The development of Infrared Spectrometry as a High Performance Liquid Chromatographic detector is presented. Early work with both a conventional dispersive instrument and a Fourier Transform Infrared (FTIR) Spectrometer is presented coupled via a flow cell to size exclusion chromatography. These were used for the analysis of the non-volatile components produced in the liquefaction of coal. Additional work is presented for the coupling of FTIR to analytical scale normal phase chromatography via a flow cell technique. Analysis of both model mixtures as well as a complex process solvent used in the liquefaction process is discussed. Use of deuterochloroform as an improved IR transparent solvent is demonstrated. Work with microbore (1 mm i.d.) columns coupled with on-line flow cell detection is presented. Modification of the flow cell design for microbore compatability is shown as well as the benefits of microbore columns for fiow cell FTIR. Detection limits as amount injected for both analytical and microbore scale HPLC-FTIR are shown. / Ph. D.

Recently, there has been an expanding interest in the packaging industry concerning thermoplastic film laminations. These types of materials provide a packaging material that can be tailored to the consumers' needs. An understanding of the bonding mechanisms between plastics might prove useful in the improvement or development of film lamination. Infrared spectrometry has been used to study the structures of plastics in the 3.0 - 100 micron region. It was decided that a study of infrared spectrometry in the 1.0 - 3.5 region could provide a tool for studying bonding mechanisms between thermoplastic material. The results of the qualitative study of the structural groups of nine polymers showed that the spectral identification in the 1.0 - 3.5 micron region was possible. These results could provide a means of determining the groups involved in bonding mechanisms. Beer's law has normally been applied to the quantitative analysis of homogeneous gaseous and liquid mixtures. A study shewed that Beer's law was applicable, with limited quantitative accuracy, to solid thermoplastic mixtures. The results indicate that a base-line analysis technique, based on Beer's law can be used to determine concentration gradients. A study of such concentration gradients across the interface of a lamination could indicate the types of bending mechanisms. All samples were analyzed in the form of films with a Beckman DK-2 ratio recording spectrophotometer. An improved method for the preparation of film samples was developed. Thermoplastic resins were pressed between 10 mil Mylar and Teflon FEP films on a Carver laboratory press. / Master of Science

Unwanted and distressing visual imagery is a persistent and emotionally taxing symptom characteristic of several mental illnesses, including depression, schizophrenia, and posttraumatic stress disorder. Intrusive imagery symptoms have been linked to maladaptive memory formation, abnormal visual cortical activity during viewing, gaze pattern deficits, and trait characteristics of mental imagery. Emotional valence of visual stimuli has been shown to alter perceptual processes that influence the direction of attention to visual information, which may result in enhanced attention to suboptimal and generalizable visual properties. This study tested the hypothesis that aberrant gaze patterns to central and peripheral image regions influence the formation of decontextualized visual details which may facilitate involuntary and emotionally negative mental imagery experiences following a stressful or traumatic event. Gaze patterns and hemodynamic response from occipital cortical locations were recorded while healthy participants (N = 39) viewed and imagined scenes with negative or neutral emotional valence. Self-report behavioral assessments of baseline vividness of visual imagery and various cognitive factors were combined with these physiological measures to investigate the potential relationship between visual perception and mental recreation of negative scenes. Results revealed significant effects of task and valence conditions on specific fixation measures and hemodynamic response patterns in ventral visual areas, which interacted with cognitive factors such as imagery vividness and familiarity. Findings further suggest that behaviors observed during mental imagery reveal processes related to representational formation over and above perceptual performance and may be applied to the study of disorders such as PTSD. / Ph. D.

The Anthropocene epoch in which we are currently living, also known as the Holocene, has brought about unprecedented losses in planet Earth’s biodiversity. Numerous extirpations of floral and faunal species have been influenced by human encroachment and more specifically, the exploitation of such species and the respective habitats in which they reside. It is this notion that has propelled many scientists to take up intellectual arms in an effort to protect these invaluable resources. The purpose of this research was to develop technologies to measure and evaluate various variables that influence animal physiology, specifically in amphibians who represent the most threatened class of all animal taxa. Species-specific knowledge including life history and an understanding of evolutionary traits are often needed to effectively guide the management decisions surrounding any given animal population. Specific objectives of this project were to develop non-invasive methods, such as hormone monitoring, machine learning-aided ultrasonography, and near-infrared spectroscopy (NIRS), to assess vital physiological traits, such as biological sex, reproductive status, and chytrid fungus pathogen detection in threatened amphibian species. The novel technologies developed and applied in amphibians here may provide insights for addressing conservation related questions in other animal as well as plant species. Additionally, automation of physiological monitoring techniques through the use of machine learning methods reduces barrier to entry and enables these technologies to be operated by a larger practitioner base. This research also serves to advance methods surrounding chemometric analyses as it pertains to the discipline of wildlife spectroscopy, where large multivariate datasets require data manipulation strategies to produce robust prediction models for the physiological trait of interest for qualitative or quantitative assessment. To that end, a multi-model framework is provided for optimizing predictive outcomes to address questions relating to wildlife management and conservation initiatives.

