Analysis of probe level patterns in Affymetrix microarray data

<p>Abstract</p> <p>Background</p> <p>Microarrays have been used extensively to analyze the expression profiles for thousands of genes in parallel. Most of the widely used methods for analyzing Affymetrix Genechip microarray data, including RMA, GCRMA and Model Based Expression Index (MBEI), summarize probe signal intensity data to generate a single measure of expression for each transcript on the array. In contrast, other methods are applied directly to probe intensities, negating the need for a summarization step.</p> <p>Results</p> <p>In this study, we used the Affymetrix rat genome Genechip to explore variability in probe response patterns within transcripts. We considered a number of possible sources of variability in probe sets including probe location within the transcript, middle base pair of the probe sequence, probe overlap, sequence homology and affinity. Although affinity, middle base pair and probe location effects may be seen at the gross array level, these factors only account for a small proportion of the variation observed at the gene level. A BLAST search and the presence of probe by treatment interactions for selected differentially expressed genes showed high sequence homology for many probes to non-target genes.</p> <p>Conclusion</p> <p>We suggest that examination and modeling of probe level intensities can be used to guide researchers in refining their conclusions regarding differentially expressed genes. We discuss implications for probe sequence selection for confirmatory analysis using real time PCR.</p

Elastic anomalies associated with domain switching in BaTiO3 single crystals under in-situ electrical cycling

The elastic response of BaTiO3 single crystals during electric field cycling at room temperature has been studied using in-situ Resonant Ultrasound Spectroscopy (RUS), which allows monitoring of both the elastic and anelastic changes caused by ferroelectric polarization switching. We find that the first ferroelectric switching of a virgin single crystal is dominated by ferroelastic 90° switching. In subsequent ferroelectric switching, ferroelastic switching is reduced by domain pinning and by the ferroelectric domains, as confirmed by polarized light microscopy. RUS under in-situ electric field therefore demonstrates to be an effective technique for the investigation of electromechanical coupling in ferroelectrics

A variable absorption feature in the X-ray spectrum of a magnetar

Soft gamma-ray repeaters (SGRs) and anomalous X-ray pulsars (AXPs) are slowly rotating, isolated neutron stars that sporadically undergo episodes of long-term flux enhancement (outbursts) generally accompanied by the emission of short bursts of hard X-rays. This behaviour can be understood in the magnetar model, according to which these sources are mainly powered by their own magnetic energy. This is supported by the fact that the magnetic fields inferred from several observed properties of AXPs and SGRs are greater than - or at the high end of the range of - those of radio pulsars. In the peculiar case of SGR 0418+5729, a weak dipole magnetic moment is derived from its timing parameters, whereas a strong field has been proposed to reside in the stellar interior and in multipole components on the surface. Here we show that the X-ray spectrum of SGR 0418+5729 has an absorption line, the properties of which depend strongly on the star's rotational phase. This line is interpreted as a proton cyclotron feature and its energy implies a magnetic field ranging from 2E14 gauss to more than 1E15 gauss.Comment: Nature, 500, 312 (including Supplementary Information

Parallelization of Kinetic Theory Simulations

Numerical studies of shock waves in large scale systems via kinetic simulations with millions of particles are too computationally demanding to be processed in serial. In this work we focus on optimizing the parallel performance of a kinetic Monte Carlo code for astrophysical simulations such as core-collapse supernovae. Our goal is to attain a flexible program that scales well with the architecture of modern supercomputers. This approach requires a hybrid model of programming that combines a message passing interface (MPI) with a multithreading model (OpenMP) in C++. We report on our approach to implement the hybrid design into the kinetic code and show first results which demonstrate a significant gain in performance when many processors are applied.Comment: 10 pages, 3 figures, conference proceeding

Multifrequency Strategies for the Identification of Gamma-Ray Sources

More than half the sources in the Third EGRET (3EG) catalog have no firmly established counterparts at other wavelengths and are unidentified. Some of these unidentified sources have remained a mystery since the first surveys of the gamma-ray sky with the COS-B satellite. The unidentified sources generally have large error circles, and finding counterparts has often been a challenging job. A multiwavelength approach, using X-ray, optical, and radio data, is often needed to understand the nature of these sources. This chapter reviews the technique of identification of EGRET sources using multiwavelength studies of the gamma-ray fields.Comment: 35 pages, 22 figures. Chapter prepared for the book "Cosmic Gamma-ray Sources", edited by K.S. Cheng and G.E. Romero, to be published by Kluwer Academic Press, 2004. For complete article and higher resolution figures, go to: http://www.astro.columbia.edu/~muk/mukherjee_multiwave.pd

Redox linked flavin sites in extracellular decaheme proteins involved in microbe-mineral electron transfer

Extracellular microbe-mineral electron transfer is a major driving force for the oxidation of organic carbon in many subsurface environments. Extracellular multi-heme cytochromes of the Shewenella genus play a major role in this process but the mechanism of electron exchange at the interface between cytochrome and acceptor is widely debated. The 1.8 Å x-ray crystal structure of the decaheme MtrC revealed a highly conserved CX8C disulfide that, when substituted for AX8A, severely compromised the ability of S. oneidensis to grow under aerobic conditions. Reductive cleavage of the disulfide in the presence of flavin mononucleotide (FMN) resulted in the reversible formation of a stable flavocytochrome. Similar results were also observed with other decaheme cytochromes, OmcA, MtrF and UndA. The data suggest that these decaheme cytochromes can transition between highly reactive flavocytochromes or less reactive cytochromes, and that this transition is controlled by a redox active disulfide that responds to the presence of oxygen

