bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial genome organization: comparative expression profiling, operons, regulons, and beyond
Authors: Peterson Scott N. 
Published: July 2005

AbstractThe sequencing of complete microbial genomes has provided a molecular basis for the diversity of bacterial species. Bacterial gene expression in response to environmental stimuli may be equally diverse and raises the question as to how well what we learn about gene expression in one species translates to another. A problem common to all scientists performing global gene expression lies in determining the significance of gene expression changes as they relate to the functional requirements of the encoded proteins in the biological process under investigation. Four recent studies are presented that highlight some of the issues that confound direct interpretation of gene expression data, including operon structure, functional redundancy of proteins, and the occurrence of nonorthologous genes in bacteria. The concept of comparative expression profiling (CEP) is introduced and discussed in the context of the experimental results observed.
Tissue microarrays
Authors: Simon Ronald , Mirlacher Martina , Sauter Guido 
Published: July 2005

AbstractTissue microarrays (TMAs) allow for simultaneous analysis of thousands of well‐characterized tissues and have, therefore, become a standard research tool for tissue‐based studies. All types of in situ analysis can be applied to tissue microarrays, including immunohistochemistry, fluorescence in situ hybridization, and RNA in situ hybridization. The TMA technology thus enables highly standardized, fast, and affordable translational research studies of unprecedented scale that substantially facilitate translational research.
Separation‐dependent approaches for protein expression profiling
Authors: Dunn Michael J. , Pennington Stephen R. 
Published: July 2005

Abstract
The depth and breadth of genomic data now available for a wide variety of prokaryotic and eukaryotic organisms provides a previously unimagined opportunity to perform comprehensive profiling studies of patterns of protein expression in complex biological systems that will result in new insights into cellular functions that determine biologically relevant phenotypes. In this chapter, we give an introduction to protein expression profiling in which the individual proteins in a complex sample are separated prior to semiquantitative analysis. We outline the alternative approaches based either on the use of one‐ and two‐dimensional gel electrophoresis or on the application of so‐called gel‐free methods based on the use of liquid chromatography coupled either on‐ or off‐line to mass spectrometry.
Protein arrays
Authors: Murphy Derek , Cahill Dolores J. 
Published: July 2005

Abstract
Protein array technology is becoming an increasingly important tool in the drive toward proteome‐scale analysis of protein activity and interactions. Presently, this technology compliments the more traditional methods for proteomic analysis, including two‐dimensional gel electrophoresis/chromatography and mass spectrometry. While the task of producing a “whole‐proteome” chip, containing active proteins, is a daunting one, current protein and antibody arrays represent the first steps toward that goal. In this review, we discuss current approaches for the generation of protein arrays, and their applications, including their use in the study of protein–protein, protein–nucleic acid, enzyme–substrate, and so on, interactions. Potential applications of protein arrays in interaction screening, such as compound–protein interactions are also discussed.
Quantum dots for multiparameter measurements
Authors: Bruchez Marcel P. 
Published: July 2005

Abstract
Quantum dot materials have emerged as powerful alternatives to conventional fluorescent molecules. Their optical properties are perfectly suited to the information‐intensive requirements of modern molecular and cellular biology assays, and have enabled a number of new ways of investigating cellular systems. Multicolor labeling with quantum dots allows collection of information on location, distribution, and abundance of multiple proteins in cellular and blot‐based systems with ratio‐based quantitation. The brightness and photostability of these materials provide researchers the means to investigate protein dynamics and changes in cellular and animal models over physiologically relevant timescales, and in situations where organic fluorescence probes fail. The spectral properties can be used effectively to extend the capability of multiplexed assays using multicolor beads as assay supports that are easily decoded to provide quantitative information on nucleic acids and proteins. A variety of researchers exploit these properties to open new avenues for biological investigation of the action and interactions of many molecules simultaneously.
Imaging protein function using fluorescence lifetime imaging microscopy (
FLIM
)
Authors: Gu Yan , Zicha Daniel 
Published: July 2005

