Recent Submissions

  • High-speed colour-converting photodetector with all-inorganic CsPbBr3 perovskite nanocrystals for ultraviolet light communication

    Kang, Chun Hong; Dursun, Ibrahim; Liu, Guangyu; Sinatra, Lutfan; Sun, Xiaobin; Kong, Meiwei; Pan, Jun; Maity, Partha; Ooi, Ee-Ning; Ng, Tien Khee; Mohammed, Omar F.; Bakr, Osman; Ooi, Boon S. (Light: Science & Applications, Springer Science and Business Media LLC, 2019-10-16) [Article]
    Optical wireless communication (OWC) using the ultra-broad spectrum of the visible-to-ultraviolet (UV) wavelength region remains a vital field of research for mitigating the saturated bandwidth of radio-frequency (RF) communication. However, the lack of an efficient UV photodetection methodology hinders the development of UV-based communication. The key technological impediment is related to the low UV-photon absorption in existing silicon photodetectors, which offer low-cost and mature platforms. To address this technology gap, we report a hybrid Si-based photodetection scheme by incorporating CsPbBr3 perovskite nanocrystals (NCs) with a high photoluminescence quantum yield (PLQY) and a fast photoluminescence (PL) decay time as a UV-to-visible colour-converting layer for high-speed solar-blind UV communication. The facile formation of drop-cast CsPbBr3 perovskite NCs leads to a high PLQY of up to ~73% and strong absorption in the UV region. With the addition of the NC layer, a nearly threefold improvement in the responsivity and an increase of ~25% in the external quantum efficiency (EQE) of the solar-blind region compared to a commercial silicon-based photodetector were observed. Moreover, time-resolved photoluminescence measurements demonstrated a decay time of 4.5 ns under a 372-nm UV excitation source, thus elucidating the potential of this layer as a fast colour-converting layer. A high data rate of up to 34 Mbps in solar-blind communication was achieved using the hybrid CsPbBr3–silicon photodetection scheme in conjunction with a 278-nm UVC light-emitting diode (LED). These findings demonstrate the feasibility of an integrated high-speed photoreceiver design of a composition-tuneable perovskite-based phosphor and a low-cost silicon-based photodetector for UV communication.
  • Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment.

