Recent Submissions

  • 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.
  • 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.
  • Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs.

    Alam, Tanvir; Alazmi, Meshari; Naser, Rayan Mohammad Mahmoud; Huser, Franceline; Momin, Afaque Ahmad Imtiyaz; Astro, Veronica; Hong, Seungbeom; Walkiewicz, Katarzyna Wiktoria; Canlas, Christian G; Huser, Raphaël; Ali, Amal J.; Merzaban, Jasmeen; Adamo, Antonio; Jaremko, Mariusz; Jaremko, Lukasz; Bajic, Vladimir B.; Gao, Xin; Arold, Stefan T. (Bioinformatics (Oxford, England), Oxford University Press (OUP), 2019-10-05) [Article]
    MOTIVATION:Leucine-aspartic acid (LD) motifs are short linear interaction motifs (SLiMs) that link paxillin family proteins to factors controlling cell adhesion, motility and survival. The existence and importance of LD motifs beyond the paxillin family is poorly understood. RESULTS:To enable a proteome-wide assessment of LD motifs, we developed an active-learning based framework (LDmotif finder; LDMF) that iteratively integrates computational predictions with experimental validation. Our analysis of the human proteome revealed a dozen new proteins containing LD motifs. We found that LD motif signalling evolved in unicellular eukaryotes more than 800 Myr ago, with paxillin and vinculin as core constituents, and nuclear export signal (NES) as a likely source of de novo LD motifs. We show that LD motif proteins form a functionally homogenous group, all being involved in cell morphogenesis and adhesion. This functional focus is recapitulated in cells by GFP-fused LD motifs, suggesting that it is intrinsic to the LD motif sequence, possibly through their effect on binding partners. Our approach elucidated the origin and dynamic adaptations of an ancestral SLiM, and can serve as a guide for the identification of other SLiMs for which only few representatives are known. AVAILABILITY:LDMF is freely available online at www.cbrc.kaust.edu.sa/ldmf; Source code is available at https://github.com/tanviralambd/LD/. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.
  • Optimal 3D trajectory planning for AUVs using ocean general circulation models

    Albarakati, Sultan Saud; Lima, Ricardo; Giraldi, Loic; Hoteit, Ibrahim; Knio, Omar (Ocean Engineering, Elsevier Ltd, 2019-09-15) [Article]
    In this paper, we consider the autonomous underwater vehicle (AUV) trajectory planning problem under the influence of a realistic 3D current as simulated by an ocean general circulation model (OGCM). Attention is focused on the case of a deterministic steady OGCM field, which is used to specify data for both the ocean current and for ocean bathymetry. A general framework for optimal trajectory planning is developed for this setting, accounting for the 3D ocean current and for static obstacle avoidance constraints. A nonlinear programming approach is used for this purpose, which leads to a low complexity discrete-time model that can be efficiently solved. To demonstrate the efficiency of the model, we consider the optimal time trajectory planning of an AUV operating in the Red Sea and Gulf of Aden, with velocity, and bathymetric data provided by an eddy-resolving MITgcm. Different optimal-time trajectory planning scenarios are implemented to demonstrate the capabilities of the model to identify trajectories that adapt to favorable and adverse currents and to avoid obstacles corresponding to a complex bathymetry environment. The simulations are also used to evaluate the performance of the proposed approach, and to illustrate the application of advanced visualization tools to interpret the model predictions.
  • Mining biosynthetic gene clusters in Virgibacillus genomes.

