277 research outputs found
Non-Gaussian Component Analysis using Entropy Methods
Non-Gaussian component analysis (NGCA) is a problem in multidimensional data
analysis which, since its formulation in 2006, has attracted considerable
attention in statistics and machine learning. In this problem, we have a random
variable in -dimensional Euclidean space. There is an unknown subspace
of the -dimensional Euclidean space such that the orthogonal
projection of onto is standard multidimensional Gaussian and the
orthogonal projection of onto , the orthogonal complement
of , is non-Gaussian, in the sense that all its one-dimensional
marginals are different from the Gaussian in a certain metric defined in terms
of moments. The NGCA problem is to approximate the non-Gaussian subspace
given samples of .
Vectors in correspond to `interesting' directions, whereas
vectors in correspond to the directions where data is very noisy. The
most interesting applications of the NGCA model is for the case when the
magnitude of the noise is comparable to that of the true signal, a setting in
which traditional noise reduction techniques such as PCA don't apply directly.
NGCA is also related to dimension reduction and to other data analysis problems
such as ICA. NGCA-like problems have been studied in statistics for a long time
using techniques such as projection pursuit.
We give an algorithm that takes polynomial time in the dimension and has
an inverse polynomial dependence on the error parameter measuring the angle
distance between the non-Gaussian subspace and the subspace output by the
algorithm. Our algorithm is based on relative entropy as the contrast function
and fits under the projection pursuit framework. The techniques we develop for
analyzing our algorithm maybe of use for other related problems
In Arabidopsis thaliana Heterosis Level Varies among Individuals in an F1 Hybrid Population.
Heterosis or hybrid vigour is a phenomenon in which hybrid progeny exhibit superior yield and biomass to parental lines and has been used to breed F1 hybrid cultivars in many crops. A similar level of heterosis in all F1 individuals is expected as they are genetically identical. However, we found variation in rosette size in individual F1 plants from a cross between C24 and Columbia-0 accessions of Arabidopsis thaliana. Big-sized F1 plants had 26.1% larger leaf area in the first and second leaves than medium-sized F1 plants at 14 days after sowing in spite of the identical genetic background. We identified differentially expressed genes between big- and medium-sized F1 plants by microarray; genes involved in the category of stress response were overrepresented. We made transgenic plants overexpressing 21 genes, which were differentially expressed between the two size classes, and some lines had increased plant size at 14 or 21 days after sowing but not at all time points during development. Change of expression levels in stress-responsive genes among individual F1 plants could generate the variation in plant size of individual F1 plants in A. thaliana
Activation of native TRPC1/C5/C6 channels by endothelin-1 is mediated by both PIP3 and PIP2 in rabbit coronary artery myocytes
We investigate activation mechanisms of native TRPC1/C5/C6 channels (termed TRPC1 channels) by stimulation of endothelin-1 (ET-1) receptor subtypes in freshly dispersed rabbit coronary artery myocytes using single channel recording and immunoprecipitation techniques. ET-1 evoked non-selective cation channel currents with a unitary conductance of 2.6 pS which were not inhibited by either ET(A) or ET(B) receptor antagonists, respectively BQ-123 and BQ788, when administered separately. However, in the presence of both antagonists, ET-1-evoked channel activity was abolished indicating that both ET(A) and ET(B) receptor stimulation activate this conductance. Stimulation of both ET(A) and ET(B) receptors evoked channel activity which was inhibited by the protein kinase C (PKC) inhibitor chelerythrine and by anti-TRPC1 antibodies indicating that activation of both receptor subtypes causes TRPC1 channel activation by a PKC-dependent mechanism. ET(A) receptor-mediated TRPC1 channel activity was selectively inhibited by phosphoinositol-3-kinase (PI-3-kinase) inhibitors wortmannin (50 nm) and PI-828 and by antibodies raised against phosphoinositol-3,4,5-trisphosphate (PIP(3)), the product of PI-3-kinase-mediated phosphorylation of phosphatidylinositol 4,5-bisphosphate (PIP(2)). Moreover, exogenous application of diC8-PIP(3) stimulated PKC-dependent TRPC1 channel activity. These results indicate that stimulation of ET(A) receptors evokes PKC-dependent TRPC1 channel activity through activation of PI-3-kinase and generation of PIP(3). In contrast, ET(B) receptor-mediated TRPC1 channel activity was inhibited by the PI-phospholipase C (PI-PLC) inhibitor U73122. 1-Oleoyl-2-acetyl-sn-glycerol (OAG), an analogue of diacylglycerol (DAG), which is a product of PI-PLC, also activated PKC-dependent TRPC1 channel activity. OAG-induced TRPC1 channel activity was inhibited by anti-phosphoinositol-4,5-bisphosphate (PIP(2)) antibodies and high concentrations of wortmannin (20 μm) which depleted tissue PIP(2) levels. In addition exogenous application of diC8-PIP(2) activated PKC-dependent TRPC1 channel activity. These data indicate that stimulation of ET(B) receptors evokes PKC-dependent TRPC1 activity through PI-PLC-mediated generation of DAG and requires a permissive role of PIP(2). In conclusion, we provide the first evidence that stimulation of ET(A) and ET(B) receptors activate native PKC-dependent TRPC1 channels through two distinct phospholipids pathways involving a novel action of PIP(3), in addition to PIP(2), in rabbit coronary artery myocytes
Self-optimization, community stability, and fluctuations in two individual-based models of biological coevolution
We compare and contrast the long-time dynamical properties of two
individual-based models of biological coevolution. Selection occurs via
multispecies, stochastic population dynamics with reproduction probabilities
that depend nonlinearly on the population densities of all species resident in
the community. New species are introduced through mutation. Both models are
amenable to exact linear stability analysis, and we compare the analytic
results with large-scale kinetic Monte Carlo simulations, obtaining the
population size as a function of an average interspecies interaction strength.
