bluuebunny/crossref_metadata_2025_split huggingface dataset:
Promoter methylation of cyclin A1 is associated with human papillomavirus 16 induced head and neck squamous cell carcinoma independently of p53 mutation
Authors: Weiss Daniel , Basel Tuerker , Sachse Florian , Braeuninger Andreas , Rudack Claudia 
Published: May 2011

AbstractAberrant promoter methylation of specific genes and infection with human papillomavirus 16 (HPV16) are known risk factors for the development of Head and Neck Squamous Cell Carcinoma (HNSCC). Little knowledge exists on the interaction of HPV16 infection and promoter methylation in HNSCC. The promoter methylation status of 12 genes (TIMP3, CDH1, CDKN2A, DAPK1, transcription factor 21 (TCF21), CD44, MLH1, MGMT, RASSF1, cyclin A1 (CCNA1), LARS2, and CEBPA) was evaluated by methylation‐specific polymerase chain reaction in 55 primary HNSCC and 31 controls. The results were correlated with HPV16 status and clinicopathological characteristics. CCNA1 and p53 protein expression were additionally determined by immunohistochemistry and compared with p53 mutation status. Methylation of DAPK1 (P = 0.043), CCNA1 (P = 0.016) and TCF21 (P = 0.0005) was significantly more present in HNSCC than in controls. The genes TIMP3 (P = 0.018) and CCNA1 (P = 0.015) showed higher methylation frequency in HPV16 positive HNSCC compared to HPV16 negative tumors. CCNA1 methylation did not correlate with CCNA1 protein expression and p53 mutation, respectively. Methylation of TCF21 was associated with higher age (P = 0.044) and nicotine abuse (P = 0.035). Methylation of CCNA1 was significantly more present in females (P = 0.003). Methylation of TCF21 and CCNA1 are important risk factors for HNSCC development. CCNA1 methylation may play a crucial role in HPV16‐induced carcinogenesis of HNSCC independently of p53. © 2011 Wiley‐Liss, Inc.
TMKink: A method to predict transmembrane helix kinks
Authors: Meruelo Alejandro D. , Samish Ilan , Bowie James U. 
Published: May 2011

AbstractA hallmark of membrane protein structure is the large number of distorted transmembrane helices. Because of the prevalence of bends, it is important to not only understand how they are generated but also to learn how to predict their occurrence. Here, we find that there are local sequence preferences in kinked helices, most notably a higher abundance of proline, which can be exploited to identify bends from local sequence information. A neural network predictor identifies over two‐thirds of all bends (sensitivity 0.70) with high reliability (specificity 0.89). It is likely that more structural data will allow for better helix distortion predictors with increased coverage in the future. The kink predictor, TMKink, is available at http://tmkinkpredictor.mbi.ucla.edu/.
Charged residues at protein interaction interfaces: Unexpected conservation and orchestrated divergence
Authors: Zhao Nan , Pang Bin , Shyu Chi‐Ren , Korkin Dmitry 
Published: May 2011

AbstractProtein–protein interactions play an essential role in the functioning of cell. The importance of charged residues and their diverse role in protein–protein interactions have been well studied using experimental and computational methods. Often, charged residues located in protein interaction interfaces are conserved across the families of homologous proteins and protein complexes. However, on a large scale, it has been recently shown that charged residues are significantly less conserved than other residue types in protein interaction interfaces. The goal of this work is to understand the role of charged residues in the protein interaction interfaces through their conservation patterns. Here, we propose a simple approach where the structural conservation of the charged residue pairs is analyzed among the pairs of homologous binary complexes. Specifically, we determine a large set of homologous interactions using an interaction interface similarity measure and catalog the basic types of conservation patterns among the charged residue pairs. We find an unexpected conservation pattern, which we call the correlated reappearance, occurring among the pairs of homologous interfaces more frequently than the fully conserved pairs of charged residues. Furthermore, the analysis of the conservation patterns across different superkingdoms as well as structural classes of proteins has revealed that the correlated reappearance of charged residues is by far the most prevalent conservation pattern, often occurring more frequently than the unconserved charged residues. We discuss a possible role that the new conservation pattern may play in the long‐range electrostatic steering effect.
Probing the structure of membrane proteins with electron spin echo envelope modulation spectroscopy
Authors: Mayo Daniel , Zhou Andy , Sahu Indra , McCarrick Robert , Walton Parker , Ring Adam , Troxel Kaylee , Coey Aaron , Hawn Jaclyn , Emwas Abdul‐Hamid , Lorigan Gary A. 
Published: May 2011

