High-resolution imaging of densely connected samples such as pathology slides using digital in-line holographic microscopy requires the acquisition of several holograms, e.g., at >6–8 different sample-to-sensor distances, to achieve robust phase recovery and coherent imaging of specimen. Reducing the number of these holographic measurements would normally result in reconstruction artifacts and loss of image quality, which would be detrimental especially for biomedical and diagnostics-related applications. Inspired by the fact that most natural images are sparse in some domain, here we introduce a sparsity-based phase reconstruction technique implemented in wavelet domain to achieve at least 2-fold reduction in the number of holographic measurements for coherent imaging of densely connected samples with minimal impact on the reconstructed image quality, quantified using a structural similarity index. We demonstrated the success of this approach by imaging Papanicolaou smears and breast cancer tissue slides over a large field-of-view of ~20 mm2 using 2 in-line holograms that are acquired at different sample-to-sensor distances and processed using sparsity-based multi-height phase recovery. This new phase recovery approach that makes use of sparsity can also be extended to other coherent imaging schemes, involving e.g., multiple illumination angles or wavelengths to increase the throughput and speed of coherent imaging.
Xie, Yu; Wodo, Olga; Ganapathysubramanian, Baskar(Advances in Computational Fluid-Structure Interaction and Flow Simulation, Springer Nature, 2016-10-04)[Book Chapter]
In this chapter, we explore numerical simulations of incompressible and immiscible two-phase flows. The description of the fluid–fluid interface is introduced via a diffuse interface approach. The two-phase fluid system is represented by a coupled Cahn–Hilliard Navier–Stokes set of equations. We discuss challenges and approaches to solving this coupled set of equations using a stabilized finite element formulation, especially in the case of a large density ratio between the two fluids. Specific features that enabled efficient solution of the equations include: (i) a conservative form of the convective term in the Cahn–Hilliard equation which ensures mass conservation of both fluid components; (ii) a continuous formula to compute the interfacial surface tension which results in lower requirement on the spatial resolution of the interface; and (iii) a four-step fractional scheme to decouple pressure from velocity in the Navier–Stokes equation. These are integrated with standard streamline-upwind Petrov–Galerkin stabilization to avoid spurious oscillations. We perform numerical tests to determine the minimal resolution of spatial discretization. Finally, we illustrate the accuracy of the framework using the analytical results of Prosperetti for a damped oscillating interface between two fluids with a density contrast.
Bernstein, W. N.; Hughen, K. A.; Langdon, C.; McCorkle, D. C.; Lentz, S. J.(Coral Reefs, Springer Nature, 2016-01-23)[Article]
Coral growth and carbonate accumulation form the foundation of the coral reef ecosystem. Changes in environmental conditions due to coastal development, climate change, and ocean acidification may pose a threat to net carbonate production in the near future. Controlled laboratory studies demonstrate that calcification by corals and coralline algae is sensitive to changes in aragonite saturation state (Ωa), as well as temperature, light, and nutrition. Studies also show that the dissolution rate of carbonate substrates is impacted by changes in carbonate chemistry. The sensitivity of coral reefs to these parameters must be confirmed and quantified in the natural environment in order to predict how coral reefs will respond to local and global changes, particularly ocean acidification. We estimated the daytime hourly net community metabolic rates, both net community calcification (NCC) and net community productivity (NCP), at Sheltered Reef, an offshore platform reef in the central Red Sea. Average NCC was 8 ± 3 mmol m−2 h−1 in December 2010 and 11 ± 1 mmol m−2 h−1 in May 2011, and NCP was 21 ± 7 mmol m−2 h−1 in December 2010 and 44 ± 4 mmol m−2 h−1 in May 2011. We also monitored a suite of physical and chemical properties to help relate the rates at Sheltered Reef to published rates from other sites. While previous research shows that short-term field studies investigating the NCC–Ωa relationship have differing results due to confounding factors, it is important to continue estimating NCC in different places, seasons, and years, in order to monitor changes in NCC versus Ω in space and time, and to ultimately resolve a broader understanding of this relationship.
