Les développements continus en micro-spectroscopie vibrationnelle IR et en analyse numérique de données multidimensionnelles ont permis récemment l'émergence de l'histologie spectrale. A l'échelle tissulaire et sur une base biomoléculaire, cette nouvelle approche représente un outil prometteur pour une meilleure analyse et caractérisation de différents états physiopathologiques, et potentiellement une aide au diagnostic clinique. Dans ce travail, en utilisant un modèle tissulaire de côlon normal chez la Souris et chez l’Homme, nous avons apporté des améliorations à la chaîne de traitements des données afin d'automatiser et d'optimiser cette histologie spectrale.En effet, dans un premier temps, le développement d’une double application hiérarchique d'indices de validité a permis de déterminer le nombre optimal de classes nécessaire à une caractérisation complète des structures histologiques. Dans un second temps, cette méthode a été généralisée à l'échelle interindividuelle par couplage d'un prétraitement par EMSC (Extended Multiplicative Signal Correction) et d'une classification non-supervisée k-Means; ce couplage étant appliqué conjointement à toutes les images spectrales IR. Enfin, compte tenu de l'essor des métaheuristiques et de leur capacité à résoudre des problèmes complexes d'optimisation numérique, nous avons transposé un algorithme mémétique aux données spectrales IR. Ce nouvel algorithme se compose d'un algorithme génétique et d'un raffinement par classification non-supervisée k-Means. Comparé aux méthodes classiques de clustering, cet algorithme mémétique appliqué aux images spectrales IR, a permis de réaliser une classification non-supervisée optimale et indépendante de l'initialisation. / Recent developments in IR vibrational microspectroscopy and numerical multidimensional analysis have led to the emergence of spectral histology. At the tissue level, this new approach represents an attractive tool for a better analysis and characterization of pathophysiological states and for diagnostic challenges. Here, using normal murine and human colon tissues, data processing steps have been improved for automating and optimizing this spectral histology. First, the development of a hierarchical double application of validity indices permitted to determine the optimal number of clusters that correctly identified the different colon histological components. Second, this method has been improved to perform spectral histology at the inter-individual level. For this, EMSC (Extended Multiplicative Signal Correction) preprocessing has been successfully combined to k-Means clustering. Finally, given the ability of metaheuristics to solve complex optimization problems, a memetic algorithm has been developed for IR spectral data clustering. This algorithm is composed of a genetic algorithm and a k-Means clustering refinement. Compared with conventional clustering methods, our memetic algorithm allowed to generate an optimal and initialization-independent clustering.

Chain of custody in the forest sector is very dependent on effectively tracking products though the supply chain and manufacturing processes, including sawmilling, drying, planing, and pulp processes. The effectiveness of a tracking system is largely influenced by the characteristics of the process it works within, the nature of the tracking system being used, and increasingly by the penetration of technologically advanced material tracking methods into on-the-ground CoC practices. A variety of CoC systems that exist in the global marketplace accommodate the use of advanced materials tracking systems as a tool for their their implementation. These advances not only offer the potential to reinforce the traceability of products in inventory, but also promote maintenance of their certified status between the various organizations that exist along the wood product supply chain, and ultimately to the end consumer. In the past, a number of different product tracking methods have been used, all of which suffer certain shortcomings in the challenging environment of the forest industry, and the extremely complex nature of Chain of Custody tracking. This work explores the development of a novel material tracking method using the innate IR signatures of polymeric compounds, varied by compound and concentration to develop millions of potential combinations, and consequently millions of unique identities. The combined variation of multiple IR peak frequencies and magnitudes provide the conceptual basis of a chemical barcode system, named "Chemi-Code", to be explored. To prove the validity of this concept, a series of polymers were assayed for suitability in such a system by tracking their IR response stability in the presence of solar UV radiation and over time. As well, the feasibility of varying polymer concentration, and subsequently identification of concentrations by DRIFT spectroscopy was explored by constructing response curves between polymer concentration and peak absorbance, and assessing associated error. Seven polymers were identified and assessed. Only two of these polymers were found to be sufficiently stable for use in the context of the forest industry, and of those two, only one behaved in a manner that would allow peak absorbance to be used as an identifiable chemical variable. Although only one of the seven polymers was suitable for use in the "Chemi-Code" system, the study did demonstrate the validity of the concept by showing that polymers can be exploited for use in such a system. / Forestry, Faculty of / Graduate