    Othoum, Ghofran K.; Bougouffa, Salim; Bokhari, Ameerah; Lafi, Feras Fawzi; Gojobori, Takashi; Hirt, Heribert; Mijakovic, Ivan; Bajic, Vladimir B.; Essack, Magbubah (BMC genomics, Springer Science and Business Media LLC, 2019-09-05) [Article]
    BACKGROUND:Biosynthetic gene clusters produce a wide range of metabolites with activities that are of interest to the pharmaceutical industry. Specific interest is shown towards those metabolites that exhibit antimicrobial activities against multidrug-resistant bacteria that have become a global health threat. Genera of the phylum Firmicutes are frequently identified as sources of such metabolites, but the biosynthetic potential of its Virgibacillus genus is not known. Here, we used comparative genomic analysis to determine whether Virgibacillus strains isolated from the Red Sea mangrove mud in Rabigh Harbor Lagoon, Saudi Arabia, may be an attractive source of such novel antimicrobial agents. RESULTS:A comparative genomics analysis based on Virgibacillus dokdonensis Bac330, Virgibacillus sp. Bac332 and Virgibacillus halodenitrificans Bac324 (isolated from the Red Sea) and six other previously reported Virgibacillus strains was performed. Orthology analysis was used to determine the core genomes as well as the accessory genome of the nine Virgibacillus strains. The analysis shows that the Red Sea strain Virgibacillus sp. Bac332 has the highest number of unique genes and genomic islands compared to other genomes included in this study. Focusing on biosynthetic gene clusters, we show how marine isolates, including those from the Red Sea, are more enriched with nonribosomal peptides compared to the other Virgibacillus species. We also found that most nonribosomal peptide synthases identified in the Virgibacillus strains are part of genomic regions that are potentially horizontally transferred. CONCLUSIONS:The Red Sea Virgibacillus strains have a large number of biosynthetic genes in clusters that are not assigned to known products, indicating significant potential for the discovery of novel bioactive compounds. Also, having more modular synthetase units suggests that these strains are good candidates for experimental characterization of previously identified bioactive compounds as well. Future efforts will be directed towards establishing the properties of the potentially novel compounds encoded by the Red Sea specific trans-AT PKS/NRPS cluster and the type III PKS/NRPS cluster.
  • Redox control of vascular biology.

    Obradovic, Milan; Essack, Magbubah; Zafirovic, Sonja; Sudar-Milovanovic, Emina; Bajic, Vladan P; Van Neste, Christophe Marc; Trpkovic, Andreja; Stanimirovic, Julijana; Bajic, Vladimir B.; Isenovic, Esma R (BioFactors (Oxford, England), Wiley, 2019-09-05) [Article]
    Redox control is lost when the antioxidant defense system cannot remove abnormally high concentrations of signaling molecules, such as reactive oxygen species (ROS). Chronically elevated levels of ROS cause oxidative stress that may eventually lead to cancer and cardiovascular and neurodegenerative diseases. In this review, we focus on redox effects in the vascular system. We pay close attention to the subcompartments of the vascular system (endothelium, smooth muscle cell layer) and give an overview of how redox changes influence those different compartments. We also review the core aspects of redox biology, cardiovascular physiology, and pathophysiology. Moreover, the topic-specific knowledgebase DES-RedoxVasc was used to develop two case studies, one focused on endothelial cells and the other on the vascular smooth muscle cells, as a starting point to possibly extend our knowledge of redox control in vascular biology.
  • Regularization of vertical-cavity surface-emitting laser emission by periodic non-Hermitian potentials

    Ahmed, Waqas Waseem; Herrero, Ramon; Botey, Muriel; Wu, Ying; Staliunas, Kestutis (Optics Letters, OSA - The Optical Societycustserv@osa.org, 2019-08-15) [Article]
    We propose a novel physical mechanism based on periodic non-Hermitian potentials to efficiently control the complex spatial dynamics of broad-area lasers, particularly in vertical-cavity surface-emitting lasers (VCSELs), achieving a stable emission of maximum brightness. A radially dephased periodic refractive index and gain-loss modulations accumulate the generated light from the entire active layer and concentrate it around the structure axis to emit narrow, bright beams. The effect is due to asymmetric inward radial coupling between transverse wave vectors for particular phase differences of the refractive index and gain-loss modulations. Light is confined into a central beam with large intensity, opening the path to design compact, bright, and efficient broad-area light sources. We perform a comprehensive analysis to explore the maximum central intensity enhancement and concentration regimes. This Letter reveals that the optimum schemes are those holding unidirectional inward coupling, but not fulfilling a perfect local PT-symmetry.
  • Subwavelength acoustic monopole source emission enhancement through dual gratings

    Mei, Jun; Wu, Ying (Scientific Reports, Springer Science and Business Media LLC, 2019-08-12) [Article]
    Acoustic source emission rate is generally low at low frequencies. In this work, we propose a simple design of ‘LEGO’-type acoustic metamaterial that can significantly enhance the low frequency emission rate of an acoustic monopole source. Such enhancement is resulted from the coupling between resonances of a cavity and a dual grating comprised of two concentric layers of periodically distributed narrow slits. We develop an effective medium model to characterize the enhancement. Because of its simple structure, the metamaterial is easy to fabricate and thus facilitates the applications in various domains such as oil exploration.
  • Corner states in a second-order acoustic topological insulator as bound states in the continuum

