bluuebunny/crossref_metadata_2025 huggingface dataset:
Proteomic studies support the use of multi‐product immunoassays to monitor host cell protein impurities
Authors: Krawitz Denise C. , Forrest William , Moreno G. Tony , Kittleson Joshua , Champion Kathleen M.
Published: November 2005

In the biopharmaceutical industry, recombinant protein drugs are commonly produced in Chinese hamster ovary (CHO) cells. During the development process, removal of CHO cell‐derived proteins from the biopharmaceutical product is monitored using multi‐product immunoassays. Such immunoassays are developed by raising antibodies to a single CHO cell protein preparation. However, these assays are utilized to monitor CHO cell protein impurities during the recovery of products from different CHO cell lines. To address whether underlying differences between CHO cell lines result in sufficient protein expression changes to exclude the suitability of multi‐product immunoassays, a comparative proteomics study of three independently generated CHO cell lines was performed. Statistical analysis of over 1000 proteins resolved by 2‐D PAGE demonstrated that the protein expression profiles of three different CHO cell lines exhibit very few differences in protein expression. Only 11 qualitative changes in protein expression and 26 quantitative changes greater than two‐fold were observed. Identification of protein spots by mass spectrometry revealed that many of the observed changes were due to post‐translational modifications rather than expression of novel proteins in each cell line. These results suggest that multi‐product immunoassays are suitable for monitoring host cell proteins in biopharmaceuticals produced in different CHO cell lines.
2‐D protein maps of rat gastrocnemius and soleus muscles: A tool for muscle plasticity assessment
Authors: Gelfi Cecilia , Viganò Agnese , De Palma Sara , Ripamonti Marilena , Begum Shajna , Cerretelli Paolo , Wait Robin
Published: November 2005

Functional characterization of muscle fibers relies on ATPase activity and on differential measurements of metabolic proteins, including mitochondrial and glycolytic enzymes, glucose, lactate and lactic acid transporters, calcium cycling proteins and components of the contractile machinery. The recent introduction of microarray technology has enabled detailed gene expression studies under different physiological and pathological conditions, thus generating novel hypotheses on muscle function. However, microarray approaches are limited by the incomplete genome coverage of currently available chips, and by poor correlation between mRNA concentration and protein expression level. We have used 2‐DE and MS to build a reference map of proteins from rat mixed gastrocnemius and soleus muscle, and to assess qualitative and quantitative differences in protein distribution between these two functionally dissimilar muscles. More than 800 spots on each gel were detected by silver staining, of which 167 were excised, digested in‐gel with trypsin and analyzed by ESI‐MS/MS. One hundred and twenty eight distinct gene products were identified, including metabolic, transport and contractile proteins. Forty one spots displayed differences in relative expression level between mixed gastrocnemius and soleus samples. These data not only enable differentiation of functionally distinct slow‐twitch and fast‐twitch fiber types, but also provide tools for investigating muscle plasticity in response to physiological and environmental conditions such as aging or hypoxia.
Cancer‐related beliefs and health behavior change among breast cancer survivors and their first‐degree relatives
Authors: Rabin Carolyn , Pinto Bernardine
Published: November 2005

It is unclear why some cancer survivors and their relatives are motivated by the (personal or vicarious) cancer experience to make positive health behavior changes while others are not. Consistent with Leventhal's Commonsense Model, we hypothesized that breast cancer survivors and their first‐degree relatives (FDRs) would change behaviors they believed: (1) had caused the survivor's cancer or (2) could prevent a future cancer incidence. Sixty‐five breast cancer survivors (stages 0–III) and 33 FDRs were recruited. Assessments occurred within three months of the survivor completing treatment (i.e. all surgery, chemotherapy, and radiation) and again three months later. Findings indicate that survivors who believed that unhealthy diet, insufficient exercise, or alcohol consumption contributed to their cancer were more likely to modify the relevant behavior. Likewise, survivors were more likely to implement healthy changes they believed would ward off a recurrence. Findings were similar when data from FDRs was added to the sample. Thus, healthy lifestyle changes after a personal (and possibly a vicarious) cancer diagnosis are tied to whether individuals believe changes can affect cancer outcomes. Given the role of health behavior change in reducing medical risks, these findings have important implications for maintaining the health of cancer survivors. Copyright © 2005 John Wiley & Sons, Ltd.
Requests for information by family and friends of cancer patients calling the National Cancer Institute's Cancer Information Service
Authors: Rutten Lila J. Finney , Squiers Linda , Treiman Katherine
Published: November 2005

Purpose: To characterize their information needs, we examined the main topics of inquiry and discussion (subjects of interaction, SOI) of calls made by family and friends of cancer patients to the National Cancer Institute's Cancer Information Service's (CIS) 1‐800‐4‐CANCER telephone information service and summarized differences by sociodemographic characteristics.

Design and analysis: Data from 26 789 family or friends of cancer patients calling the CIS between September 2002 and August 2003 were analyzed. Frequencies, χ2's, and logistic regressions were conducted to ascertain sample characteristics and sociodemographic correlates of each SOI.

