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.     

The Lazy Cook Problem, or Scheduling Two Parallel Machines to Optimize Vehicle Utilization

A cook has to prepare n cakes using an oven with two racks. According to the recipe, the i-th cake has to be baked for exactly a _i minutes. Cakes to be cooked are taken from a table and carried to the oven, and once cooked are carried back to the table by means of a trolley that can carry two cakes at a time. What is the minimum number q ^* of round trips required of the cook? This problem has application to the operation scheduling of transportation systems and to material cutting. A different problem arises according to whether the cook accepts or not to stay near the oven for awhile with the trolley. If the trolley cannot be idle at the oven, an optimum schedule with no oven idle-time always exists: consequently, the trolley schedule is trivial, and the problem is transformed into a set packing. For this case, we propose and test a heuristic method which generates all of the promising columns of the set packing, and solves the resulting problem by branch-and-bound. Instead, if the trolley can be idle at the oven for a limited amount of time, a problem arises to find an optimal schedule of the trolley: in this case we show how to use a scaling technique in order to obtain a very good feasible solution by the method above.     

Pulse height defect in pCVD and scCVD diamond based detectors

Polycrystalline (pCVD) and single crystal (scCVD) diamond films grown from Chemical Vapour Deposition (CVD), if sufficiently pure at Raman analysis, are very good materials for beam or flux monitors inside accelerators or nuclear reactors. This is because they are very hard to damage in high radiation fields and very resistant to high temperatures. Films of pCVD diamond are, however, not so good as spectroscopy detectors due to inhomogeneities induced by their growth in grains with the consequent presence of grain boundaries which worsen their energy resolution. The latter can be significantly improved by growing scCVD diamond films onto HPHT synthetic diamond substrates. We have shown that it is possible to measure the density of defects inside diamond specimens using as probes suitable penetrating nuclear radiations. With the preliminary results reported here we'll show that, bombarding CVD diamond films grown at Roma “Tor Vergata” with energetic protons and ⁴He, ⁶Li and ¹²C ions produced in the accelerators of Catania laboratories, the pulse height defects are higher than those in silicon detectors and likewise well described by a power law in the deposited energy. Furthermore, we'll show that pulse heights for the same particles seem to depend on the duration of the measurement, thus exhibiting a sort of depolarization of the insulator when exposed to the electric voltage which makes it a particle detector.     

Cold sintering of diatomaceous earth

Diatomite, a natural silicate-based sedimentary rock, was densified by cold sintering at room temperature and 150°C under various pressures (100, 200, and 300 MPa) and using different NaOH water solutions (0–3 M). The relative density of cold sintered diatomite can be as high as 90%, a condition that can be achieved by conventional firing only at 1200–1300°C. The cold sintered materials maintain the same mineralogical composition of the starting powder (quartz, glass, and illite) and are constituted by well-deformed and flattened grains oriented orthogonally to the applied pressure. Conversely, an evident phase evolution takes place upon conventional firing with the formation of cristobalite and mullite. The bending strength of cold sintered artifacts can exceed 40 MPa and increases to ≈80 MPa after post-annealing at 800°C, such mechanical strength is much larger than that of conventionally pressed samples sintered at 800°C, which is only ≈1 MPa.     

An optimization framework for “build-or-buy” decisions in software architecture

Building a software architecture that meets functional requirements is a quite consolidated activity, whereas keeping high quality attributes is still an open challenge. In this paper we introduce an optimization framework that supports the decision whether to buy software components or to build them in-house upon designing a software architecture. We devise a non-linear cost/quality optimization model based on decision variables indicating the set of architectural components to buy and to build in order to minimize the software cost while keeping satisfactory values of quality attributes. From this point of view, our tool can be ideally embedded into a Cost Benefit Analysis Method to provide decision support to software architects. The novelty of our approach consists in building costs and quality attributes on a common set of decision variables related to software development. We start from a special case of the framework where the quality constraints are related to the delivery time and the product reliability, and the model solution also devises the amount of unit testing to be performed on built components. We generalize the framework formulation to represent a broader class of architectural cost-minimization problems under quality constraints, and discuss advantages and limitations of such approach.     