Over time, the models self-optimize through mutation and selection to
approximately maximize a community fitness function, subject only to
constraints internal to the particular model. If the interspecies interactions
are randomly distributed on an interval including positive values, the system
evolves toward self-sustaining, mutualistic communities. In contrast, for the
predator-prey case the matrix of interactions is antisymmetric, and a nonzero
population size must be sustained by an external resource. Time series of the
diversity and population size for both models show approximate 1/f noise and
power-law distributions for the lifetimes of communities and species. For the
mutualistic model, these two lifetime distributions have the same exponent,
while their exponents are different for the predator-prey model. The difference
is probably due to greater resilience toward mass extinctions in the food-web
like communities produced by the predator-prey model.Comment: 26 pages, 12 figures. Discussion of early-time dynamics added. J.
Math. Biol., in pres
Elevation of circulating big endothelin-1: an independent prognostic factor for tumor recurrence and survival in patients with esophageal squamous cell carcinoma
<p>Abstract</p> <p>Background</p> <p>Endothelin(ET) axis plays a key role in many tumor progression and metastasis via various mechanisms such as angiogenesis, mediating extracellular matrix degradation and inhibition of apoptosis. However, there is limited information regarding the clinical significance of plasma big ET-1 levels in esophageal cancer patients. Circulating plasma big ET-1 levels were measured in patients with esophageal squamous cell carcinoma(ESCC) to evaluate the value of ET-1 as a biomarker for predicting tumor recurrence and patients survival.</p> <p>Methods</p> <p>Preoperative plasma big ET-1 concentrations were measured by an enzyme linked immunosorbent assay(ELISA) in 108 ESCC patients before surgery, and then again at 1,2,3,10 and 30 days after curative radical resection for ESCC. The association between preoperative plasma big ET-1 levels and clinicopathological features, tumor recurrence and patient survival, and their changes following surgery were evaluated.</p> <p>Results</p> <p>The preoperative plasma big ET-1 levels in ESCC patients were significantly higher than those in controls. And there was a significant association between plasma big ET-1 levels and disease stage, as well as invasion depth of the tumor and lymph node status. Furthermore, plasma big ET-1 levels decreased significantly after radical resection of the primary tumor and patients with postoperative recurrence had significantly higher plasma big ET-1 levels than that of patients without recurrence. Finally, the survival rate of patients with higher plasma big ET-1 concentrations (>4.3 pg/ml) was significantly lower than that of patients with lower level (≤ 4.3 pg/ml). Multivariate regression analysis showed that plasma big ET-1 level is an independent prognostic factor for survival in patients with ESCC.</p> <p>Conclusion</p> <p>Plasma big ET-1 level in ESCC patients may reflect malignancy and predict tumor recurrence and patient survival. Therefore, the preoperative plasma big ET-1 levels may be a clinically useful biomarker for choice of multimodality therapy in ESCC patients.</p
Non-Gaussian component analysis: testing the dimension of the signal subspace
Dimension reduction is a common strategy in multivariate data analysis which
seeks a subspace which contains all interesting features needed for the
subsequent analysis. Non-Gaussian component analysis attempts for this purpose
to divide the data into a non-Gaussian part, the signal, and a Gaussian part,
the noise. We will show that the simultaneous use of two scatter functionals
can be used for this purpose and suggest a bootstrap test to test the dimension
of the non-Gaussian subspace. Sequential application of the test can then for
example be used to estimate the signal dimension
A three month controlled intervention of intermittent whole body vibration designed to improve functional ability and attenuate bone loss in patients with rheumatoid arthritis