Results and conclusions: The greatest proportion of calls concerned specific treatment information (54.9%) and general cancer site information (36.9%). Calls about specific treatment information were more likely among Asians, Hawaiian Natives, and Pacific Islanders (OR=1.23, 1.04–1.45), and those with higher education (OR=1.21, 1.18–1.25). As age increased, the odds of calls about specific treatment information also increased (OR=1.05, 1.03–1.07). Females (OR=0.78, 0.72–0.84), Hispanics (OR=0.77, 0.67–0.89), African‐Americans (OR=0.68, 0.61–0.76), and American‐Indians and Alaskan Natives (OR=0.74, 0.58–0.93) were less likely to inquire about specific treatment information. Inquiries about general cancer site information were more likely among females (OR=1.14, 1.06–1.23) and less likely among younger callers (OR=0.95, 0.93–0.97) and African‐Americans (OR=0.87, 0.78–0.98). Differences in inquiries made by sociodemographic subgroups can inform the CIS' and other cancer‐related organizations' efforts to develop and disseminate cancer information for family and friends of cancer patients. Copyright © 2005 John Wiley & Sons, Ltd.
Pulmonary Tuberculosis in a Child Presenting with Acute Hemoptysis
Authors: Teeratakulpisarn Jamaree , Srinakarin Jiraporn , Tontisirin Cherdchai , Lumbiganon Pagakrong , Mitchai Jumphol
Published: November 2005

We report on a tuberculous child whose only presenting symptom was acute hemoptysis. His chest radiograph revealed a mass‐like lesion occupying the posterior basal segment of the right lower lung field. Multidetector computerized tomography (MDCT) of the chest showed a hypodense mass supplied by the bronchial artery and drained by the pulmonary vein. Surgical specimens revealed caseating granulomatous inflammation, positive for acid‐fast bacilli. The child was successfully treated with a short‐course (6‐month) regimen of antituberculous drugs. Pediatr Pulmonol. © 2005 Wiley‐Liss, Inc.
A preliminary analysis and model of prostate injection distributions
Authors: Chowning Scott L. , Susil Robert C. , Krieger Axel , Fichtinger Gabor , Whitcomb Louis L. , Atalar Ergin
Published: November 2005

PURPOSE

Understanding the internal dynamics of prostate injections, particularly injection pattern distribution is a key step to developing new therapies for prostate disease that may be best served with a direct injection approach. Due to excellent properties involving liquid contrast agents, MRI can be used for targeting and monitoring of injections into organs and tissues.

MATERIALS AND METHODS

Eleven intraprostatic injections were performed in vivo with canines using a custom transrectal guiding and imaging system for use in a standard 1.5 T MR scanner. In addition, 25 injections were performed on excised cadaveric human prostates, using a MedRad Spectris™ injector system. MRI was used to guide the injections and monitor intraparenchymal injection distribution.

RESULTS

T1 and T2‐weighted MR images were correlated with histology to produce three‐dimensional data sets that can be used to analyze trends in injection patterns. This analysis was used to develop strategies for injection prediction such as gadolinium preinjections and diffusion‐weighted imaging guidance. In addition, a rough model of prostate injections is described, and a preliminary injection guide is developed that takes into account the individual clinician's goals for therapy.

CONCLUSIONS

MR visualization of injected therapeutic agents allows for prediction and monitoring of drug distributions, possibly improving efficacy and reducing side effects. Injection analysis and modeling may be used to assist in optimizing clinical treatments that require or would benefit from focal parenchymal injections into the prostate. © 2005 Wiley‐Liss, Inc.
Polymorphisms in genes involved in sex hormone metabolism may increase risk of benign prostatic hyperplasia
Authors: Roberts Rosebud O. , Bergstralh Erik J. , Farmer Sara A. , Jacobson Debra J. , Hebbring Scott J. , Cunningham Julie M. , Thibodeau Stephen N. , Lieber Michael M. , Jacobsen Steven J.
Published: November 2005

Background

This study investigates associations between polymorphisms in genes involved in sex hormone metabolism and measures of benign prostatic hyperplasia (BPH).

Methods

Community‐dwelling Caucasian men (n = 510, median age 60 years in 2000) from the Olmsted County, MN, participated in a longitudinal study of BPH. From 1990 through 2000, urologic measures of BPH were assessed biennially from lower urinary tract symptom severity, peak flow rates, prostate volume, serum prostate specific antigen (PSA) level, acute urinary retention, and treatment for BPH. Men were genotyped for polymorphisms in genes involved in sex hormone metabolism.

Results

With the wildtype genotype as reference, men with HSD3B1 (c.1100 A/C) heterozygous genotype (hazard ratio (HR) = 0.7, 95% confidence intervals (CI) = 0.6, 0.9) were at decreased risk of an enlarged prostate and men with CYP19 (TTTA)n genotype homozygous for ≥175 TTTA repeats (HR = 1.5, 95% CI = 1.1, 2.1), and CYP19 (c.1531 C/T) homozygous T variant (HR = 1.6, 95% CI = 1.1, 2.2) were at increased risk of an enlarged prostate. The homozygous A variant of the PSA gene (g.‐252 G/A), was associated with treatment for BPH (HR = 2.3, 95% CI = 1.2, 4.4). In multivariate analyses, the homozygous variant genotypes of AKR1C3 (c.15 G/A and c.90 G/A) were associated with a decreased risk of an enlarged prostate (HR = 0.56, 95% CI = 0.35, 0.90 and HR = 0.57, 95% CI = 0.33, 0.98).

Conclusions

Polymorphisms in HSD3B1, CYP19, AKR1C3 genes may be associated with an enlarged prostate in older men. These data provide insights into genes that should be examined further for their potential role in the pathogenesis of BPH. © 2005 Wiley‐Liss, Inc.
Allelotyping analysis at chromosome 13q of high‐grade prostatic intraepithelial neoplasia and clinically insignificant and significant prostate cancers
Authors: Lu Wei , Takahashi Hiroyuki , Furusato Masakuni , Maekawa Suguru , Nakano Masataka , Meng Chenxi , Kikuchi Yasushi , Sudo Akemi , Hano Hiroshi
Published: November 2005

BACKGROUND

Loss of heterozygosity (LOH) at 13q is one of the most common chromosomal alterations in high‐stage prostate cancer, yet little is known about genetic changes in earlier‐stage prostate cancer.

