In many physiological studies, variables of interest are not directly accessible, requiring that they be estimated indirectly from noisy measured signals. Here, we introduce two empirical methods to estimate the true physiological signals from indirectly measured, noisy data. The first method is an extension of Tikhonov regularization to large-scale problems, using a sequential update approach. In the second method, we improve the conditioning of the problem by assuming that the input is uniform over a known time interval, and then we use a least-squares method to estimate the input. These methods were validated computationally and experimentally by applying them to flow-through respirometry data. Specifically, we infused CO2 in a flow-through respirometry chamber in a known pattern, and used the methods to recover the known input from the recorded data. The results from these experiments indicate that these methods are capable of sub-second accuracy. We also applied the methods on respiratory data from a grasshopper to investigate the exact timing of abdominal pumping, spiracular opening, and CO2 emission. The methods can be used more generally for input estimation of any linear system. / Master of Science / The goal of an inverse problem is to determine some signal or parameter of interest that is not directly accessible but can be obtained from an observed effect or a processed version that is measurable. Finding the gas exchange signal in animals is an example of an inverse problem. One method to noninvasively measure the gas exchange rate of animals is to put them in a respirometry chamber, flow air through the chamber, and measure the concentration of the respiratory gasses outside the chamber. However, because the gasses mix in the chamber and gradually flow through the gas analyzer, the pattern of the measured gas concentration can be dramatically different than the true pattern of real instantaneous gas exchange of the animal. In this thesis, we present two methods to recover the true signal from the recorded data (i.e., for inverse reconstruction), and we evaluate them computationally and experimentally.

More than 20 million clonal loblolly pines have been planted throughout the southeastern United States. Fertilizer has been applied to more than 6.5 million hectares of plantations to alleviate deficiencies of nitrogen and phosphorus that limit growth. Because cloning loblolly pine in large numbers has only become possible in the last decade, it is unknown how clones may respond differently to fertilizer application. Growth, growth efficiency, and biomass partitioning responses to fertilizer application were investigated among 25 clones planted in the Virginia Piedmont. Closely related clones varied in their fertilizer stem volume responses, but not enough to be statistically significant (p = 0.11). Clones varied in growth efficiency and partitioning to individual tissues, but clone-by-fertilizer interactions were not observed. Clonal variability was observed in root morphology, and maximum rooting depth showed a significant clone-by-fertilizer interaction. Clones with rapid growth rates can be selected with a range of other desirable traits. Short-term (i.e. weeks) responses to fertilization are often inconsistent with long-term (i.e. years) responses, but are critical to understanding growth responses. We investigated carbon allocation in two full-sibling clones of loblolly pine under two levels of fertilizer application over four months in a greenhouse. Using monthly harvests of some trees and ecophysiological measurements throughout, we determined carbon allocation on a monthly scale. In response to fertilizer application, both clones reduced allocation belowground and increased allocation to foliage to some extent, increasing whole-canopy photosynthetic capacity. However, these changes in allocation were ephemeral. By the end of the experiment, root-shoot ratios were no longer significantly affected by fertilizer application. Clones had allocation patterns distinct from one another, with one allocating more belowground and the other allocating more to stem mass. While their overall growth responses to fertilizer application were similar, the physiological mechanisms that resulted in these responses were different between clones. Results of the two studies indicate that while fertilizer responses may not need to be included when testing clones for deployment, knowledge of the fertilizer responses of widely-deployed clones would offer forest managers opportunities to apply clone-specific precision-silvicultural systems to optimize growth rates and manage for a range of products. / Ph. D.

