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  • American Meteorological Society (AMS)
  • Annual Reviews
  • 2005-2009  (3,514)
  • 1965-1969  (2,107)
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  • 1
    Publication Date: 2022-05-25
    Description: Author Posting. © Annual Reviews, 2003. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Environment and Resources 28 (2003): 521-558, doi:10.1146/annurev.energy.28.011503.163443.
    Description: Agriculture and industrial development have led to inadvertent changes in the natural carbon cycle. As a consequence, concentrations of carbon dioxide and other greenhouse gases have increased in the atmosphere and may lead to changes in climate. The current challenge facing society is to develop options for future management of the carbon cycle. A variety of approaches has been suggested: direct reduction of emissions, deliberate manipulation of the natural carbon cycle to enhance sequestration, and capture and isolation of carbon from fossil fuel use. Policy development to date has laid out some of the general principles to which carbon management should adhere. These are summarized as: how much carbon is stored, by what means, and for how long. To successfully manage carbon for climate purposes requires increased understanding of carbon cycle dynamics and improvement in the scientific capabilities available for measurement as well as for policy needs. The specific needs for scientific information to underpin carbon cycle management decisions are not yet broadly known. A stronger dialogue between decision makers and scientists must be developed to foster improved application of scientific knowledge to decisions. This review focuses on the current knowledge of the carbon cycle, carbon measurement capabilities (with an emphasis on the continental scale) and the relevance of carbon cycle science to carbon sequestration goals.
    Description: The National Center for Atmospheric Research is supported by the National Science Foundation.
    Keywords: Carbon sequestration ; Measurement techniques ; Climate ; Kyoto protocol
    Repository Name: Woods Hole Open Access Server
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  • 2
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    Annual Reviews
    Publication Date: 2022-05-25
    Description: Author Posting. © Annual Reviews, 2006. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Fluid Mechanics 38 (2006): 395-425, doi:10.1146/annurev.fluid.38.050304.092129.
    Description: Over the past four decades, the combination of in situ and remote sensing observations has demonstrated that long nonlinear internal solitary-like waves are ubiquitous features of coastal oceans. The following provides an overview of the properties of steady internal solitary waves and the transient processes of wave generation and evolution, primarily from the point of view of weakly nonlinear theory, of which the Korteweg-de Vries equation is the most frequently used example. However, the oceanographically important processes of wave instability and breaking, generally inaccessible with these models, are also discussed. Furthermore, observations often show strongly nonlinear waves whose properties can only be explained with fully nonlinear models.
    Description: KRH acknowledges support from NSF and ONR and an Independent Study Award from the Woods Hole Oceanographic Institution. WKM acknowledges support from NSF and ONR, which has made his work in this area possible, in close collaboration with former graduate students at Scripps Institution of Oceanography and MIT.
    Keywords: Solitary waves ; Nonlinear waves ; Stratified flow ; Physical Oceanography
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  • 3
    Publication Date: 2022-05-25
    Description: First published online as a Review in Advance on October 24, 2005. (Some corrections may occur before final publication online and in print)
    Description: Author Posting. © Annual Reviews, 2005. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Physiology 68 (2006): 22.1-22.29, doi:10.1146/annurev.physiol.68.040104.105418.
    Description: Superfast muscles of vertebrates power sound production. The fastest, the swimbladder muscle of toadfish, generates mechanical power at frequencies in excess of 200 Hz. To operate at these frequencies, the speed of relaxation has had to increase approximately 50-fold. This increase is accomplished by modifications of three kinetic traits: (a) a fast calcium transient due to extremely high concentration of sarcoplasmic reticulum (SR)-Ca2+ pumps and parvalbumin, (b) fast off-rate of Ca2+ from troponin C due to an alteration in troponin, and (c) fast cross-bridge detachment rate constant (g, 50 times faster than that in rabbit fast-twitch muscle) due to an alteration in myosin. Although these three modifications permit swimbladder muscle to generate mechanical work at high frequencies (where locomotor muscles cannot), it comes with a cost: The high g causes a large reduction in attached force-generating cross-bridges, making the swimbladder incapable of powering low-frequency locomotory movements. Hence the locomotory and sound-producing muscles have mutually exclusive designs.
    Description: This work was made possible by support from NIH grants AR38404 and AR46125 as well as the University of Pennsylvania Research Foundation.
    Keywords: Parvalbumin ; Ca2+ release ; Ca2+ uptake ; Cross-bridges ; Adaptation ; Sound production ; Whitman Center
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  • 4
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 295-318 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Toroidal DNA condensates have attracted the attention of biophysicists, biochemists, and polymer physicists for more than thirty years. In the biological community, the quest to understand DNA toroid formation has been motivated by its relevance to gene packing in certain viruses and by the potential use of DNA toroids in artificial gene delivery (e.g., gene therapy). In the physical sciences, DNA toroids are appreciated as a superb model system for studying particle formation by the collapse of a semiflexible, polyelectrolyte polymer. This review focuses on experimental studies from the past few years that have significantly increased our understanding of DNA toroid structure and the mechanism of their formation. Highlights include structural studies that show the DNA strands within toroids to be packed in an ideal hexagonal lattice, and also in regions with a nonhexagonal lattice that are required by the topological constraints associated with winding DNA into a toroid. Recent studies of DNA toroid formation have also revealed that toroid size limits result from a complex interplay between kinetic and thermodynamic factors that govern both toroid nucleation and growth. The work discussed in this review indicates that it will ultimately be possible to obtain substantial control over DNA toroid dimensions.
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  • 5
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 267-294 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: With genome sequencing nearing completion for the model organisms used in biomedical research, there is a rapidly growing appreciation that proteomics, the study of covalent modification to proteins, and transcriptional regulation will likely dominate the research headlines in the next decade. Protein methylation plays a central role in both of these fields, as several different residues (Arg, Lys, Gln) are methylated in cells and methylation plays a central role in the "histone code" that regulates chromatin structure and impacts transcription. In some cases, a single lysine can be mono-, di-, or trimethylated, with different functional consequences for each of the three forms. This review describes structural aspects of methylation of histone lysine residues by two enzyme families with entirely different structural scaffolding (the SET proteins and Dot1p) and methylation of protein arginine residues by PRMTs.
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  • 6
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 153-171 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Potassium (K+) channels are tetrameric membrane-spanning proteins that provide a selective pore for the conductance of K+ across the cell membranes. These channels are most remarkable in their ability to discriminate K+ from Na+ by more than a thousandfold and conduct at a throughput rate near diffusion limit. The recent progress in the structural characterization of K+ channel provides us with a unique opportunity to understand their function at the atomic level. With their ability to go beyond static structures, molecular dynamics simulations based on atomic models can play an important role in shaping our view of how ion channels carry out their function. The purpose of this review is to summarize the most important findings from experiments and computations and to highlight a number of fundamental mechanistic questions about ion conduction and selectivity that will require further work.
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  • 7
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 91-118 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Proteins have become accessible targets for chemical synthesis. The basic strategy is to use native chemical ligation, Staudinger ligation, or other orthogonal chemical reactions to couple synthetic peptides. The ligation reactions are compatible with a variety of solvents and proceed in solution or on a solid support. Chemical synthesis enables a level of control on protein composition that greatly exceeds that attainable with ribosome-mediated biosynthesis. Accordingly, the chemical synthesis of proteins is providing previously unattainable insight into the structure and function of proteins.
