bluuebunny/crossref_metadata_2025 huggingface dataset:
Pseudogout: An unusual and forgotten metabolic sequela of parathyroidectomy
Authors: Doshi Jayesh , Wheatley Hugh
Published: March 2008

Background

Parathyroidectomy is increasingly being performed by otolaryngology units. The well‐known metabolic sequela is hypocalcaemia; it may be transient or permanent depending on presence and/or activity of any residual parathyroid tissue. A more unusual metabolic sequela of a parathyroidectomy is the development of pseudogout. We summarize the clinical presentation and pathophysiology of pseudogout following parathyroidectomy.

Methods

We present a case of a 71‐year‐old woman who developed pseudogout following removal of a parathyroid adenoma.

Results

Although infrequent, pseudogout predominately occurs in the immediate postoperative period.

Conclusion

We propose that otolaryngology units should be more aware of the unusual sequelae of pseudogout following parathyroidectomy; it can lead to a prompt referral and commencement of early treatment. © 2008 Wiley Periodicals, Inc. Head Neck, 2008
Solitary extramedullary plasmacytoma of the head and neck—Long‐term outcome analysis of 68 cases
Authors: Bachar Gideon , Goldstein David , Brown Dale , Tsang Richard , Lockwood Gina , Perez‐Ordonez Bayardo , Irish Jonathan
Published: March 2008

Background

Head and neck solitary extramedullary plasmacytomas are rare plasma cell neoplasms. Literature review reveals only small numbers of reports. The objective was to review our experience with treating patients with this neoplasm.

Methods

A retrospective chart review between 1960 and 2000 was performed. Sixty‐eight patients with head and neck extramedullary plasmacytomas were included.

Results

The sinonasal tract was the most common site. Thirty‐nine patients were treated with radiation, 8 with surgery, 14 with surgery and radiation, and 3 with chemoradiation. Median follow‐up was 8 years. The 5‐year local recurrence–free rate (LRFR) was 81%. There was a trend toward improved LRFR in patients treated primarily with radiation. Regional recurrence at 5 years was 5%. Multiple myeloma developed in 23% of patients. The 5‐year survival was 76%.

Conclusions

Radiation is the treatment of choice with surgery reserved for large tumors and extensive bone destruction. Long‐term follow‐up is essential because local recurrence and disseminated disease can occur many years postdiagnosis. © 2008 Wiley Periodicals, Inc. Head Neck, 2008
Synovial sarcoma presenting as a parotid mass: Case report and review of literature
Authors: Jay Amrita , Hutchison Iain , Piper Kim , Farthing Paula M. , Richards Polly S.
Published: March 2008

Background

Synovial sarcoma is an unusual neoplasm of mesenchymal derivation, which is uncommon in the head and neck sites. In the parotid gland, it is most likely to be misdiagnosed as a myoepithelial, primary mesenchymal, or metastatic neoplasm.

Methods

We report a case of synovial sarcoma in a young woman who was seen with temporomandibular joint symptoms with a 10‐year history. A review of the literature was undertaken to highlight the radiologic and histologic features that help in diagnosis as well as the suggested therapeutic protocols most likely to ensure better survival.

Results

Radiologic and histologic studies of the parotid mass led to a diagnosis of synovial sarcoma. A total parotidectomy was performed, and the individual remains tumor free at 36months.

Conclusions

Review of the literature suggests an aggressive long‐term outcome for synovial sarcoma and advocates early diagnosis and radical surgical excision for a favorable prognosis. © 2008 Wiley Periodicals, Inc. Head Neck, 2008
Do current beliefs predict hypomanic symptoms beyond personality style? Factor analysis of the hypomanic attitudes and positive predictions inventory (HAPPI) and its association with hypomanic symptoms in a student population
Authors: Mansell Warren , Rigby Zoe , Tai Sara , Lowe Christine
Published: March 2008

