Ranking Preserving Nonnegative Matrix Factorization

Nonnegative matrix factorization (NMF), a wellknown technique to find parts-based representations of nonnegative data, has been widely studied. In reality, ordinal relations often exist among data, such as data i is more related to j than to q. Such relative order is naturally available, and more importantly, it truly reflects the latent data structure. Preserving the ordinal relations enables us to find structured representations of data that are faithful to the relative order, so that the learned representations become more discriminative. However, this cannot be achieved by current NMFs. In this paper, we make the first attempt towards incorporating the ordinal relations and propose a novel ranking preserving nonnegative matrix factorization (RPNMF) approach, which enforces the learned representations to be ranked according to the relations. We derive iterative updating rules to solve RPNMF’s objective function with convergence guaranteed. Experimental results with several datasets for clustering and classification have demonstrated that RPNMF achieves greater performance against the state-of-the-arts, not only in terms of accuracy, but also interpretation of orderly data structure

Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses?

<p>Abstract</p> <p>Background</p> <p>How photosynthetic organelles, or plastids, were acquired by diverse eukaryotes is among the most hotly debated topics in broad scale eukaryotic evolution. The history of plastid endosymbioses commonly is interpreted under the "chromalveolate" hypothesis, which requires numerous plastid losses from certain heterotrophic groups that now are entirely aplastidic. In this context, discoveries of putatively algal genes in plastid-lacking protists have been cited as evidence of gene transfer from a photosynthetic endosymbiont that subsequently was lost completely. Here we examine this evidence, as it pertains to the chromalveolate hypothesis, through genome-level statistical analyses of similarity scores from queries with two diatoms, <it>Phaeodactylum tricornutum </it>and <it>Thalassiosira pseudonana</it>, and two aplastidic sister taxa, <it>Phytophthora ramorum </it>and <it>P. sojae</it>.</p> <p>Results</p> <p>Contingency tests of specific predictions of the chromalveolate model find no evidence for an unusual red algal contribution to <it>Phytophthora </it>genomes, nor that putative cyanobacterial sequences that are present entered these genomes through a red algal endosymbiosis. Examination of genes unrelated to plastid function provide extraordinarily significant support for both of these predictions in diatoms, the control group where a red endosymbiosis is known to have occurred, but none of that support is present in genes specifically conserved between diatoms and oomycetes. In addition, we uncovered a strong association between overall sequence similarities among taxa and relative sizes of genomic data sets in numbers of genes.</p> <p>Conclusion</p> <p>Signal from "algal" genes in oomycete genomes is inconsistent with the chromalveolate hypothesis, and better explained by alternative models of sequence and genome evolution. Combined with the numerous sources of intragenomic phylogenetic conflict characterized previously, our results underscore the potential to be mislead by <it>a posteriori </it>interpretations of variable phylogenetic signals contained in complex genome-level data. They argue strongly for explicit testing of the different <it>a priori </it>assumptions inherent in competing evolutionary hypotheses.</p

Dose-related liver injury of Geniposide associated with the alteration in bile acid synthesis and transportation.

Fructus Gardenia (FG), containing the major active constituent Geniposide, is widely used in China for medicinal purposes. Currently, clinical reports of FG toxicity have not been published, however, animal studies have shown FG or Geniposide can cause hepatotoxicity in rats. We investigated Geniposide-induced hepatic injury in male Sprague-Dawley rats after 3-day intragastric administration of 100 mg/kg or 300 mg/kg Geniposide. Changes in hepatic histomorphology, serum liver enzyme, serum and hepatic bile acid profiles, and hepatic bile acid synthesis and transportation gene expression were measured. The 300 mg/kg Geniposide caused liver injury evidenced by pathological changes and increases in serum alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP) and γ-glutamytransferase (γ-GT). While liver, but not sera, total bile acids (TBAs) were increased 75% by this dose, dominated by increases in taurine-conjugated bile acids (t-CBAs). The 300 mg/kg Geniposide also down-regulated expression of Farnesoid X receptor (FXR), small heterodimer partner (SHP) and bile salt export pump (BSEP). In conclusion, 300 mg/kg Geniposide can induce liver injury with associated changes in bile acid regulating genes, leading to an accumulation of taurine conjugates in the rat liver. Taurocholic acid (TCA), taurochenodeoxycholic acid (TCDCA) as well as tauro-α-muricholic acid (T-α-MCA) are potential markers for Geniposide-induced hepatic damage

What can we learn about solar coronal mass ejections, coronal dimmings, and Extreme-Ultraviolet jets through spectroscopic observations?