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  • 8
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 415-440 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: A powerful approach to understanding protein enzyme catalysis is to examine the structural context of essential amino acid side chains whose deletion or modification negatively impacts catalysis. In principle, this approach can be even more powerful for RNA enzymes, given the wide variety and subtlety of functionally modified nucleotides now available. Numerous recent success stories confirm the utility of this approach to understanding ribozyme function. An anomaly, however, is the hammerhead ribozyme, for which the structural and functional data do not agree well, preventing a unifying view of its catalytic mechanism from emerging. To delineate the hammerhead structure-function comparison, we have evaluated and distilled the large body of biochemical data into a consensus set of functional groups unambiguously required for hammerhead catalysis. By examining the context of these functional groups within available structures, we have established a concise set of disagreements between the structural and functional data. The number and relative distribution of these inconsistencies throughout the hammerhead reaffirms that an extensive conformational rearrangement from the fold observed in the crystal structure must be necessary for cleavage to occur. The nature and energetic driving force of this conformational isomerization are discussed.
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  • 9
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 399-414 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: The development of single-molecule detection and manipulation has allowed us to monitor the behavior of individual biological molecules and molecular complexes in real time. This approach significantly expands our capability to characterize complex dynamics of biological processes, allowing transient intermediate states and parallel kinetic pathways to be directly observed. Exploring this capability to elucidate complex dynamics, recent single-molecule experiments on RNA folding and catalysis have improved our understanding of the folding energy landscape of RNA and allowed us to better dissect complex RNA catalytic reactions, including translation by the ribosome.
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  • 10
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 173-199 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Water plays a central role in the structures and properties of biomoleculesĐ??proteins, nucleic acids, and membranesĐ??and in their interactions with ligands and drugs. Over the past half century, our understanding of water has been advanced significantly owing to theoretical and computational modeling. However, like the blind men and the elephant, different models describe different aspects of water's behavior. The trend in water modeling has been toward finer-scale properties and increasing structural detail, at increasing computational expense. Recently, our labs and others have moved in the opposite direction, toward simpler physical models, focusing on more global propertiesĐ??water's thermodynamics, phase diagram, and solvation properties, for exampleĐ??and toward less computational expense. Simplified models can guide a better understanding of water in ways that complement what we learn from more complex models. One ultimate goal is more tractable models for computer simulations of biomolecules. This review gives a perspective from simple models on how the physical properties of waterĐ??as a pure liquid and as a solventĐ??derive from the geometric and hydrogen bonding properties of water.
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  • 11
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 379-398 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Structural data on protein-DNA complexes provide clues for understanding the mechanism of protein-DNA recognition. Although the structures of a large number of protein-DNA complexes are known, the mechanisms underlying their specific binding are still only poorly understood. Analysis of these structures has shown that there is no simple one-to-one correspondence between bases and amino acids within protein-DNA complexes; nevertheless, the observed patterns of interaction carry important information on the mechanisms of protein-DNA recognition. In this review, we show how the patterns of interaction, either observed in known structures or derived from computer simulations, confer recognition specificity, and how they can be used to examine the relationship between structure and specificity and to predict target DNA sequences used by regulatory proteins.
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  • 12
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 457-483 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: The field of lymphatic research has been recently invigorated by the identification of genes and mechanisms that control various aspects of lymphatic development. We are beginning to understand how, starting from a subgroup of embryonic venous endothelial cells, the whole lymphatic system forms in a stepwise manner. The generation of genetically engineered mice with defects in different steps of the lymphangiogenic program has provided models that are increasing our understanding of the lymphatic system in health and disease. This knowledge, in turn, should lead to the development of better diagnostic methods and treatments of lymphatic disorders and tumor metastasis.
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  • 13
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    Annual Review of Materials Research 35 (2005), S. 127-142 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The preparation of skeletal catalysts is considered, with particular reference to the preparation of skeletal nickel and skeletal copper. Skeletal catalysts have physical properties that are highly desired for some industrial processes, and the means of controlling these properties to optimize performance is reviewed. The preparation can be affected by the initial alloy composition, the quenching process, the leaching procedure, aging and by the addition of promoters. These processes may affect either or both the chemical and physical characteristics of the catalysts. Preparation procedures need to be adjusted for individual reactions if optimal performance is required. The effect of the preparation conditions on the structure and catalytic performance of these systems is reviewed.
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  • 14
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    Annual Review of Materials Research 35 (2005), S. 167-207 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: We review here the theory of the early stages of oxidation of the (110) surface of Ni1x Alx, based on ab initio calculations using a plane-wave pseudopotential method. The clean surface and several oxidized surfaces have been investigated, with oxygen coverages up to 2ML of oxygen (1ML = 3 O atoms per 2 surface Al atoms). The theory to date is a description in terms of equilibrium thermodynamics, with a comparison of the free energies of several surfaces of different composition, implemented at the atomic scale. Three environmental parameters are singled out as control variables in this treatment, namely the alloy composition x (assumed to be near 0.5), the temperature T and the partial pressure of oxygen pO2. With certain reasonable approximations an analytic formula for the surface energy ?? is derived in terms of these variables and some constants that are calculated ab initio together with others that are derived from experimental thermodynamic tables. At oxygen pressures just above the threshold for bulk oxidation of NiAl, the calculations explain the observed formation of a thin film of alumina in place of NiAl surface layers, with the consequent dissolution of Ni into the bulk. Ab initio calculations illustrate how the energetics of supplying Al to the surface depends on bulk stoichiometry, which alters the relative stability of different surface oxidation states so as to favour oxidation more if the alloy is Al-rich than if it is Ni-rich.
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  • 15
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    Annual Review of Materials Research 35 (2005), S. 315-350 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: There is a pressing need for cleaner fuels (free or aromatics and of minimal sulfur content) or ones that convert chemical energy directly to electricity, silently and without production of noxious oxides and particulates; chemical, petrochemical and pharmaceutical processes that may be conducted in a one-step, solvent-free manner and that use air as the preferred oxidant; and industrial processes that minimize consumption of energy, production of waste, or the use of corrosive, explosive, volatile, and nonbiodegradable materials. All these needs and other desiderata, such as the in situ production and containment of aggressive and hazardous reagents, and the avoidance of use of ecologically harmful elements, may be achieved by designing the appropriate heterogeneous inorganic catalyst, which ideally should be cheap, readily preparable and fully characterizable, preferably under in situ reaction conditions. A range of nanoporous and nanoparticle catalysts that meet most of the stringent demands of sustainable development and responsible (clean) technology is described. Specific examples that are highlighted include the production of adipic acid (precursor of polyamides and urethanes) without the use of concentrated nitric acid nor the production of greenhouse gases such as nitrous oxide; the production of caprolactam (precursor of nylon) without the use of oleum and hydroxylamine sulfate; and the terminal oxyfunctionalization of linear alkanes in air. The topic of biocatalysis and sustainable development is also briefly discussed for the epoxidation of terpenes and fatty acid methyl esters; for the generation of polymers, polylactides, and polyesters; and for the production of 1,3-propanediol from corn.
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    Annual Review of Materials Research 35 (2005), S. 351-395 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: This review covers the synthesis, characterization, and physico-chemical properties of microporous and mesoporous aluminophosphates and silicoaluminophosphates molecular sieves. Particular emphasis is given to the materials that have found applications as acid catalysts. We consider the evolution of the synthesis procedures from the first discoveries to the current methodologies and give perspectives for new possible synthesis strategies. Emphasis is given to the use of specially prepared precursors/reactants designed for the use as molecular sieves. Experimental (especially MAS-NMR and FTIR spectroscopy) and theoretical approaches to the description of the Si insertion into the ALPO framework and to the acidic properties of SAPOs and MeAPSOs materials are discussed.
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  • 17
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    Annual Review of Materials Research 35 (2005), S. 51-73 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The diffusion-multiple approachĐ??the creation of composition gradients and intermetallic phases by long-term annealing of junctions of three or more phases/alloysĐ??enables the generation of a large number of phases and compositions for efficient mapping of phase diagrams, phase properties, and kinetics. With an efficiency much higher than that of a conventional approach, many critical materials data, which otherwise would be too time-consuming and expensive to acquire, can be obtained and employed to accelerate alloy design. The critical data for structural materials design include phase diagrams, diffusion coefficients, precipitation kinetics, solution-strengthening effects, and precipitation-strengthening effects. All these data can be obtained from diffusion multiples. The combination of the diffusion-multiple approach with the CALPHAD approach can impact computational design of structural materials. The diffusion-multiple approach can also be applied to combinatorial screening of functional materials having unique physical, chemical, or other properties when micro-scale measurement techniques are available for these properties. Examples are shown to illustrate the progress made to date on applying the diffusion-multiple approach to accelerated design/discovery of materials.
