bluuebunny/crossref_metadata_2025_split huggingface dataset:
Carotid atherosclerotic plaques: Proteomics study after a low‐abundance protein enrichment step
Authors: Malaud Eric , Piquer Dominique , Merle Delphine , Molina Laurence , Guerrier Luc , Boschetti Egisto , Saussine Max , Marty‐Ané Charles , Albat Bernard , Fareh Jeannette 
Published: January 2012

AbstractAtherosclerosis is one of the most important causes of cardiovascular and cerebrovascular events. Although phenotypic differentiation between stable and unstable plaques is currently possible, proteomic analysis of the atherosclerotic plaque could offer a global view of the atherosclerosis pathology. With the objective to highlight the detection of low‐abundance proteins, we reduced the dynamic range of proteins by combinatorial peptide ligand library treatment of human carotid artery atherosclerotic plaques. After enrichment step, abundance of major proteins was decreased, revealing different protein profiles as assessed by both SDS‐polyacrylamide gel electrophoresis and two‐dimensional electrophoresis comparative analyses. Identification of proteins that were contained in a spot allowed finding large differences between noncomplicated and complicated plaques from carotid atherosclerotic lesions. Novel low‐abundance proteins were detected correlating very well with biological alterations related to atherosclerosis (heat shock protein 27 (HSP27) isoforms, aldehyde dehydrogenase, moesin, Protein kinase C delta‐binding protein, and inter‐α trypsin inhibitor family heavy chain‐related protein (ITIH4)). At the same time, the differential expression of known proteins of interest such as hemoglobin β‐chain and heat shock protein 27 between noncomplicated and hemorrhagic complicated plaques was maintained after enrichment step. The detection of different isoforms of a low‐abundance protein such as heat shock protein 27 species was actually improved after enrichment of tissue protein extracts. All of these findings clearly support further investigations in view to confirm the role of these proteins as possible biomarkers.
Electromembrane extraction combined with cyclodextrin‐modified capillary electrophoresis for the quantification of trimipramine enantiomers
Authors: Fakhari Ali R. , Tabani Hadi , Nojavan Saeed , Abedi Hamid 
Published: January 2012

AbstractA sensitive, simple and reproducible method was developed for preconcentration and determination of trimipramine (TPM) enantiomers in biological samples using electromembrane extraction combined with cyclodextrin‐modified capillary electrophoresis (CE). During the extraction, TPM enantiomers migrated from a 5 mL sample solution through a thin layer of 2‐nitrophenyl octyl ether NPOE immobilized in the pores of a hollow fiber, and into a 20 μL acidic aqueous acceptor phase presented inside the lumen of the fiber. A Box–Behnken design and the response surface methodology (RSM) were used for the optimization of different variables on extraction efficiency. Optimized extraction conditions were: NPOE as supported liquid membrane, inter‐electrode distance of 5 mm, stirring rate of 1000 rpm, 51 V potential difference, 34 min as the extraction time, acceptor phase pH 1.0 and donor phase pH 4.5. Then, the extract was analyzed using optimized cyclodextrin (CD)‐modified CE method for the separation of TPM enantiomers. Best results were achieved using 100 mM phosphate running buffer (pH 2.0) containing 10 mM α‐CD as the chiral selector, applied voltage of 18 kV and 20°C. The range of quantitation for both enantiomers was 20–500 ng/mL. The method was very reproducible so that intra‐ and interday RSDs (n=6) were <6%. The limits of quantitation and detection for both enantiomers were 20 and 7 ng/mL, respectively. Finally, this method was successfully applied to determine the concentration of TPM enantiomers in plasma and urine samples without any pre‐treatment.
Structural performance of a base‐isolated reinforced concrete building subjected to seismic pounding
Authors: Pant Deepak R. , Wijeyewickrema Anil C. 
Published: January 2012

SUMMARYThe effects of seismic pounding on the structural performance of a base‐isolated reinforced concrete (RC) building are investigated, with a view to evaluate the influence of adjacent structures and separation between structures on the pounding response. In particular, seismic pounding of a typical four‐story base‐isolated RC building with retaining walls at the base and with a four‐story fixed‐base RC building is studied. Three‐dimensional finite element analyses are carried out considering material and geometric nonlinearities. The structural performance of the base‐isolated building is evaluated considering various earthquake excitations. It is found that the performance of the base‐isolated building is substantially influenced by the pounding. The investigated base‐isolated building shows good resistance against shear failure and the predominant mode of failure due to pounding is flexural. Copyright © 2012 John Wiley & Sons, Ltd.
Mean and turbulent flow fields in a simulated ice‐covered channel with a gravel bed: some laboratory observations
Authors: Robert André , Tran Thang 
Published: January 2012

