bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bisulfite Modification for Analysis of DNA Methylation
Authors: Hayatsu Hikoya , Shiraishi Masahiko , Negishi Kazuo 
Published: June 2008

AbstractBisulfite is known to deaminate cytosine in nucleic acids, while 5‐methylcytosine resists this bisulfite action. For this reason, bisulfite treatment has been used for detecting 5‐methylcytosine in DNA, a minor component of eukaryotic DNA, presently recognized as playing an important role in the control of gene function. This procedure, called bisulfite genomic sequencing, is a principal method for the analysis of DNA methylation in various biological phenomena, including human diseases such as cancer. This unit describes an efficient procedure utilizing a newly developed high‐concentration bisulfite solution. Protocols for this methodology are supplemented with discussions focused on chemical aspects of the bisulfite treatment. Curr. Protoc. Nucleic Acid Chem. 33:6.10.1‐6.10.15. © 2008 by John Wiley & Sons, Inc.
Cardiac Function Evaluation with Cine MRI of the Heart
Authors: Stillman Arthur E. , Jerosch‐Herold Michael 
Published: June 2008

AbstractThis unit describes how to determine hemodynamic parameters of cardiac function such as ejection fraction (EF), end diastolic volume (EDV), end systolic volume (ESV), stroke volume (SV), and cardiac mass, based on experience using a Siemens 1.5 T Sonata scanner. Briefly, cine loops are acquired over several heartbeats, synchronized with the heart cycle by gating of the encoding steps with the patients electrocardiogram (ECG). Recently, it has become feasible to acquire cine loops in real time, although the temporal resolution is not optimal. Options discussed in this unit include breath hold versus free breathing, prospective triggering versus retrospective gating, and volumetric data sets versus biplanar approaches. Patient parameters such as heart rate or rhythm, degree of functional impairment, the presence of valvular disease, and the need to assess for jets from shunts or valve dysfunction are also treated.
MR Imaging of the Ankle and Hindfoot
Authors: Bencardino Jenny , Rosenberg Zehava S. 
Published: June 2008

AbstractMagnetic Resonance Imaging (MRI) is the diagnostic modality of choice for evaluation of traumatic ligamentous and tendinous injuries of the ankle and hindfoot. MRI is also valuable in the detection of occult bony trauma, osteochondral injuries, avascular necrosis, osteomyelitis, and a variety of other osseous conditions. This unit presents basic protocols for T1‐ and T2‐weighted sequences and short tau inversion recovery (STIR) imaging. Additional imaging following intravenous gadolinium is indicated in selected cases.
Fluorescence Imaging Techniques for Studying Drosophila Embryo Development
Authors: Mavrakis Manos , Rikhy Richa , Lilly Mary , Lippincott‐Schwartz Jennifer 
Published: June 2008

AbstractThis unit describes fluorescence‐based techniques for noninvasive imaging of development in living Drosophila embryos, discussing considerations for fluorescent imaging within living embryos and providing protocols for generation of flies expressing fluorescently tagged proteins and for preparation of embryos for fluorescent imaging. The unit details time‐lapse confocal imaging of live embryos and discusses optimizing image acquisition and performing three‐dimensional imaging. Finally, the unit provides a variety of specific methods for optical highlighting of specific subsets of fluorescently tagged proteins and organelles in the embryo, including fluorescence recovery after photobleaching (FRAP), fluorescence loss in photobleaching (FLIP), and photoactivation techniques, permitting analysis of specific movements of fluorescently tagged proteins within cells. These protocols, together with the relative ease of generating transgenic animals and the ability to express tagged proteins in specific tissues or at specific developmental times, provide powerful means for examining in vivo behavior of any tagged protein in embryos in myriad mutant backgrounds. Curr. Protoc. Cell Biol. 39:4.18.1‐4.18.43. © 2008 by John Wiley & Sons, Inc.
Visualizing Protease Activity in Living Cells: From Two Dimensions to Four Dimensions
Authors: Jedeszko Christopher , Sameni Mansoureh , Olive Mary B. , Moin Kamiar , Sloane Bonnie F. 
Published: June 2008

