chromatography/tandem mass spectrometry (LC/MS/MS), while SP‐C was analyzed by MS/MS in its intact form. The amino acid sequence of bovine SP‐B determined here matches the observed molecular mass. The sequence is almost identical to the sheep SP‐B except for two amino acid residues, consistent with the proximity of the two species. The correct sequence contains seven cysteine residues. Bovine SP‐B exists as dimers and all cysteines are oxidized to form disulfide bonds in physiological conditions, which is in agreement with the observed mass shift upon reduction of the SP‐B dimer. These cysteine residues are completely conserved across all species indicating their importance for the biological functions of this surfactant protein. The sequence of SP‐C determined here also reveals an L to V substitution at its position 22 compared with the published bovine SP‐B sequence. Copyright © 2007 John Wiley & Sons, Ltd.
Considerations for the design of organic mulch permeable reactive barriers
Authors: Ahmad Farrukh , McGuire Travis M. , Lee Robert S. , Becvar Erica 
Published: December 2007

AbstractOrganic mulch consists of insoluble carbon biopolymers that are enzymatically hydrolyzed during decomposition to release aqueous total organic carbon (TOC). The released TOC is utilized by microorganisms as an electron donor to transform electrophilic contaminants via reductive pathways. Over the last decade, organic mulch permeable reactive barriers (PRBs), or biowalls, have received increased interest as a relatively inexpensive slow‐release electron donor technology for addressing contaminated groundwater. To date, biowalls have been installed to enhance the passive bioremediation of groundwater contaminated with a variety of electrophilic compounds, including chlorinated solvents, explosives, and perchlorate. In addition, several mulch biowall projects are currently under way at several U.S. Department of Defense facilities. However, at the present time, the guidelines available for the design of mulch PRBs are limited to a few case studies published in the technical literature. A biowall design, construction, and operation protocol document is expected to be issued by the Air Force Center for Environmental Excellence in 2007. In this publication, three technical considerations that can have a significant impact on the design and performance of mulch PRBs are presented and discussed. These technical considerations are: (1) hydraulic characteristics of the mulch bed; (2) biochemical characteristics of different types of organic amendments used as mulch PRB fill materials; and (3) a transport model that can be used to estimate the required PRB thickness to attain cleanup standards. © 2007 Wiley Periodicals, Inc.
Bayesian modeling of multivariate average bioequivalence
Authors: Ghosh Pulak , Gönen Mithat 
Published: December 2007

AbstractBioequivalence trials are usually conducted to compare two or more formulations of a drug. Simultaneous assessment of bioequivalence on multiple endpoints is called multivariate bioequivalence. Despite the fact that some tests for multivariate bioequivalence are suggested, current practice usually involves univariate bioequivalence assessments ignoring the correlations between the endpoints such as AUC and Cmax. In this paper we develop a semiparametric Bayesian test for bioequivalence under multiple endpoints. Specifically, we show how the correlation between the endpoints can be incorporated in the analysis and how this correlation affects the inference. Resulting estimates and posterior probabilities ‘borrow strength’ from one another where the amount and the direction of the strength borrowed are determined by the prior correlations. The method developed is illustrated using a real data set. Copyright © 2007 John Wiley & Sons, Ltd.
Analysis of recurrent event data under the case‐crossover design with applications to elderly falls
Authors: Luo Xianghua , Sorock Gary S. 
Published: December 2007

AbstractThe case‐crossover design is useful for studying the effects of transient exposures on short‐term risk of diseases or injuries when only data on cases are available. The crossover nature of this design allows each subject to serve as his/her own control. While the original design was proposed for univariate event data, in many applications recurrent events are encountered (e.g. elderly falls, gout attacks, and sexually transmitted infections). In such situations, the within‐subject dependence among recurrent events needs to be taken into account in the analysis. We review three existing conditional logistic regression (CLR)‐based approaches for recurrent event data under the case‐crossover design. A simple approach is to use only the first event for each subject; however, we would expect loss of efficiency in estimation. The other two reviewed approaches rely on independence assumptions for the recurrent events, conditionally on a set of covariates. Furthermore, we propose new methods that adjust the CLR using either a within‐subject pairwise resampling technique or a weighted estimating equation. No specific dependency structure among recurrent events is needed therein, and hence, they have more flexibility than the existing methods in the situations with unknown correlation structures. We also propose a weighted Mantel–Haenszel estimator, which is easy to implement for data with a binary exposure. In simulation studies, we show that all discussed methods yield virtually unbiased estimates when the conditional independence assumption holds. These methods are illustrated using data from a study of the effect of medication changes on falls among the elderly. Copyright © 2007 John Wiley & Sons, Ltd.
Grammar‐driven generation of domain‐specific language debuggers
Authors: Wu Hui , Gray Jeff , Mernik Marjan 
Published: December 2007

