bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strategies to recover proteins from ocular tissues for proteomics
Authors: Patel Nikhil , Solanki Ekta , Picciani Renata , Cavett Valerie , Caldwell‐Busby Jennifer A. , Bhattacharya Sanjoy K. 
Published: March 2008

AbstractWe present here the results of protein extraction from different ocular regions using different detergents. Extraction strategies used to determine optimal protein extraction included: pressure cycling and aqueous–organic phase extraction in combination with electrophoretic fractionation for anterior, posterior, and peripapillary sclera. Detergent extraction of proteins from freshly enucleated porcine eyes (n = 8) showed significant differences for different eye regions. Protein yield ranged from 2.3 to 50.7 μg protein/mg for different ocular tissues, with the lens yielding the most protein. ASB‐14 and Triton X‐100 provided the best protein yields (n = 10) for anterior and posterior sclera. The spectrophotometric measurements for ASB‐14 were not consistent with SDS‐PAGE densitometry. A combination of 0.5% Triton X‐100, 0.5% Tween‐20, and 0.1% Genapol C‐100 was found optimal for extraction from sclera. Proteins from different regions of the eye are best extracted with different detergents. The pressure cycling technology provided superior extraction compared to the other methods. Additional aqueous–organic phase partitioning enables superior fractionation when compared to SDS‐PAGE alone. Organic phase fractionation is compatible with MS and allowed identification of 34, 71, and 77 proteins respectively from anterior, posterior, and peripapillary sclera. The extraction strategy may affect the final outcome in protein profiling by MS or by other methods.
An immunoproteomic approach for identification of clinical biomarkers of Whipple's disease
Authors: Kowalczewska Malgorzata , Fenollar Florence , Villard Claude , Azza Saïd , Roux Maurice , Raoult Didier 
Published: March 2008

AbstractWhipple's disease (WD) is a chronic multisystemic infection, caused by the bacterium Tropheryma whipplei. The main clinical presentations are classic WD (CWD) with histologic lesions in the gastrointestinal tract, endocarditis, and isolated neurologic infection. The current strategy for diagnosis remains invasive.The present study aimed to select the protein candidates for serological diagnosis of WD. The first step was to identify candidate proteins by an immunoproteomic approach combining 2‐DE using a total extract of a T. whipplei, immunoblotting, and MS. The second step was to validate the discovered biomarkers using a recombinant protein‐based ELISA. Serum samples from 18 patients with WD and from 54 control individuals were tested. A sugar ABC transporter, TWT328 (sensitivity (Se) 61%, specificity (Sp) 87%, positive predictive value (PPV) 61%, negative predictive value (NPV) 87%, and positive likelihood ratio (PLR) 4.69) was the best marker for development of serodiagnosis for CWD. We also obtained a reproducible immunoreactive protein pattern for patients with isolated neurological infection due to T. whipplei (Se 100%, Sp 93%, PPV 55.5%, NPV 100%, and PLR 13.51) as an encouraging step towards noninvasive diagnosis of this particular manifestation. Nine recombinant candidates have been successfully screened with serum samples. Results from these ELISA assays skewed with those obtained with immunoblots.
Annexin A4: A novel molecular marker for gastric cancer with Helicobacter pylori infection using proteomics approach
Authors: Lin Li‐Ling , Chen Chiung‐Nien , Lin Wei‐Chou , Lee Po‐Huang , Chang King‐Jen , Lai Yo‐Ping , Wang Jin‐Town , Juan Hsueh‐Fen 
Published: March 2008

AbstractHelicobacter pylori was reported to be an important risk factor for the carcinogenesis of gastric cancer. Here, we used a proteomic approach to find differentially expressed proteins between the normal and tumor tissue of gastric cancer patients infected with H. pylori. In our results, we found annexin A4 was over‐expressed in patients infected with H. pylori and was found in tumor cells, and over‐expressed in gastric cancer SCM‐1 cells after H. pylori infection. Ca2+ can be induced by H. pylori and interact with annexin A4 Ca2+ binding site to block the calmodulin‐activated chloride conductance activation; therefore, it produces a new environment that benefits the malignant existence of H. pylori and raises the risk for gastric cancer. We also found interleuken‐8 (IL‐8) expression levels were increased in H. pylori infected SCM‐1 cells. Combined with previous reports and our results, we summarize that the over‐expression of annexin A4 in SCM‐1 cells with H. pylori infection may subsequently induce IL‐8 which can further cause tumor angiogenesis. In this paper, we show that annexin A4 is a potential novel molecular marker for gastric cancer with H. pylori infection, and our results may provide a new insight in the development of new anti‐cancer drugs.
Proteomic analysis of early urinary biomarkers of renal changes in type 2 diabetic patients
Authors: Bellei Elisa , Rossi Elena , Lucchi Leonardo , Uggeri Simona , Albertazzi Alberto , Tomasi Aldo , Iannone Anna 
Published: March 2008