AbstractA new approach has been developed to probe the structural properties of membrane peptides and proteins using the pulsed electron paramagnetic resonance technique of electron spin echo envelope modulation (ESEEM) spectroscopy and the α‐helical M2δ subunit of the acetylcholine receptor incorporated into phospholipid bicelles. To demonstrate the practicality of this method, a cysteine‐mutated nitroxide spin label (SL) is positioned 1, 2, 3, and 4 residues away from a fully deuterated Val side chain (denoted i + 1 to i + 4). The characteristic periodicity of the α‐helical structure gives rise to a unique pattern in the ESEEM spectra. In the i + 1 and i + 2 samples, the 2H nuclei are too far away to be detected. However, with the 3.6 residue per turn pattern of an α‐helix, the i + 3 and i + 4 samples reveal a strong signal from the 2H nuclei of the Val side chain. Modeling studies verify these data suggesting that the closest 2H‐labeled Val to SL distance would in fact be expected in the i + 3 and i + 4 samples. This technique is very advantageous, because it provides pertinent qualitative structural information on an inherently difficult system like membrane proteins in a short period of time (minutes) with small amounts of protein (μg).
Quantification of extraprostatic perineural spread and its prognostic value in pT3a pN0 M0 R0 prostate cancer patients
Authors: Aumayr Klaus , Breitegger Michael , Mazal Peter R. , Koller Anke , Marberger Michael , Susani Martin , Haitel Andrea 
Published: May 2011

AbstractBACKGROUNDThe prognostic relevance of the amount of extraprostatic cancer spread in nerves in prostate cancer patients is not well established.METHODSEighty‐eight patients were included in our study with pT3a pN0 M0 R0 prostate cancer treated with retropubic prostatectomy. Eighty‐seven of them showed perineural invasion, 54 were confined to the prostate, 33 showed cancer spread in extraprostatic nerves, which was quantified by counting each transverse section of nerves infiltrated by cancer in totally embedded specimens. Biochemical relapse was established by serum PSA levels of ≥0.2 ng/ml as well as PSA ≥ 0.4 ng/ml and higher according to the EAU guidelines.RESULTSExtraprostatic but not intraprostatic perineural infiltration was significantly more often found in tumors of higher Gleason score. Intraprostatic number of infiltrated nerves (NIN) correlated with extraprostatic NIN. There was no association between extraprostatic or intraprostatic NIN and Gleason score, lymphatic, or blood vessel invasion. Extraprostatic neural infiltration in ≤10 nerves extended relapse free survival in univariate analysis for PSA 0.2 and 0.4 ng/ml (P = 0.002 and P < 0.000001, respectively) and remained significant in multivariate analysis for PSA 0.4 ng/ml (P = 0.039).CONCLUSIONSHigh amount of extraprostatic NIN correlates with tumor progression and seems to be an independent prognostic parameter. Prostate 71:1790–1795, 2011. © 2011 Wiley Periodicals, Inc.
Pathological significance and predictive value for biochemical recurrence of c‐Fes expression in prostate cancer
Authors: Miyata Yasuyoshi , Watanabe Shin‐ichi , Matsuo Tomohiro , Hayashi Tomayoshi , Sakai Hideki , Xuan Jim W. , Greer Peter A. , Kanda Shigeru 
Published: May 2011

AbstractBACKGROUNDc‐Fes is a proto–oncogene encoded non‐receptor protein–tyrosine kinase (PTK). However, genetic studies have indicated that it has anti‐tumorigenic effects in certain cancers. The pathological and clinical significance of c‐Fes in prostate cancer are unknown.METHODSExpression of c‐Fes was evaluated in normal glands, prostatic intraepithelial neoplasia (PIN), cancer cells in tissues of knock‐in mouse adenocarcinoma prostate (KIMAP) model, and prostate cancer patients free of metastasis. Expression of c‐Fes was analyzed by immunohistochemistry, and quantified by using the immunoreactivity score (IRS) (staining intensity × percentage of positive cells). Relationships between c‐Fes expression and pT stage, Gleason's score (GS), and biochemical recurrence in patients who underwent radical surgery were also investigated.RESULTSIn KIMAP, the percentage in normal glands, PIN and cancer cells positive for c‐Fes expression were 0 (0/7), 25.0 (2/8), and 100% (7/7), respectively. In human tissues, c‐Fes expression was also significantly higher in cancer cells than in normal cells and PIN, and it correlated with pT stage (P < 0.001) and GS (P = 0.047). Multivariate analysis showed that c‐Fes expression was an independent predictor of poor outcome poor prognosis (hazard ratio = 3.21, 95% confidence interval = 1.11–9.37, P = 0.032).CONCLUSIONThe results suggested that c‐Fes expression is a useful predictor of biochemical recurrence after radical surgery. The results also suggested that c‐Fes is a potentially useful therapeutic target in prostate cancer and a predictor of biochemical recurrence after radical prostatectomy. Prostate 72:201–208, 2012. © 2011 Wiley Periodicals, Inc.
Functional surfaces in heterogeneous catalysis: A short review
Authors: Rosenthal Dirk 
Published: May 2011