Abstract
Fluorescence lifetime has been used in various protein function studies in both fixed and living cells, including contrast enhancement, colocalization, and interactions. In this review, current FLIM (fluorescence lifetime imaging microscopy) technologies and data processing methodologies are briefly summarized. Special attention is paid to the lifetime retrieval of multicomponent complexes, where the combination of confocal‐based time‐domain FLIM with spectral unmixing technique can provide more accurate estimation. Typical examples of protein function interpretations using FLIM are also discussed.
Glycosylation
Authors: Cummings Richard D. 
Published: July 2005

Abstract
Glycosylation is an enzymatic process in which sugars are added to other molecules to produce a glycosylated product. The major classes of enzymes that catalyze the process of glycosylation are transferases that use sugar nucleotide and lipid‐linked sugar donors. Examples of the products of glycosylation reactions are glycoproteins, glycolipids, glycosaminoglycans, oligosaccharides, and polysaccharides. Glycosylation reactions occur in all animals, plants, fungi, and microorganisms. In animals, glycosylation reactions occur mainly in the cytoplasm, endoplasmic reticulum, Golgi apparatus, and the plasma membrane. Glycans are important in many aspects of cellular and developmental regulation, and defects in glycosylation in humans and animals result in developmental abnormalities and embryonic death. Glycosylation is a common and essential process in all organisms.
Large complexes by
X
‐ray methods
Authors: Nissen Poul 
Published: July 2005

Abstract
The atomic structures of large complexes such as ribosomes and viruses can be solved by X‐ray crystallography. The purification and crystallization, together with data collection and crystallographic phasing, all present unusual problems compared to ordinary high‐throughput crystallography. Yet, several examples show how these obstacles can be solved.
Microbial sequence assembly
Authors: Weinstock George 
Published: July 2005

Abstract
Microbial genomes are assembled by the whole‐genome shotgun method, where random sequencing is performed to high redundancy and the sequencing reads are assembled en masse. Although the early microbial genome projects relied on a large insert clone tiling path and a clone‐by‐clone sequencing approach, current assembly software makes it possible to overcome challenges posed by repeated sequences and perform whole‐genome shotgun assemblies.
Errors in sequence assembly and corrections
Authors: Tammi Martti T. , Andersson Björn 
Published: July 2005

Abstract
The shotgun sequencing method is the most economical and easily automated sequencing technique and has thus become the method of choice. Computer software is used to put the pieces together very much like a jigsaw puzzle, but they can usually only produce a good estimate of a correct assembly, and extensive manual finishing is needed to generate the final sequence.
Pair hidden
M
arkov models
Authors: Alexandersson Marina , Bray Nicolas , Pachter Lior 
Published: July 2005

Abstract
We describe pair hidden Markov models, with an emphasis on their relationship to evolutionary models and hidden Markov models. We then explain the statistical interpretation of alignment with pair hidden Markov models, and highlight connections to the Needleman–Wunsch algorithm and other dynamic programming–based alignment algorithms.
Exonic splicing enhancers and exonic splicing silencers
Authors: Mount Stephen M. 
Published: July 2005

Abstract
Splicing signals that promote splicing and lie within exons are known as exonic splicing enhancers (ESEs), while signals within exons that repress splicing are known as exonic splicing silencers (ESSs). Both ESEs and ESSs act in conjunction with more highly conserved splicing signals at the two splice sites. ESEs are bound and activated by splicing factors known as SR proteins that are thought to act by recruiting core splicing factors such as the U1 snRNP or U2AF to appropriate splice sites. The mechanism of action of ESSs is less well understood and may be more variable. A variety of methods, both experimental and computational, have been used successfully to identify functional ESEs and ESSs; mutations in these splicing signals are increasingly recognized as responsible for human genetic disease.
Gene finding using multiple related species: a classification approach
Authors: Kellis Manolis 
Published: July 2005

