bluuebunny/crossref_metadata_2025 huggingface dataset:
In Situ Characterization of
Cymbidium Ringspot Tombusvirus
Infection-Induced Posttranscriptional Gene Silencing in
Nicotiana benthamiana
Authors: Havelda Zoltán , Hornyik Csaba , Crescenzi Aniello , Burgyán József
Published: April 2003

In plants, posttranscriptional gene silencing (PTGS) is an ancient and effective defense mechanism against viral infection. A number of viruses encode proteins that suppress virus-activated PTGS. The p19 protein of tombusviruses is a potent PTGS suppressor which interferes with the onset of PTGS-generated systemic signaling and is not required for viral replication or for viral movement in
Nicotiana benthamiana.
This unique feature of p19 suppressor allowed us to analyze the mechanism of PTGS-based host defense and its viral suppression without interfering with other viral functions. In contrast to the necrotic symptoms caused by wild-type tombusvirus, the infection of p19-defective mutant virus results in the development of a typical PTGS-associated recovery phenotype in
N. benthamiana
. In this report we show the effect of PTGS on the viral infection process for
N. benthamiana
infected with either wild-type
Cymbidium Ringspot Tombusvirus
(CymRSV) or a p19-defective mutant (Cym19stop). In situ analyses of different virus-derived products revealed that PTGS is not able to reduce accumulation of virus in primary infected cells regardless of the presence of p19 PTGS suppressor. We also showed that both CymRSV and Cym19stop viruses move systemically in the vasculature, with similar efficiencies. However, in contrast to the uniform accumulation of CymRSV throughout systemically infected leaves, the presence of Cym19stop virus was confined to and around the vascular bundles. These results suggest that the role of p19 is to prevent the onset of mobile signal-induced systemic PTGS ahead of the viral infection front, leading to generalized infection.
Determination of bearing capacity of shallow foundations without using superposition approximation
Authors: Zhu D Y , Lee C F , Law K T
Published: April 2003

The Terzaghi superposition assumption has been widely used to determine the bearing capacity of shallow footings. Although this assumption always errs on the safe side, a rigorous procedure to calculate the bearing capacity is still of engineering value. This paper presents such a procedure that is free from errors as a result of the superposition assumption. It demonstrates that the ultimate bearing capacity can be precisely expressed by the Terzaghi equation, except that the bearing capacity factor Nγis dependent upon the surcharge ratio. A recently developed numerical method, i.e., the critical slip field method, is used to calculate the modification coefficient for modifying Nγ. It is found that this modification coefficient increases with the surcharge ratio at small values of surcharge ratio and then remains constant for large values of surcharge ratio. However, the errors invoked by the superposition assumption do not exceed 10%. On the basis of numerical calculations, a simple closed-form expression of the modification coefficient is proposed that yields the theoretically rigorous ultimate bearing capacity. In the later part of the paper, errors in bearing capacity calculations owing to the use of conventional procedures are analyzed. It is concluded that the continued use of conventional procedures is justified, but the inherent errors should not be neglected in assessing the performance of shallow foundations.Key words: shallow foundation, strip footing, ultimate bearing capacity, critical slip field.
The effect of strength envelope nonlinearity on slope stability computations
Authors: Jiang J -C , Baker R , Yamagami T
Published: April 2003

Engineering analysis of slope stability includes three separate but interrelated phases: (a) experimental strength measurements, (b) determination of a strength envelope that best fits the experimental results, and (c) formal limiting equilibrium analysis using the resulting strength envelopes. Studying the interrelations between these phases leads to an integrated approach to slope stability analysis. The present work uses a single experimental database that is fitted with both linear (MohrCoulomb) and nonlinear failure envelopes and investigates the effect of different forms of the failure criterion on slope stability computations for both 2D and 3D problems. It has been indicated that calculated minimum safety factors could be significantly overestimated by the linear approximation of a nonlinear strength envelope. The effect of neglecting strength envelope nonlinearity is more pronounced under 3D conditions than in a 2D simplification. As a result, the use of nonlinear failure criterions in slope stability analyses is recommended to account for the stress-dependent nature of the shear strength of soils.Key words: nonlinear strength envelope, MohrCoulomb failure criterion, limit equilibrium, critical slip surface, minimum factor of safety, three-dimensional stability analysis.
Shallow landsliding, root reinforcement, and the spatial distribution of trees in the Oregon Coast Range
Authors: Roering Joshua J , Schmidt Kevin M , Stock Jonathan D , Dietrich William E , Montgomery David R
Published: April 2003

The influence of root reinforcement on shallow landsliding has been well established through mechanistic and empirical studies, yet few studies have examined how local vegetative patterns influence slope stability. Because root networks spread outward from trees, the species, size, and spacing of trees should influence the spatial distribution of root strength. We documented the distribution and characteristics of trees adjacent to 32 shallow landslides that occurred during 1996 in the Oregon Coast Range. Although broadly classified as a conifer-dominated forest, we observed sparse coniferous and abundant hardwood trees near landslide scars in an industrial forest (Mapleton) that experienced widespread burning in the 19th century. In industrial forests that were burned, selectively harvested, and not replanted (Elliott State Forest), swordfern was ubiquitous near landslides, and we observed similar numbers of live conifer and hardwood trees proximal to landslide scarps. We demonstrate that root strength quantified in landslide scarps and soil pits correlates with a geometry-based index of root network contribution derived from mapping the size, species, condition, and spacing of local trees, indicating that root strength can be predicted by mapping the distribution and characteristics of trees on potentially unstable slopes. In our study sites, landslides tend to occur in areas of reduced root strength, suggesting that to make site-specific predictions of landslide occurrence slope stability analyses must account for the diversity and distribution of vegetation in potentially unstable terrain.Key words: slope stability, vegetation, root strength, shallow landslide, debris flow, Oregon Coast Range.
THE NUCLEON'S MIRROR IMAGE: REVEALING THE STRANGE AND UNEXPECTED
Authors: MCKEOWN R. D.
Published: April 2003

