bluuebunny/crossref_metadata_2025 huggingface dataset:
The lipophilicity indices of flavonoids estimated by reversed‐phase liquid chromatography using different computation methods
Authors: Briciu Rodica Domnica , Kot‐Wasik Agata , Namiesnik Jacek , Sârbu Costel
Published: June 2009

The chromatographic behavior of some flavonoids was established by RP‐HPLC on RP‐18 (LiChroCART, LiChrosphere RP‐18e), RP‐8 (Zorbax, Eclipse XDB‐C8), CN (Säulentechnik, LiChrosphere CN100) columns. The mobile phases were mixtures of methanol‐water in different volume proportions from 70 to 80% v/v for RP‐18 and RP‐8, while for the CN column the proportions were between 66 and 70% v/v. The lipophilicity was expressed through different lipophilicity descriptors such as mean of k (mk), mean of log k (mlog k), log kW, S, f0, and scores of k and log k corresponding to the first principal component. The experimental lipophilicity indices are directly correlated with the computed values, via computer software and internet module, at a high analytical level. Furthermore, the results obtained applying principal component analysis to k and/or log k values allow the prediction and explanation of the interaction involved in the retention mechanism which takes place between the compounds and the employed stationary phases during the development.
Determination of nonylphenol and nonylphenol ethoxylates in wastewater using MEKC
Authors: Núñez Laura , Wiedmer Susanne K. , Parshintsev Jevgeni , Hartonen Kari , Riekkola Marja‐Liisa , Tadeo José L. , Turiel Esther
Published: June 2009

Nonylphenol ethoxylates (NPEOx) are surfactants which are used worldwide and can be transformed in the environment by microorganisms to form nonylphenol (NP). Analysis of these compounds was carried out with micellar electrokinetic capillary chromatography (MEKC). Different parameters such as background electrolyte (BGE) solution, pH, type of surfactant, and sample stacking were optimized. The use of CHES (20 mM, pH 9.1) in combination with 50 mM sodium cholate as a surfactant as BGE solution, together with sample stacking using 50 mM NaCl in the sample and an injection time of 20 s, provided the best separation of the compounds studied. The method was applied to the determination of target analytes in two types of sludge water coming from two steps of a wastewater treatment plant. Liquid–liquid extraction was carried out using toluene as solvent, resulting in recoveries around 100% for all studied analytes. The presence of NPEOx was observed in the first step of the sludge water treatment, based on migration time and UV spectra. Identification was confirmed using tandem MS. LOQs of the studied compounds were in the range of 12.7 to 30.8 ng/mL, which is satisfactory for the analysis of real wastewater samples.
Kinetic study of the condensation of salicylaldehyde with diethyl malonate in a nonpolar solvent catalyzed by secondary amines
Authors: Bednarz Szczepan , Bogdal Dariusz
Published: June 2009

The kinetics of condensation between salicylaldehyde and diethylmalonate in a toluene solution in the presence of secondary amines (i.e., piperidine and 4‐piperidinopiperidine) as catalysts was investigated. It was found that the reaction proceeds via the Knoevenagel mechanism, and the kinetic model was numerically verified. © 2009 Wiley Periodicals, Inc. Int J Chem Kinet 41: 589–598, 2009
Evaluation of data for atmospheric models: Master Equation/RRKM calculations on the combination reaction ClO + NO2 → ClONO2, a recurring issue
Authors: Golden David M.
Published: June 2009

Experimental data for the title reaction have been modeled using Master Equation/RRKM methods based on the Multiwell suite of programs. The starting point for the exercise was the empirical fitting provided by the NASA and IUPAC data evaluation panels, which represent the data in the experimental pressure ranges rather well. Despite the availability of quite reliable parameters for these calculations (molecular vibrational frequencies and a value of the bond dissociation energy of ClONO2, DH298(ClONO2) = 26.5 kcal mol−1, corresponding to ΔH00 = 25.35 kcal mol−1 at 0 K) and use of RRKM/Master Equation methods, fitting calculations to the reported data was anything but straightforward. Using these molecular parameters resulted in a discrepancy between the calculations and the database of rate constants of a factor of ca 4 at, or close to, the low‐pressure limit. © 2009 Wiley Periodicals, Inc. Int J Chem Kinet 41: 573–581, 2009
Abnormal salt effects on reactions between ions: The coupling of salt and solvent effects
Authors: Martin V. I. , Lopez‐Cornejo P. , Sanchez F.
Published: June 2009

Salt effects on the reactions [Fe(CN)6]4− + S2O=8 and [Ru(NH3)5py]2+ + S2O have been studied in media of different dielectric constants constituted by mixtures of water with organic cosolvents. It is known that salt and solvent effects are coupled and, consequently, cannot be treated separately. This implies that salt (and solvent) effects need to be carefully analyzed before using them as a tool for mechanistic discrimination. © 2009 Wiley Periodicals, Inc. Int J Chem Kinet 41: 582–588, 2009
Fungal rhinosinusitis
Authors: Chakrabarti Arunaloke , Denning David W. , Ferguson Berrylin J. , Ponikau Jens , Buzina Walter , Kita Hirohito , Marple Bradley , Panda Naresh , Vlaminck Stephan , Kauffmann‐Lacroix Catherine , Das Ashim , Singh Paramjeet , Taj‐Aldeen Saad J. , Kantarcioglu A. Serda , Handa Kumud K. , Gupta Ashok , Thungabathra M. , Shivaprakash Mandya R. , Bal Amanjit , Fothergill Annette , Radotra Bishan D.
Published: June 2009

Background:

Fungal (rhino‐) sinusitis encompasses a wide spectrum of immune and pathological responses, including invasive, chronic, granulomatous, and allergic disease. However, consensus on terminology, pathogenesis, and optimal management is lacking. The International Society for Human and Animal Mycology convened a working group to attempt consensus on terminology and disease classification.

