bluuebunny/crossref_metadata_2025_split huggingface dataset:
Halide Activation by Heme Peroxidases: Theoretical Predictions on Putative Adducts of Halides with Compound I
Authors: Silaghi‐Dumitrescu Radu 
Published: October 2008

AbstractThe first density functional theory (DFT) results on models of the putative FeIII–OX and FeIII–HOX (X = halogen) adducts of chloroperoxidase (CPO) and myeloperoxidase (MPO) are reported, and their stability and electronic structure assessed. The oxygen–halogen bonds are computed to be particularly weak, to the extent where ferric hypohalous acid complexes with intact oxygen–halide bonds should be difficult to observe in heme peroxidases; a ‘caged' adduct, featuring a ferric species in close (but not covalent) contact with the oxidized halide, appears as a likely alternative for an observable intermediate in CPO and MPO. The presence of an axial thiolate (CPO) or imidazole (MPO) ligand in a position trans to the hypohalous moiety is calculated to have a distinct effect on halide activation, with relevance to the TSR (two‐state reactivity) concept.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)
Heterolignans: Stereoselective Synthesis of an 11‐Amino Analog of Azaelliptitoxin
Authors: Routier Julie , Calancea Mihaela , David Marion , Vallée Yannick , Denis Jean‐Noël 
Published: October 2008

AbstractThe 11‐amino‐azaelliptitoxin analog (11R,11aS,5R)‐15 has been prepared stereoselectively in eight steps and 24 % overall yield from commercially available (S)‐glycidol (7) via the original enantiopure chiral α‐amino aldehyde 9, used as chiral precursor for the creation of the two other stereogenic centers of the target framework. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)
The Synthesis and Physical Properties of Novel Polyaromatic Profluorescent Isoindoline Nitroxide Probes (Eur. J. Org. Chem. 32/2008)
Authors: Fairfull‐Smith Kathryn E. , Bottle Steven E. 
Published: October 2008

AbstractThe cover picture shows the minimal fluorescence emitted from a nitroxide‐quenched diphenylanthracene fluorophore (left‐hand side) and the contrasting strongly fluorescent result after the spin of the nitroxide radical has been removed by reduction or radical trapping (second from left). The same differential can be seen for the acetylene‐extended system. The top right of the picture shows the same four flasks viewed in visible light. Details are discussed in the article by K. E. Fairfull‐Smith and S. E. Bottle on p. 5391 ff. Photo courtesy of Dr. Aaron Micallef, AIBN, University of Queensland, Australia.
An adaptive cut‐cell method for environmental fluid mechanics
Authors: Barad Michael F. , Colella Phillip , Schladow S. Geoffrey 
Published: October 2008

AbstractIn this work we present a numerical method for solving the incompressible Navier–Stokes equations in an environmental fluid mechanics context. The method is designed for the study of environmental flows that are multiscale, incompressible, variable‐density, and within arbitrarily complex and possibly anisotropic domains. The method is new because in this context we couple the embedded‐boundary (or cut‐cell) method for complex geometry with block‐structured adaptive mesh refinement (AMR) while maintaining conservation and second‐order accuracy. The accurate simulation of variable‐density fluids necessitates special care in formulating projection methods. This variable‐density formulation is well known for incompressible flows in unit‐aspect ratio domains, without AMR, and without complex geometry, but here we carefully present a new method that addresses the intersection of these issues. The methodology is based on a second‐order‐accurate projection method with high‐order‐accurate Godunov finite‐differencing, including slope limiting and a stable differencing of the nonlinear convection terms. The finite‐volume AMR discretizations are based on two‐way flux matching at refinement boundaries to obtain a conservative method that is second‐order accurate in solution error. The control volumes are formed by the intersection of the irregular embedded boundary with Cartesian grid cells. Unlike typical discretization methods, these control volumes naturally fit within parallelizable, disjoint‐block data structures, and permit dynamic AMR coarsening and refinement as the simulation progresses. We present two‐ and three‐dimensional numerical examples to illustrate the accuracy of the method. Copyright © 2008 John Wiley & Sons, Ltd.
Robustness and accuracy of SPH formulations for viscous flow
Authors: Basa Mihai , Quinlan Nathan J. , Lastiwka Martin 
Published: October 2008