AbstractHeterogeneous catalysis and functional surfaces are intimately connected. Surface functionalities mediate the catalytic reactions. However, the surface must fulfil several requirements: adsorption of the reactants on the surface must be energetically favoured (but reversible), the surface functionalities must enhance the dissociation of chemical bonds in the reactant and the formation of new ones which will lead to the reaction's product(s), and finally the product(s) must be able to desorb and leave the surface. It was shown that for the ammonia synthesis on ruthenium single crystalline surfaces, both the geometric and electronic functionalities of step edges are crucial to dissociate nitrogen. Another well‐investigated reaction is the catalytic oxidation of carbon monoxide over platinum and oxidized ruthenium. For both metals, the surface is dynamic, which leads to a change in its functionalities during reaction. These few examples of simple reactions already show the complexity of the necessary surface functionalities for heterogeneous catalysis and the problems connected with the understanding of rather simple reaction mechanisms. The key objective in catalysis research consists in tailoring the geometric and electronic properties of catalysts depending on the target reactions. One attempt in this direction is the investigation of binary alloys and, more recently, of intermetallic compounds. Here, the adsorption properties of the reactants could be drastically changed. A completely different way of changing adsorption properties also exists for semiconductor surfaces: the direct application of electric fields leads to a change of charge carriers near the surface – the electro‐adsorptive effect (EAE).
Spectral phase interference: A tool for the study of adsorption processes on solid surfaces
Authors: Kusterer Jan , Bakowsky Udo , Keusgen Michael 
Published: May 2011

AbstractSpectral phase interference (SPI) has attracted considerable attention during last years as method for biomolecular interaction analysis (BIA). The advantages of this method are real time measurements independently from the refraction index of the investigated solution. Therefore, this method was applied for evaluating the influence of mouth rinsing solutions like chlorhexidine digluconate (CHX)‐solutions on the pellicle formation upon a tooth model. The tooth model was a based glass chip, type ‘K0’. The surface of this activated glass chip is comparable to the surface of the enamel of a tooth. After surface activation, saliva was applied in order to deposit a pellicle layer. The pellicle is the primary protein layer formed on the surface of a tooth. This layer has the function to prevent a direct contact of bacteria with the tooth surface. As a disadvantage, this layer is the docking point and primary nutrition reservoir for bacteria forming the plaque. Analysing the interaction of this bio layer with mouth rinsing solutions is essential to evaluate effects on the formation of plaque. In this investigation, evidences for positive effects of CHX‐solutions and amino fluorides on the formation of the pellicle have been found. Treatment with these solutions resulted in a dose dependent enhanced thickness of the pellicle. It can be assumed, that these modified pellicle layers are more resistant against bacteria attack.
Effect of magnetic field on the capacitance of the La0.5Ca0.5MnO3‐based heterojunction
Authors: Lu H. X. , Sun J. R. , Zhao J. L. , Shen B. G. 
Published: May 2011

AbstractEffects of interface decoration and ac frequency, under which the impedance is measured, on the magnetoelectric property have been experimentally studied for the heterojunctions of La0.5Ca0.5MnO3/SrTiO3:Nb and La0.5Ca0.5MnO3/LaMnO3(3nm)/SrTiO3:Nb. It is found that the impedance of the junction can be well described by an effective circuit of two R–C sub‐circuits in series well above 100 K. Magnetocapacitance emerges and develops as temperature decreases, and shows a strong frequency‐dependent character. The maximal magnetocapacitance, under a field of 5 T, is ∼30 and ∼35% with and without the buffer layer, respectively. The incorporation of the LaMnO3 layer shifts the upper temperature limit for significant magnetocapacitance from ∼120 to ∼200 K. Shrinkage of the depletion layer of the junction under magnetic field may be a main reason for the magnetoelectric effect observed here.
Pressure effects in PrT2B2C (T = Co, Ni, Pt): Applied and chemical pressure
Authors: Falconi R. , Durán A. , Núñez‐Regueiro M. , Escudero R. 
Published: May 2011

