EM algorithm for reconstructing 3D structures of human chromosomes from chromosomal contact data

Recent research suggested that chromosomes have preferred spatial conformations to facilitate necessary long-range interactions and regulations within a nucleus. So that, getting the 3D shape of chromosomes of a genome is very important for understanding how the genome folds and how the genome interact, which can know more about the secrete of life. The introduction of the chromosome conformation capture (3C) based techniques has risen the development of construct the 3D structure of chromosome model. Several works have been done to build the 3D model, among which can be divided into two groups one is consensus methods in early work, the other is ensemble method. In this paper I proposed an ensemble method for reconstructing the 3D structure of chromosome structure. First step is to process Hi-C data, and then do normalization. After that I applied the Bayesian inference model to get an objective function. Finally I used EM based algorithm along with using gradient descent method which is applied in expectation step. I applied the objective function and the optimization method to all 23 Hi-C chromosomal data at a resolution of 1MB

An Open Source Testing Tool for Evaluating Handwriting Input Methods

This paper presents an open source tool for testing the recognition accuracy of Chinese handwriting input methods. The tool consists of two modules, namely the PC and Android mobile client. The PC client reads handwritten samples in the computer, and transfers them individually to the Android client in accordance with the socket communication protocol. After the Android client receives the data, it simulates the handwriting on screen of client device, and triggers the corresponding handwriting recognition method. The recognition accuracy is recorded by the Android client. We present the design principles and describe the implementation of the test platform. We construct several test datasets for evaluating different handwriting recognition systems, and conduct an objective and comprehensive test using six Chinese handwriting input methods with five datasets. The test results for the recognition accuracy are then compared and analyzed.Comment: 5 pages, 3 figures, 11 tables. Accepted to appear at ICDAR 201

Characterization of a glucose-tolerant β-1,4-glucosidase BglC from Cytophaga hutchinsonii

rapidly and sufficiently through a unique mechanism without cellulosome and free cellulases. It was speculated to degrade cellulose with cell-bound cellulases. In this study, a putative GH3 β-glucosidase, BglC, was functionally expressed in Escherichia coli JM109, and the recombinant protein was purified and characterized. BglC was identified as a β-glucosidase with wide substrate specificity. It could not only degrade cellobiose and p-nitrophenyl β-D-glucopyranoside (pNPG) but also degrade cellodextrins such as cellotriose, cellotetrase and cellopentose. BglC had similar specific activity with both cellobiose and pNPG as the substrates. When cellobiose was used as the substrate, certain amount of cellotriose, cellotetrase and cellopentose could be produced besides glucose showing that BglC also had transglycosylation activity. Glucose could inhibite its transglycosylation activity rather than increase it. Study on the biochemical properties of BglC showed that its optimum reaction temperature was 420C and its optimum pH was pH6.5. Mg2 +, Co 2+, Mn2 +, Fe3 + could increase BglC’s activity, while Ni + and Cu2 + decreased its activity. Moreover, BglA was also found to be highly tolerant to glucose as it retained 60 % activity when the concentration of glucose was 100 times higher than that of the substrate (Fig. 1), showing potential application in the bioenergy industry. Point mutations including D303A, E513A, W443A, I336M, D122A, M268A, E188A/R, K224A, R185A/V and S271A led to disappearance of BglC activity indicating these residues were essential for the hydrolytic activity of the enzyme. Point mutations in S82A and I83A increased the hydrolysis activity of BglC by 20% and 30%, repectively. Mutations in I83A, I336S and I336L led to reduce of tolerance to glucose obviously indicating residues I83 and I336 were important not only for the hydrolytic activity of the enzyme but also for its tolerance to glucose. Please click Additional Files below to see the full abstract

Traveling waves for a diffusive SIR-B epidemic model with multiple transmission pathways

In this work, we consider a diffusive SIR-B epidemic model with multiple transmission pathways and saturating incidence rates. We first present the explicit formula of the basic reproduction number R0. Then we show that if R0 > 1, there exists a constant c ∗ > 0 such that the system admits traveling wave solutions connecting the disease-free equilibrium and endemic equilibrium with speed c if and only if c ≥ c Since the system does not admit the comparison principle, we appeal to the standard Schauder’s fixed point theorem to prove the existence of traveling waves. Moreover, a suitable Lyapunov function is constructed to prove the upward convergence of traveling waves

Bistable travelling waves in competitive recursion systems

AbstractThis paper is devoted to the study of spatial dynamics for a class of discrete-time recursion systems, which describes the spatial propagation of two competitive invaders. The existence and global stability of bistable travelling waves are established for such systems under appropriate conditions. The methods involve the upper and lower solutions, spreading speeds of monostable systems, and the monotone semiflows approach