bluuebunny/crossref_metadata_2025 huggingface dataset:
Massage therapy reduces physical discomfort and improves mood disturbances in women with breast cancer
Authors: Listing Miriam , Reißhauer Anett , Krohn Michaela , Voigt Barbara , Tjahono Gracia , Becker Janine , Klapp Burghard F. , Rauchfuß Martina
Published: February 2009

Background. A randomized controlled trial was conducted to investigate the efficacy of classical massage treatment in reducing breast cancer‐related symptoms and in improving mood disturbances.

Methods. Women diagnosed with primary breast cancer were randomized into an intervention group and a control group. For a period of 5 weeks, the intervention group received bi‐weekly 30‐min classical massages in the back and head–neck areas. The control group received no additional treatment to their routine healthcare. To evaluate treatment efficacy, the following validated questionnaires were administrated at baseline (T1), at the end of the intervention (T2), and at a followup at 11 weeks (T3): the Short Form‐8 Health Survey™, the European Organization of Research and Treatment of Cancer quality of life questionnaire breast module (EORTC QLQ‐BR23), the Giessen Complaints Inventory (GBB), and the Berlin Mood Questionnaire (BSF).

Results. Eighty‐six eligible women (mean age: 59 years) were enrolled in the study. A significantly higher reduction of physical discomfort was found in the intervention group compared with the control group at T2 (p=0.001) and at T3 (p=0.038). A decrease in fatigue was also observed. Women in the intervention group reported significantly lower mood disturbances at T2 (p<0.01) but not at T3. The effect of treatment on mood disturbances was significantly higher if a patient was treated continuously by the same masseur.

Conclusion. Classical massage seems to be an effective adjuvant treatment for reducing physical discomfort and fatigue, and improving mood disturbances in women with early stage breast cancer. Copyright © 2009 John Wiley & Sons, Ltd.
Illness perceptions in Greek patients with cancer: a validation of the Revised‐Illness Perception Questionnaire
Authors: Giannousi Zoe , Manaras Irene , Georgoulias Vassilis , Samonis George
Published: February 2009

Objective: The Revised‐Illness Perception Questionnaire (IPQ‐R) assesses illness perceptions according to Leventhal's self‐regulatory model. The aim of this paper is to present findings on the reliability and validity of the IPQ‐R in a population of Greek cancer patients.

Methods: A total of 206 patients completed a Greek translation of the IPQ‐R and the Greek version of the Beck Depression Inventory (BDI). The scale's reliability was investigated by examining its internal consistency (Cronbach's alpha) and its test–retest reliability. Structural validity was examined through factor analyses. Predictive validity was tested by regressing BDI scores on IPQ subscale scores. Inter‐relationships between IPQ‐R dimensions were also examined by computing Pearson's Correlation Coefficients.

Results: Cronbach's alpha showed satisfactory internal consistency for the IPQ‐R subscales. Paired samples' t‐test showed good test–retest reliability. Factor analysis of the IPQ‐R items revealed that the Greek version reflects the structure of the original with the only difference being that the ‘Consequences’ and ‘Emotional Representations’ subscales loaded on one factor. Factor analysis of the causal dimension items revealed a different structure of Causal Representations than that of the original questionnaire yielding three main factors: Psychological Attributions, Behavioral, and External Factors. Multiple regression analyses showed that Consequences, Emotional Representations, Illness Identity, and Psychological Attributions were the best predictors for depression.

Conclusions: Translation of the IPQ‐R has good reliability and similar structure to that of the original. Difficulties to confirm the structure of Causal Representations may represent cultural differences in understanding illness causation. Copyright © 2009 John Wiley & Sons, Ltd.
Plasma Process. Polym. 2/2009
Authors: Tran Dung Thi , Mori Shinsuke , Tsuboi Daisuke , Suzuki Masaaki
Published: February 2009

Cover: SEM images and separation properties of plasma‐polymerized composite membranes, as well as a series of OES spectra of allylamine‐discharge emission generated at different conditions, are shown. By overlap deposition of plasma polymer, a thin barrier layer with a high cross‐linking degree is formed, improving the separation efficiency of composite membranes. Further details can be found in the article by D. T. Tran,* S. Mori, D. Tsuboi, and M. Suzuki on page 110.
Prostatic chondroitin sulfate is increased in patients with metastatic disease but does not predict survival outcome
Authors: Ricciardelli Carmela , Sakko Andrew J. , Stahl Jürgen , Tilley Wayne D. , Marshall Villis R. , Horsfall David J.
Published: February 2009

BACKGROUND

Previous studies from our laboratory demonstrated a strong association between an elevated level of chondroitin sulfate (CS) in peritumoral stroma and PSA‐relapse in patients with early stage disease. In this study we determined whether CS levels could predict overall survival in men diagnosed with advanced prostate cancer subsequently treated by orchiectomy alone.

METHODS

CS was localized in archived prostatic tissues by immunohistochemistry, and the level of CS expression as measured by video image analysis was compared in cohorts of 157 and 60 men with early stage or advanced disease, respectively.

