bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extrapolation-Based Acceleration of Iterative Solvers: Application to Simulation of 3D Flows
Authors: Grinberg Leopold , Karniadakis George Em 
Published: September 2010

AbstractWe investigate the effectiveness of two extrapolation-based methods aiming to approximate the initial state required by an iterative solver in simulations of unsteady flow problems. The methods lead to about a ten-fold reduction in the iteration count while requiring only negligible computational overhead. They are particularly suitable for parallel computing since they are based almost exclusively on data stored locally on each processor. Performance has been evaluated in simulations of turbulent flow in a stenosed carotid artery and also in laminar flow in a very large domain containing the human intracranial arterial tree.
The Debt-Growth Nexus in Poor Countries: A Reassessment
Authors: Presbitero Andrea F. 
Published: September 2010

Abstract
The paper investigates the relationship between external debt and economic growth, focusing on the role played by the policy and institutional framework. Results for a panel of 114 developing countries show that the debt-growth nexus depends on institutions and policies. The Debt-Laffer curve looses statistical significance once institutional quality is controlled for and debt overhang seems to be at work exclusively in countries with sound institutions. On the contrary, external debt proves to be irrelevant for countries with weak institutions. A policy implication is that efficient debt relief policies should be tailored to country-specific characteristics and conditional to a certain level of institutional quality.
Price-Concentration Analysis in Merger Cases with Differentiated Products
Authors: Beckert Walter , Mazzarotto Nicola 
Published: September 2010

AbstractThis paper considers the empirical assessment of the relationship between prices and number of firms in local markets in geographic or, more generally, characteristic space and its use as evidence in merger cases. It outlines a structural, semi-nonparametric econometric model of competition in such markets, examines its testable implications in terms of price-concentration relationships, and demonstrates that the model is non-parametrically identified. This general approach to price-concentration analysis in differentiated product markets is illustrated in a small-scale application to cinemas in the UK. The application highlights the main decision points faced by an authority when assessing the weight that can be attached to this type of analysis as evidence.
The Triffin Dilemma Again
Authors: Campanella Edoardo 
Published: September 2010

Abstract
Tiny changes in the American monetary policy can have dramatic effects on the rest of the world because of dollar’s double role of national and international currency. This is the Triffin dilemma. The paper shows how it works through three examples: price of commodities, dollarization, and the international financial position of the US. And it makes a proposal to solve these issues, creating a more stable monetary system. In particular, it suggests the creation of an international monetary system of block regional currencies. Globalization and regionalization should be the two forces leading towards the new monetary system. The US and Europe should consider to adopt the same currency through a system of fixed exchange rates (global currency). This currency should perform its duty of anchor of the system, reducing global imbalances and gyrations in price of commodities. Developing countries, by contrast, should create regional monetary unions (regional currencies), preserving the real exchange rate as shock absorber, but gaining in terms of time consistency and credibility.
DNA
‐Binding Proteins From Starved Cells (
Dps
Proteins)
Authors: Stefanini Simonetta , Ceci Pierpaolo , Ardini Matteo , Ilari Andrea 
Published: September 2010

Abstract
In the recent past over 200 Dps (DNA‐binding proteins from starved cells) proteins have been identified in bacterial genomes. Dps proteins belong to the ferritin superfamily. They are expressed under conditions of oxidative and/or nutritional stress and are characterized by a highly conserved shell‐like structure of 12 identical subunits assembled with 23 symmetry. The internal cavity is designed to accommodate up to 500 iron/atoms per molecule in a soluble and bioavailable form. Dps proteins play an important role in the complex protection mechanism against oxidative damage. The presence of a highly conserved ferroxidase center, which uses hydrogen peroxide as physiological iron oxidant, confers to all Dps proteins the capacity to decrease the production of the hydroxyl‐radicals and, hence, to prevent the damage to DNA and other cellular components. Ferroxidase activity is of special importance in pathogenic bacteria since production of hydrogen peroxide in macrophages and neutrophiles represents one of the first host defense mechanisms. The capacity to bind DNA in a nonspecific manner and pack it into condensed structures, an attribute limited to some members of the family, represents the second distinctive mechanism used to advantage by Dps proteins for the survival of the organism.
Bases and Base Catalysis—Heterogeneous
Authors: Ono Yoshio 
Published: September 2010

