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.     

Treatment of a colored groundwater by ozone-biofiltration: pilot studies and modeling interpretation

Pilot studies investigated the fates of color, dissolved organic carbon (DOC), and biodegradable organic matter (BOM) by the tandem of ozone plus biofiltration for treating a source water having significant color (50 cu) and DOC (3.2 mg/l). Transferred ozone doses were from 1.0 to 1.8 g O3/g C. Rapid biofilters used sand, anthracite, or granular activated carbon as media with empty-bed contact time (EBCT) up to 9 min. The pilot studies demonstrated that ozonation plus biofiltration removed most color and substantial DOC, and increasing the transferred ozone dose enhanced the removals. For the highest ozone dose, removals were as high as 90% for color and 38% for DOC. While most of the color removal took place during ozonation, most DOC removal occurred in the biofilters, particularly when the ozone dose was high. Compared to sand and anthracite biofilters, the GAC biofilter gave the best performance for color and DOC removal, but some of this enhanced performance was caused by adsorption, since the GAC was virgin at the beginning of the pilot studies. Backwashing events had no noticeable impact of the performance of the biofilters. The Transient-State, Multiple-Species Biofilm Model (TSMSBM) was used to interpret the experimental results. Model simulations show that soluble microbial products, which comprised a significant part of the effluent BOM, offset the removal of original BOM, a factor that kept the removal of DOC relatively constant over the range of EBCTs of 3.5-9 min. Although improved biofilm retention, represented by a small detachment rate, allowed more total biofilm accumulation and greater removal of original BOM, it also caused more release of soluble microbial products and the build up of inert biomass in the biofilm. Backwashing had little impact on biofilter performance, because it did not remove more than 25% of the biofilm under any condition simulated.     

大S的红酒美容秘诀

3月22日,三亚的一场奢华婚礼为台湾女星大S"闪婚"事件划上一个完美的句号。女明星中,大S不是最漂亮的,但作为一个35岁、演技屡遭诟病的剩女,能如此持久地盘踞各大娱乐媒体的头版头条,除了她的真性情,更因为她一直以来不断的努力与成长。到目前为止,大S已经身兼唱片歌手、主持人、电影演员、电视明星、作家等多     

The Role of the Prefrontal Cortex in the Maintenance of Verbal Working Memory: An Event-Related fMRI Analysis.

Neuroimaging studies have been inconclusive in characterizing the role of the prefrontal cortex (PFC) for maintaining increasingly larger amounts of information in working memory (WM). To address this question, the authors collected event-related functional MRI data while participants performed an item-recognition task in which the number of to-be-remembered letters was parametrically modulated. During maintenance of information in WM, the dorsolateral and the ventrolateral PFC exhibited linearly increasing activation in response to increasing WM load. Prefrontal regions could not be distinguished from one another on the basis of load sensitivity, but the dorsolateral PFC had stronger functional connectivity with the parietal and motor cortex than the ventrolateral PFC. These results suggest an increasingly important role for the PFC in actively maintaining information as the amount of that information increases. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Hydrogen production by methane cracking using Ni-supported catalysts in a fluidized bed

Nickel, supported on porous alumina (γAl₂O₃), non-porous alumina (αAl₂O₃), and porous silica, was used to catalyze methane cracking in a fluidized bed reactor for hydrogen production. The effects of temperature, PCH₄${\text{P}}_{{\text{CH}}_4}$, and particle diameter, and their interactions, on methane conversion were studied with each catalyst. Temperature was the dominant parameter affecting the hydrogen production rate for all catalysts and particle diameter had the strongest effect on the total amount of carbon deposited. Maximum methane conversion as a function of support type followed the order Ni/SiO₂ > Ni/αAl₂O₃ > Ni/γAl₂O₃. Nonetheless, better fluidization quality was obtained with Ni/γAl₂O₃. Methane conversion was increased by increasing temperature and particle size from 108 to 275 μm due to better fluidization achieved with 275 μm particles. Increasing the flow rate and methane partial pressure (PCH₄${\text{P}}_{{\text{CH}}_4}$) caused a drop in methane conversion. Tests were also run in a fixed bed reactor, and at constant weight hourly space velocity (WHSV), higher conversion was achieved in the fixed bed, but at the same time faster deactivation occurred since a higher methane conversion led to increase in carbon filament and encapsulating carbon formation rates. A critical problem with the fixed bed was the pressure build-up inside the reactor due to carbon accumulation. Finally, a series of cracking/regeneration cycle experiments were carried out in the fluidized bed reactor. The regeneration was performed through product carbon gasification in air. Ni/αAl₂O₃ and Ni/γAl₂O₃ activity decreased significantly with the first regeneration, which is attributed to Ni sintering during exothermic regeneration/carbon oxidation. However, Ni/SiO₂ was thermally stable over at least three cracking/regeneration cycles, but mechanical attrition was observed.     

