bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression of p16INK4A but not hypoxia markers or poly adenosine diphosphate‐ribose polymerase is associated with improved survival in patients with pancreatic adenocarcinoma
Authors: Chang Daniel T. , Chapman Christopher H. , Norton Jeffrey A. , Visser Brendan , Fisher George A. , Kunz Pamela , Ford James M. , Koong Albert C. , Pai Reetesh K. 
Published: July 2010

AbstractBACKGROUND:Pancreatic cancer is associated with mutations in the tumor suppressor gene cyclin‐dependent kinase inhibitor 2A (p16INK4A), a regulator of the cell cycle and apoptosis. This study investigates whether immunohistochemical expression of p16INK4A as well as hypoxia markers and poly adenosine diphosphate‐ribose polymerase (PARP) correlates with survival in patients with resected pancreatic adenocarcinoma.METHODS:Seventy‐three patients with pancreatic adenocarcinoma who underwent curative resection at Stanford University were included. From the surgical specimens, a tissue microarray was constructed using triplicate tissue cores from the primary tumor and used for immunohistochemical staining for the following markers: carbonic anhydrase IX, dihydrofolate reductase, p16INK4A, and PARP1/2. Staining was scored as either positive or negative and percentage positive staining. Staining score was correlated with overall survival (OS) and progression‐free survival (PFS).RESULTS:Of the markers tested, only immunohistochemical expression of p16INK4A correlated with clinical outcome. On univariate analysis, p16INK4A expression in the tumor was associated with improved OS (P = .038) but not PFS (P = .28). The median survival for patients with positive versus negative p16INK4A staining was 28.8 months versus 18 months. On multivariate analysis, p16INK4A expression was associated with improved OS (P = .026) but not PFS (P = .25). Age (P = .0019) and number of nodes involved (P = .025) were also significant for OS. Adjuvant chemotherapy and margin status did not correlate with OS or PFS.CONCLUSIONS:Expression of p16INK4A is associated with improved OS in patients with resected pancreatic adenocarcinoma. Further investigation is needed for validation, given conflicting data in the published literature. Cancer 2010. © 2010 American Cancer Society.
Combination of gemcitabine and cisplatin is highly active in women with endometrial carcinoma
Authors: Brown Jubilee , Smith Judith A. , Ramondetta Lois M. , Sood Anil K. , Ramirez Pedro T. , Coleman Robert L. , Levenback Charles F. , Munsell Mark F. , Jung Maria , Wolf Judith K. 
Published: July 2010

AbstractBACKGROUND:The treatment of patients with advanced or recurrent endometrial cancer remains problematic, because chemotherapy and hormonal therapy have yielded low response rates and limited progression‐free survival. Because the combination of gemcitabine and cisplatin demonstrated synergism in preclinical studies, the authors attempted to determine the efficacy and toxicity of this combination in women with advanced or recurrent endometrial cancer.METHODS:A prospective, single‐institution, phase 2 study was performed in women with histologically documented International Federation of Gynecology and Obstetrics (FIGO) stage III or IV or recurrent endometrioid endometrial carcinoma. Gemcitabine at a dose of 1000 mg/m2 and cisplatin at a dose of 35 mg/m2 were administered intravenously on Days 1 and 8 of each 21‐day cycle; because of myelosuppression, the protocol was revised to gemcitabine at a dose of 900 mg/m2 and cisplatin at a dose of 30 mg/m2. Patients were treated until disease progression, unacceptable toxicity, or complete response.RESULTS:A total of 21 patients were enrolled and received a median of 5 courses of therapy (range, 1‐9 courses). The median age at the time of study enrollment was 62 years (range, 41‐75 years). Of 20 evaluable patients, 2 (10%) had a confirmed complete response, 8 (40%) had a partial response, 6 (30%) had stable disease, and 4 (20%) developed progressive disease. The median progression‐free survival was 7.5 months (range, 2.3‐33.6 months), and the median overall survival was 18.2 months (range, 2.5‐49.4 months). The development of toxicity mandated dose reductions in 16 of 20 patients (80%). Eighteen patients experienced grade 3 or 4 toxic effects (graded according to the Common Terminology Criteria for Adverse Events [version 3.0]).CONCLUSIONS:The objective response rate of 50% noted with gemcitabine and cisplatin combination chemotherapy merits the further development of this regimen in women with advanced or recurrent endometrial cancer. Cancer 2010. © 2010 American Cancer Society.
Computerized analysis of cytology and fluorescence in situ hybridization (FISH) in induced sputum for lung cancer detection
Authors: Guber Alexander , Greif Joel , Rona Roni , Fireman Elizabeth , Madi Lea , Kaplan Tal , Yemini Zipi , Gottfried Maya , Katz Ruth L , Daniely Michal 
Published: July 2010

