Tellipsoid: Exploiting inter-gene correlation for improved detection of differential gene expression

Motivation: Algorithms for differential analysis of microarray data are vital to modern biomedical research. Their accuracy strongly depends on effective treatment of inter-gene correlation. Correlation is ordinarily accounted for in terms of its effect on significance cut-offs. In this paper it is shown that correlation can, in fact, be exploited {to share information across tests}, which, in turn, can increase statistical power. Results: Vastly and demonstrably improved differential analysis approaches are the result of combining identifiability (the fact that in most microarray data sets, a large proportion of genes can be identified a priori as non-differential) with optimization criteria that incorporate correlation. As a special case, we develop a method which builds upon the widely used two-sample t-statistic based approach and uses the Mahalanobis distance as an optimality criterion. Results on the prostate cancer data of Singh et al. (2002) suggest that the proposed method outperforms all published approaches in terms of statistical power. Availability: The proposed algorithm is implemented in MATLAB and in R. The software, called Tellipsoid, and relevant data sets are available at http://www.egr.msu.edu/~desaikeyComment: 19 pages, Submitted to Bioinformatic

CosmoDM and its application to Pan-STARRS data

The Cosmology Data Management system (CosmoDM) is an automated and flexible data management system for the processing and calibration of data from optical photometric surveys. It is designed to run on supercomputers and to minimize disk I/O to enable scaling to very high throughput during periods of reprocessing. It serves as an early prototype for one element of the ground-based processing required by the Euclid mission and will also be employed in the preparation of ground based data needed in the eROSITA X-ray all sky survey mission. CosmoDM consists of two main pipelines. The first is the single-epoch or detrending pipeline, which is used to carry out the photometric and astrometric calibration of raw exposures. The second is the co- addition pipeline, which combines the data from individual exposures into deeper coadd images and science ready catalogs. A novel feature of CosmoDM is that it uses a modified stack of As- tromatic software which can read and write tile compressed images. Since 2011, CosmoDM has been used to process data from the DECam, the CFHT MegaCam and the Pan-STARRS cameras. In this paper we shall describe how processed Pan-STARRS data from CosmoDM has been used to optically confirm and measure photometric redshifts of Planck-based Sunyaev-Zeldovich effect selected cluster candidates.Comment: 11 pages, 4 figures. Proceedings of Precision Astronomy with Fully Depleted CCDs Workshop (2014). Accepted for publication in JINS

Line shifts in the first overtone of DF broadened by HF

Line spectra shifts in HF and in first overtone band of DF induced by HF pressure

SYNTHESIS, IN VITRO ANTIMICROBIAL ACTIVITY OF SCHIFF'S BASE, AZETIDINONES AND THIAZOLIDINONES

Objective: The objective of the present study is to synthesize 3-Chloro-4-[3-(2,4-dichloro-5-fluoro phenyl)-1H-pyrazol-4-yl]-1-(substituted) azetidin-2-one [4a-n] and 2-[3-(2,4-Dichloro-5-fluoro phenyl)-1H-pyraol-4-yl]-3-(substituted phenyl)-1,3-thiazolidin-4-one [5a-n]. The structure of all synthesized compounds were characterized by IR, 1H NMR, 13C NMR and mass spectral studies. Methods: The titled compounds 3-Chloro-4-[3-(2,4-dichloro-5-fluoro phenyl)-1H-pyrazol-4-yl]-1-(substituted) azetidin-2-one [4a-n] and 2-[3-(2,4-Dichloro-5-fluoro phenyl)-1H-pyraol-4-yl]-3-(substituted phenyl)-1,3-thiazolidin-4-one [5a-n] were synthesized by the reaction of N-{[3-(2,4-dichloro-5-fluoro phenyl)-1H-pyraol-4-yl] methylene } substituted anilin [3a-n] with chloro acetyl chloride and thioglycolic acid respectively. Compounds N-{[3-(2,4-dichloro-5-fluoro phenyl)-1H-pyraol-4-yl] methylene} substituted aniline [3a-n] were synthesized by the reaction of 3-(2,4-dichloro-5-fluoro phenyl)-1H-pyrazol-4-carbaldehyde [2] with primary aromatic amine in alcohol. All compounds were evaluated for their antimicrobial activity.Results: Compounds 3a,3b,3d,3j,3l,4d,4e,4j,4l,4m,5e,5g,5h,5n exhibited excellent to good antibacterial activity as compared to reference drugs.Conclusion: In summary, N-{[3-(2,4-dichloro-5-fluoro phenyl)-1H-pyraol-4-yl] methylene } substituted anilin [3a-n], 3-Chloro-4-[3-(2,4-dichloro-5-fluoro phenyl)-1H-pyrazol-4-yl]-1-(substituted) azetidin-2-one [4a-n] and 2-[3-(2,4-Dichloro-5-fluoro phenyl)-1H-pyraol-4-yl]-3-(substituted phenyl)-1,3-thiazolidin-4-one [5a-n] derivatives have been synthesized and characterized. In vitro antimicrobial testing of the compounds was carried out by microdilution Method. Amongst the synthesised compounds, many of them had proven their antimicrobial potency which varies from good to excellent

