bluuebunny/crossref_metadata_2025_split huggingface dataset:
BRACHYURY confers cancer stem cell characteristics on colorectal cancer cells
Authors: Sarkar Debalina , Shields Brian , Davies Melanie L. , Müller Jürgen , Wakeman Jane A. 
Published: March 2011

AbstractCancer stem cells (CSCs) are initiating cells in colorectal cancer (CRC). Colorectal tumours undergo epithelial to mesenchymal transition (EMT)‐like processes at the invasive front, enabling invasion and metastasis, and recent studies have linked this process to the acquisition of stem cell‐like properties. It is of fundamental importance to understand the molecular events leading to the establishment of cancer initiating cells and how these mechanisms relate to cellular transitions during tumourigenesis. We use an in vitro system to recapitulate changes in CRC cells at the invasive front (mesenchymal‐like cells) and central mass (epithelial‐like cells) of tumours. We show that the mesoderm inducer BRACHYURY is expressed in a subpopulation of CRC cells that resemble invasive front mesenchymal‐like cells, where it acts to impose characteristics of CSCs in a fully reversible manner, suggesting reversible formation and modulation of such cells. BRACHYURY, itself regulated by the oncogene β‐catenin, influences NANOG and other ‘stemness’ markers including a panel of markers defining CRC‐CSC whose presence has been linked to poor patient prognosis. Similar regulation of NANOG through BRACHYURY was observed in other cells lines, suggesting this might be a pathway common to cancer cells undergoing mesenchymal transition. We suggest that BRACHYURY may regulate NANOG in mesenchymal‐like CRC cells to impose a ‘plastic‐state’, allowing competence of cells to respond to signals prompting invasion or metastasis.
Optimization of a molecular mechanics force field for type‐II polyoxometalates focussing on electrostatic interactions: A case study
Authors: Courcot Blandine , Bridgeman Adam J. 
Published: March 2011

AbstractIn this study, we have focussed on type‐II polyanions such as [M7O24]6−, and we have developed and validated optimized force fields that include electrostatic and van der Waals interactions. These contributions to the total steric energy are described by the nonbonded term, which encompasses all interactions between atoms that are not transmitted through the bonds. A first validation of a stochastic technique based on genetic algorithms was previously made for the optimization of force fields dedicated to type‐I polyoxometalates. To describe the new nonbonded term added in the functional, a fixed‐charged model was chosen. Therefore, one of the main issues was to analyze that which partial atomic charges could be reliably used to describe these interactions in such inorganic compounds. Based on several computational strategies, molecular mechanics (MM) force field parameters were optimized using different types of atomic charges. Moreover, the influence of the electrostatic and van der Waals buffering constants and 1,4‐interactions scaling factors used in the force field were also tested, either being optimized as well or fixed with respect to the values of CHARMM force field. Results show that some atomic charges are not well adapted to CHARMM parameters and lead to unrealistic MM‐optimized structures or a MM divergence. As a result, a new scaling factor has been optimized for Quantum Theory of Atoms in Molecules charges and charges derived from the electrostatic potential such as ChelpG. The force fields optimized can be mixed with the CHARMM force field, without changing it, to study for the first time hepta‐anions interacting with organic molecules. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Force fields for metallic clusters and nanoparticles
Authors: Legenski Nicole , Zhou Chenggang , Zhang Qingfan , Han Bo , Wu Jinping , Chen Liang , Cheng Hansong , Forrey Robert C. 
Published: March 2011

AbstractAtomic force fields for simulating copper, silver, and gold clusters and nanoparticles are developed. Potential energy functions are obtained for both monatomic and binary metallic systems using an embedded atom method. Many cluster configurations of varying size and shape are used to constrain the parametrization for each system. Binding energies for these training clusters were computed using density functional theory (DFT) with the Perdew‐Wang exchange‐correlation functional in the generalized gradients approximation. Extensive testing shows that the many‐body potentials are able to reproduce the DFT energies for most of the structures that were included in the training set. The force fields were used to calculate surface energies, buk structures, and thermodynamic properties. The results are in good agreement with the DFT values and consistent with the available experimental data. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Rate constants for hydrogen abstraction reactions by the hydroperoxyl radical from methanol, ethenol, acetaldehyde, toluene, and phenol
Authors: Altarawneh Mohammednoor , Al‐Muhtaseb Ala'A H. , Dlugogorski Bogdan Z. , Kennedy Eric M. , Mackie John C. 
Published: March 2011

