Highly Mutable Linker Regions Regulate HIV-1 Rev Function and Stability.

HIV-1 Rev is an essential viral regulatory protein that facilitates the nuclear export of intron-containing viral mRNAs. It is organized into structured, functionally well-characterized motifs joined by less understood linker regions. Our recent competitive deep mutational scanning study confirmed many known constraints in Rev's established motifs, but also identified positions of mutational plasticity, most notably in surrounding linker regions. Here, we probe the mutational limits of these linkers by testing the activities of multiple truncation and mass substitution mutations. We find that these regions possess previously unknown structural, functional or regulatory roles, not apparent from systematic point mutational approaches. Specifically, the N- and C-termini of Rev contribute to protein stability; mutations in a turn that connects the two main helices of Rev have different effects in different contexts; and a linker region which connects the second helix of Rev to its nuclear export sequence has structural requirements for function. Thus, Rev function extends beyond its characterized motifs, and is tuned by determinants within seemingly plastic portions of its sequence. Additionally, Rev's ability to tolerate many of these massive truncations and substitutions illustrates the overall mutational and functional robustness inherent in this viral protein

Anisotropic constitutive modeling for nickel base single crystal superalloy Rene N4 at 982 C

A back stress/drag stress constitutive model based on a crystallographic approach to model single crystal anisotropy is presented. Experimental results demonstrated the need for the back stress variable in the inelastic flow equations. Experimental findings suggested that back stress is orientation dependent and controls both strain hardening and recovery characteristics. Due to the observed stable fatigue loops at 1800 F, drag stress is considered constant for this temperature. The constitutive model operated with constraints determined only from tensile data was extensively tested from simple tensile and fatigue to complicated strain hold tests. The model predicted very well under those conditions

ShapeCodes: Self-Supervised Feature Learning by Lifting Views to Viewgrids

We introduce an unsupervised feature learning approach that embeds 3D shape information into a single-view image representation. The main idea is a self-supervised training objective that, given only a single 2D image, requires all unseen views of the object to be predictable from learned features. We implement this idea as an encoder-decoder convolutional neural network. The network maps an input image of an unknown category and unknown viewpoint to a latent space, from which a deconvolutional decoder can best "lift" the image to its complete viewgrid showing the object from all viewing angles. Our class-agnostic training procedure encourages the representation to capture fundamental shape primitives and semantic regularities in a data-driven manner---without manual semantic labels. Our results on two widely-used shape datasets show 1) our approach successfully learns to perform "mental rotation" even for objects unseen during training, and 2) the learned latent space is a powerful representation for object recognition, outperforming several existing unsupervised feature learning methods.Comment: To appear at ECCV 201

Characterization of the domain chaos convection state by the largest Lyapunov exponent

Using numerical integrations of the Boussinesq equations in rotating cylindrical domains with realistic boundary conditions, we have computed the value of the largest Lyapunov exponent lambda1 for a variety of aspect ratios and driving strengths. We study in particular the domain chaos state, which bifurcates supercritically from the conducting fluid state and involves extended propagating fronts as well as point defects. We compare our results with those from Egolf et al., [Nature 404, 733 (2000)], who suggested that the value of lambda1 for the spiral defect chaos state of a convecting fluid was determined primarily by bursts of instability arising from short-lived, spatially localized dislocation nucleation events. We also show that the quantity lambda1 is not intensive for aspect ratios Gamma over the range 20<Gamma<40 and that the scaling exponent of lambda1 near onset is consistent with the value predicted by the amplitude equation formalism

The origin and evolution of the zodiacal dust cloud

We have now analyzed a substantial fraction of the IRAS observations of the zodiacal cloud, particularly in the 25 micron waveband. We have developed a gravitational perturbation theory that incorporates the effects of Poynting-Robertson light drag (Gomes and Dermott, 1992). We have also developed a numerical model, the SIMUL mode, that reproduces the exact viewing geometry of the IRAS telescope and calculates the distribution of thermal flux produced by any particular distribution of dust particle orbits (Dermott and Nicholson, 1989). With these tools, and using a distribution of orbits based on those of asteroidal particles with 3.4 micron radii whose orbits decay due to Poynting-Robertson light drag and are perturbed by the planets, we have been able to: (1) account for the inclination and node of the background zodiacal cloud observed by IRAS in the 25 micron waveband; (2) relate the distribution of orbits in the Hirayama asteroid families to the observed shapes of the IRAS solar system dustbands; and (3) show that there is observational evidence in the IRAS data for the transport of asteroidal particles from the main belt to the Earth by Poynting-Robertson light drag

