Inferring meta-covariates in classification

This paper develops an alternative method for gene selection that combines model based clustering and binary classification. By averaging the covariates within the clusters obtained from model based clustering, we define “meta-covariates” and use them to build a probit regression model, thereby selecting clusters of similarly behaving genes, aiding interpretation. This simultaneous learning task is accomplished by an EM algorithm that optimises a single likelihood function which rewards good performance at both classification and clustering. We explore the performance of our methodology on a well known leukaemia dataset and use the Gene Ontology to interpret our results

Flow field characteristics in the housing of noncircular gear flowmeter

Paper presented at the 6th International Conference on Heat Transfer, Fluid Mechanics and Thermodynamics, South Africa, 30 June - 2 July, 2008.In order to find the factors which affect the accuracy of the flow rate measurement, the inner flow characteristics of an oval-gear flowmeter were investigated. Inner flow field was analyzed by using the fluid-structure coupling technique with ADINA-FSI (Fluid-Structure Interactions) module. The results were compared with experimental results such as flow visualization and measurements of flow rate, rpm, and pressure drop. As a result, the pressure on the rotor surface was periodically changed with respect to the rotational angle, from the maximum value of the inlet pressure to the minimum value of the outlet pressure. The rotor tip velocity showed the periodical changes with respect to the rotational angle. The creation, movement, and discharge of vortices were observed by turns around the upper and the lower rotor, which are produced by the rotation of the rotor and the changes in the flow passage area and contour in the housing. Larger pressure difference between the inlet and the exit of the housing showed higher flow rate. The flowmeter used in the present experiment had the precision of 1%, in view of the ppl (pulse per liter) variation as a function of flow rate. The power loss, the difference between the theoretical driving power of the rotor due to the pressure difference and the actual power of the rotor, was increased as the flow rate was increased.vk201

Synchronization in a System of Globally Coupled Oscillators with Time Delay

We study the synchronization phenomena in a system of globally coupled oscillators with time delay in the coupling. The self-consistency equations for the order parameter are derived, which depend explicitly on the amount of delay. Analysis of these equations reveals that the system in general exhibits discontinuous transitions in addition to the usual continuous transition, between the incoherent state and a multitude of coherent states with different synchronization frequencies. In particular, the phase diagram is obtained on the plane of the coupling strength and the delay time, and ubiquity of multistability as well as suppression of the synchronization frequency is manifested. Numerical simulations are also performed to give consistent results

The in vitro effects of dehydroepiandrosterone on human osteoarthritic chondrocytes

AbstractObjective: To investigate the in vitro effects of dehydroepiandrosterone (DHEA) on human osteoarthritic chondrocytes.Design: Chondrocytes isolated from human osteoarthritic knee cartilage were three-dimensionally cultured in alginate beads, except for cell proliferation experiment. Cells were treated with DHEA in the presence or absence of IL-1β. The effects on chondrocytes were analyzed using a 3-(4,5-dimethylthiazol-2yl)-5-(3-carboxymethoxy-phenyl)-2-(4-sulfophenyl)-2H-tetrazolium inner salt (MTS) assay (for chondrocyte proliferation), a dimethylmethylene blue (DMB) assay (for glycosaminoglycan (GAG) synthesis), and an indole assay (for DNA amount). Gene expressions of type I and II collagen, metalloproteinase-1 and -3 (MMP-1 and -3), and tissue inhibitor of metalloproteinase-1 (TIMP-1) as well as the IL-1β-induced gene expressions of MMP-1 and -3 were analyzed by reverse transcription-polymerase chain reaction (RT-PCR). The protein synthesis of MMP-1 and -3 and TIMP-1 was determined by Western blotting.Results: The treatment of chondrocytes with DHEA did not affect chondrocyte proliferation or GAG synthesis up to 100μM of concentration. The gene expression of type II collagen increased in a dose-dependent manner, while that of type I decreased. DHEA suppressed the expression of MMP-1 significantly at concentrations exceeding 50μM. The gene expression of MMP-3 was also suppressed, but this was without statistical significance. The expression of TIMP-1 was significantly increased by DHEA at concentrations exceeding 10μM. The effects of DHEA on the gene expressions of MMP-1 and -3 were more prominent in the presence of IL-1β, in which DHEA suppressed not only MMP-1, but also MMP-3 at the lower concentrations, 10 and 50μM, respectively. Western blotting results were in agreement with RT-PCR, which indicates that DHEA acts at the gene transcription level.Conclusions: Our study demonstrates that DHEA has no toxic effect on chondrocytes up to 100μM of concentration and has an ability to modulate the imbalance between MMPs and TIMP-1 during OA at the transcription level, which suggest that it has a protective role against articular cartilage loss

Theory of Melting and the Optical Properties of Gold/DNA Nanocomposites

We describe a simple model for the melting and optical properties of a DNA/gold nanoparticle aggregate. The optical properties at fixed wavelength change dramatically at the melting transition, which is found to be higher and narrower in temperature for larger particles, and much sharper than that of an isolated DNA link. All these features are in agreement with available experiments. The aggregate is modeled as a cluster of gold nanoparticles on a periodic lattice connected by DNA bonds, and the extinction coefficient is computed using the discrete dipole approximation. Melting takes place as an increasing number of these bonds break with increasing temperature. The melting temperature corresponds approximately to the bond percolation threshold.Comment: 5 pages, 4 figure. To be published in Phys. Rev.

