bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermoplastic polyurethane/silica nanocomposite fibers by electrospinning
Authors: Zhang Xu‐Cheng , Chen Yi‐Zhang , Yu Jian , Guo Zhao‐Xia 
Published: September 2011

AbstractThermoplastic polyurethane/silica nanocomposite fibers with good mechanical properties were prepared by electrospinning, using colloidal silica as the source of silica and dimethyl formamide as the solvent. The fiber morphology was examined by field emission scanning electron microscopy. The average fiber diameter is about 0.8 μm with 0–10 wt % silica, and silica nanoparticles were observed on all fiber surfaces. X‐ray photoelectron spectroscopy analysis of Si in combination with transmission electron microscopy observation suggest that silica nanoparticles have a fairly uniform distribution in the fibers rather than enriching on the fiber surfaces. Tensile tests show that the incorporation of silica nanoparticles can bring about a significant reinforcing effect without decreasing the ductility. The reinforcing effect is further confirmed by dynamic mechanical analysis. The thermoplastic polyurethane/silica composite fiber mats can adsorb gold nanoparticles after further treatment with 3‐aminopropyltriethoxysilane, demonstrating that the composite fibers could be used as functional fibers by using the properties of silica nanoparticles. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011
Assessment of ligand‐binding residue predictions in CASP9
Authors: Schmidt Tobias , Haas Jürgen , Cassarino Tiziano Gallo , Schwede Torsten 
Published: September 2011

AbstractInteractions between proteins and their ligands play central roles in many physiological processes. The structural details for most of these interactions, however, have not yet been characterized experientially. Therefore, various computational tools have been developed to predict the location of binding sites and the amino acid residues interacting with ligands. In this manuscript, we assess the performance of 33 methods participating in the ligand‐binding site prediction category in CASP9. The overall accuracy of ligand‐binding site predictions in CASP9 appears rather high (average Matthews correlation coefficient of 0.62 for the 10 top performing groups) and compared to previous experiments more groups performed equally well. However, this should be seen in context of a strong bias in the test data toward easy template‐based models. Overall, the top performing methods have converged to a similar approach using ligand‐binding site inference from related homologous structures, which limits their applicability for difficult de novo prediction targets. Here, we present the results of the CASP9 assessment of the ligand‐binding site category, discuss examples for successful and challenging prediction targets in CASP9, and finally suggest changes in the format of the experiment to overcome the current limitations of the assessment. Proteins 2011. © 2011 Wiley‐Liss, Inc.
Raptorx: Exploiting structure information for protein alignment by statistical inference
Authors: Peng Jian , Xu Jinbo 
Published: September 2011

AbstractThis work presents RaptorX, a statistical method for template‐based protein modeling that improves alignment accuracy by exploiting structural information in a single or multiple templates. RaptorX consists of three major components: single‐template threading, alignment quality prediction, and multiple‐template threading. This work summarizes the methods used by RaptorX and presents its CASP9 result analysis, aiming to identify major bottlenecks with RaptorX and template‐based modeling and hopefully directions for further study. Our results show that template structural information helps a lot with both single‐template and multiple‐template protein threading especially when closely‐related templates are unavailable, and there is still large room for improvement in both alignment and template selection. The RaptorX web server is available at http://raptorx.uchicago.edu. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Reduction of switching time in pentalayer magnetic tunnel junctions with a composite‐free layer
Authors: Makarov Alexander , Sverdlov Viktor , Osintsev Dmitry , Selberherr Siegfried 
Published: September 2011

AbstractWe have performed micromagnetic simulations of the magnetization dynamics of the composite‐free magnetic layer in a pentalayer structure. We have found a substantial decrease of the switching time in this system as compared to the pentalayer structure of similar dimensions with a monolithic free layer. The physical reasons for the switching time reduction at the same current density are discussed. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Defect engineering of room‐temperature ferromagnetism of carbon‐doped ZnO
Authors: Hsu H. S. , Tung Y. , Chen Y. J. , Chen M. G. , Lee J. S. , Sun S. J. 
Published: September 2011