AbstractAn important step in the initial oxidation of hydrocarbons at low to intermediate temperatures is the abstraction of H by hydroperoxyl radical (HO2). In this study, we calculate energy profiles for the sequence: reactant + HO2 → [complex of reactants] → transition state → [complex of products] → product + H2O2 for methanol, ethenol (i.e., C2H3OH), acetaldehyde, toluene, and phenol. Rate constants are provided in the simple Arrhenius form. Reasonable agreement was obtained with the limited literature data available for acetaldehyde and toluene. Addition of HO2 to the various distinct sites in phenol is investigated. Direct abstraction of the hydroxyl H was found to dominate over HO2 addition to the ring. The results presented herein should be useful in modeling the lower temperature oxidation of the five compounds considered, especially at low temperature where the HO2 is expected to exist at reactive levels. © 2011 Wiley Periodicals, Inc. J Comput Chem 2011
Accurate macromodeling algorithm for time domain identification of transient port responses
Authors: Deschrijver D. , Dhaene T. 
Published: March 2011

SUMMARYOrthonormal vector fitting is a robust method for broadband macromodeling of frequency domain responses. The use of orthonormal rational basis functions makes the conditioning of the system equations less sensitive to the initial pole specification when compared with the classical Vector Fitting procedure. This paper presents a time domain generalization of the technique to compute broadband rational macromodels from transient input–output port responses. The efficacy of the approach is illustrated by two numerical examples. Copyright © 2011 John Wiley & Sons, Ltd.
Phase transitions in Pb8O5(XO4)2 (X = As and V) compounds
Authors: Oliveira E. A. , Silva E. N. , Paschoal A. R. , Dantas S. M. , Guedes I. , Mendes‐Filho J. , Polla G. , Ayala A. P. 
Published: March 2011

AbstractRaman spectroscopy, polarized microscopy and thermal measurements were used to investigate the sequence of phase transition in the lead oxide salts Pb8O5(XO4)2 (where X = As and V). For Pb8O5(AsO4)2, a second‐order phase transition is observed at 500 K. For Pb8O5(VO4)2, a second‐order and a first‐order structural phase transitions are observed at 425 and 525 K, respectively. The ferroelastic character of Pb8O5(VO4)2 is also discussed. Copyright © 2011 John Wiley & Sons, Ltd.
A highly efficient and versatile microchip capillary electrophoresis method for DNA separation using gold nanoparticle as a tag
Authors: Cao Wei , Chen Lei , Fu Youjian , Tan Zhenyi , Qu Bin 
Published: March 2011

AbstractA highly efficient and versatile method for DNA separation using Au nanoparticles (Au NPs) as a tag based on microchip capillary electrophoresis (MCE) was developed. The thiol‐modified DNA‐binding Au NPs were utilized as a tag. Target DNA was sandwiched between Au NPs and probe DNA labeled with horseradish peroxidase (HRP). In electrophoresis separation, the difference in electrophoretic mobility between free probe and probe‐target complex was magnified by Au NPs, which enabled the resulting mixture to be separated with high efficiency by microchip capillary electrophoresis. Horseradish peroxidase was used as a catalytic label to achieve sensitive electrochemical DNA detection via fast catalytic reactions. With this protocol, 27‐mer DNA fragments with different sequences were separated with high speed and high resolution. The proposed method was critical to achieve improved DNA separations in hybridization analyses.
Fluorinated FeF3 catalyst interactions in three different oil formulations using design of experiment optimization and chemistry characterization of tribofilms
Authors: Nehme Gabi 
Published: March 2011

ABSTRACTThe influence of fluorinated FeF3 catalyst on the formation and properties of tribofilms was examined using design of experiment (DOE) under extreme boundary lubrication (385 N or maximum Hertzian contact pressure of 2.72 GPa). A closed loop boundary condition test was developed to examine the behaviour of lubricants under boundary conditions. The reduction of phosphorus in engine oil was examined using two different plain oils and one fully formulated oil. Results indicate the formation of a thicker tribofilm in plain fluorinated oil when compared with fluorinated fully formulated oils.Several chemistry combinations were prepared and tested. Wear and frictional properties were evaluated using DOE, and the interactions of fluorinated FeF3 catalyst with minimum phosphorus were studied and compared with respect to fully formulated and plain zinc dialkyl dithiophosphate oils. Tribofilms with thickness ranging from 150 to 350 nm were developed during wear tests and were analysed for fluorinated plain and fully formulated oils that target reducing phosphorus. Three specific tests with optimised 0.6% FeF3 catalyst concentrations were used with 0.05% phosphorus in plain and fully formulated oil to verify the model optimised conditions with respect to wear and time to full break down. Scanning electron microscopy, hardness of the tribofilms and Auger spectroscopy confirm the presence of fluorine and phosphorus. These tests confirm the optimised prediction of the DOE model. Copyright © 2011 John Wiley & Sons, Ltd.
Addressing the Conformational Flexibility of Serine Racemase by Combining Targeted Molecular Dynamics, Conformational Sampling and Docking Studies
Authors: Bruno Agostino , Amori Laura , Costantino Gabriele 
Published: March 2011

