bluuebunny/crossref_metadata_2025 huggingface dataset:
NUCLEAR SHADOWING IN INCLUSIVE AND TAGGED DEUTERON STRUCTURE FUNCTIONS AND EXTRACTION OF $F_2^p-F_2^n$ AT SMALL x FROM ELECTRON–DEUTERON COLLIDER DATA
Authors: FRANKFURT L. , GUZEY V. , STRIKMAN M.
Published: January 2006

We review predictions of the theory of leading twist nuclear shadowing for inclusive unpolarized and polarized deuteron structure functions [Formula: see text], [Formula: see text] and [Formula: see text] and for the tagged deuteron structure function [Formula: see text]. We analyze the possibility to extract the neutron structure function [Formula: see text] from electron–deuteron data and demonstrate that an account of leading twist nuclear shadowing leads to large corrections for the extraction of [Formula: see text] from the future deuteron collider data both in the inclusive and in the tagged structure function modes. We suggest several strategies to address the extraction of [Formula: see text] and to measure at the same time the effect of nuclear shadowing via the measurement of the distortion of the proton spectator spectrum in the semi-inclusive eD → e′NX process. We address the issue of the final state interactions in the eD → e′NX process and examine how they affect the extraction of [Formula: see text].
TUNNELING THROUGH THE QUANTUM HORIZON
Authors: ARZANO MICHELE
Published: January 2006

The emergence of quantum-gravity induced corrective terms for the probability of emission of a particle from a black hole in the Parikh–Wilczek tunneling framework is studied. It is shown, in particular, how corrections might arise from modifications of the surface gravity due to near horizon Planck-scale effects. Our derivation provides an example of the possible linking between Planck-scale departures from Lorentz invariance and the appearance of higher order quantum gravity corrections in the black-hole entropy-area relation.
NO BOUND FOR THE FIRST FIXED POINT
Authors: GITIK MOTI
Published: January 2006

Our aim is to show that it is impossible to find a bound for the power of the first fixed point of the aleph function.
RELATIVIZING CHAITIN'S HALTING PROBABILITY
Authors: DOWNEY ROD , HIRSCHFELDT DENIS R. , MILLER JOSEPH S. , NIES ANDRÉ
Published: January 2006

As a natural example of a 1-random real, Chaitin proposed the halting probability Ω of a universal prefix-free machine. We can relativize this example by considering a universal prefix-free oracle machine U. Let [Formula: see text] be the halting probability of UA; this gives a natural uniform way of producing an A-random real for every A ∈ 2ω. It is this operator which is our primary object of study. We can draw an analogy between the jump operator from computability theory and this Omega operator. But unlike the jump, which is invariant (up to computable permutation) under the choice of an effective enumeration of the partial computable functions, [Formula: see text] can be vastly different for different choices of U. Even for a fixed U, there are oracles A =* B such that [Formula: see text] and [Formula: see text] are 1-random relative to each other. We prove this and many other interesting properties of Omega operators. We investigate these operators from the perspective of analysis, computability theory, and of course, algorithmic randomness.
EXISTENCE OF STRONG TRACES FOR GENERALIZED SOLUTIONS OF MULTIDIMENSIONAL SCALAR CONSERVATION LAWS
Authors: PANOV E. YU.
Published: January 2006

In the half-space t > 0 a multidimensional scalar conservation law with only continuous flux vector is considered. For the wide class of functions including generalized entropy sub- and super-solutions to this equation, we prove existence of the strong trace on the initial hyperspace t = 0. No nondegeneracy conditions on the flux are required.
ON ONE BLOW UP POINT SOLUTIONS TO THE CRITICAL NONLINEAR SCHRÖDINGER EQUATION
Authors: MERLE FRANK , RAPHAEL PIERRE
Published: January 2006

We consider the L2 critical nonlinear Schrödinger equation [Formula: see text] in the energy space H1. In the series of papers [11–15,18], we studied finite time blow up solutions for which lim t↑T < + ∞ |∇ u(t)|L2 = + ∞ and proved classification results of the blow up dynamics for the specific class of small super critical L2 mass initial data. We extend these results here to a wider class of finite time blow up solutions corresponding to the ones which accumulate at one point exactly the ground state mass. In particular, we prove the existence and stability of large L2 mass log-log type solutions which are believed to describe the generic blow up dynamics.
FROM THE KLEIN–GORDON–ZAKHAROV SYSTEM TO THE NONLINEAR SCHRÖDINGER EQUATION
Authors: MASMOUDI NADER , NAKANISHI KENJI
Published: January 2006

In this paper, we study the convergence of solutions in the limit from the Klein–Gordon–Zakharov system to the nonlinear Schrödinger equation. The major difficulties are resonant bilinear interactions whose frequency are going to infinity, and the diverging total energy. We overcome them by combining bilinear estimates for non-resonant interactions and a modified nonlinear energy at the resonant frequency.
Wanderings of a DNA Enzymologist: From DNA Polymerase to Viral Latency
Authors: Lehman I. Robert
Published: January 2006

