Microarray sub-grid detection: A novel algorithm

This is the post print version of the article. The official published version can be obtained from the link below - Copyright 2007 Taylor & Francis LtdA novel algorithm for detecting microarray subgrids is proposed. The only input to the algorithm is the raw microarray image, which can be of any resolution, and the subgrid detection is performed with no prior assumptions. The algorithm consists of a series of methods of spot shape detection, spot filtering, spot spacing estimation, and subgrid shape detection. It is shown to be able to divide images of varying quality into subgrid regions with no manual interaction. The algorithm is robust against high levels of noise and high percentages of poorly expressed or missing spots. In addition, it is proved to be effective in locating regular groupings of primitives in a set of non-microarray images, suggesting potential application in the general area of image processing

Orchard: building large cancer phylogenies using stochastic combinatorial search

Phylogenies depicting the evolutionary history of genetically heterogeneous subpopulations of cells from the same cancer i.e., cancer phylogenies, provide useful insights about cancer development and inform treatment. Cancer phylogenies can be reconstructed using data obtained from bulk DNA sequencing of multiple tissue samples from the same cancer. We introduce Orchard, a fast algorithm that reconstructs cancer phylogenies using point mutations detected in bulk DNA sequencing data. Orchard constructs cancer phylogenies progressively, one point mutation at a time, ultimately sampling complete phylogenies from a posterior distribution implied by the bulk DNA data. Orchard reconstructs more plausible phylogenies than state-of-the-art cancer phylogeny reconstruction methods on 90 simulated cancers and 14 B-progenitor acute lymphoblastic leukemias (B-ALLs). These results demonstrate that Orchard accurately reconstructs cancer phylogenies with up to 300 mutations. We then introduce a simple graph based clustering algorithm that uses a reconstructed phylogeny to infer unique groups of mutations i.e., mutation clusters, that characterize the genetic differences between cancer cell populations, and show that this approach is competitive with state-of-the-art mutation clustering methods

Extinction toward the Compact HII Regions G-0.02-0.07

The four HII regions in the Sgr A East complex: A, B, C, and D, represent evidence of recent massive star formation in the central ten parsecs. Using Paschen-alpha images taken with HST and 8.4 GHz VLA data, we construct an extinction map of A-D, and briefly discuss their morphology and location.Comment: 2 pages, 1 figure. To be published in the Astronomical Society of the Pacific Conference Series Proceedings of the Galactic Center Workshop 2009, Shangha

HST Palpha Survey of the Galactic Center -- Searching the missing young stellar populations within the Galactic Center

We present preliminary results of our \hst Pa$\alpha$ survey of the Galactic Center (\gc), which maps the central 0.65$\times$0.25 degrees around Sgr A*. This survey provides us with a more complete inventory of massive stars within the \gc, compared to previous observations. We find 157 Pa$\alpha$ emitting sources, which are evolved massive stars. Half of them are located outside of three young massive star clusters near Sgr A*. The loosely spatial distribution of these field sources suggests that they are within less massive star clusters/groups, compared to the three massive ones. Our Pa$\alpha$ mosaic not only resolves previously well-known large-scale filaments into fine structures, but also reveals many new extended objects, such as bow shocks and H II regions. In particular, we find two regions with large-scale Pa$\alpha$ diffuse emission and tens of Pa$\alpha$ emitting sources in the negative Galactic longitude suggesting recent star formation activities, which were not known previously. Furthermore, in our survey, we detect $\sim$0.6 million stars, most of which are red giants or AGB stars. Comparisons of the magnitude distribution in 1.90 $\mu$m and those from the stellar evolutionary tracks with different star formation histories suggest an episode of star formation process about 350 Myr ago in the \gc .Comment: 10 pages, 6 figures, Proceedings of the Galactic Center Workshop 2009, Shangha

SiS in the circumstellar envelope of IRC +10126: maser and quasi-thermal emission