AbstractThree years after the initial sequencing of the human genome, the actual number of functional human genes remains uncertain. Several expression‐based analyses still argue for a hundred thousand transcribed genes, whereas more conservative estimates range between 20 000 and 25 000 genes. The central question in such debates still remains: what constitutes arealgene? In this paper, we address this question and present a comparative genomics approach for systematic gene identification, which observes gene‐specific signatures of evolutionary selection across multiple related species. First, we formulate the gene identification problem as a classification problem between genes and noncoding regions, on the basis of their distinct patterns of nucleotide change. We then summarize the results of applying this approach to reannotate the yeast genome, with changes affecting nearly 15% of all genes, and the rejection of more than 500 previously annotated genes. Finally, we discuss the implications of this analysis on understanding the human genome, and strategies for the systematic reannotation of higher eukaryotes.
Protein domains in eukaryotic signal transduction systems
Authors: Hofmann Kay 
Published: July 2005

Abstract
Eukaryotic proteins involved in signal transduction processes are frequently characterized by a modular architecture. These modules, also known as functional domains, are able to fold independently from the rest of the molecule. Typically, they also fulfill particular unit functions that can be separated from each other. Eukaryotic cells must respond to a large array of biological stimuli, and evolution has invented a sophisticated signal transduction network consisting of many different components to cope with the situation. Despite that complexity, the analysis of signaling proteins on the level of functional domains reveals a number of recurrent motifs. For most signaling systems, the unit functions of signal generation, signal detection, and signal destruction are carried out by classes of dedicated functional domains. While the similarity within those classes reflects a similar signaling mechanism, the required specificity is either conferred by the subtle differences between the class members or by highly specific targeting domains. Key examples for highly modularized signal transduction systems include protein phosphorylation or ubiquitination, GTPase signaling, and the multiadaptor mechanism of apoptosis signaling.
Large‐scale protein annotation
Authors: Kummerfeld Sarah K. 
Published: July 2005

Abstract
In recent years, genome projects have scaled up production so that they are now producing hundreds of protein sequences everyday. This has created a wealth of sequence data and raises several questions, such as: (1) what do these proteins do? (2) how do they fold? (3) what are their evolutionary relationships? Large‐scale protein annotation aims to address these questions using approaches that can quickly be applied to millions of proteins. This review traces the annotation of a hypothetical proteome in order to illustrate the computational techniques and data sources available for large‐scale annotation. We begin by outlining some of the most extensive catalogs of experimentally determined protein annotation and then discuss how homology methods can be used to relate these small‐ to medium‐scale information sources to the large‐scale annotation problem. Finally, we discuss some of the biological questions that are being addressed now that we have whole‐proteome annotations.
IMPALA
/
RPS
‐
BLAST
/
PSI
‐
BLAST
in protein sequence analysis
Authors: Wolf Yuri I. 
Published: July 2005

Abstract
Pairwise sequence comparison works well if the sequence similarity is high; as the similarity decreases, alignment scores become less and less reliable. Profile‐based approaches allow to extend the analysis into the “twilight zone”. Several NCBI tools – PSI‐BLAST, IMPALA, and RPS‐BLAST – can be used to iteratively build position‐specific scoring matrices and use them in direct (query profile against a sequence database) and reverse (query sequence against a profile database) similarity searches.
Phylogenetic analysis of
BLAST
results
Authors: Brinkman Fiona S. L. 
Published: July 2005