RESULTS

The CS levels in the peritumoral stroma of patients without relapse after treatment for early stage disease was significantly reduced compared to levels in prostate tissue from patients who either relapsed (P = 0.003) or were diagnosed with advanced prostate cancer (P < 0.00001). There was no difference between the median CS level in the peritumoral prostatic stroma of early stage patients that relapsed after treatment and patients diagnosed with advanced prostate cancer. Increased CS levels (P < 0.0001) and high Gleason score (P < 0.0001) were associated with an increased rate of PSA‐relapse in the cohort of patients with early stage disease. However, neither CS level nor Gleason score alone or in combination could predict survival outcome in patients with advanced prostate cancer following androgen deprivation therapy.

CONCLUSIONS

Although peritumoral CS levels and Gleason score are strong predictors of relapse‐free survival in early stage prostate cancer patients, neither peritumoral CS levels nor Gleason score can predict survival outcome in patients with advanced disease. Prostate 69: 761–769, 2009. © 2009 Wiley‐Liss, Inc.
Selective expression of CD44, a putative prostate cancer stem cell marker, in neuroendocrine tumor cells of human prostate cancer
Authors: Palapattu Ganesh S. , Wu Chengyu , Silvers Christopher R. , Martin Heather B. , Williams Karin , Salamone Linda , Bushnell Timothy , Huang Li‐Shan , Yang Qi , Huang Jiaoti
Published: February 2009

BACKGROUND

Hormonal therapy is effective for advanced prostate cancer (PC) but the disease often recurs and becomes hormone‐refractory. It is hypothesized that a subpopulation of cancer cells, that is, cancer stem cells (CSCs), survives hormonal therapy and leads to tumor recurrence. CD44 expression was shown to identify tumor cells with CSC features. PC contains secretory type epithelial cells and a minor population of neuroendocrine cells. Neuroendocrine cells do not express androgen receptor and are quiescent, features associated with CSCs. The purpose of the study was to determine the expression of CD44 in human PC and its relationship to neuroendocrine tumor cells.

METHODS

Immunohistochemistry and immunofluorescence were performed to study CD44 expression in PC cell lines, single cells from fresh PC tissue and archival tissue sections of PC. We then determined if CD44+ cells represent neuroendocrine tumor cells.

RESULTS

In human PC cell lines, expression of CD44 is associated with cells of NE phenotype. In human PC tissues, NE tumor cells are virtually all positive for CD44 and CD44+ cells, excluding lymphocytes, are all NE tumor cells.

CONCLUSIONS

Selective expression of the stem cell‐associated marker CD44 in NE tumor cells of PC, in combination with their other known features, further supports the significance of such cells in therapy resistance and tumor recurrence. Prostate 69: 787–798, 2009. © 2009 Wiley‐Liss, Inc.
Quantitative RT‐PCR analysis of estrogen receptor gene expression in laser microdissected prostate cancer tissue
Authors: Walton Thomas J. , Li Geng , McCulloch Thomas A. , Seth Rashmi , Powe Desmond G. , Bishop Michael C. , Rees Robert C.
Published: February 2009

BACKGROUND

Real‐time quantitative RT‐PCR analysis of laser microdissected tissue is considered the most accurate technique for determining tissue gene expression. The discovery of estrogen receptor beta (ERβ) has focussed renewed interest on the role of estrogen receptors in prostate cancer, yet few studies have utilized the technique to analyze estrogen receptor gene expression in prostate cancer.

METHODS

Fresh tissue was obtained from 11 radical prostatectomy specimens and from 6 patients with benign prostate hyperplasia. Pure populations of benign and malignant prostate epithelium were laser microdissected, followed by RNA isolation and electrophoresis. Quantitative RT‐PCR was performed using primers for androgen receptor (AR), estrogen receptor beta (ERβ), estrogen receptor alpha (ERα), progesterone receptor (PGR) and prostate specific antigen (PSA), with normalization to two housekeeping genes. Differences in gene expression were analyzed using the Mann–Whitney U‐test. Correlation coefficients were analyzed using Spearman's test.

RESULTS

Significant positive correlations were seen when AR and AR‐dependent PSA, and ERα and ERα‐dependent PGR were compared, indicating a representative population of RNA transcripts. ERβ gene expression was significantly over‐expressed in the cancer group compared with benign controls (P < 0.01). In contrast, PGR expression was significantly down‐regulated in the cancer group (P < 0.05). There were no significant differences in AR, ERα or PSA expression between the groups. This study represents the first to show an upregulation of ERβ gene expression in laser microdissected prostate cancer specimens.

CONCLUSIONS

In concert with recent studies the findings suggest differential production of ERβ splice variants, which may play important roles in the genesis of prostate cancer. Prostate 69: 810–819, 2009. © 2009 Wiley‐Liss, Inc.
Significance of preoperative HbA1c level in patients with diabetes mellitus and clinically localized prostate cancer
Authors: Hong Sung Kyu , Lee Seung Tae , Kim Sung Soo , Min Kyung Eun , Byun Seok‐Soo , Cho Sung Yong , Choe Gheeyoung , Lee Sang Eun
Published: February 2009

INTRODUCTION

We investigated potential relationships of history of diabetes mellitus (DM) and glycemic control, represented by hemoglobin A1c (HbA1c) level, with characteristics of tumor among patients who received radical prostatectomy (RP) for clinically localized prostate cancer.

METHODS

We reviewed data of 740 patients who underwent RP for clinically localized prostate cancer between 2004 and 2008 without receiving preoperative radiation or hormonal treatment. Univariate and multivariate logistic regression analyses addressed the associations of history of DM and HbA1c level with known prognostic variables of prostate cancer.

