• Multilevel Monte Carlo in approximate Bayesian computation

      Jasra, Ajay; Jo, Seongil; Nott, David; Shoemaker, Christine; Tempone, Raul (Stochastic Analysis and Applications, Informa UK Limited, 2019-02-01) [Article]
      In the following article, we consider approximate Bayesian computation (ABC) inference. We introduce a method for numerically approximating ABC posteriors using the multilevel Monte Carlo (MLMC). A sequential Monte Carlo version of the approach is developed and it is shown under some assumptions that for a given level of mean square error, this method for ABC has a lower cost than i.i.d. sampling from the most accurate ABC approximation. Several numerical examples are given.
    • A Survey of Channel Modeling for UAV Communications

      Khuwaja, Aziz Altaf; Chen, Yunfei; Zhao, Nan; Alouini, Mohamed-Slim; Dobbins, Paul (IEEE Communications Surveys & Tutorials, Institute of Electrical and Electronics Engineers (IEEE), 2018-07-16) [Article]
      Unmanned aerial vehicles (UAVs) have attracted great interest in rapid deployment for both civil and military applications. UAV communication has its own distinctive channel characteristics compared to the widely used cellular or satellite systems. Accurate channel characterization is crucial for the performance optimization and design of efficient UAV communication. However, several challenges exist in UAV channel modeling. For example, the propagation characteristics of UAV channels are under explored for spatial and temporal variations in non-stationary channels. Additionally, airframe shadowing has not yet been investigated for small size rotary UAVs. This paper provides an extensive survey of the measurement methods proposed for UAV channel modeling that use low altitude platforms and discusses various channel characterization efforts. We also review from a contemporary perspective of UAV channel modeling approaches, and outline future research challenges in this domain.
    • Improving Shadow Suppression for Illumination Robust Face Recognition

      Zhang, Wuming; Zhao, Xi; Morvan, Jean-Marie; Chen, Liming (IEEE Transactions on Pattern Analysis and Machine Intelligence, Institute of Electrical and Electronics Engineers (IEEE), 2018-02-07) [Article]
      2D face analysis techniques, such as face landmarking, face recognition and face verification, are reasonably dependent on illumination conditions which are usually uncontrolled and unpredictable in the real world. The current massive data-driven approach, e.g., deep learning-based face recognition, requires a huge amount of labeled training face data that hardly cover the infinite lighting variations that can be encountered in real-life applications. An illumination robust preprocessing method thus remains a very interesting but also a significant challenge in reliable face analysis. In this paper we propose a novel model driven approach to improve lighting normalization of face images. Specifically, we propose to build the underlying reflectance model which characterizes interactions between skin surface, lighting source and camera sensor, and elaborate the formation of face color appearance. The proposed illumination processing pipeline enables generation of the Chromaticity Intrinsic Image (CII) in a log chromaticity space which is robust to illumination variations. Moreover, as an advantage over most prevailing methods, a photo-realistic color face image is subsequently reconstructed, which eliminates a wide variety of shadows whilst retaining the color information and identity details. Experimental results under different scenarios and using various face databases show the effectiveness of the proposed approach in dealing with lighting variations, including both soft and hard shadows, in face recognition.
    • Engineering resistance against Tomato yellow leaf curl virus via the CRISPR/Cas9 system in tomato