AbstractBACKGROUND:Lung cancer results from a multistep process, whereby genetic and epigenetic alterations lead to a malignant phenotype. Somatic mutations, deletions, and amplifications can be detected in the tumor itself, but they can also be found in histologically normal bronchial epithelium as a result of field cancerization. The present feasibility study describes a computer‐assisted analysis of induced sputum employing morphology and fluorescence in situ hybridization (target–FISH), using 2 biomarkers located at chromosomes 3p22.1 and 10q22.3.METHODS:Induced sputum samples were collected using a standardized protocol from 12 patients with lung cancer and from 15 healthy, nonsmoking controls. We used an automated scanning system that allows consecutive scans of morphology and FISH of the same slide. Cells derived for the lower airways were analyzed for the presence of genetic alterations in the 3p22.1 and 10q22.3 loci.RESULTS:The cutoff for a positive diagnosis was defined as >4% of cells showing genetic alterations. Eleven of 12 lung cancer patients and 12 of 15 controls were identified correctly, giving an overall sensitivity and specificity of 91.66% and 80%, respectively.CONCLUSIONS:This study describes a new technology for detecting lung cancer noninvasively in induced sputum via a combination of morphology and FISH analysis (target–FISH) using computer‐assisted technology. This approach may potentially be utilized for mass screening of high‐risk populations. Cancer (Cancer Cytopathol) 2010. © 2010 American Cancer Society.
Reversible Single Molecular Switch Operating at 300 K on a Surface
Authors: El Garah Mohamed , Baris Bulent , Luzet Vincent , Palmino Frank , Chérioux Frédéric 
Published: July 2010

AbstractA single 4‐pyridylazobenzene molecule is observed at room temperature on a Si(111)‐B surface by using scanning tunnel microscopy. The reversible conformational switching of this molecule is induced by tunneling electrons and observed at room temperature. This process is based on an intramolecular rotation of a single phenyl group without isomerization of the NN double bond.
A Dynamically Entangled Coordination Polymer: Synthesis, Structure, Luminescence, Single‐Crystal‐to‐Single‐Crystal Reversible Guest Inclusion and Structural Transformation
Authors: Aijaz Arshad , Lama Prem , Bharadwaj Parimal K. 
Published: July 2010

AbstractA ZnII coordination polymer {[Zn2(cpa)2(bpy)]·3H2O}n (1) (cpa2– = 4‐(methoxycarbonyl)benzoate and bpy = 4,4′‐bipyridine) has been synthesized under solvothermal condition and structurally characterized. This coordination polymer has nanotubular threefold entangled (2D→3D) structure with embedded water molecules; the water molecules can be partially exchanged in reversible single‐crystal‐to‐single‐crystal (SC‐SC) fashion by different solvent molecules like methanol, ethanol and acetone giving rise to {[Zn2(cpa)2(bpy)]·(0.5MeOH)·(2.5H2O)}n (2), {[Zn2(cpa)2(bpy)]·(0.5EtOH)·(0.5H2O)}n (3) and {[Zn2(cpa)2(bpy)]·(0.5Me2CO)·(H2O)}n (4). Inclusion of EtOH or MeOH leaves the size of the voids in the framework unaltered. Inclusion of acetone, however, is accompanied by shrinking of the voids in the framework. Heating of 1 at 100 °C under vacuum for 4 h affords the de‐solvated compound, {Zn2(cpa)2(bpy)}n (1′). Single‐crystal X‐ray structure of 1′ shows sliding of the individual nanotubular components expanding the overall framework. Thus, the coordination polymer exhibits dynamic motion of the molecular components in SC‐SC fashion. All compounds were further characterized via IR spectroscopy, PXRD, elemental and TGA analysis. When 1 is placed in benzene at 100 °C for 2 days, compound {[Zn2(cpa)2(bpy)]·(2.5H2O)}n (5) is formed in a SC‐SC fashion where coordination number of ZnII ion increases from four to five. Compound 1 also exhibits reversible guest‐dependent photoluminescence properties.
Combinatorial peptide ligand library plasma treatment: Advantages for accessing low‐abundance proteins
Authors: Beseme Olivia , Fertin Marie , Drobecq Hervé , Amouyel Philippe , Pinet Florence 
Published: July 2010