The Sizes of 1720 MHz OH Masers: VLBA and MERLIN Observations of the Supernova Remnants W44 and W28

We have used the NRAO Very Long Baseline Array (VLBA) to image OH(1720 MHz) masers in the supernova remnants W28 and W44 at a resolution of 40 mas. We also used MERLIN to observe the same OH(1720 MHz) masers in W44 at a resolution of 290 x 165 mas. All the masers are resolved by these VLBA and MERLIN observations. The measured sizes range from 50 to 180 mas and yield brightness temperature estimates from 0.3--20 x 10**8 K. We investigate whether these measured angular sizes are intrinsic and hence originate as a result of the physical conditions in the supernova remnant shock, or whether they are scatter broadened sizes produced by the turbulent ionized gas along the line of sight. While the current data on the temporal and angular broadening of pulsars, masers and extragalactic soures toward W44 and W28 can be understood in terms of scattering, we cannot rule out that these large sizes are intrinsic. Recent theoretical modeling by Lockett et al. suggests that the physical parameters in the shocked region are indicative of densities and OH abundances which lead to estimates of sizes as large as what we measure. If the sizes and structure are intrinsic, then the OH(1720 MHz) masrs may be more like the OH(1612 MHz) masers in circumstellar shells than OH masers associated with HII regions. At two locations in W28 we observe the classical S-shapes in the Stokes V profiles caused by Zeeman splitting and use it to infer magnetic fields of order 2 milliGauss.Comment: 24 pages, 6 figures, accepted by Ap

Quantifying the effects of harvesting on carbon fluxes and stocks in northern temperate forests

Harvest disturbance has substantial impacts on forest carbon (C) fluxes and stocks. The quantification of these effects is essential for the better understanding of forest C dynamics and informing forest management in the context of global change. We used a process-based forest ecosystem model, PnET-CN, to evaluate how, and by what mechanisms, clear-cuts alter ecosystem C fluxes, aboveground C stocks (AGC), and leaf area index (LAI) in northern temperate forests. We compared C fluxes and stocks predicted by the model and observed at two chronosequences of eddy covariance flux sites for deciduous broadleaf forests (DBF) and evergreen needleleaf forests (ENF) in the Upper Midwest region of northern Wisconsin and Michigan, USA. The average normalized root mean square error (NRMSE) and the Willmott index of agreement (d) for carbon fluxes, LAI, and AGC in the two chronosequences were 20% and 0.90, respectively. Simulated gross primary productivity (GPP) increased with stand age, reaching a maximum (1200–1500 g C m−2 yr−1) at 11–30 years of age, and leveled off thereafter (900–1000 g C m−2 yr−1). Simulated ecosystem respiration (ER) for both plant functional types (PFTs) was initially as high as 700–1000 g C m−2 yr−1 in the first or second year after harvesting, decreased with age (400–800 g C m−2 yr−1) before canopy closure at 10–25 years of age, and increased to 800–900 g C m−2 yr−1 with stand development after canopy recovery. Simulated net ecosystem productivity (NEP) for both PFTs was initially negative, with net C losses of 400–700 g C m−2 yr−1 for 6–17 years after clear-cuts, reaching peak values of 400–600 g C m−2 yr−1 at 14–29 years of age, and eventually stabilizing in mature forests (\u3e 60 years old), with a weak C sink (100–200 g C m−2 yr−1). The decline of NEP with age was caused by the relative flattening of GPP and gradual increase of ER. ENF recovered more slowly from a net C source to a net sink, and lost more C than DBF. This suggests that in general ENF may be slower to recover to full C assimilation capacity after stand-replacing harvests, arising from the slower development of photosynthesis with stand age. Our model results indicated that increased harvesting intensity would delay the recovery of NEP after clear-cuts, but this had little effect on C dynamics during late succession. Future modeling studies of disturbance effects will benefit from the incorporation of forest population dynamics (e.g., regeneration and mortality) and relationships between age-related model parameters and state variables (e.g., LAI) into the model

