M-BISON: Microarray-based integration of data sources using networks

BACKGROUND: The accurate detection of differentially expressed (DE) genes has become a central task in microarray analysis. Unfortunately, the noise level and experimental variability of microarrays can be limiting. While a number of existing methods partially overcome these limitations by incorporating biological knowledge in the form of gene groups, these methods sacrifice gene-level resolution. This loss of precision can be inappropriate, especially if the desired output is a ranked list of individual genes. To address this shortcoming, we developed M-BISON (Microarray-Based Integration of data SOurces using Networks), a formal probabilistic model that integrates background biological knowledge with microarray data to predict individual DE genes. RESULTS: M-BISON improves signal detection on a range of simulated data, particularly when using very noisy microarray data. We also applied the method to the task of predicting heat shock-related differentially expressed genes in S. cerevisiae, using an hsf1 mutant microarray dataset and conserved yeast DNA sequence motifs. Our results demonstrate that M-BISON improves the analysis quality and makes predictions that are easy to interpret in concert with incorporated knowledge. Specifically, M-BISON increases the AUC of DE gene prediction from .541 to .623 when compared to a method using only microarray data, and M-BISON outperforms a related method, GeneRank. Furthermore, by analyzing M-BISON predictions in the context of the background knowledge, we identified YHR124W as a potentially novel player in the yeast heat shock response. CONCLUSION: This work provides a solid foundation for the principled integration of imperfect biological knowledge with gene expression data and other high-throughput data sources

Experimental evidence of a natural parity state in 26^{26}Mg and its impact to the production of neutrons for the s process

We have studied natural parity states in $^{26}$Mg via the $^{22}$Ne($^{6}$Li,d)$^{26}$Mg reaction. Our method significantly improves the energy resolution of previous experiments and, as a result, we report the observation of a natural parity state in $^{26}$Mg. Possible spin-parity assignments are suggested on the basis of published $\gamma$-ray decay experiments. The stellar rate of the $^{22}$Ne($\alpha$,$\gamma$)$^{26}$Mg reaction is reduced and may give rise to an increase in the production of s-process neutrons via the $^{22}$Ne($\alpha$,n)$^{25}$Mg reaction.Comment: Published in PR

Deep H{\alpha} Observations of NGC 253: a Very Extended and Possibly Declining Rotation Curve?

This study presents a deep H{\alpha} kinematical analysis of the Sculptor Group galaxy NGC253. The Fabry-Perot data were taken with the 36-cm Marseille Telescope in La Silla, Chile, using an EMCCD detector. Typical emission measures of ~0.1 cm^-6 pc are reached. The observations allow the detection of the Diffuse Ionized Gas component through [N II] emission at very large radii of 11.5', 12.8' and 19.0', on the receding side of the galaxy. No H{\alpha} emission is observed at radii larger than the neutral component (11.5'). The very extended rotation curve confirms previous results and shows signs of a significant decline, on the order of 30 per cent vmax . Using the rotation data, mass models are constructed with and without the outer [N II] data points, and similar results are found. The declining part of the rotation curve is very well modeled, and seems to be truly declining.Comment: Accepted for publication in MNRAS. 16 pages, 10 figures, 4 table

GHASP : An Halpha kinematic survey of spiral and irregular galaxies - VI. New Halpha data cubes for 108 galaxies

We present the Fabry-Perot observations obtained for a new set of 108 galaxies that completes the GHASP survey (Gassendi HAlpha survey of SPirals). The GHASP survey consists of 3D Ha data cubes for 203 spiral and irregular galaxies, covering a large range in morphological types and absolute magnitudes, for kinematics analysis. The GHASP sample is by now the largest sample of Fabry-Perot data ever published. We have derived Ha data cubes from which are computed Ha maps, radial velocity fields as well as residual velocity fields, position-velocity diagrams, rotation curves and the kinematical parameters for almost all galaxies. Original improvements in the determination of the kinematical parameters, rotation curves and their uncertainties have been implemented in the reduction procedure. This new method is based on the whole 2D velocity field and on the power spectrum of the residual velocity fieldrather than the classical method using successive crowns in the velocity field. Among the results, we point out that morphological position angles have systematically higher uncertainties than kinematical ones, especially for galaxies with low inclination. Morphological inclination of galaxies having no robust determination of their morphological position angle cannot be constrained correctly. Galaxies with high inclination show a better agreement between their kinematical inclination and their morphological inclination computed assuming a thin disk. The consistency of the velocity amplitude of our rotation curves have been checked using the Tully-Fisher relationship. Our data are in good agreement with previous determinations found in the literature. Nevertheless, galaxies with low inclination have statistically higher velocities than expected and fast rotators are less luminous than expected.Comment: accepted in MNRAS for publication, 60 pages, 25 figures, usues biblio.bib for bibliography (.bbl included in the archive), natbib.sty, epsfig.st

An improved method for statistical studies of the internal kinematics of HII regions: the case of M 83

We present the integrated Halpha emission line profile for 157 HII regions in the central 3.4' x 3.4' of the galaxy M 83 (NGC 5236). Using the Fabry-Perot interferometer GHaFaS, on the 4.2 m William Herschel on La Palma, we show the importance of a good characterization of the instrumental response function for the study of line profile shapes. The luminosity-velocity dispersion relation is also studied, and in the log(L)-log(sigma) plane we do not find a linear relation, but an upper envelope with equation log(L)=0.9 *log(sigma)+38.1. For the adopted distance of 4.5 Mpc, the upper envelope appears at the luminosity L=10^38.5 ergs, in full agreement with previous studies of other galaxies, reinforcing the idea of using HII regions as standard candles.Comment: 13 pages, 9 figures, accepted for publication in MNRA

Atomic and Molecular Gas Components in Spiral Galaxies of the Virgo Cluster

Based on two models, we investigate the molecular-to-atomic gas ratio in Virgo cluster galaxies in comparison with field galaxies. We show that the enhanced metallicity for cluster members and the ram pressure stripping of atomic gas from the disk periphery cannot fully explain the observed gas component ratios. The additional environmental factors affecting the interstellar medium and leading to an increase in the molecular gas fraction should be taken into account for cluster galaxies.Comment: 11 pages, 4 figure

First Case Start Times for Vascular Surgery

Problem/Impact Statement: 85% of first cases at Maine Medical Center for Vascular Surgery start late. According to one study done by Aurora Health Care; of 5,500 first case surgeries, 88% of them started late. The impact of this is far reaching. It is not in alignment with MMC value of Patient Centered Care because the patient becomes dissatisfied waiting to be brought in to surgery , they are fasting for longer than anticipated, and being away from their family while they wait causing anxiety. The financial impact is $1995 for each 1⁄2 hr. of O.R. time. Furthermore, this may result in elective cases being canceled, late cases create a back log of cases to be done, the hospital loses potential revenue, and staff stay later causing overtime accrual