METHODS

We used five microsatellite markers at 13q14, 21, and 33 to compare LOH frequencies in 51 lesions of high‐grade prostatic intraepithelial neoplasia (HGPIN), 21 cases of incidental prostate cancers (IPCs), 31 cases of latent prostate cancers (LPCs), and 102 cases of clinical prostate cancers (CPCs).

RESULTS

The frequency of LOH at 13q with at least 1 marker was 0%, 38%, 56%, and 49% in HGPIN, IPCs, LPCs, and CPCs, respectively. No statistically significant difference was found between the types of prostate cancer. Allelic loss at 13q14 was significantly more frequent in pT4 tumors than in earlier‐stage tumors (P = 0.011).

CONCLUSIONS

Allelic loss at 13q is not only an important event in the metastasis of prostate cancer, but also associated with the initiation of the tumor. © 2005 Wiley‐Liss, Inc.
The androgen receptor pathway is by‐passed in prostate cancer cells generated after prolonged treatment with bicalutamide
Authors: Hobisch Alfred , Fritzer Andreas , Comuzzi Barbara , Fiechtl Matthias , Malinowska Kamilla , Steiner Hannes , Bartsch Georg , Culig Zoran
Published: November 2005

Background

Experimental work in various prostate cancer models revealed that the androgen receptor is frequently upregulated and implicated in tumor progression. However, little attention has been paid to the androgen receptor‐signaling pathway in the development of therapy resistance in patients who receive chronic treatment with a non‐steroidal anti‐androgen.

Methods

We have generated a novel subline, LNCaP‐Bic, after prolonged treatment with androgen and bicalutamide in vitro. Proliferation of LNCaP‐Bic cells in the absence or presence of androgen, tocopherol succinate, and/or bicalutamide was assessed by cell counting. Androgen receptor expression was determined by Western blot. Luciferase activity was measured in cells transfected with an androgen‐responsive reporter.

Results

In basal conditions, proliferation of LNCaP‐Bic cells increased more than threefold over that of control LNCaP cells. Neither synthetic androgen R1881 nor bicalutamide showed any effect on LNCaP‐Bic growth in vitro. Androgen receptor expression did not differ between the cell subline generated in the presence of bicalutamide and parental LNCaP cells. The ability of R1881 to induce reporter gene activity in LNCaP‐Bic cells was reduced by 56%. Tocopherol succinate caused inhibition of proliferation only in the parental cell line although the androgen receptor and prostate‐specific antigen were downregulated by the vitamin E derivative in both parental LNCaP and LNCaP‐Bic cells.

Conclusions

Androgen receptor‐mediated signal transaction is not enhanced in cells selected in the presence of bicalutamide. Our data may suggest that a more differentiated approach in targeting the androgen receptor is needed in prostate cancers that become resistant to classic endocrine treatment. © 2005 Wiley‐Liss, Inc.
An architectural pattern for designing component‐based application frameworks
Authors: Parsons David , Rashid Awais , Telea Alexandru , Speck Andreas
Published: November 2005

A widely used architecture for the development of software systems is the component‐based application framework. Such frameworks offer two mechanisms. First, they provide component integration and interoperability services which make it possible to extend the framework with various third‐party components. Second, they provide mechanisms to customize the integrated components to the specific needs of applications to be built using the framework. This paper describes an architectural pattern for designing such frameworks so that the appropriate mix of fixed and flexible elements can be integrated into architectures that maximize scalability and extensibility. The pattern is illustrated by frameworks developed for three different application domains: electronic design automation, scientific visualization and numerical simulation, and industrial control systems. Copyright © 2005 John Wiley & Sons, Ltd.
Applying a framework for the improvement of software process maturity
Authors: Canfora Gerardo , García Félix , Piattini Mario , Ruiz Francisco , Visaggio C. A.
Published: November 2005

This article presents the results and lessons learned in the application of the Framework for the Modelling and Measurement of Software Processes (FMESP) in a software company dedicated to the development and maintenance of software for information systems. The aim of FMESP is to provide companies with a conceptual and technological framework for the management of their process models and measurement models in an integrated way. Modelling and measurement are two key factors to promote continuous process improvement. As a result, important benefits were obtained. The company improved the maturity of its processes which allowed it to obtain the ISO 9000 certification. From a research point of view, Action‐Research was successfully applied and as a result the framework was improved and important feedback was obtained, bringing to light new important issues which will be tacked in future work. Copyright © 2005 John Wiley & Sons, Ltd.
Adenovirus‐mediated expression of the C‐terminal domain of SARS‐CoV spike protein is sufficient to induce apoptosis in Vero E6 cells
Authors: Chow Ken Y.C. , Yeung Yin Shan , Hon Chung Chau , Zeng Fanya , Law Ka Man , Leung Frederick C.C.
Published: November 2005

