Influence of recombination on acquisition and reversion of immune escape and compensatory mutations in HIV-1

Following transmission, HIV-1 adapts in the new host by acquiring mutations that allow it to escape from the host immune response at multiple epitopes. It also reverts mutations associated with epitopes targeted in the transmitting host but not in the new host. Moreover, escape mutations are often associated with additional compensatory mutations that partially recover fitness costs. It is unclear whether recombination expedites this process of multi-locus adaptation. To elucidate the role of recombination, we constructed a detailed population dynamics model that integrates viral dynamics, host immune response at multiple epitopes through cytotoxic T lymphocytes, and viral evolution driven by mutation, recombination, and selection. Using this model, we compute the expected waiting time until the emergence of the strain that has gained escape and compensatory mutations against the new host's immune response, and reverted these mutations at epitopes no longer targeted. We find that depending on the underlying fitness landscape, shaped by both costs and benefits of mutations, adaptation proceeds via distinct dominant pathways with different effects of recombination, in particular distinguishing escape and reversion. When adaptation at a single epitope is involved, recombination can substantially accelerate immune escape but minimally affects reversion. When multiple epitopes are involved, recombination can accelerate or inhibit adaptation depending on the fitness landscape. Specifically, recombination tends to delay adaptation when a purely uphill fitness landscape is accessible at each epitope, and accelerate it when a fitness valley is associated with each epitope. Our study points to the importance of recombination in shaping the adaptation of HIV-1 following its transmission to new hosts, a process central to T cell-based vaccine strategies. (C) 2015 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license.

Numerical simulation of an adaptive optics system with laser propagation in the atmosphere

A comprehensive model of laser propagation in the atmosphere with a complete adaptive optics (AO) system for phase compensation is presented, and a corresponding computer program is compiled. A direct wave-front gradient control method is used to reconstruct the wave-front phase. With the long-exposure Strehl ratio as the evaluation parameter, a numerical simulation of an AO system in a stationary state with the atmospheric propagation of a laser beam was conducted. It was found that for certain conditions the phase screen that describes turbulence in the atmosphere might not be isotropic. Numerical experiments show that the computational results in imaging of lenses by means of the fast Fourier transform (FFT) method agree well with those computed by means of an integration method. However, the computer time required for the FFT method is 1 order of magnitude less than that of the integration method. Phase tailoring of the calculated phase is presented as a means to solve the problem that variance of the calculated residual phase does not correspond to the correction effectiveness of an AO system. It is found for the first time to our knowledge that for a constant delay time of an AO system, when the lateral wind speed exceeds a threshold, the compensation effectiveness of an AO system is better than that of complete phase conjugation. This finding indicates that the better compensation capability of an AO system does not mean better correction effectiveness. (C) 2000 Optical Society of America.

Investigation of High-Speed Combustible Gas Ignited by a Hot Gas Jet Produced in the Shock Tube

The high-speed combustible gas ignited by a hot gas jet, which is induced by shock focusing, was experimentally investigated. By use of the separation mode of shock tube, the test section of a single shock tube is split into two parts, which provide the high-speed flow of combustible gas and pilot flame of hot gas jet, respectively. In the interface of two parts of test sections the flame of jet was formed and spread to the high-speed combustible gas. Two kinds of the ignitions, 3-D “line-flame ignition” and 2-D “plane-flame ignition”, were investigated. In the condition of 3-D “lineflame ignition” of combustion, thicker hot gas jet than pure air jet, was observed in schlieren photos. In the condition of 2-D “plane-flame ignition” of combustion, the delay time of ignition and the angle of flame front in schlieren photos were measured, from which the velocity of flame propagation in the high-speed combustible gas is estimated in the range of 30–90 m/s and the delay time of ignition is estimated in the range of 0.12–0.29 ms.

Direct Numerical Simulation of Supersonic Turbulent Boundary Layer Flow

Direct numerical simulations of a spatially evolving supersonic flat-plate turbulent boundary layer flow with free Mach number M = 2.25 and Reynolds number Re = 365000/in are performed. The transition process from laminar to turbulent flow is obtained by solving the three-dimensional compressible Navier-Stokes, equations, using high-order accurate difference schemes. The obtained statistical results agree well with the experimental and theoretical data. From the numerical results it can be seen that the transition process under the considered conditions is the process which skips the Tolimien-Schlichting instability and the second instability through the instability of high gradient shear layer and becomes of laminar flow breakdown. This means that the transition process is a bypass-type transition process. The spanwise asymmetry of the disturbance locally upstream imposed is important to induce the bypass-type transition. Furthermore, with increasing the time disturbance frequency the transition will delay. When the time disturbance frequency is large enough, the transition will disappear.

