bluuebunny/crossref_metadata_2025 huggingface dataset:
Purification of a candidate gonadotrophin surge‐inhibiting/attenuating factor (GnSIF/AF) showing MAPK as a possible target
Authors: Hendriks M.L. , Lambalk C.B. , Helder M.N. , de Koning J.
Published: March 2011

Gonadotrophin surge‐inhibiting/attenuating factor (GnSIF/AF) has been known for over two decades, but its molecular structure has not been completely characterized yet. In the last 20 years, five different putative GnSIF/AF sequences have been published. In this article, we describe a procedure to isolate and characterize GnSIF/AF from bovine follicular fluid, a GnSIF/AF‐derived synthetic peptide (SP‐GnSIF/AF) was produced, and the intracellular bioactivity of GnSIF/AF was tested for intracellular action with a MAPK‐assay. Two different bioactive molecular weight forms of GnSIF/AF were isolated, a 160 kDa heteromeric and a monomeric 40 kDa protein. The 40 kDa form appeared to be a subunit of the 160 kDa protein. The synthetic peptide mimicked the actions of GnSIF/AF, such as inhibition of GnRH‐induced LH secretion and attenuation of the MAPK phosphorylation. The two GnSIF/AF candidates do not show similarities with previously published GnSIF/AF sequences. These are the first data showing the influence of GnSIF/AF on intracellular processes involved in GnRH self‐priming and that the biological action of GnSIF/AF was preserved in the produced synthetic peptide. The results provide strong evidence that the identified candidate proteins are the true GnSIF/AF. Mol. Reprod. Dev. 78:292–304, 2011. © 2011 Wiley‐Liss, Inc.
Topology optimization for unsteady flow
Authors: Kreissl Sebastian , Pingen Georg , Maute Kurt
Published: March 2011

A computational methodology for optimizing the conceptual layout of unsteady flow problems at low Reynolds numbers is presented. The geometry of the design is described by the spatial distribution of a fictitious material with continuously varying porosity. The flow is predicted by a stabilized finite element formulation of the incompressible Navier–Stokes equations. A Brinkman penalization is used to enforce zero‐velocities in solid material. The resulting parameter optimization problem is solved by a non‐linear programming method. The paper studies the feasibility of the material interpolation approach for optimizing the topology of unsteady flow problems. The derivation of the governing equations and the adjoint sensitivity analysis are presented. A design‐dependent stabilization scheme is introduced to mitigate numerical instabilities in porous material. The emergence of non‐physical artifacts in the optimized material distribution is observed and linked to an insufficient resolution of the flow field and an improper representation of the pressure field within solid material by the Brinkman penalization. Two numerical examples demonstrate that the designs optimized for unsteady flow differ significantly from their steady‐state counterparts. Copyright © 2011 John Wiley & Sons, Ltd.
A reduced stabilized mixed finite element formulation based on proper orthogonal decomposition for the non‐stationary Navier–Stokes equations
Authors: Luo Zhendong , Du Juan , Xie Zhenghui , Guo Yan
Published: March 2011

In this paper, a proper orthogonal decomposition (POD) method is applied to reducing a classical stabilized mixed finite element (SMFE) formulation for the non‐stationary Navier–Stokes equations. Error estimates between the classical SMFE solutions and the reduced SMFE solutions based on the POD method are provided. The reduced SMFE formulation based on the POD method could not only greatly reduce its degrees of freedom but also circumvent the constraint of Brezzi–Babuka (BB) condition so that the combination of finite element subspaces could be chosen freely and allow optimal‐order error estimates to be obtained. Numerical experiments show that the errors between the reduced SMFE solutions and the classical SMFE solutions are consistent with theoretical results. Moreover, it is shown that the reduced SMFE formulation based on the POD method is feasible and efficient for solving the non‐stationary Navier–Stokes equations. Copyright © 2011 John Wiley & Sons, Ltd.
Richtig beleuchtet, richtig erkannt
Authors: Henzler Tobias
Published: March 2011

Bei der Realisierung einer Bildverarbeitungs­Lösung ist die Auswahl der geeigneten Beleuchtung ausschlaggebend für die Qualität der Bildaufnahme und kann damit gleichzeitig auch die anschließende Bildauswertung stark vereinfachen. Dennoch zählt die Entscheidung über die Lichtquelle häufig zu den komplizierteren und gerne vernachlässigten Problemstellungen in der Bildverarbeitung.
Qualitätssicherung durch Zeilenkameras
Authors: Zimmermann Ralf
Published: March 2011

Dank intelligenter Signalverarbeitung und leistungsstarker Zeilensensoren haben sich Zeilenkameras in der Bahnwareninspektion fest etabliert. Sie sind ein Garant für ökonomische Qualitätssicherungslösungen. Zahlreiche Beispiele aus der Industrie bestätigen die großen Vorteile von Zeilenkameras — von der qualitativen Klassifizierung unterschiedlichster Rohstoffe und Materialien, wie zum Beispiel Hölzer, Fliesen oder Textilien, bis hin zur Überprüfung des Reifegrades von Gemüse und Obst.
Qualitätssicherung von Endlosmaterial
Authors: Schreiber Miriam
Published: March 2011

