bluuebunny/crossref_metadata_2025 huggingface dataset:
High throughput testing platform for organic Solar Cells
Authors: Riede Moritz K. , Sylvester‐Hvid Kristian O. , Glatthaar Markus , Keegan Nicholas , Ziegler Tobias , Zimmermann Birger , Niggemann Michael , Liehr Andreas W. , Willeke Gerhard , Gombert Andreas
Published: July 2008

In this paper we present a high throughput testing setup for organic solar cells that is necessary for an efficient analysis of their behaviour. The setup comprises process parameter logging, automated measurement data acquisition and subsequent data management and analysis. Utilising this setup the reproducibility of solar cells and the effect of production parameter variations has been tested with a set of 360 solar cells based on the poly‐3‐hexylthiophene:1‐(3‐methoxycarbonyl)‐propyl‐1‐1‐phenyl‐(6,6)C61 bulk heterojunction. Variations in power conversion efficiency between 1 and 3% were observed on varying production parameters hardly mentioned in literature. The conditions during the vacuum deposition of the aluminium cathode turned out to have a significant effect. The key solar cell parameter affecting the performance was the fill factor (FF).

As such the work exemplifies the necessity for a combined approach to analyse the complex behaviour of organic solar cells. The developed high throughput testing setup provides a basis for an efficient testing of production parameter variations and materials and additionally opens the door for statistical analysis. Copyright © 2008 John Wiley & Sons, Ltd.
Der Mensch ändert das Klima. Vierter Sachstandsbericht des IPCC
Authors: Kohl Harald
Published: July 2008

Das Intergovernmental Panel on Climate Change (IPCC) stellt in seinem Vierten Sachstandsbericht von 2007 mit großer Gewissheit fest: Die Erde wird messbar wärmer, weil der Mensch das Klima beeinflusst. Vor allem der messbare Anstieg der anthropogenen Treibhausgasemissionen korreliert mit der Tendenz zu wärmeren Jahrestemperaturen. Das IPCC hat erneut Zukunftsszenarien für die Klimaentwicklung aufgestellt. Sie hängen von den globalen Emissionszielen ab, die erreicht werden können. Demnach wird die globale Durchschnittstemperatur bis zum Ende des 21. Jahrhunderts um 1,8 bis 4,0 K ansteigen. Eine Erwärmung oberhalb 2 K wird dramatische langfristige Folgen für die Umwelt haben. Der neue Bericht bezieht nun die zentrale Rolle der Ozeane im Kohlenstoffkreislauf der Biosphäre ein. Er macht auch erstmals Aussagen über die Entwicklung einzelner Regionen.
Genie mit großer Bescheidenheit
Authors: Huebener Rudolf
Published: July 2008

John Bardeen war ein bedeutender Pionier der Festkörperphysik. Als bisher Einziger erhielt er zwei Mal den Nobelpreis für Physik: 1956 zusammen mit Walter Brattain und William Shockley für die Entwicklung des Transistors und 1972 gemeinsam mit Leon Cooper und John Schrieffer für die quantenmechanische Deutung der Supraleitung. In diesen Tagen jährt sich sein Geburtstag zum hundertsten Mal.
Das Hochspannungskarussell
Authors: Müller Andreas
Published: July 2008

In einem sehr guten Handbuch für Schulexperimente wird eine Art Hochspannungskarussell gezeigt. Es beginnt sich zu drehen, wenn es an den negativen Pol einer Hochspannungsquelle angeschlossen wird, wobei eine Styroporunterlage der besseren Isolation gegenüber der Erde dient. Als Erklärung wird vorgeschlagen: “An den Spitzen strömt die negative Ladung heraus und erzeugt einen Rückstoß.” Oft wird als Analogie zudem die Rückstoßbewegung beim Rasensprenger (Segnersches Wasserrrad) genannt. Kann das sein?
Farben im Eis und anderswo
Authors: Schlichting H. Joachim
Published: July 2008

Eine gesprungene Eisschicht auf einem zugefrorenen See macht manchmal durch intensive Farben auf sich aufmerksam. Auch in anderen transparenten Medien wie einer Glasscheibe oder einem Bergkristall lassen sich derartige Farben beobachten.
Improved image analysis workflow for 2‐D gels enables large‐scale 2‐D gel‐based proteomics studies – COPD biomarker discovery study
Authors: Bandow Julia E. , Baker John D. , Berth Matthias , Painter Cory , Sepulveda Osvaldo J. , Clark Kelly A. , Kilty Iain , VanBogelen Ruth A.
Published: July 2008

2‐D gel electrophoresis has been used for more than three decades to study the protein complement of organisms, tissues, and cells. Three issues are holding back large‐scale proteomics studies: low‐throughput, high technical variation, and study designs lacking statistical power. We identified image analysis as the central factor connecting these three issues. By developing an improved image analysis workflow we shortened project timelines, decreased technical variation, and thus enabled large‐scale proteomics studies that are statistically powered. Rather than detecting protein spots on each gel image and matching spots across gel images, the improved workflow is based on aligning images first, then creating a consensus spot pattern and finally propagating the consensus spot pattern to all gel images for quantitation. This results in a data table without gaps. As an example we show here a study aimed at discovering circulating biomarkers for chronic obstructive pulmonary disease (COPD). Eight candidate biomarkers were identified by comparing plasma from 24 smokers with COPD and 24 smokers without COPD. Among the candidates are proteins such as plasma retinal‐binding protein (RETB) and fibrinogen that had previously been linked to the disease and are frequently monitored in COPD patients, as well as other proteins such as apolipoprotein E (ApoE), inter‐α‐trypsininhibitor heavy chain H4 (ITIH4), and glutathione peroxidase.
Binding of ciguatera toxins to the voltage‐gated Kv1.5 potassium channel in the open state. Docking of gambierol and molecular dynamics simulations of a homology model
Authors: Pietra Francesco
Published: July 2008

