bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aberrant expression of glycosylation in juvenile gastrointestinal stromal tumors
Authors: Takahashi Tsuyoshi , Naka Tetsuji , Fujimoto Minoru , Serada Satoshi , Horino Jirou , Terabe Fumitaka , Hirota Seiichi , Miyoshi. Eiji , Hirai Toshihiro , Nakajima Kiyokazu , Nishitani Akiko , Souma Yoshihito , Sawa Yoshiki , Nishida Toshirou 
Published: July 2008

AbstractMost adult gastrointestinal stromal tumors (GIST) are thought to be caused by activating mutations in the KIT or PDGFRA gene. However, many juvenile GIST lack either mutation and are considered to develop with a different pathogenesis. To investigate the molecular characteristics of juvenile GIST, we analyzed the proteome difference in phosphorylated protein between adult and juvenile GIST. Eleven GIST samples (seven adult cases and four juvenile cases lacking either mutation) were analyzed by using immunostaining and LC‐MS/MS. Comparative analysis of tyrosine‐phosphorylated protein levels showed that juvenile GIST possessed phosphorylated KIT in spite of lacking mutation in the KIT gene. Moreover, downstream signals of KIT were also activated as in adult GIST. Although, SDS‐PAGE gels showed that there was a difference of each KIT bands between adult and juvenile GIST, they became the same after removal of N‐glycans or sialic acids. Moreover, one of the most typical enzymes, ST6Gal1, which transfers Neu5Ac residues in α2‐6 linkage to Gal β1‐4GlcNAc units on N‐glycans, is significantly less expressed in juvenile GIST. This suggests that the difference in KIT is generated by post‐translational modification and may play a role in the progression of juvenile GIST.
Sample handling for mass spectrometric proteomic investigations of human urine
Authors: Petri Anette Lykke , Høgdall Claus , Christensen Ib Jarle , Simonsen Anja Hviid , T'Jampens Davy , Hellmann Marja‐Leena , Kjaer Susanne Krüger , Fung Eric T. , Høgdall Estrid 
Published: July 2008

AbstractBecause of its non‐invasive sample collection method, human urine is an attractive biological material both for discovering biomarkers and for use in future screening trials for different diseases. Before urine can be used for these applications, standardized protocols for sample handling that optimize protein stability are required. In this explorative study, we examine the influence of different urine collection methods, storage temperatures, storage times, and repetitive freeze‐thaw procedures on the protein profiles obtained by surface‐enhanced laser desorption/ionization time‐of‐flight mass spectrometry (SELDI‐TOF‐MS). Prospectively collected urine samples from 11 women were collected as either morning or midday specimens. The effects of storage temperature, time to freezing, and freeze‐thaw cycles were assessed by calculating the number, intensity, and reproducibility of peaks visualized by SELDI‐TOF‐MS. On the CM10 array, 122 peaks were detected and 28 peaks were found to be significantly different between urine types, storage temperature and time to freezing. On the IMAC‐Cu array, 65 peaks were detected and 1 peak was found to be significantly different according to time to freezing. No significant differences were demonstrated for freeze‐thaw cycles. Optimal handling and storage conditions are necessary in clinical urine proteomic investigations. Collection of urine with a single and consistently performed protocol is needed to reduce analytical bias. Collecting only one urine type, which is stored for a limited period at 4°C until freezing at −80°C prior to analysis will provide the most stable profiles.
MS‐based phenotypic characterization of a human blood protein from urinary waste products
Authors: Kiernan Urban A. , Hernandez Lisa , Niederkofler Eric E. , Tubbs Kemmons A. , Nelson Randall W. 
Published: July 2008

AbstractThe urine proteome (urineome) has become an ideal biological fluid for biomarker study and detection due to its rich protein content as well as its ease and abundance in collection. Protein variation in human plasma has been linked to the presence of disease states in humans; however, it stands to reason that the same is true of the equally complex urineome. In this manuscript we present the combination of two proteomics technologies, mass spectrometric immunoassay and a bioreactive probe, for the detection and characterization of the protein variants of transthyretin (TTR) found in human urine. Coupling these two technologies we could precisely identify protein variants within a population of normal individuals. This is the first report of the detailed characterization of urinary TTR using this combination of proteomic analytical techniques, and demonstrates a novel non‐invasive methodology for the routine analysis of this clinically significant urine protein target.
Urinary proteomic analysis of chronic allograft nephropathy
Authors: O'Riordan Edmond , Orlova Tatyana N. , Mendelev Natalia , Patschan Daniel , Kemp Rowena , Chander Praveen N. , Hu Rena , Hao Gang , Gross Steven S. , Iozzo Renato V. , Delaney Veronica , Goligorsky Michael S. 
Published: July 2008