Discussion:

Key conclusions reached were: rhinosinusitis is preferred to sinusitis; acute invasive fungal rhinosinusitis is preferred to fulminant, or necrotizing and should refer to disease of <4 weeks duration in immunocompromised patients; both chronic invasive rhinosinusitis and granulomatous rhinosinusitis were useful terms encompassing locally invasive disease over at least 3 months duration, with differing pathology and clinical settings; fungal ball of the sinus is preferred to either mycetoma or aspergilloma of the sinuses; localized fungal colonization of nasal or paranasal mucosa should be introduced to refer to localized infection visualized endoscopically; eosinophilic mucin is preferred to allergic mucin; and allergic fungal rhinosinusitis (AFRS), eosinophilic fungal rhinosinusitis, and eosinophilic mucin rhinosinusitis (EMRS) are imprecise and require better definition. In particular, to implicate fungi (as in AFRS and EMRS), hyphae must be visualized in eosinophilic mucin, but this is often not processed or examined carefully enough by histologists, reducing the universality of the disease classification. A schema for subclassifying these entities, including aspirin‐exacerbated rhinosinusitis, is proposed allowing an overlap in histopathological features, and with granulomatous, chronic invasive, and other forms of rhinosinusitis. Recommendations for future research avenues were also identified. Laryngosope, 2009
The assessment of pharyngocutaneous fistula rate in patients treated primarily with definitive radiotherapy followed by salvage surgery of the larynx and hypopharynx
Authors: Dirven Richard , Swinson Brian D. , Gao Kan , Clark Jonathan R.
Published: June 2009

Objectives/Hypothesis:

To determine whether definitive radiotherapy prior to surgery increases the rate of pharyngocutaneous fistula (PCF) following laryngectomy or hypopharyngectomy and to determine if differences in duration of time between definitive radiotherapy and surgery alters PCF rate.

Study Design:

A retrospective review of 152 patients treated surgically for primary laryngeal or hypopharyngeal squamous cell carcinoma.

Methods:

Following previous definitive radiotherapy treatment 38 patients underwent salvage surgery and 114 patients underwent primary surgery with curative intent. The PCF rate was assessed in both groups.

Results:

The rate of PCF was found to be significantly higher in the salvage surgery group than those undergoing primary surgery (34.2% vs. 15.7%) (P < .05). Fistula rate was also higher in the subgroup that received concurrent chemoradiation to radiotherapy alone (P = .002). The patients who developed PCF in the salvage surgery group had significantly lower median time to surgery (5.8 months) than the nonfistula group (9.8 months) (P = .032). PCF rate was 75% within 4 months of radiotherapy to salvage surgery compared to 25% after 4 months (P = .034). Within 12 months of radiotherapy this percentage was 48% compared to 0% after 12 months (P = .014). The median radiotherapy dose was significantly higher in those whose surgery was complicated by PCF (70 Gy) compared to patients who did not develop a fistula (64 Gy) (P = .001).

Conclusions:

Patients undergoing salvage surgery within 12 months, and in particular within 4 months, who have received high dose radiotherapy (>64 Gy) or concurrent chemoradiation are at high risk of developing PCF.
On extensions of some Flugede–Putnam type theorems involving (p, k)‐quasihyponormal, spectral, and dominant operators
Authors: Tanahashi Kotaro , Patel S. M. , Uchiyama Atsushi
Published: June 2009

A Hilbert space operator S is called (p, k)‐quasihyponormal if S *k ((S *S)p – (SS *)p )Sk ≥ 0 for an integer k ≥ 1 and 0 < p ≤ 1. In the present note, we consider (p, k)‐quasihyponormal operator S ∈ B (H) such that SX = XT for some X ∈ B (K,H) and prove the Fuglede–Putnam type theorems when the adjoint of T ∈ B (K) is either (p, k)‐quasihyponormal or dominant or a spectral operator (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Cooperativity in the Conformational Rearrangements of Polymer Chain Segments as Seen by Bond Fluctuation Model
Authors: Torregrosa Cabanilles Constantino , Meseguer Dueñas José María , Gómez Ribelles José Luis , Molina‐Mateo José
Published: June 2009

The kinetics of structural relaxation was simulated using the bond fluctuation model. Annealing of the system in the glassy state produces a clearly nonexponential decrease in the energy in a certain temperature interval. At lower temperatures, the decrease in energy takes place by successive small steps, due to the change of the energy of individual polymer chains that modify their conformation into small neighbourhoods. This cooperativity is behind the nonexponential behaviour shown by structural relaxation at higher temperatures. A second order Markov chain is able to reproduce the nonexponentiality with quite good agreement with the bond fluctuation simulated curves. Cooperativity comes from the fact that the transition probability of a polymer chain between two energy levels depends on the history of previous transitions that took place in its neighbourhood.