AbstractDomain‐specific languages (DSLs) assist a software developer (or end‐user) in writing a program using idioms that are similar to the abstractions found in a specific problem domain. Tool support for DSLs is lacking when compared with the capabilities provided for standard general‐purpose languages (GPLs), such as Java and C++. For example, support for debugging a program written in a DSL is often non‐existent. The lack of a debugger at the proper abstraction level limits an end‐user's ability to discover and locate faults in a DSL program. This paper describes a grammar‐driven technique to build a debugging tool generation framework from existing DSL grammars. The DSL grammars are used to generate the hooks needed to interface with a supporting infrastructure constructed for an integrated development environment that assists in debugging a program written in a DSL. The contribution represents a coordinated approach to bring essential software tools (e.g. debuggers) to different types of DSLs (e.g. imperative, declarative, and hybrid). This approach hides from the end‐users the accidental complexities associated with expanding the focus of a language environment to include debuggers. The research described in this paper addresses a long‐term goal of empowering end‐users with development tools for particular DSL problem domains at the proper level of abstraction without depending on a specific GPL. Copyright © 2007 John Wiley & Sons, Ltd.
Lexical frequency and third-graders' stress accuracy in derived English word production
Authors: JARMULOWICZ LINDA , TARAN VALENTINA L. , HAY SARAH E. 
Published: December 2007

ABSTRACTThis study examined the effects of lexical frequency on children's production of accurate primary stress in words derived with nonneutral English suffixes. Forty-four third-grade children participated in an elicited derived word task in which they produced high-frequency, low-frequency, and nonsense-derived words with stress-changing suffixes (i.e., -tion, -ic, -ity). Derived word frequency affected stress production accuracy; however, the individual suffix also played an important role in stress placement, with -tionproductions more accurate than either -icor -ityproductions. For the real words, derived word frequencyrelativeto stem frequency was related to performance. Stress was less accurate on derived words that were much lower in frequency than their stems (e.g.,tranquil/tranquility) and more accurate on derived words that approximated or exceeded their stem frequency (e.g.,motivate/motivation). In addition to derived word and stem frequency, results are discussed with reference to several phonological characteristics that may also influence stress production accuracy.
The effects of training on automatization of word recognition in English as a foreign language
Authors: AKAMATSU NOBUHIKO 
Published: December 2007

ABSTRACTThe present study investigated the effects of word-recognition training on the word-recognition processing of learners of English as a foreign language (EFL). Providing 7-week word-recognition training, the study examined whether such training improves EFL learners' word-recognition performance. The main aspects of this study concerned word frequency and working-memory capacity in automatization of word recognition. Analysis of variance and correlational analyses revealed qualitative differences in the improvement of EFL word-recognition performance with respect to word frequency. The improvement in the processing of high-frequency words was associated with simple speedup; conversely, the processing of low-frequency words was associated with automatization. Results also showed that working-memory capacity might not play a noticeable role in improving word-recognition speed or efficiency.
Public health and economic costs of investigating a suspected outbreak of Legionnaires' disease
Authors: LOCK K. , MILLETT C. , HEATHCOCK R. , JOSEPH C. A. , HARRISON T. G. , LEE J. V. , RAO G. , SURMAN-LEE S. ,   on behalf of the Outbreak Control Team
Published: December 2007

SUMMARYThis paper provides one of the first assessments of the burden of both the public health investigation and the economic costs associated with an apparent outbreak of Legionnaires' disease (LD) in South East London. In addition to epidemiological, microbiological and environmental investigations, we collected data on the staff time and resources committed by the 11 main organizations responsible for managing the outbreak. Of the overall estimated costs of £455 856, only 14% (£64 264) was spent on investigation and control of the outbreak compared with 86% (£391 592) spent on the hospital treatment of the patients. The time and money spent on public health services in this investigation appear to represent good value for money considering the potential costs of a major outbreak, including the high case-fatality rate in LD generally and the high health-care costs. Further research is needed to determine optimum strategies for the cost-effective use of health system resources in investigations of LD. Whether the threshold for investigation of cases should be based on observed incidence rates or the cost-effectiveness of investigations, or both, should be debated further.
A novel genome-scale repeat finder geared towards transposons
Authors: Li Xuehui , Kahveci Tamer , Settles A. Mark 
Published: December 2007

