bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural and Functional Characterization of the Interdomain Interaction in the Mineralocorticoid Receptor
Authors: Pippal Jyotsna B. , Yao Yizhou , Rogerson Fraser M. , Fuller Peter J. 
Published: June 2009

Abstract
The mineralocorticoid receptor (MR) plays a central role in electrolyte homeostasis and in cardiovascular disease. We have previously reported a ligand-dependent N/C-interaction in the MR. In the present study we sought to fully characterize the MR N/C-interaction. By using a range of natural and synthetic MR ligands in a mammalian two-hybrid assay we demonstrate that in contrast to aldosterone, which strongly induces the interaction, the physiological ligands deoxycorticosterone and cortisol weakly promote the interaction but predominantly inhibit the aldosterone-mediated N/C-interaction. Similarly, progesterone and dexamethasone antagonize the interaction. In contrast, the synthetic agonist 9α-fludrocortisol robustly induces the interaction. The ability of the N/C interaction to discriminate between MR agonists suggests a subtle conformational difference in the ligand-binding domain induced by these agonists. We also demonstrate that the N/C interaction is not cell specific, consistent with the evidence from a glutathione-S-transferase pull-down assay, of a direct protein-protein interaction between the N- and C-terminal domains of the MR. Examination of a panel of deletions in the N terminus suggests that several regions may be critical to the N/C-interaction. These studies have identified functional differences between physiological MR ligands, which suggest that the ligand-specific dependence of the N/C-interaction may contribute to the differential activation of the MR that has been reported in vivo.
Subcellular Trafficking of the TRH Receptor: Effect of Phosphorylation
Authors: Jones Brian W. , Hinkle Patricia M. 
Published: June 2009

AbstractActivation of the G protein-coupled TRH receptor leads to its phosphorylation and internalization. These studies addressed the fundamental question of whether phosphorylation regulates receptor trafficking or endosomal localization regulates the phosphorylation state of the receptor. Trafficking of phosphorylated and dephosphorylated TRH receptors was characterized using phosphosite-specific antibody after labeling surface receptors with antibody to an extracellular epitope tag. Rab5 and phosphoreceptor did not colocalize at the plasma membrane immediately after TRH addition but overlapped extensively by 15 min. Dominant-negative Rab5-S34N inhibited receptor internalization. Later, phosphoreceptor was in endosomes containing Rab5 and Rab4. Dephosphorylated receptor colocalized with Rab4 but not with Rab5. Dominant-negative Rab4, -5, or -11 did not affect receptor phosphorylation or dephosphorylation, showing that phosphorylation determines localization in Rab4+/Rab5− vesicles and not vice versa. No receptor colocalized with Rab7; a small amount of phosphoreceptor colocalized with Rab11. To characterize recycling, surface receptors were tagged with antibody, or surface receptors containing an N-terminal biotin ligase acceptor sequence were labeled with biotin. Most recycling receptors did not return to the plasma membrane for more than 2 h after TRH was removed, whereas the total cell surface receptor density was largely restored in less than 1 h, indicating that recruited receptors contribute heavily to early repopulation of the plasma membrane.
Comparative Analysis of PCR-Based Biomarker Assay Methods for Colorectal Polyp Detection from Fecal DNA
Authors: Ausch Christoph , Kim Young-Ho , Tsuchiya Karen D , Dzieciatkowski Slavomir , Washington Mary K , Paraskeva Christos , Radich Jerry , Grady William M 
Published: June 2009