An extensive program of parity-violating electron scattering experiments is providing new insight into the structure of the nucleon. Measurement of the vector form factors enables a definitive study of potential strange quark-antiquark contributions to the nucleon's electromagnetic structure, including the magnetic moment and charge distribution. Recent experimental results have already indicated that effects of strangeness are much smaller than theoretically expected. In addition, the neutral axial form factor appears to display substantial corrections as one might expect from an anapole effect.
GAMMA SPECTROSCOPY OF P-SHELL HYPERNUCLEI AND ΛN SPIN-DEPENDENT INTERACTIONS-REPORT OF BNL E930
Authors:   BNL E930 collaboration, TAMURA H. , AJIMURA S. , AKIKAWA H. , ALBURGER D. E. , BANU A. , CHRIEN R. E. , EUGENIO P. , FRANKLIN G. B. , FRANZ J. , GAN L. , HASHIMOTO O. , HAYAKAWA T. , HOTCHI H. , IMAI K. , KISHIMOTO T. , KHAUSTOV P. , MAY M. , MINAMI S. , MIURA Y. , MIYOSHI T. , MIZUNUMA K. , NAGAE T. , NAKAMURA S. N. , NAKAZAWA K. , OKAYASU Y. , PILE P. H. , QUINN B. P. , RUSEK A. , SASAO J. , SATO Y. , SAWAFTA R. , SCHMITT H. , SUTTER R. , TAKAHASHI H. , TANG L. , TANIDA K. , UKAI M. , YUAN L. , ZHOU S. H. , ZHU L. H. , ZHU X. F.
Published: April 2003

High resolution γ spectroscopy of hypernuclei using Hyperball has revealed detailed level structure of several p-shell Λ hypernuclei and allowed us to extract the strengths of ΛN spin-dependent interactions. In the experiment BNL E930, we observed E2(3/2+, 5/2+ → 1/2+) transitions in [Formula: see text] and confirmed a small size of the Λ-spin-dependent spin-orbit force. Recently we took data for [Formula: see text] and [Formula: see text] in order to investigate the strength of the ΛN tensor force. In a preliminary analysis, we observed γ rays of [Formula: see text] and [Formula: see text].
SYSTEMATIC STUDY OF DOUBLE STRANGENESS SYSTEM BY EMULSION-COUNTER HYBRID METHOD
Authors:   AGS-E964 (BNL) collaborators: BNL(US), CIAE(CN), CMU(US), Gifu(JPN), GNU(KR), Houston(US), Kyoto(JPN), New MX(US), OCU(JPN), Osaka E-C(JPN), Pusan(KR), RIKEN(JPN), Tohoku(JPN)., NAKAZAWA KAZUMA
Published: April 2003

It was successfully decided that the ΛΛ interaction was weakly attractive, by the E373 (KEK-PS) experiment with hybrid-emulsion method, recently. To get systematic understanding for double strangeness system, the experiment E964 has been approved at BNL-AGS. The experiment should provide us one hundred samples of light and heavy double-hypernuclei and information for the existence of the H dibaryon resonance. We will also get the first data of X-ray from Ξ--atom which shall give us information of Ξ--nuclear potential.
SYSTEMATIC STUDIES OF STRANGE NUCLEAR SYSTEMS: UNUSUAL STRUCTURES FORMED BY A K- MESON
Authors: DOTÉ AKINOBU , AKAISHI YOSHINORI , YAMAZAKI TOSHIMITSU
Published: April 2003

We have developed a new framework of Antisymmetrized Molecular Dynamics (AMD) for the study of kaonic nuclei. We have improved AMD in the following two points : 1) [Formula: see text] mixing and 2) J & T projections. These improvements enable us to investigate various kaonic nuclei systematically. We have investigated ppnK -, pppK -, pppnK -, 6 BeK -, and 9 BK -.
STABILITY OF STRANGELETS IN THE QUARK MASS DENSITY- AND TEMPERATURE-DEPENDENT MODEL
Authors: ZHANG YUN , SU RU-KENG
Published: April 2003

By means of the quark mass density- and temperature-dependent model, we have investigated the stability of strangelets at finite temperature. We have found two stable strangelets for the baryon number A equal to five and the temperature 20MeV.
POSSIBLE EXOTIC STRUCTURE IN LIGHT PROTON-RICH NUCLEI
Authors: ZHANG H. Y. , SHEN W. Q. , MA Y. G. , CAI X. Z. , FANG D. Q. , ZHONG C. , WEI Y. B. , CHEN J. G. , ZHOU X. F. , MA G. L. , WANG K. , REN Z. Z. , ZHAN W. L. , GUO Z. Y. , XIAO G. Q. , XU H. S. , WANG J. S. , SUN Z. Y. , LI J. X. , WANG M. , CHEN Z. Q. , XIAO Z. G. , LI W. F. , LI J. F. , HU Z. G. , BAI J. , CHEN L. X.
Published: April 2003

