bluuebunny/crossref_metadata_2025 huggingface dataset:
The implementation of temperature control to an inductive‐coil photoconductance instrument for the range of 0–230°C
Authors: Paudyal B. B. , McIntosh K. R. , Macdonald D. H. , Richards B. S. , Sinton R. A.
Published: July 2008

A new device setup for temperature and injection‐dependent lifetime spectroscopy (TIDLS) is described. It comprises two off‐the‐shelf components: a heating and cooling stage (HCS) from INSTEC and an inductive‐coil photoconductance (PC) instrument (WCT‐100) from Sinton Consulting Inc. The HCS was fitted to the WCT‐100 in a manner that circumscribes the inductive coil (the sensor) of the RF bridge circuit and controls the temperature of the wafer effectively. This setup has the advantage of requiring minor modifications to industry standard instruments while attaining a large temperature range. As experimental verification, injection‐dependent lifetimes were measured over a temperature range, 0–230°C, in three iron‐implanted silicon wafers. The measured lifetimes are consistent with the Shockley–Read–Hall equation using the impurity concentration calculated from the implant dose and the energy level and capture cross‐sections of interstitial iron from the literature. Copyright © 2008 John Wiley & Sons, Ltd.
Communication disorders in the school: Perspectives on academic and social success an introduction
Authors: Thatcher Karen L. , Fletcher Kathryn , Decker Blair
Published: July 2008

The critical role of communication in schools cannot be understated. Communication skills are a necessity both in the academic and social atmosphere of the school environment. Unfortunately, there are a large number of children in the schools today identified with speech and language disorders. This special edition of Psychology in the Schools examined issues that impact the academic and social functioning of such children. Several articles are focused on potential early intervention strategies or services surrounding literacy and social skills that may enhance the success of children with communication disorders and/or at risk for communication disorders (e.g., Chapman, Denning, & Jamison, 2008; Thatcher & Fletcher, 2008; van Kleeck, 2008). Two other articles tackle promising strategies that may be used in academic settings with children who stutter (Logan, Mullins, & Jones, 2008) or with children with cognitive impairments (Gillette & DePompei, 2008). Despite promising avenues of intervention and practice, there are also barriers to providing instruction to children with communication disorders in a regular classroom (Pufpaff, 2008). Each article provides insight into the importance of communication skills for academic and social success in the schools. The key to the success of children with or at risk for communication is for all school personnel to be aware of and proactive with children with communication disorders. © 2008 Wiley Periodicals, Inc.
Professionals' perceptions of the role of literacy in early intervention services
Authors: Thatcher Karen , Fletcher Kathryn
Published: July 2008

The purpose of the current study was to examine therapists' perceptions about literacy in early intervention services. Little effort has been devoted to the incorporation of literacy into therapy services for very young children with special needs. In an attempt to understand how therapy providers view the role of literacy in their services, 168 providers were surveyed. Responses were compared and in general, speech therapists and developmental therapists reported similar rates of use of books and rhymes and similar attitudes about the role of literacy in services. In contrast, occupational and physical therapists were often similar in their responses, yet, in most analyses, their responses were significantly different than the speech and developmental therapists'. This trend mirrors the existing literature that more attention has been devoted to encouraging the incorporation of literacy into speech services than other therapy services. Implications for these different practices and attitudes across disciplines are discussed. © 2008 Wiley Periodicals, Inc.
Do PDAs enhance the organization and memory skills of students with cognitive disabilities?
Authors: Gillette Yvonne , Depompei Roberta
Published: July 2008

The project studied the on‐time behavior of 35 students with intellectual disabilities (ID) or traumatic brain injury (TBI) under three conditions – times and tasks list, paper planner, and two different personal data assistants (PDAs). Students participated for two 4‐week periods, receiving one morning reminder during Period 1 and no reminders during Period 2. Students were on time more often using a PDA compared to a list (p < .024) or a planner (p < .002). Students were on time 50% more often in Period 1 with a single daily morning reminder as compared to no reminder across all conditions. When applying results, clinicians and researchers should note that only the alarm function prompting on‐time behavior was studied, and the influence of the small sample size and short time frame. Future researchers will find a framework for studying PDAs and cell phones with larger samples, over longer time periods, and with a wider range of functions. © 2008 Wiley Periodicals, Inc.
Ein Quanten‐Abakus aus Licht und Atomen. Manipulation von neutralen Atomen
Authors: Rauschenbeutel Arno
Published: July 2008

In mit Laserlicht erzeugten periodischen Mikropotentialen lassen sich einzelne neutrale Atome fangen. Durch Navigation der Laserstrahlen lassen sie sich zu gleichmäßigen Ketten anordnen. Solche Neutralatom‐Register eignen sich sehr gut zur Speicherung und Manipulation von Quanteninformation. Insbesondere lassen sich durch eine Kombination von Mikrowellen und Magnetfeldern die Atome des Registers selektiv mit Quanteninformation beschreiben. Darüber hinaus konnten durch Präzisionsmanipulation zwei Atome in demselben Mikropotential zusammengeführt werden. So konnte erstmals deterministisch eine Wechselwirkung zwischen individuellen Neutralatomen induziert werden.
Eingesperrtes Licht. Photonische Kristallfasern
Authors: Russell Philip
Published: July 2008