AbstractThis study investigates the role of carbon (C) in room‐temperature (RT) ferromagnetic C:ZnO films. RT ferromagnetism can be observed in air‐annealed C:ZnO samples. However, no feature that could be attributed to the incorporation of carbon at O sites (CO) was observed. An analysis of MCD spectra of the ferromagnetic C:ZnO sample included a non‐ferromagnetic peak and a ferromagnetic one. These are related to the loss of carbon and the creation of defects in an air‐annealed C:ZnO film by the reaction between C dopants and oxygen. We suggest even if the C dopants are not at CO sites, C is still a novel dopant to make ZnO ferromagnetic in controlling the defects in the structure formed by suitable post‐annealing. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Nanoscale hot electron transport across Cu/n‐Si(100) and Cu/n‐Si(111) interfaces
Authors: Parui S. , van der Ploeg J. R. R. , Rana K. G. , Banerjee T. 
Published: September 2011

AbstractBallistic electron emission microscopy (BEEM) has been used to investigate hot electron transmission, at the nanoscale, in thin films of Cu on Si(100) and Si(111). For all Cu thicknesses studied here, the BEEM transmission is observed to be twice larger for Si(111) than for Si(100). Further, the attenuation length in Cu is found to be larger for Si(111) than for Si(100) substrates, in spite of the highly textured growth of Cu on both the substrates. Our results can be explained by the incorporation of elastic scattering at the metal–semiconductor (M/S) interface as well as the increased availability of parallel momentum states at the interface. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The impact of global and local cohesion on innovation in the pharmaceutical industry
Authors: Guler Isin , Nerkar Atul 
Published: September 2011

AbstractIn this paper, we examine how the configuration of intraorganizational networks, and in particular, cohesion among members of an organization, influences organizations' innovative output. We argue that the cohesion among R&D scientists could be at a local level or a global level, and that local and global cohesion may have different impacts on firms' innovation performance. We test our hypotheses by examining the structure of the R&D collaboration networks within firms that operated in the pharmaceutical industry between 1981 and 1989, and their innovative outcomes—patents that led to new product launches. We find that local cohesion has a positive impact on the innovative performance of a firm, and global cohesion has a negative impact. Copyright © 2011 John Wiley & Sons, Ltd.
Plasmonic Coupling Interference (PCI) Nanoprobes for Nucleic Acid Detection
Authors: Wang Hsin‐Neng , Vo‐Dinh Tuan 
Published: September 2011

AbstractA label‐free approach using plasmonic coupling interference (PCI) nanoprobes for nucleic acid detection using surface‐enhanced Raman scattering (SERS) is described. To induce a strong plasmonic coupling effect, a nanonetwork of silver nanoparticles with the Raman label located between adjacent nanoparticles is assembled by Raman‐labeled DNA‐locked nucleic acid (LNA) duplexes. The PCI method then utilizes specific nucleic acid sequences of interest as competitor elements for the Raman‐labeled DNA strands to interfere the formation of nanonetworks in a competitive binding process. As a result, the plasmonic coupling effect induced through the formation of the nanonetworks is significantly diminished, resulting in a reduced SERS signal. The potential of the PCI technique for biomedical applications is illustrated by detecting single‐nucleotide polymorphism (SNP) and microRNA sequences involved in breast cancers. The results of this study could lead to the development of nucleic acid diagnostic tools for biomedical diagnostics and biosensing applications using SERS detection.
Extraordinary Responsive Intermetallic Compounds: the R5T4 Family (R = Rare Earth, T = Group 13–15 Element)
Authors: Mudryk Yaroslav , Pecharsky Vitalij K. , Gschneidner, Jr. Karl A. 
Published: September 2011