Radioactive ion beams were produced through the projectile fragmentation induced by 69MeV/nucleon 36 Ar primary beam on a 9 Be target. Measurements of reaction cross section (σR) for some proton-rich nuclei on carbon target at intermediate energies around 30MeV/nucleon have been performed on RIBLL of HIRFL by transmission method and transmission plus transportation method. The experimental σR values for 23Al and 27P are abnormally large compared with their neighboring nuclei and that of 17F has an enhancement compared with the neighboring isotopes. It suggests anomalously large matter root-mean-square radii and proton halo structure in 23 Al and 27 P . The experimental σR values and momentum distribution of fragmentation reaction product for 31 Cl , 32 Cl , 33 Cl , 28 S , 29 S were performed also on RIBLL by transmission and transportation method. These data are in analyzing. The calculation of relativistic density-dependent Hartree shows that the nuclei 23 Al , 27 P , 31 Cl may have proton-halo structure and 17F, 32Cl may have proton-skin structure. New experiment on the search for new nuclides 25 P and 26 S in proton drip line is also described. The significance of these measurements and possible proton halo and skin for light proton-rich nuclei has been discussed.
DESCRIPTION OF 8Be AS DEFORMED GAS-LIKE TWO-ALPHA-PARTICLE STATES
Authors: FUNAKI Y. , HORIUCHI H. , TOHSAKI A. , SCHUCK P. , RÖPKE G.
Published: April 2003

In order to study non-zero spin excitations of the recently proposed α-cluster condensation in the self-conjugate 4n nuclei, spatial deformation is introduced into the model wave function of the α-cluster condensate. The rotational band states of 8 Be are investigated as a first step of a test case for the study of the deformation of the α-cluster condensate. Calculations reproduce well the binding energy of the 0+ ground state and also the excitation energy of the 2+ state. Our 0+ wave function is found to be exactly equal to the 0+ wave function obtained by the generator coordinate method using Brink's 2α wave function. The study shows that both the 0+ ground and 2+ excited states can be considered as having a gas-like (i.e. weakly bound) 2α-cluster structure.
NEW CLUSTER MODEL BASED ON THE GENERATOR COORDINATE METHOD
Authors: ITO MAKOTO , KATŌ KIYOSHI , IKEDA KIYOMI
Published: April 2003

New cluster model based on the Generator Coordinate Method (GCM) is proposed for the studies on the molecular resonances recently observed in the neutron-rich Be isotope. The new model is applied to the 10 Be =4 He +6 He system and its adiabatic energy surface is calculated. It is found that both the weak-coupling states and the strong-coupling ones are quite naturally generated depending on the 4He-6He relative distance. The stability of both states is also discussed.
QUARK-EXCHANGE MECHANISM OF γd → np REACTION AT 2-6 GEV
Authors: JULIA-DIAZ BRUNO , LEE T.-S. H.
Published: April 2003

Within the constituent quark model, we examine the extent to which the deuteron photo-disintegration at 2-6 GeV can be described by the quark-exchange mechanism. With the parameters constrained by the np scattering, the calculated differential cross sections disagree with the data in both magnitude and energy-dependence. The results can be improved if we use a smaller size parameter for quark wavefunctions. We also find that the on-shell approximation used in a previous investigation is not accurate.
CHARGED PION PHOTOPRODUCTION FROM HYDROGEN AND DEUTERIUM AT JEFFERSON LAB
Authors:   On behalf of the Jefferson Lab Hall A Collaboration, E94-104 Collaboration and E02-010 Collaboration., GAO HAIYAN
Published: April 2003

The γn → π-p and γp → π+n reactions are essential probes of the transition from meson-nucleon degrees of freedom to quark-gluon degrees of feedom in exclusive processes. The cross sections of these processes are also, advantageous, for the investigation of oscillatory behavior around the quark counting prediction, since they decrease relatively slower with energy compared with other photon-induced processes. Moreover, these photoreactions in nuclei can probe the QCD nuclear filtering and color transparency effects. In this talk, I discuss the preliminary results on the γp → π+n and γn → π-p processes at a center-of-mass angle of 90° from Jefferson Lab experiment E94-104. I also discuss a new experiment in which singles γp → π+n measurement from hydrogen, and coincidence γn → π-p measurements at the quasifree kinematics from deuterium and 12 C for photon energies between 2.25 GeV to 5.8 GeV in fine steps at a center-of-mass angle of 90° are planned. The proposed measurement will allow a detailed investigation of the oscillatory scaling behavior in photopion production processes and the study of the nuclear dependence of rather mysterious oscillations with energy that previous experiments have indicated. The various nuclear and perturbative QCD approaches, ranging from Glauber theory, to quark-counting, to Sudakov-corrected independent scattering, make dramatically different predictions for the experimental outcomes.
PHOTOREACTIONS ON 3He AND 4He UP TO 1.6 GEV AT JEFFERSON LAB
Authors:   For the CLAS Collaboration., BERMAN B. L.
Published: April 2003