Ciguatera poisoning is a toxinological syndrome from ingestion of seafood contaminated by dinoflagellate toxins which has serious social and economic consequences from the Indo‐Pacific to the Caribbean. These polyannealed ethereal‐ring toxins, which comprise ciguatoxins, maitotoxin, and gambierol, are known to affect ion channels. Reported here are the first indications at molecular level as to the mode of interaction of these toxins with ion channels. The study concerns gambierol, an eight‐ring ladder polyether which is known to affect TRPV1‐type of thermal and pain sensation channels, as well as to inhibit voltage‐gated currents in K+ channels of mouse taste cells. Automated docking of gambierol on a homology model of the voltage‐gated Kv1.5 potassium ion channel in implicit solvent is followed by molecular dynamics (MD) simulation of the complex in a POPC membrane solvated with water. It is found that gambierol binds to the internal helices of the channel, unequally to the different subunits of the tetramer. Such unequal binding is a novel observation that should stimulate and aid developing a much demanded medical treatment of ciguatera poisoning. Copyright © 2008 John Wiley & Sons, Ltd.
3H‐1,2‐Dithiole‐3‐thione derivatives as novel solvatochromic dyes
Authors: Fracaroli Alejandro M. , Silva O. Fernando , Granados Alejandro M. , de Rossi Rita H.
Published: July 2008

The UV–Vis spectrum of 5‐(1‐butylthio)‐3H‐1,2‐dithiole‐3‐thione (1a) and that of the chromium pentacarbonyl complex of 5‐methyl‐3H‐1,2‐dithiole‐3‐thione (3) present significant changes with the solvent polarity. The two absorption bands shown by the compounds in the region above 300 nm were identified by theoretical calculations. For Compound 1a these are n→π* and →π* transitions and for Compound 3 the longest wavelength absorption corresponds to a charge transfer band and shows a remarkably negative solvatochromism. Not only has the wavelength of maximum absorption changed with the solvent but also the ratio of the absorbances at the two wavelengths. The effect of solvents was correlated with solvatochromic parameters such as π* and α. The spectrum of 5‐(1‐butylthio)‐3H‐1,2‐dithiole‐3‐one (2) was also measured in different solvents but in this case the changes observed are less significant than for the other two compounds. The spectra of 1a and 3 were also determined in the presence of anionic (SDS), cationic (CTAB), and neutral surfactants (Brig‐35) and it is shown that these compounds can be used as probes for the polarity of the binding sites of organized assemblies. Copyright © 2008 John Wiley & Sons, Ltd.
Nano‐Structured Cell‐Adhesive and Cell‐Repulsive Plasma‐Deposited Coatings: Chemical and Topographical Effects on Keratinocyte Adhesion
Authors: Sardella Eloisa , Detomaso Loredana , Gristina Roberto , Senesi Giorgio S. , Agheli Hossein , Sutherland Duncan S. , d'Agostino Riccardo , Favia Pietro
Published: July 2008

Cell‐adhesive and cell‐repulsive coatings have been plasma‐deposited on poly(ethylene terephthalate) surfaces previously structured with nano‐metric conical features by means of colloidal lithography. Surface analysis revealed that both coatings are conformal on nano‐structured substrates, with their wettability depending on the substrate morphology. The effect of surface chemistry and surface topography on cell adhesion has been investigated and clarified. The adhesion of a human keratinocyte cell‐line was found to be strongly dependent on the surface topography for plasma‐deposited acrylic acid (cell‐adhesive), and on the surface chemistry for poly(ethylene oxide)‐like (cell‐repulsive) coatings.

magnified image
Global Model of He/O2 and Ar/O2 Atmospheric Pressure Glow Discharges
Authors: Park Ganyoung , Lee Hyunwoo , Kim Gyoocheon , Lee Jae Koo
Published: July 2008

Atmospheric pressure glow discharges (APGDs) have widespread applications, including sterilization, cancer cell treatment, deposition, and surface modification due to their rather simple configurations, thanks to no need for vacuum system and their great capability to generate reactive species such as radical oxygen species. Helium and argon are widely used as feeding gases, achieving stable operations for wide ranges of parameters in atmospheric pressure, and oxygen is added into these gases to generate more reactive oxygen species (ROS), which play a significant role in sterilization. As the measurements of species densities and electron temperature in APGDs are difficult, we have developed the zero‐dimensional global model of He/O2 and Ar/O2 APGDs to calculate the densities of several kinds of species and electron temperature. It was shown that even though small fraction of oxygen less than 1% was added to helium or argon, electrons dissipated most of their energy through collisions with oxygen molecules rather than helium or argon atoms. The densities of electron, atomic oxygen, and ozone of Ar/O2 were higher than those of He/O2; however, the electron temperature of He/O2 was higher than that of Ar/O2. When the pulsed power is applied, the time‐averaged electron temperature for the shorter pulse period and the larger duty ratio increased, and the electron density decreased as the duty ratio increased.