Photonische Kristallfasern sind Glasfasern, deren Mantel in Längsrichtung von Kanälen mit mikroskopischem Querschnitt durchzogen ist. Über den Faserquerschnitt betrachtet bilden diese ein periodisches Lochmuster. Sie wirken auf das transportierte Licht wie ein zweidimensionaler photonischer Kristall. Im Kern sind die Fasern entweder hohl oder mit Glas gefüllt. Solche Fasern können zum Beispiel Laserlicht selektiv in der Grundschwingungsmode transportieren. Mit ihnen lassen sich auch extrem lange Fokustiefen erzielen. Das Licht leiten sie so gut, dass sie bei den internen Reflexionen zu den weltbesten Spiegeln gehören. Gasgefüllte Kanäle machen sie zu empfindlichen Gassensoren und hocheffizienten Frequenzvervielfachern. Letztere lassen sich einfach in optische Bauelemente der Telekommunikation integrieren. Hohlkernfasern können sogar als lasergetriebene Teilchenbeschleuniger funktionieren. Nicht zuletzt stellen die Fasern ein wichtiges Bauteil im nobelpreisgekrönten optischen Frequenzkamm dar. Sie eröffnen noch viele weitere Anwendungsfelder.
Hüpfende Nanotropfen. Nanostrukturen unter intensiven Laserpulsen
Authors: Boneberg Johannes
Published: July 2008

Wenn Tropfen auf eine Oberfläche treffen, können sie komplett von ihr abprallen, falls sie diese nicht benetzen. Sie verhalten sich dann wie Gummibälle. Allerdings kann man einen Ball auch springen lassen, indem man ihn auf den Boden drückt, deformiert und dann plötzlich loslässt. Mit makroskopischen Tropfen, zum Beispiel aus Wasser, ist das nicht möglich. Überraschenderweise funktioniert es aber mit Nanotröpfchen aus geschmolzenem Metall, wie Gold. Als Ausgangszustand benötigt man dafür flache Nanostrukturen auf einer Oberfläche, die das flüssige Metall nicht benetzt. Schmilzt man sie mit einem starken Laserpuls, dann ziehen sie sich schnell zu Tröpfchen zusammen. Dabei wandelt sich die Oberflächenenergie in kinetische Energie um und lässt die Tröpfchen wie Bälle von der Oberfläche weghüpfen.
Die radioaktive Galaxis. Astrophysik im Gammabereich
Authors: Diehl Roland , Hartmann Dieter
Published: July 2008

Gammalinien aus dem Zerfall von Isotopen, die im Innern von Sternen oder Supernovae fusioniert wurden, sind Gegenstand aktueller astrophysikalischer Forschung. Damit sind prinzipiell direkte Messungen der Kernfusionsbedingungen sowohl im Innern von Supernovae als auch insgesamt in den jüngsten Sterngenerationen in der Galaxis möglich. Neueste Instrumente illustrieren dies mit der Messung von Gammalinien der Isotope 56Ni, 44Ti und 26Al. Überdies haben sie mit der Beobachtung der Annihilationslinie von Positronen und Elektronen eine fundamentale astrophysikalische Frage über die Herkunft dieser Form von Antimaterie aufgeworfen.
Nichtlineare Optik mit einzelnen Licht‐ und Materieteilchen
Authors: Rempe Gerhard
Published: July 2008

Optische Mikroresonatoren erlauben es, mit einzelnen Atomen und Photonen zu experimentieren und dabei eine starke Kopplung zwischen Licht und Materie herzustellen. Dies ermöglicht tiefe Einblicke in die Quantenphysik und bietet Perspektiven für neuartige Anwendung. Nun ist es unserer Gruppe am Max‐Planck‐Institut für Quantenoptik in Garching gelungen, zwei Photonen über ein Atom miteinander in Kontakt zu bringen.
Strom aus Osmose‐Kraftwerken
Authors: Peinemann Klaus‐Viktor , Skilhagen Stein‐Erik , Nielsen Werner Kofod
Published: July 2008

Die zunehmende Knappheit von Öl und Gas und die Notwendigkeit, den Ausstoß von Kohlendioxid zu reduzieren, verhilft auch unkonventionellen Kraftwerkskonzepten zu Aufmerksamkeit. Der norwegische Energiekonzern Statkraft plant für 2008 den Bau des weltweit ersten Prototypen eines Omose‐Kraftwerkes in Toft südwestlich von Oslo. Maßgeblich an der Membranentwicklung beteiligt ist das GKSS‐Forschungszentrum Geesthacht.
Hat das Urkilogramm bald ausgedient?
Authors: Becker Peter , Nicolaus Arnold
Published: July 2008

Fast alle Basiseinheiten des Internationalen Systems der Einheiten (SI) sind inzwischen durch atomare Konstanten oder Fundamentalkonstanten der Physik definiert. Nur das Kilogramm wird noch durch einen Prototypen, das Urkilogramm, repräsentiert. Seit langem schon laufen weltweit Versuche, auch das Kilogramm an Fundamentalkonstanten anzuschließen. Bei der Physikalisch‐Technischen Bundesanstalt in Braunschweig sind die Experten bei ihrem so genannten Avogadro‐Experiment einen wichtigen Schritt vorangekommen.
Kinetics and mechanism of the anilinolysis of S‐aryl N‐arylthiocarbamates in acetonitrile
Authors: Sung Dae Dong , Jang Hee Man , Jung Dae Il , Lee Ikchoon
Published: July 2008