Qualitätssicherung ist eines der großen Themen im Bereich der industriellen Produktion. Im Mittelpunkt stehen dabei die Ansprüche des Kunden, der oftmals eine Null‐Fehler‐Strategie fordert. Die optische Prüfung mithilfe von Kamerasystemen stellt hier eine einfache und effiziente Lösung für den Hersteller dar. Parallel zum Fortschritt der technologischen Entwicklungen setzen deshalb mehr und mehr produzierende Industriebetriebe in der Qualitätssicherung industrielle Bildverarbeitung ein. Die stetig steigenden Qualitätsansprüche der Kunden führen immer öfter dazu, dass nicht nur große Unternehmen sondern auch mittelständische Firmen auf diese Art der Qualitätsprüfung zurückgreifen. Besonders bei Produkten, die sicherheitsrelevant sind, ist eine lückenlose Qualitätskontrolle unabdingbar.
Applications for THz Systems
Authors: Jansen Christian , Wietzke Steffen , Scheller Maik , Krumbholz Norman , Järdens Christian , Baaske Kai , Hochrein Thomas , Koch Martin , Wilk Rafal
Published: March 2011

The terahertz regime is sandwiched between the microwaves and the infrared, bridging the gap between electronics and optics. Due to this exposed position in the electromagnetic spectrum, a plethora of metrological applications with high impact on a variety of industries exists. Recent advances in terahertz system technology suggest that its market introduction is rapidly approaching. This article serves as introduction into selected fields of THz applications, especially focusing on those where existing measuring methods cannot deliver satisfactory solutions. Thus, the reader gets insight into the opportunities and perspectives of this exciting, new technology.
Manufacturing and Application of Micro‐Optics
Authors: Homburg Oliver , Hauschild Dirk , Lissotschenko Vitalij
Published: March 2011

Widely, the 20th century is regarded as the century of micro‐electronics. In contrast the 21st century is expected to become the century of the photon. In fact since the 1980s many new technical developments which we experience in everyday life are based on photonics, e. g. telecommunication, the internet, CDs, DVDs, scanners, mobile phones, digital cameras, LED lighting, personal computers and flat panel displays. Micro‐optics is an enabling technology in a large variety of applications — consumer as well as industrial.
Molecular Optical Switches and Waveguides
Authors: Tinnefeld Philip , Sauer Markus
Published: March 2011

Complementary metal oxide semiconductor technology, i.e. CMOS chip structures, currently have dimensions of about 40 nm. For the progression of Moore's law which states that the transistor density of semiconductor chips will double roughly every 18 months size reductions down to the molecular level are required. Further miniaturization introduces fundamental physical limitations. Optical interconnections and optical integrated circuits will provide a way out of the limitations to computational speed and complexity. In optical computers, photons will travel on optical fibers or thin films instead of electrons to perform the appropriate functions. Further down the road, for both electronic computers and optical computers the building blocks could reach molecular dimensions: Molecular (optical) switches and wires or waveguides could pave the way towards single‐molecule optical data storage and readout.
Laser Microtomy
Authors: Lubatschowski Holger
Published: March 2011

The laser microtome (LMT) has been designed to slice biological tissue and various materials with high precision. The cutting process is performed by ultra short laser pulses in the near infrared region, inducing an optical breakdown below the surface of the material. Biological Tissue can be processed in its native state without prior fixation and embedding. This is of great importance for many biological applications such as immunohistological investigations.
Advances in Fluorescence Microscopy
Authors: Gaethje Heiko
Published: March 2011

Fluorescence microscopy is a powerful tool in life science research and recent years have witnessed a rapid development of techniques and applications. These achievements have been driven by new hardware like sensitive CCD cameras and new lasers, by development of application oriented software and integration of these innovations into dedicated live cell imaging systems and confocal laser scanning microscopes. Hard‐ and software improvements were accompanied by the design of new fluorescent probes and labelling chemistries. This report summarises some of the latest trends in fluorescence microscopy.
Electrical transport and magnetic properties of PEDOT‐ferrite nanocomposites
Authors: Poddar Asok , Mukherjee Sanjoy , De Amitabha , Sen Pintu , Banerjee Sangam
Published: March 2011

We have studied the temperature‐dependent transport and magnetic properties of the nanocomposites, containing varied amounts of CoFe2O4, NiFe2O4, and Fe3O4 nanoparticles embedded in the conducting poly(3,4‐ethylenedioxythiophene) or PEDOT matrix, in the temperature range 77–300 K. Resistivities of all the composites, including pure PEDOT follows the Mott VRH relation ρ = ρ0
T−1/4 over the studied temperature range. This suggests that hopping is the mechanism of transport in these systems. Plots of (lnρ − lnρ0)/A as a function of temperature for all the studied samples are found to collapse on a single curve. Although, the conduction mechanism does not change with nanoparticle inclusions in the polymer matrix, the hopping parameters change in the nanocomposites. Magnetic studies of ferrite nanoparticles and nanocomposites show signature of superparamagnetic blocking, with a distribution of particle size. The spin structure on the surface of any particle is different from that of the core. POLYM. COMPOS., 2011. © 2011 Society of Plastics Engineers
Drug induced hepatotoxicity: data from the Serbian pharmacovigilance database
Authors: Petronijevic Marija , Ilic Katarina , Suzuki Ayako
Published: March 2011

Purpose

The main aim of this study was to determine the most frequently reported drugs to the Serbian Pharmacovigilance Database (SPD) with suspected induced hepatotoxicity. Additionally, reasons for the low reporting rate of adverse drug reactions (ADRs) in Serbia were identified.