A bacterial colony growth algorithm for mobile robot localization

Achieving robot autonomy is a fundamental objective in Mobile Robotics. However in order to realize this goal, a robot must be aware of its location within an environment. Therefore, the localization problem (i.e.,the problem of determining robot pose relative to a map of its environment) must be addressed. This paper proposes a new biology-inspired approach to this problem. It takes advantage of models of species reproduction to provide a suitable framework for maintaining the multi-hypothesis. In addition, various strategies to track robot pose are proposed and investigated through statistical comparisons. The Bacterial Colony Growth Algorithm (BCGA) provides two different levels of modeling: a background level that carries on the multi-hypothesis and a foreground level that identifies the best hypotheses according to an exchangeable strategy. Experiments, carried out on the robot ATRV-Jr manufactured by iRobot, show the effectiveness of the proposed BCGA.

Design and control of an IPMC wormlike robot.

This paper presents an innovative wormlike robot controlled by cellular neural networks (CNNs) and made of an ionic polymer-metal composite (IPMC) self-actuated skeleton. The IPMC actuators, from which it is made of, are new materials that behave similarly to biological muscles. The idea that inspired the work is the possibility of using IPMCs to design autonomous moving structures. CNNs have already demonstrated their powerfulness as new structures for bio-inspired locomotion generation and control. The control scheme for the proposed IPMC moving structure is based on CNNs. The wormlike robot is totally made of IPMCs, and each actuator has to carry its own weight. All the actuators are connected together without using any other additional part, thereby constituting the robot structure itself. Worm locomotion is performed by bending the actuators sequentially from "tail" to "head," imitating the traveling wave observed in real-world undulatory locomotion. The activation signals are generated by a CNN. In the authors' opinion, the proposed strategy represents a promising solution in the field of autonomous and light structures that are capable of reconfiguring and moving in line with spatial-temporal dynamics generated by CNNs.     

A covert attention P300-based brain-computer interface: Geospell

The Farwell and Donchin P300 speller interface is one of the most widely used brain-computer interface (BCI) paradigms for writing text. Recent studies have shown that the recognition accuracy of the P300 speller decreases significantly when eye movement is impaired. This report introduces the GeoSpell interface (Geometric Speller), which implements a stimulation framework for a P300-based BCI that has been optimised for operation in covert visual attention. We compared the Geospell with the P300 speller interface under overt attention conditions with regard to effectiveness, efficiency and user satisfaction. Ten healthy subjects participated in the study. The performance of the GeoSpell interface in covert attention was comparable with that of the P300 speller in overt attention. As expected, the effectiveness of the spelling decreased with the new interface in covert attention. The NASA task load index (TLX) for workload assessment did not differ significantly between the two modalities. PRACTITIONER SUMMARY: This study introduces and evaluates a gaze-independent, P300-based brain-computer interface, the efficacy and user satisfaction of which were comparable with those off the classical P300 speller. Despite a decrease in effectiveness due to the use of covert attention, the performance of the GeoSpell far exceeded the threshold of accuracy with regard to effective spelling.     

Diffusive Behavior of Bedform-Induced Hyporheic Exchange in Rivers

Solute transport in natural streams is a complex phenomenon that involves both in-stream dispersion and mass exchange with the porous zones surrounding the water body. Due to the complex nature of the riverine systems several models may be used to simulate and analyze the transport of solutes with different degrees of complexity. The bedform-induced hyporheic transport is a stream-subsurface exchange mechanism that can be reproduced in controlled systems, such as laboratory flumes. Application of a simple Fickian diffusion model to laboratory data obtained with passive solutes and stationary bedforms proves successful within a range of durations of the contamination process. A dimensionless form of the diffusion coefficient, scaled with dynamic, physical, and geometric properties of the system is derived by comparison with another physically based model. A prediction of the dimensionless diffusion coefficient is obtained as a function of the timescale of the exchange process and is validated with a few sets of results from laboratory tests.     

The use of EEG modifications due to motor imagery for brain-computer interfaces

The opening of a communication channel between brain and computer [brain-computer interface (BCI)] is possible by using changes in electroencephalogram (EEG) power spectra related to the imagination of movements. In this paper, we present results obtained by recording EEG during an upper limb motor imagery task in a total of 18 subjects by using low-resolution surface Laplacian, different linear and quadratic classifiers, as well as a variable number of scalp electrodes, from 2 to 26. The results (variable correct classification rate of mental imagery between 75% and 95%) suggest that it is possible to recognize quite reliably ongoing mental movement imagery for BCI applications.