AbstractThe pathogenesis of progressive renal allograft injury, which is termed chronic allograft nephropathy (CAN), remains obscure and is currently defined by histology. Prospective protocol‐biopsy trials have demonstrated that clinical and standard laboratory tests are insufficiently sensitive indicators of the development and progression of CAN. The study aim was to determine if CAN could be characterized by urinary proteomic data and identify the proteins associated with disease. The urinary proteome of 75 renal transplant recipients and 20 healthy volunteers was analyzed using surface enhanced laser desorption and ionization MS. Patients could be classified into subgroups with normal histology and Banff CAN grades 2‐3 with a sensitivity of 86% and a specificity of 92% by applying the classification algorithm Adaboost to urinary proteomic data. Several urinary proteins associated with advanced CAN were identified including α1‐microglobulin, β2‐microglobulin, prealbumin, and endorepellin, the antiangiogenic C‐terminal fragment of perlecan. Increased urinary endorepellin was confirmed by ELISA and increased tissue expression of the endorepellin/perlecan ratio by immunofluoresence analysis of renal biopsies. In conclusion, analysis of urinary proteomic data has further characterized the more severe CAN grades and identified urinary endorepellin, as a potential biomarker of advanced CAN.
The glomerular proteome in a model of chronic kidney disease
Authors: Potthoff Sebastian A. , Sitek Barbara , Stegbauer Johannes , Schulenborg Thomas , Marcus Katrin , Quack Ivo , Rump Lars C. , Meyer Helmut E. , Stühler Kai , Vonend Oliver 
Published: July 2008

AbstractAdequate kidney function is crucial in sustaining vertebrate homeostasis. Certain diseases can diminish renal function and lead to end‐stage renal disease. Diabetes mellitus and hypertension are the main causes of glomerulosclerosis and albuminuria in adults. The molecular mechanisms that trigger these maladaptive changes are still unsatisfyingly described. We previously introduced 2‐D DIGE in combination with focused tissue isolation methods to analyze protein expression in glomeruli. Glomeruli, the crucial compartments in albuminuric renal diseases, were extracted using magnetic particles from subtotally nephrectomized FVB mice (n = 6); this 5/6 nephrectomy in FVB mice is a model of chronic kidney disease. Analysis of protein expression levels from glomerular protein lysates was performed using 2‐D DIGE and compared with glomerular protein lysates from mice that underwent sham surgery. The comparison of about 2100 detectable spots between both groups revealed 48 protein spots that showed significant differential expression. Of those, 33 proteins could be identified using nanoLC‐ESI MS. The metalloproteinase meprin 1 alpha, the beta galactoside‐binding‐lectin galectin‐1 and dimethylarginine dimethylaminohydrolase 1, a key enzyme in NO metabolism, were found to be differentially regulated, thus implying a role in the pathogenesis and pathophysiology of progressive kidney disease. In conclusion, 2‐D DIGE protein analysis of smallest sample sizes from specific organ compartments provides focused protein expression results, which help in gaining an understanding of the molecular mechanisms of chronic kidney disease.
Relationship between serum adiponectin and prostate cancer grade
Authors: Sher David J. , Oh William K. , Jacobus Susanna , Regan Meredith M. , Lee Gwo‐Shu , Mantzoros Christos 
Published: July 2008