In this investigation a number of post-genomic technologies have be applied to study the dermatological disorders of psoriasis and keloid disease. In spite of considerable research focus on these diseases the pathogenesis remains unclear and currently no cure is available however, both diseases are manageable by drug intervention. It is common place that patients who are suffering from skin disorders are diagnosed and the extent of the disease assessed by a dermatologist which may be subjective due to human error. The availability and application of methods to screen patients and quantify the level of disease or response to treatment has obvious benefits in disease management. The work has incorporated a two-pronged approach combining the spectroscopic analysis of excised tissue samples and the phenotypic profiling of a rapidly proliferating cell line in response to drug intervention. The initial analysis of psoriatic skin samples by MALDI-MS provided poor results which remain relatively unexplained; however similar problems have been observed by other research groups. In a complementary approach the HaCaT cell line was exposed to increasing concentrations of three anti-psoriatic drugs namely dithranol, methotrexate and ciclosporin and the cells profiled using both metabolomic and proteomic methods. A number of metabolic pathways were highlighted including glycolysis and the TCA cycle. This has resulted in a selection of potential biomarkers which could be investigated in further work. In a small follow on study a collection of plasma samples from patients undergoing methotrexate treatment were analysed. The level of patient metadata and the number of samples was relatively limiting however, a subset of metabolites were significantly altered between responders and non-responders and with further validation could be potential biomarkers of successful treatment. The analysis of excised keloid samples was conducted using FT-IR microspectroscopy where it was possible to successfully discriminate between keloid and normal tissue. The use of imaging FTIR illustrated the complex cellular composition within a keloid scar, with increased lipid, amide and phosphate levels being observed. These measurable variations could, in the future, be incorporated into surgical procedures to allow targeted excision ensuring all keloid areas are removed. Finally a SERS-based analysis was conducted to investigate the possibility of probing dynamic enzymatic processes. This was successful and with the use of varying reporter molecules could be a beneficial tool for the analysis of metabolic processes.This project has successfully used a number of bio-analytical techniques to investigate dermatological problems. While the ultimate goal would be the application of a single analytical technique to provide answers to biological questions, it has been found that a number of complimentary techniques and statistical data handling approaches can provide a valuable insight into the problems posed.

Prostate cancer is the second most common cause of cancer fatalities in males in the UK (2006) [1]. Therefore any advances in the diagnosis or screening for this form of cancer will yield significant benefits in the treatment of this disease. FT-IR has already been successfully used to assess and grade prostate biopsies by Gazi et al 2006 [2]. The collection of prostate biopsy is however a highly invasive procedure and as current screening methods are highly sensitive, but not very specific, large numbers of patients are referred for biopsy procedures that later come back as negative for prostate cancer [3]. Harvey et al used Raman spectroscopy to classify live cells of a number of prostate cell lines as a first step towards a possible urine screening protocol for prostate cancer [3]. Due to the complementary nature of Raman and FT-IR spectroscopy a similar live cell study should be possible using FT-IR and the combination of this technique with a high-throughput microfluidic device could lead to a useful screening tool for prostate cancer.The aim of the project was therefore to develop a microfluidic system which would enable higher through-put FT-IR analysis of live single cells in an aqueous carrier solution such as PBS or urine than has been previously possible. The design of the microfluidic device must also account for the fact that the materials used to produce the analysis chamber must be highly transparent to mid-IR radiation. The microfluidic device and peripheral systems must be easily transportable as it will be necessary to perform experiments in multiple locations. A design and manufacturing protocol for such a device has been developed.The development of a spectral contribution removal algorithm for the aqueous carrier fluid will also be necessary in order to allow the accurate interpretation of the IR data obtained. A least squares fitting based spectral subtraction algorithm was developed and validated for this purpose.Although it did not prove possible during the project to investigate the possible application of this device to a prostate cancer screening protocol other applications in cell line classification and drug cell interaction studies were performed and yielded encouraging results.