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Activation of p53/p21/PUMA alliance and disruption of PI‐3/Akt in multimodal targeting of apoptotic signaling cascades in cervical cancer cells by a pentacyclic triterpenediol fromBoswellia serrata
Authors: Bhushan Shashi , Malik Fayaz , Kumar Ajay , Isher Harpreet Kaur , Kaur Indu Pal , Taneja Subhash Chandra , Singh Jaswant
Published: June 2009

Cervical carcinoma is a growing menace to women health worldwide. This study reports the apoptotic cell death in human cervical cancer HeLa and SiHa cells by a pentacyclic triterpenediol (TPD) fromBoswellia serrataby a mechanism different from reported in HL‐60 cells. It caused oxidative stress by early generation of nitric oxide and reactive oxygen species that robustly up regulated time‐dependent expression of p53/p21/PUMA while conversely abrogating phosphatidylinositol‐3‐kinase (PI3K)/Akt pathways in parallel. TPD also decreased the expression of PI3K/pAkt, ERK1/2, NF‐κB/Akt signaling cascades which coordinately contribute to cancer cell survival through these distinct pathways. The tumor suppressor p53 pathway predominantly activated by TPD further up‐regulated PUMA, which concomitantly decreased the Bcl‐2 level, caused mitochondrial membrane potential loss with attendant translocation of Bax and drp1 to mitochondria and release of pro‐apoptotic factors such as cytochromecand Smac/Diablo to cytosol leading to caspases‐3 and ‐9 activation. In addition both the phospho‐p53 and p21 were found to accumulate heavily in the nuclear fraction with attendant decrease in topoisomarase II and survivin levels. On the contrary, TPD did not affect the extrinsic signaling transduction pathway effectively through apical death receptors. Interestingly,N‐acetyl cysteine, ascorbate and s‐methylisothiourea (sMIT) rescued cells significantly from TPD induced DNA damage and caspases activation. TPD may thus find usefulness in managing and treating cervical cancer. © 2009 Wiley‐Liss, Inc.
Structure elucidation and complete NMR spectral assignments of new furostanol glycosides from Solanum torvum
Authors: Lu Yuanyuan , Luo Jianguang , Kong Lingyi
Published: June 2009

Two new furostanol glycosides, torvosides O (1) and P (2), were isolated from leaves of Solanum torvum. Their structures were completely and unambiguously assigned by one‐ and two‐dimensional NMR techniques (1H NMR, 13C NMR, TOCSY, HSQC, ROESY and HMBC), ESI‐MS spectrometry and chemical methods. Copyright © 2009 John Wiley & Sons, Ltd.
Elasto‐plastic analytical model for the design of grouted bolts in a Hoek–Brown medium
Authors: Osgoui Reza. R. , Oreste Pierpaolo
Published: June 2009

This paper presents an elasto‐plastic analytical solution of an axi‐symmetrical problem for a circular tunnel reinforced by grouted bolts. Considered as the improved model of Indraratna and Kaiser (Int. J. Rock. Mech. Min. Sci. Geomech. Abstr. 1990; 27:269–281; Int. J. Numer. Anal. Meth. Geomech. 1990; 14:227–251), in proposed solution the rock mass obeys the non‐linear Hoek–Brown yield criterion (version 2002) in terms of its peak and residual strength parameters (the most spread strength criterion for the rock masses). The proposed approach considers a⩾0.5 for the rock mass and is based on the assumption that after the peak strength of the rock is reached, the material loses its strength, as dictated by a strength loss parameter. The strength loss parameter makes it possible to model either elastic–perfectly plastic or elastic–brittle–plastic behaviour. Because of the mathematical complexity, numerical treatments have been used to assist the solution in order to evaluate the equilibrium and compatibility equations. The concept of equivalent material for Hoek–Brown strength parameters is introduced to describe the rock mass improvement due to bolting effect. The results of the numerical analyses reveal a linear relation between the improved Hoek–Brown strength parameters and residual ones, taking into consideration the bolt density parameter (β). The proposed solution is able to analyse the stress and displacement state in the presence of a bolting intervention with the objective of improving the degree of stability of the rock around the tunnel. Descriptive applications of the derived elasto‐plastic solutions are also presented to explain the effectiveness of the grouted bolts in convergence reduction. Evidences obtained by numerical analysis verify the analytical solution. Copyright © 2009 John Wiley & Sons, Ltd.
A compact local one‐dimensional scheme for solving a 3D N‐carrier system with Neumann boundary conditions
Authors: Dai Weizhong
Published: June 2009

We consider a mathematical model for thermal analysis in a 3D N‐carrier system with Neumann boundary conditions, which extends the concept of the well‐known parabolic two‐step model for micro heat transfer. To solve numerically the complex system, we first reduce 3D equations in the model to a succession of 1D equations by using the local one‐dimensional (LOD) method. The obtained 1D equations are then solved using a fourth‐order compact finite difference scheme for the interior points and a second‐order combined compact finite difference scheme for the points next to the boundary, so that the Neumann boundary condition can be applied directly without discretizing. By using matrix analysis, the compact LOD scheme is shown to be unconditionally stable. The accuracy of the solution is tested using two numerical examples. Results show that the solutions obtained by the compact LOD finite difference scheme are more accurate than those obtained by a Crank‐Nicholson LOD scheme, and the convergence rate with respect to spatial variables is about 2.6. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 2010
Fast Legendre spectral method for computing the perturbation of a gradient temperature field in an unbounded region due to the presence of two spheres
Authors: Chowdhury A. , Christov C. I.
Published: June 2009

The temperature distribution around two spheres is considered when the main field has a constant gradient at infinity. Bispherical coordinates are used, together with a transformation of the dependent variable that leads to separation of variables. Then the solution can be sought in Legendre series with respect to one of the bispherical coordinates. An important element of the proposed work is the effective way to reduce an essentially 3D problem to a set of three 2D problems. The Legendre spectral method is shown to have an exponential convergence which is confirmed by the computations. The efficiency is so high that even for the hard cases of two closely situated spheres, an accuracy of 10−10 is achieved with as few as 20 terms in the expansion.