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  • 18
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    Annual Review of Materials Research 35 (2005), S. 505-538 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Renewable energy resources, of which wind energy is prominent, are part of the solution to the global energy problem. Wind turbine and the rotorblade concepts are reviewed, and loadings by wind and gravity as important factors for the fatigue performance of the materials are considered. Wood and composites are discussed as candidates for rotorblades. The fibers and matrices for composites are described, and their high stiffness, low density, and good fatigue performance are emphasized. Manufacturing technologies for composites are presented and evaluated with respect to advantages, problems, and industrial potential. The important technologies of today are prepreg (pre-impregnated) technology and resin infusion technology. The mechanical properties of fiber composite materials are discussed, with a focus on fatigue performance. Damage and materials degradation during fatigue are described. Testing procedures for documentation of properties are reviewed, and fatigue loading histories are discussed, together with methods for data handling and statistical analysis of (large) amounts of test data. Future challenges for materials in the field of wind turbines are presented, with a focus on thermoplastic composites, new structural materials concepts, new structural design aspects, structural health monitoring, and the coming trends and markets for wind energy.
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  • 19
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    Annual Review of Materials Research 35 (2005), S. 397-426 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: This review illustrates how catalytically active molecular structures are created on oxide surfaces by attachment of metal complexes with subsequent structural transformation and molecular imprinting on the surfaces. Also discussed is how the designed surfaces are characterized in situ by physical techniques including conventional and time-resolved X-ray absorption fine structure. The structural transformation and molecular imprinting for attached metal complexes can provide a new class of catalytic materials with a high complexity for selective catalysis including shape-selective and asymmetric catalysis.
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    Annual Review of Materials Research 35 (2005), S. 29-49 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: This paper describes the use of extended X-ray absorption fine structure spectroscopy (EXAFS) to examine the structure of molten salts and ionic liquids and species dissolved in them. The EXAFS theory is briefly described as are the methods by which EXAFS of these systems can be studied. A range of applications have used EXAFS to investigate the structure of metallic species in ionic liquids from extraction studies to catalysts. The area of structural investigations of ionic liquids is still being developed, although growing rapidly, whereas the structure of molten salts has been studied using EXAFS in more detail.
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    Annual Review of Materials Research 35 (2005), S. 539-569 
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: In the nanoscience era, the properties of many exciting new materials and devices will depend on the details of their composition down to the level of single atoms. Thus the characterization of the structure and electronic properties of matter at the atomic scale is becoming ever more vital for economic and technological as well as for scientific reasons. The combination of atomic-resolution Z-contrast scanning transmission electron microscopy (STEM) and electron energy loss spectroscopy (EELS) represents a powerful method to link the atomic and electronic structure to macroscopic properties, allowing materials, nanoscale systems, and interfaces to be probed in unprecedented detail. Z-contrast STEM uses electrons that have been scattered to large angles for imaging. The relative intensity of each atomic column is roughly proportional to Z2, where Z is the atomic number. Recent developments in correcting the aberrations of the lenses in the electron microscope have pushed the achievable spatial resolution and the sensitivity for imaging and spectroscopy in the STEM into the sub-A??ngstrom (sub-A??) regime, providing a new level of insight into the structure/property relations of complex materials. Images acquired with an aberration-corrected instrument show greatly improved contrast. The signal-to-noise ratio is sufficiently high to allow sensitivity even to single atoms in both imaging and spectroscopy. This is a key achievement because the detection and measurement of the response of individual atoms has become a challenging issue to provide new insight into many fields, such as catalysis, ceramic materials, complex oxide interfaces, or grain boundaries. In this article, the state-of-the-art for the characterization of all of these different types of materials by means of aberration-corrected STEM and EELS are reviewed.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 47-79 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Mixed mating, in which hermaphrodite plant species reproduce by both self- and cross-fertilization, presents a challenging problem for evolutionary biologists. Theory suggests that inbreeding depression, the main selective factor opposing the evolution of selfing, can be purged with self-fertilization, a process that is expected to yield pure strategies of either outcrossing or selfing. Here we present updated evidence suggesting that mixed mating systems are frequent in seed plants. We outline the floral and pollination mechanisms that can lead to intermediate outcrossing, review the theoretical models that address the stability of intermediate outcrossing, and examine relevant empirical evidence. A comparative analysis of estimated inbreeding coefficients and outcrossing rates suggests that mixed mating often evolves despite strong inbreeding depression. The adaptive significance of mixed mating has yet to be fully explained for any species. Recent theoretical and empirical work suggests that future progress will come from a better integration of studies of floral mechanisms, genetics, and ecology, and recognition of how selective pressures vary in space and time.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 191-218 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: We explore empirical and theoretical evidence for the functional significance of plant-litter diversity and the extraordinary high diversity of decomposer organisms in the process of litter decomposition and the consequences for biogeochemical cycles. Potential mechanisms for the frequently observed litter-diversity effects on mass loss and nitrogen dynamics include fungi-driven nutrient transfer among litter species, inhibition or stimulation of microorganisms by specific litter compounds, and positive feedback of soil fauna due to greater habitat and food diversity. Theory predicts positive effects of microbial diversity that result from functional niche complementarity, but the few existing experiments provide conflicting results. Microbial succession with shifting enzymatic capabilities enhances decomposition, whereas antagonistic interactions among fungi that compete for similar resources slow litter decay. Soil-fauna diversity manipulations indicate that the number of trophic levels, species identity, and the presence of keystone species have a strong impact on decomposition, whereas the importance of diversity within functional groups is not clear at present. In conclusion, litter species and decomposer diversity can significantly influence carbon and nutrient turnover rates; however, no general or predictable pattern has emerged. Proposed mechanisms for diversity effects need confirmation and a link to functional traits for a comprehensive understanding of how biodiversity interacts with decomposition processes and the consequences of ongoing biodiversity loss for ecosystem functioning.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 445-466 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Investigation into model selection has a long history in the statistical literature. As model-based approaches begin dominating systematic biology, increased attention has focused on how models should be selected for distance-based, likelihood, and Bayesian phylogenetics. Here, we review issues that render model-based approaches necessary, briefly review nucleotide-based models that attempt to capture relevant features of evolutionary processes, and review methods that have been applied to model selection in phylogenetics: likelihood-ratio tests, AIC, BIC, and performance-based approaches.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 295-317 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: One of the greatest mass extinctions in Earth's history occurred at the end of the Cretaceous era, sixty-five million years (Myr) ago. Considerable evidence indicates that the impact of a large asteroid or comet was the ultimate cause of this extraordinary event. At the time of mass extinction, the organic flux to the deep sea collapsed, and production of calcium carbonate by marine plankton radically declined. These biogeochemical processes did not fully recover for a few million years. The drastic decline and long lag in final recovery of these processes are most simply explained as consequences of open-ocean ecosystem alteration by the mass extinction. If this explanation is correct, the extent and timing of marine biogeochemical recovery from the end-Cretaceous event was ultimately contingent on the extent and timing of open-ocean ecosystem recovery. The biogeochemical recovery may in turn have created new evolutionary opportunities for a diverse array of marine organisms.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 1-21 
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    Topics: Biology