    Lensink, Marc F.; Brysbaert, Guillaume; Nadzirin, Nurul; Velankar, Sameer; Chaleil, Raphaël A G; Gerguri, Tereza; Bates, Paul A; Laine, Elodie; Carbone, Alessandra; Grudinin, Sergei; Kong, Ren; Liu, Ran-Ran; Xu, Xi-Ming; Shi, Hang; Chang, Shan; Eisenstein, Miriam; Karczynska, Agnieszka; Czaplewski, Cezary; Lubecka, Emilia; Lipska, Agnieszka; Krupa, Paweł; Mozolewska, Magdalena; Golon, Łukasz; Samsonov, Sergey; Liwo, Adam; Crivelli, Silvia; Pagès, Guillaume; Karasikov, Mikhail; Kadukova, Maria; Yan, Yumeng; Huang, Sheng-You; Rosell, Mireia; Rodríguez-Lumbreras, Luis Angel; Romero-Durana, Miguel; Díaz-Bueno, Lucía; Fernandez-Recio, Juan; Christoffer, Charles; Terashi, Genki; Shin, Woong-Hee; Aderinwale, Tunde; Raghavendra Maddhuri Venkata Subraman, Sai; Kihara, Daisuke; Kozakov, Dima; Vajda, Sandor; Porter, Kathyn; Padhorny, Dzmitry; Desta, Israel; Beglov, Dmitri; Ignatov, Mikhail; Kotelnikov, Sergey; Moal, Iain H; Ritchie, David W; Chauvot de Beauchêne, Isaure; Maigret, Bernard; Devignes, Marie-Dominique; Echartea, Maria Elisa Ruiz; Barradas Bautista, Didier; Cao, Zhen; Cavallo, Luigi; Oliva, Romina; Cao, Yue; Shen, Yang; Baek, Minkyung; Park, Taeyong; Woo, Hyeonuk; Seok, Chaok; Braitbard, Merav; Bitton, Lirane; Scheidman-Duhovny, Dina; DapkŪnas, Justas; Olechnovič, Kliment; Venclovas, Česlovas; Kundrotas, Petras J; Belkin, Saveliy; Chakravarty, Devlina; Badal, Varsha D; Vakser, Ilya A; Vreven, Thom; Vangaveti, Sweta; Borrman, Tyler; Weng, Zhiping; Guest, Johnathan D; Gowthaman, Ragul; Pierce, Brian G; Xu, Xianjin; Duan, Rui; Qiu, Liming; Hou, Jie; Ryan Merideth, Benjamin; Ma, Zhiwei; Cheng, Jianlin; Zou, Xiaoqin; Koukos, Panos I; Roel-Touris, Jorge; Ambrosetti, Francesco; Geng, Cunliang; Schaarschmidt, Jörg; Trellet, Mikael E; Melquiond, Adrien S J; Xue, Li; Jiménez-García, Brian; van Noort, Charlotte W; Honorato, Rodrigo V; Bonvin, Alexandre M.J.J.; Wodak, Shoshana J (Proteins, Wiley, 2019-10-16) [Article]
    We present the results for CAPRI Round 46, the 3rd joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 20 targets including 14 homo-oligomers and 6 hetero-complexes. Eight of the homo-oligomer targets and one hetero-dimer comprised proteins that could be readily modeled using templates from the Protein Data Bank, often available for the full assembly. The remaining 11 targets comprised 5 homo-dimers, 3 hetero-dimers and two higher-order assemblies. These were more difficult to model, as their prediction mainly involved 'ab-initio' docking of subunit models derived from distantly related templates. A total of ~30 CAPRI groups, including 9 automatic servers, submitted on average ~2000 models per target. About 17 groups participated in the CAPRI scoring rounds, offered for most targets, submitting ~170 models per target. The prediction performance, measured by the fraction of models of acceptable quality or higher submitted across all predictors groups, was very good to excellent for the 9 easy targets. Poorer performance was achieved by predictors for the 11 difficult targets, with medium and high quality models submitted for only 3 of these targets. A similar performance 'gap' was displayed by scorer groups, highlighting yet again the unmet challenge of modeling the conformational changes of the protein components that occur upon binding or that must be accounted for in template-based modeling. Our analysis also indicates that residues in binding interfaces were less well predicted in this set of targets than in previous Rounds, providing useful insights for directions of future improvements. This article is protected by copyright. All rights reserved.
  • Apocarotenoids Involved in Plant Development and Stress Response.

    Felemban, Abrar; Braguy, Justine; Zurbriggen, Matias D; Al-Babili, Salim (Frontiers in plant science, Frontiers Media SA, 2019-10-16) [Article]
    Carotenoids are isoprenoid pigments synthesized by all photosynthetic organisms and many heterotrophic microorganisms. They are equipped with a conjugated double-bond system that builds the basis for their role in harvesting light energy and in protecting the cell from photo-oxidation. In addition, the carotenoids polyene makes them susceptible to oxidative cleavage, yielding carbonyl products called apocarotenoids. This oxidation can be catalyzed by carotenoid cleavage dioxygenases or triggered nonenzymatically by reactive oxygen species. The group of plant apocarotenoids includes important phytohormones, such as abscisic acid and strigolactones, and signaling molecules, such as β-cyclocitral. Abscisic acid is a key regulator of plant's response to abiotic stress and is involved in different developmental processes, such as seed dormancy. Strigolactone is a main regulator of plant architecture and an important signaling molecule in the plant-rhizosphere communication. β-Cyclocitral, a volatile derived from β-carotene oxidation, mediates the response of cells to singlet oxygen stress. Besides these well-known examples, recent research unraveled novel apocarotenoid growth regulators and suggests the presence of yet unidentified ones. In this review, we describe the biosynthesis and biological functions of established regulatory apocarotenoids and touch on the recently identified anchorene and zaxinone, with emphasis on their role in plant growth, development, and stress response.
  • Apocarotenoids: Old and New Mediators of the Arbuscular Mycorrhizal Symbiosis.