AbstractNumerous methods are available for the modelling of viscous stress terms in smoothed particle hydrodynamics (SPH). In this work, the existing methods are investigated systematically and evaluated for a range of Reynolds numbers using Poiseuille channel and lid‐driven cavity test cases. The best results are obtained using two methods based on combinations of finite difference and SPH approximations, due to Morris et al. and Cleary. Gradients of high‐valued functions are shown to be inaccurately estimated with standard SPH. A method that reduces the value of functions (in particular, pressure) before calculating the gradients reduces this inaccuracy and is shown to improve performance. A mode of instability in Poiseuille channel flows, also reported in other works, is examined and a qualitative explanation is proposed. The choice of boundary implementation is shown to have a significant effect on transient velocity profiles in start‐up of the flow. The use of at least linear extrapolation for in‐wall velocities is shown to be preferable to mirroring of velocities. Consistency corrections to the kernel are also found to result in significant accuracy and stability improvements with most methods, though not in all cases. Copyright © 2008 John Wiley & Sons, Ltd.
A fast method for solving fluid–structure interaction problems numerically
Authors: Murea C. M. , Sy S. 
Published: October 2008

AbstractThe paper presents a semi‐implicit algorithm for solving an unsteady fluid–structure interaction problem. The algorithm for solving numerically the fluid–structure interaction problems was obtained by combining the backward Euler scheme with a semi‐implicit treatment of the convection term for the Navier–Stokes equations and an implicit centered scheme for the structure equations. The structure is governed either by the linear elasticity or by the non‐linear St Venant–Kirchhoff elasticity models. At each time step, the position of the interface is predicted in an explicit way. Then, an optimization problem must be solved, such that the continuity of the velocity as well as the continuity of the stress hold at the interface. During the Broyden, Fletcher, Goldforb, Shano (BFGS) iterations for solving the optimization problem, the fluid mesh does not move, which reduces the computational effort. The term ‘semi‐implicit’ used for the fully algorithm means that the interface position is computed explicitly, while the displacement of the structure, velocity and the pressure of the fluid are computed implicitly. Numerical results are presented. Copyright © 2008 John Wiley & Sons, Ltd.
Numerical investigation of the effect of inlet condition on self‐excited oscillation of wet steam flow in a supersonic turbine cascade
Authors: Xiaoming Wu , Liang Li , Guojun Li , Zhenping Feng 
Published: October 2008

AbstractSelf‐excited oscillation can be induced due to the interaction between condensation process and local transonic condition in condensing flow, which is an important problem in wet steam turbine. With an Eulerian/Eulerian numerical model, the self‐excited oscillation of wet steam flow is investigated in a supersonic turbine cascade. Owing to supercritical heat addition to the subsonic flow in the convergent part of the cascade, the oscillation frequency decreases with increased inlet supercooling. Mass flow rate increases in the oscillating flow due to the greater supersaturation in condensation process, while the increase will be suppressed with the flow oscillation. Higher inlet supercooling leads to the fact that the condensation process moves upstream and the loss increases. Moreover, some predictions of oscillation effects on outflow angle and aerodynamic force are also presented. Finally, heterogeneous condensations with inlet wetness and periodic inlet conditions, as a result of the interference between stator and rotor, are discussed. Copyright © 2008 John Wiley & Sons, Ltd.
Edge‐based finite element implementation of the residual‐based variational multiscale method
Authors: Lins Erb F. , Elias Renato N. , Guerra Gabriel M. , Rochinha Fernando A. , Coutinho Alvaro L. G. A. 
Published: October 2008

