• Two symmetric arginine residues play distinct roles in Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage

      Lei, Jinping; Sheng, Gang; Cheung, Peter Pak-Hang; Wang, Shenglong; Li, Yu; Gao, Xin; Zhang, Yingkai; Wang, Yanli; Huang, Xuhui (Proceedings of the National Academy of Sciences, 2018-12-28)
      Bacterium Thermus thermophilus Argonaute (Ago; TtAgo) is a prokaryotic Ago (pAgo) that acts as the host defense against the uptake and propagation of foreign DNA by catalyzing the DNA cleavage reaction. The TtAgo active site consists of a plugged-in glutamate finger with two arginine residues (R545 and R486) located symmetrically around it. An interesting challenge is to understand how they can collaboratively facilitate enzymatic catalysis. In Kluyveromyces polysporus Ago, a eukaryotic Ago, the evolutionarily symmetrical residues are arginine and histidine, both of which function to stabilize the plugged-in catalytic tetrad conformation. Surprisingly, our simulation results indicated that, in TtAgo, only R545 is involved in the cleavage reaction by serving as a critical structural anchor to stabilize the catalytic tetrad Asp-Glu-Asp-Asp that is completed by the insertion of the glutamate finger, whereas R486 is not involved in target cleavage. The TtAgo-mediated target DNA cleavage occurs in a substrate-assisted mechanism, in which the pro-Rp (Rp, a tetrahedral phosphorus center with "R-type" chirality) oxygen of scissile phosphate acts as a general base to activate the nucleophilic water. Our unexpected theoretical findings on distinct roles played by R545 and R486 in TtAgo catalysis have been validated by single-point site-mutagenesis experiments, wherein the target cleavage is abolished for all mutants of R545. In sharp contrast, the cleavage activity is maintained for all mutants of R486. Our work provides mechanistic insights on the catalytic specificity of Ago proteins and could facilitate the design of new gene-editing tools in the long term.
    • Giant planar Hall effect in the Dirac semimetal ZrTe5−δ

      Li, P.; Zhang, C. H.; Zhang, Junwei; Wen, Yan; Zhang, Xixiang (American Physical Society (APS), 2018-09-24)
      Exploration and understanding of exotic topics in quantum physics such as Dirac and Weyl semimetals have become highly popular in the area of condensed matter. It has recently been predicted that a theoretical giant planar Hall effect can be induced by a chiral anomaly in Dirac and Weyl semimetals. ZrTe5 is considered an intriguing Dirac semimetal at the boundary of weak and strong topological insulators, though this claim is still controversial. In this study, we report the observation in ZrTe5 of giant planar Hall resistivity. We have also noted three different dependences of this resistivity on the magnetic field, as predicted by theory, maximum planar Hall resistivity occurs at the Lifshitz transition temperature. In addition, we have discovered a nontrivial Berry phase, as well as a chiral-anomaly-induced negative longitudinal and a giant in-plane anisotropic magnetoresistance. All these experimental observations coherently demonstrate that ZrTe5 is a Dirac semimetal.
    • Possible Evidence for Spin-Transfer Torque Induced by Spin-Triplet Supercurrents

      Li, Lai-Lai; Zhao, Yue-Lei; Zhang, Xixiang; Sun, Young (IOP Publishing, 2018-07-06)
    • High-Mobility Two-Dimensional Electron Gas at InGaN/InN Heterointerface Grown by Molecular Beam Epitaxy

