A docking and modelling strategy for peptide–RNA complexes: applications to BIV Tat–TAR and HIV Rev–RBE

Background: In spite of the great interest in the interaction between RNAs and proteins, no general protocol for modelling these complexes is presently available. This methodological vacuum is particularly acute because the structure of few such complexes is known.Results: A general strategy for docking and modelling RNA–protein complexes has been developed. The docking procedure involves minimizing electrostatic and van der Waals’ interaction energies of conformationally rigid structures during docking. After docking, libraries of amino acid sidechain conformations are searched to obtain the best interactions between the peptide and the RNA. Using this method, we have reproduced the structure of a bovine immunodeficiency virus (BIV) Tat peptide bound to BIV TAR RNA and have developed a model for the structure of the arginine-rich HIV-1 Rev peptide (Rev34–50) interacting with the Rev-binding element (RBE).Conclusions: The resulting model of the Rev34–50–RBE complex predicts that although no single arginine sidechain is responsible for complex formation, residues Arg2, Arg5 and Arg11 are more important for binding than the other arginine residues in the peptide. One model is supported by binding measurements performed on wild-type and mutant RBE molecules with the peptide

A validated finite element model for predicting dynamic responses of cylinder liners in an IC engine*

Vibration of cylinder liners affects not only engine combustion performances but also tribological behaviour and noise radiations. However, it is difficult to characterize it experimentally due to multiple sources, strong background noise, and nonlinear transfer paths. Therefore, a finite element model is established in this study to predict the dynamic responses of cylinder liners under respective sources. The model takes into account both the characteristics of structural modes and nonlinearities of assembly constraints when selecting adequate elements for efficient computation of the responses under both the highly nonlinear combustion pressure excitations and subsequent piston slap impacts. The predictions are then evaluated against experimental results under different engine operating conditions. In addition, continuous wavelet analysis is employed to process the complicated responses for key response events and their frequency ranges. The results show agreeable correspondences between the numerical predictions and measured vibration signals, paving the way for investigating its effect on combustion and lubrication processes

Sensing-aided Uplink Channel Estimation for Joint Communication and Sensing

The joint communication and sensing (JCAS) technique has drawn great attention due to its high spectrum efficiency by using the same transmit signal for both communication and sensing. Exploiting the correlation between the uplink (UL) channel and the sensing results, we propose a sensing-aided Kalman filter (SAKF)-based channel state information (CSI) estimation method for UL JCAS, which exploits the angle-of-arrival (AoA) estimation to improve the CSI estimation accuracy. A Kalman filter (KF)-based CSI enhancement method is proposed to refine the least-square CSI estimation by exploiting the estimated AoA as the prior information. Simulation results show that the bit error rates (BER) of UL communication using the proposed SAKF-based CSI estimation method approach those using the minimum mean square error (MMSE) method, while at significantly reduced complexity.Comment: 4 pages, 5 figures, IEEE lette

Downlink and Uplink Cooperative Joint Communication and Sensing

Downlink (DL) and uplink (UL) joint communication and sensing (JCAS) technologies have been individually studied for realizing sensing using DL and UL communication signals, respectively. Since the spatial environment and JCAS channels in the consecutive DL and UL JCAS time slots are generally unchanged, DL and UL JCAS may be jointly designed to achieve better sensing performance. In this paper, we propose a novel DL and UL cooperative (DUC) JCAS scheme, including a unified multiple signal classification (MUSIC)-based JCAS sensing scheme for both DL and UL JCAS and a DUC JCAS fusion method. The unified MUSIC JCAS sensing scheme can accurately estimate AoA, range, and Doppler based on a unified MUSIC-based sensing module. The DUC JCAS fusion method can distinguish between the sensing results of the communication user and other dumb targets. Moreover, by exploiting the channel reciprocity, it can also improve the sensing and channel state information (CSI) estimation accuracy. Extensive simulation results validate the proposed DUC JCAS scheme. It is shown that the minimum location and velocity estimation mean square errors of the proposed DUC JCAS scheme are about 20 dB lower than those of the state-of-the-art separated DL and UL JCAS schemes.Comment: 14 pages, 10 figures, submitted to IEEE Transactions on Communication

