bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying Mutations for MYH‐Associated Polyposis
Authors: Prior Thomas W. , Bridgeman Scott J. 
Published: January 2010

AbstractPolyposis associated with mutations in the gene MYH is an autosomal recessive syndrome characterized by the development of colorectal adenomas and cancer. Two common mutations, p.Tyr165Cys (exon 7) and p.Glu382Asp (exon 13), have been shown to account for the majority of the mutations occurring in individuals of Caucasian ancestry. Other mutations have been found throughout the gene and many have been shown to have very low frequencies. Ethnic differences in the mutation spectrum have also been observed. Thus, in order to achieve the highest clinical sensitivity, it is necessary to perform whole‐gene sequencing of the MYH gene. The sequencing protocol described allows one to identify mutations throughout the MYH gene. Curr. Protoc. Hum. Genet. 64:10.13.1‐10.13.14. © 2010 by John Wiley & Sons, Inc.
Acylcarnitine Analysis by Tandem Mass Spectrometry
Authors: Smith Emily H. , Matern Dietrich 
Published: January 2010

AbstractCarnitine plays an essential role in fatty acid metabolism, as well as modulation of intracellular concentrations of free coenzyme A by esterification of acyl residues. Acylcarnitine analysis of various biological fluids is a sensitive method to detect >20 inborn errors of metabolism that result in abnormal accumulation of acylcarnitine species due to several organic acidemias and most fatty acid β‐oxidation disorders. In addition, acylcarnitine analysis may aid in monitoring treatment of known patients affected with these inborn errors of metabolism. This unit describes protocols that can be used to measure acylcarnitine species of various carbon chain lengths in several biological specimen types including plasma, dried blood and bile spots, and urine, by derivatization to butylesters and flow‐injection electrospray ionization tandem mass spectrometry (ESI‐MS/MS). Curr. Protoc. Hum. Genet. 64:17.8.1‐17.8.20. © 2010 by John Wiley & Sons, Inc.
Atomic Spectrometry and Elemental Analysis
Authors: Welz Bernhard , Borges Daniel L.G. 
Published: January 2010

AbstractThis chapter starts with an introduction to the early history of spectroscopic investigations in the nineteenth century, followed by general considerations about atomic spectra and interferences that might be encountered. This chapter discusses optical atomic spectroscopy with its three main techniques, optical emission spectrometry (OES), atomic absorption spectrometry (AAS) and atomic fluorescence spectrometry (AFS), as well as X‐Ray spectroscopy, also including X‐ray emission, absorption, and fluorescence. The section on optical atomic spectroscopy begins with the basic principles of this technique, followed by a description of the physics of atomization and excitation, atomic spectra and spectral lines, and the measurement of radiation, calibration, and evaluation. The section on OES covers excitation sources, including arc and spark sources, glow discharges and inductively coupled plasmas, as well as lasers, which are being used increasingly in laser‐induced breakdown spectroscopy (LIBS). The section on spectrometers deals with mono‐ and polychromators, including the detectors used in this kind of equipment. The section on AAS includes a discussion on the atomizers used for this technique, mainly flames and graphite furnaces, and also on chemical vapor generation techniques, such as cold vapor and hydride generation. Radiation sources and spectrometers for line source AAS as well as those for high‐resolution continuum‐source AAS are described, with a detailed discussion on the new potentialities of the latter technique. The general principles and the instrumentation of AFS are discussed briefly, according to the limited application of this technique, which includes the use of laser‐excited AFS. The section on X‐ray spectroscopy provides the theoretical principles behind the emission and absorption of X‐rays, in particular, X‐ray fluorescence (XRF), using different kind of equipment, that is, wavelength‐dispersive and energy‐dispersive instrumentation. Total‐reflection XRF is discussed as also particle‐induced X‐ray emission (PIXE) and portable instrumentation. The chapter concludes with an outlook on the potential future development in the field of atomic spectroscopy and elemental analysis.
Neutron Spectroscopy
Authors: Anton Heidemann 
Published: January 2010