magnified image
Modeling High‐Pressure Microplasmas: Comparison of Fluid Modeling and Particle‐in‐Cell Monte Carlo Collision Modeling
Authors: Hong Yong Jun , Lee Seung Min , Kim Gyoo Cheon , Lee Jae Koo
Published: July 2008

The results of simulations using a fluid model and a PIC‐MCC model are compared, and the PIC‐MCC is used to explore the kinetics of energetic ions and electrons in microplasmas. The kinetics are studied under helium discharges at 760 Torr and Ne/Xe DBD discharges at 300 Torr with various driving currents and geometries. While EEPFs of microplasmas at high pressure show strong nonequilibrium behavior near the sheath region, EEDFs on the powered and grounded electrodes have qualitatively different features depending on input power. The effective temperature and energy flux of charged particles can be obtained from the slopes in EEPFs and IEPFs. The effects of input power, discharge length, and mixture gas concentration on the IEDFs on each electrode are discussed.

magnified image
States of Biological Components in Bacteria and Bacteriophages during Inactivation by Atmospheric Dielectric Barrier Discharges
Authors: Yasuda Hachiro , Hashimoto Mai , Rahman Md. Masudur , Takashima Kazunori , Mizuno Akira
Published: July 2008

Atmospheric DBD has been applied to the wet state of Escherichia coli and bacteriophage‐λ. Upon DBD treatment, both E.coli and λphage were immediately inactivated. The states of different biological components were monitored during the course of inactivation. Only minor and slow degradation of proteins, DNA, and membranes was observed, a remarkable degradation was seen only after the completion of sterilization. Analysis of GFP recombinantly introduced into E.coli cells proved that the DBD has a prominent protein denaturation activity without affecting peptide bonds. The irreversible denaturation of proteins, seen in the early stage of DBD application, may play a central role in inactivation of both the bacteria and bacteriophages.

magnified image
An uncommon cause of a vascular mass in the left lung in neonate: A case report with a brief review of literature
Authors: Reddy Sreenivas , Kumar Rohit
Published: July 2008

A 20‐day‐old female child presented with mild respiratory distress since first week of life. On examination there was an ejection systolic murmur at left sternal border. Chest x‐ray revealed well‐defined mass in the left lung. Echocardiogram showed features suggestive tetrology of fallot with absent pulmonary valve with massively dilated main and left pulmonary artery. We report a rare cause of vascular mass in a neonate due to tetrology fallot with absent pulmonary valve. Pediatr Pulmonol. 2008; 43:822–823. © 2008 Wiley‐Liss, Inc.
A novel sidestream ultrasonic flow sensor for multiple breath washout in children
Authors: Fuchs Susanne I. , Sturz J. , Junge S. , Ballmann M. , Gappa M.
Published: July 2008

Objective

Inert gas multiple breath washout (MBW) for measuring Lung Clearance Index using mass spectrometry and 4% sulfur hexafluoride (SF6) as the tracer gas has been shown to be sensitive for detecting early Cystic Fibrosis (CF) lung disease. However, mass spectrometry requires bulky equipment and is expensive to buy and maintain. A novel sidestream ultrasonic device may overcome this problem. The aims of this study were to assess the feasibility and clinical validity of measuring lung volume (functional residual capacity, FRC) and the LCI using the sidestream ultrasonic flow sensor in children and adolescents with CF in relation to spirometry and plain chest radiographs.

Patients and Methods

MBW using the sidestream ultrasonic device and conventional spirometry were performed in 26 patients with CF and 22 healthy controls.

Results

In the controls (4.7–17.7 years) LCI was similar to that reported using mass spectrometry (mean (SD) 6.7 (0.5)). LCI was elevated in 77% of the CF children (6.8–18.9 years), whereas spirometry was abnormal in only 38.5%, 61.5%, and 26.9% for FEV1, MEF25, and FEV1/FVC, respectively. This was more marked in children <10 years. LCI correlated with the Crispin‐Norman score, whereas FEV1 did not.

Conclusions

Sidestream ultrasonic MBW is a valid and simple alternative to mass spectrometry for assessing ventilation homogeneity in children. Pediatr Pulmonol. 2008; 43:731–738. © 2008 Wiley‐Liss, Inc.
Effect of bacterial filter on measurement of interrupter resistance in preschool and school‐aged children
Authors: Thamrin C. , Frey U.
Published: July 2008

Background

The interrupter technique is increasingly used in preschool children to assess airway resistance (Rint). Use of a bacterial filter is essential for prevention of cross‐infection in a clinical setting. It is not known how large an effect this extra resistance and compliance exert upon interrupter measurements, especially on obstructive airways and in smaller children. We aim to determine the contribution of the filter to Rint, in a sample of children attending lung function testing at an asthma clinic.

Methods

Interrupter measurements were performed according to ATS/ERS guidelines during quiet normal breathing at an expiratory flow trigger of 200 ml s−1, with the child seated upright with cheeks supported and wearing a nose clip. A minimum of 10 interrupter measurements was made with and without a bacterial filter. Spirometric and plethysmographic tests were also performed.

Results

A small but significant difference (0.12 (95% CI 0.06–0.17) kPa s L−1, P = 0.0002) with 2× SD of 0.34 kPa s L−1 was observed between Rint with and without filter in 39 children, with a large spread. This difference was not dependent on Rint magnitude, age or height, nor on lung function parameters (effective resistance, forced expiratory volume in 1 sec, and maximal expiratory flow at 50% of expired vital capacity).

