bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new smoothed aggregation multigrid method for anisotropic problems
Authors: Gee Michael W. , Hu Jonathan J. , Tuminaro Raymond S. 
Published: December 2008

AbstractA new prolongator is proposed for smoothed aggregation (SA) multigrid. The proposed prolongator addresses a limitation of standard SA when it is applied to anisotropic problems. For anisotropic problems, it is fairly standard to generate small aggregates (used to mimic semi‐coarsening) in order to coarsen only in directions of strong coupling. Although beneficial to convergence, this can lead to a prohibitively large number of non‐zeros in the standard SA prolongator and the corresponding coarse discretization operator. To avoid this, the new prolongator modifies the standard prolongator by shifting support (non‐zeros within a prolongator column) from one aggregate to another to satisfy a specified non‐zero pattern. This leads to a sparser operator that can be used effectively within a multigrid V‐cycle. The key to this algorithm is that it preserves certain null space interpolation properties that are central to SA for both scalar and systems of partial differential equations (PDEs). We present two‐dimensional and three‐dimensional numerical experiments to demonstrate that the new method is competitive with standard SA for scalar problems, and significantly better for problems arising from PDE systems. Copyright © 2008 John Wiley & Sons, Ltd.
Phase I study of SU5416, a small molecule inhibitor of the vascular endothelial growth factor receptor (VEGFR) in refractory pediatric central nervous system tumors
Authors: Kieran Mark W. , Supko Jeffrey G. , Wallace Dana , Fruscio Robert , Poussaint Tina Young , Phillips Peter , Pollack Ian , Packer Roger , Boyett James M. , Blaney Susan , Banerjee Anu , Geyer Russ , Friedman Henry , Goldman Stewart , Kun Larry E. , MacDonald Tobey ,   on behalf of the Pediatric Brain Tumor Consortium
Published: December 2008

AbstractSU5416 is a novel small molecule tyrosine kinase inhibitor of the VEGF receptors 1 and 2. A phase I dose escalation study stratified by concurrent use (stratum II) or absence (stratum I) of enzyme‐inducing anticonvulsant drugs was undertaken to estimate the maximum‐tolerated dose (MTD) and to describe the toxicity profile of SU5416 in pediatric patients with refractory brain tumors. Dose escalations were conducted independently for stratum I starting at 110 mg/m2while stratum II started at 48 mg/m2. Thirty‐three eligible patients were treated on stratum I (n = 23) and stratum II (n = 10). Tumor types included 23 glial tumors, 4 neural tumors, 4 ependymomas, and 2 choroid plexus carcinomas. The MTD in stratum I was initially estimated to be 110 mg/m2. The protocol was amended to determine the MTD after excluding transient AST elevation. Re‐estimation of the MTD began at the 145 mg/m2dose level but due to development of SU5416 being stopped by the sponsor, the trial was closed before completion. The most serious drug‐related toxicities were grade 3 liver enzyme abnormalities, arthralgia, and hallucinations. The plasma pharmacokinetics of SU5416 was not significantly affected by the concurrent administration of enzyme‐inducing anticonvulsant drugs. Mean values of the total body clearance, apparent volume of distribution, and terminal phase half‐life of SU5416 for the 19 patients in stratum I were 26.1 ± 12.5 l/hr/m2, 41.9 ± 21.4 l/m2, and 1.11 ± 0.41 hr, respectively. The plasma pharmacokinetics of SU5416 in children was similar to previously reported findings in adult cancer patients. Prolonged disease stabilization was observed in 4 of 16 stratum I patients. Pediatr Blood Cancer 2009;52:169–176. © 2008 Wiley‐Liss, Inc.
Ionic and radical fragmentations of alkoxyhalocarbenes – a perspective
Authors: Moss Robert A. 
Published: December 2008

