Hybrid error correction and de novo assembly of single-molecule sequencing reads.

Single-molecule sequencing instruments can generate multikilobase sequences with the potential to greatly improve genome and transcriptome assembly. However, the error rates of single-molecule reads are high, which has limited their use thus far to resequencing bacteria. To address this limitation, we introduce a correction algorithm and assembly strategy that uses short, high-fidelity sequences to correct the error in single-molecule sequences. We demonstrate the utility of this approach on reads generated by a PacBio RS instrument from phage, prokaryotic and eukaryotic whole genomes, including the previously unsequenced genome of the parrot Melopsittacus undulatus, as well as for RNA-Seq reads of the corn (Zea mays) transcriptome. Our long-read correction achieves >99.9% base-call accuracy, leading to substantially better assemblies than current sequencing strategies: in the best example, the median contig size was quintupled relative to high-coverage, second-generation assemblies. Greater gains are predicted if read lengths continue to increase, including the prospect of single-contig bacterial chromosome assembly.

Accurate localized resolution of identity approach for linear-scaling hybrid density functionals and for many-body perturbation theory

© 2015 IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.A key component in calculations of exchange and correlation energies is the Coulomb operator, which requires the evaluation of two-electron integrals. For localized basis sets, these four-center integrals are most efficiently evaluated with the resolution of identity (RI) technique, which expands basis-function products in an auxiliary basis. In this work we show the practical applicability of a localized RI-variant ('RI-LVL'), which expands products of basis functions only in the subset of those auxiliary basis functions which are located at the same atoms as the basis functions. We demonstrate the accuracy of RI-LVL for Hartree-Fock calculations, for the PBE0 hybrid density functional, as well as for RPA and MP2 perturbation theory. Molecular test sets used include the S22 set of weakly interacting molecules, the G3 test set, as well as the G2-1 and BH76 test sets, and heavy elements including titanium dioxide, copper and gold clusters. Our RI-LVL implementation paves the way for linear-scaling RI-based hybrid functional calculations for large systems and for all-electron many-body perturbation theory with significantly reduced computational and memory cost.

Investigation and Development of a Fully 3D Tilt Capable Hybrid SPECT - CT System for Dedicated Breast Imaging

X-ray mammography has been the gold standard for breast imaging for decades, despite the significant limitations posed by the two dimensional (2D) image acquisitions. Difficulty in diagnosing lesions close to the chest wall and axilla, high amount of structural overlap and patient discomfort due to compression are only some of these limitations. To overcome these drawbacks, three dimensional (3D) breast imaging modalities have been developed including dual modality single photon emission computed tomography (SPECT) and computed tomography (CT) systems. This thesis focuses on the development and integration of the next generation of such a device for dedicated breast imaging. The goals of this dissertation work are to: [1] understand and characterize any effects of fully 3-D trajectories on reconstructed image scatter correction, absorbed dose and Hounsifeld Unit accuracy, and [2] design, develop and implement the fully flexible, third generation hybrid SPECT-CT system capable of traversing complex 3D orbits about a pendant breast volume, without interference from the other. Such a system would overcome artifacts resulting from incompletely sampled divergent cone beam imaging schemes and allow imaging closer to the chest wall, which other systems currently under research and development elsewhere cannot achieve.

The dependence of x-ray scatter radiation on object shape, size, material composition and the CT acquisition trajectory, was investigated with a well-established beam stop array (BSA) scatter correction method. While the 2D scatter to primary ratio (SPR) was the main metric used to characterize total system scatter, a new metric called ‘normalized scatter contribution’ was developed to compare the results of scatter correction on 3D reconstructed volumes. Scatter estimation studies were undertaken with a sinusoidal saddle (±15° polar tilt) orbit and a traditional circular (AZOR) orbit. Clinical studies to acquire data for scatter correction were used to evaluate the 2D SPR on a small set of patients scanned with the AZOR orbit. Clinical SPR results showed clear dependence of scatter on breast composition and glandular tissue distribution, otherwise consistent with the overall phantom-based size and density measurements. Additionally, SPR dependence was also observed on the acquisition trajectory where 2D scatter increased with an increase in the polar tilt angle of the system.

