VictorJuiz/thesis huggingface dataset:
The role of protein-protein interactions and phosphorylation in the function of the homeodomain protein fushi tarazu

The discovery of the homeobox in 1984 revolutionized the field of developmental biology. Since its initial cloning in Drosophila, the homeobox has been found in every class of higher eukaryote. The polypeptide encoded by the homeobox, the homeodomain, is a 60 amino acid DNA-binding motif. It has been shown that homeodomain proteins bind DNA as part of their function in vivo, and that once bound to DNA they are able to regulate transcription. In every case so far examined, homeodomain-containing proteins function to determine cell fate. They carry out this function by controlling the expression of their downstream target genes. However, the indeterminate DNA-binding specificity that homeodomain proteins exhibit in vitro is not sufficient to explain their specific function in vivo. In addition, the same homeodomain protein is often responsible for the regulation of very divergent processes during the life cycle of the organism. The regulation of very different developmental processes may require the regulation of different sets or subsets of target genes at these different stages. Therefore, mechanisms must exist to first establish the functional specificity of a given homeodomain protein in vivo, and subsequently to change target gene specificity as the protein works to determine different cell fates. To better understand the factors that control homeodomain function in vivo, we have chosen to study the homeodomain protein fushi tarazu (FTZ), a member of the pair-rule class of segmentation genes in Drosophila. The ftz gene goes through three phases of expression during Drosophila embryogenesis, and it is required to determine very different cell fates during these phases of expression. The results presented in this thesis show that the ftz protein can function in vivo in the absence of its homeodomain, and that loss of DNA-binding ability is compensated for, in part, by the interaction of FTZ with two DNA-binding transcription factors, Paired (Chapter 2) and FTZ-F1 (Chapter 3). In addition, FTZ has been shown to be extensively phosphorylated in a tissue-dependent manner during embryogenesis. In vitro studies presented here, using FTZ expressed in the baculovirus system, suggest that phosphorylation may also regulate FTZ activity (Chapter 4).
Autonomy, liberalism, and advance care planning

The justification for advance directives is typically grounded in the notion that they preserve, enhance and extend patient autonomy into future states of incompetency through active patient participation in decision making about end-of-life care. However, the weight given to autonomy has become questionable in the light of recent empirical studies revealing the significance of other important values of social justice, paternalism, and personal relationships that emerge in the decision-making process. Such findings, along with objections on theoretical grounds, suggest that the value of autonomy, perceived to be a defining feature of liberal philosophical theory, is an inappropriate model for advance care planning. From a philosophical perspective, I explore the meaning and role of the value of individual autonomy within contemporary liberal writings to determine (i) whether the liberal concept of autonomy is a purely individualistic concept and (ii) whether the concept of autonomy is overemphasized by liberals at the expense of other important values of social justice, paternalism, and personal relationships. As a result of this analysis, I challenge the claim that liberalism, being a theory defined strictly in terms of its emphasis on individual autonomy, is an inappropriate framework in accounting for advance care planning. I suggest that liberalism is an indispensable component in a complete framework for advance care planning, but that it needs to be supplemented with theoretical models that explicitly focus on relevant values besides individual autonomy.
Pokeweed antiviral protein gene, expression and applications

Pokeweed antiviral protein (PAP) is a specific glycosidase which inactivates ribosomes by cleaving a single adenine at A$\sp{4324}$ of 28S ribosomal RNA. Full-length PAP cDNA $(PAP\sb{f})$ was synthesized from pokeweed (Phytolacca americana) mRNA and was expressed in E. coli. The expressed PAP was biologically active. In order to investigate the significance of the N- and C-terminal regions for toxicity, deletion mutagenesis on N- and C-terminal regions was performed. Results revealed that the N-terminal signal peptide (22 amino acids) but not the C-terminal region may be necessary for PAP gene expression. To achieve a higher expression level of PAP, $PAP\sb{f}$ was cloned in an expression vector containing a sequence (PL) derived from a polylinker instead of a Shine-Dalgarno (SD) sequence. Surprisingly, E. coli cells transformed with this vector produced over two times more PAP than with the vector containing the consensus SD sequence. Analysis of the sequence in front of the AUG codon revealed that the two boxes, ACCUACU (box I) and GAGUUAG (box II), were complementary to 1434-1440 and 507-513 in the 16S rRNA, respectively. Mutational study indicates that $PAP\sb{f}$ expression was dependent on the presence of both boxes. It is proposed that the two domains (507-513 and 1434-1440) in the 16S rRNA are organized in close proximity on the surface of the small ribosomal subunit and form a new mRNA binding site alternative to SD. The PAP gene was transformed into tobacco plants and mammalian cells to test for antiviral resistance. The PAP gene with a deletion of 36 codons from the C-terminus was expressed in transgenic tobacco plants and conferred an antiviral activity as high as 99%. The PAP gene devoid of the sequence for the N-terminal signal $(PAP\sb{\Delta N})$ was also introduced into CD$\sb4\sp+$ cells and the transformed cells were subjected to HIV-1 infection. Preliminary results indicated that the $PAP\sb{\Delta N}$ gene did not render transformed CD$\sb4\sp+$ cells resistant to HIV-1 infection. Since the $PAP\sb{\Delta N}$ gene was functional in vitro, it is suggested that the $PAP\sb{\Delta N}$ gene may be mutated after integration into the cellular genome perhaps due to toxicity to the CD$\sb4\sp+$ cells.
The development of a modern agricultural enterprise, beef cattle farming in Ontario, 1870-1924