AbstractThe R5T4 intermetallic compounds of rare earth elements (R) with the group 14 elements (T) adopt a number of layered crystal structures that reversibly transform into each other. The transformations proceed through massive shear displacements of their main structural units, i.e. slabs, which are pseudo two dimensional blocks of atoms stacked along a certain crystallographic direction. These transformations can be triggered by change in chemical composition of the compounds (including partial substitutions of the group 14 elements by the group 13 or 15 elements), temperature, applied pressure, or applied magnetic field. The physical properties of these compounds are usually intimately related to their crystallography, and especially the concomitant magnetic and crystallographic transitions. As a result, strong magnetocaloric, magnetostrictive, magnetoresistance, and other effects are commonly observed. Consequently, a large change of the materials' properties can be achieved by a relatively weak change of external thermodynamic conditions.
Risk Factor Analysis of Postoperative Complications After Robotic Rectal Cancer Surgery
Authors: Kang Jeonghyun , Min Byung Soh , Park Yoon Ah , Hur Hyuk , Baik Seung Hyuk , Kim Nam Kyu , Sohn Seung Kook , Lee Kang Young 
Published: September 2011

AbstractBackgroundThe robotic system has been adopted as the new modality for minimally invasive surgery for rectal cancer. However, analysis of risk factors for complications after robotic rectal cancer surgery (RRS) has been limited. This study aimed to identify the risk factors for complications after RRS.MethodsThe records of 389 consecutive patients who underwent RRS between June 2006 and October 2010 were retrieved from our prospectively collected database.ResultsThe overall complication rate was 19%. The most common complication was anastomotic leakage (7.0%), followed by voiding difficulty, intrapelvic abscess, and ileus/obstruction. Multivariate analysis revealed the following as risk factors for postoperative complications: male gender, history of previous abdominal surgery, and lower tumor level (hazard ratio [HR] = 1.8, 95% confidence interval [CI] = 1.0–3.1, p = 0.041; HR = 2.3; 95% CI = 1.2–4.6, p = 0.012; and HR = 1.9, 95% CI = 1.1–3.3, p = 0.020, respectively). With regard to pelvic septic complications, lower tumor level, large tumor size, and preoperative chemoradiation remained variables that retained their statistical significance in multivariate analysis (HR = 2.6, 95% CI = 1.1–6.1, p = 0.029; HR = 2.7, 95% CI = 1.1–6.1, p = 0.017; HR = 2.9, 95% CI = 1.3–6.5, p = 0.007, respectively). The rate of postoperative complications was not influenced by the difference in laparoscopic surgery experience or the technique of robotic surgery.ConclusionSurgeons should be more cautious with these patient factors to optimize the benefits of robotic rectal resection.
Rethinking theoretical and methodological issues in intergenerational family relations research
Authors: LOWENSTEIN ARIELA , KATZ RUTH , BIGGS SIMON 
Published: September 2011

ABSTRACTThis paper introduces some key theoretical and methodological developments in the study of intergenerational family relations. It draws on observations that a number of social issues are emerging that have an intergenerational dimension, that there is growing recognition that to study adult ageing one has also to study intergenerational relationships, and that a new architecture for social relations is beginning to take shape in the wake of demographic change. How individuals, families and societies cope with such changes provokes the question of how gerontologically-informed research, theorisation and policy will also adapt. Seven positions are summarised which attempt two things. First, to map out some new conceptual directions for intergenerational research through a critical use of concepts such as transition, generational self-awareness and empathy, metaphors of cultural translation, and the deployment of social and moral capital. Second, to examine changing gender roles, the balance between family and welfare-state support frameworks, ethnicity and immigration as important elements of this process. A critical review of approaches to intergenerational relationships hopefully emerges.
Estimating the force of infection for HCV in injecting drug users using interval-censored data
Authors: CASTRO-SÁNCHEZ A. , SHKEDY Z. , HENS N. , AERTS M. , GESKUS R. , PRINS M. , WIESSING L. , KRETZSCHMAR M. 
Published: September 2011

SUMMARYInjecting drug users (IDUs) account for most new HCV infections. The objectives of this study were: to estimate the force of infection for hepatitis C virus in IDUs within the interval-censoring framework and to determine the impact of risk factors such as frequency of injection, drug injected, sharing of syringes and time of first injection on the time to HCV infection. We used data from the Amsterdam Cohort Study collected in The Netherlands and focused on those individuals who were HCV negative upon entry into the study. Based on the results, the force of infection was found to vary with time of first injection. The risk of infection was higher in the first 3 years of an IDU's career, implying estimates based on single cross-sectional studies could be biased. Frequency of injection and type of drug injected were found to be highly significant predictors, whereas sharing syringes was not.
The BinProlog experience: Architecture and implementation choices for continuation passing Prolog and first-class logic engines
Authors: TARAU PAUL 
Published: September 2011

