bluuebunny/crossref_metadata_2025 huggingface dataset:
Case‐finding algorithm for post‐stroke depression in the veterans health administration
Authors: Damush Teresa M. , Jia Huanguang , Ried L. Doug , Qin Haijing , Cameon Randi , Plue Laurie , Williams Linda S.
Published: November 2007

Objectives

Post‐stroke depression (PSD) is prevalent, often undiagnosed, and undertreated. The accuracy of detecting patients with post‐stroke depression in administrative databases has not been examined.The objective was to validate a case‐finding algorithm for post‐stroke depression (PSD) among veteran stroke survivors.

Methods

We conducted a retrospective cohort study of veterans admitted to two local VHA facilities for an inpatient episode of care for acute ischemic stroke. Our cohort included all patients from two medical centers who were identified in the fiscal year (FY) 2001 VHA inpatient database using high specificity stroke ICD‐9 codes. FY 2002 VHA and Medicare inpatient, outpatient, and pharmacy data were used to examine the patients' 12‐month PSD status by using ICD‐9 depression codes and antidepressant use. We assessed our accuracy about patients' PSD from the administrative databases through standardized chart reviews.

Results

Of our 185 subject cohort, 50 (27%) were identified as having PSD. The most sensitive case‐finding algorithm for PSD included having an ICD‐9 code diagnosis for depression or receiving a prescription for an approved‐dosage of antidepressant medication. However, the algorithm of receiving an ICD‐9 code for primary or secondary diagnoses of depression revealed the largest positive predictive value.

Conclusions

A case‐finding algorithm using outpatient ICD‐9 codes or medication was the most sensitive in identifying cases of PSD. The use of ICD‐9 codes alone may be adequate for characterizing a cohort with PSD. Intention for use should be considered when choosing an algorithm to detect PSD. Copyright © 2007 John Wiley & Sons, Ltd.
Modulating in vitro bone cell and macrophage behavior by immobilized enzymatically tailored pectins
Authors: Bussy Cyrill , Verhoef René , Haeger Ash , Morra Marco , Duval Jean‐Luc , Vigneron Pascale , Bensoussan Anne , Velzenberger Elodie , Cascardo Giovanna , Cassinelli Clara , Schols Henk , Knox J. Paul , Nagel Marie‐Danielle
Published: November 2007

Previous work has reported the results of a multidisciplinary effort producing a proof‐of‐concept on the use of pectic polysaccharides in the surface modification of medical devices. This study was designed to learn more about the capability of engineered rhamnogalacturonan‐I (RG‐I) fractions of apple pectin to control bone cell and macrophage behavior. Thermanox® or polystyrene Petri dishes were surface modified with two different modified hairy regions (MHRs) obtained by different enzymatic liquefaction processes of apples differing in relative amounts and lengths of their neutral side chains: (long‐haired) MHR‐α and (short‐haired) MHR‐B. Bone explants from 14‐day‐old chick embryos were cultured for 14 days on both pectic substrata. MHR‐B promoted cell migration and differentiation, MHR‐α did not. On MHR‐α, J774.2 macrophages grew well, their percentage in G1 phase was decreased and in S phase increased, and they did not secrete either proinflammatory‐cytokines or nitrites. Contrasting results were gained from macrophages on MHR‐B, except for nitrite secretion. Thus, we conclude that coatings from tailored pectins show different biological activities in vitro and are potential innovative candidates for improving the biocompatibility of medical devices in various applications. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res, 2008
Short‐term TNF‐Alpha treatment induced A2Badenosine receptor desensitization in human astroglial cells
Authors: Trincavelli Maria Letizia , Tonazzini Ilaria , Montali Marina , Abbracchio Maria Pia , Martini Claudia
Published: November 2007

Long‐term glial cell treatment with the proinflammatory cytokine TNF‐alpha has been demonstrated to increase the functional responsiveness of A2Badenosine receptors (A2BARs), which in turn synergize with the cytokine inducing chronic astrogliosis. In the present study, we investigated the short‐term effects of TNF‐alpha on A2BAR functional responses in human astroglial cells (ADF), thus simulating the acute phase of cerebral damage which is characterized by both cytokine and adenosine high level release. Short‐term TNF‐alpha cell treatment caused A2BAR phosphorylation inducing, in turn, impairment in A2BAR‐G protein coupling and cAMP production. These effects occurred in a time‐dependent manner with a maximum following 3‐h cell exposure. Moreover, we showed PKC intracellular kinase is mainly involved in the TNF‐alpha‐mediated regulation of A2BAR functional responses. The results may indicate the A2BAR functional impairment as a cell defense mechanism to counteract the A2Breceptor‐mediated effects during the acute phase of brain damage, underlying A2BAR as a target to modulate early inflammatory responses. J. Cell. Biochem. 104: 150–161, 2008. © 2007 Wiley‐Liss, Inc.
Mechanisms of inhibition of dehydroepiandrosterone upon corticosterone release from rat zona fasciculata‐reticularis cells
Authors: Chang Ling‐Ling , Wun Wan‐Song Alfred , Wang Paulus S.
Published: November 2007