    Notes: Variation in the subtle differences between right and left sides of bilateral characters, or fluctuating asymmetry (FA), has long been considered to be primarily environmental in origin, and this has promoted its use as a measure of developmental instability (DI) in populations. There is little evidence for specific genes that govern FA per se. Numerous studies show that FA levels in various characters are influenced by dominance and especially epistatic interactions among genes. An epistatic genetic basis for FA may complicate its primary use in comparisons of DI levels in outbred or wild populations subjected or not subjected to various environmental stressors. Although the heritability of FA typically is very low or zero, epistasis can generate additive genetic variation for FA that may allow it to evolve especially in populations subjected to bottlenecks, hybridizations, or periods of rapid environmental changes caused by various stresses.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 419-444 
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    Topics: Biology
    Notes: Understanding and predicting the dynamics of multispecies systems generally require estimates of interaction strength among species. Measuring interaction strength is difficult because of the large number of interactions in any natural system, long-term feedback, multiple pathways of effects between species pairs, and possible nonlinearities in interaction-strength functions. Presently, the few studies that extensively estimate interaction strength suggest that distributions of interaction strength tend to be skewed toward few strong and many weak interactions. Modeling studies indicate that such skewed patterns tend to promote system stability and arise during assembly of persistent communities. Methods for estimating interaction strength efficiently from traits of organisms, such as allometric relationships, show some promise. Methods for estimating community response to environmental perturbations without an estimate of interaction strength may also be of use. Spatial and temporal scale may affect patterns of interaction strength, but these effects require further investigation and new multispecies modeling frameworks. Future progress will be aided by development of long-term multispecies time series of natural communities, by experimental tests of different methods for estimating interaction strength, and by increased understanding of nonlinear functional forms.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 643-689 
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    Topics: Biology
    Notes: Oysters have been introduced worldwide to 73 countries, but the ecological consequences of the introductions are not fully understood. Economically, introduced oysters compose a majority of oyster harvests in many areas. Oysters are ecosystem engineers that influence many ecological processes, such as maintenance of biodiversity, population and food web dynamics, and nutrient cycling. Consequently, both their loss, through interaction of overharvest, habitat degradation, disease, poor water quality, and detrimental species interactions, and their gain, through introductions, can cause complex changes in coastal ecosystems. Introductions can greatly enhance oyster population abundance and production, as well as populations of associated native species. However, introduced oysters are also vectors for non-native species, including disease-causing organisms. Thus, substantial population, community, and habitat changes have accompanied new oysters. In contrast, ecosystem-level consequences of oyster introductions, such as impacts on flow patterns, sediment and nutrient dynamics, and native bioengineering species, are not well understood. Ecological risk assessments for future introductions must emphasize probabilities of establishment, spread, and impacts on vulnerable species, communities, and ecosystem properties. Many characteristics of oysters lead to predictions that they would be successful, high-impact members of recipient ecosystems. This conclusion leaves open the discussion of whether such impacts are desirable in terms of restoration of coastal ecosystems, especially where restoration of native oysters is possible.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 219-242 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The multi-gene family that encodes ribosomal RNA (the rDNA) has been the subject of numerous review articles examining its structure and function, as well as its use as a molecular systematic marker. The purpose of this review is to integrate information about structural and functional aspects of rDNA that impact the ecology and evolution of organisms. We examine current understanding of the impact of length heterogeneity and copy number in the rDNA on fitness and the evolutionary ecology of organisms. We also examine the role that elemental ratios (biological stoichiometry) play in mediating the impact of rDNA variation in natural populations and ecosystems. The body of work examined suggests that there are strong reciprocal feedbacks between rDNA and the ecology of all organisms, from microbes to metazoans, mediated through increased phosphorus demand in organisms with high rRNA content.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 23-46 
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    Topics: Biology
    Notes: Two consequences of terrestrial ectothermy (low energy needs and behavioral control of body temperatures) have had major consequences for the evolution of reptile life-history traits. For example, reproducing females can manipulate incubation temperatures and thus phenotypic traits of their offspring by retaining developing eggs in utero. This ability has resulted in multiple evolutionary transitions from oviparity to viviparity in cool-climate reptile populations. The spatial and temporal heterogeneity of operative temperatures in terrestrial habitats also has favored careful nest-site selection and a matching of embryonic reaction norms to thermal regimes during incubation (e.g., via temperature-dependent sex determination). Many of the life-history features in which reptiles differ from endothermic vertebratesĐ??such as their small offspring sizes, large litter sizes, and infrequent reproductionĐ??are direct consequences of ectothermy, reflecting freedom from heat-conserving constraints on body size and energy storage. Ectothermy confers immense flexibility, enabling a dynamic matching of life-history traits to local circumstances. This flexibility has generated massive spatial and temporal variation in life-history traits via phenotypic plasticity as well as adaptation. The diversity of life histories in reptiles can best be interpreted within a conceptual framework that views reptiles as low-energy, variable-temperature systems.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 541-562 
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    Topics: Biology
    Notes: The continuous flow of genomic data is creating unprecedented opportunities for the reconstruction of molecular phylogenies. Access to whole-genome data means that phylogenetic analysis can now be performed at different genomic levels, such as primary sequences and gene order, allowing for reciprocal corroboration of the results. We critically review the different kinds of phylogenomic methods currently available, paying particular attention to method reliability. Our emphasis is on methods for the analysis of primary sequences because these are the most advanced. We discuss the important issue of statistical inconsistency and show how failing to fully capture the process of sequence evolution in the underlying models leads to tree reconstruction artifacts. We suggest strategies for detecting and potentially overcoming these problems. These strategies involve the development of better models, the use of an improved taxon sampling, and the exclusion of phylogenetically misleading data.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 267-294 
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    Topics: Biology
    Notes: It has often been argued that conserving biodiversity is necessary for maintaining ecosystem functioning. We critically evaluate the current evidence for this argument. Although there is substantial evidence that diversity is able to affect function, particularly for plant communities, it is unclear if these patterns will hold for realistic scenarios of extinctions, multitrophic communities, or larger spatial scales. Experiments are conducted at small spatial scales, the very scales at which diversity tends to increase owing to exotics. Stressors may affect function by many pathways, and diversity-mediated effects on function may be a minor pathway, except in the case of multiple-stressor insurance effects. In general, the conservation case is stronger for stability measures of function than stock and flux measures, in part because it is easier to attribute value unambiguously to stability and in part because stock and flux measures of functions are anticipated to be more affected by multitrophic dynamics. Nor is biodiversity-ecosystem function theory likely to help conservation managers in practical decisions, except in the particular case of restoration. We give recommendations for increasing the relevance of this area of research for conservation.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 597-620 
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    Topics: Biology
    Notes: The diversity and composition of herbivore assemblages was a favored theme for community ecology in the 1970s and culminated in 1984 with Insects on Plants by Strong, Lawton and Southwood. We scrutinize findings since then, considering analyses of country-wide insect-host catalogs, field studies of local herbivore communities, and comparative studies at different spatial scales. Studies in tropical forests have advanced significantly and offer new insights into stratification and host specialization of herbivores. Comparative and long-term data sets are still scarce, which limits assessment of general patterns in herbivore richness and assemblage structure. Methods of community phylogenetic analysis, complex networks, spatial and among-host diversity partitioning, and metacommunity models represent promising approaches for future work.