    Chen, Zeguo; Xu, Changqing; Al Jahdali, Rasha; Mei, Jun; Wu, Ying (Physical Review B, American Physical Societyrevtex@aps.org, 2019-08-09) [Article]
    A second-order topological insulator is designed on a platform of a two-dimensional (2D) square lattice with all coupling coefficients having the same sign. Simulated results show the existence of two types of nontrivial corner states in this system, with one type being identified as bound states in the continuum (BIC). The non-BIC corner states are also found by surrounding a nontrivial sample by a trivial one, and interestingly, these perfectly confined corner states can be gradually delocalized and merge into edge states by tuning the intersystem coupling coefficient. Both BIC and non-BIC corner states originate from bulk dipole moments rather than quantized quadrupole moments, with the corresponding topological invariant being the 2D Zak phase. Full wave simulations based on realistic acoustic waveguide structures are demonstrated. Our proposal provides an experimentally feasible platform for the study of the interplay between BIC and a high-order topological insulator, and the evolution from corner states to edge states.
  • A rezoning-free CESE Scheme for solving the Compressible Euler Equations on Moving Unstructured Meshes

    Shen, Hua; Parsani, Matteo (Journal of Computational Physics, Elsevier BV, 2019-08-02) [Article]
    We construct a space-time conservation element and solution element (CESE) scheme for solving the compressible Euler equations on moving meshes (CESE-MM) which allow an arbitrary motion for each of the mesh points. The scheme is a direct extension of a purely Eulerian CESE scheme that was previously implemented on hybrid unstructured meshes (Shen et al., J. Comput. Phys., 2015). It adopts a staggered mesh in space and time such that the physical variables are continuous across the interfaces of the adjacent space-time control volumes and, therefore, a Riemann solver is not required to calculate interface fluxes or the node velocities. Moreover, the staggered mesh can significantly alleviate mesh tangles so that the time step can be kept at an acceptable level without using any rezoning operation. The discretization of the integral space-time conservation law is completely based on the physical space-time control volume, thereby satisfying the physical and geometrical conservation laws. Plenty of numerical examples are carried out to validate the accuracy and robustness of the CESE-MM scheme.
  • Conservative and entropy stable solid wall boundary conditions for the compressible Navier–Stokes equations: Adiabatic wall and heat entropy transfer

    Dalcin, Lisandro; Rojas, Diego B.; Zampini, Stefano; Del Rey Fernández, David C.; Carpenter, Mark H.; Parsani, Matteo (Journal of Computational Physics, Elsevier BV, 2019-08-01) [Article]
    We present a novel technique for the imposition of non-linear entropy conservative and entropy stable solid wall boundary conditions for the compressible Navier–Stokes equations in the presence of an adiabatic wall, or a wall with a prescribed heat entropy flow. The procedure relies on the formalism and mimetic properties of diagonal-norm, summation-by-parts and simultaneous-approximation-term operators, and is a generalization of previous works on discontinuous interface coupling [1] and solid wall boundary conditions [2]. Using the method of lines, a semi-discrete entropy estimate for the entire domain is obtained when the proposed numerical imposition of boundary conditions are coupled with an entropy-conservative or entropy-stable discrete interior operator. The resulting estimate mimics the global entropy estimate obtained at the continuous level. The boundary data at the wall are weakly imposed using a penalty flux approach and a simultaneous-approximation-term technique for both the conservative variables and the gradient of the entropy variables. Discontinuous spectral collocation operators (mass lumped nodal discontinuous Galerkin operators), on high-order unstructured grids, are used for the purpose of demonstrating the robustness and efficacy of the new procedure for weakly enforcing boundary conditions. Numerical simulations confirm the non-linear stability of the proposed technique, with applications to three-dimensional subsonic and supersonic flows. The procedure described is compatible with any diagonal-norm summation-by-parts spatial operator, including finite element, finite difference, finite volume, discontinuous Galerkin, and flux reconstruction schemes.
  • Metagenomic Methods: From Seawater to the Database