Pinhole SPECT imaging: compact projection/backprojection operator for efficient algebraic reconstruction

We describe the efficient algebraic reconstruction (EAR) method, which applies to cone-beam tomographic reconstruction problems with a circular symmetry. Three independant steps/stages are presented, which use two symmetries and a factorization of the point spread functions (PSFs), each reducing computing times and eventually storage in memory or hard drive. In the case of pinhole single photon emission computed tomography (SPECT), we show how the EAR method can incorporate most of the physical and geometrical effects which change the PSF compared to the Dirac function assumed in analytical methods, thus showing improvements on reconstructed images. We also compare results obtained by the EAR method with a cubic grid implementation of an algebraic method and modeling of the PSF and we show that there is no significant loss of quality, despite the use of a noncubic grid for voxels in the EAR method. Data from a phantom, reconstructed with the EAR method, demonstrate 1.08-mm spatial tomographic resolution despite the use of a 1.5-mm pinhole SPECT device and several applications in rat and mouse imaging are shown. Finally, we discuss the conditions of application of the method when symmetries are broken, by considering the different parameters of the calibration and nonsymmetric physical effects such as attenuation.     

Outdoor Visual Position Estimation for Planetary Rovers

This paper describes (1) a novel, effective algorithm for outdoor visual position estimation; (2) the implementation of this algorithm in the Viper system; and (3) the extensive tests that have demonstrated the superior accuracy and speed of the algorithm. The Viper system (Visual Position Estimator for Rovers) is geared towards robotic space missions, and the central purpose of the system is to increase the situational awareness of a rover operator by presenting accurate position estimates. The system has been extensively tested with terrestrial and lunar imagery, in terrains ranging from moderate—the rounded hills of Pittsburgh and the high deserts of Chile—to rugged—the dramatic relief of the Apollo 17 landing site—to extreme—the jagged peaks of the Rockies. Results have consistently demonstrated that the visual estimation algorithm estimates position with an accuracy and reliability that greatly surpass previous work.     

Ubiquitous robotics: Recent challenges and future trends

Ambient intelligence, ubiquitous and networked robots, and cloud robotics are new research hot topics that have started to gain popularity among the robotics community. They enable robots to acquire richer functionalities and open the way for the composition of a variety of robotic services with three functions: semantic perception, reasoning and actuation. Ubiquitous robots (ubirobots) overcome the limitations of stand-alone robots by integrating them with web services and ambient intelligence technologies. The overlap that exists now between ubirobots and ambient intelligence makes their integration worthwhile. It targets to create a hybrid physical–digital space rich with a myriad of proactive intelligent services that enhance the quality and the way of our living and working. Furthermore, the emergence of cloud computing initiates the massive use of a new generation of ubirobots that enrich their cognitive capabilities and share their knowledge by connecting themselves to cloud infrastructures. The future of ubirobots will certainly be open to an unlimited space of applications such as physical and virtual companions assisting people in their daily living, ubirobots that are able to co-work alongside people and cooperate with them in the same environment, and physical and virtual autonomic guards that are able to protect people, monitor their security and safety, and rescue them in indoor and outdoor spaces. This paper introduces the recent challenges and future trends on these topics.     

Vademecum‐based GFEM (V‐GFEM): optimal enrichment for transient problems

This paper proposes a generalized finite element method based on the use of parametric solutions as enrichment functions. These parametric solutions are precomputed off‐line and stored in memory in the form of a computational vademecum so that they can be used on‐line with negligible cost. This renders a more efficient computational method than traditional finite element methods at performing simulations of processes. One key issue of the proposed method is the efficient computation of the parametric enrichments. These are computed and efficiently stored in memory by employing proper generalized decompositions. Although the presented method can be broadly applied, it is particularly well suited in manufacturing processes involving localized physics that depend on many parameters, such as welding. After introducing the vademecum‐generalized finite element method formulation, we present some numerical examples related to the simulation of thermal models encountered in welding processes. Copyright © 2016 John Wiley & Sons, Ltd.     

Predicting long-term creep failure of bimodal polyethylene pipe from short-term fatigue tests

Short-term fatigue testing was used to predict long-term creep failure of a bimodal polyethylene (BMPE) pipe with superior creep resistance. The stepwise crack propagation was studied by increasing the R-ratio (defined as the ratio of the minimum to the maximum stress intensity factor in the fatigue loading cycle) at 50 °C from 0.1 approaching creep (R = 1). Crack growth rate (da/dt) was related to the maximum stress intensity factor K _I,max and R-ratio by a power law relationship \frac\textda\textdt = B^￠ K_\textI,max⁴ (1 + R) ^{- 8.5} {\frac{{{\text{d}}a}}{{{\text{d}}t}}} = B^{\prime } K_{{{\text{I}},\max }}^{4} (1 + R)^{ - 8.5} . The correlation in crack growth kinetics allowed for extrapolation to creep fracture from short-term fatigue testing. The temperature dependence of crack growth rate was contained in the prefactor B′. A change in slope of the Arrhenius plot of B′ at 67 °C indicated that at least two mechanisms contributed to crack propagation, each dominating in a different temperature region. This implied that a simple extrapolation to ambient temperature creep fracture from elevated temperature tests might not be reliable.