The pro‐apoptotic properties of severe acute respiratory syndrome coronavirus (SARS‐CoV) structural proteins were studied in vitro. By monitoring apoptosis indicators including chromatin condensation, cellular DNA fragmentation and cell membrane asymmetry, we demonstrated that the adenovirus‐mediated over‐expression of SARS‐CoV spike (S) protein and its C‐terminal domain (S2) induce apoptosis in Vero E6 cells in a time‐ and dosage‐dependent manner, whereas the expression of its N‐terminal domain (S1) and other structural proteins, including envelope (E), membrane (M) and nucleocapsid (N) protein do not. These findings suggest a possible role of S and S2 protein in SARS‐CoV induced apoptosis and the molecular pathogenesis of SARS.
Modulation of p53 expression and its role in the conversion to a fully immortalized chicken embryo fibroblast line
Authors: Christman Shelly A. , Kong Byung-Whi , Landry Megan M. , Kim Hyunggee , Foster Douglas N.
Published: November 2005

We have established a spontaneously immortalized chicken embryo fibroblast (CEF) cell line (SC‐1) that has been in continuous culture for more than three years. This is only the second report of a spontaneously immortalized reverse transcriptase (RT)‐negative chicken cell line. The SC‐1 cells emerged from crisis (at about passage 29–31) with a slower growth rate than primary cells. Passage 50 SC‐1 cells expressed similar levels of p53 mRNA, but slightly lower levels of p53 protein than passage 6 CEF cells. By passage 120, p53 mRNA levels were significantly decreased in the SC‐1 cells, while protein levels were slightly increased compared to passage 6 CEF cells. However, functional analysis of p53 revealed reduced activity in later passage SC‐1 cells. Other p53‐related genes including p21WAF1, p27Kip1, MDM‐2, and the p16INK4a alternate reading frame (ARF) sequence showed similar patterns of differential mRNA expression. Levels of p15INK4b mRNA and protein were dramatically decreased in SC‐1 cells, suggesting that the Rb pathway also has been compromised. Telomerase expression was undetectable in SC‐1 cells. Fluorescence‐activated cell sorting analysis showed that SC‐1 and primary cells contained a similar proportion of G0/G1 phase cells, unlike the only other spontaneously immortalized chicken cell line (DF‐1). The present study suggests that alterations in the p53 and Rb pathways cause fluctuations in expression levels of important cell‐cycle regulatory genes during crucial transition periods as the SC‐1 spontaneously immortalized chicken fibroblast cells progress toward becoming a fully committed cell line.
Transgenic potato expressing Aβ reduce Aβ burden in Alzheimer's disease mouse model
Authors: Youm Jung Won , Kim Hee , Han Jee Hye Lo , Jang Chang Hwan , Ha Hee Jin , Mook-Jung Inhee , Jeon Jae Heung , Choi Cheol Yong , Kim Young Ho , Kim Hyun Soon , Joung Hyouk
Published: November 2005

Beta amyloid (Aβ) is believed one of the major pathogens of Alzheimer's disease (AD), and the reduction of Aβ is considered a primary therapeutic target. Immunization with Aβ can reduce Aβ burden and pathological features in transgenic AD model mice. Transgenic potato plants were made using genes encoding 5 tandem repeats of Aβ1–42 peptides with an ER retention signal. Amyloid precursor protein transgenic mice (Tg2576) fed with transgenic potato tubers with adjuvant showed a primary immune response and a partial reduction of Aβ burden in the brain. Thus, Aβ tandem repeats can be expressed in transgenic potato plants to form immunologically functional Aβ, and these potatoes has a potential to be used for the prevention and treatment of AD.
Molecular insights into the mechanism of ATP‐hydrolysis by the NBD of the ABC‐transporter HlyB
Authors: Hanekop N. , Zaitseva J. , Jenewein S. , Holland I.B. , Schmitt L.
Published: November 2005

The ABC‐transporter HlyB is a central element of the Type I protein secretion machinery, dedicated to export the E. coli toxin HlyA in a single step across the two membranes of the cell envelope. Here, we discuss recent insights into the structure and the mechanism of ATP‐hydrolysis by the NBD of HlyB. Combining structural and biochemical data, we have suggested that substrate‐assisted catalysis (SAC), but not general base catalysis, is responsible for ATP‐hydrolysis in this NBD and might also operate in other NBDs. Finally, the implications and advantages of SAC are discussed in the context of ATP‐induced dimerization of the NBDs.
The cysteine‐desulfurase IscS promotes the production of the rhodanese RhdA in the persulfurated form
Authors: Forlani Fabio , Cereda Angelo , Freuer Andrea , Nimtz Manfred , Leimkühler Silke , Pagani Silvia
Published: November 2005

After heterologous expression in Escherichia coli, the Azotobacter vinelandii rhodanese RhdA is purified in a persulfurated form (RhdA‐SSH). We identified l‐cysteine as the most effective sulfur source in producing RhdA‐SSH. An E. coli soluble extract was required for in vitro persulfuration of RhdA, and the addition of pyridoxal‐5′‐phosphate increased RhdA‐SSH production, indicating a likely involvement of a cysteine desulfurase. We were able to show the formation of a covalent complex between IscS and RhdA. By combining a time‐course fluorescence assay and mass spectrometry analysis, we demonstrated the transfer of sulfur from E. coli IscS to RhdA.
Psychosocial and demographic factors associated with response to prophylactic lithium. A systematic review for bipolar disorders
Authors: KLEINDIENST N. , ENGEL R. R. , GREIL W.
Published: November 2005

Background. The aim was to systematically integrate the available evidence on psychosocial and demographic factors associated with response prediction to prophylactic lithium.

Method. Each psychosocial or demographic variable that was related to lithium response in at least one study was examined with respect to response prediction. If several studies were located for the same variable results were integrated using a meta-analytical approach. To account for heterogeneity of primary studies aggregation of results was based on a random-effects model.