      Wang, Tao; Wang, Xinqiang; Chen, Zhaoying; Sun, Xiaoxiao; Wang, Ping; Zheng, Xiantong; Rong, Xin; Yang, Liuyun; Guo, Weiwei; Wang, Ding; Cheng, Jianpeng; Lin, Xi; Li, Peng; Li, Jun; He, Xin; Zhang, Qiang; Zhang, Jian; Yang, Xuelin; Xu, Fujun; Ge, Weikun; Zhang, Xixiang; Shen, Bo (Wiley, 2018-06-27)
      Due to the intrinsic spontaneous and piezoelectric polarization effect, III‐nitride semiconductor heterostructures are promising candidates for generating 2D electron gas (2DEG) system. Among III‐nitrides, InN is predicted to be the best conductive‐channel material because its electrons have the smallest effective mass and it exhibits large band offsets at the heterointerface of GaN/InN or AlN/InN. Until now, that prediction has remained theoretical, due to a giant gap between the optimal growth windows of InN and GaN, and the difficult epitaxial growth of InN in general. The experimental realization of 2DEG at an InGaN/InN heterointerface grown by molecular beam epitaxy is reported here. The directly probed electron mobility and the sheet electron density of the InGaN/InN heterostructure are determined by Hall‐effect measurements at room temperature to be 2.29 × 103 cm2 V−1 s−1 and 2.14 × 1013 cm−2, respectively, including contribution from the InN bottom layer. The Shubnikov–de Haas results at 3 K confirm that the 2DEG has an electron density of 3.30 × 1012 cm−2 and a quantum mobility of 1.48 × 103 cm2 V−1 s−1. The experimental observations of 2DEG at the InGaN/InN heterointerface have paved the way for fabricating higher‐speed transistors based on an InN channel.
    • Manipulating the Topology of Nanoscale Skyrmion Bubbles by Spatially Geometric Confinement

      Hou, Zhipeng; Zhang, Qiang; Xu, Guizhou; Zhang, Senfu; GONG, CHEN; Ding, Bei; Li, Hang; Xu, Feng; Yao, Yuan; Liu, Enke; Wu, Guangheng; Zhang, Xixiang; Wang, Wenhong (American Chemical Society (ACS), 2019-01-07)
    • OFDM with Index Modulation Assisted by Multiple Amplify-and-Forward Relays

      Sheng, Guo; Dang, Shuping; Zhang, Zhenrong; Kocan, Enis; Pejanovic-Djurisic, Milica (IEEE, 2019-01-15)
      A multi-relay assisted orthogonal frequency division multiplexing (OFDM) system with index modulation (OFDM-IM) is proposed in this letter, assuming that amplify-and-forward (AF) relaying protocol is adopted at relays. Two commonly used AF protocols are considered: fixed-gain (FG) AF and variable-gain (VG) AF relaying protocols. To utilize relays in an efficient manner, we also employ two multi-carrier relay selection schemes termed bulk and per-subcarrier (PS) relay selection in the proposed system. We analyze the outage performance of the proposed system and derive closed-form expressions of the average outage probabilities (AOPs) for all cases with different AF relaying protocols and multi-carrier relay selection schemes. In addition, we obtain the asymptotic expressions of AOPs in the high signal-to-noise ratio (SNR) region, by which it is proven that the full diversity gain equaling the number of relays is attainable.
    • Experimental and Numerical Investigation of the Response of a Swirled Flame to Flow Modulations in a Non-Adiabatic Combustor

      Chatelier, Adrien; Guiberti, Thibault; Mercier, Renaud; Bertier, Nicolas; Fiorina, Benoît; Schuller, Thierry (Springer Nature, 2019-01-11)
      Turbulent combustion models for Large Eddy Simulation (LES) aims at predicting the flame dynamics. So far, they have been proven to predict correctly the mean flow and flame properties in a wide range of configurations. A way to challenge these models in unsteady situations is to test their ability to recover turbulent flames submitted to harmonic flow modulations. In this study, the Flame Transfer Function (FTF) of a CH4/H2/air premixed swirled-stabilized flame submitted to harmonic flowrate modulations in a non-adiabatic combustor is compared to the response computed using the Filtered TAbulated Chemistry for LES (F-TACLES) formalism. Phase averaged analysis of the perturbed flow field and flame response reveal that the velocity field determined with Particle Image Velocimetry measurements, the heat release distribution inferred from OH* images and the probability of presence of burnt gases deduced from OH-Planar Laser Induced Fluorescence measurements are qualitatively well reproduced by the simulations. However, noticeable differences between experiments and simulations are also observed in a narrow frequency range. A detailed close-up view of the flow field highlight differences in experimental OH* and numerical volumetric heat release rate distributions which are at the origin of the differences observed between the numerical and experimental FTF. These differences mainly originate from the outer shear layer of the swirling jet where a residual reaction layer takes place in the simulations which is absent in the experiments. Consequences for turbulent combustion modeling are suggested by examining the evolution of the perturbed flame brush envelope along the downstream distance of the perturbed flames. It is shown that changing the grid resolution and the flame subgrid scale wrinkling factor in these regions does not alter the numerical results. It is finally concluded that the combined effects of strain rate and enthalpy defect due to heat losses are the main factors leading to small but sizable differences of the flame response to coherent structures synchronized by the acoustic forcing in the outer shear layer of the swirling flow. These small differences in flame response lead in turn to a misprediction of the FTF at specific forcing frequencies.
    • Molecular Simulation Study of Montmorillonite in Contact with Water

