Penalized Orthogonal-Components Regression for Large p Small n Data

We propose a penalized orthogonal-components regression (POCRE) for large p small n data. Orthogonal components are sequentially constructed to maximize, upon standardization, their correlation to the response residuals. A new penalization framework, implemented via empirical Bayes thresholding, is presented to effectively identify sparse predictors of each component. POCRE is computationally efficient owing to its sequential construction of leading sparse principal components. In addition, such construction offers other properties such as grouping highly correlated predictors and allowing for collinear or nearly collinear predictors. With multivariate responses, POCRE can construct common components and thus build up latent-variable models for large p small n data.Comment: 12 page

Sandpile avalanche dynamics on scale-free networks

Avalanche dynamics is an indispensable feature of complex systems. Here we study the self-organized critical dynamics of avalanches on scale-free networks with degree exponent $\gamma$ through the Bak-Tang-Wiesenfeld (BTW) sandpile model. The threshold height of a node $i$ is set as $k_i^{1-\eta}$ with $0\leq\eta<1$, where $k_i$ is the degree of node $i$. Using the branching process approach, we obtain the avalanche size and the duration distribution of sand toppling, which follow power-laws with exponents $\tau$ and $\delta$, respectively. They are given as $\tau=(\gamma-2 \eta)/(\gamma-1-\eta)$ and $\delta=(\gamma-1-\eta)/(\gamma-2)$ for $\gamma<3-\eta$, 3/2 and 2 for $\gamma>3-\eta$, respectively. The power-law distributions are modified by a logarithmic correction at $\gamma=3-\eta$.Comment: 8 pages, elsart styl

Classification of scale-free networks

While the emergence of a power law degree distribution in complex networks is intriguing, the degree exponent is not universal. Here we show that the betweenness centrality displays a power-law distribution with an exponent \eta which is robust and use it to classify the scale-free networks. We have observed two universality classes with \eta \approx 2.2(1) and 2.0, respectively. Real world networks for the former are the protein interaction networks, the metabolic networks for eukaryotes and bacteria, and the co-authorship network, and those for the latter one are the Internet, the world-wide web, and the metabolic networks for archaea. Distinct features of the mass-distance relation, generic topology of geodesics and resilience under attack of the two classes are identified. Various model networks also belong to either of the two classes while their degree exponents are tunable.Comment: 6 Pages, 6 Figures, 1 tabl

Probability distribution of persistent spins in a Ising chain

We study the probability distribution $Q(n,t)$ of $n(t)$, the fraction of spins unflipped till time $t$, in a Ising chain with ferromagnetic interactions. The distribution shows a peak at $n=n_{max}$ and in general is non-Gaussian and asymmetric in nature. However for $n>n_{max}$ it shows a Gaussian decay. A data collapse can be obtained when $Q(n,t)/L^{\alpha}$ versus $(n-n_{max})L^{\beta}$ is plotted with $\alpha \sim 0.45$ and $\beta \sim 0.6$. Interestingly, $n_{max}(t)$ shows a different behaviour compared to $= P(t)$, the persistence probability which follows the well-known behaviour $P(t)\sim t^{-\theta}$. A quantitative estimate of the asymmetry and non-Gaussian nature of $Q(n,t)$ is made by calculating its skewness and kurtosis.Comment: 4 pages, submitted to J. Phys

CDC20 regulates sensitivity to chemotherapy and radiation in glioblastoma stem cells

Glioblastoma stem cells (GSCs) are an important subpopulation in glioblastoma, implicated in tumor growth, tumor recurrence, and radiation resistance. Understanding the cellular mechanisms for chemo- and radiation resistance could lead to the development of new therapeutic strategies. Here, we demonstrate that CDC20 promotes resistance to chemotherapy and radiation therapy. CDC20 knockdown does not increase TMZ- and radiation-induced DNA damage, or alter DNA damage repair, but rather promotes cell death through accumulation of the pro-apoptotic protein, Bim. Our results identify a CDC20 signaling pathway that regulates chemo- and radiosensitivity in GSCs, with the potential for CDC20-targeted therapeutic strategies in the treatment of glioblastoma

Evolution of community structure in the world trade web

In this note we study the bilateral merchandise trade flows between 186 countries over the 1948-2005 period using data from the International Monetary Fund. We use Pajek to identify network structure and behavior across thresholds and over time. In particular, we focus on the evolution of trade "islands" in the a world trade network in which countries are linked with directed edges weighted according to fraction of total dollars sent from one country to another. We find mixed evidence for globalization.Comment: To be submitted to APFA 6 Proceedings, 8 pages, 3 Figure

Mechanisms of Groucho-mediated repression revealed by genome-wide analysis of Groucho binding and activity

Antibody validation (A) Chromatin isolated and sheared exactly as for the ChIP-seq analysis was subjected to immunoprecipitation with the indicated amounts (in μl) of affinity purified antibody against the Gro GP domain used for the ChIP-seq analysis, and then probed in a western blot with both an anti-Gro monoclonal antibody (mAb) or the anti-GP antibody. The band indicated by the asterisk is a cross-reacting protein that is recognized in the western blot but that is not efficiently immunoprecipitated by the anti-GP antibody. Ab HC – antibody heavy chain. (B) Heat map showing overlap (Jacard similarity coefficient [96]) between the peaks called in the duplicate ChIP-seq experiments at each time point. (C) Representative genome browser tracts comparing duplicate ChIP-seq experiments. (D and E) Comparison of Gro binding patterns obtained by ChIP-seq using our anti-GP antibody with that obtained by ChIP-chip (0–12 hr embryos; modENCODE #597) and ChIP-seq (white pre-pupae; modENCODE #4981) using independently derived antibodies [40]. (PDF 588 kb

Laser interstitial thermal therapy in grade 2/3 IDH1/2 mutant gliomas: A preliminary report and literature review

Laser interstitial thermal therapy (LITT) has become an increasingly utilized alternative to surgical resection for the treatment of glioma in patients. However, treatment outcomes in isocitrate dehydrogenase 1 and 2

Three Dimensional Hydrodynamic-Sedimentation Modeling Study : Hampton Roads Crossing, Lower James River, Virginia

A three-dimensional hydrodynamic-sedimentation computer model, HYSED-3D, was used to evaluate the effect of bridge-tunnel infrastructure for a proposed highway crossing of Hampton Roads on the physical characteristics (tides, currents, circulation, salinity, and sedimentation) of the James River estuary in Virginia. Model-represented infrastructure included tunnel islands and bridges on pilings connecting the islands to interstate highways in Newport News, Hampton, Norfolk, and Portsmouth, Virginia. Combinations of these elements occur in each of three proposed crossing routes designated Alternative 1 (Hampton-Norfolk), Alternative 2 (Hampton-Norfolk, Norfolk-Portsmouth), and Alternative 9 (Newport News-Portsmouth-Norfolk). Simulation comparisons were made between the existing waterways and infrastructure in Hampton Roads (Base Case) and the proposed construction in a series of model test runs representing both normal and extreme hydrologic conditions. Variations in tidal range were simulated using a three constituent tide model. Three levels of freshwater inflow into the headwaters of the James River were represented using historical stream gauge data. The simulation of sedimentation was designed based on the existence of a \u27turbidity maximum\u27 upstream from the area of concern