RESULTS

No significant differences were observed in various preoperative and pathological parameters between those with (n = 89) and without DM (n = 651). When only the subjects with DM were divided into two groups (group 1 and 2) according to HbA1c level (<6.5% vs. ≥6.5%), group 2 demonstrated significantly higher rate of extraprostatic extension of tumor (P = 0.043) and high (≥7) pathological Gleason score (P = 0.005) than group 1. Also among those with DM, HbA1c level was observed to be an independent predictor for high pathologic Gleason score (P = 0.010) and extraprostatic extension of tumor (P = 0.035), respectively in multivariate analyses.

CONCLUSION

Although simple history of having DM may not be a significant factor regarding aggressiveness of clinically localized prostate cancer, the glycemic control, as represented by HbA1c level, may be a useful preoperative predictor of aggressive tumor profile among patients with DM who are also diagnosed with clinically localized prostate cancer. Prostate 69: 820–826, 2009. © 2009 Wiley‐Liss, Inc.
Structural comparison of chromosomal and exogenous dihydrofolate reductase from Staphylococcus aureus in complex with the potent inhibitor trimethoprim
Authors: Heaslet Holly , Harris Melissa , Fahnoe Kelly , Sarver Ronald , Putz Henry , Chang Jeanne , Subramanyam Chakrapani , Barreiro Gabriela , Miller J. Richard
Published: February 2009

Dihydrofolate reductase (DHFR) is the enzyme responsible for the NADPH‐dependent reduction of 5,6‐dihydrofolate to 5,6,7,8‐tetrahydrofolate, an essential cofactor in the synthesis of purines, thymidylate, methionine, and other key metabolites. Because of its importance in multiple cellular functions, DHFR has been the subject of much research targeting the enzyme with anticancer, antibacterial, and antimicrobial agents. Clinically used compounds targeting DHFR include methotrexate for the treatment of cancer and diaminopyrimidines (DAPs) such as trimethoprim (TMP) for the treatment of bacterial infections. DAP inhibitors of DHFR have been used clinically for >30 years and resistance to these agents has become widespread. Methicillin‐resistant Staphylococcus aureus (MRSA), the causative agent of many serious nosocomial and community acquired infections, and other gram‐positive organisms can show resistance to DAPs through mutation of the chromosomal gene or acquisition of an alternative DHFR termed “S1 DHFR.” To develop new therapies for health threats such as MRSA, it is important to understand the molecular basis of DAP resistance. Here, we report the crystal structure of the wild‐type chromosomal DHFR from S. aureus in complex with NADPH and TMP. We have also solved the structure of the exogenous, TMP resistant S1 DHFR, apo and in complex with TMP. The structural and thermodynamic data point to important molecular differences between the two enzymes that lead to dramatically reduced affinity of DAPs to S1 DHFR. These differences in enzyme binding affinity translate into reduced antibacterial activity against strains of S. aureus that express S1 DHFR. Proteins 2009. © 2009 Wiley‐Liss, Inc.
An all‐atom knowledge‐based energy function for protein‐DNA threading, docking decoy discrimination, and prediction of transcription‐factor binding profiles
Authors: Xu Beisi , Yang Yuedong , Liang Haojun , Zhou Yaoqi
Published: February 2009

How to make an accurate representation of protein‐DNA interaction by an energy function is a long‐standing unsolved problem in structural biology. Here, we modified a statistical potential based on the distance‐scaled, finite ideal‐gas reference state so that it is optimized for protein‐DNA interactions. The changes include a volume‐fraction correction to account for unmixable atom types in proteins and DNA in addition to the usage of a low‐count correction, residue/base‐specific atom types, and a shorter cutoff distance for protein‐DNA interactions. The new statistical energy functions are tested in threading and docking decoy discriminations and prediction of protein‐DNA binding affinities and transcription‐factor binding profiles. The results indicate that new proposed energy functions are among the best in existing energy functions for protein‐DNA interactions. The new energy functions are available as a web‐server called DDNA 2.0 at http://sparks.informatics.iupui.edu. The server version was trained by the entire 212 protein‐DNA complexes. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Construct optimization for protein NMR structure analysis using amide hydrogen/deuterium exchange mass spectrometry
Authors: Sharma Seema , Zheng Haiyan , Huang Yuanpeng J. , Ertekin Asli , Hamuro Yoshitomo , Rossi Paolo , Tejero Roberto , Acton Thomas B. , Xiao Rong , Jiang Mei , Zhao Li , Ma Li‐Chung , Swapna G. V. T. , Aramini James M. , Montelione Gaetano T.
Published: February 2009