A self‐report scale called the Hypomanic Attitudes and Positive Predictions Inventory (HAPPI) has been developed to assess cognitions that distinguish between bipolar disorder and nonclinical controls (Mansell, 2006; Mansell & Jones, 2006). We recruited 191 undergraduate students to assess the associations between the HAPPI and self‐reported past (MDQ; Hirschfeld et al., 2000) and present (ISS; Bauer et al., 1991) bipolar symptoms, and to explore the factor structure of the scale. The HAPPI correlated with past and present symptoms independently of the BIS/BAS subscales (Carver & White, 1994) and the HPS (Eckblad & Chapman, 1986). Five factors of the HAPPI were identified: success activation and triumph over fear, activating response style, reduced social regulation, loss of control when activated, and catastrophic beliefs about internal states. The HAPPI factors showed specific relationships with current bipolar symptoms that largely fitted with predictions based on the model. Further work is required to establish whether they have a causal role. © 2008, Wiley Periodicals, Inc. J Clin Psychol 64: 1–16, 2008.
Enhancement of cell‐specific transgene expression from a Tet‐Off regulatory system using a transcriptional amplification strategy in the rat brain
Authors: Liu Beihui , Wang Shu , Brenner Michael , Paton Julian F.R. , Kasparov Sergey
Published: March 2008

Background

The Tet‐Off system uses a tetracycline‐controlled transactivator protein (tTA) and a tetracycline‐responsive promoter element (TRE) to regulate expression of a target gene. This system can be used to achieve regulatable transgene expression in specific cell types by employing a cell‐specific promoter to drive tTA expression. Wide applications of this attractive approach are, however, hindered by relatively weak transcriptional activity of most cell‐specific promoters. We report here the feasibility of using a transcriptional amplification strategy to overcome the problem.

Methods and results

In the developed cell‐type‐specific, Tet‐inducible lentiviral system, two distinct cellular promoters were tested, a human synapsin‐1 promoter for neurons and a compact glial fibrillary acidic protein promoter for astroglial cells. Lentiviral vectors were constructed that contained two copies of one or the other of these two promoters. One copy was used to drive the expression of a chimeric transactivator consisting of a part of the transcriptional activation domain of the NF‐κB p65 protein fused to the DNA‐binding domain of the yeast GAL4 protein. The second copy of the cell‐specific promoter was modified by introduction of the GAL4 binding sequences at its 5′ end. This copy was used to drive expression of tTA. A gene encoding a red fluorescent protein was cloned into another lentiviral vector under transcriptional control of TRE. Co‐transduction with the two types of viral vectors provided doxycycline‐regulated transgene expression in a neuron‐ or astrocyte‐specific manner. Compared to control viruses without transcriptional amplification, our enhanced systems were approximately 8‐fold more potent in cultured neurons and astroglial cells and at least 8‐ to 12‐fold more potent in the rat brain in vivo.

Conclusions

Our results demonstrate the effectiveness of the transcriptional amplification strategy in developing viral gene delivery systems that combine the advantages of specific cell type targeting and Tet‐inducible expression. Copyright © 2008 John Wiley & Sons, Ltd.
Upregulation of α‐skeletal muscle actin and myosin heavy polypeptide gene products in degenerating rotator cuff muscles
Authors: Fuchs Bruno , Zumstein Matthias , Regenfelder Felix , Steinmann Patrick , Fuchs Thomas , Husmann Knut , Hellermann Jens , Jost Bernhard , Hodler Jürg , Born Walter , Gerber C.
Published: March 2008

Impaired function of shoulder muscles, resulting from rotator cuff tears, is associated with abnormal deposition of fat in muscle tissue, but corresponding cellular and molecular mechanisms, likely reflected by altered gene expression profiles, are largely unknown. Here, an analysis of muscle gene expression was carried out by semiquantitative RT‐PCR in total RNA extracts of supraspinatus biopsies collected from 60 patients prior to shoulder surgery. A significant increase of α‐skeletal muscle actin (p = 0.0115) and of myosin heavy polypeptide 1 (p = 0.0147) gene transcripts was observed in parallel with progressive fat deposition in the muscle, assessed on parasagittal T1‐weighted turbo‐spin‐echo magnetic resonance images according to Goutallier. Upregulation of α‐skeletal muscle actin and of myosin heavy polypeptide‐1 has been reported to be associated with increased muscle tissue metabolism and oxidative stress. The findings of the present study, therefore, challenge the hypothesis that increased fat deposition in rotator cuff muscle after injury reflects muscle degeneration. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:1007–1011, 2008
Gradual stretching of the proximal nerve stump induces the growth of regenerating sprouts in rats
Authors: Saijilafu  , Nishiura Yasumasa , Hara Yuki , Yoshii Yuichi , Ochiai Naoyuki
Published: March 2008