Yes / The aim of this work was to investigate the possibility of covalent cross-linker-free, polyelectrolyte complex formation at the nanoscale between alginic acid (as sodium alginate, ALG) and protamine (PROT). Optimisation of the self-assembly conditions was performed by varying the type of polymer used, pH of component solutions, mass mixing ratio of the components and the speed and order of component addition on the properties of complexes. Homogenous particles with nanometric sizes resulted when an aqueous dispersion of ALG was rapidly mixed with a solution of PROT. The polyelectrolyte complex between ALG and PROT was confirmed by infrared spectroscopy. To facilitate incorporation of drugs soluble at low pH, pH of ALG dispersion was decreased to 2; however, no nanoparticles (NPs) were formed upon complexation with PROT. Adjusting pH of PROT solution to 3 resulted in the formation of cationic or anionic NPs with a size range 70–300 nm. Colloidal stability of selected alginic acid low/PROT formulations was determined upon storage at room temperature and in liquid media at various pH. Physical stability of NPs correlated with the initial surface charge of particles and was time- and pH-dependent. Generally, better stability was observed for anionic NPs stored as native dispersions and in liquids covering a range of pH. / This study was funded by Merrion Pharmaceuticals Ireland. This work was also supported by the Synthesis and Solid State Pharmaceutical Centre funded by the Science Foundation Ireland under grant number 12/RC/2275.

This thesis is a study of the near infra-red absorption spectrum of ethylidene fluoride.

This work discusses the development of a compact Tunable Diode Laser Absorption Spectrometer (TDLAS) for gas phase mixing ratio and temperature measurements of condensible vapors, in particular H2O and D2O, in supersonic flows. Through extensive pressure trace measurements and mass balances on the incoming species, the expected mixing ratio and temperature profiles of the condensible species along the supersonic nozzle have been characterized. Using a Tunable Diode Infrared laser operating in the 8 microns region, the possibility of nonintrusively measuring the gas phase mixing ratio and the temperature (even simultaneously) in a supersonic nozzle is demonstrated. The acquired spectroscopic data and the pressure trace measurements are compared and the results suggest the possibility to improve the instrument set-up and to improve the quality of the measurements. Also, the interpretation of our initial experimental results and the comparison with the pressure traces measurements suggest reasons to further investigate the condensation behavior of D2O and H2O.

