bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytoskeletal scaffolding proteins interact with Lynch‐Syndrome associated mismatch repair protein MLH1
Authors: Brieger Angela , Adryan Boris , Wolpert Fabian , Passmann Sandra , Zeuzem Stefan , Trojan Jörg 
Published: July 2010

AbstractThe involvement of MLH1 in several mismatch repair‐independent cellular processes has been reported. In an attempt to gain further insight into the protein's cellular functions, we screened for novel interacting partners of MLH1 utilizing a bacterial two‐hybrid system. Numerous unknown interacting proteins were identified, suggesting novel biological roles of MLH1. The network of MLH1 and its partner proteins involves a multitude of cellular processes. Integration of our data with the “General Repository for Interaction Datasets” highlighted that MLH1 exhibits relationships to three interacting pairs of proteins involved in cytoskeletal and filament organization: Thymosin β 4 and Actin γ, Cathepsin B and Annexin A2 as well as Spectrin α and Desmin. Coimmunoprecipitation and colocalization experiments validated the interaction of MLH1 with these proteins. Differential mRNA levels of many of the identified proteins, detected by microarray analysis comparing MLH1‐deficient and ‐proficient cell lines, support the assumed interplay of MLH1 and the identified candidate proteins. By siRNA knock down of MLH1, we demonstrated the functional impact of MLH1–Actin interaction on filament organization and propose that dysregulation of MLH1 plays an essential role in cytoskeleton dynamics. Our data suggest novel roles of MLH1 in cellular organization and colorectal cancerogenesis.
Upregulation of plasma C9 protein in gastric cancer patients
Authors: Chong Poh‐Kuan , Lee Huiyin , Loh Marie Chiew Shia , Choong Lee‐Yee , Lin Qingsong , So Jimmy Bok Yan , Lim Khong Hee , Soo Ross Andrew , Yong Wei Peng , Chan Siew Pang , Smoot Duane T. , Ashktorab Hassan , Yeoh Khay Guan , Lim Yoon Pin 
Published: July 2010

AbstractGastric cancer is one of the leading causes of cancer‐related deaths worldwide. Current biomarkers used in the clinic do not have sufficient sensitivity for gastric cancer detection. To discover new and better biomarkers, protein profiling on plasma samples from 25 normal, 15 early‐stage and 21 late‐stage cancer was performed using an iTRAQ‐LC‐MS/MS approach. The level of C9 protein was found to be significantly higher in gastric cancer compared with normal subjects. Immunoblotting data revealed a congruent trend with iTRAQ results. The discriminatory power of C9 between normal and cancer states was not due to inter‐patient variations and was independent from gastritis and Helicobacter pylori status of the patients. C9 overexpression could also be detected in a panel of gastric cancer cell lines and their conditioned media compared with normal cells, implying that higher C9 levels in plasma of cancer patients could be attributed to the presence of gastric tumor. A subsequent blind test study on a total of 119 plasma samples showed that the sensitivity of C9 could be as high as 90% at a specificity of 74%. Hence, C9 is a potentially useful biomarker for gastric cancer detection.
Illuminating the molecular basis of diabetic arteriopathy: A proteomic comparison of aortic tissue from diabetic and healthy rats
Authors: Jüllig Mia , Chen Xiuyin , Middleditch Martin J. , Vazhoor Greeshma , Hickey Anthony J. , Gong Deming , Lu Jun , Zhang Shaoping , Phillips Anthony R. J. , Cooper Garth J. S. 
Published: July 2010

