Now showing items 1-20 of 10995

    • 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.
    • Low Abundances but High Growth Rates of Coastal Heterotrophic Bacteria in the Red Sea

      Silva, Luis; Calleja, Maria L.; Huete-Stauffer, Tamara Megan; Ivetic, Snjezana; Ansari, Mohd Ikram; Viegas, Miguel; Moran, Xose Anxelu G. (Frontiers Media SA, 2019-01-07)
      Characterized by some of the highest naturally occurring sea surface temperatures, the Red Sea remains unexplored regarding the dynamics of heterotrophic prokaryotes. Over 16 months, we used flow cytometry to characterize the abundance and growth of four physiological groups of heterotrophic bacteria: membrane-intact (Live), high and low nucleic acid content (HNA and LNA) and actively respiring (CTC+) cells in shallow coastal waters. Chlorophyll a, dissolved organic matter (DOC and DON) concentrations, and their fluorescent properties were also measured as proxies of bottom-up control. We performed short-term incubations (6 days) with the whole microbial community (Community treatment), and with the bacterial community only after removing predators by filtration (Filtered treatment). Initial bacterial abundances ranged from 1.46 to 4.80 × 105 cells mL-1. Total specific growth rates in the Filtered treatment ranged from 0.76 to 2.02 d-1. Live and HNA cells displayed similar seasonal patterns, with higher values during late summer and fall (2.13 and 2.33 d-1, respectively) and lower in late spring (1.02 and 1.01 d-1, respectively). LNA cells were outgrown by the other physiological groups (0.33–1.08 d-1) while CTC+ cells (0.28–1.85 d-1) showed weaker seasonality. The Filtered treatment yielded higher bacterial abundances than the Community treatment in all but 2 of the incubations, and carrying capacities peaked in November 2016 (1.04 × 106 cells mL-1), with minimum values (3.61 × 105 cells mL-1) observed in May 2017. The high temperatures experienced from May through October 2016 (33.4 ± 0.4∘C) did not constrain the growth of heterotrophic bacteria. Indeed, bacterial growth efficiencies were positively correlated with environmental temperature, reflecting the presence of more labile compounds (high DON concentrations resulting in lower C:N ratios) in summer. The overall high specific growth rates and the consistently higher carrying capacities in the Filtered treatment suggest that strong top-down control by protistan grazers was the likely cause for the low heterotrophic bacteria abundances.
    • Fast Poynting-Vector based wave-mode separation and RTM in 2D elastic TI media

      Liu, Qiancheng; Zhang, Jianfeng; Lu, Yongming; Gao, Hongwei; Liu, Shaolin; Zhang, Hao (Elsevier BV, 2019-01-05)
      The wave-modes in isotropic elastic media are easy to get separated by using Helmholtz decomposition. This method, however, fails in TI (transverse isotropic) media due to the anisotropy, and more sophisticated operators are required. Most of these existing operators are implemented and limited in FD (finite-difference) stencil. We propose a Poynting-vector based method, which separates wave-modes pointwisely, independent of the modeling stencils. In TI media, the Poynting-vector indicates the group-velocity direction while the wave-modes get separated in the polarization-vector direction. We write the relationship between these two directions into a small numerical table by exploiting the phase-velocity direction as a bridge prior to wavefield propagation. During the modeling process, it is easy to estimate the group-velocity direction from the Poynting vector, and then we can get the polarization-vector direction to separate wave-modes by checking the numerical table. We test our method on several TI models. We furthermore apply our method to elastic reverse-time migration (RTM) in TI media.
    • A standard primary energy approach for comparing desalination processes

