Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models

RNA is a unique biomolecule that is involved in a variety of fundamental biological functions, all of which depend solely on its structure and dynamics. Since the experimental determination of crystal RNA structures is laborious, computational 3D structure prediction methods are experiencing an ongoing and thriving development. Such methods can lead to many models; thus, it is necessary to build comparisons and extract common structural motifs for further medical or biological studies. Here, we introduce a computational pipeline dedicated to reference-free high-throughput comparative analysis of 3D RNA structures. We show its application in the RNA-Puzzles challenge, in which five participating groups attempted to predict the three-dimensional structures of 5′- and 3′-untranslated regions (UTRs) of the SARS-CoV-2 genome. We report the results of this puzzle and discuss the structural motifs obtained from the analysis. All simulated models and tools incorporated into the pipeline are open to scientific and academic use.     

Compact Wideband Meandered Slotted Multi Frequency Microstrip Antenna

A compact wideband multi frequency microstrip antenna for wireless communication is proposed in this paper. The antenna is designed by introducing meandered slot on the patch and a pair of spur lines along the triangular notch on the finite ground plane. The overall size of the fabricated antenna is very small and low profile as the total dimension is 20?×?16 mm². The proposed antenna operates at 3.7 GHz, 4.27 GHz and 5.1 GHz which may be suitable for WiMAX and WLAN applications. In addition with multi frequency operation a wide bandwidth (VSWR?≤?2) has been achieved from 6 to 13.7 GHz i.e. 78.2% bandwidth of center frequency, which is suitable for X-band communication and ITU band applications. The meandered slot on the patch causes multi frequency operation of the antenna with 60% compactness and the spur line along with triangular notch on finite ground plane cause bandwidth enhancement.

     

A Stereo‐Matching Technique for Recovering 3D Information from Underwater Inspection Imagery

Underwater inspections stand to gain from using stereo imaging systems to collect three‐dimensional measurements. Although many stereo‐matching algorithms have been devised to solve the correspondence problem, that is, find the same points in multiple images, these algorithms often perform poorly when applied to images of underwater scenes due to the poor visibility and the complex underwater light field. This article presents a new stereo‐matching algorithm, called PaLPaBEL (Pyramidal Loopy Propagated BELief) that is designed to operate on challenging imagery. At its core, PaLPaBEL is a semiglobal method based on a loopy belief propagation message passing algorithm applied on a Markov random field. A pyramidal scheme is adopted that enables wide disparity ranges and high‐resolution images to be handled efficiently. For performance evaluation, PaLPaBEL is applied to underwater stereo images captured under various visibility conditions in a laboratory setting, and to synthetic imagery created in a virtual underwater environment. The technique is also demonstrated on stereo images obtained from a real‐world inspection. The successful results indicate that PaLPaBEL is well suited for underwater application and has value as a tool for the cost‐effective inspection of marine structures.     

Perception of safety of cyclists in Dublin City

In recent years, cycling has been recognized and is being promoted as a sustainable mode of travel. The perception of cycling as an unsafe mode of travel is a significant obstacle in increasing the mode share of bicycles in a city. Hence, it is important to identify and analyze the factors which influence the safety experiences of the cyclists in an urban signalized multi-modal transportation network. Previous researches in the area of perceived safety of cyclists primarily considered the influence of network infrastructure and operation specific variables and are often limited to specific locations within the network. This study explores the factors that are expected to be important in influencing the perception of safety among cyclists but were never studied in the past. These factors include the safety behavior of existing cyclists, the users of other travel modes and their attitude toward cyclists, facilities and network infrastructures applicable to cycling as well as to other modes in all parts of an urban transportation network. A survey of existing cyclists in Dublin City was conducted to gain an insight into the different aspects related to the safety experience of cyclists. Ordered Logistic Regression (OLR) and Principal Component Analysis (PCA) were used in the analysis of survey responses. This study has revealed that respondents perceive cycling as less safe than driving in Dublin City. The new findings have shown that the compliance of cyclists with the rules of the road increase their safety experience, while the reckless and careless attitudes of drivers are exceptionally detrimental to their perceived safety. The policy implications of the results of analysis are discussed with the intention of building on the reputation of cycling as a viable mode of transportation among all network users.     

Zinc oxide nanorod mediated visible light photoinactivation of model microbes in water

The inactivation of model microbes in aqueous matrix by visible light photocatalysis as mediated by ZnO nanorods was investigated. ZnO nanorods were grown on glass substrate following a hydrothermal route and employed in the inactivation of gram-negative Escherichia coli and gram-positive Bacillus subtilis in MilliQ water. The concentration of Zn(2+) ions in the aqueous matrix, bacterial cell membrane damage, and DNA degradation at post-exposure were also studied. The inactivation efficiencies for both organisms under light conditions were about two times higher than under dark conditions across the cell concentrations assayed. Anomalies in supernatant Zn(2+) concentration were observed under both conditions as compared to control treatments, while cell membrane damage and DNA degradation were observed only under light conditions. Inactivation under dark conditions was hence attributed to the bactericidal effect of Zn(2+) ions, while inactivation under light conditions was due to the combined effects of Zn(2+) ions and photocatalytically mediated electron injection. The reduction of pathogenic bacterial densities by the photocatalytically active ZnO nanorods in the presence of visible light implies potential ex situ application in water decontamination at ambient conditions under sunlight.     