We have demonstrated that dehydroepiandrosterone (DHEA) acts directly on rat zona fasciculata‐reticularis (ZFR) cells to diminish corticosterone secretion by an inhibition of post‐cAMP pathway, and decreases functions of steroidogenic enzymes after P450scc as well as steroidogenic acute regulatory (StAR) protein expression. However, the mechanisms by which DHEA engages with environmental messenger signals which translate into interfering StAR protein expression are still unclear. This study explored the effects of DHEA on the phosphorylation/activation of extracellular signal‐regulated kinases (ERKs). ERK activation resulted in enhancing phosphorylation of steroidogenic factor‐1 (SF‐1) and increased StAR protein expression. ZFR cells were incubated in the presence or absence of adrenocorticotropin (ACTH), forskolin (FSK), 25‐OH‐cholesterol, U0126, and H89 at 37°C. The concentration of corticosterone released into the media was measured by radioimmunoassay (RIA). The cells were used to extract protein for Western blot analysis of ERKs or StAR protein expression or immunoprecipitation of SF‐1 analysis. The results suggested that (1) ERK pathway of rat ZFR cells might be PKA dependent, (2) ERK activity was required for SF‐1 phosphorylation to upregulate steroidogenesis in rat ZFR cells, and (3) DHEA did not affect ERK phosphorylation, however, it attenuated forskolin‐stimulated SF‐1 phosphorylation to affect StAR protein expression. J. Cell. Biochem. 104: 359–368, 2008. © 2007 Wiley‐Liss, Inc.
Diagnostic accuracy of endometrial thickness to exclude polyps in women with postmenopausal bleeding
Authors: Timmermans Anne , Gerritse Maaike B.E. , Opmeer Brent C. , Jansen Frank W. , Mol Ben W. J. , Veersema Sebastiaan
Published: November 2007

Purpose

To determine the accuracy of endometrial thickness measurement with transvaginal ultrasonography (TVUS) to diagnose endometrial polyps in women with postmenopausal bleeding in whom a carcinoma has been ruled out.

Methods

In women with postmenopausal bleeding, endometrial thickness was measured with TVUS. If endometrial thickness was >4 mm, office hysteroscopy was performed. At hysteroscopy, the uterine cavity was assessed for the presence of polyps. Patients with malignancy were excluded. We used receiver operating characteristics (ROC) analysis to assess the capacity of TVUS endometrial thickness measurement to diagnose endometrial polyps. Findings at hysteroscopy were considered to be the reference standard.

Results

We included 178 patients with postmenopausal bleeding and endometrial thickness >4 mm. Hysteroscopy showed an endometrial polyp in 90 patients (50%). The ROC analysis revealed that endometrial thickness had an area under the curve of 0.64 in the diagnosis of endometrial polyps.

Conclusion

In women with postmenopausal bleeding in whom carcinoma has been ruled out, measurement of endometrial thickness with TVUS is not useful in the diagnosis of endometrial polyps. © 2007 Wiley Periodicals, Inc. J Clin Ultrasound, 2008
An AFM study on mechanical properties of native and dimethyl suberimidate cross‐linked pericardium tissue
Authors: Matyka K. , Matyka M. , Mróz I. , Zalewska‐Rejdak J. , Ciszewski A.
Published: November 2007

Changes in the stiffness of hog pericardium tissue, native and treated with dimethyl suberimidate (DMS), are investigated by atomic force microscopy (AFM). Young's modulus is calculated on the basis of the Hertz–Sneddon model. The cross‐linking process increases the stiffness of the tissue. The values of Young's modulus are higher for the DMS stabilized pericardium than for the native one. We also observe that the Young's modulus of native tissue increases when the time between getting the biological material and performing the measurements is longer. This process is probably connected with natural degradation of the biological samples. Copyright © 2007 John Wiley & Sons, Ltd.
Cyclical long‐range dependence and the warming effect in a long temperature time series
Authors: Gil‐Alana L. A.
Published: November 2007

In this paper, we propose a new approach for modelling a long temperature time series, using fractional cyclical integration. This model is based on the observation that the estimated spectrum of the series (the average annual temperature in Central England, 1659–2001) has its highest value at a frequency which is not zero, thus suggesting the existence of cycles at other frequencies. The results based on a fractional cyclical model show that there is a significant warming effect throughout the sample of about 0.22 °C/century. However, if we concentrate exclusively on the data corresponding to the 20th century that value increases to 0.64%. Moreover, the results in the paper show that a fractionally cyclically integrated model can be a competing alternative to other approaches based on fractional integration at the zero frequency. Copyright © 2007 Royal Meteorological Society
Effects of delayed stabilization on fracture healing
Authors: Miclau Theodore , Lu Chuanyong , Thompson Zachary , Choi Paul , Puttlitz Christian , Marcucio Ralph , Helms Jill A.
Published: November 2007

Previous studies have revealed that delayed internal fixation can stimulate fracture callus formation and decrease the rate of nonunion. However, the effect of delayed stabilization on stem cell differentiation is unknown. To address this, we created fractures in mouse tibiae and applied external fixation immediately, at 24, 48, 72, or 96 h after injury. Fracture healing was analyzed at 10 days by histological methods for callus, bone, and cartilage formation, and the mechanical properties of the calluses were assessed at 14 days postinjury by tension testing. The results demonstrate that delaying stabilization for 24–96 h does not significantly affect the volume of the callus tissue (TV) and the new bone (BV) that formed by 10 days, or the mechanical properties of the calluses at 14 days, compared to immediate stabilization. However, delaying stabilization for 24–96 h induces 10–40× more cartilage in the fracture calluses compared with fractures stabilized immediately. These findings suggest that delaying stabilization during the early phase of fracture healing may not significantly stimulate bone repair, but may alter the mode of bone repair by directing formation of more cartilage. Fractures that are not rigidly stabilized form a significantly larger amount of callus tissue and cartilage by 10 days postinjury than fractures stabilized at 24–96 h, indicating that mechanical instability influences chondrocytes beyond the first 96 h of fracture healing. © 2007 Orthopaedic Research Society. © 2007 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 25:1552–1558, 2007
Characterization of indigo carmine with surface‐enhanced resonance Raman spectroscopy (SERRS) using silver colloids and island films, and theoretical calculations
Authors: Peica N. , Kiefer W.
Published: November 2007