We have measured photoreactions on 3 He and 4 He in Hall B at Jefferson Lab, using real photons from the Photon Tagger and the CEBAF Large-Acceptance Spectrometer (CLAS). We obtained data over the full range of the Tagger — 0.33 to 1.56 GeV with an incident electron-beam energy of 1.645 GeV. Tagged, circularly polarized photons, produced by the 70% longitudinally polarized electrons, were incident on 1.2-g/cm2 liquid-helium targets positioned at the center of the CLAS. We were able to collect data at rates exceeding 3 kHz, and succeeded in collecting approximately 1.2 billion events for 3 He and 0.8 billion for 4 He . Over 5 Tb of data were obtained. The data show very good stability throughout the experimental run. Preliminary results from the analysis of several reaction channels are given here.
TWO-BODY ELECTRO DISINTEGRATION OF THE TRINUCLEON BOUND STATE
Authors: YUAN L. P. , CHMIELEWSKI K. , DELTUVA A. , OELSNER M. , SAUER P. U. , ADAM J.
Published: April 2003

The contribution describes inelastic electron scattering from 3 He with two-body final states. The description allows for single Δ-isobar excitation and includes final-state interaction and meson exchange currents.
SPIN RESPONSE OF THE NUCLEON IN THE RESONANCE REGION
Authors: BURKERT VOLKER D.
Published: April 2003

I discuss recent results from CLAS and Hall A at Jefferson Lab on the measurement of inclusive spin structure functions in the nucleon resonance region using polarized electron beams and polarized targets. Results on the first moment of the spin structure function for protons and neutrons will be discussed, as well as the Bjorken integral. I will argue that the helicity structure of individual resonances plays a vital role in understanding the nucleon's spin response in the domain of strong interaction QCD, and must be considered in any analysis of the nucleon spin structure at low and intermediate photon virtuality.
NEUTRON SPIN STRUCTURE WITH POLARIZED 3He AT JEFFERSON LAB HALL A
Authors: GILMAN R.
Published: April 2003

Several experiments at Jefferson Lab Hall A have used a polarized 3He target for studying the spin structure of the neutron. Measurements have been published for the neutron magnetic form factor, and are being published for the extended Gerasimov-Drell-Hearn sum rule. The [Formula: see text] asymmetry and the [Formula: see text] structure function have been measured above the resonance region. Further measurements in the resonance region will be performed in the near future.
ANALYZING POWER FOR THE PHOTODISINTEGRATION OF THE DEUTERON BETWEEN Eγ = 2.4 AND 4.0 MEV
Authors: TORNOW W. , CZAKON N. G. , HOWELL C. R. , HUTCHESON A. , KELLEY J. H. , LITVINENKO V. N. , MIKHAILOV S. , PINAYEV I. V. , WEISEL G. J. , WITAŁA H.
Published: April 2003

The photon analyzing power for the photodisintegration of the deuteron was measured for seven gamma-ray energies between 2.39 and 4.05 MeV using the linearly polarized gamma-ray beam of the High-Intensity Gamma-ray Source at the Duke Free-Electron Laser Laboratory. The data provide a stringent test of theoretical calculations for the inverse reaction, the neutron-proton radiative capture reaction at energies important for Big-Bang nucleosynthesis. Our data are in excellent agreement with potential model and effective field theory calculations.
MEASUREMENT OF DIFFERENTIAL CROSS SECTIONS AND VECTOR ANALYZING POWERS FOR THE ${\vec n}d$ REACTION AT 250 MEV
Authors: MAEDA Y. , SAKAI H. , TAMII A. , SAKODA S. , KATO H. , HATANO M. , SAITO T. , UCHIGASHIMA N. , KUBOKI H. , HATANAKA K. , HIROOKA D. , SHIMIZU Y. , KITAMURA Y. , FUJITA K. , SAKAMOTO N. , OKAMURA H. , SUDA K. , IKEDA T. , ITOH K. , SAKEMI Y. , WAKASA T. , KAMIYA J. , YAKO K. , SEKIGUCHI K. , SATO Y. , GREENFIELD M. B. , RAPAPORT J. , KAMADA H.
Published: April 2003

To study the three-nucleon force (3NF) effects without ambiguities from the Coulomb effect, the differential cross sections and the vector analyzing powers for the [Formula: see text] elastic scattering at En = 245 MeV have been measured at θcm = 85° - 180°. The data are compared to the results of Faddeev calculations using modern nucleon-nucleon (NN) forces with and without 3NF. Additionally we have a plan to extend our measurement to the forward angular region where the Coulomb effect is expected to be large. We carried out the test experiment and measured the differential cross sections at θcm = 21°.
POLARIZATION EFFECTS IN THE 3He(d,p)4He FUSION REACTION
Authors: GOJUKI S. , ORYU S.
Published: April 2003

We calculate the cross section of the reaction 3 He(d,p) 4 He at very low energies using the three-body Faddeev formalism in which the target nucleus 3 He is considered as a cluster with spin 1/2 and the projectile deuteron as a proton and a neutron. For the n-p interaction we adopted the AV14 potential while for the p -3 He and n -3 He channel we constructed effective potentials based on the well known Resonating Group Method (RGM). Since the n-3He and p -3 He effective potentials are essentially different, the three-body system is treated as a three-channel problem. A resonance state is found using the 1 S 0 and 3 S 1-3 D 1 input states for the n-p and the 1 S 0 and 3 S 1 input states for both nucleon-cluster interactions. Coulomb effects were taken into account for the initial and the final states only. The polarization effects on the total cross section around the resonance region are discussed.
Nd SCATTERING AT INTERMEDIATE ENERGY AND THREE-NUCLEON FORCE EFFECTS
Authors: SAKAI HIDEYUKI
Published: April 2003