AbstractIn this work we extend our edge‐based stabilized finite element incompressible flow solver to turbulence modeling with the residual‐based variational multiscale (RB‐VMS) method. Using the advective‐form of the convection term of the Navier–Stokes equations, RB‐VMS is implemented as a straightforward extension of standard stabilized methods with a modified advective velocity. This requires minimum modification of the existing highly optimized code. Two test cases were solved to assess accuracy and performance of the present implementation. First, the laminar incompressible flow past a circular cylinder at Re = 100 and second, the fully turbulent incompressible flow in a lid‐driven cubic cavity at Re = 12000. Comparisons were made with standard stabilized finite element formulations, highly resolved numerical simulations and experimental data. Results have shown that the present implementation is able to achieve reasonable accuracy without performance degradation in different flow regimes. Copyright © 2008 John Wiley & Sons, Ltd.
Related‐variables selection in temporal disaggregation
Authors: Fukuda Kosei 
Published: October 2008

AbstractTwo related‐variables selection methods for temporal disaggregation are proposed. In the first method, the hypothesis tests for a common feature (cointegration or serial correlation) are first performed. If there is a common feature between observed aggregated series and related variables, the conventional Chow–Lin procedure is applied. In the second method, alternative Chow–Lin disaggregating models with and without related variables are first estimated and the corresponding values of the Bayesian information criterion (BIC) are stored. It is determined on the basis of the selected model whether related variables should be included in the Chow–Lin model. The efficacy of these methods is examined via simulations and empirical applications. Copyright © 2008 John Wiley & Sons, Ltd.
Effectiveness of a psychoeducational intervention program in the reduction of caregiver burden in alzheimer's disease patients' caregivers
Authors: Martín‐Carrasco Manuel , Martín Manuel Franco , Valero Carmelo Pelegrín , Millán Pedro Roy , García Celso Iglesias , Montalbán Salvador Ros , Vázquez Ana Luisa Gobartt , Piris Sonia Pons , Vilanova Montserrat Balañá 
Published: October 2008

AbstractObjectivesCaregivers of patients with Alzheimer's disease (AD) experience physical and psychological stress due to the caring experience. This study evaluated the benefits of a Psychoeducational Intervention Program (PIP) on caregiver burden in southern Europe.MethodsA multicentre, prospective, randomised study was conducted. One hundred and fifteen caregivers of patients with clinical diagnosis of AD (DSM‐IV‐TR criteria, mini‐mental score = 10–26) and functional impairment (Lawton and Brody Scale and Katz Index) were recruited. Caregivers were randomised to receive either PIP (IG: intervention group, n = 60) or standard care (CG: control group, n = 55). PIP consisted of eight individual sessions over 4 months for teaching strategies for confronting problems of AD patient care. Caregivers' stress, quality of life and perceived health were measured using validated scales (Zarit, SF‐36, GHQ‐28, respectively) at baseline and after 4 and 10‐months follow‐up.ResultsMean change in caregiver burden (Zarit baseline–Zarit final scores) was statistically significant (p = 0.0083) showing an improvement in the IG (−8.09 points) and a worsening in the CG (2.08 points). The IG showed significant improvements in all the well‐being perception areas measured by the SF‐36 and a significantly lower score in the GHQ‐28 (p = 0.0004). 97.7% of caregivers and 88.6% of therapists considered PIP ‘useful/very useful’ at 4 months (the end of PIP) whereas at 10 months the estimates were 93.2% and 86.3%, respectively.ConclusionsPsychosocial training of caregivers can minimise caregiver distress and help them to develop problem‐solving strategies. A PIP improves quality of life and the perceived health of caregivers of patients with AD. Copyright © 2008 John Wiley & Sons, Ltd.
Allelic imbalances and homozygous deletion on 8p23.2 for stepwise progression of hepatocarcinogenesis # †
Authors: Midorikawa Yutaka , Yamamoto Shogo , Tsuji Shingo , Kamimura Naoko , Ishikawa Shumpei , Igarashi Hisaki , Makuuchi Masatoshi , Kokudo Norihiro , Sugimura Haruhiko , Aburatani Hiroyuki 
Published: October 2008

