510 research outputs found
Competition and Cooperation in the U.S. Liner Industry : A Case Study of the North Atlantic Trade Routes
No full textDTR557-P-80466RUEBEN KYLE MIDDLE TENNESSEE STATE UNIVERSITY, DEPARTMENT OF ECONOMICS AND FINANCE ADDL PLACE OF PUBLCATION: SPRINGFIELD, VA ADDL PUBLISHER: NATIONAL TECHNICAL INFORMATION SERVICE COVER TITLE SPONSORED BY THE U.S. DEPT. OF TRANSPORTATION, OFFICE OF THE SECRETARY OF TRANSPORTATION UNDER CONTRACT TO THE TRANSPORTATION SYSTEMS CENTER MARCH 1985 CONTRACT NO.: DTR557-P-80466 ADDL CORP. AUTHOR INFO: UNITED STATES. OFFICE OF THE SECRETARY OF TRANSPORTATION ADDL CORP. AUTHOR INFO: TRANSPORTATION SYSTEMS CENTER ADDL CORP. AUTHOR INFO: MIDDLE TENNESSEE STATE UNIVERSITY. DEPT. OF ECONOMICS AND FINANC
Protein Threading for Genome-Scale Structural Analysis
No full textProtein structure prediction is a necessary tool in the field of bioinformatic analysis. It is a non-trivial process that can add a great deal of information to a genome annotation. This dissertation deals with protein structure prediction through the technique of protein fold recognition and outlines several strategies for the improvement of protein threading techniques. In order to improve protein threading performance, this dissertation begins with an outline of sequence/structure alignment energy functions. A technique called Violated Inequality Minimization is used to quickly adapt to the changing energy landscape as new energy functions are added. To continue the improvement of alignment accuracy and fold recognition, new formulations of energy functions are used for the creation of the sequence/structure alignment. These energies include a formulation of a gap penalty which is dependent on sequence characteristics different from the traditional constant penalty. Another proposed energy is dependent on conserved structural patterns found during threading. These structural patterns have been employed to refine the sequence/structure alignment in my research. The section on Linear Programming Algorithm for protein structure alignment deals with the optimization of an alignment using additional residue-pair energy functions. In the original version of the model, all cores had to be aligned to the target sequence. Our research outlines an expansion of the original threading model which allows for a more flexible alignment by allowing core deletions. Aside from improvements in fold recognition and alignment accuracy, there is also a need to ensure that these techniques can scale for the computational demands of genome level structure prediction. A heuristic decision making processes has been designed to automate the classification and preparation of proteins for prediction. A graph analysis has been applied to the integration of different tools involved in the pipeline. Analysis of the data dependency graph allows for automatic parallelization of genome structure prediction. These different contributions help to improve the overall performance of protein threading and help distribute computations across a large set of computers to help make genome scale protein structure prediction practically feasible
A reductive theory of justification and excuse
No full textLegal theorists commonly employ a distinction between justification defenses and excuse defenses, but there are significant theoretical disagreements about the nature of the distinction as well as about what the distinction entails. This dissertation is concerned with finding the best way to describe the distinction between the moral concepts of justification and excuse that underlie the concepts employed by legal theorists. Chapter 1 begins by examining moral defenses in general, with emphasis on their purpose, nature, function, and epistemology. Chapter 2 critically examines many of the traditional theoretical assumptions made about justification and excuse in the literature with the goal of winnowing them down to an uncontroversial core that can provide the foundation for a fuller, more specific account. Chapter 3 examines the ordinary language meaning of the words "justification" and "excuse" in order to identify any analytic constraints on what a correct theoretical account of justification and excuse may legitimately include. Finally, Chapter 4 offers and defends a reductive theory of justification and excuse which I call "the praise/blame theory." This theory identifies justified acts with those prima facie wrongful acts for which the actor is morally praiseworthy and excused acts with those prima facie wrongful acts for which the actor is merely not to blame. This simple account is consistent with the logical form of moral defenses, requires minimal elaboration on the terms' ordinary language content, avoids the conceptual mistakes that plague more traditional theories, and has the potential help resolve nagging theoretical issues in related fields.Ph.D.Includes bibliographical references (p. 232-241)by Kyle David Haide
Genetic and morphological discrimination of species within the nominal Brachidontes exustus (Mollusca: bivalvia) cryptic species complex from the Florida Keys:
No full textThe discovery of sibling and cryptic species complexes in the oceans has dramatically increased the estimated number of extant marine species. However, most cryptic species complexes remain taxonomically obscure, lacking descriptions of the morphological or
ecological differences defining the species. The distributions and morphologies of species in the nominal Brachidontes exustus complex in the Florida Keys were investigated utilizing molecular and multivariate statistical techniques.