Thermovibrational Instability Of Rayleigh-Marangoni-Benard Convection In Two-Layer Fluid Systems

The thermovibrational instability of Rayleigh-Marangoni-Benard convection in a two-layer system under the high-frequency vibration has been investigated by linear instability analysis in the present paper. General equations for the description of the convective flow and within this framework, the generalized Boussinesq approximation are formulated. These equations are dealt with using the averaging method. The theoretical analysis results show that the high-frequency thermovibrations can change the Marangoni-Benard convection instabilities as well as the oscillatory gaps of the Rayleigh-Marangoni-Benard convection in two-layer liquid systems. It is found that vertical high-frequency vibrations can delay convective instability of this system, and damp the convective flow down. (C) 2007 COSPAR. Published by Elsevier Ltd. All rights reserved.

The plastic instability behaviour of laser-textured steel sheet

As the production of a new technique that can offer both good formability and high image clarity for texturing metal sheet, laser-textured sheet has attracted the attention of many manufacturers and users. Among the many subjects to be studied, plastic instability behaviour of the laser-textured sheet is one of most important to understand its ability in extending material ductility and to appropriately control this technique. Experimental investigations are carried out in this paper to study the macroscopic behaviour and microstructural mechanism of the laser-textured sheet, and comparison is made with the normal sheet taken from the same coil of metal sheet. It is demonstrated that, the difference in the behaviour of plastic instability obviously shows tendency to delay strain localization and the onset of thickness necking. Shear banding and internal void damage are spread to a much wider region in the sheet being laser-textured. The prestrained microcraters enforced on the surface of the textured sheet act as hardening spots, which are likely to share out deformation and inhibit the increasing rate of voiding, and eventually favouring the ductility of the material used.

Direct dynamical test for deterministic chaos and optimal embedding of a chaotic time-series

We propose here a local exponential divergence plot which is capable of providing an alternative means of characterizing a complex time series. The suggested plot defines a time-dependent exponent and a ''plus'' exponent. Based on their changes with the embedding dimension and delay time, a criterion for estimating simultaneously the minimal acceptable embedding dimension, the proper delay time, and the largest Lyapunov exponent has been obtained. When redefining the time-dependent exponent LAMBDA(k) curves on a series of shells, we have found that whether a linear envelope to the LAMBDA(k) curves exists can serve as a direct dynamical method of distinguishing chaos from noise.

Local exponential divergence plot and optimal embedding of a chaotic time-series

we propose here a local exponential divergence plot which is capable of providing a new means of characterizing chaotic time series. The suggested plot defines a time dependent exponent LAMBDA and a ''plus'' exponent LAMBDA+ which serves as a criterion for estimating simultaneously the minimal acceptable embedding dimension, the proper delay time and the largest Lyapunov exponent.

Valuing Flexibility: The case of an Integrated Gasification Combined Cycle Power Plant

In this paper we analyze the valuation of options stemming from the flexibility in an Integrated Gasification Combined Cycle (IGCC) Power Plant. First we use as a base case the opportunity to invest in a Natural Gas Combined Cycle (NGCC) Power Plant, deriving the optimal investment rule as a function of fuel price and the remaining life of the right to invest. Additionally, the analytical solution for a perpetual option is obtained. Second, the valuation of an operating IGCC Power Plant is studied, with switching costs between states and a choice of the best operation mode. The valuation of this plant serves as a base to obtain the value of the option to delay an investment of this type. Finally, we derive the value of an opportunity to invest either in a NGCC or IGCC Power Plant, that is, to choose between an inflexible and a flexible technology, respectively. Numerical computations involve the use of one- and two-dimensional binomial lattices that support a mean-reverting process for the fuel prices. Basic parameter values refer to an actual IGCC power plant currently in operation.

Career Planning in Spain: Do temporary contracts delay marriage and motherhood?

The aim of this paper is to find an empirical connection between the impressive increase in the use of temporary contracts in Spain and the observed increase in age at marriage and maternity. Using a pool of the six available waves of individual information from the European Household Panel for Spain, we find that holding temporary contracts rather than permanent ones delays marriage for males, but not for females. Concerning maternity, the labor market situation of both members of the household affects entry into motherhood. In particular, if woman has a temporary contract rather than a permanent one, motherhoods is delayed independently of the husband's contract. As expected, postponement of maternity is not found for non-working women. These results give strong support to the career planning, motive to delay maternity in Spain, given that an unstable labor market situation of female workers is found to be the main deterrent to entry into motherhood.

