The first chapter presents new methods for identifying the structural parameters of linear triangular systems, simultaneous systems, and structural vector autoregressions. The second chapter presents a new method for identifying an endogenous regressor in linear models of time series data. / Thesis (PhD) — Boston College, 2006. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Economics.

Diss. (sammanfattning) Uppsala : Uppsala universitet, 2005. / Härtill 5 uppsatser.

BACKGROUND: Retroviruses infect a wide range of vertebrates. However, little is known about the diversity of retroviruses in basal vertebrates. Endogenous retrovirus (ERV) provides a valuable resource to study the ecology and evolution of retrovirus. FINDINGS: I performed a genome-scale screening for ERVs in the elephant shark (Callorhinchus milii) and identified three complete or nearly complete ERVs and many short ERV fragments. I designate these retroviral elements "C. milli ERVs" (CmiERVs). Phylogenetic analysis shows that the CmiERVs form three distinct lineages. The genome invasions by these retroviruses are estimated to take place more than 50 million years ago. CONCLUSIONS: My results reveal the extensive retroviral diversity in the elephant shark. Diverse retroviruses appear to have been associated with cartilaginous fishes for millions of years. These findings have important implications in understanding the diversity and evolution of retroviruses.

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The thesis consists of five chapters. The first of them contains introduction. Chapter 2 considers a broad class of two player symmetric games, which display a fundamental non-concavity when actions of both players are about to be the same. This implies that no symmetric equilibrium is possible. We distinguish different properties of the payoff functions, like strategic substitutes, complements and quasi-concavity, which are not necessarily imposed globally on the joint action space. For each of these cases we provide conditions to secure the existence of exclusively asymmetric equilibria. Moreover we consider the case of convex payoff functions. A number of applications from industrial organization and applied microeconomics literature are provided. In Chapter 3 we generalize to the extent possible the known results for the case of games with one-dimensional action sets to the general case of games with strategic complemantarities with action spaces that are complete lattices. One key issue addressed is the extent to which all equilibria tend to be symmetric for the general case of multi-dimensional (i.e. only partially ordered) strategy spaces. We find that the scope for asymmetric equilibrium behavior is definitely broader than in the one-dimensional case, though still quite limited. Another key question investigated here is whether asymmetric pure strategy Nash equilibria are always Pareto dominated by symmetric pure strategy Nash equilibria. While this need not hold in general for games with strategic complementarities, we identify different sufficient conditions that guarantee that such dominance holds. In Chapter 4 we deal with the effects of market transparency on prices in the Bertrand duopoly model. The analysis is intuitive and simple when we consider two types of strategic interaction between firms in an industry - strategic complementarities and substitutabilities. We present also traditional comparative statics analyses, demanding additionally some other regularity conditions, to cover those problems, when neither of these situations is the case. In the first case, the results are close to conventional wisdom, especially, when in the same time products are substitutes. Namely, equilibrium prices and profits are always decreasing in transparency level, while the consumer's surplus is increasing. For a special case when supermodularity holds, but products are not substitutes, the result on profits is not valid anymore. Considering price competition with strategic substitutes, an ambiguity in the direction of change of prices appears. This leads to ambiguity concerning equilibrium profits and surplus changes caused by increasing transparency. In Chapter 5 we provide general conditions for Cournot oligopoly with product differentiation to have monotonic reaction correspondences. We give a proof for the conditions stated by Vives (1999). Moreover we elaborate more general requirements. They allow for identifying increasing best responses even in case inverse demand is submodular, and similarly, decreasing best responses in case of supermodular inverse demand. Examples illustrating the scope of applicability of these results are provided.