AbstractArterial disease is a major diabetic complication, yet the component molecular mechanisms of diabetic arteriopathy remain poorly understood. In order to identify major proteins/pathways implicated in diabetic arteriopathy, we studied the effect of 16‐wk untreated streptozotocin‐induced diabetes on the rat aortic proteome. Specific protein levels in isolated aortas were compared in six discrete, pair‐wise (streptozotocin‐diabetic and non‐diabetic age‐matched controls) experiments in which individual proteins were identified and quantified by iTRAQ combined with LC‐MS/MS. A total of 398 unique non‐redundant proteins were identified in at least one experiment and 208 were detected in three or more. Between‐group comparisons revealed significant changes or trends towards changes in relative abundance of 51 proteins (25 increased, 26 decreased). Differences in levels of selected proteins were supported by Western blotting and/or enzyme assays. The most prominent diabetes‐associated changes were in groups of proteins linked to oxidative stress responses and the structure/function of myofibrils and microfilaments. Indexes of mitochondrial content were measurably lower in aortic tissue from diabetic animals. Functional cluster analysis also showed decreased levels of glycolytic enzymes and mitochondrial electron transport system‐complex components. These findings newly implicate several proteins/functional pathways in the pathogenesis of arteriosclerosis/diabetic arteriopathy.
Large pore gels to separate mega protein complexes larger than 10 MDa by blue native electrophoresis: Isolation of putative respiratory strings or patches
Authors: Strecker Valentina , Wumaier Zibiernisha , Wittig Ilka , Schägger Hermann 
Published: July 2010

AbstractHere, we expand the application of blue native electrophoresis to the separation of mega protein complexes larger than 10 MDa by introducing novel large pore acrylamide gels. We tailored the bis‐acrylamide cross‐linker amounts relative to the acrylamide monomer to enlarge the pore size of acrylamide gels and to obtain elastic and sufficiently stable gels. The novel gel types were then used to search for suprastructures of mitochondrial respiratory supercomplexes, the hypothetical respiratory strings, or patches. We identified 4–8 MDa assemblies that contain respiratory complexes I, III, and IV and most likely represent dimers, trimers, and tetramers of respiratory supercomplexes. We also isolated multimeric respiratory supercomplexes with apparent masses of 35–45 MDa, the presumed core pieces of respiratory strings or patches. Electron microscopic investigations will be required to clarify whether the isolated assemblies of complexes are ordered and specific, as predicted for respiratory strings and patches in the mitochondrial membrane.
The stromal‐vascular fraction of adipose tissue contributes to major differences between subcutaneous and visceral fat depots
Authors: Peinado Juan R. , Jimenez‐Gomez Yolanda , Pulido Marina R. , Ortega‐Bellido Maria , Diaz‐Lopez Cesar , Padillo Francisco J. , Lopez‐Miranda Jose , Vazquez‐Martínez Rafael , Malagón María M. 
Published: July 2010

AbstractAdipose tissue represents a complex tissue both in terms of its cellular composition, as it includes mature adipocytes and the various cell types comprising the stromal‐vascular fraction (SVF), and in relation to the distinct biochemical, morphological and functional characteristics according to its anatomical location. Herein, we have characterized the proteomic profile of both mature adipocyte and SVF from human visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT) fat depots in order to unveil differences in the expression of proteins which may underlie the distinct association of VAT and SAT to several pathologies. Specifically, 24 proteins were observed to be differentially expressed between SAT SVF versus VAT SVF from lean individuals. Immunoblotting and RT‐PCR analysis confirmed the differential regulation of the nuclear envelope proteins lamin A/C, the membrane‐cytoskeletal linker ezrin and the enzyme involved in retinoic acid production, aldehyde dehydrogenase 1A2, in the two fat depots. In sum, the observation that proteins with important cell functions are differentially distributed between VAT and SAT and their characterization as components of SVF or mature adipocytes pave the way for future research on the molecular basis underlying diverse adipose tissue‐related pathologies such as metabolic syndrome or lipodystrophy.
Hydrogen‐bonded nucleophile effects in ANS: the reactions of 1‐chloro and 1‐fluoro‐2,4‐dinitrobenzene with 2‐guanidinobenzimidazole, 1‐(2‐aminoethyl)piperidine andN‐(3‐aminopropyl)morpholine in aprotic solvents
Authors: Alvaro Cecilia E. Silvana , Ayala Alicia D. , Nudelman Norma S. 
Published: July 2010