    Fiorilli, Valentina; Wang, Jian You; Bonfante, Paola; Lanfranco, Luisa; Al-Babili, Salim (Frontiers in plant science, Frontiers Media SA, 2019-10-16) [Article]
    Plants utilize hormones and other small molecules to trigger and coordinate their growth and developmental processes, adapt and respond to environmental cues, and communicate with surrounding organisms. Some of these molecules originate from carotenoids that act as universal precursors of bioactive metabolites arising through oxidation of the carotenoid backbone. This metabolic conversion produces a large set of compounds known as apocarotenoids, which includes the plant hormones abscisic acid (ABA) and strigolactones (SLs) and different signaling molecules. An increasing body of evidence suggests a crucial role of previously identified and recently discovered carotenoid-derived metabolites in the communication with arbuscular mycorrhizal (AM) fungi and the establishment of the corresponding symbiosis, which is one of the most relevant plant-fungus mutualistic interactions in nature. In this review, we provide an update on the function of apocarotenoid hormones and regulatory metabolites in AM symbiosis, highlighting their effect on both partners.
  • Single-Molecule Förster Resonance Energy Transfer Methods for Real-Time Investigation of the Holliday Junction Resolution by GEN1.

    Sobhy, Mohamed Abdelmaboud; Bralic, Amer; Raducanu, Vlad-Stefan; Tehseen, Muhammad; Ouyang, Yujing; Takahashi, Masateru; Rashid, Fahad; Zaher, Manal; Hamdan, Samir (Journal of visualized experiments : JoVE, MyJove Corporation, 2019-10-15) [Article]
    Bulk methods measure the ensemble behavior of molecules, in which individual reaction rates of the underlying steps are averaged throughout the population. Single-molecule Förster resonance energy transfer (smFRET) provides a recording of the conformational changes taking place by individual molecules in real-time. Therefore, smFRET is powerful in measuring structural changes in the enzyme or substrate during binding and catalysis. This work presents a protocol for single-molecule imaging of the interaction of a four-way Holliday junction (HJ) and gap endonuclease I (GEN1), a cytosolic homologous recombination enzyme. Also presented are single-color and two-color alternating excitation (ALEX) smFRET experimental protocols to follow the resolution of the HJ by GEN1 in real-time. The kinetics of GEN1 dimerization are determined at the HJ, which has been suggested to play a key role in the resolution of the HJ and has remained elusive until now. The techniques described here can be widely applied to obtain valuable mechanistic insights of many enzyme-DNA systems.
  • A Method for 3D Reconstruction and Virtual Reality Analysis of Glial and Neuronal Cells.

    Cali, Corrado; Kare, Kalpana; Agus, Marco; Veloz Castillo, Maria Fernanda; Boges, Daniya; Hadwiger, Markus; Magistretti, Pierre J. (Journal of visualized experiments : JoVE, MyJove Corporation, 2019-10-15) [Article]
    Serial sectioning and subsequent high-resolution imaging of biological tissue using electron microscopy (EM) allow for the segmentation and reconstruction of high-resolution imaged stacks to reveal ultrastructural patterns that could not be resolved using 2D images. Indeed, the latter might lead to a misinterpretation of morphologies, like in the case of mitochondria; the use of 3D models is, therefore, more and more common and applied to the formulation of morphology-based functional hypotheses. To date, the use of 3D models generated from light or electron image stacks makes qualitative, visual assessments, as well as quantification, more convenient to be performed directly in 3D. As these models are often extremely complex, a virtual reality environment is also important to be set up to overcome occlusion and to take full advantage of the 3D structure. Here, a step-by-step guide from image segmentation to reconstruction and analysis is described in detail.
  • More efficient time integration for Fourier pseudo-spectral DNS of incompressible turbulence