Rhythmic collapse and reinflation of tracheal tubes is a form of active ventilation that augments convective gas exchange in multiple orders of insects. The underlying mechanism driving this phenomenon is not known. Among other things, tracheal tube collapse could be caused by either direct impingement of trachea or by a difference of pressure gradients between the intra-tracheal air and the surrounding hemolymph. To determine the relationship between hemolymph pressure and tracheal tube collapse in the ground beetle (Pterostichus commutabulis), we performed direct measurements of hemolymph pressure inside the beetle's prothorax while simultaneously using synchrotron phase contrast imaging to observe morphological changes in the trachea. We observed that a pressure pulse co-occurred with every tube compression observed throughout the body, suggesting that pulses in hemolymph pressure are responsible for tracheal collapse. To assess the effects of the experimental x-ray conditions imposed on the subjects during imaging, hemolymph pressure was also directly measured in the prothorax of beetles less restricted in non-x-ray trials. To compare the pressure patterns in the two experiments, a novel method of identifying and analyzing pressure pulses was developed and applied to the data sets. The comparison provides the first quantitative characterization of a directly measured hemolymph pressure environment, and demonstrates strong similarities in the pressure patterns recorded in both tests. However, pulses occurring during the x-ray experiments exhibited larger average magnitudes. Further video analysis however shows that collapse of the primary tracheal tubes was observed to occur even in the presence of the smallest simultaneously measured pressure pulse (1.01 kPa), suggesting that collapse of the primary tracheal tubes. / Master of Science

Gluconobacter oxydans is characterized by extreme acid tolerance and the ability to carry out rapid, single-step polyol oxidation catalyzed by membrane bound ehydrogenases. Experiments were designed to determine whether acid tolerance is associated with rapid polyol oxidation in this organism. Washed cells were exposed to 0.1 M or 0.5 !vt NaCI at pH 3.20; subsequent alkalinization of the suspending solution suggested a NaCl-dependent flow of protons (H+) into the cells. Cells were then exposed to NaCI at pH 3.20 followed by the addition of glycerol to determine whether polyol oxidation resulted in H + explusion from the cells. Following glycerol addition, immediate acidification of the suspending solution occurred. To verify that H + effiux was a result of respiration, experiments were conducted using sodium azide and 2,4-dinitrophenol; both compounds prevented the acidification that otherwise occurred following glycerol addition. Because glycerol oxidation reversed the NaCl-induced flow of H + into the cell, it appeared that respiration might function to protect acid-labile cell interiors. Cells exposed to NaCl at pH 3.20 in the presence of glycerol maintained cellular viability while loss of viability occurred in the absence of glyceroL To verify the effect of H+ extrusion on pH homeostasis, radioactively labeled organic-acid probes were used to determine intracellular pH in respiring and nonrespiring cells in the presence of 0.1 M NaCI at pH 3.20. No differences in cytoplasmic pH values between respiring and nonrespiring cells were detected. However, because substantial evidence exists for the role of respiration dependent H + extrusion in the acid tolerance of G. oxydans, use of an alternate method for measurement of internal pH, such as 31 P nuclear magnetic resonance spectroscopy, is suggested. / Master of Science

The quality of healthcare in low-resource countries is often limited by the environment, lack of funds, staff availability, electricity availability, and more. In the words of a Malawian physician, medicine can feel like improvisation, wherein one must make due with available resources rather than desired resources. One prevalent problem among low-resource hospitals is the functionality and longevity of medical equipment. A large percentage of all medical equipment in Malawian hospitals is donated, resulting in a wide spectrum of models, necessary spare parts, and functionality. These machines can break quickly due to heavy use prior to donation, missing user and maintenance manuals, and a lack of replacement parts. Thus, finding necessary life-saving equipment in Malawian hospital wards can be a challenge. One such piece of equipment is the oxygen concentrator, necessary for treatment of respiratory disease, use with CPAP machines, and in the administration of surgical anesthesia. This device fills many roles in low-resource hospitals, but in many Malawian hospitals it is the most frequently malfunctioning piece of equipment. A survey administered to medical personnel and maintenance personnel in hospitals in Malawi’s Central and Southern Regions isolated some common causes of oxygen concentrator malfunction. Prominent among these were poor oxygen concentrator ventilation and the lack of consumable replacement parts such as the intake bacterial filter. A stand made from locally-sourced materials was developed to encourage better oxygen concentrator exhaust and raise the device out of dust and cleaning fluids on ward floors. Intake bacterial filter alternatives were researched, designed, constructed, and tested, manufactured from housing materials and filter media available in Malawi or continental Africa. A primary source of difficulty for low-resource hospitals is lack of autonomy, requiring aid from affluent nations to supply equipment and consumable materials. This work suggests that sustainable innovations, such as allowing consumables to be produced in-country, can replace aid with development and create more accessible materials to hospital maintenance personnel. Collaboration with material suppliers and engineers in Malawi can provide sustainable designs and systems to help hospitals access the supplies they need to service oxygen concentrators and other equipment. / Master of Science / The quality of healthcare in low-resource countries is often limited by the environment, lack of funds, staff availability, electricity availability, and more. In the words of a Malawian physician, medicine can feel like improvisation, wherein one must make due with available resources rather than desired resources. One prevalent problem among low-resource hospitals is the functionality and longevity of medical equipment. A large percentage of all medical equipment in Malawian hospitals is donated, resulting in a wide spectrum of models, necessary spare parts, and functionality. These machines can break quickly due to heavy use prior to donation, missing user and maintenance manuals, and a lack of replacement parts. Thus, finding necessary life-saving equipment in Malawian hospital wards can be a challenge. One such piece of equipment is the oxygen concentrator. This device fills many roles in low-resource hospitals, but in many Malawian hospitals it is the most frequently malfunctioning piece of equipment. A survey was used in hospitals in Malawi’s Central and Southern Regions to collect information on why oxygen concentrators malfunction. Common reported causes of malfunction were oxygen concentrators overheating due to clogged exhaust vents, and the unavailability of necessary disposable filters. A stand made from locally-available materials was developed to improve oxygen concentrator ventilation. Replaceable filter alternatives were researched, designed, constructed, and tested, made from housing materials and filter materials available in Malawi or continental Africa. A primary source of difficulty for low-resource hospitals is dependence on more developed nations for supplies and aid. This work suggests that designing materials from locally-available materials can lessen this dependency and make necessary medical materials more accessible. Collaboration with material suppliers and engineers in Malawi can provide sustainable designs and systems to help hospitals access the supplies they need to service oxygen concentrators and other equipment.

