bluuebunny/crossref_metadata_2025 huggingface dataset:
Computational methods for the prediction of protein interaction partners
Authors: Valencia Alfonso , Juan David
Published: November 2009

Several computational methods have been recently developed for the prediction of protein interactions. The first class of these methods exclusively uses sequence information for the predictions, including three methods rooted in comparative genomics (phylogenetic profiles,conserved gene neighborhood, andgene fusion), and two other methods that use multiple sequence alignments as input information (in silico two‐hybridandMirrorTreemethods). Interestingly, these two methods can be extended beyond the prediction of interaction partners to the detection of regions of interactions and key functional residues, as demonstrated in various experimental systems. The second type of computational methods exploits the information of protein structures by analyzing the observed combinatorial of protein domains or by extrapolating the structural information of protein complexes to compatible sequences.

Several studies have addressed the interesting possibilities of combining predicted and experimentally derived interactions. The current view is that the overlap between the interactions predicted by different methods is relatively small, and the various experimental and computational methods seem to be able to detect specific types of protein interactions.

A number of computational methods for predicting functional and/or physical relations between proteins have been developed in the last 4 years. The computational methods are strongly rooted in the traces left by the evolution in the organization and composition of bacterial genomes (seeMicrobial genomes). The methods developed can be divided into three categories: those methods that only use the information from genomes and sequences for the prediction of interaction partners, those methods that use the information of protein complexes of known structures (seeFundamentals of protein structure and function,Large complexes by X‐ray methods, andLarge complexes and molecular machines by electron microscopy), and those methods that use the puzzle composition of proteins in domains (seeClassification of proteins into families,Pfam: the protein families database, andCOGs) to predict the probability of interaction between the corresponding proteins.
GPIanchors
Authors: Hooper Nigel M.
Published: November 2009

Many proteins are attached to the outer surface of the membrane by a glycosyl‐phosphatidylinositol (GPI) anchor covalently linked to the C‐terminal amino acid. All GPI anchors have the core structure “ethanolamine‐PO4‐6Manα1‐2Manα1‐6Manα1‐4GlcNH2α1‐6myo‐inositol‐1‐PO4‐lipid” but vary in the nature of the lipid moiety and in side‐chain modifications to the core glycan (seeGlycosylphosphatidylinositol anchors‐ a structural perspective). The GPI anchor is built up by sequential addition of sugars and ethanolamine phosphate to phosphatidylinositol and then transferred by a transamidase enzyme to the protein. Proteins destined to be GPI anchored have an N‐terminal signal peptide for translocation into the lumen of the endoplasmic reticulum and a C‐terminal signal that directs addition of the GPI anchor. Experimentally, the presence of a GPI anchor can be determined by digestion with bacterial phosphatidylinositol‐specific phospholipase C, detection of the cross‐reacting determinant, metabolic labeling with components of the anchor, or relative detergent insolubility. In addition to the stable association of a protein with the membrane, GPI anchors convey other properties on proteins including susceptibility to cleavage by phospholipases, association with detergent‐insoluble lipid rafts, intracellular targeting, transmembrane signaling, endocytosis via caveolae, and intercellular transfer.
Classification of proteins by sequence signatures
Authors: Hofmann Kay
Published: November 2009

The prediction of a protein's function from its amino acid sequence is one of the most important tasks in bioinformatics. The traditional procedure of searching databases for related sequences and inferring the function from the best matches has several shortcomings and pitfalls. Alternatively, the sequence under study can be scrutinized for the occurrence of particular sequence signatures that can be associated with certain protein functionalities. Useful sequence signatures not only include short motifs such as protein modification sites or specific binding motifs but also encompass larger protein regions, such as homology domains. There exist a number of fundamentally different bioinformatical data structures, which can be used to store information about sequence signatures, thus making them available for the purpose of protein classification.
Metabolic dynamics in cells viewed as multilayered, distributed, mass‐energy‐information networks
Authors: Aon Miguel A. , Cortassa Sonia
Published: November 2009

The role of mathematical models in integrating available information on metabolic networks is highlighted. General modeling and other quantitative methodologies currently available are critically reviewed and the potential contributions of proteomics complemented by theoretical concepts derived from these modeling frameworks are assessed. The multilayered, distributed, view of cells increases the necessity of a more fundamental understanding of the dynamics of complex reaction networks as well as cytoplasmic organization, on cell physiology. The future of mathematical modeling will be largely determined by the trade‐off betweencompletenessandunderstandability.
Statistical signals
Authors: Gentles Andrew J. , Karlin Samuel
Published: November 2009

Statistical signals play a central role in a wide range of bioinformatics tools and analyses. The basic theory underlying general scoring schemes, particularly maximal aggregate scoring segments, is reviewed briefly. Applications include homology detection using BLAST, alignment algorithms that incorporate global normalization, analysis of distributions of sequence markers (
r
‐scans), and characterization of frequent words and repeat abundances in DNA and protein sequences.
Polymorphism and sequence assembly
Authors: Rana Brinda K. , Smith Douglas W. , Schork Nicholas J.
Published: November 2009

DNA sequence information is being deposited into public databases at a rapid rate, largely through worldwide genomic efforts to sequence the human genome as well as the genomes of other species. This information has enabled the identification of over a million of naturally occurring genetic variations in humans, in particular, single‐nucleotide polymorphisms (SNPs). SNPs have become a focal point in the study of the genetic basis of multifactorial diseases and traits and human evolutionary history. In this article, we will outline bioinformatic and molecular approaches for using available sequence information and technology to identify SNPs in the human population. These approaches may be extended to study SNPs in other organisms as well as other types of polymorphisms.
In silico
approaches to functional analysis of proteins
Authors: Aravind L.
Published: November 2009