AbstractHigh pressure electrical resistivity ρab measurements on intermetallic Pr(Co, Ni, Pt)2B2C compounds were performed down to 2 K. At ambient pressure the $\rho _{ab} (T)$ curves for the non‐superconducting Pr(Co, Ni)2B2C compounds exhibit magnetic correlations at about 10 and 4 K, respectively. At low temperatures, PrCo2B2C shows a large spin‐dependent electron scattering in comparison to PrNi2B2C. Under applied pressure, the magnetic scattering tends to be suppressed more effectively in PrCo2B2C than in PrNi2B2C. The low‐temperature behavior of $\rho _{ab} (T,P)$ for PrNi2B2C and PrCo2B2C suggests a spin fluctuation mechanism. On the other hand, the PrPt2B2C compound shows superconductivity at about 6 K and under pressure its superconducting transition temperature tends to be degraded at a rate ${\rm d}T_{{\rm c}} /{\rm d}P = {-} 0.34\;{\rm K/GPa}$, as expected in compounds with transition metals. The experimental results in Co‐, Ni‐, and Pt‐based compounds are analyzed from the point of view of the external and chemical internal pressure effects.
Ultrafast magnetization dynamics in the half‐metallic Heusler alloy Co2Cr0.6Fe0.4Al
Authors: Wüstenberg Jan‐Peter , Steil Daniel , Alebrand Sabine , Roth Tobias , Aeschlimann Martin , Cinchetti Mirko 
Published: May 2011

AbstractUltrafast demagnetization upon excitation with intense laser pulses has been observed for a variety of ferromagnetic materials. In half‐metals, long demagnetization times are expected due to the band gap for one spin direction. We have investigated the theoretically half‐metallic Heusler alloy Co2Cr0.6Fe0.4Al (CCFA), using the time‐resolved magnetooptical Kerr effect. A demagnetization time in the range of typical transition metal ferromagnets with lower spin polarization has been found, while magnetization recovery proceeds on a slower time scale. The results are discussed in the context of recent models and experimental results. We propose that for Heusler alloys the initial stage of recovery could be a better measure for the spin polarization than the demagnetization time. A simple estimate leads to a bulk spin polarization value of 0.86 for CCFA.
Physical and optical properties of mineral dust aerosol measured by aircraft during the GERBILS campaign
Authors: Johnson B. T. , Osborne S. R. 
Published: May 2011

AbstractThis paper presents aircraft measurements of the physical and optical properties of mineral dust from the GERBILS campaign. The campaign involved ten flights of the UK Facility for Airborne Atmospheric Measurements (FAAM) BAe‐146 aircraft over the western region of the Sahara desert. Vertical profiles showed dust layers at varying altitudes extending as high as 6.5 km. Dust layers were typically associated with a deep well‐mixed boundary layer or a residual boundary layer above (the Saharan air layer). Aerosol optical depths (AODs), measured by integrating vertical profiles of extinction coefficient, ranged from 0.3 to 2.4 (at 0.55 μm). Aircraft AODs were generally within 20% of AERONET and Microtops sun‐photometer measurements. Single‐scattering albedos at 0.55 μm were measured in the range 0.92–0.99 with a campaign mean of 0.97. The in situ size distribution compared well with AERONET retrievals made at Banizoumbou (Niger) and Dakar (Senegal). The proportion of aerosol volume associated with particles of radii >1.5 μm was highly variable and also more difficult to measure. Models of dust as spheres, spheroids and more complex irregular‐shaped particles were used to calculate single‐scattering optical properties. The single‐scattering albedo showed a low sensitivity to particle shape. The asymmetry parameter and specific extinction coefficient showed greater sensitivity to particle shape. Copyright © 2011 British Crown copyright, the Met Office. Published by John Wiley & Sons Ltd.
Assignable causes of variation and statistical models: another approach to an old topic
Authors: Adler, Y. , Shper V. , Maksimova O. 
Published: May 2011

AbstractThis paper presents a fresh approach to the analysis of Shewhart control chart's performance. We consider two different types of assignable causes of variation. One—called type I—affects only the parameters of a model of the underlying distribution. The other—called type X—impacts the type of the original distribution. We analyze cases when the underlying normal distribution transforms into a uniform and log‐normal distribution after the intervention of an assignable cause of variation. It is shown that the Power Functions for control charts for individual measurements and control charts for means differ significantly from the well‐known traditional studies. We believe that this approach may open up new areas of research in the field of Statistical Process Control (SPC) and extend the spheres of SPC applications in practice. Copyright © 2011 John Wiley & Sons, Ltd.
The variable sampling interval X̄ chart with estimated parameters
Authors: Zhang Ying , Castagliola Philippe , Wu Zhang , Khoo Michael B. C. 
Published: May 2011