Several examples of recent experimental activities in Japan on the study of three-nucleon-force effects via the Nd elastic scattering at intermediate energies are briefly reviewed. Differences between the data and theoretical predictions are identified.
TENSOR ANOMALY IN pd RADIATIVE CAPTURE
Authors: YAGITA T. , SAGARA K. , ISHIDA T. , MINAMI S. , TSURUTA K. , NORO T. , KAMIYA J. , WAKASA T. , YOSHIDA H. , YOSHIMURA M. , HATANAKA K. , AKIYOSHI H.
Published: April 2003

Cross section and analyzing powers of pd → 3 He + γ reaction were measured at Ed = 200 MeV . Low background data were obtained by using a liquid hydrogen target and by detecting 3 He . The cross section and Ay are well reproduced by a Faddeev calculation with a 3-nucleon force included, however, Ayy deviates from the calculation and Axx is completely different from the calculation.
WHICH CONSTITUENT QUARK MODEL IS BETTER?
Authors: WANG FAN , PING JIA-LUN , PANG HOU-RONG , GOLDMAN T.
Published: April 2003

A comparative study has heen done by calculating the effective baryon-baryon interactions of the 64 lowest channels consisting of octet and decuplet baryons with three constituent quark models: the extended quark gluon exchange model, the Goldstone boson exchange model and the quark gluon meson exchange hybrid model. We find that these three models give similar results for 44 channels. Further tests of these models are discussed.
DESCRIPTION OF SU(3) S-WAVE AND P-WAVE BARYONS
Authors: FURUICHI MIKITO , SHIMIZU KIYOTAKA , Takeuchi Sachiko
Published: April 2003

We investigate the structure of the SU(3) octet and decuplet baryons employing a constituent chiral quark model. We study the ground, s-wave and p-wave excited states of the three-quark system with many range gaussian bases. The method, which we employ here, is shown to work quite well in describing the structure of the SU(3) s-wave and p-wave baryons. It is found that the mass differences between positive and negative parity states are well reproduced. It is also found that the pseudoscalar (ps) meson exchange potential plays a very important role in describing the mass of the nucleon resonance N*(1440) (roper). We also discuss how the semirelativistic approach works in the chiral quark model, and how to treat the potential terms in the semirelativistic approach.
STRUCTURE FUNCTION IN NUCLEAR MATTER IN THE NJL MODEL
Authors: MINEO H. , BENTZ W. , THOMAS A. W. , ISHII N. , YAZAKI K.
Published: April 2003

In this work we discuss the EMC effect on the nucleon structure functions in nuclear matter, using a simple approximation to the relativistic Faddeev description of the nucleon in the framework of the Nambu-Jona-Lasinio (NJL) model. We adopt a stable nuclear matter equation of state, calculated in the NJL model, which incorporates confinement effects phenomenologically so as to avoid unphysical thresholds for the decay into quarks. We will compare our results for the EMC ratio in nuclear matter in the NJL model with the parametrized fits to the experimental data.
HIGH-PRECISION COULOMB THREE-BODY CALCULATION OF ANTIPROTONIC HELIUM ATOMS
Authors: KINO YASUSHI , KUDO HIROSHI , KAMIMURA MASAYASU
Published: April 2003

Using the non-adiabatic coupled rearrangement channel method, energy levels of metastable states of antiprotonic helium atoms are precisely calculated. A dual character of the atom is effectively described with atomic and molecular type coordinate systems. By introducing three rearrangement channels, correlation effects in the three-body system has been sufficiently incorporated. The complex coordinate rotation method is employed to take a resonant boundary condition of metastable states into account. The relativistic and QED corrections are considered with the first order perturbation theory. Calculated transition frequencies are in excellent agreement with observed values. This agreement gives best limit of the antiproton mass with 54 ppb uncertainty. This uncertainty is estimated by calculated transition frequencies with the antiproton mass slightly shifted from the proton mass.
PURE VIBRATIONAL DEPHASING OF TRIIODIDE IN LIQUIDS AND GLASSES
Authors: ZHANG F. S. , LYNDEN-BELL R. M.
Published: April 2003

A molecular dynamics model is developed to investigate the pure vibrational dephasing of [Formula: see text] in solvent at temperatures ranging from room temperature to 100 K. The triiodide ion is described by a valence bond model which responds to the field of the classical solvent molecules. We find that the pure dephasing rate does not change much with temperature. This result can then be interpreted in terms of of Kubo lineshape theory.
NUCLEAR THREE-BODY RESONANCES
Authors: KOIKE YASURO
Published: April 2003

A concept of nuclear three-body potential resonance, which is described by three-body Schrödinger equation above the scattering threshold, is introduced and discussed. As one of the example, resonances in 9 Be is investigated. It is shown that the thresholds, which may be caused by the two-body structure or by the breakup reaction, dramatically affect the energy levels and widths of three-body potential resonances.
NUCLEON-DEUTERON SCATTERING WITH Δ-ISOBAR EXCITATION: NEW TECHNICAL DEVELOPMENTS
Authors: DELTUVA A. , CHMIELEWSKI K. , SAUER P. U.
Published: April 2003

A new technique for solving three-particle scattering equations is developed. It is based on the two-dimensional Chebyshev expansion of the two-baryon transition matrix. Its validity and its effectiveness is demonstrated. Furthermore, a new perturbative technique for simulating exact scattering results is developed. It has the potential for understanding three-particle reaction mechanisms in detail. The dynamics of the examples is based on a two-baryon potential which allows for the excitation or a nucleon to a Δ-isobar; the coupled-channel potential yields an effective three-nucleon force in the three-nucleon system. The purely nucleonic reference potential is the charge-dependent Bonn potential.
CLOSING REMARKS
Authors: THOMAS ANTHONY W.
Published: April 2003