AbstractThe kinetics of the reactions of 2,4‐dinitrofluorobenzene (DNFB) and 2,4‐dinitrochlorobenzene (DNClB) with 2‐guanidinobenzimidazole (2‐GB) at 40 ± 0.2 °C in dimethylsulphoxide (DMSO), toluene, and in toluene–DMSO mixtures, and with 1‐(2‐aminoethyl)piperidine (2‐AEPip) andN‐(3‐aminopropyl)morpholine (3‐APMo) in toluene at 25 ± 0.2 °C were studied under pseudo first‐order conditions. For the reactions of 2‐GB carried out in pure DMSO, the second‐order rate coefficients were independent of the amine concentration. In contrast, the reactions of 2‐GB with DNFB in toluene, showed a kinetic behaviour consistent with a base‐catalysed decomposition of the zwitterionic intermediate. These results suggest an intramolecular H‐bonding of 2‐GB in toluene, which is not present in DMSO. To confirm this interpretation the reactions were studied in DMSO–toluene mixtures. Small amounts of DMSO produce significant increase in rate that is not expected on the basis of the classical effect of a dipolar aprotic medium; the effect is consistent with the formation of a nucleophile/co‐solventmixed aggregate. For the reactions of 3‐APMo with both substrates in toluene, the second‐order rate coefficients,kA, show a linear dependence on the [amine]. 3‐APMo is able to form a six‐membered ring by an intramolecular H‐bond which prevents the formation of self‐aggregates. In contrast, a third order was observed in the reactions with 2‐AEPip: these results can be interpreted as a H‐bonded homo‐aggregate of the amine acting as a better nucleophile than the monomer. Most of these results can be well explained within the frame of the ‘dimer nucleophile’ mechanism. Copyright © 2010 John Wiley & Sons, Ltd.
Paracrine factors produced by bone marrow stromal cells induce apoptosis and neuroendocrine differentiation in prostate cancer cells
Authors: Zhang Chu , Soori Mehrnoosh , Miles Fayth L. , Sikes Robert A. , Carson Daniel D. , Chung Leland W.K. , Farach‐Carson Mary C. 
Published: July 2010

AbstractBACKGROUNDPreferential bony metastasis of human prostate cancer (PCa) cells contributes to disease mortality and morbidity. Local factors in bone stromal extracellular matrix microenvironment affect tumor growth through paracrine interactions between tumor and stromal cells.METHODSUsing co‐culture and medium transfer, we used several methods to assess interactions between PCa and bone stromal cells using three PCa cell lines: PC3, LNCaP, and the LNCaP derivative, C4‐2B.RESULTSCo‐culture of LNCaP and C4‐2B cells with bone marrow stromal cell lines, HS27a and HS5, decreased cell number, as did culture with conditioned medium (CM) harvested from these two cell lines suggesting a soluble paracrine factor was responsible. PC3 cell growth was unaffected. CM harvested from bone stromal cell lines triggered apoptosis in LNCaP and C4‐2B cell lines, but not in PC3 cells. Surviving C4‐2B cells grown in bone stromal cell CM over several days were growth arrested, suggesting presence of a growth inhibitor. Apoptosis induced by CM was dose‐dependent. Flow cytometry demonstrated that over a 5‐day culture period in stromal cell CM, LNCaP, and C4‐2B cell lines, but not PC3 cells, underwent greater apoptosis than parallel cultures in SF medium. The LNCaP and C4‐2B cells showed morphology and biomarker expression consistent with transdifferentiation towards a neuroendocrine phenotype after exposure to stromal cell CM.CONCLUSIONSThe reactive bone stromal microenvironment initially is hostile to PCa cells producing widespread apoptosis. Activation of transdifferentiation in a subset of apoptotic resistant cells may support phenotypic adaptation during disease progression in bone, eventually favoring lethal disease. Prostate 71: 157–167, 2011. © 2010 Wiley‐Liss, Inc.
Micro‐ and nano‐electromechanical resonators based on SiC and group III‐nitrides for sensor applications
Authors: Brueckner K. , Niebelschuetz F. , Tonisch K. , Foerster Ch. , Cimalla V. , Stephan R. , Pezoldt J. , Stauden T. , Ambacher O. , Hein M. A. 
Published: July 2010