AbstractThermal and cold neutrons have wavelengths of a few angstroms (1 Å =10−10 m) and energies of the order of a few millielectronvolts. They are electrically neutral. Neutron scattering is therefore a powerful tool for the investigation of condensed matter on a microscopic scale. After an introduction to the field of neutron scattering and a short outline of its theoretical foundations, we mention the two main domains in neutron scattering without and with energy analysis. The latter, calledneutron spectroscopy,is presented in more detail. The different types of experimental techniques, such as three‐axis, time‐of‐flight, back‐scattering, and neutron spin echo spectroscopy, are described. An overview of the different types of applications of neutron spectroscopy is given, together with some typical examples.
Linear Laser Spectroscopies
Authors: Ashworth Stephen H. 
Published: January 2010

Abstract
Laser spectroscopies have developed along with the lasers used as light sources and may be applied in diverse situations. Techniques and approaches that generally involve a linear response to laser radiation are covered. These are divided broadly into direct and proxy techniques. The former detects the absorption of radiation directly, whereas the latter detects a side effect of absorption such as fluorescence or heating. A selection of the methods outlined are cavity ring‐down spectroscopy and its variants, laser‐induced fluorescence, photoacoustic spectroscopy, and some double‐resonance techniques. The range of topics covered is not intended to be exhaustive and the selection probably indicates the direct experience of the author.
Ultrafast Spectroscopy
Authors: Kühn Oliver , Lochbrunner Stefan 
Published: January 2010

Abstract
This chapter introduces the concepts, theoretical approaches, and experimental techniques of ultrafast spectroscopy. By pushing the time resolution to a few femtoseconds the observation of atomic and molecular motions in real time becomes possible. This is illustrated by means of applications including molecular dynamics from isolated diatomics via clusters to biomolecules as well as processes in semiconductors and at surfaces. Perspectives are given on the emerging fields of attosecond physics and time‐resolved diffraction techniques.
Raman Scattering for Speciation and Analysis
Authors: Esmonde‐White Karen , Raghavan Mekhala , Morris Michael 
Published: January 2010

AbstractThe article contains sections titled:IntroductionRaman Spectroscopy BasicsTheoryEnhancementSubsurface Measurements — Spatially OffsetRaman Spectroscopy (SORS)InstrumentationLaser SafetyBasic InstrumentationFiber Optic ProbesMicroprobesData ReductionIdentification and Quantification of Inorganic MaterialsIntroductionMineralsArt, Archaeology, and ArchitectureForensicsNanoscale SemiconductorsIndustrial Process ControlIdentification and Quantification of Organic MaterialsPharmaceutical ApplicationsPolymer Chemistry and PhysicsForensic and Homeland Security ApplicationsBiological Applications ofRaman SpectroscopySubcellular LevelTissue LevelEpithelial TissueMuscular TissueNervous TissueConnective TissueMicroorganisms
Mössbauer Spectroscopy
Authors: Yang De‐Ping 
Published: January 2010

AbstractMössbauer spectroscopy is a unique technique based on nuclear resonance via recoil‐free emission, absorption, and scattering of γ‐rays. Because of its extremely high energy resolution and its particular timescale, a Mössbauer spectrum can provide valuable information on structural, chemical, magnetic, and dynamical properties of a variety of solid materials. Mössbauer spectroscopy finds applications in various fields of scientific research, such as physics, metallurgy, materials science, chemistry, mineralogy, biology, medicine, environmental science, archeology, and art.Mössbauer effect has been observed in about 100 isotopes.57Fe is by far the most important one, followed by119Sn. A typical Mössbauer spectrometer operates in the transmission geometry where the γ‐rays emitted from the source and modulated via Doppler effect are resonantly absorbed in a solid sample. The amount of transmitted γ‐rays is recorded and analyzed as a function of γ‐photon energy, resulting in a Mössbauer spectrum. The shape, location, and intensity of the absorption peaks in a Mössbauer spectrum can reveal hyperfine interactions between the Mössbauer isotope and its surroundings, and therefore provide information on the chemical, magnetic, and structural properties of the material under investigation.The emission, absorption, and scattering of γ‐rays may also involve the creation or annihilation of phonons. This process is intricately related to lattice dynamics and strongly dependent on temperature. Therefore, Mössbauer spectroscopy can be used for studying lattice vibrations and phonon density of states, as well as their dependence on temperature, pressure, crystallinity, impurity, and so on.As synchrotron radiation became available, new elastic and inelastic scattering methods have been developed. The emergence of time‐domain Mössbauer spectroscopy has provided not only evidence for the coherent decay of nuclear excitons but also a new methodology for extracting parameters of hyperfine interactions and lattice dynamics.
Ultraviolet and Visible Absorption Spectrometers
Authors: Lipson Robert H. 
Published: January 2010