Time and Amplitude of Afterpulse Measured with a Large Size Photomultiplier Tube

We have studied the afterpulse of a hemispherical photomultiplier tube for an upcoming reactor neutrino experiment. The timing, the amplitude, and the rate of the afterpulse for a 10 inch photomultiplier tube were measured with a 400 MHz FADC up to 16 \ms time window after the initial signal generated by an LED light pulse. The time and amplitude correlation of the afterpulse shows several distinctive groups. We describe the dependencies of the afterpulse on the applied high voltage and the amplitude of the main light pulse. The present data could shed light upon the general mechanism of the afterpulse.Comment: 11 figure

Synchronization and resonance in a driven system of coupled oscillators

We study the noise effects in a driven system of globally coupled oscillators, with particular attention to the interplay between driving and noise. The self-consistency equation for the order parameter, which measures the collective synchronization of the system, is derived; it is found that the total order parameter decreases monotonically with noise, indicating overall suppression of synchronization. Still, for large coupling strengths, there exists an optimal noise level at which the periodic (ac) component of the order parameter reaches its maximum. The response of the phase velocity is also examined and found to display resonance behavior.Comment: 17 pages, 3 figure

Comparison of computed tomographic findings in pulmonary mucormycosis and invasive pulmonary aspergillosis

AbstractBecause there are no available molecular markers for pulmonary mucormycosis (PM), which has low culture sensitivity, early diagnosis and treatment rely heavily on imaging modes such as computed tomography (CT). However, there are limited data comparing CT findings for PM with those for invasive pulmonary aspergillosis (IPA). Adult patients who met the modified criteria for proven and probable PM (over an 11-year period) and IPA (over a 6-year period, owing to the availability of the galactomannan assay) according to the modified European Organization for Research and Treatment of Cancer/Mycosis Study Group definitions were retrospectively enrolled. IPA cases were selected at a 1 : 4 (PM/IPA) ratio. Thoracic CT scans were reviewed by two experienced radiologists blinded to the patients' demographics and clinical outcomes. A total of 24 patients with PM, including 20 (83%) with proven PM and four (17%) with probable PM, and 96 patients with IPA, including 12 (13%) with proven IPA and 84 (87%) with probable IPA, were eventually analysed. The reverse halo sign was more common in patients with PM (54%) than in those with IPA (6%, p < 0.001), whereas some airway-invasive features, such as clusters of centrilobular nodules, peribronchial consolidations, and bronchial wall thickening, were more common in patients with IPA (IPA 52% vs. PM 29%, p 0.04; IPA 49% vs. PM 21%, p 0.01; IPA 34% vs. PM 4%, p 0.003, respectively). The reverse halo sign was more common, and airway-invasive features were less common, in patients with PM than in those with IPA. These findings may help physicians to initiate Zygomycetes-active antifungal treatment earlier

Developing Tautai Lavea‘i, a Breast Cancer Patient Nativation Program in American Samoa

This article focuses on development of the psychosocial-cultural components of a breast cancer patient navigation program (PNP) in the medically underserved, albeit culturally-rich Territory of American Samoa. Efforts to reduce cancer morbidity and mortality in American Samoa must necessarily consider the territory’s limited cancer resources and indigenous culture, as well as the individuals at risk for poor health outcomes and premature death. Within this complex set of challenges resides the prospect of health equity and opportunities for advancing service innovations that meaningfully plait native ways of knowing with Western evidence- based practice. Increasing adherence to diagnostic and treatment procedures is of significant concern to the American Samoa Cancer Community Network who initiated this inquiry to assess patients lost to follow-up, describe treatment-seeking influences, and identify cultural preferences for inclusion in a PNP tailored on fa‘aSamoa or the Samoan worldview

Phase synchronization and noise-induced resonance in systems of coupled oscillators

We study synchronization and noise-induced resonance phenomena in systems of globally coupled oscillators, each possessing finite inertia. The behavior of the order parameter, which measures collective synchronization of the system, is investigated as the noise level and the coupling strength are varied, and hysteretic behavior is manifested. The power spectrum of the phase velocity is also examined and the quality factor as well as the response function is obtained to reveal noise-induced resonance behavior.Comment: to be published in Phys. Rev.