Few-body physics covers a broad range of problems from the traditional two- and three- nucleon systems to the study of hadron structure in QCD. We present a personal view of those areas that seem most promising at the present time.
ASSESSING THE IMPACT OF PREDICTIVE BIOSIMULATION ON DRUG DISCOVERY AND DEVELOPMENT
Authors: MICHELSON SETH
Published: April 2003

Systems biology is creating a context for interpreting the vast amounts of genomic and proteomic data being produced by pharmaceutical companies in support of drug development. While major data collection efforts capitalize on technical advances in miniaturization and automation and represent an industrialization of existing laboratory research, the transition from mental models to predictive computer simulations is setting the pace for advances in this field. This article addresses current approaches to the mathematical modeling of biological systems and assesses the potential impact of predictive biosimulation on drug discovery and development.
CUBIC: IDENTIFICATION OF REGULATORY BINDING SITES THROUGH DATA CLUSTERING
Authors: OLMAN VICTOR , XU DONG , XU YING
Published: April 2003

Transcription factor binding sites are short fragments in the upstream regions of genes, to which transcription factors bind to regulate the transcription of genes into mRNA. Computational identification of transcription factor binding sites remains an unsolved challenging problem though a great amount of effort has been put into the study of this problem. We have recently developed a novel technique for identification of binding sites from a set of upstream regions of genes, that could possibly be transcriptionally co-regulated and hence might share similar transcription factor binding sites. By utilizing two key features of such binding sites (i.e. their high sequence similarities and their relatively high frequencies compared to other sequence fragments), we have formulated this problem as a cluster identification problem. That is to identify and extract data clusters from a noisy background. While the classical data clustering problem (partitioning a data set into clusters sharing common or similar features) has been extensively studied, there is no general algorithm for solving the problem of identifying data clusters from a noisy background. In this paper, we present a novel algorithm for solving such a problem. We have proved that a cluster identification problem, under our definition, can be rigorously and efficiently solved through searching for substrings with special properties in a linear sequence. We have also developed a method for assessing the statistical significance of each identified cluster, which can be used to rule out accidental data clusters. We have implemented the cluster identification algorithm and the statistical significance analysis method as a computer software CUBIC. Extensive testing on CUBIC has been carried out. We present here a few applications of CUBIC on challenging cases of binding site identification.
EFFICIENT RECONSTRUCTION OF HAPLOTYPE STRUCTURE VIA PERFECT PHYLOGENY
Authors: ESKIN ELEAZAR , HALPERIN ERAN , KARP RICHARD M.
Published: April 2003

Each person's genome contains two copies of each chromosome, one inherited from the father and the other from the mother. A person's genotype specifies the pair of bases at each site, but does not specify which base occurs on which chromosome. The sequence of each chromosome separately is called a haplotype. The determination of the haplotypes within a population is essential for understanding genetic variation and the inheritance of complex diseases. The haplotype mapping project, a successor to the human genome project, seeks to determine the common haplotypes in the human population.

Since experimental determination of a person's genotype is less expensive than determining its component haplotypes, algorithms are required for computing haplotypes from genotypes. Two observations aid in this process: first, the human genome contains short blocks within which only a few different haplotypes occur; second, as suggested by Gusfield, it is reasonable to assume that the haplotypes observed within a block have evolved according to a perfect phylogeny, in which at most one mutation event has occurred at any site, and no recombination occurred at the given region.

We present a simple and efficient polynomial-time algorithm for inferring haplotypes from the genotypes of a set of individuals assuming a perfect phylogeny. Using a reduction to 2-SAT we extend this algorithm to handle constraints that apply when we have genotypes from both parents and child. We also present a hardness result for the problem of removing the minimum number of individuals from a population to ensure that the genotypes of the remaining individuals are consistent with a perfect phylogeny.

Our algorithms have been tested on real data and give biologically meaningful results. Our webserver () is publicly available for predicting haplotypes from genotype data and partitioning genotype data into blocks.
DATA MINING TOOLS FOR BIOLOGICAL SEQUENCES
Authors: LIU HUIQING , WONG LIMSOON
Published: April 2003

We describe a methodology, as well as some related data mining tools, for analyzing sequence data. The methodology comprises three steps: (a) generating candidate features from the sequences, (b) selecting relevant features from the candidates, and (c) integrating the selected features to build a system to recognize specific properties in sequence data. We also give relevant techniques for each of these three steps. For generating candidate features, we present various types of features based on the idea of k-grams. For selecting relevant features, we discuss signal-to-noise, t-statistics, and entropy measures, as well as a correlation-based feature selection method. For integrating selected features, we use machine learning methods, including C4.5, SVM, and Naive Bayes. We illustrate this methodology on the problem of recognizing translation initiation sites. We discuss how to generate and select features that are useful for understanding the distinction between ATG sites that are translation initiation sites and those that are not. We also discuss how to use such features to build reliable systems for recognizing translation initiation sites in DNA sequences.
Serum Level of the Antiinflammatory Cytokine Interleukin-10 Is an Important Prognostic Determinant in Patients With Acute Coronary Syndromes
Authors: Heeschen Christopher , Dimmeler Stefanie , Hamm Christian W. , Fichtlscherer Stephan , Boersma Eric , Simoons Maarten L. , Zeiher Andreas M.
Published: April 2003

Background—

Convincing evidence suggests that atherosclerosis is an inflammatory disease. The inflammatory response is an important determinant of atherosclerotic plaque instability. Therefore, we investigated the prognostic impact of key inflammatory players, namely the inflammatory marker C-reactive protein (CRP) and the antiinflammatory cytokine interleukin-10 (IL-10), in patients with acute coronary syndromes.