AbstractBACKGROUNDObesity is associated with prostate cancer (PCA) grade, but the mechanism behind this relationship is not understood. Adiponectin is an adipokine that has been linked with the development of hormonally sensitive carcinomas, including prostate cancer. We evaluated the relationship between serum adiponectin and Gleason score (GS) in a prospective series of patients seen in a single institution.METHODSLocalized PCA patients evaluated at Dana‐Farber Cancer Institute between 2001 and 2005 who enrolled in a prospective serum banking protocol were eligible for this study. Patients with prior hormonal therapy and/or metastatic disease were excluded. High‐grade disease was defined as biopsy or radical prostatectomy (RP) GS of 7 or higher. Logistic regression models were used to assess the relationship between high‐grade disease and adiponectin levels while adjusting for other potential prognostic variables.RESULTSThere were 539 patients included in this study, of whom 199 had undergone RP. Median age was 60 years. Median PSA was 5.1 ng/dl. Biopsy GS of 7 or higher was seen in 46.9% of patients. For biopsy GS, higher PSA, older age, and higher BMI were significantly associated with increased odds of GS 7 or higher, but adiponectin was not. In men undergoing RP, there was a significant inverse relationship between pathologic GS and adiponectin dichotomized at the median, due to a significantly higher rate of upgrading in patients with lower adiponectin (P = 0.014).CONCLUSIONSAlthough there was no association between biopsy GS and adiponectin, in patients who had undergone RP, lower adiponectin was independently associated with high‐grade prostate cancer. Prostate 68: 1592–1598, 2008. © 2008 Wiley‐Liss, Inc.
Family history of prostate and breast cancer and the risk of prostate cancer in the PSA era
Authors: Chen Yen‐Ching , Page John H. , Chen Rong , Giovannucci Edward 
Published: July 2008

AbstractBACKGROUNDA family history of prostate cancer (PCa) or breast cancer (BCa) has been associated with the risk of PCa, but the risks were inconsistent in terms of the affected family members, and data in the PSA era are limited.METHODSThis study included a subcohort of the Health Professionals Follow‐Up Study composed of a highly PSA screened population from 1986 to 2004 with 3,695 PCa cases identified. Questionnaires and a food frequency questionnaire were administered every other and every 4 years, respectively. Family history of PCa and BCa was ascertained in 1990, 1992, and 1996. All statistics were two‐sided.RESULTSA family history of PCa in both a father and brother(s) was associated with a 2.3‐fold increased risk of PCa [95% confidence interval (CI) = 1.76–3.12]. Men with a father or brother(s) with a PCa diagnosis at age<60 and ≥60 had 2.16‐ and 1.95‐fold increased risk of PCa, respectively. A family history of PCa was related to early‐onset PCa (<65 years: RR = 2.25, 95% CI = 1.95–2.60) and weakly to late‐onset PCa (≥65 years: RR = 1.67, 95% CI = 1.52–1.85). History of BCa in a mother or a sister was associated with a 1.22‐fold increased risk of PCa (95% CI = 1.08–1.38).CONCLUSIONA family history of PCa or BCa significantly increases PCa risk. These associations are evident in a population with widespread PSA screening. Prostate 68: 1582–1591, 2008. © 2008 Wiley‐Liss, Inc.
Theoretical models for doping diamond for semiconductor applications
Authors: Goss J. P. , Eyre R. J. , Briddon P. R. 
Published: July 2008

AbstractDiamond is a material with superlative properties in terms of carrier mobilities and device characteristics for high power electronics applications. Although p‐type diamond is routinely available using boron, n‐type material via impurity doping during the growth of diamond has historically been limited in success, partly because nitrogen is a hyper‐deep donor, but compounded by the compact lattice leading to low solubilities for alternative species. Implantation doping is often hampered by persistent residual damage leading to significant levels of compensation and the formation of dopant complexes with lattice vacancies. Experiment has been augmented by the application of quantum‐chemical methods to assess the likely properties should specific impurities or impurity complexes be realisable in real materials. The review outlines many of the doping strategies explored for diamond, including simple impurity doping and co‐doping. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Recombination of free and bound excitons in GaN
Authors: Monemar B. , Paskov P. P. , Bergman J. P. , Toropov A. A. , Shubina T. V. , Malinauskas T. , Usui A. 
Published: July 2008