Inference of protein function from sequence data by means of computational techniques is one of the essential requirements for biological investigations in the postgenomic era. While the basic principles of functional inference are derived from standard ideas in structural and evolutionary biology, their practical application is far from trivial. In this introductory article, we provide an overview of these principles and some definitions for frequently encountered concepts pertaining to the sequence analysis of proteins, such as conserved domains, domain architectures, nonglobular segments, and the trends in sequence conservation. We also discuss various extraneous sources of information that emerge from different contextual associations of proteins and their utility in function prediction. The remaining articles in this section delve into the specific aspects of the various themes introduced here.
Transmembrane topology prediction
Authors: Käll Lukas , Sonnhammer Erik
Published: November 2009

We describe the most popular transmembrane topology predictors and highlight their advantages and shortcomings. We also review different benchmark studies on transmembrane predictors.
The domains of life and their evolutionary implications
Authors: Woese Carl R.
Published: November 2009

After almost a century in virtual stasis, Darwin's world, the world of biology as fundamentally an expression of the evolutionary process, is once again emerging at the forefront of the discipline of biology. This has followed a century in which biology was perceived in mechanistic, reductionist terms, and the gene was effectively taken as the be‐all and end‐all of biology. The evolutionary renaissance is the result of intra‐ and interdisciplinary factors. On the one hand, the molecular paradigm, which so successfully guided biology during the twentieth century, is being recognized for what it was; an incomplete, superficial (and now failed) conception of the living world. In addition to this, the advent of genome sequencing (in the last decade of the 1990s) has provided huge amounts of information that require evolutionary explanation. On the other hand, developments in the physical sciences and mathematics over the past 50 years have shown us that classical physics (which served as the basis for the twentieth century view of biology), is far from a complete world view, and with the aid of computers, we have come to appreciate and begin to understand the vast “nonlinear” side of reality. The fact that evolution is fundamentally a nonlinear (complex dynamic) process explains why: (1) it was neglected (not recognized as important) during the twentieth century and (2) it is now reemerging as the essence of biology.
Phylogenomic approaches to bacterial phylogeny
Authors: Daubin Vincent
Published: November 2009

Reconstructing the history of bacterial species is one of the most challenging question molecular phylogeneticists have to answer. Both the antiquity of bacteria and their mode of evolution constitute barriers to the elucidation of the relationships among phyla. Time, on one side, has eroded the phylogenetic signal that would allow reconstructing the deep branches of this several billion years old tree. In addition, because of frequent gene exchanges among distantly related bacteria, even an accurate gene phylogeny may no longer represent the species tree. Methods aimed at using complete genomes for phylogenetic inference may however help resolve this issue.
Mass spectrometry and computational proteomics
Authors: Bafna Vineet , Reinert Knut
Published: November 2009

Mass Spectrometry is the tool of choice for proteomics, with applications to peptide sequencing, protein structure prediction, protein–protein interactions, and many others. Continued improvements in instrumentation and computational technologies will only help accelerate this trend. A short overview of algorithms for interpreting mass spectrometry (MS) data is provided. This overview is not intended as an introduction to the technology itself or to proteomics. Instead, an abstract overview of MS data is presented in order to describe key algorithmic ideas required for its interpretation. Three proteomic applications are considered:protein identification,protein interactions, anddifferential analysis of protein expression.
Integrating statistical approaches in experimental design and data analysis
Authors: Wit Ernst , Khanin Raya
Published: November 2009

In complex experiments such as microarray studies, the quantity of interest is measured via a long path of intermediate technologies. It is not surprising that the final signal is partially corrupted by the measurement process itself. Statistical design is aimed at assigning the replicates in an optimal way to the conditions of interest. It should be seamlessly integrated with the statistical methods to recover the signal, so that it is possible to evaluate the scientific question of interest most efficiently.
Algorithms for gene expression analysis
Authors: Brazma Alvis , Culhane Aedín C.
Published: November 2009

A new genre of algorithms, which blends bioinformatics, statistics, and machine learning, is emerging to tackle the challenges of gene expression data analysis. Microarrays enable genome‐scale high‐throughout measurement of gene expression, and have produced unprecedented amounts of gene expression data. In this chapter, we present an overview of some of the many algorithms that have been employed in the analysis of these data. These include many well‐known algorithms and new algorithms developed to address data‐specific issues. We describe various clustering algorithms, including hierarchical andk‐means, and ordination methods, such as principal component analysis, that can be applied to unsupervised exploration of data. We also provide an introduction to a number of supervised, meta‐analysis, and gene selection methods. Where possible, we mention software tools that implement these algorithms. Finally, we stress the importance of a standard data format and data repositories for sharing of microarray gene expression data.
Differential expression with the Bioconductor Project
Authors: von Heydebreck Anja , Huber Wolfgang , Gentleman Robert
Published: November 2009

A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. We discuss different approaches to this task and illustrate how they can be applied using software from the Bioconductor Project. A central problem is the high dimensionality of gene expression space, which prohibits a comprehensive statistical analysis without focusing on particular aspects of the joint distribution of the genes' expression levels. Possible strategies are to do univariate gene‐by‐gene analysis, and to perform data‐driven nonspecific filtering of genes before the actual statistical analysis. However, more focused strategies that make use of biologically relevant knowledge are more likely to increase our understanding of the data.
Extracting networks from expression data
Authors: Hatzimanikatis Vassily , Papoutsakis Eleftherios T.
Published: November 2009