      Li, Yiteng; Nair, Arun Kumar Narayanan; Kadoura, Ahmad Salim; Yang, Yafan; Sun, Shuyu (American Chemical Society (ACS), 2019-01-05)
      Grand canonical Monte Carlo and molecular dynamics simulations were applied to understand the molecular mechanism of ion and water transport in montmorillonite clays as a function of relative humidity (RH). The variation of basal spacings of montmorillonite as a function of RH predicted based on the swelling free energy profiles was consistent with X-ray data. The hydration of the montmorillonite shows the following well-known order: Mg2+ > Ca2+ > Sr2+ > Li+ > Na+ > K+. The relative contribution of water on external surfaces only becomes significant close to the saturation pressure. However, this behavior for K-montmorillonite starts to occur well below the saturation pressure due to the clay-swelling inhibition by potassium ions. The diffusion of water and ions generally increases with RH in all samples. However, for samples with weakly hydrated ions, the water mobility in thin films adsorbed on external basal surfaces of clay can be higher than that in the water-saturated mesopores. For a given RH, mobility of interlayer species is typically lower than that from the external surfaces. The results of the simulations were applied to interpret recent laboratory measurements of ion mobility with changing RH. We also assess the effect of layer charge distribution on such sorption and diffusion processes.
    • Distributed Robust Power Minimization for the Downlink of Multi-Cloud Radio Access Networks

      Dhif-Allah, Oussama; Dahrouj, Hayssam; Al-Naffouri, Tareq Y.; Alouini, Mohamed-Slim (Institute of Electrical and Electronics Engineers (IEEE), 2017-12-06)
    • On the Effect of Uplink Power Control on Temporal Retransmission Diversity

      Arshad, Rabe; Afify, Laila H.; Elsawy, Hesham; Al-Naffouri, Tareq Y.; Alouini, Mohamed-Slim (Institute of Electrical and Electronics Engineers (IEEE), 2018-09-24)
      Using stochastic geometry, this article studies the retransmission performance in uplink cellular networks with fractional path-loss inversion power control (FPC). We first show that the signal-to-interference-ratio (SIR) is correlated across time, which imposes temporal diversity loss in the retransmission performance. In particular, FPC with lower path-loss compensation factor decreases inter-cell interference but suffers from degraded retransmission diversity. On the other hand, full path-loss inversion achieves almost full temporal diversity (i.e., temporal SIR independence) at the expense of increased inter-cell interference. To this end, the results show that ramping-down the power upon transmission failure improves the overall coverage probability in interference-limited uplink networks.
    • Instantly Decodable Network Coding: From Centralized to Device-to-Device Communications