Agriculture dominated Canadian life in late Victorian times, yet we know little about its dynamics. This dissertation describes one aspect of agriculture, beef cattle raising in Ontario, from a broad perspective in order to illustrate how farming enterprises functioned. The work does so by addressing three basic questions. What type of livestock did farmers think was suitable for the production of cattle commodities in relation to economic reality? What was that economic reality? And what shaped that economic reality? Chapter One gives the background to the situation in 1870, and assesses general concerns between 1850 and 1920. Chapter Two describes the purebred cattle industry. Chapter Three looks at the production of the ordinary farmer within the framework of breeder/feeder production systems, animal improvement, and specialization of livestock for beef and dairy purposes. Chapter Four outlines policy regulations by reviewing international quarantine problems, attitudes to bovine tuberculosis, and the development of other regulatory concerns. Chapter Five places Ontario's industry within the nation, the continent, and the international market. Chapter Six explains how the cattle industry related to the meat industry through consumption. chapter Seven reassesses patterns that emerge in earlier chapters and then outlines some international developments in the industry from 1924 to 1996. As early as 1865 beef cattle raising in Ontario was part of an international industry, which had developed by 1875 into a transatlantic system in which Canada and the United States functioned together. Regulation of the modern Canadian beef cattle industry was laid down in response to this pattern. While Canadian beef cattle raising remained centered in Ontario, not in the west, cattle bred on Ontario farms after 1890 reflected the needs of the province's dairying enterprise, not its beef cattle industry. As a result, the quality of beef cattle declined in Ontario. Because of production linkages, the Ontario situation affected how the western arm of the national industry functioned. The rise of Ontario's dairy industry, therefore, was intimately related to the decline of beef cattle everywhere in the nation. Farming for beef in Ontario from 1870 to 1924 was a complex operation with national implications, and international linkages.

Keywords: Cattle trade
History
Beef cattle
Bovins
Industrie
Histoire
Bovins de boucherie
The genesis and spirit of imagination (Hegel's theory of imagination between 1801-1807)

Given the importance of imagination for Kant, Fichte and Schelling, it is significant that the word only comes up once in Hegel's Phenomenology of Spirit, and that it is not a chapter heading alongside "Sense-Certainty," "Perception," "Understanding" and "Reason." Part I. "Imagination in Theory" looks at the development in Hegel's theory of imagination from the Differenzschrift and Faith and Knowledge, through three different versions of the Philosophy of Spirit (1803, 1805, 1830). Part II. "Imagination in Practice," focuses on the final moment of the imagination according to the 1830 Philosophy of Spirit--Sign-making Phantasie. I discuss two examples--the artist's activity as described in the Aesthetics, and the 'religion of imagination'--Hinduism as Hegel understood it in the Lectures on the Philosophy of Religion. Part III synthesizes the two previous parts, showing that the Phenomenology of Spirit is the culmination of the imagination's theoretical and practical activity: while in theory imagination is the middle moment of Vorstellen, practically it is at the heart of Aufhebung and thus of Spirit's inception and development. The Phenomenology is the story of consciousness' progress through its self-presentations. Imagination is therefore present throughout the entire book. I do not engage the moments of the Phenomenology, but focus instead on the single appearance of the word imagination in the Preface, and on how Hegel reinterprets Fichte's wavering imagination as a moment within the reflection--the "medium" of this 'Science of Experience.' Between 1801-1807 language becomes an increasingly important moment of imagination; by 1830 the externalizing of representations in communication (sign-making) is a moment of imagination. Hegel's psychology of the genesis of imagination and its moments reveals Spirit to be the community of interpreters. In the thesis Hegel's imagination is thought through to the Phenomenology, however, it is in the final transition of the Phenomenology--from Religion to Absolute Knowing, from picture thinking to knowing according to the Concept--that Hegel thinks the imagination through to its end. My Epilogue briefly discusses that transition, and the end of imagination in Absolute Knowing.
The relationship between the pricing of linear infrastructure and urban development patterns, the Metro Toronto experience

