• Global mapping of protein subcellular location in apicomplexans: the parasite as we’ve never seen it before

      Barylyuk, Konstantin; Koreny, Ludek; Ke, Huiling; Butterworth, Simon; Lassadi, Imen; Mourier, Tobias; Breckels, Lisa; Gatto, Laurent; Pain, Arnab; Lilley, Kathryn; Waller, Ross (Access Microbiology, Microbiology Society, 2019-04-24) [Presentation]
      Apicomplexans are human and animal protozoan pathogens responsible for diseases including malaria, cryptosporidiosis and toxoplasmosis. As obligate intracellular parasites they are highly organised cells with numerous novel and specialised sub-compartments that form the basis of their invasion biology, host defence evasion, and novel metabolic traits. However, our understanding of these cells is highly constrained by our limited knowledge of the locations and functions of most of the cell’s proteome. Even in the best-studied apicomplexans (Plasmodium spp. and Toxoplasma gondii) only a small fraction of proteins’ locations have been experimentally determined, with most assignments based on predictions from orthologues in distant relatives. Moreover, many parasite proteins are annotated as ‘hypotheticals’, for example 4113 of 8121 Toxoplasma proteins, and many are unique to parasites stymying even predictions of location or function by comparative biology. To address this deficit in our basic understanding of the compositional organisation of the apicomplexan cell, we have used a spatial proteomics method called hyper LOPIT to simultaneously capture the steady-state subcellular association of thousands of proteins in the apicomplexan Toxoplasma. These protein atlases reveal: extensive protein association networks throughout the cell providing testable hypotheses of their function; conservation and novelty of compartment proteomes between apicomplexans; differential selective pressures across the different cell compartments; and clear instances of protein relocation from one organelle to a different one during apicomplexan speciation. This new, global view of the organisation of the apicomplexan cell proteome provides a much more complete framework for understanding the mechanisms of function and biology of these cells.
    • Using ePosters to promote scientific outcomes through Open Access

      Hall, Garry; Vijayakumar, J.K. (2018-10-10) [Presentation]
      King Abdullah University of Science and Technology (KAUST), established in 2009 as an international research University in Saudi Arabia, has adopted the first Open Access mandate for scientific publications in the region and leads with a well-established research repository managed and promoted by the University Library. Having several scientific poster events annually at the campus, with hosting supported by the Library, printed posters have remained static, highly localized and short-lived. These characteristics are at odds with what is often the first formal communication of scientific research and, as such would be of great interest to other researchers. Addressing these limitations was a major motivator behind the trialing of an ePoster alternative at KAUST. This project was conceived, piloted and will be implemented and managed by the University Library, in collaboration with IT Services. In addition to digitally capturing research content for display and preservation, ePoster functionality changes the engagement dynamics whilst helping to bridge the gap between academia and professional practice. ePosters have been extensively embraced by international professional organizations, however, academic institutions remain bound to printed posters. This project identified a short-list of possible companies that responded to criteria identified by KAUST as requirements for its campus wide ePoster management system. The evaluation process included student and researcher participation, as well as webinars and demonstrations and culminated with site visits to the company headquarters of the two finalists. The preferred supplier was then involved with several pilot conferences at KAUST to demonstrate their system’s capabilities and, as importantly, to expose academic staff to ePosters in operational settings. Surveys were conducted of conference participants, academic staff, students and conference organizers to obtain feedback and reaction to this approach. Advantages were both obvious and embraced by respondents; they appreciated the functionality which included ongoing editing and/or updating of content by authors, the ability of organizers to monitor progress of submissions and control content display and statistics being available via a dashboard. ePoster presentations engage the audience better; they are more interactive, dynamic and informative as a result of incorporating high resolution images and videos (with associated zoom capabilities) and audio. In addition, the elimination of print and poster mounting aligns with KAUST commitment to environmental stewardship and open access to scientific output through a direct upload of content to the Research Repository. Interest in ePosters is expanding; this has seen the Library involved in associated skills training and outreach. Academia is notably behind this practitioner-driven trend. KAUST Library believes that, by rolling out an ePoster system to the University, it is the first campus in the world to offer this as a campus-wide solution, truly reflecting a digital smart campus vision of KAUST.
    • ePosters Replace Print Posters: KAUST Library Initiative to Better Prepare Students and Preserve Scholarly Resources

