Generalized power method for sparse principal component analysis

In this paper we develop a new approach to sparse principal component analysis (sparse PCA). We propose two single-unit and two block optimization formulations of the sparse PCA problem, aimed at extracting a single sparse dominant principal component of a data matrix, or more components at once, respectively. While the initial formulations involve nonconvex functions, and are therefore computationally intractable, we rewrite them into the form of an optimization program involving maximization of a convex function on a compact set. The dimension of the search space is decreased enormously if the data matrix has many more columns (variables) than rows. We then propose and analyze a simple gradient method suited for the task. It appears that our algorithm has best convergence properties in the case when either the objective function or the feasible set are strongly convex, which is the case with our single-unit formulations and can be enforced in the block case. Finally, we demonstrate numerically on a set of random and gene expression test problems that our approach outperforms existing algorithms both in quality of the obtained solution and in computational speed. © 2010 Michel Journée, Yurii Nesterov, Peter Richtárik and Rodolphe Sepulchre.

Molecular cloning, promoter analysis and induced expression of the complement component C9 gene in the grass carp Ctenopharyngodon idella

Complement-mediated killing of pathogens through lytic pathway is an important effector mechanism of innate immune response. C9 is the ninth member of complement components, creating the membrane attack complex (MAC). In the present study, a putative cDNA sequence encoding the 650 amino acids of C9 and its genomic organization were identified in grass carp Ctenopharyngodon idella. The deduced amino acid sequence of grass carp C9 (gcC9) showed 48% and 38.5% identity to Japanese flounder and human C9, respectively. Domain search revealed that gcC9 contains a LDL receptor domain, an EGF precursor domain, a MACPF domain and two TSP domain located in the N-terminal and C-terminal, respectively. Phylogenetic analysis demonstrated that gcC9 is clustered in a same clade with Japanese flounder, pufferfish and rainbow trout C9. The gcC9 gene consists of 11 exons with 10 introns, spacing over approximately 7 kb of genomic sequence. Analysis of gcC9 promoter region revealed the presence of a TATA box and some putative transcription factor such as C/EBP, HSF, NF-AT, CHOP-C, HNF-3B, GATA-2, IK-2, EVI- 1, AP-1, CP2 and OCT-1 binding sites. The first intron region contains C/EBPb, HFH-1 and Oct-1 binding sites. RT-PCR and Western blotting analysis demonstrated that the mRNA and protein of gcC9 gene have similar expression patterns, being constitutively expressed in all organs examined of healthy fish, with the highest level in hepatopancreas. By real-time quantitative RT-PCR analysis, gcC9 transcripts were significantly up-regulated in head kidney, spleen, hepatopancreas and down-regulated in intestine from inactivated fish bacterial pathogen Flavobacterium columnare-stimulated fish, demonstrating the role of C9 in immune response. (c) 2007 Elsevier B.V. All rights reserved.

Contamination and distribution of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/F) in agriculture fields in Ya-Er Lake area, China

The contamination and distribution of polychlorinated dibeinizo-p-dioxins and dibenzofurans (PCDD/Fs) from two agricultural fields of a heavily polluted lake area in China (Ya-Er Lake) are presented. The vertical distribution pattern of total PCDD/Fs in soil cores reveals that the maximum concentration was in the layer of 20-30 cm. The concentrations in the top layer of soil at the two sites were similar (17.48 ng/kg at Site 1 and 18.10 ng/kg at Site 2), but the maximum concentration of Site 1 (120.8 ng/kg) was two times higher than that of Site 2 (64.39 ng/kg). The maximum concentration of PCDD/Fs in mud cores in rice fields (0-50 cm) at Sites 1 and 2 was in the layer of 0-10 cm. The maximum PCDD/F concentration in the top layer in mud at Site 1 (203.1 ng/kg) was higher than that at Site 2: (143.3 ng/kg). Significant correlations were found between the mind PCDD/Fs and the organic carbon content (R = 0.9743, P< 0,05 at Site 1; R = 0.9821, P< 0.05 at Site 2), the two variables being highly correlated (R = 0.9049, P< 0.05, at Site 1; R = 0.9916, P< 0.05 at Site 2). All correlation coefficients were significant at the 95% level. Concentrations were highly correlated with organic carbon, indicating that sorption to organic carbon was the dominant mechanism. Using principal component analysis, the homologue profiles of soil, mud, and plants (rice and radish) were compared. The PCDD/F patterns in plants were found not to be correlated to those in soil and mud. This suggests that atmospheric deposition may be the main source of PCDD/Fs in rice grain. However, mixed exposure involving uptake mechanisms and atmospheric deposition is considered main the source of PCDD/F pollution in radishes. (C) 2002 Elsevier Science (USA).