Abstract
An overview of spectroscopy fundamentals for atoms and molecules is provided as they pertain to the ultraviolet (UV) and visible spectral regions. Topics include state labels, electronic selection rules, the Born–Oppenheimer approximation, and the Franck–Condon principle. The Beer–Lambert law, chemometrics, derivative spectroscopy, and circular dichroism spectroscopy are explained as are the origins of UV/visible transitions in organic and inorganic compounds as well as solids. Relevant experimental methods and instrumentation such as light sources, monochromators, and detectors, which can be used to record UV/visible absorption spectra, are described. A brief discussion on laser‐based techniques, including fluorescence excitation spectroscopy, excitation spectroscopy with mass detection, and cavity ring‐down spectroscopy, is also given.
Molecular Fluorescence
Authors: Valeur Bernard 
Published: January 2010

AbstractFluorescence is extensively used as a tool of investigation in physical, chemical, material, biological, and medical sciences. The description of the characteristics of fluorescence emission is followed by a discussion on the effects of intermolecular photophysical processes. The last part of the chapter is devoted to the applications of fluorescence: estimation of local physical parameters, chemical sensing, tracers in biology, clinical diagnostics, fluorescence LIDAR (light detection and ranging), food science, forensics and counterfeit detection.
Surface Second Harmonic and Sum‐Frequency Generation
Authors: Iwamoto Mitsumasa , Manaka Takaaki , Lim Eunju 
Published: January 2010

Abstract
The use of optical second harmonic generation (SHG) measurement of the exploration of dielectric polarization and related surface phenomena is described. Paying attention to the specific nature of material systems on the surface, orientational order parameters are introduced to characterize surface layers, and the SHG enhancement is described in terms of the order parameters. Also the sum‐frequency generation (SFG) and electric‐field‐induced SHG(EFISHG) are described as a tool of probing carrier motions in surface layers. The experimental system is shown with some results.
Antibody, Purification: Monoclonal (MAB) and Polyclonal
Authors: Reilly James J. , Ultee Michiel E. 
Published: January 2010

AbstractThe purification of antibodies relies both on the specialized properties of this class of homologous proteins as well as more typical properties of proteins, in general. Typically, the antibody is isolated from the crude feedstock using an affinity chromatographic step, usually one exploiting the highly specific and potent binding interaction betweenimmunoglobulin G(IgG) antibodies and Protein A or G. Following this initial capture of the antibody, the partially purified antibody is further polished using ion exchange, hydrophobic interaction, or hydroxyapatite chromatographic methods. New specialized methods have recently been developed using mixed‐mode chromatographic methods that combine two modalities of purification in one step. Other advances have come from the development of membrane supports that offer much higher throughput than conventional resin‐based chromatography. This review also addresses purification of IgM antibodies, whose large size and tendency to precipitate present additional challenges. Finally, we note that the structural similarity of IgG antibodies presents an opportunity for platform or generic processes and describe the advantages of such an approach.
Biocers, Industrial Applications
Authors: Coradin Thibaud , Amoura Makhlouf , Roux Cécile , Livage Jacques 
Published: January 2010

AbstractAfter 20 years of research, the inorganic sol–gel process can now be considered as a suitable technological alternative for the encapsulation of living cells. Strategies have been developed and optimized that allow the formation of glasses and ceramics in conditions compatible with the preservation of cell membrane integrity and metabolic activity over several weeks. These biocer(amic)s can be prepared as gels, coatings, films, and capsules, which can host a wide variety of organisms including bacteria, protists, yeasts, and plant and animal cells. It was demonstrated that biocers can be used for the design of bioreactors, biosensors, as well as for bioremediation systems, at least at the laboratory scale. Moreover, hybrid materials associating biopolymers and silica were shown to be suitable for the elaboration of bioartificial organs that have been patented and are currently under clinical evaluation. The biocer technology has now reached its maturity, suggesting that industrial developments can now be foreseen in the near future.
Cell Cycle, Importance in Bioprocesses
Authors: Naciri Mariam , Al‐Rubeai Mohamed 
Published: January 2010