      Tashkandi, Manal; Ali, Zahir; Aljedaani, Fatimah R.; Shami, Ashwag; Mahfouz, Magdy M. (Plant Signaling & Behavior, Informa UK Limited, 2019-01-29) [Article]
      CRISPR/Cas systems confer molecular immunity against phages and conjugative plasmids in prokaryotes. Recently, CRISPR/Cas9 systems have been used to confer interference against eukaryotic viruses. Here, we engineered Nicotiana benthamiana and tomato (Solanum lycopersicum) plants with the CRISPR/Cas9 system to confer immunity against the Tomato yellow leaf curl virus (TYLCV). Targeting the TYLCV genome with Cas9-single guide RNA at the sequences encoding the coat protein (CP) or replicase (Rep) resulted in efficient virus interference, as evidenced by low accumulation of the TYLCV DNA genome in the transgenic plants. The CRISPR/Cas9-based immunity remained active across multiple generations in the N. benthamiana and tomato plants. Together, our results confirmed the efficiency of the CRISPR/Cas9 system for stable engineering of TYLCV resistance in N. benthamiana and tomato, and opens the possibilities of engineering virus resistance against single and multiple infectious viruses in other crops.
    • Entropy stable modeling of non-isothermal multi-component diffuse-interface two-phase flows with realistic equations of state

      Kou, Jisheng; Sun, Shuyu (Computer Methods in Applied Mechanics and Engineering, Elsevier BV, 2018-07-05) [Article]
      In this paper, we consider mathematical modeling and numerical simulation of non-isothermal compressible multi-component diffuse-interface two-phase flows with realistic equations of state. A general model with the general reference velocity is derived rigorously through thermodynamical laws and Onsager’s reciprocal principle, and it is capable of characterizing compressibility and partial miscibility between multiple fluids. We prove a novel relation between the pressure, temperature and chemical potentials, which results in a new formulation of the momentum conservation equation indicating that the gradients of chemical potentials and temperature become the primary driving force of the fluid motion except for the external forces. A key challenge in numerical simulation is to develop entropy stable numerical schemes preserving the laws of thermodynamics. Based on the convex–concave splitting of Helmholtz free energy density with respect to molar densities and temperature, we propose an entropy stable numerical method, which solves the total energy balance equation directly, and thus, naturally satisfies the first law of thermodynamics. Unconditional entropy stability (the second law of thermodynamics) of the proposed method is proved by estimating the variations of Helmholtz free energy and kinetic energy with time steps. Numerical results validate the proposed method.
    • Laser-Induced Reversion of δ′ precipitates in an Al-Li Alloy

      Khushaim, Muna S.; Gemma, Ryota; Al-Kassab, Talaat (Microscopy and Microanalysis, Cambridge University Press (CUP), 2017-08-09) [Article]
    • A Randomized Exchange Algorithm for Computing Optimal Approximate Designs of Experiments

      Harman, Radoslav; Filová, Lenka; Richtarik, Peter (Journal of the American Statistical Association, Informa UK Limited, 2018-12-15) [Article]
      We propose a class of subspace ascent methods for computing optimal approximate designs that covers existing algorithms as well as new and more efficient ones. Within this class of methods, we construct a simple, randomized exchange algorithm (REX). Numerical comparisons suggest that the performance of REX is comparable or superior to that of state-of-the-art methods across a broad range of problem structures and sizes. We focus on the most commonly used criterion of D-optimality, which also has applications beyond experimental design, such as the construction of the minimum-volume ellipsoid containing a given set of data points. For D-optimality, we prove that the proposed algorithm converges to the optimum. We also provide formulas for the optimal exchange of weights in the case of the criterion of A-optimality, which enable one to use REX and some other algorithms for computing A-optimal and I-optimal designs.
    • Investigation of high contrast and reversible luminescence thermochromism of the quantum confined Cs4PbBr6 perovskite solid