      Vijayakumar, J.K.; Hall, Garry; Afandi, Eman (2019-04-05) [Presentation]
      Scientific posters are popular in conferences run by professional organizations in the UK, Europe, and North America, with the majority focused on medicine and health care disciplines. Individual events may include hundreds (and even thousands) of posters with cumulative numbers from all events (including academia) estimated in the millions annually (1). Generally, posters are not retained, in spite of their value as scholarly resources; many are the first reporting of new research and contain information months in advance of peer-reviewed articles. Printed posters have been around for many years and, with recent digital advances can be transformed into dynamic displays through multimedia inclusion and zoom functionality, whilst being made available via the web to large, geographically distributed audiences. Electronic posters (ePosters) are environmentally friendly, they eliminate printing and transport problems, and they scale well for large conferences (e.g. American Society of Anesthesiologists has used ePosters since 2013, recently with over 3000 posters at multiple sites). Most importantly, they lend themselves to being easily captured and retained as scientific resources. Following successful pilot projects (for which data on student and faculty support and cost-effectiveness will be presented), KAUST University Library has introduced a campus-wide ePoster service for the University beginning in January 2019. This service replaces printed posters and better prepares students for ePoster presentation scenarios commonplace within professional organizations and provides open access via the KAUST Research Repository. Training overheads for both students and organizers are low and uptake has been high, with weekly events scheduled for the first four months of 2019. Academia is notably behind this practitioner-driven trend. KAUST Library believes that, by rolling out an ePoster system to the University, it is the first campus in the world to offer such a campus-wide solution, reflecting a digital smart campus vision of KAUST.
    • Solution of Density Driven Groundwater Flow with Uncertain Porosity and Permeability Coefficients

      Litvinenko, Alexander; Tempone, Raul; Logashenko, Dmitry; Wittum, Gabriel; Keyes, David E. (2019-03) [Presentation]
      In many countries, groundwater is the strategic reserve, which is used as drinking water and as an irrigation resource. Therefore, accurate modeling of the pollution of the soil and groundwater aquifer is highly important. As a model, we consider a density-driven groundwater flow problem with uncertain porosity and permeability. This problem may arise in geothermal reservoir simulation, natural saline-disposal basins, modeling of contaminant plumes and subsurface flow. This strongly non-linear problem describes how salt or polluted water streams down building 'fingers". The solving process requires a very fine unstructured mesh and, therefore, high computational resources. Consequently, we run the parallel multigrid solver UG4 (https://github.com/UG4/ughub.wiki.git) on Shaheen II supercomputer. The parallelization is done in both - the physical space and the stochastic space. The novelty of this work is the estimation of risks that the pollution will achieve a specific critical concentration. Additionally, we demonstrate how the multigrid UG4 solver can be run in a black-box fashion for testing different scenarios in the density-driven flow. We solve Elder's problem in 2D and 3D domains, where unknown porosity and permeability are modeled by random fields. For approximations in the stochastic space, we use the generalized polynomial chaos expansion.
    • Integer programming for layout problems

      Wonka, Peter (SIGGRAPH Asia 2018 Courses on - SA '18, ACM Press, 2018-11-29) [Presentation]
    • GPU-based large-scale scientific visualization

      Beyer, Johanna; Hadwiger, Markus (SIGGRAPH Asia 2018 Courses on - SA '18, ACM Press, 2018-11-29) [Presentation]
      Display-aware processing with flexible new image pyramid (spdf map). Consistent, sparse representation of pixel footprint pdfs Unified evaluation of many important non-linear image operations. Local Laplacian filtering for gigapixel images Efficient CUDA implementation Pre-computation costly, but only performed once Run time storage and computation similar to standard pyramids.
    • Efficient Simulations for Contamination of Groundwater Aquifers under Uncertainties

      Litvinenko, Alexander; Logashenko, Dmitry; Tempone, Raul; Keyes, David E.; Wittum, Gabriel (2019-02-25) [Presentation]
      Accidental contamination of groundwater can be extremely hazardous and thus, accurately predicting the fate of pollutants in groundwater is essential. Certain pollutants are soluble in water and can leak into groundwater systems, such as seawater into coastal aquifers or wastewater leaks. Indeed, some pollutants can change the density of a fluid and induce density-driven flows within the aquifer. This causes faster propagation of the contamination due to convection. Thus, simulation and analysis of this density-driven flow plays an important role in predicting how pollution can migrate through an aquifer. We propose the new parallel algorithm to compute a functional approximation of the QoI. Namely, we approximate the QoI with the polynomial chaos expansion (PCE), where all PCE coefficients are computed in parallel. We demonstrate 2D and 3D examples.
    • Numerical methods for density driven groundwater ow with uncertain data