Cytogenetic and genotoxic effects of zinc oxide nanoparticles on root cells of Allium cepa

Increasing use of zinc oxide nanoparticles (ZnO NP) in consumer products may enhance its release into the environment. Phytotoxicity study is important to understand its possible environmental impact. Allium cepa (Onion bulb) is the best model organism to study genetic toxicology of nanoparticles. Here we have reported cytogenetic and genotoxic effects of ZnO NPs on the root cells of A. cepa. The effects of ZnO NPs on the mitotic index (MI), micronuclei index (MN index), chromosomal aberration index, and lipid peroxidation were determined through the hydroponic culturing of A. cepa. A. cepa roots were treated with the dispersions of ZnO NPs at four different concentrations (25, 50, 75, and 100 μg ml(-1)). With the increasing concentrations of ZnO NPs MI decreased with the increase of pycnotic cells, on the other hand MN and chromosomal aberration index increased. The frequency of micronucleated cells was higher in ZnO NPs treated cells as compared to control (deionized distilled water). The number of cells in each mitotic phase changed upon ZnO NPs treatment. The effect of ZnO NPs on lipid peroxidation as examined by measuring TBARS concentration was evident at all the concentrations compared to bulk ZnO. The TEM image showed internalization of ZnO NPs like particles. SEM image of treated A. cepa demonstrated that the internalized nanoparticles agglomerated depending on the physico-chemical environment inside the cell. Our results demonstrated that ZnO NPs can be a clastogenic/genotoxic and cytotoxic agent. In conclusion, the A. cepa cytogenetic test can be used for the genotoxicity monitoring of novel nanomaterials like ZnO NPs, which is used in many consumer products.     

Studies on interfacial interactions of TiO2 nanoparticles with bacterial cells under light and dark conditions

The probable underlying mechanism(s) of bacterial cell–TiO₂ nanoparticles (TiO₂ NPs) interaction in the absence of photo-irradiation has been less studied since most of the prior cytotoxicity studies focused on irradiated TiO₂. The present study draws attention to the possible role of cell surface–TiO₂ NP interactions under dark conditions, through an array of spectroscopic and microscopic investigations. A dominant freshwater bacterial isolate, Bacillus licheniformis, which interacted with environmentally relevant concentrations of TiO₂ NPs (1 μg/mL), was analysed and compared under both light and dark conditions. Aggregation of cells upon NP interaction and adsorption of NPs onto the cell membrane was evident from the scanning electron micrographs under both light and dark conditions. The FT–IR and FT–Raman spectra suggested stress response of bacterial cells by elevated protein and polysaccharide content in the cell–NP interaction. The Xray photoelectron spectroscopic data substantiated the reduction of titanium from Ti(IV) to Ti(III) species which might have contributed to the redox interactions on the cell surface under light as well as dark conditions. The internalization of NPs in the cytoplasm were obvious from the transmission electron micrographs. The consequent cell death/damage was confirmed through fluorescence spectroscopy and microscopy. To conclude, the current study established the substantial role of interfacial interactions in cytotoxicity of the TiO₂ NPs irrespective of the irradiation conditions.     

Hydrothermal growth of ZnO nanostructures

One-dimensional nanostructures exhibit interesting electronic and optical properties due to their low dimensionality leading to quantum confinement effects. ZnO has received lot of attention as a nanostructured material because of unique properties rendering it suitable for various applications. Amongst the different methods of synthesis of ZnO nanostructures, the hydrothermal method is attractive for its simplicity and environment friendly conditions. This review summarizes the conditions leading to the growth of different ZnO nanostructures using hydrothermal technique. Doping of ZnO nanostructures through hydrothermal method are also highlighted.     

Effect of Road Surface,Vehicle, and Device Characteristics on Energy Harvesting from Bridge–Vehicle Interactions

Energy harvesting to power sensors for structural health monitoring (SHM) has received huge attention worldwide. A number of practical aspects affecting energy harvesting and the possibility of health monitoring directly from energy harvesters is investigated here. The key idea is the amount of power received from a damaged and an undamaged structure varying and the signature of such variation can be used for SHM. For this study, a damaged bridge and an undamaged bridge are considered with harvesters located at different positions and the power harvested is accessed numerically to determine how energy harvesting can act as a damage detector and monitor. Bridge–vehicle interaction is exploited to harvest energy. For a damaged bridge, a bilinear breathing crack is considered. Variable surface roughness according to ISO 8606:1995(E) is considered such that the real values can be considered in the simulation. The possibility of a drive‐by type health monitoring using energy harvesting is highlighted and the effects of road surface on such monitoring are identified. The sensitivity of the harvester health monitoring to locations and extents of crack damage are reported. This study investigates the effects of multiple harvesters and the effects of vehicular parameters on the harvested power. Continuous harvesting over a length of the bridge is considered semianalytically. A comparison among the numerical simulations, detailed finite element analysis, and experimental results emphasizes the feasibility of the proposed method.