Solutions with both longitudinal and transverse gradients at infinity are obtained, and the contour lines of the temperature field are presented graphically. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 2010
Effect of noise on the pattern formation in an epidemic model
Authors: Sun Gui‐Quan , Li Li , Jin Zhen , Li Bai‐Lian
Published: June 2009

We present novel numerical evidence of complicated phenomenon controlled by noise in a spatial epidemic model. The number of the spot is decreased as the noise intensity being increased, which we show by performing a series of numerical simulations. Moreover, when the noise intensity and temporal correlation are both large enough, the model dynamics exhibits a noise controlled transition from spotted pattern to stripe growth. In addition to that, we show in details the number of the spotted and stripe pattern, with the identification of a wide range of noise intensity and temporal correlation. The obtained results show that noise plays an important role in the pattern formation of the epidemic model, which may provide guidance to prevent and control the spread of disease. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 2010
Numerical solution of a class of complex differential equations by the Taylor collocation method in elliptic domains
Authors: Sezer Mehmet , Tanay Bekir , Gülsu Mustafa
Published: June 2009

An approximate method for solving higher‐order linear complex differential equations in elliptic domains is proposed. The approach is based on a Taylor collocation method, which consists of the matrix represantation of expressions in the differential equation and the collocation points defined in an elliptic domain. Illustrative examples are included to demonstrate the validity and applicability of the technique. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 2010
Numerical simulations of the improved Boussinesq equation
Authors: Irk Dursun , Dağ İdris
Published: June 2009

In this study, numerical simulations of the improved Boussinesq equation are obtained using two finite difference schemes and two finite element methods, based on the second‐and third‐order time discretization. The methods are tested on the problems of propagation of a soliton and interaction of two solitons. After the L∞ error norm is used to measure differences between the exact and numerical solutions, the results obtained by the proposed methods are compared with recently published results. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 2010
Fluorophilic cobalt phthalocyanine‐containing Nafion membrane: high oxygen permeability and proton conductivity in the membrane
Authors: Shoji Masami , Nishide Hiroyuki
Published: June 2009

A multiply‐fluorinated cobalt phthalocyanine (CoFPC) was prepared, which could reversibly interact with oxygen. CoFPC was introduced into the hydrophobic perfluoroethylene‐backbone domain of the Nafion membrane. The localization of CoFPC did not reduce the high proton conductivity (10−2–10−3 S cm−1) ascribed to the hydrophilic channel of Nafion. The oxygen permeability through the CoFPC/Nafion membrane was higher than the nitrogen permeability and that of the pristine Nafion membrane, and was significantly enhanced at the lower upstream pressure. The permselectivity of oxygen versus nitrogen increased beyond 20 with the CoFPC content in the membrane. The CoFPC/Nafion membrane was coated on a glassy carbon modified with a Pt/C catalyst. The high electrochemical reduction current of oxygen suggested that the CoFPC/Nafion membrane efficiently supplied oxygen to the Pt/C catalyst. Copyright © 2009 John Wiley & Sons, Ltd.
β1 integrin/FAK/ERK signalling pathway is essential for human fetal islet cell differentiation and survival
Authors: Saleem Saira , Li Jinming , Yee Siu‐Pok , Fellows George F , Goodyer Cynthia G , Wang Rennian
Published: June 2009

β1 integrin and collagen matrix interactions regulate the survival of cells by associating with focal adhesion kinase (FAK) and initiating MAPK/ERK signalling, but little is known about these signalling pathways during human fetal islet ontogeny. The purpose of this study was to investigate whether β1 integrin/FAK activation of the MAPK/ERK pathway regulates human fetal islet cell expression of endocrine cell markers and survival. Isolated human (18–21 weeks fetal age) islet–epithelial cell clusters, cultured on collagen I, were examined using β1 integrin blocking antibody, β1 integrin siRNA and FAK expression vector. Perturbing β1 integrin function in the human fetal islet–epithelial cell clusters resulted in a marked decrease in cell adhesion, in parallel with a reduction in the number of cells expressing PDX‐1, insulin and glucagon (p < 0.05). β1 integrin blockade disorganized focal adhesion contacts in the PDX‐1+ cells and decreased activation of FAK and ERK1/2 signalling in parallel with an increase in expression of cleaved caspases 9 and 3 (p < 0.01). Similar results were obtained following an siRNA knock‐down of β1 integrin expression. In contrast, over‐expression of FAK not only increased phospho‐ERK and the expression of PDX‐1, insulin and glucagon (p < 0.05) but also abrogated the decreases in phospho‐ERK and PDX‐1 by β1 integrin blockade. This study demonstrates that activation of the FAK/ERK signalling cascade by β1 integrin is involved in the differentiation and survival of human fetal pancreatic islet cells. Copyright © 2009 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Up‐regulation of autophagy in small intestine Paneth cells in response to total‐body γ‐irradiation
Authors: Gorbunov Nikolai V. , Kiang Juliann G.
Published: June 2009