The dose delivered by any imaging system is of primary importance from the patient’s point of view, and therefore trajectory related differences in the dose distribution in a target volume were evaluated. Monte Carlo simulations as well as physical measurements using radiochromic film were undertaken using saddle and AZOR orbits. Results illustrated that both orbits deliver comparable dose to the target volume, and only slightly differ in distribution within the volume. Simulations and measurements showed similar results, and all measured dose values were within the standard screening mammography-specific, 6 mGy dose limit, which is used as a benchmark for dose comparisons.

Hounsfield Units (HU) are used clinically in differentiating tissue types in a reconstructed CT image, and therefore the HU accuracy of a system is very important, especially when using non-traditional trajectories. Uniform phantoms filled with various uniform density fluids were used to investigate differences in HU accuracy between saddle and AZOR orbits. Results illustrate the considerably better performance of the saddle orbit, especially close to the chest and nipple region of what would clinically be a pedant breast volume. The AZOR orbit causes shading artifacts near the nipple, due to insufficient sampling, rendering a major portion of the scanned phantom unusable, whereas the saddle orbit performs exceptionally well and provides a tighter distribution of HU values in reconstructed volumes.

Finally, the third generation, fully-suspended SPECT-CT system was designed in and developed in our lab. A novel mechanical method using a linear motor was developed for tilting the CT system. A new x-ray source and a custom made 40 x 30 cm2 detector were integrated on to this system. The SPECT system was nested, in the center of the gantry, orthogonal to the CT source-detector pair. The SPECT system tilts on a goniometer, and the newly developed CT tilting mechanism allows ±15° maximum polar tilting of the CT system. The entire gantry is mounted on a rotation stage, allowing complex arbitrary trajectories for each system, without interference from the other, while having a common field of view. This hybrid system shows potential to be used clinically as a diagnostic tool for dedicated breast imaging.

Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi.

Although cell cycle control is an ancient, conserved, and essential process, some core animal and fungal cell cycle regulators share no more sequence identity than non-homologous proteins. Here, we show that evolution along the fungal lineage was punctuated by the early acquisition and entrainment of the SBF transcription factor through horizontal gene transfer. Cell cycle evolution in the fungal ancestor then proceeded through a hybrid network containing both SBF and its ancestral animal counterpart E2F, which is still maintained in many basal fungi. We hypothesize that a virally-derived SBF may have initially hijacked cell cycle control by activating transcription via the cis-regulatory elements targeted by the ancestral cell cycle regulator E2F, much like extant viral oncogenes. Consistent with this hypothesis, we show that SBF can regulate promoters with E2F binding sites in budding yeast.

We want to touch IT. Are hybrid laptops just new fancy gadgets or a new revolution?

While the number of traditional laptops and computers sold has dipped slightly year over year, manufacturers have developed new hybrid laptops with touch screens to build on the tactile trend. This market is moving quickly to make touch the rule rather than the exception and the sales of these devices have tripled since the launch of Windows 8 in 2012, to reach more than sixty million units sold in 2015. Unlike tablets, that benefit from easy-to-use applications specially designed for tactile interactions, hybrid laptops are intended to be used with regular user-interfaces. Hence, one could ask whether tactile interactions are suited for every task and activity performed with such interfaces. Since hybrid laptops are increasingly used in educational situations, this study focuses on information search tasks which are commonly performed for learning purposes. It is hypothesized that tasks that require complex and/or less common gestures will increase user's cognitive load and impair task performance in terms of efficacy and efficiency. A study was carried out in a usability laboratory with 30 participants for whom prior experience with tactile devices has been controlled. They were asked to perform information search tasks on an online encyclopaedia by using only the touch screen of and hybrid laptop. Tasks were selected with respect to their level of cognitive demand (amount of information that had to be maintained in working memory) and the complexity of gestures needed (left and/or right clicks, zoom, text selection and/or input.), and grouped into 4 sets accordingly. Task performance was measured by the number of tasks succeeded (efficacy) and time spent on each task (efficiency). Perceived cognitive load was assessed thanks to a questionnaire given after each set of tasks. An eye tracking device was used to monitor users' attention allocation and to provide objective cognitive load measures based on pupil dilation and the Index of Cognitive Activity. Each experimental run took approximately one hour. The results of this within-subjects design indicate that tasks involving complex gestures led to a lower efficacy, especially when the tasks were cognitively demanding. Regarding efficacy, there is no significant differences between sets of tasks excepted for tasks with low cognitive demand and complex gestures that required more time to be achieved. Surprisingly, users that declared the biggest experience with tactile devices spent more time than less frequent users. Cognitive load measures indicate that participants reported having devoted more mental effort in the interaction when they had to use complex gestures.