Pesticides are commonly used around the world for a multitude of different purposes and on diverse habitats, including agricultural fields, wetlands, and personal lawns and gardens. Currently, acetylcholinesterase (AChE)-inhibiting pesticides are among the most prevalently used chemical pesticides in the United States. A wealth of information exists on sub-cellular responses of organisms, primarily birds, mammals, and fish, exposed to these compounds. However, the effects of AChE-inhibiting pesticides at the whole-organism level, most importantly effects relevant to an individual's fitness, have received less attention. My Master's research focused on describing the effects of carbaryl, an AChE-inhibiting pesticide, on several fitness-related traits in the western fence lizard (Sceloporus occidentalis). Reptiles are the least studied vertebrate taxon in ecotoxicological studies even though contaminants are suspected in contributing to recent population declines. Using multiple dose concentrations within the range expected to occur in nature (based on EPA application rates and published pesticide residues on insects), I quantified the effects of carbaryl on sprint performance energy acquisition, and energy allocation, traits which could have important implications for the animal's ability to avoid predators, capture prey, and grow and reproduce. I found that at the highest dose concentration, lizards experienced a decrease in arboreal and terrestrial locomotor performance, a decrease in energy acquisition, and alterations in energy allocation. My findings suggest that acute exposure to high concentrations of carbaryl can have important sublethal consequences on fitness-related traits in S. occidentalis. Future studies should examine the consequences of multiple-pulse exposures to AChE-inhibiting pesticides on reptiles. / Master of Science

No description available.

Le rythme respiratoire est un signe vital qui permet le diagnostic de plusieurs maladies respiratoires. Cependant, la surveillance du rythme respiratoire à l'extérieur du milieu hospitalier pose un défi qui a présentement peu de solutions. La plupart des capteurs existants ont des problèmes qui causent un non-fonctionnement dans certains environnements ; il n'existe pas de capteurs qui donnent l'information de manière quasi-parfaite en tout temps. Le mémoire présente une solution incluant plusieurs capteurs pour répondre à ce problème. La solution proposée permet de fusionner les informations en provenance de plusieurs capteurs hétérogènes afin d'obtenir l'information complète sur le rythme respiratoire, même dans des conditions ou un capteur individuel ne peut fournir cette information. Cette solution proposée utilise deux capteurs disponibles couramment sur le marché, soit un microphone MEMS et des accéléromètres. La solution comprend aussi une mesure de bioimpédance par un système qui pourrait être adapté pour être portable. Le mémoire présente ces capteurs et la procédure pour transmettre les signaux de ceux-ci vers un ordinateur. Le mémoire traite toutes les étapes de traitement de signal nécessaires pour tirer les informations du signal de respiration donné par ces capteurs. Le traitement de signal permet de réduire plusieurs types de bruits ainsi que de trouver des informations spécifiques au type de signal étudié. Le système cherche à reconnaître chacune des phases du cycle respiratoire pour chaque capteur individuel. Il utilise les informations sur les états possibles fournis par chaque capteur pour les fusionner ensuite avec un système de poids. Dans un environnement contrôlé, le système avec les données fusionnées permet d'avoir un taux d'erreur pouvant atteindre 0,88% pour un segment de 30 secondes, par rapport à des systèmes avec des capteurs uniques qui donnent des taux d'erreur variant entre 4,42% et 17,70% pour ces mêmes 30 secondes.

