Developing an Unnatural Amino Acid-Specific Aminoacyl tRNA Synthetase

Unnatural Amino Acids (UAAs), amino acids not present in the human genetic code, have been synthesized to have a broad range of useful properties, in this case, as metal-binders which could have drug delivery applications. In order for the cell to place a UAA into the protein, two components, a unique aminoacyl tRNA synthetase and a corresponding tRNA must be present. If an amino acid is successfully charged to the tRNA, a stop codon is suppressed and a functional protein is built with the UAA at the mutation site. Such a tRNA molecule has previously been developed, as well as many synthetases specific to UAAs. In this work, the range of UAAs which can be incorporated into proteins using the E. coli’s own machinery is expanded by the development of a novel aminoacyl tRNA synthetase. By making a library of synthetase-coding plasmid variants and performing positive and negative screenings, the binding pocket of the synthetase can be modified for specificity to a UAA while not allowing the tRNA to be charged with a natural amino acid. In this work, we are attempting to evolve new tRNA synthetases for the incorporation of metal-binding amino acids by developing the plasmid library and a screening system to find synthetase variants meeting these criteria

Projections Onto Convex Sets (POCS) Based Optimization by Lifting

Two new optimization techniques based on projections onto convex space (POCS) framework for solving convex and some non-convex optimization problems are presented. The dimension of the minimization problem is lifted by one and sets corresponding to the cost function are defined. If the cost function is a convex function in R^N the corresponding set is a convex set in R^(N+1). The iterative optimization approach starts with an arbitrary initial estimate in R^(N+1) and an orthogonal projection is performed onto one of the sets in a sequential manner at each step of the optimization problem. The method provides globally optimal solutions in total-variation, filtered variation, l1, and entropic cost functions. It is also experimentally observed that cost functions based on lp, p<1 can be handled by using the supporting hyperplane concept

Bilateral step length estimation using a single inertial measurement unit attached to the pelvis

BACKGROUND: The estimation of the spatio-temporal gait parameters is of primary importance in both physical activity monitoring and clinical contexts. A method for estimating step length bilaterally, during level walking, using a single inertial measurement unit (IMU) attached to the pelvis is proposed. In contrast to previous studies, based either on a simplified representation of the human gait mechanics or on a general linear regressive model, the proposed method estimates the step length directly from the integration of the acceleration along the direction of progression. METHODS: The IMU was placed at pelvis level fixed to the subject's belt on the right side. The method was validated using measurements from a stereo-photogrammetric system as a gold standard on nine subjects walking ten laps along a closed loop track of about 25 m, varying their speed. For each loop, only the IMU data recorded in a 4 m long portion of the track included in the calibrated volume of the SP system, were used for the analysis. The method takes advantage of the cyclic nature of gait and it requires an accurate determination of the foot contact instances. A combination of a Kalman filter and of an optimally filtered direct and reverse integration applied to the IMU signals formed a single novel method (Kalman and Optimally filtered Step length Estimation - KOSE method). A correction of the IMU displacement due to the pelvic rotation occurring in gait was implemented to estimate the step length and the traversed distance. RESULTS: The step length was estimated for all subjects with less than 3% error. Traversed distance was assessed with less than 2% error. CONCLUSIONS: The proposed method provided estimates of step length and traversed distance more accurate than any other method applied to measurements obtained from a single IMU that can be found in the literature. In healthy subjects, it is reasonable to expect that, errors in traversed distance estimation during daily monitoring activity would be of the same order of magnitude of those presented

Compressive sensing using the modified entropy functional

Cataloged from PDF version of article.In most compressive sensing problems, 1 norm is used during the signal reconstruction process. In this article, a modified version of the entropy functional is proposed to approximate the 1 norm. The proposed modified version of the entropy functional is continuous, differentiable and convex. Therefore, it is possible to construct globally convergent iterative algorithms using Bregman’s row-action method for compressive sensing applications. Simulation examples with both 1D signals and images are presented. © 2013 Elsevier Inc. All rights reserved

Special issue on microscopic image processing

Cataloged from PDF version of article

How Do You Like Me in This: User Embodiment Preferences for Companion Agents

We investigate the relationship between the embodiment of an artificial companion and user perception and interaction with it. In a Wizard of Oz study, 42 users interacted with one of two embodiments: a physical robot or a virtual agent on a screen through a role-play of secretarial tasks in an office, with the companion providing essential assistance. Findings showed that participants in both condition groups when given the choice would prefer to interact with the robot companion, mainly for its greater physical or social presence. Subjects also found the robot less annoying and talked to it more naturally. However, this preference for the robotic embodiment is not reflected in the users’ actual rating of the companion or their interaction with it. We reflect on this contradiction and conclude that in a task-based context a user focuses much more on a companion’s behaviour than its embodiment. This underlines the feasibility of our efforts in creating companions that migrate between embodiments while maintaining a consistent identity from the user’s point of view

Content-adaptive color transform for image compression

Cataloged from PDF version of article.In this paper, an adaptive color transform for image compression is introduced. In each block of the image, coefficients of the color transform are determined from the previously compressed neighboring blocks using weighted sums of the RGB pixel values, making the transform block-specific. There is no need to transmit or store the transform coeffi- cients because they are estimated from previous blocks. The compression efficiency of the transform is demonstrated using the JPEG image coding scheme. In general, the suggested transformation results in better peak signal-to-noise ratio (PSNR) values for a given compression level. ( C) 2011 Society of Photo-Optical Instrumentation Engineer

3D Model compression using Connectivity-Guided Adaptive Wavelet Transform built into 2D SPIHT

Cataloged from PDF version of article.Connectivity-Guided Adaptive Wavelet Transform based mesh compression framework is proposed. The transformation uses the connectivity information of the 3D model to exploit the inter-pixel correlations. Orthographic projection is used for converting the 3D mesh into a 2D image-like representation. The proposed conversion method does not change the connectivity among the vertices of the 3D model. There is a correlation between the pixels of the composed image due to the connectivity of the 3D mesh. The proposed wavelet transform uses an adaptive predictor that exploits the connectivity information of the 3D model. Known image compression tools cannot take advantage of the correlations between the samples. The wavelet transformed data is then encoded using a zero-tree wavelet based method. Since the encoder creates a hierarchical bitstream, the proposed technique is a progressive mesh compression technique. Experimental results show that the proposed method has a better rate distortion performance than MPEG-3DGC/MPEG-4 mesh coder. © 2009 Elsevier Inc. All rights reserved