    Ketcheson, David I.; Mortensen, Mikael; Parsani, Matteo; Schilling, Nathanael (International Journal for Numerical Methods in Fluids, Wiley, 2019-10-15) [Article]
    Time integration of Fourier pseudo-spectral DNS is usually performed using the classical fourth-order accurate Runge–Kutta method, or other methods of second or third order, with a fixed step size. We investigate the use of higher-order Runge–Kutta pairs and automatic step size control based on local error estimation. We find that the fifth-order accurate Runge–Kutta pair of Bogacki & Shampine gives much greater accuracy at a significantly reduced computational cost. Specifically, we demonstrate speedups of 2x-10x for the same accuracy. Numerical tests (including the Taylor–Green vortex, Rayleigh–Taylor instability, and homogeneous isotropic turbulence) confirm the reliability and efficiency of the method. We also show that adaptive time stepping provides a significant computational advantage for some problems (like the development of a Rayleigh–Taylor instability) without compromising accuracy.
  • Low-Power Hardware Implementation of a Support Vector Machine Training and Classification for Neural Seizure Detection

    Elhosary, Heba; Zakhari, Michael H.; ElGammal, Mohamed A.; Elghany, Mohamed Abd; Salama, Khaled N.; Mostafa, Hassan (IEEE Transactions on Biomedical Circuits and Systems, IEEE, 2019-10-14) [Article]
    In this paper, a low power support vector machine (SVM) training, feature extraction, and classification algorithm are hardware implemented in a neural seizure detection application. The training algorithm used is the sequential minimal optimization (SMO) algorithm. The system is implemented on different platforms: such as field programmable gate array (FPGA), Xilinx Virtex-7 and application specific integrated circuit (ASIC) using hardware-calibrated UMC 65nm CMOS technology. The implemented training hardware is introduced as an accelerator intellectual property (IP), especially in the case of large number of training sets, such as neural seizure detection. Feature extraction and classification blocks are implemented to achieve the best trade-off between sensitivity and power consumption. The proposed seizure detection system achieves a sensitivity around 96.77% when tested with the implemented linear kernel classifier. A power consumption evaluation is performed on both the ASIC and FPGA platforms showing that the ASIC power consumption is improved by a factor of 2X when compared with the FPGA counterpart.
  • Arc-discharge synthesis of nitrogen-doped C embedded TiCN nanocubes with tunable dielectric/magnetic properties for electromagnetic absorbing applications.

    Zhou, Yuanliang; Wang, Ning; Qu, Xinghao; Huang, Feirong; Duan, Yuping; Zhang, Xuefeng; Dong, Xinglong; Zhang, Zhidong (Nanoscale, Royal Society of Chemistry (RSC), 2019-10-12) [Article]
    The development of novel composites consisting of ceramic and C materials to alleviate increasingly serious electromagnetic radiation is of great significance in the microwave absorption (MA) field, considering their superior anti-oxidation/corrosion performances and good mechanical strength as well as adjustable dielectric loss capabilities. However, it is still a great challenge to broaden their effective absorption bandwidth (reflection loss value ≤ -10 dB) and strengthen the absorption intensity simultaneously, which is mostly attributed to the unreliable impedance matching degree at the absorber/air interface. Herein, a feasible strategy is adopted to synthesize TiCN@N-doped C nanocubes, whose low graphitization degree provides desirable impedance matching conditions. In the meantime, masses of core/shell hetero interfaces ensure strong microwave absorption capability. Experimental results reveal that the optimal effective absorption bandwidth of the prepared TiCN@N-doped C nanocubes can reach up to 5.44 GHz with a thickness of 1.88 mm. Our work demonstrates that the TiCN@N-doped C nanocubes have potential for electromagnetic absorbing applications.
  • Comment on “A periodic grain consolidation model of porous media” [Phys. Fluids A 1, 38 (1989)]