      Litvinenko, Alexander; Logashenko, Dmitry; Keyes, David E.; Wittum, Gabriel; Tempone, Raul (2019-02-20) [Presentation]
      Accurate modeling of contamination in subsurface flow and water aquifers is crucial for agriculture and environmental protection. We consider the density-driven subsurface flow and estimate how uncertainty from permeability and porosity propagates to the solution - mass fraction. We take an Elder-like problem as a numerical benchmark and we use random fields to model the limited knowledge on the porosity and permeability. We construct a low-cost generalized polynomial chaos expansion (gPCE) surrogate model, where the gPCE coefficients are computed by projection on sparse and full tensor grids. We parallelize both the numerical solver for the deterministic problem based on the multigrid method, and the quadrature over the parametric space.
    • Integration Strategy for Heterogeneously Integrated Wearable and Implantable Electronics

      Hussain, Muhammad Mustafa (2018 International Flexible Electronics Technology Conference (IFETC), IEEE, 2019-01-09) [Presentation]
      We live in a world where electronics play critical enabling role. Specifically, matured and advanced CMOS technology with its arts and science of miniaturization has propelled variety of CMOS devices to a level where their lofty performance over cost benefit has ushered into a wide range of application spectrum ranging from computers to display to today's home automation. Going forward we may want to ask ourselves a few important questions: 1. Can CMOS technology be expanded further to add new functionalities to CMOS devices while retaining their existing attributes in tact? 2. Whether this exercise will have a better functionalities over cost metric? 3. If the first two questions are addressed well, whether the existing applications will be strengthened and/or diversified? Whether new applications may emerge?
    • Adaptive Strategies in Date Palm Revealed by Confocal Imaging Technologies

      Xiao, Ting Ting; Blilou, Ikram (2018-06-22) [Presentation]
      Date palm are confronted by harsh environmental conditions and have therefore adapted various strat-egies to survive the hostile environment. To unravel the underlying mechanisms of adaptation to desert conditions we conducted a detailed analysis of date palm tissue anatomy at different developmental stag-es. Using confocal imaging we reveal new anatomical features and complex structures in roots, shoot and leaves explaining strategies of adaptation of date palm to desert conditions.
    • Integrative Approach Toward Revealing and Understanding Complexity of Root System Architecture in Date Palm

      Blilou, Ikram (2018-06-22) [Presentation]
      The evolution from the primordial aquatic organisms to vascular terrestrial plants has been accompanied by increasing complexity in the structure and functions of their vegetative and reproductive organs. Plants have undergone dramatic changes in their root systems to adapt to terrestrial life. The development of complex diverse root architectures gave plants the advantage ability to colonize new and particularly arid and dry environments. Date palm Phoenix dactylifera fruits are known for their high nutritive, economic and social values. In arid and semi-arid areas, it plays an impor-tant role in affecting the microclimate by creating a microsystem allowing desert farming. Understanding the properties of growth and development in date palm is an essential step towards gaining insights as to how plants have evolved their strategies to cope with changes in their surrounding and survive in chal-lenged habitats like the desert. To unravel the under-lying mechanisms of date palm adaptation to desert conditions we conducted a detailed analysis of date palm anatomy during different stages of develop-ment from germination to adult plants. Using the art of state imaging technologies, we unraveled new devel-opmental mechanisms in date palm occurring during germination, plant growth and development. MicroCT Xray imaging technology combined with high resolu-tion microscopy revealed that date palm roots bear structures that have not been previously described. Some of these structures are conserved only among desert palm species. In addition, a comparative stud-ies of date palm cultivars originated from different geographical habitat, Tunisia, UAE and KSA and hav-ing distinct levels of tolerance to soil salinity revealed substantial differences in root system architecture.
    • Multilevel hybrid split-step implicit tau-leap

      Ben Hammouda, Chiheb; Moraes, Alvaro; Tempone, Raul (2016-08-15) [Presentation]
      In biochemically reactive systems with small copy numbers of one or more reactant molecules, the dynamics is dominated by stochastic effects. To approximate those systems, discrete state-space and stochastic simulation approaches have been shown to be more relevant than continuous state-space and deterministic ones. In systems characterized by having simultaneously fast and slow timescales, existing discrete space-state stochastic path simulation methods, such as the stochastic simulation algorithm (SSA) and the explicit tau-leap method, can be very slow. Implicit approximations have been developed to improve numerical stability and provide efficient simulation algorithms for those systems. Here, we propose an efficient Multilevel Monte Carlo (MLMC) method in the spirit of the work by Anderson and Higham (2012). This method uses split-step implicit tau-leap (SSI-TL) at levels where the explicit-TL method is not applicable due to numerical stability issues. We present numerical examples that illustrate the performance of the proposed method.
    • Multilevel Monte Carlo Acceleration of Seismic Wave Propagation under Uncertainty

