New Generations: Sequencing Machines and Their Computational Challenges

New generation sequencing systems are changing how molecular biology is practiced. The widely promoted ＄1000 genome will be a reality with attendant changes for healthcare, including personalized medicine. More broadly the genomes of many new organisms with large samplings from populations will be commonplace. What is less appreciated is the explosive demands on computation, both for CPU cycles and storage as well as the need for new computational methods. In this article we will survey some of these develo...     

A strategy for allowing meaningful and comparable scores in approximate matching

Approximate data matching aims at assessing whether two distinct instances of data represent the same real-world object. The comparison between data values is usually done by applying a similarity function which returns a similarity score. If this score surpasses a given threshold, both data instances are considered as representing the same real-world object. These score values depend on the algorithm that implements the function and have no meaning to the user. In addition, score values generated by different functions are not comparable. This will potentially lead to problems when the scores returned by different similarity functions need to be combined for computing the similarity between records. In this article, we propose that thresholds should be defined in terms of the precision that is expected from the matching process rather than in terms of the raw scores returned by the similarity function. Precision is a widely known similarity metric and has a clear interpretation from the user's point of view. Our approach defines mappings from score values to precision values, which we call adjusted scores. In order to obtain such mappings, our approach requires training over a small dataset. Experiments show that training can be reused for different datasets on the same domain. Our results also demonstrate that existing methods for combining scores for computing the similarity between records may be enhanced if adjusted scores are used.     

Effective visualization of short routes

In this work we develop a new alternative to conventional maps for visualization of relatively short paths as they are frequently encountered in hotels, resorts or museums. Our approach is based on a warped rendering of a 3D model of the environment such that the visualized path appears to be straight even though it may contain several junctions. This has the advantage that the beholder of the image gains a realistic impression of the surroundings along the way which makes it easy to retrace the route in practice. We give an intuitive method for generation of such images and present results from user studies undertaken to evaluate the benefit of the warped images for orientation in unknown environments.     

Towards the development of a virtual environment-based training system for mechanical assembly operations

In this paper, we discuss the development of Virtual Training Studio (VTS), a virtual environment-based training system that allows training supervisors to create training instructions and allows trainees to learn assembly operations in a virtual environment. Our system is mainly focused on the cognitive side of training so that trainees can learn to recognize parts, remember assembly sequences, and correctly orient the parts during assembly operations. Our system enables users to train using the following three training modes: (1) Interactive Simulation, (2) 3D Animation, and (3) Video. Implementing these training modes required us to develop several new system features. This paper presents an overview of the VTS system and describes a few main features of the system. We also report user test results that show how people train using our system. The user test results indicate that the system is able to support a wide variety of training preferences and works well to support training for assembly operations.

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Isoperimetric graph partitioning for image segmentation

Spectral graph partitioning provides a powerful approach to image segmentation. We introduce an alternate idea that finds partitions with a small isoperimetric constant, requiring solution to a linear system rather than an eigenvector problem. This approach produces the high quality segmentations of spectral methods, but with improved speed and stability.     

On the complexity of approximating k-set packing

Given a k-uniform hypergraph, the Maximum k -Set Packing problem is to find the maximum disjoint set of edges. We prove that this problem cannot be efficiently approximated to within a factor of unless P = NP. This improves the previous hardness of approximation factor of by Trevisan. This result extends to the problem of k-Dimensional-Matching.     

Fatigue Crack Propagation in Intercritically Tempered Fe-9Ni-0.1C and Fe-4Mn-0.15C

Fatigue crack propagation was studied for two intercritically tempered cryogenic steels, Fe-9Ni-0.1C and Fe-4Mn-0.15C, at both intermediate (stage II) and low (stage I, near threshold) stress intensity ranges. Propagation rates were determined for varying intercritical tempering times corresponding to varying amounts of retained austenite and untempered martensite. The results show that the heat treatments that optimize impact fracture properties in the nickel steel are also beneficial with respect to the fatigue crack propagation rate in stage I, while no beneficial effect beyond that attributable to carbon redistribution was observed for stage II. For the manganese steel, heat treatments leading to increased concentrations of retained austenite also increased the threshold stress even though no improvement in fracture toughness was observed. To clarify the origin of this improved behavior, the fracture surface was analyzed by Mössbauer Spectroscopy and Auger Electron Microprobe. The Mössbauer results indicated that the retained austenite in the crack path is transformed to martensite as was earlier shown in this laboratory for Charpy specimens. Auger composition analysis suggested a tendency for a stage I crack tip to avoid the mechanically induced brittle untempered martensite in the Fe-Mn steel, while no such preference was observed for stage II.     

Characterization of brevin, a serum protein that shortens actin filaments

We have purified a protein from rabbit serum with a molecular weight of 90,000 that inhibits the polymerization of actin measured viscometrically and that we have named "brevin" (from the Latin breviare, to shorten). From the extent of purification, we estimate that this inhibitor constitutes 0.3% of the total protein in plasma and serum. Brevin is also present in sera from humans and rats. Almost all of the activity in blood is extracellular; only 1% is present in platelets or other cellular elements. Several lines of evidence indicate that brevin is the same protein as the factor described by Fagraeus and Norberg [Fagraeus, A. & Norberg, R. (1978) Curr. Top. Microbiol. Immunol. 82, 1-13] as an actin-depolymerizing factor (ADF). If ADF and brevin are identical, then "ADF" is an inappropriate name because we find that the protein shortens actin filaments without depolymerizing them. Thus, brevin causes little change in the critical concentration of monomeric actin, even though the inhibitor binds to monomeric actin complexed to DNase I-agarose. Binding of brevin to filaments was demonstrated by sedimenting the inhibitor with F-actin. From the amounts of actin and brevin sedimented, and from the lengths of filaments measured by electron microscopy, we calculated that the stoichiometry of binding is one brevin molecule per filament over a wide range of inhibitor concentrations. This stoichiometry suggests that brevin inhibits polymerization by binding at the end of elongating actin filaments, a mechanism similar to that proposed for several intracellular actin-binding proteins and for the cytochalasins. Its abundance suggests that brevin plays an important physiological role in serum, but one not directly concerned with intracellular motility. Therefore its relationship to cytoplasmic actin-binding proteins remains to be determined.     

Experimental demonstration of real-time spectrum analysis using dispersive microstrip

We demonstrate the use of dispersive microstrip as a mechanism for obtaining the real-time Fourier transform of a time-limited signal within a predefined bandwidth. By etching a linearly-chirped impedance modulation into the upper plane strip-width, dispersive microstrip lines are created in which group-delay depends linearly on frequency within a prescribed bandwidth. When the group-delay satisfies a condition that is the temporal analog of the spatial Fraunhofer (far-field) condition of diffraction, the spectral components of an input signal are reordered in time such that the temporal envelope of the output signal corresponds to the Fourier-transform of the input. Experimental results are demonstrated for signals with frequency content from 4 to 8GHz in a 1.2-ns window.