Results. Out of 27 psychosocial and demographic variables investigated in this review, nine variables were identified as significantly related to outcome under to prophylactic lithium: (1) high social status, (2) social support, (3) good compliance, and (4) dominance may be protective against a recurrence under lithium. In contrast, (5) stress, (6) high expressed emotions, (7) neurotic personality traits, (8) unemployment, and (9) a high number of life events were identified as possible risk factors for poor response.

Conclusions. This systematic review shows a surprisingly high number of psychosocial variables to be related to lithium response. Effect sizes were, however, small to moderate. Many variables should, therefore, be considered simultaneously to predict response.
Applying the Clark-Wells Model of Social Phobia to Children: The Case of a “Dictation Phobia”
Authors: Ahrens-Eipper Sabine , Hoyer Jürgen
Published: November 2005

A specific type of social phobia – dictation phobia – was the main and unusual treatment problem in the cognitive-behavioural therapy for an 11-year-old schoolboy. For case formulation and treatment rationale, the social phobia model by Clark and Wells was used. The posttreatment assessment revealed clear positive treatment effects with respect to school grades, social anxiety and overall functioning. The model's applicability for children and adolescents is discussed.
Bisphosphonates and the prevention of osteoporosis in the adjuvant setting
Authors: Gnant Michael
Published: November 2005

Endocrine adjuvant therapy for breast cancer has been associated with a decrease in bone mineral density (BMD) and bone loss. For aromatase inhibitors, this bone loss is likely to be the most significant limitation to their long-term use. Treatments traditionally used to counteract his effect include exercise and supplementation with calcium and vitamin D. A newer treatment is the use of bisphosphonates, a class of drugs that reduce osteoclast activity. Clinical trials currently underway to examine the effect of bisphosphonate treatment on breast cancer patients have shown improvement in bone strength. Additional benefits of bisphosphonates, currently under study, give this class of drugs an important role to play in the treatment of cancer treatment-induced bone loss.
Breast cancer, stem cells, and the stem cell niche
Authors: Chepko G.
Published: November 2005

At least four cell types in mouse mammary epithelium, three in human, and three in cow are now known to be proliferation competent. Some evidence indicates that pregnancy may confer proliferative competency on a new cell type. These cells are widely seen as stem and progenitor cells that maintain the epithelium and produce lactational units during pregnancy. Evolutionarily conserved developmental signaling pathways active in germinal and neuronal stem cell proliferation and differentiation in drosophila and mammalian development are implicated in mammary tumorigenesis. In adult tissues this signaling is retained, is regulated by stem cell niches and operates to create new tissue and maintain tissue form and integrity. Disruption of this signaling may abrogate maintenance of the stem cell niche and lead to preneoplastic conditions.
Atmospheric pressure loading corrections applied to GPS data at the observation level
Authors: Tregoning P. , van Dam T.
Published: November 2005

Space‐geodetic techniques can detect elastic deformation of the Earth caused by atmospheric pressure loading (ATML). However, it has not yet been demonstrated whether these surface displacements should be accounted for at the time of reduction of the observations or by applying time‐averaged values to the coordinates after the analysis of the observations. An analysis of the power spectral density of the ATML predicted vertical deformation shows that, aside from the diurnal and semi‐diurnal periods, there is very little power in the sub‐daily frequencies. The present tidal ATML models improve the analysis at sites near the equator but seem to degrade the height estimates elsewhere. The majority of the non‐tidal deformation can be modelled by applying a daily‐averaged correction to daily estimates of coordinates but a greater improvement in height RMS is found if non‐tidal ATML is applied at the observation level.
Cool‐skin simulation by a one‐column ocean model
Authors: Tu Chia‐Ying , Tsuang Ben‐Jei
Published: November 2005

A one‐column ocean model is used to simulate the cool‐skin effect of sea surface temperatures. Four schemes for determining the thickness of the cool skin are compared. It is established that all four schemes can capture the cool skin for wind speeds ≤ 7.5 m s−1; however, for wind speeds > 7.5 m s−1, Artale et al.'s (2002) scheme performs better. This study demonstrates that the cool‐skin effect can be reproduced by the one‐column model, while a proper vertical resolution in the top 1 mm is embedded.
On the generation of enhanced sunward convection and transpolar aurora in the high‐latitude ionosphere by magnetic merging
Authors: Eriksson S. , Baker J. B. H. , Petrinec S. M. , Wang H. , Rich F. J. , Kuznetsova M. , Dunlop M. W. , Rème H. , Greenwald R. A. , Frey H. U. , Lühr H. , Ergun R. E. , Balogh A. , Carlson C. W.
Published: November 2005