Enzyme design is a steadily growing field of computational chemistry, but its successes are limited by the current available knowledge and application of enzyme conformational dynamics. In this work a series of FTIR and 2D IR spectroscopic methods, for observing the conformational dynamics of an enzymatic active site and its surrounding residues, are characterized. The enzyme model system for these studies is the promiscuous ene-reductase from Pyrococcus horikoshii (PhENR) which is capable of binding substrates in multiple orientations. In one method, the spectral lineshape of an aryl-nitrile substrate-analog vibrational label is analyzed using a frequency fluctuation correlation function (FFCF) and compared to the lineshape of a corresponding aryl-azide label. This analysis revealed dynamic and electrostatic active site anisotropy which may influence substrate catalysis. The second method utilizes the intramolecular vibrations of the enzymatic cofactor, flavin mononucleotide (FMN), which is shown to be sensitive to electric field changes associated with substrate binding. The final method places a site-specific nonnatural amino acid containing an azide probe within the enzyme’s hydrophobic core. Additionally, a double-mutant cycle was identified via a common design program, the Rosetta Modeling Suite, and used to analyze the effects of mutation on enzyme dynamics. Altogether, these methods demonstrate the ability of 2D IR spectroscopy to observe enzyme conformational dynamics. Application of these methods to various other enzyme model systems should provide valuable insight for the improvement of future dynamic enzyme design protocols.

Cílem této diplomové práce bylo nastudovat problematiku klasifikačních systémů v nemocnicích, které sledují především hospodářské požadavky hospitalizace. Následně bylo navrženo a naprogramováno webové rozhraní v prostředí Caché Server Pages (CSP), které poskytuje přístup k databázi CLINICOM. Pomocí webového rozhraní, je možno provádět klasifikaci pacientů do tříd MDC (Major Diagnostic Category), archivaci dat, výpočet DRG a další vybrané úkony. Webovou aplikaci by mohli využívat technicko-hospodářští pracovníci nemocnic a klinik jako jednoduchou pomůcku při své práci, respektive jako učební pomůcka biomedicínských oborů pří výuce zdravotnických informačních a klasifikačních systémů.

Une pénurie de C4 s'est produite au cours des dernières années en partie à cause de la révolution naissante du gaz de schiste. Le faible coût et la grande abondance de cette source d'énergie nouvellement découverte sont rapidement devenues un facteur de changement pour l'industrie chimique. Bien que la concurrence avec cette source d'énergie non renouvelable ne soit pas une tâche facile, ses lacunes, telles qu'une production minimale en C3 et en C4, créent de nouvelles opportunités pour les molécules biosourcées. Dans ce travail, nous rapportons la conversion nouvellement découverte du (bio) isobutanol en n-butènes sur un catalyseur zéolitique. Ce catalyseur conduit à un rendement exceptionnel en butènes linéaires, ce qui est paradoxal car la FER est un catalyseur bien connu pour l'isomérisation squelettale des butènes. Bien que la recherche sur le dernier ait débuté il y a 30 ans, aucune conclusion définitive n'a encore été faite sur le mécanisme dominant : une réaction de monomoléculaire ou un mécanisme de "carbon pool". Acquérir des connaissances plus approfondies sur ce sujet est alors nécessaire pour expliquer la sélectivité inattendue en n-butène de cette réaction.Un criblage de catalyseurs a confirmé la sélectivité supérieure de FER pour les n-butènes (81%). Ceci est une augmentation significative par rapport aux catalyseurs de déshydratation couramment utilisés, alumine  (1%) et MFI (23%). Comme la sélectivité en n-butène pour les deux zéolites est significativement plus élevée que pour l’alumine un premier indice est que l'environnement confiné et cristallin de la porosité de la zéolite est crucial pour la sélectivité du n-butène. Cependant nous avons démontré que l'isobutanol est incapable d'accéder aux micropores de la structure FER; sa déshydratation doit donc se produire sur la surface externe de la zéolithe, en particulier sur ses sites acides de Brønsted.Nous avons déterminé l'identité du site actif responsable de l'isomérisation. En raison des similitudes avec la réaction d'isomérisation squelettale de du butène 1 à l'isobutène, un mécanisme de "carbon pool" a dû être envisagé. Cependant, aucun lien n'a été trouvé entre ces espèces et l’évolution de la sélectivité du n-butène, ne permettant pas de conclure quant à la participation de ces espèces carbonées comme sites actifs d'isomérisation. Par la suite, nous avons cherché à déterminer si les n-butènes sont formés directement ou via un mécanisme de type râteau dans lequel l'isobutène serait un intermédiaire. Nous avons établi que les constantes de vitesse pour l'isomérisation individuelle des butènes sont très inférieures à la constante de vitesse globale, excluant ainsi le mécanisme de type râteau. Par conséquent, le site actif d'isomérisation doit être identique ou situé à proximité du site actif de déshydratation pour éviter la désorption des espèces intermédiaires de surface sous forme