AbstractFragmentations of secondary or tertiary alkoxyhalocarbenes in polar solvents generate carbocations as components of ion pairs. A variety of carbocations can be produced including acyclic, alicyclic, benzyl, bridgehead, cyclopropyl, cyclopropylcarbinyl, and norbornyl examples. Laser flash photolysis (LFP) studies provide kinetics and activation parameters for the carbene fragmentations, which are orders of magnitude faster, and require considerably reduced activation energies, compared to analogous solvolytic carbocation‐generative processes. In some cases, the time required for solvent and anion equilibration of the ion pairs can be estimated. In nonpolar solvents, the gas phase, or cryogenic matrices, homolytic carbene fragmentation may, in certain cases, supplant heterolytic fragmentation. Copyright © 2008 John Wiley & Sons, Ltd.
Tracing pathway activities with kinase inhibitors and reverse phase protein arrays
Authors: van Oostrum Jan , Calonder Claudio , Rechsteiner Daniel , Ehrat Markus , Mestan Jürgen , Fabbro Doriano , Voshol Hans 
Published: December 2008

AbstractControlling aberrant protein kinase activity is a promising strategy for a variety of diseases, particularly cancer. Hence, the development of kinase inhibitors is currently a focal point for pharmaceutical research. In this study we utilize a chip‐based reverse phase protein array (RPA) platform for profiling of kinase inhibitors in cell‐based assays. In combination with the planar wave‐guide technology the assay system has an absolute LOD down to the low zeptomole range. A431 cell lysates were analyzed for the activation state of key effectors in the epidermal growth factor (EGF) and insulin signaling pathways to validate this model for compound screening. A microtiter‐plate format for growing, treating, and lysing cells was shown to be suitable for this approach, establishing the value of the technology as a screening tool for characterization of large numbers of kinase inhibitors against a wide variety of cellular signaling pathways. Moreover, the reverse array format allows rapid development of site‐specific phosphorylation assays, since in contrast to ELISA type systems only a single antigen‐specific antibody is required.
The proteome of the human breast cancer cell line MDA‐MB‐231: Analysis by LTQ‐Orbitrap mass spectrometry
Authors: Strande Vaïk , Canelle Ludovic , Tastet Christophe , Burlet‐Schiltz Odile , Monsarrat Bernard , Hondermarck Hubert 
Published: December 2008

AbstractWe have used a combination of SDS‐PAGE and LTQ‐Orbitrap MS to explore the proteome of the highly invasive MDA‐MB‐231 breast cancer cell line. Based on about 520 000 MS/MS spectra, a total of 3481 proteins were identified and subsequently classified according to their cellular distribution and molecular function. Interestingly, a large proportion of proteins (38%) were from cellular membranes and we were able to characterize numerous proteins involved in cancer initiation and progression such as the tumor suppressor p53 and the epidermal growth factor receptor. Together, this study represents the largest proteome database of breast cancer cells realized to date and demonstrates the value of using Orbitrap MS for deeper proteome analysis.
A method for the analysis of domain movements in large biomolecular complexes
Authors: Poornam Guru Prasad , Matsumoto Atsushi , Ishida Hisashi , Hayward Steven 
Published: December 2008

AbstractA new method for the analysis of domain movements in large, multichain, biomolecular complexes is presented. The method is applicable to any molecule for which two atomic structures are available that represent a conformational change indicating a possible domain movement. The method is blind to atomic bonding and atom type and can, therefore, be applied to biomolecular complexes containing different constituent molecules such as protein, RNA, or DNA. At the heart of the method is the use of blocks located at grid points spanning the whole molecule. The rotation vector for the rotation of atoms from each block between the two conformations is calculated. Treating components of these vectors as coordinates means that each block is associated with a point in a “rotation space” and that blocks with atoms that rotate together, perhaps as part of the same rigid domain, will have colocated points. Thus a domain can be identified from the clustering of points from blocks that span it. Domain pairs are accepted for analysis of their relative movements in terms of screw axes based upon a set of reasonable criteria. Here, we report on the application of the method to biomolecules covering a considerable size range: hemoglobin, liver alcohol dehydrogenase, S‐Adenosylhomocysteine hydrolase, aspartate transcarbamylase, and the 70S ribosome. The results provide a depiction of the conformational change within each molecule that is easily understood, giving a perspective that is expected to lead to new insights. Of particular interest is the allosteric mechanism in some of these molecules. Results indicate that common boundaries between subunits and domains are good regions to focus on as movement in one subunit can be transmitted to another subunit through such interfaces. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Isoform‐specific variation in the intrinsic disorder of the ecdysteroid receptor N‐terminal domain
Authors: Nocula‐Ługowska Małgorzata , Rymarczyk Grzegorz , Lisowski Marek , Ożyhar Andrzej 
Published: December 2008