We investigated the effect of direct gradual stretching on the proximal nerve stump morphologically. A 10‐mm‐long nerve segment was resected from the sciatic nerve of a rat. The end of the proximal nerve stump was fixed to a small ring and the marking suture was placed at a point 1 mm proximal to the ring. Then, the nerve stump was lengthened at a rate of 1 mm/day via a stretching of the ring using an original external device. After a stretching of 20 days, the distance from the ring to the marking suture became 12 mm. Whereas large mature myelinated axons were observed in the proximal part of the marking, only small axons with thin myelin sheath were observed in the distal part, and the mean axonal diameter showed a significant difference between the two parts. Moreover, the mean internodal length was 172.4 ± 13.4 µm in the distal part of the marking and 1019.0 ± 56.2 µm in the proximal part. The internodal length also showed a significant difference between the two parts. Thus, the axonal diameter and internodal length were consistent with the characteristics of regenerating axons in the distal part. Furthermore, ultrastructural analysis also showed the histological characteristics of axonal regeneration. Thus, a transected proximal nerve stump may be lengthened by axonal regeneration during gradual stretching, and the stimulus of mechanical stretching may induce the growth of regenerating axons. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:1012–1017, 2008
Antisense oligonucleotide targeting TNF‐α can suppress co‐cr‐mo particle‐induced osteolysis
Authors: Dong Lei , Wang Rui , Zhu Yi‐an , Wang Chunming , Diao Huajia , Zhang Chenyu , Zhao Jianning , Zhang Junfeng
Published: March 2008

The most common cause of implant failure in joint replacement is aseptic loosening due to particle‐induced osteolysis. TNF‐α has been shown to be one of the key factors in the process of osteoclastogenesis. Anti‐TNF agents are useful in the treatment of joint inflammation related to osteolysis. This study investigated the effect of a single subcutaneous dose of an antisense oligonucleotide (ASO) on particle‐induced osteolysis. We utilized the murine calvaria osteolysis model in C57BL/J6 mice. Bone resorption was measured by the toluidine blue staining. Osteoclasts were detected by tartrate resistant acid phosphatase (TRAP) staining assay and were quantified by a TRAP quantification kit. Results show that bone resorption is 0.347 ± 0.09 mm2 in mice with particle implantation, and decreased to 0.123 ± 0.05 mm2 and 0.052 ± 0.02 mm2 after ASO treatment with low and high doses, respectively. The number of osteoclasts in animal calvaria treated with ASO is reduced compared with that of untreated animals, and the quantification results indicate that about 90% of osteoclastogenesis is suppressed by the ASO. In addition, the osteoclastogenesis can be reestablished by the addition of TNF‐α. In conclusion, we demonstrate that the antisense oligonucleotide targeting to TNF‐α can suppress osteolysis induced by metal particles in a murine calvaria model. This new finding may be of value in the search for novel therapeutic methods for implant loosening. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:1114–1120, 2008
Increased IL‐1β expression and myofibroblast recruitment in subacromial bursa is associated with rotator cuff lesions with shoulder stiffness
Authors: Ko Jih‐Yang , Wang Feng‐Sheng , Huang Hsuan‐Ying , Wang Ching‐Jen , Tseng Shin‐Ling , Hsu Chin
Published: March 2008