Macroautophagy (mAG) is a lysosomal mechanism of degradation of cell self‐constituents damaged due to variety of stress factors, including ionizing irradiation. Activation of mAG requires expression of mAG protein Atg8 (LC3) and conversion of its form I (LC3‐I) to form II (LC3‐II), mediated by redox‐sensitive Atg4 protease. We have demonstrated upregulation of this pathway in the innate host defense Paneth cells of the small intestine (SI) due to ionizing irradiation and correlation of this effect with induction of pro‐oxidant inducible nitric oxide synthase (iNOS). CD2F1 mice were exposed to 9.25 Gy γ‐ionizing irradiation. Small intestinal specimens were collected during 7 days after ionizing irradiation. Assessment of ionizing irradiation‐associated alterations in small intestinal crypt and villus cells and activation of the mAG pathway was conducted using microscopical and biochemical techniques. Analysis of iNOS protein and the associated formation of nitrites and lipid peroxidation products was performed using immunoblotting and biochemical analysis, and revealed increases in iNOS protein, nitrate levels and oxidative stress at day 1 following ionizing irradiation. Increase in immunoreactivity of LC3 protein in the crypt cells was observed at day 7 following ionizing irradiation. This effect predominantly occurred in the CD15‐positive Paneth cells and was associated with accumulation of LC3‐II isoform. The formation of autophagosomes in Paneth cells was confirmed by transmission electron microscopy (TEM). Up‐regulation of LC3 pathway in the irradiated SI was accompanied by a decreased protein–protein interaction between LC3 and chaperone heat shock protein 70. A high‐level of LC3‐immunoreactivity in vacuole‐shaped structures was spatially co‐localized with immunoreactivity of 3‐nitro‐tyrosine. The observed effects were diminished in iNOS knockout B6.129P2‐NOS2tm1Lau/J mice subjected to the same treatments. We postulate that the observed up‐regulation of mAG in the irradiated small intestine is at least in part mediated by the iNOS signalling mechanism. Published in 2009 by John Wiley & Sons, Ltd.
Adamalysins in biology and disease
Authors: van Goor Harry , Melenhorst Wynand BWH , Turner Anthony J , Holgate Stephen T
Published: June 2009

ADAMs (a disintegrin and metalloprotease) are membrane‐bound enzymes, capable of shedding a multitude of proteins from the surface of the cell. They are therefore considered crucial modulators of physiological and pathophysiological processes. The structure and function of ADAMs is related to those of a family of snake venom metalloproteases which also possess a potential adhesion domain as well as a potential protease domain. Mammalian ADAMs are involved in various biological and disease‐related processes, such as cell–cell fusion, adhesion and intracellular signalling. Functional involvement has been described in sperm–egg binding and fusion, trophoblast invasion and matrix degradation during pregnancy, angiogenesis and neovascularization. Clinically, ADAMs are implicated in pathological processes, including cancer, inflammation, neurodegeneration and fibrosis, through shedding of the apoptosis‐inducing FAS ligand, cytokines and growth factors. A second group of proteins within the ADAM family has recently been discovered. These contain several thrombospondin‐like repeats in their C‐terminal regions, in the absence of the transmembrane domain known to be present in ADAMs. These proteins were called the ADAMTS (ADAM with thrombospondin domains) family. The relevance of ADAMTS enzymes has become evident in patients with a deficiency in ADAMTS‐13, a von Willebrand factor cleaving protease. These patients develop thrombotic thrombocytopenic purpura, a devastating thrombotic disorder caused by widespread microvascular thrombi composed of platelets and von Willebrand factor (VWF). Here we focus on the genetic, developmental, functional and disease‐related aspects of ADAMs and ADAMTS. Finally we discuss the perspectives of the therapeutical potential of ADAMs in disease. Copyright © 2009 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Over‐expression of AEG‐1 significantly associates with tumour aggressiveness and poor prognosis in human non‐small cell lung cancer
Authors: Song Libing , Li Wen , Zhang Huizhong , Liao Wenting , Dai Ting , Yu Chunping , Ding Xiaofan , Zhang Lanjun , Li Jun
Published: June 2009

Astrocyte elevated gene 1 (AEG‐1), a novel oncoprotein, has been implicated in oncogenesis and cancer progression in various types of human cancers. The clinical significance and biological role of AEG‐1 in non‐small cell lung cancer (NSCLC), however, remain unclear. In the present study, we found that the expression of AEG‐1 was markedly up‐regulated in NSCLC cell lines and NSCLC tissues at the level of both transcription and translation. Ectopically expressed AEG‐1 enhanced the migratory and invasive abilities of NSCLC cells, whereas knockdown of endogenous AEG‐1 by specific shRNAs significantly inhibited these abilities. The function of AEG‐1 on metastasis modulation was associated with the activation of the PI3K–Akt and NF‐κB signalling pathways. Furthermore, we showed high expression of AEG‐1 in 99/200 (49.5%) paraffin‐embedded archival NSCLC specimens. Moreover, statistical analysis displayed a significant correlation in AEG‐1 expression with the clinical stage (p < 0.001), T classification (p = 0.001), N classification (p = 0.015), distant metastasis (p = 0.004) and differentiation (p = 0.027). Patients with higher AEG‐1 expression had an overall shorter survival time, whereas patients with lower expression of AEG‐1 had a better survival time. Multivariate analysis suggested that AEG‐1 expression might be an independent prognostic indicator for the survival of NSCLC patients. Taken together, our results suggest that elevated expression of AEG‐1 plays an important role in the aggressiveness of NSCLC, leading to a poor clinical outcome. Copyright © 2009 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
ADAM12s as a first‐trimester screening marker of trisomy
Authors: Wortelboer E. J. , Linskens I. H. , Koster M. P. H. , Stoutenbeek P. , Cuckle H. , Blankenstein M. A. , Visser G. H. A. , van Vugt J. M. G. , Schielen P. C. J. I.
Published: June 2009

Objective

To evaluate the potential of maternal serum A Disintegrin And Metalloprotease 12‐S (ADAM12s) as an additional marker for the combined test in the Dutch first‐trimester national Down syndrome (DS) screening program.