Abstract
Motivation: Repeats are ubiquitous in genomes and play important roles in evolution. Transposable elements are a common kind of repeat. Transposon insertions can be nested and make the task of identifying repeats difficult.
Results: We develop a novel iterative algorithm, called Greedier, to find repeats in a target genome given a repeat library. Greedier distinguishes itself from existing methods by taking into account the fragmentation of repeats. Each iteration consists of two passes. In the first pass, it identifies the local similarities between the repeat library and the target genome. Greedier then builds graphs from this comparison output. In each graph, a vertex denotes a similar subsequence pair. Edges denote pairs of subsequences that can be connected to form higher similarities. In the second pass, Greedier traverses these graphs greedily to find matches to individual repeat units in the repeat library. It computes a fitness value for each such match denoting the similarity of that match. Matches with fitness values greater than a cutoff are removed, and the rest of the genome is stitched together. The similarity cutoff is then gradually reduced, and the iteration is repeated until no hits are returned from the comparison. Our experiments on the Arabidopsis and rice genomes show that Greedier identifies approximately twice as many transposon bases as those found by cross_match and WindowMasker. Moreover, Greedier masks far fewer false positive bases than either cross_match or WindowMasker. In addition to masking repeats, Greedier also reports potential nested transposon structures.
Contact: xli@cise.ufl.edu
Structural flexibility in proteins: impact of the crystal environment
Authors: Hinsen Konrad 
Published: December 2007

Abstract
Motivation: In the study of the structural flexibility of proteins, crystallographic Debye-Waller factors are the most important experimental information used in the calibration and validation of computational models, such as the very successful elastic network models (ENMs). However, these models are applied to single protein molecules, whereas the experiments are performed on crystals. Moreover, the energy scale in standard ENMs is undefined and must be obtained by fitting to the same data that the ENM is trying to predict, reducing the predictive power of the model.
Results: We develop an elastic network model for the whole protein crystal in order to study the influence of crystal packing and lattice vibrations on the thermal fluctuations of the atom positions. We use experimental values for the compressibility of the crystal to establish the energy scale of our model. We predict the elastic constants of the crystal and compare with experimental data. Our main findings are (1) crystal packing modifies the atomic fluctuations considerably and (2) thermal fluctuations are not the dominant contribution to crystallographic Debye-Waller factors.
Availability: The programs developed for this work are available as supplementary material at Bioinformatics Online.
Contact: hinsen@cnrs-orleans.fr
Supplementary information: (1) A full derivation of the normal mode equations in a crystal and in a continuous medium. (2) A movie illustrating the lattice vibrations. Both supplements are available at Bioinformatics Online.
Power of monitoring surveys to detect abundance trends in depleted populations: the effects of density-dependent habitat use, patchiness, and climate change
Authors: Blanchard Julia L. , Maxwell David L. , Jennings Simon 
Published: December 2007

Abstract
Blanchard, J. L., Maxwell, D. L., and Jennings, S. 2008. Power of monitoring surveys to detect abundance trends in depleted fish populations: the effects of density-dependent habitat use, patchiness, and climate change. – ICES Journal of marine Science, 65: 111–120. Traditionally, trawl surveys were designed to collect fishery-independent data for assessing the population dynamics of commercially exploited species. However, trawl survey data are increasingly used to describe the abundance, distribution and ecology of a wide range of species in studies of climate change and fishing effects. These new uses of survey data suggest that improved understanding of the value and limitations of existing survey designs is required. We compared the power of different survey designs (where stations are fixed, fixed stratified, random, or random stratified) to detect known trends in the abundance of depleted populations. Modelled populations were characterized by different temperature preference, density-dependent habitat selection, and patterns of small-scale aggregation (patchiness). Temperature preferences and local patchiness had an influence on the power of different surveys to detect increases in abundance, and in some scenarios, survey-area indices would consistently underestimate or overestimate trends in overall abundance. As the distributions of many fish populations have shifted in response to climate change, exhibit distribution-abundance relationships, and have been depleted by fishing, we conclude that survey indices may provide partial or unreliable information on changes in the true abundance of the wider range of species now of interest. To disentangle the effects of fishing, climate, and biology on the abundance of fish populations, and to monitor the depletion and recovery of species threatened by fishing, there should be greater emphasis on coordinating the timing, areas of coverage, and methods of sampling of surveys of the Northeast Atlantic continental shelf.
Phylogeny of cytoplasmic incompatibility microorganisms in the parasitoid wasp genus Nasonia (Hymenoptera: Pteromalidae) based on 16S ribosomal DNA sequences
Authors: Breeuwer J. A. J. , Stouthamer R. , Barns S. M. , Pelletier D. A. , Weisburg W. G. , Werren J. H. 
Published: December 2007

AbstractCytoplasmic incompatibility results in embryo mortality in diploids, or all male offspring in haplodiploids, when individuals carrying different cytoplasmic factors are crossed. Cytoplasmic factors have been identified as intracellular micro‐organisms. Microbeinduced cytoplasmic incompatibility is found in many insect taxa and may play a role in reproductive isolation between populations. Such micro‐organisms cause bidirectional incompatibility between species of the parasitoid wasp genus Nasonia. The phylogenetic relationship of cytoplasmic incompatibility microorganisms (CIM) of different Nasonia species was analysed using their 16S ribosomal DNA (rDNA) sequence. Two 16S rDNA operons were detected in the CIM of each Nasonia species. Sequence analysis indicates that the Nasonia CIM are closely related and belong to the alpha group of the Proteobacteria.