bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultraviolet radiation stimulates expression of Snail family transcription factors in keratinocytes
Authors: Hudson Laurie G. , Choi Changsun , Newkirk Kimberly M. , Parkhani Jaipriya , Cooper Karen L. , Lu Ping , Kusewitt Donna F. 
Published: February 2007

AbstractThe related zinc finger transcription factors Slug and Snail modulate epithelial mesenchymal transformation (EMT), the conversion of sessile epithelial cells into migratory fibroblast‐like cells. EMT occurs during development, wound healing, and tumor progression. Growth factors, acting through mitogen‐activated protein kinase (MAPK) cascades, regulate expression of Slug and Snail. Expression of Snail family transcription factors appears to be elevated in UVR‐induced murine squamous cell carcinomas (SCC). We report here that ultraviolet radiation (UVR), which activates MAPK cascades, also stimulates Snail and Slug expression in epidermal keratinocytes. UVR exposure transiently elevated Slug and Snail mRNA expression in human keratinocytes in vitro and mouse epidermis in vivo. This induction was mediated, at least in part, through the ERK and p38 MAPK cascades, as pharmacological inhibition of these cascades partially or completely blocked Slug and Snail induction by UVR. On the other hand, UVR induction of Slug and Snail was enhanced by inhibition of JNK. Slug appears to play a functional role in the acute response of keratinocytes to UVR, as UVR induction of keratin 6 in the epidermis of Slug knockout mice was markedly delayed compared to wild‐type mice. Slug and Snail are known to regulate molecules important in the cytoskeleton, intercellular adhesion, cell motility, and apoptosis, thus it seems probable that transiently or persistently elevated expression of these factors fosters the progression of UVR‐induced SCC. © 2007 Wiley‐Liss, Inc.
Epidermal hyperplasia and oral carcinoma in mice overexpressing the transcription factor ATF3 in basal epithelial cells
Authors: Wang Aijin , Arantes Stacey , Conti Claudio , McArthur Mark , Aldaz C. Marcelo , MacLeod Michael C. 
Published: February 2007

AbstractATF3 is a highly conserved eukaryotic transcription factor that is ubiquitously upregulated transcriptionally during cellular responses to a variety of stresses, in particular DNA damage. However, the role of ATF3 in the DNA damage response is unclear. Transgenic mice that overexpress human ATF3 in basal epithelial cells under the control of the bovine keratin 5 (K5) promoter were constructed and characterized for epidermal alterations. Strong, nuclear expression of the exogenous ATF3 protein was seen in basal cells of the epidermis, hair follicles, and oral mucosa. Hyperplastic changes in the K5‐expressing, outer root sheath (ORS) cells of the hair follicle were observed in young mice, resulting in multiple layers of ORS cells in the mature follicle and large aberrantly shaped follicles. Mild hyperplasia of the interfollicular epidermis was also noted, increasing with age. However, no epidermal tumors were identified in BK5.ATF3 mice observed for 16 mo. At 16 mo of age, most transgenic mice exhibited multi‐focal areas of hyperplasia and dysplasia in the oral mucosa, with cellular atypia and underlying acute inflammatory changes. Neoplastic lesions were also seen in the oral cavity of BK5.ATF3 mice, including oral squamous cell carcinoma (60% incidence) and basal cell tumors with follicular differentiation (70% incidence), but not in non‐transgenic FVB/N littermates. Heterogeneous nuclear expression (or stabilization) of p53 protein was seen in some oral dysplasias, with a patchy distribution primarily in the least differentiated layers of the lesions. This represents the first indication that ATF3 may have oncogenic properties in epithelial cells. © 2007 Wiley‐Liss, Inc.
Aneuploidy of chromosome Y in prostate tumors and seminal vesicles: A possible sign of aging rather than an indicator of carcinogenesis?
Authors: Nadal Marga , Pera Guillem , Pujadas Jaume , Abril Jesús , González Laura , Aguiló Fernando , Condom Enric , Gómez‐Zaera Montserrat , Nunes Virginia 
Published: February 2007