I am a member of what has been called, perhaps too grandiosely, “The Greatest Generation.” I grew up during the Great Depression and served in the U.S. Army during World War II. Because of my military service and the benefits of the GI Bill, I was able to attend college and, later, graduate school. Early in my graduate studies, I became fascinated with enzymes and the biochemical reactions that they catalyze. This fascination has never left me during the 50 years I have been a “DNA enzymologist.” I was fortunate to have had as a mentor Arthur Kornberg, one of the great biochemists of the twentieth century, and a splendid group of postdocs and graduate students. I have studied DNA polymerases, DNA nucleases, DNA ligases, and DNA recombinases, enzymes that are critical to our understanding of DNA replication, repair, and recombination. Most recently, I have been studying herpes virus replication and inadvertently wandered into an entirely new area—viral latency.
ELECTRON TOMOGRAPHY OF MEMBRANE-BOUND CELLULAR ORGANELLES
Authors: Frey Terrence G. , Perkins Guy A. , Ellisman Mark H.
Published: January 2006

Electron microscope tomography produces three-dimensional reconstructions and has been used to image organelles both isolated and in situ, providing new insight into their structure and function. It is analogous to the various tomographies used in medical imaging. Compared with light microscopy, electron tomography offers an improvement in resolution of 30- to 80-fold and currently ranges from 3 to 8 nm, thus filling the gap between high-resolution structure determinations of isolated macromolecules and larger-scale studies on cells and tissues by light microscopy. Here, we provide an introduction to electron tomography and applications of the method in characterizing organelle architecture that also show its power for suggesting functional significance. Further improvements in labeling modalities, imaging tools, specimen preparation, and reconstruction algorithms promise to increase the quality and breadth of reconstructions by electron tomography and eventually to allow the mapping of the cellular proteomes onto detailed three-dimensional models of cellular structure.
Methodological and Conceptual Issues in Functional Magnetic Resonance Imaging: Applications to Schizophrenia Research
Authors: Brown Gregory G. , Eyler Lisa T.
Published: January 2006

Functional magnetic resonance imaging (MRI) is a noninvasive, highly repeatable, and increasingly available method to study disordered brain activity among patients with psychological or neurological disorders. In this chapter the biophysical principles underlying functional MRI are presented, and methodological limitations of the method are discussed. Artifacts related to the biophysical basis of the functional MRI signal or associated with image acquisition methods are presented, as are artifacts related to baseline effects—especially those associated with medication, caffeine, and nicotine use. The difficulties associated with the comparison of groups of subjects differing in performance receive special attention. The limitations of cognitive subtraction designs for functional MRI are also discussed. Functional MRI studies of schizophrenia patients are used to illustrate these points.
Doctoral Training in Clinical Psychology
Authors: McFall Richard M.
Published: January 2006

Competing models of doctoral training in clinical psychology are described and compared within their historical contexts. Trends in the field are examined critically with a focus on the impact of managed care on doctoral training and clinical practice. Implications for the future of doctoral training are considered, and a blueprint for the future of doctoral training in clinical psychology is presented.
Personality and Risk of Physical Illness
Authors: Smith Timothy W. , MacKenzie Justin
Published: January 2006

Several personality characteristics have been linked in multiple well-designed prospective studies to subsequent physical health outcomes, such as longevity and the development and course of cardiovascular disease. The evidence is strongest for negative affectivity/neuroticism, anger/hostility and related traits, and optimism. Models of mechanisms underlying these associations have emphasized physiological effects of stress, exposure to stressors, and health behavior. Preliminary evidence supports the viability of some mechanisms, but formal mediational tests are lacking. In addition to addressing limitations and inconsistencies in this literature, future research should address developmental aspects of these psychosocial risk factors, contextual moderators of their health effects, and intervention applications in the prevention and management of disease. In these efforts, greater incorporation of concepts and methods in the structural, social-cognitive, and interpersonal perspectives in the field of personality are needed.
PHANEROZOIC BIODIVERSITY MASS EXTINCTIONS
Authors: Bambach Richard K.
Published: January 2006

Recent analyses of Sepkoski's genus-level compendium show that only three events form a statistically separate class of high extinction intensities when only post-Early Ordovician intervals are considered, but geologists have called numerous events mass extinctions. Is this a conflict? A review of different methods of tabulating data from the Sepkoski database reveals 18 intervals during the Phanerozoic have peaks of both magnitude and rate of extinction that appear in each tabulating scheme. These intervals all fit Sepkoski's definition of mass extinction. However, they vary widely in timing and effect of extinction, demonstrating that mass extinctions are not a homogeneous group of events. No consensus has been reached on the kill mechanism for any marine mass extinction. In fact, adequate data on timing in ecologic, rather than geologic, time and on geographic and environmental distribution of extinction have not yet been systematically compiled for any extinction event.
BED MATERIAL TRANSPORT AND THE MORPHOLOGY OF ALLUVIAL RIVER CHANNELS
Authors: Church Michael
Published: January 2006

The morphology of an alluvial river channel is the consequence of sediment transport and sedimentation in the river. Morphological style is determined chiefly by the caliber and quantity of sediment delivered to the channel, although modulated by channel scale. Yet the relations between sediment transport and river morphology have received only limited, qualitative attention. In this review, the problem is studied by defining sediment transport regimes on the basis of the Shields number, a nondimensional measure of the capacity of the channel to move sediment of a given caliber. The problem is also approached from an inverse perspective by which the quantity and character of sediment deposits are used to infer details about the variation of sediment transport and sedimentation along a channel. Coupling the two approaches establishes a basis to gain new insights into the origins of alluvial channel morphology.
COSMIC DUST COLLECTION IN AEROGEL
Authors: Burchell Mark J. , Graham Giles , Kearsley Anton
Published: January 2006