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    Annual Review of Astronomy and Astrophysics 3 (1965), S. 135-216 
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    Annual Review of Astronomy and Astrophysics 3 (1965), S. 217-234 
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    Annual Review of Astronomy and Astrophysics 3 (1965), S. 297-350 
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    Annual Review of Astronomy and Astrophysics 3 (1965), S. 377-411 
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    Annual Review of Astronomy and Astrophysics 5 (1967), S. 481-524 
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    Annual Review of Astronomy and Astrophysics 5 (1967), S. 453-464 
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    Annual Review of Astronomy and Astrophysics 5 (1967), S. 525-570 
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    Annual Review of Astronomy and Astrophysics 6 (1968), S. 135-164 
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    Annual Review of Astronomy and Astrophysics 6 (1968), S. 417-448 
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    Annual Review of Astronomy and Astrophysics 7 (1969), S. 1-38 
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    Annual Review of Astronomy and Astrophysics 7 (1969), S. 39-66 
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    Annual Review of Astronomy and Astrophysics 7 (1969), S. 121-148 
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    Annual Review of Astronomy and Astrophysics 7 (1969), S. 201-248 
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    Annual Review of Astronomy and Astrophysics 7 (1969), S. 177-200 
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    Annual Review of Astronomy and Astrophysics 7 (1969), S. 303-352 
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    Annual Review of Astronomy and Astrophysics 7 (1969), S. 473-526 
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    Annual Review of Fluid Mechanics 1 (1969), S. 73-110 
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    Annual Review of Fluid Mechanics 1 (1969), S. 197-222 
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    Annual Review of Fluid Mechanics 1 (1969), S. 245-264 
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    Annual Review of Fluid Mechanics 1 (1969), S. 293-316 
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    Annual Review of Fluid Mechanics 1 (1969), S. 317-340 
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    Annual Review of Fluid Mechanics 1 (1969), S. 413-446 
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    Annual Review of Fluid Mechanics 37 (2005), S. 357-392 
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    Notes: The objective of this review is to critically assess the different approaches developed in recent years to understand the dynamics of open flows such as mixing layers, jets, wakes, separation bubbles, boundary layers, and so on. These complex flows develop in extended domains in which fluid particles are continuously advected downstream. They behave either as noise amplifiers or as oscillators, both of which exhibit strong nonlinearities ( Huerre & Monkewitz 1990 ). The local approach is inherently weakly nonparallel and it assumes that the basic flow varies on a long length scale compared to the wavelength of the instability waves. The dynamics of the flow is then considered as a superposition of linear or nonlinear instability waves that, at leading order, behave at each streamwise station as if the flow were homogeneous in the streamwise direction. In the fully global context, the basic flow and the instabilities do not have to be characterized by widely separated length scales, and the dynamics is then viewed as the result of the interactions between Global modes living in the entire physical domain with the streamwise direction as an eigendirection. This second approach is more and more resorted to as a result of increased computational capability. The earlier review of Huerre & Monkewitz (1990) emphasized how local linear theory can account for the noise amplifier behavior as well as for the onset of a Global mode. The present survey first adopts the opposite point of view by demonstrating how fully global theory accounts for the noise amplifier behavior of open flows. From such a perspective, there is strong emphasis on the very peculiar nonorthogonality of linear Global modes, which in turn allows a novel interpretation of recent numerical simulations and experimental observations. The nonorthogonality of linear Global modes also imposes severe constraints on the extension of linear global theory to the fully nonlinear re??gime. When the flow is weakly nonparallel, this limitation is so severe that the linear Global mode theory is of little help. It is then much more appropriate to develop a fully nonlinear formulation involving the presence of a front separating the base state region from the bifurcated state region.
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    Annual Review of Fluid Mechanics 37 (2005), S. 129-149 
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    Notes: We review the fluid mechanics and rheology of dense suspensions, emphasizing investigations of microstructure and total stress. "Dense" or "highly concentrated" suspensions are those in which the average particle separation distance is less than the particle radius. For these suspensions, multiple-body interactions as well as two-body lubrication play a significant role and the rheology is non-Newtonian. We include investigations of multimodal suspensions, but not those of suspensions with dominant nonhydrodynamic interactions. We consider results from both physical experiments and computer simulations and explore scaling theories and the development of constitutive equations.
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    Annual Review of Fluid Mechanics 37 (2005), S. 239-261 
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    Annual Review of Fluid Mechanics 37 (2005), S. 23-42 
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    Notes: George Gabriel Stokes died just over 100 years ago, and it has been more than 150 years since he published his great 1847 paper on water waves. The work of Stokes' precursors, which informed his early publications of 1842Đ??50, is described in the previous volume of the Annual Review of Fluid Mechanics ( Craik 2004 ). Here I examine Stokes' papers and letters concerning water waves.
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    Annual Review of Fluid Mechanics 37 (2005), S. 295-328 
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    Notes: Chaotic advection and, more generally, ideas from dynamical systems, have been fruitfully applied to a diverse, and varied, collection of mixing and transport problems arising in engineering applications over the past 20 years. Indeed, the "dynamical systems approach" was developed, and tested, to the point where it can now be considered a standard tool for understanding mixing and transport issues in many disciplines. This success for engineering-type flows motivated an effort to apply this approach to transport and mixing problems in geophysical flows. However, there are fundamental difficulties arising in this endeavor that must be properly understood and overcome. Central to this approach is that the starting point for analysis is a velocity field (i.e., the "dynamical system"). In many engineering applications this can be obtained sufficiently accurately, either analytically or computationally, so that it describes particle trajectories for the actual flow. However, in geophysical flows (and we concentrate here almost exclusively on oceanographic flows), the wide range of dynamically significant time and length scales makes the justification of any velocity field, in the sense of reproducing particle trajectories for the actual flow, a much more difficult matter. Nevertheless, the case for this approach is compelling due to the advances in observational capabilities in oceanography (e.g., drifter deployments, remote sensing capabilities, satellite imagery, etc.), which reveal space-time structures that are highly suggestive of the structures one visualizes in the global, geometrical study of dynamical systems theory. This has been pursued in recent years through a combination of laboratory studies, kinematic models, and dynamically consistent models that have all been compared with observational data. During the course of these studies it has become apparent that a new type of dynamical system is necessary to consider in these studies (i.e., a finite time, aperiodically time-dependent velocity field defined as a data set), which requires the development of new analytical and computational tools, as well as the necessity to discard some of the standard ideas and results from dynamical systems theory. In this article we review a number of the key developments to date in this young, but rapidly developing, area at the interface between geophysical fluid dynamics and applied and computational mathematics. We also describe the wealth of new directions for research that this approach unlocks.
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    Annual Review of Fluid Mechanics 38 (2006), S. 225-249 
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    Notes: The gas-lift technique comprises the injection of gas bubbles in vertical oil wells to increase production. It is based on a reduction of the tubing gravitational pressure gradient. Several fluid-flow phenomena influencing such vertical gas-liquid flows are discussed. These effects include the radial distribution of void fraction and of gas and liquid velocity, flow regime changes, and system stability problems. Associated consequences for gas-lift performance and related optimization approaches are also discussed.
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    Annual Review of Fluid Mechanics 38 (2006), S. 193-224 
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    Notes: What mechanisms of flow control do animals use to enhance hydrodynamic performance? Animals are capable of manipulating flow around the body and appendages both passively and actively. Passive mechanisms rely on structural and morphological components of the body (i.e., humpback whale tubercles, riblets). Active flow control mechanisms use appendage or body musculature to directly generate wake flow structures or stiffen fins against external hydrodynamic loads. Fish can actively control fin curvature, displacement, and area. The vortex wake shed by the tail differs between eel-like fishes and fishes with a discrete narrowing of the body in front of the tail, and three-dimensional effects may play a major role in determining wake structure in most fishes.
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    Annual Review of Fluid Mechanics 38 (2006), S. 395-425 
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    Notes: Over the past four decades, the combination of in situ and remote sensing observations has demonstrated that long nonlinear internal solitary-like waves are ubiquitous features of coastal oceans. The following provides an overview of the properties of steady internal solitary waves and the transient processes of wave generation and evolution, primarily from the point of view of weakly nonlinear theory, of which the Korteweg-de Vries equation is the most frequently used example. However, the oceanographically important processes of wave instability and breaking, generally inaccessible with these models, are also discussed. Furthermore, observations often show strongly nonlinear waves whose properties can only be explained with fully nonlinear models.