We discuss the properties of some of the model‐based identification methods used for the development of genetic networks from gene expression data. The performance of these methods is evaluated with respect to their ability to deal with different type of data, the dimensionality of the data, the combinatorial nature of gene expression regulation, and the mathematical representation of the genetic network. We identify several key issues that must be resolved in order to improve our ability to extract networks from expression data.
A comparison of existing tools for ontological analysis of gene expression data
Authors: Khatri Purvesh , Draghici Sorin
Published: November 2009

Independent of the platform and the analysis methods used, the result of a microarray experiment is, in most cases, a list of differentially expressed genes. An automatic ontological analysis approach has been recently proposed to help with the biological interpretation of such results. Currently, this approach is the de facto standard for the secondary analysis of high‐throughput experiments, and a large number of tools have been developed for this purpose. We present a detailed comparison of 14 such tools using the following criteria: scope of the analysis, visualization capabilities, statistical model(s) used, correction for multiple comparisons, reference microarrays available, installation issues, and sources of annotation data. This detailed analysis of the capabilities of these tools will help researchers choose the most appropriate tool for a given type of analysis.
Large error models for microarray intensities
Authors: Huber Wolfgang , von Heydebreck Anja , Vingron Martin
Published: November 2009

We derive the additive‐multiplicative error model for microarray intensities, and describe two applications. For the detection of differentially expressed genes, we obtain a statistic whose variance is approximately independent of the mean intensity. For the post hoc calibration (“normalization”) of data with respect to experimental factors, we describe a method for parameter estimation.
Protein structure analysis and prediction
Authors: Taylor William R.
Published: November 2009

The comparative analysis of protein sequence and structure has provided great insights into the function and evolution of proteins. This approach relies on both sequence comparison and structure comparison with the latter, giving the deepest view on distant relationships, especially when just the overall fold of the proteins is compared. The establishment of correlation between sequence features and structural features can allow structure to be predicted from sequence. This can range from isolated fragments of structure (sometimes called motifs) to the overall fold of the proteins. With the progress in the determination of genomes and many new structures from structural genomics programs, there is an increasing wealth of data for comparative analysis.
Unified Medical Language System and associated vocabularies
Authors: Chute Christopher G.
Published: November 2009

Vocabularies and ontologies comprise conceptual underpinnings of science, biology, and medicine. The 400‐year heritage of medical classification has evolved into a broadly diverse spectrum of discrete vocabularies, nomenclatures, terminologies, and ontologies about terms and concepts of clinical and basic science interest. The Unified Medical Language System (UMLS) of the National Library Medicine (NLM) is an effective form in which about 100 major terminologies are compiled in a common format. For many source systems, complex relationships between and among terms are faithfully represented in the UMLS Metathesaurus. Many sophisticated relationships exist across terms among these terminologies. Complementing the core Metathesaurus are rich components of UMLS that have tremendous value and generalizability to the UMLS suite. The major UMLS components are (1) the Semantic Network, which enumerates a shared network of meaning applied across all Metathesaurus sources and (2) the Specialist Lexicon, which provides a rich linguistic body of knowledge about English words and terms together with an open‐source suite of natural language processing tools and applications.
Ontologies for the life sciences
Authors: Schulze‐Kremer Steffen , Smith Barry
Published: November 2009

Where humans can manipulate and integrate the information they receive in subtle and ever‐changing ways from context to context, computers need structured and context‐free background information of a sort that ontologies can help to provide. A domain ontology captures the stable, highly general, and commonly accepted core knowledge for an application domain. The domain at issue here is that of the life sciences, in particular, molecular biology and bioinformatics. Contemporary life science research includes components drawn from physics, chemistry, mathematics, medicine, and many other areas, and all of these dimensions, as well as fundamental philosophical issues, must be taken into account in the construction of a domain ontology. Here we describe the basic features of domain ontologies in the life sciences and show how they can be used.
Applications of
RNA
minimum free energy computations
Authors: Clote Peter
Published: November 2009

Several applications of RNA secondary structure energy minimization are surveyed, including a recent noncoding RNA gene finder.
Relational databases in bioinformatics
Authors: Kriegel Hans‐Peter , Kröger Peer , Schönauer Stefan
Published: November 2009

In this article, we survey relational database management in bioinformatics, emphasizing advantages and limitations.
Acrolein and Derivatives
Authors: Etzkorn W. G. , Kurland J. J. , Neilsen W. D.
Published: November 2009

Economic Aspects

Reactions and Derivatives

Direct Uses of Acrolein
Acrylonitrile Polymers
Authors: Ball Lawrence E. , Curatolo Benedict S. , Kulich Donald M. , Pace John E. , Fritch Leroy W.
Published: November 2009

SAN

SANPhysical Properties and Test Methods

SANChemical Properties and Analytical Methods

SANManufacture

Other Copolymers

Economic Aspects

Health and Toxicology

ABSResins

Applications
Adipic Acid
Authors: Davis Darwin D. , Kemp Donald R.
Published: November 2009

Chemical and Physical Properties

Chemical Reactions

Manufacture and Processing

Storage, Handling, and Shipping

Economic Aspects

Toxicity, Safety, and Industrial Hygiene
Alkyd Resins
Authors: Lin K. F.
Published: November 2009