The low biomass in environmental samples is a major challenge for microbial metagenomic studies. The amplification of a genomic DNA was frequently applied to meeting the minimum requirement of the DNA for a high-throughput next-generation-sequencing technology. Using a synthetic bacterial community, the amplification efficiency of the Multiple Annealing and Looping Based Amplification Cycles (MALBAC) kit that is originally developed to amplify the single-cell genomic DNA of mammalian organisms is examined. The DNA template of 10 pg in each reaction of the MALBAC amplification may generate enough DNA for Illumina sequencing. Using 10 pg and 100 pg templates for each reaction set, the MALBAC kit shows a stable and homogeneous amplification as indicated by the highly consistent coverage of the reads from the two amplified samples on the contigs assembled by the original unamplified sample. Although GenomePlex whole genome amplification kit allows one to generate enough DNA using 100 pg of template in each reaction, the minority of the mixed bacterial species is not linearly amplified. For both of the kits, the GC-rich regions of the genomic DNA are not efficiently amplified as suggested by the low coverage of the contigs with the high GC content. The high efficiency of the MALBAC kit is supported for the amplification of environmental microbial DNA samples, and the concerns on its application are also raised to bacterial species with the high GC content.
Rosen, Paul; Burton, Brett; Potter, Kristin; Johnson, Chris R.(Visualization in Medicine and Life Sciences III, Springer Nature, 2016-05-23)[Book Chapter]
In this paper we describe the Myocardial Uncertainty Viewer (muView or μView) system for exploring data stemming from the simulation of cardiac ischemia. The simulation uses a collection of conductivity values to understand how ischemic regions effect the undamaged anisotropic heart tissue. The data resulting from the simulation is multi-valued and volumetric, and thus, for every data point, we have a collection of samples describing cardiac electrical properties. μView combines a suite of visual analysis methods to explore the area surrounding the ischemic zone and identify how perturbations of variables change the propagation of their effects. In addition to presenting a collection of visualization techniques, which individually highlight different aspects of the data, the coordinated view system forms a cohesive environment for exploring the simulations. We also discuss the findings of our study, which are helping to steer further development of the simulation and strengthening our collaboration with the biomedical engineers attempting to understand the phenomenon.
Li, Yan Vivian; Cathles, Lawrence M.(Journal of Nanoparticle Research, Springer Nature, 2016-03-02)[Article]
A new class of nearly charge-neutral carbon-cored nanoparticle tracers are remarkably non-interactive with solid surfaces and could provide a valuable baseline for diverse hydrological and environmental studies of subsurface flow and particle transport. We investigate the causes of inertness by studying the interactions with calcite of a nanoparticle of this class synthesized from malic acid and ethanolamine (M-dots) dispersed in brine (NaCl, CaCl2, and MgCl2) solutions. None of the M-dots are retained in calcite sand-packed columns when dispersed in DI water. Dispersed in the NaCl and mixed brine solutions, 5.6 % of and 7.3 % of the M-dots are initially retained, but 65 and 13 % of these retained particles are subsequently released when the column is flushed with DI water. When dispersed in the CaCl2 and MgCl2 solutions, 65 and 54 % of the M-dots are initially retained, and 28 and 26 % subsequently released in the DI water flush. The M-dots have a small negative zeta potential in all solutions, but the calcite zeta potential changes from strongly negative to strongly positive across the solution series, and the particle retention tracks this change. Derjaguin–Landau–Verwey–Overbeek (DLVO) modeling of the force between a calcite probe and an M-dot coated surface shows that hydration forces repel the particles in the DI water, NaCl, and mixed solutions, but not in the CaCl2 and MgCl2 solutions. These results show that near-zero charge and strongly hydrophilic decoration are the causes of the remarkable inertness of carbon-cored nanoparticles, and also suggest that nanoparticles could be useful in solute-surface interaction studies.
Solution-processed photovoltaic technologies represent a promising way to reduce the cost and increase the efficiency of solar energy harvesting. Among these, colloidal semiconductor quantum dot photovoltaics have the advantage of a spectrally tuneable infrared bandgap, which enables use in multi-junction cells, as well as the benefit of generating and harvesting multiple charge carrier pairs per absorbed photon. Here we review recent progress in colloidal quantum dot photovoltaics, focusing on three fronts. First, we examine strategies to manage the abundant surfaces of quantum dots, strategies that have led to progress in the removal of electronic trap states. Second, we consider new device architectures that have improved device performance to certified efficiencies of 10.6%. Third, we focus on progress in solution-phase chemical processing, such as spray-coating and centrifugal casting, which has led to the demonstration of manufacturing-ready process technologies.