      Shahzad, Muhammad Wakil; Burhan, Muhammad; Ng, Kim Choom (Springer Nature, 2019-01-04)
      Considering different grades of energy as equivalent in the desalination industry could have negative economic and environmental consequences. Whereas this approach will suffice for the comparison of same energy input processes, omitting the grade of energy when comparing diverse technologies may lead to incorrect conclusions and, resultantly, inefficient installations. Here, a standard primary energy-based thermodynamic framework is presented that addresses the energy efficacy of assorted desalination processes. Example calculations show that a thermal desalination plant integrated with a power plant consumes 2–3% of input standard primary energy. We also propose a standard universal performance ratio methodology to provide a level playing field for the comparison of desalination processes; this suggest that the majority of desalination processes are operating far from the sustainable zone, with only ~10–13% at the ideal or thermodynamic limit. A proposed roadmap shows that attaining an efficacy level of up to 25–30% of the thermodynamic limit is crucial for achieving the 2030 sustainability development goals for seawater desalination, which will require a technological shift in the capability of dissolved salts separation processes.
    • Design of intense nanoscale stray fields and gradients at magnetic nanorod interfaces

      Ivanov, Yurii P.; Leliaert, Jonathan; Crespo, Adrian; Pancaldi, Matteo; Tollan, Christopher; Kosel, Jürgen; Chuvilin, Andrey; Vavassori, Paolo (American Chemical Society (ACS), 2019-01-04)
      We explore electrodeposited ordered arrays of Fe, Ni and Co nanorods embedded in anodic alumina membranes as a source of intense magnetic stray field gradients localized at the nanoscale. We perform a multiscale characterization of the stray fields using a combination of experimental methods (Magneto-optical Kerr effect, Virtual Bright Field Differential Phase Contrast Imaging) and micromagnetic simulations, and establish a clear correlation between the stray fields and the magnetic configurations of the nanorods. For uniformly magnetized Fe and Ni wires the field gradients vary following saturation magnetization of corresponding metal and the diameter of the wires. In the case of Co nanorods, very localized (~10 nm) and intense (> 1T) stray field sources are associated with the cores of magnetic vortexes. Confinement of that strong field at extremely small dimensions leads to exceptionally high field gradients up to 108 T/m. These results demonstrate a clear path to design and fine-tune nanoscale magnetic stray field ordered patterns with a broad applicability in key nanotechnologies, such as nanomedicine, nanobiology, nanoplasmonics and sensors.
    • Polyoxometalate−Cyclodextrin Metal−Organic Frameworks: From Tunable Intrinsic Microporosity to Customized Storage Functionality

      Yang, Peng; zhao, Wenli; Shkurenko, Aleksander; Belmabkhout, Youssef; Eddaoudi, Mohamed; Dong, Xiaochen; Alshareef, Husam N.; Khashab, Niveen M. (American Chemical Society (ACS), 2019-01-04)
      Self-assembly allows structures to organize themselves into regular patterns by using local forces to find the lowest-energy configuration. However, assembling organic and inorganic building blocks in an ordered framework is hampered by the difficulties of interfacing two dissimilar materials. Herein, the ensemble of polyoxometalates (POMs) and cyclodextrins (CDs) as molecular building blocks (MBBs) has yielded two unprecedented POM-CD-MOFs, namely [PW12O40]3− & α-CD MOF (POT-CD) and [P10P15.5O50]19− & γ-CD MOF (POP-CD), with distinct properties not shared by their isolated parent MBBs. Markedly, the POT-CD features a nontraditional enhanced Li storage behavior by virtue of a unique “amorphization & pulverization” process. This opens the door to a new generation of hybrid materials with tuned structures and customized functionalities.
    • 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.
    • Revisiting area risk classification of visceral leishmaniasis in Brazil

