• 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.
    • End-to-end Performance Analysis of Delay-sensitive Multi-relay Networks

      Makki, Behrooz; Alouini, Mohamed-Slim (IEEE Communications Letters, IEEE, 2019-10-07) [Article]
      We study the end-to-end (E2E) performance of multi-relay networks in delay-constrained applications. The results are presented for both decode-and-forward (DF) and AF (A: amplify) relaying schemes. We use some fundamental results on the achievable rates of finite-length codes to analyze the system performance in the cases with short packets. Taking the message decoding delays and different numbers of hops into account, we derive closed-form expressions for the E2E packet transmission delay, the E2E error probability as well as the E2E throughput. Moreover, for different message decoding delays, we determine the appropriate codeword length and the relay power such that the same E2E error probability and packet transmission delay are achieved in the AF-and DF-relay networks. As we show, for different codeword lengths and numbers of hops, the E2E performance of multi-relay networks are affected by the message decoding delay of the nodes considerably.
    • Barcoding Amino Acids for Mutation Screening in Amyloid Beta Peptides

      Hoang, Phuong Mai; Khashab, Niveen M. (Small Methods, Wiley, 2019-10-04) [Article]
      Amino acid (AA) substitutions are directly correlated with specific pathologies such as Alzheimer's disease, making their rapid screening and detection critical to treatment and scientific study. A proof-of-concept implementation of the label-free and noninvasive Raman spectroscopy technique for the detection of AA substitutions in primary peptide fragments is demonstrated. By encoding the Raman “fingerprint” of individual AAs into binary formats called optical identification tags (OITs), a library of identifiers is created, which can then be used for detecting mutations. When the recorded Raman signal is enhanced by using surface-enhanced Raman scattering substrate, the mutation screening strategy can detect a single point missense mutation in an 11-AA peptide fragment of amyloid beta Aβ(25–35) and a frameshift mutation in a 42-AA fragment Aβ(1–42) down to picomolar concentrations. The combination of high sensitivity and simple operation makes the use of OITs a promising approach for high-throughput automated screening.
    • Richtmyer-Meshkov instability of an unperturbed interface subjected to a diffracted convergent shock

      Zou, Liyong; Al-Marouf, Mahamad; Cheng, W.; Samtaney, Ravi; Ding, Juchun; Luo, Xisheng (Journal of Fluid Mechanics, Cambridge University Press (CUP), 2019-01-01) [Article]
      The Richtmyer-Meshkov (RM) instability is numerically investigated on an unperturbed interface subjected to a diffracted convergent shock created by diffracting an initially cylindrical shock over a rigid cylinder. Four gas interfaces are considered with Atwood number ranging from 0.18 to 0.67. Results indicate that the diffracted convergent shock increases its strength gradually and reduces its amplitude quickly when it propagates towards the convergence centre. After the strike of the diffracted convergent shock, the initially unperturbed interface deforms with a bulge structure at the centre and two interface steps at both sides, which can be ascribed to the non-uniformity of the pressure distribution behind the diffracted convergent shock. With the decrease of Atwood number, the bulge structure becomes more pronounced. Quantitatively, the interface amplitude experiences a fast but short growing stage and then enters a linear stage. A good collapse of the dimensionless amplitude is found for all cases, which indicates a weak dependence of the growth rate on Atwood number in the deformed shock-induced RM instability. Then the impulsive theory is modified by eliminating the Atwood number and considering the geometry convergence, which well predicts the amplitude growth for the deformed shock-induced RM instability. Finally, the underlying mechanism is decoupled into three parts, and it is found that both the impulsive pressure perturbation and the geometry convergence promote the growth of interface perturbation while the continuous pressure perturbation inhibits the growth. As the Atwood number decreases, the impulsive perturbation plays an increasingly important role, which suggests that the impulsive perturbation dominates the deformed shock-induced RM instability at the linear stage.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • Antioxidant enzymes expression in lymphocytes of patients undergoing carotid endarterectomy

      Obradovic, Milan; Zafirovic, Sonja; Essack, Magbubah; Dimitrov, Jelena; Zivkovic, Lada; Spremo-Potparevic, Biljana; Radak, Djordje; Bajic, Vladimir B.; Isenovic, Esma R. (Medical Hypotheses, Elsevier BV, 2019-10-03) [Article]
      To remedy carotid artery stenosis and prevent stroke surgical intervention is commonly used, and the gold standard being carotid endarterectomy (CEA). During CEA cerebrovascular hemoglobin oxygen saturation decreases and when this decrease reaches critical levels it leads to cerebral hypoxia that causes neuronal damage. One of the proposed mechanism that affects changes during CEA and contribute to acute brain ischemia (ABI) is oxidative stress. The increased production of reactive oxygen species and reactive nitrogen species during ABI may cause an unregulated inflammatory response and further lead to structural and functional injury of neurons. Antioxidant activity are involved in the protection against neuronal damage after cerebral ischemia. We hypothesized that neuronal injury and poor outcomes in patients undergoing CEA may be results of oxidative stress that disturbed function of antioxidant enzymes and contributed to the DNA damage in lymphocytes.
    • 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.
    • MAPbI3 Single Crystals Free from Hole-Trapping Centers for Enhanced Photodetectivity

      Yang, Chen; El Demellawi, Jehad K.; Yin, Jun; Velusamy, Dhinesh; Emwas, Abdul-Hamid M.; El-Zohry, Ahmed M.; Gereige, Issam; AlSaggaf, Ahmed; Bakr, Osman; Alshareef, Husam N.; Mohammed, Omar F. (ACS Energy Letters, American Chemical Society (ACS), 2019-10-01) [Article]
      Perovskite single crystals (PSCs) are considered the next breakthrough in optoelectronics research due to their free-grain boundary and much lower density of trap states compared to those of their polycrystalline counterparts. However, the inevitable formation of triiodide-based intrinsic defects during high-temperature crystal growth is one of the major challenges impeding the further development of optoelectronic devices based on PSCs. Here, we not only identified the existence of these triiodide ions as hole-trapping centers and their tremendous negative impact on the performance of PSCs, but more importantly, we used a reduction treatment to prevent their formation during crystal growth. The removal of such defect centers resulted in much higher charge carrier mobility and longer carrier lifetime than the untreated counterparts, leading to enhanced photodetection properties. The I3–-free MAPbI3 single crystal (MSC) devices consistently generated a more than 100 times higher photocurrent than that generated by I3–-rich devices under the same light intensity.
    • Institutional Repositories Services and Impact

      Baessa, Mohamed A. (Electronic Resources and Libraries (ERL), Electronic Resources and Libraries (ERL), 2018-10-16) [Article]
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.