ABSTRACTNorthern rivers experience freeze‐up over the winter, creating asymmetric under‐ice flows. Field and laboratory measurements of under‐ice flows typically exhibit flow asymmetry and its characteristics depend on the presence of roughness elements on the ice cover underside. In this study, flume experiments of flows under a simulated ice cover are presented. Open water conditions and simulated rough ice‐covered flows are discussed. Mean flow and turbulent flow statistics were obtained from an Acoustic Doppler Velocimeter (ADV) above a gravel‐bed surface. A central region of faster flow develops in the middle portion of the flow with the addition of a rough cover. The turbulent flow characteristics are unambiguously different when simulated ice covered conditions are used. Two distinct boundary layers (near the bed and in the vicinity of the ice cover, near the water surface) are clearly identified, each being characterized by high turbulent intensity levels. Detailed profile measurements of Reynolds stresses and turbulent kinetic energy indicate that the turbulence structure is strongly influenced by the presence of an ice cover and its roughness characteristics. In general, for y/d > 0·4 (where y is height above bed and d is local flow depth), the addition of cover and its roughening tends to generate higher turbulent kinetic energy values in comparison to open water flows and Reynolds stresses become increasingly negative due to increased turbulence levels in the vicinity of the rough ice cover. The high negative Reynolds stresses not only indicate high turbulence levels created by the rough ice cover but also coherent flow structures where quadrants one and three dominate. Copyright © 2012 John Wiley & Sons, Ltd.
Investigating landslide‐related cracks along the edge of two loess platforms in northwest China
Authors: Xu L. , Dai F. C. , Tham L. G. , Zhou Y. F. , Wu C. X. 
Published: January 2012

ABSTRACTCracks are widely developed along the edge of loess platforms in northwest China. Field surveys reveal that these cracks can be grouped into shallow and deeply penetrating ones. The former occur at a small distance from the platform edge, normally penetrate into the top unsaturated loess with the penetration depth being controlled by the joints in loess. The latter penetrate deeper into the saturated loess farther away from the platform edge. These cracks control the inflow and drainage of irrigation water. The shallow penetrating crack can fail as a slide or fall with a volume of up to hundreds of cubic meters. The deeply penetrating crack can fail as a flow‐like landslide with a volume of thousands of cubic meters or more. A full‐scale field test simulating irrigation on the platform surface was conducted. The two types of crack can be interconnected so that the water applied in the test finally flowed into the deep crack and was discharged from the platform. Analysis of soil stress states and the results of field test show that the deeply‐penetrating cracks could have both positive as well as negative effects on slope stability. On the one hand, water can flow more freely in the cracks, and the loess could be saturated and trigger a landslide. On the other hand, the water can drain more easily along the crack and slope stability could be enhanced as the groundwater level is suppressed. Copyright © 2012 John Wiley & Sons, Ltd.
Development of a lattice Boltzmann method for two‐layered shallow‐water flow
Authors: Rocca Michele La , Adduce Claudia , Lombardi Valentina , Sciortino Giampiero , Hinkelmann Reinhard 
Published: January 2012

SUMMARYIn this paper the dynamics of a two‐layered liquid, made of two immiscible shallow‐layers of different density, has been investigated within the framework of the lattice Boltzmann method (LBM). The LBM developed in this paper for the two‐layered, shallow‐water flow has been obtained considering two separate sets of LBM equations, one for each layer. The coupling terms between the two sets have been defined as external forces, acted on one layer by the other. Results obtained from the LBM developed in this paper are compared with numerical results obtained solving the two‐layered, shallow‐water equations, with experimental and other numerical results published in literature. The results are interesting. First, the numerical results obtained by the LBM and by the shallow‐water model can be considered as equivalent. Second, the LBM developed in this paper is able to simulate motion conditions on nonflat topography. Third, the agreement between the LBM (and also shallow‐water model) numerical results and the experimental results is good when the evolution of the flow does not depend on the viscosity, that is, during the initial phase of the flow, dominated by gravity and inertia forces. When the viscous forces dominate the evolution of the flow the agreement between numerical and experimental results depends strongly on the viscosity; it is good if the numerical LBM viscosity has the same order of magnitude of the liquid's kinematic viscosity. Copyright © 2012 John Wiley & Sons, Ltd.
LES of temporally evolving mixing layers by an eighth‐order filter scheme
Authors: Hadjadj Abdellah , Yee Helen C. , Sjögreen Bjorn 
Published: January 2012