AbstractDiabetic nephropathy (DN) is a complication associated with diabetes, leading to end‐stage renal disease (ESRD). Despite significant progress in understanding DN, the cellular mechanisms leading to the renal damage are incompletely defined. In this study, with the aim to identify urine biomarkers for the early renal alterations in type 2 diabetes mellitus (T2D), we performed urinary proteomic analysis of 10 normoalbuminuric patients with T2D, 12 patients with type 2 DN (T2DN), and 12 healthy subjects. Proteins were separated by 2‐DE and identified with ESI‐Q‐TOF MS/MS. Comparing the patients proteomic profiles with those of normal subjects, we identified 11 gradually differently changed proteins. The decreased proteins were the prostatic acid phosphatase precursor, the ribonuclease and the kallikrein‐3. Eight proteins were progressively increased in both patients groups: transthyretin precursor, Ig κ chain C region, Ig κ chain V‐II region Cum, Ig κ‐chain V‐III region SIE, carbonic anhydrase 1, plasma retinol‐binding protein, β‐2‐microglobulin precursor, β‐2‐glycoprotein 1.The proteomic analysis allowed us to identify several increased urinary proteins, not only in T2DN but also in T2D patients in which the microalbuminuria was in the normal range. These patterns of urinary proteins might represent a potential tool for a better understanding of diabetic renal damage.
Comparative investigation of the Si/SiO2 interface layer containing SiC crystallites using spectroscopic ellipsometry, ion beam analysis and XPS
Authors: Lohner T. , Pongrácz A. , Khánh N. Q. , Krafcsik O. H. , Josepovits K. V. , Deák P. 
Published: March 2008

AbstractIt is known from earlier publications that SiC crystallites grow at the interface of a Si/SiO2 system during heat treatment in CO containing ambient. First 100 nm thick SiO2 layers were thermally grown on <100> Si substrates. The Si/SiO2 structures were heat treated in CO containing atmosphere for 20 and 102 hours at 1190 oC for investigation. Spectroellipsometry was applied to study the microstructure of the heat‐treated samples. We assumed a layer at the Si/SiO2 interface that contains crystalline Si and crystalline SiC. After 20 and 102 hour annealing the layer thickness extracted from evaluation of ellipsometric data was 15 nm and 25 nm, the volume fraction of SiC was 38% and 89%, respectively. To confirm the results of the ellipsometry characterization we applied ion beam analysis and X‐ray photoelectron spectroscopy. For determination of the carbon content a 4He+ ion beam of 3.5 MeV was selected to take advantage of the scattering cross section of carbon at 165o detection angle is about six times larger than the Rutherford type one. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Temperature dependence of ellipsometric spectra of Fe and CrNiAl steel
Authors: Nebojsa A. , Zrzavecká O. Fikarová , Navrátil K. , Humlíček J. 
Published: March 2008

AbstractWe report on the temperature dependence of optical response of pure bcc iron and CrNiAl steel. Ellipsometric spectra, covering the 1.4‐3.0 eV spectral range, have been obtained during temperature cycles reaching 650 °C in UHV chamber. Since the penetration depth of light is rather small and the data are sensitive to the quality of sample surfaces, we have examined polished, etched and annealed samples. We identify characteristic features of the temperature dependence, consisting in spectral shifts of interband transitions and a redistribution of spectral weight. We have also detected reproducible irreversible changes in the initial stages of annealing cycles when the samples are heated to at least 300 °C. With increasing temperature, we observe a pronounced reduction of the minority‐spin interband contribution. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Multilayer optical filters control by multi‐channel kinetic ellipsometry
Authors: Ibrahim B. Haj , Botha R. , Bulkin P. , Drévillon B. 
Published: March 2008