    Reza, Md. Shaheed; Kobiyama, Atsushi; Rashid, Jonaira; Yamada, Yuichiro; Ikeda, Yuri; Ikeda, Daisuke; Mizusawa, Nanami; Yanagisawa, Saki; Ikeo, Kazuho; Sato, Shigeru; Ogata, Takehiko; Kudo, Toshiaki; Kaga, Shinnosuke; Watanabe, Shiho; Naiki, Kimiaki; Kaga, Yoshimasa; Segawa, Satoshi; Mineta, Katsuhiko; Bajic, Vladimir B.; Gojobori, Takashi; Watabe, Shugo (Springer Singapore, 2019-07-24) [Book Chapter]
    In this article, methods or techniques of metagenomics including targeted 16S/18S rRNA analyses and shotgun sequencing will be discussed. It is sometimes difficult, especially for beginners, to follow the manufacturer’s recommendation as mentioned in the protocol and to go through different steps from the preparation of starting material (e.g., DNA), library preparation, and so on. We will try to explain all the steps in detail and share our experience here. It all starts with collection of samples and collection of ecological/environmental metadata followed by sample fractionation (optional), extraction of DNA, sequencing, and finally data analyses to interpret results. Sample collection has always been the most important part of a study as it requires proper planning, a good workforce to execute, permission(s) of sampling from appropriate authority, and precaution(s) about endangered species during sampling. Here, we first describe methodology for a shallow river and in the later section methodology for a deep marine bay. In either case, slight modifications can be made to succeed in sampling. Determination of physicochemical parameters as metadata simultaneously is also an important task. These samples are then processed to extract DNA which needs to be representative of all cells present in the sample. Finally, sequencing is done by a next-generation sequencer, and data analyses are completed. Through these methods, scientists are now able to overcome the unculturability problem of more than 99% of environmental microorganisms and uncovered functional gene diversity of environmental microorganisms.
  • Marine Metagenomic Sequence Counts of Reads Assigned to Taxa Consistently Proportionate to Read Counts Obtained for per g of Seawater Sample

    Kudo, Toshiaki; Reza, Md. Shaheed; Kobiyama, Atsushi; Rashid, Jonaira; Yamada, Yuichiro; Ikeda, Yuri; Ikeda, Daisuke; Mizusawa, Nanami; Yanagisawa, Saki; Ikeo, Kazuho; Sato, Shigeru; Ogata, Takehiko; Kaga, Shinnosuke; Watanabe, Shiho; Naiki, Kimiaki; Kaga, Yoshimasa; Segawa, Satoshi; Mineta, Katsuhiko; Bajic, Vladimir B.; Gojobori, Takashi; Watabe, Shugo (Springer Singapore, 2019-07-24) [Book Chapter]
    Development of high-throughput DNA sequencing technologies has enabled scientists to generate vast amounts of genetic information that may provide a comprehensive understanding of key roles played by environmental microorganisms. Generally the microorganisms inhabit a particular niche and correlate well with environmental changes. It is accepted that the read counts obtained through metagenomic analyses correlate semi-quantitatively with the relative abundance of bacterial species. In our marine metagenomic study conducted on the Ofunato Bay, Iwate Prefecture, Japan, we observed such correlation which exists for bacterioplankton Candidatus Pelagibacter ubique, identified as the dominant bacterial species of the bay. Shotgun metagenomic analyses identified three strains of Ca. Pelagibacter in the bay, viz., dmdA-HTCC1062, dmdA-HTCC9022, and O19-dmdA, that showed a dynamic change throughout the year particularly in the 10-m depth zone. Interestingly, the total abundances of those strains that fall in the Ca. Pelagibacter genus were found to correlate well with the read counts per g seawater samples used for analyses. It is assumed that whole-genome sequence (WGS) reads for members of the metagenome would show similar trend provided that proper precautions are taken to ensure collection of representative sample from the environment.
  • HLIBCov: Parallel hierarchical matrix approximation of large covariance matrices and likelihoods with applications in parameter identification