      Douik, Ahmed; Sorour, Sameh; Al-Naffouri, Tareq Y.; Alouini, Mohamed-Slim (Institute of Electrical and Electronics Engineers (IEEE), 2017-02-07)
      From its introduction to its quindecennial, network coding has built a strong reputation for enhancing packet recovery and achieving maximum information flow in both wired and wireless networks. Traditional studies focused on optimizing the throughput of the system by proposing elaborate schemes able to reach the network capacity. With the shift toward distributed computing on mobile devices, performance and complexity become both critical factors that affect the efficiency of a coding strategy. Instantly decodable network coding presents itself as a new paradigm in network coding that trades off these two aspects. This paper review instantly decodable network coding schemes by identifying, categorizing, and evaluating various algorithms proposed in the literature. The first part of the manuscript investigates the conventional centralized systems, in which all decisions are carried out by a central unit, e.g., a base-station. In particular, two successful approaches known as the strict and generalized instantly decodable network are compared in terms of reliability, performance, complexity, and packet selection methodology. The second part considers the use of instantly decodable codes in a device-to-device communication network, in which devices speed up the recovery of the missing packets by exchanging network coded packets. Although the performance improvements are directly proportional to the computational complexity increases, numerous successful schemes from both the performance and complexity viewpoints are identified.
    • Rate Aware Instantly Decodable Network Codes

      Douik, Ahmed; Sorour, Sameh; Al-Naffouri, Tareq Y.; Alouini, Mohamed-Slim (Institute of Electrical and Electronics Engineers (IEEE), 2016-12-05)
      This paper addresses the problem of reducing the delivery time of data messages to cellular users using instantly decodable network coding (IDNC) with physical-layer rate awareness. While most of the existing literature on IDNC does not consider any physical layer complications and abstracts the model as equally slotted time for all users, this paper proposes a cross-layer scheme that incorporates the different channel rates of the various users in the decision process of both the transmitted message combinations and the rates with which they are transmitted. The consideration of asymmetric rates for receivers reflects more practical application scenarios and introduces a new tradeoff between the choice of coding combinations for various receivers and the broadcasting rates. The completion time minimization problem in such a scenario is first shown to be intractable. The problem is thus approximated by reducing, at each transmission, the increase of an anticipated version of the completion time. This paper solves the problem by formulating it as a maximum weight clique problem over a newly designed rate-aware IDNC graph. The highest weight clique in the created graph being potentially not unique, this paper further suggests a multi-layer version of the proposed solution to improve the obtained results from the employed completion time approximation. Simulation results indicate that the cross-layer design largely outperforms the uncoded transmissions strategies and the classical IDNC scheme.
    • Implied Stopping Rules for American Basket Options from Markovian Projection

      Bayer, Christian; Häppölä, Juho; Tempone, Raul (Taylor and Francis, 2018-08-01)
      This work addresses the problem of pricing American basket options in a multivariate setting, which includes among others, the Bachelier and Black–Scholes models. In high dimensions, nonlinear PDE methods for solving the problem become prohibitively costly due to the curse of dimensionality. Instead, this work proposes to use a stopping rule that depends on the dynamics of a low-dimensional Markovian projection of the given basket of assets. From a numerical analysis point of view, we split the given non-smooth high-dimensional problem into two subproblems, namely one dealing with a smooth high-dimensionality integration in the parameter space and the other dealing with a low-dimensional, non-smooth optimal stopping problem in the projected state space. Assuming that we know the density of the forward process and using the Laplace approximation, we first efficiently evaluate the diffusion coefficient corresponding to the low-dimensional Markovian projection of the basket. Then, we approximate the optimal early exercise boundary of the option by solving an HJB PDE in the projected, low-dimensional space. The resulting near-optimal early exercise boundary is used to produce an exercise strategy for the high-dimensional option, thereby providing a lower bound for the price of the American basket option. A corresponding upper bound is also provided. These bounds allow one to assess the accuracy of the proposed pricing method. Indeed, our approximate early exercise strategy provides a straightforward lower bound for the American basket option price. Following a duality argument due to Rogers, we derive a corresponding upper bound solving only the low-dimensional optimal control problem. Numerically, we show the feasibility of the method using baskets with dimensions up to 50. In these examples, the resulting option price relative errors are only of the order of few percent.
    • Comparing theory based and higher-order reduced models for fusion simulation data