Methods and Results—

IL-10, CRP, and troponin T were measured at baseline and before discharge in 547 patients enrolled in the placebo group of the c7E3 Anti Platelet Therapy in Unstable Refractory angina (CAPTURE) trial. Death and nonfatal myocardial infarction were recorded during 6-month follow-up. IL-10 levels did not correlate with troponin T concentrations but were inversely correlated with CRP levels (
P
<0.001). Patients with elevated IL-10 levels (>3.5 pg/mL; n=276) were at significantly lower risk compared with patients with elevated IL-10 levels (hazard ratio, 0.33; 95% confidence interval [CI], 0.25 to 0.76;
P
=0.002). The predictive value of IL-10 was independent of myocardial necrosis but significantly interacted with CRP levels. CRP-positive patients with IL-10 serum levels above the calculated threshold value of 3.5 pg/mL were protected from the increased cardiac risk of CRP-positive patients with low IL-10 levels (adjusted hazard ratio, 0.25; 95% CI, 0.10 to 0.63;
P
=0.003). Moreover, discharge IL-10 levels >2.5 pg/mL were associated with lower cardiac risk during 6-month follow-up (hazard ratio, 0.38; 95% CI, 0.19 to 0.83;
P
=0.005).

Conclusions—

Elevated IL-10 serum levels are associated with a more favorable prognosis in patients with acute coronary syndromes and elevated CRP levels. These data demonstrate the importance of the balance between proinflammatory and antiinflammatory markers as a major determinant of patients’ outcome in acute coronary syndromes.
Strain-Rate Imaging During Dobutamine Stress Echocardiography Provides Objective Evidence of Inducible Ischemia
Authors: Voigt Jens-Uwe , Exner Bert , Schmiedehausen Kristin , Huchzermeyer Cord , Reulbach Udo , Nixdorff Uwe , Platsch Günther , Kuwert Torsten , Daniel Werner G. , Flachskampf Frank A.
Published: April 2003

Background—

Interpretation of dobutamine stress echocardiography (DSE) is subjective and strongly dependent on the skills of the reader. Strain-rate imaging (SRI) by tissue Doppler may objectively analyze regional myocardial function. This study investigated SRI markers of stress-induced ischemia and analyzed their applicability in a clinical setting.

Methods and Results—

DSE was performed in 44 patients with known or suspected coronary artery disease. Simultaneous perfusion scintigraphy served as a “gold standard” to define regional ischemia. All patients underwent coronary angiography. Segmental strain and strain rate were analyzed at all stress levels by measuring amplitude and timing of deformation and visual curved M-mode analysis. Results were compared with conventional stress echo reading. In nonischemic segments, peak systolic strain rate increased significantly with dobutamine stress (−1.6±0.6 s
−1
versus −3.4±1.4 s
−1
,
P
<0.01), whereas strain during ejection time changed only minimally (−17±6% versus −16±9%,
P
<0.05). During DSE, 47 myocardial segments in 19 patients developed scintigraphy-proven ischemia. Strain-rate increase (−1.6±0.8 s
−1
versus −2.0±1.1 s
−1
,
P
<0.05) and strain (−16±7% versus −10±8%,
P
<0.05) were significantly reduced (both
P
<0.01 compared with nonischemic). Postsystolic shortening (PSS) was found in all ischemic segments. The ratio of PSS to maximal segmental deformation was the best quantitative parameter to identify stress-induced ischemia. Compared with conventional readings, SRI curved M-mode assessment improved sensitivity/specificity from 81%/82% to 86%/90%.

Conclusions—

During DSE, SRI quantitatively and qualitatively differentiates ischemic and nonischemic regional myocardial response to dobutamine stress. The ratio of PSS to maximal strain may be used as an objective marker of ischemia during DSE.
The Environment of American Higher Education: A Constellation of Changes
Authors: Benjamin Roger
Published: April 2003

The American university is one of society’s key institutions, perhaps the lead institution available today to respond to changing societal imperatives. However, for the university to continue to play a leading role, it is important to match the functions of the institution with the societal imperatives presented by a changed environment. In short, for purposeful, intelligent redesign of the university to take place, new blueprints for changes in the role of the university must be constructed. This article aims at such a blueprint. A heterogeneous set of changes in the environment—globalization, immigration, rising social-economic inequality, centrality of the knowledge economy, and issues surrounding cultural identity—are the new changes that will transform the American university in coming decades. The implications of each of the challenges, particularly the recognition that the university must take a stronger responsibility to improve the nation’s human capital, are discussed.
Corporatization of the University: Seeking Conceptual Clarity
Authors: Steck Henry
Published: April 2003

The notion of corporatization is the most ominous buzzword in contemporary academic circles. A significant literature on the subject deals with the transformation of the American university. There has been substantial change—perhaps fundamental—in the direction of a university that displays the culture, practices, policies, and workforce strategies more appropriate to corporations. The article seeks to show what corporatization is and is not and to suggest some historical and contextual factors producing the change. The article seeks to deconstruct the term “corporatization” or “entepreneurial” to demonstrate the wide variety of meanings that the term covers. To the extent that a corporatized university is no university or corporate values are not academic values, the article concludes, it is the burden for faculty to address the issue of protecting traditional academic values.
Issues in University Governance: More “Professional” and Less Academic
Authors: Waugh William L.
Published: April 2003