Methods

Retrospective observational study of spontaneously reported ADRs recorded in the SPD from January 1995 to December 2008 was performed. The Medical Dictionary for Regulatory Activities (MedDRA) was used to identify cases of hepatobiliary disorders (HD). Drugs were classified using the Anatomical Therapeutic Chemical (ATC) classification. Medline and WHO‐UMC databases were used to address specific queries suggested by our results. The questionnaire was used to investigate the health care professionals' knowledge and practice related to spontaneous reporting.

Results

Among the 1804 reports of ADRs recorded in the SPD between 1995 and 2008, 70 (3.9%) cases of HD were identified. Drugs most frequently associated with hepatotoxicity were anti‐infectives for systemic use, drugs affecting the nervous system, herbal products, hypolipemics, and anticoagulant drugs (26.83, 24.39, 12.20, 9.76, and 8.54% cases, respectively). Four cases (5.71%) of liver injury resulted in death, which accounted for 10.26% of all ADR fatalities reported to the SPD. The main reasons for not reporting ADRs were lack of reporting knowledge (30.26%), well‐known ADRs (29.89%), and insecurity about causality relationship (15.50%).

Conclusions

Anti‐infectives, nervous system drugs, and herbal products were the most common drug classes reported for hepatotoxicity in Serbia. There is a need for additional education about ADRs, and enhanced reporting by health care professionals. Copyright © 2011 John Wiley & Sons, Ltd.
Construction of temperature responsive hybrid crosslinked self‐assemblies based on PEG‐b‐P(MMA‐co‐MPMA)‐b‐PNIPAAm triblock copolymer: ATRP synthesis and thermoinduced association behavior
Authors: Wei Hua , Ravarian Roya , Dehn Sabrina , Perrier Sebastien , Dehghani Fariba
Published: March 2011

A novel amphiphilic thermosensitive poly(ethylene glycol)45‐b‐poly(methyl methacrylate46‐co‐3‐(trimethoxysilyl)propyl methacrylate)2‐b‐poly(N‐isopropylacrylamide)429 (PEG45‐b‐P(MMA46‐co‐MPMA2)‐b‐PNIPAAm429) triblock copolymer was synthesized via consecutive atom transfer radical polymerization techniques. The thermoinduced association behavior of the resulting triblock copolymers in aqueous medium was further investigated in detail by 1H NMR, transmission electron microscopy, and dynamic light scattering. The results showed that at the temperature (25 °C) below the LCST, PEG45‐b‐P(MMA46‐co‐MPMA2)‐b‐PNIPAAm429 triblock copolymers self‐assembled into the core crosslinked micelles with the hydrophobic P(MMA‐co‐MPMA) block constructing a dense core, protected by the mixed soluble PEG and PNIPAAm chains acting as a hydrophilic shell simultaneously. With an increase in temperature, the resulting core‐shell micelles converted into a new type of micelles with the hydrophilic PEG chains stretching out from the hydrophobic core through the collapsed PNIPAAm shell. On the other hand, at the temperature (40 °C) above the LCST, such triblock copolymers formed the crosslinked vesicles with the hydrophobic PNIPAAm and P(MMA‐co‐MPMA) blocks constructing a membrane core and the soluble PEG chains building the hydrophilic lumen and the shell. On further decreasing the temperature, the resulting vesicles underwent transformation from the shrunken to the expanded status, leading to the formation of swollen vesicles with enlarged size. This study is believed to present the first formation of two types of hybrid crosslinked self‐assemblies by thermoinduced regulation. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Synthesis of repeating sequence copolymers of lactic, glycolic, and caprolactic acids
Authors: Weiss Ryan M. , Jones Evan M. , Shafer David E. , Stayshich Ryan M. , Meyer Tara Y.
Published: March 2011

Repeating sequence copolymers of poly(lactic‐co‐caprolactic acid) (PLCA), poly(glycolic‐co‐caprolactic acid) (PGCA), and poly(lactic‐co‐glycolic‐co‐caprolactic acid) (PLGCA) have been synthesized by polymerizing segmers with a known sequence in yields of 50–85% with Mns ranging from 18–49 kDa. The copolymers exhibited well‐resolved NMR resonances indicating that the sequence encoded in the segmers used in their preparation is retained and that transesterification is minimal. The exact sequences allowed for unambiguous assignment of the NMR spectra, and these standards were compared with the data previously reported for random copolymers. The glass transition temperatures (Tgs) of the PLCA and PGCA copolymers were found to depend primarily on monomer ratio rather than sequence. Sequence dependent Tgs were, however, noted for the PLGCA polymers with 1:1:1 L:G:C ratios; poly LGC and poly GLC exhibited Tgs that differed by nearly 8 °C. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Synthesis, optical and electrochemical properties of arylenevinylene‐based π‐conjugated polymers with imidazolium units in the main chain
Authors: Toba Masaya , Nakashima Takuya , Kawai Tsuyoshi
Published: March 2011

