Biomedical optics is a rapidly expanding field of research focusing on the development of methods to detect, diagnose, and treat disease using light. While there are a myriad of optical systems that have been developed for biological tissue imaging, optical diagnostics, and optical therapeutics, all of these methods suffer severely limited penetration depths due to attenuation of light by tissue constituent chromophores, including cells, water, blood, and protein structures. Tissue optical clearing is a recent area of study within biomedical optics and photonics, where chemical agents have been used to alter tissue optical properties, reducing optical absorption and scattering and enabling light delivery to and collection from deeper tissue regions. However, there are concerns as to the safety and efficacy of these chemical clearing agents in vivo, especially in the skin, where the projective barrier function of the stratum corneum must be removed. Mechanical optical clearing is a recently developed technology which utilizes mechanical loading to reversibly modify light transport through soft tissues, and much of the work published on this technique has focused on applications in skin tissue. This clearing technique enables deeper light delivery into soft tissues but does not require use of exogenous chemicals, nor does it compromise the skin barrier function. While this clearing effect is thought to be resultant from interstitial water and blood transport, the underlying mechanism has not been concretely identified nor characterized. The hypothesis of this body of work was that interstitial transport of tissue chromophores (e.g. water and blood) causes intrinsic optical property changes, reduces tissue optical absorption and scattering, and improves light delivery in diagnostic applications. To test this hypothesis, we first developed a mathematical framework to simulate mechanical optical clearing, using both mechanical finite element models and optical Monte Carlo simulations. By directly simulating interstitial water transport in response to loading, data from mechanical simulations was combined with optical Monte Carlo simulations, which enabled prediction of light transmission measurements made during mechanical indentation experiments. We also investigated changes in optical properties during mechanical indentation using diffuse reflectance spectroscopy. These studies used controlled flat indentation by a fiberoptic probe to dynamically measure intrinsic optical properties as they changed over time. Finally, we apply mechanical optical clearing principles to functional near-infrared spectroscopy for neuroimaging. By building a prototypical mechanical optical clearing device for measuring cerebral hemodynamics, we demonstrated that mechanical optical clearing devices modify measured cerebral hemodynamic signals in human subjects, improving signal quality. / Ph. D.

Thesis (MScEng (Process Engineering))--University of Stellenbosch, 2010. / Thesis submitted in partial fulfilment of the requirements for the degree of MASTER OF SCIENCE IN ENGINEERING (MINERAL PROCESSING) in the Department of Processing Engineering at the University of Stellenbosch / ENGLISH ABSTRACT: This work evaluates the use of inverse least squares (ILS) and classical least squares (CLS) models for calibration of a diffuse reflectance spectrophotometer for on-line monitoring of the aqueous phase in a flotation cells. Both models use a Beer's law for the quantification of the metals. The formulated statistical models are compared to a proprietary Blue Cube model in terms of prediction ability to determine the potential applicability of the models. A diffuse reflectance spectrophotometry was used for simultaneous analysis of copper (Cu), cobalt (Co) and zinc (Zn) in the solutions. The laboratory set-up of Blue Cube instrument was used for the experimental analysis. The concentrations and matrix compositions of the samples are simulated according to Skorpion zinc mine plant conditions. The calibration samples were prepared using a simplex-centroid mixture design with the triplicates of the centroid run. The unknown or test samples were prepared randomly within the same concentration of the calibration samples. The effects of temperature and nickel concentration on absorption of the metals were evaluated in the following range, 20 - 80 °C and 125 - 400 ppm, respectively. The statistical models (ILS and CLS) were calibrated from visible and near infrared (VNIR) spectra data of the calibration samples. A modified Beer's method was used as a preprocessing technique to convert the raw data into absorbance values. The manual wavelength selection procedure was used to select the wavelengths to be used in both models. The quality of the models was evaluated based on Rª and % root mean squared error (RMSE) values with 0.90 and 10% used as the guideline for the respective statistical parameters. Both ILS and CLS models showed good results for all three metals (Cu, Co and Zn) during their calibration steps. It was further shown that both models give worse predictions for Zn as compared to other metals due to its