La relation entre la mère et l'enfant a un impact sur le développement du système nerveux du nouveau-né. La séparation maternelle néonatale (SMN) est un modèle de stress, chez le rat, perturbant cette relation. Nous nous sommes intéressés aux conséquences à long terme de ce stress néonatal sur les mécanismes contrôlant la ventilation lors d'un excès sanguin de CO2 (hypercapnie). Une altération de ce réflexe ventilatoire est une des causes de plusieurs troubles respiratoires tels que les apnées du sommeil. Il a été observé, dans notre laboratoire, que la SMN altère la réponse ventilatoire à l'hypercapnie (RVHC) de façon différente selon le sexe de l'animal. Cette thèse a pour but de trouver les mécanismes, affectés par la SMN, responsables des altérations de la RVHC. Nous nous sommes premièrement intéressés à la contribution des chémorécepteurs et barorécepteurs carotidiens chez les mâles. Cette étude a révélé une inhibition de la contribution des chémorécepteurs carotidiens à la ventilation et une augmentation du baroréflexe inhibant la ventilation. Par contre, il subsiste toujours une diminution de la sensibilité de la RVHC qui n'est pas attribuable aux corps carotidiens. Nous avons donc évalué la chémodétection centrale, mais elle ne semble pas responsable du phénotype. Par la suite, nous avons testé l'influence des récepteurs bronchopulmonaires d'étirement sur la ventilation. Nous avons observé une inhibition du réflexe d'Hering-Breuer chez les rats SMN qui pourrait expliquer l'altération de la RVHC dans certaines conditions. Finalement, chez les rates adultes, nous avons découvert que la SMN n'affecte pas la production d'hormones sexuelles et que l'augmentation de la RVHC est inhibée par l'anesthésie. Nous concluons que, chez les rats mâles, la SMN affecte la contribution des afférences périphériques probablement par une altération de l'intégration au niveau central et que, chez les femelles, l'augmentation de la RVHC, chez les rats éveillés, est probablement causée par l'effet anxiogène du CO2.

Nous avons conduit un programme de recherche portant sur l’impact du port d’un masque à gaz sur l’effort respiratoire et les échanges gazeux chez des sujets sains au repos et à l’effort et chez des patients MPOC au repos. Ces données ont été acquises en mesurant les débits respiratoires et la pression œsophagienne. Une étude sur banc a évalué les composantes résistives du masque à gaz C4 (Airboss Defense) et de 8 différents cartouches filtrantes. Chez les sujets sains, tous les indices d’effort respiratoires ont été significativement augmentés (WOB; PTP; Swing Pes) au repos et à l’effort. Quant aux patients, les augmentations des indices respiratoires ont été modérées au repos. La cartouche filtrante semble expliquer en partie ces effets et nous avons constaté que les résistances de cet élément du masque varient en fonction des modèles. Nos conclusions se destinent à optimiser de nouveaux masques pour limiter le «stress respiratoire» de ces dispositifs. / We conducted a research program on the impact of wearing a gas mask on respiratory effort and gas exchanges in healthy subjects at rest and during exercise and in COPD patients at rest. These data were acquired by measuring respiratory flow and esophageal pressure. A bench study evaluated the resistive components of the C4 gas mask (Airboss Defense) and of 8 different canisters. In healthy subjects, all indexes of respiratory effort (WOB; PTP; Swing Pes) were increased with mask at rest and during exercise. In COPD patients, the increases in respiratory index of effort were moderate. The canister of the mask seems to explain part of these effects and we found that resistances of this element of the mask vary according to the tested models. Our conclusions aimed at optimizing new masks to limit the «respiratory stress» of these devices.