AbstractSerine racemase (SR) is a PLP‐dependent enzyme catalyzing the racemization of L‐Ser into D‐Ser, which is now recognized as an endogenous co‐agonist at the NMDA receptor complex. As indicated by available X‐ray structures, SR undergoes significant conformational changes during ligand recognition, and it is conceivable that, in addition to the reported X‐ray structures, other intermediate conformational states may have relevance in drug discovery studies. Targeted molecular dynamics (TMD) simulations are an effective tools to follow the conformational transition of a protein under the constrain of reaching a known target states. In this study we use TMD to simulate the transition between the open and closed form of SR in the presence of the endogenous substrate or an orthosteric inhibitor. The trajectories thus obtained are then clustered to collect an ensemble of intermediate conformational states. Docking of a small library of known SR inhibitors or closely related inactive analogs demonstrates that ensemble docking performs better than docking on available crystal structures, thus indicating that inclusion of conformational flexibility into ligand design strategies will be crucial for the development of new classes of SR inhibitors.
Expression of Hsf1, Hsf2, and Phlda1 in cells undergoing cryptorchid‐induced apoptosis in rat testes
Authors: Liu Fang , Xu Zeng‐Lu , Qian Xiao‐Jing , Qiu Wen‐Ying , Huang Hui 
Published: March 2011

AbstractSurgery‐induced cryptorchidism, in which the testes are prevented from descending into the scrotal sac, results in testicular germ cell death, and it is commonly used as an experimental tool in the study of spermatogenesis. However, the molecular events underlying the activation of germ cell death remain poorly understood. In the present study, we investigate selective cell loss from cryptorchid rat testis by using DNA flow cytometry and by determining protein and mRNA expression of Hsf1, Hsf2, and Phlda1. The hypo‐haploid cell fraction is significantly decreased as early as 3 days after surgical induction of cryptorchidism (from 42.01 ± 5.74% to 15.98 ± 3.88%), followed by a significant decrease in the haploid cell fraction at Day 7. At the latter time point, an apoptotic peak of spermatocytes appears in DNA histograms just before the tetraploid peak; the percentage of aneuploid cells between diploid and tetraploid rises as high as 14.05 ± 2.98% of the total cells in 7‐day cryptorchid testis, suggesting that a large number of spermatocytes are undergoing apoptosis. The expression of Phlda1 mRNA is significantly elevated 3 days after induction of cryptorchidism. After 7 days of cryptorchidism, Hsf1 and Phlda1 are strongly expressed in the nucleus and cytoplasm, respectively, of primary spermatocytes. Numerous apoptotic spermatocytes are also observed at this time point. These results suggest that the Hsf1/Phlda1 pathway plays an important role in the apoptosis of primary spermatocytes in cryptorchid testis. We present evidence suggesting that Hsf2 is also involved in germ cell removal in cryptorchid testis. Mol. Reprod. Dev. 78:283–291, 2011. © 2011 Wiley‐Liss, Inc.
Thermodynamic‐based model for coupling temperature‐dependent viscoelastic, viscoplastic, and viscodamage constitutive behavior of asphalt mixtures
Authors: Darabi Masoud K. , Al‐Rub Rashid K. Abu , Masad Eyad A. , Little Dallas N. 
Published: March 2011

SUMMARYBased on the continuum damage mechanics, a general and comprehensive thermodynamic‐based framework for coupling the temperature‐dependent viscoelastic, viscoplastic, and viscodamage behaviors of bituminous materials is presented. This general framework derives systematically Schapery‐type nonlinear viscoelasticity, Perzyna‐type viscoplasticity, and a viscodamage model analogous to the Perzyna‐type viscoplasticity. The resulting constitutive equations are implemented in the well‐known finite element code Abaqus via the user material subroutine UMAT. A systematic procedure for identifying the model parameters is discussed. Finally, the model is validated by comparing the model predictions with a comprehensive set of experimental data on hot mix asphalt that include creep‐recovery, creep, uniaxial constant strain rate, and repeated creep‐recovery tests in both tension and compression over a range of temperatures, stress levels, and strain rates. Comparisons between model predictions and experimental measurements show that the presented constitutive model is capable of predicting the nonlinear behavior of asphaltic mixes under different loading conditions. Copyright © 2011 John Wiley & Sons, Ltd.
An improved convergence analysis of smoothed aggregation algebraic multigrid
Authors: Brezina Marian , Vaněk Petr , Vassilevski Panayot S. 
Published: March 2011