We evaluated whether proinflammatory cytokine expression and myofibroblast recruitment in subacromial bursa was linked to rotator cuff lesions with shoulder stiffness. We analyzed expressions of IL‐1β, IL‐6, and TNF‐α in subacromial bursa and joint fluid collected from 14 patients with cuff tears with stiffness as a study group (Group I) and 14 patients with rotator cuff tears without shoulder stiffness as a control group (Group II) using real‐time RT‐PCR, immunohistochemistry, and ELISA. Myofibroblast apoptosis in subacromial bursa was analyzed using terminal deoxynucleotidyl transferase ‐mediated deoxyuridine triphosphate‐biotin nick end‐labeling (TUNEL) and α‐smooth muscle actin immunofluorescence staining. Shoulder function was evaluated using the Constant score. Group I had higher mRNA expression (p < 0.001) and immunoreactivities (p < 0.001) of IL‐1β. They also had higher levels of IL‐1β, IL‐6, and TNF‐α in joint fluid. Increased IL‐1β mRNA expression in the subacromial bursa and IL‐1β levels in joint fluid were correlated with a preoperative deficit in shoulder motion (p < 0.001) and preoperative Constant scores (p < 0.001). Immunofluorescence observations showed that Group I subjects had more myofibroblasts (p < 0.001) than Group II. In Group II, a significant correlation was found between apoptotic myofibroblasts and total myofibroblasts (p = 0.002), but not in Group I (p = 0.510). Increased expression of IL‐1β and myofibroblast recruitment in the subacromial bursa in rotator cuff lesions are linked to shoulder stiffness. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:1090–1097, 2008
Chemotransport contributes to the effect of oscillatory fluid flow on human bone marrow stromal cell proliferation
Authors: Riddle Ryan C. , Hippe Karen R. , Donahue Henry J.
Published: March 2008

Mechanical loads produce a diverse set of biophysical signals that may regulate bone cell activity, but accumulating evidence suggests that interstitial fluid flow is the primary signal that bone cells perceive. Because we previously demonstrated that oscillatory fluid flow increases human bone marrow stromal cell proliferation, we investigated the contribution of fluid shear stress and chemotransport, two stimuli induced by interstitial fluid flow. Alterations in flow rate at a constant peak shear stress were associated with decreases in oscillatory fluid flow‐induced marrow stromal cell proliferation, while variations in peak fluid shear stress had no significant effect. Modulation of marrow stromal cell proliferation by flow rate may be attributed to changes in the release of ATP and intracellular calcium signaling. We found that if the flow rate is decreased while maintaining a constant peak fluid shear stress, marrow stromal cells release less ATP into the extracellular environment. Moreover, as the flow rate decreased fewer cells respond to fluid flow with an increase in intracellular calcium concentration. These data suggest that chemotransport is a prerequisite for marrow stromal cells to respond to interstitial fluid flow. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:918–924, 2008
A computerized analysis‐by‐synthesis algorithm improves precision of linear wear measurements in total hip replacements
Authors: Dora Claudio , Burckhardt Kathrin , Székely Gábor , Rousson Valentin , Hodler Juerg , Gerber Christian
Published: March 2008

Precision is important if small polyethylene wear rates are to be detected early and in small sample sizes. Using an automatic, computerized algorithm relying on a synthetic X‐ray generated from a computer‐assisted design (CAD) model of the implant may significantly improve precision of linear wear measurements. We compared this method to provide improved in vivo precision compared to the widely used Hip Analysis Suite™ software (version 8.0.1.7). Two anterior–posterior pelvic X‐rays were taken on the same day of 18 total hip implants, and wear was measured by three observers using the two methods. Expected real wear was zero and defined as a reference value. Two sources of variability were estimated: one due to the instrument, and one due to different operators. A Wilcoxon Signed Rank Test was used for statistical comparisons. The overall precision (instrument variability and multioperator variability) given a 95% precision limit was significantly higher (p < 0.001) using the proposed method (±0.15 mm) when compared to the Hip Analysis Suite (±0.84 mm). Due to the availability of the full CAD data of the implant and to further automation of the measuring process, the newly proposed method provided improved precision in measuring polyethylene wear. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:1121–1126, 2008
Generating ultrafilters in a reasonable way
Authors: Rosłanowski Andrzej , Shelah Saharon
Published: March 2008

We continue investigations of reasonable ultrafilters on uncountable cardinals defined in Shelah [8]. We introduce a general scheme of generating a filter on λ from filters on smaller sets and we investigate the combinatorics of objects obtained this way. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On countable choice and sequential spaces
Authors: Gutierres Gonçalo
Published: March 2008

Under the axiom of choice, every first countable space is a Fréchet‐Urysohn space. Although, in its absence even ℝ may fail to be a sequential space.