AbstractChromosome Y aneuploidies have been reported as one of the recurrent cytogenetic findings in prostate cancer (PCa) and many other solid and hematological tumors. We have studied this aneuploidy in 28 patients with PCa undergoing radical prostatectomy, one patient with benign hyperplasia (BPH) and four organ donors. A total of 72 samples have been studied: 17 tumors, 25 nontumor prostate tissues, 1 BPH, 21 seminal vesicles samples obtained along with the prostate when patients underwent radical prostatectomy and prostate tissues and seminal vesicles from four organ donors. We have also studied the aneuploidy of chromosome Y in peripheral blood from four of the patients and in seminal vesicles of 11 individuals with bladder cancer (BC). The study has been performed by Fluorescence in situ hybridization (FISH) in uncultured cells. Our results indicate that complete loss of chromosome Y is found in almost all the seminal vesicles both from patients with PCa and patients with BC (samples obtained from the tissue bank), and is more frequent in prostate tumors than in nontumor samples. The percentages of chromosome Y loss in the tissues analyzed are significatively higher than expected in lymphocytes considering the patient's age as reported in the literature. The high percentage of chromosome Y loss found in the nonmalignant seminal vesicles of these patients may be an indicator of an ageing process rather than a primary cytogenetic alteration in the carcinogenesis of the prostate. However, a contribution of this loss to chromosomal instability and therefore, to the multistep tumorigenic process, cannot be discarded. © 2007 Wiley‐Liss, Inc.
Computational analysis of martensitic thin films using subdivision surfaces
Authors: Dondl Patrick W. , Shen Ching‐Ping , Bhattacharya Kaushik 
Published: February 2007

AbstractThis paper studies numerically the deformation of thin films made of materials undergoing martensitic phase transformations by using subdivision surfaces. These thin films have received interest as potential microactuators, and specifically a tent‐like configuration has recently been proposed. In order to model martensitic materials we use a multi‐well strain energy combined with an interfacial energy penalizing strain gradients. The study of such configurations requires adequate resolution of inhomogeneous in‐plane stretch, out‐of‐plane deformation and transition regions across which the deformation gradient changes sharply. This paper demonstrates that subdivision surfaces provide an attractive tool in the numerical study of such configurations, and also provides insights into the tent‐like deformations. Copyright © 2007 John Wiley & Sons, Ltd.
Hybrid pseudospectral–finite difference method for solving a 3D heat conduction equation in a submicroscale thin film
Authors: Momeni‐Masuleh S.H. , Malek A. 
Published: February 2007

AbstractThis research aims to develop a time‐dependent pseudospectral‐finite difference scheme for solving a 3D dual‐phase‐lagging heat transport equation in a submicroscale thin film. The scheme uses periodic pseudospectral discretization in space and a fully second‐order finite difference discretization in time. The three consecutive time steps model is then solved explicitly, by using a preconditioned conjugate gradient method. The scheme is illustrated by an example which is used to investigate the heat transfer in a gold submicroscale thin film. Comparisons are made with available literature. © 2007 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2007
Finite volume method based on stabilized finite elements for the nonstationary Navier–Stokes problem
Authors: He Guoliang , He Yinnian , Feng Xinlong 
Published: February 2007

AbstractA finite volume method based on stabilized finite element for the two‐dimensional nonstationary Navier–Stokes equations is investigated in this work. As in stabilized finite element method, macroelement condition is introduced for constructing the local stabilized formulation of the nonstationary Navier–Stokes equations. Moreover, for P1 − P0 element, the H1 error estimate of optimal order for finite volume solution (uh,ph) is analyzed. And, a uniform H1 error estimate of optimal order for finite volume solution (uh, ph) is also obtained if the uniqueness condition is satisfied. © 2007 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2007
Arrested Reactive Milling Synthesis and Characterization of Sodium‐Nitrate Based Reactive Composites
Authors: Umbrajkar Swati , Trunov Mikhaylo A. , Schoenitz Mirko , Dreizin Edward L. , Broad Russell 
Published: February 2007