      Machado, Gustavo; Alvarez, Julio; Bakka, Haakon Christopher; Perez, Andres; Donato, Lucas Edel; de Ferreira Lima Júnior, Francisco Edilson; Alves, Renato Vieira; Del Rio Vilas, Victor Javier (Springer Nature, 2019-01-03)
      BACKGROUND:Visceral leishmaniasis (VL) is a neglected tropical disease of public health relevance in Brazil. To prioritize disease control measures, the Secretaria de Vigilância em Saúde of Brazil's Ministry of Health (SVS/MH) uses retrospective human case counts from VL surveillance data to inform a municipality-based risk classification. In this study, we compared the underlying VL risk, using a spatiotemporal explicit Bayesian hierarchical model (BHM), with the risk classification currently in use by the Brazil's Ministry of Health. We aim to assess how well the current risk classes capture the underlying VL risk as modelled by the BHM. METHODS:Annual counts of human VL cases and the population at risk for all Brazil's 5564 municipalities between 2004 and 2014 were used to fit a relative risk BHM. We then computed the predicted counts and exceedence risk for each municipality and classified them into four categories to allow comparison with the four risk categories by the SVS/MH. RESULTS:Municipalities identified as high-risk by the model partially agreed with the current risk classification by the SVS/MH. Our results suggest that counts of VL cases may suffice as general indicators of the underlying risk, but can underestimate risks, especially in areas with intense transmission. CONCLUSION:According to our BHM the SVS/MH risk classification underestimated the risk in several municipalities with moderate to intense VL transmission. Newly identified high-risk areas should be further evaluated to identify potential risk factors and assess the needs for additional surveillance and mitigation efforts.
    • Low temperature autoignition of 5-membered ring naphthenes: Effects of substitution

      Fridlyand, Aleksandr; Goldsborough, S. Scott; Rachidi, Mariam El; Sarathy, Mani; Mehl, Marco; Pitz, William J. (Elsevier BV, 2018-12-31)
      The development and design of future internal combustion engines requires fundamental understanding and the capability to model the autoignition and pollutant formation behavior of petroleum-based and other fuels. Naphthenes are an important constituent of gasoline, and they can comprise larger portions of unconventionally-derived gasoline. There is a lack of data and validated models for 5-membered ring naphthenes. In this work, the autoignition characteristics of cyclopentane, and two of its substituted analogues, methylcyclopentane, and ethylcyclopentane are investigated using a twin-piston rapid compression machine. Each fuel is studied at engine-representative conditions: 20, 50 bar and 700–980 K, with mixtures containing stoichiometric fuel/oxygen ratios at various extents of dilution with inert gases. Negative temperature coefficient (NTC) behavior is observed for cyclopentane, though first-stage ignition and associated low temperature heat release behavior are only evident at temperatures below that for the transition to NTC. Pressure is found to have a larger impact on the reactivity than oxygen dilution, with both effects amplified in the NTC region. The cyclopentane experiments in this study are challenged by the sensitivity of this molecule to non-uniform, or mild ignition phenomena within the NTC region. The addition of saturated sidechains in methyl- and ethylcyclopentane significantly increases the reactivity of the molecules, especially at low temperature and NTC conditions. At the highest temperatures though, there is little difference between the three naphthenes. Typical two-stage ignition behavior is observed across a wide range of temperatures for these alkyl cyclopentanes with no mild ignition observed within the NTC region. A recently developed model for cyclopentane is extended to include reactions for methylcyclopentane, and this is used to simulate the new experiments. The simulation results indicate that low temperature reactivity of cyclopentane is dominated by HO2 elimination of the RO2 species producing cyclopentene, and this inhibits autoignition since it is a very stable molecule. When a methyl group is substituted on the ring, additional RO2 isomerization pathways are available, and these substantially increase the fuel reactivity. HO2 elimination is also important with methylcyclopentane, and this leads to significant production of cyclic olefins which can further react to produce diolefins. These findings are consistent with observations that have been made in other experimental apparatuses.
    • 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.
    • Ordered Sequence Detection and Barrier Signal Design for Digital Pulse Interval Modulation in Optical Wireless Communications