AbstractThe cell cycle is the name given to the process by which a cell matures, synthesizes DNA, and divides to form daughter cells. Thus the cell cycle is a fundamental process with analogous mechanisms found in all cells, from the most primitive bacterium to higher animals and plants, from the unicellular to the most complex multicellular organism. It is regulated by several ordered and directional molecular events and controlled by an elaborate system that if altered could result in physiological damage and cell death (1). Here we describe the mammalian cell cycle, highlight its importance in biotechnology, and describe some cell cycle applications in animal cell biotechnology.
Cell Separation: Yeast Flocculation
Authors: Soares Eduardo V. 
Published: January 2010

AbstractYeast flocculation is a process wherein cells are gathered together into multicellular masses, calledflocs.Due to their mass, yeast flocs sediment rapidly from the medium in which they are suspended. Flocculation is an easy, off‐cost and eco‐friendly process of cell separation that reduces the costs of equipment and energy demand associated with cell separation. Yeast flocculation can be seen as a self‐immobilization process; in this way, flocculent yeasts can be used in high cell density reactors and increase the efficiency of the fermentation process. These advantages fit quite well with the idea of “White” Biotechnology, which advises the optimization of the processes and reduction of energy consumption in order to contribute to a more sustainable future. Yeast flocculation is a complex phenomenon, influenced by multiple factors. This review discusses and updates the current knowledge on the flocculation ofSaccharomyces cerevisiae. The expression of several genes (such asFLO1,FLO5,FLO8, andLg‐FLO1), the cell surface characteristics, the chemical characteristics of the medium (such as pH and the presence of bivalent ions) and the fermentation conditions (oxygen, sugars availability, growth temperature, and ethanol concentration) that affect yeast flocculation are outlined. In addition, the present knowledge about the molecular mechanism of flocculation inS. cerevisiae, as well as the different phenotypes [Flo1, NewFlo,mannose insensitive(MI) phenotype and strains that only flocculate in the presence of ethanol] is presented. This review highlights the advantages of yeast flocculation when compared with yeast immobilization and other cell separation processes. In the last part of the work, the advantages and importance of flocculation in many industrial processes (such as in the production of wine, bio‐ethanol, heterologous proteins, and particularly in the brewing industry) and environmental applications is reviewed and critically discussed.
Fluorescence Spectroscopy
Authors: Lee Claudia Y. 
Published: January 2010

AbstractFluorescence is an extremely powerful tool in modern biology, physics, and chemistry laboratories. This unit focuses on methods that can be applied to biological studies. Starting with the preparation of fluorescently conjugated antibodies, the first part explains the physical principles of fluorescence and the features in an absorption spectrum, and how these are used to measure the degree of labeling on conjugated antibodies. The protocols describe how to obtain and interpret a fluorescence emission spectrum and utilize this information as a fluorescence indicator for protein detection. Curr. Protoc. Essential Lab. Tech. 2:2.4.1‐2.4.29. © 2009 by John Wiley & Sons, Inc.
Mass Spectrometry: An Outsourcing Guide
Authors: DeSouza Leroi V. , Siu K.W. Michael , Pearlman Ronald E. 
Published: January 2010

AbstractProteomics is the study of the proteins expressed from the genome of a cell or organism. Analytical mass spectrometry has recently become a powerful tool to study a cell or organism's proteome and is the focus of this chapter. Mass spectrometry can be used for both qualitative and quantitative analysis of proteomes. This chapter will focus on qualitative analysis, addressing questions of what proteins are present in a proteome and what post‐translational modifications may be associated with these proteins. The instrumentation required for mass spectrometric analysis is generally not available in a standard research laboratory or as part of an undergraduate laboratory, being associated in general with a core facility. We will not describe here details of specific operation of the instruments. Here we focus on the common types of analysis presently in routine use and on preparation of samples for routine biological mass spectrometric analysis that will allow most laboratories, including undergraduate and graduate teaching laboratories, to prepare and analyze samples in experiments designed to obtain proteomic information. Curr. Protoc. Essential Lab. Tech. 2:12.2.1‐12.1.18. © 2009 by John Wiley & Sons, Inc.
FBN1 mutations in patients with descending thoracic aortic dissections
Authors: Brautbar Ariel , LeMaire Scott A. , Franco Luis M. , Coselli Joseph S. , Milewicz Dianna M. , Belmont John W. 
Published: January 2010

