bluuebunny/crossref_metadata_2025_split huggingface dataset:
Met160Val polymorphism in the TRMPSS2 gene and risk of prostate cancer in a population‐based case‐control study
Authors: Lubieniecka Joanna M. , Cheteri Mahesh Keitheri , Stanford Janet L. , Ostrander Elaine A. 
Published: March 2004

AbstractBACKGROUNDSerine proteases play an important role in prostate cancer (PCa) invasion through the degradation of extracellular matrix proteins and interaction with growth modulating factors. The transmembrane serine protease 2 (TMPRSS2) gene encodes a type II transmembrane protein which, due to its cell surface localization, could be a potentially useful predictive marker for PCa.METHODSWe screened a population of 24 unrelated individuals for sequence variants in the TMPRSS2 gene, and found a Met160Val change in 33%. We then tested 559 cases and 523 controls from a population‐based case‐control study of middle‐aged men from Washington State.RESULTSMen with the GG genotype and a first‐degree family history of PCa had a significantly higher risk for PCa relative to men without a family history (OR = 2.05; 95% CI = 1.3–3.2). However, the interaction between genotype and family history of PCa was not significant (P = 0.52).CONCLUSIONSLarger, more detailed studies are needed to fully investigate the role of serine proteases in PCa. © 2004 Wiley‐Liss, Inc.
In vivo real‐time imaging of TGF‐β‐induced transcriptional activation of the RANK ligand gene promoter in intraosseous prostate cancer
Authors: Zhang Jian , Lu Yi , Dai Jinlu , Yao Zhi , Kitazawa Riko , Kitazawa Sohei , Zhao Xinping , Hall Daniel E. , Pienta Kenneth J. , Keller Evan T. 
Published: March 2004

AbstractBACKGROUNDCurrent animal models of prostate cancer (CaP) bone metastasis do not allow measurement of either tumor growth in bone over time or activation of gene promoters in intraosseous tumors. To develop these methods, we used bioluminescent imaging (BLI) to determine if expression of receptor activator of NF‐κB ligand (RANKL), a pro‐osteoclastogenic factor that promotes CaP bone metastases, is modulated by the bone matrix protein transforming growth factor‐β (TGF‐β) in vivo.METHODSC4‐2B human CaP cells were treated with TGF‐β in vitro and RANKL mRNA and protein production were measured by polymerase chain reaction (PCR) and ELISA, respectively. Then C4‐2B cells stably transfected with the RANKL promoter driving luciferase (lux) were injected intra‐tibially into severe combined immundeficient (SCID) mice. Tumors were subjected to BLI every 2 weeks for 6 weeks and serum prostate specific antigen (PSA) was measured using ELISA. Vehicle (V), 1,25 dihydroxyvitamin D (VitD), or TGF‐β was administered to mice with established tumors and BLI to measure RANKL promoter activity was performed. Tumors were then subjected to immunohistochemistry for lux and assayed for RANKL mRNA levels.RESULTSTGF‐β induced RANKL protein and mRNA expression and activated the RANKL promoter activity in a dose‐dependent manner in vitro. BLI demonstrated an increase in intraosseous tumor size over time, which correlated with serum PSA levels. Administration of TGF‐β and VitD to mice with established intraosseous tumors increased lux activity compared to V. Intratibial tumor RANKL mRNA expression paralleled the increased promoter activity. Immunohistochemistry confirmed the presence of lux in the intraosseous tumors.CONCLUSIONSThese results demonstrate the ability to measure intraosseous tumor growth over time and gene promoter activation in an established intraosseous tumor in vivo and also demonstrate that TGF‐β induces activates the RANKL promoter. These results provide a novel method to explore the biology of CaP bone metastases. © 2004 Wiley‐Liss, Inc.
An inherently safer process of cyclohexane oxidation using pure oxygen—An example of how better process safety leads to better productivity
Authors: Chen Jenq‐Renn 
Published: March 2004