Aerogel is an ultra-low-density material that can be used to capture small particles incident upon it at speeds in excess of 1 km s−1. This permits capture of cosmic dust in space where the high speeds usually result in destructive impact events. The performance of aerogel in laboratory impact tests is described. Completely intact capture is rare; most studies show that between 10% to 100% of the incident particle's mass is captured. However, in all cases unaltered domains were found in the particles captured in the laboratory at speeds up to 6 or 7 km s−1. Several analytic techniques can be applied in situ to particles captured in aerogel, yielding data on the preimpact composition of the particle. Extraction techniques for removing small particles from aerogel are described, and after extraction, handling and analysis in the laboratory can proceed as for any small-sized particle. Coupled with the survival of intact regions in the captured particles, this allows detailed identification of the composition of the dust. Examples are given of current space missions using aerogel dust collectors: Data on these will soon be supplemented by cometary dust particles captured in aerogel on the NASA Stardust spacecraft.
DYNAMICS OF LAKE ERUPTIONS AND POSSIBLE OCEAN ERUPTIONS
Authors: Zhang Youxue , Kling George W.
Published: January 2006

Dissolved gas in liquid is able to power violent eruptions. Two kinds of such gas-driven eruptions are known in nature: explosive volcanic eruptions driven by dissolved H2O in magma at high temperatures and lake eruptions driven by dissolved CO2 in water at low temperatures. There are two known occurrences of lake eruptions, one in 1984 (Lake Monoun) and one in 1986 (Lake Nyos), both in Cameroon, Africa. The erupted CO2 gas asphyxiated ∼1700 people in the Lake Nyos eruption and 37 people at Lake Monoun. Here we review experimental simulations of CO2-driven water eruptions and dynamic models of such eruptions, and a bubble plume theory is applied to the dynamics of lake eruptions. Field evidence, experimental results, and theoretical models show that lake eruptions can be violent, and theoretical calculations are consistent with the high exit velocities and eruption columns inferred from observations. Furthermore, the dynamics of lake degassing experiments are consistent with theoretical models. Other kinds of gas-driven eruptions are possible and may have occurred in nature in the past. A concentrated and large release of methane gas or hydrate from marine sediment may result in an ocean eruption. Furthermore, injection of liquid CO2 into oceans might also lead to ocean eruptions if care is not taken. The various kinetic and dynamic processes involved are examined and quantified.
HIGH-MG ANDESITES IN THE SETOUCHI VOLCANIC BELT, SOUTHWESTERN JAPAN: Analogy to Archean Magmatism and Continental Crust Formation?
Authors: Tatsumi Yoshiyuki
Published: January 2006

The occurrence of unusual high-Mg andesite (HMA) characterizes the Setouchi volcanic belt in SW Japan, which was activated at 13.7±1.0 Ma by subduction of the young and hot Shikoku Basin lithosphere into the high-temperature upper mantle. This tectonic setting may be analogous to the thermal regime during Archean times, which suggests more ubiquitous production of HMA. A plausible process that can comprehensively account for the petrological and geochemical characteristics of Setouchi HMAs involves partial melting of subducting lithosphere, subsequent melt-mantle interactions, and final equilibration with the upper-most mantle. HMAs and more differentiated andesites, which are coined sanukitoids, are distinct in that they are phenocryst-poor (<10%), compact, and nearly anhydrous, despite HMA magmas originally containing ∼7 wt% H2O, and commonly form composite lava flows. One mechanism for explaining these features is formation of a mostly solidified HMA pluton, remelting of the HMA pluton by intrusion of a high-temperature basaltic magma, consequent production of a nearly dry HMA magma, and mixing of this HMA magma with overlying residual felsic melts during ascent to form a zoned magma reservoir.
PLANETESIMALS TO BROWN DWARFS: What is a Planet?
Authors: Basri Gibor , Brown Michael E.
Published: January 2006

The past 15 years have brought about a revolution in our understanding of our Solar System and other planetary systems. During this time, discoveries include the first Kuiper belt objects (KBOs), the first brown dwarfs, and the first extrasolar planets. Although discoveries continue apace, they have called into question our previous perspectives on planets, both here and elsewhere. The result has been a debate about the meaning of the word “planet” itself. It is clear that scientists do not have a widely accepted or clear definition of what a planet is, and both scientists and the public are confused (and sometimes annoyed) by its use in various contexts. Because “planet” is a very widely used term, it seems worth the attempt to resolve this problem. In this essay, we try to cover all the issues that have come to the fore and bring clarity (if not resolution) to the debate.
SEISMIC TRIGGERING OF ERUPTIONS IN THE FAR FIELD: Volcanoes and Geysers
Authors: Manga Michael , Brodsky Emily
Published: January 2006

Approximately 0.4% of explosive volcanic eruptions occur within a few days of large, distant earthquakes. This many “triggered” eruptions is much greater than expected by chance. Several mechanisms have been proposed to explain triggering through changes in magma overpressure, including the growth of bubbles, the advection of large pressures by rising bubbles, and overturn of magma chambers. Alternatively, triggered eruptions may occur through failure of rocks surrounding stored magma. All these mechanisms require a process that enhances small static stress changes caused by earthquakes or that can convert (the larger) transient, dynamic strains into permanent changes in pressure. All proposed processes, in addition to viscoelastic relaxation of stresses, can result in delayed triggering of eruptions, although quantifying the connection between earthquakes and delayed, triggered eruptions is much more challenging. Mud volcanoes and geysers also respond to distant earthquakes. Mud volcanoes that discharge mud from depths greater than many hundreds of meters may be triggered by liquefaction caused by shaking, and may thus be similar to small mud volcanoes that originate within a few meters of the surface. Changes in permeability of the matrix surrounding main geyser conduits, by opening or creating new fractures, may explain the observed changes in their eruption frequency.
THE YARKOVSKY AND YORP EFFECTS: Implications for Asteroid Dynamics
Authors: Bottke William F. , Vokrouhlický David , Rubincam David P. , Nesvorný David
Published: January 2006