AbstractAlthough catalysis by solid bases has received much attention due to its importance in petroleum refining and petrochemical processes, relatively few studies have focused on catalysis by solid bases. Base catalysts, however, play a decisive role in a number of organic reactions essential for fine‐chemical synthesis. Solid‐base catalysis has many advantages over liquid bases in many respects from environmental aspects. This article offer general accounts of solid‐base catalysis and consists of three parts. The first part, gives the definition and concepts of solid bases and the methods for characterizing basic sites on solid surfaces. In the second part the typical solid‐base catalysts are surveyed. The solid bases include alkaline earth oxides, hydrotalcites and related materials, oxynitrides, zeolites, and modified zeolites alkaline metals and alkaline compounds such as KF/Al2O3and KNH2/Al2O3and amines anchored on mesoporous silica. The third part will show that a great variety of organic reactions is catalyzed by solid bases. The reactions described include the isomerization of alkenes and alkyns, aldol condensation, nitroaldol condensation, Knoevenagel condensation, Michael addition, substitution reactions, reactions of silicon compounds, and alkylation reactions.
Biphasic Catalysis—Homogeneous
Authors: Joó Ferenc 
Published: September 2010

AbstractHomogeneous catalysis offers advantages over heterogeneous catalytic methods in that all catalyst molecules are available for the substrate, and the catalyst can be tailored to the desired chemical transformation by choosing (designing) the proper ligand environment. In most cases, however, industry uses heterogeneous catalysts because (in addition to their high activity and selectivity) catalyst–product separation poses no serious problems. A successful way of heterogenization of homogeneous catalysts is the separation of the reactants (products) and the catalyst into immiscible liquid phases (liquid multiphase catalysis).This article reviewsbiphasic catalysiswith homogeneously (molecularly) dispersed catalysts. Attention is focused on liquid–liquid biphasic systems, containing all the reactants and the catalyst(s) in dissolved state. Such biphasic systems are built up of two or more solvents with limited mutual solubility.Aqueous–organicandorganic–organic(including alsofluorous) biphasic systems have been studied for long; however, the use of biphasic reaction mixtures designed by usingfluorous solvents,ionic liquids, andsupercritical gasesin combination with each other or with appropriate aqueous or organic solvents has been rapidly developing recently. The properties of such systems together with the need of special ligand design or modifications are discussed, and their use is illustrated by describing typical reactions (hydrogenation, hydrogen transfer, hydroformylation, hydrocarboxylation, carbonylation, alkene metathesis, dimerization, polymerization, and other CC coupling reactions).
Mononuclear Ruthenium Catalysis
Authors: Woolley Graham , Rosenberg Edward 
Published: September 2010

Abstract
The various reactions catalyzed by mononuclear ruthenium complexes are reviewed through 2008. The reactions discussed are hydrogenation with dihydrogen of carbon–carbon multiple bonds and carbon–heteroatom bonds, hydrogenation via hydrogen transfer, oxidation of carbon–heteroatom bonds, oxidation of carbon–carbon bonds, oxidation of alkanes, nucleophilic addition to alkynes, reactions involving C–H activation, olefin metathesis, reactions involving allyl ruthenium intermediates, and a brief discussion of radical reactions involving mononuclear ruthenium complexes. The article attempts to emphasize the use of chiral auxiliaries for obtaining enantiospecific transformations and the impact of ligand structure on the mechanistic aspects of a particular transformation. The article is not intended to be comprehensive but tries to survey the range of organic transformations currently employing mononuclear ruthenium reactions. More than half of the references are from the past 10 years.
Extremophiles
Authors: Ozdemir Inci , Kelly Robert M. 
Published: September 2010