Arylenevinylene‐based π‐conjugated polymers containing imidazolium cationic units in the main chain and their model compounds were synthesized and characterized in terms of optical and electrochemical properties. 9,9‐Bisoctylfluorene, 2,5‐bisdodecyloxybenzene, and 3‐dodecylthiophene were introduced as arylene units with different donor characteristics to evaluate the effect on the highest occupied molecular orbital‐lowest unoccupied molecular orbital (HOMO‐LUMO) gap energy. The UV–vis and fluorescence spectra of cationic polymers and model compounds with iodide counter anion exhibited a significant blue shift with respect to the parent neutral molecules. X‐ray single crystal analysis for model compounds revealed that the effective π‐conjugation length of cationic model compounds decreased compared to the neutral model compounds by means of twisted conformation directed by CH‐π interactions between N‐methyl groups of imidazolium and neighboring aryl units. The cyclic voltammetry measurement suggested the negative shift of LUMO levels by the conversion of imidazole to imidazolium, indicating the electron‐accepting characteristics of cationic imidazolium unit. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Linear tetrablock quaterpolymers via triple click reactions, azide‐alkyne, diels–alder, and nitroxide radical coupling in a one‐pot fashion
Authors: Durmaz Hakan , Hizal Gurkan , Tunca Umit
Published: March 2011

Azide‐alkyne and Diels–Alder click reactions together with a click‐like nitroxide radical coupling reaction were used in a one‐pot fashion to generate tetrablock quaterpolymer. The various living polymerization generated linear polymers with orthogonal end‐functionalities, maleimide‐terminated poly(ethylene glycol) (PEG‐MI), anthracene‐ and azide‐terminated polystyrene, alkyne‐ and bromide‐terminated poly(tert‐butyl acrylate) or alkyne‐poly(n‐butyl acrylate), and tetramethylpiperidine‐1‐oxyl (TEMPO)‐terminated poly(ε‐caprolactone) (PCL‐TEMPO) were clicked together in a one‐pot fashion to generate PEG‐b‐PS‐b‐PtBA‐b‐PCL or PEG‐b‐PS‐b‐PnBA‐b‐PCL quaterpolymer using Cu(0), CuBr, and N,N,N′,N″,N″‐pentamethyldiethylenetriamine as catalyst in dimethyl formamide at 80 °C for 36 h. Linear precursors and target quaterpolymers were analyzed via 1H NMR and gel permeation chromatography. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Partially fluorinated sulfonated poly(arylene sulfone)s blended with polybenzimidazole
Authors: Katzfuß Anika , Krajinovic Katica , Chromik Andreas , Kerres Jochen
Published: March 2011

A partially fluorinated and sulfonated poly(arylene sulfone) (SPSO) was successfully synthesized via nucleophilic polycondensation of 2,2‐bis(4‐fluorophenyl)hexafluoro‐propane with 4,4′‐thiobisbenzenethiol (TBBT). In a second step, the prepared poly(arylene sulfide) was oxidized to SPSO. The polymer was blended with the polybenzimidazole PBIOO® to obtain a mechanically stable membrane. This film was compared with other polymer blends, which were synthesized in our group in the last years. We were especially interested in the influence of different bridging groups such as ether, ketone, and sulfone groups. The affect on properties such as water uptake (WU), thermal stability, proton conductivity, and oxidative stability were analyzed in this work. Additionally, the blend membranes were characterized by gel permeation chromatography. The novel SPSO blend shows a high molecular weight, and its blend membrane with PBIOO has an excellent onset of SO3H group splitting‐off temperature (Tonset) of 334 °C. The proton conductivity amounts to 0.11 S cm−1, and the water uptake reaches 30%. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Conjugated polymers for pure UV light emission: Poly(meta‐phenylenes)
Authors: Patel Dinesh G. “Dan” , Ohnishi Yu‐ya , Yang Yixing , Eom Sang‐Hyun , Farley Richard T. , Graham Kenneth R. , Xue Jiangeng , Hirata So , Schanze Kirk S. , Reynolds John R.
Published: March 2011

We report the synthesis of a 3‐ethylhexyloxy substituted poly(meta‐phenylene), EHO‐PMP that shows absorption and solid state photoluminescence exclusively in the UV region of the electromagnetic spectrum with an emission maximum of 345 nm. Computational analysis of model oligomers by DFT methods indicates that EHO‐PMP is a wide bandgap polymer with the HOMO being localized on a dimeric (biphenyl) unit and with the LUMO being more delocalized. The energy of the LUMO, however, suggests that inefficient electron injection would occur from currently available cathode materials in standard light‐emitting device architectures, and this was observed experimentally. The computational results, coupled with experimental observation, lead us to believe that efficient electroluminescence from organic polymer UV emitters requires advances in electron transport layers and cathode materials. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011
The multidimensionality of spiritual wellbeing: peace, meaning, and faith and their association with quality of life and coping in oncology
Authors: Whitford Hayley S. , Olver Ian N.
Published: March 2011

Objective

This study explored associations between the recently proposed three‐factor structure of the 12‐item Functional Assessment of Chronic Illness Therapy—Spiritual Well‐being (FACIT‐Sp) subscale (Peace, Meaning, and Faith), quality of life (QoL), and coping in an oncology population.

Methods

A total of 999 newly diagnosed, study eligible, consecutive cancer patients completed the FACIT‐Sp and the Mental Adjustment to Cancer (MAC) scale.