The aminolysis reactions of S‐aryl N‐arylthiocarbamates (YC6H4NHC(O)SC6H4Z, 1) with anilines in acetonitrile are studied. The reaction rates are more influenced by the nucleophilicity of the nucleophile than the nucleofugality of the leaving group, but the change in the effective charge from reactants to the TS for formation of the tetrahedral intermediate is slightly greater in the leaving group (βZ from−0.07 to −0.14) than in the nucleophile (βX = 0.04–0.12). The magnitude of the Brönsted coefficients are in the range of values that are consistent for a stepwise mechanism with rate‐limiting formation of the zwitterionic tetrahedral intermediate. Signs of cross‐interaction constants, ρXY (>0), ρXZ (>0) and ρYZ (<0), are all consistent with a stepwise mechanism. It is concluded that the change of the amine from benzylamines to anilines causes a shift of the aminolysis mechanism from a concerted to a stepwise process. Copyright © 2008 John Wiley & Sons, Ltd.
The enthalpies of dissociation of the NO bonds in two quinoxaline derivatives
Authors: Gomes José R. B. , Monteiro André R. , Campos Bruno B. , Gomes Paula , da Silva Maria D. M. C. Ribeiro
Published: July 2008

The present work reports the first experimental thermochemical study of mono‐N‐oxides derived from quinoxaline, namely, 3‐methoxycarbonyl‐2‐methyl‐quinoxaline N‐oxide and 3‐ethoxycarbonyl‐2‐methyl‐quinoxaline N‐oxide. The values of the enthalpies of formation, in the condensed state, and of the enthalpies of sublimation, derived from static bomb calorimetry and Calvet microcalorimetry measurements, respectively, are combined to derive the standard molar enthalpies of formation in the gaseous phase for these two compounds. From the latter values, the first and second NO bond dissociation enthalpies for the corresponding di‐N‐oxides have been obtained. The gas‐phase experimental results are also compared with calculated data obtained with a density functional theory approach. Copyright © 2008 John Wiley & Sons, Ltd.
Plasma Sterilization: What are the Conditions to Meet this Claim?
Authors: von Woedtke Thomas , Kramer Axel , Weltmann Klaus‐Dieter
Published: July 2008

Plasma‐based processes to inactivate micro‐organisms are usually called ‘plasma sterilization’. Based on the debatable assumption of exponential first‐order micro‐organism inactivation kinetics, sterilization process validation is realizable by a combination of experimental tests and data extrapolation. In this article, an alternative concept for a solid and reproducible process qualification is proposed to guarantee reliable microbiological safety on a sufficient level for products that must be sterilized by alternative procedures like plasma processes. A proof of antimicrobial efficacy on the highest experimentally accessible level under experimentally realizable, reproducible, and statistically evaluable conditions is demanded.

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Power Supply for Plasma Torches Based on a Class‐E Amplifier Configuration
Authors: Pérez‐Martínez José A. , Peña‐Eguiluz Rosendo , López‐Callejas Régulo , Mercado‐Cabrera Antonio , Alvarado Raúl Valencia , Barocio Samuel R. , de la Piedad‐Beneitez Aníbal
Published: July 2008

A new RF power supply intended for low‐power plasma torches is presented. It is based on a class‐E amplifier, modified on the principle of a parallel LC resonant circuit, and is used here to supply the so‐called ‘plasma needle’. The latter is matched with a shunt inductor, and both are connected in parallel to the resonant capacitor C. This configuration is particularly useful for the control of stable discharge characteristics, for example, to resist naturally occurring variations in the load impedance, by providing the high voltage necessary to ignite and maintain the plasma. The overall system has been tested at atmospheric pressure by producing glow discharges in flows of helium and argon. We present early results that describe the device's characteristics.

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Mechanical Characterization of Protein Crystals
Authors: Tait Stephan , White Edward T. , Litster James D.
Published: July 2008

The mechanical properties (critical stress intensity factor, hardness and Young's modulus) of 4 crystalline materials (two proteins, lysozyme and glucose isomerase and two non‐proteins, glutamic acid and potassium sulphate) were measured with an indentation technique. It was found that the mechanical properties of lysozyme crystals depend on their state – dried, partly dried and moisture saturated – and their surroundings. The hardness, Young's modulus and the critical stress intensity factor of lysozyme crystals were observed to be much lower than those for the tested non‐proteins, leading to the conclusion that crystalline lysozyme is comparatively more fragile and softer. In combination the mechanical properties of lysozyme and the non‐proteins indicated that these materials were fairly brittle. Mechanical properties for crystals of the other protein, glucose isomerase, could not be quantified by indentation. However, qualitatively crystalline glucose isomerase was found to be more ductile and less fragile than crystalline lysozyme. The experimental findings were interpreted in terms of relative susceptibility to attrition and secondary nucleation in stirred industrial crystallizers.
Acute respiratory distress syndrome by cytomegalovirus infection in an immunocompetent infant
Authors: Choi Jungi , Kim You‐Suk , Kim Mun‐Sup , Callaway Zak , Youn Un‐Ki , Kim Hyo‐Bin , Kim Chang‐Keun
Published: July 2008

A 2‐month‐old female infant was admitted with progressive respiratory distress, fever, and diagnosed with acute respiratory distress syndrome (ARDS). The primary pulmonary pathogen was proven to be cytomegalovirus (CMV) from bronchoalveolar lavage fluid, urine, and blood specimens. Other immunologic findings were normal. CMV‐induced ARDS has not been reported previously in immunocompetent infants. Pediatr Pulmonol. 2008; 43:824–827. © 2008 Wiley‐Liss, Inc.
Hering–Breuer reflex, lung volume and position in prematurely born infants
Authors: Landolfo Francesca , Saiki Tolulope , Peacock Janet , Hannam Simon , Rafferty Gerrard F. , Greenough Anne
Published: July 2008

Objectives

To investigate the effect of position on the strength of the Hering–Breuer reflex in prematurely born infants and determine whether any differences seen were related to differences in lung or tidal volume between positions.