SUMMARYWe present an improved analysis of the smoothed aggregation algebraic multigrid method extending the original proof in [Numer. Math. 2001; 88:559–579] and its modification in [Multilevel Block Factorization Preconditioners. Matrix‐based Analysis and Algorithms for Solving Finite Element Equations. Springer: New York, 2008]. The new result imposes fewer restrictions on the aggregates that makes it easier to verify in practice. Also, we extend a result in [Appl. Math. 2011] that allows us to use aggressive coarsening at all levels. This is due to the properties of the special polynomial smoother that we use and analyze. In particular, we obtain bounds in the multilevel convergence estimates that are independent of the coarsening ratio. Numerical illustration is also provided. Copyright © 2011 John Wiley & Sons, Ltd.
Implementation of the Jäger contact model for discrete element simulations
Authors: Kuhn Matthew R. 
Published: March 2011

AbstractIn three‐dimensional discrete element method (DEM) simulations, the particle motions within a granular assembly can produce bewildering sequences of movements at the contacts between particle pairs. With frictional contacts, the relationship between contact movement and force is non‐linear and path‐dependent, requiring an efficient means of computing the forces and storing their histories. By cleverly applying the principles of Cattaneo, Mindlin, and Deresiewicz, J”urgen Jäger developed an efficient approach for computing the full three‐dimensional force between identical elastic spheres that have undergone difficult movement sequences (J. Jäger, New Solutions in Contact Mechanics. WIT Press: Southampton, U.K.). This paper presents a complete Jäger algorithm that can be incorporated into DEM codes and also describes three special provisions for DEM simulations: (1) a method for handling particle pairs that undergo complex tumbling and twirling motions in three‐dimensions; (2) a compact data structure for storing the loading history of the many contacts in a large assembly; and (3) an approximation of the Jäger algorithm that reduces memory demand. The algorithm addresses contact translations between elastic spheres having identical properties, but it does not resolve the tractions produced by twisting or rolling motions. A performance test demonstrates that the algorithm can be applied in a DEM code with modest increases in computation time but with more substantial increases in required storage. Copyright © 2011 John Wiley & Sons, Ltd.
A partitioning strategy for the coupled hygromechanical analysis with application to wood structures of cultural heritage
Authors: Dureisseix David , Marcon Bertrand 
Published: March 2011

AbstractOne of the main causes for damage of panel paintings of cultural heritage is due to the environmental micro‐climatic variations. Wood science and numerical modeling may help to analyze and calibrate restoration interventions, to predict the behavior of the artwork, taking into account the individual painted panels and the conservation environment. In this article, a partitioning numerical strategy is proposed to predict by simulation the behavior of such artworks. It is based on a multiphysics partition focusing on the interactions between the different physics that are described in a thermodynamical framework. It is applied to the case study of Mona Lisa, modeled as a strongly coupled hygromechanical structure. The strategy is designed to couple two different modelings: a plate model for the mechanical behavior of the panel and 1D transverse diffusion for the moisture evolution. Copyright © 2011 John Wiley & Sons, Ltd.
Bildverarbeitungstechnologie aus Europa
Authors: Schwarzkopf Patrick 
Published: March 2011

AbstractEuropa hat in den vergangenen Jahren maßgeblich zur technologischen Entwicklung der Bildverarbeitungstechnologie beigetragen. Dabei sind die europäischen Hersteller weltweit erfolgreich. Das belegen die neuesten Daten der Marktstudie der European Machine Vision Association (EMVA).
Zukunftsperspektiven der industriellen Bildverarbeitung
Authors: Jähne Bernd 
Published: March 2011