AbstractBackground: Aberrantly methylated genes are promising biomarkers for the detection of colon adenomas and colorectal cancers (CRCs). The optimal assay type and specific methylated genes for these assays remain to be determined.Methods: We used genomewide microarray-based assays to identify methylated genes as candidate biomarkers for colon neoplasms. The frequency of aberrant methylation of these genes in primary tumors was assessed with methylation-specific PCR (MSP). The limits of detection and specificities for different types of PCR-based assays were then assessed with the most promising genes identified in this screen. Finally, we assessed the best-performing MSP assay as an early-detection marker using fecal DNA samples.Results: ITGA4 [integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)] was identified as a novel gene frequently methylated in CRC. Methylated ITGA4 is present in 75% of colon adenomas (n = 36) and 92% of colon adenocarcinomas (n = 75). Comparison of end point MSP, end point MSP with clamped primers, and quantitative fluorescent MSP (qMSP) approaches revealed that both types of end point MSP assays could routinely detect as little as 70 pg DNA, whereas the qMSP assay could routinely detect as little as 7 pg. A fecal DNA qMSP assay for methylated ITGA4 can detect 69% of individuals with colon adenomas (n = 13) with a diagnostic specificity of 79% (n = 28).Conclusions: Methylated ITGA4 is a promising marker gene for the early detection of colonic neoplasms. qMSP has the lowest limit of detection of the MSP assay types tested, and a qMSP assay that detects methylated ITGA4 has potential as an early-detection assay for colon neoplasms.
CYP2D6 Genotyping for Functional-Gene Dosage Analysis by Allele Copy Number Detection
Authors: Hosono Naoya , Kato Mamoru , Kiyotani Kazuma , Mushiroda Taisei , Takata Sadaaki , Sato Hiroko , Amitani Hanae , Tsuchiya Yumiko , Yamazaki Keiko , Tsunoda Tatsuhiko , Zembutsu Hitoshi , Nakamura Yusuke , Kubo Michiaki 
Published: June 2009

Abstract
Background: Cytochrome P450 2D6 (CYP2D6), one of the most important drug-metabolizing enzymes, has been reported to possess variation in the encoding CYP2D6 gene (cytochrome P450, family 2, subfamily D, polypeptide 6) that affects enzymatic activity. For the pharmacogenetic study of CYP2D6, accurate measurement of the dosage of the functional gene is essential; however, current genotyping techniques are insufficient because of their inability to provide the exact copy number of functional CYP2D6 genes.
Methods: We developed 3 quantitative real-time PCR (qPCR) assays for estimating the total copy number of the CYP2D6 gene, as well as 24-multiplex PCR-based real-time Invader assays (mPCR-RETINAs) for estimating the allele ratio at each variation locus. After determining the allele copy number at each locus, we estimated the frequencies of CYP2D6 alleles in a population and the diplotype in each individual by a CNVphaser (copy number variation phaser). The qPCR assays and RETINAs used for HapMap Japanese and Chinese samples were applied to 455 Japanese individuals.
Results: Forty-two individuals (9.2%) had one CYP2D6 gene copy, 207 (45.5%) had 2 copies, 161 (35.4%) had 3 copies, 40 (8.8%) had 4 copies, and 5 (1.1%) had 5 copies of the CYP2D6 gene. We found 16 different CYP2D6 alleles, with frequencies similar to those described in previous reports. In the diplotype analysis, we observed that CYP2D6*1/*1 and *1/*10-*36 were the most common diplotypes (approximately 20%) in our population.
Conclusions: Our method is the first to determine the exact number of functional CYP2D6 gene copies. We believe our method will facilitate and accelerate the detailed pharmacogenetic analysis of CYP2D6.
Asymmetric Dimethylarginine Reference Intervals Determined with Liquid Chromatography–Tandem Mass Spectrometry: Results from the Framingham Offspring Cohort
Authors: Schwedhelm Edzard , Xanthakis Vanessa , Maas Renke , Sullivan Lisa M , Schulze Friedrich , Riederer Ulrich , Benndorf Ralf A , Böger Rainer H , Vasan Ramachandran S 
Published: June 2009

AbstractBackground: Accumulating evidence links higher circulating asymmetric dimethylarginine (ADMA) to greater risk of cardiovascular disease (CVD). Relatively small differences in ADMA concentrations between healthy individuals and those with disease underscore the need to formulate reference intervals that may aid risk stratification of individuals.Methods: We formulated reference intervals for plasma ADMA concentrations using a community-based reference sample from the Framingham Offspring Study consisting of 1126 nonsmoking individuals [mean (SD) age 56 (9) years; 60% women] who were free of clinical CVD, hypertension, diabetes, and obesity and who attended a routine examination at which ADMA was assayed. ADMA concentrations were determined using a validated tandem mass spectrometry–liquid chromatography assay.Results: In the study sample, the mean ADMA concentration was 0.52 (0.11) μmol/L, and the reference limits were 0.311 and 0.732 (2.5th and 97.5th percentile). The sex-specific reference limits were 0.310 and 0.745 in men and 0.313 and 0.721 μmol/L in women. In multivariable regression analysis, ADMA plasma concentrations were positively correlated with age and total plasma homocysteine (both P &lt; 0.001).Conclusions: Reference limits calculated for circulating ADMA in our large community-based healthy reference sample confirm the previous observation of a relatively narrow distribution of concentrations. This suggests a tight physiological control of ADMA plasma concentrations, presumably by dimethylarginine dimethylaminohydrolase (DDAH) metabolism of ADMA.
Multiplex Detection of 60 Hepatitis B Virus Variants by MALDI-TOF Mass Spectrometry
Authors: Luan Ju , Yuan Jing , Li Xiaohe , Jin Shengnan , Yu Ling , Liao Mingfeng , Zhang Hongmei , Xu Cheng , He Qing , Wen Bin , Zhong Xunhua , Chen Xinchun , Chan Henry L Y , Sung Joseph J Y , Zhou Boping , Ding Chunming 
Published: June 2009

