The question of adverbs and the meaning of the present perfect across varieties of English is central to sociolinguistic variationist methodologies that have approached the study of the present perfect (Winford, 1993; Tagliamonte, 1997; van Herk, 2008, 2010; Davydova, 2010; Tagliamonte, 2013). This dissertation attempts to disentangle the effect of adverbial support from the three canonical readings of the present perfect (Resultative, Experiential and Continuative). Canadian English, an understudied variety of English, is used to situate the results seen in the Early Modern English data. Early Modern English reflects the time period in which English has acquired the full modern use of the present perfect with the three readings. In order to address both these questions and current controversies over statistical models in sociolinguistics, different statistical models are used: both the traditional Goldvarb X (Sankoff, Tagliamonte and Smith, 2005) and the newer mixed-effects logistic regression (Johnson, 2009). What is missing from the previous literature in sociolinguistics that advocates logistic mixed-effects models, and provided in this dissertation, is a clear statement of where they are inappropriate to use and their limitations. The rate of adverbial marking of the present perfect in Canadian English falls between rates reported for US and British English in previous studies. The data show in both time periods that while adverbs are highly favored in continuative contexts, they are strongly disfavored in experiential and resultative contexts. In Early Modern English, adverbial support functions statistically differently for resultatives and experientials, but that difference collapses in the Canadian English sample. Both this and the other linguistic contexts support a different analysis for each set of data with respect to adverbial independence from the meaning of the present perfect form. Finally, when the focus of the analysis is on linguistic rather than social factors, both the traditional and newer models provide similar results. Where there are differences, however, these can be accounted for by the number of tokens and different estimation techniques for each model.

京都大学 / 0048 / 新制・課程博士 / 博士(人間健康科学) / 甲第21703号 / 人健博第69号 / 新制||人健||5(附属図書館) / 京都大学大学院医学研究科人間健康科学系専攻 / (主査)教授 山田 重人, 教授 古田 真里枝, 教授 万代 昌紀 / 学位規則第4条第1項該当 / Doctor of Human Health Sciences / Kyoto University / DFAM

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Ancestral Sequence Reconstruction is a technique used to statistically infer the most likely ancestor of a set of evolutionarily related sequences, but research which relies solely on protein data has the disadvantage of sequence information being lost upon translation of a protein from its gene transcript, due to the redundancy inherent in the genetic code. In this project, the amino acid sequences, and separately the corresponding codon sequences, of 184 homologous Acetylcholine receptor protein sequences were aligned, and phylogenetic analysis and ancestral sequence reconstruction was performed based on both alignments to infer several ancestral sequences representing important milestones in the evolutionary history of the homologous protein family. To further extract meaningful information from the nucleotide sequences, positive selection analysis was performed on the codon alignment using the Mixed Effects Model of Evolution method, which estimates and compares between the rates of synonymous and non- synonymous mutations across the alignment to detect the occurrence of positive selection events throughout their evolution. The Mixed Effects Model of Evolution can infer positive selection across both sites and evolutionary branches in a sequence alignment, thus highlighting residues along the evolutionary trajectory of the proteins which may have been functionally important in their evolution. Positive selection analysis detected positive selection at a multitude of sites and branches, and by mapping signatures at which selection is strongest with changes in the trajectory of ancestral states, several important sites were chosen as likely to be most valuable for future experimental testing. The implications of this study on the benefits of conducting ancestral sequence reconstruction with protein and codon sequences are discussed.