Abstract
Early hepatocellular carcinoma (eHCC) originates from the hepatocytes of chronic liver disease and develops into classical hepatocellular carcinoma (HCC). To identify sequential genetic changes in multistep hepatocarcinogenesis, we analyzed molecular karyotypes using oligonucleotide genotyping 50K arrays. First, 1q21.3-44 gain and loss of heterozygosity (LOH) on 1p36.21-36.32 and 17p13.1-13.3 were frequently observed in eHCC, but not in chronic liver diseases, suggesting that such chromosomal aberrations are early, possibly causative events in liver cancer. Next, we detected 25 chromosomal loci associated with liver cancer progression in five HCCs with nodule-in-nodule appearance, in which the inner nodule develops within eHCC lesion. Using these chromosomal regions as independent variables, decision tree analysis was applied on 14 early and 25 overt HCCs, and extracted combination of chromosomal gains on 5q11.1-35.3 and 8q11.1-24.3 and LOH on 4q11-34.3 and 8p11.21-23.3 as distinctive attributes, which can classify early and overt HCCs recursively. In these four altered regions identified as late events of hepatocarcinogenesis, two tumors in 32 overt HCCs analyzed in the present study and one in a set of independent samples of 36 overt HCCs in our previous study harbored a homozygous deletion near the CSMD1 locus on 8p23.2. CSMD1 messenger RNA expression was decreased in HCC without 8p23.2 deletion, possibly due to hypermethylation of the CpG islands in its promoter region. Conclusion: 1q gain and 1p and 17p LOH are early molecular events, whereas gains in 5q and 8q and LOH on 4q and 8p only occur in advanced HCC, and inactivation of the putative suppressor gene, CSMD1, may be the key event in progression of liver cancer. (Hepatology 2009.)
Lumican, a small leucine‐rich proteoglycan
Authors: Nikitovic Dragana , Katonis Paulos , Tsatsakis Aristidis , Karamanos Nikos K. , Tzanakakis George N. 
Published: October 2008

AbstractLumican belongs to the family of small leucine‐rich repeat proteoglycans. Recent studies have shown that lumican participates in the maintenance of tissue homeostasis and modulates cellular functions including cell proliferation, migration, and differentiation. The expression of lumican has been correlated to the growth and metastasis of various malignancies; however, its exact role in tumorogenesis remains elusive. This review focuses upon the role of lumican in cell biology, providing insights into molecular mechanisms that lumican likely utilizes to control processes relevant to tumorogenesis. © 2008 IUBMB IUBMB Life, 60(12): 818–823, 2008
Firefly bioluminescence: A mechanistic approach of luciferase catalyzed reactions
Authors: Marques Simone M. , Esteves da Silva Joaquim C. G. 
Published: October 2008

AbstractLuciferase is a general term for enzymes catalyzing visible light emission by living organisms (bioluminescence). The studies carried out with Photinus pyralis (firefly) luciferase allowed the discovery of the reaction leading to light production. It can be regarded as a two‐step process: the first corresponds to the reaction of luciferase's substrate, luciferin (LH2), with ATP‐Mg2+ generating inorganic pyrophosphate and an intermediate luciferyl‐adenylate (LH2‐AMP); the second is the oxidation and decarboxylation of LH2‐AMP to oxyluciferin, the light emitter, producing CO2, AMP, and photons of yellow‐green light (550– 570 nm). In a dark reaction LH2‐AMP is oxidized to dehydroluciferyl‐adenylate (L‐AMP). Luciferase also shows acyl‐coenzyme A synthetase activity, which leads to the formation of dehydroluciferyl‐coenzyme A (L‐CoA), luciferyl‐coenzyme A (LH2‐CoA), and fatty acyl‐CoAs. Moreover luciferase catalyzes the synthesis of dinucleoside polyphosphates from nucleosides with at least a 3′‐phosphate chain plus an intact terminal pyrophosphate moiety. The LH2 stereospecificity is a particular feature of the bioluminescent reaction where each isomer, D‐LH2 or L‐LH2, has a specific function. Practical applications of the luciferase system, either in its native form or with engineered proteins, encloses the analytical assay of metabolites like ATP and molecular biology studies with luc as a reporter gene, including the most recent and increasing field of bioimaging. © 2008 IUBMB IUBMB Life, 61(1): 6–17, 2009
Chartering new territory: diversification, legitimacy, and practice area creation in professional service firms
Authors: Gardner Heidi K. , Anand N. , Morris Timothy 
Published: October 2008