AbstractBackground: Variations in the hepatitis B virus (HBV) genome may develop spontaneously or under selective pressure from antiviral therapy. Such variations may confer drug resistance or affect virus replication capacity, resulting in failure of antiviral therapy.Methods: A duplex PCR was used to amplify the region of the reverse transcriptase gene, the precore promoter, and the basal core promoter of the HBV genome. Four multiplex primer-extension reactions were used to interrogate 60 frequently observed HBV variants during antiviral therapy. Automated MALDI-TOF mass spectrometry (MS) was used for mutation detection. Capillary sequencing was used to confirm the MS results.Results: The limit of quantification was 1000 HBV copies/mL for multiplex detection of HBV variants. Fifty-three variants (88.3%) were analyzed successfully in at least 90% of the sera from 88 treatment-naive patients and 80 patients with virologic breakthrough. MS was able to detect twice as many minor variants as direct sequencing while achieving close to full automation. MS and direct sequencing showed only 0.1% discordance in variant calls.Conclusions: This platform based on multiplex primer extension and MALDI-TOF MS was able to detect 60 HBV variants in 4 multiplex reactions with accuracy and low detection limits.
Contribution of the Bituminous Mortar and Stone Skeleton to the Resistance to Permanent Deformation in Asphalt Mixtures
Authors: Muraya P. M. , Molenaar A. A. A. , van de Ven M. F. C. 
Published: June 2009

Abstract
This paper describes the results of a research that was conducted to investigate the contribution of the different components in an asphalt mixture to the resistance to permanent deformation. As part of this research, extensive triaxial tests were performed on the stone skeletons of dense, stone mastic, and porous asphalt concrete. An extensive characterization of the bituminous mortar was also performed using the dynamic shear rheometer and the direct tension tests. The results showed that aggregate skeletons exhibit a high tendency to dilate implying tensile stresses and strains in the bituminous mortar. The results also showed that plastic deformation is much more important than viscous deformation for the stone skeleton mixtures and that viscous deformation is more important for the dense mixture. The findings of the research were used to analyze the permanent deformation that occurred in accelerated pavement test sections.
Infrared Photoconductivity in Heavily Nitrogen Doped a-Si:H
Authors: Shelton David J , Ginn James C , Coffey Kevin R , Boreman Glenn D 
Published: June 2009

AbstractThe generation of high frequency steady-state photoconductivity in nitrogen doped hydrogenated amorphous silicon (a-Si:H-N) films has been demonstrated at infrared (IR) frequencies of 650 to 2000 cm-1 or 15 to 5 μm in wavelength. This allows IR photoconductivity to be observed using a simple thermal source. In order to produce high frequency photoconductivity effects the plasma frequency must be increased to the desired device operation frequency or higher as described by the Drude model. IR ellipsometry was used to measure the steady-state permittivity of the a-Si:H-N films as a function of pump illumination intensity. The largest permittivity change was found to be Δεr = 2 resulting from a photo-carrier concentration on the order of 1022 cm-3. IR photoconductivity is shown to be limited by the effective electron mobility at IR frequencies.
SIMULATION OF PLASMONIC CRYSTAL ENHANCEMENT OF THIN FILM SOLAR CELL ABSORPTION
Authors: Biswas Rana , Zhou Dayu , Garcia Luis 
Published: June 2009