AbstractThe use of multi‐wavelength kinetic ellipsometry control for the deposition of multilayer filters is presented. Two different control methods are described and their use for the fabrication of different types of optical filters is illustrated. We fit the ellipsometric data with a model and adjust the physical thickness during deposition to ensure the conservation of the optical thickness. In order to illustrate this method and to show its importance in the case of periodic structures or single layer control, a Bragg mirror and a resonator layer in a Fabry‐Perot filter were grown using Matrix Distributed Electron Cyclotron Resonance Plasma Enhanced Chemical Vapor Deposition (MDECR‐PECVD). The use of fitting both the index and thickness for control of the physical thickness is also shown. The importance of this method for manufacturing non‐periodic multilayer structures is demonstrated by the controlled deposition of an antireflection coating. The different features of these two methods are presented. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Analysis of carrier parameters and bandgap of electroplated Bi2Te3films by infrared spectroscopic ellipsometry
Authors: Zimmer A. , Stein N. , Terryn H. , Johann L. , Boulanger C. 
Published: March 2008

AbstractPolycrystalline thin films have been grown on gold substrates by electrodeposition, leading to different film compositions. In particular, our conditions allow growing smooth and shiny surface films in a thickness range of nanometers to micrometers. In this article, electroplated layers were analysed by InfraRed Spectroscopic ellipsometry. The dielectric functions have been obtained from ellipsometry analyses using the Drude and Tauc‐Lorentz models. We attributed the scattering distribution of the mobility with the carrier concentration to the presence of grain boundaries in the films. The energy bandgap appears to be constant whatever the carrier concentration. This result can be interpreted by bandgap shrinkage that occurs simultaneously with bandgap widening. These results were supported by additional Hall Effect Measurements. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Structural order of thin film silicon made at 100 °C
Authors: Rath Jatindra K. , Schropp Ruud E. I. , Cabarocas Pere Roca i 
Published: March 2008

AbstractSpectroscopic ellipsometric measurements showed that amorphous silicon thin films made by very high frequency plasma enhanced chemical vapour deposition at 100 °C using an optimum H2dilution has denseness (A parameter) and structural order (C parameter) that are comparable to the sample made at 200 °C. The materials made by hot wire chemical vapour deposition (HWCVD) at low hydrogen dilution conditions have a less dense structure and higher roughness compared to the plasma deposited samples. The C parameter reaches the lowest value (C=1.67) for the HWCVD sample made at an optimum H2/SiH4ratio of 20, even though it was made only at 100 °C. The importance of filament to substrate distance in HWCVD process in suppressing the undesirable species reaching at the growing surface has been put forward to achieve materials with very small structural disorder and fabrication of thin film silicon solar cells with high stability. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On the determination of anisotropy in polymer thin films: A comparative study of optical techniques
Authors: Campoy‐Quiles M. , Nelson J. , Etchegoin P. G. , Bradley D. D. C. , Zhokhavets V. , Gobsch G. , Vaughan H. , Monkman A. , Ingänas O. , Persson N. K. , Arwin H. , Garriga M. , Alonso M. I. , Herrmann G. , Becker M. , Scholdei W. , Jahja M. , Bubeck C. 
Published: March 2008

AbstractWe have used seven different techniques to measure the anisotropic refractive index of poly(vinylcarbazole) films. These techniques are: two types of variable angle spectroscopic ellipsometry (VASE) with multiple sample analysis, Interference enhanced VASE, Transmittance combined with VASE, Polarised Reflectance, beta‐scan VASE, and prism coupling. We have found the average ordinary and extraordinary indices at 633 nm to be no = nTE = 1.675 ± 0.008, and ne = nTM = 1.722 ± 0.018, respectively, consistent amongst methods and conclusive on the magnitude of Δn in polymer films. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Catalyst‐referred etching of 4HSiC substrate utilizing hydroxyl radicals generated from hydrogen peroxide molecules
Authors: Yagi Keita , Murata Junji , Kubota Akihisa , Sano Yasuhisa , Hara Hideyuki , Okamoto Takeshi , Arima Kenta , Mimura Hidekazu , Yamauchi Kazuto 
Published: March 2008

AbstractWe describe a new environmentally friendly planarization technique for 4H‐silicon carbide (SiC) substrates. The method uses hydroxyl (OH) radicals generated from hydrogen peroxide (H2O2) molecules. The surface morphology and the removal rate show strong dependencies on the plane direction of the substrate. This is attributed to the oxidation mechanism wherein oxidation progresses through the exchange of the surface C‐sites with O atoms. A difference in the number of CSi bonds around the surface C‐sites causes a difference in the removal rate between the opposite faces. On the (0001) face, the oxidation progresses preferentially at the step edge, where the C‐sites are locally exposed. As a result, a step‐terrace structure is formed. Copyright © 2008 John Wiley & Sons, Ltd.
In situ B‐doped Si epitaxial growth at low temperatures by atmospheric‐pressure plasma CVD
Authors: Kirihata Y. , Nomura T. , Ohmi H. , Kakiuchi H. , Yasutake K. 
Published: March 2008

