bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generation of high‐quality protein extracts from formalin‐fixed, paraffin‐embedded tissues
Authors: Addis Maria Filippa , Tanca Alessandro , Pagnozzi Daniela , Crobu Salvatore , Fanciulli Giuseppe , Cossu‐Rocca Paolo , Uzzau Sergio 
Published: July 2009

AbstractA wealth of information on proteins involved in many aspects of disease is encased within formalin‐fixed paraffin‐embedded (FFPE) tissue repositories stored in hospitals worldwide. Recently, access to this “hidden treasure” is being actively pursued by the application of two main extraction strategies: digestion of the entangled protein matrix with generation of tryptic peptides, or decrosslinking and extraction of full‐length proteins. Here, we describe an optimised method for extraction of full‐length proteins from FFPE tissues. This method builds on the classical “antigen retrieval” technique used for immunohistochemistry, and allows generation of protein extracts with elevated and reproducible yields. In model animal tissues, average yields of 16.3 μg and 86.8 μg of proteins were obtained per 80 mm2 tissue slice of formalin‐fixed paraffin‐embedded skeletal muscle and liver, respectively. Protein extracts generated with this method can be used for the reproducible investigation of the proteome with a wide array of techniques. The results obtained by SDS‐PAGE, western immunoblotting, protein arrays, ELISA, and, most importantly, nanoHPLC‐nanoESI‐Q‐TOF MS of FFPE proteins resolved by SDS‐PAGE, are presented and discussed. An evaluation of the extent of modifications introduced on proteins by formalin fixation and crosslink reversal, and their impact on quality of MS results, is also reported.
What can the geometry tell about the charge distribution in the mesoionic heterocycles? A DFT study on the SCN4R2 system
Authors: Irshaidat Tareq 
Published: July 2009

AbstractThis computational organic chemistry study was performed using the hybrid functional B3LYP. Many basis sets were evaluated and the basis set 6‐31G(d) was found to be the most practical in terms of time and accuracy. The study presents the first method in the chemical literature that allows estimation of submolecular charges in mesoionic compounds. The theory was built on a reference model structure for which the absolute value of charge of the aromatic p‐orbitals is known. This is the cornerstone, and by employing the harmonic oscillator model of aromaticity (HOMA) many parameters can be quantified. The electronic structure of the title compound was the subject of this approach. The study addressed the following points: geometries, infrared frequencies, NMR chemical shifts, calculated charges, a chemical reactivity, and the frontier orbitals. The calculations illustrate that the π‐system of the CN4 segment includes considerable aromatic character and carries a positive charge while the overall charge is negative. This allows classifying it as a σ‐acceptor/π‐donor while the exocyclic counter anion, the sulfur atom, is a σ‐donor/π‐acceptor. The substituents (R groups) in this case are only σ‐donors. The approach may be applied to other mesoionic and mesoaromatic systems. Copyright © 2009 John Wiley & Sons, Ltd.
Electron reorganization in allowed and forbidden pericyclic reactions: multicenter bond indices as a measure of aromaticity and/or anti‐aromaticity in transition states of pericyclic electrocyclizations
Authors: Mandado Marcos , Ponec Robert 
Published: July 2009

AbstractThe multicenter bond indices (MCI), recently proposed as quantitative measures of cyclic delocalization in aromatic systems, have been applied to characterize the differences in the nature of the electron reorganization in a series of allowed and forbidden electrocyclic reactions of linear neutral polyenes of general formula CnHn+2and related charged systems of formula CnHn+2(+) and CnHn+2(−) fornranging from 4 to 7. The proposed methodology, which is based on the monitoring of the variation of the extent of cyclic delocalization along the concerted reaction paths, is shown to be completely consistent with the empirical Evans/Dewar classification anticipating aromatic transition states for allowed and anti‐aromatic transition states for forbidden electrocyclic reactions. Although the study reports the results of the analysis of electron reorganization just for the above‐mentioned particular class of electrocyclic reactions, the proposed approach is completely general and its conclusions remain valid for any pericyclic reaction. Copyright © 2009 John Wiley & Sons, Ltd.
Polyrotaxanes based on polyethers and β‐cyclodextrin
Authors: Chelli Saloua , Majdoub Mustapha , Aeiyach Salah , Jouini Mohamed 
Published: July 2009

