bluuebunny/crossref_metadata_2025_split huggingface dataset:
Matrix‐Assisted Laser Desorption/Ionization Time‐of‐Flight Mass Spectrometry of Oligonucleotides
Authors: Castleberry Colette M. , Chou Chau‐Wen , Limbach Patrick A. 
Published: June 2008

AbstractMALDI‐MS is one of the most useful techniques available for determining biomolecule mass. It offers high mass accuracy, good sensitivity, simplicity, and speed. Because singly charged ions of oligonucleotides are typically observed, MALDI‐MS spectra are easy to interpret. This unit presents protocols for sample preparation and purification, matrix preparation, and matrix/analyte sample preparation. It provides an introduction to the instrumentation and its calibration, and a discussion of some of the useful applications of MALDI‐MS analysis in the study of oligonucleotides. This technique is typically used for 120‐mer or smaller oligonucleotides. Curr. Protoc. Nucleic Acid Chem. 33:10.1.1‐10.1.21. © 2008 by John Wiley & Sons, Inc.
Solid‐Supported Diphosphitylating and Triphosphitylating Reagents for Nucleoside Modification
Authors: Ahmadibeni Yousef , Parang Keykavous 
Published: June 2008

AbstractThis unit describes procedures for synthesis of diphosphitylating and triphosphitylating reagents. The synthesized reagents are first immobilized on appropriate polymer‐bound linkers. Rigid and sterically hindered polymer‐bound diphosphitylating and triphosphitylating reagents are then reacted selectively with the 5′‐hydroxyl group of nucleosides in the presence of excess nucleosides. Typical oxidation with tert‐butyl hydroperoxide, deprotection, and final cleavage of the products from the resins using a trifluoroacetic acid cocktail afford various nucleoside 5′‐O‐diphosphate and nucleoside 5′‐O‐triphosphate analogs. The use of the diphosphitylating and polymer‐bound diphosphitylating reagents in preparation of oligodeoxynucleotides containing diphosphodiester internucleotide bridges is also described. This solid‐phase strategy allows for the synthesis of the phosphorylated compounds without the need for nucleoside phosphate precursors, protected nucleosides, or purification of intermediates. Curr. Protoc. Nucleic Acid Chem. 33:13.8.1‐13.8.29. © 2008 by John Wiley & Sons, Inc.
Head and Neck MRA at 3.0T
Authors: Bernstein Matt A. , Huston John 
Published: June 2008

Abstract3.0T MRI scanners are becoming more widely used in clinical practice, particularly for neurological applications. The increased signal‐to‐noise ratio (SNR) provided by 3.0T compared to 1.5T is particularly useful for applications like magnetic resonance angiography (MRA). A protocol to image the intracranial circulation with 3‐D time of flight (3DTOF), and a protocol to image the carotid, vertebral, and basilar arteries with contrast‐enhanced MRA are presented. The increased SNR at 3.0T is used to increase the spatial resolution. For the 3DTOF exam, the acquisition time is also reduced with the use of parallel imaging.
Coronary MRA
Authors: Deshpande Vibhas S. , Li Debiao 
Published: June 2008

AbstractCoronary X‐ray angiography is the gold standard for coronary artery imaging, but is an invasive procedure, with a minor risk of potentially serious complications in addition to the drawback of exposure to ionizing radiation. Coronary magnetic resonance angiography (MRA) is a noninvasive method of imaging the coronary arteries, with no known adverse effects. In addition to morphologic evaluation of coronary artery disease with coronary MRA, cardiac MRI offers exciting possibilities to study the functional significance of coronary artery disease in the same setting. Three widely used coronary MRA approaches are presented‐‐two free‐breathing navigator‐gated methods, and a breath‐hold method. Although the positive predictive value of coronary MRA for detecting stenoses remains lower than that of X‐ray angiography, coronary MRA can reliably detect anomalous origins of coronary arteries, and has a high negative predictive value for stenoses. In conclusion, coronary MRA is a promising tool to study coronary artery disease.
MR Imaging of the Midfoot and Forefoot
Authors: Bencardino Jenny , Rosenberg Zehava S. 
Published: June 2008

