A MOSAIC of methods: Improving ortholog detection through integration of algorithmic diversity

Ortholog detection (OD) is a critical step for comparative genomic analysis of protein-coding sequences. In this paper, we begin with a comprehensive comparison of four popular, methodologically diverse OD methods: MultiParanoid, Blat, Multiz, and OMA. In head-to-head comparisons, these methods are shown to significantly outperform one another 12-30% of the time. This high complementarity motivates the presentation of the first tool for integrating methodologically diverse OD methods. We term this program MOSAIC, or Multiple Orthologous Sequence Analysis and Integration by Cluster optimization. Relative to component and competing methods, we demonstrate that MOSAIC more than quintuples the number of alignments for which all species are present, while simultaneously maintaining or improving functional-, phylogenetic-, and sequence identity-based measures of ortholog quality. Further, we demonstrate that this improvement in alignment quality yields 40-280% more confidently aligned sites. Combined, these factors translate to higher estimated levels of overall conservation, while at the same time allowing for the detection of up to 180% more positively selected sites. MOSAIC is available as python package. MOSAIC alignments, source code, and full documentation are available at http://pythonhosted.org/bio-MOSAIC

Development of a Multiband Remote Sensing System for Determination of Unsaturated Soil Properties

A multiband system including active microwave sensing and visible-near infrared reflectance spectroscopy was developed to measure unsaturated soil properties in both field and laboratory environments. Remote measurements of soil volumetric water content (θv), soil water matric potential (ψ), and soil index properties (liquid limit [LL], plastic limit [PL], and clay fraction [CF]) were conducted. Field-based measurement of θv was conducted using a ground-based radar system and field measurements within 10 percentage points of measurements acquired with traditional sampling techniques were obtained. Laboratory-based, visible and near infrared spectroscopy was found to be capable of obtaining empirical, soil specific regression functions (partial least squares [PLS]) with coefficient of determination (R2) values greater than 0.9 for the LL, PL, and CF. A silt sized granite material, a silt sized illite clay, and a silt sized kaolinite clay were optically characterized within the visible to near-infrared wavelength range and were found to have absorption coefficient values of 0.81 to 78.8cm-1, 0.93 to 150.0cm-1, and 0.12 to 4.02cm-1, respectively. Measurements of θv and ψ using an analytical solution based on the Kubelka-Munk color theory were found not to provide viable results. Soil water characteristic curves (SWCC) were fitted to both laboratory-obtained and remotely-sensed data between -10 and -1500kPa. θv for the laboratory-obtained SWCC (SWCC-L) and remotely-obtained SWCC (SWCC-R) for the granite silt were within 1 percentage points for ψ values less than -100kPa. The SWCC-L and SWCC-R values for the silt sized illite clay were within 2 percentage points for values of ψ greater than 400kPa. The SWCC-L and SWCC-R for the silt sized kaolinite clay were within 8 percentage points for all ψ values. For the Donna Fill and illite soil types ψ values within 150kPa of the applied pressure were obtained. Specific contributions of this research project were the evaluation of remote and proximal (active microwave and diffuse reflectance spectroscopy) sensing techniques as a means of acquiring measurements of soil properties. Microwave measurements of field θv were demonstrated for ground based systems. Additional areas of research in both laboratory- and field-scale measurements of soil hydraulic and index properties are identified and discussed

The construction and validation of a test of music vocabulary.

Thesis (Ed.D.)--Boston University

Exalt the Word

Is it not high time for those who teach the Bible to give a truce to nervousness, and go ahead as though nothing had happened? As, indeed, nothing has happened to affect in the slightest degree the substance of the faith or the all-conquering power of the word. ... The great business of the pulpit and of the Sunday-school is to teach the Bible, and to urge its claim on the belief and obedience of all who listen. Let us teach it, and not busy ourselves in suggesting doubts about it. Children, youth, and the masses of churchgoing people urgently need to know what the Bible says.https://place.asburyseminary.edu/ecommonsatsdigitalresources/1092/thumbnail.jp

Exact Level And Power Of Permutation, Bootstrap, And Asymptotic Tests Of Trend

We develop computational tools that can evaluate the exact size and power of three tests of trend (e.g., permutation, bootstrap and asymptotic) without resorting to large-sample theory or simulations. We then use these tools to compare the operating characteristics of the three tests. It is seen that the bootstrap test is ultra-conservative relative to the other two tests and as a result suffers from a severe deterioration in power. The power of the asymptotic test is uniformly larger than that of the other two tests, but it fails to preserve the Type I error for most of the range of the baseline response probability. The permutation test, being exact, is guaranteed to preserve the Type I error throughout the range of the baseline response probability. The price paid for this guarantee is a loss of power relative to the asymptotic test. The power loss is, however, small in most situations

Law Day 1977

Lecture delivered by Cyrus R. Vance, U.S. Secretary of State. Luncheon address delivered by George D. Busbee, Governor of Georgia. Distinguished Service Scrolls awarded to M. Cook Barwick and A.G. Cleveland, Jr