AbstractThe Drosophila melanogaster ecdysteroid receptor (EcR) is a member of the nuclear hormone receptor superfamily. EcR controls animal development and metamorphosis by activating or repressing the transcription of target genes. There are three EcR isoforms, EcRA, EcRB1, and EcRB2 that exhibit diverse spatial and temporal distributions within various tissues and reveal essential functional differences. These differences can be attributed to the isoform‐specific N‐terminal domains (NTDs), which differ in length and primary structure. To lay a foundation for understanding of the molecular mechanism underlying functional diversity of the isoforms, we have carried out a comprehensive biochemical and biophysical analysis of purified hexahistidine‐tagged EcRA and EcRB1 NTDs (EcRA‐NTD and EcRB1‐NTD). The results, along with in silico examinations of the primary structures indicate that the EcR NTDs exhibit properties of premolten globule‐like intrinsically disordered proteins. Furthermore, we demonstrate for the first time that NTDs of isoforms of a particular nuclear hormone receptor exhibit distinct structural properties. In silico analysis revealed that the EcRA‐NTD sequence has a bigger tendency for disorder than the EcRB1‐NTD sequence. Accordingly, the circular dichroism experiments demonstrated that EcRA‐NTD has lower regular secondary structure content than EcRB1‐NTD and the size‐exclusion chromatography showed that EcRA‐NTD is less compact than EcRB1‐NTD. Furthermore, the limited proteolysis analysis revealed that the C‐terminal region common to both NTDs is more susceptible to the enzymatic cleavage in EcRA‐NTD than in EcRB1‐NTD. We postulate that unique conformational states of EcRA‐NTD and EcRB1‐NTD might act as the starting points for the functional diversity of EcRA and EcRB1 isoforms. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Spot the Hazard! A cultural extension of hazard identification training
Authors: Wasileski Robert F. 
Published: December 2008

AbstractHazard identification training (HIT) programs have been used in the chemical processing industry to raise awareness with employees on what constitutes a process hazard and techniques for identifying these hazards. Quite often these HIT programs will deliver the course material to the participants as classroom instruction, computer‐based training, organized field reviews, or a combination of these formats. These presentations tend to be one‐time efforts or cyclic programs that reach the target audience on some periodic basis (e.g., triennially). Although the content of the course material may be educational, these programs often have limited success because of their inability to make a lasting impression with the participants. Organizational and personnel changes, employee turnover, vanishing corporate memory, and shifting priorities can all have an undermining effect on the well‐intended efforts of traditional HIT programs. The challenge thus becomes finding ways to keep the knowledge both relevant and current, to effect lasting cultural change in a dynamic environment.This article presents a unique HIT program known as “Spot the Hazard,” which uses the facility's intranet to reinforce the concepts taught in the classroom. Spot the Hazard blends photographic examples and technical knowledge with aspects of behavior modification. The photographs that are presented have not been staged and thus are germane to the employees. The inherent on‐going nature of the program ensures the knowledge remains current, while at the same time it provides a platform for making a positive cultural change.The concepts of Spot the Hazard are explained in greater detail in the current article, along with a representative number of actual examples. © 2008 American Institute of Chemical Engineers Process Saf Prog, 2009
Superconductivity in diamond induced by boron doping at high pressure
Authors: Ekimov E. A. , Sidorov V. A. , Zoteev A. , Lebed' Yu. , Thompson J. D. , Bauer E. D. , Stishov S. M. 
Published: December 2008