The ongoing opioid crisis presents a significant public health challenge particularly for people who use opioids (PWUO). Naloxone is an opioid antagonist crucial to reducing opioid overdose mortality. Inconsistencies exist among PWUO in obtaining, carrying, discussing, and administering naloxone. Using sequential mixed methods, this study was aimed at investigating the use of implementation intentions on naloxone use among PWUO. Semi-structured interviews were conducted with 83 PWUO to gather individual experiences with using naloxone and contextual details regarding its use. An essentialist thematic analysis with inductive coding revealed valuable insights into where, for whom, and when naloxone is implemented. The analysis identified major themes such as caring for others' needs, knowledge gaps, reinforcement through overdose experiences, duality of overdose and compassion, and stigma. Minor themes related to syringe services program implementation and drug use were identified. Building on these qualitative findings a quantitative analysis determined the impact of implementation intentions on naloxone implementation. Participants were randomly assigned to develop implementation intentions or goal intentions for the use of naloxone. Follow-up surveys assessed changes in participants' intentions to obtain, carry, discuss, and administer naloxone and their actual implementation over a 6-month period. At the 3-month follow-up the experimental condition exhibited statistically significant positive intentions to obtain naloxone and engage in discussions about naloxone in social contexts of drug use. Changes in the magnitude of naloxone implementation were observed at the 3- and 6-month timepoints. Specifically, the self-reported discussion of naloxone showed noticeable changes in implementation frequency over time. This suggests that while implementation intentions may not have statistically significant effects on the use of naloxone it had some influence on the frequency of discussing naloxone prior to drug use. This work makes a valuable contribution to the existing literature because of its attempt to apply the Theory of Planned Behavior and implementation intentions in a novel way. Though the experimental hypothesis was not supported statistically significant observations were made for some behaviors at the 3-month follow-up. The pragmatic nature of the setting enhances the relevance of the findings and provides valuable insights for future interventions supporting PWUO. / Doctor of Philosophy / The ongoing crisis of opioid addiction poses a significant public health challenge particularly for individuals who use opioids. Naloxone is a medication that can reverse opioid overdoses and it plays a crucial role in saving lives. People who use opioids often face difficulties in accessing, carrying, discussing, and using naloxone consistently. This study was aimed at investigating the use of naloxone by employing qualitative and quantitative methods. We conducted interviews with 83 individuals who use opioids to explore their experiences and gather insights into naloxone use. These interviews provided valuable information about when, where, and for whom naloxone is used. Several important themes emerged including the significance of helping others, knowledge gaps, the influence of personal experiences, the conflict between the fear of overdose and caring for others, and the stigma associated with drug use. We investigated the impact of a specific approach called "implementation intentions" in improving naloxone use. Participants were randomly assigned to create specific plans or general goals for naloxone use. Through surveys conducted over a 6-month period we examined changes in participants' intentions and actions related to naloxone use. Although the specific approach did not yield significant improvements, we observed changes in how people discussed naloxone over time. This study contributes to the existing research by introducing innovative ideas to support positive behavioral changes among individuals who use opioids. The real-world setting in which the study took place enhances the applicability of the findings and offers valuable insights for future programs supporting individuals who use opioids.

My thesis examines nonlinearity between catch and effort. I use a meta-analysis of published literature and generalized linear mixed-effects models (GLMM) on both fixed and mobile gear fisheries of Atlantic Canada. The meta-analysis examines the proportionality of catch to effort using the slope of the reduced major axis (RMA) log-log regression, which accounts for “errors-in-variables”. The GLMMs explored proportionality while accounting for variation among fishing vessels. Both analyses found evidence for disproportionality between catch and effort. Catch that increases disproportionally to effort could result from either facilitation or recruitment of effort into the fishery. Catch increases that are less than proportional are expected from competitive interactions among fishers or gear saturation. The GLMM also revealed that the level of aggregation (by set, trip, monthly, or annually) can affect the apparent proportionality between catch and effort. In general, catch and effort should not be considered to be proportional. / May 2016

The concern of this thesis is to discuss classification of different objects based on longitudinal observations. In the first instance the reader is introduced to a linear mixed-effects model which is useful for longitudinal data modeling. Description of discriminant analysis methods follows. These methods ares usually used for classification based on longitudinal observations. Individual methods are introduced in the theoretic aspect. Random effects approach is generalized to continuous time. Subsequently the methods and features of the linear mixed-effects model are applied to real data. Finally features of the methods are studied with help of simulations.