Fitting stochastic epidemic models to gene genealogies using linear noise approximation

Phylodynamics is a set of population genetics tools that aim at reconstructing demographic history of a population based on molecular sequences of individuals sampled from the population of interest. One important task in phylodynamics is to estimate changes in (effective) population size. When applied to infectious disease sequences such estimation of population size trajectories can provide information about changes in the number of infections. To model changes in the number of infected individuals, current phylodynamic methods use non-parametric approaches, parametric approaches, and stochastic modeling in conjunction with likelihood-free Bayesian methods. The first class of methods yields results that are hard-to-interpret epidemiologically. The second class of methods provides estimates of important epidemiological parameters, such as infection and removal/recovery rates, but ignores variation in the dynamics of infectious disease spread. The third class of methods is the most advantageous statistically, but relies on computationally intensive particle filtering techniques that limits its applications. We propose a Bayesian model that combines phylodynamic inference and stochastic epidemic models, and achieves computational tractability by using a linear noise approximation (LNA) --- a technique that allows us to approximate probability densities of stochastic epidemic model trajectories. LNA opens the door for using modern Markov chain Monte Carlo tools to approximate the joint posterior distribution of the disease transmission parameters and of high dimensional vectors describing unobserved changes in the stochastic epidemic model compartment sizes (e.g., numbers of infectious and susceptible individuals). We apply our estimation technique to Ebola genealogies estimated using viral genetic data from the 2014 epidemic in Sierra Leone and Liberia.Comment: 43 pages, 6 figures in the main tex

Compressive Sensing Based on HQS for Image reconstruction

This work solves the image distortion problem caused by the noise generated during the sampling and reconstruction process, a compressive sensing algorithm based on half quadratic splitting (CS-HQS) is proposed to reconstruct images in this paper. For the part dominated by error terms, the regularization term is introduced and the second-order momentum adaptive gradient descent method is used to get the auxiliary variables. For the part dominated by the sparse prior of compressive sensing, the Bayesian maximum posterior inference is used to get the sparse coeffi cient. The combination of the two methods not only avoids the generation of random noise, but also enhances the stability of the model. The experimental results demonstrate that the strong robustness of the proposed algorithm

Far-field Super-resolution Chemical Microscopy

Far-field chemical microscopy providing molecular electronic or vibrational fingerprint information opens a new window for the study of three-dimensional biological, material, and chemical systems. Chemical microscopy provides a nondestructive way of chemical identification without exterior labels. However, the diffraction limit of optics hindered it from discovering more details under the resolution limit. Recent development of super-resolution techniques gives enlightenment to open this door behind far-field chemical microscopy. Here, we review recent advances that have pushed the boundary of far-field chemical microscopy in terms of spatial resolution. We further highlight applications in biomedical research, material characterization, environmental study, cultural heritage conservation, and integrated chip inspection.Comment: 34 pages, 8 figures,1 tabl

Microwave-assisted non-thermal hemp degumming

The microwave-assisted non-thermal degumming of hemp fibre has been studied and then compared with the water bath heating under different time and temperature conditions. The results show that the residual gum content of the lean hemp using microwave-assisted heating method is lower than that obtained using water bath heating. The residual gum content gap between the two degumming processes increases first and then decreases as the heating time and temperature are increased. This proves the existence of non-thermal effects in microwave heating process besides the thermal effects in water bath heating. In addition, the structures of the lean hemp fibres obtained from these two methods are also studied by scanning electron microscopy and fourier transform infrared spectroscopy.

MicroRNA-9-5p inhibits osteosarcoma cell promotion, metastasis and resistance to apoptosis via negatively targeting Grb2-associated binding protein 2

521-529The study explores the inhibition effects of MicroRNAs in osteosarcoma, as a means of suggesting it as treatment for bone cancer. MicroRNAs (miRNAs) are a sort of noncoding RNA molecules that regulates gene expression by targeting mRNAs and play critical roles in tumor development. This study probed the effect of miR-9-5p on osteosarcoma development. Human osteosarcoma cell lines U2-OS, 143B, MG63 and HOS and normal human osteoblast cell line hFOB were cultivated and expression of miR-9-5p and Grb2-associated binding protein 2 (Gab2) measured. The binding of miR-9-5p and Gab2 was confirmed using a bio-information program and dual luciferase reporter gene assay. Loss-of-functions of miR-9-5p and Gab2 were performed to measure their roles in osteosarcoma cell proliferation, invasion, migration and resistance to death. Result showed high miR-9-5p expression and low Gab2 expression in osteosarcoma cells, particularly in U2-OS cells. miR-9-5p directly bound to the 3¢untranslated region of Gab2. Down-regulated miR-9-5p induced U2-OS cell proliferation, invasion and the resistance to death, while conversely, silenced Gab2 led to an opposite trend on U2-OS cell growth and metastasis. Moreover, co-effect of inhibited miR-9-5p and silenced Gab2 led to decreased cell proliferation but promoted cell apoptosis compared to inhibited miR-9-5p alone, while it led to enhanced cell proliferation and invasion, but reduced cell apoptosis compared to silenced Gab2 alone. To conclude, this study demonstrated that miR-9-5p could inhibit osteosarcoma cell proliferation, invasion, migration and resistance to death via negatively targeting Gab2

LATS kinase-mediated CTCF phosphorylation and selective loss of genomic binding.

Chromatin topological organization is instrumental in gene transcription. Gene-enhancer interactions are accommodated in the same CTCF-mediated insulated neighborhoods. However, it remains poorly understood whether and how the 3D genome architecture is dynamically restructured by external signals. Here, we report that LATS kinases phosphorylated CTCF in the zinc finger (ZF) linkers and disabled its DNA-binding activity. Cellular stress induced LATS nuclear translocation and CTCF ZF linker phosphorylation, and altered the landscape of CTCF genomic binding partly by dissociating it selectively from a small subset of its genomic binding sites. These sites were highly enriched for the boundaries of chromatin domains containing LATS signaling target genes. The stress-induced CTCF phosphorylation and locus-specific dissociation from DNA were LATS-dependent. Loss of CTCF binding disrupted local chromatin domains and down-regulated genes located within them. The study suggests that external signals may rapidly modulate the 3D genome by affecting CTCF genomic binding through ZF linker phosphorylation

On-Chip Super-Resolution Imaging with Fluorescent Polymer Films

Wide field of view (FOV), label-free super-resolution imaging is demonstrated using a specially designed waveguide chip that can illuminate a sample with multi-colour evanescent waves travelling along different directions. The method is enabled by a polymer fluorescent film which emits over a broad wavelength range. Its polygonal geometry ensures coverage over all illumination directions, enabling high fidelity image reconstruction whilst minimizing distortion and image blurring. By frequency shifting and iterative stitching of different spatial frequencies in Fourier space, the reconstruction of two dimensional samples is achieved without distortion over wide FOVs. The fabrication process is facile and compatible with conventional semiconductor-fabrication methods. The super-resolution chip (SRC) can thus be produced with high yield, offer opportunities for potential conjunction of super-resolution techniques integrated optical circuits or for the development of single-use diagnostic kits