AbstractLight management and enhanced photon harvesting is a critical area for improving efficiency of thin film solar cells. Red and near infrared photons with energies just above the band edge have large absorption lengths in amorphous silicon and can not be efficiently collected. We previously demonstrated that a photonic crystal back reflector involving a periodically patterned ZnO layer can enhance absorption of band edge photons. We propose and design alternative new plasmonic crystal structures that enhance absorption in thin film solar cell structures. These plasmonic crystals consist of a periodically patterned metal back reflector with a periodic array of holes An amorphous/nanocrystalline silicon layer resides on top of this plasmonic crystal followed by a standard anti-reflecting coating. We have found plasmonic crystal structures enhance average photon absorption by more than 10%, and by more than a factor of 10 at wavelengths just above the band edge, and should lead to improved cell efficiency. The plasmonic crystal diffracts band edge photons within the absorber layer, increasing their path length and dwell time. In addition there is concentration of light within the plasmonic crystal. Design simulations are performed with rigorous scattering matrix simulations where both polarizations of light are accounted for.
Light Trapping in Thin-film μc-Si:H Solar Cells using Self-ordered 2D Grating Reflector
Authors: Sai Hitoshi , Kanamori Yoshiaki , Kondo Michio 
Published: June 2009

AbstractEffect of back reflectors on light trapping in μc-Si:H cells has been investigated with self-ordered Al substrates obtained by anodic oxidation. With increasing the period of the patterned substrates from 0 to 1.1 μm, 1-μm-thick μc-Si:H cells on the patterned substrates have shown a significant enhancement of spectral response in the near infrared region, giving an increment of the short circuit current density from 18 to 24 mA/cm2. This enhanced light trapping effect are attributed to the improved reflectivity of the rear side and effective light scattering at the front side, as well as light scattering at the rear side.
Amorphous Semiconductors Studied by First-principles Simulations: Structure and Electronic Properties
Authors: Jarolimek Karol , de Groot Robert A. , de Wijs Gilles A. , Zeman Miro 
Published: June 2009

AbstractAtomistic models of amorphous solids enable us to study properties that are difficult to address with experimental methods. We present a study of two amorphous semiconductors with a great technological importance, namely a- Si:H and a-SiN:H. We use first-principles density functional theory (DFT), i.e. the interatomic forces are derived from basic quantum mechanics, as only that provides accurate interactions between the atoms for a wide range of chemical environments (e.g. brought about by composition changes). This type of precision is necessary for obtaining the correct short range order. Our amorphous samples are prepared by a cooling from liquid approach. As DFT calculations are very demanding, typically only short simulations can be carried out. Therefore most studies suffer from a substantial amount of defects, making them less useful for modeling purposes. We varied the cooling rate during the thermalization process and found it has a considerable impact on the quality of the resulting structure. A rate of 0.02 K/fs proves to be sufficient to prepare realistic samples with low defect concentrations. To our knowledge these are the first calculations that are entirely based on first-principles and at the same time are able to produce defect-free samples. Because of the high computational load also the size of the systems has to remain modest. The samples of a-Si:H and a-SiN:H contain 72 and 110 atoms, respectively. To examine the convergence with cells size, we utilize a large cell of a-Si:H with a total of 243 atoms. As we obtain essentially the same structure as with the smaller sample, we conclude that the use of smaller cells is justified.
Although creating structures without any defects is important, on the other hand a small number of defects can give valuable information about the structure and electronic properties of defects in a-Si:H and a-SiN:H. In our samples we observe the presence of both the dangling bond (undercoordinated atom) and the floating bond (over-coordinated atom). We relate structural defects to electronic defect states within the band gap. In a-SiN:H the silicon-silicon bonds induce states at the valence and conduction band edges, thus decreasing the band gap energy. This finding is in agreement with measurements of the optical band gap, where increasing the nitrogen content increases the band gap.
High Temperature Post-deposition Annealing Studies of Layer-by-layer (LBL) Deposited Hydrogenated Amorphous Silicon Films
Authors: Tong Goh Boon , Gani Siti Meriam Ab. , Muhamad Muhamad Rasat , Rahman Saadah Abdul 
Published: June 2009