Results

Hierarchical multiple regressions revealed that Peace alone added 3% to the prediction of QoL and accounted for 15.8% of the overlap in Total Functional Assessment of Cancer Therapy—General (FACT‐G) scores (both p<0.001). Meaning alone added 1.3% to QoL prediction and accounted for 5.8% in overlap (both p<0.001). Faith did not significantly contribute to the unique prediction or overlap of QoL. Correlational analyses revealed that Peace was most prominently associated with the QoL subscales of Functional (r = 0.64) and Emotional Wellbeing (r = 0.61) and the coping styles of Helpless/Hopeless (r = −0.53), Fighting Spirit (r = 0.47), and Anxious Preoccupation (r = −0.34). Meaning was also highly associated with Functional Wellbeing (r = 0.56), Helpless/Hopeless (r = −0.53), and Fighting Spirit (r = 0.54), but in addition, Social Wellbeing (r = 0.49).

Conclusions

The three‐factor model of spiritual wellbeing appears psychometrically superior to previous models as it further discriminates between which components are most highly associated with improved QoL facets and coping styles. This study provides normative data on newly diagnosed patients with cancer and further highlights the clinical contribution of such detailed assessment.

Copyright © 2011 John Wiley & Sons, Ltd.
One‐step Fabrication of π‐Conjugated Polymer Thin Films from Naphthalenes via Plasma Polymerization for Efficient Optoelectronic Devices: White Polymer Light‐emitting Diodes
Authors: Chang Chun‐Chih , Chang Yi‐Hsin , Hwang Kuo‐Chu , Jou Jwo‐Huei , Yang Arnold C.‐M.
Published: March 2011

We describe a facile one‐step fabrication process of thin film conjugated polymers for efficient optoelectronic devices from naphthalenes by plasma polymerization through a new monomer feeding method. The resulting 3‐D aromatic chain networks of the polymerized films were in good agreement with the predictions based on monomer bond rupture routes analysis. The photoluminescence (PL) spectra of plasma‐polymerized films featured short‐lived inter‐molecular emissions arising from self‐assembly of the naphthalene units in the crosslinked architectures. When functioning between the electrodes for light emitting, the plasma films manifested electroluminescence (EL) spectra that showed a steep rise at the threshold wavelength red‐shifted relative to the PL spectra, indicating prevailing charge tunneling to lower excited states by the accumulated interfacial charges. The wide distribution of conjugation lengths in the plasma films provided the subsequent energy transfer routes and gave rise to the broad EL emission band that produced stable pure white light of CIE coordinates of (0.34, 0.33) with excellent efficiencies. This dry deposition process allows the use of multiple monomers for property tailoring and may be used for large‐area depositions.

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Structural modeling and molecular dynamics simulation of the actin filament
Authors: Splettstoesser Thomas , Holmes Kenneth C. , Noé Frank , Smith Jeremy C.
Published: March 2011

Actin is a major structural protein of the eukaryotic cytoskeleton and enables cell motility. Here, we present a model of the actin filament (F‐actin) that not only incorporates the global structure of the recently published model by Oda et al. but also conserves internal stereochemistry. A comparison is made using molecular dynamics simulation of the model with other recent F‐actin models. A number of structural determents such as the protomer propeller angle, the number of hydrogen bonds, and the structural variation among the protomers are analyzed. The MD comparison is found to reflect the evolution in quality of actin models over the last 6 years. In addition, simulations of the model are carried out in states with both ADP or ATP bound and local hydrogen‐bonding differences characterized. Proteins 2011; © 2011 Wiley‐Liss, Inc.
A parameterized, continuum electrostatic model for predicting protein pKa values
Authors: Burger Steven K. , Ayers Paul W.
Published: March 2011

Recognizing the limits of trying to achieve chemical accuracy for pKa calculations with a purely electrostatic model, we include empirical corrections into the Poisson–Boltzmann solver macroscopic electrostatics with atomic detail (Bashford, Biochemistry 1990;29:10219–10225), to improve the reliability and accuracy of the model. The total number of parameters is kept to a minimum to maximize the robustness of the model for compounds outside of the fitting dataset. The parameters are based on: (a) the electrostatic interaction between functional groups close to the titratable site, (b) the electrostatic work required to desolvate the residue, and (c) the site‐to‐site interactions. These interactions are straightforward to calculate once the electrostatic field has been solved for each residue using the linearized Poisson–Boltzmann equation and are assumed to be linearly related to the intrinsic pKa. Two hundred and eighty‐six residues from 30 proteins are used to determine the empirical parameters, which result in a root mean square error (RMSE) of 0.70 for the entire set. Eight proteins with 46 experimentally known values were excluded from the parameterization to test the model. This test set had a RMSE of 1.08. We show that the parameterized model improves the results over other models, although like other models the error is strongly correlated with the degree to which a residue is buried. The parameters themselves indicate that local effects are most important for determining the pKa, whereas site‐to‐site interactions are found to be less significant. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Structure‐based identification of catalytic residues
Authors: Yahalom Ran , Reshef Dan , Wiener Ayana , Frankel Sagiv , Kalisman Nir , Lerner Boaz , Keasar Chen
Published: March 2011