The application of resonance Raman (RR) and surface‐enhanced resonance Raman (SERR) spectroscopies to the qualitative and semiquantitative analysis of the artificial dye indigo carmine has been examined using sodium‐citrate‐reduced silver colloid and island films with various roughnesses. Additional, the Raman spectrum of the solid state and density functional theory (DFT) calculations helped to a better understanding of the fully optimized geometry and of the vibrational wavenumbers of the dye. A strong chemical interaction of indigo carmine with the silver colloidal particles was observed mainly at very low concentration of 0.03 × 10−9 M and with silver film surfaces at a concentration of 10−4 M. The indigo carmine orientation possibilities while going to different metallic substrates are discussed. Copyright © 2007 John Wiley & Sons, Ltd.
Vibrational relaxation study in carbonyl containing molecule: role of hydrodynamic and dispersion forces
Authors: Devi T. Gomti
Published: November 2007

The isotropic Raman component of the C = O stretching mode of ethyl acetate (EA) was analyzed using various polar and nonpolar solvents. It was found that the bandshape approaches towards Lorentzian at high dilution using the curve‐fitting method. The isotropic Raman band was also analyzed by estimating the correlation coefficient with reference to the Lorentzian lineshape using a simple method of linear‐curve fitting. The effects of dispersion and hydrodynamic forces on bandwidth were studied in details. The vibrational relaxation rate was studied using certain parameters and it was found that the microscopic based parameter can explain the complexities occurring in solute–solvent interactions. Copyright © 2007 John Wiley & Sons, Ltd.
Raman and IR spectra of the unstable ionic species potassium trimethylsilanolate: The role of the counterion in its theoretical interpretation
Authors: Montejo Manuel , Ureña Francisco Partal , Márquez Fernando , Ingraín Antonio Marchal , González Juan Jesús López
Published: November 2007

We have accomplished a reliable assignment of the vibrational spectra of the ionic species potassium trimethylsilanolate, which is unstable towards hydrolysis and self‐condensation, by means of the combined use of experimental data and theoretical density functional theory (DFT) calculations. We report the first record of the Raman spectrum of the pure solid. Additionally, we have newly recorded its IR spectrum in Nujol mull and for the first time in Fluorolube mull, completing the experimental data available in the literature about this chemical species. Further, in order to discuss the convenience of including the counterion in the model used for the quantum‐mechanical calculations of its vibrational spectra, we have compared the performance of three different theoretical models, namely, the isolated trimethylsilanolate anion, a theoretical monomer of potassium trimethylsilanolate and a simplified ionic cluster model based on its crystalline structure. Copyright © 2007 John Wiley & Sons, Ltd.
Hochleistungsbremsscheiben aus Faserverbundkeramik
Authors: Rosenlöcher J. , Deinzer G. , Waninger R. , Münchhoff J.
Published: November 2007

Die Audi AG ist einer der weltweit führenden Automobilhersteller der Premiumklasse. Eines der Hauptziele der Technischen Entwicklung bei Audi ist der Einsatz neuartiger und innovativer Werkstoffe. Daher bietet die Audi AG nach intensiver Entwicklung und Erprobung für mehrere Fahrzeugmodelle Keramikbremsscheiben an. Diese Bremsscheiben bestehen aus einer kohlenstoffkurzfaserverstärkten Siliziumkarbidkeramik, einem sog. CMC‐Werkstoff. Dieser Werkstoff wird in einem aufwendigen Verfahren über die Schmelzinfiltration von Kohlenstoff‐Preformen mit Silizium hergestellt. Die Vorteile dieser innovativen und leistungsfähigen Bremsscheiben aus C/SiC‐Keramik sind das geringe Gewicht und dadurch die Reduzierung der ungefederten rotierenden Massen, der geringe Verschleiß über Betriebsdauer, die Temperatur‐ und Fadingstabilität und die Korrosionsbeständigkeit. Aufgrund der materialspezifischen Eigenschaften wurde das gesamte Bremssystem überarbeitet und die Systemperipherie angepasst.
Teilautomatisiertes preforming zur Qualitätssicherung und Verkürzung von Fertigungszeiten bei der Herstellung von Rotorblättern von Windenergieanlagen
Authors: Dörsch C. , Ohlendorf J. H. , Gebauer I. , Müller D. H. , Weigel L.
Published: November 2007

Rotorblätter von Windenergieanlagen werden aufgrund des guten Verhältnisses von Steifigkeit und Gewicht zu großen Teilen aus Faserverbundwerkstoffen gefertigt. Dabei kommen hauptsächlich Glasfasern (GF) als verstärkendes Material sowie duroplastische Harze als Matrix zur Anwendung.

Um die wachsenden Herausforderungen des Offshore‐Einsatzes von Windenergieanlagen, insbesondere die steigende Rotorblattgröße, technisch und wirtschaftlich erfolgreich bewältigen zu können, wird die Verkürzung der Fertigungszeit sowie der zunehmende Qualitätsanspruch an die Rotorblätter eine immer stärkere Rolle einnehmen.

Um diese Ansprüche erfüllen zu können, beschäftigen sich das Bremer Institut für Konstruktionstechnik und das Unternehmen Abeking & Rasmussen Rotec GmbH & Co KG unter anderem mit der Handhabung und Erstellung von sogenannten Preforms, dies sind trockene, textile Halbzeuglagen, die als vorgeformter Lagenstapel in den Fertigungsprozess des Rotorblattes eingebracht werden.