      Bernholdt, David E.; Ciancosa, Mark R.; Green, David L.; Law, Kody J.H.; Litvinenko, Alexander; Park, Jin M. (AIMS Press, 2018-12-06)
      We consider using regression to fit a theory-based log-linear ansatz, as well as higher order approximations, for the thermal energy confinement of a Tokamak as a function of device features. We use general linear models based on total order polynomials, as well as deep neural networks. The results indicate that the theory-based model fits the data almost as well as the more sophisticated machines, within the support of the data set. The conclusion we arrive at is that only negligible improvements can be made to the theoretical model, for input data of this type.
    • On the Sum of Order Statistics and Applications to Wireless Communication Systems Performances

      Ben Rached, Nadhir; Botev, Zdravko; Kammoun, Abla; Alouini, Mohamed-Slim; Tempone, Raul (IEEE, 2018-09-26)
      We consider the problem of evaluating the cumulative distribution function (CDF) of the sum of order statistics, which serves to compute outage probability (OP) values at the output of generalized selection combining receivers. Generally, closed-form expressions of the CDF of the sum of order statistics are unavailable for many practical distributions. Moreover, the naive Monte Carlo (MC) method requires a substantial computational effort when the probability of interest is sufficiently small. In the region of small OP values, we instead propose two effective variance reduction techniques that yield a reliable estimate of the CDF with small computing cost. The first estimator, which can be viewed as an importance sampling estimator, has bounded relative error under a certain assumption that is shown to hold for most of the challenging distributions. A possible improvement of this estimator is then proposed for the Pareto and the Weibull cases. The second is a conditional MC estimator that achieves the bounded relative error property for the generalized Gamma case and the logarithmic efficiency for the Log-normal case. Finally, the efficiency of these estimators is compared via various numerical simulations.
    • Unified Statistical Channel Model for Turbulence-Induced Fading in Underwater Wireless Optical Communication Systems

      Zedini, Emna; Oubei, Hassan M.; Kammoun, Abla; Hamdi, Mounir; Ooi, Boon S.; Alouini, Mohamed-Slim (IEEE, 2019-01-09)
      A unified statistical model is proposed to characterize turbulence-induced fading in underwater wireless optical communication (UWOC) channels in the presence of air bubbles and temperature gradient for fresh and salty waters, based on experimental data. In this model, the channel irradiance fluctuations are characterized by the mixture Exponential-Generalized Gamma (EGG) distribution. We use the expectation maximization (EM) algorithm to obtain the maximum likelihood parameter estimation of the new model. Interestingly, the proposed model is shown to provide a perfect fit with the measured data under all channel conditions for both types of water. The major advantage of the new model is that it has a simple mathematical form making it attractive from a performance analysis point of view. Indeed, we show that the application of the EGG model leads to closed-form and analytically tractable expressions for key UWOC system performance metrics such as the outage probability, the average bit-error rate, and the ergodic capacity. To the best of our knowledge, this is the first-ever comprehensive channel model addressing the statistics of optical beam irradiance fluctuations in underwater wireless optical channels due to both air bubbles and temperature gradient.
    • The anatomy of phenotype ontologies: principles, properties and applications

      Gkoutos, Georgios V; Schofield, Paul N; Hoehndorf, Robert (Oxford University Press (OUP), 2017-03-07)
      The past decade has seen an explosion in the collection of genotype data in domains as diverse as medicine, ecology, livestock and plant breeding. Along with this comes the challenge of dealing with the related phenotype data, which is not only large but also highly multidimensional. Computational analysis of phenotypes has therefore become critical for our ability to understand the biological meaning of genomic data in the biological sciences. At the heart of computational phenotype analysis are the phenotype ontologies. A large number of these ontologies have been developed across many domains, and we are now at a point where the knowledge captured in the structure of these ontologies can be used for the integration and analysis of large interrelated data sets. The Phenotype And Trait Ontology framework provides a method for formal definitions of phenotypes and associated data sets and has proved to be key to our ability to develop methods for the integration and analysis of phenotype data. Here, we describe the development and products of the ontological approach to phenotype capture, the formal content of phenotype ontologies and how their content can be used computationally.
    • Carbohydrate composition of mucus from scleractinian corals from the central Red Sea