DNA barcoding, a method of comparing newly generated sequences of the mitochondrial cytocrome c oxidase I gene (COI) from specimens of unknown species to a database of known sequences from voucher specimens, identified two cryptic species on Long Key, Florida Keys. Two differing habitats, which were <5 km apart, had single-species populations, even though both locations were within the dispersal range of larval recruits from the other location. This was the first record from the Florida Keys for these species
to be encountered as single species populations.
Tests for pseudo-crypsis among three species of the B. exustus morphospecies complex collected throughout the Florida Keys were performed with multivariate morphometics. Specimens were assigned to species using RFLP-based molecular methods. A discriminant function was constructed that, based on shell morphology, assigns individual mussels to a certain species with a high confidence (95%). Morphological differences among the species were sufficient to create robust statistical methods of resolving species using shell morphology alone. The suite of functions will facilitate future manipulation experiments with live specimens. The morphologies of the two most common species, provisionally called Bahamian and Gulf, were more similar in locations of coexistence than in locations of exclusivity.
An improved molecular-based technique for determining species, a multiplex PCR with species-specific forward oligonucleotides, was designed and tested. The method discriminates species by visualization of PCR products after electrophoresis on an agarose gel stained with ethidium brominde. This is a low cost, high throughput method that can effectively screen large numbers of specimens from the entire geographic range of the nominal species. This method can be used to identify species using larvae or juveniles which are unlikely to have the shell differences that can be used in the multivariate morphometric approach.Ph.D.Includes bibliographical references (p. 130-143)by Kyle Francis Bennet
Data from: "Non-metabolizable" glucose analogue shines new light on priming mechanisms: Triggering of microbial metabolism
No full text<p>Raw data for the article:</p>
<p>Kyle Mason-Jones*, Yakov Kuzyakov (2017)<br>
“Non-metabolizable” glucose analogue shines new light on priming mechanisms: Triggering of microbial metabolism</p>
<p>Soil Biology and Biochemistry 107, 68-76</p>
<p>https://doi.org/10.1016/j.soilbio.2016.12.015</p>
<p>* corresponding author: [email protected]</p>== Recommended citation ==
Mason-Jones, K., Kuzyakov, Y. (2017) Data from: "Non-metabolizable" glucose analogue shines new light on priming mechanisms: Triggering of microbial metabolism. Zenodo repository. doi:10.5281/zenodo.114678
Author-level coefficients and standard error of citation impact by repeat authorship for economics journals.
No full text(DOCX)</p
Trichodesma nancyae Schnepp 2023, new species
No full text<i>Trichodesma nancyae</i> Schnepp, new species <p>Figures 23–28</p> <p> Two specimens were seen by the author, the holotype with the following labels “ MEXICO: Guerrero / 10 km. N Chilpancingo / 22 July 1987 / R. Turnbow // [on red] HOLOTYPE / <i>Trichodesma nancyae</i> / Schnepp, 2023 ”; deposited in the FSCA.</p>Published as part of <i>Schnepp, Kyle E., 2023, An illustrated type catalog of Trichodesma LeConte, 1861 (Coleoptera: Ptinidae) from Mexico, with description of a new species, pp. 1-19 in Insecta Mundi 2023 (24)</i> on page 9, DOI: <a href="http://zenodo.org/record/10621762">10.5281/zenodo.10621762</a>
Influence of vegetation structure and landscape context on the occupancy of shrubland birds
No full textLimited Restriction Lifted for Item 109948 on 2021-02-09T10:15:34Z.Across the guild of shrubland birds, some species have been experiencing long-term population declines while other have been increasing. One potential reason for these differences is that various shrubland bird species prefer different types of shrubland habitat and some habitats are more common than others. However, we lack a clear understanding of the attributes of shrublands that shrubland birds prefer. Specifically, we lack information on how the percent shrub cover, the proportion of shrubs comprised of non-native shrubs, the patchiness of shrubs, and the surrounding landscape context influence occupancy (the probability that a given species will be at a site) of shrubland birds. To better understand these relationships I used bird survey and vegetation data from a long-term