With the incorporation of Metro Toronto in 1953, privileged linear infrastructure subsidies, which were particularly high on roads, were granted to the upper tier Metropolitan Toronto government and its outlying suburbs of North York, Scarborough and Etobicoke. These high subsidies enabled Metro to provide a fine web of high quality, rapid arterials and highways across the Metro Toronto jurisdiction--accelerating urban development into the region. However, it was not just that the outlying Metro suburbs were quickly serviced and urbanized, but the new subdivisions that were facilitated by these subsidies were low density, or alternatively stated, land extensive developments characterized largely by single family detached housing. The framework used for the research is welfare economics, which establishes the basis for the work on the optimal allocation of resources, public goods and services, and externalities. The text develops a framework for recognizing particular market failures and resource misallocations within an urban economy based on the characteristics of building prototypes. Through a study of these prototypes, it is then demonstrated that the discriminatory subsidies to the three outlying Metro suburbs had generated the under-pricing of linear infrastructure, not only encouraging premature urban encroachment into farmlands and natural areas, but also, an inefficient built form. The text not only covers the impacts of linear infrastructure pricing on the built environment, but it also includes assessments of social equity conditions of various policy initiatives that have generated a particular built form.
Imagining affirmative action and equal opportunity: American failures, Canadian challenges

The dissertation offers a critique of American affirmative action law in employment as it pertains to African-Americans. Specifically, it argues that the law contains an impoverished understanding of equal opportunity. American law describes affirmative action as measures designed to remedy instances of discrimination in work forces, and asserts that equal opportunity has been achieved in those work forces when specific numbers of minority workers have been hired. This formulation, however, does not adequately address the complex effects of past discrimination which limit the employment opportunities of many African-Americans. For example, inferior educational resources, inadequate housing, and concentration in inner-city ghettos affect the ability of African-Americans to find well-paying jobs. In addition, the understanding of affirmative action as remedy for work force discrimination allows no way to distinguish levels of disadvantage within the black community. Canadian law, rather than describing affirmative action as remedy for workforce discrimination, describes it as a way to ameliorate disadvantage. Canadian law states that the pursuit of equal opportunity requires lawmakers to examine the actual economic conditions of certain groups to gauge the full extent of the disadvantages they face and to devise programs to address them. The Canadian law articulates a richer understanding of equal opportunity than the one presented in American affirmative action law. This understanding, however, resonates with arguments for equal opportunity that have been voiced by important public figures throughout American history. Therefore, inspired by the Canadian experience and employing arguments expressed in the American setting, the dissertation presents a novel justification for affirmative action directed toward the group which has come to be know as "the truly disadvantaged," poor urban African-Americans, based on a fuller understanding of equal opportunity than presented in contemporary American law.
Model reduction of discrete real-time systems

In many Discrete-Event Systems (DES) both state and event information are of importance to the systems designer. To obtain compositionally consistent hierarchical models of systems, the behavior of Discrete-Event Systems with unobservable transitions and state output maps is considered. Observers for deterministic DES are generalized to nondeterministic DES and characterized using the join semilattice of compatible partitions of a transition system. This characterization points to efficient algorithms for computing both strong and weak state-event observers as solutions to the Relational Coarsest Partition problem (RCP). The strong and weak observation equivalences of Milner are shown to be special cases of our observers under the trivial (constant) state output map. The state-event equivalence based upon the observers is shown to be a congruence for a parallel composition operator, allowing the replacement of modules by their quotient systems. Logics such as Ostroff'S RTTL allow for the specification and verification of a system's state-event behavior. To make realistic problems amenable to analysis, a designer must typically decompose the system into subsystems (modules) land use algebraic abstraction (quotient systems) to obtain hierarchical system models that preserve the properties to be verified. In this thesis we use state-event observational equivalence to perform compositionally consistent model reduction for a subclass of formulas of state-event linear temporal logics, with particular attention to a discrete time temporal logic that is a simplification of RTTL. The reduction technique allows limited use of immediate operators. In the process, we develop a method of specifying modules' input/output behavior by defining observable satisfaction for RTTL-style temporal logics. The results are applied to the shut-down system of a nuclear reactor.
Immunoglobulin heavy chain gene expression in hybridoma cells

