Three-dimensional structure of RK-1: A novel alpha-defensin peptide

NMR spectroscopy and simulated annealing calculations have been used to determine the three-dimensional structure of RK-1, an antimicrobial peptide from rabbit kidney recently discovered from homology screening based on the distinctive physicochemical properties of the corticostatins/defensins. RK-1 consists of 32 residues, including six cysteines arranged into three disulfide bonds. It exhibits antimicrobial activity against Escherichia coli and activates Ca2+ channels in vitro. Through its physicochemical similarity, identical cysteine spacing, and linkage to the corticostatins/defensins, it was presumed to be a member of this family. However, RK-1 lacks both a large number of arginines in the primary sequence and a high overall positive charge, which are characteristic of this family of peptides. The three-dimensional solution structure, determined by NMR, consists of a triple-stranded antiparallel beta -sheet and a series of turns and is similar to the known structures of other alpha -defensins. This has enabled the definitive classification of RK-1 as a member of this family of antimicrobial peptides. Ultracentrifuge measurements confirmed that like rabbit neutrophil defensins, RK-1 is monomeric in solution, in contrast to human neutrophil defensins, which are dimeric.

Quantum measurement and stochastic processes in mesoscopic conductors

In quantum measurement theory it is necessary to show how a, quantum source conditions a classical stochastic record of measured results. We discuss mesoscopic conductance using quantum stochastic calculus to elucidate the quantum nature of the measurement taking place in these systems. To illustrate the method we derive the current fluctuations in a two terminal mesoscopic circuit with two tunnel barriers containing a single quasi bound state on the well. The method enables us to focus on either the incoming/ outgoing Fermi fields in the leads, or on the irreversible dynamics of the well state itself. We show an equivalence between the approach of Buttiker and the Fermi quantum stochastic calculus for mesoscopic systems.

Dual processes in recognition: Does a focus on measurement operations provide a sufficient foundation?

Current theoretical thinking about dual processes in recognition relies heavily on the measurement operations embodied within the process dissociation procedure. We critically evaluate the ability of this procedure to support this theoretical enterprise. We show that there are alternative processes that would produce a rough invariance in familiarity (a key prediction of the dual-processing approach) and that the process dissociation procedure does not have the power to differentiate between these alternative possibilities. We also show that attempts to relate parameters estimated by the process dissociation procedure to subjective reports (remember-know judgments) cannot differentiate between alternative dual-processing models and that there are problems with some of the historical evidence and with obtaining converging evidence. Our conclusion is that more specific theories incorporating ideas about representation and process are required.

Finite element modelling of three-dimensional convection problems in fluid-saturated porous media heated from below

We use the finite element method to model three-dimensional convective pore-fluid flow in fluid-saturated porous media when they are heated from below. In particular, we employ the particle-tracking technique to mimic the trajectories of particles in three-dimensional fluid flow problems. The related numerical results demonstrated that: (1) The progressive asymptotic approach procedure, which was previously developed for the finite element modelling of two-dimensional convective pore-fluid flow problems, is equally applicable to the finite element modelling of three-dimensional convective pore-fluid flow in fluid-saturated porous media heated from below. (2) The perturbation of gravity at different planes has a significant effect on the pattern of three-dimensional convective pore-fluid flow and therefore, may influence the pattern of orebody formation and mineralization in three-dimensional hydrothermal systems. Copyright (C) 2001 John Wiley & Sons, Ltd.

In vivo measurement of the effect of intra-abdominal pressure on the human spine

In humans, intra-abdominal pressure (IAP) is elevated during many everyday activities. This experiment aimed to investigate the extent to which increased IAP-without concurrent activity of the abdominal or back extensor muscles-produces an extensor torque. With subjects positioned in side lying on a swivel table with its axis at L3, moments about this vertebral level were measured when IAP was transiently increased by electrical stimulation of the diaphragm via the phrenic nerve. There was no electromyographic activity in abdominal and back extensor muscles. When IAP was increased artificially to similar to 15% of the maximum IAP amplitude that could be generated voluntarily with the trunk positioned in flexion, a trunk extensor moment (similar to6 Nm) was recorded. The size of the effect was proportional to the increase in pressure. The extensor moment was consistent with that predicted from a model based on measurements of abdominal cross-sectional area and IAP moment arm. When IAP was momentarily increased while the trunk was flexed passively at a constant velocity, the external torque required to maintain the velocity was increased. These results provide the first in vivo data of the amplitude of extensor moment that is produced by increased IAP. Although the net effect of this extensor torque in functional tasks would be dependent on the muscles used to increase the IAP and their associated flexion torque, the data do provide evidence that IAP contributes, at least in part, to spinal stability. (C) 2001 Elsevier Science Ltd. All rights reserved.

Integrable Kondo impurity in one-dimensional q-deformed t-J models

Integrable Kondo impurities in two cases of one-dimensional q-deformed t-J models are studied by means of the boundary Z(2)-graded quantum inverse scattering method. The boundary K matrices depending on the local magnetic moments of the impurities are presented as nontrivial realizations of the reflection equation algebras in an impurity Hilbert space. Furthermore, these models are solved by using the algebraic Bethe ansatz method and the Bethe ansatz equations are obtained.