Disordered or unstructured regions of proteins, while often very important biologically, can pose significant challenges for resonance assignment and three‐dimensional structure determination of the ordered regions of proteins by NMR methods. In this article, we demonstrate the application of 1H/2H exchange mass spectrometry (DXMS) for the rapid identification of disordered segments of proteins and design of protein constructs that are more suitable for structural analysis by NMR. In this benchmark study, DXMS is applied to five NMR protein targets chosen from the Northeast Structural Genomics project. These data were then used to design optimized constructs for three partially disordered proteins. Truncated proteins obtained by deletion of disordered N‐ and C‐terminal tails were evaluated using 1H‐15N HSQC and 1H‐15N heteronuclear NOE NMR experiments to assess their structural integrity. These constructs provide significantly improved NMR spectra, with minimal structural perturbations to the ordered regions of the protein structure. As a representative example, we compare the solution structures of the full length and DXMS‐based truncated construct for a 77‐residue partially disordered DUF896 family protein YnzC from Bacillus subtilis, where deletion of the disordered residues (ca. 40% of the protein) does not affect the native structure. In addition, we demonstrate that throughput of the DXMS process can be increased by analyzing mixtures of up to four proteins without reducing the sequence coverage for each protein. Our results demonstrate that DXMS can serve as a central component of a process for optimizing protein constructs for NMR structure determination. Proteins 2009. © 2009 Wiley‐Liss, Inc.
The molecular evolution of HIV‐1 protease simulated at atomic detail
Authors: Tiana G. , Broglia R. A.
Published: February 2009

Progress in understanding protein folding allows to simulate, with atomic detail, the evolution of amino‐acid sequences folding to a given native conformation. A particularly attractive example is the HIV‐1 protease, main target of therapies to fight AIDS, which under drug pressure is able to develop resistance within few months from the starting of therapy. By comparing the results of simulations of the evolution of the protease with the corresponding proteomic data, one can approximately determine the value of the associated evolution pressure under which the enzyme has become and, as a consequence, map out the energy landscape in sequence space of the HIV‐1 protease. It is found that there are several families of sequences folding to the native conformations of the enzyme. Each of these families are characterized by different sets of highly conserved (“hot”) amino acids which play a critical role in the folding and stability of the protease. There are two main possibilities for the virus to move from one family to a different one: (a) in a single generation, through the concerted mutations of the hot amino acids, a highly unlikely event, (b) through a folding path (if it exists), again a very improbable event. In fact, the number of generations needed by the virus to change stepwise its sequence from one family to another is astronomically large. These results point to the “hot” segments of the protease as promising targets for a nonconventional inhibition strategy, likely not to create resistance. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Molecular dynamics studies of the P pilus rod subunit PapA
Authors: Vitagliano Luigi , Ruggiero Alessia , Pedone Carlo , Berisio Rita
Published: February 2009

Adhesion of uropathogenic Escherichia coli to host tissues is mediated by pili, which extend from the outer cell membrane of the bacterium. Here we report molecular dynamics (MD) characterizations of the major constituent of P pili from the uropathogenic E. coli, PapA, in unliganded state and in complex with the G1 strand of the chaperone PapD. To mimic the PapA response to the gradual dissociation of the PapD G1 strand and to evaluate the role of PapA chaperone recognition sites, we also carried out MD simulations of complexes of PapA with fragments of PapD G1 strand, that leave either the P4 or both P3 and P4 sites unoccupied. Data on the unbound form of PapA indicate that, upon release of the chaperone, PapA evolves toward compact states that are likely not prone to subunit–subunit association. In line with recent experimental reports, this finding implies that chaperone release and subunit–subunit association must be concerted. Our data also indicated that the gradual unbinding of the chaperone from the PapA groove has increasingly strong structural consequences. Indeed, the release of the chaperone from the site P4, which is closest to the initiation site (P5), does not have dramatic effects on the domain structure, whereas its release from both the P4 and the adjacent P3 sites induces a quick structural transition toward a collapsed state, where the subunit groove is obstructed. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.
N‐(ureidoethyl)amides of cyclic enkephalin analogs
Authors: Ciszewska Małgorzata , Kwasiborska Maria , Nowakowski Michał , Oleszczuk Marta , Wójcik Jacek , Chung Nga N. , Schiller Peter W. , Izdebski Jan
Published: February 2009

Novel N‐(ureidoethyl)amides of cyclic enkephalin analogs have been synthesized. The p‐nitrophenyl carbamate of 1‐Boc‐1,2‐diaminoethane was coupled with 4‐methylbenzhydrylamine (MBHA) resin. The Boc group was removed by treatment with HCl/dioxane, and the peptide chain was assembled using Boc strategy. For deprotection of amino function, HCl/dioxane was used. D‐Lys or D‐Orn were incorporated in position 2, and the side chains of Lys, Orn, Dab, or Dap in position 5 were protected with Fmoc group. Side chain protection was removed by treatment with 55% piperidine in DMF, and cyclization was achieved by treatment with bis‐(4‐nitrophenyl)carbonate to form a urea bridge. The peptide was cleaved from the resin by treatment with 45% TFA in DCM. The peptides were tested in the guinea‐pig ileum (GPI) and mouse vas deferens (MVD) assays. Divers opioid activities were observed, depending on the size of the ring. In comparison with [Leu5]enkephalin, all peptides were more active in the GPI assay (between 125 and 12 times), and some of them were also more potent in the MVD assay. The conformational propensities of each peptide were determined using the EDMC method in conjunction with NMR experiments. This approach allows treating the dynamical behavior of small peptides properly. The results were compared with those obtained previously for corresponding nonsubstituted amides and are in agreement with the biologically active conformation proposed by us earlier. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.
Antiestrogenic and anticancer activities of peptides derived from the active site of alpha‐fetoprotein
Authors: Joseph Leroy C. , Bennett James A. , Kirschner Karl N. , Shields George C. , Hughes John , Lostritto Nicole , Jacobson Herbert I. , Andersen Thomas T.
Published: February 2009

