On pairwise distances and median score of three genomes under DCJ

In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evolutionary remoteness. Generalization of this measure to three genomes is known as the median score (while a resulting genome is called median genome). In contrast to the rearrangement distance between two genomes which can be computed in linear time, computing the median score for three genomes is NP-hard. This inspires a quest for simpler and faster approximations for the median score, the most natural of which appears to be the halved sum of pairwise distances which in fact represents a lower bound for the median score. In this work, we study relationship and interplay of pairwise distances between three genomes and their median score under the model of Double-Cut-and-Join (DCJ) rearrangements. Most remarkably we show that while a rearrangement may change the sum of pairwise distances by at most 2 (and thus change the lower bound by at most 1), even the most "powerful" rearrangements in this respect that increase the lower bound by 1 (by moving one genome farther away from each of the other two genomes), which we call strong, do not necessarily affect the median score. This observation implies that the two measures are not as well-correlated as one's intuition may suggest. We further prove that the median score attains the lower bound exactly on the triples of genomes that can be obtained from a single genome with strong rearrangements. While the sum of pairwise distances with the factor 2/3 represents an upper bound for the median score, its tightness remains unclear. Nonetheless, we show that the difference of the median score and its lower bound is not bounded by a constant.Comment: Proceedings of the 10-th Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG), 2012. (to appear

Low frequency noise in chemical vapor deposited MoS2

Inherent low frequency noise is a ubiquitous phenomenon, which limits operation and performance of electronic devices and circuits. This limiting factor is very important for nanoscale electronic devices, such as 2D semiconductor devices. In this work, low frequency noise in high mobility single crystal MoS2 grown by chemical vapor deposition (CVD) is investigated. The measured low frequency noise follows an empirical formulation of mobility fluctuations with Hooge' s parameter ranging between 1.44E-3 and 3.51E-2. Small variation of Hooge's parameter suggests superior material uniformity and processing control of CVD grown MoS2 devices than reported single-layer MoS2 FET. The extracted Hooge's parameter is one order of magnitude lower than CVD grown graphene. The Hooge's parameter shows an inverse relationship with the field mobility

Human Arm simulation for interactive constrained environment design

During the conceptual and prototype design stage of an industrial product, it is crucial to take assembly/disassembly and maintenance operations in advance. A well-designed system should enable relatively easy access of operating manipulators in the constrained environment and reduce musculoskeletal disorder risks for those manual handling operations. Trajectory planning comes up as an important issue for those assembly and maintenance operations under a constrained environment, since it determines the accessibility and the other ergonomics issues, such as muscle effort and its related fatigue. In this paper, a customer-oriented interactive approach is proposed to partially solve ergonomic related issues encountered during the design stage under a constrained system for the operator's convenience. Based on a single objective optimization method, trajectory planning for different operators could be generated automatically. Meanwhile, a motion capture based method assists the operator to guide the trajectory planning interactively when either a local minimum is encountered within the single objective optimization or the operator prefers guiding the virtual human manually. Besides that, a physical engine is integrated into this approach to provide physically realistic simulation in real time manner, so that collision free path and related dynamic information could be computed to determine further muscle fatigue and accessibility of a product designComment: International Journal on Interactive Design and Manufacturing (IJIDeM) (2012) 1-12. arXiv admin note: substantial text overlap with arXiv:1012.432

What promotes greater use of the corporate bond market? A study of the issuance behaviour of firms in Asia

This paper investigates bond market development in Asia by exploring the determinants of firms' decisions to issue public debt in a range of Asian economies. Using a novel database covering the period 1995 to 2007, we use comparable micro level panel of nine countries - China, Hong Kong, Indonesia, Korea, Malaysia, Philippines, Singapore, Taiwan and Thailand - to explore factors that promote bond issuance by firms. We control for firm characteristics and market features such as bond market depth and liquidity; we also consider supra-national policy initiatives to improve bond market function. Our paper demonstrates that regional initiatives have been an important step towards greater bond issuance by firms in Asia, mostly by fostering market deepening and improving liquidity

Simplified three-dimensional tissue clearing and incorporation of colorimetric phenotyping.

Tissue clearing methods promise to provide exquisite three-dimensional imaging information; however, there is a need for simplified methods for lower resource settings and for non-fluorescence based phenotyping to enable light microscopic imaging modalities. Here we describe the simplified CLARITY method (SCM) for tissue clearing that preserves epitopes of interest. We imaged the resulting tissues using light sheet microscopy to generate rapid 3D reconstructions of entire tissues and organs. In addition, to enable clearing and 3D tissue imaging with light microscopy methods, we developed a colorimetric, non-fluorescent method for specifically labeling cleared tissues based on horseradish peroxidase conversion of diaminobenzidine to a colored insoluble product. The methods we describe here are portable and can be accomplished at low cost, and can allow light microscopic imaging of cleared tissues, thus enabling tissue clearing and imaging in a wide variety of settings

A critical analysis of mobility management related issues of wireless sensor networks in cyber physical systems

Mobility management has been a long-standing issue in mobile wireless sensor networks and especially in the context of cyber physical systems; its implications are immense. This paper presents a critical analysis of the current approaches to mobility management by evaluating them against a set of criteria which are essentially inherent characteristics of such systems on which these approaches are expected to provide acceptable performance. We summarize these characteristics by using a quadruple set of metrics. Additionally, using this set we classify the various approaches to mobility management that are discussed in this paper. Finally, the paper concludes by reviewing the main findings and providing suggestions that will be helpful to guide future research efforts in the area