The Promises and Pitfalls of Machine Learning for Detecting Viruses in Aquatic Metagenomes

Tools allowing for the identification of viral sequences in host-associated and environmental metagenomes allows for a better understanding of the genetics and ecology of viruses and their hosts. Recently, new approaches using machine learning methods to distinguish viral from bacterial signal using k-mer sequence signatures were published for identifying viral contigs in metagenomes. The promise of these content-based approaches is the ability to discover new viruses, with no or few known relatives. In this perspective paper, we examine the use of the content-based machine learning tool VirFinder for the identification of viral sequences in aquatic metagenomes and explore the possibility of using ecosystem-focused models targeted to marine metagenomes. We discuss the impact of the training set composition on the tool performance and the current limitation for the retrieval of low abundance viral sequences in metagenomes. We identify potential biases that could arise from machine learning approaches for viral hunting in real-world datasets and suggest possible avenues to overcome them.National Science Foundation [1640775]Open access journal.This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Nicalon/siliconoxycarbide ceramic composites

A series of silsesquioxane copolymers was synthesized by acid hydrolysis and condensation of trimethoxysilanes of the form RSi(OCH3)3, where R = methyl or phenyl. By varying pH, water/methoxy and methyl/phenyl ratios, the molecular structure, polymer rheology and ceramic composition can be controlled. The polymers form an amorphous siliconoxycarbide on pyrolysis. Composites of Nicalon/siliconoxycarbide were fractured in four-point flexure and in tension to evaluate the influence of matrix composition, final fabrication temperature and use of filler on composite mode of failure, modulus, strain capability and strength. Incorporation of filler was found to increase matrix compressive strength. Employment of processing temperatures of 1375 to 1400 C enhanced strain to failure and reduced the tendency toward brittle fracture. Mixed mode (compression/shear and tension/shear) failures were observed in flexural samples processed to the higher temperatures, giving rise to nonlinear stress-strain curves. Tensile samples pyrolyzed to 1400 C showed linear-elastic behavior and failed by fracture of fiber bundles. Matrix material was found to be adherent to the fiber surface after failure. These results demonstrate the need for tensile testing to establish composite behavior

The Promises and Pitfalls of Machine Learning for Detecting Viruses in Aquatic Metagenomes

Tools allowing for the identification of viral sequences in host-associated and environmental metagenomes allows for a better understanding of the genetics and ecology of viruses and their hosts. Recently, new approaches using machine learning methods to distinguish viral from bacterial signal using k-mer sequence signatures were published for identifying viral contigs in metagenomes. The promise of these content-based approaches is the ability to discover new viruses, with no or few known relatives. In this perspective paper, we examine the use of the content-based machine learning tool VirFinder for the identification of viral sequences in aquatic metagenomes and explore the possibility of using ecosystem-focused models targeted to marine metagenomes. We discuss the impact of the training set composition on the tool performance and the current limitation for the retrieval of low abundance viral sequences in metagenomes. We identify potential biases that could arise from machine learning approaches for viral hunting in real-world datasets and suggest possible avenues to overcome them

Structured matrices, continued fractions, and root localization of polynomials

We give a detailed account of various connections between several classes of objects: Hankel, Hurwitz, Toeplitz, Vandermonde and other structured matrices, Stietjes and Jacobi-type continued fractions, Cauchy indices, moment problems, total positivity, and root localization of univariate polynomials. Along with a survey of many classical facts, we provide a number of new results.Comment: 79 pages; new material added to the Introductio

Bacterial Infection and Immune Responses in Lutzomyia longipalpis Sand Fly Larvae Midgut

Citation: Heerman, M., Weng, J. L., Hurwitz, I., Durvasula, R., & Ramalho-Ortigao, M. (2015). Bacterial Infection and Immune Responses in Lutzomyia longipalpis Sand Fly Larvae Midgut. Plos Neglected Tropical Diseases, 9(7), 18. doi:10.1371/journal.pntd.0003923The midgut microbial community in insect vectors of disease is crucial for an effective immune response against infection with various human and animal pathogens. Depending on the aspects of their development, insects can acquire microbes present in soil, water, and plants. Sand flies are major vectors of leishmaniasis, and shown to harbor a wide variety of Gram-negative and Gram-positive bacteria. Sand fly larval stages acquire microorganisms from the soil, and the abundance and distribution of these microorganisms may vary depending on the sand fly species or the breeding site. Here, we assess the distribution of two bacteria commonly found within the gut of sand flies, Pantoea agglomerans and Bacillus subtilis. We demonstrate that these bacteria are able to differentially infect the larval digestive tract, and regulate the immune response in sand fly larvae. Moreover, bacterial distribution, and likely the ability to colonize the gut, is driven, at least in part, by a gradient of pH present in the gut