AbstractExtremophiles are microorganisms with the ability to survive under extreme environmental conditions, including geothermal and arctic waters, glacial ices, deserts, saline lakes, and acidic, sulfurous hot springs. Adaptation of extremophiles to harsh conditions and unique stability of the enzymes (extremozymes) from these organisms have recently attracted a great deal of attention. Extremozymes have been replacing enzymes, which do not cope with harsh conditions, in many industries, such as pharmaceutical, food, chemical, laundry detergents, and bioremediation. Furthermore, there is an increasing demand of novel applications of these biocatalysts, working optimally over a range of extreme conditions, such as high temperature, high salinity, and high alkalinity. Developments in gene discovery and gene expression technologies hopefully will expand the exploitation of these biocatalysts. In this study, different types of extremophiles are introduced and the adaptations to extreme conditions for each condition are pointed. The biocatalysts from overlooked extremophiles and the applications of these biocatalysts are highlighted.
Reforming—Industrial
Authors: Moser Mark , Sadler Clayton C. 
Published: September 2010

AbstractCatalytic reforming is one of the primary processes of refining. It is used widely today throughout the petroleum and petrochemical industries. The catalytic reforming unit is used for the production of the primary component of high‐octane motor fuels and also for the production of feedstocks for petrochemical processes. This article discusses the history of the technology, its various adaptations and current developments. The chemical reactions, their rates, thermodynamics, and reaction conditions are described. The properties of the feed and products are listed, as are process contaminants and their removal. Catalyst deactivation and the subsequent regeneration of the catalyst are discussed. Various methods of process modeling are listed. The composition and properties of the catalysts used are provided. Finally, a case study of an evaluation of process economics is given.
Understanding Enzyme Catalysis Using Computer Simulation
Authors: Parks Jerry M. , Imhof Petra , Smith Jeremy C. 
Published: September 2010

AbstractEnzymes catalyze biochemical reactions with remarkable specificity and efficiency, usually under physiological conditions. Computer simulation is a powerful tool for understanding enzyme catalytic mechanisms, particularly in cases where standard experimental techniques may be of limited utility. Here, we present an overview of the application of computer simulation techniques to understand enzyme catalytic mechanisms. Examples using quantum chemical methods and quantum mechanical/molecular mechanical approaches are provided.
Virtual Screening
Authors: Muegge Ingo , Oloff Scott 
Published: September 2010

AbstractVirtual screening can be considered asin silicoanalog to high‐throughput screening. It is a knowledge‐driven approach toward finding new lead structures for drug discovery. There are a large variety of different virtual screening approaches and strategies available today. They include ligand‐based approaches such as compound similarity searching, pharmacophore searching, and applying predictive models derived using machine learning techniques as well as structure‐based approaches such as docking and scoring that use information about the protein target structures. Triaging hit sets using target‐independent filters such as drug‐likeness and diversity is an additional component of virtual screening. Using different virtual screening approaches in synergy has become more prevalent. Virtual screening applications have been combined with modern drug discovery technologies such as fragment‐based screening, combinatorial chemistry, and scaffold hopping methods to increase their effectiveness as lead identification tools.
Gene Therapy with PlasmidDNA
Authors: Bathula Surendar Reddy , Huang Leaf 
Published: September 2010