The identification of catalytic residues is an essential step in functional characterization of enzymes. We present a purely structural approach to this problem, which is motivated by the difficulty of evolution‐based methods to annotate structural genomics targets that have few or no homologs in the databases. Our approach combines a state‐of‐the‐art support vector machine (SVM) classifier with novel structural features that augment structural clues by spatial averaging andZscoring. Special attention is paid to the class imbalance problem that stems from the overwhelming number of non‐catalytic residues in enzymes compared to catalytic residues. This problem is tackled by: (1) optimizing the classifier to maximize a performance criterion that considers both Type I and Type II errors in the classification of catalytic and non‐catalytic residues; (2) under‐sampling non‐catalytic residues before SVM training; and (3) during SVM training, penalizing errors in learning catalytic residues more than errors in learning non‐catalytic residues. Tested on four enzyme datasets, one specifically designed by us to mimic the structural genomics scenario and three previously evaluated datasets, our structure‐based classifier is never inferior to similar structure‐based classifiers and comparable to classifiers that use both structural and evolutionary features. In addition to the evaluation of the performance of catalytic residue identification, we also present detailed case studies on three proteins. This analysis suggests that many false positive predictions may correspond to binding sites and other functional residues. A web server that implements the method, our own‐designed database, and the source code of the programs are publicly available athttp://www.cs.bgu.ac.il/∼meshi/functionPrediction. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Progress in the structural prediction of G protein‐coupled receptors: D3 receptor in complex with eticlopride
Authors: Obiol‐Pardo Cristian , López Laura , Pastor Manuel , Selent Jana
Published: March 2011

Predicting the three‐dimensional structure of ligand–receptor complexes involving G protein‐coupled receptors (GPCRs) is still a challenging task in rational drug design. To evaluate the reliability of the GPCR structural prediction, only a couple of community‐wide assessments have been carried out. Our participation in the last edition, DOCK2010, involved the blind prediction of the dopaminergic D3 receptor in complex with the D2/D3 selective antagonist eticlopride for which the crystal structure has been recently released. Here, we describe a methodology that succeeded to produce a correctly predicted eticlopride‐D3 receptor complex out of three submitted models. Ranking the obtained models in the correct order is the main challenge due to subtle structural differences in the complex that are not sufficiently captured by conventional scoring functions. Importantly, our work reveals that a correct ranking is obtained by including a more sophisticated description of conformational ligand energy on binding. All in all, this case study highlights the current progress in modeling GPCR complexes and underlines that in silico modeling can be a valuable complement in GPCR drug discovery. Proteins 2011; © 2011 Wiley‐Liss, Inc.
X‐ray, ESR, and quantum mechanics studies unravel a spin well in the cofactor‐less urate oxidase
Authors: Gabison Laure , Chopard Claude , Colloc'h Nathalie , Peyrot Fabienne , Castro Bertrand , Hajji Mohamed El , Altarsha Muhannad , Monard Gerald , Chiadmi Mohamed , Prangé Thierry
Published: March 2011

Urate oxidase (EC 1.7.3.3 or UOX) catalyzes the conversion of uric acid using gaseous molecular oxygen to 5‐hydroxyisourate and hydrogen peroxide in absence of any cofactor or transition metal. The catalytic mechanism was investigated using X‐ray diffraction, electron spin resonance spectroscopy (ESR), and quantum mechanics calculations. The X‐ray structure of the anaerobic enzyme–substrate complex gives credit to substrate activation before the dioxygen fixation in the peroxo hole, where incoming and outgoing reagents (dioxygen, water, and hydrogen peroxide molecules) are handled. ESR spectroscopy establishes the initial monoelectron activation of the substrate without the participation of dioxygen. In addition, both X‐ray structure and quantum mechanic calculations promote a conserved base oxidative system as the main structural features in UOX that protonates/deprotonates and activate the substrate into the doublet state now able to satisfy the Wigner's spin selection rule for reaction with molecular oxygen in its triplet ground state. Proteins 2011; © 2011 Wiley‐Liss, Inc.
UTIs: the challenge of treatment failure and recurrent infections
Authors: Mayer Rachel
Published: March 2011

Our series on Prescribing challenges focuses on areas of therapeutics that can present a particular challenge in general practice. Here, the author considers the management of patients with urinary tract infection who reconsult having failed to respond to first‐line treatment. Copyright © 2011 Wiley Interface Ltd
Paracetamol use in children: is it as safe as we think?
Authors: Paul Siba , Whibley Jennifer
Published: March 2011

The authors explain why they think paracetamol, one of the commonest drugs prescribed, should be used with caution in young children. Copyright © 2011 Wiley Interface Ltd
Current approaches to the management of stable angina
Authors: Cruden Nick , Fox Keith
Published: March 2011

Current angina management focuses on the prevention of future cardiac events and control of symptoms. Our Drug review describes the various antianginal drugs available, followed by sources of further information and an analysis of prescription data. Copyright © 2011 Wiley Interface Ltd
Fabrication and study of porous PbTe layers on silicon substrates
Authors: Zimin Sergey , Vasin Vladimir , Gorlachev Egor , Naumov Viktor , Petrakov Anatoly , Shilov Sergey
Published: March 2011

Fabrication of porous PbTe layers on Si substrates using a developed technique based on anodic electrochemical etching of PbTe/CaF2/Si(111) heteroepitaxial structures in a Norr electrolyte with anodizing current density 2‐4 mA/cm2 is reported. The structural and morphological parameters of such layers are investigated with x‐ray reflectometry and diffractometry methods and with high‐resolution scanning electron microscopy. The influence of anodizing conditions on the parameters of the layers is discussed, as well as the morphological peculiarities of the anodized structures. The presence of cylindrical mesopores with diameter of 7‐26 nm inclined at the angle of ∼35° to the surface normal is shown. The value of the porosity for the near‐surface layer of lead telluride films is in the interval of 41‐68% and depends on the anodic electrochemical treatment conditions. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Ultra thin porous silicon films investigated by X‐ray reflectometry
Authors: Ennejah Nessima , Aouida Selma , Bessais Brahim
Published: March 2011

