A Thesis submitted to The University of Arizona College of Medicine - Phoenix in partial fulfillment of the requirements for the Degree of Doctor of Medicine. / Obstructive sleep apnea (OSA) is a condition characterized by upper airway obstruction during sleep causing intermittent hypoxia and nighttime awakening. It is a common condition in the United States that is often undiagnosed. It is a significant risk factor for decreased daytime productivity, quality of life, cardiovascular disease, and death. The current gold standard for diagnosis of OSA is laboratory‐based polysomnography (PSG). While PSG is necessary for the diagnosis and monitoring of OSA, many patients have limited access to PSG due to wait times at PSG laboratories or economic or geographic limitations. Portable sleep monitoring has been studied as a possible solution for patients who do not have access to timely PSG. This study aimed to use the Zephyr BioHarness 3, a chest‐worn physical activity monitor that records movement and physiologic data in real‐time, to detect apnea events in patients with suspected OSA undergoing single‐night laboratory PSG. Twenty patients underwent single‐night laboratory‐based PSG while simultaneously wearing the Zephyr BioHarness 3. The Zephyr BioHarness 3 data was analyzed using three methods. First, apnea events were identified in 10‐second windows of Zephyr data via support vector machine, logistic regression, and neural network (sensitivity = 76.0 ± 0.3%, specificity = 62.7 ± 0.2%, accuracy = 63.7 ± 0.1%). Second, apnea events were identified using the mean, median, and variance of the 10‐second windows (sensitivity = 72.3 ± 0.3%, specificity = 69.4 ± 0.1%), accuracy 69.6 ± 0.1%). Third, apnea events were identified using phase‐space transformation of the Zephyr BioHarness 3 data (sensitivity = 76.9 ± 0.3%, specificity = 77.9 ± 0.1 %, accuracy = 77.9 ± 0.1%). The Zephyr BioHarness shows initial promise as a possible OSA screening tool for patients suspected of OSA but who lack access to timely laboratory‐based PSG.

Modern health care systems are information dense and increasingly relying on computer-based information systems. Regrettably, many of these information systems behave only as an information repository, and the interoperability between different systems remains a challenge even with decades of investment in health information exchange standards. Medical records are complex data models and developing medical data import / export functions a is difficult, prone to error and hard to maintain process. Bidirectional transformations (bx) theories have been developed within the last decade in the fields of software engineering, programming languages and databases as a mechanism for relating different data models and keeping them consistent with each other. Current bx theories and tools have been applied to hand-picked, small-size problems outside of the health care sector. However, we believe that medical record exchange is a promising industrial application case for applying bx theories and may resolve some of the interoperability challenges in this domain. We introduce BXE2E, a proof-of-concept framework which frames the medical record interoperability challenge as a bx problem and provides a real world application of bx theories. During our experiments, BXE2E was able to reliably import / export medical records correctly and with reasonable performance. By applying bx theories to the medical document exchange problem, we are able to demonstrate a method of reducing the difficulty of creating and maintaining such a system as well as reducing the number of errors that may result. The fundamental BXE2E design allows it to be easily integrated to other data systems that could benefit from bx theories. / Graduate / 0984

In this article we summarize histories of nonlinear, complex interactions among societal, legal, and ecosystem dynamics in six North American water basins, as they respond to changing climate. These case studies were chosen to explore the conditions for emergence of adaptive governance in heavily regulated and developed social-ecological systems nested within a hierarchical governmental system. We summarize resilience assessments conducted in each system to provide a synthesis and reference by the other articles in this special feature. We also present a general framework used to evaluate the interactions between society and ecosystem regimes and the governance regimes chosen to mediate those interactions. The case studies show different ways that adaptive governance may be triggered, facilitated, or constrained by ecological and/or legal processes. The resilience assessments indicate that complex interactions among the governance and ecosystem components of these systems can produce different trajectories, which include patterns of (a) development and stabilization, (b) cycles of crisis and recovery, which includes lurches in adaptation and learning, and (3) periods of innovation, novelty, and transformation. Exploration of cross scale (Panarchy) interactions among levels and sectors of government and society illustrate that they may constrain development trajectories, but may also provide stability during crisis or innovation at smaller scales; create crises, but may also facilitate recovery; and constrain system transformation, but may also provide windows of opportunity in which transformation, and the resources to accomplish it, may occur. The framework is the starting point for our exploration of how law might play a role in enhancing the capacity of social-ecological systems to adapt to climate change.