AbstractIn situ B‐doped Si epitaxial growth by atmospheric‐pressure plasma chemical vapor deposition (AP‐PCVD) using porous carbon electrode was investigated. Heavy B doping for a carrier concentration of 8 × 1019 cm−3 was achieved using B2H6 as a doping gas, with a high average growth rate of 0.20 µm min−1 at 570 °C. The relation between the hole mobility and carrier concentration in heavily B‐doped Si films can be well fitted with that reported for bulk Si single crystals up to the carrier concentration of 5 × 1019 cm−3. This result demonstrates that the electrical quality of heavily doped Si epitaxial films grown by AP‐PCVD is sufficiently high for semiconductor device applications. The activation ratio of B atoms as acceptors in the heavily doped films is nearly 100% for a carrier concentration range reaching approximately 2 × 1019 cm−3. Cross‐sectional transmission electron microscopy examination of heavily B‐doped epitaxial Si with a carrier concentration of 2 × 1019 cm−3 revealed both a defect‐free film and film/substrate interface. In the present experiment, the required B2H6/SiH4 ratio is much higher than the resultant B composition in the Si films, due to thermal decomposition of B2H6 molecules in the porous carbon electrode. To increase the efficiency of B2H6 gas usage, cooling of the porous carbon electrode during the AP‐PCVD process may be effective. Copyright © 2008 John Wiley & Sons, Ltd.
Spatially resolved detection of plasmon‐enhanced fluorescence using scanning tunneling microscopy
Authors: Uemura T. , Akai‐Kasaya M. , Saito A. , Aono M. , Kuwahara Y. 
Published: March 2008

AbstractWe have measured a nanoscale fluorescence image of copper phthalocyanine (CuPc)/Au nanostructures on an indium tin oxide (ITO) substrate using a scanning tunneling microscope (STM). The quantum efficiency (QE) of the intrinsic fluorescence of CuPc is very low; however, the plasmon enhancement effect on an Au surface increases fluorescence efficiency. To obtain the nanoscale fluorescence image, in this study, we used up‐conversion fluorescence through a triplet‐triplet annihilation (TTA) process. Tunnel electrons induced fluorescence and tip‐induced plasmon (TIP) emission simultaneously; however, the up‐conversion fluorescence from CuPc could be clearly separated from TIP emission by spectroscopic filtering. The TIP showed different properties between the ITO substrate and the Au surface, and the CuPc fluorescence was enhanced only on the TIP of Au nanostructures. This study would lead to the application of a new fluorescence imaging method based on plasmon‐assisted STM‐induced light emission (STM‐LE). Copyright © 2008 John Wiley & Sons, Ltd.
Trace element mapping using a high‐resolution scanning X‐ray fluorescence microscope equipped with a Kirkpatrick‐Baez mirror system
Authors: Matsuyama S. , Mimura H. , Katagishi K. , Yumoto H. , Handa S. , Fujii M. , Sano Y. , Shimura M. , Yabashi M. , Nishino Y. , Tamasaku K. , Ishikawa T. , Yamauchi K. 
Published: March 2008

AbstractWe have developed a scanning X‐ray fluorescence microscope (SXFM) using Kirkpatrick‐Baez mirror optics, which enables achromatic and highly efficient focusing, at BL29XUL of SPring‐8. The SXFM enables observations of multielement distributions inside a sample with high resolution and high sensitivity. Previously, we have reported the high spatial resolution of a newly developed SXFM. In the present paper, we focus on the high sensitivity of the SXFM. By observations of fine test patterns using the X‐ray beam probe having a size of 100 × 100 nm2 and an energy of 15 keV, the lower detection limit for the visualization of elemental distributions was investigated. As a result, the lower detection limits were found to be 0.009 fg (gallium) and 0.012 fg (tungsten). Copyright © 2008 John Wiley & Sons, Ltd.
Do Benign Thyroid Nodules Have Malignant Potential? An Evidence‐Based Review
Authors: Arora Nimmi , Scognamiglio Theresa , Zhu Baixin , Fahey Thomas J. 
Published: March 2008