      Choi, Jin Woo; Cho, Namchul; Woo, Hee Chul; Oh, Byeong M; Almutlaq, Jawaher; Bakr, Osman; Kim, Sung-Hoon; Lee, Chang-Lyoul; Kim, Jong H (Nanoscale, Royal Society of Chemistry (RSC), 2019-02-16) [Article]
      Thermochromism of organic/inorganic halide perovskites has attracted particular interest due to their potential applications as photoluminescence (PL)-based temperature sensors. However, despite the outstanding PL characteristics, their use as a thermochromic material in practical temperature ranges has been limited because of their poor thermal stability. In this study, we used the quantum confinement effect and exceptional PL quantum efficiency of the Cs4PbBr6 perovskite to demonstrate their high on/off ratio (20) and reversible PL thermochromism in the solid state in practical temperature ranges including room temperature (RT). Systematic photophysical and optical characterization studies, including exciton-phonon scattering, exciton binding energy, exciton decay dynamics, and crystal structure change, were performed to investigate the origin of this unique thermochromic PL property. The results showed that the efficient and highly reversible thermochromic PL emission of the Cs4PbBr6 perovskite is due to its desirable optical properties such as highly luminescent emission, efficient PL quenching at high temperatures, and thermally reversible structural changes.
    • Exfoliated nanosheets of Co3O4 webbed with polyaniline nanofibers: A novel composite electrode material for enzymeless glucose sensing application

      Yassin, Mohamed A.; Shrestha, Bishnu Kumar; Ahmad, Rafiq; Shrestha, Sita; Park, Chan Hee; Kim, Cheol Sang (Journal of Industrial and Engineering Chemistry, Elsevier BV, 2019-01-16) [Article]
      A novel glucose biosensor was designed using cobalt oxide (CoO) nanosheets patterned by π-conjugated polyaniline nanofibers (PANINFs). A facile synthesis process was conducted to obtain cost-effective and ecofriendly mesoporous CoO@PANINFs hybrid nanomaterial for the first time. The CoO@PANINFs on glassy carbon electrode (GCE), working as a biosensor electrode based on electrochemical technique, showed electrocatalytic activity to glucose with sensitivity of 14.25 μA mM cm, linear range from (0.1 to 8) mM, minimum detection limit of 0.06 mM, and response time <6 s. Moreover, the biosensor was employed to monitor glucose concentration in human serum sample to provide effective sensing results.
    • Groundfish and invertebrate community shift in coastal areas off Iceland

      Jónsdóttir, Ingibjörg G.; Bakka, Haakon; Elvarsson, Bjarki T. (Estuarine, Coastal and Shelf Science, Elsevier BV, 2019-01-30) [Article]
      Biodiversity is a key concept for conservation and management and is fundamental for ecosystem-based approaches. It is of importance to consider whole areas in which communities and their ecological processes can be maintained. To effectively manage ecosystems for sustainable use and conservation, it is important to understand changes in the ecosystems. The objective of this study was to investigate the species diversity of groundfish and invertebrates, including both commercially exploited species as well as unexploited species, and identify long-term changes in the composition and abundance of the groundfish community and the northern shrimp (Pandalus borealis) in six fjords off Iceland in the period from 1995 to 2016 using data from annual shrimp survey. The results showed a strong indication of species replacement during the study period and a top-down control, where the abundance of cod and haddock increased at the same time as the abundance of northern shrimp, eelpouts, blennies and flatfish species decreased. Moreover, the increase in gadoid abundance seemed to have less effect in more open systems, which showed greater variability in species diversity and evenness compared with more closed ecosystems.
    • A Novel One-Pot Three-Component Reaction for Rapid Access of Arylidene 2-Aminoimidazolone Derivatives

      Hanif, Aansa; Sardar, Aniqa; Alazmi, Meshari; Tariq, Haniya; Emwas, Abdul-Hamid; Gao, Xin; Chotana, Ghayoor Abbas; Zaib Saleem, Rahman Shah (ChemistrySelect, Wiley, 2019-02-05) [Article]
      A simple and convenient one-pot reaction for the synthesis of arylidene 2-aminoimidazolone derivatives from structurally diverse benzaldehydes, amines and 2-(methylthio)-1H-imidazol-4(5H)-one is described. The reaction offers flexibility of use of electron-rich and electron-deficient benzaldehydes and mono and di-substituted amines for the rapid development of combinatorial library.
    • De Novo Variants Disrupting the HX Repeat Motif of ATN1 Cause a Recognizable Non-Progressive Neurocognitive Syndrome