Working Hypothesis

Position related differences in the strength of the Hering–Breuer reflex relate to differences in lung or tidal volume.

Study Design

Prospective observational study.

Patient/Subject Selection

Eighteen infants, median gestational age 30 (range 25–32) weeks were studied.

Methodology

Infants were examined in the supine and prone position, each position was maintained for 2 hr. At the end of each 2‐hr period, the strength of the Hering–Breuer reflex was assessed by determining the prolongation of expiration following an end inspiratory occlusion. In addition, tidal volume and functional residual capacity (FRC) were assessed in each position.

Results

The strength of the Hering–Breuer reflex was greater (P = 0.01) and the mean FRC was higher (P < 0.0001) in the prone compared to the supine position. The position related differences in the strength of the reflex correlated significantly with position related differences in FRC (P = 0.05).

Conclusions

The Hering–Breuer reflex is stronger in the prone compared to the supine position. Our results suggest this is explained by position related differences in lung volume. Pediatr Pulmonol. 2008; 43:767–771. © 2008 Wiley‐Liss, Inc.
A combination therapy of whole lung lavage and GM‐CSF inhalation in pulmonary alveolar proteinosis
Authors: Yamamoto Hajime , Yamaguchi Etsuro , Agata Hiroatsu , Kandatsu Nobuhisa , Komatsu Toru , Kawai Seiko , Baba Kenji , Awaya Tomonari , Nishikomori Ryuta , Tsurusawa Masahito , Nakata Koh
Published: July 2008

Systemic and inhalation therapy of granulocyte‐macrophage colony‐stimulating factor (GM‐CSF) is usually effective in controlling autoimmune pulmonary alveolar proteinosis (PAP), but some cases are refractory to GM‐CSF therapy and subjected to whole lung lavage (WLL). A 9‐year‐old girl developed severe respiratory failure due to autoimmune PAP was treated with inhalational 250 µg of GM‐CSF daily, however, it was ineffective. Unilateral WLL was performed three times and subsequent GM‐CSF inhalation therapy yielded marked physiological and radiological improvement and was continued for 1 year. Pediatr Pulmonol. 2008; 43:828–830. © 2008 Wiley‐Liss, Inc.
Human urine biomarkers of renal cell carcinoma evaluated by ClinProt
Authors: Bosso Niccolò , Chinello Clizia , Picozzi Stefano Carlo Maria , Gianazza Erica , Mainini Veronica , Galbusera Carmen , Raimondo Francesca , Perego Roberto , Casellato Stefano , Rocco Francesco , Ferrero Stefano , Bosari Silvano , Mocarelli Paolo , Kienle Marzia Galli , Magni Fulvio
Published: July 2008

Renal cell carcinoma (RCC) is one of the major causes of cancer death and is radio‐ and chemoresistant. Urine of 29 healthy subjects and 39 clear cell RCC patients were analyzed using the ClinProt technique to search for possible biomarkers for early RCC diagnosis. A cluster of three signals (marker A= at m/z 1827 ± 8 Da, marker B = 1914 ± 8 Da and marker C = 1968 ± 8 Da) was able to discriminate patients from controls. A receiver operating characteristic curve analysis showed values of area under the curve (AUC) higher than 0.9 for marker A and B, corresponding to a sensitivity of 85–90% and a specificity of 90%, while marker C gave a lower AUC (0.84) corresponding to sensitivity of 70% and specificity of 100%. The combination of three markers lead to an improvement in diagnostic efficacy, with specificity and sensitivity of 100% and 95%, respectively, in the training test and of 100% and of 85% in the test experiment. The efficacy of this cluster of signals to distinguish RCC patients grouped by tumor stage showed a sensibility of 100% for patients at the primary tumor 1 stage. One of the signals present in the cluster was identified as a fragment of Tamm‐Horsfall protein.
Characterization of the renal cyst fluid proteome in autosomal dominant polycystic kidney disease (ADPKD) patients
Authors: Lai Xianyin , Bacallao Robert L. , Blazer‐Yost Bonnie L. , Hong David , Mason Stephen B. , Witzmann Frank A.
Published: July 2008

Autosomal dominant polycystic kidney disease (ADPKD) is characterized by localized autonomous cellular proliferation, fluid accumulation within the cysts, and intraparenchymal fibrosis of the kidney. Little is known about the cyst fluid's protein composition. We hypothesized that the complex collection of cyst fluid proteins (cyst fluid proteome) plays a major role in cyst formation/maintenance and contains yet unknown diagnostic and mechanistic features that are common to all forms of PKD. We analyzed five kidney cyst fluids from four patients with ADPKD. Tryptic peptides from plasma‐protein immunodepleted (ProteoPrep®) and undepleted cyst fluid samples were analyzed by LC‐MS/MS. Proteins were identified by SEQUEST™ and validated via the Trans‐Proteomic Pipeline; 391 proteins were identified with >90% confidence; 251 of them in undepleted and 362 in immunodepleted samples. Immunodepletion removed >94% of the cyst fluid protein. A surprisingly large and functionally diverse number of proteins common to most cysts were identified. These proteins may be of mechanistic interest and include Ig γ, κ, and fragments; complement components; vitronectin; orosomucoid; prostaglandin D2 synthase; vitamin D‐binding protein; clusterin; SERPIN family proteins; hemopexin; and fetuin‐A. Additionally, these results suggest that further prefractionation and enhanced chromatographic separation of tryptic peptides is likely to expose an even greater number of relevant proteins.
Using proteomics to identify preprocedural risk factors for contrast induced nephropathy
Authors: Bennett Michael R. , Ravipati Neelima , Ross Gary , Nguyen Mai T. , Hirsch Russel , Beekman Robert H. , Rovner Leon , Devarajan Prasad
Published: July 2008