monitoring program that randomly monitored shrublands across the state of Illinois. I examined the influence of landscape and site-level variables on the occupancy of 22 shrubland bird species. Generally, the proportion of non-native shrubs at a site had little influence on shrubland bird occupancy. Shrubland birds responded positively to both the percent shrub cover and to the patchiness of shrubs; however the strength of the relationship differed between species. Over half (6/10) of the species that are experiencing population declines in the region (as determined by Breeding Bird Survey data) responded strongly to the patchiness of the shrubs, whereas, only 3 of the 12 shrubland species whose populations were either stable or increased responded to the patchiness of shrubs. The difference in population trends across the suite of shrubland birds may be driven by preferences for patchy shrublands. When creating or managing shrubland habitat, it is important to consider that the presence of shrubs is not enough and that the patchiness of shrubs may be important for a subset of shrubland birds.Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2020-12-01The student, Kyle Van den Bosch, accepted the attached license on 2018-11-27 at 20:44.The student, Kyle Van den Bosch, submitted this Thesis for approval on 2018-11-27 at 20:56.This Thesis was approved for publication on 2018-11-30 at 13:12.DSpace SAF Submission Ingestion Package generated from Vireo submission #13128 on 2019-02-08 at 11:40:20Made available in DSpace on 2019-02-08T18:39:52Z (GMT). No. of bitstreams: 2
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Author-level coefficients and standard error of citation Impact by repeat authorship for <i>Nature</i>/<i>Science</i>/<i>PNAS</i>.
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Regulation of matrix metalloproteinase expression and activity by the aryl hydrocarbon receptor in A2058 human melanoma cells
No full textMalignant melanoma has a high incidence of mortality due to its resistance to chemotherapy and tendency to metastasize, and in the past 60 years has seen an increase in industrialized nations. HYPOTHESIS: We propose that activation of the aryl hydrocarbon receptor (AhR) by environmental chemicals contributes to melanoma invasion through enhancing expression and activity of the matrix metalloproteinases (MMPs). Further, we hypothesize that AhR interactions with other signaling pathways are critical for AhR-induced MMP expression in these cells. The AhR, originally identified as the receptor for the polycyclic aromatic hydrocarbon (PAH) family of environmental contaminants, is activated by endogenous and exogenous compounds, including: flavonoids, UV photoproducts of tryptophan, as well as some synthetic retinoids. We have previously shown that TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin)-activation of the AhR results in increased expression and activity of MMPs -1, -2 and -9. MMPs are a family of zinc- and calcium-dependent proteinases that degrade extracellular matrix (ECM) substrates that are involved in melanoma progression and metastasis. In this thesis we show that maximal TCDD-induced MMP-1 activation in A2058 melanoma cells requires 3 cis-acting response elements in the distal portion of the MMP-1 promoter, the NFκB, CCAAT and MITF sites. These elements are known to be downstream targets of the Ras/Raf signaling pathway, and our data also show that Ras/Raf activation is critical for AhR-induced MMP-1, -2 and -9 expression. Our data further suggest that AhR-Ras/Raf interactions result in deregulation of ECM metabolism, through alterations in expression of MMPs and their endogenous inhibitors, TIMP-1/-2 (tissue inhibitor of metalloproteinases). Lastly we demonstrate crosstalk between Ras/Raf signaling and the AhR pathway, and show that loss of AhR results in a reduction in Ras/Raf-mediated phosphorylation of ERK. Crosstalk is also demonstrated by a reduction of AhR expression and activity observed following Ras/Raf inhibition. Interestingly, 60% of all melanomas contain an activating mutation, V600EBRAF, in the Ras/Raf pathway, suggesting that melanomas may be more sensitive to AhR-activation. These data demonstrate that AhR-activated expression of MMPs in A2058 melanoma cells requires Ras/Raf signaling and that these pathways are directly involved in the regulation of enzymes vital to melanoma progression.Ph.D.Includes bibliographical references (p. 123-133)
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