AbstractDiversification into innovative domains through new practice area creation is a critical imperative for professional services firms. Using theories of organizational territoriality and corporate charters, we conceptualize professional firms as federations of distinct practice areas and argue that the chartering of a new practice is an inherently political act. New practice area founders need to engage in appropriate legitimacy‐mobilizing efforts in order to sustain diversification efforts. Our analysis of 46 cases of new practice area creation efforts in consulting and law firms shows that the mix of legitimacy required for new practice areas created through radical diversification is very different from that required for incremental diversification efforts. Our findings have important implications for studying how innovation is structurally accomplished in professional firms. Copyright © 2008 John Wiley & Sons, Ltd.
Recognising subtidal foraminiferal assemblages: implications for quantitative sea‐level reconstructions using a foraminifera‐based transfer function
Authors: Woodroffe Sarah A. 
Published: October 2008

AbstractMicrofossil‐based transfer function models are increasingly used to provide decimeter‐scale sea‐level change reconstructions. In this paper I demonstrate that in the tropical location of northern Australia problems arise in selecting the appropriate elevation range for the modern training set used to calibrate fossil calcareous foraminiferal assemblages. Most calcareous foraminiferal species found in cores occur in both modern intertidal and shallow subtidal environments. A lack of independent measures to indicate whether fossil assemblages come from intertidal environments forces use of a training set that includes intertidal and subtidal environments. This results in decreased precision compared to using a training set solely from intertidal environments. The widely used method of assessing model fit to fossil assemblages (modern analogue technique) often fails to discriminate between acceptable and unacceptable reconstructions. It is important to investigate a number of different measures including modern analogue technique, canonical correspondence analysis and changing bootstrapped sample specific transfer function errors to fully understand the level of similarity between modern and fossil foraminiferal samples, to judge the reliability of transfer function‐predicted sea‐level reconstructions. Copyright © 2008 John Wiley & Sons, Ltd.
Marine geophysical evidence for former expansion and flow of the Greenland Ice Sheet across the north‐east Greenland continental shelf
Authors: Evans Jeffrey , Ó Cofaigh Colm , Dowdeswell Julian A. , Wadhams Peter 
Published: October 2008

AbstractHigh‐resolution swath bathymetry and TOPAS sub‐bottom profiler acoustic data from the inner and middle continental shelf of north‐east Greenland record the presence of streamlined mega‐scale glacial lineations and other subglacial landforms that are formed in the surface of a continuous soft sediment layer. The best‐developed lineations are found in Westwind Trough, a bathymetric trough connecting Nioghalvfjerdsfjorden Gletscher and Zachariae Isstrøm to the continental shelf edge. The geomorphological and stratigraphical data indicate that the Greenland Ice Sheet covered the inner‐middle shelf in north‐east Greenland during the most recent ice advance of the Late Weichselian glaciation. Earlier sedimentological and chronological studies indicated that the last major delivery of glacigenic sediment to the shelf and Fram Strait was prior to the Holocene during Marine Isotope Stage 2, supporting our assertion that the subglacial landforms and ice sheet expansion in north‐east Greenland occurred during the Late Weichselian. Glacimarine sediment gravity flow deposits found on the north‐east Greenland continental slope imply that the ice sheet extended beyond the middle continental shelf, and supplied subglacial sediment direct to the shelf edge with subsequent remobilisation downslope. These marine geophysical data indicate that the flow of the Late Weichselian Greenland Ice Sheet through Westwind Trough was in the form of a fast‐flowing palaeo‐ice stream, and that it provides the first direct geomorphological evidence for the former presence of ice streams on the Greenland continental shelf. The presence of streamlined subglacially derived landforms and till layers on the shallow AWI Bank and Northwind Shoal indicates that ice sheet flow was not only channelled through the cross‐shelf bathymetric troughs but also occurred across the shallow intra‐trough regions of north‐east Greenland. Collectively these data record for the first time that ice streams were an important glacio‐dynamic feature that drained interior basins of the Late Weichselian Greenland Ice Sheet across the adjacent continental margin, and that the ice sheet was far more extensive in north‐east Greenland during the Last Glacial Maximum than the previous terrestrial–glacial reconstructions showed. Copyright © 2008 John Wiley & Sons, Ltd.