The Yarkovsky and YORP (Yarkovsky-O'Keefe-Radzievskii-Paddack) effects are thermal radiation forces and torques that cause small objects to undergo semimajor axis drift and spin vector modifications, respectively, as a function of their spin, orbit, and material properties. These mechanisms help to (a) deliver asteroids (and meteoroids) with diameter D < 40 km from their source locations in the main belt to chaotic resonance zones capable of transporting this material to Earth-crossing orbits; (b) disperse asteroid families, with drifting bodies jumping or becoming trapped in mean-motion and secular resonances within the main belt; (c) modify the rotation rates and obliquities of D < 40 km asteroids; and (d) allow asteroids to enter into spin-orbit resonances, which affect the evolution of their spin vectors and feedback into the Yarkovsky-driven semimajor axis evolution. Accordingly, we suggest that nongravitational forces should now be considered as important as collisions and gravitational perturbations to our overall understanding of asteroid evolution.
USING THERMOCHRONOLOGY TO UNDERSTAND OROGENIC EROSION
Authors: Reiners Peter W. , Brandon Mark T.
Published: January 2006

Erosion of orogenic mountain ranges exhumes deeply buried rocks and controls weathering, climate, and sediment production and transport at a variety of scales. Erosion also affects the topographic form and kinematics of orogens, and it may provide dynamic feedbacks between climate and tectonics by spatially focused erosion and rock uplift. Thermochronology measures the timing and rates at which rocks approach the surface and cool as a result of exhumation. Relatively well-understood noble gas and fission-track thermochronometric systems have closure temperatures ranging from ∼60 to ∼550°C, making them sensitive to exhumation through crustal depths of about one to tens of kilometers. Thus, thermochronology can constrain erosion rates and their spatial-temporal variations on timescales of ∼105–107 years, commensurate with orogenic growth and decay cycles and possible climate-tectonic feedback response times. Useful methods for estimating erosion rates include inverting ages for erosion rates using crustal thermal models, vertical transects, and detrital approaches. Spatial-temporal patterns of thermochronometrically determined erosion rates help constrain flow of material through orogenic wedges, orogenic growth and decay cycles, paleorelief, and relationships with structural, geomorphic, or climatic features.
A CENTRAL ROLE FOR CENTRAL TOLERANCE
Authors: Kyewski Bruno , Klein Ludger
Published: January 2006

Recent elucidation of the role of central tolerance in preventing organ-specific autoimmunity has changed our concepts of self/nonself discrimination. This paradigmatic shift is largely attributable to the discovery of promiscuous expression of tissue-restricted self-antigens (TRAs) by medullary thymic epithelial cells (mTECs). TRA expression in mTECs mirrors virtually all tissues of the body, irrespective of developmental or spatio-temporal expression patterns. This review summarizes current knowledge on the cellular and molecular regulation of TRA expression in mTECs, outlines relevant mechanisms of antigen presentation and modes of tolerance induction, and discusses implications for the pathogenesis of autoimmune diseases and other biological processes such as fertility, pregnancy, puberty, and tumor defense.
HOW TCRS BIND MHCS, PEPTIDES, AND CORECEPTORS
Authors: Rudolph Markus G. , Stanfield Robyn L. , Wilson Ian A.
Published: January 2006

Since the first crystal structure determinations of αβ T cell receptors (TCRs) bound to class I MHC-peptide (pMHC) antigens in 1996, a sizable database of 24 class I and class II TCR/pMHC complexes has been accumulated that now defines a substantial degree of structural variability in TCR/pMHC recognition. Recent determination of free and bound γδ TCR structures has enabled comparisons of the modes of antigen recognition by αβ and γδ T cells and antibodies. Crystal structures of TCR accessory (CD4, CD8) and coreceptor molecules (CD3ɛδ, CD3ɛγ) have further advanced our structural understanding of most of the components that constitute the TCR signaling complex. Despite all these efforts, the structural basis for MHC restriction and signaling remains elusive as no structural features that define a common binding mode or signaling mechanism have yet been gleaned from the current set of TCR/pMHC complexes. Notwithstanding, the impressive array of self, foreign (microbial), and autoimmune TCR complexes have uncovered the diverse ways in which antigens can be specifically recognized by TCRs.
B CELL IMMUNOBIOLOGY IN DISEASE: Evolving Concepts from the Clinic
Authors: Martin Flavius , Chan Andrew C.
Published: January 2006

The pathogenic roles of B cells in autoimmune diseases occur through several mechanistic pathways that include autoantibodies, immune complexes, dendritic and T cell activation, cytokine synthesis, chemokine-mediated functions, and ectopic neolymphogenesis. Each of these pathways participate to different degrees in autoimmune diseases. The use of B cell–targeted and B cell subset–targeted therapies in humans is illuminating the mechanisms at work in a variety of human autoimmune diseases. In this review, we highlight some of these recent findings that provide insights into both murine models of autoimmunity and human autoimmune diseases.
THE EVOLUTION OF ADAPTIVE IMMUNITY
Authors: Pancer Zeev , Cooper Max D.
Published: January 2006