    Khirevich, Siarhei; Patzek, Tadeusz (Physics of Fluids, AIP Publishing, 2019-10-11) [Article]
    In this document, we correct the friction coefficient values presented in Table III in a study by Larson and Higdon [“A periodic grain consolidation model of porous media,” Phys. Fluids A 1, 38 (1989)]. The authors addressed the problem of Stokes flow through periodic arrays of (non)overlapping spheres and determined the friction coefficients. It appears that the volume of the overlapping region of spheres was not taken into account, which affected the total solid concentration and systematically biased the corresponding friction coefficient values. We correct the sphere concentration and friction coefficients, and validate our approach with lattice-Boltzmann simulations. The suggested correction is valid in the case of overlapping spheres only, when the volume of the overlapping region is positive.
  • Plasmodium kinesin-8X associates with mitotic spindles and is essential for oocyst development during parasite proliferation and transmission.

    Zeeshan, Mohammad; Shilliday, Fiona; Liu, Tianyang; Abel, Steven; Mourier, Tobias; Ferguson, David J P; Rea, Edward; Stanway, Rebecca R; Roques, Magali; Williams, Desiree; Daniel, Emilie; Brady, Declan; Roberts, Anthony J; Holder, Anthony A.; Pain, Arnab; Le Roch, Karine G; Moores, Carolyn A; Tewari, Rita (PLoS pathogens, Public Library of Science (PLoS), 2019-10-11) [Article]
    Kinesin-8 proteins are microtubule motors that are often involved in regulation of mitotic spindle length and chromosome alignment. They move towards the plus ends of spindle microtubules and regulate the dynamics of these ends due, at least in some species, to their microtubule depolymerization activity. Plasmodium spp. exhibit an atypical endomitotic cell division in which chromosome condensation and spindle dynamics in the different proliferative stages are not well understood. Genome-wide shared orthology analysis of Plasmodium spp. revealed the presence of two kinesin-8 motor proteins, kinesin-8X and kinesin-8B. Here we studied the biochemical properties of kinesin-8X and its role in parasite proliferation. In vitro, kinesin-8X has motility and depolymerization activities like other kinesin-8 motors. To understand the role of Plasmodium kinesin-8X in cell division, we used fluorescence-tagging and live cell imaging to define its location, and gene targeting to analyse its function, during all proliferative stages of the rodent malaria parasite P. berghei life cycle. The results revealed a spatio-temporal involvement of kinesin-8X in spindle dynamics and an association with both mitotic and meiotic spindles and the putative microtubule organising centre (MTOC). Deletion of the kinesin-8X gene revealed a defect in oocyst development, confirmed by ultrastructural studies, suggesting that this protein is required for oocyst development and sporogony. Transcriptome analysis of Δkinesin-8X gametocytes revealed modulated expression of genes involved mainly in microtubule-based processes, chromosome organisation and the regulation of gene expression, supporting a role for kinesin-8X in cell division. Kinesin-8X is thus required for parasite proliferation within the mosquito and for transmission to the vertebrate host.
  • Adhesion to coral surface as a potential sink for marine microplastics.