In this thesis, I have investigated gas phase infrared spectroscopy of environmentally as well as astrophysical important large organic molecules such as naphthalene, methy-lated naphthalene, fluorine, methyalted fluorine etc. which are commonly known as polycyclic aromatic hydrocarbons (PAHs). Depending upon the molecular weight these organic molecules can exist both in gaseous as well as in the particulate state at room temperature hence they are the major environmental pollutants. They are also responsible for the unidentified infrared emission bands in the interstellar medium. Chapter 1 provides a brief introduction to my thesis work. A detailed literature survey on the importance, abundance of the PAHs in the environment as well as various spectroscopic techniques useful for identifying the PAHs has been done. Since the objective of my thesis work is to assign the observed fundamental infrared bands of large organic molecules with the help of high level quantum mechanical calculations, a brief introduction to the various high level quantum mechanical techniques that I have used in assigning the bands have been described in this chapter. In Chapter 2 I have presented the experimental and the theoretical methodologies in details. The chapter begins with a detailed description of the experimental procedure used for recording the infrared spectrum of these molecules followed by the theoretical methodologies used for the assignment of the observed infrared bands as well as for identifying the Fermi resonances. In Chapters 3 and 4, of this thesis I have recorded infrared spectrum of 1-and 2-methylnaphthalene (1-and 2-MN), fluorine (FL), 1-methylfluorene (1-MFL) and 1,8-dimethylfluorene (1,8-DMF) in the gas phase. The observed bands were assigned with the help of scaled harmonic frequency, scaled quantum mechanical harmonic force field (SQMFF) and enharmonic frequency calculations. The first two methods are based on the harmonic approximation, whereas the enharmonic frequency calculation is based on the standard second order perturbation theory. All these calculations gave me a partial fit to the fundamental bands in both aromatic and aliphatic C-H stretching as well as in the non C-H stretching region. At the end of both the chapters an error analysis in fitting the spectrum from all the three different calculations have been presented. Evidently the non linear least square fitting method employed in SQMFF calculation gives much better agreement between the experiment and theory than the other two methods. It has been observed in the experimental spectrum of methylated naphthalene that the band structure near the C-H stretch around 3000 cm−1 is very complicated and many bands and shoulders remain unassigned by the methods described in Chapters 3 and 4. Fermi resonance is one of the potential reason for the complicated band structure in this region. In Chapter 5, I have taken naphthalene and have investigated the Fermi resonance around the C-H stretching region using an effective vibrational hamiltonian (EVH) approach. In this method I have constructed an EVH consisting of 8 C-H stretches and 8 H-C-C in-plane bend overtones and 28 H-C-C in-plane bend combination modes as the basis. Both type 1 (stretch overtone) and type 2 (stretch combination) Fermi resonances were investigated. Calculated frequencies belonging to B1u and B2u irreducible representation were compared with the observed bands. Many bands and shoulders have been assigned as the overtone and combination modes of low frequency H-C-C bend motion obtained from the EVH approach. How-ever some bands remain unassigned in this method. This is perhaps due to the neglect of the carbon framework motion in the construction of the EVH. To improve upon the results obtained from the EVH formalism I included the carbon frame degrees of freedom and have carried out a full variation treatment in curvilinear coordinates. I have considered the 8 C-H stretches and 8 H-C-C in-plane bends of naphthalene as local mode oscillators and 17 coordinates belonging to the carbon framework motion as curvilinear normal mode oscillators. A quartic hamiltonian in a mixed local mode -normal mode basis was constructed including up to three body terms in both kinetic and potential energy part. The hamiltonian was subsequently recast into the ladder operator form and diagonal zed in a symmetry adapted basis with polyad constraints. Frequencies so obtained were compared to the experiment All these findings have been presented in Chapter 6 of this thesis. The concluding remark of the thesis and the future direction is presented in Chapter 7

Natural archives such as lake sediments allow us to assess contemporary ecosystem responses to climate and environmental changes in a long-term context beyond the few decades to at most few centuries covered by monitoring or historical data. To achieve a comprehensive view of the changes preserved in sediment records, multi-proxy studies – ideally in high resolution – are necessary. However, this combination of including a range of analyses and high resolution constrains the amount of material available for analyses and increases the analytical costs. Infrared spectroscopic methods are a cost-efficient alternative to conventional methods because they offer a) a simple sample pre-treatment, b) a rapid measurement time, c) the non- or minimal consumption of sample material, and d) the potential to extract quantitative and qualitative information about organic and inorganic sediment components from a single measurement. The main objective of this doctoral thesis was twofold. The first part was to further explore the potential of Fourier transform infrared (FTIR) and visible-near infrared (VNIR) spectroscopy in paleolimnological studies as a) an alternative tool to conventional methods for quantifying biogenic silica (bSi) – a common proxy of paleoproductivity in lakes – in sediments and b) as a tool to infer past lake-water total organic carbon (TOC) levels from sediments. In a methodological study, I developed an independent application of FTIR spectroscopy and PLS modeling for determining bSi in sediments by using synthetic sediment mixtures with known bSi content. In contrast to previous models, this model is independent from conventional wet-chemical techniques, which had thus far been used as the calibration reference, and their inherent measurement uncertainties. The second part of the research was to apply these techniques as part of three multi-proxy studies aiming to a) improve our understanding of long-term element cycling in boreal and arctic landscapes in response to climatic and environmental changes, and b) to assess ongoing changes, particularly in lake-water TOC, on a centennial to millennial time scale. In the first applied study, high-resolution FTIR measurements of the 318-m long sediment record of Lake El’gygytgyn provided a detailed insight into long-term climate variability in the Siberian Arctic over the past 3.6 million years. Highest bSi accumulation occurred during the warm middle Pliocene (3.6-3.3 Ma), followed by a gradual but variable decline, which reflects the first onset of glacial periods and then the finally full establishment of glacial–interglacial cycles during the Quaternary. The second applied study investigated the sediment record of Torneträsk in subarctic northern Sweden also in relation to climate change, but only over the recent post-glacial period (~10 ka). By comparing responses to past climatic and environmental forcings that were recorded in this large-lake system with those recorded in small lakes from its catchment, I determined the significance and magnitude of larger-scale changes across the study region. Three different types of response were identified over the Holocene: i) a gradual response to the early landscape development following deglaciation (~10000-5300 cal yr BP); ii) an abrupt but delayed response following climate cooling during the late Holocene, which occurred c. 1300 cal yr BP – about 1000-2000 years later than in smaller lakes from the area; and iii) an immediate response to the ongoing climate change during the past century. The rapid, recent response in a previously rather insensitive lake-ecosystem emphasizes the unprecedented scale of ongoing climate change in northern Fennoscandia. In the third applied study, VNIR-inferred lake-water TOC concentrations from lakes across central Sweden showed that the ongoing, observed increase in surface water TOC in this region was in fact preceded by a long-term decline beginning already AD 1450-1600. These dynamics coincided with early human land use activities in the form of widespread summer forest grazing and farming that ceased over the past century. The results of this study show the strong impact of past human activities on past as well as ongoing TOC levels in surface waters, which has thus far been underestimated. The research in this thesis demonstrates that infrared spectroscopic methods can be an essential component in high-resolution, multi-proxy studies of past environmental and climate changes.