low relative intensity in the mixture. The derivative orders of absorbance spectra that were used to enhance the prediction results of Zn had no positive effect but they rather lowered accuracy of predictions. An increase in temperature was found to increase the intensities of the absorption spectra of all the metals while an increase in nickel concentration decreases the prediction ability of model. The developed statistical models were compared to a Blue Cube model in terms of prediction ability using analysis of variance (ANOVA) test. The ANOVA results revealed that there is no statistical difference between the developed models and Blue Cube model since the F-values for all the metals were below the critical F-value. Furthermore, the partial least squares (PLS) model shows an increased accuracy results for prediction of zinc metal as compared to both the ILS and CLS models. Finally, good comparisons of the statistical models results with atomic absorption spectroscopy (AAS) analyses were establish for the unknown samples. The study demonstrates that chemometric models (ILS and CLS) developed here can be used for quantification of several metals in real hydrometallurgical solutions as samples were simulated according to a plant conditions. However, in order to have confidence in the results of the models, a factorial-mixture design must be used to study the effect of temperature and nickel concentration. Moreover the models must be further tested and validated on the real samples from a plant. / AFRIKAANSE OPSOMMING: Hierdie werkstuk evalueer die gebruik van inverse kleinste kwadraatmetodes (IKK) en klassieke kleinste kwadraatmetodes (KKK) vir die kalibrasie van 'n diffuse reflektansiespektrofotometer vir die aanlyn monitering van die waterige fase in flottasieselle. Beer se wet word vir die kwantifisering van metale vir albei modelle gebruik. Die omskrewe data-gebaseerde modelle is op grond van voorspellingsvermoë vergelyk met'n. Blue Cube model, sodat die moontlike toepaslikheid van hierdie modelle bepaal kan word. 'n Diffuse reflectantie spektrofotometrie is ingespan vir die gelyktydige analise van koper (Cu), kobalt (Co) en sink (Zn) in oplossing. Eksperimentele analises is met behulp van 'n laboratoriumopstelling met 'n Blue Cube instrument uitgevoer. Die konsentrasies en matriks-samestellings van monsters is gesimuleer om Skorpion sinkmyn aanlegkondisies na te boots. Kalibrasie monsters is voorberei volgens . simpleks-sentroïed mengselontwerp met drievoudige sentroïede lopies. Onbekende (toets) monsters is ewekansig voorberei binne dieselfde konsentrasie spesifikasies as die kalibrasie monsters. Die invloed van temperatuur en nikkelkonsenstrasie op die absorpsie van die metale is in die bestek van 20 - 80 °C en 125 - 400 dpm, onderskeidelik, bepaal. Die data-gebaseerde modelle (IKK en KKK) is met sigbare en naby infrarooi (SNIR) spektra data van die kalibrasie monsters gekalibreer. 'n Gewysigde Beer metode is vir data voorbereiding benut om rou data na absorbansie waardes om te skakel. Die handgolflengte-seleksieprosedure is vir beide modelle gebruik om die golflengtes te kies. Die kwaliteit van die modelle is op grond van Rª en % wortel gemiddelde kwadratiese fout (WGKF) geevalueer, met waardes van 0.90 en 10% (onderskeidelik) as riglyne vir hierdie statistiese parameters. Beide IKK en KKK modelle het vir hul kalibrasie stappe vir al drie metale (Cu, Co en Zn) goeie resultate getoon. Dit is verder getoon dat albei modelle die slegste voorspellings lewer vir Zn (vergeleke met die ander metale) as gevolg van Zn se lae relatiewe intensiteit in die mengsel. Afgeleide ordes van absorbansie spektra is gebruik om die Zn voorspellings te versterk, maar het geen positiewe effek gehad nie; inteendeel, voorspellingakkuraatheid is verlaag. ʼn Verhoging in temperatuur het die intensiteite van die absorpsie spektra van alle metale verhoog, terwyl ʼn verhoging in nikkelkonsentrasie die voorspellingakkuraatheid van die modelle verlaag het. Die ontwikkelde data-gebaseerde modelle is met ʼn Blue Cube model vergelyk in terme van voorspellingsvermoë met behulp van variansie-analise (ANOVA). Die ANOVA resultate toon dat daar geen statistiese verskil tussen die ontwikkelde modelle en die Blue Cube model is nie, aangesien die F-waardes vir al die metale onder die kritiese F-waarde is. Die gedeeltelike kleinste kwadraatmodel (GKK) toon verder verhoogde voorspellingakkuraat-heid vir sinkmetaal tenoor beide die IKK en KKK modelle. Ten slotte, goeie ooreenstemming van die data-gebaseerde modelresultate met atoomabsorpsie spektroskopie (AAS) analise is vir die onbekende monsters gevind. Hierdie werkstuk toon dat die chemometriese modelle (IKK en KKK) wat hier ontwikkel is, gebruik kan word vir die kwantifisering van verskeie metale in werklike hidrometallurgiese oplossings, aangesien monsters gesimuleer is volgens aanlegkondisies. Om egter verdere vertroue te hê in die modelresultate, sal ʼn faktoriaal-mengselontwerp toegepas moet word om die effek van temperatuur en nikkelkonsentrasie te ondersoek. Voorts moet die modelle verder getoets en gevalideer word op werklike monsters van ʼn aanleg.