Mit Hilfe der Technologie des Preformings ist es möglich, Bereiche der Fertigung zu parallelisieren. Dies ist ein großer Vorteil bei der Produktion, da aufgrund der notwendigen Temperzeiten, alle anderen Fertigungsschritte möglichst zeitoptimiert gestaltet werden müssen, um kurze Zykluszeiten zu realisieren.

Betrachtet werden soll die Handhabung von textilen Halbzeugen, insbesondere das preforming und dessen Auswirkungen auf die Wirtschaftlichkeit der Faserverbundfertigung. Ebenfalls sollen die Aspekte der Qualitätssicherung in Verbindung mit dem preforming aufgezeigt werden und mögliche Ansätze zu einer Teilautomatisierung gegeben werden.
Entwicklung der Konnektivität der Phasen in einer kurzfaserverstärkten Aluminium‐Kolbenlegierung unter Kriechbelastung
Authors: Requena G.C. , Degischer H.P. , Marks E.D. , Boller E.
Published: November 2007

Das drei‐dimensionale Gefüge einer AlSi12CuMgNi‐Kolbenlegierung verstärkt mit 15 vol% Al2O3‐Kurzfasern wird mittels Synchrotron Mikro‐Tomographie dargestellt. Der lösungsgeglühte Ausgangszustand enthält ein zusammenhängendes Netzwerk aus Kurzfasern und Fe‐ und Ni‐reichen Primärausscheidungen, das darüber hinaus durch eine Vielzahl von Si‐Brücken des Eutektikums verbunden wird. Die Konnektivität nimmt mit der Dauer der Kriechbelastung bei 300 °C zu, besonders durch die Reifung der Si‐Teilchen, die zu einer in sich zusammenhängenden Struktur zusammenwachsen, die mit dem bereits vorhandenen Netzwerk mit den Fasern verbunden ist. Nach 6400 h Belastungsdauer ist die Konnektivität der steifen Phasen nahezu vollständig. Die Orientierung der Fasern wird mit drei‐dimensionalen Fast Fourier Transformationen analysiert, was auf keine Umorientierung der Fasern in die Lastrichtung schließen lässt. Die früher beobachtete Verfestigung des Materials während der Kriechbelastung wird mit der zunehmenden Steifigkeit der hybriden Verstärkungsstruktur erklärt.

Die Proben enthalten im Ausgangszustand bereits Poren an den Grenzflächen der Verstärkungsphasen. Die Porenanzahl ändert sich während der Kriechbelastung im sekundären Kriechstadium nicht, jedoch wachsen die Poren, sodass der Porenvolumenanteil verdoppelt wird. In der α‐Aluminiummatrix wurden keine Kriechporen gefunden.
Verbundwerkstoffe mit Aluminiumschaum – Anwendungen im Schienenfahrzeugbau
Authors: Baumeister J. , Rausch G. , Stöbener K. , Lehmhus D. , Busse M.
Published: November 2007

Nach ihrer Wiederentdeckung Anfang der 90er Jahre werden geschäumte Metalle inzwischen im industriellen Maßstab hergestellt. In den meisten Fällen handelt es sich dabei um Anwendungen, bei denen der Metallschaum im Verbund mit anderen Werkstoffen eingesetzt wird.

Die Verbundkörper können in ebene oder komplex geformte Sandwichstrukturen und 3‐dimensionale Formkörper eingeteilt werden. Die erforderlichen Prozessschritte und realisierbaren Geometrien werden beschrieben. Die Eigenschaften der Werkstoffe werden beleuchtet und die industriellen Anwendungen anhand von Beispielen erläutert.

Im Rahmen eines öffentlich geförderten Projekts wurde die Verwendung von Sandwichverbunden mit einer Kernlage aus Aluminiumschaum für Anwendungen im Schienenfahrzeugbau evaluiert. Insbesondere stand die Herstellung eines Frontmodulsegments im Mittelpunkt der Untersuchungen. Die Ergebnisse dieses Projekts werden vorgestellt.
Joining of cemented carbides to steel by laser beam welding
Authors: Barbatti C. , Garcia J. , Liedl G. , Pyzalla A.
Published: November 2007

Welding of dissimilar materials such as steel and cemented carbides (hardmetals, cermets) is particularly challenging e.g. because mismatches in their thermal expansion coefficients and thermal conductivities result in residual stress formation and because of the formation of brittle intermetallic phases. Laser beam welding of cemented carbides to steel appears as an attractive complementary technique to conventional brazing processes due to its high precision, high process speed, low heat input and the option of welding without filler.

Here a laser welding process including pre‐heat treatment and post‐heat treatment was applied successfully to joining as‐sintered and nitrided hardmetals and cermets to low alloyed steel. The microstructure and mechanical properties of the welds are investigated by microscopy, X‐ray diffraction, microhardness measurements, and bending tests. The results reveal that the three‐step laser beam welding process produced crack‐free and non‐porous joints. Nitridation of the cemented carbides results in a significant reduction of the amount of brittle intermetallic phases. The mechanical properties of the joints are competitive to those of the conventional brazed steel‐cemented carbide joints.
Thermische Ausdehnung, innere Spannungen und Porenverteilung in AlSiCp Metallmatrix‐ verbundwerkstoffen
Authors: Schöbel M. , Requena G. , Degischer H. P , Kaminski H. , Buslaps T. , di Michiel M.
Published: November 2007

AlSi7Mg/SiC/70p (AlSiC) eignet sich als Kühlkörper wegen seiner guten Leitfähigkeit bei gleichzeitig niedrigem thermischen Ausdehnungskoeffizienten (CTE) für Applikationen in der Hochleistungselektronik. Ein niedriger CTE ermöglicht dauerhaft einen guten thermischen Kontakt zwischen der Kühlplatte und dem Elektronikbauteil. Materialien mit hohem Ausdehnungskoeffizienten würden durch thermische induzierte makroskopische Spannungen in der Grenzfläche zu Delaminationen in der Kontaktfläche führen. Aus diesem Grund ersetzt AlSiC Kupfer als Kühlkörpermaterial in der Leistungselektronik.