The IMAGE Wideband Imaging Camera (WIC) instrument observed the duskside development of an oval‐aligned transpolar auroral arc (TPA) in the Northern Hemisphere (NH) on 16 December 2001 during strong IMF ∣B∣ ∼ 18 nT and a generally steady ∼56° clock angle (positive IMF By and Bz). Observational evidence suggests that the dayside part of the duskside TPA formed due to quasi‐continuous merging between the IMF and the lobe magnetic field tailward of the cusp while the nightside part is associated with the Harang discontinuity. The low‐altitude CHAMP satellite confirms an upward northward IMF Bz (NBZ) field‐aligned current (FAC) over the dayside TPA while associating a downward NBZ current with the region of diminished WIC emissions in between the auroral oval and the TPA. DMSP F14 suggests that the dayside region of the downward NBZ current coincides with precipitating magnetosheath‐like ions of reversed energy‐latitude dispersion consistent with high‐latitude reconnection. SuperDARN observes enhanced ionospheric sunward flows generally centered between the oppositely directed NBZ currents. We associate these flows with a clockwise lobe convection vortex and the dayside part of the TPA. The nightside TPA, however, is related to stagnant or antisunward flow and the upward FAC region of the Harang discontinuity. Cluster observations confirm the simultaneous presence of rotational discontinuities across the duskside magnetopause with changes in the magnetosheath plasma velocity that indicate an active merging region poleward of Cluster. A global MHD simulation generates sunward flow between a pair of opposite FACs on either side of a lobe reconnection site near (X, Y, Z)GSM = (−4.7, 5.4, 10.2) RE thus conforming with Cluster and SuperDARN expectations. The sense of these FACs agrees with the low‐altitude NBZ observations.
The non-Markovian quantum master equation in the collective-mode representation: Application to barrier crossing in the intermediate friction regime
Authors: Pomyalov Anna , Tannor David J.
Published: November 2005

The calculation of chemical reaction rates in the condensed phase is a central preoccupation of theoretical chemistry. At low temperatures, quantum-mechanical effects can be significant and even dominant; yet quantum calculations of rate constants are extremely challenging, requiring theories and methods capable of describing quantum evolution in the presence of dissipation. In this paper we present a new approach based on the use of a non-Markovian quantum master equation (NM-QME). As opposed to other approximate quantum methods, the quantum dynamics of the system coordinate is treated exactly; hence there is no loss of accuracy at low temperatures. However, because of the perturbative nature of the NM-QME it breaks down for dimensionless frictions larger than about 0.1. We show that by augmenting the system coordinate with a collective mode of the bath, the regime of validity of the non-Markovian master equation can be extended significantly, up to dimensionless frictions of 0.5 over the entire temperature range. In the energy representation, the scaling goes as the number of levels in the relevant energy range to the third power. This scaling is not prohibitive even for chemical systems with many levels; hence we believe that the current method will find a useful place alongside the existing techniques for calculating quantum condensed-phase rate constants.
Structures and stability of B-doped Al clusters: AlnB and AlnB2 (n=1–7)
Authors: Jiang Zhen-Yi , Yang Cheng-Jun , Li Sheng-Tao
Published: November 2005

Various structural possibilities for AlnBm (n=1–7, m=1–2) neutral isomers were investigated using B3LYP∕6-311G(d) and CCSD(T)∕6-311G(d) methods. Our calculations predicted the existence of a number of previously unknown isomers. The B atom favors to locate over/inside of all clusters in this series. All structures of the AlnB (n=2–7) may be derived from capping/putting a B atom over/inside the Aln cluster. All AlnB2 (n=1–5) may be understood as two substitutions of Al atoms by B atoms in the Aln+2 molecule. The strong B–B bond is a dominant factor in the building-up principle of mixed AlnB2 neutral clusters. The second difference in energy showed that the AlnBm clusters with even n+m are more stable than those with odd n+m. Our results and analyses revealed that the mixed Al–B clusters exhibit aromatic behaviors.
Compact antenna for two-dimensional beam scan in the JT-60U electron cyclotron heating/current drive system
Authors: Moriyama S. , Kajiwara K. , Takahashi K. , Kasugai A. , Seki M. , Ikeda Y. , Fujii T. ,   JT-60 Team
Published: November 2005

A compact antenna system was designed and fabricated to enable millimeter-wave beam scanning in the toroidal and poloidal directions of the JT-60U tokamak for electron cyclotron heating (ECH) and electron cyclotron current drive (ECCD) experiments. The antenna consists of a fast movable flat mirror mounted on the tokamak vacuum vessel and a rotary focusing mirror attached at the end of the waveguide that is supported from outside the vacuum vessel. This separate support concept enables a compact structure inside a shallow port (0.68×0.54×0.2m) that is shared with a subport for an independent diagnostic system. During a plasma shot, the flat mirror is driven by a servomotor with a 3-m-long drive shaft to reduce the influence of the high magnetic field on the motor. The focusing mirror is rotated by a simple mechanism utilizing a push rod and an air cylinder. The antenna has been operated reliably for 3 years after a small improvement to the rotary drive mechanism. It has made significant contributions to ECH and ECCD experiments, especially the current profile control in JT-60U.
Development of a compact electron-cyclotron-resonance ion source for high-energy carbon-ion therapy
Authors: Muramatsu M. , Kitagawa A. , Sakamoto Y. , Sato S. , Sato Y. , Ogawa Hirotsugu , Yamada S. , Ogawa Hiroyuki , Yoshida Y. , Drentje A. G.
Published: November 2005

Ion sources for medical facilities should have characteristics of easy maintenance, low electric power consumption, good stability, and long operation time without problems (one year or longer). For this, a 10GHz compact electron-cyclotron-resonance ion source with all-permanent magnets (Kei2 source) was developed. The maximum mirror magnetic fields on the beam axis are 0.59T at the extraction side and 0.87T at the gas-injection side, while the minimum B strength is 0.25T. These parameters have been optimized for the production of C4+ based on the experience at the 10GHz NIRS-ECR ion source and a previous prototype compact source (Kei source). The Kei2 source has a diameter of 320mm and a length of 295mm. The beam intensity of C4+ was obtained to be 530μA under an extraction voltage of 40kV. The beam stability was better than 6% at C4+ of 280μA during 90h with no adjustment of the operation parameters. The details of the design and beam tests of the source are described in this paper.
Fabrication of narrow-band self-filtering GaAs photodetector by epitaxy
Authors: Shie Jin Shown , Hwang Thunter S. D.
Published: November 2005