AbstractProteolytic degradation of extracellular matrix (ECM) components by cells is an important metabolic activity as cells grow, remodel, and migrate through the ECM. The ability to analyze ECM degradation can be valuable in the study of developmental processes as well as pathologies, such as cancer. In this unit we describe an in vitro live cell–based method to image and quantitatively measure the degradation of ECM components by live cells. Cells are grown in the presence of fluorescent dye‐quenched protein substrates (DQ‐gelatin, DQ‐collagen I, and DQ‐collagen IV) that are mixed with protein matrices. Upon proteolytic cleavage, fluorescence is released that directly reflects the level of proteolysis by the cells. Using confocal microscopy and advanced imaging software, the fluorescence is detected and accurate measurements of proteolytic degradation in three and four dimensions can be assessed. Curr. Protoc. Cell Biol. 39:4.20.1‐4.20.15. © 2008 by John Wiley & Sons, Inc.
Visualization and Measurement of DNA Methyltransferase Activity in Living Cells
Authors: Schermelleh Lothar , Spada Fabio , Leonhardt Heinrich 
Published: June 2008

AbstractIn this unit, a live‐cell assay to measure DNA (cytosine‐5) methyltransferase (MTase) activity at the single‐cell level is described. This method takes advantage of the irreversible binding of enzymatically active MTases to genomic DNA substituted with the mechanism‐based inhibitor 5‐aza‐2′‐deoxycytidine (5‐aza‐dC). The procedure comprises incorporation of this nucleoside analog into DNA during replication and quantification of the time‐dependent MTase immobilization by fluorescence recovery after photobleaching (FRAP). This trapping assay monitors kinetic properties and activity‐dependent immobilization of MTases in their native environment and enables direct comparison of mutations and inhibitors that affect MTase regulation and catalytic activity in single living cells. In addition, a simplified protocol to obtain qualitative information on the activity of either endogenously or exogenously expressed MTases is provided. Curr. Protoc. Cell Biol. 39:22.12.1‐22.12.16. © 2008 by John Wiley & Sons, Inc.
Using ZINC to Acquire a Virtual Screening Library
Authors: Irwin John J. 
Published: June 2008

AbstractThe ZINC database of commercially available compounds contains biologically relevant representations of purchasable compounds in ready‐to‐screen formats. ZINC uses catalogs from over 50 compound vendors, changing from time to time to reflect newly available compounds and depleted stock. ZINC is available in subsets that reflect current opinion in the field such as “fragment‐like” and “lead‐like,” and has a facility to create additional small ad hoc subsets. ZINC has a search facility, as well as a service to process molecules that are not in ZINC by uploading them to a server. Curr. Protoc. Bioinform. 22:14.6.1–14.6.23. © 2008 by John Wiley & Sons, Inc.
The Catalytic Asymmetric
S
trecker Reaction
Authors: Shibasaki Masakatsu , Kanai Motomu , Mita Tsuyoshi 
Published: June 2008

Abstract
Alpha‐amino acids are important building blocks for proteins, peptides, and pharmaceuticals. Among a variety of methods to synthesize optically active alpha‐amino acids, the Strecker reaction is one of the simplest and most powerful. This reaction consists of three steps (1) condensation of an aldehyde or ketone with an amine to produce and imine, (2) nucleophilic attack of cyanide on the imine to produce and amino nitrile, and (3) hydrolysis of the amino nitrile to the corresponding alpha‐amino acid. These steps can be conducted in one pot. Conversion of the nitrile group to amide, amine, or aldehyde functionalities is also possible. The catalytic promotion and enantiocontrol of the cyanide addition to the imines is the main focus of the Strecker reaction. Therefore, isolated and purified imines are normally used as substrates. The catalyst turnover efficiency and enantioselectivity of this step are intimately related to the electronic and steric characteristics of the substrate imines, with nitrogen substituent greatly contributing to these factors. However, since optically active alpha‐amino acids are generally the synthetic target of the catalytic asymmetric Strecker reaction, the accessibilty of the starting imines and ease of final deprotection of the product are also important considerations. This chapter focuses on catalytic enantioselective Strecker and Reissert reactions.
Mass Spectrometry of Biological Molecules
Authors: Fuchs Beate , Arnold Klaus , Schiller Jürgen 
Published: June 2008