The pressures for efficiency and the achievement of performance goals are encouraging college and university presidents to focus more on the management of their institutions and less on the more collegial processes of academic decision making. Presidents are being held more accountable to external constituencies, particularly the public officials and business leaders involved in hiring them and the foundations and businesses that supplement their salaries and benefits, and, therefore, feel less accountable to the faculty and other internal constituencies. To increase efficiency and meet goals, presidents are increasingly hiring professional administrators without academic experience, who feel more accountable to their administrative superiors and less accountable to faculty, students, and others within the institution. The focus on managerial values is also filtering down to academic departments and nonacademic offices. The net effect is that the faculty role in university governance is decreasing and may be extinguished if current trends continue.
Housing Students: Fraternities and Residential Colleges
Authors: De Los Reyes Guillermo , Rich Paul
Published: April 2003

Many American campuses are dominated by their fraternities and sororities. Administrators are caught on the horns of a dilemma because the housing that these Greek letter societies offer would require an enormous capital investment to replace. Moreover, old graduates are often more devoted to their “frat” than to their alma mater. But there seems no end to the difficulties, including hazing, poor study habits, de facto segregation, and alcoholism, attributable to the fraternity system. The historical background dating back to the eighteenth century, the arcane rituals, and the future prospects of one of the most controversial aspects of college and university life are surveyed, along with the arguments of both enemies and friends.
Trends in Postsecondary Science in the United States
Authors: Kumar David D.
Published: April 2003

This article deals with trends in postsecondary science in the United States. Analysis of the literature indicates that science is undergoing a subtle but steady metamorphosis in higher education as follows: a shift in the research paradigm, the rising tide of commercialism, more stringent human subject research regulations, teaching for a scientific workforce, the instructional technology invasion, pressure to participate in teacher education, ethnic and gender inequalities, a proliferation of research disciplines, and fading public influence. It is time that the university science community comes to the realization that science in higher education, like any other human enterprise, is as good as the people who learn, teach, research, and work in it and, most important, that the future of science depends on how it is used for the welfare of all mankind.
Information Communication Technology and the New University: A View on eLearning
Authors: Oh Cheol H.
Published: April 2003

The purpose of this study is to explore aspects of learning that are perceived as helping foster successful eLearning for all participants separated by time and distance. The author argues that learner-centered practice is necessary to improve the quality of learning on the Internet. To this end, this study deals with the issues of potential or actual students as they relate to eLearning. In two different surveys, most respondents expected information communication technology to play a key role in shaping the form of future education. The surveys also revealed several real or potential problems facing students taking courses on the Internet. Most important, students’ needs and demands are perceived as being given a lower priority than other aspects of designing courses on the Internet. In short, client orientation is the key mode of operation in the information age, and a user friendly environment is thus critical to ensuring the success of eLearning.
Markets, Management, and “Reengineering” Higher Education
Authors: Green Roger
Published: April 2003

Recent years have witnessed a variety of efforts to reengineer higher education into closer alignment with market principles and management approaches drawn from business. However, critical debates on these efforts typically fail to discern a number of significant issues. Many such reengineering efforts involve an intermingling of three distinctively different organizational paradigms: a professional paradigm characteristic of traditional higher education organization, a bureaucratic machine paradigm representative of traditional business organization, and an innovative or “adhocratic” paradigm defended by its proponents as a timely alternative to traditional bureaucratic organization. This intermingling typically is carried out in a fashion oblivious to the nuances of organizational design and with little or no attention to the conflicts likely to result. Continued neglect of these issues, however, will condemn proponents of higher education adhocracy to problems in the future.
The Uneven Distribution of Employee Training by Community Colleges: Description and Explanation
Authors: Dougherty Kevin J.
Published: April 2003

Community colleges have recently attracted great attention because of their important role in supplying employee training to many business establishments. But despite this major role, there is surprising variability in community colleges’ supply of, and employers’ demand for, employee training. While a few community colleges supply a lot of employee training, many provide little. Moreover, although large employers and ones in industries such as manufacturing tend to utilize the community college heavily, smaller employers and ones in industries such as retail trade use it much less. This article analyzes the causes of this variability in the demand for and supply of employee training and suggests policy responses. Public policy, while encouraging broader community college and industry partnership in employee training, must also move to counteract the harmful impacts of extensive employee training on other missions of the community college such as transfer preparation, remedial education, and general education.
Cognitive and Institutional Barriers to New Forms of Cooperation on Environmental Protection
Authors: HOFFMAN ANDREW J. , RILEY HANNAH C. , TROAST JOHN G. , BAZERMAN MAX H.
Published: April 2003

Many perceive the predominantly command-and-control structure of regulatory policy to be overly restrictive and inefficient in achieving America's emerging environmental goals. In response, the U.S. government has introduced several voluntary programs to develop innovative, beyond-compliance environmental management solutions through the collaboration between government agencies and regulated entities. Yet, these programs have not gained widespread acceptance. This article analyzes the cognitive and institutional barriers to that acceptance by looking specifically at two programs—Project XL and Habitat Conservation Plans. These barriers act out of force of habit, creating a resistance to change and a rejection of new forms of regulatory policy. The authors argue that policy change requires a shift in how individuals think and how institutions guide that thinking.