bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expanding the data depth for the analysis of complex crude oil samples by Fourier transform ion cyclotron resonance mass spectrometry using the spectral stitching method
Authors: Gaspar Andras , Schrader Wolfgang 
Published: March 2012

RATIONALECrude oil samples are very complex mixtures of compounds and only Fourier transform ion cyclotron resonance mass spectrometry (FT‐ICR MS) provides the ultra‐high mass resolution necessary to resolve them. However, FT‐ICR MS operates best when only a small amount of ions is present during each transient. This cannot be accomplished with crude oil samples without chromatography because more than 50 000 compounds can be present, with the result that species with low intensity may be suppressed and are detected either with low intensity or not at all.METHODSSpectral stitching was used to overcome the problems associated with suppression effects, where only short mass windows of 30 amu were scanned to reduce the amount of ions present in each individual scan. Afterwards, all the scans were co‐added and the subsequent spectrum was used to calculate individual class distributions.RESULTSA heavy crude oil sample was analyzed using spectral stitching and this approach was compared with analysis using a broadband‐method in order to illustrate the enhancement in depth of information. Although both methods took the same analysis time a seven‐times increase in the number of detected species was observed when the spectral stitching method was used compared with the commonly applied broadband method in a 900 amu mass window.CONCLUSIONSSpectral stitching using smaller selected ion monitoring (SIM) windows for complex crude oil samples allows better class distribution to be obtained because less ion suppression is observed. Copyright © 2012 John Wiley & Sons, Ltd.
Dual approaches to strictly positive real controller synthesis with a performance using linear matrix inequalities
Authors: Forbes James Richard 
Published: March 2012

SUMMARYThe synthesis of controllers that minimize a performance index subject to a strictly positive real (SPR) constraint is considered. Two controller synthesis methods are presented that are then combined into an iterative algorithm. Each method synthesizes optimal SPR controllers by posing a convex optimization problem where constraints are enforced via linear matrix inequalities. Additionally, each method fixes the controller state‐feedback gain matrix and finds an observer gain matrix such that an upper bound on the closed‐loop ‐norm is minimized and the controller is SPR. The first method retools the standard ‐optimal control problem by using a common Lyapunov matrix variable to satisfy both the criteria and the SPR constraint. The second method overcomes bilinear matrix inequality issues associated with the performance and the SPR constraint by employing a completing the square method and an overbounding technique. Both synthesis methods are used within an iterative scheme to find optimal SPR controllers in a sequential manner. Comparison of our synthesis methods to existing methods in the literature is presented. Copyright © 2012 John Wiley & Sons, Ltd.
Decentralized sliding‐mode control for attitude synchronization in spacecraft formation
Authors: Wu Baolin , Wang Danwei , Poh Eng Kee 
Published: March 2012

SUMMARYThis paper addresses attitude synchronization and tracking problems in spacecraft formation in the presence of model uncertainties and external disturbances. A decentralized adaptive sliding mode control law is proposed using undirected interspacecraft communication topology and analyzed based on algebraic graph theory. A multispacecraft sliding manifold is derived, on which each spacecraft approaches desired time‐varying attitude and angular velocity while maintaining attitude synchronization with the other spacecraft in the formation. A control law is then developed to ensure convergence to the sliding manifold. The stability of the resulting closed‐loop system is proved by application of Barbalat's Lemma. Simulation results demonstrate the effectiveness of the proposed attitude synchronization and tracking methodology. Copyright © 2012 John Wiley & Sons, Ltd.
Betti numbers of graphs with an application to anomaly detection
Authors: Johannsen David A. , Marchette David J. 
Published: March 2012

AbstractThis article describes an application of research that sits at the intersection of commutative algebra and combinatorics: Betti numbers of graphs. In particular, we describe a correspondence between simple undirected graphs and a class of ideals in a polynomial ring. We then briefly introduce some of the algebraic invariants that can be associated to the ideal and the relation of these invariants to the existence of induced subgraphs in the original graph. We discuss a novel application of the theory to a problem in anomaly detection—detection of a local non‐homogeneity in a graph. We describe some variants of these ideas designed to make the computations more tractable. © 2012 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 5: 235–242, 2012
Are all ‘sharks’ dangerous? new biotechnology ventures and partner selection in R&D alliances
Authors: Diestre Luis , Rajagopalan Nandini 
Published: March 2012