A narrow-band self-filtering (NBSF) GaAs photodiode has been fabricated by the LPE technique, where epilayers of high-low-high N doping were grown on a P-type substrate. By proper control of the thickness and doping concentration of each layer, it can be demonstrated that the fabricated NBSF detector has a spectral bandwidth as narrow as 315 Å at 880 nm peak wavelength. This means over 98% of the blue-side light is suppressible, indicating that the NBSF photodetector is a useful device for many applications where the suppression of high background light is necessary.
Viscosity measurements on micron-size scale using optical tweezers
Authors: Pesce G. , Sasso A. , Fusco S.
Published: November 2005

We describe how a single optical tweezer can be used as a quantitative tool to perform absolute and accurate viscosity measurements on a micrometer-size scale. Our method combines an unbiased position detector calibration procedure and frequency analysis of the Brownian motion of optically confined polystyrene microspheres. The position detector used to monitor the displacement of the particle is properly calibrated using the same trapped particle. With respect to the standard calibration method based on beads attached over the cover slip surface, our approach eliminates bias caused by surface effects and spherical aberrations. We apply our method to pure water samples determining their viscosity with a precision of 12%.
Absolute determination of inelastic mean-free paths and surface excitation parameters by absolute reflection electron energy loss spectrum analysis
Authors: Nagatomi T. , Goto K.
Published: November 2005

An analytical approach was proposed for simultaneously determining an inelastic mean-free path (IMFP) and a surface excitation parameter (SEP) with absolute units by the analysis of an absolute experimental reflection electron energy loss spectrum. The IMFPs and SEPs in Ni were deduced for electrons of 300 to 3000 eV. The obtained IMFPs were in good agreement with those calculated using the TPP-2M equation. The Chen-type empirical formula was proposed for determining the SEP. The results confirmed the applicability of the present approach for determining the IMFP and SEP for medium-energy electrons.
Effect of surface bond-order loss on the dc conductance of a metallic nanosolid
Authors: Yeung T. C. Au , Sun Chang Q. , Chiam T. C. , Ramanathan R. , Shangguan W. Z. , Kam C. H.
Published: November 2005

With the miniaturization of a solid device, quantum and interface effects become dominant not only in the static properties but also in the transport dynamics in the solid. Here we examine the dc conductance of a nanosolid by introducing the depression of the intra-atomic trapping potential in the surface skin [Sun, Phys. Rev. B 69, 045105 (2004)] as a perturbation to the conventional “quantum well” for tunneling electrons. It is derived that downshifts of the dc conductance peaks (that is, the incident energies for resonant tunneling) happens in an oscillatory way, depending on the strength of the perturbation. Besides, the downshifts of the peak positions due to the trapping potential well depression decrease as the size of the nanosolid is increased.
Frequency and field dependence of magnetoelectric interactions in layered ferromagnetic transition metal-piezoelectric lead zirconate titanate
Authors: Laletin V. M. , Paddubnaya N. , Srinivasan G. , De Vreugd C. P. , Bichurin M. I. , Petrov V. M. , Filippov D. A.
Published: November 2005

The strength of magnetoelectric (ME) coupling at 10Hz–3MHz has been measured in trilayers of Fe, Co, or Ni and lead zirconate titanate (PZT). The strongest ME coupling is measured for trilayers with Ni and the weakest in Co. Data on ME voltage coefficient αE versus bias magnetic field H for Fe–PZT–Fe show unique features including zero crossing and sign reversal. Measurements of frequency dependence of αE reveal a giant ME coupling due to the electromechanical resonance at 200–300kHz for radial modes and at ∼2.7MHz for thickness modes. Theoretical estimates of field and frequency dependence of αE are in very good agreement with the data.
Aggregated nanoparticle structures prepared by thermal decomposition of poly(vinyl)-N-pyrrolidone/Ag nanoparticle composite films
Authors: Rast L. , Stanishevsky A.
Published: November 2005

Silver nanoparticle layers were fabricated using spin coating and rapid thermal processing of poly(vinyl)-N-pyrrolidone/Ag nanoparticle composite thin films on glass. Fast thermal degradation of the polymeric matrix at 420°C results in spontaneous aggregation of Ag nanoparticles, accompanied by strong enhancement and a shift toward longer wavelengths of the absorption peak due to surface plasmon resonance (SPR). Longer annealing times lead initially to fragmentation of the aggregates, and then to partial coalescence of the nanoparticles with a corresponding shift of SPR towards shorter wavelengths. We investigated the dependence of the shape, size, and absorbance spectra of these aggregates on the spin speed and the conditions of thermal processing.
Controlled nonuniformity in macroporous silicon pore growth
Authors: Matthias Sven , Müller Frank , Gösele Ulrich
Published: November 2005

Photoelectrochemical etching of uniform prestructured silicon wafers in hydrofluoric acid containing solutions yields periodic structures that can be applied to two- and three-dimensional photonic crystals or microfluidics. Here we demonstrate experimentally macroporous silicon etching initiated by a nonuniform predefined lattice. For conveniently chosen parameters we observe a stable growth of pores whose geometrical appearance depends strongly on the spatially different nucleation conditions. Moreover, we show preliminary results on three-dimensionally shaped pores. This material can be used to realize hybrid photonic crystal structures and incorporate waveguides in three-dimensional photonic crystals.
Resonant scattering and second-harmonic spectroscopy of planar photonic crystal microcavities
Authors: McCutcheon Murray W. , Rieger Georg W. , Cheung Iva W. , Young Jeff F. , Dalacu Dan , Frédérick Simon , Poole Philip J. , Aers Geof C. , Williams Robin L.
Published: November 2005