AbstractMR imaging is the diagnostic modality of choice for the evaluation of traumatic, inflammatory and neoplastic processes affecting the midfoot and forefoot soft tissue structures including muscles, ligaments, and tendons. MR imaging is also valuable in the diagnosis of occult bony trauma, stress reaction or fractures, and osteomyelitis. Exquisite contrast resolution, noninvasiveness, and multiplanar capabilities are unique features that make MR imaging a powerful diagnostic technique. The authors employ a basic protocol using T1‐weighted, fast spin echo proton density with and without frequency‐selective fat saturation, and fast spin echo T2‐weighted sequences as well as short‐tau inversion recovery (STIR) imaging. Additional imaging following intravenous gadolinium administration is indicated when osteomyelitis and neoplastic processes are suspected. Post‐contrast fat‐suppressed T1‐weighted sequences are necessary if intravenous or intra‐articular gadolinium is utilized.
Isolation of Microtubules and Microtubule Proteins
Authors: Avila J. , Soares H. , Fanarraga M.L. , Zabala J.C. 
Published: June 2008

AbstractThis unit describes various protocols for the isolation and purification of the main constituents of microtubules, chiefly α‐ and β‐tubulin, and the most significant microtubule associated proteins (MAPs), specifically MAP1A, MAP1B, MAP2, and tau. We include a classical isolation method for soluble tubulin heterodimer as the first basic purification protocol. In addition, we show how to analyze the tubulin and MAPs obtained after a phosphocellulose chromatography purification procedure. This unit also details a powerful and simple method to determine the native state of the purified tubulin based on one‐dimensional electrophoresis under nondenaturing conditions (UNIT 6.5). The last protocol describes the application of a new technique that allows visualizing the quality of polymerized microtubules based on atomic force microscopy (AFM). Curr. Protoc. Cell Biol. 39:3.29.1‐3.29.28. © 2008 by John Wiley & Sons, Inc.
Quantitative Colocalization Analysis of Confocal Fluorescence Microscopy Images
Authors: Zinchuk Vadim , Zinchuk Olga 
Published: June 2008

AbstractColocalization is an important finding in many cell biological studies. This unit describes a protocol for quantitative evaluation of images with colocalization based on the calculation of a number of specialized coefficients. First, images of double‐stained sections are subjected to background correction. Then, various coefficients are calculated. Meanings of the coefficients and a guide to interpretation of their results indicating either presence or absence of colocalization are given. Success in colocalization studies depends on the quality of analyzed images, proper preparation of them for coefficients calculations, and correct interpretation of obtained results. This protocol helps to ensure reliability of colocalization coefficients calculations. Curr. Protoc. Cell Biol. 39:4.19.1‐4.19.16. © 2008 by John Wiley & Sons, Inc.
Assays for Ribosomal RNA Processing and Ribosome Assembly
Authors: Pestov Dimitri G. , Lapik Yevgeniya R. , Lau Lester F. 
Published: June 2008

AbstractThe synthesis of ribosomes is a major metabolic activity critical for cell growth and homeostasis. Understanding the mechanisms of ribosome biogenesis has important implications for studying both protein synthesis and cell cycle control. This unit describes several techniques for the analysis of rRNA maturation and ribosome assembly adapted for mammalian cells. Metabolic labeling of rRNA and hybridization analysis of precursors can be used to assess changes in rRNA processing that occur under experimental conditions of interest. Separation of preribosomal particles by sucrose gradient centrifugation is suitable for the analysis of proteins associated with preribosomes during their assembly and maturation in the cell nucleus. Curr. Protoc. Cell Biol. 39:22.11.1‐22.11.16. © 2008 by John Wiley & Sons, Inc.
Using GenePattern for Gene Expression Analysis
Authors: Kuehn Heidi , Liberzon Arthur , Reich Michael , Mesirov Jill P. 
Published: June 2008