Approximately 500 mya two types of recombinatorial adaptive immune systems appeared in vertebrates. Jawed vertebrates generate a diverse repertoire of B and T cell antigen receptors through the rearrangement of immunoglobulin V, D, and J gene fragments, whereas jawless fish assemble their variable lymphocyte receptors through recombinatorial usage of leucine-rich repeat (LRR) modular units. Invariant germ line–encoded, LRR-containing proteins are pivotal mediators of microbial recognition throughout the plant and animal kingdoms. Whereas the genomes of plants and deuterostome and chordate invertebrates harbor large arsenals of recognition receptors primarily encoding LRR-containing proteins, relatively few innate pattern recognition receptors suffice for survival of pathogen-infected nematodes, insects, and vertebrates. The appearance of a lymphocyte-based recombinatorial system of anticipatory immunity in the vertebrates may have been driven by a need to facilitate developmental and morphological plasticity in addition to the advantage conferred by the ability to recognize a larger portion of the antigenic world.
GP120: Target for Neutralizing HIV-1 Antibodies
Authors: Pantophlet Ralph , Burton Dennis R.
Published: January 2006

The glycoprotein (gp) 120 subunit is an important part of the envelope spikes that decorate the surface of HIV-1 and a major target for neutralizing antibodies. However, immunization with recombinant gp120 does not elicit neutralizing antibodies against multiple HIV-1 isolates (broadly neutralizing antibodies), and gp120 failed to demonstrate vaccine efficacy in recent clinical trials. Ongoing crystallographic studies of gp120 molecules from HIV-1 and SIV increasingly reveal how conserved regions, which are the targets of broadly neutralizing antibodies, are concealed from immune recognition. Based on this structural insight and that from studies of antibody structures, a number of strategies are being pursued to design immunogens that can elicit broadly neutralizing antibodies to gp120. These include (a) the construction of mimics of the viral envelope spike and (b) the design of antigens specifically tailored to induce broadly neutralizing antibodies.
DIVERSE FUNCTIONS OF IL-2, IL-15, AND IL-7 IN LYMPHOID HOMEOSTASIS
Authors: Ma Averil , Koka Rima , Burkett Patrick
Published: January 2006

IL-2, IL-15, and IL-7 are cytokines that are critical for regulating lymphoid homeostasis. These cytokines stimulate similar responses from lymphocytes in vitro, but play markedly divergent roles in lymphoid biology in vivo. Their distinct physiological functions can be ascribed to distinct signaling pathways initiated by proprietary cytokine receptor chains, differential expression patterns of the cytokines or their receptor chains, and/or signals occurring in distinct physiological contexts. Recently, the discovery of a novel mechanism of cytokine signaling, trans-presentation, has provided further insights into the different ways these cytokines function. Trans-presentation also raises several novel cell biological and cellular implications concerning how cytokines support lymphoid homeostasis.
ION PAIR DISSOCIATION: Spectroscopy and Dynamics
Authors: Suits Arthur G. , Hepburn John W.
Published: January 2006

▪ Abstract  Ion pair dissociation processes may be studied using coherent vacuum ultraviolet laser sources in a manner entirely analogous to photoelectron spectroscopy, albeit with the anion playing the role of a heavy electron. If the excitation energy is above the dissociation energy and the kinetic energy of the fragment is measured using ion imaging, this approach is termed ion pair imaging spectroscopy (IPIS) and is related to conventional photoelectron spectroscopy. If the excitation energy is just below the dissociation energy and pulsed-field dissociation is employed, this approach is analogous to mass analyzed threshold ionization (MATI) spectroscopy and is termed threshold ion pair production spectroscopy (TIPPS). These approaches provide a novel means of investigating ion thermochemistry and spectroscopy and superexcited state decay dynamics at high resolution.
REACTIVITY OF THE GERMANIUM SURFACE: Chemical Passivation and Functionalization
Authors: Loscutoff Paul W. , Bent Stacey F.
Published: January 2006

▪ Abstract  With the rapidly changing materials needs of modern microelectronics, germanium provides an opportunity for future-generation devices. Controlling germanium interfaces will be essential for this purpose. We review germanium surface reactivity, beginning with a description of the most commonly used surfaces, Ge(100) and Ge(111). An analysis of oxide formation shows why the poor oxide properties have hindered practical use of germanium to date. This is followed by an examination of alternate means of surface passivation, with particular attention given to sulfide, chloride, and hydride termination. Specific tailoring of the interface properties is possible through organic functionalization. The few solution functionalization methods that have been studied are reviewed. Vacuum functionalization has been studied to a much greater extent, with dative bonding and cycloaddition reactions emerging as principle reaction mechanisms. These are reviewed through molecular reaction studies that demonstrate the versatility of the germanium surface.
RAMAN CRYSTALLOGRAPHY AND OTHER BIOCHEMICAL APPLICATIONS OF RAMAN MICROSCOPY
Authors: Carey Paul R.
Published: January 2006