AbstractArrested reactive milling was used to synthesize three composite powders using sodium nitrate as an oxidizer, and magnesium, aluminum, and mechanically alloyed aluminum‐magnesium (Al0.5Mg0.5) as respective fuels. Both magnesium and aluminum powders formed flakes with varying thickness from hundreds of nm to several μm sandwiched between sodium nitrate particles. Three‐dimensional composite and nanocomposite particles were formed with AlMg mechanically alloyed powder. No change in the crystallinity of any components was observed from X‐ray diffraction patterns of the composite materials. Materials were characterized using differential thermal analysis (DTA) and simultaneous thermogravimetry (TG), carried out in argon. In composite materials, the decomposition of sodium nitrate starts at lower temperatures than for pure sodium nitrate. Weight loss is observed to start at relatively low temperatures. The most significant exothermic events occur at substantially higher temperatures, and therefore in a material that may have been significantly altered from its initial state. The results of thermal analysis indicate that the composite with mechanically alloyed AlMg powder is most stable at low temperatures. Ignition of the prepared composites was studied using a thin layer of powder coated on an electrically heated filament. These experiments showed that the composite with mechanically alloyed AlMg powder ignites at lowest temperatures and thus is expected to have the shortest ignition delays in practical applications. The emission spectra of the prepared composites burning in air are presented.
High Energy Propellants for Advanced Gun Ammunition Based on RDX, GAP and TAGN Compositions
Authors: Damse Ramdas S. , Singh Amarjit , Singh Harihar 
Published: February 2007

AbstractA number of gun propellant compositions based on RDX, GAP, TAGN and combinations thereof were formulated and studied with the aim to select the suitable composition for advanced gun ammunition in respect of processability and ballistic performance. Theoretical thermochemical properties of the compositions were computed using a ‘THERM’ programme and the ballistic performance was evaluated on the basis of closed vessel tests. In addition, sensitivity, thermal characterization, thermal stability and mechanical properties of the compositions were also determined for assessing the suitability for application. A composition containing 28% NC, 45% RDX, 20% TAGN, 6% GAP, 0.7% carbamite and 0.3% resorcinol was found to provide higher level of force constant at relatively lower flame temperature, reasonably good burning rate characteristics and mechanical properties.
A Detonation Model of High/Low Velocity Detonation
Authors: Hu Shaoming , Li Chenfang , Ma Yunhua , Cui Junmin 
Published: February 2007

AbstractA new detonation model that can simulate both high and low velocity detonations is established using the least action principle. The least action principle is valid for mechanics and thermodynamics associated with a detonation process. Therefore, the least action principle is valid in detonation science. In this model, thermodynamic equilibrium state is taken as the known final point of the detonation process. Thermodynamic potentials are analogous to mechanical ones, and the Lagrangian function in the detonation process is L=T−V. Under certain assumptions, the variation calculus of the Lagrangian function gives two solutions: the first one is a constant temperature solution, and the second one is the solution of an ordinary differential equation. A special solution of the ordinary differential equation is given.
Local motions in a benchmark of allosteric proteins
Authors: Daily Michael D. , Gray Jeffrey J. 
Published: February 2007

AbstractAllosteric proteins have been studied extensively in the last 40 years, but so far, no systematic analysis of conformational changes between allosteric structures has been carried out. Here, we compile a set of 51 pairs of known inactive and active allosteric protein structures from the Protein Data Bank. We calculate local conformational differences between the two structures of each protein using simple metrics, such as backbone and side‐chain Cartesian displacement, and torsion angle change and rearrangement in residue–residue contacts. Thresholds for each metric arise from distributions of motions in two control sets of pairs of protein structures in the same biochemical state. Statistical analysis of motions in allosteric proteins quantifies the magnitude of allosteric effects and reveals simple structural principles about allostery. For example, allosteric proteins exhibit substantial conformational changes comprising about 20% of the residues. In addition, motions in allosteric proteins show strong bias toward weakly constrained regions such as loops and the protein surface. Correlation functions show that motions communicate through protein structures over distances averaging 10–20 residues in sequence space and 10–20 Å in Cartesian space. Comparison of motions in the allosteric set and a set of 21 nonallosteric ligand‐binding proteins shows that nonallosteric proteins also exhibit bias of motion toward weakly constrained regions and local correlation of motion. However, allosteric proteins exhibit twice as much percent motion on average as nonallosteric proteins with ligand‐induced motion. These observations may guide efforts to design flexibility and allostery into proteins. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Phylogenetic analysis of haloalkane dehalogenases
Authors: Chovancová Eva , Kosinski Jan , Bujnicki Janusz M. , Damborský Jiří 
Published: February 2007