We present new Effelsberg-100 m, ATCA, and VLA observations of rotational SiS transitions in the circumstellar envelope (CSE) of IRC +10216. Thanks to the high angular resolution achieved by the ATCA observations, we unambiguously confirm that the molecule's J=1-0 transition exhibits maser action in this CSE, as first suggested more than thirty years ago. The maser emission's radial velocity peaking at a local standard of rest velocity of -39.862$\pm$0.065 km/s indicates that it arises from an almost fully accelerated shell. Monitoring observations show time variability of the SiS (1-0) maser. The two lowest-$J$ SiS quasi-thermal emission lines trace a much more extended emitting region than previous high-J SiS observations. Their distributions show that the SiS quasi-thermal emission consists of two components: one is very compact (radius<1.5", corresponding to <3$\times 10^{15}$ cm), and the other extends out to a radius >11". An incomplete shell-like structure is found in the north-east, which is indicative of existing SiS shells. Clumpy structures are also revealed in this CSE. The gain of the SiS (1-0) maser (optical depths of about -5 at the blue-shifted side and, assuming inversion throughout the entire line's velocity range, about -2 at the red-shifted side) suggests that it is unsaturated. The SiS (1-0) maser can be explained in terms of ro-vibrational excitation caused by infrared pumping, and we propose that infrared continuum emission is the main pumping source.Comment: Accepted for publication in ApJ. A high-resolution version can be found at https://gongyan2444.github.io/pdf/cw-leo-sis.pdf 3D movies of SiS cubes can be found at https://gongyan2444.github.io/movie/sis10-3d.avi and https://gongyan2444.github.io/movie/sis21-3d.av

Local stabilisation of polar order at charged antiphase boundaries in antiferroelectric (Bi_0.85Nd_0.15)(Ti_0.1Fe_0.9)O₃

Observation of an unusual, negatively-charged antiphase boundary in (Bi&lt;sub&gt;0.85&lt;/sub&gt;Nd&lt;sub&gt;0.15&lt;/sub&gt;)(Ti&lt;sub&gt;0.1&lt;/sub&gt;Fe&lt;sub&gt;0.9&lt;/sub&gt;)O&lt;sub&gt;3&lt;/sub&gt; is reported. Aberration corrected scanning transmission electron microscopy is used to establish the full three dimensional structure of this boundary including O-ion positions to ~ ± 10 pm. The charged antiphase boundary stabilises tetragonally distorted regions with a strong polar ordering to either side of the boundary, with a characteristic length scale determined by the excess charge trapped at the boundary. Far away from the boundary the crystal relaxes into the well-known Nd-stabilised antiferroelectric phase

Assortative mixing in networks

A network is said to show assortative mixing if the nodes in the network that have many connections tend to be connected to other nodes with many connections. We define a measure of assortative mixing for networks and use it to show that social networks are often assortatively mixed, but that technological and biological networks tend to be disassortative. We propose a model of an assortative network, which we study both analytically and numerically. Within the framework of this model we find that assortative networks tend to percolate more easily than their disassortative counterparts and that they are also more robust to vertex removal.Comment: 5 pages, 1 table, 1 figur

Simulations and cosmological inference: A statistical model for power spectra means and covariances

We describe an approximate statistical model for the sample variance distribution of the non-linear matter power spectrum that can be calibrated from limited numbers of simulations. Our model retains the common assumption of a multivariate Normal distribution for the power spectrum band powers, but takes full account of the (parameter dependent) power spectrum covariance. The model is calibrated using an extension of the framework in Habib et al. (2007) to train Gaussian processes for the power spectrum mean and covariance given a set of simulation runs over a hypercube in parameter space. We demonstrate the performance of this machinery by estimating the parameters of a power-law model for the power spectrum. Within this framework, our calibrated sample variance distribution is robust to errors in the estimated covariance and shows rapid convergence of the posterior parameter constraints with the number of training simulations.Comment: 14 pages, 3 figures, matches final version published in PR