AbstractThe abundance of genomic data now available in biomedical research has stimulated the development of sophisticated statistical methods for interpreting the data, and of special visualization tools for displaying the results in a concise and meaningful manner. However, biologists often find these methods and tools difficult to understand and use correctly. GenePattern is a freely available software package that addresses this issue by providing more than 100 analysis and visualization tools for genomic research in a comprehensive user‐friendly environment for users at all levels of computational experience and sophistication. This unit demonstrates how to prepare and analyze microarray data in GenePattern. Curr. Protoc. Bioinform. 22:7.12.1–7.12.39. © 2008 by John Wiley & Sons, Inc.
Prediction of Protein‐Protein Interaction Networks
Authors: Gomez Shawn M. , Choi Kwangbom , Wu Yang 
Published: June 2008

AbstractThis unit offers a general overview of several techniques that have been developed for inferring functional and/or protein‐protein interaction networks. The majority of these use whole‐genome sequences as their primary input source of data. In addition, a few methods that utilize both protein features and experimental protein‐protein interaction data directly in the prediction of new interactions have recently been developed. While an exhaustive list of approaches is not presented, it is hoped that the reader will gain a sense of how these approaches are implemented and an idea of their relative strengths and weaknesses, and a broader perspective on the type of work being conducted in this highly active area of research. Curr. Protoc. Bioinform. 22:8.2.1–8.2.14. © 2008 by John Wiley & Sons, Inc.
Searching the MINT Database for Protein Interaction Information
Authors: Cesareni Gianni , Chatr‐aryamontri Andrew , Licata Luana , Ceol Arnaud 
Published: June 2008

AbstractThe Molecular Interactions Database (MINT) is a relational database designed to store information about protein interactions. Expert curators extract the relevant information from the scientific literature and deposit it in a computer readable form. Currently (April 2008), MINT contains information on almost 29,000 proteins and more than 100,000 interactions from more than 30 model organisms. This unit provides protocols for searching MINT over the Internet, using the MINT Viewer. Curr. Protoc. Bioinform. 22:8.5.1–8.5.13. © 2008 by John Wiley & Sons, Inc.
Using ChemBank to Probe Chemical Biology
Authors: Petri Seiler Kathleen , Kuehn Heidi , Pat Happ Mary , DeCaprio Dave , Clemons Paul A. 
Published: June 2008

AbstractChemBank (http://chembank.broad.harvard.edu/) is a public, Web‐based informatics environment. ChemBank stores and makes freely available data derived from small molecules and small‐molecule screens and has resources for relating and studying these data. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays performed at the Broad Institute screening center. Web‐based analysis tools are available within ChemBank to study the relationships between small molecules, cell measurements, and cell states. This unit demonstrates the use of ChemBank data to ask and answer questions relating to chemical biology and screening experiments contained within ChemBank. Curr. Protoc. Bioinform. 22:14.5.1–14.5.26. © 2008 by John Wiley & Sons, Inc.
The Synthesis of Phenols and Quinones viaFischer Carbene Complexes
Authors: Waters Marcey L. , Wulff William D. 
Published: June 2008

AbstractFischer carbene complexes can be broadly defined as those transition‐metal carbene complexes that have a low oxidation state, have an electrophilic carbene carbon , and usually have a heteroatom‐stabilizing substituent on the carbene carbon. Fischer complexes were the first examples of any type of transition metal carbene complexes to be reported. The reaction of Fischer carbene complexes with alkynes is facile, occurring just above ambient temperature, and resulting in the assembly of a benzene ring from the three carbons of the alpha, beta‐unsaturated carbine complex, the two carbons of the alkyne, and the carbon of a carbon monoxide ligand. The synthetic value of this reaction stems from its broad scope, the generally high yields for the process, and the fact that that the products can function as intermediates for the synthesis of a variety of aromatic compounds includingpara‐quinones. It is the most synthetically valuable of the large number of Fischer carbene complexes that have been developed for applications in synthetic organic chemistry. This chapter is the first comprehensive review that is limited to the synthesis of phenols and quinones from the reactions of Fischer carbene complexes with alkynes.
Literature Searching Methodology
Authors: Roth Dana L. 
Published: June 2008