Cellular life is highly complex. In order to expand our understanding of the workings of human cells, in particular in the context of health and disease, detailed knowledge about the underlying molecular systems is needed. The unifying theme of this thesis concerns the use of data derived from sequencing of RNA, both within the field of transcriptomics itself and as a guide for further studies at the level of protein expression. In paper I, we showed that publicly available RNA-seq datasets are consistent across different studies, requiring only light processing for the data to cluster according to biological, rather than technical characteristics. This suggests that RNA-seq has developed into a reliable and highly reproducible technology, and that the increasing amount of publicly available RNA-seq data constitutes a valuable resource for meta-analyses. In paper II, we explored the ability to extrapolate protein concentrations by the use of RNA expression levels. We showed that mRNA and corresponding steady-state protein concentrations correlate well by introducing a gene-specific RNA-to-protein conversion factor that is stable across various cell types and tissues. The results from this study indicate the utility of RNA-seq also within the field of proteomics. The second part of the thesis starts with a paper in which we used transcriptomics to guide subsequent protein studies of the molecular mechanisms underlying malignant transformation. In paper III, we applied a transcriptomics approach to a cell model for defined steps of malignant transformation, and identified several genes with interesting expression patterns whose corresponding proteins were further analyzed with subcellular spatial resolution. Several of these proteins were further studied in clinical tumor samples, confirming that this cell model provides a relevant system for studying cancer mechanisms. In paper IV, we continued to explore the transcriptional landscape in the same cell model under moderate hypoxic conditions. To conclude, this thesis demonstrates the usefulness of RNA-seq data, from a transcriptomics perspective and beyond; to guide in analyses of protein expression, with the ultimate goal to unravel the complexity of the human cell, from a holistic point of view. / <p>QC 20161121</p>

The crystal structure of metarossite, ideally CaV2O6 center dot 2H(2)O [chemical name: calcium divanadium(V) hexaoxide dihydrate], was first determined using precession photographs, with fixed isotropic displacement parameters and without locating the positions of the H atoms, leading to a reliability factor R = 0.11 [Kelsey & Barnes (1960). Can. Mineral. 6, 448- 466]. This communication reports a structure redetermination of this mineral on the basis of single- crystal X- ray diffraction data of a natural sample from the Blue Cap mine, San Juan County, Utah, USA (R1 = 0.036). Our study not only confirms the structural topology reported in the previous study, but also makes possible the refinement of all non- H atoms with anisotropic displacement parameters and all H atoms located. The metarossite structure is characterized by chains of edge- sharing [CaO8] polyhedra parallel to [100] that are themselves connected by chains of alternating [VO5] trigonal bipyramids parallel to [010]. The two H2O molecules are bonded to Ca. Analysis of the displacement parameters show that the [VO5] chains librate around [010]. In addition, we measured the Raman spectrum of metarossite and compared it with IR and Raman data previously reported. Moreover, heating of metarossite led to a loss of water, which results in a transformation to the brannerite- type structure, CaV2O6, implying a possible dehydration pathway for the compounds M2+V2O6 center dot xH(2)O, with M = Cu, Cd, Mg or Mn, and x = 2 or 4.

In the past two years my paintings have fluctuated from figuration to abstraction. Dense surfaces, physical weight, and sense of touch have been dominant characteristics of my work. I have tried to animate oil paint by pushing it to the outer edges of the painting support and by using it to perform unorthodox tasks. I have stretched the limits of oil paint, creating works that reference flesh and the figure even while the forms remain amorphous and minimal. My work is a way for me to question the meaning of material and spiritual transformation.