AbstractHaloalkane dehalogenases (HLDs) are enzymes that catalyze the cleavage of carbon–halogen bonds by a hydrolytic mechanism. Although comparative biochemical analyses have been published, no classification system has been proposed for HLDs, to date, that reconciles their phylogenetic and functional relationships. In the study presented here, we have analyzed all sequences and structures of genuine HLDs and their homologs detectable by database searches. Phylogenetic analyses revealed that the HLD family can be divided into three subfamilies denoted HLD‐I, HLD‐II, and HLD‐III, of which HLD‐I and HLD‐III are predicted to be sister‐groups. A mismatch between the HLD protein tree and the tree of species, as well as the presence of more than one HLD gene in a few genomes, suggest that horizontal gene transfers, and perhaps also multiple gene duplications and losses have been involved in the evolution of this family. Most of the biochemically characterized HLDs are found in the HLD‐II subfamily. The dehalogenating activity of two members of the newly identified HLD‐III subfamily has only recently been confirmed, in a study motivated by this phylogenetic analysis. A novel type of the catalytic pentad (Asp‐His‐Asp+Asn‐Trp) was predicted for members of the HLD‐III subfamily. Calculation of the evolutionary rates and lineage‐specific innovations revealed a common conserved core as well as a set of residues that characterizes each HLD subfamily. The N‐terminal part of the cap domain is one of the most variable regions within the whole family as well as within individual subfamilies, and serves as a preferential site for the location of relatively long insertions. The highest variability of discrete sites was observed among residues that are structural components of the access channels. Mutations at these sites modify the anatomy of the channels, which are important for the exchange of ligands between the buried active site and the bulk solvent, thus creating a structural basis for the molecular evolution of new substrate specificities. Our analysis sheds light on the evolutionary history of HLDs and provides a structural framework for designing enzymes with new specificities. Proteins 2007. © 2007 Wiley‐Liss, Inc.
COMBINE analysis of the specificity of binding of Ras proteins to their effectors
Authors: Tomić Sanja , Bertoša Branimir , Wang Ting , Wade Rebecca C. 
Published: February 2007

AbstractThe small guanosine triphosphate (GTP)‐binding proteins of the Ras family are involved in many cellular pathways leading to cell growth, differentiation, and apoptosis. Understanding the interaction of Ras with other proteins is of importance not only for studying signalling mechanisms but also, because of their medical relevance as targets, for anticancer therapy. To study their selectivity and specificity, which are essential to their signal transfer function, we performed COMparative BINding Energy (COMBINE) analysis for 122 different wild‐type and mutant complexes between the Ras proteins, Ras and Rap, and their effectors, Raf and RalGDS. The COMBINE models highlighted the amino acid residues responsible for subtle differences in binding of the same effector to the two different Ras proteins, as well as more significant differences in the binding of the two different effectors (RalGDS and Raf) to Ras. The study revealed that E37, D38, and D57 in Ras are nonspecific hot spots at its effector interface, important for stabilization of both the RalGDS–Ras and Raf–Ras complexes. The electrostatic interaction between a GTP analogue and the effector, either Raf or RalGDS, also stabilizes these complexes. The Raf–Ras complexes are specifically stabilized by S39, Y40, and D54, and RalGDS–Ras complexes by E31 and D33. Binding of a small molecule in the vicinity of one of these groups of amino acid residues could increase discrimination between the Raf–Ras and RalGDS–Ras complexes. Despite the different size of the RalGDS–Ras and Raf–Ras complexes, we succeeded in building COMBINE models for one type of complex that were also predictive for the other type of protein complex. Further, using system‐specific models trained with only five complexes selected according to the results of principal component analysis, we were able to predict binding affinities for the other mutants of the particular Ras‐effector complex. As the COMBINE analysis method is able to explicitly reveal the amino acid residues that have most influence on binding affinity, it is a valuable aid for protein design. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Effects of telephone counselling on mortality and adherence
Authors: Holland Richard , Rechel Boika , Wright David 
Published: February 2007