SUMMARYAn eighth‐order filter method for a wide range of compressible flow speeds (H. C. Yee and B. Sjogreen, Proceedings of ICOSAHOM09, June 22–26, 2009, Trondheim, Norway) is employed for large eddy simulations (LES) of temporally evolving mixing layers (TML) for different convective Mach numbers (Mc) and Reynolds numbers. The high‐order filter method is designed for accurate and efficient simulations of shock‐free compressible turbulence, turbulence with shocklets, and turbulence with strong shocks with minimum tuning of scheme parameters. The value of the Mc considered is for the TML range from the quasi‐incompressible regime to the highly compressible supersonic regime. The three main characteristics of compressible TML (the self‐similarity property, compressibility effects, and the presence of large‐scale structures with shocklets for high Mc) are considered for the LES study. The LES results that used the same scheme parameters for all studied cases agree well with experimental results and published direct numerical simulations (DNS). Published 2012. This article is a US Government work and is in the public domain in the USA.
Maxillary reconstruction using the scapular tip free flap: A radiologic comparison of 3D morphology
Authors: Pagedar Nitin A. , Gilbert Ralph W. , Chan Harley , Daly Michael J. , Irish Jonathan C. , Siewerdsen Jeffrey H. 
Published: January 2012

AbstractBackgroundScapular tip osteomyogenous free flaps have been described for complex palate reconstruction. Minimal osteotomies are needed because of the similar shapes of the scapula and palate. We compared the bony morphology of the palate and scapular tip to determine the suitability of the scapular tip for palate reconstruction.MethodsWe analyzed facial and chest CT images of 10 patients, comparing the morphology of 3 simulated palate resection specimens (total palate, subtotal palate, and hemipalate) with corresponding simulated scapular tip bone flaps from the same patient.ResultsConformance distances between palates and simulated flaps were small, indicating close shape similarity. Median conformance distances were 3.44 mm for hemipalatectomy, 3.56 mm for subtotal palatectomy, and 3.71 mm for total palatectomy. Six outlier observations accrued from 2 patients.ConclusionsBased on this analysis, there is close similarity between the shapes of the palate and the scapular tip. This similarity supports use of the scapular tip flap for selected palate defects. © 2012 Wiley Periodicals, Inc. Head Neck, 2012
Clinical significance of elevated spleen tyrosine kinase expression in nasopharyngeal carcinoma
Authors: Du Zi–Ming , Kou Chang–Wei , Wang Hai–Yun , Huang Ma–Yan , Liao Ding–Zhun , Hu Chun–Fang , Chen Jing , Yan Li–Xu , Hu Li–Fu , Ernberg Ingemar , Zeng Yi–Xin , Shao Jian–Yong 
Published: January 2012

AbstractBackgroundSpleen tyrosine kinase (Syk) is a nonreceptor tyrosine kinase and often aberrantly expressed in human cancers. However, Syk expression pattern has not yet been investigated in nasopharyngeal carcinoma (NPC).MethodsSamples of 223 NPC tissues were immunohistochemically stained for Syk expression and survival analysis was then performed. Interaction and co‐localization of Syk with Epstein–Barr virus encoded latent membrane protein 2A (LMP2A) was explored.ResultsHigh expression of Syk was detected in 24% of NPC cases, and correlated significantly with T classification, local recurrence, a lower 5‐year survival rate, and a lower 5‐year disease‐free survival (DFS) rate. Syk expression was a significant, independent prognosis predictor for patients with NPC. LMP2A induced Syk expression in NPC and LMP2A high expression correlated with Syk high expression in NPC clinical samples.ConclusionHigh expression of Syk, which results partly from LMP2A expression in NPC, is associated with tumor recurrence and poor prognosis of patients with NPC. © 2012 Wiley Periodicals, Inc. Head Neck, 2012
Expression of hedgehog signaling molecules as a prognostic indicator of oral squamous cell carcinoma
Authors: Wang Yi–Fen , Chang Chun–Ju , Lin Chin–Ping , Chang Shyue–Yih , Chu Pen–Yuan , Tai Shyh–Kuan , Li Wing–Yin , Chao K.S. Clifford , Chen Yu–Jen 
Published: January 2012