Das Problem der unterschiedlichen Ausdehnungskoeffizienten ist in den Verbundwerkstoff transferiert und wirkt sich durch innere Mikrospannungen zwischen der Aluminiummatrix und den SiC‐Partikeln aus. Insitu Messungen während thermischer Aufheizzyklen bis 400 °C an AlSi7Mg/SiC/70p Proben wurden vorgenommen, um den Porenanteil und die inneren Spannungen zu bestimmen. Der Porenanteil wird aus Synchrotron Tomografie und die inneren Spannungen mittels Synchrotron Diffraktion (ESFR/ID15A) gemessen. Messungen während des Heizens, Kühlens und nach mehrfachem Zyklieren zeigen einen Zusammenhang zwischen den inneren Spannungen und dem Porenvolumenanteil und der Temperatur.

AlSiC verhält sich von Raumtemperatur bis etwa 200 °C thermo‐elastisch, wobei sich die dominanten Zugspannungen in der Matrix in Druckspannungen umkehren. Mit zunehmender Temperatur verformt sich die Matrix plastisch und vermindert dabei den Porenvolumenanteil. Beim Kühlen von 500 °C wird nach einer elastischen Spannungsumkehr in die Zugrichtung wieder eine Erhöhung des Porenvolumenanteils beobachtet. Unter 200 °C verhält sich AlSiC bis Raumtemperatur wieder thermo‐elastisch. Nach mehreren, extremen Temperaturzyklen von –100 °C bis 400 °C wird die Haftung der SiC‐Partikel an die Al‐Matrix des MMCs lokal gelöst und Porenwachstum beobachtet.
Danon disease due to a novel splice mutation in the LAMP2 gene
Authors: Nadeau Amelie , Therrien Christian , Karpati George , Sinnreich Michael
Published: November 2007

Danon disease is a rare X‐linked dominant disorder caused by lysosomal‐associated membrane protein 2 (LAMP2) deficiency and is characterized by hypertrophic cardiomyopathy, cardiac conduction abnormalities, skeletal vacuolar myopathy, variable degree of mental retardation, and peripheral pigmentary retinopathy. We describe a novel splice mutation in the LAMP2 gene in a French Canadian family. By identifying this novel mutation we were able to offer genetic screening and counseling to all family members. Presymptomatic diagnosis is important as cardiac surveillance can be life‐saving. Muscle Nerve, 2007
A basis function for approximation and the solutions of partial differential equations
Authors: Tian H. Y. , Reutskiy S. , Chen C. S.
Published: November 2007

In this article, we introduce a type of basis functions to approximate a set of scattered data. Each of the basis functions is in the form of a truncated series over some orthogonal system of eigenfunctions. In particular, the trigonometric eigenfunctions are used. We test our basis functions on recovering the well‐known Franke's and Peaks functions given by scattered data, and on the extension of a singular function from an irregular domain onto a square. These basis functions are further used in Kansa's method for solving Helmholtz‐type equations on arbitrary domains. Proper one level and two level approximation techniques are discussed. A comparison of numerical with analytic solutions is given. The numerical results show that our approach is accurate and efficient. © 2007 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2008
Numerical solution of the free‐surface viscous flow on a horizontal rotating elliptical cylinder
Authors: Hunt Roland
Published: November 2007

The numerical solution of the free‐surface fluid flow on a rotating elliptical cylinder is presented. Up to the present, research has concentrated on the circular cylinder for which steady solutions are the main interest. However, for noncircular cylinders, such as the ellipse, steady solutions are no longer possible, but there will be periodic solutions in which the solution is repeated after one full revolution of the cylinder. It is this new aspect that makes the investigation of noncircular cylinders novel. Here we consider both the time‐dependent and periodic solutions for zero Reynolds number fluid flow. The numerical solution is expedited by first mapping the fluid film domain onto a rectangle such that the position of the free‐surface is determined as part of the solution. For the time‐dependent case a simple time‐marching method of lines approach is adopted. For the periodic solution the discretised nonlinear equations have to be solved simultaneously over a time period. The resulting large system of equations is solved using Newton's method in which the form of the Jacobian enables a straightforward decomposition to be implemented, which makes matrix inversion manageable. In the periodic case all derivatives have been approximated pseudospectrally with the time derivative approximated by a differentiation matrix which has been specially derived so that the weight of fluid is algebraically conserved. Of interest is the solution for which the weight of fluid is at its maximum possible value, and this has been obtained by increasing the weight until a consistency break‐down occurs. Time‐dependent solutions do not produce the periodic solution after a long time‐scale but have protuberances which are constantly appearing and disappearing. Periodic solutions exhibit spectral accuracy solutions and maximum supportable weight solutions have been obtained for ranges of eccentricity and angular velocity. The maximum weights are less than and approximately proportional to those obtained for the circular case. The shapes of maximum weight solutions is distinctly different from sub‐maximum weight solutions. © 2007 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2008
The blind search for the closed states of hinge‐bending proteins
Authors: Yesylevskyy Semen O. , Kharkyanen Valery N. , Demchenko Alexander P.
Published: November 2007