Thesis (MSportSc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: There are a growing number of men and women world-wide who are suffering strokes due to poor lifestyle-related habits. While there is evidence of the differences in cerebral haemodynamics between stroke patients and both elderly and young healthy individuals, limited evidence has examined the effect of rehabilitation on cerebral haemodynamics. Furthermore, most studies have examined changes in cerebral haemodynamics during cognitive and functional tasks in isolation, with no literature published on them simultaneously. The primary aim of this study was to examine whether differences in cerebral haemodynamics exist between stroke patients and healthy elderly individuals while performing a simple and complex cognitive task. Thirty two men and women (age 75 ± 8 years) volunteered to participate in the study and were split into an experimental (n = 14) group consisting of stroke patients and a control (n = 18) group consisting of healthy individuals. Each participant was required to attend one testing session where measurements of oxyhaemoglobin (O2Hb), deoxy-haemoglobin (HHb), tissue oxygenation index (TOI) and total haemoglobin index (THI) were obtained. Measurements were obtained with the participants at rest, while performing the Mini Mental State Exam (MMSE) and the modified Stroop Task as cognitive tests, and the Timed Up-and-Go (TuG) and six minute walk test (6MWT) or Toe Taps (TT) as the functional tests. Furthermore, the outcome scores of the various tests were also recorded. Change in O2Hb levels were lower in the experimental group than in the control group, especially in the left prefrontal cortex (LPFC) while HHb values were higher in the right prefrontal cortex (RPFC) (p > 0.05). There were almost no differences in TOI between the two groups in either the LPFC or RPFC, however, statistically significant differences were seen in THI in the RPFC during the MMSE (p = 0.03), rest period 2 (p = 0.03), the first modified Stroop Task (p = 0.04), as well as the TuG (p = 0.02). Furthermore, significant differences were seen between the two groups with respect to the time taken to complete the TuG, with the experimental group completing it much faster (p = 0.04). The experimental group participants who had received regular rehabilitation performed consistently better across most of the testing phases, with a number of practically significant findings. The results show that definite differences exist between stroke patients and healthy elderly individuals when performing a simple and complex task. The positive effect of low intensity exercise on task performance was clearly seen in both groups, and holds a great deal of practical significance for the development of exercise programmes for healthy individuals, as well as stroke patients. Furthermore, rehabilitation following a stroke has obvious benefits as shown by the positive results of the current study, however, limited research exists to validate these findings, highlighting the need for further research in this area. / AFRIKAANSE OPSOMMING: Daar is ʼn wêreld wye toename in die aantal mans en dames wat beroertes ondervind as gevolg van swak lewenstyl-verwante gewoontes. Alhoewel baie navorsing beskikbaar is oor die verskille in serebrale hemodinamika tussen beroerte pasiënte en bejaardes, asook jong gesonde individue, is daar ʼn beperkte aantal studies oor die effek van rehabilitasie op serebrale hemodinamika. Meeste van hierdie studies het die veranderinge in serebrale hemodinamika tydens kognitiewe of funksionele take in isolasie ondersoek, met geen literatuur waar die effek van albei gesamentlik gemeet word nie. Die hoofdoel van hierdie studie was om die verskille in serebrale hemodinamika tussen beroerte pasiënte en gesonde bejaardes, tydens die uitvoering van ʼn eenvoudige en komplekse kognitiewe taak, te ondersoek. Twee-en-dertig mans en vroue (ouderdom 75 ± 8 jaar) het aan die studie deelgeneem. Die eksperimentele groep (n = 14) het bestaan uit die beroerte pasïente en die kontrole groep (n = 18) was gesonde bejaardes. Elke deelnemer het een toets sessie bygewoon waartydens oksihemoglobien (O2Hb), deoksihemoglobien (HHb), weefsel oksigenasie indeks (TOI) en totale hemoglobien indeks (THI) gemeet is. Metings is tydens rus geneem, asook tydens die kognitiewe toetse, die “Mini Mental State Exam” (MMSE) en die gewysigde Stroop taak gemeet, en die funksionele toetse, naamlik die “Timed Up-and-Go” (TuG) en die ses minute loop toets (6MWT) of “Toe Taps” (TT). Die eksperimentele groep se O2Hb was laer as die kontrole groep, veral in die linker voor frontale korteks (LPFC), en