bluuebunny/crossref_metadata_2025 huggingface dataset:
Ciliate Telomerase Biochemistry
Authors: Collins Kathleen
Published: July 2002

▪ Abstract  Telomerase is a cellular reverse transcriptase specialized for use of a template carried within the RNA component of the enzyme ribonucleoprotein complex. Substrates for telomerase are single-stranded oligonucleotides in vitro and chromosome ends in vivo. In vitro, a bound substrate is extended by an initial round of DNA synthesis on the internal RNA template and in some cases by multiple rounds of template copying before product dissociation. In vivo, de novo synthesis of one strand of a telomeric repeat sequence by telomerase balances the sequence loss resulting from incomplete replication of linear chromosome ends by RNA primer-requiring DNA polymerases. Telomerase biochemistry has been studied extensively by using partially purified cell extracts. Telomerase components are being identified and beginning to be produced in recombinant form. This review focuses on the enzyme mechanism of telomerases from ciliate species, thus far the most intensively studied systems.
Advancing Our Knowledge in Biochemistry, Genetics, and Microbiology Through Studies on Tryptophan Metabolism
Authors: Yanofsky Charles
Published: July 2002

I was fortunate to practice science during the last half of the previous century, when many basic biological and biochemical concepts could be experimentally addressed for the first time. My introduction to research involved isolating and identifying intermediates in the niacin biosynthetic pathway. These studies were followed by investigations focused on determining the properties of genes and enzymes essential to metabolism and examining how they were alterable by mutation. The most challenging problem I initially attacked was establishing the colinear relationship between gene and protein. Subsequent research emphasized identification and characterization of regulatory mechanisms that microorganisms use to control gene expression. An elaborate regulatory strategy, transcription attenuation, was discovered that is often based on selection between alternative RNA structures. Throughout my career I enjoyed the excitement of solving basic scientific problems. Most rewarding, however, was the feeling that I was helping young scientists experience the pleasure of performing creative research.
Automatic Implantable Cardioverter-defibrillators
Authors: Smith William M. , Ideker Raymond E.
Published: July 2002

▪ Abstract  Ventricular fibrillation, a loss of synchronus electrical activity in the heart which leads to hemodynamic collapse, is a leading cause of death. Because of the devastating personal and societal effects of this phenomenon, the automatic cardioverter-defibrillator has been developed for automatic detection and termination of the arrhythmia and is in widespread clinical use. Advances in circuits, leads, waveforms, and signal processing along with increased knowledge of the mechanisms of fibrillation have led to continuing improvements in this device, extending its use to many patients. A device has also been developed for the automatic or semiautomatic treatment of atrial fibrillation, an arrhythmia less life-threatening than ventricular fibrillation, but still a serious health problem. Continued improvement of these devices and the development of qualitatively new approaches hold great promise for exciting therapeutic advances in this area.
PROTEIN FOLDS IN THE ALL-β AND ALL-α CLASSES
Authors: Chothia Cyrus , Hubbard Tim , Brenner Steven , Barns Hugh , Murzin Alexey
Published: July 2002

▪ Abstract  Analysis of the structures in the Protein Databank, released in June 1996, shows that the number of different protein folds, i.e. the number of different arrangements of major secondary structures and/or chain topologies, is 327. Of these folds, approximately 25% belong to the all-α class, 20% belong to the all-β class, 30% belong to the α/β class, and 25% belong to the α + β class. We describe the types of folds now known for the all-β and all-α classes, emphasizing those that have been discovered recently. Detailed theories for the physical determinants of the structures of most of these folds now exist, and these are reviewed.
BACTERIAL CELL DIVISION
Authors: Bramhill David
Published: July 2002

▪ Abstract  Bacteria usually divide by building a central septum across the middle of the cell. This review focuses on recent results indicating that the tubulin-like FtsZ protein plays a central role in cytokinesis as a major component of a contractile cytoskeleton. Assembly of this cytoskeletal element abutting the membrane is a key point for regulation. The characterization of FtsZ homologues in Mycoplasmas, Archaea, and chloroplasts implies that the constriction mechanism is conserved and that FtsZ can constrict in the absence of peptidoglycan synthesis. In most Eubacteria, the internal cytoskeleton must also regulate synthesis of septal peptidoglycan. The Escherichia coli septum-specific penicillin-binding protein 3 (PBP3) forms a complex with other enzymes involved in murein metabolism, suggesting a centrally located transmembrane complex capable of splicing multiple new strands of peptidoglycan into the cell wall. Important questions remain about the spatial and temporal control of bacterial division.
MECHANISMS OF WNT SIGNALING IN DEVELOPMENT
Authors: Wodarz Andreas , Nusse Roel
Published: July 2002

