GPD: A Graph Pattern Diffusion Kernel for Accurate Graph Classification with Applications in Cheminformatics

Graph data mining is an active research area. Graphs are general modeling tools to organize information from heterogeneous sources and have been applied in many scientific, engineering, and business fields. With the fast accumulation of graph data, building highly accurate predictive models for graph data emerges as a new challenge that has not been fully explored in the data mining community. In this paper, we demonstrate a novel technique called graph pattern diffusion (GPD) kernel. Our idea is to leverage existing frequent pattern discovery methods and to explore the application of kernel classifier (e.g., support vector machine) in building highly accurate graph classification. In our method, we first identify all frequent patterns from a graph database. We then map subgraphs to graphs in the graph database and use a process we call “pattern diffusion” to label nodes in the graphs. Finally, we designed a graph alignment algorithm to compute the inner product of two graphs. We have tested our algorithm using a number of chemical structure data. The experimental results demonstrate that our method is significantly better than competing methods such as those kernel functions based on paths, cycles, and subgraphs

Quantifying Properties of the QCD Matter at RHIC

We will review recent results on quantitative description of global properties of bulk partonic matter at RHIC. These results include strangeness phase space factor of the partonic matter, azimuthal angular anisotropy $v_2$, and transverse momentum $p_T$ distributions of effective partons at the hadronization of bulk partonic matter. We present empirical constraints on parton energy loss in the high $p_T$ region ($>$ 5 GeV/c). A flat $R_{AA}$ as a function of $p_T$ at mid-rapidity implies a constant fraction of the parton energy loss ($\Delta p_T/p_T$) and the fraction reaches 25% for neutral $\pi$, charged hadrons and non-photonic electrons of heavy quark decays from central Au+Au collisions at $\sqrt{s_{NN}}$ 200 GeV. Collision centrality dependence of $\Delta p_T/p_T$ from Au+Au and Cu+Cu collisions indicates that the fraction is approximately proportional to particle rapidity density $dn/dy$ divided by the initial transverse overlapping area of the colliding nuclei. Implications on dynamics of parton energy loss will be discussed.Comment: To Appear in SQM2008 Conference Proceeding

Angular dependence of resistivity in the superconducting state of NdFeAsO0.82_{0.82}F0.18_{0.18} single crystals

We report the results of angle dependent resistivity of NdFeAsO$_{0.82}$F$_{0.18}$ single crystals in the superconducting state. By doing the scaling of resistivity within the frame of the anisotropic Ginzburg-Landau theory, it is found that the angle dependent resistivity measured under different magnetic fields at a certain temperature can be collapsed onto one curve. As a scaling parameter, the anisotropy $\Gamma$ can be determined for different temperatures. It is found that $\Gamma(T)$ increases slowly with decreasing temperature, varying from $\Gamma \simeq$ 5.48 at T=50 K to $\Gamma \simeq$ 6.24 at T=44 K. This temperature dependence can be understood within the picture of multi-band superconductivity.Comment: 7 pages, 4 figure

Life-Detection Technologies for the Next Two Decades

Since its inception six decades ago, astrobiology has diversified immensely to encompass several scientific questions including the origin and evolution of Terran life, the organic chemical composition of extraterrestrial objects, and the concept of habitability, among others. The detection of life beyond Earth forms the main goal of astrobiology, and a significant one for space exploration in general. This goal has galvanized and connected with other critical areas of investigation such as the analysis of meteorites and early Earth geological and biological systems, materials gathered by sample-return space missions, laboratory and computer simulations of extraterrestrial and early Earth environmental chemistry, astronomical remote sensing, and in-situ space exploration missions. Lately, scattered efforts are being undertaken towards the R&D of the novel and as-yet-space-unproven life-detection technologies capable of obtaining unambiguous evidence of extraterrestrial life, even if it is significantly different from Terran life. As the suite of space-proven payloads improves in breadth and sensitivity, this is an apt time to examine the progress and future of life-detection technologies.Comment: 6 pages, the white paper was submitted to and cited by the National Academy of Sciences in support of the Astrobiology Science Strategy for the Search for Life in the Univers

Generalized glycogen storage and cardiomegaly in a knockout mouse model of Pompe disease

Glycogen storage disease type II (GSDII; Pompe disease), caused by inherited deficiency of acid alpha-glucosidase, is a lysosomal disorder affecting heart and skeletal muscles. A mouse model of this disease was obtained by targeted disruption of the murine acid alpha-glucosidase gene (Gaa) in embryonic stem cells. Homozygous knockout mice (Gaa -/-) lack Gaa mRNA and have a virtually complete acid alpha-glucosidase deficiency. Glycogen-containing lysosomes are detected soon after birth in liver, heart and skeletal muscle cells. By 13 weeks of age, large focal deposits of glycogen have formed. Vacuolar spaces stain positive for acid phosphatase as a sign of lysosomal pathology. Both male and female knockout mice are fertile and can be intercrossed to produce progeny. The first born knockout mice are at present 9 months old. Overt clinical symptoms are still absent, but the heart is typically enlarged and the electrocardiogram is abnormal. The mouse model will help greatly to understand the pathogenic mechanism of GSDII and is a valuable instrument to explore the efficacy of different therapeutic interventions

Re-expression of ARHI (DIRAS3) induces autophagy in breast cancer cells and enhances the inhibitory effect of paclitaxel