In this study, we report on structural variation of ultrathin of p‐type Porous Silicon (PS) films during the early stage growth process using X‐Ray Reflectometry (XRR). The PS samples were firstly characterized by Fourier Transform Infrared spectroscopy (FTIR) measurements. The homogeneity and surface roughness of the PS films, which enable characterizing the PS films by XRR, were investigated by UV‐visible spectroscopy and atomic force microscopy (AFM) measurements. The PS layers were then analyzed by specular X‐Ray Reflectivity (XRR). XRR reveals a linear thickness behavior as a function of etching time, while the porosity increases before reaching a constant value around 72%. These results were compared to those obtained from other characterization. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Correlation between spin density and photoluminescence intensity in thermally oxidized porous silicon
Authors: Pavlikov Alexander , Konstantinova Elizaveta , Timoshenko Victor
Published: March 2011

We have investigated the optoelectronic properties of thermally oxidized meso ‐PS layers. The correlation between photoluminescence (PL) intensity in the visible spectral ranges and defect density detected by electron spin resonance method has been established. The observed PL is explained by the radiative recombination of excitons trapped on the electronic states (Si=O bonds) in Si nanocrystals. The thermal treatment of meso ‐PS results in both the oxidation and coalescence of Si nanocrystals. Then, the simultaneous increase of both Si=O bond concentration and the density of Pb‐like centers at Si/SiO2 interfaces takes place. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Combination of silicon nitride and porous silicon induced optoelectronic features enhancement of multicrystalline silicon solar cells
Authors: Rabha Mohamed Ben , Dimassi Wissem , Gaidi Mounir , Ezzaouia Hatem , Bessais Brahim
Published: March 2011

The effects of antireflection (ARC) and surface passivation films on optoelectronic features of multicrystalline silicon (mc‐Si) were investigated in order to perform high efficiency solar cells. A double layer consisting of Plasma Enhanced Chemical Vapor Deposition (PECVD) of silicon nitride (SiNx) on porous silicon (PS) was achieved on mc‐Si surfaces. It was found that this treatment decreases the total surface reflectivity from about 25% to around 6% in the 450‐1100 nm wavelength range. As a result, the effective minority carrier diffusion length, estimated from the Laser‐beam‐induced current (LBIC) method, was found to increase from 312 µm for PS‐treated cells to about 798 µm for SiNx/PS‐treated ones. The deposition of SiNx was found to impressively enhance the minority carrier diffusion length probably due to hydrogen passivation of surface, grain boundaries and bulk defects. Fourier Transform Infrared Spectroscopy (FTIR) shows that the vibration modes of the highly suitable passivating Si‐H bonds exhibit frequency shifts toward higher wavenumber, depending on the x ratio of the introduced N atoms neighbors. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On the origin of photoluminescence from silicon nanostructures: a new perspective
Authors: Sa'ar Amir
Published: March 2011

This review is aimed at describing recent developments in the field of silicon nanostructures, particularly those properties and phenomena that are connected with the room‐temperature, photoluminescence (PL) from these nanostructures. Two classes of models are the most notable ones: the quantum confinement model that assigns the PL to quantum size effects in the nanocrystalline silicon core, and the surface chemistry model that assigns the PL to surface phenomena at the interface between the crystalline core and the host matrix that wrap the nanostructures. In recent years, with the improvement in growth techniques and methods to control dimensionality and shape, it has been suggested that none of the above models alone can explain the entire spectrum of optical phenomena in silicon nanostructures. Instead, a refined model that takes into accounts both phenomena should be considered. This review describes some of these recent developments in the field of silicon nanostructures, particularly those experiments and models that indicate the mutual role of quantum confinement and surface chemistry in shaping the optical properties of these nanostructures. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
State and parameter estimation with the extended Kalman filter: an alternative formulation of the model error dynamics
Authors: Carrassi Alberto , Vannitsem Stéphane
Published: March 2011

An alternative formulation of the extended Kalman filter for state and parameter estimation is presented, referred to as Short‐Time Augmented Extended Kalman Filter (ST‐AEKF). In this algorithm, the evolution of the model error generated by the uncertain parameters is described using a truncated short‐time Taylor expansion within the assimilation interval. This allows for a simplification of the forward propagation of the augmented error covariance matrix with respect to the classical state augmented approach. The algorithm is illustrated in the case of a scalar unstable dynamics and is then more extensively analyzed in the context of the Lorenz 36‐variable model. The results demonstrate the ability of the ST‐AEKF to provide accurate estimate of both the system's state and parameters with a skill comparable to that of the full state augmented approach and in some cases close to the EKF in a perfect model scenario. The performance of the filter is analyzed for different initial parametric errors and assimilation intervals, and for the estimates of one or more model parameters. The filter accuracy is sensitive to the nature of the estimated parameter but more importantly to the assimilation interval, a feature connected to the short‐time approximation on which the filter formulation relies. The conditions and the context of applications of the present approach are also discussed. Copyright © 2011 Royal Meteorological Society
Does needle rotation improve lesion targeting?
Authors: Badaan Shadi , Petrisor Doru , Kim Chunwoo , Mozer Pierre , Mazilu Dumitru , Gruionu Lucian , Patriciu Alex , Cleary Kevin , Stoianovici Dan
Published: March 2011

Background

Image‐guided robots are manipulators that operate based on medical images. Perhaps the most common class of image‐guided robots are robots for needle interventions. Typically, these robots actively position and/or orient a needle guide, but needle insertion is still done by the physician. While this arrangement may have safety advantages and keep the physician in control of needle insertion, actuated needle drivers can incorporate other useful features.