AbstractBackgroundRecent studies have indicated hedgehog pathway plays a role in carcinogenesis of certain cancers. We investigated the clinical significance of its signaling components, including Sonic hedgehog (Shh), Patched (Ptch), and Gli‐1, in oral squamous cell carcinoma (OSCC).MethodsBy immunohistochemistry, we determined Shh, Ptch, and Gli‐1 expression in surgical specimens from 40 patients with OSCC. The relationship between expression of these molecules and clinicopathologic variables were assessed by chi‐square analysis. Statistical difference of survival was compared using log‐rank test.ResultsPtch overexpression was associated with lymphatic metastasis (p = .028). Nuclear Gli‐1 overexpression correlated with primary tumor size (p = .001), lymphatic metastasis (p = .011), and tumor recurrence (p = .008). Overexpression of Ptch (p = .020) or Gli‐1 (p = .002) in OSCC indicated poor prognosis in the univariate survival analysis.ConclusionOur results suggest sonic hedgehog (Shh) pathway plays an important role in OSCC progression and should be considered a potential therapeutic target. © 2012 Wiley Periodicals, Inc. Head Neck, 2012
t(3;8) as the sole chromosomal abnormality in a myoepithelial carcinoma ex pleomorphic adenoma: A putative progression event
Authors: Bell Diana , N. Myers Jeffrey , Rao Pulivarthi H. , El‐Naggar Adel K. 
Published: January 2012

AbstractBackgroundCarcinoma ex pleomorphic adenoma (Ca ex‐PA) is defined as a carcinoma arising from a primary (de novo) or recurrent benign pleomorphic adenoma (PA).MethodsWe present a parotid myoepithelial carcinoma ex pleomorphic adenoma in a 38‐year‐old man with a t(3;8)(p21;q13) as the only chromosomal alteration by cytogenetic and spectral karyotypic analysis (SKY).ResultsThe finding of this translocation in a subset of PA and in the present case suggests a critical role for this event in the malignant transformation of PA.ConclusionsCollectively, both the cytogenetic and the molecular studies suggest the concept that PA lacking alterations pursue a benign behavior, whereas those with the t(3;8) translocation may progress to carcinoma. © 2012 Wiley Periodicals, Inc. Head Neck, 2012
The use of GIS and remote sensing for the assessment of waterlogging in the dryland irrigated catchments of Farafra Oasis, Egypt
Authors: El Bastawesy Mohammed , Ali Rafat Ramadan 
Published: January 2012

AbstractThis paper investigates the interplay of the hydrogeological characteristics, soil properties and recent land reclamation projects on the distribution of waterlogging and salinization within the Farafra Oasis. The multi‐temporal remote sensing data and field observations show that new reclaimed areas have been recently cultivated in distant areas from the old agricultural land. These new cultivations have developed widespread waterlogging, seepage channels and soil salinization. Analyses of the Shuttle Radar Topography Mission digital elevation model (DEM) showed that both old and new agricultural areas are located within same closed drainage basin. The fluvial channels of these catchments, which were developed during wet climatic pluvial, have largely been obliterated by the prevailing aridity and often buried under aeolian deposits. However, the new cultivations have been developed on the fingertips of these fluvial channels, while the old fields occupy the low‐level playas. The soil of the new cultivated areas is mainly lithic with a high calcium carbonate content, thus limiting the downward percolation of excess irrigation water and therefore developing perched water table and seepage through the palaeo‐channels. The automatically extracted drainage networks from DEM resemble fluvial patterns and coincide with the seepage channels slowly heading toward old cultivation. The inactive alluvial channels and landforms have to be considered when planning for new cultivation in dryland catchments to better control waterlogging and salinization hazard. It is highly recommended that newly developed seepage channels have to be detected and intercepted before reaching old agriculture areas. Therefore, the ‘dry‐drainage’ concept can be implemented as the seepage water can be conveyed into nearby playas reserved for evaporation. Copyright © 2012 John Wiley & Sons, Ltd.
Determination of the conduit structure in a karst aquifer based on tracer data—Lurbach system, Austria
Authors: Kübeck Christine , Maloszewski Piotr Jan , Benischke Ralf 
Published: January 2012