Conclusions

A bacterial filter causes a small difference but is not clinically significant, with a wide spread comparable to the variability of the technique and recommended cut‐offs for assessing repeatability and bronchodilation. Age, height or severity of obstruction need not be corrected for in general. Pediatr Pulmonol. 2008; 43:781–787. © 2008 Wiley‐Liss, Inc.
Spirometry in an unselected group of 6‐year‐old children: The DARC birth cohort study
Authors: Kjaer Henrik Fomsgaard , Eller Esben , Bindslev‐Jensen Carsten , Høst Arne
Published: July 2008

This study presents reference equations for spirometric parameters in 6‐year‐old children and evaluates the ability of spirometry to discriminate healthy children from children with asthma. Baseline spirometry and respiratory symptoms were assessed in 404 children participating in a longitudinal birth cohort study. Children with known asthma, possible asthma and a control group also performed bronchodilator measurements. At least two acceptable flow‐volume curves at baseline were obtained by 368/404 children (91%). The two best values for FEV1 and FVC were within 5% of each other in 88% and 83% of children, respectively. Linear regression analyses for 242 children included in the reference population demonstrated height to be the main predictor of all spirometric indices except FEV1/FVC. FEV1, FEV75, and FVC correlated reasonably to anthropometric data in contrast to flow parameters. Gender differences were found for FEV1, FVC, and FEV75, but not for flow parameters. Asthma was diagnosed in 25/404 children. Baseline lung function in healthy children and children with asthma overlapped, although asthmatic children could be discriminated to some extent. Bronchodilator tests showed a difference in ΔFEV1(mean) between healthy children and children with asthma (3.1% vs. 6.1%, P < 0.05). At a cut‐off point of ΔFEV1 = 7.8%, bronchodilator tests had a sensitivity of 46% and a specificity of 92% for current asthma. Spirometry including bronchodilator measurements was demonstrated to be feasible in 6‐year‐old children and reference values were determined. Spirometry aids the diagnosis of asthma in young children, but knowledge on sensitivity and specificity of these measurements is a prerequisite. Pediatr Pulmonol. 2008; 43:806–814. © 2008 Wiley‐Liss, Inc.
Clinical application of antibody microarray in chronic kidney disease: How far to go?
Authors: Lv Lin‐Li , Liu Bi‐Cheng
Published: July 2008

Chronic kidney disease (CKD) that affects about 10% of the adult population has been shown as a worldwide public health problem in recent years. Both basic and clinical investigations have identified complex disease‐associated protein networks involved in the pathophysiologic processes of CKD. The traditional single‐assay approach and proteomic analysis of those related proteins have given birth to a steadily increasing panel of molecules that may have the potential to serve as biomarkers for CKD. However, both approaches suffered from some shortcomings from a technological point of view. Antibody microarray (AbM) is characterized by high sensitivity, specificity, and quantitative ability for a particular set of known proteins. However, its application in CKD has been very limited so far. The objective of this review, therefore, is to address the potential applications of AbM in studying of CKD. We will briefly discuss the proteins involved in the development of CKD, future directions in which AbM approaches would probably display its potential and also some key issues that need to be considered in application of this novel technique.
Analysis of molecular forms of albumin in urine
Authors: Hortin Glen L. , Sviridov Denis
Published: July 2008

Albumin is not only one of the most abundant urinary protein components and one of the most widely used clinical markers for kidney disease, it also is a significant source of molecular complexity of the urinary proteome and peptidome. Urine contains multiple fragments and modified forms of albumin. Analysis of molecular forms of albumin in urine is of fundamental importance for understanding clinical assays for albumin quantification, specimen stability, and proteomic and peptidomic analysis of urine.
Proteomic strategies in bladder cancer: From tissue to fluid and back
Authors: Gromov Pavel , Moreira José M. A. , Gromova Irina , Celis Julio E.
Published: July 2008

We have applied protein expression profiling technologies in combination with immunohistochemistry, using fresh tissue and urine samples, to assess bladder cancer heterogeneity and prognosis as well as to generate protein markers for tumor progression and early diagnosis of the disease. Here, we review some selected lines of investigation and approaches undertaken by our laboratory, drawing on more than 15 years of experience in bladder cancer proteomics, to highlight a number of issues that may be useful for researchers entering the field. In particular, we address the identification of markers for bladder cancer progression and exemplify the potential of gel‐based proteomic profiling of urine samples for the early detection of urothelial carcinomas. In addition, we provide a brief description of a novel and highly promising source of biomarkers, the tumor interstitial fluid (TIF) that perfuses the tumor microenvironment.
Analysis of the urine proteome in patients with pancreatic ductal adenocarcinoma
Authors: Weeks Mark E. , Hariharan Deepak , Petronijevic Ljiljana , Radon Tomasz P. , Whiteman Hannah J. , Kocher Hemant M. , Timms John F. , Lemoine Nicholas R. , Crnogorac‐Jurcevic Tatjana
Published: July 2008

Pancreatic ductal adenocarcinoma (PDAC) accounts for over 213 000 deaths worldwide each year, largely due to late diagnosis. One of the risk factors for the development of PDAC is chronic pancreatitis (CP); the intense desmoplastic reaction makes differentiation between the two conditions extremely difficult. In order to identify biomarkers for noninvasive diagnosis, we performed 2‐D DIGE analysis of urine samples from healthy individuals and patients with PDAC and CP. Despite considerable intersample heterogeneity, a total of 127 statistically valid (p<0.05), differentially expressed protein spots were detected, 101 of which were identified using MALDI‐TOF MS. A number of these, including annexin A2, gelsolin and CD59 have already been associated with PDAC, however, their validation using immunoblotting proved challenging. This is probably due to extensive PTMs and processing thus indicating the need for raising specific antibodies for urinary proteins. Despite this, our study clearly demonstrates that urine is a valid source of noninvasive biomarkers in patients with pancreatic diseases.
The urinary proteome in diabetes and diabetes‐associated complications: New ways to assess disease progression and evaluate therapy
Authors: Rossing Kasper , Mischak Harald , Rossing Peter , Schanstra Joost P. , Wiseman Alex , Maahs David M.
Published: July 2008