Contrast induced nephropathy (CIN) is the third leading cause of hospital acquired acute kidney injury (AKI). We conducted a cross‐sectional study in children undergoing elective cardiac catheterization to determine if there is a distinct preprocedural urinary proteomic profile in subjects who subsequently develop CIN. Of 90 patients enrolled, AKI due to CIN (defined as a 50% or greater increase in serum creatinine) occurred in 10 participants by the 24 h postcontrast time point. Seven patients who did not develop AKI served as age and gender matched controls. SELDI‐TOF‐MS was performed using ProteinChips with different chromatographic surfaces. A 4480 Da biomarker displayed significantly greater peak intensities on three chromatographic surfaces (p = 0.02–0.001) in control patients at time = 0 with an area under the curve (AUC) of 0.89–0.99. This biomarker was identified as the 41 amino acid (a.a.) variant of human beta‐defensin‐1. Another biomarker of 4631 Da was found to have a significantly greater peak intensity (p = 0.03) in AKI patients at time = 0, with an AUC of 0.84. Thus, the presence of a 4631 Da peptide, as well as the absence of the 41 a.a. variant of human beta‐defensin‐1 in the preprocedural urine, may prove to be useful biomarkers for the early prediction of CIN.
Proteomic analysis to improve adequacy of hemo‐ and peritoneal dialysis: Removal of small and high molecular weight proteins with high‐ and low‐flux filters or a peritoneal membrane
Authors: Dihazi Hassan , Müller Claudia A. , Mattes Harry , Müller Gerhard A.
Published: July 2008

The reduction of morbidity and mortality in patients undergoing hemo‐ or peritoneal dialysis is strongly related to an efficient and selective clearance of uremic toxins. We used proteomics methods to analyze and further characterize the dialytic removal of still undefined middle and high molecular weigh proteins as a basis for further improvement of dialysis assessment. Dialysates from 26 hemodialysis patients treated with different types of low‐ (F6HPS®) and high‐flux (FX80®, APS650®, FX60®) filters as well as peritoneal fluids from 10 continuous ambulatory peritoneal dialysis (CAPD) patients were analyzed by SELDI‐TOF and 2‐DE. The protein patterns showed selective differences in the proteins cleared depending on the dialysis method used and the filter membrane. While SELDI analyses of dialysates from the F6HPS revealed almost no protein clearance, high‐flux filters and CAPD dialysates showed protein release of different molecular weight ranges. Furthermore, 2‐DE and MS analysis identified 48 different proteins from the dialysate of high‐flux filters and 21 from peritoneal dialysis fluids. In F6HPS dialysates, however, only few proteins could be identified.
A proteomic approach to immune‐mediated epithelial‐mesenchymal transition
Authors: Feighery Ronan , Maguire Patricia , Ryan Michael P. , McMorrow Tara
Published: July 2008

Increasing evidence suggests epithelial‐mesenchymal transition (EMT) plays an important role in renal fibrosis. Initial renal injury enables the infiltration of mononuclear cells into the interstitium, and the resulting generation of inflammatory mediators that favour EMT may have a direct role in the development of renal fibrosis. The aim of this study was to investigate the proteome of renal tubular epithelial cells undergoing EMT in vitro. The human proximal tubular cell line (HK‐2), exposed to conditioned medium from activated peripheral blood mononuclear cells (PBMC‐CM), undergo phenotypic change, from an epithelial towards a fibroblastic phenotype, as evidenced by decreased E‐cadherin and increased fibronectin protein expression. Further proteomic analysis, using 2‐DE and Progenesis software, revealed the down‐regulation of 4 proteins and up‐regulation of 23 proteins. MS analysis allowed the positive identification of 15 differentially expressed proteins, including annexin A2, adipocyte plasma membrane‐associated protein, T‐complex protein 1, reticulocalbin‐1 precursor and moesin among others. Western blotting and quantitative real‐time PCR confirmed the increase in annexin A2 at the protein and gene level, respectively. Since annexin A2 and S100A6 exist as complexes in B‐1 cells, we investigated the S100A6 gene expression further and show an increased expression in HK‐2 cells following exposure to activated PBMC‐CM. Therefore, we have identified several potential proteins that could play key roles in immune‐mediated EMT.
CE‐MS analysis of the human urinary proteome for biomarker discovery and disease diagnostics
Authors: Coon Joshua J. , Zürbig Petra , Dakna Mohammed , Dominiczak Anna F. , Decramer Stéphane , Fliser Danilo , Frommberger Moritz , Golovko Igor , Good David M. , Herget‐Rosenthal Stefan , Jankowski Joachim , Julian Bruce A. , Kellmann Markus , Kolch Walter , Massy Ziad , Novak Jan , Rossing Kasper , Schanstra Joost P. , Schiffer Eric , Theodorescu Dan , Vanholder Raymond , Weissinger Eva M. , Mischak Harald , Schmitt‐Kopplin Philippe
Published: July 2008