AbstractGene therapy is a promising therapeutic modality for the treatment of inherited as well as acquired genetic disorders. It can be defined as the use of nucleic acid transfer, either RNA or DNA, to treat or prevent a disease. Although initially most research on gene therapy has focused on the development of viral‐mediated approaches to deliver therapeutic genes to cells bothex vivoandin vivo, nonviral gene medicines have emerged as a potentially safe and effective gene therapy method for the treatment of a wide variety of acquired and inherited disorders. Compared to viral vectors, this delivery system has received great attention due to their several favorable properties, including low toxicity and immunogenicity, resistance to nuclease, and their efficiency is independent on size of the genetic cargo. One of the simplest approaches of delivery is direct gene transfer with naked plasmid DNA to the organs of interest.Plasmid DNAs (pDNAs), which carry recombinant genes of interest, are used for introducing genes to cells and organs. Various physical methods, for example, gene gun, electroporation, sonoporation, and laser irradiation increase the efficiency of the naked DNA incorporation. Synthetic gene delivery vectors such as cationic lipids and cationic polymers have the advantage of protecting the DNA against degradation by endogenous DNasein vivo, and can be targeted to a specific cellular site in some special cases. Varieties of lipid‐based systems have been designed, mostly containing cationic lipids of different structures. Vectors containing polymers, either synthetic or natural, have also been developed. Although significant progress has been made, nonviral vectors are still limited in their efficiency and by some cytotoxicity inherited in the bacterial pDNA, which hosts the gene of interest. Understanding mechanisms and means to overcome the cellular barriers for the DNA delivery will undoubtedly promote further development of pDNA‐mediated gene delivery. Great advancement has recently been made in the delivery of oligonucleotides, including siRNA, by nonviral vectors. This is because the nuclear membrane is not a delivery barrier for most of the oligonucleotides.
Recent Trends in Structure‐Based Drug Design and Energetics
Authors: Andricopulo Adriano D. , Guido Rafael V.C. , Trivella Daniela B.B. , Polikarpov Igor , Leitão Andrei , Montanari Carlos 
Published: September 2010

AbstractThe integration of cheminformatics tools, thermodynamic data, and structural information play a major role in the drug discovery process. Altogether, these methods can describe the molecular forces that govern the affinity and selectivity of bioactive molecules for their macromolecular targets. By being able to uncover the relationships between structure and energetics when using high‐resolution structural information and modern biophysical methods, one can fulfill the challenge of correctly interpreting drug–macromolecular interactions. These interactions are prone to be unveiled and scrutinized when structure‐based drug design is applied to a known three‐dimensional (3D) structure of a given protein. If fully integrated with structure‐based ligand design in an iterative way, computational methods can be of invaluable help to describe the ligand–target (cocomplex) formation. Structure‐based virtual screening can be used to rapid cherry‐pick the best candidates from a large pool of compounds in a chemical library after docking into the active sites of 3D protein structures. To pursue this, the quantification of favorable and unfavorable interactions requires knowledge of the thermodynamics of the interactions. Docking algorithms and molecular dynamics simulations can be used to predict binding energies for positioning ligands in target binding sites, but they only provide information regarded to the prediction of the change in the Gibbs free energy change, which hampers the thoroughly dissection of all other very important thermodynamic parameters—enthalpy, entropy, and heat capacity change. The major goal of this chapter is to show the integration of structure‐based drug design with the energetic. Microcalorimetric measurement of the drug–macromolecular interaction is an effective way to enhance the power, the medicinal chemists have on hand, to pursue a knowledge‐based approach toward the description of all of the noncovalent bond terms that take place in the cocomplex formation.
Use of Biological Fingerprints Versus Structure/Chemotypes to Describe Molecules
Authors: Mason Jonathan S. 
Published: September 2010

AbstractMolecules are usually described by their chemical structure and by fingerprints derived from this. These range from 2D structure based, that only represent the underlying structure that gives rise to the properties recognized by a biological target to 3D pharmacophores or molecular interaction fields, that much better represent how the protein binding sites would “see” a molecule. However, all of these have many limitations, including conformation for the 3D structure‐based approaches. More recently, experimental profiling data have been generated that enables a molecule to be described by a fingerprint of binding affinity to a diverse set of biological targets (pharmacological and “antitargets” such as CYP450 metabolic enzymes). These results show that small changes in structure can cause large changes in broad biological profile, and that a structure‐based analysis/clustering of compounds, such as different hits, leads, or clinical candidates, often does not provide a differentiation that is relevant in biological space. The data show that “selective” versus “nonselective” compounds, and the type of off‐target effects are not evident from a “chemotype” approach. The concept of “biological fingerprints” as a better way to describe compounds of biological interest is described in this chapter, focusing on the power of these descriptors versus structure‐based descriptors to differentiate compounds and enable the selection of the best lead compounds.
Process Development of Protein Therapeutics
Authors: Thomas James N. , Guhan S. Sam , Pettit Dean K. 
Published: September 2010