Our goal in this paper is to discuss under which set‐theoretic conditions some topological classes, such as the first countable spaces, the metric spaces, or the subspaces of ℝ, are classes of Fréchet‐Urysohn or sequential spaces.

In this context, it is seen that there are metric spaces which are not sequential spaces. This fact raises the question of knowing if the completion of a metric space exists and it is unique. The answer depends on the definition of completion.

Among other results it is shown that: every first countable space is a sequential space if and only if the axiom of countable choice holds, the sequential closure is idempotent in ℝ if and only if the axiom of countable choice holds for families of subsets of ℝ, and every metric space has a unique $ \hat \sigma $‐completion. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Nutritional concerns in pediatric inflammatory bowel disease patients
Authors: Kappelman Michael D. , Bousvaros Athos
Published: March 2008

In approximately one‐fourth of patients with Crohn's disease (CD) and ulcerative colitis (UC), disease onset occurs during childhood and adolescence. In addition to gastrointestinal and extraintestinal symptoms of inflammatory bowel disease (IBD), children with these conditions often experience one or more nutritional complications of their disease including growth failure, delayed puberty, osteoporosis, anemia, and micronutrient deficiencies. This article provides an overview of the epidemiology, pathophysiology, evaluation, and management of selected nutritional complications in pediatric IBD.
Predicting interactions between conventional medications and botanical products on the basis ofin vitroinvestigations
Authors: Markowitz John S. , von Moltke Lisa L. , Donovan Jennifer L.
Published: March 2008

The potential for various natural products to perturb the metabolism and disposition of medications has been recognized for decades. There are numerousin vitroandin vivomethods available to screen botanical products for drug interaction potential. Although many normal volunteer botanical‐drug interaction studies have been performed, clearly,in vitrostudies assessing the potential for drug interactions with various natural products represent the predominant type of published research performed to date. In addition to the recognized limitations ofin vitroscreening methodologies to assess conventional drug interactions, further difficulties emerge when examining botanical products. Primary challenges include assigning hepatic concentrations and accounting for bioavailability, distribution, first‐pass metabolism and active metabolites. Additionally, variability in the chemical composition of commercially available botanical supplements, the lack of analytical standards and the inability to accurately screen the entities as mixtures add to complexities in experimental design. This mini‐review is intended to address the particular problems and challenges in evaluating botanical supplements usingin vitromethods, and review what can and cannot be learned from such investigations.
Time‐course regulation of quercetin on cell survival/proliferation pathways in human hepatoma cells
Authors: Granado‐Serrano Ana Belén , Angeles Martín María , Bravo Laura , Goya Luis , Ramos Sonia
Published: March 2008

Quercetin, a dietary flavonoid, has been shown to possess anticarcinogenic properties, but the precise molecular mechanisms of action are not thoroughly elucidated. This study was aimed at investigating the time‐course regulation effect of quercetin on survival/proliferation pathways in a human hepatoma cell line (HepG2). Quercetin induced a significant time‐dependent inactivation of the major survival signaling proteins, i. e., phosphatidylinositol 3‐kinase (PI 3‐kinase)/protein kinase B (AKT), extracellular regulated kinase (ERK), protein kinase C‐α (PKC‐α), in concert with a time‐dependent activation of key death‐related signals: c‐jun amino‐terminal kinase (JNK) and PKC‐δ. These data suggest that quercetin exerts a tight regulation of survival/proliferation pathways that requires the integration of different signals and persists over time, being the balance of these regulatory signals what determines the fate of HepG2 cells.
Carbon‐13 NMR of fluorocyclopropanes
Authors: Brey Wallace S.
Published: March 2008