As a child growing up, I was always in love with the ritual of “dress up”. Whether it was my dolls, various reluctant pets, or myself, it was always an activity I loved. It is not surprising then that adornment has become the medium through which I express myself and bring my fantasy world to life. Jewelry and accessory have the potential to lead many lives. One particular piece can change entirely by putting it on one body as opposed to another, or by removing it to see it as an object. In fashion, the body is the canvas and the runway becomes the moment of performance. My work uses the body in much the same way where the wearer becomes performer. Through this act, we construct personal forms of armor, or “power suits”, to face the battlefield of the outside world. In harnessing this act of adorning and what it encompasses, I am consistently challenged as both designer and maker. Creating alter egos, whether subtly flirtatious or overtly sexual, demure or flamboyant, are some of the many ways in which these “power suits” can be concocted. The stories we project about ourselves daily, through how we adorn our naked bodies, become empowering. Myths versus reality, ascetic versus sensual, and beautiful versus ugly are some of the concepts from which I draw inspiration. These dualities are conceptually expressed in my work through physical combinations of opposing materials. Mixing mediums, through methods such as collaging, beading, needlepointing, knitting, and sewing, are integral in my designs. With alternative materials, such as feathers, textiles, and yarns, I add softness and new scintillating sensations when juxtaposed with the hard, cold qualities of metal. Through combining such materials, I construct pieces that not only challenge one’s notion of what “pretty” is, but also inspire the way one thinks about body adornment. The objects I create become vessels that actualize the dualities I strive to express. In producing hybrids of materials, my need to explore these dichotomies is satisfied.

Background: Mindfulness-based cognitive therapy (MBCT) is a promising new alternative to anti-depressant medication (Kuyken et al., 2015) and whilst some qualitative studies have explored participants' experiences of MBCT, none yet have explored experiences of participants who are considering coming off their antidepressant medication alongside MBCT or how patients experience change in relationships with self, others and illness. Aim: To examine MBCT participants' experience of change across 24 months, particularly in relation to change in views of their self and their illness over time. Method: Thematic analysis of in-depth retrospective interviews with 42 participants, two years after attending an 8 week MBCT group with an invitation to taper their antidepressant medication (ADM). Each participant took part in one retrospective interview which was semi-structured and focused on experiences of MBCT and ADM over the previous two years since attending an MBCT group and how these have impacted on a change in self and experience of illness. Findings and conclusion: Four over-arching themes were found: taking control, relationships (with self, other and illness), rebuilding the self and shifts in perspective. The findings in the current study are very similar to those found in transformation in the physical chronic illness literature (e.g. Paterson et al., 1999). Perhaps MBCT could be the challenge which lead patients suffering from chronic depression towards change and creates a context in which patients can consider self and identity.