Abstract
Descriptions of analytical methods and instrumental techniques are found in an astonishing variety of resources. Because of this wide variety of sources and the extensive time period over which they have been published, developing an effective literature searching methodology is absolutely essential for students, research faculty, and practicing chemists. This article covers traditional methodologies and basic resources. In addition, recent widespread adoption of electronic journals and reference works, plus the virtually universal adoption of Google searching, are substantially transforming literature searching methodology.
Multivariate and Hyperspectral Image Analysis
Authors: Geladi Paul , Grahn Hans F. 
Published: June 2008

AbstractMultivariate image analysis (MIA) and hyperspectral image analysis (HIA) are methodologies for analyzing multivariate images, where the image coordinates are position (two or three dimensions) and variable number. Multivariate/hyperspectral images can have typical sizes 1024 × 1024, 512 × 512, 256 × 256, etc. and have between two and many hundreds of variables. The variables can be wavelength, electron energy, particle mass, and many others. Classical image analysis concentrates mainly on spatial relationships between pixels in a gray level image. MIA/HIA concentrates on the correlation of structure between the variables to provide extra information useful for exploring images and classifying regions in them. The many variables can be transformed into a few latent variable images containing condensed information. The sheer size of the data arrays necessitates visualization of raw data, intermediate data, model parameters, and residuals. When the images consist of continuous spectra having more than 100 variables, the name hyperspectral is used and the emphasis of the analysis is often on the spectral interpretation.All physical techniques for measuring materials can be made into imaging techniques, describing not only a property but also its position in a plane or volume. All imaging techniques can be expanded to become multivariate/hyperspectral. Multivariate imaging is used in many fields of research, but for practical reasons a subdivision in the classes remote sensing, medical imaging, and microscopy (including macroscopy) can be made. In microscopy, MIA/HIA can be used to study materials and biological processes by optical, electron, and charged particle techniques.
Agent‐Oriented Software Engineering
Authors: Perini Anna 
Published: June 2008

Abstract

Agent‐oriented software engineering (AOSE) is an approach to construct software systems based on the
agent
paradigm. An agent can be thought of as an
autonomous
and
social
entity, which can communicate, coordinate, and cooperate with other agents to achieve goals. The agent paradigm offers useful abstractions to design today's complex networked applications.

Several AOSE methodologies have been proposed so far, each one providing its own modeling language and analysis techniques. Efforts toward unification of AOSE methodologies and the definition of standards are in progress, in parallel with research to address challenging issues, such as designing software with autonomic properties.
Aspect‐Oriented Software Development: an Introduction
Authors: Brichau Johan , Chitchyan Ruzanna , Rashid Awais , D'Hondt Theo 
Published: June 2008

AbstractModularity of software has long been the primary mechanism used in software development to improve reuse and support maintainability. However, certain concerns do not fit the module boundaries in contemporary software‐development paradigms. The consequence of such crosscutting concerns, such as logging, persistence, security, and so forth, is that the responsibilities of the individual modules are not clearly demarcated. Not only is a module responsible for its core state and behavior (pertaining to its business functionality, for instance) but also for that of the crosscutting concern (such as logging). This phenomenon is referred to as tangling. At the same time, we observe the scattering effect whereby a given crosscutting concem,for example, logging, is not modularized in a single element and hence hampers our ability to reason about its effect and behavior with respect to the other modules; such reasoning requires inspection of all the modules where logging is realized. This requirement goes against the established best practice of separation of concerns because the crosscutting effect results in software that is difficult to understand and maintain. Addressing this problem of crosscutting is the main focus of aspect‐oriented software‐development (AOSD) techniques. In this article, we provide an introduction to AOSD by highlighting how it provides systematic support for identification, modularization, and composition of crosscutting concerns throughout the software lifecycle.
Finite Element Method
Authors: Bathe Klaus‐Jürgen 
Published: June 2008