AbstractBackgroundBenign thyroid tumors account for most nodular thyroid disease. Determination of whether a thyroid nodule is benign or malignant is a major clinical dilemma and underlies the decision to proceed to surgery in many patients. Although the accuracy of thyroid nodule fine‐needle aspiration (FNA) has reduced the need for surgery over the years, questions regarding how to follow FNA‐designated benign nodules remain unresolved. This is true at least in part because of uncertainty over whether some benign nodules harbor malignant potential.MethodsAn evidence‐based review of recent clinical, pathologic, and molecular data is presented. A summary of data and observations from our own experience is also provided.ResultsReview of our recent 10‐year experience indicates that 2% of thyroid malignancies arise within a preexisting benign thyroid nodule. In addition, both cytologic and molecular tumor markers, including Gal‐3, CITED1, HBME‐1, Ras, RET/PTC, and PAX8/PPARγ, have been identified in some histopathologically classified benign nodules. Gene expression profiling suggests that follicular adenomas and Hürthle cell adenomas have similarities to both benign and malignant tumors, suggesting that some of these tumors are premalignant. In addition, 10% of surgically excised follicular tumors are encapsulated follicular lesions with nuclear atypia, which have been termed “well‐differentiated tumors of uncertain malignant potential.” The data available suggest that these tumors could be precursors to carcinoma.ConclusionSome benign thyroid nodules have malignant potential. Further molecular testing of these tumors can shed light on the pathogenesis of early malignant transformation.
Surgical Treatment of Graves’ Disease: Evidence‐Based Approach
Authors: Stålberg Peter , Svensson Anna , Hessman Ola , Åkerström Göran , Hellman Per 
Published: March 2008

AbstractBackgroundThe optimal treatment of Graves´ disease (GD) is still controversial. Surgery is one treatment option along with radioactive iodine (RAI) and antithyroid medication. In this evidence‐based review, we examine four issues: (1) Is surgery better than RAI or long‐term antithyroid medication? (2) What is the recommended surgical approach? (3) How does the presence of Graves’ ophthalmopathy (GO) influence the role of surgery? (4) What is the role of surgery in children with GD?MethodsWe conducted a systematic review of the literature using evidence‐based criteria regarding these four issues.Results(1) There are no recommendations reaching any grade of evidence for which treatment to choose for adults with GD. (2) Total thyroidectomy has complication rates equal to those seen with lesser resections but it has higher cure rates and negligible recurrence rates (Level I–IV data leading to a grade A recommendation). (3) Data support surgery when severe GO is present, but RAI combined with glucocorticoids may be equally safe (Level II–IV data, grade B recommendation). The extent of thyroid resection does not influence the outcome of GO (Level II data, grade B recommendation). (4) Based on the available data, definitive treatment can be advocated for children (Level IV data, grade C recommendation) using either RAI or surgery. No recommendation can be given as to whether RAI or surgery is preferred owing to the lack of studies addressing this issue. Increased cancer risk with RAI in children below the age of 5 years supports surgery in this setting (Level I data, grade A recommendation).ConclusionIf surgery is considered for definitive management, evidence‐based criteria support total thyroidectomy as the surgical technique of choice for GD. Available evidence also supports surgery in the presence of severe endocrine GO. Children with GD should be treated with an ablative strategy. Whether this is achieved by total thyroidectomy or RAI may still be debatable. Data on long‐term cancer risk are missing or conflicting; and until RAI has proven harmless in children, we continue to recommend surgery in this group.
Process Evaluation of an Intensified Preventive Intervention to Reduce Cardiovascular Risk in General Practices in Deprived Neighbourhoods
Authors: El Fakiri Fatima , Hoes Arno W. , Uitewaal Paul J.M. , Frenken Rianne A.A. , Bruijnzeels Marc A. 
Published: March 2008

Background: A RCT, conducted to examine the effectiveness of a structured collaboration in general practice to provide intensified preventive care in patients at high cardiovascular risk yielded no effect in the total group but differences across healthcare centres and ethnic groups become apparent. We conducted a process evaluation to explain these differences. Methods: We assessed the reach of the target group and whether key intervention components (individual educational sessions, structured team meetings, and risk assessments) were performed as planned (maximum score for protocol completion is 11). Results: The reach was initially 91%, but only a minority of patients completed the intervention activities as planned. The average score of the number of intervention components was low (5.66 out of 11 (sd 2.8)) and varied between centres (4.84 to 7.40) and ethnic groups (4.89 to 7.38), with team meetings as the least implemented activity conform plan. Conclusion: This study indicates that adding a practice nurse and a peer health educator to the general practice did not seem to result in the desired collaboration between the healthcare personnel. Further research is needed to investigate the reasons behind the low participation rate of the patients in the intervention.