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Avec la population en constante croissance, les besoins alimentaires sont de plus en plus importants. Afin de répondre à la demande des populations, ainsi que pour s’assurer d’un bon rendement agricole, les agriculteurs suivant un mode d’agriculture qualifié de conventionnel doivent palier aux limitations naturelles des cultures. C’est par exemple en utilisant des pesticides ou herbicides pour la gestion des espèces nuisibles. Ce peut être aussi en utilisant des matières résiduelles fertilisantes pour apporter dans les sols les éléments essentiels à la bonne croissance des végétaux. Ces matières peuvent être des boues récupérées en sortie de station d’épuration, ou des fumiers. Les traitements mis en œuvre pour traiter ces matières étant insuffisants, divers contaminants sont introduits en même temps que les nutriments essentiels lors de leurs épandages. Pour les boues, ce sont les produits issus des activités humaines quotidiennes (produits pharmaceutiques et de soin corporel). Il est donc possible de retrouver dans les sols de cultures conventionnelles, un mélange de pesticides, herbicides, produits pharmaceutiques et de soin corporel et autres contaminants organiques. Ces substances, présentes dans les sols sous leurs formes initiales (ingrédient actif) ou dégradées (produits de dégradation), peuvent potentiellement interagir avec les organismes biologiques des sols et causer d’éventuels effets toxiques. Les vers de terre représentent une grande partie de la biomasse animale des sols et contribuent à la régulation des processus majeurs des sols. Vivant dans les sols et s’en nourrissant, ils sont par conséquent directement exposés à tous les contaminants qui s’y trouvent. Il apparaît dans ces conditions importantes de déterminer les potentiels effets toxiques des mélanges de contaminants organiques (pesticides et produits pharmaceutiques) sur les vers de terre. Les concentrations en contaminants organiques dans les sols sont faibles, de l’ordre du ng.g-1 (poids sec), et des effets létaux sur des organismes robustes comme les vers de terre sont peu probables. D’autres effets peuvent cependant apparaître, en altérant par exemple le comportement reproducteur des vers, leur croissance, ou encore en causant des dommages à leur ADN. Ces molécules organiques peuvent aussi s’accumuler dans les tissus des vers de terre, ce qui présente des risques supplémentaires pour les maillons supérieurs du réseau trophique. Des méthodes standardisées pour évaluer ces risques existent. Cela dit, elles ont été mises en place pour estimer les limites en termes de concentrations dans les sols auxquelles les effets toxiques vont apparaître. Les molécules sont par conséquent étudiées seules et à de hautes concentrations. L’objectif principal de ces présents travaux est de mettre en place un protocole nous permettant de détecter un ensemble d’effets sublétaux des contaminants organiques sur les vers de terre de l’espèce Eisenia andrei en exposant les vers à des mélanges de pesticides et de produits pharmaceutiques à faibles concentrations (environnementales), ou bien à des produits marqueurs d’une contamination spécifique. Le protocole expérimental retenu est basé sur un test de reproduction, auquel des analyses chimiques des tissus des vers de terre et des échantillons de sol pour évaluer la bioaccumulation des contaminants sont ajoutés. Dans ce cas d’étude, la bioaccumulation fait référence à l’accumulation des contaminants organiques provenant de toutes les sources d’exposition (alimentation, contact) dans les tissus des vers de terre. L’essai comètes appliqué aux vers de terre adultes pour déterminer l’endommagement de l’ADN vient compléter les données. Ce protocole a été appliqué à plusieurs reprises, en exposant les vers de terre à des mélanges divers de contaminants organiques (pesticides et produits pharmaceutiques) ajoutés directement au sol artificiel, en concentrations environnementales (< 100 ng.g-1 , masse sèche). L’effet le plus marquant est la bioaccumulation sélective des insecticides de la famille des néonicotinoides dans les tissus des vers de terre, quelle que soit la composition de mélange de contaminants organiques ajoutés au sol. Lorsqu’exposés au triclosan à 50 ng.g-1 (dw), les vers de terre modifient leur comportement de reproduction, et accumule cette molécule. Lorsque le triclosan est ajouté par l’intermédiaire d’une boue contaminée dans ces mêmes sol artificiel et à une concentration finale équivalente, la bioaccumulation est du même ordre de grandeur que précédemment. C’est la forme dérivée du triclosan, le méthyl-triclosan, qui apparaît progressivement dans les sols et est accumulé plus fortement que le triclosan lui-même. Ce phénomène n’était pas observé lors de l’ajout du triclosan dissous dans un solvant. Bien que réalisés dans un système artificiel, les travaux présentés dans ce mémoire montrent l’importance de rechercher les effets écotoxicologiques des contaminants en conditions les plus réalistes possibles (mélanges, concentrations faibles). Le suivi de la composition chimique des sols d’exposition au cours des expériences permet de mieux comprendre l’origine des effets observés, particulièrement lorsque les produits de transformation peuvent également être analysés. Pour aller plus loin dans les études des effets sublétaux de contaminants organiques sur les vers de terre, des expériences incluant un suivi de plusieurs générations successives apporteraient de nombreuses informations sur la sensibilisation des jeunes vers et le risque pour les populations à long terme.