▪ Abstract  Wnt genes encode a large family of secreted, cysteine-rich proteins that play key roles as intercellular signaling molecules in development. Genetic studies in Drosophila and Caenorhabditis elegans, ectopic gene expression in Xenopus, and gene knockouts in the mouse have demonstrated the involvement of Wnts in processes as diverse as segmentation, CNS patterning, and control of asymmetric cell divisions. The transduction of Wnt signals between cells proceeds in a complex series of events including post-translational modification and secretion of Wnts, binding to transmembrane receptors, activation of cytoplasmic effectors, and, finally, transcriptional regulation of target genes. Over the past two years our understanding of Wnt signaling has been substantially improved by the identification of Frizzled proteins as cell surface receptors for Wnts and by the finding that β-catenin, a component downstream of the receptor, can translocate to the nucleus and function as a transcriptional activator. Here we review recent data that have started to unravel the mechanisms of Wnt signaling.
Stem and Progenitor Cells: Origins, Phenotypes, Lineage Commitments, and Transdifferentiations
Authors: Weissman Irving L. , Anderson David J. , Gage Fred
Published: July 2002

▪ Abstract  Multipotent stem cells are clonal cells that self-renew as well as differentiate to regenerate adult tissues. Whereas stem cells and their fates are known by unique genetic marker studies, the fate and function of these cells are best studied by their prospective isolation. This review is about the properties of various highly purified tissue-specific multipotent stem cells and purified oligolineage progenitors. We contend that unless the stem or progenitor cells in question have been purified to near homogeneity, one cannot know whether their generation of expected (or unexpected) progeny is a property of a known cell type. It is interesting that in the hematopoietic system the only long-term self-renewing cells in the stem and progenitors pool are the hematopoietic stem cells. This fact is discussed in the context of normal and leukemic hematopoiesis.
THE ENIGMA OF THE NEW MADRID EARTHQUAKES OF 1811–1812
Authors: Johnston Arch C. , Schweig Eugene S.
Published: July 2002

▪ Abstract  Continental North America's greatest earthquake sequence struck on the western frontier of the United States. The frontier was not then California but the valley of the continent's greatest river, the Mississippi, and the sequence was the New Madrid earthquakes of the winter of 1811–1812. Their described impacts on the land and the river were so dramatic as to produce widespread modern disbelief. However, geological, geophysical, and historical research, carried out mostly in the past two decades, has verified much in the historical accounts. The sequence included at least six (possibly nine) events of estimated moment magnitude M ≥ 7 and two of M ≃ 8. The faulting was in the intruded crust of a failed intracontinental rift, beneath the saturated alluvium of the river valley, and its violent shaking resulted in massive and extensive liquefaction. The largest earthquakes ruptured at least six (and possibly more than seven) intersecting fault segments, one of which broke the surface as a thrust fault that disrupted the bed of the Mississippi River in at least 2 (and possibly four) places.

…it is a riddle wrpped in a mystery inside an enigma.

     Winston Churchill
The Evolutionary Ecology of Tolerance to Consumer Damage
Authors: Stowe Kirk A. , Marquis Robert J. , Hochwender Cris G. , Simms Ellen L.
Published: July 2002

▪ Abstract  Recent theoretical studies suggest that the ability to tolerate consumer damage can be an important adaptive response by plants to selection imposed by consumers. Empirical studies have also found that tolerance is a common response to consumers among plants. Currently recognized mechanisms underlying tolerance include several general sets of traits: allocation patterns; plant architecture; and various other traits that may respond to consumer damage, e.g., photosynthetic rate. Theoretical studies suggest that tolerance to consumer damage may be favored under a range of conditions, even when the risk and intensity of damage varies. However, most of these models assume that the evolution of tolerance is constrained by internal resource allocation trade-offs. While there is some empirical evidence for such trade-offs, it is also clear that external constraints such as pollinator abundance or nutrient availability may also limit the evolution of tolerance. Current research also suggests that a full understanding of plant adaptation to consumers can only be achieved by investigating the joint evolution of tolerance and resistance. While tolerance to consumer damage has just recently received significant attention in the ecological literature, our understanding of it is rapidly increasing as its profound ecological and evolutionary implications become better appreciated.
Impact of the Internet on Extension Entomology
Authors: VanDyk J.K.
Published: July 2002

▪ Abstract  Acceptance of the Internet as a common method for transferring entomological information has forced a re-evaluation of extension entomology’s role. The discipline of entomology was an early adopter of Internet-based information delivery and organization on both Gopher and the World Wide Web. New opportunities exist for immediate presentation and collection of information, but organization and categorization of information for timely retrieval remains a challenge. Metadata strategies, computer literacy, and integration of the Internet with current workflow paradigms promise to change the way extension entomology is done in the near future.
FILAMENT-STRETCHINGRHEOMETRY OFCOMPLEXFLUIDS
Authors: McKinley Gareth H. , Sridhar Tamarapu
Published: July 2002

▪ Abstract  Filament-stretching rheometers are devices for measuring the extensional viscosity of moderately viscous non-Newtonian fluids such as polymer solutions. In these devices, a cylindrical liquid bridge is initially formed between two circular end-plates. The plates are then moved apart in a prescribed manner such that the fluid sample is subjected to a strong extensional deformation. Asymptotic analysis and numerical computation show that the resulting kinematics closely approximate those of an ideal homogeneous uniaxial elongation. The evolution in the tensile stress (measured mechanically) and the molecular conformation (measured optically) can be followed as functions of the rate of stretching and the total strain imposed. The resulting rheological measurements are a sensitive discriminant of molecularly based constitutive equations proposed for complex fluids. The dynamical response of the elongating filament is also coupled to the extensional rheology of the polymeric test fluid, and this can lead to complex viscoelastic-flow instabilities such as filament necking and rupture or elastic peeling from the rigid end-plates.
UBIQUITIN-DEPENDENT PROTEIN DEGRADATION
Authors: Hochstrasser Mark
Published: July 2002