Owing to its availability, ease of collection, and correlation with pathophysiology of diseases, urine is an attractive source for clinical proteomics. However, many proteomic studies have had only limited clinical impact, due to factors such as modest numbers of subjects, absence of disease controls, small numbers of defined biomarkers, and diversity of analytical platforms. Therefore, it is difficult to merge biomarkers from different studies into a broadly applicable human urinary proteome database. Ideally, the methodology for defining the biomarkers should combine a reasonable analysis time with high resolution, thereby enabling the profiling of adequate samples and recognition of sufficient features to yield robust diagnostic panels. CE‐MS, which was used to analyze urine samples from healthy subjects and patients with various diseases, is a suitable approach for this task. The database of these datasets compiled from the urinary peptides enables the diagnosis, classification, and monitoring of a wide range of diseases. CE‐MS exhibits excellent performance for biomarker discovery and allows subsequent biomarker sequencing independent of the separation platform. This approach may elucidate the pathogenesis of many diseases, and better define especially renal and urological disorders at the molecular level.
Electrostatics‐defying interaction between arginine termini as a thermodynamic driving force in protein–protein interaction
Authors: Pednekar Deepa , Tendulkar Abhijit , Durani Susheel
Published: July 2008

Apparent electrostatics‐defying clustering of arginines attributed as screening effect of solvent is in this study examined as a possible thermodynamic driving force in protein–protein interaction. A dataset of 266 protein dimers is found to have ∼22% arginines mutually paired and ∼17% pairs in interaction across interfaces and thus putative “hotspots” of protein–protein interaction. The pairing, uncorrelated with inter or intramolecular context, could be contributing in protein folding as well, and, uncorrelated with solvent access, could be driven by effects that are generic to solvent and protein structures. Mutually stacked at shorter distances but in diverse geometrical modes otherwise, the cations tend to be in gross deficit of hydrogen‐bond partners, and contributing electrostatics across protein–protein interface that, on average, is repulsive for protein–protein interaction. Embedded in local environment enriched in polarizable residues, aromatic, aliphatic, and anionic, the arginines may contribute to protein–protein interaction via environmental polarization response to electrostatics of cation clustering, a possible new principle in molecular recognition. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases
Authors: Banavali Nilesh K. , Roux Benoît
Published: July 2008

Regulated activity of Src kinases is critical for cell growth. Src kinases can be activated by trans‐phosphorylation of a tyrosine located in the central activation loop of the catalytic domain. However, because the required exposure of this tyrosine is not observed in the down‐regulated X‐ray structures of Src kinases, transient partial opening of the activation loop appears to be necessary for such processes. Umbrella sampling molecular dynamics simulations are used to characterize the free energy landscape of opening of the hydrophilic part of the activation loop in the Src kinase Hck. The loop prefers a partially open conformation where Tyr416 has increased accessibility, but remains partly shielded. An asymmetric distribution of the charged residues in the sequence near Tyr416, which contributes to shielding, is found to be conserved in Src family members. A conformational equilibrium involving exchange of electrostatic interactions between the conserved residues Glu310 and Arg385 or Arg409 affects activation loop opening. A mechanism for access of unphosphorylated Tyr416 into an external catalytic site is suggested based on these observations. Proteins 2009. © 2008 Wiley‐Liss, Inc.
NMR structural studies of the Ste11 SAM domain in the dodecyl phosphocholine micelle
Authors: Bhunia Anirban , Domadia Prerna N. , Mohanram Harini , Bhattacharjya Surajit
Published: July 2008

The sterile α‐motif (SAM), a relatively small (∼70 amino acids) interaction domain, is found in a variety of proteins involved in cell signaling, transcription regulation, and scaffolding. The Ste11 protein kinase from the mitogen activated protein kinase (MAPK) signaling cascades of the budding yeast is regulated by a SAM domain located at the N‐terminus of full‐length protein. In solution, the Ste11 SAM domain exists as a well‐folded dimeric structure that is involved in interaction with the cognate SAM domain from an adaptor protein Ste50. In this work, we show that the Ste11 SAM domain has an intrinsic affinity towards the lipid membranes. The solution conformation of the Ste11 SAM determined in perdeuterated DPC micelle, using NMR spectroscopy, is defined by five helices of different lengths connected by a number of loops. In the micelle bound state, the non‐polar and aromatic residues of the Ste11 SAM lack a native‐like packing and are presumably engaged in interactions with the micelle. Using two different paramagnetic doxyl‐lipids; we have mapped out localization of Ste11 SAM residues at the micelle surface. Most of the residues appear to localize at the interfacial region of the micelle. However, a number of non‐polar residues from the central region of the domain are found to be located inside the core of the micelle including residues from the helix 4 and a loop between helix 2 and helix 3. Isothermal titration calorimetry studies demonstrate that a facile insertion of the Ste11 SAM into the DPC micelle is primarily driven by a large change in enthalpy, −50 kcal/mol with an apparent equilibrium association constant (Ka) of 7.86 × 106 M−1. Interestingly, an interfacial mutant L60R of the Ste11 SAM lacking the dimeric structure does not show detectable interactions with the lipid micelle. The micelle‐bound structure of the Ste11 SAM domain described in this work may have potential implications in the regulation of MAPK signaling whereby positioning of the Ste11 protein in close proximity to the membrane may facilitate efficient phosphorylation of the Ste11 kinase by the membrane attached upstream Ste20/pak kinase. Proteins 2009. © 2008 Wiley‐Liss, Inc.
A complementary La/SSB epitope anchored to Sequential Oligopeptide Carrier regulates the anti‐La/SSB response in immunized animals
Authors: Voitharou Chryssa , Krikorian Dimitrios , Sakarellos Constantinos , Sakarellos‐Daitsiotis Maria , Panou‐Pomonis Eugenia
Published: July 2008