The hinge‐bending proteins provide the most pronounced example of the large‐amplitude slow motions in a number of proteins, which are critical for their functioning. They are often used as the test ground for developing novel approaches to the simulation of slow protein dynamics. In the present study, we present the algorithm, which allows physically‐consistent simulations of slow protein dynamics in globular proteins. Our algorithm is based on the hierarchical clustering of the correlation patterns (HCCP) technique of domain identification, which allows subdividing the protein into the hierarchy of the rigid‐body‐like clusters. The clusters are allowed to rotate relative to one another on the automatically identified hinges. The clusters are found in the course of automated, objective and well‐tested procedure. In the present communication, our technique is applied to 10 hinge‐bending proteins. For each of the proteins, we performed the blind search for the closed conformation, staring from the open one. Resulting closed conformations are compared with the closed states observed in crystallographic structures. It is shown that our technique produces realistic closed conformations for 8 out of 10 studied proteins. This demonstrates that HCCP technique can be used for finding alternative protein conformations and for sampling the slow motions in proteins. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Human uroporphyrinogen III synthase: NMR‐based mapping of the active site
Authors: Cunha Luis , Kuti Miklos , Bishop David F. , Mezei Mihaly , Zeng Lei , Zhou Ming‐Ming , Desnick Robert J.
Published: November 2007

Uroporphyrinogen III synthase (URO‐synthase) catalyzes the cyclization and D‐ring isomerization of hydroxymethylbilane (HMB) to uroporphyrinogen (URO'gen) III, the cyclic tetrapyrrole and physiologic precursor of heme, chlorophyl, and corrin. The deficient activity of human URO‐synthase results in the autosomal recessive cutaneous disorder, congenital erythropoietic porphyria. Mapping of the structural determinants that specify catalysis and, potentially, protein‐protein interactions is lacking. To map the active site and assess the enzyme's possible interaction in a complex with hydroxymethylbilane‐synthase (HMB‐synthase) and/or uroporphyrinogen‐decarboxylase (URO‐decarboxylase) by NMR, an efficient expression and purification procedure was developed for these cytosolic enzymes of heme biosynthesis that enabled preparation of special isotopically‐labeled protein samples for NMR characterization. Using an 800 MHz instrument, assignment of the URO‐synthase backbone 13Cα (100%), 1Hα (99.6%), and nonproline 1HN and 15N resonances (94%) was achieved as well as 85% of the side‐chain 13C and 1H resonances. NMR analyses of URO‐synthase titrated with competitive inhibitors ND‐methyl‐1‐formylbilane (NMF‐bilane) or URO'gen III, revealed resonance perturbations of specific residues lining the cleft between the two major domains of URO synthase that mapped the enzyme's active site. In silico docking of the URO‐synthase crystal structure with NMF‐bilane and URO'gen III was consistent with the perturbation results and provided a 3D model of the enzyme‐inhibitor complex. The absence of chemical shift changes in the 15N spectrum of URO‐synthase mixed with the homogeneous HMB‐synthase holoenzyme or URO‐decarboxylase precluded occurrence of a stable cytosolic enzyme complex. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Molecular dynamics simulations of ethanol binding to the transmembrane domain of the glycine receptor: Implications for the channel potentiation mechanism
Authors: Cheng Mary Hongying , Coalson Rob D. , Cascio Michael
Published: November 2007

The glycine receptor (GlyR) is potentiated by ethanol and other anesthetics. The potentiation mechanism at the molecular level is unknown and remains elusive, but mutagenic studies have shown that ethanol and other volatile anesthetics bind to a pocket between TM1, TM2, and TM3. The present study extends previous studies (Cheng et al., Proteins 2007;68:581–593) wherein we conducted homology modeling and molecular dynamics (MD) simulations to construct models of the homopentameric α1 subunits of the GlyR transmembrane domain in open and closed states. To understand the potentiation of GlyR by ethanol we compare the binding of ethanol molecules to the channel in these different states. We observe that ethanol stably resides inside solvent‐accessible cavities found in the open state of GlyR that are formed by I229 (of TM1) in one subunit and S267 and A288 (of TM2 and TM3, respectively) in the adjacent subunit. The volume of these putative binding pockets is state‐dependent. Selective binding to the open states of receptors has been proposed to explain the potentiating actions of this class of anesthetics. In accordance with this model, our MD simulations suggest that the potentiation of ethanol on GlyR may be effected through preferential binding of ethanol molecules to an inter‐subunit binding pocket in the open state. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Combining the polymerase incomplete primer extension method for cloning and mutagenesis with microscreening to accelerate structural genomics efforts
Authors: Klock Heath E. , Koesema Eric J. , Knuth Mark W. , Lesley Scott A.
Published: November 2007

Successful protein expression, purification, and crystallization for challenging targets typically requires evaluation of a multitude of expression constructs. Often many iterations of truncations and point mutations are required to identify a suitable derivative for recombinant expression. Making and characterizing these variants is a significant barrier to success. We have developed a rapid and efficient cloning process and combined it with a protein microscreening approach to characterize protein suitability for structural studies. The Polymerase Incomplete Primer Extension (PIPE) cloning method was used to rapidly clone 448 protein targets and then to generate 2143 truncations from 96 targets with minimal effort. Proteins were expressed, purified, and characterized via a microscreening protocol, which incorporates protein quantification, liquid chromatography mass spectrometry and analytical size exclusion chromatography (AnSEC) to evaluate suitability of the protein products for X‐ray crystallography. The results suggest that selecting expression constructs for crystal trials based primarily on expression solubility is insufficient. Instead, AnSEC scoring as a measure of protein polydispersity was found to be predictive of ultimate structure determination success and essential for identifying appropriate boundaries for truncation series. Overall structure determination success was increased by at least 38% by applying this combined PIPE cloning and microscreening approach to recalcitrant targets. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Evaluating the potency of HIV‐1 protease drugs to combat resistance
Authors: Hou Tingjun , McLaughlin William A. , Wang Wei
Published: November 2007