d’isobutène. Nous avons ensuite démontré la nécessité d'une densité minimale d'acidité de Brønsted externe pour une sélectivité élevée en n-butène, également valable pour différentes zéolites, (10 MR ZSM-5 et ZSM-22 et 8 MR Erionite). Ces résultats nous ont ainsi amener à conclure que la sélectivité exceptionnelle des zéolithes de type FER en n-butène est le résultat de leur forte densité de sites acide de Brønsted externes. Cependant, une trop forte densité a un effet indésirable en terme de désactivation.L’ensemble de ces résultats nous permet de conclure que le catalyseur idéal doit présenter une densité de site d'acide de Brønsted externe très spécifique, suffisamment importante pour produire une sélectivité élevée en n-butène tout en évitant une désactivation excessive. Alors que les sites acides de Brønsted internes ne semblent pas jouer le rôle de site actifs pour la transformation de l'isobutanol en butènes linéaires, il n’est pas exclus qu’elle ait un impact sur le taux de formation des espèces carbonées. / A C4-shortage has been arising during the recent years partly as a result of the nascent shale gas revolution. The low cost and vast abundance of this newly discovered energy source rapidly became a game changer for the chemical industry. Although competing with this non-renewable energy source is not an easy task, its shortcomings such as a minimal C3 and C4 production, are creating new opportunities for bio-based molecules. In this work, we report on the newly discovered conversion of (bio)isobutanol to n-butenes over a zeolitic (ferrierite, FER structure) catalyst. It displays an exceptional yield in linear butenes. However, this is remarkable since FER is a well-known catalyst for the skeletal isomerisation of n- towards iso-butene. Although research on the n- to iso-butene skeletal isomerisation started 30 years ago, no firm conclusion has yet been made on the prevailing mechanism: a monomolecular reaction or a carbon pool mechanism. Acquiring deeper knowledge on this topic is required to explain the unexpected n-butene selectivity of this reaction. A screening of catalysts confirmed the superior selectivity of FER for n-butenes (~ 80 %). This is a significant increase compared to the commonly used dehydration catalysts, γ-alumina (~ 1 %) and MFI (~ 25 %). Since n-butene selectivity for both zeolites is significantly higher, a first hint is found that the confined and crystalline zeolite environment should be crucial for n-butene selectivity. However, we have demonstrated that isobutanol is unable to access the micropores of the FER structure; its dehydration must therefore occur on the external surface, in particular its acidic Brønsted sites.We have determined the identity of the active site responsible for isomerisation. Due to similarities with the 1- to isobutene skeletal isomerisation reaction, a carbon pool mechanism had to be considered. However, no correlation was found, hence allowing to exclude the carbonaceous species as possible isomerisation active sites. Next, we have investigated whether the n-butenes are formed directly or via a rake-type mechanism where isobutene is an intermediate. We have established that the rate constants for the individual butene isomerisation are lower than the over-all rate constant of iso-butanol transformation to n-butenes, thus excluding the rake-type mechanism. Hence, either dehydration-isomerisation occur in the same site or isomerisation occurs on a site located in the immediate neighbouring of the dehydration site in order to avoid the desorption of intermediate species as isobutene. With this respect, we have subsequently demonstrated the requirement of a minimal external Brønsted acid density for a high n-butene selectivity. Strikingly, the latter held also for different zeolites, (10 MR ZSM-5 and ZSM-22 and 8 MR Erionite) which suggests a general trend relating the n-butene selectivity to the density of external Brønsted acid sites with the existence of a “critical threshold” of external BAS density beneath which the selectivity towards n-butene is severely degraded. We concluded that the exceptional n-butene selectivity of FER is a result of its high external Brønsted acid density. However, an adverse effect was observed on isobutanol conversion as a high density of external sites is also linked to a faster deactivation. Additionally, we have determined that the selectivity for a secondary set of products, octenes, decreased with increasing the external Brønsted sites density; isolated external Brønsted acid sites should therefore function as active sites for octene formation.Finally, we conclude that the ideal catalyst should contain a very specific external Brønsted acid site density, sufficiently dense to produce high n-butene selectivity while avoiding excessive deactivation. While internal Brønsted acidity does not function as active sites for the one-step transformation, it is not excluded that they can impact the rate of carbonaceous species formation