AbstractThe application of hydrostatic pressure to boron‐doped diamond samples produces a linear decrease in the superconducting transition temperature Tc. The values d ln Tc/dP obtained for samples with different Tc's collapse near an average value –2 × 10–2 GPa–1, which is in reasonable agreement with theoretical predictions based on an electron–phonon mechanism of superconductivity in diamond within the virtual crystal approximation [Y. Ma et al., Phys. Rev. B 72, 014306 (2005)]. For the first time, superconducting boron‐doped diamond samples were synthesized with 10B and 13C isotopes. Isotopic substitution permits us to relate almost all bands in the Raman spectra of heavily boron‐doped diamond with the vibrations of carbon atoms. The “500 cm–1” Raman band shifts with both carbon and boron isotope substitutions and is associated with vibrations of clustered boron. We claim the presence of a carbon isotope effect in superconducting diamond. This fact supports the importance of the electron–phonon interaction as the mechanism of superconductivity in diamond. The value of the isotope effect coefficient is β0 = –d ln Tc/d ln M = 0.5 ± 0.3. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electronic and optical properties of III‐nitrides under pressure
Authors: Christensen N. E. , Gorczyca I. , Laskowski R. , Svane A. , Albers R. C. , Chantis A. N. , Kotani T. , van Schilfgaarde M. 
Published: December 2008

AbstractResults of theoretical studies of electronic and optical properties of III–V nitride compound semiconductors under pressure are presented. As representatives InN and AlN have been chosen, and for InN the pressure effects on the fundamental gap as well as the role of conduction‐band filling are examined. Both the fundamental gap and the electron effective mass increase with pressure, but due to the strong non‐parabolicity of the conduction band, the pressure coefficient of the mass decreases with electron concentration. Particular attention is paid to the electronic states in the gap region. The “local‐density gap error” is avoided by performing Quasi Particle self‐consistent GW calculations, which produce slightly too large gaps. Including in addition the missing electron–hole excitonic states and the gap renormalization due to electron–phonon interaction a gap reduction is obtained. The e–h correlations are deduced from solutions of the Bethe‐Salpeter equation. These are further used to study excitonic states in the gap of AlN under pressure, and for the rocksalt phase a pressure induced delocalized → localized transition is predicted. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Study of UV excited white light‐emitting diodes for optimization of luminous efficiency and color rendering index
Authors: Cho Jaehee , Kim Hyungkun , Sone Cheolsoo , Park Yongjo , Kim Young Sic , Kubota Shunichi , Yoon Euijoon 
Published: December 2008

AbstractWavelength down‐converted white‐light sources excited by near ultraviolet light‐emitting diodes require specific phosphor properties in order to generate high‐quality white light (namely, light with good color rendition and stability of color coordinate). Simulation and experimental results are discussed, with particular emphasis on the spectral distribution property of red phosphor required to realize high values of luminous efficiency and color rendition. A peak wavelength of 610 nm and an FWHM of 80 nm for the spectral power distribution were proposed, and co‐doped phosphate materials were synthesized successfully. This can contribute to a white‐light source with a luminous efficiency of 45 lm/W and color rendering index greater than 90 at a color temperature of 5600 K and an operational current of 20 mA. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Exploring Equisetum arvense L., Equisetum ramosissimum L. and Equisetum telmateia L. as sources of natural antioxidants
Authors: Štajner Dubravka , Popović Boris M. , Čanadanović‐Brunet Jasna , Anačkov Goran 
Published: December 2008

AbstractThe antioxidant and scavenging activities of above ground parts of Equisetum arvense L., Equisetum ramosissimum L. and Equisetum telmateia L. phosphate buffer (pH 7) extracts were investigated. Activities of antioxidant enzymes (superoxide dismutase, catalase, guaiacol peroxidase and glutathione peroxidase), quantities of reduced glutathione, malonyldialdehyde, superoxide and hydroxyl radicals and flavonoid, soluble protein, chlorophyll a, b and carotenoid contents were determined. The total antioxidant capacity was determined by ferric reducing antioxidant power (FRAP) assay. The Equisetum telmateia extract demonstrated scavenging and antioxidant properties better than Equisetum ramosissimum and Equisetum arvense. The ESR signal of DMPO‐OH radical adducts in the presence of Equisetum telmateia phosphate buffer (pH 7) extract was reduced by 98.9% indicating that Equisetum telmateia could be a useful source of antioxidants with huge scavenging ability. Copyright © 2008 John Wiley & Sons, Ltd.
Effects of hydroxytyrosol‐20 on carrageenan‐induced acute inflammation and hyperalgesia in rats
Authors: Gong Dezheng , Geng Chengyan , Jiang Liping , Cao Jun , Yoshimura Hiroyuki , Zhong Laifu 
Published: December 2008