Ratoon stunting disease (RSD), caused by Leifsonia xyli subsp. xyli (Lxx) can cause substantial impact on biomass production in all sugarcane producing countries. Few management options exist for controlling the disease, and they are all centered on measures of hygiene and sanitation. These measures are not efficient in eliminating the bacteria and can damage bud germination. Phenotypic selection would be the best management practice. However, selection based on Lxx-restrictive multiplication is costly, time-consuming, and destructive. One potentially useful approach for identifying resistant genotypes is Fourier-transform infrared (FT-IR) spectroscopy. In this study, we demonstrate that by using qPCR to quantify bacterial titers and to determine the resistance levels of nineteen commercial varieties inoculated with Lxx and FT-IR spectroscopy we could identify resistant and susceptible genotypes based on specific functional groups. Using a non-linear machine learning techniques (SVM) and a linear partial least square regression (PLSR) we distinguished between resistant and susceptible sugarcane genotypes and predict bacteria concentration using spectral data and Lxx titer quantification. Our Results suggest that resistance may be associated with variation in chemistry. The resistant mechanisms involved against RSD are probably associated to polyamines regulation and aromatic rings compounds accumulation. The results demonstrated that both approaches, SVM and PLSR, are capable of providing accurate estimates of sugarcane resistance to Lxx and can be applied to screen resistant sugarcane in breeding programs. / O raquitismo da soqueira da cana (RS), causada pela bactéria Leifsonia xyli subsp. xyl (Lxx) pode produzir um impacto substancial negativo na produção de biomassa em todos os países produtores de cana-de-açúcar. Existem poucas opções de manejo para o controle da doença e todas são centradas em medidas de sanitização. Entretanto, este manejo não é eficiente, uma vez que não se elimina por completo a bactéria. Diante do exposto, uma alternativa interessante é a identificação e seleção de genótipos resistentes à doença. No entanto, por se tratar de um patossistema complexo, a seleção por métodos tradicionais não é viável em um programa de melhoramento. Uma nova abordagem é a identificação de genótipos resistentes por meio de técnica de espectroscopia de infravermelho com transformada de Fourier (FT-IR). Este estudo demonstrou que por meio da técnica de reação em cadeia da polimerase em tempo real (qPCR) foi possível quantificar os títulos bacterianos e determinar os níveis de resistência de dezenove variedades comerciais inoculadas com Lxx. Além disso, por meio da técnica de FT-IR foi possível distinguir genótipos resistentes de suscetíveis baseados em grupos químicos específicos. Por meio de um algoritmo não linear, support vector machine (SVM) e uma regressão linear, partial least square regression (PLSR), foi possível distinguir genótipos de cana-de-açúcar resistentes e suscetíveis à doença além de predizer a concentração de Lxx nos genótipos por meio de dados espectrais e de título bacteriano. Nossos resultados demonstram que a resistência a esta doença está associada às variações bioquímicas e que os mecanismos de resistência envolvidos podem estar associados à regulação de poliaminas e ao acúmulo de compostos que tenha como principal grupo funcional anel aromático. Os resultados evidenciaram que ambas as abordagens, SVM e PLSR, foram capazes de fornecer estimativas precisas da resistência da cana-de-açúcar à RS e que a técnica FT-IR pode ser utilizada em programas de melhoramento na seleção de genótipos de cana-de-açúcar resistentes ao RS.