    Martin, Cecilia; Corona, Elena; Mahadik, Gauri A; Duarte, Carlos M. (Environmental pollution (Barking, Essex : 1987), Elsevier BV, 2019-10-11) [Article]
    Only 1% of plastic entering the ocean is found floating on its surface, with high loads in ocean accumulation zones and semi-enclosed seas, except for the Red Sea, which supports one of the lowest floating plastic loads worldwide. Given the extension of reefs in the Red Sea, we hypothesize a major role of scleractinian corals as sinks, through suspension-feeding, and assessed microplastic removal rates by three Red Sea coral species. Experimental evidence showed removal rates ranging from 0.25 × 10-3 to 14.8 × 10-3 microplastic particles polyp-1 hour-1, among species. However, this was only 2.2 ± 0.6% of the total removal rate, with passive removal through adhesion to the coral surface being 40 times higher than active removal through suspension-feeding. These results point at adhesion of plastic to coral reef structures as a major sink for microplastics suspended in the water column after sinking, helping explain low concentrations in Red Sea surface waters.
  • Stochastic Geometry-based analysis of Airborne Base Stations with Laser-powered UAVs

    Lahmeri, Mohamed-Amine; Kishk, Mustafa Abdelsalam; Alouini, Mohamed-Slim (IEEE Communications Letters, IEEE, 2019-10-11) [Article]
    One of the most promising solutions to the problem of limited flight time of unmanned aerial vehicles (UAVs), is providing the UAVs with power through laser beams emitted from Laser Beam Directors (LBDs) deployed on the ground. In this letter, we study the performance of a laser-powered UAV-enabled communication system using tools from stochastic geometry. We first derive the energy coverage probability, which is defined as the probability of the UAV receiving enough energy to ensure successful operation (hovering and communication). Our results show that to ensure energy coverage, the distance between the UAV and its dedicated LBD must be below a certain threshold, for which we derive an expression as a function of the system parameters. Considering simultaneous information and power transmission through the laser beam using power splitting technique, we also derive the joint energy and the Signal-to-noise Ratio (SNR) coverage probability. The analytical and simulation results reveal some interesting insights. For instance, our results show that we need at least 6 LBDs/10km2 to ensure a reliable performance in terms of energy coverage probability.
  • Assessing the Range of Validity of Current Tube Models through Analysis of a Comprehensive Set of Star–Linear 1,4-Polybutadiene Polymer Blends

    Hall, Ryan; Desai, Priyanka S.; Kang, Beom-Goo; Huang, Qifan; Lee, Sanghoon; Chang, Taihyun; Venerus, David C.; Mays, Jimmy; Ntetsikas, Konstantinos; Polymeropoulos, George; Hadjichristidis, Nikolaos; Larson, Ronald G. (Macromolecules, American Chemical Society (ACS), 2019-10-10) [Article]
    We blend newly synthesized nearly monodisperse four-arm star 1,4-polybutadienes with various well-entangled linear polymers, confirming the conclusions in Desai et al. [ Macromolecules201649 (13)49644977] that advanced tube models, namely, the hierarchical 3.0 and branch-on-branch models [Wang, Z.; J. Rheol.201054 (2)223260], fail to predict the linear rheological data when the pure linear polymers have shorter relaxation times, but within 3–4 orders of magnitude of the star polymer. However, when the linear polymer has a longer relaxation time than the star, our new work, surprisingly, finds that non-monotonic dependence of terminal relaxation behavior on composition is both observed experimentally and captured by the models. Combined with previous data from the literature, we present results from over 50 1,4-polybutadiene star–linear blends, suitable for thorough testing of rheological models of entangled polymers.
  • An explicit marching-on-in-time scheme for solving the time domain Kirchhoff integral equation.

    Chen, Rui; Sayed, Sadeed B; Al-Harthi, Noha A.; Keyes, David E.; Bagci, Hakan (The Journal of the Acoustical Society of America, Acoustical Society of America (ASA), 2019-10-09) [Article]
    A fully explicit marching-on-in-time (MOT) scheme for solving the time domain Kirchhoff (surface) integral equation to analyze transient acoustic scattering from rigid objects is presented. A higher-order Nyström method and a PE(CE)m-type ordinary differential equation integrator are used for spatial discretization and time marching, respectively. The resulting MOT scheme uses the same time step size as its implicit counterpart (which also uses Nyström method in space) without sacrificing from the accuracy and stability of the solution. Numerical results demonstrate the accuracy, efficiency, and applicability of the proposed explicit MOT solver.
  • Remotely sensing phytoplankton size structure in the Red Sea