AbstractDie industrielle Bildverarbeitung in Europa und Deutschland zeigt seit Jahren ein ungebrochenes überdurchschnittliches Wachstum. Der Gesamtumsatz der deutschen Bildverarbeitungsbranche stieg nach Angaben des VDMA von 0,297 Milliarden Euro im Jahr 1997 mit einer durchschnittlichen jährlichen Wachstumsrate von 14 % auf 1,15 Milliarden Euro im Jahr 2007. In den letzten Jahren flachte allerdings die Wachstumsrate ab und für 2008 wird ein Wachstum von sechs Prozent erwartet (siehe auch Artikel von Patrick Schwarzkopf im Heft Seite 12). Was ist der Grund für diesen überdurchschnittlichen Erfolg? Wird er sich in Zukunft so fortsetzen können? Was kann die Forschung zum weiteren Erfolg der Bildverarbeitungsbranche beitragen? Dies sind die Fragen, die der folgende Beitrag zu beantworten versucht. Dabei geht es nicht um eine einfache Fortschreibung der bisherigen Trends, was in der Regel zu falschen Schlüssen führt, sondern um eine tiefgründige Analyse, die uns weit in die Vergangenheit zurück führt.
Infrarotkameras in der Automobilindustrie
Authors: Smorscek Peter , Liebelt Frank , Wandelt Michael Jens 
Published: March 2011

AbstractWärmebildkameras werden in allen größeren Unternehmen in der vorbeugenden Instandhaltung eingesetzt. Besonders bei der Erkennung von Fehlern in elektrischen Anlagen leisten sie wichtige Dienste. Aber hochwertige Infrarotkameras können viel mehr, als „nur”︁ thermisch auffällige Kabel, Sicherungen und Schaltschränke enttarnen. Dabei ist aber neben einer hochwertigen Kamera auch spezifisches Know­how beim Anwender notwendig. Dieser Beitrag zeigt Beispiele aus der Produktentwicklung und der Qualitätssicherung, die das deutlich machen.
Interferometrische Messtechnik
Authors: Osten Wolfgang , Garbusi Eugenio Garbusi , Groves Roger M. , Körner Klaus , Pedrini Giancarlo , Pruss Christof 
Published: March 2011

AbstractEine zentrale Aufgabe der optischen Messtechnik ist die präzise Vermessung von Längen und Längenänderungen, wobei letztere als eine Folge konkreter Einwirkungen auf das Messobjekt aufzufassen sind — z. B. durch mechanische oder thermische Beanspruchungen. Übertragen auf die räumliche Natur der Körper bedeutet dies die Erfassung von dreidimensionalen Formen und Formänderungen in verschiedenen Skalenbereichen von Makro bis Nano. Eine Besonderheit optischer Messtechniken besteht darin, dass die Zielgröße nicht direkt gewonnen wird, sondern indirekt aus einer primären Messgröße rekonstruiert werden muss. Primäre Messgrößen sind z. B. die Intensität, der Kontrast, die Phase, die Polarisation oder die Wellenlänge. Aus diesem indirekten Messprinzip resultiert eine Reihe von Konsequenzen.
M‐Protection Levels for Safe Application of Shortpulse Lasers
Authors: Palkoska Jürgen , Meedt Hans Christian 
Published: March 2011

AbstractIn laser safety the letter M should not be mixed with a quick lunch at an American burger restaurant or with a racy Bavarian sports car. For a few years now, mode‐locked lasers with pulses ranging from a few picoseconds to a few femtoseconds have been enjoying a continuously increasing market share. Fields of application can be found in research and development, industrial processes and also in medicine. The special properties of these lasers are well known and have been recognized since the 1980s and therefore have already gained much attention in the laser safety standards DIN EN 207 and DIN EN 208. According to this reliable laser protection is needed. Due to this requirement, manufacturers of laser safety products have certified laser safety goggles and other protection equipment for these types of lasers. In this article we present the challenges of laser safety filters against ultrashort pulse lasers.
Small, Smaller, Biochip
Authors: Schilling Niels , Klotzbach Udo , Sonntag Frank , Howitz Steffen 
Published: March 2011

AbstractBiochemical sensors have come to play an important role in the medical and pharmaceutical sciences. An essential prerequisite for modern diagnostics, they are used in the development and characterization of new drugs. The ongoing miniaturization of these sensors poses new challenges for the production technologies.
Digital Holographic Microscopy
Authors: Kemper Björn , Langehanenberg Patrik , von Bally Gert 
Published: March 2011

AbstractDigital holographic microscopy provides quantitative phase contrast imaging that is suitable for high resolving investigations on reflective surfaces as well as for marker‐free analysis of living cells. Results from engineered surfaces and living cells demonstrate applications of digital holographic microscopy for technical inspection and life cell imaging.