die eksperimentele groep se HHb waardes was hoër in die regter voor frontale korteks (RPFC) (p > 0.05). Daar was geen statisties betekenisvolle verskille in TOI tussen die twee groepe nie, maar wel in die THI in die RPFC tydens die MMSE (p = 0.03), rusperiode twee (p = 0.03), die eerste gewysigde Stroop Taak (p = 0.04) en die TuG toets (p = 0.02). Die kontrole groep was statisties betekenisvol vinniger as die eksperimentele groep in die TuG toets (p = 0.04). Deelnemers in die eksperimentele groep wat gereelde rehabilitasie ontvang het, het konsekwent beter gevaar tydens die toets sessie, en ʼn aantal prakties betekenisvolle verskille is in sekere veranderlikes gevind. Die resultate dui aan dat daar wel ʼn verskil in serebrale hemodinamika bestaan tussen beroerte pasiënte en gesonde bejaardes terwyl hulle eenvoudige en komplekse take verrig. Die positiewe effek van lae intensiteit oefening op prestasie was duidelike sigbaar van beide groepe. Hierdie resultate is prakties betekenisvol as dit kom by die ontwikkeling van oefenprogramme vir gesonde individue asook beroerte pasiënte. Rehabilitasie na ʼn beroerte hou ooglopende voordele in soos aangedui deur die positiewe bevindinge van die huidige studie, hoewel daar beperkte navorsing beskikbaar is om hierdie bevindinge te staaf. Daar is dus ʼn behoefte vir verdere navorsing in hierdie gebied.

Thesis (MScEng (Electrical and Electronic Engineering))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: Assessing the quality of fruit has become vitally important for farmers and growers. With retailers placing ever stricter requirements on fresh produce, growers have to spend a greater amount of time and effort sorting and grading their harvest. Increasingly, vendors are placing requirements not only on external factors like colour, and firmness, but on internal quality factors such as sugar content and acidity, because, although consumers buy fruit based on their external appearances, the taste of the fruit is what determines whether the consumer will buy again. Different techniques exist that probe the internal quality of fruit non-destructively. The technique most widely used today is Near Infrared Spectroscopy. This technique is powerful, but has certain limitations such as poor reliability and the need for constant recalibration. This thesis suggests an alternative method for evaluating internal fruit quality based on low-field nuclear magnetic resonance detected by superconducting quantum interference devices. It introduces the theory of SQUIDs and NMR, and evaluates the use of SQUID detected NMR spectroscopy as a method for determining the internal quality of fruit. The fabrication techniques and processes are explained in detail and a design for a SQUID detected NMR spectrometer is given. Relevant simulations and simulation results are also given. No working SQUID could be fabricated and, as such, no working NMR spectrometer was demonstrated. This thesis serves as a reference work for future research. / AFRIKAANSE OPSOMMING: Bepaling van die gehalte van vrugte het vir boere uiters belangrik geword. Met kleinhandelaars wat al strenger vereistes plaas op vars produkte moet boere meer tyd en inspanning bestee met die sortering en gradering van hul oes. Handelaars plaas nie net vereistes op eksterne kwaliteitsfaktore soos kleur en fermheid nie, maar begin al hoe strenger vereistes plaas op interne kwaliteitsfaktore soos suikerinhoud en suurgehalte, want, hoewel verbruikers vrugte koop op grond van hul eksterne kwaliteitsfaktore, is dit die smaak van die vrug wat bepaal of die verbruiker weer die vrug sal koop. Verskillende tegnieke bestaan wat die interne kwaliteit van vrugte op ’n nie-destruktiewe manier kan bepaal. Die mees algemene tegniek is Naby Infrarooi Spektroskopie. Hierdie tegniek is kragtig maar het sekere beperkings soos swak betroubaarheid en die noodsaaklikheid van konstante herkalibrasie. Hierdie tesis stel ’n alternatiewe metode vir die evaluering van interne vrugkwaliteit gebaseer op lae-veld kernmagnetiese resonans waargeneem deur supergeleidende kwantum inmenging toestelle voor. Dit stel die teorie van SKWITs en KMR bekend, en evalueer die gebruik van SKWIT-bespeurde KMR spektroskopie as ’n metode vir die bepaling van die interne kwaliteit van vrugte. Die fabrikasie tegnieke en prosesse word in detail verduidelik en ’n ontwerp vir ’n SWKIT opgevangde KMR spektrometer word gegee. Toepaslike simulasies en simulasie resultate word ook gegee. Geen werkende SKWIT kon vervaardig word nie en as gevolg daarvan kon geen werkende KMR spektrometer gedemonstreer word nie. Hierdie tesis dien as ’n naslaan werk vir toekomstige navorsing.