AbstractWe report on recent optical investigations of free and bound exciton properties in bulk GaN. In order to obtain reliable data it is important to use low defect density samples of low doping. We have used thick GaN layers (of the order of 1 mm) grown by halide vapour phase epitaxy (HVPE) with a residual doping down to <1016 cm–3 in this work. With such samples all polarisation geometries could also easily be exploited. The influence of the surface states on the photoluminescence (PL) experiments is analysed, it is concluded that surface recombination plays an important role for the free exciton (FE) recombination. The electronic structure of the FEs is discussed in detail, including the influence of spin‐exchange and polariton effects, and compared with polarised PL spectra at 2 K. The detailed structure of excited states from the PL spectra is discussed, but further data are needed to fully explain all the peaks observed. The polarized FE spectra at room temperature allow a determination of the bandgap as 3.437 eV at 290 K, assuming an exciton binding energy of 25 meV. The PL transient of the A FE is very short (about 100 ps) for the no‐phonon (NP) line interpreted as dominated by nonradiative surface recombination. The longitudinal‐optical (LO) phonon replicas of the A FE exhibit a longer decay of about 1.4 ns at 2 K, suggested to represent the bulk lifetime of the FE. The corresponding decay time at 290 K is 9 ns in our samples, a value that might be affected by nonradiative recombination. The Si and O donor bound exciton (DBE) spectra with sharp NP lines at 3.4723 eV and 3.4714 eV respectively, are well resolved together with the so‐called two‐electron transitions (TETs) and several optical phonon replicas. The electronic structure of the DBE states including excited rotational states is discussed and compared with experiment. The well‐resolved TET lines allow an accurate determination of the ground state binding energy of the Si donor as 30.4 meV and 33.2 meV for the O donor. The PL transients of the DBEs reveal a non‐exponential decay for the NP lines. The DBE NP transient lineshape is assumed to be influenced by optical dispersion and scattering in the vicinity of exciton resonances, as well as by surface effects. The DBE decay time can most properly be deduced from the PL decay of the respective TETs and LO replicas, leading to values in the range of 1.1–1.8 ns. These values differ significantly from previous theoretical predictions, where values about two orders of magnitude shorter were obtained. A tentative discussion of the main observed features of acceptor bound excitons (ABEs), which are much less studied in GaN, is given. A decay time of about 0.9 ns for the shallowest 3.466 eV ABE is estimated, i.e. shorter than that for the shallow donor BEs. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
First principles calculations of the magnetic properties of Fe–N systems
Authors: Li Dan , Roh Jong Wook , Jeon Kye Jin , Gu You Song , Lee Wooyoung 
Published: July 2008

AbstractWe report the results of the first principles calculations performed in order to investigate the electronic and magnetic properties of the Fe–N systems and to clarify the origin of giant magnetic moments in Fe–N systems. After geometrical optimization, the densities of states have been evaluated with atom resolved band populations and magnetic moments. By examining Fe–N bond lengths in the Fe–N systems, it was found that there is a linear relationship between Fe–N bond lengths and atomic magnetic moments. Our results demonstrate that the existence of N atoms can affect charge transfer between the 4s, 4p and 3d bands of Fe atoms and is responsible for the change in magnetic moments. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Scientific literacy: A Freirean perspective as a radical view of humanistic science education
Authors: Santos Wildson L. P. Dos 
Published: July 2008

AbstractIn this article, a rationale for advancing a new idea in humanistic science education is developed from a Paulo Freire perspective. Paulo Freire developed a well‐known approach to adult literacy based on his humanistic ideas through the dialogical process. From Freirean educational principles, the idea unfolds that a Freirean humanistic science education perspective is a political commitment to sociopolitical action, considering conditions of oppression in society. Although some humanistic science education approaches to school science have incorporated a sociopolitical perspective, it is showed that not all of them necessarily focus on the political purpose of transforming oppressive conditions in society as stressed by Paulo Freire. From this Freirean humanistic perspective, an approach to science education is then highlighted, which implies the introduction of socially relevant themes and socioscientific issues, the establishment of a dialogical process in classroom, and the development of sociopolitical action. Hence, a Freirean perspective of science education is presented as a radical view of scientific literacy. Some implications of a Freirean approach to science education are outlined at the end of the paper. © 2008 Wiley Periodicals, Inc.Sci Ed93:361–382, 2009
Social barriers to meaningful engagement in biology field trip group work
Authors: Anderson David , Thomas Gregory P. , Nashon Samson M. 
Published: July 2008