AbstractA randomised controlled trial published in a peer‐reviewed journal is considered to be the ‘gold standard’ of information about the effectiveness of a treatment; however, critical appraisal of trials is required in order to judge the value and implications of the results. Here, the authors present their appraisal of a study that investigated the effects of telephone calls from a pharmacist on mortality in patients taking five or more drugs.Wu JY, Leung WY, Chang S, et al. Effectiveness of telephone counselling by a pharmacist in reducing mortality in patients receiving polypharmacy: randomised controlled trial. BMJ 2006;333(7567):522. Copyright © 2006 Wiley Interface Ltd
Laser assisted densification of surface porosity in structural alumina ceramic
Authors: Harimkar S. , Dahotre N. B. 
Published: February 2007

AbstractAlumina ceramics are extensively used in structural components due to excellent thermal and mechanical properties. The effective utilization of alumina ceramic in these applications necessitates the minimization of inherent processing defects such as porosity. Laser processing can be effectively used for densification of the surface porosity of these ceramics especially desirable for the applications where ceramics are exposed to high temperatures and aggressive environments. The present study discusses the influence of laser processing fluence on the surface porosity of the alumina ceramic irradiated with a continuous wave Nd:YAG laser beam. A detailed scanning electron microscopy characterization was carried out to indicate the mechanism of densification of porosity during laser irradiation based on development of solidification microstructures. Finally, a fractal geometry based approach was introduced to characterize the surface microstructures such that useful correlation can be developed for the prediction of surface porosity directly from the fractal dimensions. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Nitride‐based heterostructures grown by MOCVD for near‐ and mid‐infrared intersubband transitions
Authors: Mosca M. , Nicolay S. , Feltin E. , Carlin J.‐F. , Butté R. , Ilegems M. , Grandjean N. , Tchernycheva M. , Nevou L. , Julien F. H. 
Published: February 2007

AbstractIntersubband (ISB) optical absorption in different nitride‐based heterostructures grown by metal‐organic chemical vapour deposition (MOCVD) is reported. The role of indium in AlInN/GaN multi‐quantum wells (MQWs) is investigated. At high concentration (15%) AlInN is quasi lattice‐matched to GaN and no cracks appear in the structure. At very low indium concentration (∼2%) the material quality is improved without decreasing the ISB transition wavelength with respect to the case of indium‐free structures. Different mechanisms of strain relaxation in pure and 2% indium‐doped AlN/GaN MQW structures are also investigated. ISB transition wavelengths of 2 μm for AlN/GaN MQWs, and 3 μm for AlInN/GaN MQWs with 15% of In are achieved. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A fragmentation study of isoflavones in negative electrospray ionization by MSn ion trap mass spectrometry and triple quadrupole mass spectrometry
Authors: Kang Jinguo , Hick Larry A. , Price William E. 
Published: February 2007

AbstractThis study has elucidated the fragmentation pathway for deprotonated isoflavones in electrospray ionization using MSn ion trap mass spectrometry and triple quadrupole mass spectrometry. Genistein‐d4 and daidzein‐d3 were used as references for the clarification of fragment structures. To confirm the relationship between precursor and product ions, some fragments were traced from MS2 to MS5. The previous literature for the structurally related flavones and flavanones located the loss of ketene (C2H2O) to ring C, whereas the present fragmentation study for isoflavones has shown that the loss of ketene occurs at ring A. In the further fragmentation of the [MHCH3]−. radical anion of methoxylated isoflavones, loss of a hydrogen atom was commonly found. [MHCH3COB‐ring]− is a characteristic fragment ion of glycitein and can be used to differentiate glycitein from its isomers. Neutral losses of CO and CO2 were prominent in the fragmentation of deprotonated anions in ion trap mass spectrometry, whereas recyclization cleavage accounted for a very small proportion. In comparison with triple quadrupole mass spectrometry, ion trap MSn mass spectrometry has the advantage of better elucidation of the relationship between precursor and product ions. Copyright © 2007 John Wiley & Sons, Ltd.