Fundamental Reactions and Resin Structure

Classification of Alkyd Resins

Oil Length‐Resin Property Relationship

Alkyd Ingredients

The Concept of Functionality and Gelation

Microgel Formation and Molecular Weight Distribution

Principles for the Designing of Alkyd Resins

Chemical Procedures for Alkyd Resin Synthesis

Alkyd Resin Production Processes

Safety and Environmental Precautions

Modification of Alkyd Resins by Blending With Other Polymers

Chemically Modified Alkyd Resins

High Solids Alkyds

Water‐Reducible Alkyds

Economic Aspects
Allyl Alcohol and Monoallyl Derivatives
Authors: Nagato Nobuyuki
Published: November 2009

Physical Properties

Chemical Properties

Industrial Manufacturing Processes for Allyl Alcohol

Monoallyl Derivatives

Reactivity of Allyl Compounds

Physical Properties of Derivatives

Allyl Chloride

Allyl Esters

Allyl Ethers

Allyl Amines

Safety and Handling
Aluminum Alloys and Engineered Materials
Authors: Sansonetti S. J.
Published: November 2009

Non‐Heat‐Treatable Alloys

Casting Alloys

Contemporary Advancements and Future Potential

ARALL
Laminates

Quasicrystals

Advances in Powdered Metallurgy (
PM
) Aluminum Alloys

Aluminum Electroplating
Aminophenols
Authors: Mitchell Stephen , Waring Rosemary
Published: November 2009

Physical Properties

Chemical Properties

Manufacture and Processing

Purification

Economic Aspects

Storage

Health and Safety Factors

Uses

Derivatives
Amyl Alcohols
Authors: Papa Anthony J.
Published: November 2009

Physical Properties

Chemical Properties

Manufacture

Health and Safety Factors

Shipping and Storage

Economic Aspects
Antibiotics: Aminoglycosides
Authors: McGregor Donald
Published: November 2009

Aminoglycosides in Medical Usage

Medical and Biological Properties

Structure‐Activity Relationships Among Aminoglycoside Derivatives
Biopolymers
Authors: Ward Timothy
Published: November 2009

Analytical Techniques

Economic Aspects
Bioremediation
Authors: Prince Roger C.
Published: November 2009

General Technological Aspects

Organic Contaminants

Inorganic Contaminants

Conclusions
Calcium Chloride
Authors: Reid Kenneth I. G. , Kust Roger
Published: November 2009

Properties

Production and Consumption

Uses

Toxicity and Environmental
Calcium Sulfate
Authors: Petersen Donald J. , Kaleta Norbert W. , Kingston Larry W.
Published: November 2009

Properties

Sources

Decomposition Thermodynamics

Manufacture

Production and Trade
Calorimetry
Authors: Albert H. J.
Published: November 2009

Calorimeters of Historical and Special Interest

Gas Calorimeters
Carboxylic Acids
Authors: Priddy Duane B.
Published: November 2009

Fatty Acids

Monohydroxy Fatty Acids

Polyhydric Monobasic Acids

Aromatic Carboxylic Acids

Formation of Carboxylic Acids
Coal Tar and Derivatives
Authors: Romovacek George R. , Lauer G.G.
Published: November 2009

Carbonization Process

Processing of Crude Tar

Tar Acids

Tar Bases

Solvent Naphtha

Naphthalene

Topped Tar

Creosote

Pitch

Roofing Pitch
Cyanohydrins
Authors: Cholod Michael S.
Published: November 2009

Properties

Preparation

Shipping, Storage, and Handling

Health and Safety

Specific Compounds
Dimer Acids
Authors: Breuer Thomas E.
Published: November 2009

Physical Properties

Chemical Properties

Manufacture

Storage and Handling

Economic and Market Aspects

Health and Safety Aspects

Uses
Dye and Dye Intermediates
Authors: Gregory Peter
Published: November 2009

Classification Systems for Dyes

Classification of Dyes by Use or Application Method

Nomenclature of Dyes

Classification of Dyes by Chemical Structure

Dye Intermediates

The Chemistry of Dye Intermediates

Equipment and Manufacture

Economic Aspects
Dyes: Anthraquinone
Authors: Hattori Makoto
Published: November 2009

Color and Structure

Method of Synthesis

Key Intermediates

Reactive Dyes

Disperse Dyes

Acid Dyes

Vat Dyes

Mordant Dyes

Functional Dyes

Economic Aspects

Consumption

Health and Safety Information
Dyes: Application and Evaluation
Authors: Glover Brian
Published: November 2009

Classification of Dyestuffs According to Application

Physical and Organic Chemistry of Dyes and the Dyeing Process

Modes of Attraction

Dyestuff Organic Chemistry

The Dyeing Process

Dyeing of Cellulosic Fibers

Direct Dyes

Fiber‐Reactive Dyes

Vat Dyes on Cellulose

Dyeing of Wool

Acid Dyes

Mordant Dyes/Metal Complex Dyes

Dyeing Wool with Fiber‐Reactive Dyes

Silk

Dyeing of Synthetic Polyamides

Dyeing of Acrylic Fibers

Dyeing of Polyester

Dyeing of Cellulose Esters

Dyeing of Fiber Blends

Cellulosic Fiber Blends

Wool Blends

Blends of Synthetic Fibers

Other Application Procedures

Dyeing Machinery

Textile Printing

Colorants for Textile Printing

Styles of Printing

Printing Machinery

Paper Coloring

Dyeing Processes

Dyeing of Leather

Fastness Tests for Textiles

Safe Handling of Dyes

Colour Index Generic Names
Electrodialysis
Authors: McRae Wayne A.
Published: November 2009

