Bayesian Subset Selection of Binomial Parameters Using Possibly Misclassified Data

Three Bayesian approaches are considered for the selection of binomial proportion parameters when data is subject to misclassification. The cases where the misclassification is non-differential and differential were considered, thus extending previous work which considered only non-differential misclassification. In this article, various selection criteria are applied to a simulated data set and a real data set

Determining the efficacy of a biosensor to detect calpastatin, a meat tenderness indicator

The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file.Title from title screen of research.pdf file (viewed on September 18, 2007)Vita.Thesis (Ph. D.) University of Missouri-Columbia 2007.An instrumental tenderness detection system used at the time of grading to sort beef carcasses on their predicted tenderness would be valuable for the beef industry. A biosensor to accurately predict calpastatin, the inhibitor of the enzyme responsible for increased tenderness due to aging, has been investigated as a detection system. Longissimus dorsi samples from between the 12th and 13th rib of the beef carcass (n = 21 and n = 11) were extracted at 0, 24, 36 and 48 h postmortem for trial one and at 0 and 48 hr for trial two. These samples were assayed for calpastatin by traditional laboratory methods and with the developed biosensors. The biosensor used in trial one was an optical fiber and trial two was a capillary tube. Warner-Bratzler shear force was also performed on a steak from each carcass. In trial one, correlations were generated from each sampling period to determine the most closely correlated sampling times between the traditional assay and the biosensor. The highest correlations between the calpastatin and optical fiber were taken at 48 hr postmortem, suggesting that this is the best time for use of the biosensor in an online grading system. The correlation was lower for the capillary tube but there was less variation in the 0 hr capillary tube than the 0 hr precolumn and post-column optical fiber, therefore this is a more promising system. This research further advances the development of the biosensor and makes online assessment of calpastatin one step closer to reality.Includes bibliographical reference

MMP-9 cleaves SP-D and abrogates its innate immune functions in vitro

Possession of a properly functioning innate immune system in the lung is vital to prevent infections due to the ongoing exposure of the lung to pathogens. While mechanisms of pulmonary innate immunity have been well studied, our knowledge of how these systems are altered in disease states, leading to increased susceptibility to infections, is limited. One innate immune protein in the lung, the pulmonary collectin SP-D, has been shown to be important in innate immune defense, as well as clearance of allergens and apoptotic cells. MMP-9 is a protease with a wide variety of substrates, and has been found to be dysregulated in a myriad of lung diseases ranging from asthma to cystic fibrosis; in many of these conditions, there are decreased levels of SP-D. Our results indicate that MMP-9 is able to cleave SP-D in vitro and this cleavage leads to loss of its innate immune functions, including its abilities to aggregate bacteria and increase phagocytosis by mouse alveolar macrophages. However, MMP-9-cleaved SP-D was still detected in a solid-phase E. coli LPS-binding assay, while NE-cleaved SP-D was not. In addition, MMP-9 seems to cleave SP-D much more efficiently than NE at physiological levels of calcium. Previous studies have shown that in several diseases, including cystic fibrosis and asthma, patients have increased expression of MMP-9 in the lungs as well as decreased levels of intact SP-D. As patients suffering from many of the diseases in which MMP-9 is over-expressed can be more susceptible to pulmonary infections, it is possible that MMP-9 cleavage of SP-D may contribute to this phenotype

Revealing the structure of the outer disks of Be stars

Context. The structure of the inner parts of Be star disks (20 stellar radii) is well explained by the viscous decretion disk (VDD) model, which is able to reproduce the observable properties of most of the objects studied so far. The outer parts, on the ther hand, are not observationally well-explored, as they are observable only at radio wavelengths. A steepening of the spectral slope somewhere between infrared and radio wavelengths was reported for several Be stars that were previously detected in the radio, but a convincing physical explanation for this trend has not yet been provided. Aims. We test the VDD model predictions for the extended parts of a sample of six Be disks that have been observed in the radio to address the question of whether the observed turndown in the spectral energy distribution (SED) can be explained in the framework of the VDD model, including recent theoretical development for truncated Be disks in binary systems. Methods. We combine new multi-wavelength radio observations from the Karl. G. Jansky Very Large Array (JVLA) and Atacama Pathfinder Experiment (APEX) with previously published radio data and archival SED measurements at ultraviolet, visual, and infrared wavelengths. The density structure of the disks, including their outer parts, is constrained by radiative transfer modeling of the observed spectrum using VDD model predictions. In the VDD model we include the presumed effects of possible tidal influence from faint binary companions. Results. For 5 out of 6 studied stars, the observed SED shows strong signs of SED turndown between far-IR and radio wavelengths. A VDD model that extends to large distances closely reproduces the observed SEDs up to far IR wavelengths, but fails to reproduce the radio SED. ... (abstract continues but did not fit here)Comment: 20 pages, 8 figure