AbstractWide‐bandgap semiconductors represent an attractive option to meet the increasing demands of micro‐ and nano‐electromechanical systems (MEMS/NEMS) by offering new functionalities, high stability, biocompatibility and the potential for miniaturization and integration. Here, we report on resonant MEMS and NEMS devices with functional layers of SiC, AlN and AlGaN/GaN heterostructures on different substrates, which have been investigated and analysed in the course of an interdisciplinary research focus programme of the German Research Foundation (DFG). The specific deposition and etching technologies necessary for the three‐dimensional micro‐structuring are explained. Further, the implementation of appropriate electromechanical transduction schemes is discussed. In case of SiC and AlN resonators, actuation and sensing was achieved by a magnetomotive scheme. A piezoelectric coupling scheme where the counter electrode is formed by the two‐dimensional electron gas at the interface of the III/V heterostructure was realized for the AlGaN/GaN resonators.Thus, flexural and longitudinal vibration modes were excited and characterized using electrical and optical techniques. The measured key parameters of resonant frequency and quality factor are related to geometry, material and environmental parameters using analytical and finite element (FE) models. Finally, potential sensor applications are experimentally investigated.
Influence of the dielectric substrate on the field emitted by a subwavelength slit in a metal film
Authors: Nikitin A. Yu. , García‐Vidal F. J. , Martín‐Moreno L. 
Published: July 2010

AbstractThe field emitted by a localized source in the metal surface bounding to a half‐media with arbitrary dielectric permittivity is studied. The far field at the surface is composed of both the surface plasmon polariton and the algebraically decaying Norton wave contributions. The crossover distance at which the Norton wave overtakes the surface plasmon, depends upon the refractive index of the bounding media. Substrates with high dielectric permittivity bring the crossover substantially closer to the source.magnified imageThe field emitted by a subwavelength slit. Far away from the source the field presents contributions from both the surface plasmon and the Norton wave.(© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Near‐field studies of arrays of chirped subwavelength apertures
Authors: Neshev Dragomir N. , Minovich Alexander , Dieing Thomas , Hattori Haroldo T. , McKerracher Ian , Tan Hark Hoe , Jagadish Chennupati , Kivshar Yuri S. 
Published: July 2010

AbstractWe study light transmission through a metal film perforated with an array of square apertures of varying size. We combine near‐field scanning optical microscopy with confocal microscopy to identify surface plasmon modes and propagating hole modes in the different size apertures. We also perform spectral measurements to reveal the complex characteristics of light transmission through the chirped subwavelength apertures. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The effect of shave‐off scanning at a fabricated section by focused ion beam
Authors: Morita Y. , Kuroda A. , Iwata T. , Owari M. 
Published: July 2010

AbstractThree‐dimensional microanalysis for a minute structure that consists of organic compounds and polymers is important to develop and to practically use the method to analyze a micronanometer order area. However, it is difficult because of the insulating nature of the material, need of structural analysis and a dose limit not to destruct surface organic structure (static limit). We developed a novel three‐dimensional microanalysis method by means of focused ion beam (FIB) for section processing (shave‐off scanning) and ToF‐SIMS for mapping method. For the purpose of realization of three‐dimensional microanalysis and a chemical and structural analysis of the organic matter, a polymer destruction of fabricated section by shave‐off scanning was examined. To determine spectrum changing, polystyrene was fabricated as a function of dose time by shave‐off scanning, and these samples were analyzed by ToF‐SIMS. As a result, a flat surface was made along with shave‐off scanning time, and a surface organic structure fabricated by FIB was detected with a certain rate. Copyright © 2010 John Wiley & Sons, Ltd.
An AFM contribution to the understanding of surface effects caused by ageing and cleaning on acrylic glass. The Shadows by Lourdes Castro, a case study
Authors: de Sá M. H. , Ferreira Joana L. , Melo M. J. , Ramos Ana M. 
Published: July 2010

AbstractAtomic Force Microscopy (AFM) was used to study the ageing and cleaning effects on the surface of acrylic glass sheets (PMMA) like the ones used by the Portuguese artist Lourdes Castro. Measurements were done in transparent (colourless and blue) samples. The samples were aged in a SolarBox; cleaning and polishing products, similar to the ones applied by the artist, were used. From the AFM images the craze/scratch phenomena in the pristine samples surface was confirmed. The experiments led to an increase of the surface roughness, more pronounced for the polished samples due to the presence of granular features. These modifications are due to the interaction of the acrylic sheets with the polishing products, which seems to be stronger in the coloured samples. These findings are useful to define the best strategy to prolong the longevity of such materials, in particular the works of art created by Lourdes Castro. Copyright © 2010 John Wiley & Sons, Ltd.
Additional requirements for process assessment in safety–critical software and systems domain
Authors: Johansson Mika , Nevalainen Risto 
Published: July 2010