Methods

Serum samples were collected between 2004 and 2007 as part of the national program. A total of 218 singleton cases of trisomy 21 (DS), 62 trisomy 18 (Edwards syndrome) and 29 trisomy 13 (Patau syndrome) were identified. All cases were matched with controls for gestation, maternal weight and maternal age. The serum concentration of ADAM12s was determined ‘blind’ to outcome and expressed in multiples of the gestation‐specific median for controls (MoM).

Results

The median ADAM12s was 1.00 MoM in controls and in the DS cases at 8, 9, 10, 11, 12, 13 weeks it was 0.45 (n = 3), 0.73 (22), 0.74 (53), 0.85 (37), 0.92 (71), 1.06 (32) MoM, respectively. The median for trisomy 18 was 0.85 MoM and for trisomy 13 0.63 MoM.

Conclusion

The ADAM12s MoM values were clearly reduced in early first‐trimester for all trisomies. However, the screening performance for DS did not greatly improve adding ADAM12s. ADAM12s could be an additional biochemical marker for first‐trimester screening for trisomies other than DS. Copyright © 2009 John Wiley & Sons, Ltd.
Risk calculation of developing type 2 diabetes in Libyan adults
Authors: Abduelkarem AR , Sharif SI , Hammrouni AM , Aldouibi SS , Albraiki WM , El‐Shareif HJ
Published: June 2009

The aim of this study was to identify nationals at risk of developing type 2 diabetes within the next 10 years in some areas across Tripoli Health Authority in Libya.

In this questionnaire‐based survey, a total of 400 Libyan nationals of both genders were randomly selected from seven areas across the central area of Tripoli Health Authority (Soug El‐Juma, Zawet Dahmani, Al‐Furnaj, Ain Zara, Al‐Madena Centre, Al‐Dhahra Centre, and Noflean).

All participants approached (400) completed the study and responded to the items of the survey. Based on a modified Finnish Type 2 Diabetes Risk Score test (FINDRISC), 129 (32.3%) were categorised as either at moderate or at high/very high risk of developing diabetes within the next 10 years of life. Among the 129 participants at risk, body mass index was >25 kg/m2 in 125 (96.9%) and waist circumferences were high (>88 cm for females;>102 cm for males) in almost 45% of the women and 22% of the men.

We found that in the sample studied the risk of developing diabetes was clear, and there is no doubt that interventions to reduce such risk are a priority rather than a need. Diabetes has a great impact on the health of the nation and also on the future resources of the country in managing the disease and its complications; a health education/health campaign could be one good answer to tackle the problem. Copyright ©2009 John Wiley & Sons.
A novel, spontaneously immortalized, human prostate cancer cell line, Bob, offers a unique model for pre‐clinical prostate cancer studies
Authors: Attard Gerhardt , Rizzo Sian , Ledaki Ioanna , Clark Jeremy , Reid Alison H.M. , Thompson Alan , Khoo Vincent , de Bono Johann S. , Cooper Colin S. , Hudson David L.
Published: June 2009

INTRODUCTION

New in vitro models of castration‐resistant prostate cancer (CRPC) are urgently required.

METHODS

Trans‐rectal needle biopsies (TRBP) of the prostate were performed for research purposes on progressing CRPC patients who had not received prior treatment to the prostate. Biopsies were immediately digested with collagenase and plated onto collagen‐coated flasks with a feeder layer of 3T6 cells and cultured in cytokine‐supplemented keratinocyte serum‐free medium.

RESULTS

Biopsies from 25 patients were collected and one of these, following an initial period of crisis, spontaneously immortalized. A series of cell lines called Bob were then established from a clone that survived CD133‐selection followed by 4 weeks under adhesion‐independent conditions in methylcellulose. Gains and losses previously described in clinical prostate tumors, most notably loss of 8(p) and gain of 8(q), were identified on comparative genomic hybridization and long‐term growth in culture, survival in methylcellulose and invasion through matrigel confirmed the malignant phenotype of Bob. Furthermore, Bob expressed high levels of p53 and markers of early differentiation, including K8, prostatic acid phosphatase and prostate stem cell antigen. There was, however, no in vivo growth and ERG and ETV1 were not rearranged. Growth in serum permitted some differentiation.

CONCLUSION

This is the first spontaneously immortalized prostate cancer cell line to be established from a TRBP of a patient with CRPC. Bob is a novel pre‐clinical model for functional studies in CRPC and especially for studying the CRPC “basal” phenotype. Prostate 69: 1507–1520, 2009. © 2009 Wiley‐Liss, Inc.
The use of automatic tools and human expertise in template‐based modeling of CASP8 target proteins
Authors: Venclovas Česlovas , Margelevičius Mindaugas
Published: June 2009

Here, we describe our template‐based protein modeling approach and its performance during the eighth community‐wide experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP8, http://predictioncenter.org/casp8). In CASP8, our modeling approach was supplemented by the newly developed distant homology detection method based on sequence profile–profile comparison. Detection of structural homologs that could be used as modeling templates was largely achieved by automated profile‐based searches. However, the other two major steps in template‐based modeling (TBM) (selection of the best template(s) and construction of the optimal sequence‐structure alignment) to a large degree relied on the combination of automatic tools and manual input. The analysis of 64 domains categorized by CASP8 assessors as TBM domains revealed that we missed correct structural templates for only four of them. The use of multiple templates or their fragments enabled us to improve over the structure of the single best PDB template in about 1/3 of our models for TBM domains. Our results for sequence‐structure alignments are mixed. Although many models have optimal or near optimal sequence mapping, a large fraction contains one or more misaligned regions. Strikingly, in spite of this, our TBM models have the best overall alignment accuracy scores. This clearly suggests that the correct mapping of protein sequence onto three‐dimensional structure remains one of the big challenges in protein structure prediction. Proteins 2009. © 2009 Wiley‐Liss, Inc.
X‐ray characterization of epi‐Ge/Pr2O3/Si(111) layer stacks by pole figures and reciprocal space mapping
Authors: Zaumseil Peter , Giussani Alessandro , Rodenbach Peter , Schroeder Thomas
Published: June 2009