Many cerebral diseases are associated with abnormal cerebral hemodynamics and impaired cerebral autoregulation (CA). CA is a mechanism to maintain cerebral blood flow (CBF) stable when mean arterial pressure (MAP) fluctuates. Evaluating these abnormalities requires direct measurements of cerebral hemodynamics and MAP. Several near-infrared diffuse optical instruments have been developed in our laboratory for hemodynamic measurements including near-infrared spectroscopy (NIRS), diffuse correlation spectroscopy (DCS), hybrid NIRS/DCS, and dual-wavelength DCS flow-oximeter. We utilized these noninvasive technologies to quantify CBF and cerebral oxygenation in different populations under different physiological conditions/manipulations. A commercial finger plethysmograph was used to continuously monitor MAP. For investigating the impact of obstructive sleep apnea (OSA) on cerebral hemodynamics and CA, a portable DCS device was used to monitor relative changes of CBF (rCBF) during bilateral thigh cuff occlusion. Compared to healthy controls, smaller reductions in rCBF and MAP following cuff deflation were observed in patients with OSA, which might result from the impaired vasodilation. However, dynamic CAs quantified in time-domain (defined by rCBF drop/MAP drop) were not significantly different between the two groups. We also evaluated dynamic CA in frequency-domain, i.e., to quantify the phase shifts of low frequency oscillations (LFOs) at 0.1 Hz between cerebral hemodynamics and MAP under 3 different physiological conditions (i.e., supine resting, head-up tilt (HUT), paced breathing). To capture dynamic LFOs, a hybrid NIRS/DCS device was upgraded to achieve faster sampling rate and better signal-to-noise. We determined the best hemodynamic parameters (i.e., CBF, oxygenated and total hemoglobin concentrations) among the measured variables and optimal physiological condition (HUT) for detecting LFOs in healthy subjects. Finally, a novel dual-wavelength DCS flow-oximeter was developed to monitor cerebral hemodynamics during HUT-induced vasovagal presyncope (VVS) in healthy subjects. rCBF was found to have the best sensitivity for the assessment of VVS among the measured variables and was likely the final trigger of VVS. A threshold of ~50% rCBF decline was observed which can completely separate subjects with or without presyncope, suggesting its potential role for predicting VVS. With further development and applications, NIRS/DCS techniques are expected to have significant impacts on the evaluation of cerebral hemodynamics and autoregulation.