Ion‐Exchange Membranes

Apparatus

Applications

Economic Aspects
Flame‐Retarding Agents
Authors: Gann Richard G. , Touval Irving , Pettigrew Alex , Weil Edward D. , Calamari Timothy A. , Harper Robert J.
Published: November 2009

Antimony and Other Inorganic Flame Retardants

Halogenated Flame Retardants

Phosphorus Flame Retardants

Flame Retardants for Textiles
Foamed Plastics
Authors: Suh Kyung W.
Published: November 2009

Classification

Theory of the Expansion Process

Manufacturing Processes

Expandable Formulations

Decompression Expansion Processes

Dispersion Processes

Properties of Cellular Polymers

Structural Variables

Other Properties

Commercial Products and Processes

Health and Safety
Formamide
Authors: Hohn A.
Published: November 2009

Properties

Reactions

Shipment

Economic Aspects

Storage

Manufacture and Processing

Health and Safety
Gelatin
Authors: Keenan Thomas R.
Published: November 2009

Chemical Composition and Structure

Physical and Chemical Properties

Economic Aspects
Glass
Authors: Dietz Earl D. , Hench L. L.
Published: November 2009

Types of Traditional Glass

Lead Glasses

Borosilicate Glasses

Special‐Purpose Traditional Glasses

Traditional Manufacturing Process

Glass Blocks

Sol‐Gel Glass
Gold
Authors: Corrigan Donald A.
Published: November 2009

Occurrence and Processing

Uses of Gold

Chemistry of Gold
Grignard Reactions
Authors: Silverman Gary S. , Rakita Philip E.
Published: November 2009

Preparation of Grignard Reagents

Industrial Manufacturing Process

Analysis of Grignard Reagents

Economic Aspects

Health and Safety Factors

Reactions and Applications of Grignard Reagents
Hemicellulose
Authors: Thompson Norman S.
Published: November 2009

Isolation and Analysis

Pulping

The Effect of Hemicellulose in Commercial Products

Applications
Hydantoin and Its Derivatives
Authors: AvendaÑo Carmen , MenÉndez J. Carlos
Published: November 2009

Physical Properties

Synthesis

Health and Safety Factors (Toxicology)

Applications
Hydrogen‐Ion Activity
Authors: Durst Richard A. , Bates Roger G.
Published: November 2009

p
H
Determination

p
H
Measurement Systems

Nonaqueous Solvents

Indicator
p
H
Measurements

Industrial Process Control
Imines, Cyclic
Authors: Scherr G. , Steuerle U. , Fikentscher R.
Published: November 2009

Physical Properties

Chemical Properties

Reactions

Preparation
Indoles
Authors: Sundberg Richard J.
Published: November 2009

Properties

Reactivity

Syntheses

Biologically Active Indole Derivatives
Initiators (Free‐Radical)
Authors: Sanchez JosÉ , Myers Terry N.
Published: November 2009

Organic Peroxides

Inorganic Peroxides

Azo Compounds

Carbon–Carbon Initiators

Other Radical Generating Systems

Initiation Through Radiation and Photoinitiators

Economic Aspects
Ionomers
Authors: Rees Richard W.
Published: November 2009

Ethylene‐Based Ionomers

Health and Safety Factors

Uses

Noncommercial Ethylene‐Based Ionomers

Ionomers Not Based on Ethylene
Isoprene
Authors: Lybarger Hugh M.
Published: November 2009

Properties

Reactions

Production

Health and Safety

Economic Aspects and Applications
Latex Technology
Authors: Gelbert Chester H. , Grady Michael C.
Published: November 2009

Synthetic Latex Manufacture

Latex Properties
Lecithin
Authors: Wendel Armin
Published: November 2009

Physical Properties

Chemical Properties

Manufacture and Processing

Purification Processes

Commercial Grades

Economic Aspects

Health and Safety Factors

Uses
Metal Anodes
Authors: Liederbach Thomas A.
Published: November 2009

Coating Structure and Morphology

Operating Performance of Coatings

Structure Design

Manufacturing Technology
Mineralogy
Authors: Rowley Elmer B.
Published: November 2009

Origin of Minerals

Crystal Structure

Crystal Forms

Physical Mineralogy

Isomorphism and Diadochy

Polymorphism

Pseudomorphism

Twinning

Rock Types, Associated Minerals and Their Uses

Minerals of Primary Industrial and Economic Importance

Ocean Sources of Minerals

Lunar Rocks

Classification of Minerals
Molecular Modeling
Authors: Profeta Salvatore
Published: November 2009

Computer Graphics In Molecular Modeling

Computational Methods for Molecular Modeling
Nitriles
Authors: McKinney Ronald J. , DeVito Stephen C.
Published: November 2009

General Preparations and Chemical Properties

Chemistry and Uses of Nitriles

General Health and Safety Factors

Acetonitrile

Adiponitrile

α‐Aminonitriles

Azobisnitriles

Benzonitrile

Cyanoacetic Acid and Esters

Isophthalonitrile

2‐Methylglutaronitrile

Pentenenitriles

Fatty Acid Nitriles

Disclaimer
Oils, Essential
Authors: Mookherjee Braja D. , Wilson Richard A.
Published: November 2009

Economic Aspects

Composition

Commercial Essential Oils

Safety and Regulatory Aspects
Oxo Process
Authors: Billig Ernst , Bryant David R.
Published: November 2009

Catalysts

Uses

Safety, Health, and Environmental Concerns
Palladium
Authors: Libby Linton
Published: November 2009

Uses
Papermaking and Finishing
Authors: Daene Robert A. , Jaakkola Jipi
Published: November 2009