AbstractWe examine how new biotechnology firms (NBFs) select pharmaceutical firms as R&D allies as a function of value creation and value appropriation considerations. We develop a theoretical framework to understand partnering decisions accounting for both, a potential partner's ability as well as incentives to appropriate and create value within an R&D alliance. Our empirical findings show that NBFs are more likely to ally with pharmaceutical firms with the ability to create value, as long as these firms have the incentives to use their skills to create rather than appropriate value. Our study highlights the double‐edged sword nature of value creation skills and provides a deeper understanding into the contextual factors that determine when potential R&D partners will perceive such skills as increasing appropriation risks. Copyright © 2012 John Wiley & Sons, Ltd.
Stem-Like Cells with Luminal Progenitor Phenotype Survive Castration in Human Prostate Cancer
Authors: Germann Markus , Wetterwald Antoinette , Guzmán-Ramirez Natalia , van der Pluijm Gabri , Culig Zoran , Cecchini Marco G. , Williams Elizabeth D. , Thalmann George N. 
Published: March 2012

Abstract
Castration is the standard therapy for advanced prostate cancer (PC). Although this treatment is initially effective, tumors invariably relapse as incurable, castration-resistant PC (CRPC). Adaptation of androgen-dependent PC cells to an androgen-depleted environment or selection of pre-existing, CRPC cells have been proposed as mechanisms of CRPC development. Stem cell (SC)-like PC cells have been implicated not only as tumor initiating/maintaining in PC but also as tumor-reinitiating cells in CRPC. Recently, castration-resistant cells expressing the NK3 homeobox 1 (Nkx3-1) (CARNs), the other luminal markers cytokeratin 18 (CK18) and androgen receptor (AR), and possessing SC properties, have been found in castrated mouse prostate and proposed as the cell-of-origin of CRPC. However, the human counterpart of CARNs has not been identified yet. Here, we demonstrate that in the human PC xenograft BM18, pre-existing SC-like and neuroendocrine (NE) PC cells are selected by castration and survive as totally quiescent. SC-like BM18 cells, displaying the SC markers aldehyde dehydrogenase 1A1 or NANOG, coexpress the luminal markers NKX3-1, CK18, and a low level of AR (ARlow) but not basal or NE markers. These CR luminal SC-like cells, but not NE cells, reinitiate BM18 tumor growth after androgen replacement. The ARlow seems to mediate directly both castration survival and tumor reinitiation. This study identifies for the first time in human PC SC-/CARN-like cells that may represent the cell-of-origin of tumor reinitiation as CRPC. This finding will be fundamental for refining the hierarchy among human PC cancer cells and may have important clinical implications.
Disclosure of potential conflicts of interest is found at the end of this article.
Oscillatory gene expression and somitogenesis
Authors: Kageyama Ryoichiro , Niwa Yasutaka , Isomura Akihiro , González Aitor , Harima Yukiko 
Published: March 2012

AbstractA bilateral pair of somites forms periodically by segmentation of the anterior ends of the presomitic mesoderm (PSM). This periodic event is regulated by a biological clock called the segmentation clock, which involves cyclic gene expression. Expression of her1 and her7 in zebrafish and Hes7 in mice oscillates by negative feedback, and mathematical models have been used to generate and test hypotheses to aide elucidation of the role of negative feedback in regulating oscillatory expression. her/Hes genes induce oscillatory expression of the Notch ligand deltaC in zebrafish and the Notch modulator Lunatic fringe in mice, which lead to synchronization of oscillatory gene expression between neighboring PSM cells. In the mouse PSM, Hes7 induces coupled oscillations of Notch and Fgf signaling, while Notch and Fgf signaling cooperatively regulate Hes7 oscillation, indicating that Hes7 and Notch and Fgf signaling form the oscillator networks. Notch signaling activates, but Fgf signaling represses, expression of the master regulator for somitogenesis Mesp2, and coupled oscillations in Notch and Fgf signaling dissociate in the anterior PSM, which allows Notch signaling‐induced synchronized cells to express Mesp2 after these cells are freed from Fgf signaling. These results together suggest that Notch signaling defines the prospective somite region, while Fgf signaling regulates the pace of segmentation. It is likely that these oscillator networks constitute the core of the segmentation clock, but it remains to be determined whether as yet unknown oscillators function behind the scenes. WIREs Dev Biol 2012 doi: 10.1002/wdev.46For further resources related to this article, please visit the WIREs website.
The History of ViSta: The Visual Statistics System
Authors: Valero‐Mora Pedro , Ledesma Rubén D. , Friendly Michael 
Published: March 2012

