11,059 research outputs found

    Microbial Diversity Across an Oxygen Gradient Using Large-scale Phylogenetic-based Analysis of Marine Metagenomes

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    Insufficient reference sequence data for annotation of unknown environmental sequences and metagenomes has driven efforts to find alternative annotation methods that mitigate biases from missing information. The use of phylogenetic-placement algorithms shows promise as a robust sequence annotation technique that deals with missing reference information by allowing for annotation of sequences at internal nodes of a phylogenetic tree. However, using these methods for community level surveys of the thousands of genes found in metagenomes requires powerful computational systems and sophisticated software workflows. The main goal of this thesis is to outline a phylogenetic analysis pipeline built to process environmental metagenomic samples using the pplacer software suite, and a pilot study performed with this software pipeline to investigate community-level patterns in gene diversity for a marine oxygen minimum zone (OMZ) off the coast of Chile, South America. Reference sequence data was used to create a custom database and custom reference packages for 9,204 functional housekeeping genes, along with small sub-unit ribosomal genes (SSU) by Domain. A comparative analysis of metagenomic samples from the OMZ using our pipeline shows that while functional and SSU genes show similar spatial patterns of diversity across the oxygen gradient, higher overall diversity was identified via the functional genes. Ecologically relevant functional genes showed higher levels of diversity than either the total from all functional genes or SSU ribosomal genes, underlining the importance of diversity in ecosystem functions

    Intersection Information based on Common Randomness

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    The introduction of the partial information decomposition generated a flurry of proposals for defining an intersection information that quantifies how much of "the same information" two or more random variables specify about a target random variable. As of yet, none is wholly satisfactory. A palatable measure of intersection information would provide a principled way to quantify slippery concepts, such as synergy. Here, we introduce an intersection information measure based on the G\'acs-K\"orner common random variable that is the first to satisfy the coveted target monotonicity property. Our measure is imperfect, too, and we suggest directions for improvement.Comment: 19 pages, 5 figure

    Hard x-ray polarimeter for gamma-ray bursts and solar flares

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    We report on the development of a dedicated polarimeter design that is capable of studying the linear polarization of hard X-rays (50-300 keV) from gamma-ray bursts and solar flares. This compact design, based on the use of a large area position-sensitive PMT (PSPMT), is referred to as GRAPE (Gamma-RAy Polarimeter Experiment). The PSPMT is used to determine the Compton interaction location within an array of small plastic scintillator elements. Some of the photons that scatter within the plastic scintillator array are subsequently absorbed by a small centrally-located array of CsI(Tl) crystals that is read out by an independent multi-anode PMT. One feature of GRAPE that is especially attractive for studies of gamma-ray bursts is the significant off-axis response (at angles \u3e 60 degrees). The modular nature of this design lends itself toward its accomodation on a balloon or spacecraft platform. For an array of GRAPE modules, sensitivity levels below a few percent can be achieved for both gamma-ray bursts and solar flares. Here we report on the latest results from the testing of a laboratory science model

    Dedicated polarimeter design for hard x-ray and soft gamma-ray astronomy

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    We have developed a modular design for a hard X-ray and soft gamma-ray polrimeter that we call GRAPE (Gamma RAy Polarimeter Experiment). Optimized for the energy range of 50-300 keV, the GRAPE design is a Compton polarimeter based on the use of an array of plastic scintillator scattering elements in conjunction with a centrally positioned high-Z calorimeter detector. Here we shall review the results from a laboratory model of the baseline GRAPE design. The baseline design uses a 5-inch diameter position sensitive PMT (PSPMT) for readout of the plastic scintillator array and a small array of CsI detectors for measurement of the scattered photon. An improved design, based on the use of large area multi-anode PMTs (MAPMTs), is also discussed along with plans for laboratory testing of a prototype. An array of GRAPE modules could be used as the basis for a dedicated science mission, either on a long duration balloon or on an orbital mission. With a large effective FoV, a non-imaging GRAPE mission would be ideal for studying polarization in transient sources (gamma ray bursts and solar flares). It may also prove useful for studying periodically varying sources, such as pulsars. An imaging system would improve the sensitivity of the polarization measurements for transient and periodic sources and may also permit the measurement of polarization in steady-state sources

    The Development of GRAPE, a Gamma Ray Polarimeter Experiment

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    The measurement of hard X‐ray polarization in γ‐ray bursts (GRBs) would add yet another piece of information in our effort to resolve the true nature of these enigmatic objects. Here we report on the development of a dedicated polarimeter design with a relatively large FoV that is capable of studying hard X‐ray polarization (50–300 keV) from GRBs. This compact design, based on the use of a large area position‐sensitive PMT (PSPMT), is referred to as GRAPE (Gamma‐RAy Polarimeter Experiment). The feature of GRAPE that is especially attractive for studies of GRBs is the significant off‐axis polarization response (at angles greater than 60°). For an array of GRAPE modules, current sensitivity estimates give minimum detectable polarization (MDP) levels of a few percent for the brightest GRBs

    The impact of firm characteristics on speed of adjustment to target leverage: a UK study

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    Responding to the need to investigate heterogeneity in the speed of adjustment (SOA) to target leverage in a manner that reflects the fractional nature of leverage, we estimate SOA across sub-samples of UK firms using the Dynamic Panel Fractional (DPF) estimator. Using firm characteristics to identify firms subject to varying costs of deviation from and adjustment to target leverage, we find significant evidence of heterogeneity in the speeds at which UK firms adjust to target leverage. Our results show that small, high growth and low dividend paying firms adjust to target leverage faster than their large, low growth and high dividend paying counterparts. We also find some evidence to suggest openly held firms adjust faster than closely held firms, though our results are not robust to the categorizing criterion employed or target leverage specification
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