Wet End

Press Section

Dryers

Size Press and Coaters

Calenders and Winders

Other Types of Machines
Pharmacodynamics
Authors: Triggle David J.
Published: November 2009

Drug Discovery and Regulation

The Receptor Concept

Pharmacokinetic Aspects of Drug Action

Pharmacodynamic Aspects of Drug Action
Phthalocyanine Compounds
Authors: Loebbert Gerd
Published: November 2009

Physical Properties

Chemical Properties

Manufacturing and Processing

Uses

Health and Safety Factors
Pigments (Inorganic)
Authors: Novotny Mirek , Solc Z. , Trojan M.
Published: November 2009

Properties

Specifications, Standards, and Quality Control

White Pigments

Other White Pigments

Colored Pigments

Black Pigments

Extenders and Opacifiers

Miscellaneous Pigments

Environmental Aspects
Pigments (Organic)
Authors: Jaffe E. E.
Published: November 2009

Color and Constitution

Properties of Pigments

Types of Pigments

Uses

Testing and Standardization

Health and Safety Factors
Polyethylene
Authors: Heinemeyer B. W.
Published: November 2009

Applications

Properties

Fabrication

Decorating

Design
Polymethine
DYES
Authors: Kachkovski Alexy D.
Published: November 2009

Electron Structure

Electron Transitions

Chemical Reactivity

Synthesis

Molecular Design
Pyridine and Derivatives
Authors: Dressler Hans
Published: November 2009

Production of Pyridine and Homologues

Major Uses of Pyridine Derivatives

Health and Safety Factors
Soaps
Authors: Dahlgren R. Marc , Kalberg John N.
Published: November 2009

Personal Cleansing Soap Products

Manufacture of Soap
Sol–Gel Technology
Authors: Hench Larry L. , Orefice Rodrigo
Published: November 2009

Compositions

Sol–Gel Process Steps

Alumina Derived from Sol–Gel

Applications
Steroids
Authors: Morgan Bradley P. , Moynihan Melinda S.
Published: November 2009

Structure and Nomenclature

Classification of Biologically Active, Natural Steroids

Biosynthesis

Manufacture and Synthesis

Partial Syntheses

Uses: Therapeutics and Toxicology

Analytical Methods
Surfactants
Authors: Lynn Jesse L. , Bory Barbara H.
Published: November 2009

Physical Chemistry of Interfaces

Anionic Surfactants

Nonionic Surfactants

Amphoteric Surfactants

Uses
Tantalum
Authors: Schussler Fansteel M.
Published: November 2009

Uses

Alloys

Chemistry and Compounds
Urethane Polymers
Authors: Ulrich Henri
Published: November 2009

Formation and Properties

Raw Materials

Uses

Health and Safety Factors

Commercial Applications
Vinyl Acetal Polymers
Authors: Knapczyk Jerome W.
Published: November 2009

Synthesis and Structure

Physical Properties

Health and Safety Factors

Poly(vinyl butyral)

Poly(vinyl formal)
Vinyl Ester Resins
Authors: Cook P. H.
Published: November 2009

Resin Properties

Cure Mechanism

Applications
Vinyl Ether Monomers and Polymers
Authors: Login Robert B.
Published: November 2009

Monomers

Homopolymerization

Living Polymerization

Homopolymer Properties

Commercial Aspects

Copolymerization

Health and Safety Factors

Applications
Waxes
Authors: Warth Albin H.
Published: November 2009

Animal and Vegetable Waxes

Mineral Waxes

Petroleum Waxes

Microcrystalline Waxes

Synthetic Waxes
X
‐Ray Analysis
Authors: Shequen W. G.
Published: November 2009

Source of
X
‐rays

Continuous Spectrum

X
‐Ray Spectral Lines

Generation of
X
‐rays

Detection of
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‐rays

X
‐ray Crystallography

X
‐Ray Analyzer, Electron‐Microprobe

Detectors

X
‐ray Fluorescence Analysis
Generation of Human Embryonic Stem Cell Reporter Knock‐In Lines by Homologous Recombination
Authors: Davis Richard P. , Grandela Catarina , Sourris Koula , Hatzistavrou Tanya , Dottori Mirella , Elefanty Andrew G. , Stanley Edouard G. , Costa Magdaline
Published: November 2009

This unit describes a series of technical procedures to form clonal human embryonic stem cell (hESC) lines that are genetically modified by homologous recombination. To develop a reporter knock‐in hESC line, a vector is configured to contain a reporter gene adjacent to a positive selection cassette. These core elements are flanked by homologous sequences that, following electroporation into hESCs, promote the integration of the vector into the appropriate genomic locus. The positive selection cassette facilitates the enrichment and isolation of genetically modified hESC colonies that are then screened by PCR to identify correctly targeted lines. The selection cassette, flanked byloxPsites, is subsequently excised from the positively targeted hESCs via the transient expression of Cre recombinase. This is necessary because the continued presence of the cassette may interfere with the regulation of the reporter or neighboring genes. Finally, these genetically modified hESCs are clonally isolated using single‐cell deposition flow cytometry. Reporter knock‐in hESC lines are valuable tools that allow easy and rapid identification and isolation of specific hESC derivatives.Curr. Protoc. Stem Cell Biol. 11:5B.1.1‐5B.1.34. © 2009 by John Wiley & Sons, Inc.
Laboratory Maintenance of Bordetella pertussis
Authors: Hulbert Robin R. , Cotter Peggy A.
Published: November 2009