An epi‐Ge/Pr2O3/Si(111) layer structure prepared by consecutive steps of epitaxial deposition and annealing is used to demonstrate the possibility of a complex characterization by combination of different X‐ray diffraction techniques. Especially pole figure measurements, reciprocal space mapping (RSM) and high resolution (HR) Θ/2Θ scans at selected inclined netplanes were successfully used to determine the in‐plane lattice orientation of the layers relative to the substrate, the strain state of all layers and the structural perfection of the epi‐Ge film. It was found that the major part of the epi‐Ge layer has the same type A stacking orientation as the Si substrate, but about 0.6% is of type B. The Pr2O3 buffer layer exhibits type B only. The strain state of oxide and epi‐Ge was determined, and a small difference in the lattice constant of type A and B epi‐Ge was found. Microtwins lying in inclined {111} planes were unambiguously identified by pole figure measurements as the dominating structural defects in the epi‐Ge layer. They cause a characteristic scattering pattern in reciprocal space maps. The proposed combination of X‐ray techniques allows a relatively fast, integral and non‐destructive analysis of heteroepitaxial semiconductor oxide semiconductor structures.
Heteroepitaxial growth of lattice matched films on GaAs(001)
Authors: Jenichen B. , Kaganer V. M. , Shayduk R. , Braun W. , Trampert A.
Published: June 2009

The thin films of lattice matched materials Fe3Si and Ge are grown on GaAs(001) by molecular beam epitaxy and studied by grazing incidence X‐ray diffraction. In the initial phase of Fe3Si growth, the surface is rough due to a formation of small islands. Two‐dimensional layer‐by‐layer growth arises later on. Germanium grows on GaAs in a layer‐by‐layer growth mode right from the beginning. A substantial improvement of the surface smoothness of the Ge film during the growth is found.
Interfacial roughness of Fe3Si/GaAs(001) films studied by X‐ray crystal truncation rods
Authors: Kaganer Vladimir , Jenichen Bernd , Shayduk Roman , Braun Wolfgang
Published: June 2009

Crystal truncation rods (CTRs) from thin Fe3Si films grown on GaAs(001) by molecular beam epitaxy (MBE) are measured at different stages of deposition. The films do not develop their own surface roughness but are conformal to the substrate, so that the substrate roughness governs the whole system. A factor that describes the roughness of a zinc blende structure in the β model of terrace height probabilities is derived and applied to describe the experimental curves. We show that the β model adequately describes the CTRs while the model of continuous Gaussian fluctuations of the surface height notably underestimates the root‐mean‐squared (rms) roughness.
Ripple structures on surfaces and underlying crystalline layers in ion beam irradiated Si wafers
Authors: Grenzer J. , Biermanns A. , Mücklich A. , Grigorian S. A. , Pietsch U.
Published: June 2009

We report on the formation of ion beam induced ripples in Si(001) wafers when bombarded with Ar+ ions at an energy of 60 keV. A set of samples varying incidence and azimuthal angles of the ion beam with respect to the crystalline surface orientation was studied by two complementary near surface sensitive techniques, namely atomic force microscopy and depth‐resolved X‐ray grazing incidence diffraction (GID). Additionally, cross‐section TEM investigations were carried out. The ripple‐like structures are formed at the sample surface as well as at the buried amorphous–crystalline interface. Best quality of the ripple pattern was found when the irradiating ion beam was aligned parallel to the (111) planes. The quality decreases rapidly if the direction of the ion beam deviates from (111).
Structural changes in Si crystals exposed to chemical etching and ion implantation
Authors: Fodchuk I. , Zaplitnyy R. , Kazemirskiy T. , Litvinchuk I. , Swiatek Z.
Published: June 2009

Results of X‐ray diffraction studies on structural changes in Si crystals caused by chemical etching for 40 s in HF, HNO3 solution and phosphorus‐ion implantation with the energy E = 100 keV and dose D = 8 × 1014 cm−2 are represented.

Two‐ and three‐crystal X‐ray diffractometry methods are used for a quantitative assessment of structural changes occurring in the near‐surface crystal layers. Analysis of experimental rocking curves was made with the use of different approaches developed on the basis of kinematic and dynamic theory of X‐ray scattering in the imperfect crystals. A model of possible system of structural defects in the near‐surface silicon layers modified by chemical etching and ion implantation is proposed. The model accounts for the availability of respective sizes and concentrations of spherical and disc‐shaped cluster formations, dislocation loops.
Three‐dimensional ordering in self‐organized (In,Ga)As quantum dot multilayer structures
Authors: Kladko V. , Slobodian M. , Lytvyn P. , Strelchuk V. , Mazur Yu. , Marega E. , Hussein M. , Salamo G.
Published: June 2009