Yields for four inbred lines and six F1 hybrid of silkworm in Argentina

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A novel neural/symbolic hybrid approach to heuristically optimized fuel allocation and automated revision of heuristics in nuclear engineering

FUELCON is an expert system for optimized refueling design in nuclear engineering. This task is crucial for keeping down operating costs at a plant without compromising safety. FUELCON proposes sets of alternative configurations of allocation of fuel assemblies that are each positioned in the planar grid of a horizontal section of a reactor core. Results are simulated, and an expert user can also use FUELCON to revise rulesets and improve on his or her heuristics. The successful completion of FUELCON led this research team into undertaking a panoply of sequel projects, of which we provide a meta-architectural comparative formal discussion. In this paper, we demonstrate a novel adaptive technique that learns the optimal allocation heuristic for the various cores. The algorithm is a hybrid of a fine-grained neural network and symbolic computation components. This hybrid architecture is sensitive enough to learn the particular characteristics of the ‘in-core fuel management problem’ at hand, and is powerful enough to use this information fully to automatically revise heuristics, thus improving upon those provided by a human expert.

A blackboard architecture for a hybrid CBR system for scientific software

This paper describes the use of a blackboard architecture for building a hybrid case based reasoning (CBR) system. The Smartfire fire field modelling package has been built using this architecture and includes a CBR component. It allows the integration into the system of qualitative spatial reasoning knowledge from domain experts. The system can be used for the automatic set-up of fire field models. This enables fire safety practitioners who are not expert in modelling techniques to use a fire modelling tool. The paper discusses the integrating powers of the architecture, which is based on a common knowledge representation comprising a metric diagram and place vocabulary and mechanisms for adaptation and conflict resolution built on the Blackboard.

A hybrid fractal video compression method

Fractal image compression is a relatively recent image compression method. Its extension to a sequence of motion images is important in video compression applications. There are two basic fractal compression methods, namely the cube-based and the frame-based methods, being commonly used in the industry. However there are advantages and disadvantages in both methods. This paper proposes a hybrid algorithm highlighting the advantages of the two methods in order to produce a good compression algorithm for video industry. Experimental results show the hybrid algorithm improves the compression ratio and the quality of decompressed images.

Adaptive partition and hybrid method in fractal video compression

Fractal image compression is a relatively recent image compression method, which is simple to use and often leads to a high compression ratio. These advantages make it suitable for the situation of a single encoding and many decoding, as required in video on demand, archive compression, etc. There are two fundamental fractal compression methods, namely, the cube-based and the frame-based methods, being commonly studied. However, there are advantages and disadvantages in both methods. This paper gives an extension of the fundamental compression methods based on the concept of adaptive partition. Experimental results show that the algorithms based on adaptive partition may obtain a much higher compression ratio compared to algorithms based on fixed partition while maintaining the quality of decompressed images.

A hybrid Laplace transform/finite difference boundary element method for diffusion problems

The solution process for diffusion problems usually involves the time development separately from the space solution. A finite difference algorithm in time requires a sequential time development in which all previous values must be determined prior to the current value. The Stehfest Laplace transform algorithm, however, allows time solutions without the knowledge of prior values. It is of interest to be able to develop a time-domain decomposition suitable for implementation in a parallel environment. One such possibility is to use the Laplace transform to develop coarse-grained solutions which act as the initial values for a set of fine-grained solutions. The independence of the Laplace transform solutions means that we do indeed have a time-domain decomposition process. Any suitable time solver can be used for the fine-grained solution. To illustrate the technique we shall use an Euler solver in time together with the dual reciprocity boundary element method for the space solution

A move toward hybrid interregionalism in Asia

The chapter provides a critical overview of European engagement with Asia, and reviews the contemporary economic cooperation and trade relations between the two regions. The chapter concludes with a critical assessment of the nature of EU interregionalism and speculates on the influence and actorness of the European Union in Asia.