Sofosbuvir Selects for Drug-Resistant Amino Acid Variants in the Zika Virus RNA-Dependent RNA-Polymerase Complex In Vitro

The nucleotide analog sofosbuvir, licensed for the treatment of hepatitis C, recently revealed activity against the Zika virus (ZIKV) in vitro and in animal models. However, the ZIKV genetic barrier to sofosbuvir has not yet been characterized. In this study, in vitro selection experiments were performed in infected human hepatoma cell lines. Increasing drug pressure significantly delayed viral breakthrough (p = 0.029). A double mutant in the NS5 gene (V360L/V607I) emerged in 3 independent experiments at 40–80 µM sofosbuvir resulting in a 3.9 ± 0.9-fold half- maximal inhibitory concentration (IC₅₀) shift with respect to the wild type (WT) virus. A triple mutant (C269Y/V360L/V607I), detected in one experiment at 80 µM, conferred a 6.8-fold IC₅₀ shift with respect to the WT. Molecular dynamics simulations confirmed that the double mutant V360L/V607I impacts the binding mode of sofosbuvir, supporting its role in sofosbuvir resistance. Due to the distance from the catalytic site and to the lack of reliable structural data, the contribution of C269Y was not investigated in silico. By a combination of sequence analysis, phenotypic susceptibility testing, and molecular modeling, we characterized a double ZIKV NS5 mutant with decreased sofosbuvir susceptibility. These data add important information to the profile of sofosbuvir as a possible lead for anti-ZIKV drug development.     

Discovery of Affinity-Based Probes for Btk Occupancy Assays

Bruton's tyrosine kinase (Btk) is an attractive target for the treatment of a wide array of B-cell malignancies and autoimmune diseases. Small-molecule covalent irreversible Btk inhibitors targeting Cys481 have been developed for the treatment of such diseases. In clinical trials, probe molecules are required in occupancy studies to measure the level of engagement of the protein by these covalent irreversible inhibitors. The result of this pharmacodynamic (PD) activity provides guidance for appropriate dosage selection to optimize inhibition of the drug target and correlation of target inhibition with disease treatment efficacy. This information is crucial for successful evaluation of drug candidates in clinical trials. Based on the pyridine carboxamide scaffold of a novel solvent-accessible pocket (SAP) series of covalent irreversible Btk inhibitors, we successfully developed a potent and selective affinity-based biotinylated probe 12 (2-[(4-{4-[5-(1-{5-[(3aS,4S,6aR)-2-oxo-hexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamido}-3,6,9,12-tetraoxapentadecan-15-amido)pentanoyl]piperazine-1-carbonyl}phenyl)amino]-6-[1-(prop-2-enoyl)piperidin-4-yl]pyridine-3-carboxamide). Compound 12 has been used in Btk occupancy assays for preclinical studies to determine the therapeutic efficacy of Btk inhibition in two mouse lupus models driven by TLR7 activation and type I interferon.     

Defocusing image to pattern contact holes using attenuated phase shift masks

The patterning of contact holes by selecting out-of-focus image plane (defocus) using attenuated phase shift masks (APSM) has been studied. Defocus is found to enhance the image modulation at low partial coherence for contact holes with negative local average of mask function. Semi-dense holes up to 130 nm in 8% APSM have been printed by 0.5 μm defocus at a partial coherence of 0.31 using KrF scanner with highest numerical aperture of 0.68. However, these holes were closed with in-focus imaging. Defocus is also found to be beneficial for patterning the pitches that have extensive side lobes with in-focus imaging.     

Adaptive motion control using neural network approximations

In this paper, we present a new adaptive technique for tracking control of mechanical systems in the presence of friction and periodic disturbances. Radial Basis Functions (RBFs) are used to compensate for the effects of nonlinearly occurring parameters in the friction and periodic disturbance model. Theoretical analysis, such as stability and transient performance, is provided. Furthermore, the performance of the adaptive RBF controller and its non-adaptive counterpart are compared.     

Topology preservation of template-based 6-subiteration reduction operations

Generally, a reduction operation (e.g., thinning and shrinking) on 3D binary images can be represented as a set of reduction templates where every object voxel of the image satisfying any template is turned to a background voxel. Generally, it is rather difficult, error-prone and time-consuming for verifying the topological soundness of a 3D parallel reduction operation. This paper proposes sufficient conditions of time complexity O(n) for verifying the topological soundness of 3D parallel 6-subiteration reduction operations of n templates where such a kind of 3D reduction operations is performed alternatively from the six orthogonal directions to turn object voxels to background voxels. By such sufficient conditions, the topology soundness of a 3D 6-subiteration parallel reduction operation can be verified by checking each and every of its templates.     

Control of discrete time nonlinear systems with a time-varying structure

In this paper, we present a control methodology for a class of discrete time nonlinear systems that depend on a possibly exogenous scheduling variable. This class of systems consists of an interpolation of nonlinear dynamic equations in strict feedback form, and it may represent systems with a time-varying nonlinear structure. Moreover, this class of systems is able to represent some cases of gain scheduling control, Takagi-Sugeno fuzzy systems, as well as input-output realizations of nonlinear systems which are approximated via localized linearizations. We present two control theorems, one using what we call a “global” approach (akin to traditional backstepping), and a “local” approach, our main result, where backstepping is again used but the control law is an interpolation of local control terms. An aircraft wing rock regulation problem with varying angle of attack is used to illustrate and compare the two approaches.     

Stability robustness of networked control systems with respect to packet loss

This paper is concerned with stability analysis of discrete-time networked control systems over a communication channel subject to packet loss whose behavior is modeled by an i.i.d Bernoulli process with a packet dropping probability bounded by a constant. A necessary and sufficient condition for stability is obtained. A packet dropping margin is introduced as a measure of stability robustness of a system against packet dropping, and a formula for it is derived. A design method is proposed for achieving a large margin subject to a constraint that the system has a set of prescribed nominal closed-loop poles.     

Decentralized adaptive coordinated control of multiple robot arms without using a force sensor

This paper presents a distributed adaptive coordinated control method for multiple robot arms grasping a common object. The cases of rigid contact and rolling contact are analyzed. In the proposed controller, the dynamic parameters of both object and robot arms are estimated adaptively. The desired motions of the robot arms are generated by an estimated object reference model. The control method requires only the measurements of the positions and velocities of the object and robot arms, but not the measurements of forces and moments at contact points. The asymptotic convergence of trajectory is proven by the Lyapunov-like Lemma. Experiments involving two robot arms handling a common object are shown.