Carbon‐13 and hydrogen NMR data are presented for several cyclopropanes with one to four fluorine atoms attached to the ring. Substituents directly attached to a ring carbon are found to unshield that carbon to an extent increasing with their electronegativity, but remote substituents may have an opposite effect. Relative orientation of the substituent groups, especially if they are bulky, also has a strong influence on the ring‐carbon shifts. Chemical shifts of carbons in methyl groups attached to the ring change to an extent which is additive in the effects of gem and cis substituents. One‐bond coupling of ring carbons with fluorines is affected both by geminal and vicinal substituents, in a way generally related to their electronegativity. It is tentatively concluded that two‐bond coupling between ring carbons and ring‐attached fluorines depends in magnitude primarily on what groups are cis to the fluorine. Two‐bond coupling between a carbon atom in a ring‐attached methyl and the hydrogen gem to the methyl appears to be vanishingly small, but there is appreciable three‐bond coupling of the methyl carbons to vicinal hydrogens. Copyright © 2008 John Wiley & Sons, Ltd.
Complete assignments of 1H and 13C NMR spectral data for three polyhydroxylated 12‐ursen‐type triterpenoids from Dischidia esquirolii
Authors: Ma Xiaoxia , Yang Chongren , Zhang Yingjun
Published: March 2008

The complete assignments of all the 1H and 13C NMR signals of three polyhydroxylated 12‐ursen‐type triterpenes, 6β,19α,22α‐trihydroxyurs‐12‐en‐3‐oxo‐28‐oic acid (1), 3β,6α,19α,23‐tetrahydroxyurs‐12‐en‐28‐ oic acid (2) and 3β,6β,19α,23‐tetrahydroxyurs‐12‐en‐28‐oic acid (3), were carried out by means of homo‐ and hetero‐nuclear two‐dimensional NMR experiments. Compounds 1–3 were isolated from the aerial parts of Dischidia esquirolii. Of them, 1 and 2 were identified as new polyhydroxylated ursolic acid derivatives. Compound 2 is the C‐6 hydroxyl epimer of 3, which was isolated first from Adina rubella, and its structure is revised in this paper. Copyright © 2008 John Wiley & Sons, Ltd.
Predictive differential equations
Authors: Ohira Toru
Published: March 2008

We propose and study a differential equation whose dynamics are governed by predictions of its future states. General formalism and concrete examples are presented. We find that the dynamical characteristics depend on both how to shape predictions as well as how far ahead in time to make them. This can be thought of one of examples of dynamical complexity caused by a temporal non‐locality. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Memory effects and ergodicity for diffusion in spatially correlated velocity fields
Authors: Suciu Nicolae , Sabelfeld Karl , Vamoş Călin , Andronache Constantin
Published: March 2008

We show that the process of diffusion in statistically homogeneous velocity fields with finite correlation range “remembers” the shape and the orientation of the source over hundreds of dimensionless times and behaves ergodically with respect to the one‐particle dispersion only asymptotically. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Simulation and solution of stochastic systems with a component‐based software design
Authors: Krosche Martin , Hautefeuille Martin
Published: March 2008

Often uncertainties occur in the numerical simulation of real‐world problems. A useful method is stochastic modelling. In this context Monte Carlo (MC) methods and the stochastic Galerkin method are well known and frequently used. In the field of component‐based software systems a component can be seen as an independent software or as a part of a software system. A corresponding architecture allows clearness, flexibility and reusability. The Component Template Library (CTL) is a so called middleware to realise component‐based software systems, and fits to the requirements of scientific computing.