AbstractThe application of recombinant DNA technology to the production of protein therapeutics has undergone considerable progress since first introduced 30 years ago. Considerable scientific effort has been devoted to developing robust processes that produce large amounts of complex proteins with the desired product quality attributes. An overview of the contributions from the four major disciplines working in concert to deliver these processes and methods will be covered. This chapter will discuss some of the tools, methods, and approaches used to produce, purify, formulate, and analyze the drugs of modern biotechnology. Future trends in each of the disciplines will also be presented.
Multiple Sclerosis
Authors: Huryn Donna M. 
Published: September 2010

Abstract

Multiple sclerosis
(
MS
) is a severe, debilitating disease that affects more than a million individuals worldwide. Unfortunately, most aspects of this disease are poorly understood, thereby making drug discovery efforts particularly challenging. Historically, therapeutics for MS have relied on broad immunosuppression, and therefore these agents cause significant limiting side effects. Many of these older drugs were developed first as cancer therapeutics, and their ability to prevent the proliferation of immune cells was exploited in treating MS patients. Other current frontline therapies include immunosuppressants and immunomodulators that originally found use in inflammatory or other automimmune disorders. Current efforts are focusing on a more subtle approach at immunomodulation that target specific aspects of the immune response or putative MS autoantigens. This chapter provides an overview of currently approved therapies, including small‐molecule and protein‐based therapeutics as well as a more detailed review of promising new approaches, particularly those with a medicinal chemistry component.
Hsp
90 Inhibitors
Authors: Blagg Brian S. J. , Hadden M. Kyle 
Published: September 2010

Abstract
The Hsp90 molecular chaperones represent a promising target for the development of anticancer and neuroprotective agents as they are responsible for the conformational maturation of numerous signaling proteins and the refolding of aggregated proteins, respectively. In this chapter, a summary of recent developments toward the treatment of these diseases by small‐molecule modulators of Hsp90 is provided.
Histone Deacetylase Inhibitors: A Brief Overview Of Their Role And Medicinal Chemistry
Authors: Angibaud P. , Van Emelen K. , Arts J. 
Published: September 2010

Abstract

Histone deacetylase
s (
HDAC
s) comprise a family of proteins that impact critical cellular processes through regulation of chromatin remodeling and gene transcription. HDACs have emerged as attractive targets for the development of new anticancer agents and a number of structurally diverse inhibitors of HDAC from natural or synthetic origin have been described in the literature. This chapter focuses on those having reached clinical phases. For each, synthesis pathway,
in vitro
properties and short clinical profiles are presented. Recent developments in medicinal chemistry of HDAC inhibition are also reported.
Polymer Light‐Emitting Diodes
Authors: Weder Christoph , Kostka James 
Published: September 2010

Abstract
Electroluminescent devices based on polymeric materials have been a primary subject of research interest because of their potential for display and solid‐state lighting applications. These types of devices, termed polymer light‐emitting diodes, or PLEDs, offer the efficiency and lifetime benefits associated with solid‐state semiconductor technology, in addition to cost effective solution processing. Due to these inherent advantages, the field has grown rapidly over the past two decades, beyond the point of commercial exploitation. This article summarizes the exciting progress of the technology, addressing a broad range of topics including operating principles, device architecture, materials selection, and application requirements.
Smart Polymers–Biotechnological and Biomedical Applications
Authors: Galaev I. Yu. 
Published: September 2010

AbstractStimuli‐responsive or “smart” polymers undergo reversible phase separation from aqueous solutions triggered by small changes in the environment. The polymers are used in bioseparation (affinity precipitation, aqueous two‐phase polymer systems, smart chromatographic matrices responding to temperature), for production of smart surfaces for the mild detachment of cultivated mammalian cells, as a “chemical valve” regulating porosity of the system, as drug‐delivery systems, and for the development of microactuators and bioanalytical systems.