AbstractThe VSI chart has been investigated by many researchers under the assumption of known process parameters. However, in practice, these parameters are usually unknown and it is necessary to estimate them from the past data. In this paper, we evaluate and compare the performance of the VSI chart in terms of its average time to signal in the case where the process parameters are known and in the case where these parameters are estimated. We also provide new chart constants taking into account the number of phase I samples. Copyright © 2011 John Wiley & Sons, Ltd.
Electric and magnetic dipole shielding constants for the ground state of the relativistic hydrogen‐like atom: Application of the Sturmian expansion of the generalized Dirac‐Coulomb Green function
Authors: Stefańska Patrycja , Szmytkowski Radosław 
Published: May 2011

AbstractThe Sturmian expansion of the generalized Dirac‐Coulomb Green function (Szmytkowski, J Phys B, 1997, 30, 825; erratum 1997, 30, 2747) is exploited to derive closed‐form expressions for electric
$(\sigma_{E})$
and magnetic $(\sigma_{M})$
dipole shielding constants for the ground state of the relativistic hydrogen‐like atom with a point‐like and spinless nucleus of charge Ze. It is found that $\sigma_{E}=Z^{-1}$
(as it should be) and

where
$\gamma_{1}=\sqrt{1-(Z\alpha)^{2}}$
(α is the fine‐structure constant). This expression for $\sigma_{M}$
agrees with earlier findings of several other authors, obtained with the use of other analytical techniques, and is elementary compared to an alternative one presented recently by Cheng et al. (J Chem Phys 2009, 130, 144102), which involves an infinite series of ratios of the Euler's gamma functions. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
A robotic endoscope based on minimally invasive locomotion and wireless techniques for human colon
Authors: Gao Peng , Yan Guozheng , Wang Zhiwu , Wang Kundong , Jiang Pingping , Zhou Yilu 
Published: May 2011

AbstractBackgroundTraditional endoscopy may cause tissue trauma and discomfort to patients because of the use of relatively long and semi‐rigid scopes.MethodsA wireless robotic endoscope has been designed based on minimally invasive locomotion and wireless techniques for energy, monitoring, and telecontrol.ResultsThe robotic endoscope can move forward or backward effectively in a smooth synthetic glass tube. The increase of the tube dip angle reduces the relative speed. The robot moves with lower efficiency because of the viscoelasticity of intestinal tissue in in vitro pig colon. The wireless power system can continuously and stably provide a minimum 378 mW energy, which exceeds the maximum system consumption. The video system realizes wireless image transmission at 30 frames per second. Doctors control the robot remotely using a communication frequency of 433 MHz.ConclusionsThe prototype robot shows the possibility of clinical application, but needs further improvement and testing. Copyright © 2011 John Wiley & Sons, Ltd.
Robotic central pancreatectomy with stented pancreaticogastrostomy: operative details
Authors: Addeo Pietro , Marzano Ettore , Nobili Cinzia , Bachellier Philippe , Jaeck Daniel , Pessaux Patrick 
Published: May 2011

AbstractBackgroundCentral pancreatectomy (CP) is increasingly being used to treat selected lesions of the central pancreatic segment. A step‐by‐step technique for robotic CP is described and a literature review provided for this minimally invasive approach.MethodsA 55‐year‐old woman was referred to the authors' center for the treatment of a single 4 cm lesion located at the proximal part of the pancreatic body. The da Vinci Robotic surgical system® with a five trocar technique was used. The pancreatic neck was transected using an endoscopic stapler. The pancreatic body was progressively dissected from the splenic vessels right to left and sectioned with an appropriate oncologic margin. A pancreaticogastrostomy protected by a transanastomotic external stent was constructed to the distal pancreatic stump.ResultsSurgery lasted 450 min (8 min docking time) with minimal blood loss. Pathology showed a 28 mm well‐differentiated neuroendocrine pancreatic tumor with tumor‐free resection margins. The patient was discharged home on postoperative day 15 in good condition.ConclusionsRobotic surgery can be safely used for complex pancreatic resection requiring pancreaticoenteric reconstruction. The experience reported so far is still limited but the results are encouraging; robotics shows the potential to bridge the gap between minimally invasive surgery and advanced pancreatic surgery. Copyright © 2011 John Wiley & Sons, Ltd.