Cerebral autoregulation describes the clinically observed phenomenon that cerebral blood flow remains relatively constant in healthy human subjects despite large systemic changes in blood pressure, dissolved blood gas concentrations, heart rate and other systemic variables. Cerebral autoregulation is known to be impaired post ischaemic stroke, after severe head injury, in patients suffering from autonomic dysfunction and under the action of various drugs. Cerebral auto-regulation is a dynamic, multivariate phenomenon. Sensitive techniques are required to monitor cerebral auto-regulation in a clinical setting. This thesis presents 4 related signal processing studies of cerebral autoregulation. The first study shows how consideration of changes in blood gas concentrations simultaneously with changes in blood pressure can improve the accuracy of an existing frequency domain technique for monitoring cerebral autoregulation from spontaneous fluctuations in blood pressure and a transcranial doppler measure of cerebral blood flow velocity. The second study shows how the continuous wavelet transform can be used to investigate coupling between blood pressure and near infrared spectroscopy measures of cerebral haemodynamics in patients with autonomic failure. This introduces time information into the frequency based assessment, however neglects the contribution of blood gas concentrations. The third study shows how this limitation can be resolved by introducing a new time-varying multivariate system identification algorithm based around the dual tree undecimated wavelet transform. All frequency and time-frequency domain methods of monitoring cerebral autoregulation assume linear coupling between the variables under consideration. The fourth study therefore considers nonlinear techniques of monitoring cerebral autoregulation, and illustrates some of the difficulties inherent in this form of analysis. The general approach taken in this thesis is to formulate a simple system model; usually in the form of an ODE or a stochastic process. The form of the model is adapted to encapsulate a hypothesis about features of cerebral autoregulation, particularly those features that may be difficult to recover using existing methods of analysis. The performance of the proposed method of analysis is then evaluated under these conditions. After this testing, the techniques are then applied to data provided by the Laboratory of Human Cerebrovascular Physiology in Alberta, Canada, and the National Hospital for Neurology and Neurosurgery in London, UK.

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.

L’atteinte de la fonction endothéliale représente une phase précoce de l’athérosclérose, un stade où les patients sont généralement asymptomatiques. Il existe donc un intérêt certain à détecter la dysfonction endothéliale. Nous avons développé une technique de mesure des variations de flot artériel au niveau des membres supérieurs, basée sur la spectroscopie proche infrarouge (NIRS). Cette approche permettrait d’étudier le niveau d’atteinte vasculaire et probablement de quantifier le degré de dysfonction endothéliale périphérique lors d’une hyperémie réactive. L'expérience a été exécutée sur deux cohortes de 13 et de 15 patients et a été comparée à la pléthysmographie par jauge de contrainte (SGP) qui est considérée comme une méthode de référence. Par la suite, nous avons caractérisé la réponse endothéliale par modélisation de la courbe hyperémique du flot artériel. Des études préliminaires avaient démontré que la réponse hyperémique adoptait majoritairement une forme bi-modale. Nous avons tenté de séparer les composantes endothéliales-dépendantes et endothéliales-indépendantes de l’hyperémie. La quantification des deux composantes de la réaction hyperémique permet de calculer un indice de la ‘santé’ du système endothélial local. Cet indice est nommé le ηfactor. Les résultats montrent une forte corrélation des mesures de flots entre la technique développée et la méthode de référence (r=0.91). Nous avons conclu que NIRS est une approche précise pour la mesure non-invasive du flot artériel. Nous avons obtenu une bonne répétabilité (ICC = 0.9313) pour le ηfactor indiquant sa robustesse. Cependant des études supplémentaires sont nécessaires pour valider la valeur de diagnostic du facteur défini. Mots clés: hyperémie réactive, réponse myogénique, oxyde nitrique, athérosclérose, spectroscopie proche infrarouge / Atherosclerotic diseases are mainly caused by coronary and peripheral blood vessel disorders. Endothelial dysfunction represents an early phase in these diseases, when patients are generally asymptomatic. We developed a technique, based on near infrared spectroscopy (NIRS), for measurement of arterial blood flow variations in limbs during reactive hyperemia. The technique allows the study of the level of vascular impairment and probably quantifying the level of endothelial dysfunction at peripheral arteries. The experiment was performed on two cohorts of 13 and 15 patients and was compared to strain gauge plethysmography (SGP) which is considered as gold standard. Afterward, we characterized endothelial reaction during reactive hyperemia through blood flow variations by modeling the hyperemic curve. Preliminary studies have shown that the hyperemic response generally adopts a bimodal form. The first peak was attributed to myogenic reaction that is endothelial independent and the second one to local endothelial cells reaction. The quantification of the two hyperemic response components makes it possible to calculate an index of ‘health’ for local endothelial cells, named ηfactor. The results showed a strong correlation (r = 0.91) of blood flow measurements between the developed method and the gold standard. We concluded that NIRS is a precise technique for non-invasive measurement of blood flow. Moreover, we found a high repeatability (ICC = 0.9313) of the ηfactor in repeated measurements indicating its robustness. Nonetheless, more studies are required to validate the diagnosis value of the defined factor. Key words: reactive hyperemia, myogenic response, endothelial dependent vasodilatation, nitric oxide, atherosclerosis, near infrared spectroscopy (NIRS)