Diabetes represents one of the main chronic diseases worldwide. Diabetes and its associated complications may be detectable even at early stages in the urinary proteome. In this article we review the current literature on urinary proteomics applied to the study of diabetes and diabetic complications. Further, we present recent data that strongly indicate urinary proteome analysis may be a valuable tool in detecting diabetes‐associated pathophysiological changes at an early stage, and also may enable assessment of disease progression and efficacy of therapy. Current data indicate that collagen‐derived peptides represent one of the main peptidic components in urine, which are consistently found at reduced levels in diabetes. It is tempting to speculate that this decrease in urinary collagen‐derived peptides is related to an increase in extracellular matrix deposition which is a major complication in diabetes. Therefore, urinary proteome analysis might enable noninvasive assessment of this process at an early stage via determination of specific collagen fragments. This may open an avenue towards targeted therapeutic intervention.
Identification of phosphoproteins in kidney tissues from patients with autosomal dominant polycystic kidney disease
Authors: Liu Yawei , Dai Bing , Mei Changlin , Zhang Yan , Xiong Xishan , Sandford Richard
Published: July 2008

Protein phosphorylation is a very important PTM. Phosphorylation/dephosphorylation of a protein can alter its behavior in almost every conceivable way. Previous studies indicate that abnormal phosphorylation is involved in the pathogenesis of autosomal dominant polycystic kidney disease (ADPKD). However, large‐scale proteomic analysis of altered phosphoproteins in ADPKD has not been reported. In this study, total proteins from ADPKD cystic kidney tissues (n = 5) and normal kidney tissues (n = 5) were extracted and phosphoproteins were enriched by phosphate metal affinity chromatography, then separated by 2‐DE and identified by LC‐MS/MS. Between the two groups, 48 protein spots showing more than a twofold difference were detected. Among them, 28 spots were up‐regulated and 20 down‐regulated in ADPKD kidney tissues. Of these, 38 different proteins were identified including cell signaling proteins, cytoskeleton proteins, mitochondria metabolic enzymes, antioxidant proteins, molecular chaperones, transcription factors and regulators. Two differential phosphoproteins, annexin II and tropomyosin, were further confirmed by immunoprecipitation and Western blot analysis. The results show that there are many kinds of abnormal phosphoproteins in ADPKD cystic kidney tissues. More studies on the functions of the differential phosphoproteins may provide us new clues for ADPKD pathogenesis and treatment.
Proteomic analysis of a podocyte vesicle‐enriched fraction from human normal and pathological urine samples
Authors: Lescuyer Pierre , Pernin Agnès , Hainard Alexandre , Bigeire Caty , Burgess Jennifer A. , Zimmermann‐Ivol Catherine , Sanchez Jean‐Charles , Schifferli Jürg A. , Hochstrasser Denis F. , Moll Solange
Published: July 2008

Podocytes (glomerular visceral epithelial cells) release vesicles into urine. Podocyte vesicle‐enriched fractions from normal and pathological human urine samples were prepared for proteomic analysis. An immunoadsorption method was applied and enrichment of podocyte vesicles was assessed. We identified 76 unique proteins. One protein, serum paraoxonase/arylesterase 1 (PON‐1), was newly identified in normal human urine sample. We confirmed this result and showed PON‐1 expression in normal human kidney. These results demonstrated the potential for using the urine samples enriched in podocyte vesicles as a starting material in studies aimed at discovery of biomarkers for diseases.
The ratio of matrix metalloproteinase to E‐cadherin expression: A pilot study to assess mRNA and protein expression among African American prostate cancer patients
Authors: Pettaway Curtis A. , Song Renduo , Wang Xuemei , Sanchez‐Ortiz Ricardo , Spiess Philippe E. , Strom Sara , Troncoso Patricia
Published: July 2008

BACKGROUND

We assessed the expression of Matrix Metalloproteinase (MMP) to E‐cadherin (M/E ratio) to determine the correlation of gene expression with pathologic variables and outcome in a cohort of African American (AA) prostate cancer patients.

METHODS

Tumors from formalin‐fixed, paraffin embedded RP specimens were examined. Gleason scores were 6, 7, and ≥8 in 7, 16, 13 tumors, respectively. Pathologic stage was organ confined (pT2) in 18 and advanced (>pT2) in 18 tumors. A colorimetric mRNA in situ hybridization (ISH) assay was performed using biotinylated anti‐sense oligonucleotide probes for MMP 2 and 9, as well as for E‐cadherin gene transcripts. Immunohistochemistry (IHC) was performed utilizing specific monoclonal antibodies to detect the above genes. Image analysis was performed to determine the intensity of both mRNA and protein expression. Two reviewers analyzed ISH gene expression independently.

RESULTS

The M/E expression ratio was significantly increased at the invasive edge (but not the center) of tumors of higher Gleason score (P = 0.02 and 0.0008) and pathologic stage (P = 0.0001 and <0.0001) when examined by both ISH and IHC. Significant variability in ISH staining interpretation was noted within and among the two study reviewers. An M/E ratio >2.5 was associated with biochemical recurrence after radical prostatectomy in addition to tumor pathologic stage subsequent to univariate statistical analysis.