AbstractHydroxytyrosol (HT) is a simple phenol compound extracted from olive leaves. The content of HT in the studied preparation was about 20%, and the preparation was called hydroxytyrosol‐20 (HT‐20). HT has antioxidant and antiinflammatory activities. There has been no report so far on the efficacy of HT‐20 in carrageenan‐induced acute inflammation and hyperalgesia in rats. Therefore, the aim of this study was to assess the inhibitory role of HT‐20 on carrageenan‐induced swelling and hyperalgesia of rat paw. Paw inflammation was assessed by the increase in paw volume and hyperalgesia. The rat paws were cut out under ether anesthesia at 270 min after administration of carrageenan. The tissue of the right paw was isolated separately from the individual rat. The levels of the tumor necrosis factor‐alpha (TNF‐α), interleukin 1β(IL‐1β) and interleukin 10 (IL‐10) mRNA in the tissue were estimated by reverse transcription‐polymerase chain reaction (RT‐PCR). The results showed that the paw pressure thresholds of rats orally administered HT‐20 significantly increased at 210, 240 and 270 min after administration of carrageenan, compared with corresponding basal paw pressure thresholds; the degree of swelling of the right hind paw showed a statistically significant reduction, compared with rats in the carrageenan‐treated control. In this model, HT‐20 appears to decrease pro‐inflammatory cytokines IL‐1βand TNF‐αand not to increase the antiinflammatory cytokine mRNA expression of IL‐10. Copyright © 2008 John Wiley & Sons, Ltd.
Using degradation data to assess reliability: a case study on train wheel degradation
Authors: Freitas Marta A. , de Toledo Maria Luíza G. , Colosimo Enrico A. , Pires Magda C. 
Published: December 2008

AbstractDegradation experiments are usually used to assess the lifetime distribution of highly reliable products, which are not likely to fail under the traditional life tests or accelerated life tests. In such cases, if there exist product characteristics whose degradation over time can be related to reliability, then collecting ‘degradation data’ can provide information about product reliability. In general, the degradation data are modeled by a nonlinear regression model with random coefficients. If we can obtain the estimates of parameters under the model, then the failure‐time distribution can be estimated. In order to estimate those parameters, three basic methods are available, namely, the analytical, numerical and the approximate. They are chosen according to the complexity of the degradation path model used in the analysis. In this paper, the numerical and the approximate methods are compared in a simulation study, assuming a simple linear degradation path model. A comparison with traditional failure‐time analysis is also performed. The mean‐squared error of the estimated 100pth percentile of the lifetime distribution is evaluated for each one of the approaches. The approaches are applied to a real degradation data set. Copyright © 2008 John Wiley & Sons, Ltd.
Characterizing future large, rapid changes in aggregated wind power using Numerical Weather Prediction spatial fields
Authors: Cutler Nicholas J. , Outhred Hugh R. , MacGill Iain F. , Kay Merlinde J. , Kepert Jeffrey D. 
Published: December 2008

AbstractA critical limiting factor to the successful deployment of a large proportion of wind power in power systems is its predictability. Power system operators play a vital role in maintaining system security, and this task is greatly aided by useful characterizations of future system operations. A wind farm power forecast generally relies on the forecast output from a Numerical Weather Prediction (NWP) model, typically at a single grid point in the model to represent the wind farm's physical location. A key limitation of this approach is the spatial misplacement of weather features often found in NWP forecasts. This paper presents a methodology to display wind forecast information from multiple grid points at hub height around the wind farm location. If the raw forecast wind speeds at hub height at multiple grid points were to be displayed directly, they would be misleading as the NWP outputs take account of the estimated local surface roughness and terrain at each grid point. Hence, the methodology includes a transformation of the wind speed at each grid point to an equivalent value that represents the surface roughness and terrain at the chosen single grid point for the wind farm site. The chosen‐grid‐point‐equivalent wind speeds for the wind farm can then be transformed to available wind farm power. The result is a visually‐based decision support tool which can help the forecast user to assess the possibilities of large, rapid changes in available wind power from wind farms. A number of methods for displaying the field for multiple wind farms are discussed. The chosen‐grid‐point‐equivalent transformation also has other potential applications in wind power forecasting such as assessing deterministic forecast uncertainty and improving downscaling results. Copyright © 2008 John Wiley & Sons, Ltd.