Methods

We first present a new needle driver that can actively insert and rotate a needle. With this device we investigate the use of needle rotation in controlled in‐vitro experiments performed with a specially developed revolving needle driver.

Results

These experiments show that needle rotation can improve targeting and may reduce errors by as much as 70%.

Conclusion

The new needle driver provides a unique kinematic architecture that enables insertion with a compact mechanism. Perhaps the most interesting conclusion of the study is that lesions of soft tissue organs may not be perfectly targeted with a needle without using special techniques, either manually or with a robotic device. The results of this study show that needle rotation may be an effective method of reducing targeting errors. Copyright © 2011 John Wiley & Sons, Ltd.
Nanoparticles: Well Shaped Mn3O4 Nano‐octahedra with Anomalous Magnetic Behavior and Enhanced Photodecomposition Properties (Small 4/2011)
Authors: Li Yu , Tan Haiyan , Yang Xiao‐Yu , Goris Bart , Verbeeck Jo , Bals Sara , Colson Pierre , Cloots Rudi , Van Tendeloo Gustaaf , Su Bao‐Lian
Published: March 2011

Very uniform and well shaped Mn3O4 nano‐octahedra are synthesized using a simple hydrothermal method under the help of polyethylene glycol (PEG200) as a reductant and shape‐directing agent. The nano‐octahedra formation mechanism is monitored. The shape and crystal orientation of the nanoparticles is reconstructed by scanning electron microscopy and electron tomography, which reveals that the nano‐octahedra only selectively expose {101} facets at the external surfaces. The magnetic testing demonstrates that the Mn3O4 nano‐octahedra exhibit anomalous magnetic properties: the Mn3O4 nano‐octahedra around 150 nm show a similar Curie temperature and blocking temperature to Mn3O4 nanoparticles with 10 nm size because of the vertical axis of [001] plane and the exposed {101} facets. With these Mn3O4 nano‐octahedra as a catalyst, the photodecomposition of rhodamine B is evaluated and it is found that the photodecomposition activity of Mn3O4 nano‐octahedra is much superior to that of commercial Mn3O4 powders. The anomalous magnetic properties and high superior photodecomposition activity of well shaped Mn3O4 nano‐octahedra should be related to the special shape of the nanoparticles and the abundantly exposed {101} facets at the external surfaces. Therefore, the shape preference can largely broaden the application of the Mn3O4 nano‐octahedra.
Sonographic ‘molar tooth’ sign in the diagnosis of Joubert syndrome
Authors: Pugash D. , Oh T. , Godwin K. , Robinson A. J. , Byrne A. , Van Allen M. I. , Osiovich H.
Published: March 2011

The characteristic imaging finding common to Joubert syndrome and related disorders is the ‘molar tooth’ sign. The prenatal diagnosis of Joubert syndrome using both ultrasound and fetal magnetic resonance imaging (MRI) in families with an affected child has been reported previously. We report two cases in which the molar tooth sign was identified by sonography at 26 + 4 weeks and at 20 + 6 weeks, respectively, prior to fetal MRI or genetic testing. In both cases the finding was subsequently confirmed on fetal MRI. As definitive prenatal genetic testing may not be conclusive in Joubert syndrome, the ability to identify the molar tooth sign sonographically before 24 weeks provides a valuable adjunct to prenatal diagnosis. Copyright © 2011 ISUOG. Published by John Wiley & Sons, Ltd.
Evaluation of a Trainer Phantom in the Learning Phase of Sentinel Lymph Node Identification in Breast Cancer
Authors: Lèguevaque Pierre , Motton Stephanie , Courbon Frédéric , Ricard Marcel , Berry Isabelle , Querleu Denis
Published: March 2011

Background

The concept of a learning phase is difficult to implement in a university setting, as it is unacceptable to subject a patient who requires only lymphadenectomy to axillary dissection for the purpose of training surgeons. We therefore sought too evaluate intraoperative sentinel node detection using a phantom, the Senti‐Trainer. Learning phases on the Senti‐Trainer and detection rate were assessed in order to determine whether the proficiency of surgeons in training improved with the number of procedures.

Methods

Twenty residents each performed 30 detection procedures of a sentinel node on the silicon phantom. Each resident was evaluated at each procedure, and an observation report was made every five procedures. Evaluation was single‐blind as the surgeons did not know the result of the previous detection and were aware of the results only after the thirtieth procedure.

Results

The mean detection rate was 75% during the first procedure and reached 95% (or 5% detection errors) at the 30th procedure (p < 0.0001; OR = 6.33 with a 95% CI = [2.31; 17.33]). Proficiency in sentinel lymph node (SLN) identification also increased with the number of procedures performed. The ability to localize SLN improved during the learning phase with the increasing number of procedures performed. Mean detection time during the 30 procedures was 150 s (range: 115–210 s).

Conclusions

Training on a phantom showed that this is a valuable teaching tool that enables surgeons to become familiar with gamma probes. It cannot replace the clinical training phase, but is an important aid to proficiency in intraoperative detection.