AbstractA polyrotaxane in which β‐cyclodextrins (β‐CDs) are threaded onto a polyether chain was prepared by polycondensation of a β‐CD/bisphenol A (BPA) inclusion complex with aromatic dihalides. Two dihalides, with and without a side chain, were used. This polycondensation results in a polyrotaxane (or pseudopolyrotaxane for polymers without stoppers) with a 1:1 threading ratio when the side chain is present and 2:3 when there is none. The long side chain prevents dethreading of the macrocycles. The best yield and a good threading ratio were obtained when the polycondensation was performed by liquid−solid phase transfer catalysis without solvent (L/S PTC) using 2,5‐bi(iodomethyl)‐4‐methoxy‐(1‐octyloxy)benzene as dihalide. The 1H NMR and FTIR spectra show that the products consist of β‐CD and polyether. The 2D NOESY NMR spectrum shows that the polyether chains are included in the β‐CD cavity. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 4391–4399, 2009
The Cancer Pain Inventory: preliminary development and validation
Authors: Deshields Teresa L. , Tait Raymond C. , Manwaring Jamie , Trinkaus Kathryn M. , Naughton Michael , Hawkins Josephine , Jeffe Donna B. 
Published: July 2009

AbstractObjective: The purpose of this study was to develop a Cancer Pain Inventory (CPI) that measures cancer patients' beliefs and concerns about pain. This paper describes development and pilot testing of a preliminary version of the CPI and describes its psychometric properties including its reliability and validity relative to established pain measures.Methods: Subjects were recruited from inpatient and outpatient oncology services of an NCI‐designated comprehensive cancer center. Participants completed the 50 potential CPI items and these standard measures—Orientation‐Memory‐Concentration Test, Survey of Pain Attitudes, Brief Pain Inventory, Pain Disability Index, and Center for Epidemiological Studies—Depression Scale. The magnitude and significance of associations between the CPI and the other measures were examined.Results: Of 366 patients who were eligible and agreed to participate in the study, 262 completed the questionnaires. Principal components analyses were used to select items most appropriate for retention in the preliminary version of the CPI and to describe its factor structure. Based on the content of items that loaded on each factor, the five factors were labeled as Catastrophizing, Interference with Functioning, Stoicism, Social Aspects, and Concerns about Pain Medication. Correlations between the CPI and other measures supported construct validity of the five CPI factors.Conclusions: The results supported the validity of the CPI as a measure of five constructs relevant to the experience of pain in the cancer setting. The results also underscored the presence of unique features of cancer‐related pain that clearly differ from commonly recognized dimensions of chronic, non‐cancer‐related pain. Copyright © 2009 John Wiley & Sons, Ltd.
Physical and mental health correlates of pregnancy following breast cancer
Authors: Gorman Jessica R. , Roesch Scott C. , Parker Barbara A. , Madlensky Lisa , Saquib Nazmus , Newman Vicky A. , Pierce John P. 
Published: July 2009

AbstractIntroduction: The safety of pregnancy after breast cancer is an important issue for many younger breast cancer survivors and their health care providers. Current research does not indicate that pregnancy negatively affects survival, but the ‘healthy mother bias,’ suggesting that survivors who go on to become pregnant are a self‐selected healthier group based on their prognosis, has led to cautious interpretation of these findings. No studies have systematically evaluated the potential for this bias.Methods: This nested case–control study includes 81 younger participants from the Women's Healthy Eating and Living (WHEL) study (N=3088). Our sample includes 27 cases who had children after breast cancer and 54 controls, matched on age and stage at diagnosis. We used hierarchical linear modeling to accommodate longitudinal data with individuals nested within matched sets (cases and controls). The primary aim was to evaluate the association between summary scores of health and childbearing after breast cancer. Covariates were added for adjustment and to improve model precision.Results: Controlling for other variables in the model, physical health scores were not different between cases and controls (B=0.14, p=0.96). Mental health scores were marginally higher among cases (B=6.40, p=0.08), as compared with controls, a difference considered clinically significant.Conclusion: This preliminary study did not find evidence of a healthy mother bias based on physical health. However, mental health was 6 points higher (p=0.08) among those who had children, indicating that the role of mental health needs evaluation in future research. Larger studies are needed to verify these findings. Copyright © 2009 John Wiley & Sons, Ltd.
Application of Thin Layer Chromatography for Monitoring of FOX‐7 Synthesis
Authors: Błądek Jan , Pietrzyk Sylwia , Cudziło Stanisław , Chyłek Zbigniew 
Published: July 2009