CONCLUSIONS

The M/E ratio characterizes an important aspect of the molecular phenotype associated with the histologic progression of prostate cancer among African American prostate cancer patients. A larger comparative study is required to determine potential racial variation and prognostic significance of gene expression. Prostate 68: 1467–1476, 2008. © 2008 Wiley‐Liss, Inc.
Phase II study of fulvestrant (faslodex®) in castration resistant prostate cancer
Authors: Chadha Manpreet K. , Ashraf Umeer , Lawrence David , Tian Lili , Levine Ellis , Silliman Carrie , Escott Paul , Payne Valencia , Trump Donald L.
Published: July 2008

BACKGROUND

Preclinical evidence supports the role of estrogen receptor signaling in prostate cancer. In this trial we investigated the tolerability and efficacy of fulvestrant, a pure estrogen receptor antagonist, in the treatment of castration resistant prostate cancer (CRPC).

METHODS

Patients with CRPC were enrolled after written informed consent. Fulvestrant was administered by intramuscular injection at a dose of 500 mg on day 0, then 250 mg on day 14, day 28 and monthly thereafter. History, physical examination, serum prostate specific antigen (PSA) levels and toxicity was evaluated monthly. Radiographic studies were repeated every 3 months to assess disease. Treatment was continued until disease progression, unacceptable toxicity, non‐compliance or consent withdrawal.

RESULTS

Twenty patients were enrolled over a period of six months. All patients were Caucasians with median age of 69.5 years [range: 47–85 years]. Sixteen patients (80%) had radiological evidence of metastasis and four patients (20%) had rising PSA as the only evidence of progressive disease. Patients received a median of three treatment cycles of fulvestrant [range: 1–11]. Median time to progression was 4.3 months (95% confidence interval of 3–5.7 months) and median overall survival was 19.4 months (range: 9.9–19.4 months) after a median follow‐up of 16 months. No patient showed ≥50% reduction in PSA or radiologic improvement. Few adverse events were noted, none of which were attributed directly to fulvestrant.

CONCLUSION

Fulvestrant was well tolerated but failed to produce clinical or PSA response in men with CRPC. Prostate 68: 1461–1466, 2008. © 2008 Wiley‐Liss, Inc.
Insulin‐like growth factor‐I, insulin‐like growth factor binding protein‐3 and risk of benign prostate hyperplasia in the prostate cancer prevention trial
Authors: Neuhouser Marian L. , Schenk Jeannette , Song Yoon Ju , Tangen Catherine M. , Goodman Phyllis J. , Pollak Michael , Penson David F. , Thompson Ian M. , Kristal Alan R.
Published: July 2008

BACKGROUND

We investigated whether peptides involved in cellular proliferation and apoptosis, [insulin‐like growth factor I (IGFI) and its major binding protein (insulin‐like growth factor binding protein 3)], predicted risk of benign prostate hyperplasia (BPH).

METHODS

We conducted a nested‐case–control study in the placebo arm of the prostate cancer prevention trial (PCPT). Cases (n = 727) were men with surgical or medical treatment for BPH; two or more IPSS scores >14; or two scores of at least five points over baseline one of which was ≥12. Controls (n = 727) were frequency matched by age to cases, reported no BPH treatment, and no IPSS score >8. Cases and controls remained on the PCPT placebo and were followed closely until their 7‐year PCPT anniversary. Baseline serum was analyzed for IGFI and IGFBP3. Unconditional logistic regression and polytomous regression estimated the multivariate‐adjusted odds ratio (OR) for BPH risk.

RESULTS

IGFBP3 was inversely and the IGFI:IGFBP3 ratio was positively associated with BPH risk, but findings were statistically significant only for men with severe symptoms (OR = 0.60, 95% CI = 0.40–0.90 for the fifth vs. first quintile of IGFBP3, P‐trend = 0.01). Associations did not differ by age (<65 or ≥65 years), and there was a suggestion that the IGFI:IGFBP3 – BPH risk association may be stronger among overweight men.

CONCLUSIONS

A high IGFI:IGFBP3 ratio was associated with increased BPH risk, and high serum IGFBP3 was associated with decreased BPH risk among men with severe symptoms. These results confirm findings from other recent studies. Prostate 68: 1477–1486, 2008. © 2008 Wiley‐Liss, Inc.
Signaling pathways of PDZ2 domain: A molecular dynamics interaction correlation analysis
Authors: Kong Yifei , Karplus Martin
Published: July 2008

PDZ domains are found in many signaling proteins. One of their functions is to provide scaffolds for forming membrane‐associated protein complexes by binding to the carboxyl termini of their partners. PDZ domains are thought also to play a signal transduction role by propagating the information that binding has occurred to remote sites. In this study, a molecular dynamics (MD) simulation‐based approach, referred to as an interaction correlation analysis, is applied to the PDZ2 domain to identify the possible signal transduction pathways. A residue correlation matrix is constructed from the interaction energy correlations between all residue pairs obtained from the MD simulations. Two continuous interaction pathways, starting at the ligand binding pocket, are identified by a hierarchical clustering analysis of the residue correlation matrix. One pathway is mainly localized at the N‐terminal side of helix α1 and the adjacent C‐terminus of loop β1‐β2. The other pathway is perpendicular to the central β‐sheet and extends toward the side of PDZ2 domain opposite to the ligand binding pocket. The results complement previous studies based on multiple sequence analysis, NMR, and MD simulations. Importantly, they reveal the energetic origin of the long‐range coupling. The PDZ2 results, as well as the earlier rhodopsin analysis, show that the interaction correlation analysis is a robust approach for determining pathways of intramolecular signal transduction. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Rapid comparison of properties on protein surface
Authors: Sael Lee , La David , Li Bin , Rustamov Raif , Kihara Daisuke
Published: July 2008