AbstractViSta is a project that focuses on dynamic and interactive graphics for statistics and was initiated by the late Forrest W. Young at the beginning of the 1990s. For over approximately 20 years, Forrest and other collaborators, including the authors of this article, have used ViSta for experimenting with these kinds of graphics in different settings, applying them to different scenarios of data and statistical analysis, searching to develop the right combination of features most appropriate in each case. In this time, ViSta evolved quite considerably, going through what we reckon were three different stages, namely: the initial one setting forth the foundations of ViSta; the second period where versions 5 and 6 of ViSta were released; and the consolidation period when a book summarizing the lessons learnt in the project was published. This book was titled ‘Visual Statistics: Seeing your data with interactive and dynamic graphics’ and was completed in the last days of life of Forrest, who continued to work enthusiastically in the project even though his health was seriously deteriorating during that time. This article is a tribute to this work, but also describes the innovative features of ViSta, many of which are still relevant today. WIREs Comput Stat 2012, 4:295–306. doi: 10.1002/wics.1203This article is categorized under:

Software for Computational Statistics > Software/Statistical Software
Fractal and multifractal geometry: scaling symmetry and statistics
Authors: Frame Michael , Martino William 
Published: March 2012

AbstractScaling symmetry is explored in several settings, deterministic, stochastic, and natural. Complexity of geometric fractals is quantified by dimension; complexity of a scaling measure is quantified by the multifractal spectrum. Some statistical examples are explored.WIREs Comput Stat2012, 4:249–274. doi: 10.1002/wics.1207This article is categorized under:Algorithms and Computational Methods > Computer GraphicsApplications of Computational Statistics > Computational MathematicsData: Types and Structure > Time Series, Stochastic Processes, and Functional Data
RNA biology in a test tube—an overview of in vitro systems/assays
Authors: Roca Xavier , Karginov Fedor V. 
Published: March 2012

AbstractIn vitro systems have provided a wealth of information in the field of RNA biology, as they constitute a superior and sometimes the unique approach to address many important questions. Such cell‐free methods can be sorted by the degree of complexity of the preparation of enzymatic and/or regulatory activity. Progress in the study of pre‐mRNA processing has largely relied on traditional in vitro methods, as these reactions have been recapitulated in cell‐free systems. The pre‐mRNA capping, editing, and cleavage/polyadenylation reactions have even been reconstituted using purified components, and the enzymes responsible for catalysis have been characterized by such techniques. In vitro splicing using nuclear or cytoplasmic extracts has yielded clues on spliceosome assembly, kinetics, and mechanisms of splicing and has been essential to elucidate the function of splicing factors. Coupled systems have been important to functionally connect distinct processes, like transcription and splicing. Extract preparation has also been adapted to cells from a variety of tissues and species, revealing general versus species‐specific mechanisms. Cell‐free assays have also been applied to newly discovered pathways such as those involving small RNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs), and Piwi‐interacting RNAs (piRNAs). The first two pathways have been well characterized largely by in vitro methods, which need to be developed for piRNAs. Finally, new techniques, such as single‐molecule studies, are continuously being established, providing new and important insights into the field. Thus, in vitro approaches have been, are, and will continue being at the forefront of RNA research. WIREs RNA 2012, 3:509–527. doi: 10.1002/wrna.1115This article is categorized under:

RNA Processing > Splicing Mechanisms
Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action
RNA Methods > RNA Analyses In Vitro and In Silico
Nonsurgical Treatment of Dupuytren's Contracture: 1-Year US Post-Marketing Safety Data for Collagenase Clostridium Histolyticum
Authors: Peimer C. A. , McGoldrick C. A. , Fiore G. J. 
Published: March 2012