The resonant modes of two-dimensional planar photonic crystal microcavities patterned in a free-standing InP slab are probed in a novel fashion using a long working distance microscope objective to obtain cross-polarized resonant scattering and second-harmonic spectra. We show that these techniques can be used to do rapid effective assays of large arrays of microcavities that do not necessarily contain resonant light-emitting layers. The techniques are demonstrated using microcavities comprised of single missing-hole defects in hexagonal photonic crystal hosts formed with elliptically shaped holes. These cavities typically support two orthogonally polarized resonant modes, and the resonant scattering and harmonic spectra are well fitted using a coherent sum of Lorentzian functions. The well-defined coherence between the two resonant features is explained in terms of a microscopic harmonic oscillator model. The relative merits of these techniques are quantitatively compared with the more commonly used cavity-enhanced photoluminescence technique.
Molecular weight dependence of a whispering gallery mode biosensor
Authors: Noto M. , Khoshsima M. , Keng D. , Teraoka I. , Kolchenko V. , Arnold S.
Published: November 2005

We report on molecular weight dependence measurements for an optical resonance biosensor. A dielectric microparticle is evanescently coupled with an optical fiber for the resonance stimulation, and a shift of the resonance wavelength is measured to monitor protein monolayer formation on the microparticle surface. Wavelength shifts for proteins over two orders of magnitude in molecular weight are measured. We show that the shift is proportional to molecular weight to the one-third power. Our result demonstrates that the optical resonance biosensor provides protein size information upon detection. This molecular weight dependency differentiates optical resonance sensing from electrical detection using field-effect transistors.
Analytical model for organic thin-film transistors operating in the subthreshold region
Authors: Calvetti E. , Savio A. , Kovács-Vajna Zs. M. , Colalongo L.
Published: November 2005

In this letter, a mathematical model for the subthreshold current of organic thin-film transistors (OTFTs) is proposed. The model is based on the variable range hopping transport theory using the channel depletion approach as in the standard junction field-effect transistor theory. Furthermore, the model is generalized to account for the complete depletion of the organic film. It describes the OTFTs behavior in the whole subthreshold region and it is suitable for computer aided design applications.
Amorphization/templated recrystallization method for changing the orientation of single-crystal silicon: An alternative approach to hybrid orientation substrates
Authors: Saenger K. L. , de Souza J. P. , Fogel K. E. , Ott J. A. , Reznicek A. , Sung C. Y. , Sadana D. K. , Yin H.
Published: November 2005

We demonstrate that the crystal orientation of single-crystal silicon layers may be changed in selected areas from one orientation to another by an amorphization/templated recrystallization (ATR) process, and then introduce ATR as an alternative approach for fabricating planar hybrid orientation substrates with surface regions of (100)- and (110)-oriented Si. The ATR technique, applied to a starting substrate comprising a thin (50–200 nm) overlayer of (100) or (110) Si on a (110) or (100) Si handle wafer, consists of two process steps: (i) Si+ or Ge+ ion implantation to create an amorphous silicon (a-Si) layer extending from the top of the overlayer to a depth below the overlayer/handle wafer interface, and (ii) a thermal anneal to produce the handle-wafer-templated epitaxial recrystallization of the a-Si layer. Regions exposed to the ATR process assume the orientation of the handle wafer while regions not exposed to the ATR process retain their original orientation. The practicality of this approach is demonstrated with the fabrication of a planar hybrid orientation substrate comprising (100) and (110) Si regions separated by SiO2-filled trenches.
Subharmonic mechanism of the mode C instability
Authors: Sheard G. J. , Thompson M. C. , Hourigan K.
Published: November 2005

The perturbation field of the recently discovered subharmonic mode C instability in the wake behind a ring is compared via a side-by-side comparison to the perturbation fields of the modes A and B instabilities familiar from past studies of the vortex street behind a circular cylinder. Snapshots of the wake are presented over a full shedding cycle, along with evidence from a linear stability analysis, to verify and better understand how the subharmonic instability is sustained.
Gene flow, colonisation and demographic history of the flat oyster Ostrea angasi
Authors: Hurwood David A. , Heasman Mike P. , Mather Peter B.
Published: November 2005

The Australian flat oyster Ostrea angasi is currently being assessed for its potential as a species for culture in New South Wales. It is considered important to determine the population genetic structure of wild stocks among estuaries before translocation of juveniles (spat) for growout in order to avoid possible deleterious effects of hybridisation of genetically divergent stocks (i.e. outbreeding depression). Five estuaries were sampled in southern New South Wales as well as another four from across the natural range of the species in Australia. Sequence analysis of a 594 base pair fragment of the mitochondrial cytochrome oxidase I gene was used to determine the degree of population structuring inferred from pairwise ΦST estimates and spatial analysis of molecular variance analysis. The analyses revealed that there is no significant genetic differentiation among the sampled New South Wales estuaries (P > 0.05) and all eastern samples represent a geographically homogeneous population. This essentially removes any potential constraints on broodstock sourcing and spat translocation within this region. Although levels of differentiation among all sites varied, little divergence was evident across the entire range of the sample. Furthermore, the study revealed extremely low levels of divergence between O. angasi and its northern hemisphere congener, O. edulis, raising the possibility that O. angasi may have only recently colonised Australian estuaries.