Au cours du vieillissement, des modifications dans la compréhension du discours ont été rapportées, attribuées en partie aux changements cognitifs encourus lors du vieillissement. Néanmoins, diverses études suggèrent une réorganisation cérébrale lors du vieillissement. Cette étude a pour but d'évaluer l'influence de l'âge lors d'une tâche de compréhension du discours à l'aide de l'imagerie optique. Comme première hypothèse, il est attendu que les participants jeunes auront plus de bonnes réponses au niveau des micropropositions et des macropropositions et des performances équivalentes au niveau du modèle de situation. La deuxième hypothèse est que les réseaux neuronaux utilisés lors de la compréhension du discours subiront une réorganisation cérébrale lors du vieillissement. Trente-deux participants ont pris part à cette étude : 16 jeunes adultes et 16 adultes âgés. Alors que les participants étaient sous enregistrement en imagerie optique au niveau du cortex préfrontal (CPF), ils ont lu des courtes histoires chacune suivie d’une phrase et devaient décider si elle était en accord ou non avec la précédente histoire. Les résultats ne montrent aucune différence entre les groupes au niveau de l’exactitude des réponses, contrairement à la littérature. Le CPF a été davantage activé par les adultes âgés comparativement aux jeunes adultes témoignant d’une réorganisation cérébrale. / During aging, changes in discourse comprehension have been reported, attributed in part by cognitive changes that occur during aging. Moreover, various studies suggest a cerebral reorganization with aging. This study aims to evaluate the influence of aging on cerebral reorganization during discourse comprehension using near infrared spectroscopy (NIRS). The first hypothesis is that younger adults will have better accuracy on micropropositions and macropropositions, but will have equivalent performance for the situation model. The second hypothesis is that the neural networks used for discourse comprehension will be reorganized during aging. Thirty-two participants took part in this study: 16 young adults and 16 older adults. While undergoing NIRS recording on the prefrontal cortex (PFC), the participants read short stories each followed by a sentence deciding if it was in agreement or not with the previous story. Results didn’t show any differences for accuracy between the group, in opposition with the literature. The PFC was more activated by the older adults compared to the younger adults showing a cerebral reorganization.

Le vieillissement normal est associé à une réorganisation cérébrale qui peut être influencée par plusieurs facteurs. Des théories comme la réserve cognitive de Stern (2002) tentent d’expliquer les effets de ces différents facteurs. Certains, le niveau de scolarité par exemple, sont encore mal connus. Pourtant, le niveau de scolarité est connu pour avoir un impact sur les performances cognitives tout au long de la vie. Le but de ce mémoire est d’étudier les effets du niveau de scolarité sur l’oxygénation cérébrale de personnes âgées en santé lors d’une tâche d’évocation lexicale orthographique et sémantique. Chaque tâche est divisée selon un critère « plus productive » et « moins productive ». Les âgés faiblement scolarisés produisent moins de mots que les âgés fortement scolarisés. De plus, la différence de mots produits entre le critère plus productif et moins productif est plus grande pour la tâche sémantique que pour la tâche orthographique. Du point de vue hémodynamique, les deux groupes ont des activations semblables, contredisant le phénomène HAROLD. De plus, les participants peu scolarisés tendent à activer de façon plus importante l’hémisphère gauche, peu importe la tâche ou la condition. Par contre, les activations varient selon la tâche et la condition dans le cas du groupe fortement scolarisé. / Normal aging is associated with cerebral reorganisation which can be influenced by many factors. For example, the theory cognitive reserve (Stern, 2002) is trying to explain how those factors can have an impact on the reorganization. However, some factors, such as educational level, are known to have an impact on cognitive performance. The aim of this dissertation is to study the effect of educational level in cerebral oxygenation of healthy older adults during both phonologic and semantic verbal fluency tasks. Each task is divided into two criteria: more productive and less productive. Behavioural data showed that less educated elderly generate fewer words than more educated ones for both tasks. Moreover, the differences between the number of words for the more productive criterion and the less productive one are higher for the semantic than for the phonologic task. NIRS data showed that both groups activated prefrontal cortex, without difference between them. In addition, less educated participants tend to have bigger activations in the left hemisphere regardless of the task and the criterion. On the other hand, higher educated participants’ activations vary according to the task and the criterion unlike the HAROLD model’s predictions.