Concurrent Downlink and Uplink Joint Communication and Sensing for 6G Networks

Joint communication and sensing (JCAS) is a promising technology for 6th Generation (6G) mobile networks, such as intelligent vehicular networks, intelligent manufacturing, and so on. Equipped with two spatially separated antenna arrays, the base station (BS) can perform downlink active JCAS in a mono-static setup. This paper proposes a Concurrent Downlink and Uplink (CDU) JCAS system where the BS can use the echo of transmitted dedicated signals for sensing in the uplink timeslot, while performing reliable uplink communication. A novel successive interference cancellation-based CDU JCAS processing method is proposed to enable the estimation of uplink communication symbols and downlink sensing parameters. Extensive simulation results verify the feasibility of the CDU JCAS system, showing a performance improvement of more than 10 dB compared to traditional JCAS methods while maintaining reliable uplink communication.Comment: 5 pages, 5 figures, submitted to IEEE transactions on vehicular technology correspondenc

Multiple Signal Classification Based Joint Communication and Sensing System

Joint communication and sensing (JCS) has become a promising technology for mobile networks because of its higher spectrum and energy efficiency. Up to now, the prevalent fast Fourier transform (FFT)-based sensing method for mobile JCS networks is on-grid based, and the grid interval determines the resolution. Because the mobile network usually has limited consecutive OFDM symbols in a downlink (DL) time slot, the sensing accuracy is restricted by the limited resolution, especially for velocity estimation. In this paper, we propose a multiple signal classification (MUSIC)-based JCS system that can achieve higher sensing accuracy for the angle of arrival, range, and velocity estimation, compared with the traditional FFT-based JCS method. We further propose a JCS channel state information (CSI) enhancement method by leveraging the JCS sensing results. Finally, we derive a theoretical lower bound for sensing mean square error (MSE) by using perturbation analysis. Simulation results show that in terms of the sensing MSE performance, the proposed MUSIC-based JCS outperforms the FFT-based one by more than 20 dB. Moreover, the bit error rate (BER) of communication demodulation using the proposed JCS CSI enhancement method is significantly reduced compared with communication using the originally estimated CSI.Comment: 30 pages, 10 figures, major revision to IEEE Transactions on Wireless Communication

Microbiota-Produced N-Formyl Peptide fMLF Promotes Obesity-Induced Glucose Intolerance.

The composition of the gastrointestinal microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine, are elevated in high-fat diet-induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon-like peptide 1. Obese Fpr1 knockout mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota. Overall, we describe a new mechanism by which the gut microbiota can modulate glucose metabolism, providing a potential approach for the treatment of metabolic disease

Altered fluvial patterns in North China indicate rapid climate change linked to the Permian-Triassic mass extinction

The causes of the severest crisis in the history of life around the Permian-Triassic boundary (PTB) remain controversial. Here we report that the latest Permian alluvial plains in Shanxi, North China, went through a rapid transition from meandering rivers to braided rivers and aeolian systems. Soil carbonate carbon isotope (δ13C), oxygen isotope (δ18O), and geochemical signatures of weathering intensity reveal a consistent pattern of deteriorating environments (cool, arid, and anoxic conditions) and climate fluctuations across the PTB. The synchronous ecological collapse is confirmed by a dramatic reduction or disappearance of dominant plants, tetrapods and invertebrates and a bloom of microbially-induced sedimentary structures. A similar rapid switch in fluvial style is seen worldwide (e.g. Karoo Basin, Russia, Australia) in terrestrial boundary sequences, all of which may be considered against a background of global marine regression. The synchronous global expansion of alluvial fans and high-energy braided streams is a response to abrupt climate change associated with aridity, hypoxia, acid rain, and mass wasting. Where neighbouring uplands were not uplifting or basins subsiding, alluvial fans are absent, but in these areas the climate change is evidenced by the disruption of pedogenesis