<p>Abstract</p> <p>Background</p> <p><it>ARHI </it>is a Ras-related imprinted gene that inhibits cancer cell growth and motility. ARHI is downregulated in the majority of breast cancers, and loss of its expression is associated with its progression from ductal carcinoma <it>in situ </it>(DCIS) to invasive disease. In ovarian cancer, re-expression of ARHI induces autophagy and leads to autophagic death in cell culture; however, ARHI re-expression enables ovarian cancer cells to remain dormant when they are grown in mice as xenografts. The purpose of this study is to examine whether ARHI induces autophagy in breast cancer cells and to evaluate the effects of ARHI gene re-expression in combination with paclitaxel.</p> <p>Methods</p> <p>Re-expression of ARHI was achieved by transfection, by treatment with trichostatin A (TSA) or by a combination of TSA and 5-aza-2'-deoxycytidine (DAC) in breast cancer cell cultures and by liposomal delivery of ARHI in breast tumor xenografts.</p> <p>Results</p> <p>ARHI re-expression induces autophagy in breast cancer cells, and ARHI is essential for the induction of autophagy. When ARHI was re-expressed in breast cancer cells treated with paclitaxel, the growth inhibitory effect of paclitaxel was enhanced in both the cell culture and the xenografts. Although paclitaxel alone did not induce autophagy in breast cancer cells, it enhanced ARHI-induced autophagy. Conversely, ARHI re-expression promoted paclitaxel-induced apoptosis and G2/M cell cycle arrest.</p> <p>Conclusions</p> <p>ARHI re-expression induces autophagic cell death in breast cancer cells and enhances the inhibitory effects of paclitaxel by promoting autophagy, apoptosis, and G2/M cell cycle arrest.</p

Superconducting properties of SmO1-xFxFeAs wires with Tc = 52 K prepared by the powder-in-tube method

We demonstrate that Ta sheathed SmO1-xFxFeAs wires were successfully fabricated by the powder-in-tube (PIT) method for the first time. Structural analysis by mean of x-ray diffraction shows that the main phase of SmO1-xFxFeAs was obtained by this synthesis method. The transition temperature of the SmO0.65F0.35FeAs wires was confirmed to be as high as 52 K. Based on magnetization measurements, it is found that a globe current can flow on macroscopic sample dimensions with Jc of ~3.9x10^3 A/cm^2 at 5 K and self field, while a high Jc about 2x10^5 A/cm^2 is observed within the grains, suggesting that a significant improvement in the globle Jc is possible. It should be noted that the Jc exhibits a very weak field dependence behavior. Furthermore, the upper critical fields (Hc2) determined according to the Werthamer-Helfand-Hohenberg formula are (T= 0 K) = 120 T, indicating a very encouraging application of the new superconductors.Comment: 14 pages, 6 figure

Constructing non-stationary Dynamic Bayesian Networks with a flexible lag choosing mechanism

<p>Abstract</p> <p>Background</p> <p>Dynamic Bayesian Networks (DBNs) are widely used in regulatory network structure inference with gene expression data. Current methods assumed that the underlying stochastic processes that generate the gene expression data are stationary. The assumption is not realistic in certain applications where the intrinsic regulatory networks are subject to changes for adapting to internal or external stimuli.</p> <p>Results</p> <p>In this paper we investigate a novel non-stationary DBNs method with a potential regulator detection technique and a flexible lag choosing mechanism. We apply the approach for the gene regulatory network inference on three non-stationary time series data. For the Macrophages and Arabidopsis data sets with the reference networks, our method shows better network structure prediction accuracy. For the Drosophila data set, our approach converges faster and shows a better prediction accuracy on transition times. In addition, our reconstructed regulatory networks on the Drosophila data not only share a lot of similarities with the predictions of the work of other researchers but also provide many new structural information for further investigation.</p> <p>Conclusions</p> <p>Compared with recent proposed non-stationary DBNs methods, our approach has better structure prediction accuracy By detecting potential regulators, our method reduces the size of the search space, hence may speed up the convergence of MCMC sampling.</p

Follow-Up of Patients with Multidrug Resistant Tuberculosis Four Years after Standardized First-Line Drug Treatment

Background: In 2004, an anti-tuberculosis (TB) drug resistance survey in Heilongjiang province, China, enrolled 1574 (79%) new and 421 (21%) retreatment patients. Multi-drug resistant (MDR) TB was detected in 7.2% of new and 30.4% of retreatment patients. All received treatment with standardized first-line drug (FLD) regimens. Methodology/Principal Findings: We report treatment outcomes of the 2004 cohort, and long-term outcomes as assessed in the second half of 2008. The reported cure rate for MDR-TB patients was 83% (94/113) among new and 66% (85/128) among retreatment patients (P<0.001). Ten of the 241 MDR-TB patients died during treatment. Of the remaining 231, 129 (56%) could be traced in 2008. The overall recurrence rates among new and retreatment cases were 46% and 66%, respectively (P=0.03). The overall death rates among new and retreatment cases were 25% and 46%, respectively (P=0.02). Forty percent of the traced new cases and 24% of the retreatment cases were alive and without recurrent TB (P=0.01). Of the 16 patients who failed or defaulted from treatment in 2004, only two patients were not re-diagnosed with TB by 2008. Of the 111 (86%) patients with an initial successful treatment outcome 63 (57%) had developed recurrent TB, 40 (36%) had died, 27 (24%) of them died of TB. The follow-up period of four years precluded follow-up of all patients. In a highly conservative sensitivity analysis in which we assumed that all non-included patients were alive and did not have recurrent TB, the recurrence and death rate were 33% and 21%. Conclusions/Significance: Documentation of cure based on conventional smear microscopy was a poor predictor of long term outcomes. MDR-TB patients in Heilongjiang province in China had high recurrence and death rates four years after treatment with standardized FLD regimens, reinforcing the need for early diagnosis and treatment of MDR-TB, including assessment of treatment outcomes with more sensitive laboratory method