The mapping of physicochemical characteristics onto the surface of a protein provides crucial insights into its function and evolution. This information can be further used in the characterization and identification of similarities within protein surface regions. We propose a novel method which quantitatively compares global and local properties on the protein surface. We have tested the method on comparison of electrostatic potentials and hydrophobicity. The method is based on 3D Zernike descriptors, which provides a compact representation of a given property defined on a protein surface. Compactness and rotational invariance of this descriptor enable fast comparison suitable for database searches. The usefulness of this method is exemplified by studying several protein families including globins, thermophilic and mesophilic proteins, and active sites of TIM β/α barrel proteins. In all the cases studied, the descriptor is able to cluster proteins into functionally relevant groups. The proposed approach can also be easily extended to other surface properties. This protein surface‐based approach will add a new way of viewing and comparing proteins to conventional methods, which compare proteins in terms of their primary sequence or tertiary structure. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Crystal structure of human carbonic anhydrase XIII and its complex with the inhibitor acetazolamide
Authors: Di Fiore Anna , Monti Simona Maria , Hilvo Mika , Parkkila Seppo , Romano Vincenza , Scaloni Andrea , Pedone Carlo , Scozzafava Andrea , Supuran Claudiu T. , De Simone Giuseppina
Published: July 2008

The cytosolic isoform XIII is a recently discovered member of the human carbonic anhydrase (hCA, EC 4.2.1.1) family. It is selectively expressed among other tissues in the reproductive organs, where it may control pH and ion balance regulation, ensuring thus proper fertilization conditions. The authors report here the X‐ray crystallographic structure of this isozyme in the unbound state and in complex with a classical sulfonamide inhibitor, namely acetazolamide. A detailed comparison of the obtained structural data with those already reported for other CA isozymes provides novel insights into the catalytic properties of the members of this protein family. On the basis of the inhibitory properties of acetazolamide against various cytosolic/transmembrane isoforms and the structural differences detected within the active site of the various CA isoforms, further prospects for the design of isozyme‐specific CA inhibitors are here proposed. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Computational protein design with side‐chain conformational entropy
Authors: Sciretti Daniele , Bruscolini Pierpaolo , Pelizzola Alessandro , Pretti Marco , Jaramillo Alfonso
Published: July 2008

Recent advances in modeling protein structures at the atomic level have made it possible to tackle “de novo” computational protein design. Most procedures are based on combinatorial optimization using a scoring function that estimates the folding free energy of a protein sequence on a given main‐chain structure. However, the computation of the conformational entropy in the folded state is generally an intractable problem, and its contribution to the free energy is not properly evaluated. In this article, we propose a new automated protein design methodology that incorporates such conformational entropy based on statistical mechanics principles. We define the free energy of a protein sequence by the corresponding partition function over rotamer states. The free energy is written in variational form in a pairwise approximation and minimized using the Belief Propagation algorithm. In this way, a free energy is associated to each amino acid sequence: we use this insight to rescore the results obtained with a standard minimization method, with the energy as the cost function. Then, we set up a design method that directly uses the free energy as a cost function in combination with a stochastic search in the sequence space. We validate the methods on the design of three superficial sites of a small SH3 domain, and then apply them to the complete redesign of 27 proteins. Our results indicate that accounting for entropic contribution in the score function affects the outcome in a highly nontrivial way, and might improve current computational design techniques based on protein stability. Proteins 2009. © 2008 Wiley‐Liss, Inc.
MADAMM: A multistaged docking with an automated molecular modeling protocol
Authors: Cerqueira N. M. F. S. A. , Bras N. F. , Fernandes P. A. , Ramos M. J.
Published: July 2008

Dealing with receptor flexibility in docking methodology is still a problem. The main reason behind this difficulty is the large number of degrees of freedom that have to be considered in this kind of calculations. In this paper, we present an automated procedure, called MADAMM, that allows flexibilization of both the receptor and the ligand during a multistaged docking with an automated molecular modeling protocol. We show that the orientation of particular residues at the interface between the protein and the ligand have a crucial influence on the way they interact during the docking process, and the standard docking methodologies failed to predict their correct mode of binding. We present some examples that demonstrate the capabilities of this approach when compared with traditional docking methodologies. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Thermodynamics of calmodulin binding to cardiac and skeletal muscle ryanodine receptor ion channels
Authors: Meissner Gerhard , Pasek Daniel A. , Yamaguchi Naohiro , Ramachandran Srinivas , Dokholyan Nikolay V. , Tripathy Ashutosh
Published: July 2008