AbstractDepletion of major blood proteins is one of the most promising approaches to accessing low‐abundance biomarkers. This study compared the use of combinatorial peptide ligand library (CPLL) and albumin and immunoglobulins (IgGs) depletion technology for accessing these low‐abundance proteins in plasma using 2‐DE in an acidic restricted pH range (4–7). Compared with native plasma, both techniques enlarge the visibility of other proteins than albumin and IgG, but there were marked differences in their composition. An increase of the number of spots was detected compared with native plasma (157 spots) with 427 and 557 spots, respectively, detected with albumin and IgG depletion, and CPLL treatment. We selected 70 spots to be identified by MALDI‐TOF related to their absence in the 2‐D gels from native or albumin and IgG‐depleted plasma. The 42 spots identified corresponded to 24 different proteins, with more than half of the proteins which did not belong to the major plasma proteins. CPLL treatment allowed the accessibility to proteolytic fragments obtained from major plasma proteins. We found a large superiority of the CPLL approach over the albumin and IgG depletion process. These findings show the utility of depleting major blood proteins to be able to access low‐abundance proteins and the potential of CPLL to select and identify candidate biomarkers in clinical studies.
Migration and internal architecture of marine dunes in the eastern English Channel over 14 and 56 year intervals: the influence of tides and decennial storms
Authors: Ferret Y. , Le Bot S. , Tessier B. , Garlan T. , Lafite R. 
Published: July 2010

AbstractSubmarine dune dynamics are controlled by tidal currents and wind forces. According to the relative influence of these forces and the nature of dune sediment, different bedform behaviors can be observed. The footprint of the different hydrodynamic agents is recorded into the internal architecture of dunes. This paper is concerned with bedforms that compose the thick sediment wedge located in the eastern English Channel, off the Bay of Somme. This sedimentary archive constitutes an interesting feature to achieve a better understanding of seabed sediment dynamics and its timeline building stages. The dynamics of large submarine dunes, which are organized in fields, are studied thanks to bathymetric and seismic data over the periods 1937–1993 and 1993–2007.Dune morphology presents low lee and stoss side slopes (on average 8° and 3°, respectively) and dune migration rate is not very high. Dune movements are in the direction of residual tidal currents, i.e. toward the east, with mean migration rates around 0·8 to 5 ± 0·25 m yr−1 and up to 6·6 ± 0·7 m yr−1, respectively, at multi‐decennial and decennial time scales. The dune internal architecture is complex with superimposed eastward prograding units, displaying locally opposite progradation. Second‐order discontinuities (dip of 0·5°–4° perpendicular to dune crests) constitute dune master bedding. By counting the number of second‐order reflectors between 1937–1993 and 1993–2007, the formation periodicity of these bounding surfaces is estimated to range from 4 to 18 years. These time intervals coincide with the long‐term tidal cyclicities and also with the inter‐annual to decennial variability of storm activity in northern Europe. Two theories were made to interpret the dune internal structures: the second‐order surfaces are interpreted either as the depositional surfaces corresponding to the marks of weak energy periods (weak tidal and storm action), or as erosive surfaces due to an opposite direction of dune migration provoked temporarily by exceptional storms from the northeast. Copyright © 2010 John Wiley & Sons, Ltd.
Geomorphic and cosmogenic nuclide constraints on escarpment evolution in an intraplate setting, Darling Escarpment, Western Australia
Authors: Jakica Sara , Quigley Mark C. , Sandiford Mike , Clark Dan , Fifield L. Keith , Alimanovic Abaz 
Published: July 2010