Background: Rheumatoid arthritis (RA) is a chronic autoimmune condition that results in pain and disability. Patients with RA have a decreased functional ability and are forced into a sedentary lifestyle and as such, these patients often become predisposed to poor bone health. Patients with RA may also experience a decreased health related quality of life (HRQoL) due to their disease. Whole body vibration (WBV) is a form of exercise that stimulates bone loading through forced oscillation. WBV has also been shown to decrease pain and fatigue in other rheumatic diseases, as well as to increase muscle strength. This paper reports on the development of a semi randomised controlled clinical trial to assess the impact of a WBV intervention aiming to improve functional ability, attenuate bone loss, and improve habitual physical activity levels in patients with RA. Methods/Design: This study is a semi randomised, controlled trial consisting of a cohort of patients with established RA assigned to either a WBV group or a CON (control) group. Patients in the WBV group will undergo three months of twice weekly intermittent WBV sessions, while the CON group will receive standard care and continue with normal daily activities. All patients will be assessed at baseline, following the three month intervention, and six months post intervention. Main outcomes will be an improvement in functional ability as assessed by the HAQ. Secondary outcomes are attenuation of loss of bone mineral density (BMD) at the hip and changes in RA disease activity, HRQoL, habitual physical activity levels and body composition. Discussion: This study will provide important information regarding the effects of WBV on functional ability and BMD in patients with RA, as well as novel data regarding the potential changes in objective habitual physical activity patterns that may occur following the intervention. The sustainability of the intervention will also be assessed
Comparison of Ion Balance and Nitrogen Metabolism in Old and Young Leaves of Alkali-Stressed Rice Plants
BACKGROUND: Alkali stress is an important agricultural contaminant and has complex effects on plant metabolism. The aim of this study was to investigate whether the alkali stress has different effects on the growth, ion balance, and nitrogen metabolism in old and young leaves of rice plants, and to compare functions of both organs in alkali tolerance. METHODOLOGY/PRINCIPAL FINDINGS: The results showed that alkali stress only produced a small effect on the growth of young leaves, whereas strongly damaged old leaves. Rice protected young leaves from ion harm via the large accumulation of Na(+) and Cl(-) in old leaves. The up-regulation of OsHKT1;1, OsAKT1, OsHAK1, OsHAK7, OsHAK10 and OsHAK16 may contribute to the larger accumulation of Na(+) in old leaves under alkali stress. Alkali stress mightily reduced the NO(3)(-) contents in both organs. As old leaf cells have larger vacuole, under alkali stress these scarce NO(3)(-) was principally stored in old leaves. Accordingly, the expression of OsNRT1;1 and OsNRT1;2 in old leaves was up-regulated by alkali stress, revealing that the two genes might contribute to the accumulation of NO(3)(-) in old leaves. NO(3)(-) deficiency in young leaves under alkali stress might induce the reduction in OsNR1 expression and the subsequent lacking of NH(4)(+), which might be main reason for the larger down-regulation of OsFd-GOGAT and OsGS2 in young leaves. CONCLUSIONS/SIGNIFICANCE: Our results strongly indicated that, during adaptation of rice to alkali stress, young and old leaves have distinct mechanisms of ion balance and nitrogen metabolism regulation. We propose that the comparative studies of young and old tissues may be important for abiotic stress tolerance research
Predicting invasions of North American basses in Japan using native range data and a genetic algorithm
Largemouth bass Micropterus salmoides and smallmouth bass M. dolomieu have been
introduced into freshwater habitats in Japan, with potentially serious consequences for native fish
populations. In this paper we apply the technique of ecological niche modeling using the genetic
algorithm for rule-set prediction (GARP) to predict the potential distributions of these two species
in Japan. This algorithm constructs a niche model based on point occurrence records and ecological
coverages. The model can be visualized in geographic space, yielding a prediction of potential
geographic range. The model can then be tested by determining how well independent point
occurrence data are predicted according to the criteria of sensitivity and specificity provided by
receiver–operator curve analysis. We ground-truthed GARP’s ability to forecast the geographic
occurrence of each species in its native range. The predictions were statistically significant for
both species (P , 0.001). We projected the niche models onto the Japanese landscape to visualize
the potential geographic ranges of both species in Japan. We tested these predictions using known
occurrences from introduced populations of largemouth bass, both in the aggregate and by habitat
type. All analyses robustly predicted known Japanese occurrences (P , 0.001). The number of
smallmouth bass in Japan was too small for statistical tests, but the 10 known occurrences were
predicted by the majority of models
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