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    Annual Review of Fluid Mechanics 38 (2006), S. 309-338 
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    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Electrophoretic separation of a mixture of chemical species is a fundamental technique of great usefulness in biology, health care, and forensics. In capillary electrophoresis (which has evolved from its predecessor, slab-gel electrophoresis), the sample migrates through a single microcapillary instead of through the network of pores in a gel. A fundamental design problem is to minimize dispersion in the separation direction. Molecular diffusion is inevitable and sets a theoretical limit on the best separation that can be achieved. But in practice, there are a number of effects arising out of the interplay between fluid flow, chemistry, thermal effects, and electric fields that result in enhanced dispersion. This paper reviews the subject of fluid flow in such capillary microchannels and examines the various causes of enhanced dispersion that limit the efficiency of separation.
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    Annual Review of Fluid Mechanics 38 (2006), S. 27-63 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Race car performance depends on elements such as the engine, tires, suspension, road, aerodynamics, and of course the driver. In recent years, however, vehicle aerodynamics gained increased attention, mainly due to the utilization of the negative lift (downforce) principle, yielding several important performance improvements. This review briefly explains the significance of the aerodynamic downforce and how it improves race car performance. After this short introduction various methods to generate downforce such as inverted wings, diffusers, and vortex generators are discussed. Due to the complex geometry of these vehicles, the aerodynamic interaction between the various body components is significant, resulting in vortex flows and lifting surface shapes unlike traditional airplane wings. Typical design tools such as wind tunnel testing, computational fluid dynamics, and track testing, and their relevance to race car development, are discussed as well. In spite of the tremendous progress of these design tools (due to better instrumentation, communication, and computational power), the fluid dynamic phenomenon is still highly nonlinear, and predicting the effect of a particular modification is not always trouble free. Several examples covering a wide range of vehicle shapes (e.g., from stock cars to open-wheel race cars) are presented to demonstrate this nonlinear nature of the flow field.
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    Annual Review of Fluid Mechanics 38 (2006), S. 453-482 
    ISSN: 0066-4189
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Large-eddy simulation (LES) of turbulent combustion is a relatively new research field. Much research has been carried out over the past years, but to realize the full predictive potential of combustion LES, many fundamental questions still have to be addressed, and common practices of LES of nonreacting flows revisited. The focus of the present review is to highlight the fundamental differences between Reynolds-averaged Navier-Stokes (RANS) and LES combustion models for nonpremixed and premixed turbulent combustion, to identify some of the open questions and modeling issues for LES, and to provide future perspectives.
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    Annual Review of Genetics 1 (1967), S. 37-70 
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    Annual Review of Genetics 1 (1967), S. 1-38 
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    Annual Review of Genetics 1 (1967), S. 87-116 
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    Annual Review of Genetics 1 (1967), S. 185-200 
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    Annual Review of Genetics 1 (1967), S. 221-244 
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    Annual Review of Genetics 1 (1967), S. 245-268 
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    Annual Review of Genetics 1 (1967), S. 295-312 
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    Annual Review of Genetics 39 (2005), S. 359-407 
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    Notes: Life is the interplay between structure and energy, yet the role of energy deficiency in human disease has been poorly explored by modern medicine. Since the mitochondria use oxidative phosphorylation (OXPHOS) to convert dietary calories into usable energy, generating reactive oxygen species (ROS) as a toxic by-product, I hypothesize that mitochondrial dysfunction plays a central role in a wide range of age-related disorders and various forms of cancer. Because mitochondrial DNA (mtDNA) is present in thousands of copies per cell and encodes essential genes for energy production, I propose that the delayed-onset and progressive course of the age-related diseases results from the accumulation of somatic mutations in the mtDNAs of post-mitotic tissues. The tissue-specific manifestations of these diseases may result from the varying energetic roles and needs of the different tissues. The variation in the individual and regional predisposition to degenerative diseases and cancer may result from the interaction of modern dietary caloric intake and ancient mitochondrial genetic polymorphisms. Therefore the mitochondria provide a direct link between our environment and our genes and the mtDNA variants that permitted our forbears to energetically adapt to their ancestral homes are influencing our health today.
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    Annual Review of Genetics 39 (2005), S. 69-94 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Cell-cycle control of transcription seems to be a universal feature of proliferating cells, although relatively little is known about its biological significance and conservation between organisms. The two distantly related yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe have provided valuable complementary insight into the regulation of periodic transcription as a function of the cell cycle. More recently, genome-wide studies of proliferating cells have identified hundreds of periodically expressed genes and underlying mechanisms of transcriptional control. This review discusses the regulation of three major transcriptional waves, which roughly coincide with three main cell-cycle transitions (initiation of DNA replication, entry into mitosis, and exit from mitosis). I also compare and contrast the transcriptional regulatory networks between the two yeasts and discuss the evolutionary conservation and possible roles for cell cycle-regulated transcription.
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    Annual Review of Genetics 39 (2005), S. 23-46 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Three processes alter genomic sequence and structure at the immunoglobulin genes of B lymphocytes: gene conversion, somatic hypermutation, and class switch recombination. Though the molecular signatures of these processes differ, they occur by a shared pathway which is induced by targeted DNA deamination by a B cellĐ??specific factor, activation induced cytidine deaminase (AID). Ubiquitous factors critical for DNA repair carry out all downstream steps, creating mutations and deletions in genomic DNA. This review focuses on the genetic and biochemical mechanisms of diversification of immunoglobulin genes.
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    Annual Review of Genetics 39 (2005), S. 561-613 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: The basic vertebrate body plan of the zebrafish embryo is established in the first 10 hours of development. This period is characterized by the formation of the anterior-posterior and dorsal-ventral axes, the development of the three germ layers, the specification of organ progenitors, and the complex morphogenetic movements of cells. During the past 10 years a combination of genetic, embryological, and molecular analyses has provided detailed insights into the mechanisms underlying this process. Maternal determinants control the expression of transcription factors and the location of signaling centers that pattern the blastula and gastrula. Bmp, Nodal, FGF, canonical Wnt, and retinoic acid signals generate positional information that leads to the restricted expression of transcription factors that control cell type specification. Noncanonical Wnt signaling is required for the morphogenetic movements during gastrulation. We review how the coordinated interplay of these molecules determines the fate and movement of embryonic cells.
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    Annual Review of Genetics 39 (2005), S. 481-501 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The zebrafish (Danio rerio) has emerged as an ideal organism for the study of hematopoiesis, the process by which all the cellular elements of the blood are formed. These elements, including erythrocytes, granulocytes, monocytes, lymphocytes, and thrombocytes, are formed through complex genetic signaling pathways that are highly conserved throughout phylogeny. Large-scale forward genetic screens have identified numerous blood mutants in zebrafish, helping to elucidate specific signaling pathways important for hematopoietic stem cells (HSCs) and the various committed blood cell lineages. Here we review both primitive and definitive hematopoiesis in zebrafish, discuss various genetic methods available in the zebrafish model for studying hematopoiesis, and describe some of the zebrafish blood mutants identified to date, many of which have known human disease counterparts.
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    Annual Review of Genetics 39 (2005), S. 339-358 
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    Notes: The moss Physcomitrella patens, like seed plants, shows alternation of generations, but its gametophyte, the haploid phase of the life cycle, is dominant, making it ideal for genetic studies. Crosses show direct segregations, so F2 or test crosses are unnecessary. Mutagenesis yields mutants, the phenotype of which is directly evident. Haploid tissue can be propagated vegetatively, allowing the maintenance of mutants blocked early in development. Protoplasts, isolated from filamentous gametophytic tissue, regenerate directly into filamentous tissue, providing an abundant supply of single haploid cells for transformation. Recombination occurs at a high frequency between genomic sequences in transforming DNA and the corresponding chromosomal sequences, allowing precise inactivation or modification of genes. RNAi technology allows the inactivation of the expression of gene families and the partial knockdown of essential genes. Over 100,000 ESTs have been sequenced and annotated, and sequencing of the genome should be completed by the end of 2005.