AbstractMass spectrometric methods may serve as powerful analytical methods in life sciences and medicine. Mass spectrometry (MS) is comparable in sensitivity to techniques based on chromatography or electrophoresis but has superior resolution. Although there are a number of suitable ionization methods, allowing the analysis of biological molecules that are of high molecular weight and low volatility, there are mainly two “soft‐ionization” techniques that confer only a minimum of degradation of the analyte: MALDI (matrix‐assisted laser desorption/ionization) and ESI (electrospray ionization).The following article provides a short overview on the advantages and drawbacks of MALDI analysis of biological samples. Whereas most applications of MALDI are in the field of protein analysis, the analyses of carbohydrates and lipids are also comprehensively discussed. It is shown that MALDI is a useful tool especially in the field of lipid analysis, whereas with carbohydrate analysis, still a number of problems have to be solved. MALDI is a rapid and very sensitive (from the low picomolar to the attomolar range) tool that tolerates high amounts of impurities (in contrast to ESI), which are typically present in biological samples. A further advantage is that mainly singly charged ions are formed; this enables MALDI to be applied even to the analysis of crude mixtures although ion yields may differ significantly in dependence on the molecules of interest. In comparison with ESI, MALDI detects compounds of higher molecular weights more sensitively, whereas ESI is more suitable for labile compounds. Therefore, the combination of both methods is, in many cases, the ideal solution for a number of analytical problems.
Quantitative Structure–Activity Relationships and Computational Methods in Drug Discovery
Authors: Balaban Alexandru T. 
Published: June 2008

AbstractQuantitative structure–activity relationships (QSARs) are mathematical equations or other types of functions (such as the weights of connections in artificial neural networks) relating chemical structures to their biological activity. The purpose of QSAR studies is to predict novel structures with either beneficial activity as drugs for human or veterinary medicine (bactericides, antiviral or anticancer drugs, and metabolic regulators, such as hypoglycemics, hypotensives, etc.), or selective toxicity for various unwanted higher organisms (pesticides such as fungicides, insecticides, acaricides, weed killers, etc.) Quantitative structure–property relationships (QSPRs) are similar, but the property may be physical or chemical. The main problems involvefinding a mathematical representation of chemical structures (usually organic molecules), represented either as molecular graphs by their constitution or connectivity without considering the three‐dimensional (3‐D) (stereochemical) factors, or as 3‐D objects including stereochemical information;measuring the biological activities of a series of molecules;finding the QSAR between each type of biological activity and the most convenient molecular descriptors.Physicochemical parameters that are closely related to drug transport and ligand binding include lipophilicity, polarity, polarizability, and electronic influence on hydrogen‐donor and hydrogen‐acceptor binding. The next task is to use the QSAR to predict which novel structures to prepare in order to obtain molecules with the desired biological activity. Then the cycle is usually repeated, because a single pass seldom affords the optimal solution.The main mathematical descriptors and the techniques for obtaining QSARs are reviewed. An important molecular parameter, which may be measured experimentally or computed from the chemical structure, is lipophilicity or hydrophobicity; Hansch introduced then‐octanol–water partition coefficient as a measure of this property, which, to a large extent, determines the ability of molecules to penetrate the lipophilic, bilayer, extra‐ or intracellular membranes. Lipophilicity levels that are too high lead to insolubility in water, i.e. it is difficult to administer the drug orally via the digestive tract. The main constitutional and 3‐D molecular descriptors are described and examples are given. To be statistically valid, correlations must involve orthogonal or orthogonalized descriptors. Linear, multilinear, and nonlinear types of correlations are reviewed. Screening of virtual combinatorial libraries together with high‐throughput combinatorial synthesis and testing provides modern tools for more efficient drug design.
Inductively Coupled Plasma‐Optical Emission Spectrometry
Authors: Hou Xiandeng , Jones Bradley T. 
Published: June 2008