    Litvinenko, Alexander; Kriemann, Ronald; Genton, Marc G.; Sun, Ying; Keyes, David E. (MethodsX, Elsevier BV, 2019-07-12) [Article]
    We provide more technical details about the HLIBCov package, which is using parallel hierarchical (H-) matrices to: • approximates large dense inhomogeneous covariance matrices with a log-linear computational cost and storage requirement; •computes matrix-vector product, Cholesky factorization and inverse with a log-linear complexity; •identify unknown parameters of the covariance function (variance, smoothness, and covariance length); These unknown parameters are estimated by maximizing the joint Gaussian log-likelihood function. To demonstrate the numerical performance, we identify three unknown parameters in an example with 2,000,000 locations on a PC-desktop.
  • Efficient Dynamical Downscaling of General Circulation Models Using Continuous Data Assimilation

    Desamsetti, Srinivas; Dasari, Hari Prasad; Langodan, Sabique; Titi, Edriss S.; Knio, Omar; Hoteit, Ibrahim (Quarterly Journal of the Royal Meteorological Society, Wiley, 2019-07-09) [Article]
    Continuous data assimilation (CDA) is successfully implemented for the first timefor efficient dynamical downscaling of a global atmospheric reanalysis. A com-parison of the performance of CDA with the standard grid and spectral nudgingtechniques for representing long- and short-scale features in the downscaled fieldsusing the Weather Research and Forecast (WRF) model is further presented andanalysed. The WRF model is configured at 0.25◦×0.25◦horizontal resolution andis driven by 2.5◦×2.5◦initial and boundary conditions from NCEP/NCAR reanal-ysis fields. Downscaling experiments are performed over a one-month period inJanuary 2016. The similarity metric is used to evaluate the performance of thedownscaling methods for large (2,000 km) and small (300 km) scales. Similarityresults are compared for the outputs of the WRF model with different downscalingtechniques, NCEP/NCAR reanalysis, and NCEP Final Analysis (FNL, available at0.25◦×0.25◦horizontal resolution). Both spectral nudging and CDA describe betterthe small-scale features compared to grid nudging. The choice of the wave number iscritical in spectral nudging; increasing the number of retained frequencies generallyproduced better small-scale features, but only up to a certain threshold after which itssolution gradually became closer to grid nudging. CDA maintains the balance of thelarge- and small-scale features similar to that of the best simulation achieved by thebest spectral nudging configuration, without the need of a spectral decomposition.The different downscaled atmospheric variables, including rainfall distribution, withCDA is most consistent with the observations. The Brier skill score values furtherindicate that the added value of CDA is distributed over the entire model domain.The overall results clearly suggest that CDA provides an efficient new approach fordynamical downscaling by maintaining better balance between the global model andthe downscaled fields
  • Incompressible models of magnetohydrodynamic Richtmyer-Meshkov instability in cylindrical geometry

    Bakhsh, A.; Samtaney, Ravi (Physical Review Fluids, American Physical Society, 2019-06-27) [Article]
    The Richtmyer-Meshkov instability (RMI) occurs when a shock impulsively accelerates an interface between two different fluids, and it is important in many technological applications such as inertial confinement fusion (ICF) and astrophysical phenomena such as supernova. Here, we present incompressible models of an impulsively accelerated interface separating conducting fluids of different densities in cylindrical geometry. The present study complements earlier investigations on linear and nonlinear simulations of RMI. We investigate the influence of a normal or an azimuthal magnetic field on the growth rate of the interface. This is accomplished by solving the linearized initial value problem using numerical inverse Laplace transform. For a finite normal magnetic field, although the initial growth rate of the interface is unaffected by the presence of the magnetic field, at late-time the growth rate of the interface decays. This occurs by transporting the vorticity by two Alfvén fronts which propagate away from the interface. For the azimuthal magnetic field configuration, the suppression mechanism is associated with the interference of two waves propagating parallel and antiparallel to the interface that transport vorticity and cause the growth rate to oscillate in time with nearly a zero mean value. Comparing the results of the incompressible models with linear compressible MHD simulations show reasonable agreement at early time of simulations.
  • Mining the deep Red-Sea brine pool microbial community for anticancer therapeutics.