Molecular beam epitaxy (MBE) grown In0.5Ga0.5As/GaAs multilayer structures with quantum dots chains (QDs), obtained under different growth conditions, were investigated by high‐resolution X‐ray diffractometry (HRXRD) and AFM. It was determined that self‐organized epitaxial growth of In0.5Ga0.5As/GaAs can lead to the formation of three‐dimensional quantum‐dot crystals with triclinic (distorted cubic) unit cell. The mechanisms of QDs ordering in dependence on As flux are analyzed.
Spatially resolved strain within a single SiGe island investigated by X‐ray scanning microdiffraction
Authors: Diaz Ana , Mocuta Cristian , Stangl Julian , Vila‐Comamala Joan , David Christian , Metzger Till H. , Bauer Günther
Published: June 2009

A submicron X‐ray beam was employed to scan a 3.2 µm SiGe island in two directions. At each scanning position, 2D cuts of the reciprocal space close to the (004) Bragg reflection of the Si substrate were recorded with a CCD. From the position of the SiGe island induced diffuse scattering peak on each CCD frame, we detected and analyzed variations of the strain within a selected single island. Our method does not require the recording of the whole 3D reciprocal space at each position in real space, thus avoiding instability problems during data acquisition. We found changes in the strain which are consistent with finite element calculations of the strain within a model island. The knowledge of the strain distribution within SiGe epitaxial structures is relevant for the correct interpretation of their electronic and optical properties.
In situ X‐ray investigation of SiGe/Si islands grown by liquid phase epitaxy
Authors: Deiter S. , Hanke M. , Eisenschmidt C. , Boeck T. , Teubner T. , Jendritzki U. , Gerlitzke A.‐K. , Schadow G.
Published: June 2009

We report on the in situ observation during liquid phase epitaxy (LPE) of Stranski–Krastanow grown SiGe/Si(001) islands with X‐ray diffraction methods. Therefore, we developed a growth chamber combined with pre‐processed samples which afford LPE under N2 atmosphere (instead of H2 which is normally used for LPE) at a synchrotron beamline. The island evolution is probed with X‐ray diffraction methods from the backside of a thin silicon substrate which floats on the melt. The way towards LPE in situ X‐ray diffraction experiments will be described. Our results show the development of X‐ray diffraction signals in dependence of the current growth state.
Influence of quantum‐dots density on average in‐plane strain of optoelectronic devices investigated by high‐resolution X‐ray diffraction
Authors: Freitas Raul O. , Diaz Beatriz , Abramof Eduardo , Quivy Alain A. , Morelhão Sérgio L.
Published: June 2009

High‐resolution X‐ray diffractometry is used to probe the nature of a diffraction‐peak broadening previously noticed in quantum dots (QDs) systems with freestanding InAs islands on top of GaAs (001) substrates [Freitas et al., Phys. Status Solidi (A) 204, 2548 (2007)]. The procedure is hence extended to further investigate the capping process of InAs/GaAs QDs. A direct correlation is established between QDs growth rates and misorientation of lattice‐planes at the samples surfaces. This effect provides an alternative tool for studying average strain fields on QDs systems in standard triple axis diffractometers running on X‐ray tube sources, which are much more common than synchrotron facilities.
Fourier transform holography in the context of coherent diffraction imaging with hard X‐rays
Authors: Stadler Lorenz‐M. , Gutt Christian , Autenrieth Tina , Leupold Olaf , Rehbein Stefan , Chushkin Yuriy , Grübel Gerhard
Published: June 2009

Coherent diffraction imaging (CDI) with 8 keV X‐rays is used to image a gold nanostructure. Experimental details are given and frequently encountered problems such as missing low spatial frequency information and parasitic slit scattering are discussed. As a possible remedy, hard X‐ray Fourier transform holography (FTH) is presented and its robustness with respect to the diffraction pattern quality is demonstrated. It is shown that even with a few‐second exposure to an unfocussed beam, the object structure can be clearly recognised. FTH in combination with CDI is ideal for single‐shot imaging of micron‐sized objects using femtosecond flashes of hard X‐rays at the upcoming free‐electron laser facilities in the USA, Japan and Germany.
Anisotropy of mosaic structure of GaAsP layers grown on GaAs substrates
Authors: Saka T. , Kato T. , Jin X. G. , Tanioku M. , Ujihara T. , Takeda Y. , Yamamoto N. , Nakagawa Y. , Mano A. , Okumi S. , Yamamoto M. , Nakanishi T. , Horinaka H. , Matsuyama T. , Yasue T. , Koshikawa T.
Published: June 2009

The crystalline structure of GaAsP layers grown on GaAs and GaP (001) substrates, used for spin polarized photocathodes, has been investigated by X‐ray diffraction. The layers on the GaAs substrate possess a mosaic structure observable by X‐ray topography and consist of many large blocks. The mosaicity is anisotropic and the distribution of the mosaic is restricted within the (110) plane, and the blocks zigzag around the [110] direction. The layer grown on the GaP substrate was uniform and no mosaic was observed in the topographs. The results indicate that different mechanisms of strain release occur in GaAsP layers for tensile and compressive strains.
Elliptical micropipes in SiC revealed by computer simulating phase contrast images
Authors: Argunova Tatiana , Kohn Victor , Jung Ji‐Won , Je Jung‐Ho
Published: June 2009

The elliptical micropipes in SiC are studied using computer simulation of the phase contrast images. The experimental measurements of “white beam” images are performed at third‐generation synchrotron radiation source in Pohang, Korea. We reveal that the transmitted X‐ray spectrum of a high brilliance with a pronounced maximum at 16 keV enables to form partially coherent images even for transparent objects. The computer simulation allows one to automatically determine the diameters of elliptical cross‐sections based on best matches between calculated and experimental intensity profiles. We show that the micropipes studied here have extended elliptical cross‐sections, sometimes rotating around the micropipe axis.