▪ Abstract  A growing number of cellular regulatory mechanisms are being linked to protein modification by the polypeptide ubiquitin. These include key transitions in the cell cycle, class I antigen processing, signal transduction pathways, and receptor-mediated endocytosis. In most, but not all, of these examples, ubiquitination of a protein leads to its degradation by the 26S proteasome. Following attachment of ubiquitin to a substrate and binding of the ubiquitinated protein to the proteasome, the bound substrate must be unfolded (and eventually deubiquitinated) and translocated through a narrow set of channels that leads to the proteasome interior, where the polypeptide is cleaved into short peptides. Protein ubiquitination and deubiquitination are both mediated by large enzyme families, and the proteasome itself comprises a family of related but functionally distinct particles. This diversity underlies both the high substrate specificity of the ubiquitin system and the variety of regulatory mechanisms that it serves.
UNDERSTANDING GENE AND ALLELE FUNCTION WITH TWO-HYBRID METHODS
Authors: Brent Roger , Finley Jr Russell L.
Published: July 2002

▪ Abstract  Two-hybrid schemes for detecting protein-protein interactions have deepened our understanding of biology by allowing scientists to identify individual important proteins. Recent developments will allow biologists to chart regulatory networks and to rapidly generate hypotheses for the function of genes, allelic variants, and the connections between proteins that make up these networks. Future developments will allow biologists to test inferences about the function of network elements, and allow global approaches to questions of biological function.
THE GENETICS OF HYPHAL FUSION AND VEGETATIVE INCOMPATIBILITY IN FILAMENTOUS ASCOMYCETE FUNGI
Authors: Glass N. Louise , Jacobson David J. , Shiu Patrick K. T.
Published: July 2002

▪ Abstract  Filamentous fungi grow as a multicellular, multinuclear network of filament-shaped cells called hyphae. A fungal individual can be viewed as a fluid, dynamic system that is characterized by hyphal tip growth, branching, and hyphal fusion (anastomosis). Hyphal anastomosis is especially important in such nonlinear systems for the purposes of communication and homeostasis. Filamentous fungi can also undergo hyphal fusion with different individuals to form heterokaryons. However, the viability of such heterokaryons is dependent upon genetic constitution at heterokaryon incompatibility (het) loci. If hyphal fusion occurs between strains that differ in allelic specificity at het loci, vegetative incompatibility, which is characterized by hyphal compartmentation and cell lysis, is induced. This review covers microscopic and genetic analysis of hyphal fusion and the molecular and genetic analysis of the consequence of hyphal fusion between individuals that differ in specificity at het loci in filamentous ascomycetes.
How Many Genes Can Make a Cell: The Minimal-Gene-Set Concept
Authors: Koonin Eugene V.
Published: July 2002

Several theoretical and experimental studies have endeavored to derive the minimal set of genes that are necessary and sufficient to sustain a functioning cell under ideal conditions, that is, in the presence of unlimited amounts of all essential nutrients and in the absence of any adverse factors, including competition. A comparison of the first two completed bacterial genomes, those of the parasites Haemophilus influenzae and Mycoplasma genitalium, produced a version of the minimal gene set consisting of ∼250 genes. Very similar estimates were obtained by analyzing viable gene knockouts in Bacillus subtilis, M. genitalium, and Mycoplasma pneumoniae. With the accumulation and comparison of multiple complete genome sequences, it became clear that only ∼80 genes of the 250 in the original minimal gene set are represented by orthologs in all life forms. For ∼15% of the genes from the minimal gene set, viable knockouts were obtained in M. genitalium; unexpectedly, these included even some of the universal genes. Thus, some of the genes that were included in the first version of the minimal gene set, based on a limited genome comparison, could be, in fact, dispensable. The majority of these genes, however, are likely to encode essential functions but, in the course of evolution, are subject to nonorthologous gene displacement, that is, recruitment of unrelated or distantly related proteins for the same function. Further theoretical and experimental studies within the framework of the minimal-gene-set concept and the ultimate construction of a minimal genome are expected to advance our understanding of the basic principles of cell functioning by systematically detecting nonorthologous gene displacement and deciphering the roles of essential but functionally uncharacterized genes.
CAPTURE AND PROCESSING OF EXOGENOUS ANTIGENS FOR PRESENTATION ON MHC MOLECULES
Authors: Watts Colin
Published: July 2002