    Esau, Luke; Zhang, Guishan; Sagar, Sunil; Stingl, Ulrich; Bajic, Vladimir B.; Kaur, Mandeep (BMC complementary and alternative medicine, Springer Science and Business Media LLC, 2019-06-22) [Article]
    BACKGROUND: Microbial species in the brine pools of the Red Sea and the brine pool-seawater interfaces are exposed to high temperature, high salinity, low oxygen levels and high concentrations of heavy metals. As adaptations to these harsh conditions require a large suite of secondary metabolites, these microbes have a huge potential as a source of novel anticancer molecules. METHODS:A total of 60 ethyl-acetate extracts of newly isolated strains from extreme environments of the Red-Sea were isolated and tested against several human cancer cell lines for potential cytotoxic and apoptotic activities. RESULTS: Isolates from the Erba brine-pool accounted for 50% of active bacterial extracts capable of inducing 30% or greater inhibition of cell growth. Among the 60 extracts screened, seven showed selectivity towards triple negative BT20 cells compared to normal fibroblasts. CONCLUSION: In this study, we identified several extracts able to induce caspase-dependent apoptosis in various cancer cell lines. Further investigations and isolation of the active compounds of these Red Sea brine pool microbes may offer a chemotherapeutic potential for cancers with limited treatment options.
  • Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