Cyclo[EKTOVNOGN] (AFPep), a cyclic 9‐amino acid peptide derived from the active site of alpha‐fetoprotein, has been shown to prevent carcinogen‐induced mammary cancer in rats and inhibit the growth of ER+ human breast cancer xenografts in mice. Recently, studies using replica exchange molecular dynamics predicted that the TOVN region of AFPep might form a dynamically stable putative Type I beta‐turn, and thus be biologically active without additional amino acids. The studies presented in this paper were performed to determine whether TOVN and other small analogs of AFPep would inhibit estrogen‐stimulated cancer growth and exhibit a broad effective‐dose range. These peptides contained nine or fewer amino acids, and were designed to bracket or include the putative pharmacophoric region (TOVN) of AFPep. Biological activities of these peptides were evaluated using an immature mouse uterine growth inhibition assay, a T47D breast cancer cell proliferation assay, and an MCF‐7 breast cancer xenograft assay. TOVN had very weak antiestrogenic activity in comparison to AFPep's activity, whereas TOVNO had antiestrogenic and anticancer activities similar to AFPep. OVNO, which does not form a putative Type I beta‐turn, had virtually no antiestrogenic and anticancer activities. A putative proteolytic cleavage product of AFPep, TOVNOGNEK, significantly inhibited E2‐stimulated growth in vivo and in vitro over a wider dose range than AFPep or TOVNO. We conclude that TOVNO has anticancer potential, that TOVNOGNEK is as effective as AFPep in suppressing growth of human breast cancer cells, and that it does so over a broader effective‐dose range. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.
Thermodynamics of partitioning of substance P in isotropic bicelles
Authors: Kim Chul , Baek Seung Bin , Kim Do Hun , Lim Sung Chul , Lee Hyeong Ju , Lee Hee Cheon
Published: February 2009

The temperature dependence of the partition of a neuropeptide, substance P (SP), in isotropic (q = 0.5) bicelles was investigated by using pulsed field gradient NMR diffusion technique. The partition coefficient decreases as the temperature is increased from 295 to 325 K, indicating a favorable (negative) enthalpy change upon partitioning of the peptide. Thermodynamic analysis of the data shows that the partitioning of SP at 300 K is driven by the enthalpic term (ΔH) with the value of − 4.03 kcal mol−1, while it is opposed by the entropic term (−TΔS) by approximately 1.28 kcal mol−1 with a small negative change in heat capacity (ΔCp). The enthalpy‐driven process for the partition of SP in bicelles is the same as in dodecylphosphocholine (DPC) micelles, however, the negative entropy change in bicelles of flat bilayer surface is in sharp contrast with the positive entropy change in DPC micelles of highly curved surface, indicating that the curvature of the membrane surface might play a significant role in the partitioning of peptides. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.
Synthetic diamond films as a platform material for label‐free protein sensors
Authors: Bijnens Nathalie , Vermeeren Veronique , Daenen Michaël , Grieten Lars , Haenen Ken , Wenmackers Sylvia , Williams Oliver A. , Ameloot Marcel , vandeVen Martin , Michiels Luc , Wagner Patrick
Published: February 2009

In the framework of developing a fast and label‐free immunosensor for C‐reactive protein (CRP) detection, H‐terminated nanocrystalline diamond (NCD) was functionalised with anti‐CRP antibodies that were physically adsorbed to the surface. Impedance spectroscopy was used to electronically detect real‐time CRP recognition. Different impedance behaviours were observed after CRP addition as compared to after FITC‐labelled ssDNA addition at low (100 Hz) as well as at high frequencies (1 MHz). Physical interpretations of the observed impedance changes were obtained by fitting the data to an equivalent electrical circuit. Concentrations of 1 μM CRP were recognised with a reaction time of 30 minutes. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
8 W single‐emitter InGaN laser in pulsed operation
Authors: Brüninghoff Stefanie , Eichler Christoph , Tautz Sönke , Lell Alfred , Sabathil Matthias , Lutgen Stephan , Strauß Uwe
Published: February 2009

We present the investigation of an optimized epitaxial layer structure in order to reach high optical output powers of several watts. The influence of an interlayer, which is located between the multiple quantum well layers and the electron blocking layer, is analysed carefully. For high current densities the leakage current density increases with increasing interlayer thickness. Correlating the leakage current density with the injection efficiency it is found that by decreasing the interlayer thickness constant injection efficiency for high current regions can be reached. This is essential for a linear laser characteristic up to high optical output power levels. Further enhancement can be achieved by enlarging the total waveguiding layer structure. As a result the optical power density in the resonator was decreased. With these improvements threshold current density and slope efficiency of 2.7 kA/cm2 and 2.1 W/A can be achieved. The optical output power is increased to 8.7 W for a 20 μm broad single‐emitter ridge‐waveguide laser in pulsed operation. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Carbonization of porous silicon optical gas sensors for enhanced stability and sensitivity
Authors: Torres‐Costa V. , Salonen J. , Jalkanen T. M. , Lehto V.‐P. , Martín‐Palma R. J. , Martínez‐Duart J. M.
Published: February 2009