      Palmer, Elizabeth E; Hong, Seungbeom; Al Zahrani, Fatema; Hashem, Mais O; Aleisa, Fajr A; Ahmed, Heba M Jalal; Kandula, Tejaswi; Macintosh, Rebecca; Minoche, Andre E; Puttick, Clare; Gayevskiy, Velimir; Drew, Alexander P; Cowley, Mark J; Dinger, Marcel; Rosenfeld, Jill A; Xiao, Rui; Cho, Megan T; Yakubu, Suliat F; Henderson, Lindsay B; Guillen Sacoto, Maria J; Begtrup, Amber; Hamad, Muddathir; Shinawi, Marwan; Andrews, Marisa V; Jones, Marilyn C; Lindstrom, Kristin; Bristol, Ruth E; Kayani, Saima; Snyder, Molly; Villanueva, María Mercedes; Schteinschnaider, Angeles; Faivre, Laurence; Thauvin, Christel; Vitobello, Antonio; Roscioli, Tony; Kirk, Edwin P; Bye, Ann; Merzaban, Jasmeen; Jaremko, Łukas; Jaremko, Mariusz; Sachdev, Rani K; Alkuraya, Fowzan S; Arold, Stefan T. (The American Journal of Human Genetics, Elsevier BV, 2019-02-28) [Article]
      Polyglutamine expansions in the transcriptional co-repressor Atrophin-1, encoded by ATN1, cause the neurodegenerative condition dentatorubral-pallidoluysian atrophy (DRPLA) via a proposed novel toxic gain of function. We present detailed phenotypic information on eight unrelated individuals who have de novo missense and insertion variants within a conserved 16-amino-acid
    • Electronic and optical properties of van der Waals vertical heterostructures based on two-dimensional transition metal dichalcogenides: First-principles calculations

      Ren, Kai; Sun, Minglei; Luo, Yi; Wang, Sake; Xu, Yujing; Yu, Jin; Tang, Wencheng (Physics Letters A, Elsevier BV, 2019-02-01) [Article]
      Four vertical heterostructures based on two-dimensional transition-metal dichalcogenides (TMDs) – MoS/GeC, MoSe/GeC, WS/GeC, and WSe/GeC, were studied by density functional theory calculations to investigate their structure, electronic characteristics, principle of photogenerated electron–hole separation, and optical-absorption capability. The optimized heterostructures were formed by van der Waals (vdW) forces and without covalent bonding. Their most stable geometric configurations and band structures display type-II band alignment, which allows them to spontaneously separate photogenerated electrons and holes. The charge difference and built-in electric field across the interface of these vdW heterostructures also contribute to preventing the photogenerated electron–hole recombination. Finally, the high optical absorption of the four TMD-based vdW heterostructures in the visible and near-infrared regions indicates their suitability for photocatalytic, photovoltaic, and optical devices.
    • A stochastic gradient approach for the reliability maximization of passively controlled structures

      Carlon, A.G.; Lopez, R.H.; Espath, L.F.R.; Miguel, L.F.F.; Beck, A.T. (Engineering Structures, Elsevier BV, 2019-02-10) [Article]
      This paper addresses the reduction of the computational burden of structural reliability maximization of passively controlled buildings subject to transient loading. Such a reduction is accomplished by means of Stochastic Gradient Descent (SGD) algorithms, which replace expensive multi-dimensional Monte Carlo integration by a singleton multi-iteration integration. In order to be able to apply SGD methods, the time-dependent structural reliability evaluation was constructed based on the out-crossing rate approach. Design of single and multi Friction Tuned Mass Dampers (FTMDs) are considered as design examples. The proposed SGD algorithm, the accelerated stochastic gradient descent (ASGD) algorithm, efficiently combines Nesterov acceleration, Polyak–Ruppert averaging and restart techniques. The main result drew from the numerical analysis is that SGD algorithms were able to maximize the structural reliability by providing more accurate results and requiring lower computational cost than well-known optimization methods. Finally, the limitation of the proposed optimization procedure is linked to the validity of the out-crossing rate to approximate the time-dependent structural reliability.
    • Supershear tsunami disaster