AbstractIn this paper, results of the research on the application of thin layer chromatography (TLC) for the determination of 1,1‐diamino‐2,2‐dinitroethene (FOX‐7, DADNE) and its precursors produced in the synthetic path starting from 2‐methylpyrimidine‐4,6(1H,5H)‐dione are presented. Analytical parameters of the substances and methodology of their quantitative analysis were determined, and the results obtained were used for monitoring the FOX‐7 synthesis process.
Structural and optical characterization of pulsed laser‐ablated potassium lithium niobate thin films
Authors: Jayasree V. , Ratheesh R. , Rao P. Prabhakar , Koshy Peter , Ganesan V. , Nayar V. U. , Pillai V. P. Mahadevan 
Published: July 2009

AbstractThin films of potassium lithium niobate (K3Li2Nb5O15: KLN) have been prepared on glass substrate, as a function of substrate temperature, using a pulsed laser‐deposition (PLD) technique for the first time. Grazing‐incidence X‐ray diffraction (GIXRD) analysis suggests that KLN films can be grown successfully at a substrate temperature as low as 300 K. The anomalous behavior of the decline of crystalline structure with increase in substrate temperature is explained. The atomic force microscopic (AFM) and scanning electron microscopic (SEM) images show an agglomerated growth mode for the films deposited at a substrate temperature of 300 K and a decrease in grain size with increase in substrate temperature. The films deposited at higher substrate temperatures show ring‐like structures. The AFM analysis shows that the rms surface roughness of the film decrease with increase in substrate temperature. The UV–Vis transmission spectra suggest that the nature of the transition in the films is directly allowed. A blue shift in optical bandgap is observed for the films compared to bulk material. The changes in the optical bandgap with substrate temperature are also discussed.
Measurement of the spatial coherence of synchrotron beams using the Talbot effect
Authors: Kluender Rafael , Masiello Fabio , van Vaerenbergh Pierre , Härtwig Jürgen 
Published: July 2009

AbstractWe present an application of the Talbot effect [Talbot et al., Philos. Mag. 11, 196 (1836)] to measure the spatial coherence of a synchrotron beam, as well as the influence of optical elements on it. One advantage of using this effect is that regions of the beams down to 50 µm × 50 µm are still analysable (in our case). This spatial resolution allows analysing the local coherence degradation caused by small regions in the investigated optical element, like windows or Bragg diffraction crystals with defects. A second advantage is the independence of the results on the detector point spread function. This method is used by the Optics and the X‐ray Imaging Group at the ESRF in the hard X‐ray domain at 20.5 keV. Although already presented by Cloetens et al., J. Synchrotron Radiat. 11, 476 (2004), this technique was mainly used to analyse the spatial beam coherence itself. In order to measure the coherence degradation due to non‐perfect optical elements, we improved the data analysis which was very deficient when applied to diffractive samples. These improvements have led to accurate and reliable results and have allowed to extend the application field of that method towards diffracting crystals.
Structural and photoluminescence studies of erbium‐implanted nanocrystalline silicon thin films
Authors: Cerqueira M. F. , Alpuim P. , Filonovich S. A. , Alves E. , Rolo A. G. , Andres G. , Soares J. , Kozanecki A. 
Published: July 2009

AbstractHydrogenated amorphous and nanocrystalline silicon thin films deposited by hot wire (HW) and radio‐frequency plasma‐enhanced chemical vapour deposition (RF‐PECVD) were erbium‐implanted. Their pre‐implantation structural properties and post‐implantation optical properties were studied and correlated. After 1 h annealing at 150 °C in nitrogen atmosphere only amorphous films showed photoluminescence (PL) activity at 1.54 µm, measured at 5 K. After further annealing at 300 °C for 1 h, all the samples exhibited a sharp PL peak positioned at 1.54 µm, with an FWHM of ∼5 nm. Amorphous films deposited by HW originated a stronger PL peak than corresponding films deposited by RF, while in nanocrystalline films PL emission was much stronger in samples deposited by RF than by HW. There was no noticeable difference in Er3+ PL activity between films implanted with 1 × 1014 and 5 × 1015 atoms cm−2 Er doses.
Electrical and optical properties of LixNi1–xO/In:MgxZn1–xO heteroepitaxial junction grown on TiN buffered Si
Authors: Wong H. F. , Wong K. H. , Lau C. H. 
Published: July 2009