Jordan-Wigner fermionization of the one-dimensional Bariev model of three coupled XY chains

The Jordan-Wigner fermionization for the one-dimensional Bariev model of three coupled XY chains is formulated. The L-matrix in terms of fermion operators and the R-matrix are presented explicitly. Furthermore, the graded reflection equations and their solutions are discussed.

Algebraic Bethe ansatz for integrable one-dimensional extended Hubbard models with open boundary conditions

Nine classes of integrable open boundary conditions, further extending the one-dimensional U-q (gl (212)) extended Hubbard model, have been constructed previously by means of the boundary Z(2)-graded quantum inverse scattering method. The boundary systems are now solved by using the algebraic Bethe ansatz method, and the Bethe ansatz equations are obtained for all nine cases.

Effect of material anisotropy on the onset of convective flow in three-dimensional fluid-saturated faults

In order to investigate the effect of material anisotropy on convective instability of three-dimensional fluid-saturated faults, an exact analytical solution for the critical Rayleigh number of three-dimensional convective flow has been obtained. Using this critical Rayleigh number, effects of different permeability ratios and thermal conductivity ratios on convective instability of a vertically oriented three-dimensional fault have been examined in detail. It has been recognized that (1) if the fault material is isotropic in the horizontal direction, the horizontal to vertical permeability ratio has a significant effect on the critical Rayleigh number of the three-dimensional fault system, but the horizontal to vertical thermal conductivity ratio has little influence on the convective instability of the system, and (2) if the fault material is isotropic in the fault plane, the thermal conductivity ratio of the fault normal to plane has a considerable effect on the critical Rayleigh number of the three-dimensional fault system, but the effect of the permeability ratio of the fault normal to plane on the critical Rayleigh number of three-dimensional convective flow is negligible.

Estimation of crystalline phase present in the glucose crystal-solution mixture by water activity measurement

The amount of crystalline fraction present in monohydrate glucose crystal-solution mixture up to 110% crystal in relation to solution (crystal:solution=110:100) was determined by water activity measurement. It was found that the water activity had a strong linear correlation (R-2=0.994) with the amount of glucose present above saturation. Difference in the water activities of the crystal-solution mixture (a(w1)) and the supersaturated solution (a(w2)) by re-dissolving the crystalline fraction allowed calculation of the amount of crystalline phase present (DeltaG) in the mixture by an equation DeltaG=846.97(a(w1)-a(w2)). Other methods such as Raoult's, Norrish and Money-Born equations were also tested for the prediction of water activity of supersaturated glucose solution. (C) 2003 Swiss Society of Food Science and Technology. Published by Elsevier Science Ltd. All rights reserved.

Characterisation of the three-dimensional structure of earthworm burrow systems using image analysis and mathematical morphology

The aim of this work was to exemplify the specific contribution of both two- and three-dimensional (31)) X-ray computed tomography to characterise earthworm burrow systems. To achieve this purpose we used 3D mathematical morphology operators to characterise burrow systems resulting from the activity of an anecic (Aporrectodea noctunia), and an endogeic species (Allolobophora chlorotica), when both species were introduced either separately or together into artificial soil cores. Images of these soil cores were obtained using a medical X-ray tomography scanner. Three-dimensional reconstructions of burrow systems were obtained using a specifically developed segmentation algorithm. To study the differences between burrow systems, a set of classical tools of mathematical morphology (granulometries) were used. So-called granulometries based on different structuring elements clearly separated the different burrow systems. They enabled us to show that burrows made by the anecic species were fatter, longer, more vertical, more continuous but less sinuous than burrows of the endogeic species. The granulometry transform of the soil matrix showed that burrows made by A. nocturna were more evenly distributed than those of A. chlorotica. Although a good discrimination was possible when only one species was introduced into the soil cores, it was not possible to separate burrows of the two species from each other in cases where species were introduced into the same soil core. This limitation, partly due to the insufficient spatial resolution of the medical scanner, precluded the use of the morphological operators to study putative interactions between the two species.

Ladder operators for integrable one-dimensional lattice models

A generalised ladder operator is used to construct the conserved operators for any one-dimensional lattice model derived from the Yang-Baxter equation. As an example, the low order conserved operators for the XYh model are calculated explicitly.

Quantum phase-space analysis of the pendular cavity

We perform a quantum-mechanical analysis of the pendular cavity, using the positive-P representation, showing that the quantum state of the moving mirror, a macroscopic object, has noticeable effects on the dynamics. This system has previously been proposed as a candidate for the quantum-limited measurement of small displacements of the mirror due to radiation pressure, for the production of states with entanglement between the mirror and the field, and even for superposition states of the mirror. However, when we treat the oscillating mirror quantum mechanically, we find that it always oscillates, has no stationary steady state, and exhibits uncertainties in position and momentum which are typically larger than the mean values. This means that previous linearized fluctuation analyses which have been used to predict these highly quantum states are of limited use. We find that the achievable accuracy in measurement is fat, worse than the standard quantum limit due to thermal noise, which, for typical experimental parameters, is overwhelming even at 2 mK