    Menden, Michael P.; Wang, Dennis; Mason, Mike J.; Szalai, Bence; Bulusu, Krishna C.; Guan, Yuanfang; Yu, Thomas; Kang, Jaewoo; Jeon, Minji; Wolfinger, Russ; Nguyen, Tin; Zaslavskiy, Mikhail; Abante, Jordi; Abecassis, Barbara Schmitz; Aben, Nanne; Aghamirzaie, Delasa; Aittokallio, Tero; Akhtari, Farida S.; Al-lazikani, Bissan; Alam, Tanvir; Allam, Amin; Allen, Chad; de Almeida, Mariana Pelicano; Altarawy, Doaa; Alves, Vinicius; Amadoz, Alicia; Anchang, Benedict; Antolin, Albert A.; Ash, Jeremy R.; Aznar, Victoria Romeo; Ba Alawi, Wail; Bagheri, Moeen; Bajic, Vladimir B.; Ball, Gordon; Ballester, Pedro J.; Baptista, Delora; Bare, Christopher; Bateson, Mathilde; Bender, Andreas; Bertrand, Denis; Wijayawardena, Bhagya; Boroevich, Keith A.; Bosdriesz, Evert; Bougouffa, Salim; Bounova, Gergana; Brouwer, Thomas; Bryant, Barbara; Calaza, Manuel; Calderone, Alberto; Calza, Stefano; Capuzzi, Stephen; Carbonell-Caballero, Jose; Carlin, Daniel; Carter, Hannah; Castagnoli, Luisa; Celebi, Remzi; Cesareni, Gianni; Chang, Hyeokyoon; Chen, Guocai; Chen, Haoran; Chen, Huiyuan; Cheng, Lijun; Chernomoretz, Ariel; Chicco, Davide; Cho, Kwang Hyun; Cho, Sunghwan; Choi, Daeseon; Choi, Jaejoon; Choi, Kwanghun; Choi, Minsoo; Cock, Martine De; Coker, Elizabeth; Cortes-Ciriano, Isidro; Cserzö, Miklós; Cubuk, Cankut; Curtis, Christina; Daele, Dries Van; Dang, Cuong C.; Dijkstra, Tjeerd; Dopazo, Joaquin; Draghici, Sorin; Drosou, Anastasios; Dumontier, Michel; Ehrhart, Friederike; Eid, Fatma Elzahraa; ElHefnawi, Mahmoud; Elmarakeby, Haitham; van Engelen, Bo; Engin, Hatice Billur; de Esch, Iwan; Evelo, Chris; Falcao, Andre O.; Farag, Sherif; Fernandez-Lozano, Carlos; Fisch, Kathleen; Flobak, Asmund; Fornari, Chiara; Foroushani, Amir B.K.; Fotso, Donatien Chedom; Fourches, Denis; Friend, Stephen; Frigessi, Arnoldo; Gao, Feng; Gao, Xiaoting; Gerold, Jeffrey M.; Gestraud, Pierre; Ghosh, Samik; Gillberg, Jussi; Godoy-Lorite, Antonia; Godynyuk, Lizzy; Godzik, Adam; Goldenberg, Anna; Gomez-Cabrero, David; Gonen, Mehmet; de Graaf, Chris; Gray, Harry; Grechkin, Maxim; Guimera, Roger; Guney, Emre; Haibe-Kains, Benjamin; Han, Younghyun; Hase, Takeshi; He, Di; He, Liye; Heath, Lenwood S.; Hellton, Kristoffer H.; Helmer-Citterich, Manuela; Hidalgo, Marta R.; Hidru, Daniel; Hill, Steven M.; Hochreiter, Sepp; Hong, Seungpyo; Hovig, Eivind; Hsueh, Ya Chih; Hu, Zhiyuan; Huang, Justin K.; Huang, R. Stephanie; Hunyady, László; Hwang, Jinseub; Hwang, Tae Hyun; Hwang, Woochang; Hwang, Yongdeuk; Isayev, Olexandr; Don’t Walk, Oliver Bear; Jack, John; Jahandideh, Samad; Ji, Jiadong; Jo, Yousang; Kamola, Piotr J.; Kanev, Georgi K.; Karacosta, Loukia; Karimi, Mostafa; Kaski, Samuel; Kazanov, Marat; Khamis, Abdullah M.; Khan, Suleiman Ali; Kiani, Narsis A.; Kim, Allen; Kim, Jinhan; Kim, Juntae; Kim, Kiseong; Kim, Kyung; Kim, Sunkyu; Kim, Yongsoo; Kim, Yunseong; Kirk, Paul D.W.; Kitano, Hiroaki; Klambauer, Gunter; Knowles, David; Ko, Melissa; Kohn-Luque, Alvaro; Kooistra, Albert J.; Kuenemann, Melaine A.; Kuiper, Martin; Kurz, Christoph; Kwon, Mijin; van Laarhoven, Twan; Laegreid, Astrid; Lederer, Simone; Lee, Heewon; Lee, Jeon; Lee, Yun Woo; Lepp_aho, Eemeli; Lewis, Richard; Li, Jing; Li, Lang; Liley, James; Lim, Weng Khong; Lin, Chieh; Liu, Yiyi; Lopez, Yosvany; Low, Joshua; Lysenko, Artem; Machado, Daniel; Madhukar, Neel; Maeyer, Dries De; Malpartida, Ana Belen; Mamitsuka, Hiroshi; Marabita, Francesco; Marchal, Kathleen; Marttinen, Pekka; Mason, Daniel; Mazaheri, Alireza; Mehmood, Arfa; Mehreen, Ali; Michaut, Magali; Miller, Ryan A.; Mitsopoulos, Costas; Modos, Dezso; Moerbeke, Marijke Van; Moo, Keagan; Motsinger-Reif, Alison; Movva, Rajiv; Muraru, Sebastian; Muratov, Eugene; Mushthofa, Mushthofa; Nagarajan, Niranjan; Nakken, Sigve; Nath, Aritro; Neuvial, Pierre; Newton, Richard; Ning, Zheng; Niz, Carlos De; Oliva, Baldo; Olsen, Catharina; Palmeri, Antonio; Panesar, Bhawan; Papadopoulos, Stavros; Park, Jaesub; Park, Seonyeong; Park, Sungjoon; Pawitan, Yudi; Peluso, Daniele; Pendyala, Sriram; Peng, Jian; Perfetto, Livia; Pirro, Stefano; Plevritis, Sylvia; Politi, Regina; Poon, Hoifung; Porta, Eduard; Prellner, Isak; Preuer, Kristina; Pujana, Miguel Angel; Ramnarine, Ricardo; Reid, John E.; Reyal, Fabien; Richardson, Sylvia; Ricketts, Camir; Rieswijk, Linda; Rocha, Miguel; Rodriguez-Gonzalvez, Carmen; Roell, Kyle; Rotroff, Daniel; de