      Ballesio, Marco; Beck, Joakim; Pandey, Anamika; Parisi, Laura; von Schwerin, Erik; Tempone, Raul (2018-09-06) [Presentation]
      We consider forward seismic wave propagation in an inhomogeneous linear viscoelastic media with random wave speeds and densities, subject to deterministic boundary and initial conditions. We study this forward problem as a first step towards the treatment of inverse problems. There the goal is to determine, for example, earthquake source locations from seismograms recorded in a small number of seismic sensors at the Earth’s surface. Existing results on earthquake source inversion for a given event show a large variability, which indicates that the inherent uncertainty of the Earth parameters should be taken into account. Here this uncertainty is modeled through random parameters. We propose multilevel Monte Carlo simulations for computing statistics of quantities of interest which are motivated by the choice of loss function for the corresponding inverse problem, presenting a case study based on experimental seismic data from a passive experiment in Tanzania. This work provides a benchmark for the implementation of multilevel algorithms to accelerate seismic inversion addressing earthquake source estimation as well as inferring Earth structure.
    • Multilevel ensemble Kalman filtering for spatio-temporal processes

      Hoel, Hakon; Chernov, Alexey; Law, Kody; Nobile, Fabio; Tempone, Raul (2018-07-04) [Presentation]
      The ensemble Kalman filter (EnKF) is a sequential filtering method that uses an ensemble of particle paths to estimate the means and covariances required by the Kalman filter by the use of sample moments, i.e., the Monte Carlo method. EnKF is often both robust and efficient, but its performance may suffer in settings where the computational cost of accurate simulations of particles is high. The multilevel Monte Carlo method (MLMC) is an extension of the classical Monte Carlo method, which by sampling stochastic realizations on a hierarchy of resolutions may reduce the computational cost of moment approximations by orders of magnitude. In this talk I will present ideas on combining MLMC and EnKF to construct the multilevel ensemble Kalman filter (MLEnKF) for the setting of finite and infinite dimensional state spaces. Theoretical results and numerical studies of the performance gain of MLEnKF over EnKF will also be presented. (Joint work with Alexey Chernov, Kody J. H. Law, Fabio Nobile, and Raul Tempone.) References: [1] H. Hoel, K. Law, and R. lTempone(2016). Multilevelensemble Kalman filtering. SIAM J. Numer. Anal. 54(3), 1813–1839. [2] A. Chernov, H. Hoel, K. Law, F. Nobile, and R. Tempone (2016). Multilevel ensemble Kalman filtering for spatially extended models. ArXiv e-prints. arXiv: 1608.08558 [math.NA].
    • Multilevel ensemble Kalman filtering for spatially extended models

      Hoel, Hakon; Chernov, Alexey; Law, Kody JH; Nobile, Fabio; Tempone, Raul (2018-01-10) [Presentation]
      The ensemble Kalman filter (EnKF) is a sequential filtering method that uses an ensemble of particle paths to estimate the means and covariances required by the Kalman filter by the use of sample moments, i.e., the Monte Carlo method. EnKF is often both robust and efficient, but its performance may suffer in settings where the computational cost of accurate simulations of particles is high. The multilevel Monte Carlo method (MLMC) is an extension of the classical Monte Carlo method, which by sampling stochastic realizations on a hierarchy of resolutions may reduce the computational cost of moment approximations by orders of magnitude. In this talk I will present ideas on combining MLMC and EnKF to construct the multilevel ensemble Kalman filter (MLEnKF) for the setting of finite and infinite dimensional state spaces. Theoretical results and numerical studies of the performance gain of MLEnKF over EnKF will also be presented. (Joint work with Alexey Chernov, Kody J. H. Law, Fabio Nobile, and Raul Tempone.)
    • Study of Regional Volcanic Impact on the Middle East and North Africa using high-resolution global and regional models

      Osipov, Sergey; Dogar, Muhammad Mubashar; Stenchikov, Georgiy L. (2016-04) [Presentation]
      High-latitude winter warming after strong equatorial volcanic eruptions caused by circulation changes associated with the anomalously positive phase of Arctic Oscillation is a subject of active research during recent decade. But severe winter cooling in the Middle East observed after the Mt. Pinatubo eruption of 1991, although recognized, was not thoroughly investigated. These severe regional climate perturbations in the Middle East cannot be explained by solely radiative volcanic cooling, which suggests that a contribution of forced circulation changes could be important and significant. To better understand the mechanisms of the Middle East climate response and evaluate the contributions of dynamic and radiative effects we conducted a comparative study using Geophysical Fluid Dynamics Laboratory global High Resolution Atmospheric Model (HiRAM) with the effectively "regional-model-resolution" of 25-km and the regional Weather Research and Forecasting (WRF) model focusing on the eruption of Mount Pinatubo on June 15, 1991 followed by a pronounced positive phase of the Arctic Oscillation. The WRF model has been configured over the Middle East and North Africa (MENA) region. The WRF code has been modified to interactively account for the radiative effect of volcanic aerosols. Both HiRAM and WRF capture the main features of the MENA climate response and show that in winter the dynamic effects in the Middle East prevail the direct radiative cooling from volcanic aerosols.
    • Regional Climate Response to Volcanic Radiative Forcing in Middle East and North Africa