The causative agent of the respiratory disease whooping cough, Bordetella pertussis, is a nutritionally fastidious microorganism but can be grown with relative ease in research laboratories. Stainer‐Scholte synthetic broth medium and Bordet‐Gengou blood agar both support growth of B. pertussis and are commonly used. B. pertussis prefers aerobic conditions and a temperature range of 35° to 37°C. Appropriate laboratory safety protocols are required to prevent the generation of aerosols, which could potentially spread this highly infectious agent. Curr. Protoc. Microbiol. 15:4B.1.1‐4B.1.9. © 2009 by John Wiley & Sons, Inc.
Differential Staining of Bacteria: Gram Stain
Authors: Moyes Rita B. , Reynolds Jackie , Breakwell Donald P.
Published: November 2009

In 1884, Hans Christian Gram, a Danish doctor, developed a differential staining technique that is still the cornerstone of bacterial identification and taxonomic division. This multistep, sequential staining protocol separates bacteria into four groups based on cell morphology and cell wall structure: Gram‐positive cocci, Gram‐negative cocci, Gram‐positive rods, and Gram‐negative rods. The Gram stain is useful for assessing bacterial contamination of tissue culture samples or for examining the Gram stain status and morphological features of bacteria isolated from mixed or isolated bacterial cultures. Curr. Protoc. Microbiol. 15:A.3C.1‐A.3C.8. © 2009 by John Wiley & Sons, Inc.
Preliminary Staining of Bacteria: Simple Stains
Authors: Moyes Rita B. , Reynolds Jackie , Breakwell Donald P.
Published: November 2009

Simple staining involves directly staining the bacterial cell with a positively charged dye in order to see bacterial detail, in contrast to negative staining where the bacteria remain unstained against a dark background. Curr. Protoc. Microbiol. 15:A.3E.1‐A.3E.5. © 2009 by John Wiley & Sons, Inc.
Fluorescent Staining of Bacteria: Viability and Antibody Labeling
Authors: Moyes Rita B.
Published: November 2009

This appendix presents several methods for using fluorescence to evaluate bacterial viability and to explore the cell surface for the presence of various antigens for diagnostic and taxonomic purposes. The use of fluorescent labeling will allow fast and accurate analysis and monitoring of microbial populations in ecological and clinical environments. Curr. Protoc. Microbiol. 15:A.3K.1‐A.3K.13. © 2009 by John Wiley & Sons, Inc.
Occupational injuries among emergency responders
Authors: Reichard Audrey A. , Jackson Larry L.
Published: November 2009

Background

Emergency responders frequently incur injuries while providing medical, fire, and law enforcement services. National surveillance systems provide fragmented perspectives on responder injuries because they omit specific classes of workers (e.g., government or volunteers); they report only selected injuries; and employment information is incomplete.

Methods

We characterized injuries among emergency medical services (EMS), firefighting, and police occupations by using data from the National Electronic Injury Surveillance System—Occupational Supplement (NEISS‐Work) for injuries treated in U.S. hospital emergency departments in 2000–2001.

Results

Sprains and strains were the leading injury (33–41%) among EMS, firefighter, and police occupations. Police officers and career firefighters had the highest injury rates (8.5 and 7.4 injuries per 100 full‐time equivalent workers, respectively).

Conclusions

The physical demands of emergency response are a leading cause of injuries that may benefit from similar interventions across the occupations. To assess risk, improved exposure data need to be acquired, particularly for volunteers. Am. J. Ind. Med. 53:1–11, 2010. Published 2009 Wiley‐Liss, Inc.
Once again, the Supreme Court takes on class action arbitration
Authors: Bleemer Russ
Published: November 2009

What the amicus filers are telling the U.S. Supreme Court in advance of next month's arguments in Stolt‐Nielsen v. AnimalFeeds Int'l Corp., an arbitration class action case.
Worldly Perspectives: Lebanon
Authors: De Palo Giuseppe , Trevor Mary B.
Published: November 2009

The international ADR profile column by Giuseppe De Palo, of Rome, and Mary B. Trevor, of St. Paul, Minn., this month visits Lebanon.
Generalized Confidence Intervals for Ratios of Regression Coefficients with Applications to Bioassays
Authors: Bebu Ionut , Seillier‐Moiseiwitsch Françoise , Mathew Thomas
Published: November 2009

The problem of constructing a confidence interval for the ratio of two regression coefficients is addressed in the context of multiple regression. The concept of a Generalized Confidence Interval is used, and the resulting confidence interval is shown to perform well in terms of coverage probability. The proposed methodology always results in an interval, unlike the confidence region generated from Fieller's theorem. The procedure can easily be implemented for parallel‐line assays, slope‐ratio assays, and quantal assays under a probit model. Furthermore, this approach can also be extended to compute confidence intervals based on data from multiple bioassays. The results are illustrated using several examples.
Minimum‐Norm Estimation for Binormal Receiver Operating Characteristic (ROC) Curves
Authors: Davidov Ori , Nov Yuval
Published: November 2009

The receiver operating characteristic (ROC) curve is often used to assess the usefulness of a diagnostic test. We present a new method to estimate the parameters of a popular semi‐parametric ROC model, called the binormal model. Our method is based on minimization of the functional distance between two estimators of an unknown transformation postulated by the model, and has a simple, closed‐form solution. We study the asymptotics of our estimators, showviasimulation that they compare favorably with existing estimators, and illustrate how covariates may be incorporated into the norm minimization framework.
A low‐cost autonomous mobile robotics experiment: Control, vision, sonar, and Handy Board
Authors: Inanc Tamer , Dinh Huan
Published: November 2009