AbstractThis paper discusses how detailed studies on flammability at elevated pressures and temperatures can be applied to liquid‐phase oxidation of cyclohexane using air/oxygen and lead to an inherently safer process with better productivity. Flammability tests of cyclohexane/oxygen vapor and vapor bubbles under actual oxidation conditions were performed. The flammability of the vapor and vapor bubbles was found to be moderated by the addition of water into the cyclohexane liquid. The added water forms minimum boiling azeotrope with cyclohexane and its vapor renders the cyclohexane vapor and vapor bubble inflammable. Oxidations of the cyclohexane/water azeotrope utilizing pure oxygen were carried out and found to outperform the traditional air oxidation process by a factor of 2. This paper summarizes our work during the past few years toward a safer and better process development for the liquid‐phase oxidation of cyclohexane. © 2004 American Institute of Chemical Engineers Process Saf Prog 23: 72–81, 2004
Effective thermal conductivity: application to photothermal experiments for the case of bulk light absorption
Authors: Gurevich Yuriy , Logvinov Georgiy , Lashkevich Igor 
Published: March 2004

AbstractWe suggest a new theoretical approach to obtain effective thermal parameters of two‐layer structures in photothermal experiments, and calculate the effective thermal conductivity in the quasistatic approximation. Unlike previous works devoted to this problem, it is supposed that a non‐equilibrium temperature originates due to the bulk modulated light absorption. It is shown that in this case the effective thermal parameters have to be obtained together with the effective optical parameters. As a result, the effective thermal parameters in the general case are dependent on the optical parameters of the layers. The role of the thermal properties of the interface between the layers is discussed. It is concluded that the effective parameters are not single‐valued. They depend on the manner of measurements and the point of these measurements. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Theory of related to shear strain u6 physical properties of ferroelectrics and antiferroelectrics of the KH2PO4 family
Authors: Levitskii R. R. , Lisnii B. M. 
Published: March 2004

AbstractWe propose an extension of the proton tunneling model in order to study related to the shear strain u6 dielectric, piezoelectric, and elastic properties of ferro‐ and antiferroelectrics of the KH2PO4 family. This strain is introduced into the proton Hamiltonian via the linear contributions into the configurational energies of protons surrounding an oxygen tetrahedron. In the four‐particle cluster approximation for the short‐range interactions and the mean field approximation for the long‐range interaction we explore the phase transition and piezoelectric effect in the KH2PO4 ferroelectrics. In the paraelectric phase the dielectric, piezoelectric, and elastic characteristics of the NH4H2PO4 antiferroelectrics are calculated. At the proper choice of the theory parameters a good agreement between theoretical and experimental results is obtained. Taking into account of the piezoelectric coupling with the shear strain u6 allows one to calculate the static dielectric permittivities of free and clamped crystals as well as to obtain a good description of ferroelectric spontaneous shear strain u6. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Stability of single‐wall carbon nanotube tori
Authors: Yang Linfeng , Chen Jiangwei , Dong Jinming 
Published: March 2004

AbstractWe obtained the formation threshold energy expression of SWNT torus by treating single‐walled carbon nanotube (SWNT) as a continuum elastic shell, the obtained formation threshold energy is the function of the radius of formed SWNT torus. The radius of SWNT torus is found to be the most probable radius (energy preferred), which corresponds to the minimum formation threshold energy. Taking into account the rebonding energy of the dangling bond of two ends, the formation energy of the SWNT torus is negative, indicating the formed SWNT torus is stable both physically and chemically. This model can well explain the average radius of 270 nm and the narrow radius distribution of the SWNT tori in experiments. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effective depths for surface excitation derived by reflection electron energy‐loss spectroscopy analysis
Authors: Zhang Zengming , Iyasu Takeshi , Shimizu Ryuichi , Goto Keisuke , Koshikawa Takanori , Tamura Keiji 
Published: March 2004

AbstractA method of estimation is proposed for determining the effective depth of surface excitation. For this, the effective differential inverse inelastic mean free path (DIIMFP) is presumed to be represented as a linear combination of theoretical DIIMFPs for surface and bulk excitation, which are derived by the use of optical dielectric constants. The effective DIIMFP in the approach is derived by a reflected electron energy‐loss spectroscopy analysis based on the extended Landau approach. The present analysis for 1 kV electrons has led to a simple estimation of the effective depth for surface excitations (∼14.5 Å for Al and ∼21 Å for Ag), agreeing well with an estimation given by υ/ωs, where υ and ωs are the velocity of the primary electrons and the average surface plasmon frequency, respectively. Copyright © 2004 John Wiley & Sons, Ltd.
Chemical environment of copper at the surface of a CuAl2 model alloy: XPS, MEIS and TEM analyses
Authors: Liu Yanwen , Bailey Paul , Noakes Timothy C. Q. , Thompson George E. , Skeldon Peter , Alexander Morgan R. 
Published: March 2004