Abstract
BLAST (Basic Local Alignment Search Theorem) is one of the most elegant, and widely used bioinformatics analysis developed to date. Like many bioinformatic analyses, BLAST uses evolutionary theory as the basis for its assumptions. Therefore, an understanding of evolutionary theory is critical to the appropriate interpretation, and further analysis, of BLAST results. Viewing essentially one‐dimensional BLAST analysis from the perspective of a two‐dimensional phylogenetic analysis has a number of benefits including more accurate identification of the true “top hit”, delineation of gene families, identification of true homologs, and improved functional assignment of orthologs and paralogs. Performing such phylogenetic analyses has become easier, now that semiautomated methods have been developed that permit rough phylogenetic overviews of the data. However, it should be emphasized that phylogenetic analysis must often be customized for a given experiment or research question. Such issues are relevant not only to the further analysis of a BLAST output, but also to similar analyses of outputs from other widely used algorithms for rapid database search. Critical analysis of results is becoming increasingly important as sequence databases increase in both size and complexity – and as we begin to understand that even these large sequence databases are only scratching the surface of the true complexity and variety of sequences that exist in nature.
Ontologies for information retrieval
Authors: Hersh William Richard 
Published: July 2005

Abstract
The goal of this review is to describe ontologies used for information retrieval (IR). We will begin with an overview of IR and its processes, followed by a description of how ontologies are used for IR, with particular emphasis on biomedical systems. Ontologies in general, the Gene Ontology (GO), and the Unified Medical Language System (UMLS) have been described in previous chapters. The explosion of data from new genomics and related research technologies provide a strong use case for the better understanding and improvement of IR systems.
Proteomics data representation and management
Authors: Paton Norman W. , Jones Andrew , Oliver Stephen G. 
Published: July 2005

Abstract
Proteomics is rapidly evolving into a high‐throughput technology, in which substantial studies are conducted on samples from a wide range of physiological, developmental, or pathological conditions. This gives rise to a need for techniques and technologies that enable the systematic description and capture of experimental data and metadata, which will allow for the archiving, sharing, and analysis of proteomic data sets. This chapter identifies the different aspects of an experiment that must be captured, and the derived information that underpins the interpretation of such data.
Gibbs sampling and bioinformatics
Authors: Liu Xiaole Shirley 
Published: July 2005

Abstract
Gibbs sampling is one of the best‐known Markov chain Monte Carlo methods. Its first and most popular application to bioinformatics is the sequence motif finding problem. Since then, Gibbs sampling has been successfully applied to many other interesting genomics and bioinformatics problems, especially haplotype inference and microarray biclustering.
Packaging, Cosmetics and Pharmaceuticals
Authors: Rosette Jack L. ,   Updated by Staff
Published: July 2005

Abstract
Cosmetics and pharmaceuticals each have their own special packaging requirements, although the primary purpose of packaging for both is to provide a means to store and distribute the product until the entire contents of the package are used. Cosmetic packaging is used to enhance the image of the product, and though pharmaceutical packaging has the same basic objectives, product stability and safe packaging requirements dictate different parameters regarding tampering prevention and child safety requirements of the FDA and the Consumer Product Safety Commission.
The FDA Rule requires the use of tamper‐evident packaging on all over‐the‐counter drugs and some cosmetics. However, if a product in an adulterated form could harm a consumer, manufacturers have the responsibility of protecting the product and consumer against tampering, meaning that tamper‐evident packaging transcends FDA regulations. No single feature is best for all products and all features can be violated in some manner, but effective tamper‐evident features provide greater difficulty in doing so. Consumers should be aware of what to look for in tamper‐evident packaging and pay attention to what product is being used.
Toluenediamine
Authors: Cartolano Anthony R. 
Published: July 2005

AbstractToluenediamine (diaminotoluene,m‐TDA) is an important industrial chemical intermediate; it is produced in the largest volume of any arylamine and is the lowest priced diamine. The principal use for TDA is in the manufacture of toluenediisocyanate (TDI), the predominant diisocyanate in the flexible foams and elastomers industries. Although all six possible toluenediamine isomers are made in the commercial synthesis, only two products are available commercially. The aromatic toluenediamines undergo typical amine reactions. The general chemistry is similar to that of the phenylenediamines or the cyclohexanediamines. Reactions of industrial importance involving commercial toluenediamines include phosgenation, ring alkylation, alkoxylation, and diazotization. Dinitrotoluenes can be catalytically hydrogenated to toluenediamines under a wide variety of temperatures, pressures, and solvents. Toluenediamine is classified as toxic and is readily absorbed through the skin, which is the major route of human exposure.
Packaging, Food
Authors: Brody Aaron L. 
Published: July 2005