AbstractThe ∼900 km long Darling Scarp in Western Australia is one of the most prominent linear topographic features on Earth. Despite the presence of over‐steepened reaches in all westerly flowing streams crossing the scarp, and significant seismic activity within 100 km of the scarp, there is no historical seismicity and no reported evidence for Quaternary tectonic displacements on the underlying Darling Fault. Consequently, it is unclear whether the scarp is a rapidly evolving landform responding to recent tectonic and/or climatic forcing or a more slowly evolving landform. In order to quantify late Quaternary rates of erosion and scarp relief processes, we obtained measurements of the cosmic‐ray produced nuclide beryllium‐10 (10Be) from outcropping bedrock surfaces along the scarp summit and face, in valley floors, and at stream knickpoints. Erosion rates of bedrock outcrops along the scarp summit surface range from 0·5 to 4·0 m Myr−1. These are in the same range as erosion rates of 2·1 to 3·6 m Myr−1 on the scarp face and similar to river incision rates of 2·6 to 11·0 m Myr−1 from valley floor bedrock straths, indicating that the Darling Scarp is a slowly eroding ‘steady state’ landform, without any significant contemporary relief production over the last several 100 kyr and possibly several million years. Knickpoint retreat rates determined from 10Be concentrations at the bases of two knickpoints on small streams incised into the scarp are 36 and 46 m Myr−1. If these erosion rates were sustained over longer timescales, then associated knickpoints may have initiated in the mid‐Tertiary to early Neogene, consistent with early‐mid Tertiary marginal uplift. Ongoing maintenance of stream disequilibrium longitudinal profiles is consistent with slow, regional base level lowering associated with recently proposed continental‐scale tilting, as opposed to differential uplift along discrete faults. Cosmogenic 10Be analysis provides a useful tool for interpreting the palaeoseismic history of intraplate near‐fault landforms over 105 to 106 years. Copyright © 2010 John Wiley & Sons, Ltd.
Essential oil from fruits and roots of Ferulago campestris (Besser) Grecescu (Apiaceae): composition and antioxidant and anti‐Candida activity
Authors: Cecchini Cinzia , Coman Maria M. , Cresci Alberto , Tirillini Bruno , Cristalli Gloria , Papa Fabrizio , Sagratini Gianni , Vittori Sauro , Maggi Filippo 
Published: July 2010

AbstractEssential oil from fruits and roots of Ferulago campestris (Apiaceae) growing in central Italy was analysed by GC–FID and GC–MS for composition and by agar diffusion and microdilution methods for antibacterial and anti‐Candida activity. The antioxidant activities were also investigated by 1,1‐diphenyl‐2‐picrylhydrazyl (DPPH) radical‐scavenging, β‐carotene/linoleic acid assay, scavenging of hydrogen peroxide (HRPO test), and hypochlorous acid scavenging (taurine test). High yields of essential oils (5.7–7.1%) were obtained by hydrodistillation from fruits, making these exploitable in the flavour and fragrance industry. Monoterpene hydrocarbons constituted the main fraction of both fruits (78.8–80.3%) and roots (67.2–81.4%), with myrcene (33.4–39.7%), α‐pinene (22.7–23.0%) and γ‐terpinene (8.1–10.9%) as the major components of fruits, and α‐pinene (58.3–75.0%) as the predominant compound in the oil from roots collected in summer. (2,3,6)‐Trimethyl benzaldehyde was an aromatic volatile detected in significant percentages (8.6–9.0% in fruits, 14.8–27.9% in roots collected in summer, 65.2% in roots collected in autumn) in both oils. The antioxidant activity was related as IC50 to Trolox or BHT; <2 ml oils had an activity equivalent to 1 mg Trolox in the DPPH radical‐scavenging, and about 1 ml oils could be compared with 1 mg Trolox or BHT in the β‐carotene/linoleic acid assay, HRPO and taurine tests. The essential oils from the roots were more active than those from fruits against the microorganisms tested, owing to the abundance of α‐pinene, a monoterpene hydrocarbon with known antimicrobial potency. In particular, it showed strong inhibition on clinically isolated Candida strains, namely C. albicans (MIC values of 39–78 μg/ml), C. tropicalis and C. glabrata (MIC values of 78 μg/ml). Copyright © 2010 John Wiley & Sons, Ltd.
A study on the mechanism of high‐lift generation by an insect wing in unsteady motion at small Reynolds number
Authors: Hamdani Hossein Raza , Naqvi Ali 
Published: July 2010

AbstractThe aerodynamic force and flow structure of a wing performing an unsteady motion at small Reynolds number (Re=4000) is calculated by solving Navier–Stokes equations. Calculations were conducted for steady motion, simple unsteady motions suc as azimuth rotation, pure translation, feathering, etc., which can provide a basis for understanding the more complicated hovering flight. At Re=4000, the delayed stall mechanism was noted during the azimuth rotation of a wing due to span wise flow. In azimuth rotation and pure translation, large value of CL could be achieved due to fast acceleration of the airfoil from rest. Large value of CL could be maintained during azimuth rotation for many chord length of travel in comparison with the pure translation due to spanwise flow that causes Dynamic Stall Vortex (DSV) to remain attached. For feathering motion, pitch oscillation motion was dominated by the azimuth rotation. Copyright © 2010 John Wiley & Sons, Ltd.
A solution adaptive simulation of compressible multi‐fluid flows with general equation of state
Authors: Zheng H. W. , Shu C. , Chew Y. T. , Qin N. 
Published: July 2010