▪ Abstract  Class I and class II MHC molecules bind peptides during their biosynthetic maturation and provide a continuously updated display of intracellular and environmental protein composition, respectively, for scrutiny by T cells. Receptor-mediated endocytosis, phagocytosis, and macropinocytosis all contribute to antigen uptake by class II MHC-positive antigen-presenting cells. Capture of antigenic peptides by class II MHC molecules is facilitated because antigen catabolism and class II MHC maturation take place in the same compartments or in communicating compartments of the endosome/lysosome system. These class II MHC-rich, multivesicular endosomes receive incoming antigen and can support not only antigen processing and class II MHC peptide loading but also the export of peptide/class II MHC complexes to the cell surface. A balance between production and destruction of antigenic peptides is achieved by the activity of local proteases and may be influenced by binding of antigen to other proteins both prior to the onset of processing (e.g. antibodies) and during antigen unfolding (e.g. MHC molecules). T cell determinants that can be released for MHC binding without a substantial processing requirement may be able to utilize a distinct minor population of cell surface class II MHC molecules that become available during peripheral recycling. Although peptides derived from exogenous protein sources are usually excluded from presentation on class I MHC molecules, recent evidence shows that this embargo may be lifted in certain professional antigen-presenting cells to increase the spectrum of antigens that may be displayed on class I MHC.
TRANSCRIPTIONAL REGULATION OF T LYMPHOCYTE DEVELOPMENT AND FUNCTION
Authors: Kuo Chay T. , Leiden Jeffrey M.
Published: July 2002

▪ Abstract  The development and function of T lymphocytes are regulated tightly by signal transduction pathways that include specific cell-surface receptors, intracellular signaling molecules, and nuclear transcription factors. Since 1988, several families of functionally important T cell transcription factors have been identified. These include the Ikaros, LKLF, and GATA3 zinc-finger proteins; the Ets, CREB/ATF, and NF-κB/Rel/NFAT transcription factors; the Stat proteins; and HMG box transcription factors such as LEF1, TCF1, and Sox4. In this review, we summarize our current understanding of the transcriptional regulation of T cell development and function with particular emphasis on the results of recent gene targeting and transgenic experiments. In addition to increasing our understanding of the molecular pathways that regulate T cell development and function, these results have suggested novel targets for genetic and pharmacological manipulation of T cell immunity.
FATAL ASTHMA
Authors: FitzGerald, M.D J.M. , Macklem, M.D P.
Published: July 2002

▪ Abstract  This brief review highlights the rise in asthma mortality witnessed in many countries. It outlines the multifactorial character of this phenomenon, which in most instances is a complex interplay between physician, patient, and environment. The pathophysiology of airflow obstruction and in particular the role of hyperinflation are outlined. These data may allow better prediction of who is at risk of fatal asthma (FA). Finally, potential approaches to the prevention of FA are outlined.
New Approaches to Supporting the Failing Liver
Authors: Cao Sean , Esquivel Carlos O. , Keeffe Emmet B.
Published: July 2002

With the continued, growing disparity between the numbers of organ donations and patients waiting for liver transplantation, various efforts have been made to optimize the allocation of organs, as well as to devise means to support the failing liver. Over the years, the development of bioartificial liver-assist devices has aimed at replacing the three main functions of hepatocytes, which are synthetic, metabolic, and excretory. The application of porcine hepatocytes in humans to carry out biotransformation, as well as other metabolic functions and refinement of the membrane separator, have yielded some promising results in supporting patients with acute liver failure. Further advances will need to be made before these bioartificial devices can be considered for routine application in clinical settings.
The Challenge of Viral Reservoirs in HIV-1 Infection
Authors: Blankson Joel N. , Persaud Deborah , Siliciano Robert F.
Published: July 2002

▪ Abstract  A viral reservoir is a cell type or anatomical site in association with which a replication-competent form of the virus accumulates and persists with more stable kinetic properties than the main pool of actively replicating virus. This article reviews several cell types and anatomical sites proposed as potential reservoirs for HIV-1. It is now clear that HIV-1 persists in a small reservoir of latently infected resting memory CD4+T cells, which shows minimal decay even in patients on highly active antiretroviral therapy (HAART). The persistence of virus in this reservoir is consistent with the biology of these cells and the long-term persistence of immunologic memory. The viral replication that continues in patients on suppressive HAART may also contribute to the stability of this reservoir. There may be other reservoirs, but the latent reservoir in resting CD4+T cells appears to be sufficient to guarantee lifetime persistence of HIV-1 in the majority of patients on current HAART regimens, and unless new approaches are developed, eradication will not be possible. The clinical implications of this and other HIV-1 reservoirs are discussed.
Recombination and the Population Structures of Bacterial Pathogens
Authors: Feil Edward J. , Spratt Brian G.
Published: July 2002