HIV‐1 protease has been an important drug target for the antiretroviral treatment of HIV infection. The efficacy of protease drugs is impaired by the rapid emergence of resistant virus strains. Understanding the molecular basis and evaluating the potency of an inhibitor to combat resistance are no doubt important in AIDS therapy. In this study, we first identified residues that have significant contributions to binding with six substrates using molecular dynamics simulations and Molecular Mechanics Generalized Born Surface Area calculations. Among the critical residues, Asp25, Gly27, Ala28, Asp29, and Gly49 are well conserved, with which the potent drugs should form strong interactions. We then calculated the contribution of each residue to binding with eight FDA approved drugs. We analyzed the conservation of each protease residue and also compared the interaction between the HIV protease and individual residues of the drugs and substrates. Our analyses showed that resistant mutations usually occur at less conserved residues forming more favorable interactions with drugs than with substrates. To quantitatively integrate the binding free energy and conservation information, we defined an empirical parameter called free energy/variability (FV) value, which is the product of the contribution of a single residue to the binding free energy and the sequence variability at that position. As a validation, the FV value was shown to identify single resistant mutations with an accuracy of 88%. Finally, we evaluated the potency of a newly approved drug, darunavir, to combat resistance and predicted that darunavir is more potent than amprenavir but may be susceptible to mutations on Val32 and Ile84. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Ion pairs and their role in modulating stability of cold‐ and warm‐active uracil DNA glycosylase
Authors: Olufsen Magne , Papaleo Elena , Smalås Arne Oskar , Brandsdal Bjørn Olav
Published: November 2007

MD simulations and continuum electrostatics calculations have been used to study the observed differences in thermostability of cold‐ and warm‐active uracil DNA glycosylase (UDG). The present study focuses on the role of ion pairs and how they affect the thermal stability of the two enzymes. Analysis of the MD generated structural ensembles show that cod UDG (cUDG) and human UDG (hUDG) have 11 and 12 ion pairs which are present in at least 30% of the conformations. The electrostatic contribution of the ion pairs, computed using continuum electrostatics, is slightly more favorable in cUDG at 298 K. This is primarily attributed to more optimized interactions between the ion pairs and nearby dipoles/charges in cUDG. More global salt bridges are found in hUDG and are more stabilizing when compared to cUDG, possibly playing a role in maintaining overall stability and reducing conformational entropy. Both enzymes contain one three‐member ionic network, but the one found in hUDG is far more stabilizing. Our results also suggest that care should be taken when performing statistical analysis of crystal structures with respect to ion pairs, and that crystallization conditions must be carefully examined when performing such analysis. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Coherence and spatial resolution of transport in quantum cascade lasers
Authors: Wacker Andreas
Published: November 2007

The method of nonequilibrium Greens functions allows for a spatial and energetical resolution of the electron current in Quantum Cascade Lasers. While scattering does not change the spatial position of carriers, the entire spatial evolution of charge can be attributed to coherent transport by complex wave functions.We discuss the hierarchy of transportmodels and derive the density matrix equations as well as the hopping model starting from the nonequilibrium Greens functions approach. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Onset of quasi‐ballistic transport and mobility degradation in ultra scaled MOSFETs: a Monte Carlo study
Authors: Martín M. J. , Rengel R. , Pascual E. , Łusakowski J. , Knap W. , González T.
Published: November 2007

A Monte Carlo investigation of quasi‐ballistic transport in scaled MOSFETs is presented. Taking into account a realistic velocity and electric field profile in ultra‐scaled transistors, the carrier mobility is calculated, observing a degradation of this macroscopic parameter strongly related to the peculiarities of the electrostatic profiles found for extremely short gate lengths. Simultaneously, the onset of ballistic phenomena within the channel is detected. A detailed investigation of the movement of carriers inside the channel allows providing numerous microscopic quantities related to electronic transport, such as mean free paths, transit times or average number of scattering mechanisms. Results evidence the existence of a significant proportion of ballistic carriers as the gate length is scaled down to few tens of nanometre. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Rashba spin‐orbit interaction of In0.53Ga0.47As/In0.7Ga0.3As/In0.53Ga0.47As shallow two‐dimensional electron gas by surface etching
Authors: Kunihashi Yoji , Nihei Takayuki , Kohda Makoto , Nitta Junsaku
Published: November 2007

We have investigated Rashba spin‐orbit interaction (SOI) of In0.53Ga0.47As/In0.7Ga0.3As/In0.53Ga0.47As two dimensional electron gas (2DEG) located below 6.4 nm ‐ 26.5 nm from the sample surface by analyzing weak antilocalization (WAL). Depth of the 2DEG from the sample surface is systematically controlled by surface etching within the identical samples. WAL is enhanced as increasing the etching depth due to the large energy‐band bending of In0.53Ga0.47As/In0.7Ga0.3As/In0.53Ga0.47As quantum well. The Rashba SOI parameter α increases with increasing the etching depth, and 2.41 × 10–12 eVm is obtained in the shallowest 2DEG which is located below 6.4 nm from the surface. Calculated α from the k · p formalism shows good agreement on the surface etching dependence with the experimental values. Dominant contribution of the Rashba SOI parameter α is originated from the In0.53Ga0.47As/In0.7Ga0.3As heterointerface as well as the energy‐band bending in the In0.7Ga0.3As quantum well. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Emission and absorption of phonons in silicon
Authors: Aksamija Z. , Hahm H.‐S. , Ravaioli U.
Published: November 2007