AbstractHigh temperature post-deposition annealing studies were done on hydrogenated amorphous silicon thin films deposited by plasma-enhanced chemical vapour deposition (PECVD) using the layer-by-layer (LBL) deposition technique. The films were annealed at temperatures of 400 °C, 600 °C, 800 °C and 1000 °C in ambient nitrogen for one hour. Auger electron spectroscopy (AES) depth profiling results showed that high concentration of O atoms were present at the substrate/film interface and at film surface. Very low concentration of O atoms was present separating silicon layers at regular intervals from the film surface and the substrate due to the nature of the LBL deposition and these silicon oxide layers were stable to high annealing temperature. Reflectance spectroscopy measurements showed that the onset of transformation from amorphous to crystalline phase in the LBL a-Si:H film structure started when annealed at temperature of 600 °C but the X-ray diffraction (XRD) and Raman scattering spectroscopy showed that this transition only started at 800 °C. The films were polycrystalline with very small grains when annealed at 800 °C and 1000 °C. Fourier transform infrared spectroscopy (FTIR), measurements showed that hydrogen was completely evolved from the film at the on-set of crystallization when annealed at 800 °C. The edge of the reflectance fringes shifted to longer wavelength decrease in hydrogen content but shifted to shorter wavelength with increase in crystallinity.
Polysilicon Films Formed on Metal Sheets by Aluminium Induced Crystallization of Amorphous Silicon: Barrier Effect
Authors: Pathi Prathap , Tüzün Ozge , Slaoui Abdelilah 
Published: June 2009

AbstractPolycrystalline silicon (pc-Si) thin films have been synthesized by aluminium induced crystallization (AIC) of amorphous silicon (a-Si) at low temperatures (≤500°C) on flexible metallic substrates for the first time. Different diffusion barrier layers were used to prepare stress free pc-Si films as well as to evaluate the effective barrier against substrate impurity diffusion. The layers of aluminum (Al) and then amorphous silicon with the thickness of 0.27 μm and 0.37 μm were deposited on barrier coated metal sheets by means of an electron beam evaporation and PECVD, respectively. The bi-layers were annealed in a tube furnace at different temperatures (400-500°C) under nitrogen flow for different time periods (1-10hours). The degree of crystallinity of the as-grown layers was monitored by micro-Raman and reflectance spectroscopies. Structure, surface morphology and impurity analysis were carried out by X-ray diffraction, scanning electron microscopy (SEM) and EDAX, respectively. The X-ray diffraction measurements were used to determine the orientation of grains. The results show that the AIC films on metal sheets are polycrystalline and the grains oriented in (100) direction preferentially. However, the properties of AIC films are highly sensitive to the surface roughness.
Improving Silicon Crystallinity by Grain Reorientation Annealing
Authors: Saenger Katherine L. , de Souza Joel P. , Inns Daniel , Fogel Keith E. , Sadana Devendra K. 
Published: June 2009

AbstractDemand for high efficiency, low-cost solar cells has led to strong interest in post-deposition processing techniques that can improve the crystallinity of thick (1 to 40 μm) silicon films deposited at high growth rates. Here we describe a high temperature grain reorientation annealing process that enables the conversion of polycrystalline silicon (poly-Si) into a single crystal material having the orientation of an underlying single crystal Si seed layer. Poly-Si films of thickness 0.5 to 1.0 μm were deposited by low pressure chemical vapor deposition (LPCVD) on substrates comprising a surface thermal oxide or a 100-oriented single crystal silicon-on-insulator (SOI) layer. After annealing at 1300 °C for 1 hour, poly-Si on oxide shows very significant grain growth, as expected. In contrast, the poly-Si deposited on SOI showed no grain boundaries after annealing, transforming into a single crystal material with a fairly high density of stacking faults. Possible uses and drawbacks of this approach for solar cell applications will be discussed.
Optimization of p-type Nanocrystalline Silicon Thin Films for Solar Cells and Photodiodes
Authors: Vygranenko Yuri , Fathi Ehsanollah , Sazonov Andrei , Vieira Manuela , Heiler Gregory , Tredwell Timothy , Nathan Arokia 
Published: June 2009

AbstractWe report on structural, electronic, and optical properties of boron-doped, hydrogenated nanocrystalline silicon (nc-Si:H) thin films deposited by plasma-enhanced chemical vapor deposition (PECVD) at a substrate temperature of 150°C. Film properties were studied as a function of trimethylboron-to-silane ratio and film thickness. The film thickness was varied in the range from 14 to 100 nm. The conductivity of 60 nm thick films reached a peak value of 0.07 S/cm at a doping ratio of 1%. As a result of amorphization of the film structure, which was indicated by Raman spectra measurements, any further increase in doping reduced conductivity. We also observed an abrupt increase in conductivity with increasing film thickness ascribed to a percolation cluster composed of silicon nanocrystallites. The absorption loss of 25% at a wavelength of 400 nm was measured for the films with optimized conductivity deposited on glass and glass/ZnO:Al substrates. A low-leakage, blue-enhanced p-i-n photodiode with an nc-Si p-layer was also fabricated and characterized.