      Mai, Paul Martin (Nature Geoscience, Springer Nature, 2019-02-04) [Article]
      A magnitude 7.5 strike-slip earthquake that struck Palu, Indonesia, in 2018 unexpectedly generated a devastating tsunami. Seismic data reveal that its rupture propagated fast, at supershear speed. Whether the two are connected remains to be seen.
    • Low NOX - LPG staged combustion double swirl flames

      Elbaz, Ayman M.; Moneib, H.A.; Shebil, K.M.; Roberts, William L. (Renewable Energy, Elsevier BV, 2019-01-30) [Article]
      As a clean, abundant energy source with demonstrated methodologies for producing liquid petroleum gas (LPG) from renewable feedstocks, the growing availability of LPG motivates this study to investigate the utilization of LPG in a staged swirl burner. The burner has an outer and annular swirlers concentric with a central jet, where the flame stability, NO emissions, and flame structure were investigated. The burner allows controlling the degree of mixing by varying swirl angles (θan, θout), and the equivalence ratios of the annular/outer streams (Φan/Φout). The stability mapping showed that the LPG admitted via the annular mixture improves the flame stability more than the outer mixture, and the central fuel injection further improves the flame’s stability. Less segregation between Φan and Φout leads to low NO emissions. Three distinct zones have featured the flame; the recirculation zone (RZ), the reaction zone; and the outer flame zone. High NO concentration was limited to the RZ, so the RZ residence time, mixture strength and temperature at the RZ boundaries are the controlling parameters for NO emissions. The largest θan together with a small θout has a significant effect on reducing the flame temperature and residence time, and thus produces low NO emissions.
    • MobiSeq: De novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements

      Rey-Iglesia, Alba; Gopalakrishan, Shyam; Carøe, Christian; Alquezar-Planas, David E.; Ahlmann Nielsen, Anne; Röder, Timo; Bruhn Pedersen, Lene; Næsborg-Nielsen, Christina; Sinding, Mikkel-Holger S.; Fredensborg Rath, Martin; Li, Zhipeng; Petersen, Bent; Gilbert, M. Thomas P.; Bunce, Michael; Mourier, Tobias; Hansen, Anders Johannes (Molecular Ecology Resources, Wiley, 2018-12-21) [Article]
      In recent years, the availability of reduced representation library (RRL) methods has catalysed an expansion of genome-scale studies to characterize both model and non-model organisms. Most of these methods rely on the use of restriction enzymes to obtain DNA sequences at a genome-wide level. These approaches have been widely used to sequence thousands of markers across individuals for many organisms at a reasonable cost, revolutionizing the field of population genomics. However, there are still some limitations associated with these methods, in particular the high molecular weight DNA required as starting material, the reduced number of common loci among investigated samples, and the short length of the sequenced site-associated DNA. Here, we present MobiSeq, a RRL protocol exploiting simple laboratory techniques, that generates genomic data based on PCR targeted enrichment of transposable elements and the sequencing of the associated flanking region. We validate its performance across 103 DNA extracts derived from three mammalian species: grey wolf (Canis lupus), red deer complex (Cervus sp.) and brown rat (Rattus norvegicus). MobiSeq enables the sequencing of hundreds of thousands loci across the genome and performs SNP discovery with relatively low rates of clonality. Given the ease and flexibility of MobiSeq protocol, the method has the potential to be implemented for marker discovery and population genomics across a wide range of organisms—enabling the exploration of diverse evolutionary and conservation questions.
    • Beyond buying time: the role of plasticity in phenotypic adaptation to rapid environmental change