AbstractAir‐formed oxide on a CuAl2 model alloy is shown to be free of copper species, with copper enriching in the alloy. With thickening of the oxide by anodizing, copper enriches further to a critical concentration at which its oxidation proceeds with incorporation of Cu(II) species into the film. Such species migrate more rapidly through the film than aluminium species. Incorporation of copper species is associated with generation of oxygen gas within the film and subsequent film rupture is due to release of the gas. Reduction of Cu(II) to Cu(I) species during XPS analysis is characterized and the accelerating role of charge neutralizing is highlighted. Copyright © 2004 John Wiley & Sons, Ltd.
Effectiveness of multimedia‐based instruction that emphasizes molecular representations on students' understanding of chemical change
Authors: Ardac Dilek , Akaygun Sevil 
Published: March 2004

AbstractThe present study makes use of the capabilities of computerized environments to enable simultaneous display of molecular representations that correspond to observations at the macroscopic level. This study questions the immediate and long‐term effects of using a multimedia instructional unit that integrates the macroscopic, symbolic, and molecular representations of chemical phenomena. Forty‐nine eighth graders received either multimedia‐based instruction that emphasized molecular representations (n = 16), or regular instruction (n = 33). Students who received multimedia‐based instruction that emphasized the molecular state of chemicals outperformed students from the regular instruction group in terms of the resulting test scores and the ease with which they could represent matter at the molecular level. However, results relating to the long‐term effects suggest that the effectiveness of a multimedia‐based environment can be improved if instruction includes additional prompting that requires students to attend to the correspondence between different representations of the same phenomena. © 2004 Wiley Periodicals, Inc. J Res Sci Teach 41: 317–337, 2004
In search of pedagogical content knowledge in science: Developing ways of articulating and documenting professional practice
Authors: Loughran John , Mulhall Pamela , Berry Amanda 
Published: March 2004

AbstractThis study examines the development of ways of documenting and portraying science teachers' pedagogical content knowledge (PCK). As a result of a longitudinal study into science teachers' pedagogical content knowledge, a method is developed for capturing and portraying PCK that comprises two important elements. The first is linked to the particular science content, termed Content Representation (CoRe), and the second is linked to teaching practice, termed Professional and Pedagogical experience Repertoire (PaP‐eR). Through this approach new understandings of PCK emerge that are of interest in terms of both academic (knowledge building about PCK) and teaching perspectives. This study includes a full CoRe and one PaP‐eR and fully demonstrates how these two elements interact to begin to portray science teachers' pedagogical content knowledge. © 2004 Wiley Periodicals, Inc. J Res Sci Teach 41: 370–391, 2004
Sodium and potassium transport in the halophilic yeast Debaryomyces hansenii
Authors: González‐Hernández J. C. , Cárdenas‐Monroy C. A. , Peña A. 
Published: March 2004

AbstractDebaryomyces hansenii, a halophile yeast found in shallow sea waters and salty food products grows optimally in 0.6 M of either NaCl or KCl, accumulating high concentrations of Na+ or K+. After growth in NaCl or KCl, a rapid efflux of either accumulated cation was observed if the cells were incubated in the presence of KCl or NaCl, respectively, accompanied by a slower accumulation of the cation present in the incubation medium. However, a similar, rapid efflux was observed if cells were incubated in buffer, in the absence of external cations. This yeast shows a cation uptake activity of both 86Rb+ and 22Na+ with saturation kinetics, and much higher affinity for 86Rb+ than for 22Na+. The pH dependence of the kinetics constants was similar for both cations, and although Km values were higher at pH 8.0, there was also an increase in the Vmax values. The accumulation of 22Na+ was found to be increased in cells grown in the presence of 0.6 M NaCl. 86Rb+ was also accumulated more in these cells, but to a slightly greater extent. The inhibition kinetics of the uptake of 22Na+ by K+, and that of 86Rb+ by Na+ was found to be non‐competitive. It can be concluded that Na+ in D. hansenii is not excluded but instead, its metabolic systems must be resistant to high salt concentrations. Copyright © 2004 John Wiley & Sons, Ltd.
The Development of Antibiotic Resistant Organisms with the Use of Ototopical Medications
Authors: Weber Peter C. , Roland Peter S. , Hannley Maureen , Friedman Rick , Manolidis Spiros , Matz Greg , Owens Fred , Rybak Leonard , Stewart Michael G. 
Published: March 2004

