2,725 research outputs found
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 Ă
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 pHâ=â7. 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 30â°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
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)
, there are () possible cycles. During each cycle the
-qubit state switches, with each cavity photon emission, between the states
, where is a Dicke state in a rotated
collective basis. The quantum number (), which distinguishes the
particular cycle, is determined by the photon counting record and varies
randomly from one trajectory to the next. For even it is also possible,
under the same conditions, to prepare probabilistically (but in steady state)
the Dicke state , i.e., an -qubit state with excitations,
which is of particular interest in the context of multipartite entanglement.Comment: 10 pages, 9 figure
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