Changes in microphytobenthos fluorescence over a tidal cycle: implications for sampling designs

Intertidal microphytobenthos (MPB) are important primary producers and provide food for herbivores in soft sediments and on rocky shores. Methods of measuring MPB biomass that do not depend on the time of collection relative to the time of day or tidal conditions are important in any studies that need to compare temporal or spatial variation, effects of abiotic factors or activity of grazers. Pulse amplitude modulated (PAM) fluorometry is often used to estimate biomass of MPB because it is a rapid, non-destructive method, but it is not known how measures of fluorescence are altered by changing conditions during a period of low tide. We investigated this experimentally using in situ changes in minimal fluorescence (F) on a rocky shore and on an estuarine mudflat around Sydney (Australia), during low tides. On rocky shores, the time when samples are taken during low tide had little direct influence on measures of fluorescence as long as the substratum is dry. Wetness from wave-splash, seepage from rock pools, run-off, rainfall, etc., had large consequences for any comparisons. On soft sediments, fluorescence was decreased if the sediment dried out, as happens during low-spring tides on particularly hot and dry days. Surface water affected the response of PAM and therefore measurements used to estimate MPB, emphasising the need for care to ensure that representative sampling is done during low tide

Inhibition of Fungi and Gram-Negative Bacteria by Bacteriocin BacTN635 Produced by Lactobacillus plantarum sp. TN635

The aim of this study was to evaluate 54 lactic acid bacteria (LAB) strains isolated from meat, fermented vegetables and dairy products for their capacity to produce antimicrobial activities against several bacteria and fungi. The strain designed TN635 has been selected for advanced studies. The supernatant culture of this strain inhibits the growth of all tested pathogenic including the four Gram-negative bacteria (Salmonella enterica ATCC43972, Pseudomonas aeruginosa ATCC 49189, Hafnia sp. and Serratia sp.) and the pathogenic fungus Candida tropicalis R2 CIP203. Based on the nucleotide sequence of the 16S rRNA gene of the strain TN635 (1,540 pb accession no FN252881) and the phylogenetic analysis, we propose the assignment of our new isolate bacterium as Lactobacillus plantarum sp. TN635 strain. Its antimicrobial compound was determined as a proteinaceous substance, stable to heat and to treatment with surfactants and organic solvents. Highest antimicrobial activity was found between pH 3 and 11 with an optimum at pH = 7. The BacTN635 was purified to homogeneity by a four-step protocol involving ammonium sulfate precipitation, centrifugal microconcentrators with a 10-kDa membrane cutoff, gel filtration Sephadex G-25, and C18 reverse-phase HPLC. SDS-PAGE analysis of the purified BacTN635, revealed a single band with an estimated molecular mass of approximately 4 kDa. The maximum bacteriocin production (5,000 AU/ml) was recorded after a 16-h incubation in Man, Rogosa, and Sharpe (MRS) medium at 30 °C. The mode of action of the partial purified BacTN635 was identified as bactericidal against Listeria ivanovii BUG 496 and as fungistatic against C. tropicalis R2 CIP203

An eclipsing binary distance to the Large Magellanic Cloud accurate to 2 per cent

In the era of precision cosmology it is essential to determine the Hubble Constant with an accuracy of 3% or better. Currently, its uncertainty is dominated by the uncertainty in the distance to the Large Magellanic Cloud (LMC) which as the second nearest galaxy serves as the best anchor point of the cosmic distance scale. Observations of eclipsing binaries offer a unique opportunity to precisely and accurately measure stellar parameters and distances. The eclipsing binary method was previously applied to the LMC but the accuracy of the distance results was hampered by the need to model the bright, early-type systems used in these studies. Here, we present distance determinations to eight long-period, late- type eclipsing systems in the LMC composed of cool giant stars. For such systems we can accurately measure both the linear and angular sizes of their components and avoid the most important problems related to the hot early-type systems. Our LMC distance derived from these systems is demonstrably accurate to 2.2 % (49.97 +/- 0.19 (statistical) +/- 1.11 (systematic) kpc) providing a firm base for a 3 % determination of the Hubble Constant, with prospects for improvement to 2 % in the future.Comment: 34 pages, 5 figures, 13 tables, published in the Nature, a part of our data comes from new unpublished OGLE-IV photometric dat

Entangled-State Cycles of Atomic Collective-Spin States

We study quantum trajectories of collective atomic spin states of $N$ effective two-level atoms driven with laser and cavity fields. We show that interesting ``entangled-state cycles'' arise probabilistically when the (Raman) transition rates between the two atomic levels are set equal. For odd (even) $N$, there are $(N+1)/2$ ($N/2$) possible cycles. During each cycle the $N$-qubit state switches, with each cavity photon emission, between the states $(|N/2,m>\pm |N/2,-m>)/\sqrt{2}$, where $|N/2,m>$ is a Dicke state in a rotated collective basis. The quantum number $m$ ($>0$), which distinguishes the particular cycle, is determined by the photon counting record and varies randomly from one trajectory to the next. For even $N$ it is also possible, under the same conditions, to prepare probabilistically (but in steady state) the Dicke state $|N/2,0>$, i.e., an $N$-qubit state with $N/2$ excitations, which is of particular interest in the context of multipartite entanglement.Comment: 10 pages, 9 figure