      Fox, Rebecca J.; Donelson, Jennifer M.; Schunter, Celia; Ravasi, Timothy; Gaitán-Espitia, Juan D. (Philosophical Transactions of the Royal Society B: Biological Sciences, The Royal Society, 2019-01-28) [Article]
      How populations and species respond to modified environmental conditions is critical to their persistence both now and into the future, particularly given the increasing pace of environmental change. The process of adaptation to novel environmental conditions can occur via two mechanisms: (1) the expression of phenotypic plasticity (the ability of one genotype to express varying phenotypes when exposed to different environmental conditions), and (2) evolution via selection for particular phenotypes, resulting in the modification of genetic variation in the population. Plasticity, because it acts at the level of the individual, is often hailed as a rapid-response mechanism that will enable organisms to adapt and survive in our rapidly changing world. But plasticity can also retard adaptation by shifting the distribution of phenotypes in the population, shielding it from natural selection. In addition to which, not all plastic responses are adaptive—now well-documented in cases of ecological traps. In this theme issue, we aim to present a considered view of plasticity and the role it could play in facilitating or hindering adaption to environmental change. This introduction provides a re-examination of our current understanding of the role of phenotypic plasticity in adaptation and sets the theme issue’s contributions in their broader context. Four key themes emerge: the need to measure plasticity across both space and time; the importance of the past in predicting the future; the importance of the link between plasticity and sexual selection; and the need to understand more about the nature of selection on plasticity itself. We conclude by advocating the need for cross-disciplinary collaborations to settle the question of whether plasticity will promote or retard species’ rates of adaptation to ever-more stressful environmental conditions.
    • Porous liquids based on porous cages, metal organic frameworks and metal organic polyhedra

      Bavykina, Anastasiya; Cadiau, Amandine; Gascon, Jorge (Coordination Chemistry Reviews, Elsevier BV, 2019-02-13) [Article]
      The possibility of creating well controlled empty space into liquids is both, conceptually and, from the application point of view, very attractive. Since James, Cooper and co-workers coined the term porous liquid a few years ago, intense research effort has been put into this new class of materials. This review highlights most of the work published to date in this field, with special emphasis on the use of metal organic frameworks, Porous Organic Cages and Metal Organic Polyhedra as pore generators. After discussing some general considerations on the fundamentals of porous liquids, we examine the different synthetic approaches proposed to date and the main challenges in terms of materials synthesis and characterization. Finally, our view on possible future research directions is outlined.
    • Road traffic density estimation and congestion detection with a hybrid observer-based strategy

      Zeroual, Abdelhafid; Harrou, Fouzi; Sun, Ying (Sustainable Cities and Society, Elsevier BV, 2018-12-31) [Article]
      Reliable detection of traffic congestion provides pertinent information for improving safety and comfort by alerting the driver to crowded roads or providing useful information for rapid decision-making. This paper addresses the problem of road traffic congestion estimation and detection from a statistical approach. First, a piecewise switched linear traffic model (PWSL)-based observer is introduced. The proposed hybrid observer (HO) estimates the unmeasured traffic density, thus reducing the cost of implementing and maintenance sensors and measurements devices. Here, the observer gains of each mode are obtained by solving a set of linear matrix inequalities. Second, a novel method for efficiently monitoring traffic congestion is proposed by combining the proposed HO with a generalized likelihood ratio (GLR) test. Also, an exponentially-weighted moving average (EWMA) filter is applied to the residual data to reduce high-frequency noise. Thus, as the EWMA filter, aggregates all of the information from past and actual samples in the decision rule, it extends the congestion detection abilities of the GLR test to the detection of incipient changes. This study shows that a better performance is achieved when GLR is applied to filtered data than to unfiltered data. The effectiveness of the proposed approach is verified on traffic data from the four-lane State Route 60 (SR-60) and the three lanes Interstate 210 (I-210) in California freeways. Results show the efficacy of the proposed HO-based EWMA-GLR method to monitor traffic congestions. Also, the proposed approach is compared to that of the conventional Shewhart and EWMA approaches and found better performance.