Abstract
Inductively coupled plasma‐optical emission spectrometry (ICP‐OES) is a powerful tool for the determination of metals in a variety of different sample matrices. With this technique, liquid samples are injected into a radiofrequency (RF)‐induced argon plasma using one of a variety of nebulizers or sample introduction techniques. The sample mist reaching the plasma is quickly dried, vaporized, and energized through collisional excitation at high temperature. The atomic emission emanating from the plasma is viewed in either a radial or axial configuration, collected with a lens or mirror, and imaged onto the entrance slit of a wavelength selection device. Single element measurements can be performed cost‐effectively with a simple monochromator‐photomultiplier tube (PMT) combination, and simultaneous multielement determinations are performed for up to 70 elements with the combination of a polychromator and an array detector. The analytical performance of such systems is competitive with most other inorganic analysis techniques, especially with regard to sample throughput and sensitivity.
Cavity Ringdown Laser Absorption Spectroscopy
Authors: Wang Chuji , Miller George P. , Winstead Christopher B. 
Published: June 2008

AbstractCavity ringdown spectroscopy (CRDS) has developed rapidly during the last two decades and has been implemented for a variety of applications ranging from fundamental spectroscopic studies, trace chemical detection for environmental monitoring, combustion flame chemistry and plasma diagnostics, elemental and isotopic measurements, breath gas analysis, and fiber ringdown chemical and physical sensor development. A host of chemical species, including atoms, ions, molecules, clusters, and free radicals, have been studied by CRDS. The experimental ringdown scheme has also evolved from an original mirror‐based format to various new forms for detection and analysis of analytes in either gas phase or liquid solutions. Recent research effort has also extended the CRDS approach for fiber optical sensor development. CRDS has become a mature spectrometric technique for a range of prototype and commercial instrumentation. This article provides a review of the latest developments in CRDS applications, specifically emphasizing new trends in elemental and isotopic analysis, plasma diagnostics, breath gas analysis, and new fiber ringdown techniques for sensor development. The introduction of cutting‐edge laser sources into CRDS methods, the combination of CRDS with conventional analytical tools, and current CRDS instrumentation are also briefly discussed.
Multidimensional Nuclear Magnetic Resonance of Biomolecules
Authors: Craik David J. , Horne James , Scanlon Martin J. 
Published: June 2008

AbstractNuclear magnetic resonance (NMR) is associated with transitions, induced by radiofrequency (RF) irradiation, between energy levels of nuclei with nonzero spin quantum numbers in a magnetic field. Traditional “one‐dimensional” (1‐D) NMR spectra are presented as a plot of signal intensity versus applied frequency and provide information about the chemical environment of magnetically active nuclei. This is used to deduce information about the chemical structure and dynamics of molecules containing the magnetically active nuclei (most often protons). The frequencies of individual nuclei are referred to as their chemical shifts. Multidimensional NMR encompasses a range of related techniques, based on the application of a variety of precisely timed RF pulses to the sample, which extends traditional 1‐D NMR into two‐, three‐, or four‐frequency dimensions. These additional frequency dimensions may be the same as the first frequency dimension, referred to as homonuclear multidimensional NMR, or different, referred to as heteronuclear NMR. In multidimensional NMR of biomolecules, the most common frequencies correspond to1Hin the directly detected dimension and one or more of1H,13C, or15Nin the additional dimensions. Peaks in such spectra are defined by their intensity and frequency coordinates in two, three, or four dimensions obtained by extrapolation back to the respective frequency axes, which are in turn determined by the nature of the applied RF pulse sequences. The intensity and chemical shifts of such peaks provide information about the chemical environment, molecular connectivity, or spatial proximity of the participating nuclei. Multidimensional NMR has major advantages over 1‐D NMR: reduction of peak overlap and provision of information on connectivity (either through bonds or through space). Multidimensional NMR spectroscopy of biomolecules is usually done for samples in solution at millimolar concentration. Where experiments require the use of13Cor15Nfrequencies, it is usually necessary to isotopically enrich the macromolecule with these nuclei to >90%. This is readily achieved with modern molecular biology techniques and does not present a major limitation. The biggest limitation relates to molecular size, with studies generally limited to macromolecules of less than approximately 35 kDa.
Discrete Event Systems: Untimed Models and their Analysis
Authors: Lafortune Stéphane 
Published: June 2008