Complementary peptide epitopes, derived from complementary RNA sequences, have been used for suppressing the autoimmune response in experimental autoimmune diseases as myasthenia gravis, allergic neuritis and allergic encephalomyelitis. Aiming at contributing to the development of a tool that could regulate the autoantibody production against La/SSB, which is the main target of autoantibodies in Sjogren's syndrome (SS) and systemic lupus erythematosus (SLE), the complementary epitope, cpep349–364, of the minor T/major B cell epitope of La/SSB, pep349–364, was utilized for the induction of neutralizing anti‐cpep349–364 antibodies in rabbit immunizations. Complementary peptides were coupled to an artificial carrier, developed in our laboratory, in order to enhance the complementary potency of cpep349–364 and its counterpart. This carrier, named Sequential Oligopeptide Carrier, SOCn, formed by the repeating tripeptide Lys‐Aib‐Gly, adopts helical conformation, which allows the anchored peptide epitopes to preserve their initial reactivity such as molecular recognition, antigenicity/immunogenicity. Our study provides proof of evidence of specific interactions between idiotypic (Id)/anti‐idiotypic (anti‐Id) antibodies generated in immunized animals by the sense epitope (conjugate I) of La/SSB and its complementary counterpart (conjugate II). It was also demonstrated that the Id/anti‐Id association is specifically disrupted by adding either the sense epitope (conjugate I) or its complementary counterpart (conjugate II). A mutual neutralization of Id/anti‐Id antibodies was observed in vivo, which implies that generation of anti‐Id antibodies by immunization with the complementary La/SSB epitope could scavenge the anti‐La/SSB response. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.
Preface: phys. stat. sol. (c) 5/9
Authors: Arakawa Yasuhiko , Hirayama Yoshiro , Sogawa Tetsuomi
Published: July 2008

The present issue of physica status solidi (c) contains the papers presented at the 34th International Symposium on Compound Semiconductors (ISCS‐2007). The symposium was held in Kyoto, Japan, 15–18 October 2007. This conference was one of the annual series, which rotates between America, Europe and Asia. The last three conferences were held in Vancouver, Canada (2006), Rust, Germany (2005) and Seoul, Korea (2004).

The symposium, whose history goes back to 1966 under the name “International Symposium on GaAs and Related Compounds” has a long standing tradition in science, technology, and applications of compound semiconductors. In this conference, 11 subcommittees (Growth and Nanostructure Formation; Transport Devices; Photonic Devices; Physics; Spintronics; Characterization, Nanoprobe and Nanomechanics; GaN and Related Semiconductors; Oxide Semiconductors; SiGe and Related Semiconductors; Carbon Related Materials; Organic Semiconductors and Other Soft Materials) cover the entire spectrum of III–V compound semiconductors as well as II–VI, SiGe, oxide semiconductors and carbon related materials.

The symposium was attended by 550 registered participants from more than 25 countries all over the world. During the course of the symposium, 4 plenary talks, 27 invited papers, 7 late news papers as well as 295 contributed papers were given as oral or poster presentation. ISCS‐2007 highlighted emerging wide‐band gap and oxide semiconductor materials and devices as well as high‐speed electronics, next‐generation photonics and physics studies based on the traditional compound semiconductors.

The symposium is also the venue for the attribution of three prestigious scientific awards, the Welker Award, the Quantum Device Award and the Young Scientist Award.

The Proceedings contain many papers presented at the conference. The chapters are organized in a way that related papers are grouped by the subjects of the subcommittees.

We would like to thank all the participants of ISCS‐2007 for contributing to the success of the symposium and acknowledge the diligent work of the committee members and referees of the manuscripts. We also thank Prof. Shizuo Fujita, Kyoto University, for the excellent local organization. Kyoto, the ancient capital of Japan with more than one thousand years of history, is full of beautiful temples, shrines, and gardens, giving us an ideal location to combine a scientific conference with motivating entertainment. Finally, we extend our thanks to Ms. Kaori Yoshida for her excellent secretary job for these proceedings.

The 35th International Symposium on Compound Semiconductors, organized by Prof. Günter Weimann and Prof. Oliver Ambacher will be held at Euro‐Park, Rust near Freiburg, Germany, 21–24 September 2008.

May 2008
Do transient gravity waves in a shear flow break?
Authors: Pulido M. , Rodas C.
Published: July 2008

The propagation of transient gravity waves in a shear flow towards their critical levels is examined using a ray tracing approximation and a higher‐degree (quasi‐optic) approximation. Because of its transient forcing, the amplitude of transient waves decays to zero in the neighbourhood of the critical region so that it is not clear whether transient gravity waves will reach the convective instability threshold or not. The analysis shows that the horizontal perturbation decays asymptotically as the inverse of the square root of time, while the vertical wavenumber depends linearly on time, thus transient gravity waves attain convective instability for long times. The theoretical results are compared with numerical simulations. The ray path approximation is not able to reproduce the maximum amplitude, but the quasi‐optic approximation gives a reasonable agreement at short and long times. There are three breaking regimes for transient gravity waves. For wave packets with a narrow frequency spectrum (quasi‐steady waves) and large enough initial wave amplitude, the wave breaking is similar to the abrupt monochromatic wave overturning. On the other hand, highly transient wave packets will dissipate near the critical region for very long times with small wave amplitudes and high vertical wavenumber. The third regime is a transition between the two extremes; in this case both wave amplitude and vertical wavenumber are important to produce the convective threshold. The dependencies of the convective instability height (a quantity that may be useful for gravity wave parametrizations) on the Richardson number and the frequency spectral width are obtained. Copyright © 2008 Royal Meteorological Society
Selecting explanatory variables with the modified version of the Bayesian information criterion
Authors: Bogdan Małgorzata , Ghosh Jayanta K. , Żak‐Szatkowska Małgorzata
Published: July 2008