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    Annual Review of Genetics 3 (1969), S. 247-268 
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    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 319-349 
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Progress in experimental and theoretical biology is likely to provide us with the opportunity to assemble detailed predictive models of mammalian cells. Using a functional format to describe the organization of mammalian cells, we describe current approaches for developing qualitative and quantitative models using data from a variety of experimental sources. Recent developments and applications of graph theory to biological networks are reviewed. The use of these qualitative models to identify the topology of regulatory motifs and functional modules is discussed. Cellular homeostasis and plasticity are interpreted within the framework of balance between regulatory motifs and interactions between modules. From this analysis we identify the need for detailed quantitative models on the basis of the representation of the chemistry underlying the cellular process. The use of deterministic, stochastic, and hybrid models to represent cellular processes is reviewed, and an initial integrated approach for the development of large-scale predictive models of a mammalian cell is presented.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 1-33 
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: In this review I describe the several stages of my research career, all of which were driven by a desire to understand the basic mechanisms responsible for the complex and beautiful organization of the eukaryotic cell. I was originally trained as an electron microscopist in Argentina, and my first major contribution was the introduction of glutaraldehyde as a fixative that preserved the fine structure of cells, which opened the way for cytochemical studies at the EM level. My subsequent work on membrane-bound ribosomes illuminated the process of cotranslational translocation of polypeptides across the ER membrane and led to the formulation, with Gunter Blobel, of the signal hypothesis. My later studies with many talented colleagues contributed to an understanding of ER structure and function and aspects of the mechanisms that generate and maintain the polarity of epithelial cells. For this work my laboratory introduced the now widely adopted Madin-Darby canine kidney (MDCK) cell line, and demonstrated the polarized budding of envelope viruses from those cells, providing a powerful new system that further advanced the field of protein traffic.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 133-153 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Chromatin can be differentiated by the deposition of variant histones at centromeres, active genes, and silent loci. Variant histones are assembled into nucleosomes in a replication-independent manner, in contrast to assembly of bulk chromatin that is coupled to replication. Recent in vitro studies have provided the first glimpses of protein machines dedicated to building and replacing alternative nucleosomes. They deposit variant H2A and H3 histones and are targeted to particular functional sites in the genome. Differences between variant and canonical histones can have profound consequences, either for delivery of the histones to sites of assembly or for their function after incorporation into chromatin. Recent studies have also revealed connections between assembly of variant nucleosomes, chromatin remodeling, and histone post-translational modification. Taken together, these findings indicate that chromosome architecture can be highly dynamic at the most fundamental level, with epigenetic consequences.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 203-222 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Plants shape their organs with a precision demanded by optimal function; organ shaping requires control over cell wall expansion anisotropy. Focusing on multicellular organs, I survey the occurrence of expansion anisotropy and discuss its causes and proposed controls. Expansion anisotropy of a unit area of cell wall is characterized by the direction and degree of anisotropy. The direction of maximal expansion rate is usually regulated by the direction of net alignment among cellulose microfibrils, which overcomes the prevailing stress anisotropy. In some stems, the directionality of expansion of epidermal cells is controlled by that of the inner tissue. The degree of anisotropy can vary widely as a function of position and of treatment. The degree of anisotropy is probably controlled by factors in addition to the direction of microfibril alignment. I hypothesize that rates of expansion in maximal and minimal directions are regulated by distinct molecular mechanisms that regulate interactions between matrix and microfibrils.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 581-603 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Over the past decades, intravital microscopy (IVM), the imaging of cells in living organisms, has become a valuable tool for studying the molecular determinants of lymphocyte trafficking. Recent advances in microscopy now make it possible to image cell migration and cell-cell interactions in vivo deep within intact tissues. Here, we summarize the principal techniques that are currently used in IVM, discuss options and tools for fluorescence-based visualization of lymphocytes in microvessels and tissues, and describe IVM models used to explore lymphoid and non-lymphoid organs. The latter will be introduced according to the physiologic itinerary of developing and differentiating T and B lymphocytes as they traffic through the body, beginning with their development in bone marrow and thymus and continuing with their migration to secondary lymphoid organs and peripheral tissues.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 411-434 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: Centrosomes, spindle pole bodies, and related structures in other organisms are a morphologically diverse group of organelles that share a common ability to nucleate and organize microtubules and are thus referred to as microtubule organizing centers or MTOCs. Features associated with MTOCs include organization of mitotic spindles, formation of primary cilia, progression through cytokinesis, and self-duplication once per cell cycle. Centrosomes bind more than 100 regulatory proteins, whose identities suggest roles in a multitude of cellular functions. In fact, recent work has shown that MTOCs are required for several regulatory functions including cell cycle transitions, cellular responses to stress, and organization of signal transduction pathways. These new liaisons between MTOCs and cellular regulation are the focus of this review. Elucidation of these and other previously unappreciated centrosome functions promises to yield exciting scientific discovery for some time to come.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 695-718 
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    Topics: Biology , Medicine
    Notes: The combined use of the new technologies of multiphoton-based intravital imaging, the chemotaxis-mediated collection of invasive cells, and high sensitivity expression profiling has allowed the correlation of the behavior of invasive tumor cells in vivo with their gene expression patterns. New insights have resulted including a gene expression signature for invasive cells and the tumor microenvironment invasion model. This model proposes that tumor invasion and metastasis can be studied as a problem resembling normal morphogenesis. We discuss how these new insights may lead to a better understanding of the molecular basis of the invasive behavior of tumor cells in vivo, which may result in new strategies for the diagnosis and treatment of metastasis.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 435-456 
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    Notes: Secretory and transmembrane proteins enter the secretory pathway through the protein-conducting Sec61 channel in the membrane of the endoplasmic reticulum. In the endoplasmic reticulum, proteins fold, are frequently covalently modified, and oligomerize before they are packaged into transport vesicles that shuttle them to the Golgi complex. Proteins that misfold in the endoplasmic reticulum are selectively transported back across the endoplasmic reticulum membrane to the cytosol for degradation by proteasomes. Depending on the topology of the defect in the protein, cytosolic or lumenal chaperones are involved in its targeting to degradation. The export channel for misfolded proteins is likely also formed by Sec61p. Export may be powered by AAA-ATPases of the proteasome 19S regulatory particle or Cdc48p/p97. Exported proteins are frequently ubiquitylated prior to degradation and are escorted to the proteasome by polyubiquitin-binding proteins.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 511-527 
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    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
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    Notes: Phagocytosis, the process by which cells engulf large particles, requires a substantial contribution of membranes. Recent studies have revealed that intracellular compartments, including endocytic organelles and the endoplasmic reticulum (ER), can engage in fusion events with the plasma membrane at the sites of nascent phagosomes. The finding that ER proteins are delivered to phagosomes, where degraded peptides are loaded onto major histocompatibility complex (MHC) class II molecules, has significantly enhanced our understanding of the immune functions associated with these organelles. Although it is well known that pathogens are killed in phagosomes, the contribution of ER proteins to phagosomes has provided a novel pathway for the loading of exogenous peptides onto MHC class I molecules, a process known as cross-presentation. Thus, phagocytosis has evolved from a nutritional function in unicellular organisms to play key roles in both innate and adaptive immunity in vertebrates.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 551-580 
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    Notes: The sensory and motor components of nervous systems are connected topographically and contain neural maps of the external world. The paradigm for such maps is the precisely ordered wiring of the output cells of the eye to their synaptic targets in the tectum of the midbrain. The retinotectal map is organized in development through the graded activity of Eph receptor tyrosine kinases and their ephrin ligands. These signaling proteins are arrayed in complementary expression gradients along the orthogonal axes of the retina and tectum, and provide both input and recipient cells with Cartesian coordinates that specify their location. Molecular genetic studies in the mouse indicate that these coordinates are interpreted in the context of neuronal competition for termination sites in the tectum. They further suggest that order in the retinotectal map is determined by ratiometric rather than absolute difference comparisons in Eph signaling along the temporal-nasal and dorsal-ventral axes of the eye.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 271-295 
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    Topics: Biology , Medicine
    Notes: The cytoskeleton plays important roles in plant cell shape determination by influencing the patterns in which cell wall materials are deposited. Cortical microtubules are thought to orient the direction of cell expansion primarily via their influence on the deposition of cellulose into the wall, although the precise nature of the microtubule-cellulose relationship remains unclear. In both tip-growing and diffusely growing cell types, F-actin promotes growth and also contributes to the spatial regulation of growth. F-actin has been proposed to play a variety of roles in the regulation of secretion in expanding cells, but its functions in cell growth control are not well understood. Recent work highlighted in this review on the morphogenesis of selected cell types has yielded substantial new insights into mechanisms governing the dynamics and organization of cytoskeletal filaments in expanding plant cells and how microtubules and F-actin interact to direct patterns of cell growth. Nevertheless, many important questions remain to be answered.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 485-509 
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    Notes: The establishment of the Angiosperm root apical meristem is dependent on the specification of a stem cell niche and the subsequent development of the quiescent center at the presumptive root pole. Distribution of auxin and the establishment of auxin maxima are early formative steps in niche specification that depend on the expression and distribution of auxin carriers. Auxin specifies stem cell niche formation by directly and indirectly affecting gene activities. Part of the indirect regulation by auxin may involve changes in redox, favoring local, oxidized microenvironments. Formation of a QC is required for root meristem development and elaboration. Many signals likely pass between the QC and the adjacent root meristem tissues. Disappearance of the QC is associated with roots becoming determinate. Given the many auxin feedback loops, we hypothesize that roots evolved as part of an auxin homeostasis mechanism.