ABSTRACTA structure model was used to analyse solute‐transport parameter estimates based on tracer breakthrough curves. In the model system, groundwater flow is envisioned to be organised in a complex conduit network providing a variety of short circuits with relative small carrying capacities along different erosion levels. The discharge through the fully filled conduits is limited owing to void geometries and turbulent flow; thus, a hierarchic overflow system evolves where conduits are (re‐)activated or dried up depending on the flow condition.Exemplified on the Lurbach–Tanneben karst aquifer, the applicability of the model approach was tested. Information derived from multi‐tracer experiments performed at different volumetric flow rates enabled to develop a structural model of the karst network, under constraint of the geomorphological and hydrological evolution of the site. Depending on the flow rate, groundwater is divided into up to eight flow paths. The spatial hierarchy of flow paths controls the sequence of flow path activation. Conduits of the topmost level are strongly influenced by reversible alteration processes. Sedimentation or blocking causes an overflow of water to the next higher conduit. Flow path specific dissolutional denudation rates were estimated using the temporal development of the partial discharge. Copyright © 2012 John Wiley & Sons, Ltd.
Watershed modelling of hydrology and water quality in the Sacramento River watershed, California
Authors: Ficklin Darren L. , Luo Yuzhou , Zhang Minghua 
Published: January 2012

AbstractAgricultural pollutant runoff is a major source of water contamination in California's Sacramento River watershed where 8500 km2 of agricultural land influences water quality. The Soil and Water Assessment Tool (SWAT) hydrology, sediment, nitrate and pesticide transport components were assessed for the Sacramento River watershed. To represent flood conveyance in the area, the model was improved by implementing a flood routing algorithm. Sensitivity/uncertainty analyses and multi‐objective calibration were incorporated into the model application for predicting streamflow, sediment, nitrate and pesticides (chlorpyrifos and diazinon) at multiple watershed sites from 1992 to 2008. Most of the observed data were within the 95% uncertainty interval, indicating that the SWAT simulations were capturing the uncertainties that existed, such as model simplification, observed data errors and lack of agricultural management data. The monthly Nash–Sutcliffe coefficients at the watershed outlet ranged from 0.48 to 0.82, indicating that the model was able to successfully predict streamflow and agricultural pollutant transport after calibration. Predicted sediment loads were highly correlated to streamflow, whereas nitrate, chlorpyrifos and diazinon were moderately correlated to streamflow. This indicates that timing of agricultural management operations plays a role in agricultural pollutant runoff. Best management practices, such as pesticide use limits during wet seasons, could improve water quality in the Sacramento River watershed. The calibrated model establishes a modelling framework for further studies of hydrology, water quality and ecosystem protection in the study area. Copyright © 2012 John Wiley & Sons, Ltd.
Hypoxia upregulates ovarian cancer invasiveness via the binding of HIF‐1α to a hypoxia‐induced, methylation‐free hypoxia response element of S100A4 gene
Authors: Horiuchi Akiko , Hayashi Takuma , Kikuchi Norihiko , Hayashi Akiko , Fuseya Chiho , Shiozawa Tanri , Konishi Ikuo 
Published: January 2012

AbstractHypoxia is known to play important roles in the development and progression of tumors. We previously demonstrated that S100A4, a critical molecule for metastasis, was upregulated in ovarian cancer cells. Therefore, we examined the mechanisms of the upregulation of S100A4 expression in ovarian carcinoma cells, with particular attention paid to the effects of hypoxia. The expression levels of S100A4 were found to be correlated with the invasiveness of ovarian carcinoma cells in vitro and in vivo, and the upregulation of S100A4 expression was associated with hypomethylation of CpG sites in the first intron of S100A4 in ovarian carcinoma cell lines and tissues. The expression of S100A4 was increased under hypoxia and was associated with elevated invasiveness, which was inhibited by S100A4 small interfering RNA (siRNA). In addition, exposure to hypoxia reduced the methylation of hypoxia‐response elements (HRE) of the S100A4 gene in a time‐dependent fashion, in association with the increased binding of HIF‐1α to a methylation‐free HRE in ovarian carcinoma cells. These results indicate that hypoxia‐induced hypomethylation plays an essential role in S100A4 overexpression and the epigenetic transformation of ovarian carcinoma cells into the “metastatic phenotype.”