AbstractWe describe theBinPrologsystem's compilation technology, runtime system and its extensions supporting first-class Logic Engines while providing a short history of its development, details of some of its newer re-implementations as well as an overview of the most important architectural choices involved in their design. With focus on its differences with conventional Warren Abstract Machine (WAM) implementations, we explain key details ofBinProlog's compilation technique, which replaces the WAM with a simplifiedcontinuation passingruntime system (the “BinWAM”), based on a mapping of full Prolog tobinary logic programs. This is followed by a description of aterm compressiontechnique using a “tag-on-data” representation. Later derivatives, the Java-basedJinni Prologcompiler and the recently developedLean Prologsystem refine theBinPrologarchitecture withfirst-class Logic Engines, made generic through the use of anInteractorinterface. An overview of their applications with focus on the ability to express at source level a wide variety of Prolog built-ins and extensions covers these newer developments.
ECLiPSe – From LP to CLP
Authors: SCHIMPF JOACHIM , SHEN KISH 
Published: September 2011

AbstractECLiPSe is a Prolog-based programming system, aimed at the development and deployment of constraint programming applications. It is also used for teaching most aspects of combinatorial problem solving, for example, problem modelling, constraint programming, mathematical programming and search techniques. It uses an extended Prolog as its high-level modelling and control language, complemented by several constraint solver libraries, interfaces to third-party solvers, an integrated development environment and interfaces for embedding into host environments. This paper discusses language extensions, implementation aspects, components, and tools that we consider relevant on the way from Logic Programming to Constraint Logic Programming.
SICStus Prolog—The first 25 years
Authors: CARLSSON MATS , MILDNER PER 
Published: September 2011

AbstractSICStus Prolog has evolved for nearly 25 years. This is an appropriate point in time for revisiting the main language and design decisions, and try to distill some lessons. SICStus Prolog was conceived in a context of multiple, conflicting Prolog dialect camps and a fledgling standardization effort. We reflect on the impact of this effort and role model implementations on our development. After summarizing the development history, we give a guided tour of the system anatomy, exposing some designs that were not published before. We give an overview of our new interactive development environment, and describe a sample of key applications. Finally, we try to identify key good and not so good design decisions.
SWI-Prolog
Authors: WIELEMAKER JAN , SCHRIJVERS TOM , TRISKA MARKUS , LAGER TORBJÖRN 
Published: September 2011

AbstractSWI-Prolog is neither a commercial Prolog system nor a purely academic enterprise, but increasingly a community project. The core system has been shaped to its current form while being used as a tool for building research prototypes, primarily forknowledge-intensiveandinteractivesystems. Community contributions have added several interfaces and the constraint (CLP) libraries. Commercial involvement has created the initial garbage collector, added several interfaces and two development tools: PlDoc (a literate programming documentation system) and PlUnit (a unit testing environment).In this article, we present SWI-Prolog as an integrating tool, supporting a wide range of ideas developed in the Prolog community and acting as glue betweenforeignresources. This article itself is the glue between technical articles on SWI-Prolog, providing context and experience in applying them over a longer period.
SBFC - The Systems Biology Format Converter Framework
Authors: Kutmon Martina , Rodriguez Nicolas 
Published: September 2011

AbstractThe System Biology Format Converter (SBFC) aims is to provide a generic framework that potentially allows any conversion between two formats. Interoperability between formats is a recurring issue in Systems Biology. Although there are various tools available to convert models from one format to another, most of them have been independently developed and cannot easily be combined, specially to provide support for more formats. The framework is written in Java and can be used as a standalone executable. Recently a prototype has been developed with OSGi to achieve a more modular framework structure. This is a collaborative project and we hope that developers will provide support for more formats by creating new modules. SBFC allows anyone to easily add new converters and to integrate existing converters with a minimum of changes. We will also allow to combine several existing converters.
A Modular Semantic Annotation Framework: CellML Metadata Specifications 2.0
Authors: Cooling Michael 
Published: September 2011