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    Annual Review of Cell and Developmental Biology 21 (2005), S. 155-176 
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    Notes: Polarization is a feature common to many cell types. Epithelial cells, for example, exhibit a characteristic apical-basolateral polarity that is critical for their function. In addition to this ubiquitous form of polarity, whole fields of cells are often polarized in a plane perpendicular to the apical-basal axis. This form of polarity, referred to as planar cell polarity (PCP), exists in all adult Drosophila cuticular tissues, as well as in numerous vertebrate tissues, including the mammalian skin and inner ear epithelia. Recent advances in the study of PCP establishment are beginning to unravel the molecular mechanisms underlying this cellular process. This review discusses new developments in the molecular understanding of PCP in Drosophila and vertebrates and integrates the current data in a model to illustrate how interactions between PCP factors might function to generate planar polarity.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 125-146 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: In contrast to Bateman's principle, there is now increasing evidence that female fitness can depend on the number of mates obtained. A number of genetic benefits have been proposed for the evolution of polyandry. A meta-analysis of available data suggests that polyandry, rather than multiple mating, can have a weak but significant general effect on embryo viability, as indicated by egg hatching success. Although this effect is generally regarded as evidence in favor of the genetic incompatibility hypothesis, appropriate data that test for intrinsic sire effects on embryo viability are generally unavailable. Moreover, maternal effects that could generate the result have not been adequately controlled, and there is little unequivocal evidence to suggest that fertilization is biased toward sperm bearing genotypes that would enhance offspring viability. Greater effort is required in these areas to elucidate the mechanisms underlying observed fitness effects of polyandry.
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    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 621-642 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The reconstruction of evolutionary trees from mitochondrial DNA (mtDNA) data is a common tool with which to infer the relationships of living organisms. The wide use of mtDNA stems from the ease of getting new sequence data for a set of orthologus genes and from the availability of many existing mtDNA sequences for a wide array of species. In this review we argue that developing a fuller understanding of the biology of mitochondria is essential for the rigorous application of mtDNA to inferences about the evolutionary history of species or populations. Though much progress has been made in understanding the parameters that shape the evolution of mitochondria and mtDNA, many questions still remain, and a better understanding of the role this organelle plays in regulating organismal fitness is becoming increasingly critical for accurate phylogeny reconstruction. In population biology, the limited information content of one nonrecombining genetic marker can compromise evolutionary inference, and the effects of nuclear genetic variationĐ??and environmental factorsĐ??in mtDNA fitness differences can compound these problems. In systematics, the limited gene set, biased amino acid composition, and problems of compensatory substitutions can cloud phylogenetic signal. Dissecting the functional bases of these biases offers both challenges and opportunities in comparative biology.
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    Notes: Quantifying the extent to which seed production is limited by the availability of pollen has been an area of intensive empirical study over the past few decades. Whereas theory predicts that pollen augmentation should not increase seed production, numerous empirical studies report significant and strong pollen limitation. Here, we use a variety of approaches to examine the correlates of pollen limitation in an effort to understand its occurrence and importance in plant evolutionary ecology. In particular, we examine the role of recent ecological perturbations in influencing pollen limitation and discuss the relation between pollen limitation and plant traits. We find that the magnitude of pollen limitation observed in natural populations depends on both historical constraints and contemporary ecological factors.
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    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 147-168 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Individual-based models (IBMs) allow the explicit inclusion of individual variation in greater detail than do classical differential-equation and difference-equation models. Inclusion of such variation is important for continued progress in ecological and evolutionary theory. We provide a conceptual basis for IBMs by describing five major types of individual variation in IBMs: spatial, ontogenetic, phenotypic, cognitive, and genetic. IBMs are now used in almost all subfields of ecology and evolutionary biology. We map those subfields and look more closely at selected key papers on fish recruitment, forest dynamics, sympatric speciation, metapopulation dynamics, maintenance of diversity, and species conservation. Theorists are currently divided on whether IBMs represent only a practical tool for extending classical theory to more complex situations, or whether individual-based theory represents a radically new research program. We feel that the tension between these two poles of thinking can be a source of creativity in ecology and evolutionary theory.
    Type of Medium: Electronic Resource
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  • 99
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 373-397 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Immune responses can cause severe disease, despite the role immunity plays in defending against parasitism. Indeed, immunopathology is a remarkably common cause of disease and has strong impacts upon both host and parasite fitness. Why has immune-mediated disease not been eliminated by natural selection? What constraints might immunopathology impose upon the evolution of resistance? In this review, we explore two major mechanistic causes of immunopathology in mammals and consider how such disease may have influenced immune system design. We then propose hypotheses that could explain the failure of natural selection to eliminate immunopathology. Finally, we suggest how the evolution of strategies for parasite virulence and host resistance may be shaped by this "double-edged sword" of immunity. Future work may reveal whether immunopathology constrains the evolution of resistance in all host taxa.
    Type of Medium: Electronic Resource
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  • 100
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 243-266 
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Plant adaptation to serpentine soil has been a topic of study for many decades, yet investigation of the genetic component of this adaptation has only recently begun. We review the defining properties of serpentine soil and the pioneering work leading to three established physiological and evolutionary mechanisms hypothesized to be responsible for serpentine tolerance: tolerance of a low calcium-to-magnesium ratio, avoidance of Mg toxicity, or a high Mg requirement. In addition, we review recent work in serpentine ecology documenting the high proportion of endemic species present, the adaptive morphologies of serpentine-tolerant plants, and the distinctive structure of serpentine communities. Studies of the physiological mechanisms proposed to confer serpentine tolerance have shown that uptake of particular ions and heavy metals varies between serpentine-tolerant and -intolerant species. Recent studies examining the genetic basis of serpentine adaptation have shown serpentine-adaptive quantitative trait loci (QTL) to have large phenotypic effects, drought tolerance to be as important as metal tolerance, and serpentine adaptation to have evolved independently multiple times within species. Investigations of plant races and species adapted to contrasting soil types have shown disparate flowering times, divergent floral morphologies, and pollen incompatibility to contribute to reproductive isolation. Finally, we propose that future studies involving serpentine systems should merge the fields of ecology, evolution, physiology, and genetics.
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