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.     

Strength and dilatancy behaviors of deep sands in Shanghai with a focus on grain size and shape effect

With rapid development of infrastructures like tunnels and open excavations in Shanghai, investigations on deeper soils have become critically important. Most of the existing laboratory works were focused on the clayey strata up to Layer 6 in Shanghai, i.e. at depth of up to 40 m. In this paper, Layers 7, 9, and 11, which were mostly formed of sandy soils at depth of up to 150 m, were experimentally investigated with respect to physico-mechanical behaviors. The stress–strain behaviors were analyzed by the consolidated drained/undrained (CD/CU) triaxial tests under monotonic loading. One-dimensional (1D) oedometer tests were performed to investigate the consolidation properties of the sandy soils. Specimens were prepared at three different relative densities for each layer. Also, the micro-images and particle size analyzers were used to analyze the shape and size of the sand grains. The influences of grain size, density, and angularity on the stress–strain behaviors and compressibility were also studied. Compared to the other layers, Layer 11 had the smallest mean grain size (D₅₀), highest compressibility, and lowest shear strength. In contrast, Layer 9 had the largest mean grain size, lowest compressibility, and highest shear strength. Layer 7 was of intermediate mean grain size, exhibiting more compressibility and less shear strength than that of Layer 9. Also, the critical state parameters and maximum dilatancy rate of different layers were discussed.     

Prediction of rock mass P wave velocity using blasthole drilling information

In this paper, the development of the models for the prediction of rock mass P wave velocity is presented. For model development, the database of 53 cases including widely used and recorded drilling parameters and P wave velocity was constructed from the field studies conducted in 13 open pit lignite mines. Both conventional linear, non-linear multiple regression and Adaptive Neuro Fuzzy Inference System (ANFIS) were used for model development. Prediction performance indicators showed that ANFIS model presented the best performance and it can successfully be used for the preliminary prediction of P wave velocities of rock masses.     

叠合盆地凸起区多期复杂断裂特征及形成机制——以准噶尔盆地车排子凸起为例

以高精度三维地震资料为基础,结合构造演化恢复和区域构造背景,系统研究了准噶尔盆地车排子凸起断裂分布和形成机制。结果表明,车排子凸起发育深部和浅部2套断裂体系,深部断裂体系和浅部断裂体系分别发育3种断裂样式。车排子凸起共经历5个构造演化阶段,其中,晚二叠世挤压-逆冲控制了深部断裂体系的初始形成,晚侏罗世逆冲-走滑控制了深部断裂体系的最终定型,新近纪叠加掀斜、局部伸展控制了浅部断裂体系的形成。不同断裂体系在油气成藏过程中均起到了重要作用。其中:深部断裂体系的红车断裂是重要的油源断裂,低序级断层控制形成了石炭系火山岩优质储集体;浅部断裂体系使得油气向浅部层系运移调整,同时形成了断块圈闭、断鼻圈闭和断层-岩性圈闭等丰富的圈闭类型。     

Systematic convergence of nonlinear stochastic estimators on the Special Orthogonal Group SO(3)

This paper introduces two novel nonlinear stochastic attitude estimators developed on the Special Orthogonal Group with the tracking error of the normalized Euclidean distance meeting predefined transient and steady‐state characteristics. The tracking error is confined to initially start within a predetermined large set such that the transient performance is guaranteed to obey dynamically reducing boundaries and decrease smoothly and asymptotically to the origin in probability from almost any initial condition. The proposed estimators produce accurate attitude estimates with remarkable convergence properties using measurements obtained from low‐cost inertial measurement units. The estimators proposed in continuous form are complemented by their discrete versions for the implementation purposes. The simulation results illustrate the effectiveness and robustness of the proposed estimators against uncertain measurements and large initialization error, whether in continuous or discrete form.     

Smart control of the assembly process with a fuzzy control system in the context of Industry 4.0

Assembly line balancing is important for the efficiency of the assembly process, however, a wide range of disruptions can break the current workload balance. Some researchers explored the task assignment plan for the assembly line balancing problem with the assumption that the assembly process is smooth with no disruption. Other researchers considered the impacts of disruptions, but they only explored the task re-assignment solutions for the assembly line re-balancing problem with the assumption that the re-balancing decision has been made already. There is limited literature exploring on-line adjustment solutions (layout adjustment and production rate adjustment) for an assembly line in a dynamic environment. This is because real-time monitoring of an assembly process was impossible in the past, and it is difficult to incorporate uncertainty factors into the balancing process because of the randomness and non-linearity of these factors. However, Industry 4.0 breaks the information barriers between different parts of an assembly line, since smart, connected products, which are enabled by advanced information and communication technology, can intelligently interact and communicate with each other and collect, process and produce information. Smart control of an assembly line becomes possible with the large amounts of real-time production data in the era of Industry 4.0, but there is little literature considering this new context. In this study, a fuzzy control system is developed to analyze the real-time information of an assembly line, with two types of fuzzy controllers in the fuzzy system. Type 1 fuzzy controller is used to determine whether the assembly line should be re-balanced to satisfy the demand, and type 2 fuzzy controller is used to adjust the production rate of each workstation in time to eliminate blockage and starvation, and increase the utilization of machines. Compared with three assembly lines without the proposed fuzzy control system, the assembly line with the fuzzy control system performs better, in terms of blockage ratio, starvation ratio and buffer level. Additionally, with the improvement of information transparency, the performance of an assembly line will be better. The research findings shed light on the smart control of the assembly process, and provide insights into the impacts of Industry 4.0 on assembly line balancing.     

Occurrence and diversity of Listeria spp. in seafood processing plant environments

Listeria contamination in processing plant environments is a major issue for the seafood industry worldwide; faster and more reliable results are therefore desired for early detection and monitoring of environmental Listeria spp. This study aimed to gain a better understanding of the prevalence and diversity of Listeria spp., and to evaluate a rapid detection method, the 3M Molecular Detection Assay (MDA) Listeria, for its ability to detect Listeria spp. in environmental samples from seafood processing plants. Duplicate environmental sponge samples (n = 444) were collected from 152 different sites within three seafood processing plants, and analyzed for Listeria spp. by the MDA method (after 26 and 48 h of enrichment) and the U.S. Food and Drug Administration Bacteriological Analytical Manual method. Overall, detection of Listeria spp. by the two methods did not differ significantly (p > 0.05); 11 (4.9%) and 13 (5.9%) samples were positive for Listeria spp. by the MDA and FDA-BAM method, respectively. The sensitivity of the MDS was 87.0% (95% CI: 77.4–96.6%), specificity was 97.6% (95% CI: 95.5–99.7%), accuracy was 95.3%, and the positive predictive value was 89.4% (95% CI: 80.5–98.2%). Classification of 19 Listeria isolates by partial SigB sequencing analysis identified three allelic types. Twelve of these isolates were ATs 58 and 60 which were classified as Listeria monocytogenes lineage I and serotypes 1/2b, 3b, 4b, 4d, 4e, by multiplex-PCR serotyping. Six Listeria isolates were classified as Listeria innocua (AT31). Our data show that the 3M Molecular Detection Assay Listeria provides rapid and reliable results for detection and monitoring of Listeria spp., which are important for seafood processing plants. Effective Listeria monitoring programs will allow for improved development of Listeria control measures in order to minimize cross-contamination in finished products.