▪ Abstract  Recent studies using a Raman microscope have shown that single protein crystals provide an ideal platform to undertake Raman difference spectroscopic analyses under nonresonance conditions. This approach, termed Raman crystallography, provides a means of characterizing chemical events within the crystal such as ligand binding and enzyme reactions. In many cases Raman crystallography goes hand in hand with X-ray crystallographic studies because the Raman results can inform the X-ray crystallographer about the status of chemical events in the crystal prior to flash freezing and X-ray analysis. In turn, the combined data from the Raman and X-ray analyses are highly synergistic and offer novel perspectives on structure and dynamics in enzyme active sites. In a related area, protein misfolding, Raman microscopy can provide detailed insights into the chemistry of the amyloid plaques associated with Alzheimer's disease and into the intermediates on the α-synuclein protein misfolding pathway implicated in Parkinson's disease.
CORRELATED ELECTRONIC STRUCTURE NONLINEAR RESPONSE METHODS FOR STRUCTURED ENVIRONMENTS
Authors: Mikkelsen Kurt V.
Published: January 2006

▪ Abstract  This contribution concerns a brief outline of structural environment models where correlated electronic structure response methods are utilized for the determination of nonlinear optical properties of molecules. The presentation provides theory and applications of a heterogeneous dielectric media model and a quantum mechanical–classical mechanical model at the level of correlated electronic structure response methods. The correlated electronic structure response methods include the multiconfigurational self-consistent field method.
ECONOMIC TRANSFORMATION AND ITS POLITICAL DISCONTENTS IN CHINA: Authoritarianism, Unequal Growth, and the Dilemmas of Political Development
Authors: Yang Dali L.
Published: January 2006

▪ Abstract  China's economic growth and transition pose fascinating questions for social scientists. In the economic realm, proponents of the market-preserving federalism (MPF) model appear to have gone too far. In reality, China's central leadership has retained the prerogative to appoint top provincial officials as well as the power to reconfigure central-provincial fiscal relations, thus defying predictions of the MPF model. In the social realm, rapid growth has propelled the expansion of the middle class, but the large increase in inequality has sharpened social cleavages and class conflicts. The uncertainties of market transition and rising social conflicts pose major challenges for the ruling elite and for China's political development.
Single-beat estimation of end-diastolic pressure-volume relationship: a novel method with potential for noninvasive application
Authors: Klotz Stefan , Hay Ilan , Dickstein Marc L. , Yi Geng-Hua , Wang Jie , Maurer Mathew S. , Kass David A. , Burkhoff Daniel
Published: January 2006

Whereas end-systolic and end-diastolic pressure-volume relations (ESPVR, EDPVR) characterize left ventricular (LV) pump properties, clinical utility of these relations has been hampered by the need for invasive measurements over a range of pressure and volumes. We propose a single-beat approach to estimate the whole EDPVR from one measured volume-pressure (Vm and Pm) point. Ex vivo EDPVRs were measured from 80 human hearts of different etiologies (normal, congestive heart failure, left ventricular assist device support). Independent of etiology, when EDPVRs were normalized (EDPVRn) by appropriate scaling of LV volumes, EDPVRns were nearly identical and were optimally described by the relation EDP = An·EDV Bn, with An = 28.2 mmHg and Bn = 2.79. V0 (the volume at the pressure of ∼0 mmHg) was predicted by using the relation V0 = Vm·(0.6 − 0.006·Pm) and V30 by V30 = V0 + (Vm,n − V0)/(Pm/ An) (1/ B n). The entire EDPVR of an individual heart was then predicted by forcing the curve through Vm, Pm, and the predicted V0 and V30. This technique was applied prospectively to the ex vivo human EDPVRs not used in determining optimal An and Bn values and to 36 in vivo human, 12 acute and 14 chronic canine, and 80 in vivo and ex vivo rat studies. The root-mean-square error (RMSE) in pressure between measured and predicted EDPVRs over the range of 0–40 mmHg was <3 mmHg of measured EDPVR in all settings, indicating a good predictive value of this approach. Volume-normalized EDPVRs have a common shape, despite different etiology and species. This allows the entire curve to be predicted by a new method with a potential for noninvasive application. The results are most accurate when applied to groups of hearts rather than to individual hearts.
Expression of slow myosin heavy chain during muscle regeneration is not always dependent on muscle innervation and calcineurin phosphatase activity
Authors: Launay Thierry , Noirez Philippe , Butler-Browne Gillian , Agbulut Onnik
Published: January 2006

In the literature, there is an ambiguity as to the respective roles played by calcineurin phosphatase activity (CPA) and muscle innervation in the reestablishment of the slow-twitch muscle phenotype after muscle regeneration in different species. In this study, we wanted to determine the role of calcineurin and muscle innervation on the appearance and maintenance of the slow phenotype during mouse muscle regeneration. The pattern of myosin expression and CPA was analyzed in adult ( n = 15), regenerating ( n = 45) and denervated-regenerating ( n = 32) slow-twitch soleus and fast-twitch extensor digitorum longus (EDL) muscles. Moreover, in a second group of denervated-regenerating mice ( n = 9), the animals were treated with a calcineurin inhibitor. Regeneration was induced by injection of cardiotoxin and in the denervated-regenerating group, denervation was carried out by cutting the sciatic nerve before the administration of cardiotoxin. In innervated-regenerating soleus muscle, CPA increased continuously after 10 days postinjury and by 21 days, there was a 3.5-fold increase in CPA compared with adult basal level, whereas in innervated-regenerating EDL muscle, CPA remained unchanged. Moreover, our results show that in denervated-regenerating muscles, the MyHC profile was identical in spite of the functional differences inherent in these muscles. In long-term denervated-regenerating muscles, a slow muscle phenotype was reexpressed both in the presence or absence of calcineurin inhibitor. Our results show that although in innervated-regenerating mouse muscle, the appearance of a slow phenotype is correlated with a peak of CPA, in denervated-regenerating muscles, a slow phenotype is triggered and maintained in a calcineurin- and nerve-independent manner.
Carbohydrate metabolism during prolonged exercise and recovery: interactions between pyruvate dehydrogenase, fatty acids, and amino acids
Authors: Mourtzakis Marina , Saltin Bengt , Graham Terry , Pilegaard Henriette
Published: January 2006