We examine in detail the rates of phonon emission and absorption in silicon at several values for the applied electric field. The effect of the field on the electron distribution is obtained from full‐band Monte Carlo simulation for bulk silicon. The electron distributions are used to numerically compute the phonon rates and learn about their behavior at high fields. The concept of electron temperature is used to understand the relationship between field and heat emission, and it is found that longitudinal acoustic (LA) phonon emission increases at high fields. Optical absorption is found to be small, while optical phonon emission stays constant across a wide range of electron temperatures. Strong emission of LA phonons at high field can be used to enable heat‐conscious design of future silicon devices. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Shelf life of vegetable oils bottled in different scavenging polyethyleneterephthalate (PET) containers
Authors: Sacchi R. , Savarese M. , Del Regno A. , Paduano A. , Terminiello R. , Ambrosino M. L.
Published: November 2007

The shelf life of extra virgin olive oil (EVOO) and sunflower oil (SO) bottled in containers with different levels of oxygen scavenger (OS) and stored at room temperature under diffuse lighting conditions for 6 months has been evaluated. Four packaging materials were tested: glass, polyethyleneterephthalate (PET), PET including 1% of OS (PET 1%) and PET including 5% of OS (PET 5%). Free acidity, peroxide value (PV), spectrophotometric indices (K232, K270, ΔK), antioxidant (biophenols and tocopherols) content, pigment (chlorophylls and carotenoids) change and the amount of oxygen dissolved in the oil were monitored during storage. A significant influence of the packaging material on the quality decay was not found. The differences in the shelf life observed between oils bottled in PET and oils bottled in glass are attributable to a difference in the initial content of dissolved oxygen in the oils. The study showed the usefulness of monitoring changes in dissolved oxygen level, antioxidant (phenols and tocopherols) and pigment (chlorophyll and carotenoids) profiles during oil storage. The change of these compounds could in fact supply important information on the oxidation processes that occur in bottled oils and on the effectiveness of the material employed in oil packaging. Copyright © 2007 John Wiley & Sons, Ltd.
Modelling capping of 28 mm beverage closures using finite element analysis
Authors: Rowson J. , Yoxall A. , Hart J.H.
Published: November 2007

Understanding the performance of packaging on production lines is of course extremely important to the packaging industry. Computer simulation techniques have improved vastly in recent years, and modelling the complex interaction of three‐dimensional threaded shapes, like closures, is now a reality. This paper outlines the work undertaken in understanding the possible mechanisms relating to the capping of 28  mm beverage closures and the use of experimental and computer simulations in order to establish that understanding. Copyright © 2007 John Wiley & Sons, Ltd.
Prediction of Volatile Components Retention Time in Blackstrap Molasses by Least‐Squares Support Vector Machine
Authors: Yuan Yongna , Zhang Ruisheng , Hu Rongjing , Ruan Xiaofang
Published: November 2007

House flies are pestiferous insects that have the potential to spread many diseases to humans and livestock, so it is very significant for us to manage house fly populations. Many commercial types of bait are available to attract house flies, but most are designed for outdoor or limited indoor use, due to their malodorous components. This study sought to identify compounds present in blackstrap molasses that might be attractive to house flies. An effective Quantitative Structure‐Property Relationship (QSPR) model between the Retention Time (RT) and five molecular descriptors of the volatile compounds in blackstrap molasses, was built using a modified algorithm of Least‐Squares Support Vector Machine (LS‐SVM). Descriptors calculated from the molecular structures alone were used to represent the characteristics of compounds. The five molecular descriptors selected by the Heuristic Method (HM) in CODESSA were used as inputs for LS‐SVM. The results obtained by LS‐SVM were compared with those obtained by the HM. The LS‐SVM model gives better results with the predicted correlation coefficient ($\rm{ R^2 }$) 0.919 and Root Mean‐Square Errors (RMSE) 2.193 for the test set, as well as that 0.824 and 2.728 in the MLR model. The prediction results of log RT are in very good agreement with the experimental values. This paper provided a new and effective method for predicting the chromatography retention index.
A Review of (Q)SAR Models for Skin and Eye Irritation and Corrosion
Authors: Saliner Ana Gallegos , Patlewicz Grace , Worth Andrew P.
Published: November 2007

This paper reviews the state‐of‐the‐art of in silico methods for assessing dermal and ocular irritation and corrosion. It is based on an in‐depth review performed by the European Chemicals Bureau of the European Commission's Joint Research Centre in support of the development of technical guidance for the implementation of the REACH legislation, and is one of a series of minireviews in this journal. The most widely used in silico approaches are classified into methods to assess (1) skin irritation, (2) skin corrosion and (3) eye irritation. In this review, emphasis is placed on literature‐based (Q)SAR models.
Optimizing port placement for robot‐assisted minimally invasive cardiac surgery
Authors: Trejos A. L. , Patel R. V. , Ross I. , Kiaii B.
Published: November 2007

Background

Proper placement of ports during robot‐assisted endoscopic surgery is critical to the success of the procedure. In current practice, port placement methods do not consider the ability of the robot to manoeuvre the tools.

Methods

This paper proposes to choose the best port location such that the performance of the robot is maximized. The Global Conditioning Index (GCI) is used to optimize port placement when using the da Vinci®surgical system during cardiac surgery.

Results

The results show that, due to a singularity at the remote centre of motion, higher performance is obtained the further away the port is from the workspace. When compared to the ports selected by an expert surgeon, our results show that it is possible to increase robot performance by at least 29% for the left arm of the robot.

Conclusions

Selecting an adequate port location can improve robot performance and ensure that the instruments reach the surgical site. Copyright © 2007 John Wiley & Sons, Ltd.