Thesis advisor: Matthias M. Waegele / Studying the visible light-driven photoredox catalysis coupled with transition-metal complexes is of overriding importance in the development of synthetic strategy. Comparing to conventional thermal catalysis, reactions catalyzed and/ or initiated by photon energy are not only attractive for establishing a more sustainable system, but also for their unique reactivity that has previously been inaccessible. However, one issue draws our attention is that such photoredox catalytic schemes often suffer from a limited substrate scope. To develop more efficient and effective synthetic strategies applicable to broader range of substrates, it is of our interest to construct an functional and reliable instrument to identify the critical mechanistic steps that lead to low product yield. To this end, we designed a time-resolved visible-pump/ infrared-probe spectroscopic measurement technique to monitor reaction dynamics in-situ. Using our transmission infrared setup, we effectively demonstrated in-situ photoexcitation and decay process of Tris(2,2′-bipyridyl)dichlororuthenium(II) hexahydrate in deuterated acetonitrile. In addition, to optimize signal resolution, an electronic filter was installed in one of the data-collecting channels to allow for concurrent AC-coupled and DC-coupled signal recording. A series of chopper wheel experiments was conducted to assure the functionality of the system and reliability of obtained data. / Thesis (MS) — Boston College, 2020. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Quantum approaches to International Relations theory have proliferated rapidly in recent years, challenging the field to come to terms with the influence of physics at its philosophical foundations. These new theoretical perspectives draw on quantum physics, quantum social theory, and prior quantum interventions in other disciplines of social science. But unlike prior debates around the desirability of "adding" science to the study of world politics (Morgenthau 1946; Kindleberger 1958; Bull 1966), the call of quantum IR theory is one for transformation (Barad 2007; Fierke 2022; Murphy 2021c; O’Brien 2021; Zanotti 2018). In this dissertation, I explore the stakes and scope of this quantum transformation to better understand the process of quantizing inquiry into International Relations. The first chapter sets out the metatheoretical stakes of quantizing IR by engaging with critical responses to prior works of quantum. Situating quantum approaches in the broader intellectual history of the field, I argue that understanding the "cost" of quantizing IR cannot take the form of a cost/benefit logic, instead recognizing the opportunity cost of remaining Newtonian. The second chapter turns to the development of quantum mechanics within physics to demonstrate the relatability of key concepts for social inquiry, despite the vernacular divide. The third chapter turns to methodology, discussing the philosophical sources supporting 'quantizing through translation,' drawing on both the quantum social theory of Karen Barad and broader influences including Walter Benjamin, actor-network theory, and Donna Haraway. The next trio of chapters serve to demonstrate the breadth of quantum's utility across the discipline through a set of conceptual case studies related to major subfields of IR. The fourth chapter speaks to debates in peace and security studies, and provides a quantized account of violence through a diffractive reading of Johan Galtung's "Violence, Peace, and Peace Research." The fifth chapter turns to foreign policy and strategic studies, arguing that the non-traditional diplomatic strategy of "track two diplomacy" abides a quantum game-theoretic logic, and that this can only be fully appreciated by interrogating its quantum-like assumptions. Chapter six then addresses international political economy through an attempt to redefine "the market" in quantum terms. Recognizing the stakes and scope of quantum IR explored through the dissertation, the conclusion reaffirms the case for quantum to be understood as transformation rather than addition, and sets out future directions for research in quantum IR.

Previously, we demonstrated that exposure to morphine during gestation increases hypothalamic norepinephrine (NE) content and turnover rate in adult male rats and decreases these measures in adult females. To investigate the basis of these alterations, the present study examined the effects of prenatal exposure to morphine on tyrosine hydroxylase immunoreactivity (TH-IR) in the brains of adult male and female progeny. In male rats, prenatal morphine exposure significantly increased the density of TH-IR in cells and fibers in the caudal paraventricular nucleus of the hypothalamus (PVN) and locus coeruleus (LC), but had no effects in the lateral hypothalamus (LH). In female rats that were ovariectomized (OVX), prenatal morphine exposure significantly decreased the density of TH-IR in cells and fibers in the LC. Interestingly, an injection of estrogen in OVX control females reduced the mean optical density of TH-IR in the LC, but it was ineffective in drug-exposed females in the same brain region. Estrogen injections also reduced the mean optical density of TH-IR in the LH but not in the PVN of females, regardless of prenatal drug exposure. Thus, the present study suggests that prenatal morphine exposure induces long-term, sex-specific alterations in TH-IR in the PVN and LC of adult progeny.