Investigation of High-Speed Combustible Gas Ignited by a Hot Gas Jet Produced in the Shock Tube

The high-speed combustible gas ignited by a hot gas jet, which is induced by shock focusing, was experimentally investigated. By use of the separation mode of shock tube, the test section of a single shock tube is split into two parts, which provide the high-speed flow of combustible gas and pilot flame of hot gas jet, respectively. In the interface of two parts of test sections the flame of jet was formed and spread to the high-speed combustible gas. Two kinds of the ignitions, 3-D "line-flame ignition" and 2-D "plane-flame ignition", were investigated. In the condition of 3-D "line-flame ignition" of combustion, thicker hot gas jet than pure air jet, was observed in schlieren photos. In the condition of 2-D "plane-flame ignition" of combustion, the delay time of ignition and the angle of flame front in schlieren photos were measured, from which the velocity of flame propagation in the high-speed combustible gas is estimated in the range of 30-90m/s and the delay time of ignition is estimated in the range of 0.12-0.29ms.

Chemical equilibrium analysis and CFD simulation of coal combustion and NOx formation

A full two-fluid model of reacting gas-particle flows with an algebraic unified second-order moment (AUSM) turbulence-chemistry model is used to simulate Beijing coal combustion and NOx formation. The sub-models are the k-epsilon-kp two-phase turbulence model, the EBU-Arrhenius volatile and CO combustion model, the six-flux radiation model, coal devolatilization model and char combustion model. The blocking effect on NOx formation is discussed. In addition, the chemical equilibrium analysis is used to predict NOx concentration at different temperature. Results of CID simulation and chemical equilibrium analysis show that, optimizing air dynamic parameters can delay the NOx formation and decrease NOx emission, but it is effective only in a restricted range. In order to decrease NOx emission near to zero, the re-burning or other chemical methods must be used.

Hopwood Hall College: Touchscreen technology overtakes interactive whiteboards as interactive teaching tool of choice

Hopwood Hall is adopting the use of touch screen technology and gradually replacing its interactive whiteboards to improve access to interactive learning. The touch screen monitors connected to LCD TV’s provide a cheaper classroom build with technology that’s more user-friendly and better suited to classroom delivery. Until now, interactive boards had been the mainstay of classrooms but they created teaching barriers for staff including the additional software to learn and master. They are also expensive and often have usability issues with 'pens' not working or having a delay when used as the mouse tool.

Widow rockfish: Proceedings of a workshop, Tiburon, California, December 11-12, 1980

This workshop was organized because of the increase between 1978 and 1980 in coastwide landings of widow rockfish, from less than 1,000 mt to more than 20,000 mt, and because of scientists' concern with the lack of knowledge both of the fishery and biology of the species. Most scientists active in research on Pacific groundfish, as well as some members of the fishing industry and fishery managers, attended the workshop. These proceedings contain the report of the workshop discussion panel, status reports on California, Oregon, and Washington fisheries through 1980, and a collection of seven papers presented at the workshop. The status reports provide an historical perspective of the development of an important fishery. The papers present a fairly complete survey of biological knowledge of widow rockfish, economic status of the fishery, and fishery-independent methods for estimation of abundance. The papers also contain some information developed after the workshop. Since the workshop, the fishery has matured. Largest landings were made in 1981, when more than 28,000 mt were landed. Maximum sustainable yield (MSY) is estimated to be slightly less than 10,000 mt, and the stock appeared to be at about the MSY level in 1985. The Pacific Fishery Management Council and National Marine Fisheries Service have implemented regulations that have maintained landings since 1983 at approximately the maximum sustainable yield level. Fishery-dependent stock assessments are being made on an annual basis for the Pacific Fishery Management Council. While these assessments are considered to be the best possible with available data, scientists responsible for the assessment have chosen to delay their publication in the formal scientific literature until more data are obtained. However, the stock assessment reports are available from the Pacific Fishery Management Council. In addition to the papers in this collection, three papers have been published on widow rockfish since 1980. BoehIert, Barss, and Lamberson (1982) estimate fecundity of the species off Oregon; Gunderson (1984) describes the fishery and management actions; and Laroche and Richardson (1981) describe the morphology and distribution of juvenile widow rockfish off Oregon. During the past decade, the fishery for widow rockfish has developed from a minor fishery to one of the more important on the Pacific Coast. Our knowledge of the biology and dynamics of the species has progressed from minimal to relatively extensive for a groundfish species. It is our intention in preparing this collection of papers to make this knowledge readily available to the scientific community. (PDF file contains 63 pages.)