Endogenous retroviruses (ERVs) comprise a significant portion of the genome of all mammals and have been implicated in placental development in multiple species. The ovine genome contains approximately 27 copies of endogenous betaretroviruses (enJSRVs) that are related to the exogenous Jaagsiekte sheep retrovirus (JSRV), an oncogenic retrovirus tropic to the lung. The enJSRV loci are abundantly expressed in the female reproductive tract and the conceptus, and they are essential to conceptus development. Studies were conducted to determine: 1) the effect of exogenous progesterone administration on conceptus development after loss of enJSRV Env; 2) the specific enJSRV env expressed in the developing conceptus; and 3) if the uterus produces enJSRV viral particles that are capable of transducing the conceptus. Study One determined the effects of exogenous progesterone on development of the conceptus in which enJSRV Env was ablated. Despite rescuing conceptus survival, the conceptuses were morphologically fragile and had reduced binucleate cell (BNC) numbers. These results suggest that mononuclear trophectoderm cell (MTC) proliferation and differentiation is dependent on enJSRV Env, even in a uterine environment supported by exogenous progesterone. Study Two assessed the enJSRV loci transcribed in the ovine conceptus during elongation before (day 13) and after (day 18) onset of BNC differentiation. The most represented loci in both day 13 and day 18 conceptuses encoded truncated Env proteins that did not contain membrane-spanning domains. Conceptuses from both time points contained evidence of the transcription of full-length, biologically active enJSRV Env, as well as completely intact proviral loci with the ability to produce viral particles in vitro. Study Three utilized a transpecies embryo transfer experiment to determine if the intact enJSRVs loci could produce viral particles in vivo. The presence of enJSRV viral particles in the uterus was confirmed, as was their ability to transduce the conceptus. Collectively, these studies provide evidence of truncated Env proteins, intact biologically active Env proteins, and enJSRVs viral particles within the ovine uterus and conceptus that are necessary to stimulate proliferation and differentiation of MTCs even in a uterine environment supported by exogenous progesterone.

Thesis (Ph. D.)--York University, 2000. Graduate Programme in Economics. / Typescript. Includes bibliographical references (leaves 143-152). Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://wwwlib.umi.com/cr/yorku/fullcit?pNQ59142

Major injury leads to host immune dysregulation and increased susceptibility to infectious challenge. Toll-like receptors (TLRs) are archetypical pattern-recognition receptors that, in addition to a role in mediating innate immune responses to components of Gram-positive and Gram-negative pathogens, have been implicated in the recognition of endogenous mediators, released during host tissue injury. A murine model of thermal injury was employed to examine the impact of injury on TLR-mediated immune cell responses. Lymph node and spleen cell suspensions were prepared from wild type, TLR4-/- and IL-1RI-/- mice at 24 hours or 7 days after injury/sham injury, cultured for 48 hours with lipid A (LA), lipopolysaccharide (LPS), lipoteichoic acid (LTA) or peptidoglycan (PGN) and production of IL-1<span style='font-family:Symbol'>b, IL-6, IL-10 and TNF<span style='font-family:Symbol'>a measured by ELISA.  Cell subset localisation of cytokine production was assessed by intracellular cytokine detection and immunomagnetic bead T-cell depletion.  TLR4/MD2 cell surface expression was measured by flow cytometry and TLR gene induction by Real Time RT-PCR. Injury caused augmented wild type splenocyte production of IL-1<span style='font-family:Symbol'>b and TNF<span style='font-family: Symbol'>a at 24 hours and of IL-1<span style='font-family:Symbol'>b and TNF<span style='font-family:Symbol'>a at 7 days in response to all stimuli. Cytokine production was localised to macrophages and dendritic cells and the injury-augmented reactivity was independent of T-cells. Responses to LA, LPS and LTA required TLR4 whereas PGN responses were TLR4-independent.  TLR4 was not required for the <i>in vivo</i> establishment of injury-augmented proinflammatory responses. Injury did not substantially change TLR gene expression assessed by Real Time RT-PCR or TLR4/MD2 cell surface expression. IL-1 signalling was not essential for the injury-augmented proinflammatory response but was required for injury-augmented production of IL-6 and IL-10 and therefore may be important for the development of anti-inflammatory responses.