AbstractP‐type Li doped NiO (LNO) and n‐type In doped cubic MgxZn1–xO (In:MZO) thin films were grown on TiN buffered Si (100) substrates by pulsed laser deposition. A heteroepitaxial relationship of (001)LNO||(001)In:MZO ||(001)TiN||(001)Si was obtained. These heterostructures showed good p–n junction current–voltage characteristics with a current rectification ratio of 400 at bias voltages of ±4 V. The typical current turn‐on voltage at room temperature was 2.8 V. It decreased to 2.6 V at 400 K. The spectral responses of these heterojunctions were measured in the near UV region. Our results have suggested that LNO/In:MZO heterojunction is a potential candidate for Solar‐blind UV detector.
Towards printed magnetic sensors based on organic diodes
Authors: Majumdar Sayani , Majumdar Himadri S. , Tobjörk Daniel , Österbacka Ronald 
Published: July 2009

AbstractWe report a study of magnetotransport properties of regio‐regular poly(3‐hexyl thiophene) (RRP3HT)‐based organic diodes. The devices were fabricated using two different techniques namely spin coating and inkjet printing. Positive magnetoresistance (MR) effect was observed at room temperature in all the devices. The highest MR magnitude reached up to 16% for some spin‐coated devices and up to 10% in inkjet printed devices. The MR magnitude and line shapes were found to depend strongly on the measuring current. We observed deviation from the theoretically predicted Lorentzian or non‐Lorentzian line shape of the MR traces, which is discussed in detail in the article. Although, the printed devices exhibit MR response as high as for the spin‐coated ones, they still need to be optimised in terms of performance and yield for large scale applications as magnetic sensors.
Semimagnetic semiconductor oxides as materials for transparent electronics and spintronics
Authors: Savchuk A. I. , Makhniy V. P. , Fediv V. I. , Kleto G. I. , Savchuk S. A. 
Published: July 2009

AbstractZinc oxide‐based semimagnetic semiconductor (SMS) ZnMnO, ZnMnFeO and ZnMnSnO thin films were deposited on sapphire and glass substrate by pulsed laser deposition (PLD) and RF sputtering techniques. Further, ZnMnO nanocrystals embedded in polyvinyl alcohol (PVA) and polyvinyl pyrrolidone (PVP) matrices were prepared by chemical method employing zinc acetate and manganese acetate as precursors. The morphology of the thin films was studied using atomic force microscopy (AFM). Large variety of the morphology images was obtained depending on the film composition and growth conditions. The most interesting feature was observed for the ZnMnSnO films, in which the formation of clusters including nanowire‐like structures was shown. Optical transmission spectra suggest that metals Mn, Fe and Sn substitute for Zn2+ ions in the ZnO lattice, resulting in the increase in the band gap energy. Magneto‐optical Faraday rotation measurements confirm ferromagnetic ordering in ZnMnFeO thin films and paramagnetic behaviour for the other films.
Micromechanical behaviour of gel grown pure and doped potassium hydrogen tartrate single crystals
Authors: Quasim I. , Firdous A. , Sahni N. , Khosa S. K. , Kotru P. N. 
Published: July 2009

AbstractMicromechanical characteristics of (001) and (111) planes of gel grown pure, sodium‐ and lithium‐doped potassium hydrogen tartrate single crystals as revealed by indentation induced technique are described. The indentation size effect (ISE) exhibited by the crystals is explained on application of proportional specimen resistance (PSR) model and the analytical law of Hays and Kendall. The load independent values of Vickers hardness of (001) and (111) planes of these crystals as indicated by indentation experiments and computed on the basis of PSR model and the analytical law are shown to be in good agreement. The doping by sodium or lithium results in the increase in hardness of potassium hydrogen tartrate crystals. The crystals exhibit hardness anisotropy. The values of yield strength of each plane of both pure and sodium and lithium doped potassium hydrogen tartrate single crystals are estimated using appropriate equations.
Enhanced red emission of CaMoO4:Eu3+ phosphor by structural adjustment for white light‐emitting diodes application
Authors: Zhang Zhan Hui , Huang Qiang , Zhao Xu , Huang Zhi Liang 
Published: July 2009