We consider the situation in which a large database needs to be analyzed to identify a few important predictors of a given quantitative response variable. There is a lot of evidence that in this case classical model selection criteria, such as the Akaike information criterion or the Bayesian information criterion (BIC), have a strong tendency to overestimate the number of regressors. In our earlier papers, we developed the modified version of BIC (mBIC), which enables the incorporation of prior knowledge on a number of regressors and prevents overestimation. In this article, we review earlier results on mBIC and discuss the relationship of this criterion to the well‐known Bonferroni correction for multiple testing and the Bayes oracle, which minimizes the expected costs of inference. We use computer simulations and a real data analysis to illustrate the performance of the original mBIC and its rank version, which is designed to deal with data that contain some outlying observations. Copyright © 2008 John Wiley & Sons, Ltd.
Conclusive evidence on the insensitivity of additive rules to the combinational details of exchange and correlation functional in hybrid DFT methods
Authors: Firouzi Rohoullah , Zahedi Mansour
Published: July 2008

This account is a quest to evaluate the sensitivity of additive rules among total electronic energies of some triple molecular sets to the employed computational level. To achieve the goal, seven randomly generated hybrid functionals have been constructed and employed for calculation on a test set of 29 molecules containing second and third row elements. The computational results based on these nonoptimized DFT methods in conjunction with those of standard B3LYP method clearly demonstrates that in contrast to atomization or isomerization energies, additive rules among total electronic energies are insensitive to reliability or precision of computational method. This insensitivity to details of exchange‐correlation functional indicates that additive rules can be generally well considered using simple computational methods. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Convergence of the generalized simulated annealing method with independent parameters for the acceptance probability, visitation distribution, and temperature functions
Authors: de Andrade M. D. , Mundim K. C. , Malbouisson L. A. C.
Published: July 2008

In their original form, the Generalized Simulated Annealing (GSA), proposed by Tsallis and Stariolo, was defined with two independent parameters, qa and qv, used in the definition of the acceptance probability, visitation distribution, and temperature functions. In the posterior applications of this algorithm, however, another independent parameter has been introduced, replacing qv in the definition of the temperature function, becoming more efficient and allowing a convergence with a small number of cycles. Nevertheless, there is no convergence proof of the GSA algorithm to the absolute minimum in this case. In this work it is presented a convergence proof of the GSA method to the absolute minimum, with three independent parameters, qa, qv, and qT, to define the acceptance probability, visitation distribution, and temperature functions, using a modified form of the distribution function, ′g, in the formulation of the algorithm. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Electrostatic properties of small molecules by means of atomic multipoles from the quantum theory of atoms in molecules
Authors: Rodrigues Eduardo F. F. , de Sá Eduardo L. , Haiduke Roberto L. A.
Published: July 2008

Atomic multipoles from the Quantum Theory of Atoms in Molecules (QTAIM), up to quadrupoles, and CHELPG charges are employed in the description of electrostatic properties of some small linear molecules: H2, HF, HCl, HBr, HCN, HNC, and CO. A proton is placed on the molecular axis in distances within the range 3–8 Å from the terminal atoms. The polarization of molecular electronic densities induced by the proton is readily included by the calculation of atomic multipoles in each proton‐molecule arrangement. Electrostatic potentials at the proton position as given by QTAIM multipoles are always in better agreement with the reference results, calculated directly at the B3LYP/6‐311G(3d,3p) level, than those predicted with CHELPG charges, particularly for cases in which QTAIM multipoles showed that the contribution of atomic charges to these potentials is not clearly predominant over other contributions as in H2, HCl, HBr, HNC, and CO. The lone pair at the carbon atoms in CO and HNC, as described by QTAIM atomic dipoles, is indispensable in studies of electrostatic properties of these molecules. Moreover, QTAIM multipoles are also able to describe properly the large polarizations induced by the proton along the proton‐molecule distances studied. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
New perspectives on the fundamental theorem of density functional theory
Authors: Pan Xiao‐Yin , Sahni Viraht
Published: July 2008

The fundamental theorem of time‐independent/time‐dependent density functional theory due to Hohenberg–Kohn (HK)/Runge–Gross (RG) proves the bijectivity between the density ρ(r)/ρ(rt) and the Hamiltonian /(t) to within a constant C/function C(t), and wave function Ψ/Ψ (t). The theorems are each proved for scalar external potential energy operators. By a unitary or equivalently a gauge transformation that preserves the density, we generalize the realm of validity of each theorem to Hamiltonians, which additionally include the momentum operator and a curl‐free vector potential energy operator defined in terms of a gauge function α (R)/α (Rt). The original HK/RG theorems then each constitute a special case of this generalization. Thereby, a fourfold hierarchy of such theorems is established. As a consequence of the generalization, the wave function Ψ/Ψ (t) is shown to be a functional of both the density ρ(r)/ρ(rt), which is a gauge‐invariant property, and a gauge function α(R)/α(Rt). The functional dependence on the gauge function ensures that as required by quantum mechanics, the wave function written as a functional is gauge variant. The hierarchy and the dependence of the wave function functional on the gauge function thus enhance the significance of the phase factor in density functional theory in a manner similar to that of quantum mechanics. Various additional perspectives on the theorem are arrived at. These understandings also address past critiques of time‐dependent theory. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008