EUV Spectra of the Full Solar Disk: Analysis and Results of the Cosmic Hot Interstellar Plasma Spectrometer (CHIPS)

We analyze EUV spectra of the full solar disk from the Cosmic Hot Interstellar Plasma Spectrometer (CHIPS) spanning a period of two years. The observations were obtained via a fortuitous off-axis light path in the 140 -- 270 Angstrom passband. The general appearance of the spectra remained relatively stable over the two-year time period, but did show significant variations of up to 25% between two sets of Fe lines that show peak emission at 1 MK and 2 MK. The variations occur at a measured period of 27.2 days and are caused by regions of hotter and cooler plasma rotating into, and out of, the field of view. The CHIANTI spectral code is employed to determine plasma temperatures, densities, and emission measures. A set of five isothermal plasmas fit the full disk spectra well. A 1 -- 2 MK plasma of Fe contributes 85% of the total emission in the CHIPS passband. The standard Differential Emission Measures (DEMs) supplied with the CHIANTI package do not fit the CHIPS spectra well as they over-predict emission at temperatures below log(T) = 6.0 and above log(T) = 6.3. The results are important for cross-calibrating TIMED, SORCE, SOHO/EIT, and CDS/GIS, as well as the recently launched Solar Dynamics Observatory.Comment: 27 Pages, 13 Figure

Anti-Trust and Economic Theory: Some Observations from the US Experience

Recent developments in US anti-trust can be characterised as reflecting the uneasy interaction of two quite separate phenomena: first, the increased emphasis on economic analysis as the overriding organising principle of anti-trust policy and on economic efficiency as the primary (perhaps only) relevant goal for anti-trust; second, the long-standing reluctance of the federal judiciary to involve itself in any substantive economic analysis, and the preference, instead, for simple rules of thumb or ‘pigeon holes’ to sort out lawful from unlawful conduct. The result has been that while economics has played a major role, it has not influenced American anti-trust as thoroughly or as uniformly as might have been imagined; rather the extent and the nature of its influence have depended on the degree to which the relevant economics could be reduced to the kind of simple rules or pigeon holes that the judiciary favours. The present paper will illustrate that theme, first by reporting on the two developments separately and then by illustrating their joint influence with reference to two important areas of American anti-trust: predatory conduct and so-called vertical restraints. Finally, a contrast will be made between judicial development in those two areas and recent American merger policy which, it is argued, is carried out largely independently of the judiciary, and hence the opportunities for economics to influence the process are less inhibited by the judicial reluctance to undertake extensive economic analysis

A New Measurement of the Average FUV Extinction Curve

We have measured the extinction curve in the far-ultraviolet wavelength region of (900 -- 1200 A) using spectra obtained with the Berkeley EUV/FUV spectrometer during the ORFEUS-I and the ORFEUS-II missions in 1993 and 1996. From the complete sample of early-type stars observed during these missions, we have selected pairs of stars with the same spectral type but different reddenings to measure the differential FUV extinction. We model the effects of molecular hydrogen absorption and exclude affected regions of the spectrum to determine the extinction from dust alone. We minimize errors from inaccuracies in the cataloged spectral types of the stars by making our own determinations of spectral types based on their IUE spectra. We find substantial scatter in the curves of individual star pairs and present a detailed examination of the uncertainties and their effects on each extinction curve. We find that, given the potentially large uncertainties inherent in using the pair method at FUV wavelengths, a careful analysis of measurement uncertainties is critical to assessing the true dust extinction. We present a new measurement of the average far-ultraviolet extinction curve to the Lyman limit; our new measurement is consistent with an extrapolation of the standard extinction curve of Savage & Mathis (1979).Comment: 13 pages text, 7 figures 4 tables. Sent as gzipped tar, with ms.tex and 7 figure

Polarization of tightly focused laser beams

The polarization properties of monochromatic light beams are studied. In contrast to the idealization of an electromagnetic plane wave, finite beams which are everywhere linearly polarized in the same direction do not exist. Neither do beams which are everywhere circularly polarized in a fixed plane. It is also shown that transversely finite beams cannot be purely transverse in both their electric and magnetic vectors, and that their electromagnetic energy travels at less than c. The electric and magnetic fields in an electromagnetic beam have different polarization properties in general, but there exists a class of steady beams in which the electric and magnetic polarizations are the same (and in which energy density and energy flux are independent of time). Examples are given of exactly and approximately linearly polarized beams, and of approximately circularly polarized beams.Comment: 9 pages, 6 figure