AbstractIn the last decade or so, model encoding efforts such as CellML and SBML have greatly facilitated model availability. But, as the complexity of models increases, the utility of these models can vary. The addition of semantic information is crucial to transforming mathematical models from esoteric to informative resources.We have developed a metadata specification framework to better enable the annotation of CellML models with metadata. The framework consists of a core specification describing, in general terms, how annotations should be attached using RDF/XML, and satellite specifications covering several domains of immediate interest, using elements from the Dublin Core, FOAF (Friend-Of-A-Friend), BIBO (Bibliographic Ontology), MIRIAM URNs and Biomodels Qualifiers.We also describe what we see as several emerging challenges in the field, uncovered during the application of this annotation scheme to mathematical models.
Towards a Modelling Ecosystem for Libraries of Modular, Reusable Components
Authors: Cooling Michael 
Published: September 2011

AbstractCellML 1.1 [1] is an XML-based model exchange protocol with inherent support for modularity.To assist in answering complex biomedical research questions, we are developing libraries of modular model components that facilitate mathematical model construction.Stored in the online, publicly accessible CellML Repository [2], the libraries vary from genetic and associated regulatory components for Synthetic Biology [3] to quantifying the Systems Biology of cardiovascular wall mal-adaptation [4,5].Currently however, using the libraries is not as easy as it should be. Here I describe progress towards a modelling ecosystem to encompasses component search and retrieval, composition, visualization and analysis services [6], building upon research in semantic annotation [7,8], graphical rendering [9], collaborative model storage [10] and large-scale parallel model simulation environments [11,12].Development of this ecosystem provides ample motivation to explore the applicability of emerging community standards as well as iteratively refine their efficacy in real biomedical problem scenarios.[1] Cuellar A. A., et al. (2003) Sim.[2] http://models.cellml.org[3] Cooling M. T., et al. (2010) Bioinf.[4] Ho H., et al. (2010) IFMBE Proc.[5] Ho H., et al. (2011) in press.[6] Cooling M. T., et al. (2010) IWBDA Proc.[7] Cooling M. T. (2011) ISMB Proc.[8] Misirli G., et al. (2011) Bioinf.[9] Wimalaratne, S. M., et al. (2009) Bioinf.[10] Yu, T., et al. (2011) Bioinf.[11] Sher, A. A. et al. (2010) IEEE EMBS Proc.[12] Cooling M. T., et al. (2010) NZ eResearch Symp.
Hypertonic stress regulates amino acid transport and cell cycle proteins in chick embryo hepatocytes
Authors: Bruscalupi Giovannella , Massimi Mara , Spagnuolo Silvana , Fiore Anna Maria , Leoni Silvia 
Published: September 2011

AbstractHyperosmotic stress affects cell growth, decreasing cell volume and increasing the uptake of organic osmolytes. However, the sensitivity of embryonic cells to osmotic treatment remains to be established. We have analysed some aspects of cell‐cycle control and amino‐acid transport in hypertonic conditions during prenatal life. The effects of hyperosmotic stress on amino‐acid uptake mediated by system A, 3H‐thymidine incorporation, and regulation of cell‐cycle proteins were analysed in chick embryo hepatocytes. Hypertonic stress increased system A activity and caused cell‐cycle delay. Effects on amino‐acid transport involved p38 kinase activation and new carrier synthesis. Cyclin D1, cdk4 (cyclin‐dependent kinase 4) and PCNA (proliferating‐cell nuclear antigen) levels decreased, whereas cyclin E, p21 and p53 levels were unchanged. Incorporation of 3H‐leucine indicated decreased synthesis of cyclin D1. In contrast, analysis of mRNA by qRT‐PCR (quantitative real‐time PCR) showed a net increase of cyclin D1 transcripts, suggesting post‐transcriptional regulation. The data show that chick embryo hepatocytes respond to hyperosmotic conditions by arresting cell growth to prevent DNA damage and increasing osmolyte uptake to regulate cell volume, indicating that the adaptive response to environmental stress exists during prenatal life.