Abstract
The objective of this article is to give an overview of finite element methods that currently are used extensively in academia and industry. The method is described in general terms, the basic formulation is presented, and some issues regarding effective finite element procedures are summarized. Various applications are given briefly to illustrate the current use of the method. Finally, the article concludes with key challenges for the additional development of the method.
Robot Kinematics
Authors: Zhang Dan , Bi Zhuming , Gao Zhen 
Published: June 2008

Abstract
In this article, kinematics of robot manipulators is presented with a systematic and general approach—Denavit‐Hartenberg convention. The basic mathematical concepts are explained in detail, including translational transformation, rotational transformation, homogeneous transformation, Euler angle, direct kinematics and inverse kinematics, and so on. The relation between joint velocities and end‐effector linear and angular velocities is described by the Jacobian matrix. As an example, a parallel manipulator with three degrees of freedom (DOFs) is presented. This 3DOF‐parallel manipulator can be used for machine tools, and it includes two rotations and one translation along the z axis. Both direct and inverse kinematic problems are conducted based on the theory described in the beginning of the article. The case study will allow readers to better understand the knowledge of robot kinematics.
Visual Programming Languages
Authors: Cox Philip T. 
Published: June 2008

AbstractDiagrams have always been used as aids in the design of programs, but because of the limitations of hardware and software, could not be directly incorporated into the software development process until the advent of low‐cost, high‐quality graphics in the 1980s. This enabled research on the pictorial representation of software structures, including an extensive study of visual programming languages. A visual programming language is one that uses diagrams to represent significant portions of the logic of a program, with the aim of making programs easier and faster to build and debug. We present several representative visual programming languages, discuss theoretical and cognitive issues, and provide a brief overview of current research in the area.
Wide Area Networks
Authors: Gu Yunhong 
Published: June 2008

Abstract
This article briefly describes wide area networks (WAN), which can be defined roughly as the computer networks that cover a broad geographical area. The Internet is the most typical WAN. Another example would be an intranet for a large enterprise that has multiple geographically distributed branches. This article explains WANs in the organization of the five‐layer TCP/IP layered model. For each layer, typical hardware and software (protocols) for WANs are discussed, especially these popular technologies used in WANs today.
Dynamic Programming
Authors: Oka Ryuichi , Wakamatsu Aizu 
Published: June 2008

AbstractDynamic programming (DP) is a powerful method for solving optimization problems. DP belongs to the mathematical programming field, which also includes linear programming. DP provides optimal algorithms for solving problems categorized by a sequential decision process. It was developed by R. Bellman in the 1950s and has been applied to various domains, including Markov decision processes, optimal control, variation methods, and numerical analysis. Recently, its fields of application have expanded to include speech recognition, bioinformatics, information retrieval, and many areas in artificial intelligence and pattern recognition. The reason for its widespread use is the simplicity of its algorithms, which are based on the principle of optimality. To emphasize the simplicity, we focus on a baseline algorithm of DP.
Process‐Aware Information Systems: Design, Enactment, and Analysis
Authors: van der Aalst Wil M.P. 
Published: June 2008

AbstractProcess‐aware information systems support operational business processes by combining advances in information technology with recent insights from management science. Workflow management systems are typical examples of such systems. However, many other types of information systems are also “process aware” even if their processes are hard‐coded or only used implicitly (e.g., ERP systems). The shift from data orientation to process orientation has increased the importance of process‐aware information systems. Moreover, advanced analysis techniques ranging from simulation and verification to process mining and activity monitoring allow for systems that support process improvement in various ways. This article provides an overview of process‐aware information systems and relates these to business process management, workflow management, process analysis techniques, and process flexibility.
Geometric Camera Calibration
Authors: Kannala Juho , Heikkilä Janne , Brandt Sami S. 
Published: June 2008

AbstractGeometric camera calibration is a prerequisite for making accurate geometric measurements from image data, and hence it is a fundamental task in computer vision. This article gives a discussion about the camera models and calibration methods used in the field. The emphasis is on conventional calibration methods in which the parameters of the camera model are determined by using images of a calibration object whose geometric properties are known. The presented techniques are illustrated with real calibration examples in which several different kinds of cameras are calibrated using a planar calibration object.