    Gittings, John; Brewin, Robert J.W.; Raitsos, Dionysios E.; Kheireddine, Malika; Ouhssain, Mustapha; Jones, Burton; Hoteit, Ibrahim (Remote Sensing of Environment, Elsevier BV, 2019-10-09) [Article]
    Phytoplankton size structure impacts ocean food-web dynamics and biogeochemical cycling, and is thus an important ecological indicator that can be utilised to quantitatively evaluate the state of marine ecosystems. Potential alterations to size structure are predicted to occur in tropical regions under future scenarios of climate change. Therefore, there is an increasing requirement for the synoptic monitoring of phytoplankton size structure in marine systems. The Red Sea remains a comparatively unexplored tropical marine ecosystem, particularly with regards to its large-scale biological dynamics. Using an in situ pigment dataset acquired in the Red Sea, we parameterise a two-component, abundance-based phytoplankton size model and apply it to remotely-sensed observations of chlorophyll-a (Chl-a) concentration, to infer Chl-a in two size classes of phytoplankton, small cells <2 μm in size (picophytoplankton) and large cells >2 μm in size. Satellite-derived estimates of phytoplankton size structure are in good agreement with corresponding in situ measurements and also capture the spatial variability related to regional mesoscale dynamics. Our analysis reveals that, for the estimation of Chl-a in the two size classes, the model performs comparably or in some cases better, to validations in other oceanic regions. Our model parameterisation will be useful for future studies on the seasonal and interannual variability of phytoplankton size classes in the Red Sea, which may ultimately be relevant for understanding trophic linkages between phytoplankton size structure and fisheries, and the development of marine management strategies.
  • Novel algorithms for efficient subsequence searching and mapping in nanopore raw signals towards targeted sequencing.

    Han, Renmin; wang, sheng; Gao, Xin (Bioinformatics (Oxford, England), Oxford University Press (OUP), 2019-10-09) [Article]
    MOTIVATION:Genome diagnostics have gradually become a prevailing routine for human healthcare. With the advances in understanding the causal genes for many human diseases, targeted sequencing provides a rapid, cost-efficient and focused option for clinical applications, such as SNP detection and haplotype classification, in a specific genomic region. Although nanopore sequencing offers a perfect tool for targeted sequencing because of its mobility, PCR-freeness, and long read properties, it poses a challenging computational problem of how to efficiently and accurately search and map genomic subsequences of interest in a pool of nanopore reads (or raw signals). Due to its relatively low sequencing accuracy, there is no reliable solution to this problem, especially at low sequencing coverage. RESULTS:Here, we propose a brand new signal-based subsequence inquiry pipeline as well as two novel algorithms to tackle this problem. The proposed algorithms follow the principle of subsequence dynamic time warping and directly operate on the electrical current signals, without loss of information in base-calling. Therefore, the proposed algorithms can serve as a tool for sequence inquiry in targeted sequencing. Two novel criteria are offered for the consequent signal quality analysis and data classification. Comprehensive experiments on real-world nanopore datasets show the efficiency and effectiveness of the proposed algorithms. We further demonstrate the potential applications of the proposed algorithms in two typical tasks in nanopore-based targeted sequencing: SNP detection under low sequencing coverage, and haplotype classification under low sequencing accuracy. AVAILABILITY:The project is accessible at https://github.com/icthrm/cwSDTWnano.git, and the presented bench data is available upon request.
  • An explicit marching-on-in-time scheme for solving the time domain Kirchhoff integral equation.