Background Collagenase clostridium histolyticum (CCH) is a Food and Drug Administration-approved treatment for adult patients with Dupuytren's contracture with a palpable cord that has been shown efficacious and safe in clinical trials. Methods This paper summarizes the most common post-marketing clinical adverse event (AE) reports received by the manufacturer of CCH and sponsor of the US Biologics License Application (Auxilium Pharmaceuticals, Malvern, PA, USA) during the first 12 months after drug approval and commercialization in the USA. Results Of the 115 AE reports describing 270 AEs voluntarily received from patients or health care providers after approximately 5,400 injections of CCH administered, the most common AEs involved local, nonserious reactions to treatment, including skin tears, peripheral edema, and contusion. There were few serious AEs observed (0.6% reporting rate per 1,000 injections), and two flexor tendon ruptures and one flexor pulley injury were reported. Conclusions Analysis of post-marketing AEs received for CCH in the first year post-approval supports the safety profile reported earlier during clinical development and did not reveal additional clinical risks or concerns about CCH.
Effects of Inorganic Salts and Polymers on the Foam Performance of 1‐Tetradecyl‐3‐methylimidazolium Bromide Aqueous Solution
Authors: Zhang Qian , Wei Xilian , Liu Jie , Sun Dezhi , Zhang Xianxi , Zhang Chong , Liu Jifeng 
Published: March 2012

AbstractThe foaming performance of 1‐tetradecyl‐3‐methylimidazolium bromide (C14mimBr) aqueous solution, in the presence of polymers (PEG or PVA) or inorganic salts (NaBr, MgCl2, NaNO3, Na2SO4 or Na3PO4), was investigated at 25.0 °C by using the self‐made apparatus and the conductivity method. The experimental results show that the foaming ability and foam stability of the ternary aqueous systems of C14mimBr coexisting with PEG or PVA are stronger than those of the C14mimBr solutions in the absence of a polymer, and both the efficiency of foaming ability and foam stability of the surfactant solutions are evidently enhanced with an increase in polymer concentration. However, the addition of inorganic salts can decrease the foaming ability and foam stability of C14mimBr solution. Especially, the inorganic salts, with high valence state of the anion (SO42− and PO43−), are good antifoam agents which can remove and inhibit foam quickly. For the aqueous solution of the surfactant, the effect of temperature on foaming properties was also examined. The results show that both the foaming ability and stability of the foams of the surfactant solutions decrease with an increase in the temperature within the range from 25.0 to 45.0 °C.
Treatment of twin reversed arterial perfusion sequence with alcohol ablation or bipolar cord coagulation
Authors: Corbacioglu Aytul , Gul Ahmet , Bakirci Isil T. , Gedikbasi Ali , Yildirim Gokhan 
Published: March 2012

AbstractObjectiveTo evaluate perinatal outcome in pregnancies complicated by TRAP sequence.MethodsThe perinatal outcomes of 15 TRAP sequence pregnancies referred to Kanuni Sultan Suleyman Research and Teaching Hospital, Turkey, were evaluated. Six cases were treated conservatively. Alcohol ablation and bipolar coagulation were performed in 5 and 4 cases, respectively.ResultsIn 12 cases, there were signs of fetal compromise and acardiac/pump twin abdominal circumference ratio of more than 50%. In 3 cases without intervention, the ratio was less than 50%. Three of the 6 pregnancies treated conservatively resulted in intrauterine death of the pump twin. Alcohol ablation was successful in 3 cases, with delivery of live fetuses at 36–38 weeks, whereas intrauterine death occurred in 1 case and abortion occurred in 1 case. In 2 of the cases involving bipolar cord coagulation, live birth occurred at 39 weeks; preterm premature rupture of membranes and abortion occurred at 18 weeks in 1 case, and pregnancy was terminated in 1 case because of ventriculomegaly.ConclusionConservative therapy is suitable for mild cases of TRAP sequence in which the pump twin dominates. If there are signs of pump twin compromise, alcohol ablation and bipolar cord coagulation can be performed successfully.
Mining Functional Gene Modules Linked with Rheumatoid Arthritis Using a SNP-SNP Network
Authors: Hua Lin , Lin Hui , Li Dongguo , Li Lin , Liu Zhicheng 
Published: March 2012