▪ Abstract  The population structures of bacterial species are complex and often controversial. To a large extent, this is due to uncertainty about the frequency and impact of recombination in bacteria. The existence of clones within bacterial populations, and of linkage disequilibrium between alleles at different loci, is often cited as evidence for low rates of recombination. However, clones and linkage disequilibrium are almost inevitable in species that divide by binary fission and can be present in populations where recombination is frequent. In recent years, it has become possible to directly compare rates of recombination in different species. These studies indicate that in many bacterial species, including Neisseria meningitidis, Streptococcus pneumoniae, and Staphylococcus aureus, evolutionary change at neutral (housekeeping) loci is more likely to occur by recombination than mutation and can result in the elimination of any deep-rooted phylogenetic signal. In such species, the long-term evolution of the population is dominated by recombination, but this does not occur at a sufficiently high frequency to prevent the emergence of adaptive clones, although these are relatively short-lived and rapidly diversify.
GROWTH CONE GUIDANCE: First Steps Towards a Deeper Understanding
Authors: Mueller Bernhard K.
Published: July 2002

▪ Abstract  Growth cones, the hand-like structures at the tip of growing neurites, possess remarkable abilities to detect directional cues. On their way to their targets they traverse a dense jungle of many different cells, expressing a variety of different molecular guidance cues. Proper reading and integration of these cues is essential for precise wiring of different parts of the peripheral and central nervous systems. Guidance cues have been classified according to the response they elicit as either attractive or repulsive. Recent work, however, suggests that this might not represent an absolute distinction and that the internal state of the growth cone can dictate whether it detects a cue as repulsive or attractive. This article reviews some new experimental approaches to understanding growth cone signal transduction mechanisms induced by extracellular guidance cues.
Flies, Genes, and Learning
Authors: Waddell Scott , Quinn William G
Published: July 2002

▪ Abstract  Flies can learn. For the past 25 years, researchers have isolated mutants, engineered mutants with transgenes, and tested likely suspect mutants from other screens for learning ability. There have been notable surprises—conventional second messenger systems co-opted for intricate associative learning tasks, two entirely separate forms of long-term memory, a cell-adhesion molecule that is necessary for short-term memory. The most recent surprise is the mechanistic kinship revealed between learning and addictive drug response behaviors in flies. The flow of new insight is likely to quicken with the completion of the fly genome and the arrival of more selective methods of gene expression.
PROPERTIES OF HADRONS IN THE NUCLEAR MEDIUM
Authors: Ming Ko Che , Koch Volker , Li Guoqiang
Published: July 2002

▪ Abstract  This review is devoted to discussion of hadron properties in the nuclear medium and their relationship to the partial restoration of chiral symmetry. Special attention is given to the difference between in-medium effects caused by conventional many-body interactions and those caused by change of the chiral condensate. In particular, we discuss medium effects on the Goldstone bosons (pion, kaon, and η), the vector mesons (ρ, ω, and φ), and the nucleon. Also, for each proposed in-medium effect the experimental consequences and results are reviewed.
DIETARY PHYTOESTROGENS
Authors: Kurzer Mindy S. , Xu Xia
Published: July 2002

▪ Abstract  Broadly defined, phytoestrogens include isoflavones, coumestans, and lignans. A number of these compounds have been identified in fruits, vegetables, and whole grains commonly consumed by humans. Soybeans, clover and alfalfa sprouts, and oilseeds (such as flaxseed) are the most significant dietary sources of isoflavones, coumestans, and lignans, respectively. Studies in humans, animals, and cell culture systems suggest that dietary phytoestrogens play an important role in prevention of menopausal symptoms, osteoporosis, cancer, and heart disease. Proposed mechanisms include estrogenic and antiestrogenic effects, induction of cancer cell differentiation, inhibition of tyrosine kinase and DNA topoisomerase activities, suppression of angiogenesis, and antioxidant effects. Although there currently are no dietary recommendations for individual phytoestrogens, there may be great benefit in increased consumption of plant foods.
Protein Allergenicity Assessment of Foods Produced Through Agricultural Biotechnology
Authors: Taylor Steve L.
Published: July 2002

Foods produced through agricultural biotechnology are reaching the consumer marketplace. These novel foods should be assessed for their safety, including their potential allergenicity. Agricultural biotechnology involves the introduction of novel proteins into the modified foods, and proteins can be allergenic. The potential allergenicity of the introduced proteins can be evaluated by focusing on the source of the gene, the homology of the newly introduced protein to known allergens, the reactivity of the novel protein with IgE antibodies from the serum of individuals with known allergies to the source of the transferred DNA or to materials that are broadly related to the source of the transferred DNA, the resistance of the novel protein to pepsin, and the immunoreactivity of the novel protein in appropriate animal models. Additional factors, such as the level of expression of the novel protein in the modified food and expression in the edible portion of the food, may also yield valuable insights. Applying such criteria provides a reasonable approach to determining whether or not the novel protein is likely to become an allergen.
CONSTRUCTINGMULTIDIMENSIONALMOLECULARPOTENTIALENERGYSURFACES FROMABINITIODATA
Authors: Hollebeek Timothy , Ho Tak-San , Rabitz Herschel
Published: July 2002