OBJECTIVEThere is growing concern over the use of systemic antibiotics and the development of bacterial resistance. The question remains as to whether ototopical medications may also promote antibiotic‐resistant organisms, either on a local level (in the ear) or in other areas of the aerodigestive tract. We performed an evidence‐based review to answer the following clinical question, “Do antibiotic ototopical medications induce antibiotic resistant organisms?”STUDY DESIGNWe performed a MEDLINE search of the published literature from 1966 to the present. We used appropriate search terms such as “ototopical antibiotics,” “ototopical drops,” “antibiotic resistance,” “topical antibiotics and otitis externa,” “otitis externa and treatment,” “otitis externa and antibiotic drops,” “otitis externa and ototopical drops,” “otitis media,” “otitis media and treatment,” “otitis media and antibiotic drops,” “chronic suppurative otitis media,” “chronic suppurative otitis media and treatment,” “chronic suppurative otitis media and antibiotic drops,” “ otitis externa and resistant organisms,” “otitis media and resistant organisms,” “chronic suppurative otitis media and resistant organisms,” “ophthalmic antibiotic drops,” “draining ear,” “P.E. tube otorrhea,” “pressure equalizing tube otorrhea,” “pressure equalizing tube otorrhea and treatment,” and “pressure equalizing tube otorrhea and ototopical therapy” to identify pertinent articles. These articles were reviewed and graded according to the evidence quality.RESULTSAfter an initial screening of over 2,500 articles, 38 articles were analyzed further; of these, 11 were determined to warrant extensive review. Eight articles evaluated chronic suppurative otitis media; 2, otitis externa; and 1, post‐tympanostomy tube otorrhea, whereas 3 others studied systemic absorption. Of the 8 chronic suppurative otitis media studies, there were thought to be 5 grade 2B studies, 1 grade 1B study, and 1 grade 2C study. These studies did not demonstrate a propensity for the development of resistant organisms. No study answered the question as to whether resistance to systemic antibiotics might occur in otitis externa.CONCLUSIONSOverall grade B evidence seems to indicate that no significant antibiotic resistance develops from the use of ototopical antibiotic treatment.
Statistical comparison of Regional Atmospheric Modelling System forecasts with observations
Authors: Buckley Robert L. , Weber Allen H. , Weber Jilene H. 
Published: March 2004

AbstractA statistical comparison of observations and forecasts using the Regional Atmospheric Modelling System (RAMS) for operations at the Savannah River Site (SRS) in South Carolina is discussed. Simulated and observed values of wind direction and wind speed, collected twice daily for a two‐year period from April 1998 to March 2000, are compared in a variety of ways for five different locations in the southeastern United States. Simulated and observed turbulence intensities are also compared for a one‐year period beginning in February 1999 for the SRS. Statistical measures used for comparison are the mean absolute error, mean relative error and standard deviation. Directional errors tend to increase with forecast time while speeds tend to be underestimated over the entire forecast range, especially those exceeding 8 m s−1. Seasonally, winds are predicted with greater accuracy during the winter and spring months, when speeds in the southeastern United States are higher and direction is less variable. Vertical turbulence intensity at SRS is slightly underestimated, while horizontal turbulence intensity is slightly overestimated. In general, the statistical measures show that the model produces results with reasonable skill for the wind speed, direction and turbulence. Copyright © 2004 Royal Meteorological Society.
Simultaneous search for multiple QTL using the global optimization algorithm DIRECT
Authors: Ljungberg K. , Holmgren S. , Carlborg Ö. 
Published: March 2004