Nanostructured porous silicon (PS) optical filters have been widely proposed for their use in biological and chemical sensing applications. Porous silicon, however, presents a reactive surface that must be adequately passivated in order to achieve the required chemical stability mandatory for sensing applications. In the present work, thermal carbonization by acetylene decomposition (TCAD) is shown to provide effective passivation of PS internal surface, as well as an enhancement of the device's sensitivity to certain species. Moreover, it is shown that the TCAD process, as opposed to more common oxidation treatments, has only minor effects on the optical properties of PS. Thus, the optical performance of PS interference filters is preserved after the carbonization process. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Terahertz transmission through p+ porous silicon membranes
Authors: Lo Shu‐Zee A. , Rossi Andrea M. , Murphy Thomas E.
Published: February 2009

We report an experimental measurement of far infrared dielectric properties of p+‐doped free‐standing porous silicon membranes, characterized using terahertz time‐domain spectroscopy. Freshly fabricated hydrogen‐terminated porous silicon samples exhibited significant absorption in the terahertz regime, and the absorption was observed to slowly drift in response to the surrounding environment and the duration of illumination. Samples that are partially oxidized, either by age or through thermal oxidation in an oven, become almost transparent in the terahertz spectral regime, and the dielectric properties stabilize to a constant value. The partially‐oxidized porous silicon samples are observed to have an absorption coefficient of approximately 2 cm–1 over the range of 0–2 THz, which corresponds to an effective resistivity of 35 ± 9 Ω cm, approximately four orders of magnitude higher than that of the crystalline silicon from which they were formed. Spectral transmission measurements further confirm that p+ porous silicon has no significant absorption peaks or other spectral variation in the 0–2 THz regime. These findings suggest that p+ porous silicon could be a useful material for fabricating future THz devices. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Biomagnetic field detection using very high sensitivity magnetoimpedance sensors for medical applications
Authors: Uchiyama Tsuyoshi , Nakayama Shinsuke , Mohri Kaneo , Bushida Kenichi
Published: February 2009

This paper demonstrates the performance of magnetoimpedance (MI) sensors for biomagnetic field recording. The rms noise of an amorphous wire MI sensor with 600 turns of pick‐up coil was estimated as approximately 3 pT/Hz1/2 at 1 Hz. Here, we demonstrate that this sensitivity is enough to clearly detect magnetic cardiogram signals. We also measured the biomagnetic field around a smooth muscle tissue sample taken from a guinea‐pig. We discovered that the magnetic‐field waveform of a small tissue sample is similar to the voltage waveform measured by a microelectrode array in a smooth muscle sheet sample. The results suggest that the localized biomagnetic field generated by smooth muscle cells can be detected by an MI sensor. We concluded that the MI sensor is a promising device for use as a noninvasive tool to test cell activity or function through magnetic‐field measurement. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Spin relaxation and domain wall dynamics in glass‐coated microwires
Authors: Sossmeier K. D. , Beck F. , Chiriac H. , Schelp L. F. , Carara M.
Published: February 2009

The dynamic properties of the magnetic domain walls in amorphous glass‐covered microwires were studied. The samples was Joule annealed with an alternate current at different frequencies and the dynamic behaviour of the samples were studied at different applied stresses. The Landau–Lifshitz–Gilbert damping parameter and the domain wall mobility have shown that the dynamic response can be improved by increasing the annealing current frequency. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Coulomb effects in type‐II Ga(As)Sb quantum dots
Authors: Gradkowski Kamil , Ochalski Tomasz J. , Williams David P. , Healy Sorcha B. , Tatebayashi Jun , Balakrishnan Ganesh , O'Reilly Eoin P. , Huyet Guillaume , Huffaker Diana L.
Published: February 2009

We present a detailed explanation of the blue‐shift that is observed in Ga(As)Sb quantum dots (QD) with increasing pump power density by employing an 8‐band k · p model with the Coulomb attractive potential added into the Hamiltonian. Two types of structures are considered: Ga(As)Sb QDs in a GaAs matrix and the same dots overgrown with an InGaAs quantum well (QW). We show that with increasing charge density the electron and hole energy levels shift relative to each other, which results in an increase of the optical transition energy (i.e. a blue‐shift). The major contribution to the effect arises from the holes and is a result of their 3D confinement inside the dot. Additionally, with increasing charge density the electrons move closer to the dot, which improves the oscillator strength of the ground‐state optical transition. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Theory of electronic and transport properties of resonant triple quantum dot molecules
Authors: Shim Y.‐P. , Delgado F. , Korkusinski M. , Gaudreau L. , Studenikin S. , Kam A. , Sachrajda A. S. , Hawrylak P.
Published: February 2009

We present a theory of electronic and transport properties of triple quantum dot molecules in the vicinity of quadruple points where four different charge configurations are on resonance. We study three different quadruple points in the presence of a magnetic field and show that a trapped particle in one of the dot plays an essential role in determining the spin character of the transport. Many‐electron states of the triple quantum dot molecules are used as transport channels in the Fermi's Golden Rule approach and it is demonstrated that the Aharonov–Bohm oscillations of the energy spectrum lead to spin‐selective oscillations in transport. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Non‐inverted electron–hole alignment in InAs/InP self‐assembled quantum dots
Authors: Reimer M. E. , Dalacu D. , Lapointe J. , Poole P. J. , McKinnon W. R. , Williams R. L.
Published: February 2009