▪ Abstract  This paper describes the reproducing kernel Hilbert space (RKHS) method for constructing accurate, smooth, and efficient global potential energy surface (PES) representations for polyatomic systems using high-level ab initio data. The RKHS method provides a rigorous and effective framework for smooth multivariate interpolation of arbitrarily scattered data points and also for incorporating various physical requirements onto the PESs. Smoothness, permutation symmetry, and the asymptotic properties of polyatomic systems can be incorporated into the construction of reproducing kernels to render globally accurate PESs. Tensor products of one-dimensional generalized-spline-reproducing kernels are amenable to a fast algorithm, which makes a single evaluation of RKHS PESs essentially independent of the number of interpolated ab initio data points. This efficient implementation enables the study of the detailed dynamics of polyatomic systems based on high-quality RKHS PESs.
A FREE RADICAL
Authors: Carrington Alan
Published: July 2002

[Figure: see text]

▪ Abstract  This chapter describes my research career, spanning the period from 1955 to 2000. My initial PhD work at the University of Southampton was concerned with the electronic structure and spectra of transition metal complexes and included studies of the electronic spin resonance (ESR) spectra of magnetically dilute single crystals. After a year at the University of Minnesota, I went to Cambridge University and for the next six years studied the ESR spectra of liquid phase organic free radicals. I commenced work on the microwave magnetic resonance (MMR) spectra of gaseous free radicals in 1965, and this work continued until 1975. I moved from Cambridge to Southampton in 1967. In 1975 I turned to the study of gas phase molecular ions, using ion beam methods. In the earlier years of this period I concentrated on simple fundamental species like H+2, HD+, and H+3. In the later years until my retirement in 1999, I concentrated on the observation and analysis of microwave spectra involving energy levels lying very close to a dissociation asymptote.

DEDICATION This chapter is dedicated to the memory of Harry E. Radford, who died while it was being written. Harry was a quiet and shy man, who often worked alone and never indulged in self-promotion. So far as I know, he was never awarded any medals or prizes, nor elected to any academies or learned societies. Nevertheless he was an experimentalist of the highest originality and quality, a theorist of true intellectual depth, and a remarkable pioneer in many of the techniques of studying free radicals that are now commonplace.
SURFACTANT PROTEINS: Molecular Genetics of Neonatal Pulmonary Diseases
Authors: Floros Joanna , Kala Padma
Published: July 2002

▪ Abstract  Genetic and phenotypic complexity has been described for diseases of varied etiology. Groups of patients with varied phenotype can be used in association studies as an initial approach to identify contributing loci. Although association studies have limitations, their value is enhanced by using candidate genes with functions related to disease. Surfactant proteins have been studied in the etiopathogenesis of neonatal pulmonary diseases. SP-A and SP-B polymorphisms are found at a higher frequency in certain groups of patients with respiratory distress syndrome (RDS), and SP-B mutations are linked to the pathogenesis of congenital alveolar proteinosis (CAP). Phenotypic heterogeneity is observed for both CAP and RDS. The available data suggest that a number of factors contribute to the etiology of CAP and RDS and, therefore, a multidisciplinary approach of clinical, genetic, epidemiologic, and statistical considerations is necessary for an in-depth understanding of the pathophysiology of these and other pulmonary diseases.
The Evolutionary Physiology of Animal Flight: Paleobiological and Present Perspectives
Authors: Dudley Robert
Published: July 2002

▪ Abstract  Recent geophysical analyses suggest the presence of a late Paleozoic oxygen pulse beginning in the late Devonian and continuing through to the late Carboniferous. During this period, plant terrestrialization and global carbon deposition resulted in a dramatic increase in atmospheric oxygen levels, ultimately yielding concentrations potentially as high as 35% relative to the contemporary value of 21%. Such hyperoxia of the late Paleozoic atmosphere may have physiologically facilitated the initial evolution of insect flight metabolism. Widespread gigantism in late Paleozoic insects and other arthropods is also consistent with enhanced oxygen flux within diffusion-limited tracheal systems. Because total atmospheric pressure increases with increased oxygen partial pressure, concurrently hyperdense conditions would have augmented aerodynamic force production in early forms of flying insects. By the late Permian, evolution of decompositional microbial and fungal communities, together with disequilibrium in rates of carbon deposition, gradually reduced oxygen concentrations to values possibly as low as 15%. The disappearance of giant insects by the end of the Permian is consistent with extinction of these taxa for reasons of asphyxiation on a geological time scale. As with winged insects, the multiple historical origins of vertebrate flight in the late Jurassic and Cretaceous correlate temporally with periods of elevated atmospheric oxygen. Much discussion of flight performance in Archaeopteryx assumes a contemporary atmospheric composition. Elevated oxygen levels in the mid- to late Mesozoic would, however, have facilitated aerodynamic force production and enhanced muscle power output for ancestral birds, as well as for precursors to bats and pterosaurs.
Surfactant Proteins A and D and Pulmonary Host Defense
Authors: Crouch Erika , Wright Jo Rae
Published: July 2002

▪ Abstract  The lung collectins, SP-A and SP-D, are important components of the innate immune response to microbial challenge and participate in other aspects of immune and inflammatory regulation within the lung. Both proteins bind to surface structures expressed by a wide variety of microorganisms and have the capacity to modulate multiple leukocyte functions, including the enhanced internalization and killing of certain microorganisms in vitro. In addition, transgenic mice with deficiencies in SP-A and SP-D show defective or altered responses to challenge with bacterial, fungal, and viral microorganisms and to bacterial lipopolysaccharides in vivo. Thus collectins could play particularly important roles in settings of inadequate or impaired specific immunity, and acquired alterations in the levels of active collectins within the airspaces and distal airways may increase susceptibility to infection.
E.M. FREEMAN: Early Research on Cereal Diseases and the Rise of Plant Pathology at the University of Minnesota
Authors: Peterson Paul D.
Published: July 2002