      Guo, Shuaishuai; Park, Ki-Hong; Alouini, Mohamed-Slim (IEEE, 2018-12-28)
      This paper proposes an ordered sequence detection (OSD) for digital pulse interval modulation (DPIM) in optical wireless communications. Leveraging the sparsity of DPIM sequences, OSD shows comparable performance to the optimal maximum likelihood sequence detection (MLSD) with much lower complexity. Compared with the widely adopted sampleby- sample optimal threshold detection (OTD), it considerably improves the bit error rate (BER) performance by mitigating error propagation. Moreover, this paper proposes a barrier signalaided digital pulse interval modulation (BDPIM), where the last of every K symbols is allocated with more power as an inserted barrier signal. BDPIM with OSD (BDPIM-OSD) can limit the error propagation between two adjacent barriers. To reduce the storing delay when using OSD to detect extremely large packets, we propose BDPIM with a combination of OTD and OSD (BDPIM-OTD-OSD), within which long sequences are cut into pieces and separately detected. Approximate upper bounds of the average BER performance of DPIM-OTD, DPIM-OSD, BDPIM-OSD and BDPIM-OTD-OSD are analyzed. Simulations are conducted to corroborate our analysis. Optimal parameter settings are also investigated in uncoded and coded systems by simulations. Simulation results show that the proposed OSD and BDPIM bring significant improvement in uncoded and coded systems over various channels.
    • 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/.
    • Excitation Wavelength Dependent Internal Quantum Efficiencies in a P3HT / Non-Fullerene Acceptor Solar Cell

      Tan, Ching-Hong; Wadsworth, Andrew; Gasparini, Nicola; Wheeler, Scot; Holliday, Sarah; Ashraf, Raja Shahid; Dimitrov, Stoichko D.; Baran, Derya; McCulloch, Iain; Durrant, James R. (American Chemical Society (ACS), 2018-12-24)
      Solar cells based on blends of the donor polymer, P3HT, with the non-fullerene acceptor, IDTBR, have been shown to exhibit promising efficiencies and stabilities for low cost organic photovoltaic (OPV) devices. We focus herein on the charge separation and recombination dynamics in such devices. By employing selective wavelength excitations of P3HT and O-IDTBR, we show that photoexcitation of the P3HT results in lower internal quantum efficiency (IQE) for photocurrent generation than observed for photoexcitation of the O-IDTBR. Transient absorption and photoluminescence quenching studies indicate that this lower IQE results primarily from higher geminate recombination losses of photogenerated charges following P3HT excitation compared with O-IDTBR excitation, rather than from differences in exciton separation efficiency. These higher geminate recombination losses result not only in a lower photocurrent generation efficiency at short circuit, but also a lower device J-V fill factor upon selective excitation of the P3HT donor, when compared with O-IDTBR excitation.
    • An ANN based hybrid chemistry framework for complex fuels

      Ranade, Rishikesh; Alqahtani, Sultan; Farooq, Aamir; Echekki, Tarek (Elsevier BV, 2018-12-22)
      The oxidation chemistry of complex hydrocarbons involves large mechanisms with hundreds or thousands of chemical species and reactions. For practical applications and computational ease, it is desirable to reduce their chemistry. To this end, high-temperature fuel oxidation for large carbon number fuels may be described as comprising two steps, fuel pyrolysis and small species oxidation. Such an approach has recently been adopted as ‘hybrid chemistry’ or HyChem to handle high-temperature chemistry of jet fuels by utilizing time-series measurements of pyrolysis products. In the approach proposed here, a shallow Artificial Neural Network (ANN) is used to fit temporal profiles of fuel fragments to directly extract chemical reaction rate information. This information is then correlated with the species concentrations to build an ANN-based model for the fragments’ chemistry during the pyrolysis stage. Finally, this model is combined with a C0-C4 chemical mechanism to model high-temperature fuel oxidation. This new hybrid chemistry approach is demonstrated using homogeneous chemistry calculations of n-dodecane (n-C12H26) oxidation. The experimental uncertainty is simulated by introducing realistic noise in the data. The comparison shows a good agreement between the proposed ANN hybrid chemistry approach and detailed chemistry results.
    • One-step growth of reduced graphene oxide on arbitrary substrates