During prolonged exercise, carbohydrate oxidation may result from decreased pyruvate production and increased fatty acid supply and ultimately lead to reduced pyruvate dehydrogenase (PDH) activity. Pyruvate also interacts with the amino acids alanine, glutamine, and glutamate, whereby the decline in pyruvate production could affect tricarboxycylic acid cycle flux as well as gluconeogenesis. To enhance our understanding of these interactions, we studied the time course of changes in substrate utilization in six men who cycled at 44 ± 1% peak oxygen consumption (mean ± SE) until exhaustion (exhaustion at 3 h 23 min ± 11 min). Femoral arterial and venous blood, blood flow measurements, and muscle samples were obtained hourly during exercise and recovery (3 h). Carbohydrate oxidation peaked at 30 min of exercise and subsequently decreased for the remainder of the exercise bout ( P < 0.05). PDH activity peaked at 2 h of exercise, whereas pyruvate production peaked at 1 h of exercise and was reduced (∼30%) thereafter, suggesting that pyruvate availability primarily accounted for reduced carbohydrate oxidation. Increased free fatty acid uptake ( P < 0.05) was also associated with decreasing PDH activity ( P < 0.05) and increased PDH kinase 4 mRNA ( P < 0.05) during exercise and recovery. At 1 h of exercise, pyruvate production was greatest and was closely linked to glutamate, which was the predominant amino acid taken up during exercise and recovery. Alanine and glutamine were also associated with pyruvate metabolism, and they comprised ∼68% of total amino-acid release during exercise and recovery. Thus reduced pyruvate production was primarily associated with reduced carbohydrate oxidation, whereas the greatest production of pyruvate was related to glutamate, glutamine, and alanine metabolism in early exercise.
Salvage of focal cerebral ischemic damage by transfusion of high O2-affinity recombinant hemoglobin polymers in mouse
Authors: Nemoto Masaaki , Mito Toshiaki , Brinigar William S , Fronticelli Clara , Koehler Raymond C.
Published: January 2006

Cell-free hemoglobin solutions with high oxygen affinity might be beneficial for selectively delivering oxygen to ischemic tissue. A recombinant hybrid hemoglobin molecule was designed using the human α-subunit and the bovine β-subunit, with placement of surface cysteines to permit disulfide bond polymerization of the tetramers. The resulting protein generated from an Escherichia coli expression system had a molecular mass >1 MDa, a P50 of ∼3 Torr, and a cooperativity of n = 1.0. Anesthetized mice were transfused during 2-h occlusion of the middle cerebral artery. Compared with transfusion with 5% albumin, cerebral infarct volume was reduced by 41% with transfusion of a 3% solution of the high oxygen-affinity hemoglobin polymer and by 50% with transfusion of a 6% solution of the polymer. Transfusion of a 6% solution of a 500-kDa polymer possessing a P50 of 17 Torr and a cooperativity of n = 2.0 resulted in a 66% reduction of infarct volume. These results indicate that cell-free Hb polymers with P50 values much lower than that of red blood cell hemoglobin are highly capable of salvaging ischemic brain. The assumption that the P50 of blood substitutes should be similar to that of blood might not be warranted when used during ischemic conditions.
Enhanced mitochondrial sensitivity to creatine in rats bred for high aerobic capacity
Authors: Walsh B. , Hooks R. B. , Hornyak J. E. , Koch L. G. , Britton S. L. , Hogan M. C.
Published: January 2006

Qualitative and quantitative measures of mitochondrial function were performed in rats selectively bred 15 generations for intrinsic aerobic high running capacity (HCR; n = 8) or low running capacity (LCR; n = 8). As estimated from a speed-ramped treadmill exercise test to exhaustion (15° slope; initial velocity of 10 m/min, increased 1 m/min every 2 min), HCR rats ran 10 times further (2,375 ± 80 m) compared with LCR rats (238 ± 12 m). Fiber bundles were obtained from the soleus and chemically permeabilized. Respiration was measured 1) in the absence of ADP, 2) in the presence of a submaximally stimulating concentration of ADP (0.1 mM ADP, with and without 20 mM creatine), and 3) in the presence of a maximally stimulating concentration of ADP (2 mM). Although non-ADP-stimulated and maximally ADP-stimulated rates of respiration were 13% higher in HCR compared with LCR, the difference was not statistically significant ( P > 0.05). Despite a similar rate of respiration in the presence of 0.1 mM ADP, HCR rats demonstrated a higher rate of respiration in the presence of 0.1 mM ADP + 20 mM creatine (HCR 33% higher vs. LCR, P < 0.05). Thus mitochondria from HCR rats exhibit enhanced mitochondrial sensitivity to creatine (i.e., the ability of creatine to decrease the Kmfor ADP). We propose that increased respiratory sensitivity to ADP in the presence of creatine can effectively increase muscle sensitivity to ADP during exercise (when creatine is increased) and may be, in part, a contributing factor for the increased running capacity in HCR rats.
A Probabilistic Functional Atlas of the VIM Nucleus Constructed from Pre-, Intra- and Postoperative Electrophysiological and Neuroimaging Data Acquired during the Surgical Treatment of Parkinson’s Disease Patients
Authors: Nowinski Wieslaw L. , Belov Dmitry , Thirunavuukarasuu A. , Benabid Alim Louis
Published: January 2006