AbstractNa+ was incorporated into red‐emitting CaMoO4:Eu3+ phosphor to form solid solutions and reduce the crystal symmetry. For a fixed Eu3+ concentration, the luminescent properties as a function of Na+ concentrations were systematically studied under near‐ultraviolet (UV) excitation. Enhanced red emission at 613 nm was observed and the strongest intensity was 4.5 times that of the sample without Na+. Differing from the charge‐compensation mechanism, this enhancement was related to the structural distortion and decreasing centrosymmetry. The increased ratios of red emission (5D0 → 7F2) to orange (5D0 → 7F1) in intensity revealed that the structural adjustment was achieved in the phosphors via the incorporation of Na+.
Mesoporous GaAs double layers for layer transfer processes
Authors: Garralaga Rojas Enrique , Terheiden Barbara , Plagwitz Heiko , Hampe Carsten , Tutuc Daniel , Haug Rolf , Brendel Rolf 
Published: July 2009

AbstractMesoporous GaAs double layers with different porosities and thicknesses up to 7 µm are formed on highly doped p‐type 4 inch GaAs substrates by means of electrochemical etching in highly concentrated hydrofluoric acid electrolytes. Small 〈111〉 oriented pyramids form at the interface between porous layer and substrate if etching current densities below 7.5 mA cm−2are applied. Porous double layers with different porosities are obtained by varying simultaneously the etching current density and the electrolyte concentration. The porosity of the porous GaAs layers decreases nearly linearly from 69 to 53% with electrolyte concentrations increasing from 30 to 50 wt.%, respectively. The etching process increases the mean roughness of the porous layer surface from 0.15 to 0.24 nm.magnified image
Oxygen‐assisted photoinduced structural transformation in amorphous Ge–S films
Authors: Sakaguchi Yoshifumi , Tenne Dmitri A. , Mitkova Maria 
Published: July 2009

AbstractWe report our results of continuous illumination of Ge46S54 chalcogenide glass films with bandgap light in air. The outcome of this process is the formation of Ge–S backbone depleted in germanium. We relate this to consumption of some of the germanium available in the initial material due to the occurrence of a photoinduced oxidation. This is proved using energy dispersion spectroscopy which shows the presence of 17.68 at.% oxygen in the glass post‐radiation. Raman spectra demonstrate that the initial material shows breathing modes, characteristic for Ge46S54 glass. After prolonged illumination Raman spectra reveal structure characteristic for the composition of the Ge–S backbone close to Ge33S67. The oxide forms a film on the surface and this changes the surface relief, studied by atomic force microscopy, but the oxidation is not surface‐limited. The oxidation process in these glasses is discussed and the higher priority of germanium oxidation compared to the oxidation of sulphur is stated.
Diffraction and luminescent structures based on chalcogenide glasses and polymers
Authors: Andriesh Andrei , Iovu Mihail 
Published: July 2009

AbstractDiffraction optical structures are the main elements of diffraction optics with the perspectives for application in the systems of filtering, multiplexing, routing, focusing, and collimating of the light, as well as for fabrication of the photonic crystals. Thin films prepared from chalcogenide glasses and polymers were used for the fabrication of diffractive structures by holographic and electron‐beam recording technology. The electric field and other technological procedures have been used during the holographic writing process in order to increase the diffraction efficiency and the spatial density of the recording media. The problem of obtaining low‐cost but efficient luminescent materials is still present. It was shown that intensive luminescence is manifested from composite materials consisting of arsenic sulfide and arsenic selenide doped with rare‐earth ions (Dy3+and Pr3+), and polymers polyvinylalcohol or polyvinylpyrrolidone.
GaN layer growth by HVPE on m‐plane sapphire substrates
Authors: Usikov Alexander , Shapovalov Lisa , Ivantsov Vladimir , Kovalenkov Oleg , Syrkin Alexander , Spiberg Philippe , Brown Robert 
Published: July 2009

AbstractSemipolar GaN layers were grown on m‐plane sapphire substrates by HVPE. Insertion of AlxGa1–xN (x ∼ 0.1‐0.6) layer in‐between m‐plane sapphire substrate and GaN layer promoted to improve crystalline quality and to grow of semipolar (11‐22) plane GaN layers. X‐ray diffraction (11‐22) ω‐scan rocking curve FWHM of 298 arcsec was measured for a 30 μm thick (11‐22) GaN layer. Depending on growth conditions, m‐plane GaN layer having micro‐crystallites of other orientations (mainly of (11‐24) plane GaN layer) was also grown. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)