A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes

Background: Highly parallel,‘second generation’ sequencing technologies have rapidly expanded the number of bacterial whole genome sequences available for study, permitting the emergence of the discipline of population genomics. Most of these data are publically available as unassembled short-read sequence files that require extensive processing before they can be used for analysis. The provision of data in a uniform format, which can be easily assessed for quality, linked to provenance and phenotype and used for analysis, is therefore necessary. Results: The performance of de novo short-read assembly followed by automatic annotation using the pubMLST. orgNeisseriadatabase was assessed and evaluated for 108 diverse, representative, and well-characterisedNeisseria meningitidisisolates. High-quality sequences were obtained for >99% of known meningococcal genes among the de novoassembled genomes and four resequenced genomes and less than 1% of reassembled genes had sequence discrepancies or misassembled sequences. A core genome of 1600 loci, present in at least 95% of the population, was determined using the Genome Comparator tool. Genealogical relationships compatible with, but at a higher resolution than, those identified by multilocus sequence typing were obtained with core genome comparisons and ribosomal protein gene analysis which revealed a genomic structure for a number of previously described phenotypes. This unified system for cataloguing Neisseria genetic variation in the genome was implemented and used for multiple analyses and the data are publically available in the PubMLST Neisseria database. Conclusions: The de novo assembly, combined with automated gene-by-gene annotation, generates high quality draft genomes in which the majority of protein-encoding genes are present with high accuracy. The approach catalogues diversity efficiently, permits analyses of a single genome or multiple genome comparisons, and is a practical approach to interpreting WGS data for large bacterial population samples. The method generates novel insights into the biology of the meningococcus and improves our understanding of the whole population structure, not just disease causing lineages.</p

A Review of Associate/Bachelor Degree Library Programs in the United States

This presentation outlines the results of a nation-wide survey and analysis of Associate and Bachelor degree programs in the United States as well as a brief comparison to those degree programs world-wide

Synthetic, Photophysical, and Catalytic Studies of Light-Harvesting Macrocyclic Complexes

Chromophores are an important class of compounds in Nature and industry, with several hundred thousand tons produced annually as dyes and pigments. Alone, these compounds absorb light unto themselves; however, several of these compounds can be combined to produce a beneficial cascading transfer of energy to a core chromophore. In this study, photophysical properties of several covalent and axially borondipyrromethene (BODIPY)-conjugated complexes of porphyrin and salphen scaffolds have been evaluated in a series of emission and catalytic studies. In the porphyrin systems, a beneficial excited energy transfer (EET) from the BODIPY moieties to the porphyrin core was observed; however, only the covalently bound BODIPY metal complexes displayed enhanced activity in the catalytic oxidation reactions in the presence of visible light. The BODIPY-porphyrin ligand displayed fluorescence quenching when excited at the porphyrin or BODIPY moieties roughly equal to 50% of the bare tetra(phenyl)porphyrin (TPP) ligand which indicated an efficient EET from the BODIPY-antennae to the porphyrin core. The axially BODIPY-porphyrin iron(III) complex displayed an intense green fluorescence corresponding to the BODIPY moiety due to an electron transfer from the phenolate ligand to the porphyrin core completely quenching the porphyrin emission. The BODIPY-salphen (L-Salphen) conjugates displayed the opposite EET compared to the porphyrin conjugates, instead transferring energy away from the salphen core to the BODIPY-moieties. A beneficial light effect was observed with the chromium L-Salphen complex; however, the effect was deemed to be the cause of visible light irradiation’s ability to destabilize the meta-stable chromium-oxo bond rather than an EET of the BODIPY-moieties to salphen core. In addition, several iron(III) phthalocyanine complexes [FeIII(Pc)Cl] were synthesized and evaluated in the catalytic oxidation of thioanisoles to compare their viability to previous metalloporphyrin systems. The [FeIII(Pc)Cl] catalysts gave quantitative conversions of the starting sulfides with moderate to excellent selectivity towards sulfoxide over sulfone but displayed an unexpected sustainability towards oxidative degradation even with mild terminal oxidants, i.e., iodobenzene diacetate [PhI(OAc)2]. Nonetheless, efforts were made to probe the active oxospecies with PhI(OAc)2, and a putative iron(IV)-oxo radical cation was spectroscopically observed in the systems of unsubstituted phthalocyanine [H2(Pc)] and the 1,4,5,8,9,12,13,16-(a)- octabutyloxyphthalocyanine [H2(α-(OBu)8-Pc)] ligands

Book Review: The Blue Ribbon Cook Book

Review of the book The Blue Ribbon Cook Book, by Jennie C. Benedict. Reprint of the 4th ed. 1922. Lexington, KY: The University Press of Kentucky, 2008

From the Editor

Column from Perry Bratcher, editor of The Southeastern Librarian