Photoluminescence from individual InAs/InP quantum dots embedded within a planar n–i structure is studied as a function of vertical electric field. We demonstrate control of the electron number and determine the Stark shift and built‐in dipole at zero electric field. In contrast to the well studied InAs/GaAs quantum dot material system, we obtain a built‐in dipole which indicates that the electron lies above the hole at zero electric field. The magnitude and direction of the measured dipole suggests a uniform quantum dot composition. The gating principles we demonstrate can be applied to pre‐positioned InAs/InP quantum dots, such that arrays of initialized single spins can be employed for quantum information applications. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effect of ethanol in an inorganic salt detector based on porous silicon
Authors: Murillo N. , Rucavado E. , Ramírez‐Porras A.
Published: February 2009

A porous silicon (PSi) chemical sensor for detection of chloride ions in aqueous solution is reported. The sensor setup is based on the semiconductor/electrolyte system used for the analysis of semiconductor surfaces. AC frequency response signals have been obtained in non‐ethanoic and ethanoic solutions containing small concentrations of chloride ions. Discussion of the results is provided. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Chemical etching of Si by Ag nanocatalysts in HF‐H2O2: application to multicrystalline Si solar cell texturisation
Authors: Bastide Stéphane , Quang Nam Le , Monna Rémi , Lévy‐Clément Claude
Published: February 2009

Metal‐assisted chemical etching (MAE) was used as an alternative route to texturise the front surface of multicrystalline Si solar cells. Ag nanoparticles deposited by an electroless method on the Si surface acted as catalysts for Si etching in a solution containing HF and H2O2, an oxidizing species. MAE formed a duplex structure at the surface of the Si wafer consisting in a mesoporous Si layer that after dissolution in NaOH revealed the second structure, which is a macrotexturised surface. After texturisation, the effective reflectivity (AM1.5G, 400‐1000 nm) ranged between 12% and 15% depending on the duration of the dissolution treatment of the mesoporous layer. MAE texturised solar cells were compared to NaOH texturised solar cells made with similar wafers (∼25% in effective reflectivity). MAE texturisation leads to a gain in fill factor (FF) but not in short‐circuit current (JSC) (from average values). The best MAE cell exhibited higher JSC (+2%) and efficiency (16.1%) compared to the best NaOH cell (15.7%). (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Detecting amine vapours with thermally carbonized porous silicon gas sensor
Authors: Björkqvist Mikko , Salonen Jarno , Tuura Jaani , Jalkanen Tero , Lehto Vesa‐Pekka
Published: February 2009

A capacitive type porous silicon based gas sensor for detecting amine vapours has been developed. The sensor is highly sensitive, e.g., to methylamine and trimethylamine vapours, and its electrical parameters recover totally after exposure to studied gases. Thermal carbonization of porous silicon under acetylene atmosphere was carried out to produce stable and attractive surface to amine vapours. The sensor response to studied amine vapours can be separated from its response to humidity changes since their electrical responses act reversely. In addition to the vapours of methylamine/water and trimethylamine/water solutions, the sensor was also used to detect different amines, which are generated during spoilage of raw shrimps and Baltic herring fillets at room temperature. Fourier Transform Infrared spectroscopy was used to detect the amine vapours and other volatile compounds simultaneously with sensor measurements. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Stress induced one‐dimensional model for current oscillations at the Si/electrolyte contact
Authors: Grzanna Jürgen , Notz Thilo , Lewerenz Hans‐J.
Published: February 2009

A cellular automata is introduced to model the locally resolved oxide thickness, the stress, and the etching rate dynamics at the silicon electrolyte contact along a macroscopically long line (1 mm). Short‐ and long‐range interaction mechanisms are considered to achieve current oscillations. Extended chronoamperometric oscillations are obtained but finally, the oscillations become increasingly damped for the case of a locally acting stress and a locally varying etching rate. The additional incorporation of a small oscillating and long‐range interacting nominal etching rate into the model leads to sustained oscillations. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
In‐situ FFT impedance spectroscopy in new modes applied to pore growth in semiconductors
Authors: Carstensen Jürgen , Föll Helmut , Cojocaru Ala , Leisner Malte
Published: February 2009

Major progress in FFT impedance spectroscopy now allows in‐situ measurements during pore growth in three modes, two of which use modulation of the back side or front side illumination intensity, respectively; with the back side illumination mode being especially useful to n‐macro(bsi) pores in Silicon. The data obtained in all modes can be interpreted on the base of fully quantitative models which give perfect fits to the measured data and therefore allow to extract in‐situ data of many parameters, including the valence of the process and the actual pore depth. Based on this, macropore growth in Si has been re‐investigated, resulting in new growth modes and especially in substantially increased macropore growth rates as well as pore quality. It is now possible to grow macropores in n‐type Si far deeper and more than twice as fast compared to the present state of the art; the quality as expressed, e.g., in the pore wall roughness, can also be substantially improved. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Fast macropore growth in n‐type silicon
Authors: Cojocaru Ala , Carstensen Jürgen , Ossei‐Wusu Emmanuel K. , Leisner Malte , Riemenschneider Oliver , Föll Helmut
Published: February 2009