AbstractAortic aneurysm and dissection cause significant morbidity and mortality. There are several known single gene disorders that predispose to isolated aortic disease and eventually aneurysm and dissection. FBN1 mutations are associated with multiple clinical phenotypes, including Marfan syndrome (MFS), MASS phenotype, and familial ectopia lentis, but rarely with isolated aortic aneurysm and dissection. In this report, we describe three patients who presented with primary descending thoracic aortic dissection and who were found to have an FBN1 mutation. None of the patients fulfilled clinical criteria for the diagnosis of MFS, and all had few or none of the skeletal features typical of the condition. Two patients had a history of long‐term hypertension, and such a history was suspected in the third patient. These observations suggest that some individuals with FBN1 mutations have significant aortic disease involvement of other systems that is typical of FBN1 mutation‐related syndromes. Superimposed risk factors, such as hypertension, may weaken the aortic wall and eventually lead to aortic dissection. Given that the cost continues to decrease, we suggest that diagnostic DNA sequencing for FBN1 mutations in patients with thoracic aortic aneurysms and dissection may be a practical clinical step in evaluating such patients and at‐risk family members. © 2010 Wiley‐Liss, Inc.
Birth incidence and prevalence of tumor‐prone syndromes: Estimates from a UK family genetic register service
Authors: Evans D.G. , Howard E. , Giblin C. , Clancy T. , Spencer H. , Huson S.M. , Lalloo F. 
Published: January 2010

AbstractAutosomal dominantly inherited tumor‐prone syndromes are a substantial health problem and are amenable to epidemiologic studies by combining cancer surveillance registries with a genetic register (GR)‐based approach. Knowledge of the frequency of the conditions provides a basis for appropriate health‐resources allocations. GRs for five tumor‐prone syndromes were established in the Manchester region of North West England in 1989 and 1990. Mapping birth dates of affected individuals from families onto regional birth rates has allowed an estimate of birth incidence, disease prevalence, and de novo mutation rates. Disease prevalence in order of frequency were for neurofibromatosis type 1 (NF1): 1 in 4,560; familial adenomatous polyposis (FAP): 1 in 18,976; nevoid basal cell carcinoma [Gorlin syndrome (GS)]: 1 in 30,827; neurofibromatosis type 2 (NF2) 1 in 56,161; and von Hippel Lindau (VHL) 1 in 91,111. Best estimates for birth incidence were: 1 in 2,699; 1 in 8,619; 1 in 14,963, 1 in 33,000; and 1 in 42,987, respectively. The proportions due to de novo mutation were: 42% (NF1); 16% (FAP); 26% (GS); 56% (NF2); and 21% (VHL). Estimates for NF1, NF2, FAP, and VHL are in line with previous estimates, and we provide the first estimates of birth incidence and de novo mutation rate for GS. © 2010 Wiley‐Liss, Inc.
High frequency of multiexonic deletion of the GCH1 gene in a Taiwanese cohort of dopa‐response dystonia
Authors: Wu‐Chou Yah‐Huei , Yeh Tu‐Hsueh , Wang Chuan‐Yu , Lin Juei‐Jueng , Huang Chin‐Chang , Chang Hsiu‐Chen , Lai Szu‐Chia , Chen Rou‐Shayn , Weng Yi‐Hsin , Huang Chia‐Ling , Lu Chin‐Song 
Published: January 2010

AbstractLarge deletions in the GCH1 gene have been reported in a minority of cases of dopa‐responsive dystonia (DRD). In this study, we performed an extensive clinical and genetic investigation of 22 affected members in eight families. Sequence analysis revealed five different mutations in five families (n = 10); Ser81Pro (novel), Ser76X, Gly203Arg, 249del A, and IVS5 + 3insT. Applying multiple ligation‐dependent probe amplification analysis, we detected a large heterozygous deletion of exons 1–3 in the remaining three families (n = 12), which was verified by quantitative real‐time PCR analysis. Therefore, the large deletion accounted for 37.5% of the total families and 55% of our DRD population. The deletion appeared to have high penetrance and was associated with multifocal dystonia and adult onset in males. Adult‐onset patients were commonly presenting with resting tremor, rigidity, and bradykinesia, indistinguishable from those in Parkinson's disease. In conclusion, a high frequency of multiexonic deletion of GCH1 was identified in the Taiwanese DRD population. By dosage analysis, we were able to detect a mutation in all patients. Our study demonstrates that dosage analysis is necessary for molecular diagnostics in DRD patients of Han Chinese ethnicity. © 2010 Wiley‐Liss, Inc.