The aim of the paper is to demonstrate a design of a low‐cost mobile robotics experiment using LEGO Mindstorms Robotic Invention System kit, Handy Board microcontroller board, CMU camera, and SRF04 sonar sensor. The experiment is designed to be used as a laboratory session of a course on Fundamentals of Autonomous Robots. This hands‐on course aims to foster students' interests from different fields to autonomous mobile robotics and improve the education in this area. © 2009 Wiley Periodicals, Inc. Comput Appl Eng Educ 20: 203–213, 2012
Guidance on Safety/Health for Process Intensification including MS Design; Part II: Explosion Hazards
Authors: Klais O. , Westphal F. , Benaissa W. , Carson D.
Published: November 2009

The implementation of process intensification by multiscale equipment will have a profound impact on the way chemicals are produced. The shift to higher space‐time yields for partial oxidation processes using micro‐designed reactors comprises the risk of having a permanent explosive atmosphere in the reaction section. In Part I, it was concluded that spontaneous reaction with hot spots can be presumed if highly exothermic reactions were performed and may cause ignition of an explosive atmosphere. The risk analysis of the situation, based on public information in the literature, leads to the conclusion that microreactors are inherently safe regarding the initiation and propagation of an explosion inside a microchannel by an uncontrolled reaction. The situation is the opposite when a propagating explosion enters the same micro‐designed reactor from one of the outside openings. The external explosion may enter the micro‐designed equipment and destroy it when the same starting conditions are present.
Fullerene Dimers (C60/C70) for Energy Harvesting
Authors: Delgado Juan L. , Espíldora Eva , Liedtke Moritz , Sperlich Andreas , Rauh Daniel , Baumann Andreas , Deibel Carsten , Dyakonov Vladimir , Martín Nazario
Published: November 2009

A new family of fullerene‐based compounds, namely, soluble [60]‐ and [70]fullerene homodimers and the [60]/[70]heterodimer linked through 2‐pyrazolino–pyrrolidino bridges, has been synthesised by simple procedures and in high yield. Electrochemical studies confirm their suitability to act as electron acceptors in combination with poly(3‐hexylthiophene‐2,5‐diyl) (P3HT). Their optical properties in solution and in the solid state were studied. A significantly stronger absorption in [70]fullerene‐containing dimers relative to [60]homodimer in solution in the visible range was observed. Furthermore, in all donor–acceptor blends studied an efficient charge transfer was observed by means of photoluminescence (PL), photoinduced absorption and light‐induced electron spin resonance spectroscopy. The [70]homodimer was found to be a distinctive species, being the strongest PL quencher and most efficient acceptor with the longest lifetime of the charge‐separated (polaron) states. As a consequence, bulk‐heterojunction solar cells based on this novel [70]homodimer blended with P3HT demonstrated the highest quantum and power conversion efficiencies of 37 and 1 %, respectively, compared to those of [60]fullerene dimers.
Modellierung von Gas/Flüssig/Fest‐Reaktionen in engen Kanälen für das Regime der Kolbenströmung
Authors: Lange R. , Haase S. , Bauer T. , Langsch R.
Published: November 2009

Mikro‐ und Monolithreaktoren profitieren in Mehrphasenanwendungen von hohen Stofftransportraten der Gas/Flüssig‐Kolbenströmung zur Kanaloberfläche, an der die chemische Reaktion stattfindet. Auf der Basis eines weiterentwickelten Pseudo‐2D‐Modells zur Vorhersage von Konzentrations‐ und Temperaturprofilen in axialer Durchströmungsrichtung sowie innerhalb der porösen Kanalwand eines einzelnen Reaktionskanals werden Teilaspekte des Stofftransports detailliert analysiert sowie günstige Betriebsbedingungen und ein vorteilhaftes Kanaldesign für die technische Anwendung diskutiert.
How to Replace the Residual Solvation Shell of Polar Active Site Residues to Achieve Nanomolar Inhibition of tRNA‐Guanine Transglycosylase
Authors: Ritschel Tina , Kohler Philipp C. , Neudert Gerd , Heine Andreas , Diederich François , Klebe Gerhard
Published: November 2009

In a computational and structural study, we investigated a series of 4‐substituted lin‐benzoguanines that are potent inhibitors of tRNA‐guanine transglycosylase (TGT), a putative target for the treatment of shigellosis. At first glance, it appears self‐evident that the placement of a positively charged ligand functional group between the carboxylate groups of two adjacent aspartate residues in the glycosylase catalytic center leads to enhanced ligand binding. The concomitant displacement of water molecules that partially solvate the aspartates prior to ligand binding appears to result as a consequence of this. However, the case study presented herein shows that this premise is much too superficial. Placement of a likely positively charged amino group at such a pivotal position, interfering with the residual water solvation shell, is at best cost‐neutral compared with the unsubstituted parent ligand not conflicting with the residual water shell. A ligand that orients a hydroxy group in this position shows even decreased binding. Based on the cost‐neutral placement of the amino functionality, hydrophobic side chains can now be further attached to fill, with increasing potency, a small hydrophobic pocket remote to the aspartates. Any attempts to cross the pivotal position between both aspartates with nonpolar scaffolds reveals only decreased binding, even though the waters of the residual solvation shell are successfully repelled. This surprising observation fostered a detailed analysis of the role of water molecules involved in the residual solvation of polar active site residues. Their geometry and putative replacement in the binding pocket of TGT has been studied by a comparative database analysis, computational active site mapping, and a series of crystal structure analyses. Furthermore, conformational preferences of attached hydrophobic moieties explain their contribution to a gradual increase in binding affinity.