We analyze several data sets obtained by Hinode/EIS and find various types of flows during CMEs and EUV jet eruptions. CME-induced dimming regions are found to be characterized by significant blueshift and enhanced line width by using a single Gaussian fit. While a red-blue (RB) asymmetry analysis and a RB-guided double Gaussian fit of the coronal line profiles indicate that these are likely caused by the superposition of a strong background emission component and a relatively weak (~10%) high-speed (~100 km s-1) upflow component. This finding suggests that the outflow velocity in the dimming region is probably of the order of 100 km s-1, not ~20 km s-1 as reported previously. Density and temperature diagnostics suggest that dimming is primarily an effect of density decrease rather than temperature change. The mass losses in dimming regions as estimated from different methods are roughly consistent with each other and they are 20%-60% of the masses of the associated CMEs. With the guide of RB asymmetry analysis, we also find several temperature-dependent outflows (speed increases with temperature) immediately outside the (deepest) dimming region. In an erupted CME loop and an EUV jet, profiles of emission lines formed at coronal and transition region temperatures are found to exhibit two well-separated components, an almost stationary component accounting for the background emission and a highly blueshifted (~200 km s-1) component representing emission from the erupting material. The two components can easily be decomposed through a double Gaussian fit and we can diagnose the electron density, temperature and mass of the ejecta. Combining the speed of the blueshifted component and the projected speed of the erupting material derived from simultaneous imaging observations, we can calculate the real speed of the ejecta.Comment: 20 figures. Ready for publication in ApJ. The quality of Figures 4,5 15 & 20 is greatly reduced as a result of the requirement of the size limit of arXiv.org. High-quality version of these figures can be found in http://download.hao.ucar.edu/pub/htian

Quantum and classical resonant escapes of a strongly-driven Josephson junction

The properties of phase escape in a dc SQUID at 25 mK, which is well below quantum-to-classical crossover temperature $T_{cr}$, in the presence of strong resonant ac driving have been investigated. The SQUID contains two Nb/Al-AlO$_{x}$/Nb tunnel junctions with Josephson inductance much larger than the loop inductance so it can be viewed as a single junction having adjustable critical current. We find that with increasing microwave power $W$ and at certain frequencies $\nu$ and $\nu$/2, the single primary peak in the switching current distribution, \textrm{which is the result of macroscopic quantum tunneling of the phase across the junction}, first shifts toward lower bias current $I$ and then a resonant peak develops. These results are explained by quantum resonant phase escape involving single and two photons with microwave-suppressed potential barrier. As $W$ further increases, the primary peak gradually disappears and the resonant peak grows into a single one while shifting further to lower $I$. At certain $W$, a second resonant peak appears, which can locate at very low $I$ depending on the value of $\nu$. Analysis based on the classical equation of motion shows that such resonant peak can arise from the resonant escape of the phase particle with extremely large oscillation amplitude resulting from bifurcation of the nonlinear system. Our experimental result and theoretical analysis demonstrate that at $T\ll T_{cr}$, escape of the phase particle could be dominated by classical process, such as dynamical bifurcation of nonlinear systems under strong ac driving.Comment: 10 pages, 9 figures, 1 tabl

Quantum and classical resonant escapes of a strongly driven Josephson junction

This is the published version, also available here: http://dx.doi.org/10.1103/PhysRevB.81.144518.The properties of phase escape in a dc superconducting quantum interference device (SQUID) at 25 mK, which is well below quantum-to-classical crossover temperature Tcr, in the presence of strong resonant ac driving have been investigated. The SQUID contains two Nb/Al-AlOx/Nb tunnel junctions with Josephson inductance much larger than the loop inductance so it can be viewed as a single junction having adjustable critical current. We find that with increasing microwave power W and at certain frequencies ν and ν/2, the single primary peak in the switching current distribution, which is the result of macroscopic quantum tunneling of the phase across the junction, first shifts toward lower bias current I and then a resonant peak develops. These results are explained by quantum resonant phase escape involving single and two photons with microwave-suppressed potential barrier. As W further increases, the primary peak gradually disappears and the resonant peak grows into a single one while shifting further to lower I. At certain W, a second resonant peak appears, which can locate at very low I depending on the value of ν. Analysis based on the classical equation of motion shows that such resonant peak can arise from the resonant escape of the phase particle with extremely large oscillation amplitude resulting from bifurcation of the nonlinear system. Our experimental result and theoretical analysis demonstrate that at T⪡Tcr, escape of the phase particle could be dominated by classical process, such as dynamical bifurcation of nonlinear systems under strong ac driving

Three-dimensional Electrochemical Micromachining on Metal and Semiconductor by Confined Etchant Layer Technique (CELT)

Contacting Author: Zhao W. Tian is with the State key laboratory for Physical Chemistry of Solid Surfaces, Xiamen, China (phone: 86-592-2185797; fax: 86-592-2085349; email: [email protected]

Evolution and Flare Activity of Delta-Sunspots in Cycle 23

The emergence and magnetic evolution of solar active regions (ARs) of beta-gamma-delta type, which are known to be highly flare-productive, were studied with the SOHO/MDI data in Cycle 23. We selected 31 ARs that can be observed from their birth phase, as unbiased samples for our study. From the analysis of the magnetic topology (twist and writhe), we obtained the following results. i) Emerging beta-gamma-delta ARs can be classified into three topological types as "quasi-beta", "writhed" and "top-to-top". ii) Among them, the "writhed" and "top-to-top" types tend to show high flare activity. iii) As the signs of twist and writhe agree with each other in most cases of the "writhed" type (12 cases out of 13), we propose a magnetic model in which the emerging flux regions in a beta-gamma-delta AR are not separated but united as a single structure below the solar surface. iv) Almost all the "writhed"-type ARs have downward knotted structures in the mid portion of the magnetic flux tube. This, we believe, is the essential property of beta-gamma-delta ARs. v) The flare activity of beta-gamma-delta ARs is highly correlated not only with the sunspot area but also with the magnetic complexity. vi) We suggest that there is a possible scaling-law between the flare index and the maximum umbral area