Structure of poly(propyl ether imine) (PETIM) dendrimer from fully atomistic molecular Dynamics Simulation and by Small Angle X-ray scattering

We study the structure of carboxylic acid terminated neutral poly (propyl ether imine) (PETIM) dendrimer from generation 1 through 6 (G1-G6) in a good solvent (water) by fully atomistic molecular dynamics (MD) simulations. We determine as a function of generation such structural properties as: radius of gyration, shape tensor, asphericity, fractal dimension, monomer density distribution, and end-group distribution functions. The sizes obtained from the MD simulations have been validated by Small Angle X-Ray Scattering (SAXS) experiment on dendrimer of generation 2 to 4 (G2-G4). A good agreement between the experimental and theoretical value of radius of gyration has been observed. We find a linear increase in radius of gyration with the generation. In contrast, Rg scales as ~ N^x with the number of monomers. We find two distinct exponents depending on the generations: x = 0.47 for G1-G3 and x = 0.28 for G3-G6 which reveals their non-space filling nature. In comparison with the amine terminated PAMAM dendrimer, we find Rg of G-th generation PETIM dendrimer is nearly equal to that of (G+1)-th generation of PAMAM dendrimer as observed by Maiti et. al. [Macromolecules,38, 979 2005]. We find substantial back folding of the outer sub generations into the interior of the dendrimer. Due to their highly flexible nature of the repeating branch units, the shape of the PETIM dendrimer deviates significantly from the spherical shape and the molecules become more and more spherical as the generation increases. The interior of the dendrimer is quite open with internal cavities available for accommodating guest molecules suggesting using PETIM dendrimer for guest-host applications. We also give a quantitative measure of the number of water molecules present inside the dendrimer.Comment: 33 page

Pressure-induced alpha-to-omega transition in titanium metal: A systematic study of the effects of uniaxial stress

We investigated the effects of uniaxial stress on the pressure-induced alpha-to-omega transition in pure titanium (Ti) by means of angle dispersive x-ray diffraction in a diamond-anvil cell. Experiments under four different pressure environments reveal that: (1) the onset of the transition depends on the pressure medium used, going from 4.9 GPa (no pressure medium) to 10.5 GPa (argon pressure medium); (2) the a and w phases coexist over a rather large pressure range, which depends on the pressure medium employed; (3) the hysteresis and quenchability of the w phase is affected by differences in the sample pressure environment; and (4) a short term laser-heating of Ti lowers the alpha-to-omega transition pressure. Possible transition mechanisms are discussed in the light of the present results, which clearly demonstrated the influence of uniaxial stress in the alpha-to-omega transition.Comment: 16 pages, 6 figures, 1 tabl

Automatic Creation of SQL Injection and Cross-Site Scripting Attacks

We present a technique for finding security vulnerabilitiesin Web applications. SQL Injection (SQLI) and cross-sitescripting (XSS) attacks are widespread forms of attackin which the attacker crafts the input to the application toaccess or modify user data and execute malicious code. Inthe most serious attacks (called second-order, or persistent,XSS), an attacker can corrupt a database so as to causesubsequent users to execute malicious code.This paper presents an automatic technique for creatinginputs that expose SQLI and XSS vulnerabilities. The techniquegenerates sample inputs, symbolically tracks taintsthrough execution (including through database accesses),and mutates the inputs to produce concrete exploits. Oursis the first analysis of which we are aware that preciselyaddresses second-order XSS attacks.Our technique creates real attack vectors, has few falsepositives, incurs no runtime overhead for the deployed application,works without requiring modification of applicationcode, and handles dynamic programming-languageconstructs. We implemented the technique for PHP, in a toolArdilla. We evaluated Ardilla on five PHP applicationsand found 68 previously unknown vulnerabilities (23 SQLI,33 first-order XSS, and 12 second-order XSS)