Mobility and profiles of polychlorinated dibenzo-p-dioxins and dibenzofurans in sediment of Ya-Er Lake, China

The sediment of Ya-Er Lake had been heavily polluted by polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) from the former chloralkali industry. The total amounts of PCDD/Fs and I-TEQ decreased along the water flow direction and also decreased from top to bottom layers of sediment cores. Sediment of Pond 1 was dominated by PCDF, especially TCDF. In contrast, in the other four ponds, PCDD dominated in all layers and octachlorinated dibenzo-p-dioxin (OCDD) predominated in all of the homologues. When homologue profiles from sediments and water samples were compared using principal component analysis (PCA), the first two principal components represented 95.2% of the variance in the data. The first component explained 75.9% of the variance and the second one 19.3%. Two clusters were most distinct, presenting a shift in PCDD/Fs composition from PCDF to heptachlorinated dibenzo-p-dioxin (HpCDD) and OCDD in sediments and water from Pond I to Ponds 2-5. The pattern variation between Pond 1 and Ponds 2-5 in Ya-Er Lake was most likely due to the change of process in the chemical plant after the dams between the ponds were built. The results of the present study also showed that log K-oc of PCDD/Fs calculated from data of sediment and water in the field were comparable with theoretical log K-oc. The results also implied that the concentrations of PCDD/Fs in water and sediments could be predicted from each other by log K-oc. (C) 2001 Elsevier Science Ltd. All rights reserved.

Measurement of the inelastic branch of the O-14(alpha, p)F-17 reaction: Implications for explosive burning in novae and x-ray bursters

A measurement of the inelastic component of the key astrophysical resonance in the 14O(α,p)17F reaction for burning and breakout from hot carbon-nitrogen-oxygen (CNO) cycles is reported. The inelastic component is found to be comparable to the ground-state branch and will enhance the 14O(α,p)17F reaction rate. The current results for the reaction rate confirm that the 14O(α,p)17F reaction is unlikely to contribute substantially to burning and breakout from the CNO cycles under novae conditions. The reaction can, however, contribute strongly to the breakout from the hot CNO cycles under the more extreme conditions found in x-ray bursters.

Measurement of the inelastic branch of the stellar O-14(alpha,p)F-17 reaction occurring in the explosive burning in Novae and X-ray busters

The inelastic component of the key astrophysical resonance (1(-), E-x=6.15 MeV) in the O-14(alpha,p)F-17 reaction has been studied by using the resonant scattering of F-17+p. The experiment was done at REX-ISOLDE CERN with the Miniball setup. The thick target method in inverse kinematics was utilized in the present experiment where a 44.2 MeV F-17 beam bombarded a similar to 40 mu m thick (CH2)(n) target. The inelastic scattering protons in coincidence with the de-excited 495 keV gamma rays have been clearly seen and they are from the inelastic branch to the first excited state in F-17 following decay of the 1(-) resonance in Ne-18. Some preliminary results are reported.

Ambipolar organic heterojunction transistors with various p-type semiconductors

Ambipolar transport has been realized in organic heterojunction transistors with metal phthalocyanines, phenanthrene-based conjugated oligomers as the first semiconductors and copper-hexadecafluoro-phthalocyanine as the second semiconductor. The electron and hole mobilities of ambipolar devices with rod-like molecules were comparable to the corresponding single component devices, while the carrier mobility of ambipolar devices with disk-like molecules was much lower than the corresponding single component devices.

Time-dependent DNA condensation induced by amyloid beta-peptide

The major protein component of the amyloid deposition in Alzheimer's disease is a 39-43 residue peptide, amyloid beta (A beta). A beta is toxic to neurons, although the mechanism of neurodegeneration is uncertain. Evidence exists for non-B DNA conformation in the hippocampus of Alzheimer's disease brains, and A beta was reportedly able to transform DNA conformation in vitro. In this study, we found that DNA conformation was altered in the presence of A beta, and A beta induced DNA condensation in a time-dependent manner. Furthermore, A beta sheets, serving as condensation nuclei, were crucial for DNA condensation, and Cu2+ and Zn2+ ions inhibited A beta sheet-induced DNA condensation. Our results suggest DNA condensation as a mechanism of A beta toxicity.