      Chen, Mingguang; Yengel, Emre; Zhang, Junwei; Zhu, Chenxu; He, Xin; Zhang, Chenhui; Huang, Jing-Kai; Hedhili, Mohamed N.; Anthopoulos, Thomas D.; Zhang, Xixiang (Elsevier BV, 2018-12-22)
      Reduced graphene oxide (rGO) has inherited the outstanding electronic, optical, thermal and mechanical properties of graphene to a large extent, while maintaining sufficient chemically active sites. Therefore, it has attracted a great deal of research attention in the fields of energy storage, electronics, photonics, catalysis, environmental engineering, etc. Currently, the most popular way to prepare rGO is to reduce graphene oxide, which is obtained by modified Hummer methods using tedious treatments in a harsh environment, to rGO flakes. Industrial applications demand advanced preparation methods that can mass produce highly uniform rGO sheets on arbitrary substrates. In this work, a one-step growth process is introduced that utilizes cellulose acetate as a precursor, without any catalysts, to produce uniform ultrathin rGO films on various substrates and free-standing rGO powders. Systematic spectroscopic and microscopic studies on the resulting rGO are performed. Prototypes of electronic and optoelectronic devices, such as field effect transistors (FETs), photodetectors, and humidity sensors, are fabricated and tested, demonstrating the intriguing applications of our rGO materials across a wide range of fields.
    • Solvent-resistant Triazine-Piperazine Linked Porous Covalent Organic Polymer Thin-film Nanofiltration Membrane

      Das, Swapan Kumar; Manchanda, Priyanka; Peinemann, Klaus-Viktor (Elsevier BV, 2018-12-21)
      We present the fabrication of a novel porous covalent organic triazine-piperazine based membrane (CTP membrane) for solvent nanofiltration. The porous CTP skin layer grows on the top surface of polyacrylonitrile (PAN) support in presence of N, N-diisopropylethylamine (DIPEA) in the water/heptane interfacial reaction. The CTP skin layer membrane showed solvent-resistant property to a wide range of common solvents such as DMF, DMSO, and NMP; the stability of the composite membrane is limited by the PAN support. Chemical bonding and elemental analyses confirm the incorporation and linking of the triazine and piperazine components in the nanofilms skeleton. Electron microscopic image analysis demonstrates that the CTP skin layer nicely covers the PAN support and has porous and crumple morphology. The membrane exhibits excellent NF properties as demonstrated by the selective dye rejection and salt rejection experiment. The CTP membrane showed dye rejection (Reactive black-5; MW 992 gmol−1) and salt rejection (Na2SO4) 96.7%, and 91.3%, respectively. The membrane comprised a stable porous robust structure, large surface area, well-defined pore topology, and solvent durability coupled with the zeta potential. All of these cooperatively benefits to achieve superior performances in separation, reusability with high permeance, leading to state of the art performance in the NF application.
    • Baroclinic tides simulation in the Red Sea: comparison to observations and basic characteristics

      Guo, Daquan; Kartadikaria, Aditya R.; Zhan, Peng; Xie, Jieshuo; Li, Mingjie; Hoteit, Ibrahim (American Geophysical Union (AGU), 2018-12-19)
      The baroclinic tides in the Red Sea are simulated using a three-dimensional, nonhydrostatic, high-resolution Massachusetts Institute of Technology general circulation model. Various observations have been used to validate the simulation results. A good match between the model results and observations from five tidal gauges has been obtained. Tidal amplitude and phase data from 21 tidal stations present high correlation coefficients and low deviations with the model results. Comparisons between model and Oregon State University Tidal Inversion Software data suggest consistent results, with only small discrepancies at the locations of the amphidromic points. Tidal currents from four mooring observations are in good agreement with the simulation results, with discrepancies appearing in shallow areas and those with complex bottom topography. Based on the simulation results, the basic characteristics of baroclinic tides in the Red Sea are analyzed. The properties of barotropic tides, and distribution of the forcing function parameter, indicate that the baroclinic tides are generated mainly in four areas: the Bab-el-Mandeb (BAM) Strait, the southern Red Sea, the Gulf of Suez, and the Strait of Tiran. This is confirmed by the spatial distributions of baroclinic tidal kinetic energy and energy flux. The properties of the conversion rate from barotropic tides to baroclinic tides, and the divergence of baroclinic energy flux, further reveal quantitatively that the southern Red Sea features the most of the generated baroclinic energy. The majority of the baroclinic energy disappears within the four areas, either dissipating due to friction and bottom drag or converting back to barotropic energy.
    • TELS: A Novel Computational Framework for Identifying Motif Signatures of Transcribed Enhancers