We have previously introduced a concept of a probabilistic functional atlas (PFA) to overcome limitations of the current electronic stereotactic brain atlases: anatomical nature, spatial sparseness, inconsistency and lack of population information. The PFA for the STN has already been developed. This work addresses construction of the PFA for the ventrointermediate nucleus (PFA-VIM). The PFA-VIM is constructed from pre-, intra- and postoperative electrophysiological and neuroimaging data acquired during the surgical treatment of Parkinson’s disease patients. The data contain the positions of the chronically implanted electrodes and their best contacts. For each patient, the intercommissural distance, height of the thalamus and width of the third ventricle were measured. An algorithm was developed to convert these data into the PFA-VIM, and to present them on axial, coronal and sagittal planes and in 3-D. The PFA-VIM gives a spatial distribution of the best contacts, and its probability is proportional to best contact concentration in a given location. The region with the highest probability corresponds to the best target. The PFA-VIM is calculated with 0.25-mm3 resolution from 107 best contacts in two situations: with and without lateral compensation against the width of the third ventricle. For the PFA-VIM compensated laterally, the anterior, lateral and dorsal coordinates of the mean value are (in mm) 6.24, 13.83, 1.68 for the left VIM and 6.54, –13.84, 2.10 for the right VIM. The coordinates of the mean value of the highest probability region along with the highest number of the best contacts (P) are: 6.25, 14.25, 1.75, P = 16, for the left VIM, and 6.0, –14.0, 1.00, P = 18, for the right VIM. The coordinate system origin is at the posterior commissure. For the PFA-VIM not compensated laterally, the coordinates of the mean value are 6.24, 13.99, 1.68 for the left VIM and 6.53, –14.13, 2.10 for the right VIM. The coordinates of the mean value of the highest probability region along with the highest number of the best contacts are 5.58, 13.67, 1.33, P = 14, for the left VIM, and 6.36, –14.03, 1.11, P = 17, for the right VIM. The PFA-VIM atlas overcomes several limitations of the current anatomical atlases and can improve targeting of thalamotomies and thalamic stimulations. It is dynamic and can easily be extended with new cases.
Multimodality Treatment of Trigeminal Neuralgia
Authors: Amirnovin Ramin , Neimat Joseph S. , Roberts Jane A. , Eskandar Emad N.
Published: January 2006

Most trigeminal neuralgia (TN) studies focus on a single strategy, microvascular decompression (MVD) or percutaneous rhizotomy (PR). We use a multimodality approach to TN. We perform MVD on patients younger than 70 years and PR on older patients or those where MVD has failed. We performed a chart review of the procedures for TN over the past 3 years and used a questionnaire for long-term follow-up. The questionnaire asked patients to rate their pre- and postoperative pain, outcome, and medication changes. Seventy-four procedures (40 MVDs and 34 PRs) were performed on 67 patients. Twenty patients had undergone previous procedures. 93% of the patients had significant initial pain relief. Over a 1.2-year mean follow-up, 51% of the patients had complete pain relief while 27% had a substantial improvement. There were no deaths and 5 complications. Our results suggest that a multimodality approach to TN yields excellent results with minimal complications.
A Novel Prostaglandin E Receptor 4–Associated Protein Participates in Antiinflammatory Signaling
Authors: Takayama Kiyoshi , Sukhova Galina K. , Chin Michael T. , Libby Peter
Published: January 2006

Prostaglandin E
2
exerts an antiinflammatory action by ligation of the heptahelical receptor EP4 in human macrophages. Because the mechanism by which EP4 receptor stimulation suppresses inflammatory activation in macrophages remains undefined, we sought interactors with the carboxyl-terminal cytoplasmic domain of the EP4 receptor. Yeast 2-hybrid screening of the human bone marrow cDNA library with the EP4 receptor as a bait identified a cDNA clone encoding a 669-amino acid protein, designated here as EP4 receptor-associated protein (EPRAP), which contains 8 ankyrin motifs that might recruit other signaling molecules. EPRAP bound to the full-length EP4 receptor in HEK293 cells cotransfected with V5-tagged EPRAP and FLAG-tagged EP4 receptor cDNA, as anti-FLAG antibody coimmunoprecipitated EPRAP with the EP4 receptor from the lysates of cotransfected cells. Human macrophages derived from peripheral blood monocytes expressed an approximately 70-kDa protein detected by Western blotting with a polyclonal anti-EPRAP antibody. Fluorescence immunohistochemistry colocalized EPRAP with the EP4 receptor in human atheromata. Interference with EPRAP function by small interference RNA limited prostaglandin E
2
–mediated suppression of chemokine expression in macrophages activated with lipopolysaccharide and tumor necrosis factor α. In conclusion, the antiinflammatory action of prostaglandin E
2
in macrophages involves EPRAP that associates directly with the cytoplasmic tail of EP4 receptor.