AbstractThe primary purpose of food packaging is to protect food against environmental contaminants. Each food category, eg, ambient temperature shelf stable, frozen, or chilled, has different requirements. Generally, product processing must be integrated with the package to optimize shelf‐life objective. Thus canned foods are both heated and hermetically sealed to exclude microbiological recontamination; dry foods are sealed against moisture access; frozen foods must be maintained at low temperatures and protected against moisture loss; and chilled foods are refrigerated while controlling the transmission of both moisture and air.The most widely used packaging materials are paper and paperboard employed mostly in distribution channels. Second are metals; aluminum for cans to contain carbonated beverages and beer dominates in this category. Steel is applied for vacuum packaged foods. Glass has been declining as a package material because of weight, relative fragility, and high energy consumption. Plastic materials constitute only about 20% of the mass of package materials, but contain proportionately larger amount of food because of low densities and exceptional surface‐to‐volume ratio to achieve functionality. A variety of plastic materials is used for packaging depending on the food requirements, eg, polyethylenes, polyesters, polypropylenes, polystyrenes, nylons, poly(vinyl chlorides), etc. Among the structures employed are extrusion and injection blow‐molded bottles, thermoformed trays and cast or blown films. High gas barrier plastics are coated, coextruded, or laminated to structural plastics to enhance properties.
Light Emitting Diodes
Authors: Schubert E. Fred , Gessmann Thomas , Kim Jong Kyu 
Published: July 2005

AbstractInorganic semiconductor light‐emitting diodes (LEDs) are environmentally benign and have already found widespread use as indicator lights, large‐area displays, and signage applications. In addition, LEDs are very promising candidates for future energy‐saving light sources suitable for office and home lighting applications. Today, the entire visible spectrum can be covered by light‐emitting semiconductors: AlGaInP and AlGaInN compound semiconductors are capable of emission in the red to yellow wavelength range and ultraviolet (uv) to green wavelength range, respectively. Currently, two basic approaches exist for white light sources: The combination of one or more phosphorescent materials with a semiconductor LED and the use of multiple LEDs emitting at complementary wavelengths. Both approaches are suitable for high efficiency sources that have the potential to replace incandescent and fluorescent lights. In this article, the properties of inorganic LEDs will be presented, including emission spectra, electrical characteristics, and current‐flow patterns. Structures providing high internal quantum efficiency, namely, heterostructures and multiple quantum well structures, will be discussed. Advanced techniques enhancing the external quantum efficiency will be reviewed, including resonant‐cavities, die shaping (chip shaping), omnidirectional reflectors, and photonic crystals. Different approaches to white LEDs will be presented and figures‐of‐merit such as the color rendering index, luminous efficacy, and luminous efficiency will be explained. Finally, the packaging of low power and high power LED dies will be discussed.
Nuclear Power Facilities, Safety
Authors: Taylor John J. 
Published: July 2005

AbstractSafety has played a dominant role in the ability to generate electricity by nuclear means because large quantities of highly radioactive fission products are generated with the energy from fission. Strict control is maintained over these radioactive materials to assure that public and worker health and safety are protected. The basic safety principles, defense‐in‐depth design philosophy, and key safety design features that apply to all nuclear facilities are discussed. Specific examples are given from nuclear power plant design. The methods of assessment of safety are described, both for self‐assessment and independent assessment. The roles of industry and government in the assessment process are outlined. Comparative risks of nuclear power are substantially lower than most other methods of generating electricity. The specific safety characteristics of the nuclear power plant that generates the electricity, and of the nuclear fuel cycle, which functions to produce nuclear fuel and dispose of radioactive wastes are each given. Special focus is placed on the safe disposal of spent fuel and radioactive waste. The basic radiation exposure and health standards which establish the foundation of public and worker protection are cited. The safety of future nuclear power plants is summarized.