      Kleftogiannis, Dimitrios; Ashoor, Haitham; Bajic, Vladimir B. (Elsevier BV, 2018-12-19)
      In mammalian cells, transcribed enhancers (TrEns) play important roles in the initiation of gene expression and maintenance of gene expression levels in a spatiotemporal manner. One of the most challenging questions is how the genomic characteristics of enhancers relate to enhancer activities. To date, only a limited number of enhancer sequence characteristics have been investigated, leaving space for exploring the enhancers’ DNA code in a more systematic way. To address this problem, we developed a novel computational framework, Transcribed Enhancer Landscape Search (TELS), aimed at identifying predictive cell type/tissue-specific motif signatures of TrEns. As a case study, we used TELS to compile a comprehensive catalogue of motif signatures for all known TrEns identified by the FANTOM5 consortium across 112 human primary cells and tissues. Our results confirm that combinations of different short motifs characterize in an optimized manner cell type/tissue-specific TrEns. Our study is the first to report combinations of motifs that maximize classification performance of TrEns exclusively transcribed in one cell type/tissue from TrEns exclusively transcribed in different cell types/tissues. Moreover, we also report 31 motif signatures predictive of enhancers’ broad activity. TELS codes and material are publicly available at http://www.cbrc.kaust.edu.sa/TELS.
    • Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions

      Alazmi, Meshari; Kuwahara, Hiroyuki; Soufan, Othman; Ding, Lizhong; Gao, Xin (Oxford University Press (OUP), 2018-12-19)
      Motivation \nAccurate and wide-ranging prediction of thermodynamic parameters for biochemical reactions can facilitate deeper insights into the workings and the design of metabolic systems. \n \nResults \nHere, we introduce a machine learning method with chemical fingerprint-based features for the prediction of the Gibbs free energy of biochemical reactions. From a large pool of 2D fingerprint-based features, this method systematically selects a small number of relevant ones and uses them to construct a regularized linear model. Since a manual selection of 2D structurebased features can be a tedious and time-consuming task, requiring expert knowledge about the structure-activity relationship of chemical compounds, the systematic feature selection step in our method offers a convenient means to identify relevant 2D fingerprint-based features. By comparing our method with state-of-the-art linear regression-based methods for the standard Gibbs free energy prediction, we demonstrated that its prediction accuracy and prediction coverage are most favorable. Our results show direct evidence that a number of 2D fingerprints collectively provide useful information about the Gibbs free energy of biochemical reactions and that our systematic feature selection procedure provides a convenient way to identify them.
    • H-NS uses an autoinhibitory conformational switch for environment-controlled gene silencing

      Shahul Hameed, Umar F; Liao, Chenyi; Radhakrishnan, Anand K; Huser, Franceline; Aljedani, Safia Salim Eid; Zhao, Xiaochuan; Momin, Afaque Ahmad Imtiyaz; Melo, Fernando A; Guo, Xianrong; Brooks, Claire; Li, Yu; Cui, Xuefeng; Gao, Xin; Ladbury, John E; Jaremko, Łukasz; Jaremko, Mariusz; Li, Jianing; Arold, Stefan T. (Oxford University Press (OUP), 2018-12-19)
      As an environment-dependent pleiotropic gene regulator in Gram-negative bacteria, the H-NS protein is crucial for adaptation and toxicity control of human pathogens such as Salmonella, Vibrio cholerae or enterohaemorrhagic Escherichia coli. Changes in temperature affect the capacity of H-NS to form multimers that condense DNA and restrict gene expression. However, the molecular mechanism through which H-NS senses temperature and other physiochemical parameters remains unclear and controversial. Combining structural, biophysical and computational analyses, we show that human body temperature promotes unfolding of the central dimerization domain, breaking up H-NS multimers. This unfolding event enables an autoinhibitory compact H-NS conformation that blocks DNA binding. Our integrative approach provides the molecular basis for H-NS-mediated environment-sensing and may open new avenues for the control of pathogenic multi-drug resistant bacteria.