Stellar Mass to Halo Mass Scaling Relation for X-ray Selected Low Mass Galaxy Clusters and Groups out to Redshift z≈1z\approx1

We present the stellar mass-halo mass scaling relation for 46 X-ray selected low-mass clusters or groups detected in the XMM-BCS survey with masses $2\times10^{13}M_{\odot}\lesssim M_{500}\lesssim2.5\times10^{14}M_{\odot}$ at redshift $0.1\le z \le1.02$. The cluster binding masses $M_{500}$ are inferred from the measured X-ray luminosities \Lx, while the stellar masses $M_{\star}$ of the galaxy populations are estimated using near-infrared imaging from the SSDF survey and optical imaging from the BCS survey. With the measured \Lx\ and stellar mass $M_{\star}$, we determine the best fit stellar mass-halo mass relation, accounting for selection effects, measurement uncertainties and the intrinsic scatter in the scaling relation. The resulting mass trend is $M_{\star}\propto M_{500}^{0.69\pm0.15}$, the intrinsic (log-normal) scatter is $\sigma_{\ln M_{\star}|M_{500}}=0.36^{+0.07}_{-0.06}$, and there is no significant redshift trend $M_{\star}\propto (1+z)^{-0.04\pm0.47}$, although the uncertainties are still large. We also examine $M_{\star}$ within a fixed projected radius of $0.5$~Mpc, showing that it provides a cluster binding mass proxy with intrinsic scatter of $\approx93\%$ (1$\sigma$ in $M_{500}$). We compare our $M_{\star}=M_{\star}(M_{500}, z)$ scaling relation from the XMM-BCS clusters with samples of massive, SZE-selected clusters ($M_{500}\approx6\times10^{14}M_{\odot}$) and low mass NIR-selected clusters ($M_{500}\approx10^{14}M_{\odot}$) at redshift $0.6\lesssim z \lesssim1.3$. After correcting for the known mass measurement systematics in the compared samples, we find that the scaling relation is in good agreement with the high redshift samples, suggesting that for both groups and clusters the stellar content of the galaxy populations within $R_{500}$ depends strongly on mass but only weakly on redshift out to $z\approx1$.Comment: 15 pages, 10 figures. Accepted for publication in MNRA

Seed populations for large solar particle events of cycle 23

Using high-resolution mass spectrometers on board the Advanced Composition Explorer (ACE), we surveyed the event-averaged ~0.1-60 MeV/nuc heavy ion elemental composition in 64 large solar energetic particle (LSEP) events of cycle 23. Our results show the following: (1) The rare isotope ^3He is greatly enhanced over the corona or the solar wind values in 46% of the events. (2) The Fe/O ratio decreases with increasing energy up to ~10 MeV/nuc in ~92% of the events and up to ~60 MeV/nuc in ~64% of the events. (3) Heavy ion abundances from C-Fe exhibit systematic M/g-dependent enhancements that are remarkably similar to those seen in ^3He-rich SEP events and CME-driven interplanetary (IP) shock events. Taken together, these results confirm the role of shocks in energizing particles up to ~60 MeV/nuc in the majority of large SEP events of cycle 23, but also show that the seed population is not dominated by ions originating from the ambient corona or the thermal solar wind, as previously believed. Rather, it appears that the source material for CME-associated large SEP events originates predominantly from a suprathermal population with a heavy ion enrichment pattern that is organized according to the ion's mass-per-charge ratio. These new results indicate that current LSEP models must include the routine production of this dynamic suprathermal seed population as a critical pre-cursor to the CME shock acceleration process