In this paper we present the design of a software system for the stochastic simulation using MC and stochastic Galerkin methods based on the CTL. For each stochastic method a number of components are realised to allow parallel features. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Large scale depletion of the high‐abundance proteins and analysis of middle‐ and low‐abundance proteins in human liver proteome by multidimensional liquid chromatography
Authors: Gao Mingxia , Deng Chunhui , Yu Wenjia , Zhang Yang , Yang Pengyuan , Zhang Xiangmin
Published: March 2008

An unbiased method for large‐scale depletion of high‐abundance proteins and identification of middle‐ or low‐abundance proteins by multidimensional LC (MDLC) was demonstrated in this paper. At the protein level, the MDLC system, coupling the first dimensional strong cation exchange (SCX) chromatography with the second dimensional RP‐HPLC, instead of immunoaffinity technology, was used to deplete high‐abundance proteins. Sixty‐two fractions from SCX were separated further by RPLC. UV absorption spectra were observed to differentiate high‐abundance proteins from middle‐ or low‐abundance proteins. After the depletion of high‐abundance proteins, middle‐ or low‐abundance proteins were enriched, digested, and separated by online 2D‐micro‐SCX/cRPLC. The eluted peptides were deposited on the MALDI target and detected by MALDI‐TOF/TOF MS. This depletion strategy was applied to the proteome of the normal human liver (NHL) provided by the China Human Liver Proteome Project (CHLPP). In total, 58 high‐abundance proteins were depleted in one experiment. The strategy increases greatly the number of identified proteins and around 1213 proteins were identified, which was about 2.7 times as that of the nondepletion method.
Identification by 2‐D DIGE of apoplastic proteins regulated by oligogalacturonides in Arabidopsis thaliana
Authors: Casasoli Manuela , Spadoni Sara , Lilley Kathryn S. , Cervone Felice , De Lorenzo Giulia , Mattei Benedetta
Published: March 2008

Oligogalacturonides (OGs) are elicitors of plant defence responses released from the homogalacturonan of the plant cell wall during the attack by pathogenic micro‐organisms. The signalling pathway mediated by OGs remains poorly understood, and no proteins involved in their signal perception and transduction have yet been identified. In order to shed light into the molecular pathways regulated by OGs, a differential proteomic analysis has been carried out in Arabidopsis. Proteins from the apoplastic compartment were isolated and their expression compared between control and OG‐treated seedlings. 2‐D gels and difference in gel electrophoresis (DIGE) techniques were used to compare control and treated proteomes in the same gel. The analysis of subcellular proteomes from seedlings allowed the identification of novel and low abundance proteins that otherwise remain masked when total cellular extracts are investigated. The DIGE technique showed to be a powerful tool to overcome the high interexperiment variation of 2‐D gels. Differentially expressed apoplastic proteins were identified by MS and included proteins putatively involved in recognition as well as proteins whose PTMs are regulated by OGs. Our findings underscore the importance of cell wall as a source of molecules playing a role in the perception of pathogens and provide candidate proteins involved in the response to OGs.
Temporal variations of the postnatal rat urinary proteome as a reflection of systemic maturation
Authors: Lee Richard S. , Monigatti Flavio , Lutchman Mohini , Patterson Thomas , Budnik Bogdan , Steen Judith A. J. , Freeman Michael R. , Steen Hanno
Published: March 2008

The rat kidney matures during the first 2 wk of life, suggesting that temporal variations in the urinary proteome may occur during this period. We describe the urine proteome during postnatal development in the rat and demonstrate specific proteomic changes corresponding to developmental milestones. Urine was collected from 30 rats at five postnatal (P) days of life (P1, P3, P7, P14, and >P30) by bladder aspiration. The proteome was assessed by nano‐ESI‐LC‐MS/MS. For identification, we used stringent criteria to provide a 1% false positive rate at the peptide level. The proteins in common at each time interval decreased during postnatal maturation. When comparing all five developmental times, six proteins were ubiquitously present. We detected 14 proteins involved with cellular adhesion, structure, or proliferation and differentiation only during neonatal development. Additionally, 30 proteins were specific to adults, of which 13 originated from the prostate or seminal vesicle. This is the first MS characterization of the normal urinary proteome in early postnatal rodent development that demonstrates distinct differences correlating with different stages of tissue maturation. Further characterization of the normal urinary proteome may provide the basis for identification of urinary biomarkers of diseases of the urinary tract.
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

We 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

Whipple'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

Helicobacter 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

Diabetic 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

It 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

We 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

The 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

Polycrystalline 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

Spectroscopic 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

We 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

We 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

In 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

We 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.