AbstractThis paper reports on a study that employed metacognition and social cognition theoretical frameworks to explore and interpret students' views of their cognitive roles and the nature of the mechanisms that they considered influenced and mediated their learning within small group contexts. An instrumental interpretive case study methodology was used to capture students' descriptive accounts of their Year 11 Biology learning experiences, as conveyed through their recollections and reflections concerning their interactions and roles, perceptions of the learning task, and their learning strategies that they considered to be manifest during a field trip visit to a nature center. We conclude that, even among apparently highly collegial student groups, deemed by their teacher to be effective learning groups, and constituted in ways consistent with the literature on effective collaborative group work, there existed metasocial metacognitive factors that influenced and shaped cognition in ways counterproductive to the effective learning of science. This study reveals the existence of metacognitive knowledge and processes, common among students and related to their views of what is appropriate thinking and behavior within small groups, which inform collective and individual task actions. We contend that students are highly aware of their social status within groups and of their individual group's social conditions and that this awareness affects cognition and behavior. Moreover, they monitor these conditions and employ strategies that simultaneously service both the task and social relationships and their learning processes to varying extents depending on individual and group factors. © 2008 Wiley Periodicals, Inc. Sci Ed 93: 511–534, 2009
Mechanism of carbon nanotube dispersion and precipitation during treatment with poly(acrylic acid)
Authors: Tran N. H. , Milev A. S. , Wilson M. A. , Bartlett J. R. , Kannangara G. S. K. 
Published: July 2008

AbstractCarbon nanotubes have been shown to be easily dispersed within an acidic aqueous solution of poly(acrylic acid) but precipitate when the pH is increased. Transmission electron microscopy showed that the nanotubes were more exfoliated under the acidic condition but highly aggregated under the basic condition. Carbon K‐edge NEXAFS spectroscopy showed that the carbon nanotubes did not chemically react with poly(acrylic acid) during the dispersion or precipitation and that the dispersion mainly involved physical adsorption of poly(acrylic acid) onto the nanotubes. Together with the carbon K‐edge NEXAFS spectra, the cobalt L3, 2‐edge NEXAFS spectra suggested that under the basic condition, the cobalt impurity within the nanotubes strongly reacted with poly(acrylic acid) resulting in complex formation. Cobalt reduces the adsorption of poly(acrylic acid) onto the nanotubes, which then reduced the nanotube dispersion and resulted in the precipitation. Copyright © 2008 John Wiley & Sons, Ltd.
Effect of Cu pre‐deposition on the interface structure between the C‐SiC coatings and stainless steel
Authors: Du J. F. , Yang S. Q. , Ren D. , Zhang R. Q. , Huang N. K. 
Published: July 2008

AbstractThe copper dispersion‐strengthened matrix composites (Cu/CSiC) were fabricated on the stainless steel by using magnetron sputtering and ion‐beam mixing. The pre‐deposition of Cu element is used to modify the interface structure, and hence, to develop the compatibility between Fe substrate and C‐SiC coating. The results show that the copper layer can effectively broaden the transition layer, where the elements of the coating could be completely mixed with the elements of the substrate. The following heat treatment on it can further broaden the transition layer, i.e. heat treatment can provide more compatibility between C‐SiC coating and Fe substrate. Copyright © 2008 John Wiley & Sons, Ltd.
Surface morphology of Ge‐modified 3C‐SiC/Si films
Authors: Nader Richard , Kazan Michel , Moussaed Elie , Stauden Thomas , Niebelschütz Merten , Masri Pierre , Pezoldt Jörg 
Published: July 2008

AbstractThe influence of Ge deposition prior to carbon interaction with 3° off‐axis Si(111) substrates on the structural and morphological properties of the formed silicon carbide (SiC) layer is studied. In situ reflection high‐energy electron diffraction (RHEED) and X‐ray diffraction (XRD) revealed the formation of the cubic silicon carbide (3C‐SiC) modification. In situ spectroscopic ellipsometry measurements revealed a decreasing 3C‐SiC thickness with increasing Ge predeposition. Atomic force microscopy (AFM) studies revealed that the surface overlayer morphology is mainly formed by periodic step arrangements whose relevant geometric parameters, i.e. lateral separation, height and terrace width, depend on the Ge content. Besides the changes of the step morphology, the surface roughness and the grain size and the strain of the formed 3C‐SiC decreases with increasing germanium precoverage. Copyright © 2008 John Wiley & Sons, Ltd.
Disordered state of adsorbed hydrogens on Ni(111) surface studied by slow‐positron beam
Authors: Komagata S. , Hirota K. , Arii S. , Kanazawa I. , Fukutani K. , Nozawa K. , Komori F. 
Published: July 2008

AbstractThe positron annihilation γ‐ray energy spectra emitted from hydrogen‐lightly adsorbed Ni(111) surface and hydrogen‐saturatedly adsorbed one are analyzed. We have discussed the disordered state of hydrogen‐saturatedly adsorbed Ni(111) surface. Copyright © 2008 John Wiley & Sons, Ltd.