The skeletal muscle (RyR1) and cardiac muscle (RyR2) ryanodine receptor calcium release channels contain a single, conserved calmodulin (CaM) binding domain, yet are differentially regulated by CaM. Here, we report that high‐affinity [35S]CaM binding to RyR1 is driven by favorable enthalpic and entropic contributions at Ca2+ concentrations from <0.01 to 100 μM. At 0.15 μM Ca2+, [35S]CaM bound to RyR2 with decreased affinity and binding enthalpy compared with RyR1. The rates of [35S]CaM dissociation from RyR1 increased as the temperature was raised, whereas at 0.15 μM Ca2+ the rate from RyR2 was little affected. The results suggest major differences in the energetics of CaM binding to and dissociation from RyR1 and RyR2. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Molecular dynamics simulation of the acidic compact state of apomyoglobin from yellowfin tuna
Authors: Bismuto Ettore , Di Maggio Emiddio , Pleus Stefan , Sikor Martin , Röcker Carlheinz , Nienhaus G. Ulrich , Lamb Don C.
Published: July 2008

A molecular model of the acidic compact state of apomyoglobin (A‐state) from yellowfin tuna was obtained using molecular dynamics simulations (MD) by calculating multiple trajectories. To cause partial unfolding within a reasonable amount of CPU time, both an acidic environment (pH 3 and 0.15M NaCl) and a temperature jump to 500 K were needed. Twenty‐five acidic structures of apomyoglobin were generated by MD, 10 of them can be clustered by RMSD in an average structure having a common hydrophobic core as was reported for acidic sperm whale apomyoglobin, with shortened helices A,G,E, and H (the helix A appears to be translated along the sequence). Prolonging the MD runs at 500 K did not cause further substantial unfolding, suggesting that the ensemble of generated structures is indicative of a region of the conformational space accessible to the apoprotein at acidic pH corresponding to a local energy minimum. The comparison of experimentally determined values of specific spectroscopic properties of the apomyoglobin in acidic salt conditions with the expected ones on the basis of the MD generated structures shows a reasonable agreement considering the characteristic uncertainties of both experimental and simulation techniques. We used frequency domain fluorometry, acrylamide fluorescence quenching, and fluorescence correlation spectroscopy together with far UV circular dichroism to estimate the helical content, the Stern–Volmer quenching constant and the radius of gyration of the protein. Tuna apomyoglobin is a single tryptophan protein and thus, interpretation of its intrinsic fluorescence is simpler than for other proteins. The high sensitivity of the applied fluorescence techniques enabled experiments to be performed under very dilute conditions, that is, at concentrations of subnanomolar for the FCS measurements and 6 μM for the other fluorescence measurements. As high concentrations of proteins can strongly affect the association equilibrium among partially unfolded states, fluorescence techniques can provide complementary information with respect to other techniques requiring higher sample concentrations, such as NMR. The analysis of exposed hydrophobic regions in each of the MD‐generated acidic structures reveals potential candidates involved in the aggregation processes of apomyoglobin in the acidic compact state. Our investigation represents an effective model system for studying amyloid fibril formation found in important diseases that are believed to proceed via aggregation of protein in the molten globule state. Proteins 2009. © 2008 Wiley‐Liss, Inc.
The structure of the PP2A regulatory subunit B56γ: The remaining piece of the PP2A jigsaw puzzle
Authors: Magnusdottir Audur , Stenmark Pål , Flodin Susanne , Nyman Tomas , Kotenyova Tetyana , Gräslund Susanne , Ogg Derek , Nordlund Pär
Published: July 2008

The PP2A serine/threonine phosphatase regulates a plethora of cellular processes. In the cell the predominant form of the enzyme is a heterotrimer, formed by a core dimer composed of a catalytic and a scaffolding subunit, which assemble together with one of a range of different regulatory B subunits. Here, we present the first structure of a free non‐complexed B subunit, B56γ. Comparison with the recent structures of a heterotrimeric complex and the core dimer reveals several significant conformational changes in the interface region between the B56γ and the core dimer. These allow for an assembly scheme of the PP2A holoenzyme to be put forth where B56γ first complexes with the scaffolding subunit and subsequently binds to the catalytic subunit and this induces the formation of a binding site for the invariant C‐terminus of the catalytic subunit that locks in the complex as a last step of assembly. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Energetics of the loop‐to‐helix transition leading to the coiled‐coil structure of influenza virus hemagglutinin HA2 subunits
Authors: Huang Qiang , Korte Thomas , Rachakonda P. Sivaramakrishna , Knapp Ernst‐Walter , Herrmann Andreas
Published: July 2008

Fusion of influenza virus with the endosomal membrane of the host cell is mediated by the homotrimer‐organized glycoprotein hemagglutinin (HA). Its fusion activity is triggered by a low pH‐mediated conformational change affecting the structure of the HA1 and HA2 subunits. The HA2 subunits undergo a loop‐to‐helix transition leading to a coiled‐coil structure, a highly conserved motif for many fusion mediating viral proteins. However, experimental studies showed that the HA2 coiled‐coil structure is stable at neutral and low pH, implying that there is no direct relationship between low pH and the HA2 loop‐to‐helix transition. To interpret this observation, we used a computational approach based on the dielectric continuum solvent model to explore the influence of water and pH on the free energy change of the transition. The computations showed that the electrostatic interaction between HA2 fragments and water is the major driving force of the HA2 loop‐to‐helix transition leading to the coiled‐coil structure, as long as the HA1 globular domain covering the HA2 subunits in the nonfusion competent conformation is reorganized and thereby allows water molecules to interact with the whole loop segments of the HA2 subunits. Moreover, we show that the energy released by the loop‐to‐helix transition may account for those energies required for driving the subsequent steps of membrane fusion. Such a water‐driven process may resemble a general mechanism for the formation of the highly conserved coiled‐coil motif of enveloped viruses. Proteins 2009. © 2008 Wiley‐Liss, Inc.