SUMMARYCertification of safety–critical software is a multi‐disciplinary topic. Process assessment is an essential part of that, but is not enough for software certification. Certification also employs several other method families, such as inspections and reviews, independent V&V, conformance with selected reference standard(s) and use of selected measurements and analyses. Process assessment directly supports qualification of safety–critical applications but is less relevant for certification of platforms and environments. Anyway, qualification and certification are closely related. Certification as a whole supports qualification and makes it more effective. It is possible to adapt and evolve process assessment so that it supports both qualification and certification. Typical process assessment is done for improvement purpose. In qualification and certification it is not so relevant as conformance and management of risks. In this article we discuss the possibilities to develop process assessment to achieve that goal. In most cases assessment is a combination of several approaches. Copyright © 2010 John Wiley & Sons, Ltd.
Lessons learned from an ISO/IEC 15504 SPI programme in a company
Authors: Mas Antonia , Fluxà Bartomeu , Amengual Esperança 
Published: July 2010

SUMMARYThis paper describes a first‐hand experience in Software Process Improvement within a Spanish Company which, since 2002, has been involved in an improvement programme led by our research group. We discuss the experience and the results of this improvement programme, as well as the lessons learned to deal with new future improvement initiatives in other companies of our environment. Copyright © 2010 John Wiley & Sons, Ltd.
UML‐based regression testing for OO software
Authors: Mansour Nashat , Takkoush Husam , Nehme Ali 
Published: July 2010

AbstractIn software maintenance, a system has to be regression tested after modifying it. The goal of regression testing is to ensure that modifications have not adversely affected the system. Regression test selection determines a subset of test cases, from the initial test suite, which concentrates on the parts of the system affected by the modification. Previous techniques have been mainly code‐based and several of them have addressed procedural programs. When working with large and complex object‐oriented systems, source code‐based regression testing is usually costly. This paper proposes a programming‐language‐independent technique for regression test selection for object‐oriented software based on Unified Modeling Language (UML 2.0) design diagrams. These diagrams are: the newly introduced interaction overview diagram, class diagrams, and sequence diagrams. We assume a test suite that contains both unit and system test cases. Based on the software changes reflected in the class and the interaction overview diagrams, our proposed technique selects test cases in phases. In the first phase, we select both unit and system test cases that directly traverse the changed methods and their calling methods. For the second phase, we present algorithms for detecting system level changes in the interaction overview diagram. If the change is at the action level, which is represented by a sequence diagram, only the test cases that execute changed methods will be selected. We apply our proposed technique to a few object‐oriented subject applications and evaluate its precision and inclusiveness in addition to the number of selected tests; the results demonstrate the advantages of the technique. Copyright © 2010 John Wiley & Sons, Ltd.
Parallelization of a dynamic SVD clustering algorithm and its application in information retrieval
Authors: Seshadri Karthick , Iyer K. Viswanathan 
Published: July 2010

AbstractWe describe an implementation of a parallel document clustering scheme based on latent semantic indexing, which uses singular value decomposition. Given a set of documents, the clustering algorithm is dynamic in the sense that it automatically infers the number of clusters to be output. The parallel version has been implemented on a LAN and on a dual‐core system. Experimental evaluation of the algorithm shows an average speed‐up of 6.22 for the LAN implementation and an average speed‐up of 3.71 for the dual‐core implementation, while still maintaining a precision and recall in the range [0.85, 1]. To put these implementations in the context of information retrieval, we use the parallel clustering algorithm and develop a document similarity search system. The similarity search system shows good performance in terms of precision and recall. Copyright © 2010 John Wiley & Sons, Ltd.
Architectural layer recovery for software system understanding and evolution
Authors: Scanniello Giuseppe , D'Amico Anna , D'Amico Carmela , D'Amico Teodora 
Published: July 2010

AbstractThis paper presents an approach to identify software layers for the understanding and evolution of software systems implemented with any object‐oriented programming language. The approach first identifies relations between the classes of a software system and then uses a link analysis algorithm (i.e. the Kleinberg algorithm) to group them into layers. Additionally to assess the approach and the underlying techniques, the paper also presents a prototype of a supporting tool and the results from a case study. Copyright © 2010 John Wiley & Sons, Ltd.