      Hadaidi, Ghaida Ali Hassan; Gegner, H. M.; Ziegler, Maren; Voolstra, Christian R. (Springer Nature, 2018-12-31)
      Coral mucus is continuously released by most corals and acts as an important protective barrier and as a substrate for host-associated microbial communities due to its complex composition of carbohydrates, lipids, and proteins. On a reef scale, coral mucus functions as a particle trap, thereby retaining nutrients and energy in the ecosystem. Given the distinct environmental conditions in the Red Sea (high temperature, high salinity, high total alkalinity), we sought to investigate the carbohydrate composition of mucus from five corals from the central Red Sea. Our aim was to assess whether mucus from Red Sea corals is different from what is known from other corals and whether those differences could be aligned to putative beneficial functions with regard to the prevailing environment. Using gas chromatography/mass spectrometry, we detected nine sugars as the main prevalent carbohydrates. Although we detected significant differences between species with regard to the relative abundance of given carbohydrates, the identified sugars resembled those found in mucus from corals elsewhere, and we could corroborate high abundance of arabinose in acroporid corals. Taken together, our results suggest the presence of a common set of carbohydrates across a broad range of coral species from geographically diverse environments, highlighting the important role of mucus with regard to coral and reef ecosystem function.
    • Promoter analysis and prediction in the human genome using sequence-based deep learning models

      Umarov, Ramzan; Kuwahara, Hiroyuki; Li, Yu; Gao, Xin; Solovyev, Victor (Oxford University Press (OUP), 2018-12-27)
      Motivation:Computational identification of promoters is notoriously difficult as human genes often have unique promoter sequences that provide regulation of transcription and interaction with transcription initiation complex. While there are many attempts to develop computational promoter identification methods, we have no reliable tool to analyze long genomic sequences. Results:In this work we further develop our deep learning approach that was relatively successful to discriminate short promoter and non-promoter sequences. Instead of focusing on the classification accuracy, in this work we predict the exact positions of the TSS inside the genomic sequences testing every possible location. We studied human promoters to find effective regions for discrimination and built corresponding deep learning models. These models use adaptively constructed negative set, which iteratively improves the model's discriminative ability. Our method significantly outperforms the previously developed promoter prediction programs by considerably reducing the number of false positive predictions. We have achieved error-per-1000-bp rate of 0.02 and have 0.31 errors per correct prediction, which is significantly better than the results of other human promoter predictors. Availability:The developed method is available as a web server at http://www.cbrc.kaust.edu.sa/PromID/.
    • High-throughput 3D modelling to dissect the genetic control of leaf elongation in barley (Hordeum vulgare )

      Ward, Ben; Brien, Chris; Oakey, Helena; Pearson, Allison; Negrão, Sónia; Schilling, Rhiannon K.; Taylor, Julian; Jarvis, David Erwin; Timmins, Andy; Roy, Stuart J.; Tester, Mark A.; Berger, Bettina; van den Hengel, Anton (Wiley, 2019-01-03)
      To optimize shoot growth and structure of cereals, we need to understand the genetic components controlling initiation and elongation. While measuring total shoot growth at high-throughput using 2D imaging has progressed, recovering the 3D shoot structure of small grain cereals at a large scale is still challenging. Here, we present a method for measuring defined individual leaves of cereals, such as wheat and barley, using few images. Plant shoot modelling over time was used to measure the initiation and elongation of leaves in a bi-parental barley mapping population under low and high soil salinity. We detected quantitative trait loci (QTL) related to shoot growth per se, using both simple 2D total shoot measurements and our approach of measuring individual leaves. In addition, we detected QTL specific to leaf elongation and not to total shoot size. Of particular importance was the detection of a QTL on Chromosome 3H specific to the early responses of leaf elongation to salt stress, a locus that could not be detected without the computer vision tools developed in this study. This article is protected by copyright. All rights reserved.