    Chen, Rui; Sayed, Sadeed B; Al-Harthi, Noha A.; Keyes, David E.; Bagci, Hakan (The Journal of the Acoustical Society of America, Acoustical Society of America (ASA), 2019-10-09) [Article]
    A fully explicit marching-on-in-time (MOT) scheme for solving the time domain Kirchhoff (surface) integral equation to analyze transient acoustic scattering from rigid objects is presented. A higher-order Nyström method and a PE(CE)m-type ordinary differential equation integrator are used for spatial discretization and time marching, respectively. The resulting MOT scheme uses the same time step size as its implicit counterpart (which also uses Nyström method in space) without sacrificing from the accuracy and stability of the solution. Numerical results demonstrate the accuracy, efficiency, and applicability of the proposed explicit MOT solver.
  • New Insight on the Role of Electrolyte Additives in Rechargeable Lithium Ion Batteries

    Ming, Jun; Cao, Zhen; Wu, Yingqiang; Wahyudi, Wandi; Wang, Wenxi; Guo, Xianrong; Cavallo, Luigi; Hwang, Jang-Yeon; Shamim, Atif; Li, Lain-Jong; Sun, Yang-Kook; Alshareef, Husam N. (ACS Energy Letters, American Chemical Society (ACS), 2019-10-08) [Article]
    Solid electrolyte interphase (SEI)-forming agents such as vinylene carbonate, sulfone, and cyclic sulfate are commonly believed to be film-forming additives in lithium-ion batteries that help to enhance graphite anode stability. However, we find that the film-forming effect and the resultant SEI may not be the only reasons for the enhanced graphite stability. This is because the as-formed SEI cannot inhibit Li+–solvent co-intercalation once the additive is removed from the electrolyte. Instead, we show that the Li+ solvation structure, which is modified by these additives, plays a critical role in achieving reversible Li+ (de)intercalation within graphite. This discovery is confirmed in both carbonate and ether-based electrolytes. We show that the problem of graphite exfoliation caused by Li+–solvent co-intercalation can be mitigated by adding ethene sulfate to tune the Li+ coordination structure. This work brings new insight into the role of additives in electrolytes, expanding the prevailing thinking over the past 2 decades. In addition, this finding can guide the design of more versatile electrolytes for advanced rechargeable metal-ion batteries.
  • Ultraviolet-to-blue color-converting scintillating-fibers photoreceiver for 375-nm laser-based underwater wireless optical communication

    Kang, Chun Hong; Trichili, Abderrahmen; Alkhazragi, Omar; Zhang, Huafan; Subedi, Ram Chandra; Guo, Yujian; Mitra, Somak; Shen, Chao; Roqan, Iman S.; Ng, Tien Khee; Alouini, Mohamed-Slim; Ooi, Boon S. (Optics Express, The Optical Society, 2019-10-08) [Article]
    Underwater wireless optical communication (UWOC) can offer reliable and secure connectivity for enabling future internet-of-underwater-things (IoUT), owing to its unlicensed spectrum and high transmission speed. However, a critical bottleneck lies in the strict requirement of pointing, acquisition, and tracking (PAT), for effective recovery of modulated optical signals at the receiver end. A large-area, high bandwidth, and wide-angle-of-view photoreceiver is therefore crucial for establishing a high-speed yet reliable communication link under non-directional pointing in a turbulent underwater environment. In this work, we demonstrated a large-area, of up to a few tens of cm2, photoreceiver design based on ultraviolet(UV)-to-blue color-converting plastic scintillating fibers, and yet offering high 3-dB bandwidth of up to 86.13 MHz. Tapping on the large modulation bandwidth, we demonstrated a high data rate of 250 Mbps at bit-error ratio (BER) of 2.2 × 10−3 using non-return-to-zero on-off keying (NRZ-OOK) pseudorandom binary sequence (PRBS) 210-1 data stream, a 375-nm laser-based communication link over the 1.15-m water channel. This proof-of-concept demonstration opens the pathway for revolutionizing the photodetection scheme in UWOC, and for non-line-of-sight (NLOS) free-space optical communication.

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