      Stenchikov, Georgiy L.; Dogar, Muhammad Mubashar (2012-04) [Presentation]
      We have tested the regional climate sensitivity in the Middle East and North Africa (MENA) to radiation perturbations caused by the large explosive equatorial volcanic eruptions of the second part of 20th century, El Chichon and Pinatubo occurred, respectively, in 1982 and 1991. The observations and reanalysis data show that the surface volcanic cooling in the MENA region is two-three times larger than the global mean response to volcanic forcing. The Red Sea surface temperature appears to be also very sensitive to the external radiative impact. E.g., the sea surface cooling, associated with the 1991 Pinatubo eruption, caused deep water mixing and coral bleaching for a few years. To better quantify these effects we use the Geophysical Fluid Dynamics Laboratory global High Resolution Atmospheric Model (HIRAM) to conduct simulations of both the El Chichon and Pinatubo impacts with the effectively 25-km grid spacing. We find that the circulation changes associated with the positive phase of the arctic oscillation amplified the winter temperature anomalies in 1982-1984 and 1991-1993. The dynamic response to volcanic cooling also is characterized by the southward shift of the inter-tropical convergence zone in summer and associated impact on the precipitation patterns. Thus, these results suggest that the climate regime in the MENA region is highly sensitive to external forcing. This is important for better understanding of the climate variability and change in this region.
    • Study of Ocean Response to Periodic and Constant Volcanic Radiative Forcing

      Dogar, Muhammad Mubashar; Stenchikov, Georgiy L. (2013-12) [Presentation]
      It is known that volcanic radiative impacts could produce long-term perturbations of the ocean heat content. In this study we systematically compare the effect of periodic volcanic forcing with an equivalent time-average radiative cooling. One could expect that a sporadic strong cooling should initiate more vigorous vertical mixing of the upper ocean layer and therefore cools the ocean more effectively than a uniform radiative forcing. However, the long-term simulations show that on average the ocean heat content responses to periodic and constant forcings are almost identical. To better understand this controversy we conducted two sets of parallel simulations, the first one with uniform volcanic forcing and the second one with periodic volcanic forcing with 10 and 50 years repeating cycle using Geophysical Fluid Dynamics Laboratory Coupled Model CM2.1. We found that average perturbations of surface temperature, precipitation, ocean heat content, and sea level rise in both sets of simulations are similar but responses of Atlantic Meridional Overturning Circulation are significantly different, which explains the differences in the relaxation processes. These findings could be important for ocean initialization in long-tern climate studies and for geoengineering applications.
    • Uncertainty quantification of groundwater contamination

      Litvinenko, Alexander; Logashenko, Dmitry (2018-10-08) [Presentation]
      In many countries, groundwater is the strategic reserve, which is used as drinking water and as an irrigation resource. Therefore, accurate modeling of the pollution of the soil and groundwater aquifer is highly important. As a model, we consider a density-driven groundwater flow problem with uncertain porosity and permeability. This problem may arise in geothermal reservoir simulation, natural saline-disposal basins, modeling of contaminant plumes and subsurface flow. This strongly non-linear problem describes how salt or polluted water streams down building ''fingers". The solving process requires a very fine unstructured mesh and, therefore, high computational resources. Consequently, we run the parallel multigrid solver UG4 (https://github.com/UG4/ughub.wiki.git) on Shaheen II supercomputer. The parallelization is done in both - the physical space and the stochastic space. The novelty of this work is the estimation of risks that the pollution will achieve a specific critical concentration. Additionally, we demonstrate how the multigrid UG4 solver can be run in a black-box fashion for testing different scenarios in the density-driven flow. We solve Elder's problem in 2D and 3D domains, where unknown porosity and permeability are modeled by random fields. For approximations in the stochastic space, we use the generalized polynomial chaos expansion. We compute different quantities of interest such as the mean, variance and exceedance probabilities of the concentration. As a reference solution, we use the solution, obtained from the quasi-Monte Carlo method.