Developing lightweight, flexible, foldable and sustainable power sources with simple transport and storage remains a challenge and an urgent need for the advancement of next-generation wearable electronics. Here, we report a micro-cable power textile for simultaneously harvesting energy from ambient sunshine and mechanical movement. Solar cells fabricated from lightweight polymer fibres into micro cables are then woven via a shuttle-flying process with fibre-based triboelectric nanogenerators to create a smart fabric. A single layer of such fabric is 320 μm thick and can be integrated into various cloths, curtains, tents and so on. This hybrid power textile, fabricated with a size of 4 cm by 5 cm, was demonstrated to charge a 2 mF commercial capacitor up to 2 V in 1 min under ambient sunlight in the presence of mechanical excitation, such as human motion and wind blowing. The textile could continuously power an electronic watch, directly charge a cell phone and drive water splitting reactions.
In light of concerns about global warming and energy crises, searching for renewable energy resources that are not detrimental to the environment is one of the most urgent challenges to the sustainable development of human civilization1,2,3. Generating electricity from natural forces provides a superior solution to alleviate expanding energy needs on a sustainable basis4,5,6,7,8,9. With the rapid advancement of modern technologies, developing lightweight, flexible, sustainable and stable power sources remains both highly desirable and a challenge10,11,12,13,14,15,16. Solar irradiance and mechanical motion are clean and renewable energy sources17,18,19,20,21,22,23,24. Fabric-based materials are most common for humans and fibre-based textiles can effectively accommodate the complex deformations induced by body motion25,26,27,28,29,30,31,32. A smart textile that generates electrical power from absorbed solar irradiance and mechanical motion could be an important step towards next-generation wearable electronics.
Here, we present a foldable and sustainable power source by fabricating an all-solid hybrid power textile with economically viable materials and scalable fabrication technologies. Based on lightweight and low-cost polymer fibres, the reported hybrid power textile introduces a new module fabrication strategy by weaving it in a staggered way on an industrial weaving machine via a shuttle-flying process. Colourful textile modules with arbitrary size and various weaving patterns are demonstrated. Featuring decent breathability and robustness, the hybrid power textile was demonstrated to harvest energy simultaneously from ambient sunshine and human biomechanical movement in a wearable manner with or without encapsulation. The hybrid power textile is highly deformable in response to human motion. Mixed with colourful wool fibres, the hybrid power textile with a size of 4 cm by 5 cm is capable of stably delivering an output power of 0.5 mW with a wide range of loading resistances from 10 KΩ to 10 MΩ for a human walking under sunlight of intensity 80 mW cm−2. More importantly, the power textile can be also adopted for large-area application such as curtains and tents. Under ambient sunlight with movement of a car or wind blowing, the textile delivered sufficient power to charge a 2 mF commercial capacitor up to 2 V in 1 min, continuously drive an electronic watch, directly charge a cell phone, as well as drive the water splitting reactions.
Burger, Martin; Papafitsoros, Konstantinos; Papoutsellis, Evangelos; Schönlieb, Carola-Bibiane(Journal of Mathematical Imaging and Vision, Springer Nature, 2016-02-03)[Article]
We study a general class of infimal convolution type regularisation functionals suitable for applications in image processing. These functionals incorporate a combination of the total variation seminorm and Lp norms. A unified well-posedness analysis is presented and a detailed study of the one-dimensional model is performed, by computing exact solutions for the corresponding denoising problem and the case p=2. Furthermore, the dependency of the regularisation properties of this infimal convolution approach to the choice of p is studied. It turns out that in the case p=2 this regulariser is equivalent to the Huber-type variant of total variation regularisation. We provide numerical examples for image decomposition as well as for image denoising. We show that our model is capable of eliminating the staircasing effect, a well-known disadvantage of total variation regularisation. Moreover as p increases we obtain almost piecewise affine reconstructions, leading also to a better preservation of hat-like structures.
Elbehery, Ali H. A.; Aziz, Ramy K.; Siam, Rania(Extremophiles, Springer Nature, 2016-12-03)[Article]
Mobile genetic elements are major agents of genome diversification and evolution. Limited studies addressed their characteristics, including abundance, and role in extreme habitats. One of the rare natural habitats exposed to multiple-extreme conditions, including high temperature, salinity and concentration of heavy metals, are the Red Sea brine pools. We assessed the abundance and distribution of different mobile genetic elements in four Red Sea brine pools including the world’s largest known multiple-extreme deep-sea environment, the Red Sea Atlantis II Deep. We report a gradient in the abundance of mobile genetic elements, dramatically increasing in the harshest environment of the pool. Additionally, we identified a strong association between the abundance of insertion sequences and extreme conditions, being highest in the harshest and deepest layer of the Red Sea Atlantis II Deep. Our comparative analyses of mobile genetic elements in secluded, extreme and relatively non-extreme environments, suggest that insertion sequences predominantly contribute to polyextremophiles genome plasticity.
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