Regulatory elements which determine gene expression in the immunoglobulin heavy chain (IgH) locus have traditionally been identified by their effects on the expression of transgenes, i.e., reporter genes which have been transfected into cell lines or animals. Such analyses have revealed that expression of immunoglobulin heavy chain transgenes requires multiple elements from the J$\rm\sb{H}$-C$\mu$ intron: the matrix attachment regions (MARs), the E$\mu$ enhancer, and several switch-associated elements. Nevertheless, expression of the endogenous heavy chain genes in some B-cell lines is maintained in the absence of these intronic elements, a result which is generally interpreted to reflect the presence of redundant but remote activating elements in the IgH locus. To investigate these discrepancies systematically, I have used gene targeting to generate recombinant hybridoma cell lines lacking various defined segments in the J$\rm\sb{H}$-C$\mu$ intron. As in earlier studies of the endogenous IgH locus, my analysis of mRNA and nuclear run-on activity indicates that expression of the endogenous $\mu$ heavy chain gene does not require the E$\mu$ enhancer. By contrast, expression of the endogenous $\mu$ gene is decreased greatly by deleting the MARs, i.e., the MARs are not functionally redundant in the recombinant IgH locus. My further analysis identified a segment of the gpt gene of the targeting vector that depresses expression of a truncated, recombinant IgH locus. I propose that this region of the gpt gene insulates the $\mu$ transcription unit from other MARs in the IgH locus. These results indicate that MARs can function in the expression of a single copy endogenous gene, and that the MARs can function independently of the normally closely linked E$\mu$ enhancer. This system provides well defined and advantageous conditions for analyzing how MARs function in gene expression. My results also underscore that vector-borne sequences can strongly affect expression of an adjoining chromosomal gene.
The semantic significance of Donnellan's referential/attributive distinction

In "Reference and Definite Descriptions", Keith Donnellan introduces the notion of referential and attributive uses of definite descriptions--phrases such as "the author of Waverly". Here and in subsequent papers he argues that Russell's Theory of Descriptions is inadequate as a semantic analysis for all uses of definite descriptions. According to Russell's theory, definite descriptions are quantifier phrases, not singular terms. Donnellan's arguments suggest that definite descriptions are ambiguous. When they are used attributively, definite descriptions should be read as quantifier phrases. When they are used referentially, they should be read as genuine singular terms. I argue that it is possible to draw a sharp distinction between referential and attributive uses of definite descriptions. Following Donnellan, I argue that whether a description is used referentially or attributively depends on the intentions of the speaker concerning the truth-conditions of the proposition he wishes to express. This provides us with a precise way to determine whether a definite description is used referentially or attributively. I turn next to the question: Does Donnellan's referential/attributive distinction show that definite descriptions are semantically ambiguous? I distinguish two positions which have emerged in the literature. What I call The Strong Referential Thesis maintains that definite descriptions are singular terms, when they are used referentially. On this account, definite descriptions are semantically ambiguous. What I call The Weak Referential Thesis maintains that definite descriptions, when used referentially, are properly analyzed according to Russell's Theory of Descriptions. This thesis maintains that in referential cases, a speaker's utterance semantically expresses one proposition, but he may succeed in communicating some other proposition. This account attempts to defend Russell's Theory of Descriptions against the apparent counterexamples offered by Donnellan and others. I present two arguments in support of The Strong Referential Thesis. First, I argue that The Weak Referential Thesis results in the ascription of contradictory beliefs to speakers. I call this The Argument from the Principle of Charity. Second, I argue that The Weak Referential Thesis cannot, in all cases, explain how speakers may succeed in communicating a determinate proposition other than that which their utterances semantically express.
The comparative analysis of the certification processes of five professional associations

Technological developments and innovations are changing the nature of work, traditional jobs are disappearing and new, more advanced forms of work requiring an expanded and growing knowledge base are emerging. More occupations are taking on the characteristics of "professions" particularly in terms of certifying and maintaining competency of their members. Professionals, whose knowledge and skills were acquired through formal education and technical training find their initial education is not longer sufficient. With the increasing demand for up-dating, up-grading and re-training, professional associations are playing a significant educational role by developing and implementing activities such as seminars and certification programs. In this study, the certification processes used by five professional associations were analyzed. The objectives were to determine: the type of certifications process or processes used by the association; why association members participate in the process; if the understanding of the requirements to participate in and successfully complete the certification program by the association membership reflect the association's requirements; whether the association leadership and members share the same understanding regarding how the certification program standards are set and who participates in setting the standards; how accessible the certification program is perceived by the membership and the types of continuing education programs offered and the participation in the programs. The research included examples of criterion-, curriculum-, and competency-based certification. The researcher found that: individuals participate in certification programs to develop new skills to strengthen their position or marketability, the documentation on how programs are developed, how standards are set and why certain courses are in a program is generally confidential to the association and generally members of the associations survey were unclear as to how the standards are set. The study was limited by the lack of association documentation and the inability to survey the membership or ask specific questions on the survey. The research findings will be of interest to individuals and associations who have or would like to have an understanding of the use of certification and the implications of the process on members of the profession who participate in the program and employers who hire the certified profession.