AbstractThe unstructured quadrilateral mesh‐based solution adaptive method is proposed in this article for simulation of compressible multi‐fluid flows with a general form of equation of state (EOS). The five equation model (J. Comput. Phys. 2002; 118:577–616) is employed to describe the compressible multi‐fluid flows. To preserve the oscillation‐free property of velocity and pressure across the interface, the non‐conservative transport equation is discretized in a compatible way of the HLLC scheme for the conservative Euler equations on the unstructured quadrilateral cell‐based adaptive mesh. Five numerical examples, including an interface translation problem, a shock tube problem with two fluids, a solid impact problem, a two‐dimensional Riemann problem and a bubble explosion under free surface, are used to examine its performance in solving the various compressible multi‐fluid flow problems with either the same types of EOS or different types of EOS. The results are compared with those calculated by the following methods: the method with ROE scheme (J. Comput. Phys. 2002; 118:577–616), the seven equation model (J. Comput. Phys. 1999; 150:425–467), Shyue's fluid‐mixture model (J. Comput. Phys. 2001; 171:678–707) or the method in Liu et al. (Comp. Fluids 2001; 30:315–337). The comparisons for the test problems show that the proposed method seems to be more accurate than the method in Allaire et al. (J. Comput. Phys. 2002; 118:577–616) or the seven‐equation model (J. Comput. Phys. 1999; 150:425–467). They also show that it can adaptively and accurately solve these compressible multi‐fluid problems and preserve the oscillation‐free property of pressure and velocity across the material interface. Copyright © 2010 John Wiley & Sons, Ltd.
An efficient method for discretizing 3D fractured media for subsurface flow and transport simulations
Authors: Mustapha Hussein , Dimitrakopoulos Roussos , Graf Thomas , Firoozabadi Abbas 
Published: July 2010

AbstractWe introduce a new method to discretize inclined non‐planar two‐dimensional (2D) fractures in three‐dimensional (3D) fractured media for subsurface flow and transport simulations. The 2D fractures are represented by ellipsoids. We first discretize the fractures and generate a 2D finite element mesh for each fracture. Then, the mesh of fractures is analyzed by searching and treating critical geometric configurations. Based on that search, the method generates a quality mesh and allows for including finer grids. A solute transport problem in fractured porous media is solved to test the method. The results show that the method (i) adequately represents the fractured domain by maintaining the geometric integrity of input surfaces and geologic data, (ii) provides accurate results for both simple and complex fractured domains, (iii) is insensitive to spatial discretization, and (iv) is computationally very efficient. For inclined and vertical fractures, analytical and numerical solutions are shown to be in good agreement. The method is therefore suitable to discretize fracture networks for flow and transport simulations in fractured porous media. Copyright © 2010 John Wiley & Sons, Ltd.
Calculation of capillary jet
Authors: Zhang Kenn K. Q. 
Published: July 2010

AbstractThe Arbitrary Lagrangian Eulerian (ALE) framework coupled with some boundary tracking techniques is proven to be an effective method for simulation of free‐surface flows. In this paper, a special ALE framework is derived with clarification of three velocities, the notion of mesh‐frozen and field‐frozen, and the notion of tentatively inertial coordinates. A weighted integral ALE governing equations are formulated on generic coordinates and discretized with a finite element method and linear implicit time scheme. The system is solved with a discrete operator splitting technique and superposition‐based logistic parallelization. The formulation and implementation are verified through several fixed‐geometry problems and a reasonably good parallel performance is observed. Capillary jet flow is the main problem of the paper and the numerical techniques for boundary tracking are elaborated, which include an indirect boundary tracking of flux method and an iterative direct boundary tracking method. Also, a high‐order compact scheme for dynamic boundary condition and a squeeze technique for kinematic boundary condition are adopted. The axisymmetric jet breakup is studied in detail and numerical results match with the published data very well. Numerical accuracy and sensitivity are studied, including effects of element type, time scheme, compact scheme, and boundary tracking techniques. Copyright © 2010 John Wiley & Sons, Ltd.