[Figure: see text]

▪ Abstract  E.M. Freeman's role in early cereal disease research and the beginning of plant pathology at the University of Minnesota has been overshadowed largely by the enormous prestige of his student, E.C. Stakman. During the first decade of the twentieth century, Freeman was responsible for the transferral from Europe to the United States and the subsequent nurturing of important conceptual and technical developments in the area of cereal disease pathology. Under Freeman's leadership, these ideas would come to shape the direction of plant pathology research at the University of Minnesota for decades to follow.
Preference-Based Measures in Economic Evaluation in Health Care
Authors: Neumann Peter J. , Goldie Sue J. , Weinstein Milton C.
Published: July 2002

▪ Abstract  Estimating preferences for states of health has been an active area of research in recent years. Unlike psychophysical approaches, which discriminate levels of health status, preference-based approaches incorporate values or utilities for health outcomes and can be used in cost-effectiveness analyses to aid resource allocation decisions. This chapter considers issues and controversies involved in using preference-based measures in economic evaluation in health care, with a particular emphasis on cost-utility analysis and the estimation of quality-adjusted life years. Topics considered include techniques for measuring preferences, the use of preference-based classification systems, the relationship between patient and community preferences, methods for obtaining utilities from clinical trials, mapping health status from health utilities, the development of “off-the-shelf” preference weights, and proposed alternatives to quality-adjusted life years. We also consider applications of cost-utility analyses to public health interventions. Although cost-utility analyses have become more popular recently, many challenges remain for the field. Widespread acceptance of the methodology likely awaits more consensus on measurement techniques, as well as educational efforts in the public health and medical communities on the usefulness of the approach.
Sociological Work in Japan
Authors: Nakao Keiko
Published: July 2002

The aim of this paper is to provide an overview of contemporary sociology in Japan. The sociological discipline in Japan has made remarkable progress since World War II. The rapid economic growth during the 1960s, which was prompted by Western influence, had an effect on the direction of the discipline's development. After providing a brief overview of historical events, I consider scholarly publications during the last 30 years to illuminate substantive trends in sociological research. As might be predicted, the changing substantive interests of Japanese sociologists have been in many ways a response to societal changes and needs. I also examine the trends in theory, methods, and empirical research. A content analysis of articles published in the major Japanese sociological journals shows the growing emphasis on theoretical scholarship and the decreasing emphasis on empirical research in recent years. The conclusion presents some considerations concerning the future direction of Japanese sociology.
Proper Nouns and Methodological Propriety: Pooling Dyads in International Relations Data
Authors: King Gary
Published: July 2002

This article provides a concluding comment on the symposium focusing on Donald P. Green, Soo Yeon Kim, and David H. Yoon's “Dirty Pool.” Although the perspectives offered by the three sets of authors participating in the symposium differ starkly, my view (supported by conversations with the authors and additional analyses and debates among all involved) is that there is now a large area of underlying agreement. I describe this agreement by first illuminating Green, Kim, and Yoon's fundamental contribution in understanding and high lighting the role of heterogeneity in dyad-level studies of international conflict. I then describe the limitations in their revised analytic strategy, including those raised by John R. Oneal and Bruce Russett and by Nathaniel Beck and Jonathan N. Katz. I also offer suggestions for future researchers, methodologists, and data collectors.
Varying methods of state violence
Authors: Ron James
Published: July 2002

At some point during 1991–92, something substantial changed in the way Israel's security agencies interrogated Palestinian detainees. The change was not in the number of detainees interrogated; on any given day in 1993, some four hundred to six hundred Palestinians continued to be interrogated by either the General Security Services (GSS) or the military (Israel Defense Forces; IDF). Overall, Israel interrogated some five thousand Palestinians every year from 1988 to 1994. Nor was the change one of interrogation results: the conviction rate of Palestinians in the military courts remained above 96 percent, with most convictions based on confessions obtained during interrogation. According to official statistics, of the 83,321 Palestinians tried in military courts in the West Bank and Gaza Strip between 1988 and 1993, only 2,731, or 3.2 percent, were acquitted. The security forces were still questioning a remarkable proportion of the adult male population, obtaining vast amounts of information on Palestinian social, political, and military activities.
Food for Growth: Trends in Indonesia's Food Supply, 1880-1995
Authors: van der Eng Pierre
Published: July 2002