Abstract
The identification of functional gene modules that are derived from integration of information from different types of networks is a powerful strategy for interpreting the etiology of complex diseases such as rheumatoid arthritis (RA). Genetic variants are known to increase the risk of developing RA. Here, a novel method, the construction of a genetic network, was used to mine functional gene modules linked with RA. A polymorphism interaction analysis (PIA) algorithm was used to obtain cooperating single nucleotide polymorphisms (SNPs) that contribute to RA disease. The acquired SNP pairs were used to construct a SNP-SNP network. Sub-networks defined by hub SNPs were then extracted and turned into gene modules by mapping SNPs to genes using dbSNP database. We performed Gene Ontology (GO) analysis on each gene module, and some GO terms enriched in the gene modules can be used to investigate clustered gene function for better understanding RA pathogenesis. This method was applied to the Genetic Analysis Workshop 15 (GAW 15) RA dataset. The results show that genes involved in functional gene modules, such as CD160 (rs744877) and RUNX1 (rs2051179), are especially relevant to RA, which is supported by previous reports. Furthermore, the 43 SNPs involved in the identified gene modules were found to be the best classifiers when used as variables for sample classification.
MotViz: A Tool for Sequence Motif Prediction in Parallel to Structural Visualization and Analyses
Authors: Nawaz Muhammad Sulaman , Rashid Sajid 
Published: March 2012

Abstract
Linking similar proteins structurally is a challenging task that may help in finding the novel members of a protein family. In this respect, identification of conserved sequence can facilitate understanding and classifying the exact role of proteins. However, the exact role of these conserved elements cannot be elucidated without structural and physiochemical information. In this work, we present a novel desktop application MotViz designed for searching and analyzing the conserved sequence segments within protein structure. With MotViz, the user can extract a complete list of sequence motifs from loaded 3D structures, annotate the motifs structurally and analyze their physiochemical properties. The conservation value calculated for an individual motif can be visualized graphically. To check the efficiency, predicted motifs from the data sets of 9 protein families were analyzed and MotViz algorithm was more efficient in comparison to other online motif prediction tools. Furthermore, a database was also integrated for storing, retrieving and performing the detailed functional annotation studies. In summary, MotViz effectively predicts motifs with high sensitivity and simultaneously visualizes them into 3D strucures. Moreover, MotViz is user-friendly with optimized graphical parameters and better processing speed due to the inclusion of a database at the back end. MotViz is available at http://www.fi-pk.com/motviz.html.
Theoretical Estimation and Modeling for Constraint-Tuning Ultrasonic Actuator
Authors: Lai M.-H. , Ouyang M. S. , Wen F.-L. 
Published: March 2012

ABSTRACTUsing a piezoelectric unimorph vibrator with constraint-tuning modified-mode (CTMM) mechanism, a novel design of a thin-disc ultrasonic actuator was developed to drive an optical sled. The theoretical estimation of in-plane wave propagation on a thin disc is introduced to explain the novel actuating mechanism, via a modal expansion technique and modal participation factors. Furthermore, the approximate wave propagations could be illustrated by the practical estimated wave equations in this study. Applying four screws at the exact distribution of angles on the thin-disc vibrator, the actuating mechanism of ultrasonic modified modes is generated and propagated. The in-plane vibration modes could be tuned by these desired screw constraints on the piezoelectric vibrator. The ultrasonic actuator offers the output force to drive an optical sled by friction contact in bilateral motions. To implement the equilibrium structure force in bilateral directions, natural and forced analysis as well as impedance comparison of FEM software ANSYS are also introduced into the constrained design. Hence, there are two various modified modes chosen at the different resonant frequencies within the electromechanical coupling of piezoelectric material to pursue more efficiency in energy conversion. Experimental results have demonstrated consistency with the approximate theoretical approach of the in-plane wave propagation and simulations based on the concept of constrained-tuning modified modes.