Ruiter, Julian R.; Rukawa, Ploy; Sadacca, Benjamin; Safikhani, Zhaleh; Safitri, Fita; Sales-Pardo, Marta; Sauer, Sebastian; Schlichting, Moritz; Seoane, Jose A.; Serra, Jordi; Shang, Ming Mei; Sharma, Alok; Sharma, Hari; Shen, Yang; Shiga, Motoki; Shin, Moonshik; Shkedy, Ziv; Shopsowitz, Kevin; Sinai, Sam; Skola, Dylan; Smirnov, Petr; Soerensen, Izel Fourie; Soerensen, Peter; Song, Je Hoon; Song, Sang Ok; Soufan, Othman; Spitzmueller, Andreas; Steipe, Boris; Suphavilai, Chayaporn; Tamayo, Sergio Pulido; Tamborero, David; Tang, Jing; Tanoli, Zia ur Rehman; Tarres-Deulofeu, Marc; Tegner, Jesper; Thommesen, Liv; Tonekaboni, Seyed Ali Madani; Tran, Hong; Troyer, Ewoud De; Truong, Amy; Tsunoda, Tatsuhiko; Turu, Gábor; Tzeng, Guang Yo; Verbeke, Lieven; Videla, Santiago; Vis, Daniel; Voronkov, Andrey; Votis, Konstantinos; Wang, Ashley; Wang, Hong Qiang Horace; Wang, Po Wei; wang, sheng; Wang, Wei; Wang, Xiaochen; Wang, Xin; Wennerberg, Krister; Wernisch, Lorenz; Wessels, Lodewyk; van Westen, Gerard J.P.; Westerman, Bart A.; White, Simon Richard; Willighagen, Egon; Wurdinger, Tom; Xie, Lei; Xie, Shuilian; Xu, Hua; Yadav, Bhagwan; Yau, Christopher; Yeerna, Huwate; Yin, Jia Wei; Yu, Michael; Yu, Min Hwan; Yun, So Jeong; Zakharov, Alexey; Zamichos, Alexandros; Zanin, Massimiliano; Zeng, Li; Zenil, Hector; Zhang, Frederick; Zhang, Pengyue; Zhang, Wei; Zhao, Hongyu; Zhao, Lan; Zheng, Wenjin; Zoufir, Azedine; Zucknick, Manuela; Jang, In Sock; Ghazoui, Zara; Aghamirzaie, Delasa; Vogel, Robert; Neto, Elias Chaibub; Norman, Thea; Tang, Eric K.Y.; Garnett, Mathew J.; Veroli, Giovanni Y.Di; Fawell, Stephen; Altarawy, Doaa; Alves, Vinicius; Dry, Jonathan R.; Anchang, Benedict (Nature Communications, Nature Publishing Group, 2019-06-17) [Article]
    The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca’s large drug combination dataset, consisting of 11,576 experiments from 910 combinations across 85 molecularly characterized cancer cell lines, and results of a DREAM Challenge to evaluate computational strategies for predicting synergistic drug pairs and biomarkers. 160 teams participated to provide a comprehensive methodological development and benchmarking. Winning methods incorporate prior knowledge of drug-target interactions. Synergy is predicted with an accuracy matching biological replicates for >60% of combinations. However, 20% of drug combinations are poorly predicted by all methods. Genomic rationale for synergy predictions are identified, including ADAM17 inhibitor antagonism when combined with PIK3CB/D inhibition contrasting to synergy when combined with other PI3K-pathway inhibitors in PIK3CA mutant cells.
  • Three-dimensional registration and shape reconstruction from depth data without matching: A PDE approach

    Gomes, Diogo A.; Costeira, João; Saúde, João (Portugaliae Mathematica, European Mathematical Publishing House, 2019-06-06) [Article]
    The widespread availability of depth sensors like the Kinect camera makes it easy to gather three-dimensional (3D) data. However, accurately and efficiently merging large datasets collected from different views is still a core problem in computer vision. This question is particularly challenging if the relative positions of the views are not known, if there are few or no overlapping points, or if there are multiple objects. Here, we develop a method to reconstruct the 3D shapes of objects from depth data taken from different views whose relative positions are not known. Our method does not assume that common points in the views exist nor that the number of objects is known a priori. To reconstruct the shapes, we use partial differential equations (PDE) to compute upper and lower bounds for distance functions, which are solutions of the Eikonal equation constrained by the depth data. To combine various views, we minimize a function that measures the compatibility of relative positions. As we illustrate in several examples, we can reconstruct complex objects, even in the case where multiple views do not overlap, and, therefore, do not have points in common. We present several simulations to illustrate our method including multiple objects, non-convex objects, and complex shapes. Moreover, we present an application of our PDE approach to object classification from depth data.

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