AbstractThis article introduces the class of dynamic systems known as discrete event systems, which are characterized by event‐driven transitions over a discrete set of states. The modeling formalism of automata is employed, and their language properties characterized. Parallel composition of automata is defined. Analysis of logical properties of discrete event systems modeled by automata is discussed, with a special focus on partially observed systems and event diagnosis using diagnoser automata.
Geometric Programming
Authors: Jefferson T. R. , Scott C. H. 
Published: June 2008

AbstractSince its initial appearance more than four decades ago, geometric programming has proved itself to be a powerful means of solving many optimization problems, particularly those that pertain to engineering design. The theory has been generalized to provide a structure for the analysis of any convex programming problem. Here we trace the development of geometric programming from its initial use as a trick for solving certain cost‐optimization problems to its current status as a fully fledged branch of optimization theory. Examples drawn from inventory theory and engineering reinforce and motivate this development.
Radiometric Camera Calibration
Authors: Hamey Leonard G.C. 
Published: June 2008

AbstractRadiometric calibration is a method of capturing digital images and processing the digital image data so that the pixel values represent actual measurements of light. Radiometric camera calibration converts ordinary digital images into radiometric images. Absolute radiometric calibration means that the image pixels are calibrated with reference to physical units such as watts per steradian per square meter (W.sr−1.m−2) or photon counts. Relative radiometric calibration means that the image pixels are calibrated with reference to each other — the ratio of two image pixels is the same as the ratio of the corresponding physical measurements of light. Radiometric calibration, both absolute and relative, has a wide range of applications in science and technology, including astronomy, remote sensing, and machine vision. Methods for radiometric calibration typically involve up to four steps. First, the camera response is corrected to be linear. Second, the camera's black response is subtracted. Third, corrections are applied for spatial variations in the effective aperture of the lens and the sensor sensitivity. This correction yields a relative radiometric calibration. A final step converts the relative calibration to absolute calibration by applying an appropriate scaling factor. This article first explains the basis of radiometric calibration — the additive property of light and the formation of digital images. Techniques for radiometric calibration are then explained, focusing on the four steps of estimating the camera response function, measuring the black response, correcting for vignetting and sensitivity, and using calibration targets. Finally, applications of radiometric imaging are discussed briefly.
Longitudinal Data
Authors: Li Hung‐Ir 
Published: June 2008

AbstractLongitudinal data have been the focus in various research such as economy, social science, public health, and biomedical research in the past few decades. These data comprise outcome measures or responses prospectively collected or naturally accrued repeatedly from the same subjects across multiple time points along with subject characteristic measures. In some observational studies in epidemiology/public heath, the data accrued over a long period of time as recorded in medical charts and are retrospectively retrieved. The data are used to answer questions regarding the change or progression of the disease over time and/or potential risk factors for the disease. Although in other studies, the existing data could be used to identify subgroups with different background characteristics or traits. The identified groups are then followed up for their health conditions for a certain period of time prospectively. The data from these groups are then compared with answer questions set out for the studies. In the clinical research and development settings, most of the longitudinal data are collected via prospectively designed clinical trials in order to assess the changes in efficacy and/or safety of certain medical intervention, drug, biologics, or devices. The longitudinal data from clinical trials in phase III of product development are intended to confirm that the clinical benefit or desired changes over time are primarily due to the target product, can be maintained for an adequate amount of time, and are applicable to a well‐defined population before regulatory approval is granted and the product is registered for public use. This article provides a summary of the definitions, features, and various types of longitudinal data resulting from clinical trials in phase III medicinal product development. The respective characteristics and the related issues along with the rules of thumb in the selection of the statistical methods for the analyses will also be provided.