Abstract
Motivation: A simultaneous search is necessary for maximizing the power to detect epistatic quantitative trait loci (QTL). The computational complexity demands that the traditional exhaustive search be replaced by a more efficient global optimization algorithm.
Results: We have the previously known algorithm adapted DIRECT, to the problem of simultaneous mapping of multiple QTL. We have compared DIRECT with standard exhaustive search and a genetic algorithm previously used for QTL mapping in two dimensions. In all two- and three-QTL test cases, DIRECT accurately finds the global optimum two to four orders of magnitude faster than when using an exhaustive search, and one order of magnitude faster than when using the genetic algorithm. Thus, randomization testing for determining empirical significance thresholds for at least three QTL is made feasible by the use of DIRECT.
Availability: The code of the prototype implementation is available at http://user.it.uu.se/~kl/qtl_software.html
CEBS object model for systems biology data, SysBio-OM
Authors: Xirasagar Sandhya , Gustafson Scott , Merrick B. Alex , Tomer Kenneth B. , Stasiewicz Stanley , Chan Denny D. , Yost Kenneth J. , Yates John R. , Sumner Susan , Xiao Nianqing , Waters Michael D. 
Published: March 2004

Abstract
Motivation: To promote a systems biology approach to understanding the biological effects of environmental stressors, the Chemical Effects in Biological Systems (CEBS) knowledge base is being developed to house data from multiple complex data streams in a systems friendly manner that will accommodate extensive querying from users. Unified data representation via a single object model will greatly aid in integrating data storage and management, and facilitate reuse of software to analyze and display data resulting from diverse differential expression or differential profile technologies. Data streams include, but are not limited to, gene expression analysis (transcriptomics), protein expression and protein–protein interaction analysis (proteomics) and changes in low molecular weight metabolite levels (metabolomics).
Results: To enable the integration of microarray gene expression, proteomics and metabolomics data in the CEBS system, we designed an object model, Systems Biology Object Model (SysBio-OM). The model is comprehensive and leverages other open source efforts, namely the MicroArray Gene Expression Object Model (MAGE-OM) and the Proteomics Experiment Data Repository (PEDRo) object model. SysBio-OM is designed by extending MAGE-OM to represent protein expression data elements (including those from PEDRo), protein–protein interaction and metabolomics data. SysBio-OM promotes the standardization of data representation and data quality by facilitating the capture of the minimum annotation required for an experiment. Such standardization refines the accuracy of data mining and interpretation. The open source SysBio-OM model, which can be implemented on varied computing platforms is presented here.
Availability: A universal modeling language depiction of the entire SysBio-OM is available at http://cebs.niehs.nih.gov/SysBioOM/. The Rational Rose object model package is distributed under an open source license that permits unrestricted academic and commercial use and is available at http://cebs.niehs.nih.gov/cebsdownloads. The database and interface are being built to implement the model and will be available for public use at http://cebs.niehs.nih.gov.
DNA microarray normalization methods can remove bias from differential protein expression analysis of 2D difference gel electrophoresis results
Authors: Kreil David P. , Karp Natasha A. , Lilley Kathryn S. 
Published: March 2004

Abstract
Motivation: Two-dimensional Difference Gel Electrophoresis (DIGE) measures expression differences for thousands of proteins in parallel. In contrast to DNA microarray analysis, however, there have been few systematic studies on the validity of differential protein expression analysis, and the effects of normalization methods have not yet been investigated. To address this need, we assessed a series of same–same comparisons, evaluating how random experimental variance influenced differential expression analysis.
Results: The strong fluctuations observed were reflected in large discrepancies between the distributions of the spot intensities for different gels. Correct normalization for pooling of multiple gels for analysis is, therefore, essential. We show that both dye-specific background levels and the differences in scale of the spot intensity distributions must be accounted for. A variance stabilizing transform that had been developed for DNA microarray analysis combined with a robust Z-score allowed the determination of gel-independent signal thresholds based on the empirical distributions from same–same comparisons. In contrast, similar thresholds holding up to cross-validation could not be proposed for data normalized using methods established in the field of proteomics.
Availability: Software is available on request from the authors.
Supplementary information: There is supplementary material available online at http://www.flychip.org.uk/kreil/pub/2dgels/