Miscibility and crystallization of poly(beta-hydroxybutyrate) and poly(p-vinylphenol) blends

The miscibility and crystallization behavior of poly(beta-hydroxybutyrate) (PHB) and poly(p-vinylphenol) (PVPh) blends were studied by differential scanning calorimetry and optical microscopy (OM). The blends exhibit a single composition-dependent glass transition temperature, characteristic of miscible systems, A depression of the equilibrium melting temperature of PHB is observed. The interaction parameter values obtained from analysis of the melting point depression are of large negative values, which suggests that PHB and PVPh blends are thermodynamically miscible in the melt. Isothermal crystallization kinetics in the miscible blend system PHB/PVPh was examined by OM. The presence of the amorphous PVPh component results in a reduction in the rate of spherulite growth of PHB. The spherulite growth rate is analyzed using the Lauritzen-Hoffman model, The isothermally crystallized blends of PHB/PVPh were examined by wide-angle X-ray diffraction and smell-angle X-ray scattering (SAXS). The long period obtained from SAXS increases with the increase in PVPh component, which implies that the amorphous PVPh is squeezed into the interlamallar region of PHB.

Growing season ecosystem respirations and associated component fluxes in two alpine meadows on the Tibetan Plateau

From 30 June to 24 September in 2003 ecosystem respiration (Re) in two alpine meadows on the Tibetan Plateau were measured using static chamber- and gas chromatography- (GC) based techniques. Simultaneously, plant removal treatments were set to partition Re into plant autotrophic respiration (Ra) and microbial heterotrophic respiration (Rh). Results indicated that Re had clear diurnal and seasonal variation patterns in both of the meadows. The seasonal variability of Re at both meadow sites was caused mainly by changes in Ra, rather than Rh. Moreover, at the Kobresia humilis meadow site (K_site), Ra and Rh accounted for 54% and 46% of Re, respectively. While at the Potentilla fruticosa scrub meadow (P_site), the counterparts accounted for 61% and 39%, respectively. T test showed that there was significant difference in Re rates between the two meadows (t = 2.387, P = 0.022). However, no significant difference was found in Rh rates, whereas a significant difference was observed in Ra rates between the two meadows. Thus, the difference in Re rate between the two meadows was mainly attributed to plant autotrophic respirations. During the growing season, the two meadows showed relatively low Q(10) values, suggesting that Re, especially Rh was not sensitive to temperature variation in the growing season. Additionally, Re and Rh at the K_site, as well as Rh at the P_site was negatively correlated with soil moisture, indicating that soil moisture would also play an important role in respirations.

大别山太湖地区榴辉岩变质P-T条件及构造意义

As far as the architecture of the south Dabie metamorphic terrain is concerned, there have been lots of different opinions for a long time. Wang et al. (1990, 1992) thought of it was a continuous terrain. Okay (1993) held that it consistes of two different tectonic terrains: the 'hot' and 'cold' eclogite belt. Liu and Wang (1998) held that it is composed of different metamorphic blocks through 'melange' in depth. For this reason, we have choiced Hualiangting reservoir of Taihu county as the study area treat eclogite as the investigated objection in this thesis, and employ the detailed 1 :10000 geological mapping, methods of Petrography and electonic probe anaylsis to probe into the architecture of the south Dabie metamorphic terrains. In the light of the eclogite occurrenc in the field, the analysis of Petrography, the research on metamoiphic P-T path and condition of the peak metamorphic P-T condition, the eclogite in the Taihu area of Dabieshan have been classified into three types eclogite from the south to the north: The zhujiachong type eclogite; The Daba type eclogite; (3) The Jinheqiao type eclogite, their mineral composition, structure, and mineral component vary continuously. These eclogites have the same rnetamoiphic stages, P-T evolution pattern, and their peak P-T condition varies continuously. The zhujiachong type eclogite is formed in the high pressure metamoiphic environment. The Jinheqiao type eclogite is formed in the typical ultra-high pressure environment. The Daba type eclogite is formed in the transformed metamorphic environment between high pressure and ultra-high pressure metamorphism. All these evidences show that the south Dabie metamorphic terrain is a continuous metamorphic block and no large fault ever existed.

The effect of tungsten additive on the surface characteristics of amorphous Ni-P alloy

The variation of surface compositions on amorphous Ni80.4W1.5P18.1 alloy by O-2 oxidation and H-2 reduction treatments have been studied by XPS, UPS and ISS. It shows that addition of tungsten in the amorphous Ni-P alloy leads to dramatic changes of the relating component distributions in the surface layers before and after these treatments. Oxidation of a Ni80.4W1.5P18.1 amorphous alloy in 1 bar of oxygen at 513 K caused a significant segregation of nickel in different oxide states at the surface. The subsequent reduction of the oxidized surface with I bar hydrogen at 553 K resulted in only a small portion of Ni and P being reduced into elemental states, while most of them was found to combine to form a kind of nickel phosphate compound. On the other hand, under the same conditions, the oxidation and reduction of a Ni80P20 alloy gave rise to metallic Ni and elemental P as the predominate species on the alloy surface. The addition of W in the amorphous alloy might act as nuclei for a favorable formation of the phosphate structure which was proposed to be an active species for hydrogen-relating catalytic reactions. (C) 1999 Elsevier Science B.V. All rights reserved.