Deep macropores can be grown in classical aqueous HF electrolytes only at slow etching speeds, fast macropores can only be grown to modest depths (150 μm). The addition of acid acetic to the electrolyte can roughly double the etching speed of the macropores, enabling quick and easy etching of pore depths as deep as 520 μm, and potentially more, if wafers thicker than 550 μm would be used. The addition of carboxymethylcellulose sodium salt (CMC) to the electrolyte decreases the roughness of the pore walls significantly. It is successfully shown that electrolytes consisting of HF + acetic acid + CMC can be utilized to produce fast, deep, and smooth macropores simultaneously in n‐type silicon, required for a multitude of potential applications. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Exploring the QSAR of Pyrazolo[3,4‐b]Pyridine, Pyrazolo[3,4‐b]Pyridone and Pyrazolo[3,4‐b]Pyrimidine Derivatives as Antagonists for A1 Adenosine Receptor
Authors: Cichero Elena , Casolino Chiara , Menozzi Giulia , Mosti Luisa , Fossa Paola
Published: February 2009

Pyrazolo[3,4‐b]pyridines have been recently presented as a novel class of adenosine A1 receptor antagonists. Depending on substitutions on some key positions of their scaffold they show selectivity towards A1, A2A or A3 receptors, which results in a variety of therapeutic potentialities of these ligands. In this work, we present a QSAR study on these analogues as antagonists for adenosine A1 receptors. Using the MOE software we identified a pool of descriptors that numerically describes the ligand features impacting the affinity at adenosine A1 receptors. The obtained information is useful to understand the main structural features that strongly correlate with the A1 antagonism in this class of compounds and will be used for the rational design of more potent and selective pyrazolo[3,4‐b]pyridine derivatives.
Combined utilization of ion mobility and ultra‐high‐resolution mass spectrometry to identify multiply charged constituents in natural organic matter
Authors: Gaspar Andras , Kunenkov Erast V. , Lock Richard , Desor Michael , Perminova Irina , Schmitt‐Kopplin Philippe
Published: February 2009

Natural organic matter as complex biogeochemical non‐repetitive material was investigated with ion mobility mass spectrometry (IMS) and ultra‐high‐resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR‐MS) approaches in order to unravel the existence of multiply charged state constituents. Hereby we describe and assign the potential molecular formulae of these doubly charged species, derived from FTICR‐MS, and the existence of these species was confirmed via IMS. The parallel application of these powerful techniques enabled the boundaries of the understanding of natural organic matter to be pushed further. Copyright © 2009 John Wiley & Sons, Ltd.
First application of the depth profile of silica species as a tracer by fast‐atom bombardment mass spectrometry: investigation of the circulation of seawater and silica uptake by diatoms
Authors: Tanaka Miho , Takahashi Kazuya , Urabe Tatsuya , Oikawa Tomohiro , Nemoto Masao , Nagashima Hideki
Published: February 2009

Silica, represented by SiO2, is the general name for the compounds composed of Si, O and H with their derivative complexes. Silica forms various chemical species in aquatic solutions, such as a monomer (Si(OH)3O−), dimer (Si2(OH)5O), and others. These species are known to vary in their relative abundances in solution depending on the chemical and physical conditions. Silica species dissolved in seawater have been examined by fast‐atom bombardment mass spectrometry (FAB‐MS) to elucidate the behavior of silica and its circulation as a novel tracer reflecting the chemical and physical conditions of seawater and the bioactivity of diatoms, which take up silica. In the seawater of Tokyo Bay, silica species such as [Si(OH)2O2Na]− ([monomer–Na]−), [Si2(OH)5O2]− ([dimer]−), [Si2(OH)4O3Na]− ([dimer–Na]−), [Si4(OH)7O5]− ([cyclic tetramer]−), [Si4(OH)6O6Na]− ([cyclic tetramer–Na]−), [Si4(OH)9O4]− ([linear tetramer]−) and [Si4(OH)8O5Na]− ([linear tetramer–Na]−) were observed and assigned by FAB‐MS. To investigate the suitability of silica species as a tracer, the relative peak intensity ratios of silica species observed in the mass spectra, i.e. the profiles of the ratio of the linear tetramer to the cyclic tetramer (m/z 329/311) and the ratio of the dimer to the cyclic tetramer (m/z 173/311) against depth, were examined to determine the annual changes and reproducibility of the depth profiles. In particular, the depth profile of the relative ratio of the linear tetramer to the cyclic tetramer, 329/311, exhibits critical changes depending on the seawater budget. These changes in the relative ratios were identified by an experiment involving a simple sodium chloride solution system. Our measurement is expected to elucidate the dynamics of silica and its role as ‘food’ for diatoms, and we showed that speciation using mass spectrometry is a powerful tool for examining elemental behavior in nature and environmental changes. Our results suggest that a silica tracer is useful for investigating the behavior of seawater in small coastal regions and the uptake of silica by diatoms. Copyright © 2009 John Wiley & Sons, Ltd.
Analysis of Steiner subtrees of random trees for traceroute algorithms
Authors: Guillemin Fabrice , Robert Philippe
Published: February 2009

We consider in this article the problem of discovering, via a traceroute algorithm, the topology of a network, whose graph is spanned by an infinite branching process. A subset of nodes is selected according to some criterion. As a measure of efficiency of the algorithm, the Steiner distance of the selected nodes, i.e. the size of the spanning subtree of these nodes, is investigated. For the selection of nodes, two criteria are considered: a node is randomly selected with a probability, which is either independent of the depth of the node (uniform model) or else in the depth biased model, is exponentially decaying with respect to its depth. The limiting behavior the size of the discovered subtree is investigated for both models. © 2009 Wiley Periodicals, Inc. Random Struct. Alg., 2009