A decline in Indonesia's per capita rice supply until the 1970s was marginal in relation to food supply as a whole. Until the 1970s, trends were determined by non-rice food crops. Indonesia was long unable to satisfy an increase in the demand for food with a higher supply of rice. From 1905 to 1920, cassava products met the additional demand for carbohydrates, which grew with purchasing power. During the interwar years, per capita food supply decreased slightly, mainly because demand shifted from staple foods to cheap manufactures. From 1943 to 1970, Indonesia experienced a drastic fall in food supply per capita due to an acceleration in population growth, restrictive regulations imposed on food markets, and the general demise of the Indonesian economy. The upward trend in per capita food supply since the 1960s was caused largely by increases in rice production, generated by government support to rice farmers. Higher incomes brought an increased demand for food, which could be met with inexpensive rice.
Gender and the “Lost” Spaces of Catholicism
Authors: Dolan Frances E.
Published: July 2002

The Reformation in England was largely a contest over space and its social meanings and uses. Gender intersected with religious affiliation in struggles over the control of several particularly fruitful sites: court chapels, prisons, households, and beds. Although Catholics lost many devotional, social, and political spaces in the wake of the Reformation, they also developed a tactical and adaptive relationship to space that fostered Catholic survival.
The Ecological Imperative: Elements of Nature in Late Twentieth-Century Art
Authors: Mańczak Aleksandra
Published: July 2002

The author draws attention to visual artworks of the 1980s and 1990s in which artists, drawing upon diverse trends, disciplines and artistic generations, applied materials directly from the surrounding environment in pieces called eco-installations. The text attempts to explain certain creative postures and artistic decisions in the context of our advanced civilization—its achievements and threats alike. The eco-installations—subtle, subdued, gentle, fragile, fleeting, whose finite existence (like that of living organisms doomed to pass away) reflects the artists' own decisions—are in urgent need of identification, analysis and documentation. Among artists recognized in international circles, the author situates two Polish artists perhaps less well known than their colleagues.
Remarks on Backcopying
Authors: Raimy Eric
Published: July 2002

This article presents a rule-based serial model of reduplication that is empirically and conceptually capable of handling backcopying effects in reduplication, contrary to McCarthy and Prince's (1995) claim that serial models of phonology are incapable of adequately accounting for this phenomenon. The model of reduplication presented here claims that reduplication is the result of loops in underlying temporal precedence structures of segments in formatives and reduces over- and underapplication effects in reduplication to cases of opacity.
The Need for Accurate Alignment in Natural Language System Evaluation
Authors: Kehler Andrew , Bear John , Appelt Douglas
Published: July 2002

As evaluations of computational linguistics technology progress toward higher-level interpretation tasks, the problem of determining alignments between system responses and answer key entries may become less straightforward. We present an extensive analysis of the alignment procedure used in the MUC-6 evaluation of information extraction technology, which reveals effects that interfere with the stated goals of the evaluation. These effects are shown to be pervasive enough that they have the potential to adversely impact the technology development process. These results argue strongly for the use of accurate alignment criteria in natural language evaluations, and for maintaining the independence of alignment criteria and mechanisms used to calculate scores.
A Machine Learning Approach to Coreference Resolution of Noun Phrases
Authors: Soon Wee Meng , Ng Hwee Tou , Lim Daniel Chung Yong
Published: July 2002

In this paper, we present a learning approach to coreference resolution of noun phrases in unrestricted text. The approach learns from a small, annotated corpus and the task includes resolving not just a certain type of noun phrase (e.g., pronouns) but rather general noun phrases. It also does not restrict the entity types of the noun phrases; that is, coreference is assigned whether they are of “organization,” “person,” or other types. We evaluate our approach on common data sets (namely, the MUC-6 and MUC-7 coreference corpora) and obtain encouraging results, indicating that on the general noun phrase coreference task, the learning approach holds promise and achieves accuracy comparable to that of nonlearning approaches. Our system is the first learning-based system that offers performance comparable to that of state-of-the-art nonlearning systems on these data sets.
Age Differences in the Frontal Lateralization of Verbal and Spatial Working Memory Revealed by PET
Authors: Reuter-Lorenz Patricia A. , Jonides John , Smith Edward E. , Hartley Alan , Miller Andrea , Marshuetz Christina , Koeppe Robert A.
Published: July 2002

Age-related decline in working memory figures prominently in theories of cognitive aging. However, the effects of aging on the neural substrate of working memory are largely unknown. Positron emission tomography (PET) was used to investigate verbal and spatial short-term storage (3 sec) in older and younger adults. Previous investigations with younger subjects performing these same tasks have revealed asymmetries in the lateral organization of verbal and spatial working memory. Using volume of interest (VOI) analyses that specifically compared activation at sites identified with working memory to their homologous twin in the opposite hemisphere, we show pronounced age differences in this organization, particularly in the frontal lobes: In younger adults, activation is predominantly left lateralized for verbal working memory, and right lateralized for spatial working memory, whereas older adults show a global pattern of anterior bilateral activation for both types of memory. Analyses of frontal subregions indicate that several underlying patterns contribute to global bilaterality in older adults: most notably, bilateral activation in areas associated with rehearsal, and paradoxical laterality in dorsolateral prefrontal sites (DLPFC; greater left activation for spatial and greater right activation for verbal). We consider several mechanisms that could account for these age differences including the possibility that bilateral activation reflects recruitment to compensate for neural decline.